WO2016075278A1 - Antigen binding molecules comprising a tnf family ligand trimer - Google Patents

Antigen binding molecules comprising a tnf family ligand trimer Download PDF

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Publication number
WO2016075278A1
WO2016075278A1 PCT/EP2015/076528 EP2015076528W WO2016075278A1 WO 2016075278 A1 WO2016075278 A1 WO 2016075278A1 EP 2015076528 W EP2015076528 W EP 2015076528W WO 2016075278 A1 WO2016075278 A1 WO 2016075278A1
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Prior art keywords
seq
amino acid
acid sequence
domain
antigen binding
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PCT/EP2015/076528
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French (fr)
Inventor
Maria AMANN
Peter Bruenker
Christina CLAUS
Claudia Ferrara Koller
Sandra GRAU-RICHARDS
Christian Klein
Viktor LEVITSKY
Ekkehard Moessner
Joerg Thomas Regula
Pablo Umaña
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F. Hoffmann-La Roche Ag
Hoffmann-La Roche Inc.
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Priority to KR1020237034293A priority Critical patent/KR20230146133A/en
Priority to CN202210001707.9A priority patent/CN114634570A/en
Priority to SG11201703597TA priority patent/SG11201703597TA/en
Application filed by F. Hoffmann-La Roche Ag, Hoffmann-La Roche Inc. filed Critical F. Hoffmann-La Roche Ag
Priority to UAA201705791A priority patent/UA125577C2/en
Priority to NZ730933A priority patent/NZ730933A/en
Priority to MYPI2017701668A priority patent/MY191428A/en
Priority to KR1020177016136A priority patent/KR102588377B1/en
Priority to JP2017525959A priority patent/JP6873901B2/en
Priority to MA40882A priority patent/MA40882B1/en
Priority to SI201531194T priority patent/SI3224275T1/en
Priority to PL15797922T priority patent/PL3224275T3/en
Priority to PE2022001462A priority patent/PE20221909A1/en
Priority to MX2020012798A priority patent/MX2020012798A/en
Priority to RS20200473A priority patent/RS60201B1/en
Priority to BR112017009006-6A priority patent/BR112017009006A2/en
Priority to EP18207248.8A priority patent/EP3489256B1/en
Priority to CA2963718A priority patent/CA2963718A1/en
Priority to EP20158607.0A priority patent/EP3738609A1/en
Priority to CN201580073211.0A priority patent/CN108064237B/en
Priority to AU2015345024A priority patent/AU2015345024B2/en
Priority to CN202110472897.8A priority patent/CN113372434B/en
Priority to IL282922A priority patent/IL282922B/en
Priority to LTEP15797922.0T priority patent/LT3224275T/en
Priority to MX2017006250A priority patent/MX2017006250A/en
Priority to CR20170194A priority patent/CR20170194A/en
Priority to PL18207248T priority patent/PL3489256T3/en
Priority to DK15797922.0T priority patent/DK3224275T3/en
Priority to ES15797922T priority patent/ES2788979T3/en
Priority to EA201791057A priority patent/EA037557B1/en
Priority to EP15797922.0A priority patent/EP3224275B1/en
Priority to US15/067,024 priority patent/US10392445B2/en
Publication of WO2016075278A1 publication Critical patent/WO2016075278A1/en
Priority to IL251317A priority patent/IL251317B/en
Priority to CONC2017/0003212A priority patent/CO2017003212A2/en
Priority to PH12017500892A priority patent/PH12017500892A1/en
Priority to HK18114659.3A priority patent/HK1255482A1/en
Priority to US16/522,412 priority patent/US11267903B2/en
Priority to US16/522,391 priority patent/US11306154B2/en
Priority to HRP20200679TT priority patent/HRP20200679T1/en
Priority to AU2020264337A priority patent/AU2020264337B2/en
Priority to US17/580,970 priority patent/US20220259326A1/en
Priority to US17/580,980 priority patent/US20220259327A1/en
Priority to AU2022201144A priority patent/AU2022201144A1/en

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    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/68—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment
    • A61K47/6835—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment the modifying agent being an antibody or an immunoglobulin bearing at least one antigen-binding site
    • A61K47/6849—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment the modifying agent being an antibody or an immunoglobulin bearing at least one antigen-binding site the antibody targeting a receptor, a cell surface antigen or a cell surface determinant
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    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70575—NGF/TNF-superfamily, e.g. CD70, CD95L, CD153, CD154
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    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70596—Molecules with a "CD"-designation not provided for elsewhere
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    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2803—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily
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    • C07K16/2803—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily
    • C07K16/2815—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily against CD8
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    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2896—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against molecules with a "CD"-designation, not provided for elsewhere
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    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/30—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants from tumour cells
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    • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
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    • C07K2319/30—Non-immunoglobulin-derived peptide or protein having an immunoglobulin constant or Fc region, or a fragment thereof, attached thereto
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    • C07K2319/00—Fusion polypeptide
    • C07K2319/33—Fusion polypeptide fusions for targeting to specific cell types, e.g. tissue specific targeting, targeting of a bacterial subspecies

Definitions

  • Antigen Binding Molecules comprising a TNF family ligand trimer
  • the invention relates to novel TNF family ligand trimer-containing antigen binding molecules comprising (a) at least one moiety capable of specific binding to a target cell antigen and (b) a first and a second polypeptide that are linked to each other by a disulfide bond, wherein the antigen binding molecules are characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof.
  • the invention further relates to methods of producing these molecules and to methods of using the same.
  • TNF tumor necrosis factor
  • TNF family ligands also called cytokines
  • the TNF ligand family comprises 18 genes encoding 19 type II (i.e. intracellular N terminus and extracellular C-terminus) transmembrane proteins, characterized by the presence of a conserved C-terminal domain coined the 'TNF homology domain' (THD).
  • TNF family ligands This domain is responsible for receptor binding and is thus critical for the biological activity of the TNF ligand family members.
  • the sequence identity between family members is ⁇ 20-30 (Bodmer, 2002).
  • Members of the TNF ligand family exert their biological function as self-assembling, noncovalent trimers (Banner et al, Cell 1993, 73, 431-445).
  • the TNF family ligands form a trimer that is able to bind to and to activate the corresponding receptors of TNFR superfamily.
  • 4-1BB (CD137), a member of the TNF receptor superfamily, has been first identified as a molecule whose expression is induced by T-cell activation (Kwon and Weissman, 1989).
  • Expression of 4- IBB in different cell types is mostly inducible and driven by various stimulatory signals, such as T-cell receptor (TCR) or B-cell receptor triggering, as well as signaling induced through co- stimulatory molecules or receptors of pro-inflammatory cytokines (Diehl et al., 2002; von Kempis et al., 1997; Zhang et al., 2010).
  • TCR T-cell receptor
  • B-cell receptor triggering signaling induced through co- stimulatory molecules or receptors of pro-inflammatory cytokines
  • 4-1BB ligand (4-1BBL or CD137L) is more restricted and is observed on professional antigen presenting cells (APC) such as B-cells, dendritic cells (DCs) and
  • Inducible expression of 4-1BBL is characteristic for T-cells, including both ⁇ and ⁇ T-cell subsets, and endothelial cells (reviewed in Shao and Schwarz, 2011).
  • CD 137 signaling is known to stimulate IFNy secretion and proliferation of NK cells (Buechele et al., 2012; Lin et al., 2008; Melero et al., 1998) as well as to promote DC activation as indicated by their increased survival and capacity to secret cytokines and upregulate co- stimulatory molecules (Choi et al., 2009; Futagawa et al., 2002; Wilcox et al., 2002).
  • CD 137 is best characterized as a co-stimulatory molecule which modulates TCR- induced activation in both the CD4+ and CD8+ subsets of T-cells.
  • agonistic 4-lBB-specific antibodies enhance proliferation of T-cells, stimulate lymphokine secretion and decrease sensitivity of T-lymphocytes to activation-induced cells death (reviewed in (reviewed in Snell et al., 2011).
  • 4- IBB antibodies In line with these co- stimulatory effects of 4- IBB antibodies on T-cells in vitro, their administration to tumor bearing mice leads to potent anti-tumor effects in many experimental tumor models (Melero et al., 1997; Narazaki et al., 2010). However, 4- IBB usually exhibits its potency as an anti-tumor agent only when administered in combination with other tumor models (Melero et al., 1997; Narazaki et al., 2010). However, 4- IBB usually exhibits its potency as an anti-tumor agent only when administered in combination with other
  • 4- IBB agonists can also induce infiltration and retention of activated T-cells in the tumor through 4- IBB -mediated upregulation of intercellular adhesion molecule 1 (ICAM1) and vascular cell adhesion molecule 1 (VCAM1) on tumor vascular endothelium (Palazon et al., 2011).
  • IAM1 intercellular adhesion molecule 1
  • VCAM1 vascular cell adhesion molecule 1
  • 4- IBB triggering may also reverse the state of T-cell anergy induced by exposure to soluble antigen that may contribute to disruption of immunological tolerance in the tumor micro- environment or during chronic infections (Wilcox et al., 2004).
  • Fusion proteins composed of one extracellular domain of a 4- IBB ligand and a single chain antibody fragment (Mueller et al., 2008; Hornig et al., 2012) or a single 4-1BB ligand fused to the C-terminus of a heavy chain (Zhang et al, 2007) have been made.
  • WO 2010/010051 discloses the generation of fusion proteins that consist of three TNF ligand ectodomains linked to each other and fused to an antibody part.
  • the antigen binding molecules of the present invention comprise both and surprisingly they provide a trimeric and thus biologically active TNF ligand, although one of the trimerizing TNF ligand ectodomains is located on another polypeptide than the other two TNF ligand ectodomains of the molecule.
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising
  • the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof.
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising
  • the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof, and
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule, comprising
  • the first polypeptide contains a CHI or CL domain and the second polypeptide contains a CL or CHI domain, respectively, wherein the second polypeptide is linked to the first polypeptide by a disulfide bond between the CHI and CL domain, and wherein the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the CHI or CL domain by a peptide linker and wherein the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to the CL or
  • the first polypeptide contains a CH3 domain and the second polypeptide contains a CH3 domain, respectively, and wherein the first polypeptide comprises two
  • ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the C-terminus of the CH3 domain by a peptide linker and wherein the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to C-terminus of the CH3 domain of said polypeptide, or
  • the first polypeptide contains a VH-CL or a VL-CH1 domain and the second
  • polypeptide contains a VL-CH1 domain or a VH-CL domain, respectively, wherein the second polypeptide is linked to the first polypeptide by a disulfide bond between the
  • the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to to VH or VL by a peptide linker and wherein the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to VL or VH of said polypeptide.
  • the TNF ligand family member is one that costimulates human T-cell activation.
  • the TNF family ligand trimer-containing antigen binding molecule comprises (a) at least one moiety capable of specific binding to a target cell antigen and
  • the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof, wherein the TNF ligand family member costimulates human T-cell activation. More particularly, the TNF ligand family member is selected from 4-1BBL and OX40L.
  • the TNF ligand family member is 4-1BBL.
  • the ectodomain of a TNF ligand family member comprises the amino acid sequence selected from the group consisting of SEQ ID NO: l, SEQ ID NO: 2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:96, SEQ ID NO: 373, SEQ ID NO:374 and SEQ ID NO:375, particularly the amino acid sequence of SEQ ID NO: l or SEQ ID NO:96.
  • the ectodomain of a TNF ligand family member or fragment thereof comprises the amino acid sequence selected from the group consisting of SEQ ID NO: l, SEQ ID NO:2, SEQ ID NO:3 , SEQ ID NO:4 and SEQ ID NO:96, particularly the amino acid sequence of SEQ ID NO: l or SEQ ID NO:96. More particularly, the ectodomain of a TNF ligand family member comprises the amino acid sequence of SEQ ID NO:96.
  • the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
  • the antigen binding molecule comprises the amino acid sequence selected from the group consisting of SEQ ID NO:5, SEQ ID NO:97, SEQ ID NO:98 and SEQ ID NO:99 and in that the second polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO: l, SEQ ID NO:96, SEQ ID NO:3 and SEQ ID NO:4.
  • the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
  • the antigen binding molecule is characterized in that the first polypeptide comprises the amino acid sequence of SEQ ID NO:5 and in that the second polypeptide comprises the amino acid sequence of SEQ ID NO:6.
  • the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
  • the antigen binding molecule is characterized in that the first polypeptide comprises the amino acid sequence of SEQ ID NO:5 and in that the second polypeptide comprises the amino acid sequence of SEQ ID NO: 183.
  • the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
  • the antigen binding molecule is characterized in that the first polypeptide comprises the amino acid sequence of SEQ ID NO:97 and in that the second polypeptide comprises the amino acid sequence of SEQ ID NO: 184 or SEQ ID NO: 185.
  • the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
  • the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other and to the CHI or CL domain by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof connected by a peptide linker to the CL or CHI domain of said polypeptide.
  • TNF family ligand trimer-containing antigen binding molecule comprising
  • the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the CHI domain by a peptide linker and in that the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to the CL domain of said polypeptide.
  • TNF family ligand trimer-containing antigen binding molecule comprising
  • the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the CL domain by a peptide linker and in that the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to the CHI domain of said polypeptide.
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule as defined herein before, wherein the moiety capable of specific binding to a target cell antigen is selected from the group consisting of an antibody, an antibody fragment and a scaffold antigen binding protein.
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule as defined herein before, wherein the moiety capable of specific binding to a target cell antigen is an antibody fragment.
  • the moiety capable of specific binding to a target cell antigen is selected from the group consisting of an antibody fragment, a Fab molecule, a crossover Fab molecule, a single chain Fab molecule, a Fv molecule, a scFv molecule, a single domain antibody, an aVH and a scaffold antigen binding protein.
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule as defined herein before, wherein the moiety capable of specific binding to a target cell antigen is a scaffold antigen binding protein.
  • the invention is concerned with a TNF family ligand trimer- containing antigen binding molecule as defined above, wherein the moiety capable of specific binding to a target cell antigen is a Fab molecule capable of specific binding to a target cell antigen.
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule that comprises at least one moiety capable of specific binding to a target cell antigen.
  • the TNF family ligand trimer-containing antigen binding molecule comprises one moiety capable of specific binding to a target cell antigen.
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising two moieties capable of specific binding to a target cell antigen.
  • TNF family ligand trimer-containing antigen binding molecule of the invention wherein the target cell antigen is selected from the group consisting of Fibroblast Activation Protein (FAP), Carcinoembryonic Antigen (CEA), Melanoma- associated Chondroitin Sulfate Proteoglycan (MCSP), Epidermal Growth Factor Receptor (EGFR), CD 19, CD20 and CD33.
  • FAP Fibroblast Activation Protein
  • CEA Carcinoembryonic Antigen
  • MCSP Melanoma- associated Chondroitin Sulfate Proteoglycan
  • EGFR Epidermal Growth Factor Receptor
  • the target cell antigen is Fibroblast Activation Protein (FAP).
  • FAP Fibroblast Activation Protein
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule, wherein the moiety capable of specific binding to FAP comprises a VH domain comprising (i) CDR-Hl comprising the amino acid sequence of SEQ ID NO:7 or SEQ ID NO: 100, (ii) CDR-H2 comprising the amino acid sequence of SEQ ID NO:8 or SEQ ID NO: 101, and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO:9 or SEQ ID NO: 102, and a VL domain comprising (iv) CDR-Ll comprising the amino acid sequence of SEQ ID NO: 10 or SEQ ID NO: 103, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO: 11 or SEQ ID NO: 104, and (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO: 12
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule, wherein the moiety capable of specific binding to FAP comprises a VH domain comprising (i) CDR-Hl comprising the amino acid sequence of SEQ ID NO:7, (ii) CDR- H2 comprising the amino acid sequence of SEQ ID NO: 8 and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO:9, and a VL domain comprising (iv) CDR-Ll comprising the amino acid sequence of SEQ ID NO: 10, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO: 11 and (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO: 12.
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule, wherein the moiety capable of specific binding to FAP comprises a VH domain comprising (i) CDR-Hl comprising the amino acid sequence of SEQ ID NO: 100, (ii) CDR-H2 comprising the amino acid sequence SEQ ID NO: 101, and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO: 102, and a VL domain comprising (iv) CDR-L1 comprising the amino acid sequence of SEQ ID NO: 103, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO: 104, and (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO:105.
  • VH domain comprising (i) CDR-Hl comprising the amino acid sequence of SEQ ID NO: 100, (ii) CDR-H2 comprising the amino acid sequence SEQ ID NO: 101, and (iii) CDR-H3 comprising the
  • a TNF family ligand trimer-containing antigen binding molecule as defined herein before, wherein the moiety capable of specific binding to FAP comprises a variable heavy chain comprising an amino acid sequence of SEQ ID NO: 16 and a variable light chain comprising an amino acid sequence of SEQ ID NO: 17 or wherein the moiety capable of specific binding to FAP comprises a variable heavy chain comprising an amino acid sequence of SEQ ID NO: 106 and a variable light chain comprising an amino acid sequence of SEQ ID
  • a TNF family ligand trimer-containing antigen binding molecule wherein a peptide comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C-terminus to the CHI or CL domain of a heavy chain by a second peptide linker and wherein one ectodomain of said TNF ligand family member or a fragment thereof is fused at the its C-terminus the CL or CHI domain on a light chain by a third peptide linker.
  • the invention relates to a TNF family ligand trimer-containing antigen binding molecule as defined above, wherein the peptide linker is (G4S) 2 , i.e. a peptide linker of SEQ ID NO: 13.
  • the first peptide linker is (G4S) 2
  • the second peptide linker is GSPGSSSSGS (SEQ ID NO:57)
  • the third peptide linker is (G4S) 2
  • the first, the second and the third peptide linker is (G4S) 2 .
  • the invention is further concerned with a TNF family ligand trimer-containing antigen binding molecule as defined herein before, comprising an Fc domain composed of a first and a second subunit capable of stable association.
  • the TNF family ligand trimer-containing antigen binding molecule of the invention comprising (c) an Fc domain composed of a first and a second subunit capable of stable association further comprises (a) a Fab molecule capable of specific binding to a target cell antigen, wherein the Fab heavy chain is fused at the C-terminus to the N-terminus of a CH2 domain in the Fc domain.
  • the Fc domain is an IgG, particularly an IgGl Fc domain or an IgG4 Fc domain. More particularly, the Fc domain is an IgGl Fc domain. In a particular aspect, the Fc domain comprises a modification promoting the association of the first and second subunit of the Fc domain.
  • the invention is concerned with a TNF family ligand trimer-containing antigen binding molecule as defined herein before, comprising
  • an Fc domain composed of a first and a second subunit capable of stable association, wherein the Fc domain comprises one or more amino acid substitution that reduces binding to an Fc receptor, in particular towards Fey receptor.
  • the Fc domain comprises amino acid substitutions at positions 234 and 235 (EU numbering) and/or 329 (EU numbering) of the IgG heavy chains. More particularly, provided is a trimeric TNF family ligand-containing antigen binding molecule according to the invention which comprises an IgGl Fc domain with the amino acid substitutions L234A, L235A and P329G (EU numbering).
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule, wherein the antigen binding molecule comprises
  • a first heavy chain and a first light chain both comprising a Fab molecule capable of specific binding to a target cell antigen
  • a first peptide comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker fused at its C-terminus by a second peptide linker to a second heavy or light chain,
  • a second peptide comprising one ectodomain of said TNF ligand family member fused at its C-terminus by a third peptide linker to a second light or heavy chain, respectively.
  • a TNF family ligand trimer-containing antigen binding molecule wherein the first peptide comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C-terminus by a second peptide linker to a CHI domain that is part of a heavy chain,
  • the second peptide comprising one ectodomain of said TNF ligand family member or a fragment thereof is fused at its C-terminus by a third peptide linker to a CL domain that is part of a light chain.
  • a TNF family ligand trimer-containing antigen binding molecule wherein the first peptide comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C-terminus by a second peptide linker to a CL domain that is part of a heavy chain,
  • the second peptide comprising one ectodomain of said TNF ligand family member or a fragment thereof is fused at its C-terminus by a third peptide linker to a CHI domain that is part of a light chain.
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule, wherein the first peptide comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C- terminus by a second peptide linker to a VH domain that is part of a heavy chain,
  • the second peptide comprising one ectodomain of said TNF ligand family member or a fragment thereof is fused at its C-terminus by a third peptide linker to a VL domain that is part of a light chain.
  • TNF family ligand trimer-containing antigen binding molecule wherein in the CL domain adjacent to the TNF ligand family member the amino acid at position 123 (EU numbering) has been replaced by arginine (R) and the amino acid at position 124 (EU numbering) has been substituted by lysine (K), and wherein in the CHI domain adjacent to the TNF ligand family member the amino acids at position 147 (EU numbering) and at position 213 (EU numbering) have been substituted by glutamic acid (E).
  • TNF family ligand trimer-containing antigen binding molecule as described herein before, wherein the antigen binding molecule comprises
  • a second heavy chain comprising an amino acid sequence selected from the group consisting of SEQ ID NO:5, SEQ ID NO:97, SEQ ID NO:98 and SEQ ID NO:99, and
  • a second light chain comprising an amino acid sequence selected from the group consisting of SEQ ID NO:l, SEQ ID NO:96, SEQ ID NO:3 and SEQ ID NO:4.
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule, wherein the antigen binding molecule comprises
  • a second heavy chain comprising an amino acid sequence selected from the group consisting of SEQ ID NO:5, SEQ ID NO:97, SEQ ID NO:98 and SEQ ID NO:99, and
  • a second light chain comprising an amino acid sequence selected from the group consisting of SEQ ID NO: l, SEQ ID NO:96, SEQ ID NO:3 and SEQ ID NO:4.
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising a moiety capable of specific binding to FAP.
  • a TNF family ligand trimer-containing antigen binding molecule wherein the antigen binding molecule comprises
  • a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO: 106 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO: 107,
  • a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 14, SEQ ID NO: 108, SEQ ID NO: 111, SEQ ID NO: 113, SEQ ID NO.115, SEQ
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule, wherein the antigen binding molecule comprises
  • a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO: 106 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO: 107,
  • a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 115, SEQ ID NO: 117, SEQ ID NO: 119 and SEQ ID NO: 173, and
  • a second light chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 116, SEQ ID NO: 118, SEQ ID NO: 120 and SEQ ID NO: 174.
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule, comprising
  • the antigen binding molecule is characterized in that the first polypeptide contains a CH3 domain and the second polypeptide contains a CH3 domain, respectively, and wherein the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the C-terminus of the CH3 domain by a peptide linker and wherein the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to C-terminus of the CH3 domain of said polypeptide.
  • a TNF family ligand trimer-containing antigen binding molecule comprises two moieties capable of specific binding to a target cell antigen.
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising two moieties capable of specific binding to FAP.
  • a TNF family ligand trimer-containing antigen binding molecule as described herein before comprises
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule as described herein before, wherein the target cell antigen is CD 19.
  • a TNF family ligand trimer-containing antigen binding molecule wherein the moiety capable of specific binding to CD 19 comprises a VH domain comprising (i) CDR-H1 comprising the amino acid sequence of SEQ ID NO: 195 or SEQ ID NO:252, (ii) CDR- H2 comprising the amino acid sequence of SEQ ID NO: 196 or SEQ ID NO:253, and (iii) CDR- H3 comprising the amino acid sequence of SEQ ID NO: 197 or SEQ ID NO:254, and a VL domain comprising (iv) CDR-L1 comprising the amino acid sequence of SEQ ID NO: 198 or SEQ ID NO:249, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO: 199 or SEQ ID NO:250, and (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO:200 or SEQ ID NO:251.
  • TNF family ligand trimer-containing antigen binding molecule wherein the moiety capable of specific binding to CD 19 comprises a variable heavy chain comprising an amino acid sequence of SEQ ID NO:201 and a variable light chain comprising an amino acid sequence of SEQ ID NO:202 or wherein the moiety capable of specific binding to FAP comprises a variable heavy chain comprising an amino acid sequence of SEQ ID NO:357 and a variable light chain comprising an amino acid sequence of SEQ ID NO:358.
  • a TNF family ligand trimer-containing antigen binding molecule wherein the antigen binding molecule comprises (i) a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO:201 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO:202 or
  • a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO:357 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO:358,
  • a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 14, SEQ ID NO: 108, SEQ ID NO: 111 and SEQ ID NO: 113, and
  • TNF family ligand trimer-containing antigen binding molecule wherein the antigen binding molecule comprises
  • a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO:357 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO:358,
  • a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 115, SEQ ID NO: 117, SEQ ID NO: 119 and SEQ ID NO: 173, and
  • a second light chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 116, SEQ ID NO: 118, SEQ ID NO: 120 and SEQ ID NO: 174.
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising two moieties capable of specific binding to CD 19.
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule as described herein before, wherein the target cell antigen is CEA.
  • a TNF family ligand trimer-containing antigen binding molecule wherein the moiety capable of specific binding to CEA comprises a VH domain comprising (i) CDR-H1 comprising the amino acid sequence of SEQ ID NO:321, (ii) CDR-H2 comprising the amino acid sequence of SEQ ID NO:322, and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO:323, and a VL domain comprising (iv) CDR-L1 comprising the amino acid sequence of SEQ ID NO:324, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO:325, and (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO:326.
  • TNF family ligand trimer-containing antigen binding molecule wherein the moiety capable of specific binding to CEA comprises a variable heavy chain comprising an amino acid sequence of SEQ ID NO:329 and a variable light chain comprising an amino acid sequence of SEQ ID NO:330.
  • TNF family ligand trimer-containing antigen binding molecule as described herein before, wherein the antigen binding molecule comprises
  • a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 14, SEQ ID NO: 108, SEQ ID NO: 111 and SEQ ID NO: 113, and
  • TNF family ligand trimer-containing antigen binding molecule wherein the antigen binding molecule comprises
  • a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 115, SEQ ID NO: 117, SEQ ID NO: 119 and SEQ ID NO: 173, and
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising two moieties capable of specific binding to CEA.
  • a TNF family ligand trimer-containing antigen binding molecule comprising two moieties capable of specific binding to CEA.
  • the antigen binding molecule comprises
  • aTNF family ligand trimer-containing antigen binding molecule as described herein before, wherein the TNF ligand family member is OX40L.
  • TNF family ligand trimer-containing antigen binding molecule wherein the ectodomain of a TNF ligand family member comprises the amino acid sequence of SEQ ID NO:53 or SEQ ID NO:54, particularly the amino acid sequence of SEQ ID NO:53.
  • TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 5, 10 to 24, 29, 30, 32 to 34, 38 to 40, 44 and 45, comprising
  • the antigen binding molecule is characterized in that the first polypeptide comprises the amino acid sequence of SEQ ID NO:371 or SEQ ID:372 and in that the second polypeptide comprises the amino acid sequence of SEQ ID NO:53 or SEQ ID NO:54.
  • a TNF family ligand trimer-containing antigen binding molecule wherein the target cell antigen is Fibroblast Activation Protein (FAP) and the moiety capable of specific binding to FAP comprises a VH domain comprising (i) CDR-H1 comprising the amino acid sequence of SEQ ID NO:7 or SEQ ID NO: 100, (ii) CDR-H2 comprising the amino acid sequence of SEQ ID NO:8 or SEQ ID NO: 101, and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO:9 or SEQ ID NO: 102, and a VL domain comprising (iv) CDR-L1 comprising the amino acid sequence of SEQ ID NO: 10 or SEQ ID NO: 103, (v) CDR- L2 comprising the amino acid sequence of SEQ ID NO: 11 or SEQ ID NO: 104, and (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO: 12 or SEQ ID NO: 105.
  • FAP Fibroblast
  • TNF family ligand trimer-containing antigen binding molecule as described herein, wherein the antigen binding molecule comprises
  • a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO: 106 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO: 107,
  • an isolated polynucleotide encoding a TNF family ligand trimer-containing antigen binding molecule as defined herein before.
  • the invention further provides a vector, particularly an expression vector, comprising the isolated polynucleotide of the invention and a host cell comprising the isolated polynucleotide or the vector of the invention.
  • the host cell is a eukaryotic cell, particularly a mammalian cell.
  • a method for producing the TNF family ligand trimer- containing antigen binding molecule of the invention comprising the steps of (i) culturing the host cell of the invention under conditions suitable for expression of the antigen binding molecule, and (ii) recovering the antigen binding molecule.
  • the invention also encompasses a TNF family ligand trimer-containing antigen binding molecule produced by the method of the invention.
  • the invention further provides a pharmaceutical composition comprising the TNF family ligand trimer-containing antigen binding molecule of the invention and at least one
  • TNF family ligand trimer-containing antigen binding molecule of the invention or the pharmaceutical composition of the invention, for use as a medicament.
  • the TNF family ligand trimer-containing antigen binding molecule of the invention, or the pharmaceutical composition of the invention for use in the treatment of a disease in an individual in need thereof.
  • the TNF family ligand trimer-containing antigen binding molecule of the invention, or the pharmaceutical composition of the invention for use in the treatment of cancer.
  • the TNF family ligand trimer-containing antigen binding molecule of the invention for the manufacture of a medicament for the treatment of a disease in an individual in need thereof, in particular for the manufacture of a medicament for the treatment of cancer, as well as a method of treating a disease in an individual, comprising administering to said individual a therapeutically effective amount of a composition comprising the TNF family ligand trimer-containing antigen binding molecule of the invention in a pharmaceutically acceptable form.
  • the disease is cancer.
  • the individual is preferably a mammal, particularly a human.
  • Figure 1 shows the components for the assembly of split trimeric human 4- IBB ligands.
  • Figure (1A) shows the dimeric ligand that is fused at the C-terminus to a human CHI or CL domain or a VL or VH domain and
  • Figure (IB) shows the monomeric ligand fused to human CL or CHI domain or a VL or VH domain.
  • Figure (1C) shows the dimeric ligand that is fused at the N-terminus to a human CH3 domain and
  • Figure (ID) shows the monomeric ligand fused at the N-terminus to a human CH3 domain.
  • Figure 2 shows the 4-lBBL-trimer-containing antigen binding molecules Constructs 1.1 to 1.10 of the invention. The preparation and production of these constructs is described in
  • VH and VL domains are those of anti-FAP antibody 28H1, the thick black point stands for the knob-into-hole modification. * symbolizes amino acid modifications in the CHI and CL domain (so-called charged residues).
  • Figure 3 shows the components for the assembly of split trimeric murine 4-1BB ligands.
  • Figure (3 A) shows the dimeric ligand that is fused at the C-terminus to murine CL domain and
  • Figure (3B) shows the monomeric ligand fused at the C-terminus to murine CHI domain.
  • Figure (3C) shows the assembled murine 4-lBBL-trimer-containing antigen binding molecules as described in more detail in Example 1.3.
  • FIG. 4 shows the 4-lBBL-trimer-containing antigen binding molecules Constructs 2.1 to 2.6 of the invention. The preparation and production of these constructs is described in Example 2.
  • the VH and VL domains are those of anti-FAP antibody 4B9, the thick black point stands for the knob-into-hole modification. * symbolizes amino acid modifications in the CHI and CL domain (so-called charged residues).
  • Figure 5A and Figure 5B show the "untargeted" variants of Constructs 1.1 and 1.2 comprising a DP47 Fab molecule instead of the anti-FAP Fab molecule.
  • the molecules are named Control A and Control B, respectively.
  • the preparation is described in Example 1.4.
  • Figure 5C is a drawing of the monomeric 4- IBB Fc(kih) construct as prepared in Example 3.
  • Figure 6 relates to the binding of FAP-targeted 4- IBB ligand trimer-containing Fc(kih) fusion antigen binding molecule (FAP split 4-1BBL trimer, filled circles) or DP-47 untargeted 4- 1BB ligand trimer-containing Fc(kih) fusion antigen binding molecule (DP47 split 4-1BBL trimer, open circles) to resting (naive) or activated human PMBCs.
  • the binding to resting (naive) or activated human CD8+ T cells is shown in Figure (6A), to resting (naive) or activated human CD4+ T cells in Figure (6B) and to resting (naive) or activated human NK cells in Figure (6C). Shown is the binding as Median of fluorescence intensity (MFI) of red
  • R-PE Phycoerythrin-labeled anti-human IgG Fcy-specific goat IgG F(ab )2 fragment which is used as secondary detection antibody.
  • MFI was measured by flow cytometry and baseline corrected by subtracting the MFI of the blank control.
  • Binding was detected with R-Phycoerythrin-fluorochrome conjugated anti-human IgG Fcy- specific goat IgG F(ab )2 fragment. Shown is the median of fluorescence intensity (MFI) versus the concentration of tested Constructs 1.1 to 1.10 of Example 1. For a better display the binding curves are split in four different blots with Construct 1.1 (monovalent FAP-targeted split trimeric human 4- IBB ligand Fc (kih)) and Control B (monovalent untargeted split trimeric human 4- 1BB ligand Fc (kih) with CH-CL cross and charged residues) as comparison curves.
  • Construct 1.1 monovalent FAP-targeted split trimeric human 4- IBB ligand Fc (kih)
  • Control B monovalent untargeted split trimeric human 4- 1BB ligand Fc (kih) with CH-CL cross and charged residues
  • Figure 8 shows the binding of different FAP-targeted or untargeted split trimeric human 4- 1BB ligand Fc (kih) constructs to CD4+ or CD8+ T cells from fresh PBMCs ( Figure 8A) or to human 4- IBB expressing PHA-L and Proleukin pre-activated and anti-human CD3/anti-human CD28 re-activated human PBMCs ( Figure 8B). Binding was detected with R-Phycoerythrin- fluorochrome conjugated anti-human IgG Fcy-specific goat IgG F(ab )2 fragment.
  • An anti-mouse CD137-specific human IgGl P329G LALA antibody (clone Lobl2.3) was used as positive control (Triangles).
  • the binding is characterized by plotting the MFI of R-PE- labeled anti-human IgG Fcy-specific goat IgG F(ab )2 fragment that is used as secondary detection antibody versus the concentration in nM of the tested split 4-1BBL trimer constructs. MFI was measured by flow cytometry and baseline corrected by subtracting the MFI of the blank control.
  • Figure 10 shows the binding of 4- IBB ligand trimer-containing Fc(kih) fusion antigen binding molecules (filled circles: FAP-targeted 4- IBB ligand trimer-containing Fc(kih) fusion antigen binding molecule Construct 1.1, open circles: DP47 untargeted 4- IBB ligand trimer- containing Fc(kih) fusion antigen binding molecule Control A to fibroblast activation protein (FAP)-expressing human melanoma (A) MV-3 cell line and (B) WM-266-4 cell line.
  • FAP fibroblast activation protein
  • the binding is characterized by plotting the MFI of R-PE-labeled anti-human IgG Fcy-specific goat IgG F(ab )2 fragment that is used as secondary detection antibody versus the concentration in nM of tested split 4-1BBL trimer constructs. MFI was measured by flow cytometry and baseline corrected by subtracting the MFI of the blank control.
  • FIG 11 the binding of different FAP-targeted or untargeted split trimeric human 4- 1BB ligand Fc (kih) constructs to human-FAP expressing human melanoma MV-3 cells ( Figure 11 A) and/or NIH/3T3-huFAP clone 39 transfected mouse embryonic fibroblast cells ( Figure 11B) is shown. Binding was detected with R-Phycoerythrin-fluorochrome or fluorescein-fluorochrome conjugated anti-human IgG Fcy-specific goat IgG F(ab )2 fragments. Shown is the median of fluorescence intensity (MFI) versus the concentration of tested constructs.
  • MFI median of fluorescence intensity
  • construct 2.1 monovalent FAP-targeted split trimeric human 4- IBB ligand Fc (kih)
  • bivalent FAP-targeted construct 2.3 It has a tendency to show lower EC50 values and lower median fluorescence intensity. This can be explained with its bivalent targeting, which results in higher avidity but less occupancy or FAP molecules on the cell surface resulting in a lower MFI.
  • Figure 13 shows the binding of different FAP-targeted or untargeted split trimeric mouse 4-1BB ligand Fc (kih) constructs to CD4+ or CD8+ T cells from fresh splenocytes ( Figure 13A) or to mouse 4- IBB expressing anti-mouse CD3/anti-mouse CD28 monoclonal agonistic antibodies activated mouse splenocytes ( Figure 13B). Binding was detected with FITC- fluorochrome conjugated anti-mouse IgG Fey- specific goat IgG F(ab )2 fragment. Shown is the median of fluorescence intensity (MFI) versus the concentration of tested constructs.
  • MFI median of fluorescence intensity
  • CD3+ CD8+ T cells left blot
  • CD3+ CD4+ T cells right blot
  • the 4- 1BB expression level on CD8 T cells is normally higher than on CD4 T cells. All constructs bind with a quite similar affinity to mouse 4- IBB.
  • Figure 15 shows a scheme that illustrates the general principal of the NFkB activity assay described in Example 6.1 using a reporter cell line. Shown is the activation assay set up with human 4- IBB expressing HeLa reporter cell line. A crosslinking of 4- IBB expressed on the reporter cells induces NFKB activation and NFKB-mediated Luciferase expression. After lysis of the cells Luciferase can catalyze the oxidation of Luciferin to Oxyluciferin. This chemical reaction correlates positively with the strength of NFKB-mediated luciferase expression and can be measured by the strength of light emission (units of released light). The ratio of FAP- expressing tumor cells to the reporter cell line HeLa-huCD137-NFkB-luc was 5 to 1.
  • FIG 16 it is shown that the activation of the NFkB signaling pathway by FAP- targeted 4- IBB ligand trimer-containing Fc(kih) fusion antigen binding molecule (Construct 1.1) is strictly dependent on its binding to FAP-expressing target cells.
  • Human CD137 expressing NFkB reporter HeLa cells were co-cultured with the indicated tumor cells exhibiting different levels of cell surface FAP expression. Luciferase activity was assessed as described in Example 6.1 after culturing cells in the absence or presence of 4-lBBL-containing molecules at the indicated concentrations for 6 hours.
  • Filled circles refer to Construct 1.1.
  • Open circles refer to DP47 untargeted 4- IBB ligand trimer-containing Fc(kih) fusion antigen binding molecule (Control A).
  • Cell line NIH/3T3-human FAP clone 39 was used as target cells in Graph (A), Graph (B) shows the activation with MV3 cell line as target cells and Graph (C) with WM-266-4 cell line as target cells.
  • Activity is characterized by blotting the units of released light (URL) measured during 0.5 s versus the concentration in nM of tested split 4-1BBL trimer constructs. URLs are emitted due to luciferase-mediated oxidation of luciferin to oxyluciferin.
  • Figure 17 shows the NFKB-activation-induced Luciferase expression and activity as measured with the assay described in Example 6.1. Counts of released light per seconds (CPS) are measured for 0.5 s/well and plotted against the used concentration of FAP-targeted or untargeted split trimeric human 4-1BB ligand Fc (kih) constructs. Human 4-lBB-expressing HeLa-reporter cells were incubated for 6 h in the absence ( Figure 17A) or presence of crosslinking human-FAP expressing human melanoma cell line MV-3 ( Figure 17B) or WM- 266-4 ( Figure 17C). CPS were measured and blotted against the concentrations of different
  • the cell ratio is one human 4-lBB-expressing HeLa reporter cell to five tumor cells.
  • activation curves were split to four different display-blots with construct 1.1 (monovalent FAP- targeted split trimeric human 4- IBB ligand Fc (kih)) and control B (monovalent untargeted split trimeric human 4- IBB ligand Fc (kih) with CH-CL cross and charged residues) as comparison curves.
  • Figure 17A shows the activation without crosslinking FAP-expressing tumor cells
  • Figure 17B shows the activation in the presence of crosslinking FAP-expressing MV-3 tumor cells and Figure 17C shows the activation in the presence of crosslinking FAP-expressing WM- 266-4 tumor cells.
  • Figure 18 shows the NFKB-activation-induced Luciferase expression and activity as measured for the constructs of Example 2. Units of released light (URL) are measured for 0.5 s/well and plotted against the used concentration of FAP-targeted or untargeted split trimeric human 4-1BB ligand Fc (kih) constructs. Human 4-lBB-expressing HeLa-reporter cells were incubated for 6 h in the absence or presence of crosslinking human-FAP expressing human melanoma cell line MV-3 or WM-266-4. URLs were measured and blotted against the
  • FIG 19 the activation assay set up with cynomolgus monkey 4- IBB expressing T293-HEK reporter cell line is shown.
  • a crosslinking of cynomolgus monkey 4- IBB expressed on the reporter cells induces NFKB activation and NFKB-mediated Luciferase expression.
  • Luciferase can catalyze the oxidation of Luciferin to Oxyluciferin. This chemical reaction correlates positively with the strength of NFKB-mediated luciferase expression and can be measured by the strength of light emission (units of released light).
  • Figure 20 shows the NFKB-activation-induced Luciferase expression and activity.
  • Units of released light are measured for 0.5 s/well and plotted against the used concentration of FAP-targeted or untargeted split trimeric human 4-1BB ligand Fc (kih) constructs.
  • Cynomolgus monkey 4-lBB-expressing T293-HEK-reporter cells were incubated for 6 h in the absence or presence of crosslinking human-FAP expressing human melanoma cell line MV-3 or WM-266-4.
  • URLs were measured and blotted against the concentrations of different FAP-targeted or untargeted split trimeric human 4-1BB ligand Fc (kih) constructs.
  • the cell ratio is one 4- 1BB- expressing T293-HEK reporter cell to five MV-3 or two WM-266-4 cells. For better display activation curves were split to two different blots with Construct 2.1 as comparison curve.
  • FIG. 21 This scheme illustrates the principal of the T-cell activation assay described in Example 6.3. Shown is the schematic assay activation set up with HLA-A2-NLV- specific CD8 T cells and NLV -pulsed HLA-A2+ FAP+ human melanoma cell line MV-3 in the presence of different titrated concentration of FAP-targeted or untargeted split trimeric human 4- IBB ligand Fc (kih) constructs. Cells were incubated for 28 h, the last 4 h in the presence of monesin- containing Golgi-Stop. The ratio of NLV- specific CD8 T cells to MV-3 tumor cells is 1 :8.
  • Figures 22A-E and 23A-E relate to the Activation assay with HLA-A2-NLV-specific CD 8
  • Construct 1.1 monovalent FAP-targeted split trimeric human 4- IBB ligand Fc (kih)
  • Control B monovalent untargeted split trimeric human 4- IBB ligand Fc (kih)
  • Results were obtained in four independent similar experiments and show that prolonged IFNy secretion and CD 137 expression of NLV- specific CD8+ T cells is strictly dependent on simultaneous activation of T-cells via recognition of NLV-HLA-A2 complexes (signal 1) and 4- lBB-triggering by FAP-targeted human split 4- 1BBL (signal 2).
  • the effect of 4- IBB upregulation is shown in graphs of Figure 22, whereas the effect of INFy expression of CD8+ T cells is presented in graphs of Figure 23. Shown is always the frequency in percentage of positive cells in the total CD8+ T cell population.
  • Figures 24 and 25 refer to the Activation assay with HLA-A2-NLV-specific CD8 T cells and NLV-pulsed HLA-A2+ FAP+ human melanoma cell line MV-3 in the presence of titrated concentration of different FAP-targeted or untargeted split trimeric human 4- IBB ligand Fc (kih) constructs of Example 2.
  • Construct 2.1 monovalent FAP-targeted split trimeric human 4- IBB ligand Fc (kih)
  • Figure 27 shows the induction of CD8+ T cell proliferation. Shown is the frequency of proliferating CD8+ T cells versus the concentration of tested constructs.
  • Figure 28A relates to the single dose PK experiment of Construct 1.2 and Control B in healthy NOG mice. Shown is the decline in Construct concentration over the time.
  • Figure 28B shows the results of the single dose PK experiment of Constructs 2.1, 2.3, Control B and Control C in tumor bearing NOG mice humaniced with stem cells.
  • Figure 28C relates to the single dose PK experiment comparing Construct 2.1 and 2.3 in healthy NOG mice.
  • Figure 29 shows components for the assembly of split trimeric human 4- IBB ligands.
  • Figure (29 A) shows the dimeric ligand that is fused at the C-terminus to a human CL domain with mutations E123R and Q124K (charged residues) and Figure (29B) shows the monomeric 4- 1BB ligand fused to human CHI domain with mutations K147E and K213E (charged residues). Components for the assembly of bivalent CD19-targeted split trimeric human 4-1BB ligand (71- 254) antigen binding molecule (construct 3.3).
  • Figure (29C) shows the dimeric ligand being fused to the C-terminus of human IgGl Fc hole chain.
  • Figure (29D) shows the monomeric ligand being fused to the C-terminus of human IgGl Fc knob chain.
  • Figure 30 shows the CD19-targeted 4-lBBL-trimer-containing antigen binding molecules Constructs 3.1 to 3.6 of the invention.
  • the preparation and production of these constructs is described in Example 3.
  • the VH and VL domains are those of anti-CD19 antibody 8B8-018, the thick black point stands for the knob-into-hole modification. * symbolizes amino acid modifications in the CHI and CL domain (so-called charged residues).
  • Figure 31A is illustrated the randomization strategy for the CDR regions of the parental clone 8B8. Shown are the variable domains of the parental clone 8B8 and the CDR regiones (boxed) according to the numbering of Kabat. (X) represents the randomized positions.
  • Figure 31B shows the schematic description of the library generation strategies. Shown is the PCR amplification and cloning strategy used for the generation of the 8B8-based library with A) randomized CDRl and CDR2 regions in the light and heavy chain or B) randomized CDRl and CDR3 regions in the light and CDR3 region in the heavy chain. Respective enzymes used for cloning into the phagemide are indicated.
  • Figure 32 shows the alignment of the parental anti-CD 19 clone 8B8 with the selected affinity-matured binders. Shown are the sequences of clone 8B8 and all selected affinity-matured binders. CDRs of both heavy and light chains are framed.
  • Figure 33 relates to the SPR analysis of the parental 8B8 clone and its affinity-matured variants.
  • Figure 34 illustrates the setup of the assay measuring Simultaneous binding of CD 19 targeted trimeric split 4-1BBL to hu4-lBB and huCD19 (Example 8.2).
  • the graphs in Figure 35 show simultaneous binding of the CD19 targeted trimeric 4-1BBL FC fusion antigen binding molecules Constructs 3.1, 3.3, 3.4, 3.5, 3.6 and 4.4 (Analyte 1) to immobilized human 4-1BB and human CD19 (Analyte 2).
  • Figure 36 shows the binding of different CD19-targeted or un targeted split trimeric human 4-1BB ligand Fc (kih) constructs to 4-lBB-expressing CD4 and CD 8 T cells of PHA-L and Proleukin pre-activated and anti-human CD3/anti-human CD28 re-activated human PBMCs. Binding was detected with R-Phycoerythrin-fluorochrome conjugated anti-human IgG Fcy- specific goat IgG F(ab )2 fragment. Shown is the median of fluorescence intensity (MFI) versus the concentration of tested constructs.
  • MFI median of fluorescence intensity
  • binding curves are split in three different blots with construct 3.4 and control F (Isotype control hulgGI P329G LALA) as comparison curves. Binding was monitored on CD45+ CD3+ CD8+ T cells ( Figure 36A) and CD45+ CD3+ CD4+ T cells ( Figure 36B). The 4- IBB expression level on CD 8 T cells is normally higher than on CD4 T cells. All constructs bind with a quite similar affinity to human 4-1BB.
  • Figure 37 shows the binding of CD19-targeted or untargeted split trimeric human 4-1BB ligand Fc (kih) antigen binding molecules to human-CD 19 expressing B cell lymphoma cell lines: diffuse large non-Hodgkin B cell lymphoma SU-DHL-8 (37A), acute B cell precursor lymphoid leukemia Nalm6 (37B), diffuse large cell lymphoblast lymphoma Toledo (37C) and diffuse large B cell lymphoma OCTLyl8 (37D). Binding was detected with R-Phycoerythrin-fluorochrome conjugated anti-human IgG Fcy-specific goat IgG F(ab )2 fragments.
  • Figure 38 relates to NFKB-activation-induced Luciferase expression and activity of CD19- targeted or untargeted split trimeric human 4- IBB ligand Fc (kih) antigen binding molecules. Units of released light (URL) are measured for 0.5 s/well and plotted against the used
  • Figure 39 shows the binding of different humanized variants of T84.66 IgG on CEA- expressing human gastric adenocarcinoma cells. Based on the data humanized variant 1 was selected for including it into CEA-targeted trimeric human 4- IBB ligand Fc (kih) antigen binding molecules.
  • FIG 40 shows the CEA targeted 4-lBBL-trimer-containing antigen binding molecules Constructs 5.1 to 5.6 of the invention.
  • the preparation and production of these constructs is described in Example 11.
  • the VH and VL domains are those of anti-CEA antibody T84.66- LCHA, the thick black point stands for the knob-into-hole modification. * symbolizes amino acid modifications in the CHI and CL domain (so-called charged residues).
  • Figure 41A shows a schematic description of human NA3B3A2-avi His, the antigen used to assess binding of CEA-targeted trimeric split 4-1BBL Fc (kih) antigen binding molecules.
  • Figure 41B illustrates the setup of the assay measuring simultaneous binding of CEA-targeted trimeric split 4-1BBL to hu4-lBB and human NA3B3A2 (Example 12.1).
  • the graphs in Figure 42 show simultaneous binding of the CEA targeted trimeric 4-1BBL Fc fusion antigen binding molecules Constructs 5.4, 5.6, 5.7 and 5.8 (Analyte 1) to immobilized human 4- IBB and human NA3B3A2 (Analyte 2).
  • Binding of different CEA-targeted or untargeted split trimeric human 4- IBB ligand Fc (kih) constructs to 4-lBB-expressing CD4 and CD8 T cells of PHA-L and Proleukin pre-activated and anti-human CD3/anti-human CD28 re-activated human PBMCs is shown in Figure 43. Binding was detected with R-Phycoerythrin-fluorochrome conjugated anti-human IgG Fey- specific goat IgG F(ab )2 fragment. Shown is the median of fluorescence intensity (MFI) versus the
  • binding curves are split in two different blots with construct 5.4 and control F (Isotype control hulgGI P329G LALA) as comparison curves. Binding was monitored on CD45+ CD3+ CD8+ T cells (blots on the bottom) and CD45+ CD3+ CD4+ T cells (blots on the top). The 4-1BB expression level on CD 8 T cells is normally higher than on CD4 T cells. All constructs bind with quite similar affinity to human 4-1BB.
  • Figure 44 shows the binding of CEA-targeted or untargeted split trimeric human 4- IBB ligand Fc (kih) constructs to human-CEA expressing human gastric cell line MKN-45 (left) and human colorectal adenocarcinoma cells line LS I 80 (right). Binding was detected with R- Phycoerythrin-fluorochrome conjugated anti-human IgG Fcy-specific goat IgG F(ab )2 fragments. Shown is the median of fluorescence intensity (MFI) versus the concentration of tested constructs.
  • MFI median of fluorescence intensity
  • Figure 45 relates to NFKB-activation-induced Luciferase expression and activity of CEA- targeted or untargeted split trimeric human 4- IBB ligand Fc (kih) antigen binding molecules. Units of released light (URL) are measured for 0.5 s/well and blotted against the used
  • Human 4- IBB -expressing HeLa-reporter cells were incubated for 6 h in the absence or presence of crosslinking human-CEA expressing human gastric cancer cell line MKN-45. The cell ratio is one 4-lBB-expressing HeLa reporter cell to three tumor cells.
  • Figures 46A and 46B are shown the components for the assembly of monovalent FAP targeted split trimeric human OX40 ligand (construct 6.1).
  • Figure 46A relates to dimeric ligand fused to human IgGl-CL domain
  • Figure 46B relates to monomeric ligand fused to human IgGl-CHl domain.
  • Figure 46C shows the FAP targeted OX40L-trimer-containing antigen binding molecule Construct 6.1.
  • Figure 46D is shown the DP47 "untargeted" human IgGl PGLALA (control F).
  • Figure 47A shows the binding of FAP targeted split trimeric human Ox40L to FAP positive WM-266-4 cells.
  • WM-266-4 cells express high levels of human fibroblast activation protein (huFAP).
  • huFAP human fibroblast activation protein
  • MFI was measured by flow cytometry.
  • the x-axis shows the concentration of antibody constructs.
  • Figure 47B shows the binding of FAP targeted 0X40 ligand Fc (kih) construct to human FAP human Ox40 negative A549 NucLight Red cells.
  • FAP targeted 0X40 ligand Fc (kih) construct showed no binding to OX40 negative FAP negative A549 tumor cells.
  • Shown is the binding as median of fluorescence intensity (MFI) of FITC labeled anti-human IgG Fey- specific goat IgG F(ab )2 fragment which is used as secondary detection antibody.
  • MFI was measured by flow cytometry and baseline corrected by subtracting the MFI of the blank control.
  • FIG 48A the binding of FAP-Ox40L to resting and activated human CD4 T cells is shown.
  • Ox40 is not expressed on resting human CD4 T cells (left side). In the absence of human Ox40 expressing cells no binding was observed (left graphs). After activation of human PBMCs Ox40 is up-regulated on CD4+ T cells (right side).
  • MFI median of fluorescence intensity
  • the x-axis shows the concentration of antibody constructs.
  • Figure 48B shows that Ox40 is not expressed on resting human CD8 T cells (left side). In the absence of human Ox40 expressing cells no binding was observed (left graphs). After activation of human PBMCs Ox40 is up- regulated on CD8+ T cells (right side). Ox40 expression on human CD8+ T cells is lower than on CD4+ T cells and varies between donors and time points. Expression of Ox40 was low on the depicted CD 8 T cells. FAp-Ox40L bound to 0x40+ activated CD 8 T cells.
  • MFI median of fluorescence intensity
  • Activity is characterized by blotting the units of released light (URL) measured during 0.5 s versus the concentration in nM of tested construct. URLs are emitted due to luciferase-mediated oxidation of luciferin to oxyluciferin.
  • the activation of NFKB by FAP-OX40L in HeLa_hOx40_NFkB_Luc 1 reporter cells in the presence of FAP positive cells is shown in Figure 50A. Shown is the activation of NFKB signaling pathway in the reporter cells by FAP-OX40L in the presence of low FAP expressing expressing NIH-3T3 human FAP cells (ratio 3 FAP+ tumor cells to 1 reporter cell).
  • the NFKB- mediated luciferase activity was characterized by blotting the units of released light (URL), measured during 0.5 s, versus the concentration in nM of tested compounds.
  • URLs are emitted due to luciferase-mediated oxidation of luciferin to oxyluciferin.
  • Values are baseline corrected by subtracting the URLs of the blank control.
  • the area under the curve of the respective blotted dose-response curves were quantified as a marker for the agonistic capacity of each construct. The comparison is illustrated in Figure 50B. The area was calculated using GraphPad Prism. Values are baseline corrected by subtracting the value of the blank control.
  • Figure 51 shows the OX40 mediated costimulation of suboptimally TCR triggered resting human PBMC (Example 15.5).
  • Hyper-crosslinking of FAP-Ox40L by the present NIH/3T3- huFAP clone 39 cells strongly promoted survival and proliferation in human CD4 and CD8 T cells. Shown is the event count of vital CD4+ (left) and CD8+ (right) T cells.
  • Baseline values of samples containing only the anti-human CD3 (clone V9, hulgGI), resting human PBMC and NIH/3T3-huFAP clone 39 were substracted.
  • antigen binding molecule refers in its broadest sense to a molecule that specifically binds an antigenic determinant.
  • antigen binding molecules are antibodies, antibody fragments and scaffold antigen binding proteins.
  • the term "moiety capable of specific binding to a target cell antigen” refers to a polypeptide molecule that specifically binds to an antigenic determinant.
  • the antigen binding moiety is able to activate signaling through its target cell antigen.
  • the antigen binding moiety is able to direct the entity to which it is attached (e.g. the TNF family ligand trimer) to a target site, for example to a specific type of tumor cell or tumor stroma bearing the antigenic determinant.
  • Moieties capable of specific binding to a target cell antigen include antibodies and fragments thereof as further defined herein.
  • moieties capable of specific binding to a target cell antigen include scaffold antigen binding proteins as further defined herein, e.g. binding domains which are based on designed repeat proteins or designed repeat domains (see e.g. WO 2002/020565).
  • the term "moiety capable of specific binding to a target cell antigen” refers to the part of the molecule that comprises the area which specifically binds to and is complementary to part or all of an antigen.
  • a moiety capable of specific antigen binding may be provided, for example, by one or more antibody variable domains (also called antibody variable regions).
  • a moiety capable of specific antigen binding comprises an antibody light chain variable region (VL) and an antibody heavy chain variable region (VH).
  • antibody herein is used in the broadest sense and encompasses various antibody structures, including but not limited to monoclonal antibodies, polyclonal antibodies, monospecific and multispecific antibodies (e.g., bispecific antibodies), and antibody fragments so long as they exhibit the desired antigen-binding activity.
  • the term "monoclonal antibody” as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical and/or bind the same epitope, except for possible variant antibodies, e.g. containing naturally occurring mutations or arising during production of a monoclonal antibody preparation, such variants generally being present in minor amounts.
  • polyclonal antibody preparations which typically include different antibodies directed against different determinants (epitopes)
  • each monoclonal antibody of a monoclonal antibody preparation is directed against a single determinant on an antigen.
  • the term "monospecific” antibody as used herein denotes an antibody that has one or more binding sites each of which bind to the same epitope of the same antigen.
  • bispecific means that the antigen binding molecule is able to specifically bind to at least two distinct antigenic determinants.
  • a bispecific antigen binding molecule comprises two antigen binding sites, each of which is specific for a different antigenic determinant.
  • the bispecific antigen binding molecule is capable of simultaneously binding two antigenic determinants, particularly two antigenic determinants expressed on two distinct cells.
  • the term “valent” as used within the current application denotes the presence of a specified number of binding sites in an antigen binding molecule.
  • the terms “bivalent”, “tetravalent”, and “hexavalent” denote the presence of two binding sites, four binding sites, and six binding sites, respectively, in an antigen binding molecule.
  • the terms “full length antibody”, “intact antibody”, and “whole antibody” are used herein interchangeably to refer to an antibody having a structure substantially similar to a native antibody structure.
  • Native antibodies refer to naturally occurring immunoglobulin molecules with varying structures. For example, native IgG-class antibodies are heterotetrameric glycoproteins of about 150,000 daltons, composed of two light chains and two heavy chains that are disulfide-bonded.
  • each heavy chain has a variable region (VH), also called a variable heavy domain or a heavy chain variable domain, followed by three constant domains (CHI, CH2, and CH3), also called a heavy chain constant region.
  • VH variable heavy domain
  • CH2 heavy chain variable domain
  • each light chain has a variable region (VL), also called a variable light domain or a light chain variable domain, followed by a light chain constant domain (CL), also called a light chain constant region.
  • the heavy chain of an antibody may be assigned to one of five types, called a (IgA), ⁇ (IgD), ⁇ (IgE), ⁇ (IgG), or ⁇ (IgM), some of which may be further divided into subtypes, e.g.
  • the light chain of an antibody may be assigned to one of two types, called kappa ( ⁇ ) and lambda ( ⁇ ), based on the amino acid sequence of its constant domain.
  • antibody fragment refers to a molecule other than an intact antibody that comprises a portion of an intact antibody that binds the antigen to which the intact antibody binds.
  • antibody fragments include but are not limited to Fv, Fab, Fab', Fab'-SH, F(ab') 2 ; diabodies, triabodies, tetrabodies, cross-Fab fragments; linear antibodies; single-chain antibody molecules (e.g. scFv); and single domain antibodies.
  • scFv single-chain antibody molecules
  • Diabodies are antibody fragments with two antigen-binding sites that may be bivalent or bispecific, see, for example, EP 404,097; WO 1993/01161; Hudson et al., Nat Med 9, 129-134 (2003); and Hollinger et al., Proc Natl Acad Sci USA 90, 6444-6448 (1993). Triabodies and tetrabodies are also described in Hudson et al., Nat Med 9, 129-134 (2003).
  • Single-domain antibodies are antibody fragments comprising all or a portion of the heavy chain variable domain or all or a portion of the light chain variable domain of an antibody.
  • a single-domain antibody is a human single-domain antibody (Domantis, Inc., Waltham, MA; see e.g. U.S. Patent No. 6,248,516 Bl).
  • Antibody fragments can be made by various techniques, including but not limited to proteolytic digestion of an intact antibody as well as production by recombinant host cells (e.g. E. coli or phage), as described herein.
  • Papain digestion of intact antibodies produces two identical antigen-binding fragments, called "Fab” fragments containing each the heavy- and light-chain variable domains and also the constant domain of the light chain and the first constant domain (CHI) of the heavy chain.
  • Fab fragment refers to an antibody fragment comprising a light chain fragment comprising a VL domain and a constant domain of a light chain (CL), and a VH domain and a first constant domain (CHI) of a heavy chain.
  • Fab' fragments differ from Fab fragments by the addition of a few residues at the carboxy terminus of the heavy chain CHI domain including one or more cysteins from the antibody hinge region.
  • Fab'-SH are Fab' fragments in which the cysteine residue(s) of the constant domains bear a free thiol group.
  • cross-Fab fragment or "xFab fragment” or “crossover Fab fragment” refers to a Fab fragment, wherein either the variable regions or the constant regions of the heavy and light chain are exchanged.
  • Two different chain compositions of a crossover Fab molecule are possible and comprised in the bispecific antibodies of the invention: On the one hand, the variable regions of the Fab heavy and light chain are exchanged, i.e.
  • the crossover Fab molecule comprises a peptide chain composed of the light chain variable region (VL) and the heavy chain constant region (CHI), and a peptide chain composed of the heavy chain variable region (VH) and the light chain constant region (CL).
  • This crossover Fab molecule is also referred to as CrossFab (VLVH)-
  • the crossover Fab molecule comprises a peptide chain composed of the heavy chain variable region (VH) and the light chain constant region (CL), and a peptide chain composed of the light chain variable region (VL) and the heavy chain constant region (CHI).
  • This crossover Fab molecule is also referred to as CrossFab (CLCHI)-
  • a “single chain Fab fragment” or “scFab” is a polypeptide consisting of an antibody heavy chain variable domain (VH), an antibody constant domain 1 (CHI), an antibody light chain variable domain (VL), an antibody light chain constant domain (CL) and a linker, wherein said antibody domains and said linker have one of the following orders in N-terminal to C-terminal direction: a) VH-CH1 -linker- VL-CL, b) VL-CL-linker-VH-CHl, c) VH-CL-linker-VL-CHl or d) VL-CH1 -linker- VH-CL; and wherein said linker is a polypeptide of at least 30 amino acids, preferably between 32 and 50 amino acids.
  • Said single chain Fab fragments are stabilized via the natural disulfide bond between the CL domain and the CHI domain.
  • these single chain Fab molecules might be further stabilized by generation of interchain disulfide bonds via insertion of cysteine residues (e.g. position 44 in the variable heavy chain and position 100 in the variable light chain according to Kabat numbering).
  • a “crossover single chain Fab fragment” or “x-scFab” is a is a polypeptide consisting of an antibody heavy chain variable domain (VH), an antibody constant domain 1 (CHI), an antibody light chain variable domain (VL), an antibody light chain constant domain (CL) and a linker, wherein said antibody domains and said linker have one of the following orders in N- terminal to C-terminal direction: a) VH-CL-linker-VL-CHl and b) VL-CH1 -linker- VH-CL; wherein VH and VL form together an antigen-binding site which binds specifically to an antigen and wherein said linker is a polypeptide of at least 30 amino acids.
  • these x-scFab molecules might be further stabilized by generation of interchain disulfide bonds via insertion of cysteine residues (e.g. position 44 in the variable heavy chain and position 100 in the variable light chain according to Kabat numbering).
  • a "single-chain variable fragment (scFv)" is a fusion protein of the variable regions of the heavy (V H ) and light chains (V L ) of an antibody, connected with a short linker peptide of ten to about 25 amino acids.
  • the linker is usually rich in glycine for flexibility, as well as serine or threonine for solubility, and can either connect the N-terminus of the V H with the C-terminus of the V L , or vice versa.
  • This protein retains the specificity of the original antibody, despite removal of the constant regions and the introduction of the linker.
  • scFv antibodies are, e.g. described in Houston, J.S., Methods in Enzymol. 203 (1991) 46-96).
  • antibody fragments comprise single chain polypeptides having the characteristics of a VH domain, namely being able to assemble together with a VL domain, or of a VL domain, namely being able to assemble together with a VH domain to a functional antigen binding site and thereby providing the antigen binding property of full length antibodies.
  • fibronectin and designed ankyrin repeat proteins have been used as alternative scaffolds for antigen- binding domains, see, e.g., Gebauer and Skerra, Engineered protein scaffolds as next- generation antibody therapeutics. Curr Opin Chem Biol 13:245-255 (2009) and Stumpp et al., Darpins: A new generation of protein therapeutics. Drug Discovery Today 13: 695-701 (2008).
  • a scaffold antigen binding protein is selected from the group consisting of CTLA-4 (Evibody), Lipocalins (Anticalin), a Protein A-derived molecule such as Z-domain of Protein A (Affibody), an A-domain (Avimer/Maxibody), a serum transferrin (trans-body); a designed ankyrin repeat protein (DARPin), a variable domain of antibody light chain or heavy chain (single-domain antibody, sdAb), a variable domain of antibody heavy chain (nanobody, aVH), V NAR fragments, a fibronectin (AdNectin), a C-type lectin domain (Tetranectin); a variable domain of a new antigen receptor beta-lactamase (V NAR fragments), a human gamma- crystallin or ubiquitin (Affilin molecules); a kunitz type domain of human protease inhibitors, microbodies such as the proteins from the knot
  • CTLA-4 Cytotoxic T Lymphocyte-associated Antigen 4
  • CTLA-4 is a CD28-family receptor expressed on mainly CD4+ T-cells. Its extracellular domain has a variable domain- like Ig fold. Loops corresponding to CDRs of antibodies can be substituted with heterologous sequence to confer different binding properties.
  • CTLA-4 molecules engineered to have different binding specificities are also known as Evibodies (e.g. US7166697B1). Evibodies are around the same size as the isolated variable region of an antibody (e.g. a domain antibody). For further details see Journal of Immunological Methods 248 (1-2), 31-45 (2001).
  • Lipocalins are a family of extracellular proteins which transport small hydrophobic molecules such as steroids, bilins, retinoids and lipids. They have a rigid beta-sheet secondary structure with a number of loops at the open end of the conical structure which can be engineered to bind to different target antigens. Anticalins are between 160-180 amino acids in size, and are derived from lipocalins. For further details see Biochim Biophys Acta 1482: 337-350 (2000), US7250297B1 and US20070224633.
  • An affibody is a scaffold derived from Protein A of Staphylococcus aureus which can be engineered to bind to antigen.
  • the domain consists of a three-helical bundle of approximately 58 amino acids. Libraries have been generated by randomization of surface residues. For further details see Protein Eng. Des. Sel. 17, 455-462 (2004) and EP 1641818A1.
  • Avimers are multidomain proteins derived from the A-domain scaffold family. The native domains of approximately 35 amino acids adopt a defined disulfide bonded structure. Diversity is generated by shuffling of the natural variation exhibited by the family of A-domains. For further details see Nature Biotechnology 23(12), 1556 - 1561 (2005) and Expert Opinion on Investigational Drugs 16(6), 909-917 (June 2007).
  • a transferrin is a monomeric serum transport glycoprotein. Transferrins can be engineered to bind different target antigens by insertion of peptide sequences in a permissive surface loop. Examples of engineered transferrin scaffolds include the Trans-body. For further details see J. Biol. Chem 274, 24066-24073 (1999).
  • DARPins Designed Ankyrin Repeat Proteins
  • Ankyrin which is a family of proteins that mediate attachment of integral membrane proteins to the cytoskeleton.
  • a single ankyrin repeat is a 33 residue motif consisting of two alpha-helices and a beta-turn. They can be engineered to bind different target antigens by randomizing residues in the first alpha-helix and a beta-turn of each repeat. Their binding interface can be increased by increasing the number of modules (a method of affinity maturation).
  • affinity maturation For further details see J. Mol. Biol. 332, 489-503 (2003), PNAS 100(4), 1700-1705 (2003) and J. Mol. Biol. 369, 1015-1028 (2007) and
  • a single-domain antibody is an antibody fragment consisting of a single monomeric variable antibody domain.
  • the first single domain were derived from the variable domain of the antibody heavy chain from camelids (nanobodies or V H H fragments).
  • the term single-domain antibody includes an autonomous human heavy chain variable domain (aVH) or V NAR fragments derived from sharks.
  • Fibronectin is a scaffold which can be engineered to bind to antigen.
  • Adnectins consists of a backbone of the natural amino acid sequence of the 10th domain of the 15 repeating units of human fibronectin type III (FN3). Three loops at one end of the .beta.-sandwich can be engineered to enable an Adnectin to specifically recognize a therapeutic target of interest. For further details see Protein Eng. Des. Sel. 18, 435- 444 (2005), US20080139791, WO2005056764 and US6818418B1.
  • Peptide aptamers are combinatorial recognition molecules that consist of a constant scaffold protein, typically thioredoxin (TrxA) which contains a constrained variable peptide loop inserted at the active site.
  • TrxA thioredoxin
  • Microbodies are derived from naturally occurring microproteins of 25-50 amino acids in length which contain 3-4 cysteine bridges - examples of microproteins include KalataBI and conotoxin and knottins.
  • the microproteins have a loop which can beengineered to include upto 25 amino acids without affecting the overall fold of the microprotein.
  • engineered knottin domains see WO2008098796.
  • an "antigen binding molecule that binds to the same epitope" as a reference molecule refers to an antigen binding molecule that blocks binding of the reference molecule to its antigen in a competition assay by 50% or more, and conversely, the reference molecule blocks binding of the antigen binding molecule to its antigen in a competition assay by 50% or more.
  • an antigen binding domain refers to the part of an antigen binding molecule that comprises the area which specifically binds to and is complementary to part or all of an antigen. Where an antigen is large, an antigen binding molecule may only bind to a particular part of the antigen, which part is termed an epitope.
  • An antigen binding domain may be provided by, for example, one or more variable domains (also called variable regions).
  • an antigen binding domain comprises an antibody light chain variable region (VL) and an antibody heavy chain variable region (VH).
  • antigenic determinant is synonymous with “antigen” and “epitope,” and refers to a site (e.g. a contiguous stretch of amino acids or a conformational configuration made up of different regions of non-contiguous amino acids) on a polypeptide macromolecule to which an antigen binding moiety binds, forming an antigen binding moiety- antigen complex.
  • Useful antigenic determinants can be found, for example, on the surfaces of tumor cells, on the surfaces of virus-infected cells, on the surfaces of other diseased cells, on the surface of immune cells, free in blood serum, and/or in the extracellular matrix (ECM).
  • ECM extracellular matrix
  • the proteins useful as antigens herein can be any native form the proteins from any vertebrate source, including mammals such as primates (e.g. humans) and rodents (e.g. mice and rats), unless otherwise indicated.
  • the antigen is a human protein.
  • the term encompasses the "full-length", unprocessed protein as well as any form of the protein that results from processing in the cell.
  • the term also encompasses naturally occurring variants of the protein, e.g. splice variants or allelic variants.
  • ELISA enzyme-linked immunosorbent assay
  • SPR Surface Plasmon Resonance
  • the extent of binding of an antigen binding molecule to an unrelated protein is less than about 10% of the binding of the antigen binding molecule to the antigen as measured, e.g. by SPR.
  • an molecule that binds to the antigen has a dissociation constant (Kd) of ⁇ 1 ⁇ , ⁇ 100 nM, ⁇ 10 nM, ⁇ 1 nM, ⁇ 0.1 nM, ⁇ 0.01 nM, or ⁇ 0.001 nM (e.g. 10 ⁇ 8 M or less, e.g. from 10 ⁇ 8 M to 10 "13 M, e.g. from 10 "9 M to 10 "13 M).
  • Binding affinity refers to the strength of the sum total of non-covalent interactions between a single binding site of a molecule (e.g. an antibody) and its binding partner (e.g. an antigen). Unless indicated otherwise, as used herein, “binding affinity” refers to intrinsic binding affinity which reflects a 1: 1 interaction between members of a binding pair (e.g.
  • the affinity of a molecule X for its partner Y can generally be represented by the dissociation constant (Kd), which is the ratio of dissociation and association rate constants (koff and kon, respectively).
  • Kd dissociation constant
  • equivalent affinities may comprise different rate constants, as long as the ratio of the rate constants remains the same.
  • Affinity can be measured by common methods known in the art, including those described herein. A particular method for measuring affinity is Surface Plasmon Resonance (SPR).
  • target cell antigen refers to an antigenic determinant presented on the surface of a target cell, for example a cell in a tumor such as a cancer cell or a cell of the tumor stroma.
  • the target cell antigen is an antigen on the surface of a tumor cell.
  • target cell antigen is selected from the group consisting of Fibroblast Activation Protein (FAP), Carcinoembryonic Antigen (CEA), Melanoma-associated Chondroitin Sulfate Proteoglycan (MCSP), Epidermal Growth Factor Receptor (EGFR), CD19, CD20 and CD33.
  • FAP Fibroblast Activation Protein
  • CEA Carcinoembryonic Antigen
  • MCSP Melanoma-associated Chondroitin Sulfate Proteoglycan
  • EGFR Epidermal Growth Factor Receptor
  • CD19, CD20 and CD33 CD19, CD20 and CD33.
  • the target cell antigen is Fibroblast Activation Protein (FAP).
  • FAP Fibroblast activation protein
  • Prolyl endopeptidase FAP or Seprase EC 3.4.21
  • FAP Fibroblast activation protein
  • mammals such as primates (e.g. humans) non-human primates (e.g. cynomolgus monkeys) and rodents (e.g. mice and rats), unless otherwise indicated.
  • the term encompasses "full-length,” unprocessed FAP as well as any form of FAP which results from processing in the cell.
  • the term also encompasses naturally occurring variants of FAP, e.g., splice variants or allelic variants.
  • the antigen binding molecule of the invention is capable of specific binding to human, mouse and/or cynomolgus FAP.
  • the amino acid sequence of human FAP is shown in UniProt (www.uniprot.org) accession no. Q12884 (version 149, SEQ ID NO:20), or NCBI (www.ncbi.nlm.nih.gov/) RefSeq NP_004451.2.
  • the extracellular domain (ECD) of human FAP extends from amino acid position 26 to 760.
  • the amino acid and nucleotide sequences of a His- tagged human FAP ECD is shown in SEQ ID NOs 15 and 16, respectively.
  • the amino acid sequence of mouse FAP is shown in UniProt accession no.
  • mouse FAP extends from amino acid position 26 to 761.
  • SEQ ID NOs 24 and 25 show the amino acid and nucleotide sequences, respectively, of a His-tagged mouse FAP ECD.
  • SEQ ID NOs 26 and 27 show the amino acid and nucleotide sequences, respectively, of a His-tagged cynomolgus FAP ECD.
  • an anti-FAP binding molecule of the invention binds to the extracellular domain of FAP. Exemplary anti-FAP binding molecules are described in International Patent Application No. WO 2012/020006 A2.
  • CEA Carcinoembryonic antigen-related cell adhesion molecule 5
  • CEACAM5 Carcinoembryonic antigen- related cell adhesion molecule 5
  • CEA cynomolgus monkeys
  • rodents e.g. mice and rats
  • the amino acid sequence of human CEA is shown in UniProt accession no. P06731 (version 151, SEQ ID NO:28).
  • CEA has long been identified as a tumor- associated antigen (Gold and Freedman, J Exp Med., 121:439-462, 1965; Berinstein N. L., J Clin Oncol., 20:2197-2207, 2002). Originally classified as a protein expressed only in fetal tissue, CEA has now been identified in several normal adult tissues.
  • tumors of epithelial origin contain CEA as a tumor associated antigen. While the presence of CEA itself does not indicate transformation to a cancerous cell, the distribution of CEA is indicative. In normal tissue, CEA is generally expressed on the apical surface of the cell (Hammarstrom S., Semin Cancer Biol.
  • CEA tends to be expressed over the entire surface of cancerous cells (Hammarstrom S., Semin Cancer Biol. 9(2):67-81 (1999)). This change of expression pattern makes CEA accessible to antibody binding in cancerous cells.
  • CEA expression increases in cancerous cells.
  • increased CEA expression promotes increased intercellular adhesions, which may lead to metastasis (Marshall J., Semin Oncol., 30(a Suppl. 8):30-6, 2003).
  • the prevalence of CEA expression in various tumor entities is generally very high. In concordance with published data, own analyses performed in tissue samples confirmed its high prevalence, with
  • CEA colorectal carcinoma
  • CRC colorectal carcinoma
  • NSCLC non-small cell lung cancer
  • HER3 non-small cell lung cancer
  • breast cancer low expression was found in small cell lung cancer and glioblastoma.
  • CEA is readily cleaved from the cell surface and shed into the blood stream from tumors, either directly or via the lymphatics.
  • the level of serum CEA has been used as a clinical marker for diagnosis of cancers and screening for recurrence of cancers, particularly colorectal cancer (Goldenberg D M., The International Journal of Biological Markers, 7: 183-188, 1992; Chau I., et al., J Clin Oncol., 22: 1420-1429, 2004; Flamini et al., Clin Cancer Res; 12(23):6985-6988, 2006).
  • MCSP Chondroitin Sulfate Proteoglycan
  • CSPG4 Chondroitin Sulfate Proteoglycan 4
  • the amino acid sequence of human MCSP is shown in UniProt accession no. Q6UVK1 (version 103, SEQ ID NO:29).
  • Epidermal Growth Factor Receptor also named Proto- oncogene c-ErbB-1 or Receptor tyrosine -protein kinase erbB-1, refers to any native EGFR from any vertebrate source, including mammals such as primates (e.g. humans) non-human primates (e.g. cynomolgus monkeys) and rodents (e.g. mice and rats), unless otherwise indicated.
  • the amino acid sequence of human EGFR is shown in UniProt accession no. P00533 (version 211, SEQ ID NO:30).
  • CD19 refers to B-lymphocyte antigen CD 19, also known as B-lymphocyte surface antigen B4 or T-cell surface antigen Leu- 12 and includes any native CD 19 from any vertebrate source, including mammals such as primates (e.g. humans) non-human primates (e.g. cynomolgus monkeys) and rodents (e.g. mice and rats), unless otherwise indicated.
  • the amino acid sequence of human CD19 is shown in Uniprot accession no. P15391 (version 160, SEQ ID NO:31). The term encompasses "full-length" unprocessed human CD19 as well as any form of human CD 19 that results from processing in the cell as long as the antibody as reported herein binds thereto.
  • CD19 is a structurally distinct cell surface receptor expressed on the surface of human B cells, including, but not limited to, pre-B cells, B cells in early development ⁇ i.e., immature B cells), mature B cells through terminal differentiation into plasma cells, and malignant B cells.
  • CD19 is expressed by most pre-B acute lymphoblastic leukemias (ALL), non- Hodgkin's lymphomas, B cell chronic lymphocytic leukemias (CLL), pro-lymphocytic leukemias, hairy cell leukemias, common acute lymphocytic leukemias, and some Null-acute lymphoblastic leukemias.
  • ALL pre-B acute lymphoblastic leukemias
  • CLL B cell chronic lymphocytic leukemias
  • pro-lymphocytic leukemias pro-lymphocytic leukemias
  • hairy cell leukemias common acute lymphocytic leukemias
  • CD19 on plasma cells further suggests it may be expressed on differentiated B cell tumors such as multiple myeloma. Therefore, the CD 19 antigen is a target for immunotherapy in the treatment of non-Hodgkin's lymphoma, chronic lymphocytic leukemia and/or acute lymphoblastic leukemia.
  • CD20 refers to B-lymphocyte antigen CD20, also known as membrane- spanning 4- domains subfamily A member 1 (MS4A1), B-lymphocyte surface antigen Bl or Leukocyte surface antigen Leu- 16, and includes any native CD20 from any vertebrate source, including mammals such as primates (e.g. humans) non-human primates (e.g. cynomolgus monkeys) and rodents (e.g. mice and rats), unless otherwise indicated.
  • the amino acid sequence of human CD20 is shown in Uniprot accession no. PI 1836 (version 149, SEQ ID NO:32).
  • CD33 refers to Myeloid cell surface antigen CD33, also known as SIGLEC3 or gp67, and includes any native CD33 from any vertebrate source, including mammals such as primates (e.g. humans) non- human primates (e.g. cynomolgus monkeys) and rodents (e.g. mice and rats), unless otherwise indicated.
  • the amino acid sequence of human CD33 is shown in Uniprot accession no. P20138 (version 157, SEQ ID NO:33).
  • variable region refers to the domain of an antibody heavy or light chain that is involved in binding the antigen binding molecule to antigen.
  • the variable domains of the heavy chain and light chain (VH and VL, respectively) of a native antibody generally have similar structures, with each domain comprising four conserved framework regions (FRs) and three hypervariable regions (HVRs). See, e.g., Kindt et al., Kuby Immunology, 6th ed., W.H. Freeman and Co., page 91 (2007).
  • a single VH or VL domain may be sufficient to confer antigen-binding specificity.
  • hypervariable region refers to each of the regions of an antibody variable domain which are hypervariable in sequence and/or form structurally defined loops ("hypervariable loops").
  • native four-chain antibodies comprise six HVRs; three in the VH (HI, H2, H3), and three in the VL (LI, L2, L3).
  • HVRs generally comprise amino acid residues from the hypervariable loops and/or from the "complementarity determining regions" (CDRs), the latter being of highest sequence variability and/or involved in antigen recognition.
  • CDRs complementarity determining regions
  • Exemplary hypervariable loops occur at amino acid residues 26-32 (LI), 50- 52 (L2), 91-96 (L3), 26-32 (HI), 53-55 (H2), and 96-101 (H3).
  • Exemplary CDRs CDR-L1, CDR-L2, CDR-L3, CDR-H1, CDR-H2, and CDR-H3 occur at amino acid residues 24-34 of LI, 50-56 of L2, 89-97 of L3, 31-35B of HI, 50-65 of H2, and 95-102 of H3.
  • Hypervariable regions are also referred to as complementarity determining regions (CDRs), and these terms are used herein interchangeably in reference to portions of the variable region that form the antigen binding regions.
  • CDRs complementarity determining regions
  • Kabat et al. also defined a numbering system for variable region sequences that is applicable to any antibody.
  • Kabat et al. also defined a numbering system for variable region sequences that is applicable to any antibody.
  • One of ordinary skill in the art can unambiguously assign this system of "Kabat numbering” to any variable region sequence, without reliance on any experimental data beyond the sequence itself.
  • Kabat numbering refers to the numbering system set forth by Kabat et al., U.S. Dept. of Health and Human Services, "Sequence of Proteins of Immunological Interest” ( 1983). Unless otherwise specified, references to the numbering of specific amino acid residue positions in an antibody variable region are according to the Kabat numbering system.
  • CDRs generally comprise the amino acid residues that form the hypervariable loops.
  • CDRs also comprise "specificity determining residues," or "SDRs,” which are residues that contact antigen. SDRs are contained within regions of the CDRs called abbreviated-CDRs, or a-CDRs.
  • Exemplary a-CDRs (a-CDR-Ll, a-CDR-L2, a-CDR-L3, a- CDR-H1, a-CDR-H2, and a-CDR-H3) occur at amino acid residues 31-34 of LI, 50-55 of L2, 89-96 of L3, 31-35B of HI, 50-58 of H2, and 95-102 of H3.
  • HVR residues and other residues in the variable domain are numbered herein according to Kabat et al., supra.
  • affinity matured in the context of antigen binding molecules (e.g., antibodies) refers to an antigen binding molecule that is derived from a reference antigen binding molecule, e.g., by mutation, binds to the same antigen, preferably binds to the same epitope, as the reference antibody; and has a higher affinity for the antigen than that of the reference antigen binding molecule.
  • Affinity maturation generally involves modification of one or more amino acid residues in one or more CDRs of the antigen binding molecule.
  • the affinity matured antigen binding molecule binds to the same epitope as the initial reference antigen binding molecule.
  • FR Framework or "FR” refers to variable domain residues other than hypervariable region (HVR) residues.
  • the FR of a variable domain generally consists of four FR domains: FR1, FR2, FR3, and FR4. Accordingly, the HVR and FR sequences generally appear in the following sequence in VH (or VL): FR1-H1(L1)-FR2-H2(L2)-FR3-H3(L3)-FR4.
  • acceptor human framework for the purposes herein is a framework comprising the amino acid sequence of a light chain variable domain (VL) framework or a heavy chain variable domain (VH) framework derived from a human immunoglobulin framework or a human consensus framework, as defined below.
  • An acceptor human framework "derived from” a human immunoglobulin framework or a human consensus framework may comprise the same amino acid sequence thereof, or it may contain amino acid sequence changes. In some embodiments, the number of amino acid changes are 10 or less, 9 or less, 8 or less, 7 or less, 6 or less, 5 or less, 4 or less, 3 or less, or 2 or less.
  • the VL acceptor human framework is identical in sequence to the VL human immunoglobulin framework sequence or human consensus framework sequence.
  • chimeric antibody refers to an antibody in which a portion of the heavy and/or light chain is derived from a particular source or species, while the remainder of the heavy and/or light chain is derived from a different source or species.
  • the "class" of an antibody refers to the type of constant domain or constant region possessed by its heavy chain.
  • the heavy chain constant domains that correspond to the different classes of immunoglobulins are called , ⁇ , ⁇ , ⁇ , and ⁇ respectively..
  • a “humanized” antibody refers to a chimeric antibody comprising amino acid residues from non-human HVRs and amino acid residues from human FRs.
  • a humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the HVRs (e.g., CDRs) correspond to those of a non- human antibody, and all or substantially all of the FRs correspond to those of a human antibody.
  • a humanized antibody optionally may comprise at least a portion of an antibody constant region derived from a human antibody.
  • a "humanized form" of an antibody, e.g., a non-human antibody refers to an antibody that has undergone humanization.
  • Other forms of "humanized antibodies” encompassed by the present invention are those in which the constant region has been additionally modified or changed from that of the original antibody to generate the properties according to the invention, especially in regard to Clq binding and/or Fc receptor (FcR) binding.
  • a "human” antibody is one which possesses an amino acid sequence which corresponds to that of an antibody produced by a human or a human cell or derived from a non-human source that utilizes human antibody repertoires or other human antibody-encoding sequences. This definition of a human antibody specifically excludes a humanized antibody comprising non- human antigen-binding residues.
  • Fc domain or "Fc region” herein is used to define a C-terminal region of an antibody heavy chain that contains at least a portion of the constant region.
  • the term includes native sequence Fc regions and variant Fc regions.
  • An IgG Fc region comprises an IgG CH2 and an IgG CH3 domain.
  • the "CH2 domain” of a human IgG Fc region usually extends from an amino acid residue at about position 231 to an amino acid residue at about position 340.
  • a carbohydrate chain is attached to the CH2 domain.
  • the CH2 domain herein may be a native sequence CH2 domain or variant CH2 domain.
  • the "CH3 domain” comprises the stretch of residues C-terminal to a CH2 domain in an Fc region (i.e.
  • the CH3 region herein may be a native sequence CH3 domain or a variant CH3 domain (e.g. a CH3 domain with an introduced "protuberance” ("knob”) in one chain thereof and a corresponding introduced “cavity” ("hole”) in the other chain thereof; see US Patent No. 5,821,333, expressly incorporated herein by reference).
  • a human IgG heavy chain Fc region extends from Cys226, or from Pro230, to the carboxyl-terminus of the heavy chain.
  • the C-terminal lysine (Lys447) of the Fc region may or may not be present.
  • numbering of amino acid residues in the Fc region or constant region is according to the EU numbering system, also called the EU index, as described in Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, MD, 1991.
  • the "knob-into-hole" technology is described e.g. in US 5,731,168; US 7,695,936;
  • the method involves introducing a protuberance ("knob”) at the interface of a first polypeptide and a corresponding cavity ("hole”) in the interface of a second polypeptide, such that the protuberance can be positioned in the cavity so as to promote heterodimer formation and hinder homodimer formation.
  • Protuberances are constructed by replacing small amino acid side chains from the interface of the first polypeptide with larger side chains (e.g. tyrosine or tryptophan).
  • Compensatory cavities of identical or similar size to the protuberances are created in the interface of the second polypeptide by replacing large amino acid side chains with smaller ones (e.g. alanine or threonine).
  • the protuberance and cavity can be made by altering the nucleic acid encoding the polypeptides, e.g. by site-specific mutagenesis, or by peptide synthesis.
  • a knob modification comprises the amino acid substitution T366W in one of the two subunits of the Fc domain
  • the hole modification comprises the amino acid substitutions T366S, L368A and Y407V in the other one of the two subunits of the Fc domain.
  • the subunit of the Fc domain comprising the knob modification additionally comprises the amino acid substitution S354C
  • the subunit of the Fc domain comprising the hole modification additionally comprises the amino acid substitution Y349C.
  • a "region equivalent to the Fc region of an immunoglobulin" is intended to include naturally occurring allelic variants of the Fc region of an immunoglobulin as well as variants having alterations which produce substitutions, additions, or deletions but which do not decrease substantially the ability of the immunoglobulin to mediate effector functions (such as antibody- dependent cellular cytotoxicity).
  • one or more amino acids can be deleted from the N-terminus or C-terminus of the Fc region of an immunoglobulin without substantial loss of biological function.
  • Such variants can be selected according to general rules known in the art so as to have minimal effect on activity (see, e.g., Bowie, J. U. et al., Science 247: 1306-10 (1990)).
  • effector functions refers to those biological activities attributable to the Fc region of an antibody, which vary with the antibody isotype.
  • antibody effector functions include: Clq binding and complement dependent cytotoxicity (CDC), Fc receptor binding, antibody-dependent cell-mediated cytotoxicity (ADCC), antibody-dependent cellular phagocytosis (ADCP), cytokine secretion, immune complex-mediated antigen uptake by antigen presenting cells, down regulation of cell surface receptors (e.g. B cell receptor), and B cell activation.
  • an “activating Fc receptor” is an Fc receptor that following engagement by an Fc region of an antibody elicits signaling events that stimulate the receptor-bearing cell to perform effector functions.
  • Activating Fc receptors include FcyRIIIa (CD16a), FcyRI (CD64), FcyRIIa (CD32), and FcaRI (CD89).
  • a particular activating Fc receptor is human FcyRIIIa (see UniProt accession no. P08637, version 141).
  • TNF ligand family member or “TNF family ligand” refers to a
  • Cytokines in general, and in particular the members of the TNF ligand family, play a crucial role in the stimulation and coordination of the immune system. At present, nineteen cyctokines have been identified as members of the TNF (tumour necrosis factor) ligand superfamily on the basis of sequence, functional, and structural similarities. All these ligands are type II transmembrane proteins with a C-terminal extracellular domain
  • TNF homology domain TNF homology domain
  • TNF ligand family are selected from the group consisting of Lymphotoxin (also known as LTA or TNFSF1), TNF (also known as TNFSF2), ⁇ (also known as TNFSF3), OX40L (also known as TNFSF4), CD40L (also known as CD 154 or TNFSF5), FasL (also known as CD95L, CD 178 or TNFSF6), CD27L (also known as CD70 or TNFSF7), CD30L (also known as CD153 or TNFSF8), 4-1BBL (also known as TNFSF9), TRAIL (also known as AP02L, CD253 or TNFSF10), RANKL (also known as CD254 or TNFSF11), TWEAK (also known as TNFSF12), APRIL (also known as CD256 or TNFSF13), BAFF (also known as CD257 or TNFSF13B), LIGHT (also known as CD258 or TNFSF14), TL1A (also known as VEGI),
  • the term refers to any native TNF family ligand from any vertebrate source, including mammals such as primates (e.g. humans), non- human primates (e.g. cynomolgus monkeys) and rodents (e.g. mice and rats), unless otherwise indicated.
  • the TNF ligand family member is selected from the group consisting of OX40L, FasL, CD27L, TRAIL, 4-1BBL, CD40L and GITRL.
  • the TNF ligand family member is selected from 4-1BBL and OX40L.
  • the human TNF ligands have the following amino acid sequences: human Lymphotoxin a (UniProt accession no. P01374, SEQ ID NO:34), human TNF (UniProt accession no. P01375, SEQ ID NO:35), human Lymphotoxin ⁇ (UniProt accession no. Q06643, SEQ ID NO:36), human OX40L (UniProt accession no. P23510, SEQ ID NO:37), human CD40L (UniProt accession no.
  • Ectodomain is the domain of a membrane protein that extends into the extracellular space (i.e. the space outside the target cell). Ectodomains are usually the parts of proteins that initiate contact with surfaces, which leads to signal transduction.
  • the ectodomain of TNF ligand family member as defined herein thus refers to the part of the TNF ligand protein that extends into the extracellular space (the extracellular domain), but also includes shorter parts or fragments thereof that are responsible for the trimerization and for the binding to the
  • TNF receptor corresponding TNF receptor.
  • ectodomain of a TNF ligand family member or a fragment thereof thus refers to the extracellular domain of the TNF ligand family member that forms the extracellular domain or to parts thereof that are still able to bind to the receptor (receptor binding domain).
  • costimulatory TNF ligand family member or “costimulatory TNF family ligand” refers to a subgroup of TNF ligand family members, which are able to costimulate proliferation and cytokine production of T-cells. These TNF family ligands can costimulate TCR signals upon interaction with their corresponding TNF receptors and the interaction with their receptors leads to recruitment of TNFR-associated factors (TRAF), which initiate signalling cascades that result in T-cell activation.
  • TNF TNFR-associated factors
  • Costimulatory TNF family ligands are selected from the group consisting of 4-lBBL, OX40L, GITRL, CD70, CD30L and LIGHT, more particularly the costimulatory TNF ligand family member is selected from 4-lBBL and OX40L.
  • 4-lBBL is a type II transmembrane protein and one member of the TNF ligand family.
  • Complete or full length 4-lBBL having the amino acid sequence of SEQ ID NO:42 has been described to form trimers on the surface of cells.
  • the formation of trimers is enabled by specific motives of the ectodomain of 4-lBBL. Said motives are designated herein as "trimerization region".
  • the amino acids 50-254 of the human 4-lBBL sequence (SEQ ID NO:52) form the extracellular domain of 4-lBBL, but even fragments thereof are able to form the trimers.
  • the term "ectodomain of 4-lBBL or a fragment thereof refers to a polypeptide having an amino acid sequence selected from SEQ ID NO:4
  • amino acids 52-254 of human 4-lBBL SEQ ID NO: l (amino acids 71-254 of human 4-lBBL), SEQ ID NO:3 (amino acids 80-254 of human 4-lBBL) and SEQ ID NO:2 (amino acids 85-254 of human 4-lBBL) or a polypeptide having an amino acid sequence selected from SEQ ID NO:96 (amino acids 71-248 of human 4-lBBL), SEQ ID NO:375 (amino acids 52-248 of human 4-lBBL), SEQ ID NO:374 (amino acids 80-248 of human 4-lBBL) and SEQ ID NO:373 (amino acids 85-248 of human 4-lBBL), but also other fragments of the ectodomain capable of trimerization are included herein.
  • OX40L is another type II transmembrane protein and a further member of the TNF ligand family.
  • Complete or full length human OX40L has the amino acid sequence of SEQ ID NO:37.
  • the amino acids 51-183 of the human OX40L sequence (SEQ ID NO:53) form the extracellular domain of OX40L, but even fragments thereof that are able to form the trimers.
  • the term "ectodomain of OX40L or a fragment thereof refers to a polypeptide having an amino acid sequence selected from SEQ ID NO:53 (amino acids 51-183 of human OX40L) or SEQ ID NO:54 (amino acids 52-183 of human OX40L), but also other fragments of the ectodomain capable of trimerization are included herein.
  • peptide linker refers to a peptide comprising one or more amino acids, typically about 2 to 20 amino acids.
  • Peptide linkers are known in the art or are described herein.
  • Suitable, non-immunogenic linker peptides are, for example, (G 4 S) n , (SG 4 ) n or G 4 (SG 4 ) n peptide linkers, wherein "n” is generally a number between 1 and 10, typically between 1 and 4, in particular 2, i.e. the peptides selected from the group consisting of GGGGS (SEQ ID NO: 128), GGGGSGGGGS (SEQ ID NO: 13), SGGGGSGGGG (SEQ ID NO:55) and
  • GGGGSGGGGSGGGG (SEQ ID NO:56), but also include the sequences GSPGSSSSGS (SEQ ID NO:57), GSGSGSGS (SEQ ID NO:58), GSGSGNGS (SEQ ID NO:59), GGSGSGSG (SEQ ID NO:60), GGSGSG (SEQ ID NO:61), GGSG (SEQ ID NO:62), GGSGNGSG (SEQ ID NO:
  • Peptide linkers of particular interest are (G4S)i or GGGGS (SEQ ID NO: 128), (G 4 S) 2 or GGGGSGGGGS (SEQ ID NO: 13) and GSPGSSSSGS (SEQ ID NO:57), more particularly (G 4 S) 2 or GGGGSGGGGS (SEQ ID NO: 13) and GSPGSSSSGS (SEQ ID NO:57).
  • amino acid denotes the group of naturally occurring carboxy a-amino acids comprising alanine (three letter code: ala, one letter code: A), arginine (arg, R), asparagine (asn, N), aspartic acid (asp, D), cysteine (cys, C), glutamine (gin, Q), glutamic acid (glu, E), glycine (gly, G), histidine (his, H), isoleucine (ile, I), leucine (leu, L), lysine (lys, K), methionine (met, M), phenylalanine (phe, F), proline (pro, P), serine (ser, S), threonine (thr, T), tryptophan (trp, W), tyrosine (tyr, Y), and valine (val, V).
  • a "single chain fusion protein” as used herein refers to a single chain polypeptide composed of one or two ectodomains of said TNF ligand family member fused to a part of antigen binding moiety or Fc part. The fusion may occur by directly linking the N or C-terminal amino acid of the antigen binding moiety via a peptide linker to the C- or N-terminal amino acid of the ectodomain of said TNF ligand family member.
  • fused or “connected” is meant that the components (e.g. a polypeptide and an ectodomain of said TNF ligand family member) are linked by peptide bonds, either directly or via one or more peptide linkers.
  • Percent (%) amino acid sequence identity with respect to a reference polypeptide (protein) sequence is defined as the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in the reference polypeptide sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, BLAST-2, ALIGN. SAWI or Megalign (DNASTAR) software. Those skilled in the art can determine appropriate parameters for aligning sequences, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared.
  • % amino acid sequence identity values are generated using the sequence comparison computer program ALIGN-2.
  • the ALIGN- 2 sequence comparison computer program was authored by Genentech, Inc., and the source code has been filed with user documentation in the U.S. Copyright Office, Washington D.C., 20559, where it is registered under U.S. Copyright Registration No. TXU510087.
  • the ALIGN-2 program is publicly available from Genentech, Inc., South San Francisco, California, or may be compiled from the source code.
  • the ALIGN-2 program should be compiled for use on a UNIX operating system, including digital UNIX V4.0D. All sequence comparison parameters are set by the ALIGN-2 program and do not vary.
  • % amino acid sequence identity of a given amino acid sequence A to, with, or against a given amino acid sequence B is calculated as follows:
  • amino acid sequence variants of the TNF ligand trimer- containing antigen binding molecules are contemplated. For example, it may be desirable to improve the binding affinity and/or other biological properties of the TNF ligand trimer-containing antigen binding molecules.
  • Amino acid sequence variants of the TNF ligand trimer-containing antigen binding molecules may be prepared by introducing appropriate modifications into the nucleotide sequence encoding the molecules, or by peptide synthesis. Such modifications include, for example, deletions from, and/or insertions into and/or substitutions of residues within the amino acid sequences of the antibody.
  • Any combination of deletion, insertion, and substitution can be made to arrive at the final construct, provided that the final construct possesses the desired characteristics, e.g., antigen-binding.
  • Sites of interest for substitutional mutagenesis include the HVRs and Framework (FRs). Conservative substitutions are provided in Table B under the heading "Preferred Substitutions" and further described below in reference to amino acid side chain classes (1) to (6). Amino acid substitutions may be introduced into the molecule of interest and the products screened for a desired activity, e.g., retained/improved antigen binding, decreased immunogenicity, or improved ADCC or CDC.
  • Amino acids may be grouped according to common side-chain properties:
  • Non-conservative substitutions will entail exchanging a member of one of these classes for another class.
  • amino acid sequence variants includes substantial variants wherein there are amino acid substitutions in one or more hypervariable region residues of a parent antigen binding molecule (e.g. a humanized or human antibody).
  • a parent antigen binding molecule e.g. a humanized or human antibody.
  • the resulting variant(s) selected for further study will have modifications (e.g., improvements) in certain biological properties (e.g., increased affinity, reduced immunogenicity) relative to the parent antigen binding molecule and/or will have substantially retained certain biological properties of the parent antigen binding molecule.
  • An exemplary substitutional variant is an affinity matured antibody, which may be conveniently generated, e.g., using phage display-based affinity maturation techniques such as those described herein.
  • one or more HVR residues are mutated and the variant antigen binding molecules displayed on phage and screened for a particular biological activity (e.g. binding affinity).
  • substitutions, insertions, or deletions may occur within one or more HVRs so long as such alterations do not substantially reduce the ability of the antigen binding molecule to bind antigen.
  • conservative alterations e.g., conservative substitutions as provided herein
  • a useful method for identification of residues or regions of an antibody that may be targeted for mutagenesis is called "alanine scanning mutagenesis" as described by Cunningham and Wells (1989) Science, 244: 1081-1085.
  • a residue or group of target residues e.g., charged residues such as Arg, Asp, His, Lys, and Glu
  • a neutral or negatively charged amino acid e.g., alanine or polyalanine
  • Further substitutions may be introduced at the amino acid locations demonstrating functional sensitivity to the initial substitutions.
  • a crystal structure of an antigen- antigen binding molecule complex to identify contact points between the antibody and antigen. Such contact residues and neighboring residues may be targeted or eliminated as candidates for substitution.
  • Variants may be screened to determine whether they contain the desired properties.
  • Amino acid sequence insertions include amino- and/or carboxyl-terminal fusions ranging in length from one residue to polypeptides containing a hundred or more residues, as well as intrasequence insertions of single or multiple amino acid residues.
  • terminal insertions include TNF family ligand trimer-containing antigen binding molecule with an N- terminal methionyl residue.
  • Other insertional variants of the molecule include the fusion to the N- or C-terminus to a polypeptide which increases the serum half-life of the TNF ligand trimer- containing antigen binding molecules.
  • the TNF family ligand trimer-containing antigen binding molecules provided herein are altered to increase or decrease the extent to which the antibody is glycosylated. Glycosylation variants of the molecules may be conveniently obtained by altering the amino acid sequence such that one or more glycosylation sites is created or removed. Where the TNF ligand trimer-containing antigen binding molecule comprises an Fc region, the carbohydrate attached thereto may be altered. Native antibodies produced by mammalian cells typically comprise a branched, biantennary oligosaccharide that is generally attached by an N- linkage to Asn297 of the CH2 domain of the Fc region. See, e.g., Wright et al. TIBTECH 15:26- 32 (1997).
  • the oligosaccharide may include various carbohydrates, e.g., mannose, N-acetyl glucosamine (GlcNAc), galactose, and sialic acid, as well as a fucose attached to a GlcNAc in the "stem" of the biantennary oligosaccharide structure.
  • modifications of the oligosaccharide in TNF family ligand trimer-containing antigen binding molecule may be made in order to create variants with certain improved properties.
  • variants of TNF family ligand trimer-containing antigen binding molecules are provided having a carbohydrate structure that lacks fucose attached (directly or indirectly) to an Fc region. Such fucosylation variants may have improved ADCC function, see e.g. US Patent Publication Nos. US
  • TNF family ligand trimer-containing antigen binding molecules of the invention include those with bisected oligosaccharides, e.g., in which a biantennary oligosaccharide attached to the Fc region is bisected by GlcNAc. Such variants may have reduced fucosylation and/or improved ADCC function., see for example WO 2003/011878 (Jean-Mairet et al.); US Patent No. 6,602,684 (Umana et al.); and US 2005/0123546 (Umana et al.). Variants with at least one galactose residue in the oligosaccharide attached to the Fc region are also provided. Such antibody variants may have improved CDC function and are described, e.g., in WO
  • cysteine engineered variants of the TNF family ligand trimer-containing antigen binding molecule of the invention e.g.,
  • thioMAbs in which one or more residues of the molecule are substituted with cysteine residues.
  • the substituted residues occur at accessible sites of the molecule.
  • reactive thiol groups are thereby positioned at accessible sites of the antibody and may be used to conjugate the antibody to other moieties, such as drug moieties or linker-drug moieties, to create an immunoconjugate.
  • any one or more of the following residues may be substituted with cysteine: V205 (Kabat numbering) of the light chain; Al 18 (EU numbering) of the heavy chain; and S400 (EU numbering) of the heavy chain Fc region.
  • Cysteine engineered antigen binding molecules may be generated as described, e.g., in U.S. Patent No. 7,521,541.
  • the TNF family ligand trimer-containing antigen binding molecules provided herein may be further modified to contain additional non-proteinaceous moieties that are known in the art and readily available.
  • the moieties suitable for derivatization of the antibody include but are not limited to water soluble polymers.
  • Non-limiting examples of water soluble polymers include, but are not limited to, polyethylene glycol (PEG), copolymers of ethylene glycol/propylene glycol, carboxymethylcellulose, dextran, polyvinyl alcohol, polyvinyl pyrrolidone, poly- 1, 3-dioxolane, poly-l,3,6-trioxane, ethylene/maleic anhydride copolymer, polyaminoacids (either homopolymers or random copolymers), and dextran or poly(n-vinyl pyrrolidone)polyethylene glycol, propropylene glycol homopolymers, prolypropylene oxide/ethylene oxide co-polymers, polyoxyethylated polyols (e.g., glycerol), polyvinyl alcohol, and mixtures thereof.
  • Polyethylene glycol propionaldehyde may have advantages in
  • the polymer may be of any molecular weight, and may be branched or unbranched.
  • the number of polymers attached to the antibody may vary, and if more than one polymer is attached, they can be the same or different molecules. In general, the number and/or type of polymers used for derivatization can be determined based on considerations including, but not limited to, the particular properties or functions of the antibody to be improved, whether the bispecific antibody derivative will be used in a therapy under defined conditions, etc.
  • conjugates of an antibody and non-proteinaceous moiety that may be selectively heated by exposure to radiation are provided.
  • the non-proteinaceous moiety is a carbon nanotube (Kam, N.W. et al., Proc.
  • the radiation may be of any wavelength, and includes, but is not limited to, wavelengths that do not harm ordinary cells, but which heat the non-proteinaceous moiety to a temperature at which cells proximal to the antibody-non-proteinaceous moiety are killed.
  • immunoconjugates of the TNF family ligand trimer-containing antigen binding molecules provided herein maybe obtained.
  • An “immunoconjugate” is an antibody conjugated to one or more heterologous molecule(s), including but not limited to a cytotoxic agent.
  • polynucleotide refers to an isolated nucleic acid molecule or construct, e.g. messenger RNA (mRNA), virally-derived RNA, or plasmid DNA (pDNA).
  • mRNA messenger RNA
  • pDNA virally-derived RNA
  • a polynucleotide may comprise a conventional phosphodiester bond or a non-conventional bond (e.g. an amide bond, such as found in peptide nucleic acids (PNA).
  • nucleic acid molecule refers to any one or more nucleic acid segments, e.g. DNA or RNA fragments, present in a polynucleotide.
  • isolated nucleic acid molecule or polynucleotide is intended a nucleic acid molecule,
  • DNA or RNA which has been removed from its native environment.
  • DNA or RNA which has been removed from its native environment.
  • recombinant polynucleotide encoding a polypeptide contained in a vector is considered isolated for the purposes of the present invention.
  • Further examples of an isolated polynucleotide include recombinant polynucleotides maintained in heterologous host cells or purified (partially or substantially) polynucleotides in solution.
  • An isolated polynucleotide includes a polynucleotide molecule contained in cells that ordinarily contain the polynucleotide molecule, but the polynucleotide molecule is present extrachromosomally or at a chromosomal location that is different from its natural chromosomal location.
  • Isolated RNA molecules include in vivo or in vitro RNA transcripts of the present invention, as well as positive and negative strand forms, and double- stranded forms. Isolated polynucleotides or nucleic acids according to the present invention further include such molecules produced synthetically.
  • a polynucleotide or a nucleic acid may be or may include a regulatory element such as a promoter, ribosome binding site, or a transcription terminator.
  • nucleic acid or polynucleotide having a nucleotide sequence at least, for example, 95% "identical" to a reference nucleotide sequence of the present invention it is intended that the nucleotide sequence of the polynucleotide is identical to the reference sequence except that the polynucleotide sequence may include up to five point mutations per each 100 nucleotides of the reference nucleotide sequence.
  • a polynucleotide having a nucleotide sequence at least 95% identical to a reference nucleotide sequence up to 5% of the nucleotides in the reference sequence may be deleted or substituted with another nucleotide, or a number of nucleotides up to 5% of the total nucleotides in the reference sequence may be inserted into the reference sequence.
  • These alterations of the reference sequence may occur at the 5' or 3' terminal positions of the reference nucleotide sequence or anywhere between those terminal positions, interspersed either individually among residues in the reference sequence or in one or more contiguous groups within the reference sequence.
  • any particular polynucleotide sequence is at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to a nucleotide sequence of the present invention can be determined conventionally using known computer programs, such as the ones discussed above for polypeptides (e.g.
  • expression cassette refers to a polynucleotide generated recombinantly or synthetically, with a series of specified nucleic acid elements that permit transcription of a particular nucleic acid in a target cell.
  • the recombinant expression cassette can be incorporated into a plasmid, chromosome, mitochondrial DNA, plastid DNA, virus, or nucleic acid fragment.
  • the recombinant expression cassette portion of an expression vector includes, among other sequences, a nucleic acid sequence to be transcribed and a promoter.
  • the expression cassette of the invention comprises polynucleotide sequences that encode bispecific antigen binding molecules of the invention or fragments thereof.
  • vector or "expression vector” is synonymous with "expression construct” and refers to a DNA molecule that is used to introduce and direct the expression of a specific gene to which it is operably associated in a target cell.
  • the term includes the vector as a self -replicating nucleic acid structure as well as the vector incorporated into the genome of a host cell into which it has been introduced.
  • the expression vector of the present invention comprises an expression cassette. Expression vectors allow transcription of large amounts of stable mRNA. Once the expression vector is inside the target cell, the ribonucleic acid molecule or protein that is encoded by the gene is produced by the cellular transcription and/or translation machinery.
  • the expression vector of the invention comprises an expression cassette that comprises polynucleotide sequences that encode bispecific antigen binding molecules of the invention or fragments thereof.
  • host cell refers to cells into which exogenous nucleic acid has been introduced, including the progeny of such cells.
  • Host cells include “transforaiants” and “transformed cells,” which include the primary transformed cell and progeny derived therefrom without regard to the number of passages. Progeny may not be completely identical in nucleic acid content to a parent cell, but may contain mutations. Mutant progeny that have the same function or biological activity as screened or selected for in the originally transformed cell are included herein.
  • a host cell is any type of cellular system that can be used to generate the bispecific antigen binding molecules of the present invention.
  • Host cells include cultured cells, e.g.
  • mammalian cultured cells such as CHO cells, BHK cells, NSO cells, SP2/0 cells, YO myeloma cells, P3X63 mouse myeloma cells, PER cells, PER.C6 cells or hybridoma cells, yeast cells, insect cells, and plant cells, to name only a few, but also cells comprised within a transgenic animal, transgenic plant or cultured plant or animal tissue.
  • an “effective amount” of an agent refers to the amount that is necessary to result in a physiological change in the cell or tissue to which it is administered.
  • a “therapeutically effective amount” of an agent refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired therapeutic or prophylactic result.
  • a therapeutically effective amount of an agent for example eliminates, decreases, delays, minimizes or prevents adverse effects of a disease.
  • mammals include, but are not limited to, domesticated animals (e.g. cows, sheep, cats, dogs, and horses), primates (e.g. humans and non- human primates such as monkeys), rabbits, and rodents (e.g. mice and rats). Particularly, the individual or subject is a human.
  • domesticated animals e.g. cows, sheep, cats, dogs, and horses
  • primates e.g. humans and non- human primates such as monkeys
  • rabbits e.g. mice and rats
  • rodents e.g. mice and rats
  • pharmaceutical composition refers to a preparation which is in such form as to permit the biological activity of an active ingredient contained therein to be effective, and which contains no additional components which are unacceptably toxic to a subject to which the formulation would be administered.
  • pharmaceutically acceptable excipient refers to an ingredient in a pharmaceutical composition, other than an active ingredient, which is nontoxic to a subject.
  • a pharmaceutically acceptable excipient includes, but is not limited to, a buffer, a stabilizer, or a preservative.
  • package insert is used to refer to instructions customarily included in commercial packages of therapeutic products, that contain information about the indications, usage, dosage, administration, combination therapy, contraindications and/or warnings concerning the use of such therapeutic products.
  • treatment refers to clinical intervention in an attempt to alter the natural course of the individual being treated, and can be performed either for prophylaxis or during the course of clinical pathology. Desirable effects of treatment include, but are not limited to, preventing occurrence or recurrence of disease, alleviation of symptoms, diminishment of any direct or indirect pathological consequences of the disease, preventing metastasis, decreasing the rate of disease progression, amelioration or palliation of the disease state, and remission or improved prognosis.
  • the molecules of the invention are used to delay development of a disease or to slow the progression of a disease.
  • cancer refers to proliferative diseases, such as lymphomas, carcinoma, lymphoma, blastoma, sarcoma, leukemia, lymphocytic leukemias, lung cancer, non- small cell lung (NSCL) cancer, bronchioloalviolar cell lung cancer, bone cancer, pancreatic cancer, skin cancer, cancer of the head or neck, cutaneous or intraocular melanoma, uterine cancer, ovarian cancer, rectal cancer, cancer of the anal region, stomach cancer, gastric cancer, colorectal cancer (CRC), pancreatic cancer, breast cancer, triple-negative breast cancer , uterine cancer, carcinoma of the fallopian tubes, carcinoma of the endometrium, carcinoma of the cervix, carcinoma of the vagina, carcinoma of the vulva, Hodgkin's Disease, cancer of the esophagus, cancer of the small intestine, cancer of the endocrine system, cancer of the thyroid gland, cancer of the parathyroid gland, cancer
  • TNF family ligand trimer-containing antigen binding molecules of the invention TNF family ligand trimer-containing antigen binding molecules of the invention
  • the invention provides novel TNF family ligand trimer-containing antigen binding molecules with particularly advantageous properties such as producibility, stability, binding affinity, biological activity, targeting efficiency and reduced toxicity.
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising
  • the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof.
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising (a) at least one moiety capable of specific binding to a target cell antigen,
  • the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof, and
  • the TNF family ligand trimer-containing antigen binding molecule comprises (a) at least one moiety capable of specific binding to a target cell antigen and
  • the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof, wherein the TNF ligand family member is costimulates human T-cell activation.
  • the TNF family ligand trimer-containing antigen binding molecule comprises (a) at least one moiety capable of specific binding to a target cell antigen and
  • the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof, wherein the ectodomains of a TNF ligand family member are identical in all instances.
  • a TNF family ligand trimer-containing antigen binding molecule of claim 1 comprising
  • the antigen binding molecule is characterized in that (i) the first polypeptide contains a CHI or CL domain and the second polypeptide contains a CL or CHI domain, respectively, wherein the second polypeptide is linked to the first polypeptide by a disulfide bond between the CHI and CL domain, and wherein the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the CHI or CL domain by a peptide linker and wherein the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to the CL or CHI domain of said polypeptide, or
  • the first polypeptide contains a CH3 domain and the second polypeptide contains a
  • ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the C-terminus of the CH3 domain by a peptide linker and wherein the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to C-terminus of the CH3 domain of said polypeptide, or
  • the first polypeptide contains a VH-CL or a VL-CH1 domain and the second
  • polypeptide contains a VL-CH1 domain or a VH-CL domain, respectively, wherein the second polypeptide is linked to the first polypeptide by a disulfide bond between the CHI and CL domain, and wherein the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to to VH or VL by a peptide linker and wherein the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to VL or VH of said polypeptide.
  • the TNF family ligand trimer-containing antigen binding molecule comprises a TNF ligand family member that costimulates human T-cell activation which is selected from 4-lBBL and OX40L. More particularly, the TNF ligand family member is 4-lBBL.
  • the ectodomain of a TNF ligand family member comprises the amino acid sequence selected from the group consisting of SEQ ID NO: l, SEQ ID NO: 2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:96, SEQ ID NO: 373, SEQ ID NO:374 and SEQ ID NO:
  • the ectodomain of a TNF ligand family member or fragment thereof comprises the amino acid sequence selected from the group consisting of SEQ ID NO: l, SEQ ID NO: 2, SEQ ID NO:3, SEQ ID NO:4 and SEQ ID NO:96, particularly the amino acid sequence of SEQ ID NO: l or SEQ ID NO:96.
  • the ectodomain of a TNF ligand family member or fragment thereof comprises the amino acid sequence of SEQ ID NO:96.
  • the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
  • the antigen binding molecule is characterized in that the first polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO:5, SEQ ID NO:97, SEQ ID NO:98 and SEQ ID NO:99 and in that the second polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO: l, SEQ ID NO:96, SEQ ID NO:3 and SEQ ID NO:4.
  • the first polypeptide comprises the amino acid sequence of SEQ ID NO:97 and the second polypeptide comprises the amino acid sequence of SEQ ID NO:96.
  • the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
  • the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
  • the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
  • the TNF ligand family member is OX40L.
  • TNF family ligand trimer-containing antigen binding molecule wherein the ectodomain of a TNF ligand family member comprises the amino acid sequence of SEQ ID NO:53 or SEQ ID NO:54, particularly the amino acid sequence of SEQ ID NO:53.
  • the invention relates to a TNF family ligand trimer-containing antigen binding molecule comprising
  • the antigen binding molecule comprises the amino acid sequence of SEQ ID NO:371 or SEQ ID:372 and in that the second polypeptide comprises the amino acid sequence of SEQ ID NO:53 or SEQ ID NO:54, respectively.
  • the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
  • the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the CHI or CL domain by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to the CL or CHI domain of said polypeptide.
  • a TNF family ligand trimer-containing antigen binding molecule comprising
  • the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the CHI domain by a peptide linker and in that the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to the CL domain of said polypeptide.
  • TNF family ligand trimer-containing antigen binding molecule comprising
  • the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the CL domain by a peptide linker and in that the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to the CHI domain of said polypeptide.
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising
  • the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof.
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising
  • the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to said polypeptide.
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising
  • the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof.
  • TNF family ligand trimer-containing antigen binding molecule comprising
  • the antigen binding molecule is characterized in that the first polypeptide contains a CH3 domain and the second polypeptide contains a CH3 domain, respectively, and wherein the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the C-terminus of the CH3 domain by a peptide linker and wherein the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to C-terminus of the CH3 domain of said polypeptide.
  • TNF family ligand trimer-containing antigen binding molecule comprises two moieties capable of specific binding to a target cell antigen.
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising
  • the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof,
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule as defined herein before, wherein the moiety capable of specific binding to a target cell antigen is selected from the group consisting of an antibody, an antibody fragment and a scaffold antigen binding protein.
  • a TNF family ligand trimer-containing antigen binding molecule as described herein before, wherein the moiety capable of specific binding to a target cell antigen is selected from the group consisting of an antibody fragment, a Fab molecule, a crossover Fab molecule, a single chain Fab molecule, a Fv molecule, a scFv molecule, a single domain antibody, an aVH and a scaffold antigen binding protein.
  • the moiety capable of specific binding to a target cell antigen is an aVH or a scaffold antigen binding protein.
  • the moiety capable of specific binding to a target cell antigen is a scaffold antigen binding protein capable of specific binding to a target cell antigen.
  • the TNF family ligand trimer-containing antigen binding molecule comprises one or two moieties capable of specific binding to a target cell antigen.
  • a TNF family ligand trimer-containing antigen binding molecule wherein the moiety capable of specific binding to a target cell antigen is a Fab molecule or a crossover Fab molecule capable of specific binding to a target cell antigen.
  • the moiety capable of specific binding to a target cell antigen is a Fab capable of specific binding to a target cell antigen.
  • TNF family ligand trimer-containing antigen binding molecule as described herein, wherein the target cell antigen is selected from the group consisting of
  • Fibroblast Activation Protein FAP
  • MCSP Melanoma-associated Chondroitin Sulfate Proteoglycan
  • EGFR Epidermal Growth Factor Receptor
  • CEA Carcinoembryonic Antigen
  • a TNF family ligand trimer-containing antigen binding molecule wherein a peptide comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C-terminus to the CHI domain of a heavy chain by a second peptide linker and wherein one ectodomain of said TNF ligand family member or a fragment thereof is fused at the its C-terminus to the CL domain on a light chain by a third peptide linker.
  • a TNF family ligand trimer-containing antigen binding molecule comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C-terminus to the CL domain of a heavy chain by a second peptide linker and wherein one ectodomain of said TNF ligand family member or a fragment thereof is fused at the its C-terminus to the CHI domain on a light chain by a third peptide linker.
  • the invention is concerned with a TNF family ligand trimer-containing antigen binding molecule according to the invention, wherein a peptide comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C-terminus to the CL domain of a light chain by a second peptide linker and wherein one ectodomain of said TNF ligand family member or a fragment thereof is fused at the its C-terminus to the CHI domain of the heavy chain by a third peptide linker.
  • the invention relates to a TNF family ligand trimer-containing antigen binding molecule as defined above, wherein the peptide linker is (G4S) 2 .
  • the first peptide linker is (G4S) 2 (SEQ ID NO: 13)
  • the second peptide linker is GSPGSSSSGS (SEQ ID NO:57)
  • the third peptide linker is (G4S) 2 (SEQ ID NO: 13).
  • the invention relates to a TNF ligand trimer-containing antigen binding molecule as defined above, wherein the first peptide linker is (G4S) 2 (SEQ ID NO: 13), the second peptide linker is (G4S) 2 (SEQ ID NO: 13), and the third peptide linker is (G4S) 2 (SEQ ID NO: 13).
  • the TNF family ligand trimer-containing antigen binding molecule as defined herein before comprises an Fc domain composed of a first and a second subunit capable of stable association.
  • the TNF family ligand trimer-containing antigen binding molecule of the invention comprises (a) a Fab molecule capable of specific binding to a target cell antigen, wherein the Fab heavy chain is fused at the C-terminus to the N-terminus of a CH2 domain in the Fc domain and (c) an Fc domain composed of a first and a second subunit capable of stable association.
  • the Fc domain is an IgG, particularly an IgGl Fc domain or an IgG4 Fc domain. More particularly, the Fc domain is an IgGl Fc domain. In a particular aspect, the Fc domain comprises a modification promoting the association of the first and second subunit of the Fc domain.
  • the Fc domain of the TNF family ligand trimer-containing antigen binding molecules of the invention consists of a pair of polypeptide chains comprising heavy chain domains of an immunoglobulin molecule.
  • the Fc domain of an immunoglobulin G (IgG) molecule is a dimer, each subunit of which comprises the CH2 and CH3 IgG heavy chain constant domains. The two subunits of the Fc domain are capable of stable association with each other.
  • the Fc domain confers favorable pharmacokinetic properties to the antigen binding molecules of the invention, including a long serum half-life which contributes to good accumulation in the target tissue and a favorable tissue-blood distribution ratio. At the same time it may, however, lead to undesirable targeting of the bispecific antibodies of the invention to cells expressing Fc receptors rather than to the preferred antigen-bearing cells. Accordingly, in particular aspects, the Fc domain of the TNF family ligand trimer-containing antigen binding molecule of the invention exhibits reduced binding affinity to an Fc receptor and/or reduced effector function, as compared to a native IgGl Fc domain. In one aspect, the Fc does not substantially bind to an Fc receptor and/or does not induce effector function.
  • the Fc receptor is an Fey receptor.
  • the Fc receptor is a human Fc receptor.
  • the Fc receptor is an activating human Fey receptor, more specifically human FcyRIIIa, FcyRI or FcyRIIa, most specifically human FcyRIIIa.
  • the Fc domain does not induce effector function.
  • the reduced effector function can include, but is not limited to, one or more of the following: reduced complement dependent cytotoxicity (CDC), reduced antibody-dependent cell-mediated cytotoxicity (ADCC), reduced antibody-dependent cellular phagocytosis (ADCP), reduced cytokine secretion, reduced immune complex-mediated antigen uptake by antigen-presenting cells, reduced binding to NK cells, reduced binding to macrophages, reduced binding to monocytes, reduced binding to polymorphonuclear cells, reduced direct signaling inducing apoptosis, reduced dendritic cell maturation, or reduced T cell priming.
  • CDC complement dependent cytotoxicity
  • ADCC reduced antibody-dependent cell-mediated cytotoxicity
  • ADCP reduced antibody-dependent cellular phagocytosis
  • reduced immune complex-mediated antigen uptake by antigen-presenting cells reduced binding to NK cells, reduced binding to macrophages, reduced binding to monocytes, reduced binding to polymorphonuclear cells, reduced direct signaling inducing apoptosis, reduced dend
  • one or more amino acid modifications may be introduced into the Fc region of a TNF family ligand trimer-containing antigen binding molecule provided herein, thereby generating an Fc region variant.
  • the Fc region variant may comprise a human Fc region sequence (e.g., a human IgGl, IgG2, IgG3 or IgG4 Fc region) comprising an amino acid modification (e.g. a substitution) at one or more amino acid positions.
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising
  • the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof, and
  • an Fc domain composed of a first and a second subunit capable of stable association, wherein the Fc domain comprises one or more amino acid substitution that reduces binding to an Fc receptor, in particular towards Fey receptor.
  • the Fc domain of the TNF family ligand trimer-containing antigen binding molecule of the invention comprises one or more amino acid mutation that reduces the binding affinity of the Fc domain to an Fc receptor and/or effector function.
  • the same one or more amino acid mutation is present in each of the two subunits of the Fc domain.
  • the Fc domain comprises an amino acid substitution at a position of E233, L234, L235, N297, P331 and P329 (EU numbering).
  • the Fc domain comprises amino acid substitutions at positions 234 and 235 (EU numbering) and/or 329 (EU numbering) of the IgG heavy chains.
  • a trimeric TNF family ligand-containing antigen binding molecule which comprises an Fc domain with the amino acid substitutions L234A, L235A and P329G ("P329G LALA", EU numbering) in the IgG heavy chains.
  • the amino acid substitutions L234A and L235A refer to the so-called LALA mutation.
  • the "P329G LALA" combination of amino acid substitutions almost completely abolishes Fey receptor binding of a human IgGl Fc domain and is described in International Patent Appl. Publ. No. WO 2012/130831 Al which also describes methods of preparing such mutant Fc domains and methods for determining its properties such as Fc receptor binding or effector functions.
  • EU numbering refers to the numbering according to EU index of Kabat et al , Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, MD, 1991.
  • Fc domains with reduced Fc receptor binding and/or effector function also include those with substitution of one or more of Fc domain residues 238, 265, 269, 270, 297, 327 and 329 (U.S. Patent No. 6,737,056).
  • Such Fc mutants include Fc mutants with substitutions at two or more of amino acid positions 265, 269, 270, 297 and 327, including the so-called "DANA" Fc mutant with substitution of residues 265 and 297 to alanine (US Patent No. 7,332,581).
  • the Fc domain is an IgG4 Fc domain. IgG4 antibodies exhibit reduced binding affinity to Fc receptors and reduced effector functions as compared to IgGl antibodies.
  • the Fc domain is an IgG4 Fc domain comprising an amino acid substitution at position S228 (Kabat numbering), particularly the amino acid substitution S228P.
  • the Fc domain is an IgG4 Fc domain comprising amino acid
  • Mutant Fc domains can be prepared by amino acid deletion, substitution, insertion or modification using genetic or chemical methods well known in the art. Genetic methods may include site- specific mutagenesis of the encoding DNA sequence, PCR, gene synthesis, and the like. The correct nucleotide changes can be verified for example by sequencing.
  • Binding to Fc receptors can be easily determined e.g. by ELISA, or by Surface Plasmon Resonance (SPR) using standard instrumentation such as a BIAcore instrument (GE Healthcare), and Fc receptors such as may be obtained by recombinant expression. A suitable such binding assay is described herein. Alternatively, binding affinity of Fc domains or cell activating bispecific antigen binding molecules comprising an Fc domain for Fc receptors may be evaluated using cell lines known to express particular Fc receptors, such as human NK cells expressing Fcyllla receptor.
  • Effector function of an Fc domain, or bispecific antibodies of the invention comprising an Fc domain can be measured by methods known in the art.
  • a suitable assay for measuring ADCC is described herein.
  • Other examples of in vitro assays to assess ADCC activity of a molecule of interest are described in U.S. Patent No. 5,500,362; Hellstrom et al. Proc Natl Acad Sci USA 83, 7059-7063 (1986) and Hellstrom et al., Proc Natl Acad Sci USA 82, 1499-1502 (1985); U.S. Patent No. 5,821,337; Bruggemann et al., J Exp Med 166, 1351-1361 (1987).
  • non- radioactive assays methods may be employed (see, for example, ACTITM non-radioactive cytotoxicity assay for flow cytometry (CellTechnology, Inc. Mountain View, CA); and CytoTox 96® non-radioactive cytotoxicity assay (Promega, Madison, WI)).
  • Useful effector cells for such assays include peripheral blood mononuclear cells (PBMC) and Natural Killer (NK) cells.
  • ADCC activity of the molecule of interest may be assessed in vivo, e.g. in a animal model such as that disclosed in Clynes et al., Proc Natl Acad Sci USA 95, 652- 656 (1998).
  • binding of the Fc domain to a complement component, specifically to Clq is reduced.
  • said reduced effector function includes reduced CDC.
  • Clq binding assays may be carried out to determine whether the bispecific antibodies of the invention is able to bind Clq and hence has CDC activity. See e.g., Clq and C3c binding ELISA in WO 2006/029879 and WO 2005/100402.
  • a CDC assay may be performed (see, for example, Gazzano-Santoro et al., J Immunol Methods 202, 163 (1996); Cragg et al., Blood 101, 1045-1052 (2003); and Cragg and Glennie, Blood 103, 2738-2743 (2004)).
  • the Fc domain comprises a modification promoting the association of the first and second subunit of the Fc domain.
  • the TNF family ligand trimer-containing antigen binding molecules of the invention comprise (a) at least one moiety capable of specific binding to a target cell antigen, (b) a first and a second polypeptide that are linked to each other by a disulfide bond,
  • the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof, and (c) an Fc domain composed of a first and a second subunit capable of stable association, wherein the Fc domain comprises one or more amino acid substitution that reduces binding to an Fc receptor, in particular towards Fey receptor.
  • they comprise different moieties, fused to one or the other of the two subunits of the Fc domain that are typically comprised in two non-identical polypetide chains ("heavy chains").
  • the Fc domain of the TNF family ligand trimer-containing antigen binding molecules of the invention comprises a modification promoting the association of the first and the second subunit of the Fc domain.
  • the site of most extensive protein-protein interaction between the two subunits of a human IgG Fc domain is in the CH3 domain of the Fc domain.
  • said modification is particularly in the CH3 domain of the Fc domain.
  • said modification is a so-called "knob-into-hole” modification, comprising a "knob” modification in one of the two subunits of the Fc domain and a "hole” modification in the other one of the two subunits of the Fc domain.
  • the invention relates to a TNF family ligand trimer-containing antigen binding molecule as described herein before which comprises an IgG molecule, wherein the Fc part of the first heavy chain comprises a first dimerization module and the Fc part of the second heavy chain comprises a second dimerization module allowing a heterodimerization of the two heavy chains of the IgG molecule and the first dimerization module comprises knobs and the second dimerization module comprises holes according to the knob into hole technology.
  • the knob-into-hole technology is described e.g.
  • the method involves introducing a protuberance ("knob") at the interface of a first polypeptide and a corresponding cavity ("hole”) in the interface of a second polypeptide, such that the
  • protuberance can be positioned in the cavity so as to promote heterodimer formation and hinder homodimer formation.
  • Protuberances are constructed by replacing small amino acid side chains from the interface of the first polypeptide with larger side chains (e.g. tyrosine or tryptophan).
  • Compensatory cavities of identical or similar size to the protuberances are created in the interface of the second polypeptide by replacing large amino acid side chains with smaller ones (e.g. alanine or threonine).
  • an amino acid residue is replaced with an amino acid residue having a larger side chain volume, thereby generating a protuberance within the CH3 domain of the first subunit which is positionable in a cavity within the CH3 domain of the second subunit, and in the CH3 domain of the second subunit of the Fc domain an amino acid residue is replaced with an amino acid residue having a smaller side chain volume, thereby generating a cavity within the CH3 domain of the second subunit within which the protuberance within the CH3 domain of the first subunit is positionable.
  • the protuberance and cavity can be made by altering the nucleic acid encoding the polypeptides, e.g. by site-specific mutagenesis, or by peptide synthesis.
  • the threonine residue at position 366 is replaced with a tryptophan residue (T366W)
  • T366W tryptophan residue
  • Y407V valine residue
  • the threonine residue at position 366 is replaced with a serine residue (T366S) and the leucine residue at position 368 is replaced with an alanine residue (L368A).
  • the serine residue at position 354 is replaced with a cysteine residue (S354C)
  • the tyrosine residue at position 349 is replaced by a cysteine residue (Y349C).
  • the introduction of these two cysteine residues results in the formation of a disulfide bridge between the two subunits of the Fc domain. The disulfide bridge further stabilizes the dimer (Carter, J Immunol Methods 248, 7-15 (2001)).
  • a modification promoting association of the first and the second subunit of the Fc domain comprises a modification mediating electrostatic steering effects, e.g. as described in PCT publication WO 2009/089004.
  • this method involves replacement of one or more amino acid residues at the interface of the two Fc domain subunits by charged amino acid residues so that homodimer formation becomes electrostatically unfavorable but heterodimerization electrostatically favorable.
  • the TNF family ligand trimer-containing antigen binding molecules can contain different charged amino acid substitutions (so-called "charged residues"). These modifications are introduced in the crossed or non-crossed CHI and CL domains.
  • the invention relates to a TNF family ligand trimer-containing antigen binding molecule, wherein in one of CL domains the amino acid at position 123 (EU numbering) has been replaced by arginine (R) and the amino acid at position 124 (EU numbering) has been substituted by lysine (K) and wherein in one of the CHI domains the the amino acids at position 147 (EU numbering) and at position 213 (EU numbering) have been substituted by glutamic acid (E).
  • the invention relates to a TNF family ligand trimer-containing antigen binding molecule, wherein in the CL domain adjacent to the TNF ligand family member the amino acid at position 123 (EU numbering) has been replaced by arginine (R) and the amino acid at position 124 (EU numbering) has been substituted by lysine (K), and wherein in the CHI domain adjacent to the TNF ligand family member the amino acids at position 147 (EU numbering) and at position 213 (EU numbering) have been substituted by glutamic acid (E).
  • TNF family ligand trimer-containing antigen binding molecules wherein in the CL domain adjacent to the TNF ligand family member the amino acid at position 123 (EU numbering) has been replaced by arginine (R) and the amino acid at position 124 (EU numbering) has been substituted by lysine (K), and wherein in the CHI domain adjacent to the TNF ligand family member the amino acids at position 147 (EU numbering) and at position 213
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule, wherein the antigen binding molecule comprises
  • a first heavy chain and a first light chain both comprising a Fab molecule capable of specific binding to a target cell antigen
  • a first peptide comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker fused at its C-terminus by a second peptide linker to a second heavy or light chain,
  • a TNF family ligand trimer-containing antigen binding molecule wherein the first peptide comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C-terminus by a second peptide linker to a CHI domain that is part of a heavy chain, and the second peptide comprising one ectodomain of said TNF ligand family member or a fragment thereof is fused at its C-terminus by a third peptide linker to a CL domain that is part of a light chain.
  • a TNF family ligand trimer-containing antigen binding molecule wherein the first peptide comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C-terminus by a second peptide linker to a CL domain that is part of a heavy chain,
  • the second peptide comprising one ectodomain of said TNF ligand family member or a fragment thereof that is fused at its C-terminus by a third peptide linker to a CHI domain that is part of a light chain.
  • a TNF family ligand trimer-containing antigen binding molecule wherein the first peptide comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C-terminus by a second peptide linker to a VH domain that is part of a heavy chain,
  • the second peptide comprising one ectodomain of said TNF ligand family member or a fragment thereof is fused at its C-terminus by a third peptide linker to a VL domain that is part of a light chain.
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule of claims 21 to 23, wherein in the CL domain adjacent to the TNF ligand family member the amino acid at position 123 (EU numbering) has been replaced by arginine (R) and the amino acid at position 124 (EU numbering) has been substituted by lysine (K), and wherein in the CHI domain adjacent to the TNF ligand family member the amino acids at position 147 (EU numbering) and at position 213 (EU numbering) have been substituted by glutamic acid (E).
  • R arginine
  • K lysine
  • E glutamic acid
  • TNF family ligand trimer-containing antigen binding molecule as described herein, wherein the target cell antigen is selected from the group consisting of
  • Fibroblast Activation Protein FAP
  • MCSP Melanoma-associated Chondroitin Sulfate Proteoglycan
  • EGFR Epidermal Growth Factor Receptor
  • CEA Carcinoembryonic Antigen
  • CD19 CD20 and CD33.
  • a TNF family ligand trimer-containing antigen binding molecule wherein the target cell antigen is Fibroblast Activation Protein (FAP).
  • FAP Fibroblast Activation Protein
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule, wherein the moiety capable of specific binding to FAP comprises a VH domain comprising (i) CDR-H1 comprising the amino acid sequence of SEQ ID NO:7 or SEQ ID NO: 100, (ii) CDR-H2 comprising the amino acid sequence of SEQ ID NO:8 or SEQ ID NO: 101, and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO:9 or SEQ ID NO: 102, and a VL domain comprising (iv) CDR-Ll comprising the amino acid sequence of SEQ ID NO: 10 or SEQ ID NO: 103, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO: 11 or SEQ ID NO: 104, and (vi
  • a TNF family ligand trimer-containing antigen binding molecule of the invention wherein the moiety capable of specific binding to a target cell antigen is a Fab molecule capable of specific binding to FAP and comprises a VH domain comprising (i) CDR-H1 comprising the amino acid sequence of SEQ ID NO:7, (ii) CDR-H2 comprising the amino acid sequence of SEQ ID NO: 8 and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO:9, and a VL domain comprising (iv) CDR-Ll comprising the amino acid sequence of SEQ ID NO: 10, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO: 1 land (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO: 12.
  • a TNF family ligand trimer-containing antigen binding molecule of the invention wherein the moiety capable of specific binding to a target cell antigen is a Fab molecule capable of specific binding to FAP and comprises a VH domain comprising (i) CDR-H1 comprising the amino acid sequence of SEQ ID NO: 100, (ii) CDR-H2 comprising the amino acid sequence of SEQ ID NO: 101 and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO: 102, and a VL domain comprising (iv) CDR-Ll comprising the amino acid sequence of SEQ ID NO: 103, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO: 104and (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO: 105.
  • the moiety capable of specific binding to FAP comprises a heavy chain variable region comprising an amino acid sequence that is at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO: 16 and a light chain variable region comprising an amino acid sequence that is at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO: 17.
  • the moiety capable of specific binding to FAP comprises a heavy chain variable region comprising an amino acid sequence that is at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO: 106 and a light chain variable region comprising an amino acid sequence that is at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO: 107.
  • the moiety capable of specific binding to FAP comprises a variable heavy chain comprising an amino acid sequence of SEQ ID NO: 16 and a variable light chain comprising an amino acid sequence of SEQ ID NO: 17 or a variable heavy chain comprising an amino acid sequence of SEQ ID NO: 106 and a variable light chain comprising an amino acid sequence of SEQ ID NO: 107.
  • the moiety capable of specific binding to FAP comprises a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 16 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 17.
  • the moiety capable of specific binding to FAP comprises a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 106 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 107.
  • the moiety capable of specific binding to FAP comprises a VH domain consisting of amino acid sequence of SEQ ID NO: 106 and a VL domain consisting of the amino acid sequence of SEQ ID NO: 107.
  • the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
  • the antigen binding molecule is characterized in that the first polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO:5, SEQ ID NO:97, SEQ ID NO:98 and SEQ ID NO:99 and in that the second polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO: l, SEQ ID NO:96, SEQ ID NO:3 and SEQ ID NO:4.
  • the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
  • the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
  • the antigen binding molecule is characterized in that the first polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO:5, SEQ ID NO:97, SEQ ID NO:98 and SEQ ID NO:99 and in that the second polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO: l, SEQ ID NO:96, SEQ ID NO:3 and SEQ ID NO:4.
  • the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
  • the antigen binding molecule is characterized in that the first polypeptide comprises the the amino acid sequence of SEQ ID NO:97 and the second polypeptide comprises the amino acid sequence of SEQ ID NO:96.
  • TNF family ligand trimer-containing antigen binding molecule wherein the antigen binding molecule comprises
  • a first heavy chain and a first light chain both comprising a Fab molecule capable of specific binding to a target cell antigen
  • a second heavy chain comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker that is fused at its C-terminus by a second peptide linker to a CHI domain, and a second light chain comprising one ectodomain of said TNF ligand family member or a fragment thereof is fused at its C-terminus by a third peptide linker to a CL domain, and wherein the antigen binding molecule comprises
  • a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO:106 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO: 107,
  • a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 14, SEQ ID NO: 108, SEQ ID NO: 111 and SEQ ID NO: 113, and
  • TNF family ligand trimer-containing antigen binding molecule wherein the antigen binding molecule comprises
  • a first heavy chain and a first light chain both comprising a Fab molecule capable of specific binding to a target cell antigen
  • a second heavy chain comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C-terminus by a second peptide linker to a CL domain, and a second light chain comprising one ectodomain of said TNF ligand family member or a fragment thereof that is fused at its C-terminus by a third peptide linker to a CHI domain , and wherein the molecule comprises
  • a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO: 106 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO: 107,
  • a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 115, SEQ ID NO: 117, SEQ ID NO: 119 and SEQ ID NO: 173, and
  • a second light chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 116, SEQ ID NO: 118, SEQ ID NO: 120 and SEQ ID NO: 174.
  • TNF family ligand trimer-containing antigen binding molecule comprising
  • a first heavy chain and a first light chain both comprising a Fab molecule capable of specific binding to a target cell antigen, wherein the first heavy chain comprises the VH domain comprising the amino acid sequence of SEQ ID NO: 106 and the first light chain comprises the VL domain comprising the amino acid sequence of SEQ ID NO: 107, and
  • a second heavy chain comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C-terminus by a second peptide linker to a CL domain, and a second light chain comprising one ectodomain of said TNF ligand family member or a fragment thereof that is fused at its C-terminus by a third peptide linker to a CHI domain , wherein the second heavy chain comprises the amino acid sequence of SEQ ID NO: 119 or SEQ ID NO: 173, and the second light chain comprises the amino acid sequence of SEQ ID NO: 120 or SEQ ID NO: 174.
  • the second heavy chain comprises the amino acid sequence of SEQ ID NO:l 19 and the second light chain comprises the amino acid sequence of SEQ ID NO: 120.
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule, comprising
  • a first and a second polypeptide that are linked to each other by a disulfide bond wherein the antigen binding molecule is characterized in that the first polypeptide contains a CH3 domain and the second polypeptide contains a CH3 domain, respectively, and wherein the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the C-terminus of the CH3 domain by a peptide linker and wherein the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to C-terminus of the CH3 domain of said polypeptide.
  • such a TNF family ligand trimer-containing antigen binding molecule comprises two moieties capable of specific binding to a target cell antigen.
  • TNF family ligand trimer-containing antigen binding molecule comprises
  • the invention relates to a TNF family ligand trimer-containing antigen binding molecule, selected from the group consisting of:
  • a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO: 18, a first light chain comprising the amino acid sequence of SEQ ID NO: 19, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 115 and a second light chain comprising the amino acid sequence of SEQ ID NO: 116;
  • a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO: 135, a first light chain comprising the amino acid sequence of SEQ ID NO: 136, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 108 and a second light chain comprising the amino acid sequence of SEQ ID NO: 109;
  • a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO: 18, a first light chain comprising the amino acid sequence of SEQ ID NO: 19, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 139 and a second light chain comprising the amino acid sequence of SEQ ID NO: 140;
  • a molecule comprising two light chains comprising the amino acid sequence of SEQ ID NO: 19, a first heavy chain comprising the amino acid sequence of SEQ ID NO: 121 and a second heavy chain comprising the amino acid sequence of SEQ ID NO: 122;
  • a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO: 18, a first light chain comprising the amino acid sequence of SEQ ID NO: 19, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 108 and a second light chain comprising the amino acid sequence of SEQ ID NO: 110;
  • a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO: 145, a first light chain comprising the amino acid sequence of SEQ ID NO: 19, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 115 and a second light chain comprising the amino acid sequence of SEQ ID NO: 116;
  • a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO: 18, a first light chain comprising the amino acid sequence of SEQ ID NO: 19, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 148 and a second light chain comprising the amino acid sequence of SEQ ID NO: 149;
  • a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO: 18, a first light chain comprising the amino acid sequence of SEQ ID NO: 19, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 111 and a second light chain comprising the amino acid sequence of SEQ ID NO: 112; and
  • the invention relates to a TNF family ligand trimer-containing antigen binding molecule, selected from the group consisting of:
  • a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO: 164, a first light chain comprising the amino acid sequence of SEQ ID NO: 125, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 117 and a second light chain comprising the amino acid sequence of SEQ ID NO: 118;
  • a molecule comprising two light chains comprising the amino acid sequence of SEQ ID NO: 125, a first heavy chain comprising the amino acid sequence of SEQ ID NO: 123 and a second heavy chain comprising the amino acid sequence of SEQ ID NO: 124;
  • a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO: 164, a first light chain comprising the amino acid sequence of SEQ ID NO: 125, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 173 and a second light chain comprising the amino acid sequence of SEQ ID NO: 174; and
  • a molecule comprising two light chains comprising the amino acid sequence of SEQ ID NO: 125, a first heavy chain comprising the amino acid sequence of SEQ ID NO: 126 and a second heavy chain comprising the amino acid sequence of SEQ ID NO: 127.
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO: 164, a first light chain comprising the amino acid sequence of SEQ ID NO: 125, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 119 and a second light chain comprising the amino acid sequence of SEQ ID NO: 120.
  • a TNF family ligand trimer-containing antigen binding molecule wherein the TNF ligand family member is OX40L and wherein the target cell antigen is Fibroblast Activation Protein (FAP) and the moiety capable of specific binding to FAP comprises a VH domain comprising (i) CDR-Hl comprising the amino acid sequence of SEQ ID NO:7 or SEQ ID NO: 100, (ii) CDR-H2 comprising the amino acid sequence of SEQ ID NO: 8 or SEQ ID NO:101, and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO:9 or SEQ ID NO: 102, and a VL domain comprising (iv) CDR-L1 comprising the amino acid sequence of SEQ ID NO: 10 or SEQ ID NO: 103, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO: 11 or SEQ ID NO: 104, and (vi) CDR-L3 comprising the amino acid sequence of
  • a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO: 106 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO: 107,
  • TNF family ligand trimer-containing antigen binding molecules wherein the target cell antigen is CD 19
  • TNF family ligand trimer-containing antigen binding molecule wherein the target cell antigen is CD 19.
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule, wherein the moiety capable of specific binding to CD 19 comprises a VH domain comprising (i) CDR-Hl comprising the amino acid sequence of SEQ ID NO: 195 or SEQ ID NO:252, (ii) CDR-H2 comprising the amino acid sequence of SEQ ID NO: 196 or SEQ ID NO:253, and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO: 197 or SEQ ID NO:254, and a VL domain comprising (iv) CDR-Ll comprising the amino acid sequence of SEQ ID NO: 198 or SEQ ID NO:249, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO: 199 or SEQ ID NO:250, and (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO:200 or SEQ ID NO:251.
  • VH domain comprising (i) CDR-Hl comprising the amino
  • a TNF family ligand trimer-containing antigen binding molecule of the invention wherein the moiety capable of specific binding to a target cell antigen is a Fab molecule capable of specific binding to CD 19 and comprises a VH domain comprising (i) CDR-Hl comprising the amino acid sequence of SEQ ID NO: 195, (ii) CDR-H2 comprising the amino acid sequence of SEQ ID NO: 196 and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO: 197, and a VL domain comprising (iv) CDR-Ll comprising the amino acid sequence of SEQ ID NO: 198, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO: 199 and (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO:200.
  • a TNF family ligand trimer-containing antigen binding molecule of the invention wherein the moiety capable of specific binding to a target cell antigen is a Fab molecule capable of specific binding to CD 19 and comprises a VH domain comprising (i) CDR-H1 comprising the amino acid sequence of SEQ ID NO:252, (ii) CDR-H2 comprising the amino acid sequence of SEQ ID NO:253 and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO:254, and a VL domain comprising (iv) CDR-L1 comprising the amino acid sequence of SEQ ID NO:249, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO:250 and (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO:251.
  • the moiety capable of specific binding to CD 19 comprises a heavy chain variable region comprising an amino acid sequence that is at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:201 and a light chain variable region comprising an amino acid sequence that is at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:202.
  • the moiety capable of specific binding to CD 19 comprises a heavy chain variable region comprising an amino acid sequence that is at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:357 and a light chain variable region comprising an amino acid sequence that is at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:358.
  • the moiety capable of specific binding to CD 19 comprises a variable heavy chain comprising an amino acid sequence of SEQ ID NO:201 and a variable light chain comprising an amino acid sequence of SEQ ID NO:202 or wherein the moiety capable of specific binding to CD 19 comprises a variable heavy chain comprising an amino acid sequence of SEQ ID NO:357 and a variable light chain comprising an amino acid sequence of SEQ ID NO:358.
  • the moiety capable of specific binding to CD 19 comprises a heavy chain variable region comprising the amino acid sequence of SEQ ID NO:201 and a light chain variable region comprising the amino acid sequence of SEQ ID NO:202.
  • the moiety capable of specific binding to CD 19 comprises a heavy chain variable region comprising the amino acid sequence of SEQ ID NO:357 and a light chain variable region comprising the amino acid sequence of SEQ ID NO:358.
  • the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
  • the antigen binding molecule is characterized in that the first polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO:5, SEQ ID NO:97, SEQ ID NO:98 and SEQ ID NO:99 and in that the second polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO: l, SEQ ID NO:96, SEQ ID NO:3 and SEQ ID NO:4.
  • the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
  • the antigen binding molecule is characterized in that the first polypeptide comprises the the amino acid sequence of SEQ ID NO:97 and the second polypeptide comprises the amino acid sequence of SEQ ID NO:96.
  • the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
  • the antigen binding molecule is characterized in that the first polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO:5, SEQ ID NO:97, SEQ ID NO:98 and SEQ ID NO:99 and in that the second polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO: l, SEQ ID NO:96, SEQ ID NO:3 and SEQ ID NO:4.
  • the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
  • the antigen binding molecule is characterized in that the first polypeptide comprises the the amino acid sequence of SEQ ID NO:97 and the second polypeptide comprises the amino acid sequence of SEQ ID NO:96.
  • TNF family ligand trimer-containing antigen binding molecule wherein the antigen binding molecule comprises
  • a first heavy chain and a first light chain both comprising a Fab molecule capable of specific binding to a target cell antigen
  • a second heavy chain comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker that is fused at its C-terminus by a second peptide linker to a CHI domain, and a second light chain comprising one ectodomain of said TNF ligand family member or a fragment thereof is fused at its C-terminus by a third peptide linker to a CL domain, and wherein the antigen binding molecule comprises
  • a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO:357 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO:358,
  • a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 14, SEQ ID NO: 108, SEQ ID NO: 111 and SEQ ID NO: 113, and
  • TNF family ligand trimer-containing antigen binding molecule wherein the antigen binding molecule comprises
  • a first heavy chain and a first light chain both comprising a Fab molecule capable of specific binding to a target cell antigen
  • a second heavy chain comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C-terminus by a second peptide linker to a CL domain, and a second light chain comprising one ectodomain of said TNF ligand family member or a fragment thereof that is fused at its C-terminus by a third peptide linker to a CHI domain, and wherein the molecule comprises
  • a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO:357 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO:358,
  • a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 115, SEQ ID NO: 117, SEQ ID NO: 119 and SEQ ID NO: 173, and
  • a second light chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 116, SEQ ID NO: 118, SEQ ID NO: 120 and SEQ ID NO: 174.
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule, comprising (a) at least one moiety capable of specific binding to a target cell antigen, and
  • a first and a second polypeptide that are linked to each other by a disulfide bond wherein the antigen binding molecule is characterized in that the first polypeptide contains a CH3 domain and the second polypeptide contains a CH3 domain, respectively, and wherein the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the C-terminus of the CH3 domain by a peptide linker and wherein the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to C-terminus of the CH3 domain of said polypeptide.
  • such a TNF family ligand trimer-containing antigen binding molecule comprises two moieties capable of specific binding to a target cell antigen.
  • TNF family ligand trimer-containing antigen binding molecule comprises
  • the invention relates to a TNF family ligand trimer-containing antigen binding molecule, selected from the group consisting of:
  • a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO:205, a first light chain comprising the amino acid sequence of SEQ ID NO:206, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 119 and a second light chain comprising the amino acid sequence of SEQ ID NO: 120;
  • a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO:205, a first light chain comprising the amino acid sequence of SEQ ID NO:206, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 173 and a second light chain comprising the amino acid sequence of SEQ ID NO: 174; and
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO:205, a first light chain comprising the amino acid sequence of SEQ ID NO:206, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 119 and a second light chain comprising the amino acid sequence of SEQ ID NO: 120.
  • the invention relates to a TNF family ligand trimer-containing antigen binding molecule, selected from the group consisting of:
  • a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO:357, a first light chain comprising the amino acid sequence of SEQ ID NO:358, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 117 and a second light chain comprising the amino acid sequence of SEQ ID NO: 118;
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO:357, a first light chain comprising the amino acid sequence of SEQ ID NO:358, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 119 and a second light chain comprising the amino acid sequence of SEQ ID NO: 120.
  • TNF family ligand trimer-containing antigen binding molecules wherein the target cell antigen is CEA
  • the target cell antigen is CEA
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule, wherein the moiety capable of specific binding to CD 19 comprises a VH domain comprising (i) CDR-H1 comprising the amino acid sequence of SEQ ID NO:321, (ii) CDR-H2 comprising the amino acid sequence of SEQ ID NO:322, and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO:323, and a VL domain comprising (iv) CDR-L1 comprising the amino acid sequence of SEQ ID NO:324, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO:325, and (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO:326.
  • VH domain comprising (i) CDR-H1 comprising the amino acid sequence of SEQ ID NO:321, (ii) CDR-H2 comprising the amino acid sequence of SEQ ID NO:322, and (iii) CDR-H3 comprising the
  • a TNF family ligand trimer-containing antigen binding molecule of the invention wherein the moiety capable of specific binding to a target cell antigen is a Fab molecule capable of specific binding to CEA and comprises a VH domain comprising (i) CDR-H1 comprising the amino acid sequence of SEQ ID NO:321, (ii) CDR-H2 comprising the amino acid sequence of SEQ ID NO:322 and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO:323, and a VL domain comprising (iv) CDR-L1 comprising the amino acid sequence of SEQ ID NO:324, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO:325 and (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO:326.
  • the moiety capable of specific binding to CEA comprises a heavy chain variable region comprising an amino acid sequence that is at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:327 and a light chain variable region comprising an amino acid sequence that is at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:328.
  • the moiety capable of specific binding to CEA comprises a variable heavy chain comprising an amino acid sequence of SEQ ID NO:327 and a variable light chain comprising an amino acid sequence of SEQ ID NO:328.
  • the moiety capable of specific binding to CEA comprises a heavy chain variable region comprising an amino acid sequence that is at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:329 and a light chain variable region comprising an amino acid sequence that is at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:330.
  • the moiety capable of specific binding to CEA comprises a variable heavy chain comprising an amino acid sequence of SEQ ID NO:329 and a variable light chain comprising an amino acid sequence of SEQ ID NO:330.
  • the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
  • the antigen binding molecule is characterized in that the first polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO:5, SEQ ID NO:97, SEQ ID NO:98 and SEQ ID NO:99 and in that the second polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO: l, SEQ ID NO:96, SEQ ID NO:3 and SEQ ID NO:4.
  • the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
  • the antigen binding molecule is characterized in that the first polypeptide comprises the the amino acid sequence of SEQ ID NO:97 and the second polypeptide comprises the amino acid sequence of SEQ ID NO:96.
  • TNF family ligand trimer-containing antigen binding molecule wherein the antigen binding molecule comprises
  • a first heavy chain and a first light chain both comprising a Fab molecule capable of specific binding to a target cell antigen
  • a second heavy chain comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker that is fused at its C-terminus by a second peptide linker to a CHI domain, and a second light chain comprising one ectodomain of said TNF ligand family member or a fragment thereof is fused at its C-terminus by a third peptide linker to a CL domain, and wherein the antigen binding molecule comprises
  • a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 14, SEQ ID NO: 108, SEQ ID NO: 111 and SEQ ID NO: 113, and
  • TNF family ligand trimer-containing antigen binding molecule wherein the antigen binding molecule comprises
  • a first heavy chain and a first light chain both comprising a Fab molecule capable of specific binding to a target cell antigen
  • a second heavy chain comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C-terminus by a second peptide linker to a CL domain, and a second light chain comprising one ectodomain of said TNF ligand family member or a fragment thereof that is fused at its C-terminus by a third peptide linker to a CHI domain, and wherein the molecule comprises
  • a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 115, SEQ ID NO: 117, SEQ ID NO: 119 and SEQ ID NO: 173, and
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule, comprising (a) at least one moiety capable of specific binding to a target cell antigen, and
  • a first and a second polypeptide that are linked to each other by a disulfide bond wherein the antigen binding molecule is characterized in that the first polypeptide contains a CH3 domain and the second polypeptide contains a CH3 domain, respectively, and wherein the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the C-terminus of the CH3 domain by a peptide linker and wherein the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to C-terminus of the CH3 domain of said polypeptide.
  • such a TNF family ligand trimer-containing antigen binding molecule comprises two moieties capable of specific binding to a target cell antigen.
  • TNF family ligand trimer-containing antigen binding molecule comprises
  • the invention relates to a TNF family ligand trimer-containing antigen binding molecule, selected from the group consisting of:
  • a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO:333, a first light chain comprising the amino acid sequence of SEQ ID NO:334, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 117 and a second light chain comprising the amino acid sequence of SEQ ID NO: 118;
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO:333, a first light chain comprising the amino acid sequence of SEQ ID NO:334, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 119 and a second light chain comprising the amino acid sequence of SEQ ID NO: 120.
  • the invention further provides isolated polynucleotides encoding a TNF family ligand trimer-containing antigen binding molecule as described herein or a fragment thereof.
  • the isolated polynucleotides encoding TNF ligand trimer-containing antigen binding molecules of the invention may be expressed as a single polynucleotide that encodes the entire antigen binding molecule or as multiple (e.g., two or more) polynucleotides that are co- expressed.
  • Polypeptides encoded by polynucleotides that are co-expressed may associate through, e.g., disulfide bonds or other means to form a functional antigen binding molecule.
  • the light chain portion of an immunoglobulin may be encoded by a separate
  • the heavy chain polypeptides When co-expressed, the heavy chain polypeptides will associate with the light chain polypeptides to form the
  • the isolated polynucleotide encodes the entire TNF family ligand trimer- containing antigen binding molecule according to the invention as described herein.
  • the isolated polynucleotide encodes a polypeptide comprised in the TNF family ligand trimer-containing antigen binding molecule according to the invention as described herein.
  • the present invention is directed to an isolated polynucleotide encoding a
  • the polynucleotide comprises (a) a sequence that encodes a moiety capable of specific binding to a target cell antigen, (b) a sequence that encodes a polypeptide comprising two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and (c) a sequence that encodes a polypeptide comprising one ectodomain of said TNF ligand family member or a fragment thereof.
  • an isolated polynucleotide encoding a 4- IBB ligand trimer- containing antigen binding molecule, wherein the polynucleotide comprises (a) a sequence that encodes a moiety capable of specific binding to a target cell antigen, (b) a sequence that encodes a polypeptide comprising two ectodomains of 4-1BBL or two fragments thereof that are connected to each other by a peptide linker and (c) a sequence that encodes a polypeptide comprising one ectodomain of 4-1BBL or a fragment thereof.
  • the invention is directed to an isolated polynucleotide comprising a sequence that encodes a polypeptide comprising two 4-1BBL fragments comprising an amino acid sequence that is at least about 90%, 95%, 98% or 100% identical to an amino acid sequence shown in SEQ ID NO: l, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4 or SEQ ID NO:96, and to a polynucleotide comprising a sequence that encodes a polypeptide comprising one 4-1BBL fragment comprising an amino acid sequence that is is at least about 90%, 95%, 98% or 100% identical to an amino acid sequence shown in SEQ ID NO: l, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4 or SEQ ID NO:96.
  • an isolated polynucleotide encoding a OX40 ligand trimer- containing antigen binding molecule, wherein the polynucleotide comprises (a) a sequence that encodes a moiety capable of specific binding to a target cell antigen, (b) a sequence that encodes a polypeptide comprising two ectodomains of OX40L or two fragments thereof that are connected to each other by a peptide linker and (c) a sequence that encodes a polypeptide comprising one ectodomain of OX40L or a fragment thereof.
  • the invention is directed to an isolated polynucleotide comprising a sequence that encodes a polypeptide comprising two 4-1BBL fragments comprising an amino acid sequence that is at least about 90%, 95%, 98% or 100% identical to an amino acid sequence shown in SEQ ID NO:53 or SEQ ID NO:54, and to a polynucleotide comprising a sequence that encodes a polypeptide comprising one 4-1BBL fragment comprising an amino acid sequence that is is at least about 90%, 95%, 98% or 100% identical to an amino acid sequence shown in SEQ ID NO:53 or SEQ ID NO:54.
  • the invention relates to the polynucleotides comprising a sequence that is at least about 90%, 95%, 98% or 100% identical to the specific cDNA sequences disclosed herein.
  • the invention relates to a polynucleotide comprising a sequence that is identical to one of the specific cDNA sequences disclosed herein.
  • the nucleic acid molecule comprises or consists of a nucleotide sequence that encodes an amino acid sequence as set forth in any one of SEQ ID NOs: 5, 6, 97, 98, 99, 183, 184 or 185.
  • the nucleic acid molecule comprises or consists of a nucleotide sequence that encodes an amino acid sequence as set forth in any one of SEQ ID NOs: 14, 15, 108, 109, 110, 111, 112, 113, 114, 115,116, 117, 118, 119, 120, 173 or 174.
  • the nucleic acid molecule comprises or consists of a nucleotide sequence selected from the group consisting of SEQ ID NOs: 66, 67, 68, 69, 129, 130, 131, 132, 133, 134, 137, 138, 141, 142, 143, 144, 146, 147, 150, 151, 152, 153, 162, 163, 165, 166, 167, 168, 169, 170, 171, 172, 175, 176, 177, 178, 203, 204, 207, 208, 211, 212, 215, 216, 273, 274, 277, 278, 281, 282, 285, 286, 289, 290, 293, 294, 297, 298, 301, 302, 305, 307, 308, 311, 312, 315, 316, 331, 332, 335, 336, 339, 340, 343, 344, 347, 348, 353 or 354.
  • the polynucleotide or nucleic acid is DNA.
  • a polynucleotide of the present invention is RNA, for example, in the form of messenger RNA (mRNA).
  • mRNA messenger RNA
  • RNA of the present invention may be single stranded or double stranded.
  • TNF family ligand trimer-containing antigen binding molecules of the invention may be obtained, for example, by solid-state peptide synthesis (e.g. Merrifield solid phase synthesis) or recombinant production.
  • solid-state peptide synthesis e.g. Merrifield solid phase synthesis
  • polynucleotide encoding the TNF family ligand trimer-containing antigen binding molecule or polypeptide fragments thereof, e.g., as described above is isolated and inserted into one or more vectors for further cloning and/or expression in a host cell.
  • Such polynucleotide may be readily isolated and sequenced using conventional procedures.
  • a vector, preferably an expression vector, comprising one or more of the polynucleotides of the invention is provided.
  • the expression vector can be part of a plasmid, virus, or may be a nucleic acid fragment.
  • the expression vector includes an expression cassette into which the polynucleotide encoding the TNF family ligand trimer- containing antigen binding molecule or polypeptide fragments thereof (i.e. the coding region) is cloned in operable association with a promoter and/or other transcription or translation control elements.
  • a "coding region” is a portion of nucleic acid which consists of codons translated into amino acids.
  • a "stop codon" (TAG, TGA, or TAA) is not translated into an amino acid, it may be considered to be part of a coding region, if present, but any flanking sequences, for example promoters, ribosome binding sites, transcriptional terminators, introns, 5' and 3' untranslated regions, and the like, are not part of a coding region.
  • Two or more coding regions can be present in a single polynucleotide construct, e.g. on a single vector, or in separate polynucleotide constructs, e.g. on separate (different) vectors.
  • any vector may contain a single coding region, or may comprise two or more coding regions, e.g.
  • a vector of the present invention may encode one or more polypeptides, which are post- or co-translationally separated into the final proteins via proteolytic cleavage.
  • a vector, polynucleotide, or nucleic acid of the invention may encode heterologous coding regions, either fused or unfused to a polynucleotide encoding the TNF family ligand trimer-containing antigen binding molecule of the invention or polypeptide fragments thereof, or variants or derivatives thereof.
  • Heterologous coding regions include without limitation specialized elements or motifs, such as a secretory signal peptide or a heterologous functional domain. An operable association is when a coding region for a gene product, e.g.
  • a polypeptide is associated with one or more regulatory sequences in such a way as to place expression of the gene product under the influence or control of the regulatory sequence(s).
  • Two DNA fragments (such as a polypeptide coding region and a promoter associated therewith) are "operably associated” if induction of promoter function results in the transcription of mRNA encoding the desired gene product and if the nature of the linkage between the two DNA fragments does not interfere with the ability of the expression regulatory sequences to direct the expression of the gene product or interfere with the ability of the DNA template to be transcribed.
  • a promoter region would be operably associated with a nucleic acid encoding a polypeptide if the promoter was capable of effecting transcription of that nucleic acid.
  • the promoter may be a cell-specific promoter that directs substantial transcription of the DNA only in predetermined cells.
  • Other transcription control elements besides a promoter, for example enhancers, operators, repressors, and transcription termination signals, can be operably associated with the polynucleotide to direct cell-specific transcription.
  • transcription control regions which function in vertebrate cells, such as, but not limited to, promoter and enhancer segments from cytomegaloviruses (e.g. the immediate early promoter, in conjunction with intron-A), simian virus 40 (e.g. the early promoter), and retroviruses (such as, e.g. Rous sarcoma virus).
  • transcription control regions include those derived from vertebrate genes such as actin, heat shock protein, bovine growth hormone and rabbit a-globin, as well as other sequences capable of controlling gene expression in eukaryotic cells.
  • tissue-specific promoters and enhancers as well as inducible promoters (e.g. promoters inducible tetracyclins).
  • inducible promoters e.g. promoters inducible tetracyclins
  • translation control elements include, but are not limited to ribosome binding sites, translation initiation and termination codons, and elements derived from viral systems (particularly an internal ribosome entry site, or IRES, also referred to as a CITE sequence).
  • the expression cassette may also include other features such as an origin of replication, and/or chromosome integration elements such as retroviral long terminal repeats (LTRs), or adeno- associated viral (AAV) inverted terminal repeats (ITRs).
  • LTRs retroviral long terminal repeats
  • AAV adeno- associated viral inverted terminal repeats
  • Polynucleotide and nucleic acid coding regions of the present invention may be associated with additional coding regions which encode secretory or signal peptides, which direct the secretion of a polypeptide encoded by a polynucleotide of the present invention.
  • additional coding regions which encode secretory or signal peptides, which direct the secretion of a polypeptide encoded by a polynucleotide of the present invention.
  • DNA encoding a signal sequence may be placed upstream of the nucleic acid encoding a TNF family ligand trimer-containing antigen binding molecule of the invention or polypeptide fragments thereof.
  • proteins secreted by mammalian cells have a signal peptide or secretory leader sequence which is cleaved from the mature protein once export of the growing protein chain across the rough endoplasmic reticulum has been initiated.
  • polypeptides secreted by vertebrate cells generally have a signal peptide fused to the N-terminus of the polypeptide, which is cleaved from the translated polypeptide to produce a secreted or "mature" form of the polypeptide.
  • the native signal peptide e.g. an immunoglobulin heavy chain or light chain signal peptide is used, or a functional derivative of that sequence that retains the ability to direct the secretion of the polypeptide that is operably associated with it.
  • a heterologous mammalian signal peptide may be used.
  • the wild-type leader sequence may be substituted with the leader sequence of human tissue plasminogen activator (TPA) or mouse ⁇ -glucuronidase.
  • TPA tissue plasminogen activator
  • DNA encoding a short protein sequence that could be used to facilitate later purification (e.g. a histidine tag) or assist in labeling the fusion protein may be included within or at the ends of the polynucleotide encoding a TNF family ligand trimer-containing antigen binding molecule of the invention or polypeptide fragments thereof.
  • a host cell comprising one or more polynucleotides of the invention.
  • a host cell comprising one or more vectors of the invention.
  • the polynucleotides and vectors may incorporate any of the features, singly or in combination, described herein in relation to polynucleotides and vectors, respectively.
  • a host cell comprises (e.g. has been transformed or transfected with) a vector comprising a polynucleotide that encodes (part of) a TNF family ligand trimer- containing antigen binding molecule of the invention of the invention.
  • the term "host cell” refers to any kind of cellular system which can be engineered to generate the fusion proteins of the invention or fragments thereof.
  • Host cells suitable for replicating and for supporting expression of antigen binding molecules are well known in the art. Such cells may be transfected or transduced as appropriate with the particular expression vector and large quantities of vector containing cells can be grown for seeding large scale fermenters to obtain sufficient quantities of the antigen binding molecule for clinical applications.
  • Suitable host cells include prokaryotic microorganisms, such as E. coli, or various eukaryotic cells, such as Chinese hamster ovary cells (CHO), insect cells, or the like.
  • polypeptides may be produced in bacteria in particular when glycosylation is not needed.
  • the polypeptide may be isolated from the bacterial cell paste in a soluble fraction and can be further purified.
  • eukaryotic microbes such as filamentous fungi or yeast are suitable cloning or expression hosts for polypeptide-encoding vectors, including fungi and yeast strains whose glycosylation pathways have been "humanized", resulting in the production of a polypeptide with a partially or fully human glycosylation pattern. See Gerngross, Nat Biotech 22, 1409-1414 (2004), and Li et al., Nat Biotech 24, 210-215 (2006).
  • Suitable host cells for the expression of (glycosylated) polypeptides are also derived from multicellular organisms (invertebrates and vertebrates).
  • invertebrate cells include plant and insect cells. Numerous baculoviral strains have been identified which may be used in conjunction with insect cells, particularly for transfection of Spodoptera frugiperda cells. Plant cell cultures can also be utilized as hosts. See e.g. US Patent Nos. 5,959,177, 6,040,498, 6,420,548, 7,125,978, and 6,417,429 (describing PLANTIBODIESTM technology for producing antibodies in transgenic plants). Vertebrate cells may also be used as hosts.
  • mammalian cell lines that are adapted to grow in suspension may be useful.
  • useful mammalian host cell lines are monkey kidney CV1 line transformed by SV40 (COS-7); human embryonic kidney line (293 or 293T cells as described, e.g., in Graham et al., J Gen Virol 36, 59 (1977)), baby hamster kidney cells (BHK), mouse Sertoli cells (TM4 cells as described, e.g., in Mather, Biol Reprod 23, 243-251 (1980)), monkey kidney cells (CV1), African green monkey kidney cells (VERO-76), human cervical carcinoma cells (HELA), canine kidney cells (MDCK), buffalo rat liver cells (BRL 3A), human lung cells (W138), human liver cells (Hep
  • mouse mammary tumor cells MMT 060562
  • TRI cells as described, e.g., in Mather et al., Annals N.Y. Acad Sci 383, 44-68 (1982)
  • MRC 5 cells MRC 5 cells
  • FS4 cells FS4 cells.
  • Other useful mammalian host cell lines include Chinese hamster ovary (CHO) cells, including dhfr- CHO cells (Urlaub et al., Proc Natl Acad Sci USA 77, 4216 (1980)); and myeloma cell lines such as YO, NS0, P3X63 and Sp2/0.
  • Host cells include cultured cells, e.g., mammalian cultured cells, yeast cells, insect cells, bacterial cells and plant cells, to name only a few, but also cells comprised within a transgenic animal, transgenic plant or cultured plant or animal tissue.
  • the host cell is a eukaryotic cell, preferably a mammalian cell, such as a Chinese Hamster Ovary (CHO) cell, a human embryonic kidney (HEK) cell or a lymphoid cell (e.g., Y0, NSO, Sp20 cell).
  • CHO Chinese Hamster Ovary
  • HEK human embryonic kidney
  • a lymphoid cell e.g., Y0, NSO, Sp20 cell.
  • Standard technologies are known in the art to express foreign genes in these systems.
  • Cells expressing a polypeptide comprising either the heavy or the light chain of an immunoglobulin may be engineered so as to also express the other of the immunoglobulin chains such that the expressed product is an immunoglobulin that has both a heavy and a light chain.
  • a method of producing a TNF family ligand trimer-containing antigen binding molecule of the invention or polypeptide fragments thereof comprises culturing a host cell comprising polynucleotides encoding the TNF family ligand trimer-containing antigen binding molecule of the invention or polypeptide fragments thereof, as provided herein, under conditions suitable for expression of the TNF family ligand trimer-containing antigen binding molecule of the invention or polypeptide fragments thereof, and recovering the TNF family ligand trimer-containing antigen binding molecule of the invention or polypeptide fragments thereof from the host cell (or host cell culture medium).
  • the components (at least one moiety capable of specific binding to a target cell antigen, one polypeptide comprising two ectodomains of a TNF ligand family member or fragments thereof and a polypeptide comprising one ectodomain of said TNF family ligand family member or a fragment thereof) are not genetically fused to each other.
  • the polypeptides are designed such that its components (two ectodomains of a TNF ligand family member or fragments thereof and other components such as CH or CL) are fused to each other directly or through a linker sequence.
  • composition and length of the linker may be determined in accordance with methods well known in the art and may be tested for efficacy.
  • Examples of linker sequences between different components of the antigen binding molecules of the invention are found in the sequences provided herein. Additional sequences may also be included to incorporate a cleavage site to separate the individual components of the fusion protein if desired, for example an endopeptidase recognition sequence.
  • the moieties capable of specific binding to a target cell antigen (e.g. Fab fragments) forming part of the antigen binding molecule comprise at least an immunoglobulin variable region capable of binding to an antigen.
  • Variable regions can form part of and be derived from naturally or non-naturally occurring antibodies and fragments thereof.
  • Methods to produce polyclonal antibodies and monoclonal antibodies are well known in the art (see e.g. Harlow and Lane, "Antibodies, a laboratory manual", Cold Spring Harbor Laboratory, 1988).
  • Non-naturally occurring antibodies can be constructed using solid phase-peptide synthesis, can be produced recombinantly (e.g. as described in U.S. patent No.
  • immunoglobulins useful in the present invention can be of murine, primate, or human origin. If the fusion protein is intended for human use, a chimeric form of immunoglobulin may be used wherein the constant regions of the immunoglobulin are from a human.
  • a humanized or fully human form of the immunoglobulin can also be prepared in accordance with methods well known in the art (see e. g. U.S. Patent No. 5,565,332 to Winter).
  • Humanization may be achieved by various methods including, but not limited to (a) grafting the non-human (e.g., donor antibody) CDRs onto human (e.g. recipient antibody) framework and constant regions with or without retention of critical framework residues (e.g. those that are important for retaining good antigen binding affinity or antibody functions), (b) grafting only the non-human specificity-determining regions (SDRs or a-CDRs; the residues critical for the antibody-antigen interaction) onto human framework and constant regions, or (c) transplanting the entire non-human variable domains, but "cloaking" them with a human-like section by replacement of surface residues.
  • a grafting the non-human (e.g., donor antibody) CDRs onto human (e.g. recipient antibody) framework and constant regions with or without retention of critical framework residues (e.g. those that are important for retaining good antigen binding affinity or antibody functions)
  • SDRs or a-CDRs the residues critical for the antibody-antigen interaction
  • Particular immunoglobulins according to the invention are human immunoglobulins.
  • Human antibodies and human variable regions can be produced using various techniques known in the art. Human antibodies are described generally in van Dijk and van de Winkel, Curr Opin Pharmacol 5, 368-74 (2001) and Lonberg, Curr Opin Immunol 20, 450-459 (2008). Human variable regions can form part of and be derived from human monoclonal antibodies made by the hybridoma method (see e.g. Monoclonal Antibody Production Techniques and Applications, pp. 51-63 (Marcel Dekker, Inc., New York, 1987)).
  • Human antibodies and human variable regions may also be prepared by administering an immunogen to a transgenic animal that has been modified to produce intact human antibodies or intact antibodies with human variable regions in response to antigenic challenge (see e.g. Lonberg, Nat Biotech 23, 1117-1125 (2005). Human antibodies and human variable regions may also be generated by isolating Fv clone variable region sequences selected from human-derived phage display libraries (see e.g., Hoogenboom et al.
  • Phage typically display antibody fragments, either as single-chain Fv (scFv) fragments or as Fab fragments.
  • the moieties capable of specific binding to a target cell antigen (e.g. Fab fragments) comprised in the antigen binding molecules of the present invention are engineered to have enhanced binding affinity according to, for example, the methods disclosed in PCT publication WO 2012/020006 (see Examples relating to affinity maturation) or U.S. Pat. Appl. Publ. No. 2004/0132066.
  • the ability of the antigen binding molecules of the invention to bind to a specific antigenic determinant can be measured either through an enzyme-linked
  • ELISA immunosorbent assay
  • ELISA immunosorbent assay
  • Other techniques familiar to one of skill in the art, e.g. surface plasmon resonance technique (Liljeblad, et al., Glyco J 17, 323-329 (2000)), and traditional binding assays (Heeley, Endocr Res 28, 217-229 (2002)).
  • Competition assays may be used to identify an antigen binding molecule that competes with a reference antibody for binding to a particular antigen.
  • such a competing antigen binding molecule binds to the same epitope (e.g. a linear or a conformational epitope) that is bound by the reference antigen binding molecule.
  • immobilized antigen is incubated in a solution comprising the first labeled antigen binding molecule but not the second unlabeled antigen binding molecule. After incubation under conditions permissive for binding of the first antibody to the antigen, excess unbound antibody is removed, and the amount of label associated with immobilized antigen is measured. If the amount of label associated with immobilized antigen is substantially reduced in the test sample relative to the control sample, then that indicates that the second antigen binding molecule is competing with the first antigen binding molecule for binding to the antigen. See Harlow and Lane (1988) Antibodies: A Laboratory Manual ch.14 (Cold Spring Harbor Laboratory, Cold Spring Harbor, NY).
  • TNF ligand trimer-containing antigen binding molecules of the invention prepared as described herein may be purified by art-known techniques such as high performance liquid chromatography, ion exchange chromatography, gel electrophoresis, affinity chromatography, size exclusion chromatography, and the like.
  • the actual conditions used to purify a particular protein will depend, in part, on factors such as net charge, hydrophobicity, hydrophilicity etc., and will be apparent to those having skill in the art.
  • affinity chromatography purification an antibody, ligand, receptor or antigen can be used to which the TNF ligand trimer-containing antigen binding molecule binds.
  • a matrix with protein A or protein G may be used for affinity chromatography purification of fusion proteins of the invention.
  • Sequential Protein A or G affinity chromatography and size exclusion chromatography can be used to isolate an antigen binding molecule essentially as described in the Examples.
  • the purity of the TNF ligand trimer-containing antigen binding molecule or fragments thereof can be determined by any of a variety of well-known analytical methods including gel electrophoresis, high pressure liquid chromatography, and the like.
  • the TNF ligand trimer-containing antigen binding molecules expressed as described in the Examples were shown to be intact and properly assembled as demonstrated by reducing and non-reducing SDS-PAGE.
  • antigen binding molecules provided herein may be identified, screened for, or characterized for their physical/chemical properties and/or biological activities by various assays known in the art.
  • the affinity of the TNF family ligand trimer-containing antigen binding molecule provided herein for the corresponding TNF receptor can be determined in accordance with the methods set forth in the Examples by surface plasmon resonance (SPR), using standard instrumentation such as a BIAcore instrument (GE Healthcare), and receptors or target proteins such as may be obtained by recombinant expression.
  • the affinity of the TNF family ligand trimer-containing antigen binding molecule for the target cell antigen can also be determined by surface plasmon resonance (SPR), using standard instrumentation such as a BIAcore instrument (GE Healthcare), and receptors or target proteins such as may be obtained by recombinant expression.
  • SPR surface plasmon resonance
  • K D is measured by surface plasmon resonance using a BIACORE® T100 machine (GE Healthcare) at 25 °C. 2. Binding assays and other assays
  • Binding of the TNF family ligand trimer-containing antigen binding molecule provided herein to the corresponding receptor expressing cells may be evaluated using cell lines expressing the particular receptor or target antigen, for example by flow cytometry (FACS).
  • FACS flow cytometry
  • fresh peripheral blood mononuclear cells (PBMCs) expressing the TNF receptor are used in the binding assay. These cells are used directly after isolation (naive PMBCs) or after stimulation (activated PMBCs).
  • activated mouse splenocytes (expressing the TNF receptor molecule) were used to demonstrate the binding of the TNF family ligand trimer- containing antigen binding molecule of the invention to the corresponding TNF receptor expressing cells.
  • cancer cell lines expressing the target cell antigen were used to demonstrate the binding of the antigen binding molecules to the target cell antigen.
  • competition assays may be used to identify an antigen binding molecule that competes with a specific antibody or antigen binding molecule for binding to the target or TNF receptor, respectively.
  • a competing antigen binding molecule binds to the same epitope (e.g., a linear or a conformational epitope) that is bound by a specific anti-target antibody or a specific anti-TNF receptor antibody.
  • epitope e.g., a linear or a conformational epitope
  • Detailed exemplary methods for mapping an epitope to which an antibody binds are provided in Morris (1996) "Epitope Mapping Protocols," in Methods in Molecular Biology vol. 66 (Humana Press, Totowa, NJ). 3. Activity assays
  • assays are provided for identifying TNF family ligand trimer-containing antigen binding molecules that bind to a specific target cell antigen and to a specific TNF receptor having biological activity.
  • Biological activity may include, e.g., agonistic signalling through the TNF receptor on cells expressing the target cell antigen.
  • TNF family ligand trimer- containing antigen binding molecules identified by the assays as having such biological activity in vitro are also provided.
  • a TNF family ligand trimer-containing antigen binding molecule of the invention is tested for such biological activity.
  • Assays for detecting the biological activity of the molecules of the invention are those described in Example 6.
  • assays for detecting cell lysis e.g. by measurement of LDH release
  • induced apoptosis kinetics e.g. by
  • apoptosis e.g. using the TUNEL assay
  • biological activity of such complexes can be assessed by evaluating their effects on survival, proliferation and lymphokine secretion of various lymphocyte subsets such as NK cells, NKT-cells or ⁇ T-cells or assessing their capacity to modulate phenotype and function of antigen presenting cells such as dendritic cells, monocytes/macrophages or B-cells.
  • the invention provides pharmaceutical compositions comprising any of the TNF family ligand trimer-containing antigen binding molecules provided herein, e.g., for use in any of the below therapeutic methods.
  • a pharmaceutical composition comprises any of the TNF family ligand trimer-containing antigen binding molecules provided herein and at least one pharmaceutically acceptable excipient.
  • a pharmaceutical composition comprises any of the TNF family ligand trimer-containing antigen binding molecules provided herein and at least one additional therapeutic agent, e.g., as described below.
  • compositions of the present invention comprise a therapeutically effective amount of one or more TNF family ligand trimer-containing antigen binding molecules dissolved or dispersed in a pharmaceutically acceptable excipient.
  • pharmaceutically acceptable refers to molecular entities and compositions that are generally non-toxic to recipients at the dosages and concentrations employed, i.e. do not produce an adverse, allergic or other untoward reaction when administered to an animal, such as, for example, a human, as appropriate.
  • compositions that contain at least one TNF family ligand trimer-containing antigen binding molecule and optionally an additional active ingredient will be known to those of skill in the art in light of the present disclosure, as exemplified by Remington's Pharmaceutical Sciences, 18th Ed. Mack Printing Company, 1990, incorporated herein by reference.
  • the compositions are lyophilized formulations or aqueous solutions.
  • pharmaceutically acceptable excipient includes any and all solvents, buffers, dispersion media, coatings, surfactants, antioxidants, preservatives (e.g. antibacterial agents, antifungal agents), isotonic agents, salts, stabilizers and combinations thereof, as would be known to one of ordinary skill in the art.
  • Parenteral compositions include those designed for administration by injection, e.g.
  • the TNF family ligand trimer-containing antigen binding molecules of the invention may be formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hanks' solution, Ringer's solution, or physiological saline buffer.
  • the solution may contain formulatory agents such as suspending, stabilizing and/or dispersing agents.
  • the fusion proteins may be in powder form for constitution with a suitable vehicle, e.g., sterile pyrogen-free water, before use.
  • Sterile injectable solutions are prepared by
  • fusion proteins of the invention in the required amount in the appropriate solvent with various of the other ingredients enumerated below, as required.
  • Sterility may be readily accomplished, e.g., by filtration through sterile filtration membranes.
  • dispersions are prepared by incorporating the various sterilized active ingredients into a sterile vehicle which contains the basic dispersion medium and/or the other ingredients.
  • the preferred methods of preparation are vacuum-drying or freeze-drying techniques which yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile- filtered liquid medium thereof.
  • the liquid medium should be suitably buffered if necessary and the liquid diluent first rendered isotonic prior to injection with sufficient saline or glucose.
  • the composition must be stable under the conditions of manufacture and storage, and preserved against the contaminating action of microorganisms, such as bacteria and fungi. It will be appreciated that endotoxin contamination should be kept minimally at a safe level, for example, less that 0.5 ng/mg protein.
  • Suitable pharmaceutically acceptable excipients include, but are not limited to: buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid and methionine; preservatives (such as octadecyldimethylbenzyl ammonium chloride; hexamethonium chloride; benzalkonium chloride; benzethonium chloride; phenol, butyl or benzyl alcohol; alkyl parabens such as methyl or propyl paraben; catechol; resorcinol; cyclohexanol; 3-pentanol; and m-cresol); low molecular weight (less than about 10 residues) polypeptides; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, histidine, arginine, or lysine; monos
  • Aqueous injection suspensions may contain compounds which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, dextran, or the like.
  • the suspension may also contain suitable stabilizers or agents which increase the solubility of the compounds to allow for the preparation of highly concentrated solutions.
  • suspensions of the active compounds may be prepared as appropriate oily injection suspensions.
  • Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty acid esters, such as ethyl cleats or triglycerides, or liposomes.
  • Active ingredients may be entrapped in microcapsules prepared, for example, by coacervation techniques or by interfacial polymerization, for example, hydroxymethylcellulose or gelatin-microcapsules and poly-(methylmethacylate) microcapsules, respectively, in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, nano- particles and nanocapsules) or in macroemulsions. Such techniques are disclosed in Remington's Pharmaceutical Sciences (18th Ed. Mack Printing Company, 1990).
  • Sustained-release preparations may be prepared. Suitable examples of sustained-release preparations include semipermeable matrices of solid hydrophobic polymers containing the polypeptide, which matrices are in the form of shaped articles, e.g. films, or microcapsules.
  • sustained-release preparations include semipermeable matrices of solid hydrophobic polymers containing the polypeptide, which matrices are in the form of shaped articles, e.g.
  • prolonged absorption of an injectable composition can be brought about by the use in the compositions of agents delaying absorption, such as, for example, aluminum monostearate, gelatin or combinations thereof.
  • agents delaying absorption such as, for example, aluminum monostearate, gelatin or combinations thereof.
  • exemplary pharmaceutically acceptable excipients herein further include insterstitial drug dispersion agents such as soluble neutral- active hyaluronidase glycoproteins (sHASEGP), for example, human soluble PH-20 hyaluronidase glycoproteins, such as rHuPH20 (HYLENEX®, Baxter International, Inc.).
  • sHASEGPs and methods of use, including rHuPH20 are described in US Patent Publication Nos. 2005/0260186 and 2006/0104968.
  • a sHASEGP is combined with one or more additional glycosaminoglycanases such as chondroitinases.
  • Exemplary lyophilized antibody formulations are described in US Patent No. 6,267,958.
  • Aqueous antibody formulations include those described in US Patent No. 6,171,586 and
  • the fusion proteins may also be formulated as a depot preparation. Such long acting formulations may be administered by implantation (for example subcutaneously or intramuscularly) or by intramuscular injection.
  • the fusion proteins may be formulated with suitable polymeric or
  • hydrophobic materials for example as an emulsion in an acceptable oil
  • ion exchange resins for example as an emulsion in an acceptable oil
  • sparingly soluble derivatives for example, as a sparingly soluble salt
  • compositions comprising the fusion proteins of the invention may be manufactured by means of conventional mixing, dissolving, emulsifying, encapsulating, entrapping or lyophilizing processes.
  • Pharmaceutical compositions may be formulated in conventional manner using one or more physiologically acceptable carriers, diluents, excipients or auxiliaries which facilitate processing of the proteins into preparations that can be used pharmaceutically. Proper formulation is dependent upon the route of administration chosen.
  • the TNF family ligand trimer-containing antigen binding molecules may be formulated into a composition in a free acid or base, neutral or salt form.
  • Pharmaceutically acceptable salts are salts that substantially retain the biological activity of the free acid or base. These include the acid addition salts, e.g. those formed with the free amino groups of a proteinaceous composition, or which are formed with inorganic acids such as for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric or mandelic acid.
  • Salts formed with the free carboxyl groups can also be derived from inorganic bases such as for example, sodium, potassium, ammonium, calcium or ferric hydroxides; or such organic bases as isopropylamine, trimethylamine, histidine or procaine. Pharmaceutical salts tend to be more soluble in aqueous and other pro tic solvents than are the corresponding free base forms.
  • composition herein may also contain more than one active ingredients as necessary for the particular indication being treated, preferably those with complementary activities that do not adversely affect each other.
  • active ingredients are suitably present in combination in amounts that are effective for the purpose intended.
  • the formulations to be used for in vivo administration are generally sterile. Sterility may be readily accomplished, e.g., by filtration through sterile filtration membranes. Therapeutic methods and compositions
  • TNF family ligand trimer-containing antigen binding molecules may be used in therapeutic methods.
  • TNF family ligand trimer-containing antigen binding molecules of the invention can be formulated, dosed, and administered in a fashion consistent with good medical practice.
  • Factors for consideration in this context include the particular disorder being treated, the particular mammal being treated, the clinical condition of the individual patient, the cause of the disorder, the site of delivery of the agent, the method of administration, the scheduling of administration, and other factors known to medical
  • TNF family ligand trimer-containing antigen binding molecules of the invention for use as a medicament are provided.
  • TNF family ligand trimer-containing antigen binding molecules of the invention for use in treating a disease, in particular for use in the treatment of cancer are provided.
  • TNF family ligand trimer- containing antigen binding molecules of the invention for use in a method of treatment are provided.
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule as described herein for use in the treatment of a disease in an individual in need thereof.
  • the invention provides a TNF family ligand trimer-containing antigen binding molecule for use in a method of treating an individual having a disease comprising administering to the individual a therapeutically effective amount of the fusion protein.
  • the disease to be treated is cancer.
  • cancers include solid tumors, bladder cancer, renal cell carcinoma, brain cancer, head and neck cancer, pancreatic cancer, lung cancer, breast cancer, ovarian cancer, uterine cancer, cervical cancer, endometrial cancer, esophageal cancer, colon cancer, colorectal cancer, rectal cancer, gastric cancer, prostate cancer, blood cancer, skin cancer, squamous cell carcinoma, bone cancer, and kidney cancer, melanoma, B-cell lymphoma, B-cell leukemia, non-Hodgkin lymphoma and acute lymphoblastic leukemia.
  • TNF family ligand trimer-containing antigen binding molecule as described herein for use in the treatment of cancer is provided.
  • the subject, patient, or "individual” in need of treatment is typically a mammal, more specifically a human.
  • a TNF family ligand trimer-containing antigen binding molecule as described herein for use in the treatment of infectious diseases, in particular for the treatment of viral infections.
  • a TNF family ligand trimer- containing antigen binding molecule as described herein for use in the treatment of autoimmune diseases such as for example Lupus disease.
  • a TNF family ligand trimer-containing antigen binding molecule for use in treating head and neck squamous cell carcinoma (HNSCC), breast cancer, colorectal cancer (CRC), pancreatic cancer (PAC), gastric cancer, non- small-cell lung carcinoma (NSCLC) and Mesothelioma, wherein the target cell antigen is FAP.
  • HNSCC head and neck squamous cell carcinoma
  • CRC colorectal cancer
  • PAC pancreatic cancer
  • gastric cancer gastric cancer
  • NSCLC non- small-cell lung carcinoma
  • NSCLC non- small-cell lung carcinoma
  • Mesothelioma wherein the target cell antigen is FAP.
  • the invention relates to the use of a TNF family ligand trimer- containing antigen binding molecule in the manufacture or preparation of a medicament for the treatment of a disease in an individual in need thereof.
  • the medicament is for use in a method of treating a disease comprising administering to an individual having the disease a therapeutically effective amount of the medicament.
  • the disease to be treated is a proliferative disorder, particularly cancer.
  • the invention relates to the use of a TNF family ligand trimer-containing antigen binding molecule of the invention in the manufacture or preparation of a medicament for the treatment of cancer.
  • cancers include solid tumors, bladder cancer, renal cell carcinoma, brain cancer, head and neck cancer, pancreatic cancer, lung cancer, breast cancer, ovarian cancer, uterine cancer, cervical cancer, endometrial cancer, esophageal cancer, colon cancer, colorectal cancer, rectal cancer, gastric cancer, prostate cancer, blood cancer, skin cancer, squamous cell carcinoma, bone cancer, and kidney cancer, melanoma, B-cell lymphoma, B-cell leukemia, non-Hodgkin lymphoma and acute lymphoblastic leukemia.
  • TNF family ligand trimer-containing antigen binding molecule of the present invention include, but are not limited to neoplasms located in the: abdomen, bone, breast, digestive system, liver, pancreas, peritoneum, endocrine glands (adrenal, parathyroid, pituitary, testicles, ovary, thymus, thyroid), eye, head and neck, nervous system (central and peripheral), lymphatic system, pelvic, skin, soft tissue, spleen, thoracic region, and urogenital system. Also included are pre-cancerous conditions or lesions and cancer metastases.
  • the cancer is chosen from the group consisting of renal cell cancer, skin cancer, lung cancer, colorectal cancer, breast cancer, brain cancer, head and neck cancer.
  • TNF family ligand trimer-containing antigen binding molecule may not provide a cure but may only provide partial benefit.
  • a physiological change having some benefit is also considered therapeutically beneficial.
  • an amount of TNF family ligand trimer-containing antigen binding molecule that provides a physiological change is considered an "effective amount" or a "therapeutically effective amount”.
  • the invention relates to the use of a TNF family ligand trimer- containing antigen binding molecule as described herein in the manufacture or preparation of a medicament for the treatment of infectious diseases, in particular for the treatment of viral infections or for the treatment of autoimmune diseases, for example Lupus disease.
  • the invention provides a method for treating a disease in an individual, comprising administering to said individual a therapeutically effective amount of a TNF family ligand trimer-containing antigen binding molecule of the invention.
  • a composition is administered to said individual, comprising a fusion protein of the invention in a
  • the disease to be treated is a proliferative disorder.
  • the disease is cancer.
  • the disease is an infectious disease or an autoimmune disease.
  • the method further comprises administering to the individual a therapeutically effective amount of at least one additional therapeutic agent, e.g. an anti-cancer agent if the disease to be treated is cancer.
  • An "individual" according to any of the above embodiments may be a mammal, preferably a human.
  • the appropriate dosage of a TNF family ligand trimer-containing antigen binding molecule of the invention (when used alone or in combination with one or more other additional therapeutic agents) will depend on the type of disease to be treated, the route of administration, the body weight of the patient, the type of fusion protein, the severity and course of the disease, whether the fusion protein is administered for preventive or therapeutic purposes, previous or concurrent therapeutic interventions, the patient's clinical history and response to the fusion protein, and the discretion of the attending physician.
  • the practitioner responsible for administration will, in any event, determine the concentration of active ingredient(s) in a composition and appropriate dose(s) for the individual subject.
  • Various dosing schedules including but not limited to single or multiple administrations over various time-points, bolus administration, and pulse infusion are contemplated herein.
  • the TNF family ligand trimer-containing antigen binding molecule is suitably
  • TNF family ligand trimer-containing antigen binding molecule can be an initial candidate dosage for administration to the patient, whether, for example, by one or more separate administrations, or by continuous infusion.
  • One typical daily dosage might range from about 1 ⁇ g/kg to 100 mg/kg or more, depending on the factors mentioned above.
  • the treatment would generally be sustained until a desired suppression of disease symptoms occurs.
  • One exemplary dosage of the fusion protein would be in the range from about 0.005 mg/kg to about 10 mg/kg.
  • a dose may also comprise from about 1 ⁇ g/kg body weight, about 5 ⁇ g/kg body weight, about 10 ⁇ g/kg body weight, about 50 ⁇ g/kg body weight, about 100 ⁇ g/kg body weight, about 200 ⁇ g/kg body weight, about 350 ⁇ g/kg body weight, about 500 ⁇ g/kg body weight, about 1 mg/kg body weight, about 5 mg/kg body weight, about 10 mg/kg body weight, about 50 mg/kg body weight, about 100 mg/kg body weight, about 200 mg/kg body weight, about 350 mg/kg body weight, about 500 mg/kg body weight, to about 1000 mg/kg body weight or more per administration, and any range derivable therein.
  • a range of about 5 mg/kg body weight to about 100 mg/kg body weight, about 5 ⁇ g/kg body weight to about 500 mg/kg body weight etc. can be administered, based on the numbers described above.
  • one or more doses of about 0.5 mg/kg, 2.0 mg/kg, 5.0 mg/kg or 10 mg/kg (or any combination thereof) may be administered to the patient.
  • Such doses may be administered intermittently, e.g. every week or every three weeks (e.g. such that the patient receives from about two to about twenty, or e.g. about six doses of the fusion protein).
  • An initial higher loading dose, followed by one or more lower doses may be administered.
  • other dosage regimens may be useful. The progress of this therapy is easily monitored by conventional techniques and assays.
  • the TNF family ligand trimer-containing antigen binding molecules of the invention will generally be used in an amount effective to achieve the intended purpose.
  • the TNF family ligand trimer-containing antigen binding molecules of the invention, or pharmaceutical compositions thereof are administered or applied in a therapeutically effective amount. Determination of a therapeutically effective amount is well within the capabilities of those skilled in the art, especially in light of the detailed disclosure provided herein.
  • a therapeutically effective dose can be estimated initially from in vitro assays, such as cell culture assays.
  • a dose can then be formulated in animal models to achieve a circulating concentration range that includes the IC 50 as determined in cell culture. Such information can be used to more accurately determine useful doses in humans.
  • Initial dosages can also be estimated from in vivo data, e.g., animal models, using techniques that are well known in the art. One having ordinary skill in the art could readily optimize administration to humans based on animal data. Dosage amount and interval may be adjusted individually to provide plasma levels of the
  • TNF family ligand trimer-containing antigen binding molecules which are sufficient to maintain therapeutic effect.
  • Usual patient dosages for administration by injection range from about 0.1 to 50 mg/kg/day, typically from about 0.5 to 1 mg/kg/day.
  • Therapeutically effective plasma levels may be achieved by administering multiple doses each day. Levels in plasma may be measured, for example, by HPLC.
  • the effective local concentration of the TNF family ligand trimer-containing antigen binding molecule may not be related to plasma concentration.
  • a therapeutically effective dose of the TNF family ligand trimer-containing antigen binding molecules described herein will generally provide therapeutic benefit without causing substantial toxicity.
  • Toxicity and therapeutic efficacy of a fusion protein can be determined by standard pharmaceutical procedures in cell culture or experimental animals. Cell culture assays and animal studies can be used to determine the LD 50 (the dose lethal to 50% of a population) and the ED 50 (the dose therapeutically effective in 50% of a population). The dose ratio between toxic and therapeutic effects is the therapeutic index, which can be expressed as the ratio
  • TNF family ligand trimer-containing antigen binding molecules that exhibit large therapeutic indices are preferred.
  • the TNF family ligand trimer-containing antigen binding molecule according to the present invention exhibits a high therapeutic index.
  • the data obtained from cell culture assays and animal studies can be used in formulating a range of dosages suitable for use in humans.
  • the dosage lies preferably within a range of circulating concentrations that include the ED 50 with little or no toxicity.
  • the dosage may vary within this range depending upon a variety of factors, e.g., the dosage form employed, the route of administration utilized, the condition of the subject, and the like.
  • the attending physician for patients treated with fusion proteins of the invention would know how and when to terminate, interrupt, or adjust administration due to toxicity, organ dysfunction, and the like. Conversely, the attending physician would also know to adjust treatment to higher levels if the clinical response were not adequate (precluding toxicity).
  • the magnitude of an administered dose in the management of the disorder of interest will vary with the severity of the condition to be treated, with the route of administration, and the like. The severity of the condition may, for example, be evaluated, in part, by standard prognostic evaluation methods. Further, the dose and perhaps dose frequency will also vary according to the age, body weight, and response of the individual patient.
  • the TNF family ligand trimer-containing antigen binding molecules of the invention may be administered in combination with one or more other agents in therapy.
  • a fusion protein of the invention may be co-administered with at least one additional therapeutic agent.
  • therapeutic agent encompasses any agent that can be administered for treating a symptom or disease in an individual in need of such treatment.
  • additional therapeutic agent may comprise any active ingredients suitable for the particular indication being treated, preferably those with complementary activities that do not adversely affect each other.
  • an additional therapeutic agent is another anti-cancer agent.
  • Such other agents are suitably present in combination in amounts that are effective for the purpose intended.
  • the effective amount of such other agents depends on the amount of fusion protein used, the type of disorder or treatment, and other factors discussed above.
  • the TNF family ligand trimer-containing antigen binding molecules are generally used in the same dosages and with administration routes as described herein, or about from 1 to 99% of the dosages described herein, or in any dosage and by any route that is empirically/clinically determined to be appropriate.
  • combination therapies noted above encompass combined administration (where two or more therapeutic agents are included in the same or separate compositions), and separate administration, in which case, administration of the TNF family ligand trimer-containing antigen binding molecule of the invention can occur prior to, simultaneously, and/or following, administration of the additional therapeutic agent and/or adjuvant.
  • an article of manufacture containing materials useful for the treatment, prevention and/or diagnosis of the disorders described above comprises a container and a label or package insert on or associated with the container.
  • Suitable containers include, for example, bottles, vials, syringes, IV solution bags, etc.
  • the containers may be formed from a variety of materials such as glass or plastic.
  • the container holds a composition which is by itself or combined with another composition effective for treating, preventing and/or diagnosing the condition and may have a sterile access port (for example the container may be an intravenous solution bag or a vial having a stopper that is pierceable by a hypodermic injection needle).
  • At least one active agent in the composition is a TNF ligand trimer-containing antigen binding molecule of the invention.
  • the label or package insert indicates that the composition is used for treating the condition of choice.
  • the article of manufacture may comprise (a) a first container with a composition contained therein, wherein the composition comprises a TNF ligand trimer- containing antigen binding molecule of the invention; and (b) a second container with a composition contained therein, wherein the composition comprises a further cytotoxic or otherwise therapeutic agent.
  • the article of manufacture in this embodiment of the invention may further comprise a package insert indicating that the compositions can be used to treat a particular condition.
  • the article of manufacture may further comprise a second (or third) container comprising a pharmaceutically-acceptable buffer, such as bacteriostatic water for injection (BWFI), phosphate-buffered saline, Ringer's solution and dextrose solution. It may further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, and syringes.
  • BWFI bacteriostatic water for injection
  • phosphate-buffered saline such as bacteriostatic water for injection (BWFI), phosphate-buffered saline, Ringer's solution and dextrose solution.
  • BWFI bacteriostatic water for injection
  • phosphate-buffered saline such as bacteriostatic water for injection (BWFI), phosphate-buffered saline, Ringer's solution and dextrose solution.
  • BWFI bacteriostatic water for injection
  • Ringer's solution such as phosphate

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Abstract

The invention relates to novel TNF family ligand trimer-containing antigen binding molecules comprising (a) at least one moiety capable of specific binding to a target cell antigen and (b) a first and a second polypeptide that are linked to each other by a disulfide bond, characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof.

Description

Antigen Binding Molecules comprising a TNF family ligand trimer
FIELD OF THE INVENTION
The invention relates to novel TNF family ligand trimer-containing antigen binding molecules comprising (a) at least one moiety capable of specific binding to a target cell antigen and (b) a first and a second polypeptide that are linked to each other by a disulfide bond, wherein the antigen binding molecules are characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof. The invention further relates to methods of producing these molecules and to methods of using the same.
BACKGROUND
Ligands interacting with molecules of the TNF (tumor necrosis factor) receptor superfamily have pivotal roles in the organization and function of the immune system. While regulating normal functions such as immune responses, hematopoiesis and morphogenesis, the TNF family ligands (also called cytokines) play a role in tumorgenesis, transplant rejection, septic shock, viral replication, bone resorption, rheumatoid arthritis and diabetes (Aggarwal, 2003). The TNF ligand family comprises 18 genes encoding 19 type II (i.e. intracellular N terminus and extracellular C-terminus) transmembrane proteins, characterized by the presence of a conserved C-terminal domain coined the 'TNF homology domain' (THD). This domain is responsible for receptor binding and is thus critical for the biological activity of the TNF ligand family members. The sequence identity between family members is ~20-30 (Bodmer, 2002). Members of the TNF ligand family exert their biological function as self-assembling, noncovalent trimers (Banner et al, Cell 1993, 73, 431-445). Thus, the TNF family ligands form a trimer that is able to bind to and to activate the corresponding receptors of TNFR superfamily.
4-1BB (CD137), a member of the TNF receptor superfamily, has been first identified as a molecule whose expression is induced by T-cell activation (Kwon and Weissman, 1989).
Subsequent studies demonstrated expression of 4- IBB in T- and B-lymphocytes (Snell et al., 2011; Zhang et al., 2010), NK-cells (Lin et al., 2008), NKT-cells (Kim et al., 2008), monocytes (Kienzle and von Kempis, 2000; Schwarz et al., 1995), neutrophils (Heinisch et al., 2000), mast (Nishimoto et al., 2005) and dendritic cells as well as cells of non-hematopoietic origin such as endothelial and smooth muscle cells (Broil et al., 2001; Olofsson et al., 2008). Expression of 4- IBB in different cell types is mostly inducible and driven by various stimulatory signals, such as T-cell receptor (TCR) or B-cell receptor triggering, as well as signaling induced through co- stimulatory molecules or receptors of pro-inflammatory cytokines (Diehl et al., 2002; von Kempis et al., 1997; Zhang et al., 2010). Expression of 4-1BB ligand (4-1BBL or CD137L) is more restricted and is observed on professional antigen presenting cells (APC) such as B-cells, dendritic cells (DCs) and
macrophages. Inducible expression of 4-1BBL is characteristic for T-cells, including both β and γδ T-cell subsets, and endothelial cells (reviewed in Shao and Schwarz, 2011).
CD 137 signaling is known to stimulate IFNy secretion and proliferation of NK cells (Buechele et al., 2012; Lin et al., 2008; Melero et al., 1998) as well as to promote DC activation as indicated by their increased survival and capacity to secret cytokines and upregulate co- stimulatory molecules (Choi et al., 2009; Futagawa et al., 2002; Wilcox et al., 2002). However, CD 137 is best characterized as a co-stimulatory molecule which modulates TCR- induced activation in both the CD4+ and CD8+ subsets of T-cells. In combination with TCR triggering, agonistic 4-lBB-specific antibodies enhance proliferation of T-cells, stimulate lymphokine secretion and decrease sensitivity of T-lymphocytes to activation-induced cells death (reviewed in (reviewed in Snell et al., 2011).
In line with these co- stimulatory effects of 4- IBB antibodies on T-cells in vitro, their administration to tumor bearing mice leads to potent anti-tumor effects in many experimental tumor models (Melero et al., 1997; Narazaki et al., 2010). However, 4- IBB usually exhibits its potency as an anti-tumor agent only when administered in combination with other
immunomodulatory compounds (Curran et al., 2011; Guo et al., 2013; Morales-Kastresana et al., 2013; Teng et al., 2009; Wei et al., 2013), chemotherapeutic reagents (Ju et al., 2008; Kim et al., 2009), tumor- specific vaccination (Cuadros et al., 2005; Lee et al., 2011) or radiotherapy (Shi and Siemann, 2006). In vivo depletion experiments demonstrated that CD8+ T-cells play the most critical role in anti-tumoral effect of 4- IBB- specific antibodies. However, depending on the tumor model or combination therapy, which includes anti-4-lBB, contributions of other types of cells such as DCs, NK-cells or CD4+ T-cells have been reported (Melero et al., 1997; Murillo et al., 2009; Narazaki et al., 2010; Stagg et al., 2011). In addition to their direct effects on different lymphocyte subsets, 4- IBB agonists can also induce infiltration and retention of activated T-cells in the tumor through 4- IBB -mediated upregulation of intercellular adhesion molecule 1 (ICAM1) and vascular cell adhesion molecule 1 (VCAM1) on tumor vascular endothelium (Palazon et al., 2011). 4- IBB triggering may also reverse the state of T-cell anergy induced by exposure to soluble antigen that may contribute to disruption of immunological tolerance in the tumor micro- environment or during chronic infections (Wilcox et al., 2004).
It appears that the immunomodulatory properties of 4- IBB agonistic antibodies in vivo require the presence of the wild type Fc -portion on the antibody molecule thereby implicating Fc-receptor binding as an important event required for the pharmacological activity of such reagents as has been described for agonistic antibodies specific to other apoptosis-inducing or immunomodulatory members of the TNFR-superfamily (Li and Ravetch, 2011; Teng et al., 2009). However, systemic administration of 4-lBB-specific agonistic antibodies with the functionally active Fc domain also induces expansion of CD8+ T-cells associated with liver toxicity (Dubrot et al., 2010) that is diminished or significantly ameliorated in the absence of functional Fc-receptors in mice. In human clinical trials (ClinicalTrials.gov, NCT00309023), Fc- competent 4-1BB agonistic antibodies (BMS-663513) administered once every three weeks for 12 weeks induced stabilization of the disease in patients with melanoma, ovarian or renal cell carcinoma. However, the same antibody given in another trial (NCT00612664) caused grade 4 hepatitis leading to termination of the trial (Simeone and Ascierto, 2012).
Collectively, the available pre-clinical and clinical data clearly demonstrate that there is a high clinical need for effective 4- IBB agonists. However, new generation drug candidates should not only effectively engage 4- IBB on the surface of hematopoietic and endothelial cells but also be capable of achieving that through mechanisms other than binding to Fc-receptors in order to avoid uncontrollable side effects. The latter may be accomplished through preferential binding to and oligomerization on tumor- specific or tumor- associated moieties.
Fusion proteins composed of one extracellular domain of a 4- IBB ligand and a single chain antibody fragment (Mueller et al., 2008; Hornig et al., 2012) or a single 4-1BB ligand fused to the C-terminus of a heavy chain (Zhang et al, 2007) have been made. WO 2010/010051 discloses the generation of fusion proteins that consist of three TNF ligand ectodomains linked to each other and fused to an antibody part.
However, there is still a need of new antigen binding molecules that combine a moiety capable of preferred binding to tumor- specific or tumor-associated targets with a moiety capable of forming a costimulatory TNF ligand trimer and that have sufficient stability to be
pharmaceutically useful. The antigen binding molecules of the present invention comprise both and surprisingly they provide a trimeric and thus biologically active TNF ligand, although one of the trimerizing TNF ligand ectodomains is located on another polypeptide than the other two TNF ligand ectodomains of the molecule. SUMMARY OF THE INVENTION
In one aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising
(a) at least one moiety capable of specific binding to a target cell antigen and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof. In a particular aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising
(a) at least one moiety capable of specific binding to a target cell antigen,
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof, and
(c) an Fc domain composed of a first and a second subunit capable of stable association.
In a further aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule, comprising
(a) at least one moiety capable of specific binding to a target cell antigen and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that
(i) the first polypeptide contains a CHI or CL domain and the second polypeptide contains a CL or CHI domain, respectively, wherein the second polypeptide is linked to the first polypeptide by a disulfide bond between the CHI and CL domain, and wherein the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the CHI or CL domain by a peptide linker and wherein the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to the CL or
CHI domain of said polypeptide, or
(ii) the first polypeptide contains a CH3 domain and the second polypeptide contains a CH3 domain, respectively, and wherein the first polypeptide comprises two
ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the C-terminus of the CH3 domain by a peptide linker and wherein the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to C-terminus of the CH3 domain of said polypeptide, or
(iii) the first polypeptide contains a VH-CL or a VL-CH1 domain and the second
polypeptide contains a VL-CH1 domain or a VH-CL domain, respectively, wherein the second polypeptide is linked to the first polypeptide by a disulfide bond between the
CHI and CL domain, and wherein the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to to VH or VL by a peptide linker and wherein the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to VL or VH of said polypeptide.
In a particular aspect, the TNF ligand family member is one that costimulates human T-cell activation. Thus, the TNF family ligand trimer-containing antigen binding molecule comprises (a) at least one moiety capable of specific binding to a target cell antigen and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof, wherein the TNF ligand family member costimulates human T-cell activation. More particularly, the TNF ligand family member is selected from 4-1BBL and OX40L.
In one aspect, the TNF ligand family member is 4-1BBL.
In a further aspect, the ectodomain of a TNF ligand family member comprises the amino acid sequence selected from the group consisting of SEQ ID NO: l, SEQ ID NO: 2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:96, SEQ ID NO: 373, SEQ ID NO:374 and SEQ ID NO:375, particularly the amino acid sequence of SEQ ID NO: l or SEQ ID NO:96.
In another aspect, the ectodomain of a TNF ligand family member or fragment thereof comprises the amino acid sequence selected from the group consisting of SEQ ID NO: l, SEQ ID NO:2, SEQ ID NO:3 , SEQ ID NO:4 and SEQ ID NO:96, particularly the amino acid sequence of SEQ ID NO: l or SEQ ID NO:96. More particularly, the ectodomain of a TNF ligand family member comprises the amino acid sequence of SEQ ID NO:96.
In a further aspect, the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
(a) at least one moiety capable of specific binding to a target cell antigen and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond, wherein the antigen binding molecule is characterized in that the first polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO:5, SEQ ID NO:97, SEQ ID NO:98 and SEQ ID NO:99 and in that the second polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO: l, SEQ ID NO:96, SEQ ID NO:3 and SEQ ID NO:4.
In one aspect, the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
(a) at least one moiety capable of specific binding to a target cell antigen and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that the first polypeptide comprises the amino acid sequence of SEQ ID NO:5 and in that the second polypeptide comprises the amino acid sequence of SEQ ID NO:6.
In a further aspect, the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
(a) at least one moiety capable of specific binding to a target cell antigen and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that the first polypeptide comprises the amino acid sequence of SEQ ID NO:5 and in that the second polypeptide comprises the amino acid sequence of SEQ ID NO: 183. In yet a further aspect, the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
(a) at least one moiety capable of specific binding to a target cell antigen and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that the first polypeptide comprises the amino acid sequence of SEQ ID NO:97 and in that the second polypeptide comprises the amino acid sequence of SEQ ID NO: 184 or SEQ ID NO: 185.
In another aspect, the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
(a) at least one moiety capable of specific binding to a target cell antigen,
(b) a first polypeptide containing a CHI or CL domain and a second polypeptide containing a CL or CHI domain, respectively, wherein the second polypeptide is linked to the first polypeptide by a disulfide bond between the CHI and CL domain,
and wherein the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other and to the CHI or CL domain by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof connected by a peptide linker to the CL or CHI domain of said polypeptide.
In one aspect, provided is a TNF family ligand trimer-containing antigen binding molecule comprising
(a) at least one moiety capable of specific binding to a target cell antigen,
(b) a first polypeptide containing a CHI domain and a second polypeptide containing a CL domain, wherein the second polypeptide is linked to the first polypeptide by a disulfide bond between the CHI and CL domain,
and wherein the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the CHI domain by a peptide linker and in that the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to the CL domain of said polypeptide.
In another aspect, provided is a TNF family ligand trimer-containing antigen binding molecule comprising
(a) at least one moiety capable of specific binding to a target cell antigen,
(b) a first polypeptide containing a CL domain and a second polypeptide containing a CHI domain, wherein the second polypeptide is linked to the first polypeptide by a disulfide bond between the CHI and CL domain,
and wherein the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the CL domain by a peptide linker and in that the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to the CHI domain of said polypeptide. In a further aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule as defined herein before, wherein the moiety capable of specific binding to a target cell antigen is selected from the group consisting of an antibody, an antibody fragment and a scaffold antigen binding protein.
In one aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule as defined herein before, wherein the moiety capable of specific binding to a target cell antigen is an antibody fragment.
In particular, the moiety capable of specific binding to a target cell antigen is selected from the group consisting of an antibody fragment, a Fab molecule, a crossover Fab molecule, a single chain Fab molecule, a Fv molecule, a scFv molecule, a single domain antibody, an aVH and a scaffold antigen binding protein. In one aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule as defined herein before, wherein the moiety capable of specific binding to a target cell antigen is a scaffold antigen binding protein.
In a particular aspect, the invention is concerned with a TNF family ligand trimer- containing antigen binding molecule as defined above, wherein the moiety capable of specific binding to a target cell antigen is a Fab molecule capable of specific binding to a target cell antigen.
The invention provides a TNF family ligand trimer-containing antigen binding molecule that comprises at least one moiety capable of specific binding to a target cell antigen. In a particular aspect, the TNF family ligand trimer-containing antigen binding molecule comprises one moiety capable of specific binding to a target cell antigen. In another aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising two moieties capable of specific binding to a target cell antigen.
In another aspect, provided is a TNF family ligand trimer-containing antigen binding molecule of the invention, wherein the target cell antigen is selected from the group consisting of Fibroblast Activation Protein (FAP), Carcinoembryonic Antigen (CEA), Melanoma- associated Chondroitin Sulfate Proteoglycan (MCSP), Epidermal Growth Factor Receptor (EGFR), CD 19, CD20 and CD33.
In a particular aspect, the target cell antigen is Fibroblast Activation Protein (FAP). In one aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule, wherein the moiety capable of specific binding to FAP comprises a VH domain comprising (i) CDR-Hl comprising the amino acid sequence of SEQ ID NO:7 or SEQ ID NO: 100, (ii) CDR-H2 comprising the amino acid sequence of SEQ ID NO:8 or SEQ ID NO: 101, and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO:9 or SEQ ID NO: 102, and a VL domain comprising (iv) CDR-Ll comprising the amino acid sequence of SEQ ID NO: 10 or SEQ ID NO: 103, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO: 11 or SEQ ID NO: 104, and (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO: 12 or SEQ ID NO: 105.
In one aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule, wherein the moiety capable of specific binding to FAP comprises a VH domain comprising (i) CDR-Hl comprising the amino acid sequence of SEQ ID NO:7, (ii) CDR- H2 comprising the amino acid sequence of SEQ ID NO: 8 and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO:9, and a VL domain comprising (iv) CDR-Ll comprising the amino acid sequence of SEQ ID NO: 10, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO: 11 and (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO: 12.
In a particular aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule, wherein the moiety capable of specific binding to FAP comprises a VH domain comprising (i) CDR-Hl comprising the amino acid sequence of SEQ ID NO: 100, (ii) CDR-H2 comprising the amino acid sequence SEQ ID NO: 101, and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO: 102, and a VL domain comprising (iv) CDR-L1 comprising the amino acid sequence of SEQ ID NO: 103, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO: 104, and (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO:105.
In one aspect, provided is a TNF family ligand trimer-containing antigen binding molecule as defined herein before, wherein the moiety capable of specific binding to FAP comprises a variable heavy chain comprising an amino acid sequence of SEQ ID NO: 16 and a variable light chain comprising an amino acid sequence of SEQ ID NO: 17 or wherein the moiety capable of specific binding to FAP comprises a variable heavy chain comprising an amino acid sequence of SEQ ID NO: 106 and a variable light chain comprising an amino acid sequence of SEQ ID
NO: 107.
In a further aspect, provided is a TNF family ligand trimer-containing antigen binding molecule according to the invention, wherein a peptide comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C-terminus to the CHI or CL domain of a heavy chain by a second peptide linker and wherein one ectodomain of said TNF ligand family member or a fragment thereof is fused at the its C-terminus the CL or CHI domain on a light chain by a third peptide linker.
In a particular aspect, the invention relates to a TNF family ligand trimer-containing antigen binding molecule as defined above, wherein the peptide linker is (G4S)2, i.e. a peptide linker of SEQ ID NO: 13. In one aspect, the first peptide linker is (G4S)2, the second peptide linker is GSPGSSSSGS (SEQ ID NO:57) and the third peptide linker is (G4S)2. In another aspect, the first, the second and the third peptide linker is (G4S)2.
The invention is further concerned with a TNF family ligand trimer-containing antigen binding molecule as defined herein before, comprising an Fc domain composed of a first and a second subunit capable of stable association.
In particular, the TNF family ligand trimer-containing antigen binding molecule of the invention comprising (c) an Fc domain composed of a first and a second subunit capable of stable association further comprises (a) a Fab molecule capable of specific binding to a target cell antigen, wherein the Fab heavy chain is fused at the C-terminus to the N-terminus of a CH2 domain in the Fc domain.
In a further aspect, the Fc domain is an IgG, particularly an IgGl Fc domain or an IgG4 Fc domain. More particularly, the Fc domain is an IgGl Fc domain. In a particular aspect, the Fc domain comprises a modification promoting the association of the first and second subunit of the Fc domain.
In another aspect, the invention is concerned with a TNF family ligand trimer-containing antigen binding molecule as defined herein before, comprising
(c) an Fc domain composed of a first and a second subunit capable of stable association, wherein the Fc domain comprises one or more amino acid substitution that reduces binding to an Fc receptor, in particular towards Fey receptor.
In particular, the Fc domain comprises amino acid substitutions at positions 234 and 235 (EU numbering) and/or 329 (EU numbering) of the IgG heavy chains. More particularly, provided is a trimeric TNF family ligand-containing antigen binding molecule according to the invention which comprises an IgGl Fc domain with the amino acid substitutions L234A, L235A and P329G (EU numbering).
In a further aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule, wherein the antigen binding molecule comprises
a first heavy chain and a first light chain, both comprising a Fab molecule capable of specific binding to a target cell antigen,
a first peptide comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker fused at its C-terminus by a second peptide linker to a second heavy or light chain,
and a second peptide comprising one ectodomain of said TNF ligand family member fused at its C-terminus by a third peptide linker to a second light or heavy chain, respectively.
In another aspect, provided is a TNF family ligand trimer-containing antigen binding molecule, wherein the first peptide comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C-terminus by a second peptide linker to a CHI domain that is part of a heavy chain,
and the second peptide comprising one ectodomain of said TNF ligand family member or a fragment thereof is fused at its C-terminus by a third peptide linker to a CL domain that is part of a light chain.
In yet another aspect, provided is a TNF family ligand trimer-containing antigen binding molecule, wherein the first peptide comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C-terminus by a second peptide linker to a CL domain that is part of a heavy chain,
and the second peptide comprising one ectodomain of said TNF ligand family member or a fragment thereof is fused at its C-terminus by a third peptide linker to a CHI domain that is part of a light chain.
In a further aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule, wherein the first peptide comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C- terminus by a second peptide linker to a VH domain that is part of a heavy chain,
and the second peptide comprising one ectodomain of said TNF ligand family member or a fragment thereof is fused at its C-terminus by a third peptide linker to a VL domain that is part of a light chain.
Provided is further a TNF family ligand trimer-containing antigen binding molecule, wherein in the CL domain adjacent to the TNF ligand family member the amino acid at position 123 (EU numbering) has been replaced by arginine (R) and the amino acid at position 124 (EU numbering) has been substituted by lysine (K), and wherein in the CHI domain adjacent to the TNF ligand family member the amino acids at position 147 (EU numbering) and at position 213 (EU numbering) have been substituted by glutamic acid (E).
In a further aspect, provided is a TNF family ligand trimer-containing antigen binding molecule as described herein before, wherein the antigen binding molecule comprises
(a) a first heavy chain and a first light chain, both comprising a Fab molecule capable of specific binding to a target cell antigen,
(b) a second heavy chain comprising an amino acid sequence selected from the group consisting of SEQ ID NO:5, SEQ ID NO:97, SEQ ID NO:98 and SEQ ID NO:99, and
a second light chain comprising an amino acid sequence selected from the group consisting of SEQ ID NO:l, SEQ ID NO:96, SEQ ID NO:3 and SEQ ID NO:4.
In one aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule, wherein the antigen binding molecule comprises
(a) a Fab molecule capable of specific binding to FAP, and
(b) a second heavy chain comprising an amino acid sequence selected from the group consisting of SEQ ID NO:5, SEQ ID NO:97, SEQ ID NO:98 and SEQ ID NO:99, and
a second light chain comprising an amino acid sequence selected from the group consisting of SEQ ID NO: l, SEQ ID NO:96, SEQ ID NO:3 and SEQ ID NO:4.
In a particular aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising a moiety capable of specific binding to FAP. In one aspect, provided is a TNF family ligand trimer-containing antigen binding molecule, wherein the antigen binding molecule comprises
(i) a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO: 16 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO: 17 or
a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO: 106 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO: 107,
(ii) a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 14, SEQ ID NO: 108, SEQ ID NO: 111, SEQ ID NO: 113, SEQ ID NO.115, SEQ
ID NO: 139 and SEQ ID NO: 148, and
(iii) a second light chain comprising the amino acid sequence of SEQ ID NO: 15, SEQ ID
NO: 109, SEQ ID NO: 110, SEQ ID NO: 112, SEQ ID NO: 114 and SEQ ID NO: 115.
In another aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule, wherein the antigen binding molecule comprises
(i) a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO: 16 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO: 17 or
a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO: 106 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO: 107,
(ii) a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 115, SEQ ID NO: 117, SEQ ID NO: 119 and SEQ ID NO: 173, and
(iii) a second light chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 116, SEQ ID NO: 118, SEQ ID NO: 120 and SEQ ID NO: 174.
In yet another aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule, comprising
(a) at least one moiety capable of specific binding to a target cell antigen, and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that the first polypeptide contains a CH3 domain and the second polypeptide contains a CH3 domain, respectively, and wherein the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the C-terminus of the CH3 domain by a peptide linker and wherein the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to C-terminus of the CH3 domain of said polypeptide. In particular, such a TNF family ligand trimer-containing antigen binding molecule comprises two moieties capable of specific binding to a target cell antigen.
In one aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising two moieties capable of specific binding to FAP. In particular, provided is a TNF family ligand trimer-containing antigen binding molecule as described herein before comprises
(i) a first heavy chain comprising the amino acid sequence of SEQ ID NO: 121, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 122, and two light chains comprising the amino acid sequence of SEQ ID NO: 19, or
(ii) a first heavy chain comprising the amino acid sequence of SEQ ID NO: 123, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 124, and two light chains comprising the amino acid sequence of SEQ ID NO: 125, or
(iii) a first heavy chain comprising the amino acid sequence of SEQ ID NO: 126, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 127, and two light chains comprising the amino acid sequence of SEQ ID NO: 125.
In another particular aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule as described herein before, wherein the target cell antigen is CD 19.
In one aspect, provided is a TNF family ligand trimer-containing antigen binding molecule, wherein the moiety capable of specific binding to CD 19 comprises a VH domain comprising (i) CDR-H1 comprising the amino acid sequence of SEQ ID NO: 195 or SEQ ID NO:252, (ii) CDR- H2 comprising the amino acid sequence of SEQ ID NO: 196 or SEQ ID NO:253, and (iii) CDR- H3 comprising the amino acid sequence of SEQ ID NO: 197 or SEQ ID NO:254, and a VL domain comprising (iv) CDR-L1 comprising the amino acid sequence of SEQ ID NO: 198 or SEQ ID NO:249, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO: 199 or SEQ ID NO:250, and (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO:200 or SEQ ID NO:251.
In a further aspect, provided is a TNF family ligand trimer-containing antigen binding molecule, wherein the moiety capable of specific binding to CD 19 comprises a variable heavy chain comprising an amino acid sequence of SEQ ID NO:201 and a variable light chain comprising an amino acid sequence of SEQ ID NO:202 or wherein the moiety capable of specific binding to FAP comprises a variable heavy chain comprising an amino acid sequence of SEQ ID NO:357 and a variable light chain comprising an amino acid sequence of SEQ ID NO:358.
In a particular aspect, provided is a TNF family ligand trimer-containing antigen binding molecule, wherein the antigen binding molecule comprises (i) a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO:201 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO:202 or
a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO:357 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO:358,
(ii) a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 14, SEQ ID NO: 108, SEQ ID NO: 111 and SEQ ID NO: 113, and
(iii) a second light chain comprising the amino acid sequence of SEQ ID NO: 15, SEQ ID
NO: 109, SEQ ID NO: 110, SEQ ID NO: 112 and SEQ ID NO: 114.
In another aspect, provided is a TNF family ligand trimer-containing antigen binding molecule, wherein the antigen binding molecule comprises
(i) a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO:201 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO:202 or
a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO:357 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO:358,
(ii) a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 115, SEQ ID NO: 117, SEQ ID NO: 119 and SEQ ID NO: 173, and
(iii) a second light chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 116, SEQ ID NO: 118, SEQ ID NO: 120 and SEQ ID NO: 174.
In one aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising two moieties capable of specific binding to CD 19. In particular, provided is a TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 14, 29, 30 and 32 to 34, wherein the antigen binding molecule comprises
(i) a first heavy chain comprising the amino acid sequence of SEQ ID NO:209, a second heavy chain comprising the amino acid sequence of SEQ ID NO:210, and two light chains comprising the amino acid sequence of SEQ ID NO:206, or
(ii) a first heavy chain comprising the amino acid sequence of SEQ ID NO:213, a second heavy chain comprising the amino acid sequence of SEQ ID NO:214, and two light chains comprising the amino acid sequence of SEQ ID NO:206, or
(iii) a first heavy chain comprising the amino acid sequence of SEQ ID NO:309, a second heavy chain comprising the amino acid sequence of SEQ ID NO:310, and two light chains comprising the amino acid sequence of SEQ ID NO:279, or
(iv) a first heavy chain comprising the amino acid sequence of SEQ ID NO:313, a second heavy chain comprising the amino acid sequence of SEQ ID NO:314, and two light chains comprising the amino acid sequence of SEQ ID NO:279.
In another particular aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule as described herein before, wherein the target cell antigen is CEA. In one aspect, provided is a TNF family ligand trimer-containing antigen binding molecule, wherein the moiety capable of specific binding to CEA comprises a VH domain comprising (i) CDR-H1 comprising the amino acid sequence of SEQ ID NO:321, (ii) CDR-H2 comprising the amino acid sequence of SEQ ID NO:322, and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO:323, and a VL domain comprising (iv) CDR-L1 comprising the amino acid sequence of SEQ ID NO:324, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO:325, and (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO:326.
In another aspect, provided is a TNF family ligand trimer-containing antigen binding molecule, wherein the moiety capable of specific binding to CEA comprises a variable heavy chain comprising an amino acid sequence of SEQ ID NO:329 and a variable light chain comprising an amino acid sequence of SEQ ID NO:330.
In one aspect, provided is a TNF family ligand trimer-containing antigen binding molecule as described herein before, wherein the antigen binding molecule comprises
(i) a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO:329 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO:330,
(ii) a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 14, SEQ ID NO: 108, SEQ ID NO: 111 and SEQ ID NO: 113, and
(iii) a second light chain comprising the amino acid sequence of SEQ ID NO: 15, SEQ ID
NO: 109, SEQ ID NO: 110, SEQ ID NO: 112 and SEQ ID NO: 114. In another aspect, provided is a TNF family ligand trimer-containing antigen binding molecule, wherein the antigen binding molecule comprises
(i) a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO:329 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO:330,
(ii) a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 115, SEQ ID NO: 117, SEQ ID NO: 119 and SEQ ID NO: 173, and
(iii) a second light chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 116, SEQ ID NO: 118, SEQ ID NO: 120 and SEQ ID NO: 174. In one aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising two moieties capable of specific binding to CEA. Particularly, provided is a TNF family ligand trimer-containing antigen binding molecule, wherein the antigen binding molecule comprises
(i) a first heavy chain comprising the amino acid sequence of SEQ ID NO:337, a second heavy chain comprising the amino acid sequence of SEQ ID NO:338, and two light chains comprising the amino acid sequence of SEQ ID NO:334, or
(ii) a first heavy chain comprising the amino acid sequence of SEQ ID NO:341, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 342, and two light chains comprising the amino acid sequence of SEQ ID NO:334.
In a further aspect, provided is aTNF family ligand trimer-containing antigen binding molecule as described herein before, wherein the TNF ligand family member is OX40L. In one aspect, provided is TNF family ligand trimer-containing antigen binding molecule, wherein the ectodomain of a TNF ligand family member comprises the amino acid sequence of SEQ ID NO:53 or SEQ ID NO:54, particularly the amino acid sequence of SEQ ID NO:53.
In a further aspect, provided is a TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 5, 10 to 24, 29, 30, 32 to 34, 38 to 40, 44 and 45, comprising
(a) at least one moiety capable of specific binding to a target cell antigen and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that the first polypeptide comprises the amino acid sequence of SEQ ID NO:371 or SEQ ID:372 and in that the second polypeptide comprises the amino acid sequence of SEQ ID NO:53 or SEQ ID NO:54.
In another aspect, provided is a TNF family ligand trimer-containing antigen binding molecule, wherein the target cell antigen is Fibroblast Activation Protein (FAP) and the moiety capable of specific binding to FAP comprises a VH domain comprising (i) CDR-H1 comprising the amino acid sequence of SEQ ID NO:7 or SEQ ID NO: 100, (ii) CDR-H2 comprising the amino acid sequence of SEQ ID NO:8 or SEQ ID NO: 101, and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO:9 or SEQ ID NO: 102, and a VL domain comprising (iv) CDR-L1 comprising the amino acid sequence of SEQ ID NO: 10 or SEQ ID NO: 103, (v) CDR- L2 comprising the amino acid sequence of SEQ ID NO: 11 or SEQ ID NO: 104, and (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO: 12 or SEQ ID NO: 105.
Particularly, provided is a TNF family ligand trimer-containing antigen binding molecule as described herein, wherein the antigen binding molecule comprises
(i) a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO: 16 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO: 17 or
a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO: 106 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO: 107,
(ii) a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO:355, and
(iii) a second light chain comprising the amino acid sequence of SEQ ID NO:356.
According to another aspect of the invention, there is provided an isolated polynucleotide encoding a TNF family ligand trimer-containing antigen binding molecule as defined herein before. The invention further provides a vector, particularly an expression vector, comprising the isolated polynucleotide of the invention and a host cell comprising the isolated polynucleotide or the vector of the invention. In some embodiments the host cell is a eukaryotic cell, particularly a mammalian cell. In another aspect, provided is a method for producing the TNF family ligand trimer- containing antigen binding molecule of the invention, comprising the steps of (i) culturing the host cell of the invention under conditions suitable for expression of the antigen binding molecule, and (ii) recovering the antigen binding molecule. The invention also encompasses a TNF family ligand trimer-containing antigen binding molecule produced by the method of the invention.
The invention further provides a pharmaceutical composition comprising the TNF family ligand trimer-containing antigen binding molecule of the invention and at least one
pharmaceutically acceptable excipient.
Also encompassed by the invention is the TNF family ligand trimer-containing antigen binding molecule of the invention, or the pharmaceutical composition of the invention, for use as a medicament. In one aspect is provided the TNF family ligand trimer-containing antigen binding molecule of the invention, or the pharmaceutical composition of the invention, for use in the treatment of a disease in an individual in need thereof. In a specific embodiment, provided is the TNF family ligand trimer-containing antigen binding molecule of the invention, or the pharmaceutical composition of the invention, for use in the treatment of cancer.
Also provided is the use of the TNF family ligand trimer-containing antigen binding molecule of the invention for the manufacture of a medicament for the treatment of a disease in an individual in need thereof, in particular for the manufacture of a medicament for the treatment of cancer, as well as a method of treating a disease in an individual, comprising administering to said individual a therapeutically effective amount of a composition comprising the TNF family ligand trimer-containing antigen binding molecule of the invention in a pharmaceutically acceptable form. In a specific embodiment, the disease is cancer. In any of the above
embodiments the individual is preferably a mammal, particularly a human. BRIEF DESCRIPTION OF THE DRAWINGS
Figure 1 shows the components for the assembly of split trimeric human 4- IBB ligands. Figure (1A) shows the dimeric ligand that is fused at the C-terminus to a human CHI or CL domain or a VL or VH domain and Figure (IB) shows the monomeric ligand fused to human CL or CHI domain or a VL or VH domain. Figure (1C) shows the dimeric ligand that is fused at the N-terminus to a human CH3 domain and Figure (ID) shows the monomeric ligand fused at the N-terminus to a human CH3 domain.
Figure 2 shows the 4-lBBL-trimer-containing antigen binding molecules Constructs 1.1 to 1.10 of the invention. The preparation and production of these constructs is described in
Example 1. The VH and VL domains are those of anti-FAP antibody 28H1, the thick black point stands for the knob-into-hole modification. * symbolizes amino acid modifications in the CHI and CL domain (so-called charged residues).
Figure 3 shows the components for the assembly of split trimeric murine 4-1BB ligands. Figure (3 A) shows the dimeric ligand that is fused at the C-terminus to murine CL domain and Figure (3B) shows the monomeric ligand fused at the C-terminus to murine CHI domain.
Components for the assembly of FAP targeted split trimeric murine 4- IBB ligand. Figure (3C) shows the assembled murine 4-lBBL-trimer-containing antigen binding molecules as described in more detail in Example 1.3.
Figure 4 shows the 4-lBBL-trimer-containing antigen binding molecules Constructs 2.1 to 2.6 of the invention. The preparation and production of these constructs is described in Example 2. The VH and VL domains are those of anti-FAP antibody 4B9, the thick black point stands for the knob-into-hole modification. * symbolizes amino acid modifications in the CHI and CL domain (so-called charged residues).
Figure 5A and Figure 5B show the "untargeted" variants of Constructs 1.1 and 1.2 comprising a DP47 Fab molecule instead of the anti-FAP Fab molecule. The molecules are named Control A and Control B, respectively. The preparation is described in Example 1.4. Figure 5C is a drawing of the monomeric 4- IBB Fc(kih) construct as prepared in Example 3.
Figure 6 relates to the binding of FAP-targeted 4- IBB ligand trimer-containing Fc(kih) fusion antigen binding molecule (FAP split 4-1BBL trimer, filled circles) or DP-47 untargeted 4- 1BB ligand trimer-containing Fc(kih) fusion antigen binding molecule (DP47 split 4-1BBL trimer, open circles) to resting (naive) or activated human PMBCs. Specifically, the binding to resting (naive) or activated human CD8+ T cells is shown in Figure (6A), to resting (naive) or activated human CD4+ T cells in Figure (6B) and to resting (naive) or activated human NK cells in Figure (6C). Shown is the binding as Median of fluorescence intensity (MFI) of red
macrophytic algae Phycoerythrin (R-PE)-labeled anti-human IgG Fcy-specific goat IgG F(ab )2 fragment which is used as secondary detection antibody. MFI was measured by flow cytometry and baseline corrected by subtracting the MFI of the blank control.
The binding of different FAP-targeted or untargeted split trimeric human 4- IBB ligand Fc (kih) constructs to human 4- IBB expressing T cells from PHA-L and Proleukin pre-activated and anti-human CD3/anti-human CD28 re-activated human PBMCs is shown in Figure 7.
Binding was detected with R-Phycoerythrin-fluorochrome conjugated anti-human IgG Fcy- specific goat IgG F(ab )2 fragment. Shown is the median of fluorescence intensity (MFI) versus the concentration of tested Constructs 1.1 to 1.10 of Example 1. For a better display the binding curves are split in four different blots with Construct 1.1 (monovalent FAP-targeted split trimeric human 4- IBB ligand Fc (kih)) and Control B (monovalent untargeted split trimeric human 4- 1BB ligand Fc (kih) with CH-CL cross and charged residues) as comparison curves. Binding was monitored on CD3+ CD8+ T cells (Figure 7A) and CD3+ CD4+ T cells (Figure 7B). The 4- IBB expression level on CD8 T cells is normally higher than on CD4 T cells. All versions bind with a quite similar affinity to human 4- IBB.
Figure 8 shows the binding of different FAP-targeted or untargeted split trimeric human 4- 1BB ligand Fc (kih) constructs to CD4+ or CD8+ T cells from fresh PBMCs (Figure 8A) or to human 4- IBB expressing PHA-L and Proleukin pre-activated and anti-human CD3/anti-human CD28 re-activated human PBMCs (Figure 8B). Binding was detected with R-Phycoerythrin- fluorochrome conjugated anti-human IgG Fcy-specific goat IgG F(ab )2 fragment. Shown is the median of fluorescence intensity (MFI) versus the concentration of tested Constructs 2.1, 2.3, 2.4, 2.5 and 2.6 of Example 2 and control molecules Control B, Control C, Control E and Control F. For a better display the binding curves are split in two different blots with construct 2.1
(monovalent FAP-targeted split trimeric human 4- IBB ligand Fc (kih)) and control B
(monovalent untargeted split trimeric human 4- IBB ligand Fc (kih) with CH-CL cross and charged residues) as comparison curves. Binding was monitored on CD45+ CD3+ CD8+ T cells (blots on the bottom) and CD45+ CD3+ CD4+ T cells (blots on the top). The 4-1BB expression level on CD8 T cells is normally higher than on CD4 T cells. All constructs bind with a quite similar affinity to human 4- IBB, whereas the bivalent construct 2.3 and its untargeted control C show a lower MFI. This can be due to sterical hindrance of 4-lBB-binding and/or less detection due to the 2nd detection antibody induced by the Fc-conjugated split 4- IBB ligand. In Figure 9 the binding of FAP-targeted 4- IBB ligand trimer-containing Fc(kih) fusion antigen binding molecules (FAP split 4-1BBL trimer, filled circles) or DP47 untargeted 4- IBB ligand trimer-containing Fc(kih) fusion antigen binding molecules (DP47 split 4-1BBL trimer; open circles) to activated mouse splenocytes is shown. In particular, the binding to activated mouse CD4+ T cells is shown in Figure (9A) and to activated mouse CD8+ T cells in Figure (9B). An anti-mouse CD137-specific human IgGl P329G LALA antibody (clone Lobl2.3) was used as positive control (Triangles). The binding is characterized by plotting the MFI of R-PE- labeled anti-human IgG Fcy-specific goat IgG F(ab )2 fragment that is used as secondary detection antibody versus the concentration in nM of the tested split 4-1BBL trimer constructs. MFI was measured by flow cytometry and baseline corrected by subtracting the MFI of the blank control.
Figure 10 shows the binding of 4- IBB ligand trimer-containing Fc(kih) fusion antigen binding molecules (filled circles: FAP-targeted 4- IBB ligand trimer-containing Fc(kih) fusion antigen binding molecule Construct 1.1, open circles: DP47 untargeted 4- IBB ligand trimer- containing Fc(kih) fusion antigen binding molecule Control A to fibroblast activation protein (FAP)-expressing human melanoma (A) MV-3 cell line and (B) WM-266-4 cell line. The binding is characterized by plotting the MFI of R-PE-labeled anti-human IgG Fcy-specific goat IgG F(ab )2 fragment that is used as secondary detection antibody versus the concentration in nM of tested split 4-1BBL trimer constructs. MFI was measured by flow cytometry and baseline corrected by subtracting the MFI of the blank control.
In Figure 11 the binding of different FAP-targeted or untargeted split trimeric human 4- 1BB ligand Fc (kih) constructs to human-FAP expressing human melanoma MV-3 cells (Figure 11 A) and/or NIH/3T3-huFAP clone 39 transfected mouse embryonic fibroblast cells (Figure 11B) is shown. Binding was detected with R-Phycoerythrin-fluorochrome or fluorescein-fluorochrome conjugated anti-human IgG Fcy-specific goat IgG F(ab )2 fragments. Shown is the median of fluorescence intensity (MFI) versus the concentration of tested constructs. For a better display binding curves were distributed to four (Figure 11 A) or two blots (Figure 1 IB), whereas construct 1.1 (monovalent FAP-targeted split trimeric human 4- IBB ligand Fc (kih)) is used a comparison curve. All constructs bind with a similar affinity to human FAP except the bivalent FAP-targeted constructs (constructs 1.5, 1.7 and 1.8). They showed a tendency to have lower EC50 values and lower median fluorescence intensity. This can be explained with their bivalent targeting (higher avidity, less molecules can bind at the same time due to occupancy of two epitopes resulting in a lower MFI). Structural differences may also explain the difference between Construct 1.8 (complete bivalent targeting) and Constructs 1.5 and 1.7 (only partial bivalent targeting). In Figure 12 the binding of different FAP-targeted or untargeted split trimeric human 4- 1BB ligand Fc (kih) Constructs 2.1, 2.3, 2.4, 2.5 and 2.6 to human-FAP expressing human melanoma MV-3 cells (Figure 12A) and WM-266-4 cells (Figure 12B) is shown. Binding was detected with R-Phycoerythrin-fluorochrome conjugated anti-human IgG Fcy-specific goat IgG F(ab )2 fragments. Shown is the median of fluorescence intensity (MFI) versus the concentration of tested contracts. For a better display binding curves were distributed to two blots, whereas construct 2.1 (monovalent FAP-targeted split trimeric human 4- IBB ligand Fc (kih)) is used as comparison curve. All constructs bind with a similar affinity to human FAP except the bivalent FAP-targeted construct 2.3. It has a tendency to show lower EC50 values and lower median fluorescence intensity. This can be explained with its bivalent targeting, which results in higher avidity but less occupancy or FAP molecules on the cell surface resulting in a lower MFI.
Figure 13 shows the binding of different FAP-targeted or untargeted split trimeric mouse 4-1BB ligand Fc (kih) constructs to CD4+ or CD8+ T cells from fresh splenocytes (Figure 13A) or to mouse 4- IBB expressing anti-mouse CD3/anti-mouse CD28 monoclonal agonistic antibodies activated mouse splenocytes (Figure 13B). Binding was detected with FITC- fluorochrome conjugated anti-mouse IgG Fey- specific goat IgG F(ab )2 fragment. Shown is the median of fluorescence intensity (MFI) versus the concentration of tested constructs. Binding was monitored on CD3+ CD8+ T cells (left blot) and CD3+ CD4+ T cells (right blot). The 4- 1BB expression level on CD8 T cells is normally higher than on CD4 T cells. All constructs bind with a quite similar affinity to mouse 4- IBB.
The binding of different FAP-targeted or untargeted split trimeric mouse 4- IBB ligand Fc (kih) constructs to human FAP expressing tumor cells is demonstrated in Figure 14. Binding was detected with FITC-fluorochrome conjugated anti-mouse IgG Fcy-specific goat IgG F(ab )2 fragment. Shown is the median of fluorescence intensity (MFI) versus the concentration of tested constructs. Binding was monitored on MV-3 cells (Figure 14A) and WM-266-4 cells (Figure 14B). FAP-targeted split trimeric mouse 4- IBB ligand Fc (kih) constructs M.l and M.2 bind with a quite similar affinity to FAP.
Figure 15 shows a scheme that illustrates the general principal of the NFkB activity assay described in Example 6.1 using a reporter cell line. Shown is the activation assay set up with human 4- IBB expressing HeLa reporter cell line. A crosslinking of 4- IBB expressed on the reporter cells induces NFKB activation and NFKB-mediated Luciferase expression. After lysis of the cells Luciferase can catalyze the oxidation of Luciferin to Oxyluciferin. This chemical reaction correlates positively with the strength of NFKB-mediated luciferase expression and can be measured by the strength of light emission (units of released light). The ratio of FAP- expressing tumor cells to the reporter cell line HeLa-huCD137-NFkB-luc was 5 to 1. In Figure 16 it is shown that the activation of the NFkB signaling pathway by FAP- targeted 4- IBB ligand trimer-containing Fc(kih) fusion antigen binding molecule (Construct 1.1) is strictly dependent on its binding to FAP-expressing target cells. Human CD137 expressing NFkB reporter HeLa cells were co-cultured with the indicated tumor cells exhibiting different levels of cell surface FAP expression. Luciferase activity was assessed as described in Example 6.1 after culturing cells in the absence or presence of 4-lBBL-containing molecules at the indicated concentrations for 6 hours. Filled circles refer to Construct 1.1. Open circles refer to DP47 untargeted 4- IBB ligand trimer-containing Fc(kih) fusion antigen binding molecule (Control A). Cell line NIH/3T3-human FAP clone 39 was used as target cells in Graph (A), Graph (B) shows the activation with MV3 cell line as target cells and Graph (C) with WM-266-4 cell line as target cells. Activity is characterized by blotting the units of released light (URL) measured during 0.5 s versus the concentration in nM of tested split 4-1BBL trimer constructs. URLs are emitted due to luciferase-mediated oxidation of luciferin to oxyluciferin.
Figure 17 shows the NFKB-activation-induced Luciferase expression and activity as measured with the assay described in Example 6.1. Counts of released light per seconds (CPS) are measured for 0.5 s/well and plotted against the used concentration of FAP-targeted or untargeted split trimeric human 4-1BB ligand Fc (kih) constructs. Human 4-lBB-expressing HeLa-reporter cells were incubated for 6 h in the absence (Figure 17A) or presence of crosslinking human-FAP expressing human melanoma cell line MV-3 (Figure 17B) or WM- 266-4 (Figure 17C). CPS were measured and blotted against the concentrations of different
FAP-targeted or untargeted split trimeric human 4- IBB ligand Fc (kih) Constructs. The cell ratio is one human 4-lBB-expressing HeLa reporter cell to five tumor cells. For better display, activation curves were split to four different display-blots with construct 1.1 (monovalent FAP- targeted split trimeric human 4- IBB ligand Fc (kih)) and control B (monovalent untargeted split trimeric human 4- IBB ligand Fc (kih) with CH-CL cross and charged residues) as comparison curves. Figure 17A shows the activation without crosslinking FAP-expressing tumor cells,
Figure 17B shows the activation in the presence of crosslinking FAP-expressing MV-3 tumor cells and Figure 17C shows the activation in the presence of crosslinking FAP-expressing WM- 266-4 tumor cells. Figure 18 shows the NFKB-activation-induced Luciferase expression and activity as measured for the constructs of Example 2. Units of released light (URL) are measured for 0.5 s/well and plotted against the used concentration of FAP-targeted or untargeted split trimeric human 4-1BB ligand Fc (kih) constructs. Human 4-lBB-expressing HeLa-reporter cells were incubated for 6 h in the absence or presence of crosslinking human-FAP expressing human melanoma cell line MV-3 or WM-266-4. URLs were measured and blotted against the
concentrations of different FAP-targeted or untargeted split trimeric human 4- IBB ligand Fc (kih) constructs 2.1, 2.3, 2.4, 2.5 and 2.6 and Controls B, C, E and F. The cell ratio is one 4- IBB- expressing HeLa reporter cell to five tumor cells. For better display activation curves were split to two different display-blots with construct 2.1 (monovalent FAP-targeted split trimeric human 4- IBB ligand Fc (kih)).
In Figure 19 the activation assay set up with cynomolgus monkey 4- IBB expressing T293-HEK reporter cell line is shown. A crosslinking of cynomolgus monkey 4- IBB expressed on the reporter cells induces NFKB activation and NFKB-mediated Luciferase expression. After lysis of the cells Luciferase can catalyze the oxidation of Luciferin to Oxyluciferin. This chemical reaction correlates positively with the strength of NFKB-mediated luciferase expression and can be measured by the strength of light emission (units of released light). Figure 20 shows the NFKB-activation-induced Luciferase expression and activity. Units of released light (URL) are measured for 0.5 s/well and plotted against the used concentration of FAP-targeted or untargeted split trimeric human 4-1BB ligand Fc (kih) constructs. Cynomolgus monkey 4-lBB-expressing T293-HEK-reporter cells were incubated for 6 h in the absence or presence of crosslinking human-FAP expressing human melanoma cell line MV-3 or WM-266-4. URLs were measured and blotted against the concentrations of different FAP-targeted or untargeted split trimeric human 4-1BB ligand Fc (kih) constructs. The cell ratio is one 4- 1BB- expressing T293-HEK reporter cell to five MV-3 or two WM-266-4 cells. For better display activation curves were split to two different blots with Construct 2.1 as comparison curve.
Figure 21: This scheme illustrates the principal of the T-cell activation assay described in Example 6.3. Shown is the schematic assay activation set up with HLA-A2-NLV- specific CD8 T cells and NLV -pulsed HLA-A2+ FAP+ human melanoma cell line MV-3 in the presence of different titrated concentration of FAP-targeted or untargeted split trimeric human 4- IBB ligand Fc (kih) constructs. Cells were incubated for 28 h, the last 4 h in the presence of monesin- containing Golgi-Stop. The ratio of NLV- specific CD8 T cells to MV-3 tumor cells is 1 :8. Figures 22A-E and 23A-E relate to the Activation assay with HLA-A2-NLV-specific CD 8
T cells and NLV -pulsed HLA-A2+ FAP+ human melanoma cell line MV-3 in the presence of different titrated concentration of different FAP-targeted or untargeted split trimeric human 4- 1BB ligand Fc (kih) constructs as prepared in Example 1. For better display expression curves were split to several different display-blots with Construct 1.1 (monovalent FAP-targeted split trimeric human 4- IBB ligand Fc (kih)) and Control B (monovalent untargeted split trimeric human 4- IBB ligand Fc (kih)) as comparison curves. Results were obtained in four independent similar experiments and show that prolonged IFNy secretion and CD 137 expression of NLV- specific CD8+ T cells is strictly dependent on simultaneous activation of T-cells via recognition of NLV-HLA-A2 complexes (signal 1) and 4- lBB-triggering by FAP-targeted human split 4- 1BBL (signal 2). The effect of 4- IBB upregulation is shown in graphs of Figure 22, whereas the effect of INFy expression of CD8+ T cells is presented in graphs of Figure 23. Shown is always the frequency in percentage of positive cells in the total CD8+ T cell population. All FAP- targeted variants induced a similar activation improvement of NLV -peptide activated CD8 T cells shown in Figure 22 as 4-lBB-upregulation (positive feedback loop) and in Figure 23 as IFNy expression after 24 h of stimulation. Differences of curves lie in the range of normal error deviation and are not significant.
Figures 24 and 25 refer to the Activation assay with HLA-A2-NLV-specific CD8 T cells and NLV-pulsed HLA-A2+ FAP+ human melanoma cell line MV-3 in the presence of titrated concentration of different FAP-targeted or untargeted split trimeric human 4- IBB ligand Fc (kih) constructs of Example 2. For better display expression curves were split to two different display- blots with Construct 2.1 (monovalent FAP-targeted split trimeric human 4- IBB ligand Fc (kih)) and Control B as comparison curves. All FAP-targeted split trimeric human 4- IBB ligand Fc (kih) constructs show a similar activation improvement of HLA-A2-NLV-peptide specific CD8 T cells shown in Figure 24 as 4-lBB-upregulation (positive feedback loop) and in Figure 25 as IFNy expression after 24 h of stimulation. Differences of curves lie in the range of normal error deviation and are not significant.
Figure 26: This scheme illustrates the experiment as described in Example 6.4.
Figure 27 shows the induction of CD8+ T cell proliferation. Shown is the frequency of proliferating CD8+ T cells versus the concentration of tested constructs. Figure 28A relates to the single dose PK experiment of Construct 1.2 and Control B in healthy NOG mice. Shown is the decline in Construct concentration over the time. Figure 28B shows the results of the single dose PK experiment of Constructs 2.1, 2.3, Control B and Control C in tumor bearing NOG mice humaniced with stem cells. Figure 28C relates to the single dose PK experiment comparing Construct 2.1 and 2.3 in healthy NOG mice. Figure 29 shows components for the assembly of split trimeric human 4- IBB ligands.
Figure (29 A) shows the dimeric ligand that is fused at the C-terminus to a human CL domain with mutations E123R and Q124K (charged residues) and Figure (29B) shows the monomeric 4- 1BB ligand fused to human CHI domain with mutations K147E and K213E (charged residues). Components for the assembly of bivalent CD19-targeted split trimeric human 4-1BB ligand (71- 254) antigen binding molecule (construct 3.3). Figure (29C) shows the dimeric ligand being fused to the C-terminus of human IgGl Fc hole chain. Figure (29D) shows the monomeric ligand being fused to the C-terminus of human IgGl Fc knob chain.
Figure 30 shows the CD19-targeted 4-lBBL-trimer-containing antigen binding molecules Constructs 3.1 to 3.6 of the invention. The preparation and production of these constructs is described in Example 3. The VH and VL domains are those of anti-CD19 antibody 8B8-018, the thick black point stands for the knob-into-hole modification. * symbolizes amino acid modifications in the CHI and CL domain (so-called charged residues).
In Figure 31A is illustrated the randomization strategy for the CDR regions of the parental clone 8B8. Shown are the variable domains of the parental clone 8B8 and the CDR regiones (boxed) according to the numbering of Kabat. (X) represents the randomized positions. Figure 31B shows the schematic description of the library generation strategies. Shown is the PCR amplification and cloning strategy used for the generation of the 8B8-based library with A) randomized CDRl and CDR2 regions in the light and heavy chain or B) randomized CDRl and CDR3 regions in the light and CDR3 region in the heavy chain. Respective enzymes used for cloning into the phagemide are indicated.
Figure 32 shows the alignment of the parental anti-CD 19 clone 8B8 with the selected affinity-matured binders. Shown are the sequences of clone 8B8 and all selected affinity-matured binders. CDRs of both heavy and light chains are framed. Figure 33 relates to the SPR analysis of the parental 8B8 clone and its affinity-matured variants.
Shown are the sensorgrams of clone 8B8 and its affinity-matured derivatives that are devoid of the LCDR1 N27d and N28 hotspots.
Figure 34 illustrates the setup of the assay measuring Simultaneous binding of CD 19 targeted trimeric split 4-1BBL to hu4-lBB and huCD19 (Example 8.2). The graphs in Figure 35 show simultaneous binding of the CD19 targeted trimeric 4-1BBL FC fusion antigen binding molecules Constructs 3.1, 3.3, 3.4, 3.5, 3.6 and 4.4 (Analyte 1) to immobilized human 4-1BB and human CD19 (Analyte 2).
Figure 36 shows the binding of different CD19-targeted or un targeted split trimeric human 4-1BB ligand Fc (kih) constructs to 4-lBB-expressing CD4 and CD 8 T cells of PHA-L and Proleukin pre-activated and anti-human CD3/anti-human CD28 re-activated human PBMCs. Binding was detected with R-Phycoerythrin-fluorochrome conjugated anti-human IgG Fcy- specific goat IgG F(ab )2 fragment. Shown is the median of fluorescence intensity (MFI) versus the concentration of tested constructs. For a better display the binding curves are split in three different blots with construct 3.4 and control F (Isotype control hulgGI P329G LALA) as comparison curves. Binding was monitored on CD45+ CD3+ CD8+ T cells (Figure 36A) and CD45+ CD3+ CD4+ T cells (Figure 36B). The 4- IBB expression level on CD 8 T cells is normally higher than on CD4 T cells. All constructs bind with a quite similar affinity to human 4-1BB. Figure 37 shows the binding of CD19-targeted or untargeted split trimeric human 4-1BB ligand Fc (kih) antigen binding molecules to human-CD 19 expressing B cell lymphoma cell lines: diffuse large non-Hodgkin B cell lymphoma SU-DHL-8 (37A), acute B cell precursor lymphoid leukemia Nalm6 (37B), diffuse large cell lymphoblast lymphoma Toledo (37C) and diffuse large B cell lymphoma OCTLyl8 (37D). Binding was detected with R-Phycoerythrin-fluorochrome conjugated anti-human IgG Fcy-specific goat IgG F(ab )2 fragments. Shown is the median of fluorescence intensity (MFI) versus the concentration of tested constructs. For a better display the binding curves are split in three different blots with construct 3.4 and control F (Isotype control hulgGI P329G LALA) as comparison curves. All constructs bind with a quite similar affinity to human CD 19.
Figure 38 relates to NFKB-activation-induced Luciferase expression and activity of CD19- targeted or untargeted split trimeric human 4- IBB ligand Fc (kih) antigen binding molecules. Units of released light (URL) are measured for 0.5 s/well and plotted against the used
concentration of CD19-targeted or untargeted split trimeric human 4- IBB ligand Fc (kih) constructs 3.1 and 3.3 and control molecules B and C. Human 4-lBB-expressing HeLa-reporter cells were incubated for 7.5 h in the absence presence of crosslinking human-CD 19 expressing SU-DHL-8 or Pfeiffer cells. URLs were measured and blotted against the concentrations of different CD19-targeted or untargeted split trimeric human 4- IBB ligand Fc (kih) constructs. The cell ratio is one 4-lBB-expressing HeLa reporter cell to 2.5 or five tumor cells. Figure 39 shows the binding of different humanized variants of T84.66 IgG on CEA- expressing human gastric adenocarcinoma cells. Based on the data humanized variant 1 was selected for including it into CEA-targeted trimeric human 4- IBB ligand Fc (kih) antigen binding molecules.
Figure 40 shows the CEA targeted 4-lBBL-trimer-containing antigen binding molecules Constructs 5.1 to 5.6 of the invention. The preparation and production of these constructs is described in Example 11. The VH and VL domains are those of anti-CEA antibody T84.66- LCHA, the thick black point stands for the knob-into-hole modification. * symbolizes amino acid modifications in the CHI and CL domain (so-called charged residues).
Figure 41A shows a schematic description of human NA3B3A2-avi His, the antigen used to assess binding of CEA-targeted trimeric split 4-1BBL Fc (kih) antigen binding molecules. Figure 41B illustrates the setup of the assay measuring simultaneous binding of CEA-targeted trimeric split 4-1BBL to hu4-lBB and human NA3B3A2 (Example 12.1).
The graphs in Figure 42 show simultaneous binding of the CEA targeted trimeric 4-1BBL Fc fusion antigen binding molecules Constructs 5.4, 5.6, 5.7 and 5.8 (Analyte 1) to immobilized human 4- IBB and human NA3B3A2 (Analyte 2). Binding of different CEA-targeted or untargeted split trimeric human 4- IBB ligand Fc (kih) constructs to 4-lBB-expressing CD4 and CD8 T cells of PHA-L and Proleukin pre-activated and anti-human CD3/anti-human CD28 re-activated human PBMCs is shown in Figure 43. Binding was detected with R-Phycoerythrin-fluorochrome conjugated anti-human IgG Fey- specific goat IgG F(ab )2 fragment. Shown is the median of fluorescence intensity (MFI) versus the
concentration of tested constructs. For a better display the binding curves are split in two different blots with construct 5.4 and control F (Isotype control hulgGI P329G LALA) as comparison curves. Binding was monitored on CD45+ CD3+ CD8+ T cells (blots on the bottom) and CD45+ CD3+ CD4+ T cells (blots on the top). The 4-1BB expression level on CD 8 T cells is normally higher than on CD4 T cells. All constructs bind with quite similar affinity to human 4-1BB.
Figure 44 shows the binding of CEA-targeted or untargeted split trimeric human 4- IBB ligand Fc (kih) constructs to human-CEA expressing human gastric cell line MKN-45 (left) and human colorectal adenocarcinoma cells line LS I 80 (right). Binding was detected with R- Phycoerythrin-fluorochrome conjugated anti-human IgG Fcy-specific goat IgG F(ab )2 fragments. Shown is the median of fluorescence intensity (MFI) versus the concentration of tested constructs.
Figure 45 relates to NFKB-activation-induced Luciferase expression and activity of CEA- targeted or untargeted split trimeric human 4- IBB ligand Fc (kih) antigen binding molecules. Units of released light (URL) are measured for 0.5 s/well and blotted against the used
concentration of CEA-targeted or untargeted split trimeric human 4- IBB ligand Fc (kih) constructs 5.4, 5.6, 5.7 and 5.8 and control molecules. Human 4- IBB -expressing HeLa-reporter cells were incubated for 6 h in the absence or presence of crosslinking human-CEA expressing human gastric cancer cell line MKN-45. The cell ratio is one 4-lBB-expressing HeLa reporter cell to three tumor cells.
In Figures 46A and 46B are shown the components for the assembly of monovalent FAP targeted split trimeric human OX40 ligand (construct 6.1). Figure 46A relates to dimeric ligand fused to human IgGl-CL domain, Figure 46B relates to monomeric ligand fused to human IgGl-CHl domain. Figure 46C shows the FAP targeted OX40L-trimer-containing antigen binding molecule Construct 6.1. In Figure 46D is shown the DP47 "untargeted" human IgGl PGLALA (control F).
Figure 47A shows the binding of FAP targeted split trimeric human Ox40L to FAP positive WM-266-4 cells. WM-266-4 cells express high levels of human fibroblast activation protein (huFAP). Only FAP targeted OX40 ligand Fc (kih) constructs (filled square) but not control 5 (filled diamond) bound to WM-266-4 cells. Shown is the binding as median of fluorescence intensity (MFI) of Fluorescein isothiocyanate (FITC)-labeled anti-human IgG Fcy-specific goat IgG F(ab )2 fragment which is used as secondary detection antibody. MFI was measured by flow cytometry. The x-axis shows the concentration of antibody constructs. Figure 47B shows the binding of FAP targeted 0X40 ligand Fc (kih) construct to human FAP human Ox40 negative A549 NucLight Red cells. FAP targeted 0X40 ligand Fc (kih) construct showed no binding to OX40 negative FAP negative A549 tumor cells. Shown is the binding as median of fluorescence intensity (MFI) of FITC labeled anti-human IgG Fey- specific goat IgG F(ab )2 fragment which is used as secondary detection antibody. MFI was measured by flow cytometry and baseline corrected by subtracting the MFI of the blank control.
In Figure 48A the binding of FAP-Ox40L to resting and activated human CD4 T cells is shown. Ox40 is not expressed on resting human CD4 T cells (left side). In the absence of human Ox40 expressing cells no binding was observed (left graphs). After activation of human PBMCs Ox40 is up-regulated on CD4+ T cells (right side). FAP-Ox40L bound to 0x40+ activated CD4 T cells. Shown is the binding as median of fluorescence intensity (MFI) of FITC labeled anti-human IgG Fcy-specific goat IgG F(ab )2 fragment which is used as secondary detection antibody. MFI was measured by flow cytometry and baseline corrected by subtracting the MFI of the blank control. The x-axis shows the concentration of antibody constructs. Figure 48B shows that Ox40 is not expressed on resting human CD8 T cells (left side). In the absence of human Ox40 expressing cells no binding was observed (left graphs). After activation of human PBMCs Ox40 is up- regulated on CD8+ T cells (right side). Ox40 expression on human CD8+ T cells is lower than on CD4+ T cells and varies between donors and time points. Expression of Ox40 was low on the depicted CD 8 T cells. FAp-Ox40L bound to 0x40+ activated CD 8 T cells. Shown is the binding as median of fluorescence intensity (MFI) of FITC labeled anti-human IgG Fcy-specific goat IgG F(ab )2 fragment which is used as secondary detection antibody. MFI was measured by flow cytometry and baseline corrected by subtracting the MFI of the blank control. The x-axis shows the concentration of antibody constructs
In Figure 49 the activation of NFKB signaling pathway by the FAP targeted split trimeric human OX40L antigen binding molecule (FAP-OX40L) in HeLa_hOx40_NFkB_Lucl reporter cells is demonstrated. Shown is the activation with (right graph) or without (left graph) crosslinking by secondary antibody. The reporter cells were cultured for 5 hours in the presence of FAP-OX40L at the indicated concentrations with or without crosslinking secondary polyclonal anti-huIgGl Fcy-specific goat IgG F(ab)2 fragment in a 1:2 ratio. Luciferase activity was assessed as described in Example 6.1. Activity is characterized by blotting the units of released light (URL) measured during 0.5 s versus the concentration in nM of tested construct. URLs are emitted due to luciferase-mediated oxidation of luciferin to oxyluciferin. The activation of NFKB by FAP-OX40L in HeLa_hOx40_NFkB_Luc 1 reporter cells in the presence of FAP positive cells is shown in Figure 50A. Shown is the activation of NFKB signaling pathway in the reporter cells by FAP-OX40L in the presence of low FAP expressing expressing NIH-3T3 human FAP cells (ratio 3 FAP+ tumor cells to 1 reporter cell). The NFKB- mediated luciferase activity was characterized by blotting the units of released light (URL), measured during 0.5 s, versus the concentration in nM of tested compounds. URLs are emitted due to luciferase-mediated oxidation of luciferin to oxyluciferin. Values are baseline corrected by subtracting the URLs of the blank control. For a better comparison the area under the curve of the respective blotted dose-response curves were quantified as a marker for the agonistic capacity of each construct. The comparison is illustrated in Figure 50B. The area was calculated using GraphPad Prism. Values are baseline corrected by subtracting the value of the blank control.
Figure 51 shows the OX40 mediated costimulation of suboptimally TCR triggered resting human PBMC (Example 15.5). Hyper-crosslinking of FAP-Ox40L by the present NIH/3T3- huFAP clone 39 cells strongly promoted survival and proliferation in human CD4 and CD8 T cells. Shown is the event count of vital CD4+ (left) and CD8+ (right) T cells. Baseline values of samples containing only the anti-human CD3 (clone V9, hulgGI), resting human PBMC and NIH/3T3-huFAP clone 39 were substracted. Thus the enhancing effect of OX40 co- stimulation but not the effect of suboptimal anti-CD3 stimulation per se is shown here. In the Figures on the bottom the rescue of suboptimal TCR stimulation of resting human PBMC with cell surface immobilized FAP-Ox40L - Proliferation is shown. DETAILED DESCRIPTION OF THE INVENTION
Definitions
Unless defined otherwise, technical and scientific terms used herein have the same meaning as generally used in the art to which this invention belongs. For purposes of interpreting this specification, the following definitions will apply and whenever appropriate, terms used in the singular will also include the plural and vice versa.
As used herein, the term "antigen binding molecule" refers in its broadest sense to a molecule that specifically binds an antigenic determinant. Examples of antigen binding molecules are antibodies, antibody fragments and scaffold antigen binding proteins.
As used herein, the term "moiety capable of specific binding to a target cell antigen" refers to a polypeptide molecule that specifically binds to an antigenic determinant. In one aspect, the antigen binding moiety is able to activate signaling through its target cell antigen. In a particular aspect, the antigen binding moiety is able to direct the entity to which it is attached (e.g. the TNF family ligand trimer) to a target site, for example to a specific type of tumor cell or tumor stroma bearing the antigenic determinant. Moieties capable of specific binding to a target cell antigen include antibodies and fragments thereof as further defined herein. In addition, moieties capable of specific binding to a target cell antigen include scaffold antigen binding proteins as further defined herein, e.g. binding domains which are based on designed repeat proteins or designed repeat domains (see e.g. WO 2002/020565).
In relation to an antibody or fragment thereof, the term "moiety capable of specific binding to a target cell antigen" refers to the part of the molecule that comprises the area which specifically binds to and is complementary to part or all of an antigen. A moiety capable of specific antigen binding may be provided, for example, by one or more antibody variable domains (also called antibody variable regions). Particularly, a moiety capable of specific antigen binding comprises an antibody light chain variable region (VL) and an antibody heavy chain variable region (VH).
The term "antibody" herein is used in the broadest sense and encompasses various antibody structures, including but not limited to monoclonal antibodies, polyclonal antibodies, monospecific and multispecific antibodies (e.g., bispecific antibodies), and antibody fragments so long as they exhibit the desired antigen-binding activity.
The term "monoclonal antibody" as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical and/or bind the same epitope, except for possible variant antibodies, e.g. containing naturally occurring mutations or arising during production of a monoclonal antibody preparation, such variants generally being present in minor amounts. In contrast to polyclonal antibody preparations, which typically include different antibodies directed against different determinants (epitopes), each monoclonal antibody of a monoclonal antibody preparation is directed against a single determinant on an antigen. The term "monospecific" antibody as used herein denotes an antibody that has one or more binding sites each of which bind to the same epitope of the same antigen. The term
"bispecific" means that the antigen binding molecule is able to specifically bind to at least two distinct antigenic determinants. Typically, a bispecific antigen binding molecule comprises two antigen binding sites, each of which is specific for a different antigenic determinant. In certain embodiments the bispecific antigen binding molecule is capable of simultaneously binding two antigenic determinants, particularly two antigenic determinants expressed on two distinct cells.
The term "valent" as used within the current application denotes the presence of a specified number of binding sites in an antigen binding molecule. As such, the terms "bivalent", "tetravalent", and "hexavalent" denote the presence of two binding sites, four binding sites, and six binding sites, respectively, in an antigen binding molecule. The terms "full length antibody", "intact antibody", and "whole antibody" are used herein interchangeably to refer to an antibody having a structure substantially similar to a native antibody structure. "Native antibodies" refer to naturally occurring immunoglobulin molecules with varying structures. For example, native IgG-class antibodies are heterotetrameric glycoproteins of about 150,000 daltons, composed of two light chains and two heavy chains that are disulfide-bonded. From N- to C-terminus, each heavy chain has a variable region (VH), also called a variable heavy domain or a heavy chain variable domain, followed by three constant domains (CHI, CH2, and CH3), also called a heavy chain constant region. Similarly, from N- to C-terminus, each light chain has a variable region (VL), also called a variable light domain or a light chain variable domain, followed by a light chain constant domain (CL), also called a light chain constant region. The heavy chain of an antibody may be assigned to one of five types, called a (IgA), δ (IgD), ε (IgE), γ (IgG), or μ (IgM), some of which may be further divided into subtypes, e.g. l (IgGl), γ2 (IgG2), γ3 (IgG3), γ4 (IgG4), al (IgAl) and a2 (IgA2). The light chain of an antibody may be assigned to one of two types, called kappa (κ) and lambda (λ), based on the amino acid sequence of its constant domain.
An "antibody fragment" refers to a molecule other than an intact antibody that comprises a portion of an intact antibody that binds the antigen to which the intact antibody binds.
Examples of antibody fragments include but are not limited to Fv, Fab, Fab', Fab'-SH, F(ab')2; diabodies, triabodies, tetrabodies, cross-Fab fragments; linear antibodies; single-chain antibody molecules (e.g. scFv); and single domain antibodies. For a review of certain antibody fragments, see Hudson et al., Nat Med 9, 129-134 (2003). For a review of scFv fragments, see e.g.
Pliickthun, in The Pharmacology of Monoclonal Antibodies, vol. 113, Rosenburg and Moore eds., Springer- Verlag, New York, pp. 269-315 (1994); see also WO 93/16185; and U.S. Patent Nos. 5,571,894 and 5,587,458. For discussion of Fab and F(ab')2 fragments comprising salvage receptor binding epitope residues and having increased in vivo half-life, see U.S. Patent No.
5,869,046. Diabodies are antibody fragments with two antigen-binding sites that may be bivalent or bispecific, see, for example, EP 404,097; WO 1993/01161; Hudson et al., Nat Med 9, 129-134 (2003); and Hollinger et al., Proc Natl Acad Sci USA 90, 6444-6448 (1993). Triabodies and tetrabodies are also described in Hudson et al., Nat Med 9, 129-134 (2003). Single-domain antibodies are antibody fragments comprising all or a portion of the heavy chain variable domain or all or a portion of the light chain variable domain of an antibody. In certain embodiments, a single-domain antibody is a human single-domain antibody (Domantis, Inc., Waltham, MA; see e.g. U.S. Patent No. 6,248,516 Bl). Antibody fragments can be made by various techniques, including but not limited to proteolytic digestion of an intact antibody as well as production by recombinant host cells (e.g. E. coli or phage), as described herein.
Papain digestion of intact antibodies produces two identical antigen-binding fragments, called "Fab" fragments containing each the heavy- and light-chain variable domains and also the constant domain of the light chain and the first constant domain (CHI) of the heavy chain. As used herein, Thus, the term "Fab fragment" refers to an antibody fragment comprising a light chain fragment comprising a VL domain and a constant domain of a light chain (CL), and a VH domain and a first constant domain (CHI) of a heavy chain. Fab' fragments differ from Fab fragments by the addition of a few residues at the carboxy terminus of the heavy chain CHI domain including one or more cysteins from the antibody hinge region. Fab'-SH are Fab' fragments in which the cysteine residue(s) of the constant domains bear a free thiol group.
Pepsin treatment yields an F(ab')2 fragment that has two antigen-combining sites (two Fab fragments) and a part of the Fc region. The term "cross-Fab fragment" or "xFab fragment" or "crossover Fab fragment" refers to a Fab fragment, wherein either the variable regions or the constant regions of the heavy and light chain are exchanged. Two different chain compositions of a crossover Fab molecule are possible and comprised in the bispecific antibodies of the invention: On the one hand, the variable regions of the Fab heavy and light chain are exchanged, i.e. the crossover Fab molecule comprises a peptide chain composed of the light chain variable region (VL) and the heavy chain constant region (CHI), and a peptide chain composed of the heavy chain variable region (VH) and the light chain constant region (CL). This crossover Fab molecule is also referred to as CrossFab (VLVH)- On the other hand, when the constant regions of the Fab heavy and light chain are exchanged, the crossover Fab molecule comprises a peptide chain composed of the heavy chain variable region (VH) and the light chain constant region (CL), and a peptide chain composed of the light chain variable region (VL) and the heavy chain constant region (CHI). This crossover Fab molecule is also referred to as CrossFab (CLCHI)-
A "single chain Fab fragment" or "scFab" is a polypeptide consisting of an antibody heavy chain variable domain (VH), an antibody constant domain 1 (CHI), an antibody light chain variable domain (VL), an antibody light chain constant domain (CL) and a linker, wherein said antibody domains and said linker have one of the following orders in N-terminal to C-terminal direction: a) VH-CH1 -linker- VL-CL, b) VL-CL-linker-VH-CHl, c) VH-CL-linker-VL-CHl or d) VL-CH1 -linker- VH-CL; and wherein said linker is a polypeptide of at least 30 amino acids, preferably between 32 and 50 amino acids. Said single chain Fab fragments are stabilized via the natural disulfide bond between the CL domain and the CHI domain. In addition, these single chain Fab molecules might be further stabilized by generation of interchain disulfide bonds via insertion of cysteine residues (e.g. position 44 in the variable heavy chain and position 100 in the variable light chain according to Kabat numbering).
A "crossover single chain Fab fragment" or "x-scFab" is a is a polypeptide consisting of an antibody heavy chain variable domain (VH), an antibody constant domain 1 (CHI), an antibody light chain variable domain (VL), an antibody light chain constant domain (CL) and a linker, wherein said antibody domains and said linker have one of the following orders in N- terminal to C-terminal direction: a) VH-CL-linker-VL-CHl and b) VL-CH1 -linker- VH-CL; wherein VH and VL form together an antigen-binding site which binds specifically to an antigen and wherein said linker is a polypeptide of at least 30 amino acids. In addition, these x-scFab molecules might be further stabilized by generation of interchain disulfide bonds via insertion of cysteine residues (e.g. position 44 in the variable heavy chain and position 100 in the variable light chain according to Kabat numbering).
A "single-chain variable fragment (scFv)" is a fusion protein of the variable regions of the heavy (VH) and light chains (VL) of an antibody, connected with a short linker peptide of ten to about 25 amino acids. The linker is usually rich in glycine for flexibility, as well as serine or threonine for solubility, and can either connect the N-terminus of the VH with the C-terminus of the VL, or vice versa. This protein retains the specificity of the original antibody, despite removal of the constant regions and the introduction of the linker. scFv antibodies are, e.g. described in Houston, J.S., Methods in Enzymol. 203 (1991) 46-96). In addition, antibody fragments comprise single chain polypeptides having the characteristics of a VH domain, namely being able to assemble together with a VL domain, or of a VL domain, namely being able to assemble together with a VH domain to a functional antigen binding site and thereby providing the antigen binding property of full length antibodies.
"Scaffold antigen binding proteins" are known in the art, for example, fibronectin and designed ankyrin repeat proteins (DARPins) have been used as alternative scaffolds for antigen- binding domains, see, e.g., Gebauer and Skerra, Engineered protein scaffolds as next- generation antibody therapeutics. Curr Opin Chem Biol 13:245-255 (2009) and Stumpp et al., Darpins: A new generation of protein therapeutics. Drug Discovery Today 13: 695-701 (2008). In one aspect of the invention, a scaffold antigen binding protein is selected from the group consisting of CTLA-4 (Evibody), Lipocalins (Anticalin), a Protein A-derived molecule such as Z-domain of Protein A (Affibody), an A-domain (Avimer/Maxibody), a serum transferrin (trans-body); a designed ankyrin repeat protein (DARPin), a variable domain of antibody light chain or heavy chain (single-domain antibody, sdAb), a variable domain of antibody heavy chain (nanobody, aVH), VNAR fragments, a fibronectin (AdNectin), a C-type lectin domain (Tetranectin); a variable domain of a new antigen receptor beta-lactamase (VNAR fragments), a human gamma- crystallin or ubiquitin (Affilin molecules); a kunitz type domain of human protease inhibitors, microbodies such as the proteins from the knottin family, peptide aptamers and fibronectin (adnectin).
CTLA-4 (Cytotoxic T Lymphocyte-associated Antigen 4) is a CD28-family receptor expressed on mainly CD4+ T-cells. Its extracellular domain has a variable domain- like Ig fold. Loops corresponding to CDRs of antibodies can be substituted with heterologous sequence to confer different binding properties. CTLA-4 molecules engineered to have different binding specificities are also known as Evibodies (e.g. US7166697B1). Evibodies are around the same size as the isolated variable region of an antibody (e.g. a domain antibody). For further details see Journal of Immunological Methods 248 (1-2), 31-45 (2001). Lipocalins are a family of extracellular proteins which transport small hydrophobic molecules such as steroids, bilins, retinoids and lipids. They have a rigid beta-sheet secondary structure with a number of loops at the open end of the conical structure which can be engineered to bind to different target antigens. Anticalins are between 160-180 amino acids in size, and are derived from lipocalins. For further details see Biochim Biophys Acta 1482: 337-350 (2000), US7250297B1 and US20070224633.
An affibody is a scaffold derived from Protein A of Staphylococcus aureus which can be engineered to bind to antigen. The domain consists of a three-helical bundle of approximately 58 amino acids. Libraries have been generated by randomization of surface residues. For further details see Protein Eng. Des. Sel. 17, 455-462 (2004) and EP 1641818A1. Avimers are multidomain proteins derived from the A-domain scaffold family. The native domains of approximately 35 amino acids adopt a defined disulfide bonded structure. Diversity is generated by shuffling of the natural variation exhibited by the family of A-domains. For further details see Nature Biotechnology 23(12), 1556 - 1561 (2005) and Expert Opinion on Investigational Drugs 16(6), 909-917 (June 2007). A transferrin is a monomeric serum transport glycoprotein. Transferrins can be engineered to bind different target antigens by insertion of peptide sequences in a permissive surface loop. Examples of engineered transferrin scaffolds include the Trans-body. For further details see J. Biol. Chem 274, 24066-24073 (1999).
Designed Ankyrin Repeat Proteins (DARPins) are derived from Ankyrin which is a family of proteins that mediate attachment of integral membrane proteins to the cytoskeleton. A single ankyrin repeat is a 33 residue motif consisting of two alpha-helices and a beta-turn. They can be engineered to bind different target antigens by randomizing residues in the first alpha-helix and a beta-turn of each repeat. Their binding interface can be increased by increasing the number of modules (a method of affinity maturation). For further details see J. Mol. Biol. 332, 489-503 (2003), PNAS 100(4), 1700-1705 (2003) and J. Mol. Biol. 369, 1015-1028 (2007) and
US20040132028A1.
A single-domain antibody is an antibody fragment consisting of a single monomeric variable antibody domain. The first single domain were derived from the variable domain of the antibody heavy chain from camelids (nanobodies or VHH fragments). Furthermore, the term single-domain antibody includes an autonomous human heavy chain variable domain (aVH) or VNAR fragments derived from sharks.
Fibronectin is a scaffold which can be engineered to bind to antigen. Adnectins consists of a backbone of the natural amino acid sequence of the 10th domain of the 15 repeating units of human fibronectin type III (FN3). Three loops at one end of the .beta.-sandwich can be engineered to enable an Adnectin to specifically recognize a therapeutic target of interest. For further details see Protein Eng. Des. Sel. 18, 435- 444 (2005), US20080139791, WO2005056764 and US6818418B1.
Peptide aptamers are combinatorial recognition molecules that consist of a constant scaffold protein, typically thioredoxin (TrxA) which contains a constrained variable peptide loop inserted at the active site. For further details see Expert Opin. Biol. Ther. 5, 783-797 (2005).
Microbodies are derived from naturally occurring microproteins of 25-50 amino acids in length which contain 3-4 cysteine bridges - examples of microproteins include KalataBI and conotoxin and knottins. The microproteins have a loop which can beengineered to include upto 25 amino acids without affecting the overall fold of the microprotein. For further details of engineered knottin domains, see WO2008098796.
An "antigen binding molecule that binds to the same epitope" as a reference molecule refers to an antigen binding molecule that blocks binding of the reference molecule to its antigen in a competition assay by 50% or more, and conversely, the reference molecule blocks binding of the antigen binding molecule to its antigen in a competition assay by 50% or more.
The term "antigen binding domain" refers to the part of an antigen binding molecule that comprises the area which specifically binds to and is complementary to part or all of an antigen. Where an antigen is large, an antigen binding molecule may only bind to a particular part of the antigen, which part is termed an epitope. An antigen binding domain may be provided by, for example, one or more variable domains (also called variable regions). Preferably, an antigen binding domain comprises an antibody light chain variable region (VL) and an antibody heavy chain variable region (VH).
As used herein, the term "antigenic determinant" is synonymous with "antigen" and "epitope," and refers to a site (e.g. a contiguous stretch of amino acids or a conformational configuration made up of different regions of non-contiguous amino acids) on a polypeptide macromolecule to which an antigen binding moiety binds, forming an antigen binding moiety- antigen complex. Useful antigenic determinants can be found, for example, on the surfaces of tumor cells, on the surfaces of virus-infected cells, on the surfaces of other diseased cells, on the surface of immune cells, free in blood serum, and/or in the extracellular matrix (ECM). The proteins useful as antigens herein can be any native form the proteins from any vertebrate source, including mammals such as primates (e.g. humans) and rodents (e.g. mice and rats), unless otherwise indicated. In a particular embodiment the antigen is a human protein. Where reference is made to a specific protein herein, the term encompasses the "full-length", unprocessed protein as well as any form of the protein that results from processing in the cell. The term also encompasses naturally occurring variants of the protein, e.g. splice variants or allelic variants.
By "specific binding" is meant that the binding is selective for the antigen and can be discriminated from unwanted or non-specific interactions. The ability of an antigen binding molecule to bind to a specific antigen can be measured either through an enzyme-linked immunosorbent assay (ELISA) or other techniques familiar to one of skill in the art, e.g. Surface Plasmon Resonance (SPR) technique (analyzed on a BIAcore instrument) (Liljeblad et al., Glyco J 17, 323-329 (2000)), and traditional binding assays (Heeley, Endocr Res 28, 217-229 (2002)). In one embodiment, the extent of binding of an antigen binding molecule to an unrelated protein is less than about 10% of the binding of the antigen binding molecule to the antigen as measured, e.g. by SPR. In certain embodiments, an molecule that binds to the antigen has a dissociation constant (Kd) of < 1 μΜ, < 100 nM, < 10 nM, < 1 nM, < 0.1 nM, < 0.01 nM, or < 0.001 nM (e.g. 10~8 M or less, e.g. from 10~8 M to 10"13 M, e.g. from 10"9 M to 10"13 M).
"Affinity" or "binding affinity" refers to the strength of the sum total of non-covalent interactions between a single binding site of a molecule (e.g. an antibody) and its binding partner (e.g. an antigen). Unless indicated otherwise, as used herein, "binding affinity" refers to intrinsic binding affinity which reflects a 1: 1 interaction between members of a binding pair (e.g.
antibody and antigen). The affinity of a molecule X for its partner Y can generally be represented by the dissociation constant (Kd), which is the ratio of dissociation and association rate constants (koff and kon, respectively). Thus, equivalent affinities may comprise different rate constants, as long as the ratio of the rate constants remains the same. Affinity can be measured by common methods known in the art, including those described herein. A particular method for measuring affinity is Surface Plasmon Resonance (SPR).
A "target cell antigen" as used herein refers to an antigenic determinant presented on the surface of a target cell, for example a cell in a tumor such as a cancer cell or a cell of the tumor stroma. In certain embodiments, the target cell antigen is an antigen on the surface of a tumor cell. In one embodiment, target cell antigen is selected from the group consisting of Fibroblast Activation Protein (FAP), Carcinoembryonic Antigen (CEA), Melanoma-associated Chondroitin Sulfate Proteoglycan (MCSP), Epidermal Growth Factor Receptor (EGFR), CD19, CD20 and CD33. In particular, the target cell antigen is Fibroblast Activation Protein (FAP). The term "Fibroblast activation protein (FAP)", also known as Prolyl endopeptidase FAP or Seprase (EC 3.4.21), refers to any native FAP from any vertebrate source, including mammals such as primates (e.g. humans) non-human primates (e.g. cynomolgus monkeys) and rodents (e.g. mice and rats), unless otherwise indicated. The term encompasses "full-length," unprocessed FAP as well as any form of FAP which results from processing in the cell. The term also encompasses naturally occurring variants of FAP, e.g., splice variants or allelic variants. In one embodiment, the antigen binding molecule of the invention is capable of specific binding to human, mouse and/or cynomolgus FAP. The amino acid sequence of human FAP is shown in UniProt (www.uniprot.org) accession no. Q12884 (version 149, SEQ ID NO:20), or NCBI (www.ncbi.nlm.nih.gov/) RefSeq NP_004451.2. The extracellular domain (ECD) of human FAP extends from amino acid position 26 to 760. The amino acid and nucleotide sequences of a His- tagged human FAP ECD is shown in SEQ ID NOs 15 and 16, respectively. The amino acid sequence of mouse FAP is shown in UniProt accession no. P97321 (version 126, SEQ ID NO:23), or NCBI RefSeq NP_032012.1. The extracellular domain (ECD) of mouse FAP extends from amino acid position 26 to 761. SEQ ID NOs 24 and 25 show the amino acid and nucleotide sequences, respectively, of a His-tagged mouse FAP ECD. SEQ ID NOs 26 and 27 show the amino acid and nucleotide sequences, respectively, of a His-tagged cynomolgus FAP ECD. Preferably, an anti-FAP binding molecule of the invention binds to the extracellular domain of FAP. Exemplary anti-FAP binding molecules are described in International Patent Application No. WO 2012/020006 A2.
The term "Carcinoembroynic antigen (CEA)", also known as Carcinoembryonic antigen- related cell adhesion molecule 5 (CEACAM5), refers to any native CEA from any vertebrate source, including mammals such as primates (e.g. humans) non-human primates (e.g.
cynomolgus monkeys) and rodents (e.g. mice and rats), unless otherwise indicated. The amino acid sequence of human CEA is shown in UniProt accession no. P06731 (version 151, SEQ ID NO:28). CEA has long been identified as a tumor- associated antigen (Gold and Freedman, J Exp Med., 121:439-462, 1965; Berinstein N. L., J Clin Oncol., 20:2197-2207, 2002). Originally classified as a protein expressed only in fetal tissue, CEA has now been identified in several normal adult tissues. These tissues are primarily epithelial in origin, including cells of the gastrointestinal, respiratory, and urogential tracts, and cells of colon, cervix, sweat glands, and prostate (Nap et al., Tumour Biol., 9(2-3): 145-53, 1988; Nap et al., Cancer Res., 52(8):2329- 23339, 1992). Tumors of epithelial origin, as well as their metastases, contain CEA as a tumor associated antigen. While the presence of CEA itself does not indicate transformation to a cancerous cell, the distribution of CEA is indicative. In normal tissue, CEA is generally expressed on the apical surface of the cell (Hammarstrom S., Semin Cancer Biol. 9(2):67-81 (1999)), making it inaccessible to antibody in the blood stream. In contrast to normal tissue, CEA tends to be expressed over the entire surface of cancerous cells (Hammarstrom S., Semin Cancer Biol. 9(2):67-81 (1999)). This change of expression pattern makes CEA accessible to antibody binding in cancerous cells. In addition, CEA expression increases in cancerous cells. Furthermore, increased CEA expression promotes increased intercellular adhesions, which may lead to metastasis (Marshall J., Semin Oncol., 30(a Suppl. 8):30-6, 2003). The prevalence of CEA expression in various tumor entities is generally very high. In concordance with published data, own analyses performed in tissue samples confirmed its high prevalence, with
approximately 95% in colorectal carcinoma (CRC), 90% in pancreatic cancer, 80% in gastric cancer, 60% in non-small cell lung cancer (NSCLC, where it is co-expressed with HER3), and 40% in breast cancer; low expression was found in small cell lung cancer and glioblastoma. CEA is readily cleaved from the cell surface and shed into the blood stream from tumors, either directly or via the lymphatics. Because of this property, the level of serum CEA has been used as a clinical marker for diagnosis of cancers and screening for recurrence of cancers, particularly colorectal cancer (Goldenberg D M., The International Journal of Biological Markers, 7: 183-188, 1992; Chau I., et al., J Clin Oncol., 22: 1420-1429, 2004; Flamini et al., Clin Cancer Res; 12(23):6985-6988, 2006).
The term "Melanoma-associated Chondroitin Sulfate Proteoglycan (MCSP)", also known as Chondroitin Sulfate Proteoglycan 4 (CSPG4) refers to any native MCSP from any vertebrate source, including mammals such as primates (e.g. humans) non-human primates (e.g. cynomolgus monkeys) and rodents (e.g. mice and rats), unless otherwise indicated. The amino acid sequence of human MCSP is shown in UniProt accession no. Q6UVK1 (version 103, SEQ ID NO:29). The term "Epidermal Growth Factor Receptor (EGFR)", also named Proto- oncogene c-ErbB-1 or Receptor tyrosine -protein kinase erbB-1, refers to any native EGFR from any vertebrate source, including mammals such as primates (e.g. humans) non-human primates (e.g. cynomolgus monkeys) and rodents (e.g. mice and rats), unless otherwise indicated. The amino acid sequence of human EGFR is shown in UniProt accession no. P00533 (version 211, SEQ ID NO:30).
The term "CD19" refers to B-lymphocyte antigen CD 19, also known as B-lymphocyte surface antigen B4 or T-cell surface antigen Leu- 12 and includes any native CD 19 from any vertebrate source, including mammals such as primates (e.g. humans) non-human primates (e.g. cynomolgus monkeys) and rodents (e.g. mice and rats), unless otherwise indicated. The amino acid sequence of human CD19 is shown in Uniprot accession no. P15391 (version 160, SEQ ID NO:31). The term encompasses "full-length" unprocessed human CD19 as well as any form of human CD 19 that results from processing in the cell as long as the antibody as reported herein binds thereto. CD19 is a structurally distinct cell surface receptor expressed on the surface of human B cells, including, but not limited to, pre-B cells, B cells in early development {i.e., immature B cells), mature B cells through terminal differentiation into plasma cells, and malignant B cells. CD19 is expressed by most pre-B acute lymphoblastic leukemias (ALL), non- Hodgkin's lymphomas, B cell chronic lymphocytic leukemias (CLL), pro-lymphocytic leukemias, hairy cell leukemias, common acute lymphocytic leukemias, and some Null-acute lymphoblastic leukemias. The expression of CD19 on plasma cells further suggests it may be expressed on differentiated B cell tumors such as multiple myeloma. Therefore, the CD 19 antigen is a target for immunotherapy in the treatment of non-Hodgkin's lymphoma, chronic lymphocytic leukemia and/or acute lymphoblastic leukemia.
"CD20" refers to B-lymphocyte antigen CD20, also known as membrane- spanning 4- domains subfamily A member 1 (MS4A1), B-lymphocyte surface antigen Bl or Leukocyte surface antigen Leu- 16, and includes any native CD20 from any vertebrate source, including mammals such as primates (e.g. humans) non-human primates (e.g. cynomolgus monkeys) and rodents (e.g. mice and rats), unless otherwise indicated. The amino acid sequence of human CD20 is shown in Uniprot accession no. PI 1836 (version 149, SEQ ID NO:32). "CD33" refers to Myeloid cell surface antigen CD33, also known as SIGLEC3 or gp67, and includes any native CD33 from any vertebrate source, including mammals such as primates (e.g. humans) non- human primates (e.g. cynomolgus monkeys) and rodents (e.g. mice and rats), unless otherwise indicated. The amino acid sequence of human CD33 is shown in Uniprot accession no. P20138 (version 157, SEQ ID NO:33).
The term "variable region" or "variable domain" refers to the domain of an antibody heavy or light chain that is involved in binding the antigen binding molecule to antigen. The variable domains of the heavy chain and light chain (VH and VL, respectively) of a native antibody generally have similar structures, with each domain comprising four conserved framework regions (FRs) and three hypervariable regions (HVRs). See, e.g., Kindt et al., Kuby Immunology, 6th ed., W.H. Freeman and Co., page 91 (2007). A single VH or VL domain may be sufficient to confer antigen-binding specificity.
The term "hypervariable region" or "HVR," as used herein refers to each of the regions of an antibody variable domain which are hypervariable in sequence and/or form structurally defined loops ("hypervariable loops"). Generally, native four-chain antibodies comprise six HVRs; three in the VH (HI, H2, H3), and three in the VL (LI, L2, L3). HVRs generally comprise amino acid residues from the hypervariable loops and/or from the "complementarity determining regions" (CDRs), the latter being of highest sequence variability and/or involved in antigen recognition. Exemplary hypervariable loops occur at amino acid residues 26-32 (LI), 50- 52 (L2), 91-96 (L3), 26-32 (HI), 53-55 (H2), and 96-101 (H3). (Chothia and Lesk, J. Mol. Biol. 196:901-917 (1987).) Exemplary CDRs (CDR-L1, CDR-L2, CDR-L3, CDR-H1, CDR-H2, and CDR-H3) occur at amino acid residues 24-34 of LI, 50-56 of L2, 89-97 of L3, 31-35B of HI, 50-65 of H2, and 95-102 of H3. (Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, MD (1991).) Hypervariable regions (HVRs) are also referred to as complementarity determining regions (CDRs), and these terms are used herein interchangeably in reference to portions of the variable region that form the antigen binding regions. This particular region has been described by Kabat et al., U.S. Dept. of Health and Human Services, "Sequences of Proteins of Immunological Interest" (1983) and by Chothia et al., J. Mol. Biol. 196:901-917 (1987), where the definitions include overlapping or subsets of amino acid residues when compared against each other.
Nevertheless, application of either definition to refer to a CDR of an antibody or variants thereof is intended to be within the scope of the term as defined and used herein. The appropriate amino acid residues which encompass the CDRs as defined by each of the above cited references are set forth below in Table A as a comparison. The exact residue numbers which encompass a particular CDR will vary depending on the sequence and size of the CDR. Those skilled in the art can routinely determine which residues comprise a particular CDR given the variable region amino acid sequence of the antibody. TABLE A. CDR Definitions1
Figure imgf000041_0001
1 Numbering of all CDR definitions in Table A is according to the numbering
conventions set forth by Kabat et al. (see below).
"AbM" with a lowercase "b" as used in Table A refers to the CDRs as
defined by Oxford Molecular's "AbM" antibody modeling software. Kabat et al. also defined a numbering system for variable region sequences that is applicable to any antibody. One of ordinary skill in the art can unambiguously assign this system of "Kabat numbering" to any variable region sequence, without reliance on any experimental data beyond the sequence itself. As used herein, "Kabat numbering" refers to the numbering system set forth by Kabat et al., U.S. Dept. of Health and Human Services, "Sequence of Proteins of Immunological Interest" ( 1983). Unless otherwise specified, references to the numbering of specific amino acid residue positions in an antibody variable region are according to the Kabat numbering system. With the exception of CDR1 in VH, CDRs generally comprise the amino acid residues that form the hypervariable loops. CDRs also comprise "specificity determining residues," or "SDRs," which are residues that contact antigen. SDRs are contained within regions of the CDRs called abbreviated-CDRs, or a-CDRs. Exemplary a-CDRs (a-CDR-Ll, a-CDR-L2, a-CDR-L3, a- CDR-H1, a-CDR-H2, and a-CDR-H3) occur at amino acid residues 31-34 of LI, 50-55 of L2, 89-96 of L3, 31-35B of HI, 50-58 of H2, and 95-102 of H3. (See Almagro and Fransson, Front. Biosci. 13: 1619-1633 (2008).) Unless otherwise indicated, HVR residues and other residues in the variable domain (e.g., FR residues) are numbered herein according to Kabat et al., supra.
As used herein, the term "affinity matured" in the context of antigen binding molecules (e.g., antibodies) refers to an antigen binding molecule that is derived from a reference antigen binding molecule, e.g., by mutation, binds to the same antigen, preferably binds to the same epitope, as the reference antibody; and has a higher affinity for the antigen than that of the reference antigen binding molecule. Affinity maturation generally involves modification of one or more amino acid residues in one or more CDRs of the antigen binding molecule. Typically, the affinity matured antigen binding molecule binds to the same epitope as the initial reference antigen binding molecule.
"Framework" or "FR" refers to variable domain residues other than hypervariable region (HVR) residues. The FR of a variable domain generally consists of four FR domains: FR1, FR2, FR3, and FR4. Accordingly, the HVR and FR sequences generally appear in the following sequence in VH (or VL): FR1-H1(L1)-FR2-H2(L2)-FR3-H3(L3)-FR4.
An "acceptor human framework" for the purposes herein is a framework comprising the amino acid sequence of a light chain variable domain (VL) framework or a heavy chain variable domain (VH) framework derived from a human immunoglobulin framework or a human consensus framework, as defined below. An acceptor human framework "derived from" a human immunoglobulin framework or a human consensus framework may comprise the same amino acid sequence thereof, or it may contain amino acid sequence changes. In some embodiments, the number of amino acid changes are 10 or less, 9 or less, 8 or less, 7 or less, 6 or less, 5 or less, 4 or less, 3 or less, or 2 or less. In some embodiments, the VL acceptor human framework is identical in sequence to the VL human immunoglobulin framework sequence or human consensus framework sequence.
The term "chimeric" antibody refers to an antibody in which a portion of the heavy and/or light chain is derived from a particular source or species, while the remainder of the heavy and/or light chain is derived from a different source or species.
The "class" of an antibody refers to the type of constant domain or constant region possessed by its heavy chain. There are five major classes of antibodies: IgA, IgD, IgE, IgG, and IgM, and several of these may be further divided into subclasses (isotypes), e.g. IgGi, IgG2, IgG3, IgG4, IgAi, and IgA2. The heavy chain constant domains that correspond to the different classes of immunoglobulins are called , δ, ε, γ, and μ respectively..
A "humanized" antibody refers to a chimeric antibody comprising amino acid residues from non-human HVRs and amino acid residues from human FRs. In certain embodiments, a humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the HVRs (e.g., CDRs) correspond to those of a non- human antibody, and all or substantially all of the FRs correspond to those of a human antibody. A humanized antibody optionally may comprise at least a portion of an antibody constant region derived from a human antibody. A "humanized form" of an antibody, e.g., a non-human antibody, refers to an antibody that has undergone humanization. Other forms of "humanized antibodies" encompassed by the present invention are those in which the constant region has been additionally modified or changed from that of the original antibody to generate the properties according to the invention, especially in regard to Clq binding and/or Fc receptor (FcR) binding.
A "human" antibody is one which possesses an amino acid sequence which corresponds to that of an antibody produced by a human or a human cell or derived from a non-human source that utilizes human antibody repertoires or other human antibody-encoding sequences. This definition of a human antibody specifically excludes a humanized antibody comprising non- human antigen-binding residues.
The term "Fc domain" or "Fc region" herein is used to define a C-terminal region of an antibody heavy chain that contains at least a portion of the constant region. The term includes native sequence Fc regions and variant Fc regions. An IgG Fc region comprises an IgG CH2 and an IgG CH3 domain. The "CH2 domain" of a human IgG Fc region usually extends from an amino acid residue at about position 231 to an amino acid residue at about position 340. In one embodiment, a carbohydrate chain is attached to the CH2 domain. The CH2 domain herein may be a native sequence CH2 domain or variant CH2 domain. The "CH3 domain" comprises the stretch of residues C-terminal to a CH2 domain in an Fc region (i.e. from an amino acid residue at about position 341 to an amino acid residue at about position 447 of an IgG). The CH3 region herein may be a native sequence CH3 domain or a variant CH3 domain (e.g. a CH3 domain with an introduced "protuberance" ("knob") in one chain thereof and a corresponding introduced "cavity" ("hole") in the other chain thereof; see US Patent No. 5,821,333, expressly incorporated herein by reference). Such variant CH3 domains may be used to promote heterodimerization of two non-identical antibody heavy chains as herein described. In one embodiment, a human IgG heavy chain Fc region extends from Cys226, or from Pro230, to the carboxyl-terminus of the heavy chain. However, the C-terminal lysine (Lys447) of the Fc region may or may not be present. Unless otherwise specified herein, numbering of amino acid residues in the Fc region or constant region is according to the EU numbering system, also called the EU index, as described in Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, MD, 1991. The "knob-into-hole" technology is described e.g. in US 5,731,168; US 7,695,936;
Ridgway et al., Prot Eng 9, 617-621 (1996) and Carter, J Immunol Meth 248, 7-15 (2001).
Generally, the method involves introducing a protuberance ("knob") at the interface of a first polypeptide and a corresponding cavity ("hole") in the interface of a second polypeptide, such that the protuberance can be positioned in the cavity so as to promote heterodimer formation and hinder homodimer formation. Protuberances are constructed by replacing small amino acid side chains from the interface of the first polypeptide with larger side chains (e.g. tyrosine or tryptophan). Compensatory cavities of identical or similar size to the protuberances are created in the interface of the second polypeptide by replacing large amino acid side chains with smaller ones (e.g. alanine or threonine). The protuberance and cavity can be made by altering the nucleic acid encoding the polypeptides, e.g. by site-specific mutagenesis, or by peptide synthesis. In a specific embodiment a knob modification comprises the amino acid substitution T366W in one of the two subunits of the Fc domain, and the hole modification comprises the amino acid substitutions T366S, L368A and Y407V in the other one of the two subunits of the Fc domain. In a further specific embodiment, the subunit of the Fc domain comprising the knob modification additionally comprises the amino acid substitution S354C, and the subunit of the Fc domain comprising the hole modification additionally comprises the amino acid substitution Y349C. Introduction of these two cysteine residues results in the formation of a disulfide bridge between the two subunits of the Fc region, thus further stabilizing the dimer (Carter, J Immunol Methods 248, 7-15 (2001)). The numbering is according to EU index of Kabat et al, Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, MD, 1991.
A "region equivalent to the Fc region of an immunoglobulin" is intended to include naturally occurring allelic variants of the Fc region of an immunoglobulin as well as variants having alterations which produce substitutions, additions, or deletions but which do not decrease substantially the ability of the immunoglobulin to mediate effector functions (such as antibody- dependent cellular cytotoxicity). For example, one or more amino acids can be deleted from the N-terminus or C-terminus of the Fc region of an immunoglobulin without substantial loss of biological function. Such variants can be selected according to general rules known in the art so as to have minimal effect on activity (see, e.g., Bowie, J. U. et al., Science 247: 1306-10 (1990)). The term "effector functions" refers to those biological activities attributable to the Fc region of an antibody, which vary with the antibody isotype. Examples of antibody effector functions include: Clq binding and complement dependent cytotoxicity (CDC), Fc receptor binding, antibody-dependent cell-mediated cytotoxicity (ADCC), antibody-dependent cellular phagocytosis (ADCP), cytokine secretion, immune complex-mediated antigen uptake by antigen presenting cells, down regulation of cell surface receptors (e.g. B cell receptor), and B cell activation.
An "activating Fc receptor" is an Fc receptor that following engagement by an Fc region of an antibody elicits signaling events that stimulate the receptor-bearing cell to perform effector functions. Activating Fc receptors include FcyRIIIa (CD16a), FcyRI (CD64), FcyRIIa (CD32), and FcaRI (CD89). A particular activating Fc receptor is human FcyRIIIa (see UniProt accession no. P08637, version 141).
The term "TNF ligand family member" or "TNF family ligand" refers to a
proinflammatory cytokine. Cytokines in general, and in particular the members of the TNF ligand family, play a crucial role in the stimulation and coordination of the immune system. At present, nineteen cyctokines have been identified as members of the TNF (tumour necrosis factor) ligand superfamily on the basis of sequence, functional, and structural similarities. All these ligands are type II transmembrane proteins with a C-terminal extracellular domain
(ectodomain), N-terminal intracellular domain and a single transmembrane domain. The C- terminal extracellular domain, known as TNF homology domain (THD), has 20-30% amino acid identity between the superfamily members and is responsible for binding to the receptor. The TNF ectodomain is also responsible for the TNF ligands to form trimeric complexes that are recognized by their specific receptors.
Members of the TNF ligand family are selected from the group consisting of Lymphotoxin (also known as LTA or TNFSF1), TNF (also known as TNFSF2), υτβ (also known as TNFSF3), OX40L (also known as TNFSF4), CD40L (also known as CD 154 or TNFSF5), FasL (also known as CD95L, CD 178 or TNFSF6), CD27L (also known as CD70 or TNFSF7), CD30L (also known as CD153 or TNFSF8), 4-1BBL (also known as TNFSF9), TRAIL (also known as AP02L, CD253 or TNFSF10), RANKL (also known as CD254 or TNFSF11), TWEAK (also known as TNFSF12), APRIL (also known as CD256 or TNFSF13), BAFF (also known as CD257 or TNFSF13B), LIGHT (also known as CD258 or TNFSF14), TL1A (also known as VEGI or TNFSF15), GITRL (also known as TNFSF18), EDA-A1 (also known as ectodysplasin Al) and EDA-A2 (also known as ectodysplasin A2). The term refers to any native TNF family ligand from any vertebrate source, including mammals such as primates (e.g. humans), non- human primates (e.g. cynomolgus monkeys) and rodents (e.g. mice and rats), unless otherwise indicated. In specific embodiments of the invention, the TNF ligand family member is selected from the group consisting of OX40L, FasL, CD27L, TRAIL, 4-1BBL, CD40L and GITRL. In a particular embodiment, the TNF ligand family member is selected from 4-1BBL and OX40L. Further information, in particular sequences, of the TNF ligand family members may be obtained from publically accessible databases such as Uniprot (www.uniprot.org). For instance, the human TNF ligands have the following amino acid sequences: human Lymphotoxin a (UniProt accession no. P01374, SEQ ID NO:34), human TNF (UniProt accession no. P01375, SEQ ID NO:35), human Lymphotoxin β (UniProt accession no. Q06643, SEQ ID NO:36), human OX40L (UniProt accession no. P23510, SEQ ID NO:37), human CD40L (UniProt accession no. P29965, SEQ ID NO:38), human FasL (UniProt accession no. P48023, SEQ ID NO:39), human CD27L (UniProt accession no. P32970, SEQ ID NO:40), human CD30L (UniProt accession no. P32971, SEQ ID NO:41), 4-lBBL (UniProt accession no. P41273, SEQ ID NO:42), TRAIL (UniProt accession no. P50591, SEQ ID NO:43), RANKL (UniProt accession no. 014788, SEQ ID NO:44), TWEAK (UniProt accession no. 043508, SEQ ID NO:45), APRIL (UniProt accession no. 075888, SEQ ID NO:46), BAFF (UniProt accession no. Q9Y275, SEQ ID NO:47), LIGHT (UniProt accession no. 043557, SEQ ID NO:48), TL1A (UniProt accession no. 095150, SEQ ID NO:49), GITRL (UniProt accession no. Q9UNG2, SEQ ID NO:50) and ectodysplasin A (UniProt accession no. Q92838, SEQ ID NO:51).
An "ectodomain" is the domain of a membrane protein that extends into the extracellular space (i.e. the space outside the target cell). Ectodomains are usually the parts of proteins that initiate contact with surfaces, which leads to signal transduction. The ectodomain of TNF ligand family member as defined herein thus refers to the part of the TNF ligand protein that extends into the extracellular space (the extracellular domain), but also includes shorter parts or fragments thereof that are responsible for the trimerization and for the binding to the
corresponding TNF receptor. The term "ectodomain of a TNF ligand family member or a fragment thereof thus refers to the extracellular domain of the TNF ligand family member that forms the extracellular domain or to parts thereof that are still able to bind to the receptor (receptor binding domain).
The term "costimulatory TNF ligand family member" or "costimulatory TNF family ligand" refers to a subgroup of TNF ligand family members, which are able to costimulate proliferation and cytokine production of T-cells. These TNF family ligands can costimulate TCR signals upon interaction with their corresponding TNF receptors and the interaction with their receptors leads to recruitment of TNFR-associated factors (TRAF), which initiate signalling cascades that result in T-cell activation. Costimulatory TNF family ligands are selected from the group consisting of 4-lBBL, OX40L, GITRL, CD70, CD30L and LIGHT, more particularly the costimulatory TNF ligand family member is selected from 4-lBBL and OX40L.
As described herein before, 4-lBBL is a type II transmembrane protein and one member of the TNF ligand family. Complete or full length 4-lBBL having the amino acid sequence of SEQ ID NO:42 has been described to form trimers on the surface of cells. The formation of trimers is enabled by specific motives of the ectodomain of 4-lBBL. Said motives are designated herein as "trimerization region". The amino acids 50-254 of the human 4-lBBL sequence (SEQ ID NO:52) form the extracellular domain of 4-lBBL, but even fragments thereof are able to form the trimers. In specific embodiments of the invention, the term "ectodomain of 4-lBBL or a fragment thereof refers to a polypeptide having an amino acid sequence selected from SEQ ID NO:4
(amino acids 52-254 of human 4-lBBL), SEQ ID NO: l (amino acids 71-254 of human 4-lBBL), SEQ ID NO:3 (amino acids 80-254 of human 4-lBBL) and SEQ ID NO:2 (amino acids 85-254 of human 4-lBBL) or a polypeptide having an amino acid sequence selected from SEQ ID NO:96 (amino acids 71-248 of human 4-lBBL), SEQ ID NO:375 (amino acids 52-248 of human 4-lBBL), SEQ ID NO:374 (amino acids 80-248 of human 4-lBBL) and SEQ ID NO:373 (amino acids 85-248 of human 4-lBBL), but also other fragments of the ectodomain capable of trimerization are included herein.
As described herein before, OX40L is another type II transmembrane protein and a further member of the TNF ligand family. Complete or full length human OX40L has the amino acid sequence of SEQ ID NO:37. The amino acids 51-183 of the human OX40L sequence (SEQ ID NO:53) form the extracellular domain of OX40L, but even fragments thereof that are able to form the trimers. In specific embodiments of the invention, the term "ectodomain of OX40L or a fragment thereof refers to a polypeptide having an amino acid sequence selected from SEQ ID NO:53 (amino acids 51-183 of human OX40L) or SEQ ID NO:54 (amino acids 52-183 of human OX40L), but also other fragments of the ectodomain capable of trimerization are included herein.
The term "peptide linker" refers to a peptide comprising one or more amino acids, typically about 2 to 20 amino acids. Peptide linkers are known in the art or are described herein. Suitable, non-immunogenic linker peptides are, for example, (G4S)n, (SG4)n or G4(SG4)n peptide linkers, wherein "n" is generally a number between 1 and 10, typically between 1 and 4, in particular 2, i.e. the peptides selected from the group consisting of GGGGS (SEQ ID NO: 128), GGGGSGGGGS (SEQ ID NO: 13), SGGGGSGGGG (SEQ ID NO:55) and
GGGGSGGGGSGGGG (SEQ ID NO:56), but also include the sequences GSPGSSSSGS (SEQ ID NO:57), GSGSGSGS (SEQ ID NO:58), GSGSGNGS (SEQ ID NO:59), GGSGSGSG (SEQ ID NO:60), GGSGSG (SEQ ID NO:61), GGSG (SEQ ID NO:62), GGSGNGSG (SEQ ID
NO:63), GGNGSGSG (SEQ ID NO:64) and GGNGSG (SEQ ID NO:65). Peptide linkers of particular interest are (G4S)i or GGGGS (SEQ ID NO: 128), (G4S)2 or GGGGSGGGGS (SEQ ID NO: 13) and GSPGSSSSGS (SEQ ID NO:57), more particularly (G4S)2 or GGGGSGGGGS (SEQ ID NO: 13) and GSPGSSSSGS (SEQ ID NO:57).
The term "amino acid" as used within this application denotes the group of naturally occurring carboxy a-amino acids comprising alanine (three letter code: ala, one letter code: A), arginine (arg, R), asparagine (asn, N), aspartic acid (asp, D), cysteine (cys, C), glutamine (gin, Q), glutamic acid (glu, E), glycine (gly, G), histidine (his, H), isoleucine (ile, I), leucine (leu, L), lysine (lys, K), methionine (met, M), phenylalanine (phe, F), proline (pro, P), serine (ser, S), threonine (thr, T), tryptophan (trp, W), tyrosine (tyr, Y), and valine (val, V).
A "single chain fusion protein" as used herein refers to a single chain polypeptide composed of one or two ectodomains of said TNF ligand family member fused to a part of antigen binding moiety or Fc part. The fusion may occur by directly linking the N or C-terminal amino acid of the antigen binding moiety via a peptide linker to the C- or N-terminal amino acid of the ectodomain of said TNF ligand family member.
By "fused" or "connected" is meant that the components (e.g. a polypeptide and an ectodomain of said TNF ligand family member) are linked by peptide bonds, either directly or via one or more peptide linkers.
"Percent (%) amino acid sequence identity" with respect to a reference polypeptide (protein) sequence is defined as the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in the reference polypeptide sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, BLAST-2, ALIGN. SAWI or Megalign (DNASTAR) software. Those skilled in the art can determine appropriate parameters for aligning sequences, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared. For purposes herein, however, % amino acid sequence identity values are generated using the sequence comparison computer program ALIGN-2. The ALIGN- 2 sequence comparison computer program was authored by Genentech, Inc., and the source code has been filed with user documentation in the U.S. Copyright Office, Washington D.C., 20559, where it is registered under U.S. Copyright Registration No. TXU510087. The ALIGN-2 program is publicly available from Genentech, Inc., South San Francisco, California, or may be compiled from the source code. The ALIGN-2 program should be compiled for use on a UNIX operating system, including digital UNIX V4.0D. All sequence comparison parameters are set by the ALIGN-2 program and do not vary. In situations where ALIGN-2 is employed for amino acid sequence comparisons, the % amino acid sequence identity of a given amino acid sequence A to, with, or against a given amino acid sequence B (which can alternatively be phrased as a given amino acid sequence A that has or comprises a certain % amino acid sequence identity to, with, or against a given amino acid sequence B) is calculated as follows:
100 times the fraction X/Y where X is the number of amino acid residues scored as identical matches by the sequence alignment program ALIGN-2 in that program's alignment of A and B, and where Y is the total number of amino acid residues in B. It will be appreciated that where the length of amino acid sequence A is not equal to the length of amino acid sequence B, the % amino acid sequence identity of A to B will not equal the % amino acid sequence identity of B to A. Unless specifically stated otherwise, all % amino acid sequence identity values used herein are obtained as described in the immediately preceding paragraph using the ALIGN-2 computer program.
In certain embodiments, amino acid sequence variants of the TNF ligand trimer- containing antigen binding molecules provided herein are contemplated. For example, it may be desirable to improve the binding affinity and/or other biological properties of the TNF ligand trimer-containing antigen binding molecules. Amino acid sequence variants of the TNF ligand trimer-containing antigen binding molecules may be prepared by introducing appropriate modifications into the nucleotide sequence encoding the molecules, or by peptide synthesis. Such modifications include, for example, deletions from, and/or insertions into and/or substitutions of residues within the amino acid sequences of the antibody. Any combination of deletion, insertion, and substitution can be made to arrive at the final construct, provided that the final construct possesses the desired characteristics, e.g., antigen-binding. Sites of interest for substitutional mutagenesis include the HVRs and Framework (FRs). Conservative substitutions are provided in Table B under the heading "Preferred Substitutions" and further described below in reference to amino acid side chain classes (1) to (6). Amino acid substitutions may be introduced into the molecule of interest and the products screened for a desired activity, e.g., retained/improved antigen binding, decreased immunogenicity, or improved ADCC or CDC.
TABLE B
Original Exemplary Preferred
Residue Substitutions Substitutions
Ala (A) Val; Leu; He Val
Arg (R) Lys; Gin; Asn Lys
Asn (N) Gin; His; Asp, Lys; Arg Gin
Asp (D) Glu; Asn Glu
Cys (C) Ser; Ala Ser
Gin (Q) Asn; Glu Asn
Glu (E) Asp; Gin Asp
Gly (G) Ala Ala
His (H) Asn; Gin; Lys; Arg Arg
He (I) Leu; Val; Met; Ala; Phe; Norleucine Leu Original Exemplary Preferred Residue Substitutions Substitutions
Leu (L) Norleucine; He; Val; Met; Ala; Phe He
Lys (K) Arg; Gin; Asn Arg
Met (M) Leu; Phe; He Leu
Phe (F) Trp; Leu; Val; He; Ala; Tyr Tyr
Pro (P) Ala Ala
Ser (S) Thr Thr
Thr (T) Val; Ser Ser
Trp (W) Tyr; Phe Tyr
Tyr (Y) Trp; Phe; Thr; Ser Phe
Val (V) He; Leu; Met; Phe; Ala; Norleucine Leu
Amino acids may be grouped according to common side-chain properties:
(1) hydrophobic: Norleucine, Met, Ala, Val, Leu, He;
(2) neutral hydrophilic: Cys, Ser, Thr, Asn, Gin;
(3) acidic: Asp, Glu;
(4) basic: His, Lys, Arg;
(5) residues that influence chain orientation: Gly, Pro;
(6) aromatic: Trp, Tyr, Phe.
Non-conservative substitutions will entail exchanging a member of one of these classes for another class.
The term "amino acid sequence variants" includes substantial variants wherein there are amino acid substitutions in one or more hypervariable region residues of a parent antigen binding molecule (e.g. a humanized or human antibody). Generally, the resulting variant(s) selected for further study will have modifications (e.g., improvements) in certain biological properties (e.g., increased affinity, reduced immunogenicity) relative to the parent antigen binding molecule and/or will have substantially retained certain biological properties of the parent antigen binding molecule. An exemplary substitutional variant is an affinity matured antibody, which may be conveniently generated, e.g., using phage display-based affinity maturation techniques such as those described herein. Briefly, one or more HVR residues are mutated and the variant antigen binding molecules displayed on phage and screened for a particular biological activity (e.g. binding affinity). In certain embodiments, substitutions, insertions, or deletions may occur within one or more HVRs so long as such alterations do not substantially reduce the ability of the antigen binding molecule to bind antigen. For example, conservative alterations (e.g., conservative substitutions as provided herein) that do not substantially reduce binding affinity may be made in HVRs. A useful method for identification of residues or regions of an antibody that may be targeted for mutagenesis is called "alanine scanning mutagenesis" as described by Cunningham and Wells (1989) Science, 244: 1081-1085. In this method, a residue or group of target residues (e.g., charged residues such as Arg, Asp, His, Lys, and Glu) are identified and replaced by a neutral or negatively charged amino acid (e.g., alanine or polyalanine) to determine whether the interaction of the antibody with antigen is affected. Further substitutions may be introduced at the amino acid locations demonstrating functional sensitivity to the initial substitutions. Alternatively, or additionally, a crystal structure of an antigen- antigen binding molecule complex to identify contact points between the antibody and antigen. Such contact residues and neighboring residues may be targeted or eliminated as candidates for substitution. Variants may be screened to determine whether they contain the desired properties.
Amino acid sequence insertions include amino- and/or carboxyl-terminal fusions ranging in length from one residue to polypeptides containing a hundred or more residues, as well as intrasequence insertions of single or multiple amino acid residues. Examples of terminal insertions include TNF family ligand trimer-containing antigen binding molecule with an N- terminal methionyl residue. Other insertional variants of the molecule include the fusion to the N- or C-terminus to a polypeptide which increases the serum half-life of the TNF ligand trimer- containing antigen binding molecules. In certain embodiments, the TNF family ligand trimer-containing antigen binding molecules provided herein are altered to increase or decrease the extent to which the antibody is glycosylated. Glycosylation variants of the molecules may be conveniently obtained by altering the amino acid sequence such that one or more glycosylation sites is created or removed. Where the TNF ligand trimer-containing antigen binding molecule comprises an Fc region, the carbohydrate attached thereto may be altered. Native antibodies produced by mammalian cells typically comprise a branched, biantennary oligosaccharide that is generally attached by an N- linkage to Asn297 of the CH2 domain of the Fc region. See, e.g., Wright et al. TIBTECH 15:26- 32 (1997). The oligosaccharide may include various carbohydrates, e.g., mannose, N-acetyl glucosamine (GlcNAc), galactose, and sialic acid, as well as a fucose attached to a GlcNAc in the "stem" of the biantennary oligosaccharide structure. In some embodiments, modifications of the oligosaccharide in TNF family ligand trimer-containing antigen binding molecule may be made in order to create variants with certain improved properties. In one aspect, variants of TNF family ligand trimer-containing antigen binding molecules are provided having a carbohydrate structure that lacks fucose attached (directly or indirectly) to an Fc region. Such fucosylation variants may have improved ADCC function, see e.g. US Patent Publication Nos. US
2003/0157108 (Presta, L.) or US 2004/0093621 (Kyowa Hakko Kogyo Co., Ltd). Further variants of the TNF family ligand trimer-containing antigen binding molecules of the invention include those with bisected oligosaccharides, e.g., in which a biantennary oligosaccharide attached to the Fc region is bisected by GlcNAc. Such variants may have reduced fucosylation and/or improved ADCC function., see for example WO 2003/011878 (Jean-Mairet et al.); US Patent No. 6,602,684 (Umana et al.); and US 2005/0123546 (Umana et al.). Variants with at least one galactose residue in the oligosaccharide attached to the Fc region are also provided. Such antibody variants may have improved CDC function and are described, e.g., in WO
1997/30087 (Patel et al.); WO 1998/58964 (Raju, S.); and WO 1999/22764 (Raju, S.).
In certain embodiments, it may be desirable to create cysteine engineered variants of the TNF family ligand trimer-containing antigen binding molecule of the invention, e.g.,
"thioMAbs," in which one or more residues of the molecule are substituted with cysteine residues. In particular embodiments, the substituted residues occur at accessible sites of the molecule. By substituting those residues with cysteine, reactive thiol groups are thereby positioned at accessible sites of the antibody and may be used to conjugate the antibody to other moieties, such as drug moieties or linker-drug moieties, to create an immunoconjugate. In certain embodiments, any one or more of the following residues may be substituted with cysteine: V205 (Kabat numbering) of the light chain; Al 18 (EU numbering) of the heavy chain; and S400 (EU numbering) of the heavy chain Fc region. Cysteine engineered antigen binding molecules may be generated as described, e.g., in U.S. Patent No. 7,521,541.
In certain aspects, the TNF family ligand trimer-containing antigen binding molecules provided herein may be further modified to contain additional non-proteinaceous moieties that are known in the art and readily available. The moieties suitable for derivatization of the antibody include but are not limited to water soluble polymers. Non-limiting examples of water soluble polymers include, but are not limited to, polyethylene glycol (PEG), copolymers of ethylene glycol/propylene glycol, carboxymethylcellulose, dextran, polyvinyl alcohol, polyvinyl pyrrolidone, poly- 1, 3-dioxolane, poly-l,3,6-trioxane, ethylene/maleic anhydride copolymer, polyaminoacids (either homopolymers or random copolymers), and dextran or poly(n-vinyl pyrrolidone)polyethylene glycol, propropylene glycol homopolymers, prolypropylene oxide/ethylene oxide co-polymers, polyoxyethylated polyols (e.g., glycerol), polyvinyl alcohol, and mixtures thereof. Polyethylene glycol propionaldehyde may have advantages in
manufacturing due to its stability in water. The polymer may be of any molecular weight, and may be branched or unbranched. The number of polymers attached to the antibody may vary, and if more than one polymer is attached, they can be the same or different molecules. In general, the number and/or type of polymers used for derivatization can be determined based on considerations including, but not limited to, the particular properties or functions of the antibody to be improved, whether the bispecific antibody derivative will be used in a therapy under defined conditions, etc. In another aspect, conjugates of an antibody and non-proteinaceous moiety that may be selectively heated by exposure to radiation are provided. In one embodiment, the non-proteinaceous moiety is a carbon nanotube (Kam, N.W. et al., Proc. Natl. Acad. Sci. USA 102 (2005) 11600-11605). The radiation may be of any wavelength, and includes, but is not limited to, wavelengths that do not harm ordinary cells, but which heat the non-proteinaceous moiety to a temperature at which cells proximal to the antibody-non-proteinaceous moiety are killed.
In another aspect, immunoconjugates of the TNF family ligand trimer-containing antigen binding molecules provided herein maybe obtained. An "immunoconjugate" is an antibody conjugated to one or more heterologous molecule(s), including but not limited to a cytotoxic agent. The term "polynucleotide" refers to an isolated nucleic acid molecule or construct, e.g. messenger RNA (mRNA), virally-derived RNA, or plasmid DNA (pDNA). A polynucleotide may comprise a conventional phosphodiester bond or a non-conventional bond (e.g. an amide bond, such as found in peptide nucleic acids (PNA). The term "nucleic acid molecule" refers to any one or more nucleic acid segments, e.g. DNA or RNA fragments, present in a polynucleotide. By "isolated" nucleic acid molecule or polynucleotide is intended a nucleic acid molecule,
DNA or RNA, which has been removed from its native environment. For example, a
recombinant polynucleotide encoding a polypeptide contained in a vector is considered isolated for the purposes of the present invention. Further examples of an isolated polynucleotide include recombinant polynucleotides maintained in heterologous host cells or purified (partially or substantially) polynucleotides in solution. An isolated polynucleotide includes a polynucleotide molecule contained in cells that ordinarily contain the polynucleotide molecule, but the polynucleotide molecule is present extrachromosomally or at a chromosomal location that is different from its natural chromosomal location. Isolated RNA molecules include in vivo or in vitro RNA transcripts of the present invention, as well as positive and negative strand forms, and double- stranded forms. Isolated polynucleotides or nucleic acids according to the present invention further include such molecules produced synthetically. In addition, a polynucleotide or a nucleic acid may be or may include a regulatory element such as a promoter, ribosome binding site, or a transcription terminator.
By a nucleic acid or polynucleotide having a nucleotide sequence at least, for example, 95% "identical" to a reference nucleotide sequence of the present invention, it is intended that the nucleotide sequence of the polynucleotide is identical to the reference sequence except that the polynucleotide sequence may include up to five point mutations per each 100 nucleotides of the reference nucleotide sequence. In other words, to obtain a polynucleotide having a nucleotide sequence at least 95% identical to a reference nucleotide sequence, up to 5% of the nucleotides in the reference sequence may be deleted or substituted with another nucleotide, or a number of nucleotides up to 5% of the total nucleotides in the reference sequence may be inserted into the reference sequence. These alterations of the reference sequence may occur at the 5' or 3' terminal positions of the reference nucleotide sequence or anywhere between those terminal positions, interspersed either individually among residues in the reference sequence or in one or more contiguous groups within the reference sequence. As a practical matter, whether any particular polynucleotide sequence is at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to a nucleotide sequence of the present invention can be determined conventionally using known computer programs, such as the ones discussed above for polypeptides (e.g.
ALIGN-2). The term "expression cassette" refers to a polynucleotide generated recombinantly or synthetically, with a series of specified nucleic acid elements that permit transcription of a particular nucleic acid in a target cell. The recombinant expression cassette can be incorporated into a plasmid, chromosome, mitochondrial DNA, plastid DNA, virus, or nucleic acid fragment. Typically, the recombinant expression cassette portion of an expression vector includes, among other sequences, a nucleic acid sequence to be transcribed and a promoter. In certain
embodiments, the expression cassette of the invention comprises polynucleotide sequences that encode bispecific antigen binding molecules of the invention or fragments thereof.
The term "vector" or "expression vector" is synonymous with "expression construct" and refers to a DNA molecule that is used to introduce and direct the expression of a specific gene to which it is operably associated in a target cell. The term includes the vector as a self -replicating nucleic acid structure as well as the vector incorporated into the genome of a host cell into which it has been introduced. The expression vector of the present invention comprises an expression cassette. Expression vectors allow transcription of large amounts of stable mRNA. Once the expression vector is inside the target cell, the ribonucleic acid molecule or protein that is encoded by the gene is produced by the cellular transcription and/or translation machinery. In one embodiment, the expression vector of the invention comprises an expression cassette that comprises polynucleotide sequences that encode bispecific antigen binding molecules of the invention or fragments thereof.
The terms "host cell", "host cell line," and "host cell culture" are used interchangeably and refer to cells into which exogenous nucleic acid has been introduced, including the progeny of such cells. Host cells include "transforaiants" and "transformed cells," which include the primary transformed cell and progeny derived therefrom without regard to the number of passages. Progeny may not be completely identical in nucleic acid content to a parent cell, but may contain mutations. Mutant progeny that have the same function or biological activity as screened or selected for in the originally transformed cell are included herein. A host cell is any type of cellular system that can be used to generate the bispecific antigen binding molecules of the present invention. Host cells include cultured cells, e.g. mammalian cultured cells, such as CHO cells, BHK cells, NSO cells, SP2/0 cells, YO myeloma cells, P3X63 mouse myeloma cells, PER cells, PER.C6 cells or hybridoma cells, yeast cells, insect cells, and plant cells, to name only a few, but also cells comprised within a transgenic animal, transgenic plant or cultured plant or animal tissue.
An "effective amount" of an agent refers to the amount that is necessary to result in a physiological change in the cell or tissue to which it is administered.
A "therapeutically effective amount" of an agent, e.g. a pharmaceutical composition, refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired therapeutic or prophylactic result. A therapeutically effective amount of an agent for example eliminates, decreases, delays, minimizes or prevents adverse effects of a disease.
An "individual" or "subject" is a mammal. Mammals include, but are not limited to, domesticated animals (e.g. cows, sheep, cats, dogs, and horses), primates (e.g. humans and non- human primates such as monkeys), rabbits, and rodents (e.g. mice and rats). Particularly, the individual or subject is a human.
The term "pharmaceutical composition" refers to a preparation which is in such form as to permit the biological activity of an active ingredient contained therein to be effective, and which contains no additional components which are unacceptably toxic to a subject to which the formulation would be administered. A "pharmaceutically acceptable excipient" refers to an ingredient in a pharmaceutical composition, other than an active ingredient, which is nontoxic to a subject. A pharmaceutically acceptable excipient includes, but is not limited to, a buffer, a stabilizer, or a preservative.
The term "package insert" is used to refer to instructions customarily included in commercial packages of therapeutic products, that contain information about the indications, usage, dosage, administration, combination therapy, contraindications and/or warnings concerning the use of such therapeutic products.
As used herein, "treatment" (and grammatical variations thereof such as "treat" or "treating") refers to clinical intervention in an attempt to alter the natural course of the individual being treated, and can be performed either for prophylaxis or during the course of clinical pathology. Desirable effects of treatment include, but are not limited to, preventing occurrence or recurrence of disease, alleviation of symptoms, diminishment of any direct or indirect pathological consequences of the disease, preventing metastasis, decreasing the rate of disease progression, amelioration or palliation of the disease state, and remission or improved prognosis. In some embodiments, the molecules of the invention are used to delay development of a disease or to slow the progression of a disease.
The term "cancer" as used herein refers to proliferative diseases, such as lymphomas, carcinoma, lymphoma, blastoma, sarcoma, leukemia, lymphocytic leukemias, lung cancer, non- small cell lung (NSCL) cancer, bronchioloalviolar cell lung cancer, bone cancer, pancreatic cancer, skin cancer, cancer of the head or neck, cutaneous or intraocular melanoma, uterine cancer, ovarian cancer, rectal cancer, cancer of the anal region, stomach cancer, gastric cancer, colorectal cancer (CRC), pancreatic cancer, breast cancer, triple-negative breast cancer , uterine cancer, carcinoma of the fallopian tubes, carcinoma of the endometrium, carcinoma of the cervix, carcinoma of the vagina, carcinoma of the vulva, Hodgkin's Disease, cancer of the esophagus, cancer of the small intestine, cancer of the endocrine system, cancer of the thyroid gland, cancer of the parathyroid gland, cancer of the adrenal gland, sarcoma of soft tissue, cancer of the urethra, cancer of the penis, prostate cancer, cancer of the bladder, cancer of the kidney or ureter, renal cell carcinoma, carcinoma of the renal pelvis, mesothelioma, hepatocellular cancer, biliary cancer, neoplasms of the central nervous system (CNS), spinal axis tumors, brain stem glioma, glioblastoma multiforme, astrocytomas, schwanomas, ependymonas, medulloblastomas, meningiomas, squamous cell carcinomas, pituitary adenoma and Ewings sarcoma, melanoma, multiple myeloma, B-cell cancer (lymphoma), chronic lymphocytic leukemia (CLL), acute lymphoblastic leukemia (ALL), hairy cell leukemia, chronic myeloblastic leukemia, including refractory versions of any of the above cancers, or a combination of one or more of the above cancers.
TNF family ligand trimer-containing antigen binding molecules of the invention
The invention provides novel TNF family ligand trimer-containing antigen binding molecules with particularly advantageous properties such as producibility, stability, binding affinity, biological activity, targeting efficiency and reduced toxicity.
In a first aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising
(a) at least one moiety capable of specific binding to a target cell antigen and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof.
In a particular aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising (a) at least one moiety capable of specific binding to a target cell antigen,
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof, and
(c) an Fc domain composed of a first and a second subunit capable of stable association.
In a particular aspect, the TNF family ligand trimer-containing antigen binding molecule comprises (a) at least one moiety capable of specific binding to a target cell antigen and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof, wherein the TNF ligand family member is costimulates human T-cell activation.
In another particular aspect, the TNF family ligand trimer-containing antigen binding molecule comprises (a) at least one moiety capable of specific binding to a target cell antigen and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof, wherein the ectodomains of a TNF ligand family member are identical in all instances. In a further aspect, provided is a TNF family ligand trimer-containing antigen binding molecule of claim 1, comprising
(a) at least one moiety capable of specific binding to a target cell antigen and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that (i) the first polypeptide contains a CHI or CL domain and the second polypeptide contains a CL or CHI domain, respectively, wherein the second polypeptide is linked to the first polypeptide by a disulfide bond between the CHI and CL domain, and wherein the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the CHI or CL domain by a peptide linker and wherein the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to the CL or CHI domain of said polypeptide, or
(ii) the first polypeptide contains a CH3 domain and the second polypeptide contains a
CH3 domain, respectively, and wherein the first polypeptide comprises two
ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the C-terminus of the CH3 domain by a peptide linker and wherein the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to C-terminus of the CH3 domain of said polypeptide, or
(iii) the first polypeptide contains a VH-CL or a VL-CH1 domain and the second
polypeptide contains a VL-CH1 domain or a VH-CL domain, respectively, wherein the second polypeptide is linked to the first polypeptide by a disulfide bond between the CHI and CL domain, and wherein the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to to VH or VL by a peptide linker and wherein the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to VL or VH of said polypeptide.
In a particular aspect, the TNF family ligand trimer-containing antigen binding molecule comprises a TNF ligand family member that costimulates human T-cell activation which is selected from 4-lBBL and OX40L. More particularly, the TNF ligand family member is 4-lBBL.
In another aspect, wherein the ectodomain of a TNF ligand family member comprises the amino acid sequence selected from the group consisting of SEQ ID NO: l, SEQ ID NO: 2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:96, SEQ ID NO: 373, SEQ ID NO:374 and SEQ ID
NO:375, particularly the amino acid sequence of SEQ ID NO: l or SEQ ID NO:96. In one aspect, the ectodomain of a TNF ligand family member or fragment thereof comprises the amino acid sequence selected from the group consisting of SEQ ID NO: l, SEQ ID NO: 2, SEQ ID NO:3, SEQ ID NO:4 and SEQ ID NO:96, particularly the amino acid sequence of SEQ ID NO: l or SEQ ID NO:96. In a particular aspect, the the ectodomain of a TNF ligand family member or fragment thereof comprises the amino acid sequence of SEQ ID NO:96. In a further aspect, the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
(a) at least one moiety capable of specific binding to a target cell antigen and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that the first polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO:5, SEQ ID NO:97, SEQ ID NO:98 and SEQ ID NO:99 and in that the second polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO: l, SEQ ID NO:96, SEQ ID NO:3 and SEQ ID NO:4. In a particular aspect, the first polypeptide comprises the amino acid sequence of SEQ ID NO:97 and the second polypeptide comprises the amino acid sequence of SEQ ID NO:96. In one aspect, the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
(a) at least one moiety capable of specific binding to a target cell antigen and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond, wherein the antigen binding molecule is characterized in that the first polypeptide comprises the amino acid sequence of SEQ ID NO:5 and in that the second polypeptide comprises the amino acid sequence of SEQ ID NO:6.
In a further aspect, the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
(a) at least one moiety capable of specific binding to a target cell antigen and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond, wherein the antigen binding molecule is characterized in that the first polypeptide comprises the amino acid sequence of SEQ ID NO:5 and in that the second polypeptide comprises the amino acid sequence of SEQ ID NO: 183.
In yet a further aspect, the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
(a) at least one moiety capable of specific binding to a target cell antigen and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond, wherein the antigen binding molecule is characterized in that the first polypeptide comprises the amino acid sequence of SEQ ID NO:97 and in that the second polypeptide comprises the amino acid sequence of SEQ ID NO: 184 or SEQ ID NO: 185.
In another aspect, the TNF ligand family member is OX40L. In a particular aspect, provided is TNF family ligand trimer-containing antigen binding molecule, wherein the ectodomain of a TNF ligand family member comprises the amino acid sequence of SEQ ID NO:53 or SEQ ID NO:54, particularly the amino acid sequence of SEQ ID NO:53. In one aspect, the invention relates to a TNF family ligand trimer-containing antigen binding molecule comprising
(a) at least one moiety capable of specific binding to a target cell antigen and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond, wherein the antigen binding molecule is characterized in that the first polypeptide comprises the amino acid sequence of SEQ ID NO:371 or SEQ ID:372 and in that the second polypeptide comprises the amino acid sequence of SEQ ID NO:53 or SEQ ID NO:54, respectively.
In one aspect, the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
(a) at least one moiety capable of specific binding to a target cell antigen,
(b) a first polypeptide containing a CHI or CL domain and a second polypeptide containing a CL or CHI domain, respectively, wherein the second polypeptide is linked to the first polypeptide by a disulfide bond between the CHI and CL domain,
and wherein the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the CHI or CL domain by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to the CL or CHI domain of said polypeptide. In one aspect, provided is a TNF family ligand trimer-containing antigen binding molecule comprising
(a) at least one moiety capable of specific binding to a target cell antigen,
(b) a first polypeptide containing a CHI domain and a second polypeptide containing a CL domain, wherein the second polypeptide is linked to the first polypeptide by a disulfide bond between the CHI and CL domain,
and wherein the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the CHI domain by a peptide linker and in that the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to the CL domain of said polypeptide.
In another aspect, provided is a TNF family ligand trimer-containing antigen binding molecule comprising
(a) at least one moiety capable of specific binding to a target cell antigen,
(b) a first polypeptide containing a CL domain and a second polypeptide containing a CHI domain, wherein the second polypeptide is linked to the first polypeptide by a disulfide bond between the CHI and CL domain,
and wherein the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the CL domain by a peptide linker and in that the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to the CHI domain of said polypeptide. In another aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising
(a) one moiety capable of specific binding to a target cell antigen and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof.
In yet another aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising
(a) more than one moiety capable of specific binding to a target cell antigen and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to said polypeptide.
In one aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising
(a) two moities capable of specific binding to a target cell antigen and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof.
In a particular aspect, provided is a TNF family ligand trimer-containing antigen binding molecule, comprising
(a) at least one moiety capable of specific binding to a target cell antigen, and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that the first polypeptide contains a CH3 domain and the second polypeptide contains a CH3 domain, respectively, and wherein the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the C-terminus of the CH3 domain by a peptide linker and wherein the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to C-terminus of the CH3 domain of said polypeptide. Particularly, such TNF family ligand trimer-containing antigen binding molecule comprises two moieties capable of specific binding to a target cell antigen.
In one aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising
(a) two moities capable of specific binding to a target cell antigen and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof,
wherein the two moieties capable of specific binding to a target cell antigen bind to two different target cell antigens.
In a further aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule as defined herein before, wherein the moiety capable of specific binding to a target cell antigen is selected from the group consisting of an antibody, an antibody fragment and a scaffold antigen binding protein.
In one aspect, provided is a TNF family ligand trimer-containing antigen binding molecule as described herein before, wherein the moiety capable of specific binding to a target cell antigen is selected from the group consisting of an antibody fragment, a Fab molecule, a crossover Fab molecule, a single chain Fab molecule, a Fv molecule, a scFv molecule, a single domain antibody, an aVH and a scaffold antigen binding protein. In one aspect, the moiety capable of specific binding to a target cell antigen is an aVH or a scaffold antigen binding protein. In one aspect, the moiety capable of specific binding to a target cell antigen is a scaffold antigen binding protein capable of specific binding to a target cell antigen. In particular, the TNF family ligand trimer-containing antigen binding molecule comprises one or two moieties capable of specific binding to a target cell antigen.
In a particular aspect, provided is a TNF family ligand trimer-containing antigen binding molecule, wherein the moiety capable of specific binding to a target cell antigen is a Fab molecule or a crossover Fab molecule capable of specific binding to a target cell antigen. In particular, the moiety capable of specific binding to a target cell antigen is a Fab capable of specific binding to a target cell antigen.
Furthermore, provided is TNF family ligand trimer-containing antigen binding molecule as described herein, wherein the target cell antigen is selected from the group consisting of
Fibroblast Activation Protein (FAP), Melanoma-associated Chondroitin Sulfate Proteoglycan (MCSP), Epidermal Growth Factor Receptor (EGFR), Carcinoembryonic Antigen (CEA), CD19, CD20 and CD33.
In a further aspect, provided is a TNF family ligand trimer-containing antigen binding molecule according to the invention, wherein a peptide comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C-terminus to the CHI domain of a heavy chain by a second peptide linker and wherein one ectodomain of said TNF ligand family member or a fragment thereof is fused at the its C-terminus to the CL domain on a light chain by a third peptide linker.
In another aspect, provided is a TNF family ligand trimer-containing antigen binding molecule according to the invention, wherein a peptide comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C-terminus to the CL domain of a heavy chain by a second peptide linker and wherein one ectodomain of said TNF ligand family member or a fragment thereof is fused at the its C-terminus to the CHI domain on a light chain by a third peptide linker. In a further aspect, the invention is concerned with a TNF family ligand trimer-containing antigen binding molecule according to the invention, wherein a peptide comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C-terminus to the CL domain of a light chain by a second peptide linker and wherein one ectodomain of said TNF ligand family member or a fragment thereof is fused at the its C-terminus to the CHI domain of the heavy chain by a third peptide linker.
In a particular aspect, the invention relates to a TNF family ligand trimer-containing antigen binding molecule as defined above, wherein the peptide linker is (G4S)2. In one aspect, the first peptide linker is (G4S)2 (SEQ ID NO: 13), the second peptide linker is GSPGSSSSGS (SEQ ID NO:57) and the third peptide linker is (G4S)2 (SEQ ID NO: 13). In particular, the invention relates to a TNF ligand trimer-containing antigen binding molecule as defined above, wherein the first peptide linker is (G4S)2 (SEQ ID NO: 13), the second peptide linker is (G4S)2 (SEQ ID NO: 13), and the third peptide linker is (G4S)2 (SEQ ID NO: 13).
In another aspect, the TNF family ligand trimer-containing antigen binding molecule as defined herein before comprises an Fc domain composed of a first and a second subunit capable of stable association.
In particular, the TNF family ligand trimer-containing antigen binding molecule of the invention comprises (a) a Fab molecule capable of specific binding to a target cell antigen, wherein the Fab heavy chain is fused at the C-terminus to the N-terminus of a CH2 domain in the Fc domain and (c) an Fc domain composed of a first and a second subunit capable of stable association.
In a further aspect, the Fc domain is an IgG, particularly an IgGl Fc domain or an IgG4 Fc domain. More particularly, the Fc domain is an IgGl Fc domain. In a particular aspect, the Fc domain comprises a modification promoting the association of the first and second subunit of the Fc domain.
Fc domain modifications reducing Fc receptor binding and/or effector function
The Fc domain of the TNF family ligand trimer-containing antigen binding molecules of the invention consists of a pair of polypeptide chains comprising heavy chain domains of an immunoglobulin molecule. For example, the Fc domain of an immunoglobulin G (IgG) molecule is a dimer, each subunit of which comprises the CH2 and CH3 IgG heavy chain constant domains. The two subunits of the Fc domain are capable of stable association with each other.
The Fc domain confers favorable pharmacokinetic properties to the antigen binding molecules of the invention, including a long serum half-life which contributes to good accumulation in the target tissue and a favorable tissue-blood distribution ratio. At the same time it may, however, lead to undesirable targeting of the bispecific antibodies of the invention to cells expressing Fc receptors rather than to the preferred antigen-bearing cells. Accordingly, in particular aspects, the Fc domain of the TNF family ligand trimer-containing antigen binding molecule of the invention exhibits reduced binding affinity to an Fc receptor and/or reduced effector function, as compared to a native IgGl Fc domain. In one aspect, the Fc does not substantially bind to an Fc receptor and/or does not induce effector function. In a particular aspect the Fc receptor is an Fey receptor. In one aspect, the Fc receptor is a human Fc receptor. In a specific aspect, the Fc receptor is an activating human Fey receptor, more specifically human FcyRIIIa, FcyRI or FcyRIIa, most specifically human FcyRIIIa. In one aspect, the Fc domain does not induce effector function. The reduced effector function can include, but is not limited to, one or more of the following: reduced complement dependent cytotoxicity (CDC), reduced antibody-dependent cell-mediated cytotoxicity (ADCC), reduced antibody-dependent cellular phagocytosis (ADCP), reduced cytokine secretion, reduced immune complex-mediated antigen uptake by antigen-presenting cells, reduced binding to NK cells, reduced binding to macrophages, reduced binding to monocytes, reduced binding to polymorphonuclear cells, reduced direct signaling inducing apoptosis, reduced dendritic cell maturation, or reduced T cell priming.
In certain aspects, one or more amino acid modifications may be introduced into the Fc region of a TNF family ligand trimer-containing antigen binding molecule provided herein, thereby generating an Fc region variant. The Fc region variant may comprise a human Fc region sequence (e.g., a human IgGl, IgG2, IgG3 or IgG4 Fc region) comprising an amino acid modification (e.g. a substitution) at one or more amino acid positions.
In a particular aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising
(a) at least one moiety capable of specific binding to a target cell antigen,
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof, and
(c) an Fc domain composed of a first and a second subunit capable of stable association, wherein the Fc domain comprises one or more amino acid substitution that reduces binding to an Fc receptor, in particular towards Fey receptor.
In one aspect, the Fc domain of the TNF family ligand trimer-containing antigen binding molecule of the invention comprises one or more amino acid mutation that reduces the binding affinity of the Fc domain to an Fc receptor and/or effector function. Typically, the same one or more amino acid mutation is present in each of the two subunits of the Fc domain. In particular, the Fc domain comprises an amino acid substitution at a position of E233, L234, L235, N297, P331 and P329 (EU numbering). In particular, the Fc domain comprises amino acid substitutions at positions 234 and 235 (EU numbering) and/or 329 (EU numbering) of the IgG heavy chains. More particularly, provided is a trimeric TNF family ligand-containing antigen binding molecule according to the invention which comprises an Fc domain with the amino acid substitutions L234A, L235A and P329G ("P329G LALA", EU numbering) in the IgG heavy chains. The amino acid substitutions L234A and L235A refer to the so-called LALA mutation. The "P329G LALA" combination of amino acid substitutions almost completely abolishes Fey receptor binding of a human IgGl Fc domain and is described in International Patent Appl. Publ. No. WO 2012/130831 Al which also describes methods of preparing such mutant Fc domains and methods for determining its properties such as Fc receptor binding or effector functions. "EU numbering" refers to the numbering according to EU index of Kabat et al , Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, MD, 1991.
Fc domains with reduced Fc receptor binding and/or effector function also include those with substitution of one or more of Fc domain residues 238, 265, 269, 270, 297, 327 and 329 (U.S. Patent No. 6,737,056). Such Fc mutants include Fc mutants with substitutions at two or more of amino acid positions 265, 269, 270, 297 and 327, including the so-called "DANA" Fc mutant with substitution of residues 265 and 297 to alanine (US Patent No. 7,332,581). In another aspect, the Fc domain is an IgG4 Fc domain. IgG4 antibodies exhibit reduced binding affinity to Fc receptors and reduced effector functions as compared to IgGl antibodies. In a more specific aspect, the Fc domain is an IgG4 Fc domain comprising an amino acid substitution at position S228 (Kabat numbering), particularly the amino acid substitution S228P. In a more specific aspect, the Fc domain is an IgG4 Fc domain comprising amino acid
substitutions L235E and S228P and P329G (EU numbering). Such IgG4 Fc domain mutants and their Fey receptor binding properties are also described in WO 2012/130831.
Mutant Fc domains can be prepared by amino acid deletion, substitution, insertion or modification using genetic or chemical methods well known in the art. Genetic methods may include site- specific mutagenesis of the encoding DNA sequence, PCR, gene synthesis, and the like. The correct nucleotide changes can be verified for example by sequencing.
Binding to Fc receptors can be easily determined e.g. by ELISA, or by Surface Plasmon Resonance (SPR) using standard instrumentation such as a BIAcore instrument (GE Healthcare), and Fc receptors such as may be obtained by recombinant expression. A suitable such binding assay is described herein. Alternatively, binding affinity of Fc domains or cell activating bispecific antigen binding molecules comprising an Fc domain for Fc receptors may be evaluated using cell lines known to express particular Fc receptors, such as human NK cells expressing Fcyllla receptor.
Effector function of an Fc domain, or bispecific antibodies of the invention comprising an Fc domain, can be measured by methods known in the art. A suitable assay for measuring ADCC is described herein. Other examples of in vitro assays to assess ADCC activity of a molecule of interest are described in U.S. Patent No. 5,500,362; Hellstrom et al. Proc Natl Acad Sci USA 83, 7059-7063 (1986) and Hellstrom et al., Proc Natl Acad Sci USA 82, 1499-1502 (1985); U.S. Patent No. 5,821,337; Bruggemann et al., J Exp Med 166, 1351-1361 (1987). Alternatively, non- radioactive assays methods may be employed (see, for example, ACTI™ non-radioactive cytotoxicity assay for flow cytometry (CellTechnology, Inc. Mountain View, CA); and CytoTox 96® non-radioactive cytotoxicity assay (Promega, Madison, WI)). Useful effector cells for such assays include peripheral blood mononuclear cells (PBMC) and Natural Killer (NK) cells.
Alternatively, or additionally, ADCC activity of the molecule of interest may be assessed in vivo, e.g. in a animal model such as that disclosed in Clynes et al., Proc Natl Acad Sci USA 95, 652- 656 (1998).
In some embodiments, binding of the Fc domain to a complement component, specifically to Clq, is reduced. Accordingly, in some embodiments wherein the Fc domain is engineered to have reduced effector function, said reduced effector function includes reduced CDC. Clq binding assays may be carried out to determine whether the bispecific antibodies of the invention is able to bind Clq and hence has CDC activity. See e.g., Clq and C3c binding ELISA in WO 2006/029879 and WO 2005/100402. To assess complement activation, a CDC assay may be performed (see, for example, Gazzano-Santoro et al., J Immunol Methods 202, 163 (1996); Cragg et al., Blood 101, 1045-1052 (2003); and Cragg and Glennie, Blood 103, 2738-2743 (2004)).
In a particular aspect, the Fc domain comprises a modification promoting the association of the first and second subunit of the Fc domain.
Fc domain modifications promoting heterodimerization
In one aspect, the TNF family ligand trimer-containing antigen binding molecules of the invention comprise (a) at least one moiety capable of specific binding to a target cell antigen, (b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof, and (c) an Fc domain composed of a first and a second subunit capable of stable association, wherein the Fc domain comprises one or more amino acid substitution that reduces binding to an Fc receptor, in particular towards Fey receptor. Thus, they comprise different moieties, fused to one or the other of the two subunits of the Fc domain that are typically comprised in two non-identical polypetide chains ("heavy chains"). Recombinant co-expression of these polypeptides and subsequent dimerization leads to several possible combinations of the two polypeptides. To improve the yield and purity of the TNF family ligand trimer-containing antigen binding molecules in recombinant production, it will thus be advantageous to introduce in the Fc domain of the TNF family ligand trimer- containing antigen binding molecules of the invention a modification promoting the association of the desired polypeptides.
Accordingly, the Fc domain of the TNF family ligand trimer-containing antigen binding molecules of the invention comprises a modification promoting the association of the first and the second subunit of the Fc domain. The site of most extensive protein-protein interaction between the two subunits of a human IgG Fc domain is in the CH3 domain of the Fc domain. Thus, said modification is particularly in the CH3 domain of the Fc domain.
In a specific aspect, said modification is a so-called "knob-into-hole" modification, comprising a "knob" modification in one of the two subunits of the Fc domain and a "hole" modification in the other one of the two subunits of the Fc domain. Thus, in a particular aspect, the invention relates to a TNF family ligand trimer-containing antigen binding molecule as described herein before which comprises an IgG molecule, wherein the Fc part of the first heavy chain comprises a first dimerization module and the Fc part of the second heavy chain comprises a second dimerization module allowing a heterodimerization of the two heavy chains of the IgG molecule and the first dimerization module comprises knobs and the second dimerization module comprises holes according to the knob into hole technology. The knob-into-hole technology is described e.g. in US 5,731,168; US 7,695,936; Ridgway et al., Prot Eng 9, 617-621 (1996) and Carter, J Immunol Meth 248, 7-15 (2001). Generally, the method involves introducing a protuberance ("knob") at the interface of a first polypeptide and a corresponding cavity ("hole") in the interface of a second polypeptide, such that the
protuberance can be positioned in the cavity so as to promote heterodimer formation and hinder homodimer formation. Protuberances are constructed by replacing small amino acid side chains from the interface of the first polypeptide with larger side chains (e.g. tyrosine or tryptophan). Compensatory cavities of identical or similar size to the protuberances are created in the interface of the second polypeptide by replacing large amino acid side chains with smaller ones (e.g. alanine or threonine). Accordingly, in a particular aspect, in the CH3 domain of the first subunit of the Fc domain of the TNF family ligand trimer-containing antigen binding molecules of the invention an amino acid residue is replaced with an amino acid residue having a larger side chain volume, thereby generating a protuberance within the CH3 domain of the first subunit which is positionable in a cavity within the CH3 domain of the second subunit, and in the CH3 domain of the second subunit of the Fc domain an amino acid residue is replaced with an amino acid residue having a smaller side chain volume, thereby generating a cavity within the CH3 domain of the second subunit within which the protuberance within the CH3 domain of the first subunit is positionable.
The protuberance and cavity can be made by altering the nucleic acid encoding the polypeptides, e.g. by site-specific mutagenesis, or by peptide synthesis. In a specific aspect, in the CH3 domain of the first subunit of the Fc domain the threonine residue at position 366 is replaced with a tryptophan residue (T366W), and in the CH3 domain of the second subunit of the Fc domain the tyrosine residue at position 407 is replaced with a valine residue (Y407V). More particularly, in the second subunit of the Fc domain additionally the threonine residue at position 366 is replaced with a serine residue (T366S) and the leucine residue at position 368 is replaced with an alanine residue (L368A). More particularly, in the first subunit of the Fc domain additionally the serine residue at position 354 is replaced with a cysteine residue (S354C), and in the second subunit of the Fc domain additionally the tyrosine residue at position 349 is replaced by a cysteine residue (Y349C). The introduction of these two cysteine residues results in the formation of a disulfide bridge between the two subunits of the Fc domain. The disulfide bridge further stabilizes the dimer (Carter, J Immunol Methods 248, 7-15 (2001)).
In an alternative aspect, a modification promoting association of the first and the second subunit of the Fc domain comprises a modification mediating electrostatic steering effects, e.g. as described in PCT publication WO 2009/089004. Generally, this method involves replacement of one or more amino acid residues at the interface of the two Fc domain subunits by charged amino acid residues so that homodimer formation becomes electrostatically unfavorable but heterodimerization electrostatically favorable.
Modifications in the CH1/CL domains To further improve correct pairing, the TNF family ligand trimer-containing antigen binding molecules can contain different charged amino acid substitutions (so-called "charged residues"). These modifications are introduced in the crossed or non-crossed CHI and CL domains. In a particular aspect, the invention relates to a TNF family ligand trimer-containing antigen binding molecule, wherein in one of CL domains the amino acid at position 123 (EU numbering) has been replaced by arginine (R) and the amino acid at position 124 (EU numbering) has been substituted by lysine (K) and wherein in one of the CHI domains the the amino acids at position 147 (EU numbering) and at position 213 (EU numbering) have been substituted by glutamic acid (E).
More particularly, the invention relates to a TNF family ligand trimer-containing antigen binding molecule, wherein in the CL domain adjacent to the TNF ligand family member the amino acid at position 123 (EU numbering) has been replaced by arginine (R) and the amino acid at position 124 (EU numbering) has been substituted by lysine (K), and wherein in the CHI domain adjacent to the TNF ligand family member the amino acids at position 147 (EU numbering) and at position 213 (EU numbering) have been substituted by glutamic acid (E). Particular TNF family ligand trimer-containing antigen binding molecules
In another aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule, wherein the antigen binding molecule comprises
a first heavy chain and a first light chain, both comprising a Fab molecule capable of specific binding to a target cell antigen,
a first peptide comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker fused at its C-terminus by a second peptide linker to a second heavy or light chain,
and a second peptide comprising one ectodomain of said TNF ligand family member fused at its C-terminus by a third peptide linker to a second light or heavy chain, respectively. In a further aspect, provided is a TNF family ligand trimer-containing antigen binding molecule, wherein the first peptide comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C-terminus by a second peptide linker to a CHI domain that is part of a heavy chain, and the second peptide comprising one ectodomain of said TNF ligand family member or a fragment thereof is fused at its C-terminus by a third peptide linker to a CL domain that is part of a light chain.
In yet another aspect, provided is a TNF family ligand trimer-containing antigen binding molecule, wherein the first peptide comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C-terminus by a second peptide linker to a CL domain that is part of a heavy chain,
and the second peptide comprising one ectodomain of said TNF ligand family member or a fragment thereof that is fused at its C-terminus by a third peptide linker to a CHI domain that is part of a light chain.
In a further aspect, provided is a TNF family ligand trimer-containing antigen binding molecule, wherein the first peptide comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C-terminus by a second peptide linker to a VH domain that is part of a heavy chain,
and the second peptide comprising one ectodomain of said TNF ligand family member or a fragment thereof is fused at its C-terminus by a third peptide linker to a VL domain that is part of a light chain.
In one aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule of claims 21 to 23, wherein in the CL domain adjacent to the TNF ligand family member the amino acid at position 123 (EU numbering) has been replaced by arginine (R) and the amino acid at position 124 (EU numbering) has been substituted by lysine (K), and wherein in the CHI domain adjacent to the TNF ligand family member the amino acids at position 147 (EU numbering) and at position 213 (EU numbering) have been substituted by glutamic acid (E). These modifications lead to so-called charged residues with advantageaous properties that avoid undesired effects such as for example mispairing.
Furthermore, provided is TNF family ligand trimer-containing antigen binding molecule as described herein, wherein the target cell antigen is selected from the group consisting of
Fibroblast Activation Protein (FAP), Melanoma-associated Chondroitin Sulfate Proteoglycan (MCSP), Epidermal Growth Factor Receptor (EGFR), Carcinoembryonic Antigen (CEA), CD19, CD20 and CD33. TNF family ligand trimer-containing antigen binding molecules, wherein the target cell antigen is FAP
In a particular aspect, provided is a TNF family ligand trimer-containing antigen binding molecule, wherein the target cell antigen is Fibroblast Activation Protein (FAP). In one aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule, wherein the moiety capable of specific binding to FAP comprises a VH domain comprising (i) CDR-H1 comprising the amino acid sequence of SEQ ID NO:7 or SEQ ID NO: 100, (ii) CDR-H2 comprising the amino acid sequence of SEQ ID NO:8 or SEQ ID NO: 101, and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO:9 or SEQ ID NO: 102, and a VL domain comprising (iv) CDR-Ll comprising the amino acid sequence of SEQ ID NO: 10 or SEQ ID NO: 103, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO: 11 or SEQ ID NO: 104, and (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO: 12 or SEQ ID NO: 105.
In a particular aspect, provided is a TNF family ligand trimer-containing antigen binding molecule of the invention, wherein the moiety capable of specific binding to a target cell antigen is a Fab molecule capable of specific binding to FAP and comprises a VH domain comprising (i) CDR-H1 comprising the amino acid sequence of SEQ ID NO:7, (ii) CDR-H2 comprising the amino acid sequence of SEQ ID NO: 8 and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO:9, and a VL domain comprising (iv) CDR-Ll comprising the amino acid sequence of SEQ ID NO: 10, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO: 1 land (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO: 12.
In another aspect, provided is a TNF family ligand trimer-containing antigen binding molecule of the invention, wherein the moiety capable of specific binding to a target cell antigen is a Fab molecule capable of specific binding to FAP and comprises a VH domain comprising (i) CDR-H1 comprising the amino acid sequence of SEQ ID NO: 100, (ii) CDR-H2 comprising the amino acid sequence of SEQ ID NO: 101 and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO: 102, and a VL domain comprising (iv) CDR-Ll comprising the amino acid sequence of SEQ ID NO: 103, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO: 104and (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO: 105. In a further aspect, the moiety capable of specific binding to FAP comprises a heavy chain variable region comprising an amino acid sequence that is at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO: 16 and a light chain variable region comprising an amino acid sequence that is at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO: 17. In another aspect, the moiety capable of specific binding to FAP comprises a heavy chain variable region comprising an amino acid sequence that is at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO: 106 and a light chain variable region comprising an amino acid sequence that is at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO: 107.
In one aspect, the moiety capable of specific binding to FAP comprises a variable heavy chain comprising an amino acid sequence of SEQ ID NO: 16 and a variable light chain comprising an amino acid sequence of SEQ ID NO: 17 or a variable heavy chain comprising an amino acid sequence of SEQ ID NO: 106 and a variable light chain comprising an amino acid sequence of SEQ ID NO: 107.
In a particular aspect, the moiety capable of specific binding to FAP comprises a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 16 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 17. In another particular aspect, the moiety capable of specific binding to FAP comprises a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 106 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 107. In a specific aspect, the moiety capable of specific binding to FAP comprises a VH domain consisting of amino acid sequence of SEQ ID NO: 106 and a VL domain consisting of the amino acid sequence of SEQ ID NO: 107.
In a further aspect, the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
(a) at least one moiety capable of specific binding to a target cell antigen comprising a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 16 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 17, and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that the first polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO:5, SEQ ID NO:97, SEQ ID NO:98 and SEQ ID NO:99 and in that the second polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO: l, SEQ ID NO:96, SEQ ID NO:3 and SEQ ID NO:4. In a particular aspect, the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
(a) at least one moiety capable of specific binding to a target cell antigen comprising a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 16 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 17, and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond, wherein the antigen binding molecule is characterized in that the first polypeptide comprises the the amino acid sequence of SEQ ID NO:97 and the second polypeptide comprises the amino acid sequence of SEQ ID NO:96.
In another aspect, the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
(a) at least one moiety capable of specific binding to a target cell antigen comprising a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 106 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 107, and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that the first polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO:5, SEQ ID NO:97, SEQ ID NO:98 and SEQ ID NO:99 and in that the second polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO: l, SEQ ID NO:96, SEQ ID NO:3 and SEQ ID NO:4. In a particular aspect, the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
(a) at least one moiety capable of specific binding to a target cell antigen comprising a heavy chain variable region comprising the amino acid sequence of SEQ ID NO: 106 and a light chain variable region comprising the amino acid sequence of SEQ ID NO: 107, and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that the first polypeptide comprises the the amino acid sequence of SEQ ID NO:97 and the second polypeptide comprises the amino acid sequence of SEQ ID NO:96.
In another aspect, provided is a TNF family ligand trimer-containing antigen binding molecule, wherein the antigen binding molecule comprises
a first heavy chain and a first light chain, both comprising a Fab molecule capable of specific binding to a target cell antigen,
a second heavy chain comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker that is fused at its C-terminus by a second peptide linker to a CHI domain, and a second light chain comprising one ectodomain of said TNF ligand family member or a fragment thereof is fused at its C-terminus by a third peptide linker to a CL domain, and wherein the antigen binding molecule comprises
(i) a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO: 16 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO: 17 or
a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO:106 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO: 107,
(ii) a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 14, SEQ ID NO: 108, SEQ ID NO: 111 and SEQ ID NO: 113, and
(iii) a second light chain comprising the amino acid sequence of SEQ ID NO: 15, SEQ ID
NO: 109, SEQ ID NO: 110, SEQ ID NO: 112 and SEQ ID NO: 114.
In a further particular aspect, provided is a TNF family ligand trimer-containing antigen binding molecule, and wherein the antigen binding molecule comprises
a first heavy chain and a first light chain, both comprising a Fab molecule capable of specific binding to a target cell antigen,
a second heavy chain comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C-terminus by a second peptide linker to a CL domain, and a second light chain comprising one ectodomain of said TNF ligand family member or a fragment thereof that is fused at its C-terminus by a third peptide linker to a CHI domain , and wherein the molecule comprises
(i) a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO: 16 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO: 17 or
a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO: 106 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO: 107,
(ii) a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 115, SEQ ID NO: 117, SEQ ID NO: 119 and SEQ ID NO: 173, and
(iii) a second light chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 116, SEQ ID NO: 118, SEQ ID NO: 120 and SEQ ID NO: 174.
More particularly, provided is a TNF family ligand trimer-containing antigen binding molecule comprising
(a) a first heavy chain and a first light chain, both comprising a Fab molecule capable of specific binding to a target cell antigen, wherein the first heavy chain comprises the VH domain comprising the amino acid sequence of SEQ ID NO: 106 and the first light chain comprises the VL domain comprising the amino acid sequence of SEQ ID NO: 107, and
(b) a second heavy chain comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C-terminus by a second peptide linker to a CL domain, and a second light chain comprising one ectodomain of said TNF ligand family member or a fragment thereof that is fused at its C-terminus by a third peptide linker to a CHI domain , wherein the second heavy chain comprises the amino acid sequence of SEQ ID NO: 119 or SEQ ID NO: 173, and the second light chain comprises the amino acid sequence of SEQ ID NO: 120 or SEQ ID NO: 174. In particular, the second heavy chain comprises the amino acid sequence of SEQ ID NO:l 19 and the second light chain comprises the amino acid sequence of SEQ ID NO: 120.
Furthermore, the invention provides a TNF family ligand trimer-containing antigen binding molecule, comprising
(a) at least one moiety capable of specific binding to a target cell antigen, and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond, wherein the antigen binding molecule is characterized in that the first polypeptide contains a CH3 domain and the second polypeptide contains a CH3 domain, respectively, and wherein the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the C-terminus of the CH3 domain by a peptide linker and wherein the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to C-terminus of the CH3 domain of said polypeptide. In a particular aspect, such a TNF family ligand trimer-containing antigen binding molecule comprises two moieties capable of specific binding to a target cell antigen.
More particular, such TNF family ligand trimer-containing antigen binding molecule comprises
(i) a first heavy chain comprising the amino acid sequence of SEQ ID NO: 121, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 122, and two light chains comprising the amino acid sequence of SEQ ID NO: 19, or
(ii) a first heavy chain comprising the amino acid sequence of SEQ ID NO: 123, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 124, and two light chains comprising the amino acid sequence of SEQ ID NO: 125, or
(iii) a first heavy chain comprising the amino acid sequence of SEQ ID NO: 126, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 127, and two light chains comprising the amino acid sequence of SEQ ID NO: 125.
In a further aspect, the invention relates to a TNF family ligand trimer-containing antigen binding molecule, selected from the group consisting of:
a) a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ
ID NO: 18, a first light chain comprising the amino acid sequence of SEQ ID NO: 19, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 14 and a second light chain comprising the amino acid sequence of SEQ ID NO: 15;
b) a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO: 18, a first light chain comprising the amino acid sequence of SEQ ID NO: 19, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 115 and a second light chain comprising the amino acid sequence of SEQ ID NO: 116;
c) a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO: 135, a first light chain comprising the amino acid sequence of SEQ ID NO: 136, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 108 and a second light chain comprising the amino acid sequence of SEQ ID NO: 109;
d) a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO: 18, a first light chain comprising the amino acid sequence of SEQ ID NO: 19, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 139 and a second light chain comprising the amino acid sequence of SEQ ID NO: 140;
e) a molecule comprising two light chains comprising the amino acid sequence of SEQ ID NO: 19, a first heavy chain comprising the amino acid sequence of SEQ ID NO: 121 and a second heavy chain comprising the amino acid sequence of SEQ ID NO: 122;
f) a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO: 18, a first light chain comprising the amino acid sequence of SEQ ID NO: 19, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 108 and a second light chain comprising the amino acid sequence of SEQ ID NO: 110;
g) a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO: 145, a first light chain comprising the amino acid sequence of SEQ ID NO: 19, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 115 and a second light chain comprising the amino acid sequence of SEQ ID NO: 116;
h) a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO: 18, a first light chain comprising the amino acid sequence of SEQ ID NO: 19, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 148 and a second light chain comprising the amino acid sequence of SEQ ID NO: 149;
i) a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO: 18, a first light chain comprising the amino acid sequence of SEQ ID NO: 19, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 111 and a second light chain comprising the amino acid sequence of SEQ ID NO: 112; and
j) a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ
ID NO: 18, a first light chain comprising the amino acid sequence of SEQ ID NO: 19, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 113 and a second light chain comprising the amino acid sequence of SEQ ID NO: 114.
In another aspect, the invention relates to a TNF family ligand trimer-containing antigen binding molecule, selected from the group consisting of:
a) a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO: 164, a first light chain comprising the amino acid sequence of SEQ ID NO: 125, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 115 and a second light chain comprising the amino acid sequence of SEQ ID NO: 116;
b) a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO: 164, a first light chain comprising the amino acid sequence of SEQ ID NO: 125, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 117 and a second light chain comprising the amino acid sequence of SEQ ID NO: 118;
c) a molecule comprising two light chains comprising the amino acid sequence of SEQ ID NO: 125, a first heavy chain comprising the amino acid sequence of SEQ ID NO: 123 and a second heavy chain comprising the amino acid sequence of SEQ ID NO: 124;
d) a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ
ID NO: 164, a first light chain comprising the amino acid sequence of SEQ ID NO: 125, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 119 and a second light chain comprising the amino acid sequence of SEQ ID NO: 120;
e) a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO: 164, a first light chain comprising the amino acid sequence of SEQ ID NO: 125, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 173 and a second light chain comprising the amino acid sequence of SEQ ID NO: 174; and
f) a molecule comprising two light chains comprising the amino acid sequence of SEQ ID NO: 125, a first heavy chain comprising the amino acid sequence of SEQ ID NO: 126 and a second heavy chain comprising the amino acid sequence of SEQ ID NO: 127.
In particular, the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO: 164, a first light chain comprising the amino acid sequence of SEQ ID NO: 125, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 119 and a second light chain comprising the amino acid sequence of SEQ ID NO: 120.
In another aspect, provided is a TNF family ligand trimer-containing antigen binding molecule, wherein the TNF ligand family member is OX40L and wherein the target cell antigen is Fibroblast Activation Protein (FAP) and the moiety capable of specific binding to FAP comprises a VH domain comprising (i) CDR-Hl comprising the amino acid sequence of SEQ ID NO:7 or SEQ ID NO: 100, (ii) CDR-H2 comprising the amino acid sequence of SEQ ID NO: 8 or SEQ ID NO:101, and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO:9 or SEQ ID NO: 102, and a VL domain comprising (iv) CDR-L1 comprising the amino acid sequence of SEQ ID NO: 10 or SEQ ID NO: 103, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO: 11 or SEQ ID NO: 104, and (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO: 12 or SEQ ID NO: 105. In a particular aspect, the TNF family ligand trimer-containing antigen binding molecule of comprises
(i) a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO: 16 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO: 17 or
a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO: 106 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO: 107,
(ii) a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO:355, and
(iii) a second light chain comprising the amino acid sequence of SEQ ID NO:356.
TNF family ligand trimer-containing antigen binding molecules, wherein the target cell antigen is CD 19
In a particular aspect, provided is a TNF family ligand trimer-containing antigen binding molecule, wherein the target cell antigen is CD 19.
In one aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule, wherein the moiety capable of specific binding to CD 19 comprises a VH domain comprising (i) CDR-Hl comprising the amino acid sequence of SEQ ID NO: 195 or SEQ ID NO:252, (ii) CDR-H2 comprising the amino acid sequence of SEQ ID NO: 196 or SEQ ID NO:253, and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO: 197 or SEQ ID NO:254, and a VL domain comprising (iv) CDR-Ll comprising the amino acid sequence of SEQ ID NO: 198 or SEQ ID NO:249, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO: 199 or SEQ ID NO:250, and (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO:200 or SEQ ID NO:251. In a particular aspect, provided is a TNF family ligand trimer-containing antigen binding molecule of the invention, wherein the moiety capable of specific binding to a target cell antigen is a Fab molecule capable of specific binding to CD 19 and comprises a VH domain comprising (i) CDR-Hl comprising the amino acid sequence of SEQ ID NO: 195, (ii) CDR-H2 comprising the amino acid sequence of SEQ ID NO: 196 and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO: 197, and a VL domain comprising (iv) CDR-Ll comprising the amino acid sequence of SEQ ID NO: 198, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO: 199 and (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO:200.
In a further aspect, provided is a TNF family ligand trimer-containing antigen binding molecule of the invention, wherein the moiety capable of specific binding to a target cell antigen is a Fab molecule capable of specific binding to CD 19 and comprises a VH domain comprising (i) CDR-H1 comprising the amino acid sequence of SEQ ID NO:252, (ii) CDR-H2 comprising the amino acid sequence of SEQ ID NO:253 and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO:254, and a VL domain comprising (iv) CDR-L1 comprising the amino acid sequence of SEQ ID NO:249, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO:250 and (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO:251.
In another aspect, the moiety capable of specific binding to CD 19 comprises a heavy chain variable region comprising an amino acid sequence that is at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:201 and a light chain variable region comprising an amino acid sequence that is at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:202.
In a further aspect, the moiety capable of specific binding to CD 19 comprises a heavy chain variable region comprising an amino acid sequence that is at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:357 and a light chain variable region comprising an amino acid sequence that is at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:358.
In one aspect, the moiety capable of specific binding to CD 19 comprises a variable heavy chain comprising an amino acid sequence of SEQ ID NO:201 and a variable light chain comprising an amino acid sequence of SEQ ID NO:202 or wherein the moiety capable of specific binding to CD 19 comprises a variable heavy chain comprising an amino acid sequence of SEQ ID NO:357 and a variable light chain comprising an amino acid sequence of SEQ ID NO:358.
In a particular aspect, the moiety capable of specific binding to CD 19 comprises a heavy chain variable region comprising the amino acid sequence of SEQ ID NO:201 and a light chain variable region comprising the amino acid sequence of SEQ ID NO:202. In another particular aspect, the moiety capable of specific binding to CD 19 comprises a heavy chain variable region comprising the amino acid sequence of SEQ ID NO:357 and a light chain variable region comprising the amino acid sequence of SEQ ID NO:358.
In another aspect, the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
(a) at least one moiety capable of specific binding to a target cell antigen comprising a heavy chain variable region comprising the amino acid sequence of SEQ ID NO:201 and a light chain variable region comprising the amino acid sequence of SEQ ID NO:202, and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that the first polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO:5, SEQ ID NO:97, SEQ ID NO:98 and SEQ ID NO:99 and in that the second polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO: l, SEQ ID NO:96, SEQ ID NO:3 and SEQ ID NO:4.
In a particular aspect, the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
(a) at least one moiety capable of specific binding to a target cell antigen comprising a heavy chain variable region comprising the amino acid sequence of SEQ ID NO:201 and a light chain variable region comprising the amino acid sequence of SEQ ID NO:202, and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that the first polypeptide comprises the the amino acid sequence of SEQ ID NO:97 and the second polypeptide comprises the amino acid sequence of SEQ ID NO:96.
In another aspect, the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
(a) at least one moiety capable of specific binding to a target cell antigen comprising a heavy chain variable region comprising the amino acid sequence of SEQ ID NO:357 and a light chain variable region comprising the amino acid sequence of SEQ ID NO:358, and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that the first polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO:5, SEQ ID NO:97, SEQ ID NO:98 and SEQ ID NO:99 and in that the second polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO: l, SEQ ID NO:96, SEQ ID NO:3 and SEQ ID NO:4.
In a particular aspect, the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
(a) at least one moiety capable of specific binding to a target cell antigen comprising a heavy chain variable region comprising the amino acid sequence of SEQ ID NO:357 and a light chain variable region comprising the amino acid sequence of SEQ ID NO:358, and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that the first polypeptide comprises the the amino acid sequence of SEQ ID NO:97 and the second polypeptide comprises the amino acid sequence of SEQ ID NO:96.
In another aspect, provided is a TNF family ligand trimer-containing antigen binding molecule, wherein the antigen binding molecule comprises
a first heavy chain and a first light chain, both comprising a Fab molecule capable of specific binding to a target cell antigen,
a second heavy chain comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker that is fused at its C-terminus by a second peptide linker to a CHI domain, and a second light chain comprising one ectodomain of said TNF ligand family member or a fragment thereof is fused at its C-terminus by a third peptide linker to a CL domain, and wherein the antigen binding molecule comprises
(i) a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO:201 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO:202 or
a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO:357 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO:358,
(ii) a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 14, SEQ ID NO: 108, SEQ ID NO: 111 and SEQ ID NO: 113, and
(iii) a second light chain comprising the amino acid sequence of SEQ ID NO: 15, SEQ ID
NO: 109, SEQ ID NO: 110, SEQ ID NO: 112 and SEQ ID NO: 114.
In a further particular aspect, provided is a TNF family ligand trimer-containing antigen binding molecule, and wherein the antigen binding molecule comprises
a first heavy chain and a first light chain, both comprising a Fab molecule capable of specific binding to a target cell antigen,
a second heavy chain comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C-terminus by a second peptide linker to a CL domain, and a second light chain comprising one ectodomain of said TNF ligand family member or a fragment thereof that is fused at its C-terminus by a third peptide linker to a CHI domain, and wherein the molecule comprises
(i) a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO:201 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO:202 or
a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO:357 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO:358,
(ii) a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 115, SEQ ID NO: 117, SEQ ID NO: 119 and SEQ ID NO: 173, and
(iii) a second light chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 116, SEQ ID NO: 118, SEQ ID NO: 120 and SEQ ID NO: 174.
Furthermore, the invention provides a TNF family ligand trimer-containing antigen binding molecule, comprising (a) at least one moiety capable of specific binding to a target cell antigen, and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond, wherein the antigen binding molecule is characterized in that the first polypeptide contains a CH3 domain and the second polypeptide contains a CH3 domain, respectively, and wherein the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the C-terminus of the CH3 domain by a peptide linker and wherein the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to C-terminus of the CH3 domain of said polypeptide. In a particular aspect, such a TNF family ligand trimer-containing antigen binding molecule comprises two moieties capable of specific binding to a target cell antigen.
More particular, such TNF family ligand trimer-containing antigen binding molecule comprises
(i) a first heavy chain comprising the amino acid sequence of SEQ ID NO:209, a second heavy chain comprising the amino acid sequence of SEQ ID NO:210, and two light chains comprising the amino acid sequence of SEQ ID NO:206, or
(ii) a first heavy chain comprising the amino acid sequence of SEQ ID NO:213, a second heavy chain comprising the amino acid sequence of SEQ ID NO:214, and two light chains comprising the amino acid sequence of SEQ ID NO:206, or
(iii) a first heavy chain comprising the amino acid sequence of SEQ ID NO:309, a second heavy chain comprising the amino acid sequence of SEQ ID NO:310, and two light chains comprising the amino acid sequence of SEQ ID NO:279, or
(iv) a first heavy chain comprising the amino acid sequence of SEQ ID NO:313, a second heavy chain comprising the amino acid sequence of SEQ ID NO:314, and two light chains comprising the amino acid sequence of SEQ ID NO:279.
In a further aspect, the invention relates to a TNF family ligand trimer-containing antigen binding molecule, selected from the group consisting of:
a) a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO:205, a first light chain comprising the amino acid sequence of SEQ ID NO:206, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 115 and a second light chain comprising the amino acid sequence of SEQ ID NO: 116;
b) a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO:205, a first light chain comprising the amino acid sequence of SEQ ID NO:206, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 117 and a second light chain comprising the amino acid sequence of SEQ ID NO: 118; c) a molecule comprising two light chains comprising the amino acid sequence of SEQ ID NO:206, a first heavy chain comprising the amino acid sequence of SEQ ID NO:209 and a second heavy chain comprising the amino acid sequence of SEQ ID NO:210;
d) a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO:205, a first light chain comprising the amino acid sequence of SEQ ID NO:206, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 119 and a second light chain comprising the amino acid sequence of SEQ ID NO: 120;
e) a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO:205, a first light chain comprising the amino acid sequence of SEQ ID NO:206, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 173 and a second light chain comprising the amino acid sequence of SEQ ID NO: 174; and
f) a molecule comprising two light chains comprising the amino acid sequence of SEQ ID NO:206, a first heavy chain comprising the amino acid sequence of SEQ ID NO:213 and a second heavy chain comprising the amino acid sequence of SEQ ID NO:214. In particular, the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO:205, a first light chain comprising the amino acid sequence of SEQ ID NO:206, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 119 and a second light chain comprising the amino acid sequence of SEQ ID NO: 120. In another aspect, the invention relates to a TNF family ligand trimer-containing antigen binding molecule, selected from the group consisting of:
a) a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO:357, a first light chain comprising the amino acid sequence of SEQ ID NO:358, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 115 and a second light chain comprising the amino acid sequence of SEQ ID NO: 116;
b) a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO:357, a first light chain comprising the amino acid sequence of SEQ ID NO:358, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 117 and a second light chain comprising the amino acid sequence of SEQ ID NO: 118;
c) a molecule comprising two light chains comprising the amino acid sequence of SEQ ID
NO:358, a first heavy chain comprising the amino acid sequence of SEQ ID NO:209 and a second heavy chain comprising the amino acid sequence of SEQ ID NO:210;
d) a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO:357, a first light chain comprising the amino acid sequence of SEQ ID NO:358, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 119 and a second light chain comprising the amino acid sequence of SEQ ID NO: 120; e) a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO:357, a first light chain comprising the amino acid sequence of SEQ ID NO:358, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 173 and a second light chain comprising the amino acid sequence of SEQ ID NO: 174; and
f) a molecule comprising two light chains comprising the amino acid sequence of SEQ ID
NO:358, a first heavy chain comprising the amino acid sequence of SEQ ID NO:213 and a second heavy chain comprising the amino acid sequence of SEQ ID NO:214.
In particular, the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO:357, a first light chain comprising the amino acid sequence of SEQ ID NO:358, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 119 and a second light chain comprising the amino acid sequence of SEQ ID NO: 120.
TNF family ligand trimer-containing antigen binding molecules, wherein the target cell antigen is CEA In a particular aspect, provided is a TNF family ligand trimer-containing antigen binding molecule, wherein the target cell antigen is CEA.
In one aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule, wherein the moiety capable of specific binding to CD 19 comprises a VH domain comprising (i) CDR-H1 comprising the amino acid sequence of SEQ ID NO:321, (ii) CDR-H2 comprising the amino acid sequence of SEQ ID NO:322, and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO:323, and a VL domain comprising (iv) CDR-L1 comprising the amino acid sequence of SEQ ID NO:324, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO:325, and (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO:326. In a particular aspect, provided is a TNF family ligand trimer-containing antigen binding molecule of the invention, wherein the moiety capable of specific binding to a target cell antigen is a Fab molecule capable of specific binding to CEA and comprises a VH domain comprising (i) CDR-H1 comprising the amino acid sequence of SEQ ID NO:321, (ii) CDR-H2 comprising the amino acid sequence of SEQ ID NO:322 and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO:323, and a VL domain comprising (iv) CDR-L1 comprising the amino acid sequence of SEQ ID NO:324, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO:325 and (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO:326. In a further aspect, the moiety capable of specific binding to CEA comprises a heavy chain variable region comprising an amino acid sequence that is at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:327 and a light chain variable region comprising an amino acid sequence that is at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:328.
In one aspect, the moiety capable of specific binding to CEA comprises a variable heavy chain comprising an amino acid sequence of SEQ ID NO:327 and a variable light chain comprising an amino acid sequence of SEQ ID NO:328.
In a further aspect, the moiety capable of specific binding to CEA comprises a heavy chain variable region comprising an amino acid sequence that is at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:329 and a light chain variable region comprising an amino acid sequence that is at least about 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence of SEQ ID NO:330.
In one aspect, the moiety capable of specific binding to CEA comprises a variable heavy chain comprising an amino acid sequence of SEQ ID NO:329 and a variable light chain comprising an amino acid sequence of SEQ ID NO:330.
In another aspect, the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
(a) at least one moiety capable of specific binding to a target cell antigen comprising a heavy chain variable region comprising the amino acid sequence of SEQ ID NO:329 and a light chain variable region comprising the amino acid sequence of SEQ ID NO:330, and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that the first polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO:5, SEQ ID NO:97, SEQ ID NO:98 and SEQ ID NO:99 and in that the second polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO: l, SEQ ID NO:96, SEQ ID NO:3 and SEQ ID NO:4.
In a particular aspect, the TNF family ligand trimer-containing antigen binding molecule of the invention comprises
(a) at least one moiety capable of specific binding to a target cell antigen comprising a heavy chain variable region comprising the amino acid sequence of SEQ ID NO:329 and a light chain variable region comprising the amino acid sequence of SEQ ID NO:330, and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond,
wherein the antigen binding molecule is characterized in that the first polypeptide comprises the the amino acid sequence of SEQ ID NO:97 and the second polypeptide comprises the amino acid sequence of SEQ ID NO:96.
In another aspect, provided is a TNF family ligand trimer-containing antigen binding molecule, wherein the antigen binding molecule comprises
a first heavy chain and a first light chain, both comprising a Fab molecule capable of specific binding to a target cell antigen,
a second heavy chain comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker that is fused at its C-terminus by a second peptide linker to a CHI domain, and a second light chain comprising one ectodomain of said TNF ligand family member or a fragment thereof is fused at its C-terminus by a third peptide linker to a CL domain, and wherein the antigen binding molecule comprises
(i) a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO:329 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO:330,
(ii) a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 14, SEQ ID NO: 108, SEQ ID NO: 111 and SEQ ID NO: 113, and
(iii) a second light chain comprising the amino acid sequence of SEQ ID NO: 15, SEQ ID
NO: 109, SEQ ID NO: 110, SEQ ID NO: 112 and SEQ ID NO: 114.
In a further particular aspect, provided is a TNF family ligand trimer-containing antigen binding molecule, and wherein the antigen binding molecule comprises
a first heavy chain and a first light chain, both comprising a Fab molecule capable of specific binding to a target cell antigen,
a second heavy chain comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C-terminus by a second peptide linker to a CL domain, and a second light chain comprising one ectodomain of said TNF ligand family member or a fragment thereof that is fused at its C-terminus by a third peptide linker to a CHI domain, and wherein the molecule comprises
i) a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO:329 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO:330,
(ii) a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 115, SEQ ID NO: 117, SEQ ID NO: 119 and SEQ ID NO: 173, and
(iii) a second light chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 116, SEQ ID NO: 118, SEQ ID NO: 120 and SEQ ID NO: 174. Furthermore, the invention provides a TNF family ligand trimer-containing antigen binding molecule, comprising (a) at least one moiety capable of specific binding to a target cell antigen, and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond, wherein the antigen binding molecule is characterized in that the first polypeptide contains a CH3 domain and the second polypeptide contains a CH3 domain, respectively, and wherein the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the C-terminus of the CH3 domain by a peptide linker and wherein the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to C-terminus of the CH3 domain of said polypeptide. In a particular aspect, such a TNF family ligand trimer-containing antigen binding molecule comprises two moieties capable of specific binding to a target cell antigen.
More particular, such TNF family ligand trimer-containing antigen binding molecule comprises
(i) a first heavy chain comprising the amino acid sequence of SEQ ID NO:337, a second heavy chain comprising the amino acid sequence of SEQ ID NO:338, and two light chains comprising the amino acid sequence of SEQ ID NO:334, or
(ii) a first heavy chain comprising the amino acid sequence of SEQ ID NO:341, a second heavy chain comprising the amino acid sequence of SEQ ID NO:342, and two light chains comprising the amino acid sequence of SEQ ID NO:334. In a further aspect, the invention relates to a TNF family ligand trimer-containing antigen binding molecule, selected from the group consisting of:
a) a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO:333, a first light chain comprising the amino acid sequence of SEQ ID NO:334, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 115 and a second light chain comprising the amino acid sequence of SEQ ID NO: 116;
b) a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO:333, a first light chain comprising the amino acid sequence of SEQ ID NO:334, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 117 and a second light chain comprising the amino acid sequence of SEQ ID NO: 118;
c) a molecule comprising two light chains comprising the amino acid sequence of SEQ ID
NO:334, a first heavy chain comprising the amino acid sequence of SEQ ID NO:337 and a second heavy chain comprising the amino acid sequence of SEQ ID NO:338;
d) a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO:333, a first light chain comprising the amino acid sequence of SEQ ID NO:334, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 119 and a second light chain comprising the amino acid sequence of SEQ ID NO: 120; e) a molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO:333, a first light chain comprising the amino acid sequence of SEQ ID NO:334, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 173 and a second light chain comprising the amino acid sequence of SEQ ID NO: 174; and
f) a molecule comprising two light chains comprising the amino acid sequence of SEQ ID
NO:334, a first heavy chain comprising the amino acid sequence of SEQ ID NO:341 and a second heavy chain comprising the amino acid sequence of SEQ ID NO:342.
In particular, the invention provides a TNF family ligand trimer-containing antigen binding molecule comprising a first heavy chain comprising the amino acid sequence of SEQ ID NO:333, a first light chain comprising the amino acid sequence of SEQ ID NO:334, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 119 and a second light chain comprising the amino acid sequence of SEQ ID NO: 120.
Polynucleotides
The invention further provides isolated polynucleotides encoding a TNF family ligand trimer-containing antigen binding molecule as described herein or a fragment thereof.
The isolated polynucleotides encoding TNF ligand trimer-containing antigen binding molecules of the invention may be expressed as a single polynucleotide that encodes the entire antigen binding molecule or as multiple (e.g., two or more) polynucleotides that are co- expressed. Polypeptides encoded by polynucleotides that are co-expressed may associate through, e.g., disulfide bonds or other means to form a functional antigen binding molecule. For example, the light chain portion of an immunoglobulin may be encoded by a separate
polynucleotide from the heavy chain portion of the immunoglobulin. When co-expressed, the heavy chain polypeptides will associate with the light chain polypeptides to form the
immunoglobulin. In some aspects, the isolated polynucleotide encodes the entire TNF family ligand trimer- containing antigen binding molecule according to the invention as described herein. In
parrticular, the isolated polynucleotide encodes a polypeptide comprised in the TNF family ligand trimer-containing antigen binding molecule according to the invention as described herein. In one aspect, the present invention is directed to an isolated polynucleotide encoding a
TNF family ligand trimer-containing antigen binding molecule, wherein the polynucleotide comprises (a) a sequence that encodes a moiety capable of specific binding to a target cell antigen, (b) a sequence that encodes a polypeptide comprising two ectodomains of a TNF ligand family member or two fragments thereof that are connected to each other by a peptide linker and (c) a sequence that encodes a polypeptide comprising one ectodomain of said TNF ligand family member or a fragment thereof.
In another aspect, provided is an isolated polynucleotide encoding a 4- IBB ligand trimer- containing antigen binding molecule, wherein the polynucleotide comprises (a) a sequence that encodes a moiety capable of specific binding to a target cell antigen, (b) a sequence that encodes a polypeptide comprising two ectodomains of 4-1BBL or two fragments thereof that are connected to each other by a peptide linker and (c) a sequence that encodes a polypeptide comprising one ectodomain of 4-1BBL or a fragment thereof. In a further aspect, the invention is directed to an isolated polynucleotide comprising a sequence that encodes a polypeptide comprising two 4-1BBL fragments comprising an amino acid sequence that is at least about 90%, 95%, 98% or 100% identical to an amino acid sequence shown in SEQ ID NO: l, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4 or SEQ ID NO:96, and to a polynucleotide comprising a sequence that encodes a polypeptide comprising one 4-1BBL fragment comprising an amino acid sequence that is is at least about 90%, 95%, 98% or 100% identical to an amino acid sequence shown in SEQ ID NO: l, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4 or SEQ ID NO:96.
Furthermore, provided is an isolated polynucleotide encoding a OX40 ligand trimer- containing antigen binding molecule, wherein the polynucleotide comprises (a) a sequence that encodes a moiety capable of specific binding to a target cell antigen, (b) a sequence that encodes a polypeptide comprising two ectodomains of OX40L or two fragments thereof that are connected to each other by a peptide linker and (c) a sequence that encodes a polypeptide comprising one ectodomain of OX40L or a fragment thereof.
In another aspect, the invention is directed to an isolated polynucleotide comprising a sequence that encodes a polypeptide comprising two 4-1BBL fragments comprising an amino acid sequence that is at least about 90%, 95%, 98% or 100% identical to an amino acid sequence shown in SEQ ID NO:53 or SEQ ID NO:54, and to a polynucleotide comprising a sequence that encodes a polypeptide comprising one 4-1BBL fragment comprising an amino acid sequence that is is at least about 90%, 95%, 98% or 100% identical to an amino acid sequence shown in SEQ ID NO:53 or SEQ ID NO:54.
In further aspects, the invention relates to the polynucleotides comprising a sequence that is at least about 90%, 95%, 98% or 100% identical to the specific cDNA sequences disclosed herein. In a particular aspect, the invention relates to a polynucleotide comprising a sequence that is identical to one of the specific cDNA sequences disclosed herein. In other aspects, the nucleic acid molecule comprises or consists of a nucleotide sequence that encodes an amino acid sequence as set forth in any one of SEQ ID NOs: 5, 6, 97, 98, 99, 183, 184 or 185. In a further aspect, the nucleic acid molecule comprises or consists of a nucleotide sequence that encodes an amino acid sequence as set forth in any one of SEQ ID NOs: 14, 15, 108, 109, 110, 111, 112, 113, 114, 115,116, 117, 118, 119, 120, 173 or 174.
In still other aspects, the nucleic acid molecule comprises or consists of a nucleotide sequence selected from the group consisting of SEQ ID NOs: 66, 67, 68, 69, 129, 130, 131, 132, 133, 134, 137, 138, 141, 142, 143, 144, 146, 147, 150, 151, 152, 153, 162, 163, 165, 166, 167, 168, 169, 170, 171, 172, 175, 176, 177, 178, 203, 204, 207, 208, 211, 212, 215, 216, 273, 274, 277, 278, 281, 282, 285, 286, 289, 290, 293, 294, 297, 298, 301, 302, 305, 307, 308, 311, 312, 315, 316, 331, 332, 335, 336, 339, 340, 343, 344, 347, 348, 353 or 354.
In certain aspects, the polynucleotide or nucleic acid is DNA. In other embodiments, a polynucleotide of the present invention is RNA, for example, in the form of messenger RNA (mRNA). RNA of the present invention may be single stranded or double stranded. Recombinant Methods
TNF family ligand trimer-containing antigen binding molecules of the invention may be obtained, for example, by solid-state peptide synthesis (e.g. Merrifield solid phase synthesis) or recombinant production. For recombinant production one or more polynucleotide encoding the TNF family ligand trimer-containing antigen binding molecule or polypeptide fragments thereof, e.g., as described above, is isolated and inserted into one or more vectors for further cloning and/or expression in a host cell. Such polynucleotide may be readily isolated and sequenced using conventional procedures. In one aspect of the invention, a vector, preferably an expression vector, comprising one or more of the polynucleotides of the invention is provided. Methods which are well known to those skilled in the art can be used to construct expression vectors containing the coding sequence of the TNF family ligand trimer-containing antigen binding molecule (fragment) along with appropriate transcriptional/translational control signals. These methods include in vitro recombinant DNA techniques, synthetic techniques and in vivo recombination/genetic recombination. See, for example, the techniques described in Maniatis et al., MOLECULAR CLONING: A LABORATORY MANUAL, Cold Spring Harbor Laboratory, N.Y. (1989); and Ausubel et al., CURRENT PROTOCOLS IN MOLECULAR BIOLOGY,
Greene Publishing Associates and Wiley Interscience, N.Y. (1989). The expression vector can be part of a plasmid, virus, or may be a nucleic acid fragment. The expression vector includes an expression cassette into which the polynucleotide encoding the TNF family ligand trimer- containing antigen binding molecule or polypeptide fragments thereof (i.e. the coding region) is cloned in operable association with a promoter and/or other transcription or translation control elements. As used herein, a "coding region" is a portion of nucleic acid which consists of codons translated into amino acids. Although a "stop codon" (TAG, TGA, or TAA) is not translated into an amino acid, it may be considered to be part of a coding region, if present, but any flanking sequences, for example promoters, ribosome binding sites, transcriptional terminators, introns, 5' and 3' untranslated regions, and the like, are not part of a coding region. Two or more coding regions can be present in a single polynucleotide construct, e.g. on a single vector, or in separate polynucleotide constructs, e.g. on separate (different) vectors. Furthermore, any vector may contain a single coding region, or may comprise two or more coding regions, e.g. a vector of the present invention may encode one or more polypeptides, which are post- or co-translationally separated into the final proteins via proteolytic cleavage. In addition, a vector, polynucleotide, or nucleic acid of the invention may encode heterologous coding regions, either fused or unfused to a polynucleotide encoding the TNF family ligand trimer-containing antigen binding molecule of the invention or polypeptide fragments thereof, or variants or derivatives thereof. Heterologous coding regions include without limitation specialized elements or motifs, such as a secretory signal peptide or a heterologous functional domain. An operable association is when a coding region for a gene product, e.g. a polypeptide, is associated with one or more regulatory sequences in such a way as to place expression of the gene product under the influence or control of the regulatory sequence(s). Two DNA fragments (such as a polypeptide coding region and a promoter associated therewith) are "operably associated" if induction of promoter function results in the transcription of mRNA encoding the desired gene product and if the nature of the linkage between the two DNA fragments does not interfere with the ability of the expression regulatory sequences to direct the expression of the gene product or interfere with the ability of the DNA template to be transcribed. Thus, a promoter region would be operably associated with a nucleic acid encoding a polypeptide if the promoter was capable of effecting transcription of that nucleic acid. The promoter may be a cell-specific promoter that directs substantial transcription of the DNA only in predetermined cells. Other transcription control elements, besides a promoter, for example enhancers, operators, repressors, and transcription termination signals, can be operably associated with the polynucleotide to direct cell-specific transcription.
Suitable promoters and other transcription control regions are disclosed herein. A variety of transcription control regions are known to those skilled in the art. These include, without limitation, transcription control regions, which function in vertebrate cells, such as, but not limited to, promoter and enhancer segments from cytomegaloviruses (e.g. the immediate early promoter, in conjunction with intron-A), simian virus 40 (e.g. the early promoter), and retroviruses (such as, e.g. Rous sarcoma virus). Other transcription control regions include those derived from vertebrate genes such as actin, heat shock protein, bovine growth hormone and rabbit a-globin, as well as other sequences capable of controlling gene expression in eukaryotic cells. Additional suitable transcription control regions include tissue-specific promoters and enhancers as well as inducible promoters (e.g. promoters inducible tetracyclins). Similarly, a variety of translation control elements are known to those of ordinary skill in the art. These include, but are not limited to ribosome binding sites, translation initiation and termination codons, and elements derived from viral systems (particularly an internal ribosome entry site, or IRES, also referred to as a CITE sequence). The expression cassette may also include other features such as an origin of replication, and/or chromosome integration elements such as retroviral long terminal repeats (LTRs), or adeno- associated viral (AAV) inverted terminal repeats (ITRs).
Polynucleotide and nucleic acid coding regions of the present invention may be associated with additional coding regions which encode secretory or signal peptides, which direct the secretion of a polypeptide encoded by a polynucleotide of the present invention. For example, if secretion of the TNF family ligand trimer-containing antigen binding molecule or polypeptide fragments thereof is desired, DNA encoding a signal sequence may be placed upstream of the nucleic acid encoding a TNF family ligand trimer-containing antigen binding molecule of the invention or polypeptide fragments thereof. According to the signal hypothesis, proteins secreted by mammalian cells have a signal peptide or secretory leader sequence which is cleaved from the mature protein once export of the growing protein chain across the rough endoplasmic reticulum has been initiated. Those of ordinary skill in the art are aware that polypeptides secreted by vertebrate cells generally have a signal peptide fused to the N-terminus of the polypeptide, which is cleaved from the translated polypeptide to produce a secreted or "mature" form of the polypeptide. In certain embodiments, the native signal peptide, e.g. an immunoglobulin heavy chain or light chain signal peptide is used, or a functional derivative of that sequence that retains the ability to direct the secretion of the polypeptide that is operably associated with it.
Alternatively, a heterologous mammalian signal peptide, or a functional derivative thereof, may be used. For example, the wild-type leader sequence may be substituted with the leader sequence of human tissue plasminogen activator (TPA) or mouse β-glucuronidase.
DNA encoding a short protein sequence that could be used to facilitate later purification (e.g. a histidine tag) or assist in labeling the fusion protein may be included within or at the ends of the polynucleotide encoding a TNF family ligand trimer-containing antigen binding molecule of the invention or polypeptide fragments thereof.
In a further aspect of the invention, a host cell comprising one or more polynucleotides of the invention is provided. In certain embodiments a host cell comprising one or more vectors of the invention is provided. The polynucleotides and vectors may incorporate any of the features, singly or in combination, described herein in relation to polynucleotides and vectors, respectively. In one aspect, a host cell comprises (e.g. has been transformed or transfected with) a vector comprising a polynucleotide that encodes (part of) a TNF family ligand trimer- containing antigen binding molecule of the invention of the invention. As used herein, the term "host cell" refers to any kind of cellular system which can be engineered to generate the fusion proteins of the invention or fragments thereof. Host cells suitable for replicating and for supporting expression of antigen binding molecules are well known in the art. Such cells may be transfected or transduced as appropriate with the particular expression vector and large quantities of vector containing cells can be grown for seeding large scale fermenters to obtain sufficient quantities of the antigen binding molecule for clinical applications. Suitable host cells include prokaryotic microorganisms, such as E. coli, or various eukaryotic cells, such as Chinese hamster ovary cells (CHO), insect cells, or the like. For example, polypeptides may be produced in bacteria in particular when glycosylation is not needed. After expression, the polypeptide may be isolated from the bacterial cell paste in a soluble fraction and can be further purified. In addition to prokaryotes, eukaryotic microbes such as filamentous fungi or yeast are suitable cloning or expression hosts for polypeptide-encoding vectors, including fungi and yeast strains whose glycosylation pathways have been "humanized", resulting in the production of a polypeptide with a partially or fully human glycosylation pattern. See Gerngross, Nat Biotech 22, 1409-1414 (2004), and Li et al., Nat Biotech 24, 210-215 (2006).
Suitable host cells for the expression of (glycosylated) polypeptides are also derived from multicellular organisms (invertebrates and vertebrates). Examples of invertebrate cells include plant and insect cells. Numerous baculoviral strains have been identified which may be used in conjunction with insect cells, particularly for transfection of Spodoptera frugiperda cells. Plant cell cultures can also be utilized as hosts. See e.g. US Patent Nos. 5,959,177, 6,040,498, 6,420,548, 7,125,978, and 6,417,429 (describing PLANTIBODIES™ technology for producing antibodies in transgenic plants). Vertebrate cells may also be used as hosts. For example, mammalian cell lines that are adapted to grow in suspension may be useful. Other examples of useful mammalian host cell lines are monkey kidney CV1 line transformed by SV40 (COS-7); human embryonic kidney line (293 or 293T cells as described, e.g., in Graham et al., J Gen Virol 36, 59 (1977)), baby hamster kidney cells (BHK), mouse Sertoli cells (TM4 cells as described, e.g., in Mather, Biol Reprod 23, 243-251 (1980)), monkey kidney cells (CV1), African green monkey kidney cells (VERO-76), human cervical carcinoma cells (HELA), canine kidney cells (MDCK), buffalo rat liver cells (BRL 3A), human lung cells (W138), human liver cells (Hep
G2), mouse mammary tumor cells (MMT 060562), TRI cells (as described, e.g., in Mather et al., Annals N.Y. Acad Sci 383, 44-68 (1982)), MRC 5 cells, and FS4 cells. Other useful mammalian host cell lines include Chinese hamster ovary (CHO) cells, including dhfr- CHO cells (Urlaub et al., Proc Natl Acad Sci USA 77, 4216 (1980)); and myeloma cell lines such as YO, NS0, P3X63 and Sp2/0. For a review of certain mammalian host cell lines suitable for protein production, see, e.g., Yazaki and Wu, Methods in Molecular Biology, Vol. 248 (B.K.C. Lo, ed., Humana Press, Totowa, NJ), pp. 255-268 (2003). Host cells include cultured cells, e.g., mammalian cultured cells, yeast cells, insect cells, bacterial cells and plant cells, to name only a few, but also cells comprised within a transgenic animal, transgenic plant or cultured plant or animal tissue. In one embodiment, the host cell is a eukaryotic cell, preferably a mammalian cell, such as a Chinese Hamster Ovary (CHO) cell, a human embryonic kidney (HEK) cell or a lymphoid cell (e.g., Y0, NSO, Sp20 cell). Standard technologies are known in the art to express foreign genes in these systems. Cells expressing a polypeptide comprising either the heavy or the light chain of an immunoglobulin, may be engineered so as to also express the other of the immunoglobulin chains such that the expressed product is an immunoglobulin that has both a heavy and a light chain. In one aspect, a method of producing a TNF family ligand trimer-containing antigen binding molecule of the invention or polypeptide fragments thereof is provided, wherein the method comprises culturing a host cell comprising polynucleotides encoding the TNF family ligand trimer-containing antigen binding molecule of the invention or polypeptide fragments thereof, as provided herein, under conditions suitable for expression of the TNF family ligand trimer-containing antigen binding molecule of the invention or polypeptide fragments thereof, and recovering the TNF family ligand trimer-containing antigen binding molecule of the invention or polypeptide fragments thereof from the host cell (or host cell culture medium).
In the TNF family ligand trimer-containing antigen binding molecule of the invention, the components (at least one moiety capable of specific binding to a target cell antigen, one polypeptide comprising two ectodomains of a TNF ligand family member or fragments thereof and a polypeptide comprising one ectodomain of said TNF family ligand family member or a fragment thereof) are not genetically fused to each other. The polypeptides are designed such that its components (two ectodomains of a TNF ligand family member or fragments thereof and other components such as CH or CL) are fused to each other directly or through a linker sequence. The composition and length of the linker may be determined in accordance with methods well known in the art and may be tested for efficacy. Examples of linker sequences between different components of the antigen binding molecules of the invention are found in the sequences provided herein. Additional sequences may also be included to incorporate a cleavage site to separate the individual components of the fusion protein if desired, for example an endopeptidase recognition sequence.
In certain embodiments the moieties capable of specific binding to a target cell antigen (e.g. Fab fragments) forming part of the antigen binding molecule comprise at least an immunoglobulin variable region capable of binding to an antigen. Variable regions can form part of and be derived from naturally or non-naturally occurring antibodies and fragments thereof. Methods to produce polyclonal antibodies and monoclonal antibodies are well known in the art (see e.g. Harlow and Lane, "Antibodies, a laboratory manual", Cold Spring Harbor Laboratory, 1988). Non-naturally occurring antibodies can be constructed using solid phase-peptide synthesis, can be produced recombinantly (e.g. as described in U.S. patent No. 4,186,567) or can be obtained, for example, by screening combinatorial libraries comprising variable heavy chains and variable light chains (see e.g. U.S. Patent. No. 5,969,108 to McCafferty). Any animal species of immunoglobulin can be used in the invention. Non-limiting immunoglobulins useful in the present invention can be of murine, primate, or human origin. If the fusion protein is intended for human use, a chimeric form of immunoglobulin may be used wherein the constant regions of the immunoglobulin are from a human. A humanized or fully human form of the immunoglobulin can also be prepared in accordance with methods well known in the art (see e. g. U.S. Patent No. 5,565,332 to Winter). Humanization may be achieved by various methods including, but not limited to (a) grafting the non-human (e.g., donor antibody) CDRs onto human (e.g. recipient antibody) framework and constant regions with or without retention of critical framework residues (e.g. those that are important for retaining good antigen binding affinity or antibody functions), (b) grafting only the non-human specificity-determining regions (SDRs or a-CDRs; the residues critical for the antibody-antigen interaction) onto human framework and constant regions, or (c) transplanting the entire non-human variable domains, but "cloaking" them with a human-like section by replacement of surface residues. Humanized antibodies and methods of making them are reviewed, e.g., in Almagro and Fransson, Front Biosci 13, 1619-1633 (2008), and are further described, e.g., in Riechmann et al., Nature 332, 323-329 (1988); Queen et al., Proc Natl Acad Sci USA 86, 10029-10033 (1989); US Patent Nos. 5,821,337, 7,527,791, 6,982,321, and 7,087,409; Jones et al., Nature 321, 522-525 (1986);
Morrison et al., Proc Natl Acad Sci 81, 6851-6855 (1984); Morrison and Oi, Adv Immunol 44, 65-92 (1988); Verhoeyen et al., Science 239, 1534-1536 (1988); Padlan, Molec Immun 31(3), 169-217 (1994); Kashmiri et al., Methods 36, 25-34 (2005) (describing SDR (a-CDR) grafting); Padlan, Mol Immunol 28, 489-498 (1991) (describing "resurfacing"); Dall'Acqua et al., Methods 36, 43-60 (2005) (describing "FR shuffling"); and Osbourn et al., Methods 36, 61-68 (2005) and Klimka et al., Br J Cancer 83, 252-260 (2000) (describing the "guided selection" approach to FR shuffling). Particular immunoglobulins according to the invention are human immunoglobulins. Human antibodies and human variable regions can be produced using various techniques known in the art. Human antibodies are described generally in van Dijk and van de Winkel, Curr Opin Pharmacol 5, 368-74 (2001) and Lonberg, Curr Opin Immunol 20, 450-459 (2008). Human variable regions can form part of and be derived from human monoclonal antibodies made by the hybridoma method (see e.g. Monoclonal Antibody Production Techniques and Applications, pp. 51-63 (Marcel Dekker, Inc., New York, 1987)). Human antibodies and human variable regions may also be prepared by administering an immunogen to a transgenic animal that has been modified to produce intact human antibodies or intact antibodies with human variable regions in response to antigenic challenge (see e.g. Lonberg, Nat Biotech 23, 1117-1125 (2005). Human antibodies and human variable regions may also be generated by isolating Fv clone variable region sequences selected from human-derived phage display libraries (see e.g., Hoogenboom et al. in Methods in Molecular Biology 178, 1-37 (O'Brien et al., ed., Human Press, Totowa, NJ, 2001); and McCafferty et al., Nature 348, 552-554; Clackson et al., Nature 352, 624-628 (1991)). Phage typically display antibody fragments, either as single-chain Fv (scFv) fragments or as Fab fragments.
In certain aspects, the moieties capable of specific binding to a target cell antigen (e.g. Fab fragments) comprised in the antigen binding molecules of the present invention are engineered to have enhanced binding affinity according to, for example, the methods disclosed in PCT publication WO 2012/020006 (see Examples relating to affinity maturation) or U.S. Pat. Appl. Publ. No. 2004/0132066. The ability of the antigen binding molecules of the invention to bind to a specific antigenic determinant can be measured either through an enzyme-linked
immunosorbent assay (ELISA) or other techniques familiar to one of skill in the art, e.g. surface plasmon resonance technique (Liljeblad, et al., Glyco J 17, 323-329 (2000)), and traditional binding assays (Heeley, Endocr Res 28, 217-229 (2002)). Competition assays may be used to identify an antigen binding molecule that competes with a reference antibody for binding to a particular antigen. In certain embodiments, such a competing antigen binding molecule binds to the same epitope (e.g. a linear or a conformational epitope) that is bound by the reference antigen binding molecule. Detailed exemplary methods for mapping an epitope to which an antigen binding molecule binds are provided in Morris (1996) "Epitope Mapping Protocols", in Methods in Molecular Biology vol. 66 (Humana Press, Totowa, NJ). In an exemplary competition assay, immobilized antigen is incubated in a solution comprising a first labeled antigen binding molecule that binds to the antigen and a second unlabeled antigen binding molecule that is being tested for its ability to compete with the first antigen binding molecule for binding to the antigen. The second antigen binding molecule may be present in a hybridoma supernatant. As a control, immobilized antigen is incubated in a solution comprising the first labeled antigen binding molecule but not the second unlabeled antigen binding molecule. After incubation under conditions permissive for binding of the first antibody to the antigen, excess unbound antibody is removed, and the amount of label associated with immobilized antigen is measured. If the amount of label associated with immobilized antigen is substantially reduced in the test sample relative to the control sample, then that indicates that the second antigen binding molecule is competing with the first antigen binding molecule for binding to the antigen. See Harlow and Lane (1988) Antibodies: A Laboratory Manual ch.14 (Cold Spring Harbor Laboratory, Cold Spring Harbor, NY). TNF ligand trimer-containing antigen binding molecules of the invention prepared as described herein may be purified by art-known techniques such as high performance liquid chromatography, ion exchange chromatography, gel electrophoresis, affinity chromatography, size exclusion chromatography, and the like. The actual conditions used to purify a particular protein will depend, in part, on factors such as net charge, hydrophobicity, hydrophilicity etc., and will be apparent to those having skill in the art. For affinity chromatography purification an antibody, ligand, receptor or antigen can be used to which the TNF ligand trimer-containing antigen binding molecule binds. For example, for affinity chromatography purification of fusion proteins of the invention, a matrix with protein A or protein G may be used. Sequential Protein A or G affinity chromatography and size exclusion chromatography can be used to isolate an antigen binding molecule essentially as described in the Examples. The purity of the TNF ligand trimer-containing antigen binding molecule or fragments thereof can be determined by any of a variety of well-known analytical methods including gel electrophoresis, high pressure liquid chromatography, and the like. For example, the TNF ligand trimer-containing antigen binding molecules expressed as described in the Examples were shown to be intact and properly assembled as demonstrated by reducing and non-reducing SDS-PAGE.
Assays The antigen binding molecules provided herein may be identified, screened for, or characterized for their physical/chemical properties and/or biological activities by various assays known in the art.
1. Affinity assays
The affinity of the TNF family ligand trimer-containing antigen binding molecule provided herein for the corresponding TNF receptor can be determined in accordance with the methods set forth in the Examples by surface plasmon resonance (SPR), using standard instrumentation such as a BIAcore instrument (GE Healthcare), and receptors or target proteins such as may be obtained by recombinant expression. The affinity of the TNF family ligand trimer-containing antigen binding molecule for the target cell antigen can also be determined by surface plasmon resonance (SPR), using standard instrumentation such as a BIAcore instrument (GE Healthcare), and receptors or target proteins such as may be obtained by recombinant expression. A specific illustrative and exemplary embodiment for measuring binding affinity is described in Example 4. According to one aspect, KD is measured by surface plasmon resonance using a BIACORE® T100 machine (GE Healthcare) at 25 °C. 2. Binding assays and other assays
Binding of the TNF family ligand trimer-containing antigen binding molecule provided herein to the corresponding receptor expressing cells may be evaluated using cell lines expressing the particular receptor or target antigen, for example by flow cytometry (FACS). In one aspect, fresh peripheral blood mononuclear cells (PBMCs) expressing the TNF receptor are used in the binding assay. These cells are used directly after isolation (naive PMBCs) or after stimulation (activated PMBCs). In another aspect, activated mouse splenocytes (expressing the TNF receptor molecule) were used to demonstrate the binding of the TNF family ligand trimer- containing antigen binding molecule of the invention to the corresponding TNF receptor expressing cells.
In a further aspect, cancer cell lines expressing the target cell antigen, for example FAP, were used to demonstrate the binding of the antigen binding molecules to the target cell antigen.
In another aspect, competition assays may be used to identify an antigen binding molecule that competes with a specific antibody or antigen binding molecule for binding to the target or TNF receptor, respectively. In certain embodiments, such a competing antigen binding molecule binds to the same epitope (e.g., a linear or a conformational epitope) that is bound by a specific anti-target antibody or a specific anti-TNF receptor antibody. Detailed exemplary methods for mapping an epitope to which an antibody binds are provided in Morris (1996) "Epitope Mapping Protocols," in Methods in Molecular Biology vol. 66 (Humana Press, Totowa, NJ). 3. Activity assays
In one aspect, assays are provided for identifying TNF family ligand trimer-containing antigen binding molecules that bind to a specific target cell antigen and to a specific TNF receptor having biological activity. Biological activity may include, e.g., agonistic signalling through the TNF receptor on cells expressing the target cell antigen. TNF family ligand trimer- containing antigen binding molecules identified by the assays as having such biological activity in vitro are also provided.
In certain aspects, a TNF family ligand trimer-containing antigen binding molecule of the invention is tested for such biological activity. Assays for detecting the biological activity of the molecules of the invention are those described in Example 6. Furthermore, assays for detecting cell lysis (e.g. by measurement of LDH release), induced apoptosis kinetics (e.g. by
measurement of Caspase 3/7 activity) or apoptosis (e.g. using the TUNEL assay) are well known in the art. In addition the biological activity of such complexes can be assessed by evaluating their effects on survival, proliferation and lymphokine secretion of various lymphocyte subsets such as NK cells, NKT-cells or γδ T-cells or assessing their capacity to modulate phenotype and function of antigen presenting cells such as dendritic cells, monocytes/macrophages or B-cells.
Pharmaceutical Compositions, Formulations and Routes of Administation
In a further aspect, the invention provides pharmaceutical compositions comprising any of the TNF family ligand trimer-containing antigen binding molecules provided herein, e.g., for use in any of the below therapeutic methods. In one embodiment, a pharmaceutical composition comprises any of the TNF family ligand trimer-containing antigen binding molecules provided herein and at least one pharmaceutically acceptable excipient. In another embodiment, a pharmaceutical composition comprises any of the TNF family ligand trimer-containing antigen binding molecules provided herein and at least one additional therapeutic agent, e.g., as described below.
Pharmaceutical compositions of the present invention comprise a therapeutically effective amount of one or more TNF family ligand trimer-containing antigen binding molecules dissolved or dispersed in a pharmaceutically acceptable excipient. The phrases "pharmaceutical or pharmacologically acceptable" refers to molecular entities and compositions that are generally non-toxic to recipients at the dosages and concentrations employed, i.e. do not produce an adverse, allergic or other untoward reaction when administered to an animal, such as, for example, a human, as appropriate. The preparation of a pharmaceutical composition that contains at least one TNF family ligand trimer-containing antigen binding molecule and optionally an additional active ingredient will be known to those of skill in the art in light of the present disclosure, as exemplified by Remington's Pharmaceutical Sciences, 18th Ed. Mack Printing Company, 1990, incorporated herein by reference. In particular, the compositions are lyophilized formulations or aqueous solutions. As used herein, "pharmaceutically acceptable excipient" includes any and all solvents, buffers, dispersion media, coatings, surfactants, antioxidants, preservatives (e.g. antibacterial agents, antifungal agents), isotonic agents, salts, stabilizers and combinations thereof, as would be known to one of ordinary skill in the art.
Parenteral compositions include those designed for administration by injection, e.g.
subcutaneous, intradermal, intralesional, intravenous, intraarterial intramuscular, intrathecal or intraperitoneal injection. For injection, the TNF family ligand trimer-containing antigen binding molecules of the invention may be formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hanks' solution, Ringer's solution, or physiological saline buffer. The solution may contain formulatory agents such as suspending, stabilizing and/or dispersing agents. Alternatively, the fusion proteins may be in powder form for constitution with a suitable vehicle, e.g., sterile pyrogen-free water, before use. Sterile injectable solutions are prepared by
incorporating the fusion proteins of the invention in the required amount in the appropriate solvent with various of the other ingredients enumerated below, as required. Sterility may be readily accomplished, e.g., by filtration through sterile filtration membranes. Generally, dispersions are prepared by incorporating the various sterilized active ingredients into a sterile vehicle which contains the basic dispersion medium and/or the other ingredients. In the case of sterile powders for the preparation of sterile injectable solutions, suspensions or emulsion, the preferred methods of preparation are vacuum-drying or freeze-drying techniques which yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile- filtered liquid medium thereof. The liquid medium should be suitably buffered if necessary and the liquid diluent first rendered isotonic prior to injection with sufficient saline or glucose. The composition must be stable under the conditions of manufacture and storage, and preserved against the contaminating action of microorganisms, such as bacteria and fungi. It will be appreciated that endotoxin contamination should be kept minimally at a safe level, for example, less that 0.5 ng/mg protein. Suitable pharmaceutically acceptable excipients include, but are not limited to: buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid and methionine; preservatives (such as octadecyldimethylbenzyl ammonium chloride; hexamethonium chloride; benzalkonium chloride; benzethonium chloride; phenol, butyl or benzyl alcohol; alkyl parabens such as methyl or propyl paraben; catechol; resorcinol; cyclohexanol; 3-pentanol; and m-cresol); low molecular weight (less than about 10 residues) polypeptides; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, histidine, arginine, or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugars such as sucrose, mannitol, trehalose or sorbitol; salt-forming counter-ions such as sodium; metal complexes (e.g. Zn-protein complexes); and/or non-ionic surfactants such as polyethylene glycol (PEG). Aqueous injection suspensions may contain compounds which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, dextran, or the like. Optionally, the suspension may also contain suitable stabilizers or agents which increase the solubility of the compounds to allow for the preparation of highly concentrated solutions. Additionally, suspensions of the active compounds may be prepared as appropriate oily injection suspensions. Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty acid esters, such as ethyl cleats or triglycerides, or liposomes. Active ingredients may be entrapped in microcapsules prepared, for example, by coacervation techniques or by interfacial polymerization, for example, hydroxymethylcellulose or gelatin-microcapsules and poly-(methylmethacylate) microcapsules, respectively, in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, nano- particles and nanocapsules) or in macroemulsions. Such techniques are disclosed in Remington's Pharmaceutical Sciences (18th Ed. Mack Printing Company, 1990). Sustained-release preparations may be prepared. Suitable examples of sustained-release preparations include semipermeable matrices of solid hydrophobic polymers containing the polypeptide, which matrices are in the form of shaped articles, e.g. films, or microcapsules. In particular
embodiments, prolonged absorption of an injectable composition can be brought about by the use in the compositions of agents delaying absorption, such as, for example, aluminum monostearate, gelatin or combinations thereof. Exemplary pharmaceutically acceptable excipients herein further include insterstitial drug dispersion agents such as soluble neutral- active hyaluronidase glycoproteins (sHASEGP), for example, human soluble PH-20 hyaluronidase glycoproteins, such as rHuPH20 (HYLENEX®, Baxter International, Inc.). Certain exemplary sHASEGPs and methods of use, including rHuPH20, are described in US Patent Publication Nos. 2005/0260186 and 2006/0104968. In one aspect, a sHASEGP is combined with one or more additional glycosaminoglycanases such as chondroitinases.
Exemplary lyophilized antibody formulations are described in US Patent No. 6,267,958. Aqueous antibody formulations include those described in US Patent No. 6,171,586 and
WO2006/044908, the latter formulations including a histidine-acetate buffer.
In addition to the compositions described previously, the fusion proteins may also be formulated as a depot preparation. Such long acting formulations may be administered by implantation (for example subcutaneously or intramuscularly) or by intramuscular injection. Thus, for example, the fusion proteins may be formulated with suitable polymeric or
hydrophobic materials (for example as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, for example, as a sparingly soluble salt.
Pharmaceutical compositions comprising the fusion proteins of the invention may be manufactured by means of conventional mixing, dissolving, emulsifying, encapsulating, entrapping or lyophilizing processes. Pharmaceutical compositions may be formulated in conventional manner using one or more physiologically acceptable carriers, diluents, excipients or auxiliaries which facilitate processing of the proteins into preparations that can be used pharmaceutically. Proper formulation is dependent upon the route of administration chosen.
The TNF family ligand trimer-containing antigen binding molecules may be formulated into a composition in a free acid or base, neutral or salt form. Pharmaceutically acceptable salts are salts that substantially retain the biological activity of the free acid or base. These include the acid addition salts, e.g. those formed with the free amino groups of a proteinaceous composition, or which are formed with inorganic acids such as for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric or mandelic acid. Salts formed with the free carboxyl groups can also be derived from inorganic bases such as for example, sodium, potassium, ammonium, calcium or ferric hydroxides; or such organic bases as isopropylamine, trimethylamine, histidine or procaine. Pharmaceutical salts tend to be more soluble in aqueous and other pro tic solvents than are the corresponding free base forms.
The composition herein may also contain more than one active ingredients as necessary for the particular indication being treated, preferably those with complementary activities that do not adversely affect each other. Such active ingredients are suitably present in combination in amounts that are effective for the purpose intended.
The formulations to be used for in vivo administration are generally sterile. Sterility may be readily accomplished, e.g., by filtration through sterile filtration membranes. Therapeutic methods and compositions
Any of the TNF family ligand trimer-containing antigen binding molecules provided herein may be used in therapeutic methods.
For use in therapeutic methods, TNF family ligand trimer-containing antigen binding molecules of the invention can be formulated, dosed, and administered in a fashion consistent with good medical practice. Factors for consideration in this context include the particular disorder being treated, the particular mammal being treated, the clinical condition of the individual patient, the cause of the disorder, the site of delivery of the agent, the method of administration, the scheduling of administration, and other factors known to medical
practitioners. In one aspect, TNF family ligand trimer-containing antigen binding molecules of the invention for use as a medicament are provided. In further aspects, TNF family ligand trimer- containing antigen binding molecules of the invention for use in treating a disease, in particular for use in the treatment of cancer, are provided. In certain aspects, TNF family ligand trimer- containing antigen binding molecules of the invention for use in a method of treatment are provided. In one aspect, the invention provides a TNF family ligand trimer-containing antigen binding molecule as described herein for use in the treatment of a disease in an individual in need thereof. In certain aspects, the invention provides a TNF family ligand trimer-containing antigen binding molecule for use in a method of treating an individual having a disease comprising administering to the individual a therapeutically effective amount of the fusion protein. In certain aspects, the disease to be treated is cancer. Examples of cancers include solid tumors, bladder cancer, renal cell carcinoma, brain cancer, head and neck cancer, pancreatic cancer, lung cancer, breast cancer, ovarian cancer, uterine cancer, cervical cancer, endometrial cancer, esophageal cancer, colon cancer, colorectal cancer, rectal cancer, gastric cancer, prostate cancer, blood cancer, skin cancer, squamous cell carcinoma, bone cancer, and kidney cancer, melanoma, B-cell lymphoma, B-cell leukemia, non-Hodgkin lymphoma and acute lymphoblastic leukemia. Thus, a TNF family ligand trimer-containing antigen binding molecule as described herein for use in the treatment of cancer is provided. The subject, patient, or "individual" in need of treatment is typically a mammal, more specifically a human. In another aspect, provided is a TNF family ligand trimer-containing antigen binding molecule as described herein for use in the treatment of infectious diseases, in particular for the treatment of viral infections. In a further aspect, provided is a TNF family ligand trimer- containing antigen binding molecule as described herein for use in the treatment of autoimmune diseases such as for example Lupus disease.
In one aspect, provided is a TNF family ligand trimer-containing antigen binding molecule according to the invention for use in treating head and neck squamous cell carcinoma (HNSCC), breast cancer, colorectal cancer (CRC), pancreatic cancer (PAC), gastric cancer, non- small-cell lung carcinoma (NSCLC) and Mesothelioma, wherein the target cell antigen is FAP. In a further aspect, the invention relates to the use of a TNF family ligand trimer- containing antigen binding molecule in the manufacture or preparation of a medicament for the treatment of a disease in an individual in need thereof. In one aspect, the medicament is for use in a method of treating a disease comprising administering to an individual having the disease a therapeutically effective amount of the medicament. In certain embodiments the disease to be treated is a proliferative disorder, particularly cancer. Thus, in one aspect, the invention relates to the use of a TNF family ligand trimer-containing antigen binding molecule of the invention in the manufacture or preparation of a medicament for the treatment of cancer. Examples of cancers include solid tumors, bladder cancer, renal cell carcinoma, brain cancer, head and neck cancer, pancreatic cancer, lung cancer, breast cancer, ovarian cancer, uterine cancer, cervical cancer, endometrial cancer, esophageal cancer, colon cancer, colorectal cancer, rectal cancer, gastric cancer, prostate cancer, blood cancer, skin cancer, squamous cell carcinoma, bone cancer, and kidney cancer, melanoma, B-cell lymphoma, B-cell leukemia, non-Hodgkin lymphoma and acute lymphoblastic leukemia.. Other cell proliferation disorders that can be treated using a TNF family ligand trimer-containing antigen binding molecule of the present invention include, but are not limited to neoplasms located in the: abdomen, bone, breast, digestive system, liver, pancreas, peritoneum, endocrine glands (adrenal, parathyroid, pituitary, testicles, ovary, thymus, thyroid), eye, head and neck, nervous system (central and peripheral), lymphatic system, pelvic, skin, soft tissue, spleen, thoracic region, and urogenital system. Also included are pre-cancerous conditions or lesions and cancer metastases. In certain embodiments the cancer is chosen from the group consisting of renal cell cancer, skin cancer, lung cancer, colorectal cancer, breast cancer, brain cancer, head and neck cancer. A skilled artisan may recognize that in some cases the TNF family ligand trimer-containing antigen binding molecule may not provide a cure but may only provide partial benefit. In some aspects, a physiological change having some benefit is also considered therapeutically beneficial. Thus, in some aspects, an amount of TNF family ligand trimer-containing antigen binding molecule that provides a physiological change is considered an "effective amount" or a "therapeutically effective amount". In a further aspect, the invention relates to the use of a TNF family ligand trimer- containing antigen binding molecule as described herein in the manufacture or preparation of a medicament for the treatment of infectious diseases, in particular for the treatment of viral infections or for the treatment of autoimmune diseases, for example Lupus disease. In a further aspect, the invention provides a method for treating a disease in an individual, comprising administering to said individual a therapeutically effective amount of a TNF family ligand trimer-containing antigen binding molecule of the invention. In one aspect a composition is administered to said individual, comprising a fusion protein of the invention in a
pharmaceutically acceptable form. In certain aspects, the disease to be treated is a proliferative disorder. In a particular aspect, the disease is cancer. In another aspect, the disease is an infectious disease or an autoimmune disease. In certain aspects, the method further comprises administering to the individual a therapeutically effective amount of at least one additional therapeutic agent, e.g. an anti-cancer agent if the disease to be treated is cancer. An "individual" according to any of the above embodiments may be a mammal, preferably a human. For the prevention or treatment of disease, the appropriate dosage of a TNF family ligand trimer-containing antigen binding molecule of the invention (when used alone or in combination with one or more other additional therapeutic agents) will depend on the type of disease to be treated, the route of administration, the body weight of the patient, the type of fusion protein, the severity and course of the disease, whether the fusion protein is administered for preventive or therapeutic purposes, previous or concurrent therapeutic interventions, the patient's clinical history and response to the fusion protein, and the discretion of the attending physician. The practitioner responsible for administration will, in any event, determine the concentration of active ingredient(s) in a composition and appropriate dose(s) for the individual subject. Various dosing schedules including but not limited to single or multiple administrations over various time-points, bolus administration, and pulse infusion are contemplated herein.
The TNF family ligand trimer-containing antigen binding molecule is suitably
administered to the patient at one time or over a series of treatments. Depending on the type and severity of the disease, about 1 μg/kg to 15 mg/kg (e.g. 0.1 mg/kg - 10 mg/kg) of TNF family ligand trimer-containing antigen binding molecule can be an initial candidate dosage for administration to the patient, whether, for example, by one or more separate administrations, or by continuous infusion. One typical daily dosage might range from about 1 μg/kg to 100 mg/kg or more, depending on the factors mentioned above. For repeated administrations over several days or longer, depending on the condition, the treatment would generally be sustained until a desired suppression of disease symptoms occurs. One exemplary dosage of the fusion protein would be in the range from about 0.005 mg/kg to about 10 mg/kg. In other examples, a dose may also comprise from about 1 μg/kg body weight, about 5 μg/kg body weight, about 10 μg/kg body weight, about 50 μg/kg body weight, about 100 μg/kg body weight, about 200 μg/kg body weight, about 350 μg/kg body weight, about 500 μg/kg body weight, about 1 mg/kg body weight, about 5 mg/kg body weight, about 10 mg/kg body weight, about 50 mg/kg body weight, about 100 mg/kg body weight, about 200 mg/kg body weight, about 350 mg/kg body weight, about 500 mg/kg body weight, to about 1000 mg/kg body weight or more per administration, and any range derivable therein. In examples of a derivable range from the numbers listed herein, a range of about 5 mg/kg body weight to about 100 mg/kg body weight, about 5 μg/kg body weight to about 500 mg/kg body weight etc., can be administered, based on the numbers described above. Thus, one or more doses of about 0.5 mg/kg, 2.0 mg/kg, 5.0 mg/kg or 10 mg/kg (or any combination thereof) may be administered to the patient. Such doses may be administered intermittently, e.g. every week or every three weeks (e.g. such that the patient receives from about two to about twenty, or e.g. about six doses of the fusion protein). An initial higher loading dose, followed by one or more lower doses may be administered. However, other dosage regimens may be useful. The progress of this therapy is easily monitored by conventional techniques and assays.
The TNF family ligand trimer-containing antigen binding molecules of the invention will generally be used in an amount effective to achieve the intended purpose. For use to treat or prevent a disease condition, the TNF family ligand trimer-containing antigen binding molecules of the invention, or pharmaceutical compositions thereof, are administered or applied in a therapeutically effective amount. Determination of a therapeutically effective amount is well within the capabilities of those skilled in the art, especially in light of the detailed disclosure provided herein.
For systemic administration, a therapeutically effective dose can be estimated initially from in vitro assays, such as cell culture assays. A dose can then be formulated in animal models to achieve a circulating concentration range that includes the IC50 as determined in cell culture. Such information can be used to more accurately determine useful doses in humans.
Initial dosages can also be estimated from in vivo data, e.g., animal models, using techniques that are well known in the art. One having ordinary skill in the art could readily optimize administration to humans based on animal data. Dosage amount and interval may be adjusted individually to provide plasma levels of the
TNF family ligand trimer-containing antigen binding molecules which are sufficient to maintain therapeutic effect. Usual patient dosages for administration by injection range from about 0.1 to 50 mg/kg/day, typically from about 0.5 to 1 mg/kg/day. Therapeutically effective plasma levels may be achieved by administering multiple doses each day. Levels in plasma may be measured, for example, by HPLC. In cases of local administration or selective uptake, the effective local concentration of the TNF family ligand trimer-containing antigen binding molecule may not be related to plasma concentration. One skilled in the art will be able to optimize therapeutically effective local dosages without undue experimentation. A therapeutically effective dose of the TNF family ligand trimer-containing antigen binding molecules described herein will generally provide therapeutic benefit without causing substantial toxicity. Toxicity and therapeutic efficacy of a fusion protein can be determined by standard pharmaceutical procedures in cell culture or experimental animals. Cell culture assays and animal studies can be used to determine the LD50 (the dose lethal to 50% of a population) and the ED50 (the dose therapeutically effective in 50% of a population). The dose ratio between toxic and therapeutic effects is the therapeutic index, which can be expressed as the ratio
LD50/ED50. TNF family ligand trimer-containing antigen binding molecules that exhibit large therapeutic indices are preferred. In one embodiment, the TNF family ligand trimer-containing antigen binding molecule according to the present invention exhibits a high therapeutic index. The data obtained from cell culture assays and animal studies can be used in formulating a range of dosages suitable for use in humans. The dosage lies preferably within a range of circulating concentrations that include the ED50 with little or no toxicity. The dosage may vary within this range depending upon a variety of factors, e.g., the dosage form employed, the route of administration utilized, the condition of the subject, and the like. The exact formulation, route of administration and dosage can be chosen by the individual physician in view of the patient's condition (see, e.g., Fingl et al., 1975, in: The Pharmacological Basis of Therapeutics, Ch. 1, p. 1, incorporated herein by reference in its entirety).
The attending physician for patients treated with fusion proteins of the invention would know how and when to terminate, interrupt, or adjust administration due to toxicity, organ dysfunction, and the like. Conversely, the attending physician would also know to adjust treatment to higher levels if the clinical response were not adequate (precluding toxicity). The magnitude of an administered dose in the management of the disorder of interest will vary with the severity of the condition to be treated, with the route of administration, and the like. The severity of the condition may, for example, be evaluated, in part, by standard prognostic evaluation methods. Further, the dose and perhaps dose frequency will also vary according to the age, body weight, and response of the individual patient.
Other agents and treatments
The TNF family ligand trimer-containing antigen binding molecules of the invention may be administered in combination with one or more other agents in therapy. For instance, a fusion protein of the invention may be co-administered with at least one additional therapeutic agent. The term "therapeutic agent" encompasses any agent that can be administered for treating a symptom or disease in an individual in need of such treatment. Such additional therapeutic agent may comprise any active ingredients suitable for the particular indication being treated, preferably those with complementary activities that do not adversely affect each other. In certain embodiments, an additional therapeutic agent is another anti-cancer agent.
Such other agents are suitably present in combination in amounts that are effective for the purpose intended. The effective amount of such other agents depends on the amount of fusion protein used, the type of disorder or treatment, and other factors discussed above. The TNF family ligand trimer-containing antigen binding molecules are generally used in the same dosages and with administration routes as described herein, or about from 1 to 99% of the dosages described herein, or in any dosage and by any route that is empirically/clinically determined to be appropriate.
Such combination therapies noted above encompass combined administration (where two or more therapeutic agents are included in the same or separate compositions), and separate administration, in which case, administration of the TNF family ligand trimer-containing antigen binding molecule of the invention can occur prior to, simultaneously, and/or following, administration of the additional therapeutic agent and/or adjuvant.
Articles of Manufacture
In another aspect of the invention, an article of manufacture containing materials useful for the treatment, prevention and/or diagnosis of the disorders described above is provided. The article of manufacture comprises a container and a label or package insert on or associated with the container. Suitable containers include, for example, bottles, vials, syringes, IV solution bags, etc. The containers may be formed from a variety of materials such as glass or plastic. The container holds a composition which is by itself or combined with another composition effective for treating, preventing and/or diagnosing the condition and may have a sterile access port (for example the container may be an intravenous solution bag or a vial having a stopper that is pierceable by a hypodermic injection needle). At least one active agent in the composition is a TNF ligand trimer-containing antigen binding molecule of the invention.
The label or package insert indicates that the composition is used for treating the condition of choice. Moreover, the article of manufacture may comprise (a) a first container with a composition contained therein, wherein the composition comprises a TNF ligand trimer- containing antigen binding molecule of the invention; and (b) a second container with a composition contained therein, wherein the composition comprises a further cytotoxic or otherwise therapeutic agent. The article of manufacture in this embodiment of the invention may further comprise a package insert indicating that the compositions can be used to treat a particular condition.
Alternatively, or additionally, the article of manufacture may further comprise a second (or third) container comprising a pharmaceutically-acceptable buffer, such as bacteriostatic water for injection (BWFI), phosphate-buffered saline, Ringer's solution and dextrose solution. It may further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, and syringes.
Table C (Sequences):
SEQ Name Sequence
ID NO:
1 Human (hu) 4-1BBL (71- REGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGP 254) LSWYSDPGLAGVSLTGGLSYKEDTKELVVAKAGVY
YVFFQLELRRVVAGEGSGSVSLALHLQPLRSAAGAA ALALTVDLPPASSEARNSAFGFQGRLLHLSAGQRLG VHLHTEARARHAWQLTQGATVLGLFRVTPEIPAGLP SPRSE
2 hu 4-lBBL (85-254) LDLRQGMFAQLVAQNVLLIDGPLSWYSDPGLAGVSL
TGGLSYKEDTKELVVAKAGVYYVFFQLELRRVVAG
EGSGSVSLALHLQPLRSAAGAAALALTVDLPPASSEA
RNSAFGFQGRLLHLSAGQRLGVHLHTEARARHAWQ
LTQGATVLGLFRVTPEIPAGLPSPRSE
3 hu 4-lBBL (80-254) DPAGLLDLRQGMFAQLVAQNVLLIDGPLSWYSDPGL
AGVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELRR
VVAGEGSGSVSLALHLQPLRSAAGAAALALTVDLPP
ASSEARNSAFGFQGRLLHLSAGQRLGVHLHTEARAR
HAWQLTQGATVLGLFRVTPEIPAGLPSPRSE
4 hu 4-lBBL (52-254) PWAVSGARASPGSAASPRLREGPELSPDDPAGLLDLR
QGMFAQLVAQNVLLIDGPLSWYSDPGLAGVSLTGGL
SYKEDTKELVVAKAGVYYVFFQLELRRVVAGEGSG
SVSLALHLQPLRSAAGAAALALTVDLPPASSEARNSA
FGFQGRLLHLSAGQRLGVHLHTEARARHAWQLTQG
ATVLGLFRVTPEIPAGLPSPRSE
5 dimeric hu 4-1BBL (71-254) REGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGP connected by (G4S)2 linker LSWYSDPGLAGVSLTGGLSYKEDTKELVVAKAGVY
YVFFQLELRRVVAGEGSGSVSLALHLQPLRSAAGAA
ALALTVDLPPASSEARNSAFGFQGRLLHLSAGQRLG
VHLHTEARARHAWQLTQGATVLGLFRVTPEIPAGLP
SPRSEGGGGSGGGGSREGPELSPDDPAGLLDLRQGM
FAQLVAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYK
EDTKELVVAKAGVYYVFFQLELRRVVAGEGSGSVSL
ALHLQPLRSAAGAAALALTVDLPPASSEARNSAFGF
QGRLLHLSAGQRLGVHLHTEARARHAWQLTQGATV
LGLFRVTPEIPAGLPSPRSE
6 monomeric hu 4-1BBL (71- REGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGP 254) plus (G4S)2 linker LSWYSDPGLAGVSLTGGLSYKEDTKELVVAKAGVY
YVFFQLELRRVVAGEGSGSVSLALHLQPLRSAAGAA ALALTVDLPPASSEARNSAFGFQGRLLHLSAGQRLG SEQ Name Sequence
ID NO:
VHLHTEARARHAWQLTQGATVLGLFRVTPEIPAGLP SPRSEGGGGSGGGGS
7 FAP(28H1) CDR-H1 SHAMS
8 FAP(28H1) CDR-H2 AIWASGEQYYADSVKG
9 FAP(28H1) CDR-H3 GWLGNFDY
10 FAP(28H1) CDR-L1 RASQSVSRSYLA
11 FAP(28H1) CDR-L2 GASTRAT
12 FAP(28H1) CDR-L3 QQGQVIPPT
13 (G4S)2 GGGGSGGGGS
14 dimeric hu 4-lBBL (71- REGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGP 254)-CHl Fc knob chain LSWYSDPGLAGVSLTGGLSYKEDTKELVVAKAGVY
YVFFQLELRRVVAGEGSGSVSLALHLQPLRSAAGAA
ALALTVDLPPASSEARNSAFGFQGRLLHLSAGQRLG
VHLHTEARARHAWQLTQGATVLGLFRVTPEIPAGLP
SPRSEGGGGSGGGGSREGPELSPDDPAGLLDLRQGM
FAQLVAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYK
EDTKELVVAKAGVYYVFFQLELRRVVAGEGSGSVSL
ALHLQPLRSAAGAAALALTVDLPPASSEARNSAFGF
QGRLLHLSAGQRLGVHLHTEARARHAWQLTQGATV
LGLFRVTPEIPAGLPSPRSEGGGGSGGGGSASTKGPS
VFPL APS SKSTS GGT A ALGCL VKD YFPEPVT VS WNS G
ALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYI
CNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAA
GGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPE
VKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLT
VLHQDWLNGKEYKCKVSNKALGAPIEKTISKAKGQP
REPQVYTLPPCRDELTKNQVSLWCLVKGFYPSDIAV
EWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKS
RWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK
15 monomeric hu 4-1BBL (71- REGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGP
254)-CL LSWYSDPGLAGVSLTGGLSYKEDTKELVVAKAGVY
YVFFQLELRRVVAGEGSGSVSLALHLQPLRSAAGAA
ALALTVDLPPASSEARNSAFGFQGRLLHLSAGQRLG
VHLHTEARARHAWQLTQGATVLGLFRVTPEIPAGLP
SPRSEGGGGSGGGGSRTVAAPSVFIFPPSDEQLKSGT
ASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVT
EQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQG
LSSPVTKSFNRGEC
16 FAP(28H1) VH EVQLLESGGGLVQPGGSLRLSCAASGFTFSSHA
MSWVRQAPGKGLEWVSArWASGEQYYADSVK GRFTISRDNS KNTLYLQMNS LR AEDT A V Y YC AK GWLGNFD YWGQGTL VTVS S
17 FAP(28H1) VL EIVLTQSPGTLSLSPGERATLSCRASQSVSRSYLA
WYQQKPGQAPRLLIIGASTRATGIPDRFSGSGSG TDFTLTISRLEPEDFAVYYCQQGQVIPPTFGQGT KVEIK
18 anti-FAP(28Hl) Fc hole see Table 2
chain
19 anti-FAP(28Hl) light chain see Table 2
20 Human (hu) FAP UniProt no. Q 12884 SEQ Name Sequence
ID NO:
21 hu FAP ectodomain+poly- RPSRVHNSEENTMRALTLKDILNGTFSYKTFFPNWIS lys-tag+his6-tag GQEYLHQSADNNIVLYNIETGQSYTILSNRTMKSVNA
SNYGLSPDRQFVYLESDYSKLWRYSYTATYYIYDLS
NGEFVRGNELPRPIQYLCWSPVGSKLAYVYQNNIYL
KQRPGDPPFQITFNGRENKIFNGIPDWVYEEEMLATK
YALWWSPNGKFLAYAEFNDTDIPVIAYSYYGDEQYP
RTINIPYPKAGAKNPVVRIFIIDTTYPAYVGPQEVPVP
AMIASSDYYFSWLTWVTDERVCLQWLKRVQNVSVL
SICDFREDWQTWDCPKTQEHIEESRTGWAGGFFVST
PVFSYDAISYYKIFSDKDGYKHIHYIKDTVENAIQITS
GKWEAINIFRVTQDSLFYSSNEFEEYPGRRNIYRISIGS
YPPSKKCVTCHLRKERCQYYTASFSDYAKYYALVCY
GPGIPISTLHDGRTDQEIKILEENKELENALKNIQLPKE
EIKKLEVDEITLWYKMILPPQFDRSKKYPLLIQVYGG
PCSQSVRSVFAVNWISYLASKEGMVIALVDGRGTAF
QGDKLLYAVYRKLGVYEVEDQITAVRKFIEMGFIDE
KRIAIWGWSYGGYVSSLALASGTGLFKCGIAVAPVSS
WEYYASVYTERFMGLPTKDDNLEHYKNSTVMARAE
YFRNVDYLLIHGTADDNVHFQNSAQIAKALVNAQV
DFQAMWYSDQNHGLSGLSTNHLYTHMTHFLKQCFS
LSDGKKKKKKGHHHHHH
22 nucleotide sequence CGCCCTTCAAGAGTTCATAACTCTGAAGAAAATAC hu FAP ectodomain+poly- AATGAGAGCACTCACACTGAAGGATATTTTAAATG lys-tag+his6-tag GAACATTTTCTTATAAAACATTTTTTCCAAACTGGA
TTTCAGGACAAGAATATCTTCATCAATCTGCAGAT
AACAATATAGTACTTTATAATATTGAAACAGGACA
ATCATATACCATTTTGAGTAATAGAACCATGAAAA
GTGTGAATGCTTCAAATTACGGCTTATCACCTGAT
CGGCAATTTGTATATCTAGAAAGTGATTATTCAAA
GCTTTGGAGATACTCTTACACAGCAACATATTACA
TCTATGACCTTAGCAATGGAGAATTTGTAAGAGGA
AATGAGCTTCCTCGTCCAATTCAGTATTTATGCTGG
TCGCCTGTTGGGAGTAAATTAGCATATGTCTATCA
AAACAATATCTATTTGAAACAAAGACCAGGAGAT
CCACCTTTTCAAATAACATTTAATGGAAGAGAAAA
TAAAATATTTAATGGAATCCCAGACTGGGTTTATG
AAGAGGAAATGCTTGCTACAAAATATGCTCTCTGG
ATTTAATGATACGGATATACCAGTTATTGCCTATTC
CTATTATGGCGATGAACAATATCCTAGAACAATAA
ATATTCCATACCCAAAGGCTGGAGCTAAGAATCCC
GTTGTTCGGATATTTATTATCGATACCACTTACCCT
GCGTATGTAGGTCCCCAGGAAGTGCCTGTTCCAGC
AATGATAGCCTCAAGTGATTATTATTTCAGTTGGC
TCACGTGGGTTACTGATGAACGAGTATGTTTGCAG
TGGCTAAAAAGAGTCCAGAATGTTTCGGTCCTGTC
TATATGTGACTTCAGGGAAGACTGGCAGACATGGG
ATTGTCCAAAGACCCAGGAGCATATAGAAGAAAG
CAGAACTGGATGGGCTGGTGGATTCTTTGTTTCAA
CACCAGTTTTCAGCTATGATGCCATTTCGTACTACA
AAATATTTAGTGACAAGGATGGCTACAAACATATT
CACTATATCAAAGACACTGTGGAAAATGCTATTCA SEQ Name Sequence
ID NO:
AATTACAAGTGGCAAGTGGGAGGCCATAAATATA
TTCAGAGTAACACAGGATTCACTGTTTTATTCTAG
CAATGAATTTGAAGAATACCCTGGAAGAAGAAAC
ATCTACAGAATTAGCATTGGAAGCTATCCTCCAAG
CAAGAAGTGTGTTACTTGCCATCTAAGGAAAGAAA
GGTGCCAATATTACACAGCAAGTTTCAGCGACTAC
GCCAAGTACTATGCACTTGTCTGCTACGGCCCAGG
CATCCCCATTTCCACCCTTCATGATGGACGCACTG
ATCAAGAAATTAAAATCCTGGAAGAAAACAAGGA
ATTGGAAAATGCTTTGAAAAATATCCAGCTGCCTA
AAGAGGAAATTAAGAAACTTGAAGTAGATGAAAT
TACTTTATGGTACAAGATGATTCTTCCTCCTCAATT
TGACAGATCAAAGAAGTATCCCTTGCTAATTCAAG
TGTATGGTGGTCCCTGCAGTCAGAGTGTAAGGTCT
GTATTTGCTGTTAATTGGATATCTTATCTTGCAAGT
AAGGAAGGGATGGTCATTGCCTTGGTGGATGGTCG
AGGAACAGCTTTCCAAGGTGACAAACTCCTCTATG
CAGTGTATCGAAAGCTGGGTGTTTATGAAGTTGAA
GACCAGATTACAGCTGTCAGAAAATTCATAGAAAT
GGGTTTCATTGATGAAAAAAGAATAGCCATATGGG
GCTGGTCCTATGGAGGATACGTTTCATCACTGGCC
CTTGCATCTGGAACTGGTCTTTTCAAATGTGGTATA
GCAGTGGCTCCAGTCTCCAGCTGGGAATATTACGC
GTCTGTCTACACAGAGAGATTCATGGGTCTCCCAA
CAAAGGATGATAATCTTGAGCACTATAAGAATTCA
ACTGTGATGGCAAGAGCAGAATATTTCAGAAATGT
AGACTATCTTCTCATCCACGGAACAGCAGATGATA
ATGTGCACTTTCAAAACTCAGCACAGATTGCTAAA
GCTCTGGTTAATGCACAAGTGGATTTCCAGGCAAT
GTGGTACTCTGACCAGAACCACGGCTTATCCGGCC
TGTCCACGAACCACTTATACACCCACATGACCCAC
TTCCTAAAGCAGTGTTTCTCTTTGTCAGACGGCAA
AAAGAAAAAGAAAAAGGGCCACCACCATCACCAT
CAC
23 mouse FAP UniProt no. P97321
24 Murine FAP RPSRVYKPEGNTKRALTLKDILNGTFSYKTYFPNWIS ectodomain+poly-lys- EQEYLHQSEDDNIVFYNIETRESYIILSNSTMKSVNAT tag+his6-tag DYGLSPDRQFVYLESDYSKLWRYSYTATYYIYDLQN
GEFVRGYELPRPIQYLCWSPVGSKLAYVYQNNIYLK
QRPGDPPFQITYTGRENRIFNGIPDWVYEEEMLATKY
ALWWSPDGKFLAYVEFNDSDIPIIAYSYYGDGQYPR
TINIPYPKAGAKNPVVRVFIVDTTYPHHVGPMEVPVP
EMIASSDYYFSWLTWVSSERVCLQWLKRVQNVSVL
SICDFREDWHAWECPKNQEHVEESRTGWAGGFFVST
PAFSQDATSYYKIFSDKDGYKHIHYIKDTVENAIQITS
GKWEAIYIFRVTQDSLFYSSNEFEGYPGRRNIYRISIG
NSPPSKKCVTCHLRKERCQYYTASFSYKAKYYALVC
YGPGLPISTLHDGRTDQEIQVLEENKELENSLRNIQLP
KVEIKKLKDGGLTFWYKMILPPQFDRSKKYPLLIQVY
GGPCSQSVKSVFAVNWITYLASKEGIVIALVDGRGTA
FQGDKFLHAVYRKLGVYEVEDQLTAVRKFIEMGFID
EERIAIWGWSYGGYVSSLALASGTGLFKCGIAVAPVS SEQ Name Sequence
ID NO:
SWEYYASIYSERFMGLPTKDDNLEHYKNSTVMARA EYFRNVDYLLIHGTADDNVHFQNSAQIAKALVNAQV DFQAMWYSDQNHGILSGRSQNHLYTHMTHFLKQCF SLSDGKKKKKKGHHHHHH
25 nucleotide sequence CGTCCCTCAAGAGTTTACAAACCTGAAGGAAACAC Murine FAP AAAGAGAGCTCTTACCTTGAAGGATATTTTAAATG ectodomain+poly-lys- GAACATTCTCATATAAAACATATTTTCCCAACTGG tag+his6-tag ATTTCAGAACAAGAATATCTTCATCAATCTGAGGA
TGATAACATAGTATTTTATAATATTGAAACAAGAG
AATCATATATCATTTTGAGTAATAGCACCATGAAA
AGTGTGAATGCTACAGATTATGGTTTGTCACCTGA
TCGGCAATTTGTGTATCTAGAAAGTGATTATTCAA
AGCTCTGGCGATATTCATACACAGCGACATACTAC
ATCTACGACCTTCAGAATGGGGAATTTGTAAGAGG
ATACGAGCTCCCTCGTCCAATTCAGTATCTATGCT
GGTCGCCTGTTGGGAGTAAATTAGCATATGTATAT
CAAAACAATATTTATTTGAAACAAAGACCAGGAG
ATCCACCTTTTCAAATAACTTATACTGGAAGAGAA
AATAGAATATTTAATGGAATACCAGACTGGGTTTA
TGAAGAGGAAATGCTTGCCACAAAATATGCTCTTT
GAATTTAATGATTCAGATATACCAATTATTGCCTA TTCTTATTATGGTGATGGACAGTATCCTAGAACTA TAAATATTCCATATCCAAAGGCTGGGGCTAAGAAT
CCTCACCACGTGGGCCCAATGGAAGTGCCAGTTCC
AGAAATGATAGCCTCAAGTGACTATTATTTCAGCT
GGCTCACATGGGTGTCCAGTGAACGAGTATGCTTG
CAGTGGCTAAAAAGAGTGCAGAATGTCTCAGTCCT
GTCTATATGTGATTTCAGGGAAGACTGGCATGCAT
GGGAATGTCCAAAGAACCAGGAGCATGTAGAAGA
AAGCAGAACAGGATGGGCTGGTGGATTCTTTGTTT
CGACACCAGCTTTTAGCCAGGATGCCACTTCTTAC
TACAAAATATTTAGCGACAAGGATGGTTACAAACA
TATTCACTACATCAAAGACACTGTGGAAAATGCTA
TTCAAATTACAAGTGGCAAGTGGGAGGCCATATAT
ATATTCCGCGTAACACAGGATTCACTGTTTTATTCT
AGCAATGAATTTGAAGGTTACCCTGGAAGAAGAA
ACATCTACAGAATTAGCATTGGAAACTCTCCTCCG
AGCAAGAAGTGTGTTACTTGCCATCTAAGGAAAGA
AAGGTGCCAATATTACACAGCAAGTTTCAGCTACA
AAGCCAAGTACTATGCACTCGTCTGCTATGGCCCT
GGCCTCCCCATTTCCACCCTCCATGATGGCCGCAC
AGACCAAGAAATACAAGTATTAGAAGAAAACAAA
GAACTGGAAAATTCTCTGAGAAATATCCAGCTGCC
TAAAGTGGAGATTAAGAAGCTCAAAGACGGGGGA
CTGACTTTCTGGTACAAGATGATTCTGCCTCCTCAG
TTTGACAGATCAAAGAAGTACCCTTTGCTAATTCA
AGTGTATGGTGGTCCTTGTAGCCAGAGTGTTAAGT
CTGTGTTTGCTGTTAATTGGATAACTTATCTCGCAA
GTAAGGAGGGGATAGTCATTGCCCTGGTAGATGGT
CGGGGCACTGCTTTCCAAGGTGACAAATTCCTGCA SEQ Name Sequence
ID NO:
TGCCGTGTATCGAAAACTGGGTGTATATGAAGTTG
AGGACCAGCTCACAGCTGTCAGAAAATTCATAGA
AATGGGTTTCATTGATGAAGAAAGAATAGCCATAT
GGGGCTGGTCCTACGGAGGTTATGTTTCATCCCTG
GCCCTTGCATCTGGAACTGGTCTTTTCAAATGTGG
CATAGCAGTGGCTCCAGTCTCCAGCTGGGAATATT
ACGCATCTATCTACTCAGAGAGATTCATGGGCCTC
CCAACAAAGGACGACAATCTCGAACACTATAAAA
ATTCAACTGTGATGGCAAGAGCAGAATATTTCAGA
AATGTAGACTATCTTCTCATCCACGGAACAGCAGA
TGATAATGTGCACTTTCAGAACTCAGCACAGATTG
CTAAAGCTTTGGTTAATGCACAAGTGGATTTCCAG
GCGATGTGGTACTCTGACCAGAACCATGGTATATT
ATCTGGGCGCTCCCAGAATCATTTATATACCCACA
TGACGCACTTCCTCAAGCAATGCTTTTCTTTATCAG
ACGGCAAAAAGAAAAAGAAAAAGGGCCACCACCA
TCACCATCAC
26 Cynomolgus FAP RPPRVHNSEENTMRALTLKDILNGTFSYKTFFPNWIS ectodomain+poly-lys- GQEYLHQSADNNIVLYNIETGQSYTILSNRTMKSVNA tag+his6-tag SNYGLSPDRQFVYLESDYSKLWRYSYTATYYIYDLS
NGEFVRGNELPRPIQYLCWSPVGSKLAYVYQNNIYL
KQRPGDPPFQITFNGRENKIFNGIPDWVYEEEMLATK
YALWWSPNGKFLAYAEFNDTDIPVIAYSYYGDEQYP
RTINIPYPKAGAKNPFVRIFIIDTTYPAYVGPQEVPVP
AMIASSDYYFSWLTWVTDERVCLQWLKRVQNVSVL
SICDFREDWQTWDCPKTQEHIEESRTGWAGGFFVST
PVFSYDAISYYKIFSDKDGYKHIHYIKDTVENAIQITS
GKWEAINIFRVTQDSLFYSSNEFEDYPGRRNIYRISIG
SYPPSKKCVTCHLRKERCQYYTASFSDYAKYYALVC
YGPGIPISTLHDGRTDQEIKILEENKELENALKNIQLP
KEEIKKLEVDEITLWYKMILPPQFDRSKKYPLLIQVY
GGPCSQSVRSVFAVNWISYLASKEGMVIALVDGRGT
AFQGDKLLYAVYRKLGVYEVEDQITAVRKFIEMGFI
DEKRIAIWGWSYGGYVSSLALASGTGLFKCGIAVAP
VSSWEYYASVYTERFMGLPTKDDNLEHYKNSTVMA
RAEYFRNVDYLLIHGTADDNVHFQNSAQIAKALVNA
QVDFQAMWYSDQNHGLSGLSTNHLYTHMTHFLKQ
CFSLSDGKKKKKKGHHHHHH
27 nucleotide sequence CGCCCTCCAAGAGTTCATAACTCTGAAGAAAATAC Cynomolgus FAP AATGAGAGCACTCACACTGAAGGATATTTTAAATG ectodomain+poly-lys- GGACATTTTCTTATAAAACATTTTTTCCAAACTGGA tag+his6-tag TTTCAGGACAAGAATATCTTCATCAATCTGCAGAT
AACAATATAGTACTTTATAATATTGAAACAGGACA
ATCATATACCATTTTGAGTAACAGAACCATGAAAA
GTGTGAATGCTTCAAATTATGGCTTATCACCTGAT
CGGCAATTTGTATATCTAGAAAGTGATTATTCAAA
GCTTTGGAGATACTCTTACACAGCAACATATTACA
TCTATGACCTTAGCAATGGAGAATTTGTAAGAGGA
AATGAGCTTCCTCGTCCAATTCAGTATTTATGCTGG
TCGCCTGTTGGGAGTAAATTAGCATATGTCTATCA
AAACAATATCTATTTGAAACAAAGACCAGGAGAT
CCACCTTTTCAAATAACATTTAATGGAAGAGAAAA SEQ Name Sequence
ID NO:
TAAAATATTTAATGGAATCCCAGACTGGGTTTATG AAGAGGAAATGCTTGCTACAAAATATGCTCTCTGG
ATTTAATGATACAGATATACCAGTTATTGCCTATTC
CTATTATGGCGATGAACAATATCCCAGAACAATAA
ATATTCCATACCCAAAGGCCGGAGCTAAGAATCCT
TTTGTTCGGATATTTATTATCGATACCACTTACCCT
GCGTATGTAGGTCCCCAGGAAGTGCCTGTTCCAGC
AATGATAGCCTCAAGTGATTATTATTTCAGTTGGC
TCACGTGGGTTACTGATGAACGAGTATGTTTGCAG
TGGCTAAAAAGAGTCCAGAATGTTTCGGTCTTGTC
TATATGTGATTTCAGGGAAGACTGGCAGACATGGG
ATTGTCCAAAGACCCAGGAGCATATAGAAGAAAG
CAGAACTGGATGGGCTGGTGGATTCTTTGTTTCAA
CACCAGTTTTCAGCTATGATGCCATTTCATACTACA
AAATATTTAGTGACAAGGATGGCTACAAACATATT
CACTATATCAAAGACACTGTGGAAAATGCTATTCA
AATTACAAGTGGCAAGTGGGAGGCCATAAATATA
TTCAGAGTAACACAGGATTCACTGTTTTATTCTAG
CAATGAATTTGAAGATTACCCTGGAAGAAGAAAC
ATCTACAGAATTAGCATTGGAAGCTATCCTCCAAG
CAAGAAGTGTGTTACTTGCCATCTAAGGAAAGAAA
GGTGCCAATATTACACAGCAAGTTTCAGCGACTAC
GCCAAGTACTATGCACTTGTCTGCTATGGCCCAGG
CATCCCCATTTCCACCCTTCATGACGGACGCACTG
ATCAAGAAATTAAAATCCTGGAAGAAAACAAGGA
ATTGGAAAATGCTTTGAAAAATATCCAGCTGCCTA
AAGAGGAAATTAAGAAACTTGAAGTAGATGAAAT
TACTTTATGGTACAAGATGATTCTTCCTCCTCAATT
TGACAGATCAAAGAAGTATCCCTTGCTAATTCAAG
TGTATGGTGGTCCCTGCAGTCAGAGTGTAAGGTCT
GTATTTGCTGTTAATTGGATATCTTATCTTGCAAGT
AAGGAAGGGATGGTCATTGCCTTGGTGGATGGTCG
GGGAACAGCTTTCCAAGGTGACAAACTCCTGTATG
CAGTGTATCGAAAGCTGGGTGTTTATGAAGTTGAA
GACCAGATTACAGCTGTCAGAAAATTCATAGAAAT
GGGTTTCATTGATGAAAAAAGAATAGCCATATGGG
GCTGGTCCTATGGAGGATATGTTTCATCACTGGCC
CTTGCATCTGGAACTGGTCTTTTCAAATGTGGGAT
AGCAGTGGCTCCAGTCTCCAGCTGGGAATATTACG
CGTCTGTCTACACAGAGAGATTCATGGGTCTCCCA
ACAAAGGATGATAATCTTGAGCACTATAAGAATTC
AACTGTGATGGCAAGAGCAGAATATTTCAGAAAT
GTAGACTATCTTCTCATCCACGGAACAGCAGATGA
TAATGTGCACTTTCAAAACTCAGCACAGATTGCTA
AAGCTCTGGTTAATGCACAAGTGGATTTCCAGGCA
ATGTGGTACTCTGACCAGAACCACGGCTTATCCGG
CCTGTCCACGAACCACTTATACACCCACATGACCC
ACTTCCTAAAGCAGTGTTTCTCTTTGTCAGACGGC
AAAAAGAAAAAGAAAAAGGGCCACCACCATCACC
ATCAC
28 human CEA UniProt no. P06731 SEQ Name Sequence
ID NO:
29 human MCSP UniProt no. Q6UVK1
30 human EGFR UniProt no. P00533
31 human CD 19 UniProt no. P15391
32 human CD20 Uniprot no. PI 1836
33 human CD33 UniProt no. P20138
34 human Lymphotoxin UniProt no. P01374
35 human TNF UniProt no. P01375
36 human Lymphotoxin β UniProt no. Q06643
37 human OX40L UniProt no. P23510
38 human CD40L UniProt no. P29965
39 human FasL UniProt no. P48023
40 human CD27L UniProt no. P32970
41 human CD30L UniProt no. P32971
42 human 4-lBBL UniProt no. P41273
43 human TRAIL UniProt no. P50591
44 human RANKL UniProt no. 014788
45 human TWEAK UniProt no. 043508
46 human APRIL UniProt no. 075888
47 human BAFF UniProt no. Q9Y275
48 human LIGHT UniProt no. 043557
49 human TL1A UniProt no. 095150
50 human GITRL UniProt no. Q9UNG2
51 human ectodysplasin A UniProt no. Q92838
52 hu 4-lBBL (50-254) ACPWAVSGARASPGSAASPRLREGPELSPDDPAGLL
DLRQGMFAQLVAQNVLLIDGPLSWYSDPGLAGVSLT
GGLSYKEDTKELVVAKAGVYYVFFQLELRRVVAGE
GSGSVSLALHLQPLRSAAGAAALALTVDLPPASSEAR
NSAFGFQGRLLHLSAGQRLGVHLHTEARARHAWQL
TQGATVLGLFRVTPEIPAGLPSPRSE
53 hu OX40L (51- 183) QVSHRYPRIQSIKVQFTEYKKEKGFILTSQKEDEIMK
VQNNSVIINCDGFYLISLKGYFSQEVNISLHYQKDEEP LFQLKKVRSVNSLMVASLTYKDKVYLNVTTDNTSL DDFHVNGGELILIHQNPGEFCVL
54 hu OX40L (52- 183) VSHRYPRIQSIKVQFTEYKKEKGFILTSQKEDEIMKV
QNNSVIINCDGFYLISLKGYFSQEVNISLHYQKDEEPL FQLKKVRSVNSLMVASLTYKDKVYLNVTTDNTSLD DFHVNGGELILIHQNPGEFCVL
55 Peptide linker (SG4)2 SGGGGSGGGG
56 Peptide linker G4(SG4)2 GGGGS GGGGSGGGG
57 Peptide linker GSPGSSSSGS
58 Peptide linker (G4S)4 GGGGS GGGGS GGGGS GGGGS
59 Peptide linker GSGSGNGS
60 Peptide linker GGSGSGSG
61 Peptide linker GGSGSG
62 Peptide linker GGSG
63 Peptide linker GGSGNGSG
64 Peptide linker GGNGSGSG SEQ Name Sequence
ID NO:
65 Peptide linker GGNGSG
66 nucleotide sequence See Table 2
dimeric hu 4-lBBL (71- 254)-CHl Fc knob chain
67 nucleotide sequence See Table 2
monomeric hu 4-lBBL (71- 254)-CLl
68 nucleotide sequence See Table 2
anti-FAP(28Hl) Fc hole
chain
69 nucleotide sequence See Table 2
anti-FAP (28H1) light chain
70 Murine (mu) 4-lBBL UniProt no. Q3U1Z9-1
71 nucleotide sequence See Table 13
dimeric mu 4-lBBL (104- 309, C137,160,246S)-CH1
Fc knob chain
72 nucleotide sequence See Table 13
monomeric mu 4-lBBL
(104-309, C137,160,246S)- CL
73 nucleotide sequence See Table 13
anti-FAP Fc KK chain
74 nucleotide sequence See Table 13
anti-FAP light chain
75 dimeric mu 4-lBBL (104- See Table 13
309, C137,160,246S) - CL
Fc DD chain
76 monomeric mu 4-lBBL See Table 13
(104-309, C137,160,246S)- CL1
77 anti-FAP Fc KK chain See Table 13
78 anti-FAP light chain See Table 13
79 nucleotide sequence DP47 See Table 18
Fc-hole chain
80 nucleotide sequence DP47 See Table 18
light chain
81 DP47 Fc-hole chain See Table 18
82 DP47 light chain See Table 18
83 Human 4- IBB Fc(kih) See Table 31
84 Cynomolgus 4- IBB Fc(kih) See Table 31
85 Murine 4- IBB Fc(kih) See Table 31
86 nucleotide sequence See Table 32
Fc hole chain
87 nucleotide sequence See Table 32
Human 4- IBB Fc(kih)
88 nucleotide sequence See Table 32 SEQ Name Sequence
ID NO:
Cynomolgus 4- IBB Fc(kih)
89 nucleotide sequence See Table 32
Murine 4- IBB Fc(kih)
90 Fc hole chain See Table 32
91 Human 4- IBB Fc(kih) See Table 32
92 Cynomolgus 4- IBB Fc(kih) See Table 32
93 Murine 4- IBB Fc(kih) See Table 32
94 nucleotide sequence See Table 33
Human 4- IBB His
95 Human 4- IBB His See Table 33
96 Human (hu) 4- 1BBL (71- REGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGP 248) LSWYSDPGLAGVSLTGGLSYKEDTKELVVAKAGVY
YVFFQLELRRVVAGEGSGSVSLALHLQPLRSAAGAA ALALTVDLPPASSEARNSAFGFQGRLLHLSAGQRLG VHLHTEARARHAWQLTQGATVLGLFRVTPEIPAGL
97 dimeric hu 4-1BBL (71-248) REGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGP connected by (G4S)2 linker LSWYSDPGLAGVSLTGGLSYKEDTKELVVAKAGVY
YVFFQLELRRVVAGEGSGSVSLALHLQPLRSAAGAA
ALALTVDLPPASSEARNSAFGFQGRLLHLSAGQRLG
VHLHTEARARHAWQLTQGATVLGLFRVTPEIPAGLG
GGGSGGGGSREGPELSPDDPAGLLDLRQGMFAQLVA
QNVLLIDGPLSWYSDPGLAGVSLTGGLSYKEDTKEL
VVAKAGVYYVFFQLELRRVVAGEGSGSVSLALHLQP
LRSAAGAAALALTVDLPPASSEARNSAFGFQGRLLH
LSAGQRLGVHLHTEARARHAWQLTQGATVLGLFRV
TPEIPAGL
98 dimeric hu 4-1BBL (80-254) DPAGLLDLRQGMFAQLVAQNVLLIDGPLSWYSDPGL connected by (G4S)2 linker AGVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELRR
VVAGEGSGSVSLALHLQPLRSAAGAAALALTVDLPP
ASSEARNSAFGFQGRLLHLSAGQRLGVHLHTEARAR
HAWQLTQGATVLGLFRVTPEIPAGLPSPRSEGGGGSG
GGGSDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWY
SDPGLAGVSLTGGLSYKEDTKELVVAKAGVYYVFFQ
LELRRVVAGEGSGSVSLALHLQPLRSAAGAAALALT
VDLPPASSEARNSAFGFQGRLLHLSAGQRLGVHLHT
EARARHAWQLTQGATVLGLFRVTPEIPAGLPSPRSE
99 dimeric hu 4-1BBL (52-254) PWAVSGARASPGSAASPRLREGPELSPDDPAGLLDLR connected by (G4S)2 linker QGMFAQLVAQNVLLIDGPLSWYSDPGLAGVSLTGGL
SYKEDTKELVVAKAGVYYVFFQLELRRVVAGEGSG
SVSLALHLQPLRSAAGAAALALTVDLPPASSEARNSA
FGFQGRLLHLSAGQRLGVHLHTEARARHAWQLTQG
ATVLGLFRVTPEIPAGLPSPRSEGGGGSGGGGSPWAV
SGARASPGSAASPRLREGPELSPDDPAGLLDLRQGMF
AQLVAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYKE
DTKELVVAKAGVYYVFFQLELRRVVAGEGSGSVSL
ALHLQPLRSAAGAAALALTVDLPPASSEARNSAFGF
QGRLLHLSAGQRLGVHLHTEARARHAWQLTQGATV
LGLFRVTPEIPAGLPSPRSE
100 FAP(4B9) CDR-H1 SYAMS
101 FAP(4B9) CDR-H2 AIIGSGASTYYADSVKG SEQ Name Sequence
ID NO:
102 FAP(4B9) CDR-H3 GWFGGFNY
103 FAP(4B9) CDR-L1 RASQSVTSSYLA
104 FAP(4B9) CDR-L2 VGSRRAT
105 FAP(4B9) CDR-L3 QQGIMLPPT
106 FAP(4B9) VH EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYA
MSWVRQAPGKGLEWVSAIIGSGASTYYADSVK GRFTISRDNS KNTLYLQMNS LR AEDT A V Y YC AK GWFGGFN YWGQGTLVT VS S
107 FAP(4B9) VL EIVLTQSPGTLSLSPGERATLSCRASQSVTSSYLA
WYQQKPGQAPRLLINVGSRRATGIPDRFSGSGSG TDFTLTISRLEPEDFAVYYCQQGIMLPPTFGQGT KVEIK
108 dimeric hu 4-lBBL (71- see Table 4
254)-CHl* Fc knob chain
109 monomeric hu 4-1BBL (71- see Table 4
254)-CL*
110 monomeric hu 4-1BBL (71- see Table 7
254)-(G4S)l-CL*
111 dimeric hu 4-lBBL (52- see Table 10
254)-CHl* Fc knob chain
112 monomeric hu 4-1BBL (52- see Table 10
254)-CL*
113 dimeric hu 4-lBBL (80- see Table 11
254)-CHl* Fc knob chain
114 monomeric hu 4-1BBL (80- see Table 11
254)-CL*
115 dimeric hu 4-lBBL (71- see Table 3
254)-CL* Fc knob chain
116 monomeric hu 4-1BBL (71- see Table 3
254)-CHl*
117 dimeric hu 4-lBBL (71- see Table 22
254)-CL Fc knob chain
118 monomeric hu 4-1BBL (71- see Table 22
254)-CHl
119 dimeric hu 4-lBBL (71- see Table 24
248)-CL* Fc knob chain
120 monomeric hu 4-1BBL (71- see Table 24
248)-CHl*
121 anti-FAP (28H1) Fc hole see Table 6
chain fused to dimeric 4- 1BBL (71-254)
122 anti-FAP (28Hl) Fc knob see Table 6
chain fused to monomeric 4- 1BBL (71-254)
123 anti-FAP (4B9) Fc hole see Table 23
chain fused to dimeric 4- 1BBL (71-254) SEQ Name Sequence ID NO:
124 anti-FAP (4B9) Fc knob see Table 23
chain fused to monomelic 4- 1BBL (71-254)
125 anti-FAP (4B9) light chain see Table 21
126 anti-FAP (4B9) Fc hole see Table 26
chain fused to dimeric 4- 1BBL (71-248)
127 anti-FAP (4B9) Fc knob see Table 26
chain fused to monomelic 4- 1BBL (71-248)
128 Peptide linker GGGGS
129 nucleotide sequence dimeric see Table 3
hu 4-lBBL (71-254) - CL*
Fc knob chain
130 nucleotide sequence see Table 3
monomeric hu 4-lBBL (71- 254) -CHI*
131 nucleotide sequence dimeric see Table 4
hu 4-lBBL (71-254) - CH1* Fc knob chain
132 nucleotide sequence see Table 4
monomeric hu 4-lBBL (71- 254) -CL*
133 nucleotide sequence anti- see Table 4
FAP (28H1) (VHCL) Fc
hole chain
134 nucleotide sequence anti- see Table 4
FAP (28H1) (VLCH1) light
chain
135 anti-FAP (VHCL) (28H1) see Table 4
Fc hole chain
136 anti-FAP (VLCH1) (28H1) see Table 4
light chain
137 nucleotide sequence see Table 5
monomeric hu 4-lBBL (71- 254) - CHI* Fc knob chain
138 nucleotide sequence dimeric see Table 5
hu 4-lBBL (71-254) -CL*
139 monomeric hu 4-lBBL (71- see Table 5
254) - CL* Fc knob chain
140 dimeric hu 4-lBBL (71-254) see Table 5
-CL*
141 nucleotide sequence anti- see Table 6
FAP (28H1) Fc hole chain
fused to dimeric hu 4-lBBL
(71-254)
142 nucleotide sequence anti- see Table 6
Figure imgf000120_0001
SEQ Name Sequence ID NO:
chain
161 monomeric murine 4- 1BBL see Table 15
(104-309, C160S) - CHI
162 nucleotide sequence see Table 21
anti-FAP (4B9) Fc hole
chain
163 nucleotide sequence see Table 21
anti-FAP (4B9) light chain
164 anti-FAP (4B9) Fc hole see Table 21
chain
165 nucleotide sequence dimeric see Table 22
hu 4-lBBL (71-254) - CL
Fc knob chain
166 nucleotide sequence see Table 22
monomeric hu 4-1BBL (71- 254) - CHI
167 nucleotide sequence anti- see Table 23
FAP (4B9) Fc hole chain
fused to dimeric hu 4-1BBL
(71-254)
168 nucleotide sequence anti- see Table 23
FAP (4B9) Fc knob chain
fused to monomeric hu 4- 1BBL (71-254)
169 nucleotide sequence dimeric see Table 24
hu 4-lBBL (71-248) - CL*
Fc knob chain
170 nucleotide sequence see Table 24
monomeric hu
4-1BBL (71-248) - CHI*
171 nucleotide sequence dimeric see Table 25
hu 4-lBBL (71-248) - CL
Fc knob chain
172 nucleotide sequence see Table 25
monomeric hu
4-1BBL (71-248) - CHI
173 Dimeric hu 4- 1BBL (71- see Table 25
248) - CL Fc knob chain
174 Monomeric hu see Table 25
4-1BBL (71-248) - CHI
175 nucleotide sequence anti- see Table 26
FAP (4B9) Fc hole chain
fused to dimeric hu 4-1BBL
(71-248)
176 nucleotide sequence anti- see Table 26
FAP (4B9) Fc knob chain SEQ Name Sequence
ID NO:
fused to monomeric hu 4- 1BBL (71-248)
177 nucleotide sequence DP47 see Table 27
Fc hole chain fused to
dimeric hu 4-1BBL (71-254)
178 nucleotide sequence DP47 see Table 27
Fc knob chain fused to
monomeric hu 4-1BBL (71- 254)
179 DP47 Fc hole chain fused to see Table 27
dimeric hu 4-1BBL (71-254)
180 DP47 Fc knob chain fused see Table 27
to monomeric hu 4-1BBL
(71-254)
181 nucleotide sequence DP47 see Table 29
heavy chain (hu IgGl
PGLALA)
182 DP47 heavy chain (hu IgGl see Table 29
PGLALA)
183 monomeric hu 4-1BBL (71- REGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGP 254) plus (G4S)i linker LSWYSDPGLAGVSLTGGLSYKEDTKELVVAKAGVY
YVFFQLELRRVVAGEGSGSVSLALHLQPLRSAAGAA ALALTVDLPPASSEARNSAFGFQGRLLHLSAGQRLG VHLHTEARARHAWQLTQGATVLGLFRVTPEIPAGLP SPRSEGGGGS
184 monomeric hu 4-1BBL (71- REGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGP 248) plus (G4S)2 linker LSWYSDPGLAGVSLTGGLSYKEDTKELVVAKAGVY
YVFFQLELRRVVAGEGSGSVSLALHLQPLRSAAGAA
ALALTVDLPPASSEARNSAFGFQGRLLHLSAGQRLG
VHLHTEARARHAWQLTQGATVLGLFRVTPEIPAGLG
GGGSGGGGS
185 monomeric hu 4-1BBL (71- REGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGP 248) plus (G4S)i linker LSWYSDPGLAGVSLTGGLSYKEDTKELVVAKAGVY
YVFFQLELRRVVAGEGSGSVSLALHLQPLRSAAGAA
ALALTVDLPPASSEARNSAFGFQGRLLHLSAGQRLG
VHLHTEARARHAWQLTQGATVLGLFRVTPEIPAGLG
GGGS
186 Nucleotide sequence see Table 43
human CD 19 antigen Fc
knob chain avi tag
187 Polypeptide sequence see Table 43
human CD 19 antigen Fc
knob chain avi tag
188 Nucleotide sequence see Table 43
cynomolgus CD 19 antigen
Fc knob chain avi tag
189 Polypeptide sequence see Table 43
cynomolgus CD 19 antigen
Fc knob chain avi tag SEQ Name Sequence
ID NO:
190 humanized CD19 (8B8) NSNGNT
HVR-L1
191 humanized CD19 (8B8) KFNG
HVR-H2
192 humanized CD19 (8B8) TEKFQGRVTM
var. l to 9 HVR-H2
193 humanized CD19 (8B8) LENPNGNT
var.5 HVR-L1
194 humanized CD19 (8B8) LENPSGNT
var.9 HVR-L1
195 CD19 (8B8-018) CDR-H1 DYIMH
196 CD19 (8B8-018) CDR-H2 YINPYNDGSKYTEKFQG
197 CD19 (8B8-018) CDR-H3 GTYYYGSALFDY
198 CD19 (8B8-018) CDR-L1 KSSQSLENPNGNTYLN
199 CD19 (8B8-018) CDR-L2 RVSKRFS
200 CD19 (8B8-018) CDR-L3 LQLTHVPYT
201 CD19 (8B8-018) VH QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMH
WVRQAPGQGLEWMGYINPYNDGSKYTEKFQGRVT MTSDTSISTAYMELSRLRSDDTAVYYCARGTYYYGS ALFD YWGQGTT VT VS S
202 CD19 (8B8-018) VL DIVMTQTPLSLSVTPGQPASISCKSSQSLENPNGNTYL
NWYLQKPGQSPQLLI YR VS KRFS GVPDRFS GSGS GTD FTLKISRVEAEDVGVYYCLQLTHVPYTFGQGTKLEIK
203 Nucleotide sequence anti- see Table 47
CD19(8B8-018)
Fc hole chain
204 Nucleotide sequence anti- see Table 47
CD19(8B8-018) light chain
205 anti-CD19(8B8-018) Fc hole see Table 47
chain
206 anti-CD19(8B8-018) light see Table 47
chain
207 Nucleotide sequence anti- see Table 49
CD19(8B8-018) Fc hole
dimeric ligand chain
208 Nucleotide sequence anti- see Table 49
CD19(8B8-018) Fc knob
monomeric ligand
209 anti-CD19(8B8-018) Fc hole see Table 49
dimeric ligand chain
210 anti-CD19(8B8-018) Fc see Table 49
knob monomeric ligand
211 Nucleotide sequence anti- see Table 52
CD19(8B8-018) Fc hole
dimeric ligand (71-248) SEQ Name Sequence
ID NO:
chain
212 Nucleotide sequence anti- see Table 52
CD19(8B8-018) Fc knob
monomeric (71-248) ligand
213 anti-CD19(8B8-018) Fc hole see Table 52
dimeric ligand (71-248)
chain
214 anti-CD19(8B8-018) Fc see Table 52
knob monomeric (71-248)
ligand
215 Nucleotide sequence CD 19 GAGGTCCAGCTGCAGCAGTCTGGACCTGAGCTGGT (8B8) VH Parental clone AAAGCCTGGGGCTTCAGTGAAGATGGCCTGCAAG
GCTTCTGGATACACATTCACTGACTATATTATGCA
CTGGGTGAAGCAGAAGACTGGGCAGGGCCTTGAG
TGGATTGGATATATTAATCCTTACAATGATGGTTCT
AAGTACACTGAGAAGTTCAACGGCAAGGCCACAC
TGACTTCAGACAAATCTTCCATCACAGCCTACATG
GAGCTCAGCAGCCTGACCTCTGAGGACTCTGCGGT
CTATTACTGTGCAAGAGGGACCTATTATTATGGTA
GCGCCCTCTTTGACTACTGGGGCCAAGGCACCACT
CTCACAGTCTCCTCG
216 Nucleotide sequence CD 19 GATGCTGTGATGACCCAAACTCCACTCTCCCTGCC (8B8) VL Parental clone TGTCAGTCTTGGAGATCAAGCCTCCATCTCTTGCA
GGTCTAGTCAGAGCCTTGAAAACAGTAATGGAAA
CACCTATTTGAACTGGTACCTCCAGAAACCAGGCC
AGTCTCCACAACTCCTGATCTACAGGGTTTCCAAA
CGATTTTCTGGGGTCCTAGACAGGTTCAGTGGTAG
TGGATCAGGGACAGATTTCACACTGAAAATCAGCA
GAGTGGAGGCTGAGGATTTGGGAGTTTATTTCTGC
CTACAACTTACACATGTCCCGTACACGTTCGGAGG
GGGGACCAAGCTGGAAATAAAA
217 CD 19 LI reverse random see Table 53
218 CD 19 L2 forward random see Table 53
219 CD 19 HI reverse random see Table 53
220 CD 19 H2 forward random see Table 53
221 CD 19 H3 reverse constant see Table 53
222 LMB3 see Table 53
223 D19 LI forward constant see Table 54
224 CD 19 L3 reverse random see Table 54
225 CD 19 L3 forward constant see Table 54
226 CD 19 H3 reverse random see Table 54
227 Nucleotide sequence SNAP GGCCGCCGCTAGCGGCATCGACTACAAGGACGAC tag human CD19 ECD- GATGACAAGGCCGGCATCGATGCCATCATGGACA PDGFR AAGACTGCGAAATGAAGCGCACCACCCTGGATAG SEQ Name Sequence
ID NO:
CCCTCTGGGCAAGCTGGAACTGTCTGGGTGCGAAC
AGGGCCTGCACGAGATCAAGCTGCTGGGCAAAGG
AACATCTGCCGCCGACGCCGTGGAAGTGCCTGCCC
CAGCCGCCGTGCTGGGCGGACCAGAGCCACTGAT
GCAGGCCACCGCCTGGCTCAACGCCTACTTTCACC
AGCCTGAGGCCATCGAGGAGTTCCCTGTGCCAGCC
CTGCACCACCCAGTGTTCCAGCAGGAGAGCTTTAC
CCGCCAGGTGCTGTGGAAACTGCTGAAAGTGGTGA
AGTTCGGAGAGGTCATCAGCTACCAGCAGCTGGCC
GCCCTGGCCGGCAATCCCGCCGCCACCGCCGCCGT
GAAAACCGCCCTGAGCGGAAATCCCGTGCCCATTC
TGATCCCCTGCCACCGGGTGGTGTCTAGCTCTGGC
GCCGTGGGGGGCTACGAGGGCGGGCTCGCCGTGA
AAGAGTGGCTGCTGGCCCACGAGGGCCACAGACT
GGGCAAGCCTGGGCTGGGTGATATCCCCGAGGAA
CCCCTGGTCGTGAAGGTGGAAGAGGGCGACAATG
CCGTGCTGCAGTGCCTGAAGGGCACCTCCGATGGC
CCTACCCAGCAGCTGACCTGGTCCAGAGAGAGCCC
CCTGAAGCCCTTCCTGAAGCTGTCTCTGGGCCTGC
CTGGCCTGGGCATCCATATGAGGCCTCTGGCCATC
TGGCTGTTCATCTTCAACGTGTCCCAGCAGATGGG
CGGCTTCTACCTGTGTCAGCCTGGCCCCCCATCTG
AGAAGGCTTGGCAGCCTGGCTGGACCGTGAACGT
GGAAGGATCCGGCGAGCTGTTCCGGTGGAACGTGT
CCGATCTGGGCGGCCTGGGATGCGGCCTGAAGAA
CAGATCTAGCGAGGGCCCCAGCAGCCCCAGCGGC
AAACTGATGAGCCCCAAGCTGTACGTGTGGGCCAA
GGACAGACCCGAGATCTGGGAGGGCGAGCCTCCT
TGCCTGCCCCCTAGAGACAGCCTGAACCAGAGCCT
GAGCCAGGACCTGACAATGGCCCCTGGCAGCACA
CTGTGGCTGAGCTGTGGCGTGCCACCCGACTCTGT
GTCTAGAGGCCCTCTGAGCTGGACCCACGTGCACC
CTAAGGGCCCTAAGAGCCTGCTGAGCCTGGAACTG
AAGGACGACAGGCCCGCCAGAGATATGTGGGTCA
TGGAAACCGGCCTGCTGCTGCCTAGAGCCACAGCC
CAGGATGCCGGCAAGTACTACTGCCACAGAGGCA
ACCTGACCATGAGCTTCCACCTGGAAATCACCGCC
AGACCCGTGCTGTGGCACTGGCTGCTGAGAACAGG
CGGCTGGAAGGTCGACGAACAAAAACTCATCTCA
GAAGAGGATCTGAATGCTGTGGGCCAGGACACGC
AGGAGGTCATCGTGGTGCCACACTCCTTGCCCTTT
AAGGTGGTGGTGATCTCAGCCATCCTGGCCCTGGT
GGTGCTCACCATCATCTCCCTTATCATCCTCATCAT
GCTTTGGCAGAAGAAGCCACGT
228 Nucleotide sequence SNAP CCGGCCGCCGCTAGCGGCATCGACTACAAGGACG tag cynomolgus CD 19 ACGATGACAAGGCCGGCATCGATGCCATCATGGA ECD- PDGFR CAAAGACTGCGAAATGAAGCGCACCACCCTGGAT
AGCCCTCTGGGCAAGCTGGAACTGTCTGGGTGCGA
ACAGGGCCTGCACGAGATCAAGCTGCTGGGCAAA
GGAACATCTGCCGCCGACGCCGTGGAAGTGCCTGC
CCCAGCCGCCGTGCTGGGCGGACCAGAGCCACTG
ATGCAGGCCACCGCCTGGCTCAACGCCTACTTTCA SEQ Name Sequence
ID NO:
CCAGCCTGAGGCCATCGAGGAGTTCCCTGTGCCAG
CCCTGCACCACCCAGTGTTCCAGCAGGAGAGCTTT
ACCCGCCAGGTGCTGTGGAAACTGCTGAAAGTGGT
GAAGTTCGGAGAGGTCATCAGCTACCAGCAGCTG
GCCGCCCTGGCCGGCAATCCCGCCGCCACCGCCGC
CGTGAAAACCGCCCTGAGCGGAAATCCCGTGCCCA
TTCTGATCCCCTGCCACCGGGTGGTGTCTAGCTCTG
GCGCCGTGGGGGGCTACGAGGGCGGGCTCGCCGT
GAAAGAGTGGCTGCTGGCCCACGAGGGCCACAGA
CTGGGCAAGCCTGGGCTGGGTGATATCCCCCAGGA
ACCCCTGGTCGTGAAGGTGGAAGAGGGCGACAAT
GCCGTGCTCCAGTGTCTCGAGGGCACCTCCGATGG
CCCTACACAGCAGCTCGTGTGGTGCAGAGACAGCC
CCTTCGAGCCCTTCCTGAACCTGTCTCTGGGCCTGC
CTGGCATGGGCATCAGAATGGGCCCTCTGGGCATC
TGGCTGCTGATCTTCAACGTGTCCAACCAGACCGG
CGGCTTCTACCTGTGTCAGCCTGGCCTGCCAAGCG
AGAAGGCTTGGCAGCCTGGATGGACCGTGTCCGTG
GAAGGATCTGGCGAGCTGTTCCGGTGGAACGTGTC
CGATCTGGGCGGCCTGGGATGCGGCCTGAAGAAC
AGAAGCAGCGAGGGCCCTAGCAGCCCCAGCGGCA
AGCTGAATAGCAGCCAGCTGTACGTGTGGGCCAA
GGACAGACCCGAGATGTGGGAGGGCGAGCCTGTG
TGTGGCCCCCCTAGAGATAGCCTGAACCAGAGCCT
GAGCCAGGACCTGACAATGGCCCCTGGCAGCACA
CTGTGGCTGAGCTGTGGCGTGCCACCCGACTCTGT
GTCCAGAGGCCCTCTGAGCTGGACACACGTGCGGC
CTAAGGGCCCTAAGAGCAGCCTGCTGAGCCTGGA
ACTGAAGGACGACCGGCCCGACCGGGATATGTGG
GTGGTGGATACAGGCCTGCTGCTGACCAGAGCCAC
AGCCCAGGATGCCGGCAAGTACTACTGCCACAGA
GGCAACTGGACCAAGAGCTTTTACCTGGAAATCAC
CGCCAGACCCGCCCTGTGGCACTGGCTGCTGAGAA
TCGGAGGCTGGAAGGTCGACGAGCAGAAGCTGAT
CTCCGAAGAGGACCTGAACGCCGTGGGCCAGGAT
ACCCAGGAAGTGATCGTGGTGCCCCACAGCCTGCC
CTTCAAGGTGGTCGTGATCAGCGCCATTCTGGCCC
TGGTGGTGCTGACCATCATCAGCCTGATCATCCTG
ATTATGCTGTGGCAGAAAAAGCCCCGC
229 Polypeptide sequence SNAP PAAASGIDYKDDDDKAGIDAIMDKDCEMKRTTLDSP
LGKLELSGCEQGLHEIKLLGKGTSAADAVEVPAPAA
tag human CD19 ECD-
VLGGPEPLMQATAWLNAYFHQPEAIEEFPVPALHHP PDGFR VFQQESFTRQVLWKLLKVVKFGEVISYQQLAALAGN
PAATAAVKTALSGNPVPILIPCHRVVSSSGAVGGYEG
GLAVKEWLLAHEGHRLGKPGLGDIPEEPLVVKVEEG
DNAVLQCLKGTSDGPTQQLTWSRESPLKPFLKLSLG
LPGLGIHMRPLAIWLFIFNVSQQMGGFYLCQPGPPSE
KAWQPGWTVNVEGSGELFRWNVSDLGGLGCGLKN
RSSEGPSSPSGKLMSPKLYVWAKDRPEIWEGEPPCLP
PRDSLNQSLSQDLTMAPGSTLWLSCGVPPDSVSRGPL SEQ Name Sequence
ID NO:
SWTHVHPKGPKSLLSLELKDDRPARDMWVMETGLL LPRATAQDAGKYYCHRGNLTMSFHLEITARPVLWH WLLRTGGWKVDEQKLISEEDLNAVGQDTQEVIVVP HSLPFKVVVISAILALVVLTIISLIILIMLWQKKPR
230 Polypeptide sequence SNAP PAAASGIDYKDDDDKAGIDAIMDKDCEMKRTTLDSP
LGKLELSGCEQGLHEIKLLGKGTSAADAVEVPAPAA
tag cynomolgus CD 19
VLGGPEPLMQATAWLNAYFHQPEAIEEFPVPALHHP ECD- PDGFR VFQQESFTRQVLWKLLKVVKFGEVISYQQLAALAGN
PAATAAVKTALSGNPVPILIPCHRVVSSSGAVGGYEG
GLAVKEWLLAHEGHRLGKPGLGDIPQEPLVVKVEEG
DNAVLQCLEGTSDGPTQQLVWCRDSPFEPFLNLSLG
LPGMGIRMGPLGIWLLIFNVSNQTGGFYLCQPGLPSE
KAWQPGWTVSVEGSGELFRWNVSDLGGLGCGLKN
RSSEGPSSPSGKLNSSQLYVWAKDRPEMWEGEPVCG
PPRDSLNQSLSQDLTMAPGSTLWLSCGVPPDSVSRGP
LSWTHVRPKGPKSSLLSLELKDDRPDRDMWVVDTG
LLLTRATAQDAGKYYCHRGNWTKSFYLEITARPAL
WHWLLRIGGWKVDEQKLISEEDLNAVGQDTQEVIV
VPHSLPFKVVVISAILALVVLTIISLIILIMLWQKKPR
231 CD19 (8B8-5H09) CDR-L1 see Table 56
232 CD19 (8B8-5H09) CDR-L2 see Table 56
233 CD19 (8B8-5H09) CDR-L3 see Table 56
234 CD19 (8B8-5H09) CDR-H1 see Table 57
235 CD19 (8B8-5H09) CDR-H2 see Table 57
236 CD19 (8B8-5H09) CDR-H3 see Table 57
237 CD19 (8B8-7H07) CDR-L1 see Table 56
238 CD19 (8B8-7H07) CDR-L2 see Table 56
239 CD19 (8B8-7H07) CDR-L3 see Table 56
240 CD19 (8B8-7H07) CDR-H1 see Table 57
241 CD19 (8B8-7H07) CDR-H2 see Table 57
242 CD19 (8B8-7H07) CDR-H3 see Table 57
243 CD19 (8B8-2B03) CDR-L1 see Table 56
244 CD19 (8B8-2B03) CDR-L2 see Table 56
245 CD19 (8B8-2B03) CDR-L3 see Table 56
246 CD19 (8B8-2B03) CDR-H1 see Table 57
247 CD19 (8B8-2B03) CDR-H2 see Table 57
248 CD19 (8B8-2B03) CDR-H3 see Table 57
249 CD19 (8B8-2B 11) CDR-L1 see Table 56
250 CD19 (8B8-2B 11) CDR-L2 see Table 56
251 CD19 (8B8-2B 11) CDR-L3 see Table 56
252 CD19 (8B8-2B 11) CDR-H1 see Table 57
253 CD19 (8B8-2B 11) CDR-H2 see Table 57
254 CD19 (8B8-2B 11) CDR-H3 see Table 57
255 CD19 (8B8-5A07) CDR-L1 see Table 56 SEQ Name Sequence ID NO:
256 CD19 (8B8-5A07) CDR-L2 see Table 56
257 CD19 (8B8-5A07) CDR-L3 see Table 56
258 CD19 (8B8-5A07) CDR-H1 see Table 57
259 CD19 (8B8-5A07) CDR-H2 see Table 57
260 CD19 (8B8-5A07) CDR-H3 see Table 57
261 CD19 (8B8-5B08) CDR-L1 see Table 56
262 CD19 (8B8-5B08) CDR-L2 see Table 56
263 CD19 (8B8-5B08) CDR-L3 see Table 56
264 CD19 (8B8-5B08) CDR-H1 see Table 57
265 CD19 (8B8-5B08) CDR-H2 see Table 57
266 CD19 (8B8-5B08) CDR-H3 see Table 57
267 CD19 (8B8-5D08) CDR-L1 see Table 56
268 CD19 (8B8-5D08) CDR-L2 see Table 56
269 CD19 (8B8-5D08) CDR-L3 see Table 56
270 CD19 (8B8-5D08) CDR-H1 see Table 57
271 CD19 (8B8-5D08) CDR-H2 see Table 57
272 CD19 (8B8-5D08) CDR-H3 see Table 57
273 nucleotide sequence CD 19 see Table 58
(8B8) parental light chain
274 nucleotide sequence CD 19 see Table 58
(8B8) parental heavy chain
275 CD19 (8B8) parental light see Table 58
chain
276 CD19 (8B8) parental heavy see Table 58
chain
277 nucleotide sequence CD 19 see Table 59
(8B8-2B 11) light chain
278 nucleotide sequence CD 19 see Table 59
(8B8-2B11) heavy chain
279 CD19 (8B8-2B11) light see Table 59
chain
280 CD19 (8B8-2B11) heavy see Table 59
chain
281 nucleotide sequence CD 19 see Table 59
(8B8-7H07) light chain
282 nucleotide sequence CD 19 see Table 59
(8B8-7H07) heavy chain
283 CD19 (8B8-7H07) light see Table 59
chain
284 CD19 (8B8-7H07) heavy see Table 59
chain
nucleotide sequence CD 19 see Table 59
285
(8B8-2B03) light chain
nucleotide sequence CD 19 see Table 59
286
(8B8-2B03) heavy chain
CD19 (8B8-2B03) light see Table 59
287
chain SEQ Name Sequence ID NO:
CD19 (8B8-2B03) heavy see Table 59
288
chain
nucleotide sequence CD 19 see Table 59
289
(8B8-5A07) light chain
nucleotide sequence CD 19 see Table 59
290
(8B8-5A07) heavy chain
CD19 (8B8-5A07) light see Table 59
291
chain
CD19 (8B8-5A07) heavy see Table 59
292
chain
nucleotide sequence CD 19 see Table 59
293
(8B8-5D08) light chain
nucleotide sequence CD 19 see Table 59
294
(8B8-5D08) heavy chain
CD19 (8B8-5D08) light see Table 59
295
chain
CD19 (8B8-5D08) heavy see Table 59
296
chain
297 nucleotide sequence CD 19 see Table 59
(8B8-5B08) light chain
298 nucleotide sequence CD 19 see Table 59
(8B8-5B08) heavy chain
299 CD19 (8B8-5B08) light see Table 59
chain
300 CD19 (8B8-5B08) heavy see Table 59
chain
301 nucleotide sequence CD 19 see Table 59
(8B8-5H09) light chain
302 nucleotide sequence CD 19 see Table 59
(8B8-5H09) heavy chain
303 CD19 (8B8-5H09) light see Table 59
chain
304 CD19 (8B8-5H09) heavy see Table 59
chain
305 Nucleotide sequence anti- see Table 62
CD19(8B8-2B11)
Fc hole chain
306 anti-CD19(8B8-2Bl l) Fc see Table 62
hole chain
307 Nucleotide sequence anti- see Table 64
CD19(8B8-2Bl l) Fc hole
dimeric ligand chain
308 Nucleotide sequence anti- see Table 64
CD19(8B8-2Bl l) Fc knob
monomeric ligand
309 anti-CD19(8B8-2Bl l) Fc see Table 64 SEQ Name Sequence
ID NO:
hole dimeric ligand chain
310 anti-CD19(8B8-2B l l) Fc see Table 64
knob monomelic ligand
311 Nucleotide sequence anti- see Table 67
CD19(8B8-2B l l) Fc hole
dimeric ligand (71-248)
chain
312 Nucleotide sequence anti- see Table 67
CD19(8B8-2B l l) Fc knob
monomeric (71-248) ligand
313 anti-CD19(8B8-2B l l) Fc see Table 67
hole dimeric ligand (71-248)
chain
314 anti-CD19(8B8-2B l l) Fc see Table 67
knob monomeric (71-248)
ligand
315 nucleotide sequence see Table 72
CD19(8B8-018) heavy chain
(hulgGI PGLALA)
316 CD19(8B8-018) heavy chain see Table 72
(hulgGI PGLALA)
317 anti-mu CEA T84.66 MKCSWVIFFL MAVVTGVNSE VQLQQSGAEL VH VEPGASVKLS CTASGFNIKD TYMHWVKQRP EQGLEWIGRI DP ANGNS KY V PKFQGKATIT ADTSSNTAYL QLTSLTSEDT AVYYCAPFGY YVSDYAMAYW GQGTSVTVSS
318 anti-mu CEA T84.66 METDTLLLWV LLLWVPGSTG DIVLTQSPAS VL LAVSLGQRAT MSCRAGESVD IFGVGFLHWY QQKPGQPPKL LIYRASNLES GIPVRFSGTG SRTDFTLIID PVEADDVATY YCQQTNEDPY TFGGGTKLEI K
319 IGHVl-69*08 TAAGGGGCTT CCTAGTCCTA AGGCTGAGGA
EVIGT Acc No. Z14309 AGGGATCCTG GTTTAGTTAA AGAGGATTTT
ATTCACCCCT GTGTCCTCTC CACAGGTGTC CAGTCCCAGG TCCAGCTGGT GCAATCTGGG GCTGAGGTGA AGAAGCCTGG GTCCTCGGTG AAGGTCTCCT GCAAGGCTTC TGGAGGCACC TTCAGCAGCT ATACTATCAG CTGGGTGCGA CAGGCCCCTG GACAAGGGCT TGAGTGGATG GGAAGGATCA TCCCTATCCT TGGTACAGCA AACTACGCAC AGAAGTTCCA GGGCAGAGTC ACGATTACCG CGGACAAATC CACGAGCACA GCCTACATGG AGCTGAGCAG CCTGAGATCT GAGGACACGG CCGTGTATTA CTGTGCGAGA GA
320 IGKV3- 11*01 CTGCAGCTGG AAGCTCAGCT CCCACCCAGC EVIGT Acc No. TGCTTTGCAT GTCCCTCCCA GCTGCCCTAC
CTTCCAGAGC CCATATCAAT GCCTGTGTCA GAGCCCTGGG GAGGAACTGC TCAGTTAGGA SEQ Name Sequence ID NO:
CCCAGAGGGA ACCATGGAAG CCCCAGCTCA GCTTCTCTTC CTCCTGCTAC TCTGGCTCCC AGGTGAGGGG AACATGAGGT GGTTTTGCAC ATTAGTGAAA ACTCTTGCCA CCTCTGCTCA GCAAGAAATA TAATTAAAAT TCAAAGTATA TCAACAATTT TGGCTCTACT CAAAGACAGT TGGTTTGATC TTGATTACAT GAGTGCATTT CTGTTTTATT TCCAATTTCA GATACCACCG GAGAAATTGT GTTGACACAG TCTCCAGCCA CCCTGTCTTT GTCTCCAGGG GAAAGAGCCA CCCTCTCCTG CAGGGCCAGT CAGAGTGTTA GCAGCTACTT AGCCTGGTAC CAACAGAAAC CTGGCCAGGC TCCCAGGCTC CTCATCTATG ATGCATCCAA CAGGGCCACT GGCATCCCAG CCAGGTTCAG TGGCAGTGGG TCTGGGACAG ACTTCACTCT CACCATCAGC AGCCTAGAGC CTGAAGATTT TGCAGTTTAT TACTGTCAGC AGCGTAGCAA CTGGCCTCCC ACAGTGATTC CACATGAAAC AAAAACCCCA ACAAGACCAT CAGTGTTTAC TAGATTATTA TACCAGCTGC TTCCTTTACA GACAGCTAGT GGGGTGGCCA CTCAGTGTTA GCATCTCAGC TCTATTTGGC CATTTTGGAG TTCAAGT
321 CEA CDR-H1 see Table 81
322 CEA CDR-H2 see Table 81
323 CEA CDR-H3 see Table 81
324 CEA CDR-L1 see Table 81
325 CEA CDR-L2 see Table 81
326 CEA CDR-L3 see Table 81
327 Parental CEA binder VH see Table 81
328 Parental CEA binder VL see Table 81
329 Humanized CEA binder VH see Table 81
330 Humanized CEA binder VL see Table 81
331 Nucleotide sequence anti- see Table 82
CEA(T84.66-LCHA) Fc
hole chain
332 Nucleotide sequence anti- see Table 82
CEA(T84.66-LCHA) light
chain
333 anti- CEA (T84.66-LCHA) see Table 82
Fc hole chain
334 anti- CEA (T84.66-LCHA) see Table 82
light chain
335 Nucleotide sequence anti- see Table 84
CEA(T84.66-LCHA) Fc
hole dimeric ligand chain SEQ Name Sequence ID NO:
336 Nucleotide sequence anti- see Table 84
CEA(T84.66-LCHA) Fc
knob monomelic ligand
337 anti- CEA(T84.66-LCHA) see Table 84
Fc hole dimeric ligand chain
338 anti- CEA(T84.66-LCHA) see Table 84
Fc knob monomelic ligand
339 Nucleotide sequence anti- see Table 87
CEA (T84.66-LCHA) Fc
hole dimeric ligand (71-248)
chain
340 Nucleotide sequence anti- see Table 87
CEA (T84.66-LCHA) Fc
knob monomelic (71-248)
ligand
341 anti- CEA (T84.66-LCHA) see Table 87
Fc hole dimeric ligand (71- 248) chain
342 anti- CEA (T84.66-LCHA) see Table 87
Fc knob monomelic (71- 248) ligand
343 Nucleotide sequence anti- see Table 88
CEA(T84.66) Fc hole chain
344 Nucleotide sequence anti- see Table 88
CEA(T84.66) light chain
345 anti- CEA (T84.66) Fc hole see Table 88
chain
346 anti- CEA (T84.66) light see Table 88
chain
347 Nucleotide sequence anti- see Table 89
CEA(T84.66) Fc hole
dimeric ligand chain
348 Nucleotide sequence anti- see Table 89
CEA(T84.66) Fc knob
monomeric ligand
349 anti- CEA(T84.66) Fc hole see Table 89
dimeric ligand chain
350 anti- CEA(T84.66) Fc knob see Table 89
monomeric ligand
351 nucleotide sequence hu see Table 92
NA3B3A2-avi His SEQ Name Sequence
ID NO:
see Table 92
352 human NA3B3A2-avi-His
353 Nucleotide sequence see Table 97
Dimeric hu OX40L (51- 183)
- CL* Fc knob chain
354 Nucleotide sequence see Table 97
Monomelic hu
OX40L (51-183) - CHI*
355 Dimeric hu OX40L (51- 183) see Table 97
- CL* Fc knob chain
356 Monomeric hu see Table 97
OX40L (51-183) - CHI*
357 CD19 (8B8-2B 11) VH QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMH
WVRQAPGQGLEWMGYINPYNDGSKYTEKFQGRVT MTSDTSISTAYMELSRLRSDDTAVYYCARGTYYYGP QLFD YWGQGTT VT VS S
358 CD19 (8B8-2B 11) VL DIVMTQTPLSLSVTPGQPASISCKSSQSLETSTGTTYL
NWYLQKPGQSPQLLI YR VS KRFS GVPDRFS GSGS GTD FTLKISRVEAEDVGVYYCLQLLEDPYTFGQGTKLEIK
359 CD19 (8B8-7H07) VH QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMH
WVRQAPGQGLEWMGYINPYNDGSKYTEKFQGRVT MTSDTSISTAYMELSRLRSDDTAVYYCARGTYYYGS ELFD YWGQGTT VTVS S
360 CD19 (8B8-7H07) VL DIVMTQTPLSLSVTPGQPASISCKSSQSLETSTGNTYL
NWYLQKPGQSPQLLI YRVS KRFS GVPDRFS GSGS GTD FTLKISRVEAEDVGVYYCLQATHIPYTFGQGTKLEIK
361 CD19 (8B8-2B03) VH QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYITH
WVRQAPGQGLEWMGYINPYNDGSKYTEKFQGRVT MTSDTSISTAYMELSRLRSDDTAVYYCARGTYYYGP DLFD YWGQGTT VTVS S
362 CD19 (8B8-2B03) VL DIVMTQTPLSLSVTPGQPASISCKSSQSLETSTGNTYL
NWYLQKPGQSPQLLI YRVS KRFS GVPDRFS GSGS GTD FTLKISRVEAEDVGVYYCLQLTHVPYTFGQGXKLEIK
363 CD19 (8B8-5A07) VH QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMH
WVRQAPGQGLEWMGYINPYNDGSKYTEKFQGRVT MTSDTSISTAYMELSRLRSDDTAVYYCARGTYYYGS ALFD YWGQGTT VTVS S
364 CD19 (8B8-5A07) VL DIVMTQTPLSLSVTPGQPASISCKSSQSLETSTGNTYL
NWYLQKPGQSPQLLI YRVS KRFS GVPDRFS GSGS GTD FTLKISRVEAEDVGVYYCLQPGHYPGTFGQGTKLEIK
365 CD19 (8B8-5D08) VH QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMH
WVRQAPGQGLEWMGYINPYNDGSKYTEKFQGRVT MTSDTSISTAYMELSRLRSDDTAVYYCARGTYYYGS ELFD YWGQGTT VTVS S
366 CD19 (8B8-5D08) VL DIVMTQTPLSLSVTPGQPASISCKSSQSLETSTGNTYL
NWYLQKPGQSPQLLI YRVS KRFS GVPDRFS GSGS GTD FTLKISRVEAEDVGVYYCLQLTHEPYTFGQGTKLEIK
367 CD19 (8B8-5B08) VH QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMH SEQ Name Sequence
ID NO:
WVRQAPGQGLEWMGYINPYNDGSKYTEKFQGRVT MTSDTSISTAYMELSRLRSDDTAVYYCARGTYYYGP QLFD YWGQGTT VT VS S
368 CD19 (8B8-5B08) VL DIVMTQTPLSLSVTPGQPASISCKSSQSLETSTGNTYL
NWYLQKPGQSPQLLI YR VS KRFS GVPDRFS GSGS GTD FTLKISRVEAEDVGVYYCLQLDSYPNTFGQGTKLEIK
369 CD19 (8B8-5H09) VH QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMH
WVRQAPGQGLEWMGYINPYNDGSKYTEKFQGRVT MTSDTSISTAYMELSRLRSDDTAVYYCARGTYYYGS ALFD YWGQGTT VTVS S
370 CD19 (8B8-5H09) VL DIVMTQTPLSLSVTPGQPASISCKSSQSLESSTGNTYL
NWYLQKPGQSPQLLI YRVS KRFS GVPDRFS GSGS GTD FTLKISRVEAEDVGVYYCLQLIDYPVTFGQGTKLEIK
371 dimeric huOX40L (51-183) QVSHRYPRIQSIKVQFTEYKKEKGFILTSQKEDEIMK connected by (G4S)2 linker VQNNSVIINCDGFYLISLKGYFSQEVNISLHYQKDEEP
LFQLKKVRSVNSLMVASLTYKDKVYLNVTTDNTSL
DDFH VNGGELILIHQNPGEFC VLGGGGS GGGGS Q VS
HRYPRIQSIKVQFTEYKKEKGFILTSQKEDEIMKVQN
NSVIINCDGFYLISLKGYFSQEVNISLHYQKDEEPLFQ
LKKVRSVNSLMVASLTYKDKVYLNVTTDNTSLDDF
HVNGGELILIHQNPGEFCVL
372 dimeric huOX40L (52-183) VSHRYPRIQSIKVQFTEYKKEKGFILTSQKEDEIMKV connected by (G4S)2 linker QNNSVIINCDGFYLISLKGYFSQEVNISLHYQKDEEPL
FQLKKVRSVNSLMVASLTYKDKVYLNVTTDNTSLD
DFHVNGGELILIHQNPGEFCVLGGGGSGGGGSVSHR
YPRIQSIKVQFTEYKKEKGFILTSQKEDEIMKVQNNS
VIINCDGFYLISLKGYFSQEVNISLHYQKDEEPLFQLK
KVRSVNSLMVASLTYKDKVYLNVTTDNTSLDDFHV
NGGELILIHQNPGEFCVL
373 hu 4-lBBL (85-248) LDLRQGMFAQLVAQNVLLIDGPLSWYSDPGLAGVSL
TGGLSYKEDTKELVVAKAGVYYVFFQLELRRVVAG
EGSGSVSLALHLQPLRSAAGAAALALTVDLPPASSEA
RNSAFGFQGRLLHLSAGQRLGVHLHTEARARHAWQ
LTQGATVLGLFRVTPEIPAGL
374 hu 4-lBBL (80-248) DPAGLLDLRQGMFAQLVAQNVLLIDGPLSWYSDPGL
AGVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELRR
VVAGEGSGSVSLALHLQPLRSAAGAAALALTVDLPP
ASSEARNSAFGFQGRLLHLSAGQRLGVHLHTEARAR
HAWQLTQGATVLGLFRVTPEIPAGL
375 hu 4-lBBL (52-248) PWAVSGARASPGSAASPRLREGPELSPDDPAGLLDLR
QGMFAQLVAQNVLLIDGPLSWYSDPGLAGVSLTGGL
SYKEDTKELVVAKAGVYYVFFQLELRRVVAGEGSG
SVSLALHLQPLRSAAGAAALALTVDLPPASSEARNSA
FGFQGRLLHLSAGQRLGVHLHTEARARHAWQLTQG
ATVLGLFRVTPEIPAGL
General information regarding the nucleotide sequences of human immunoglobulins light and heavy chains is given in: Kabat, E.A., et al., Sequences of Proteins of Immunological Interest, 5th ed., Public Health Service, National Institutes of Health, Bethesda, MD (1991). Amino acids of antibody chains are numbered and referred to according to the EU numbering systems according to Kabat (Kabat, E.A., et al., Sequences of Proteins of Immunological Interest, 5th ed., Public Health Service, National Institutes of Health, Bethesda, MD (1991)) as defined above.
EXAMPLES
The following are examples of methods and compositions of the invention. It is understood that various other embodiments may be practiced, given the general description provided above.
Recombinant DNA techniques Standard methods were used to manipulate DNA as described in Sambrook et al.,
Molecular cloning: A laboratory manual; Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1989. The molecular biological reagents were used according to the manufacturer's instructions. General information regarding the nucleotide sequences of human immunoglobulin light and heavy chains is given in: Kabat, E.A. et al., (1991) Sequences of Proteins of Immunological Interest, Fifth Ed., NIH Publication No 91-3242.
DNA sequencing
DNA sequences were determined by double strand sequencing. Gene synthesis
Desired gene segments were either generated by PCR using appropriate templates or were synthesized by Geneart AG (Regensburg, Germany) from synthetic oligonucleotides and PCR products by automated gene synthesis. In cases where no exact gene sequence was available, oligonucleotide primers were designed based on sequences from closest homologues and the genes were isolated by RT-PCR from RNA originating from the appropriate tissue. The gene segments flanked by singular restriction endonuclease cleavage sites were cloned into standard cloning / sequencing vectors. The plasmid DNA was purified from transformed bacteria and concentration determined by UV spectroscopy. The DNA sequence of the subcloned gene fragments was confirmed by DNA sequencing. Gene segments were designed with suitable restriction sites to allow sub-cloning into the respective expression vectors. All constructs were designed with a 5 '-end DNA sequence coding for a leader peptide which targets proteins for secretion in eukaryotic cells.
Cell culture techniques
Standard cell culture techniques were used as described in Current Protocols in Cell Biology (2000), Bonifacino, J.S., Dasso, M., Harford, J.B., Lippincott-Schwartz, J. and Yamada, K.M. (eds.), John Wiley & Sons, Inc. Protein purification
Proteins were purified from filtered cell culture supernatants referring to standard protocols. In brief, antibodies were applied to a Protein A Sepharose column (GE healthcare) and washed with PBS. Elution of antibodies was achieved at pH 2.8 followed by immediate neutralization of the sample. Aggregated protein was separated from monomeric antibodies by size exclusion chromatography (Superdex 200, GE Healthcare) in PBS or in 20 mM Histidine, 150 mM NaCl pH 6.0. Monomeric antibody fractions were pooled, concentrated (if required) using e.g., a MILLIPORE Amicon Ultra (30 MWCO) centrifugal concentrator, frozen and stored at -20°C or -80°C. Part of the samples were provided for subsequent protein analytics and analytical characterization e.g. by SDS-PAGE, size exclusion chromatography (SEC) or mass spectrometry.
SDS-PAGE
The NuPAGE® Pre-Cast gel system (Invitrogen) was used according to the manufacturer's instruction. In particular, 10% or 4-12% NuPAGE® Novex® Bis-TRIS Pre-Cast gels (pH 6.4) and a NuPAGE® MES (reduced gels, with NuPAGE® Antioxidant running buffer additive) or MOPS (non-reduced gels) running buffer was used.
Analytical size exclusion chromatography
Size exclusion chromatography (SEC) for the determination of the aggregation and oligomeric state of antibodies was performed by HPLC chromatography. Briefly, Protein A purified antibodies were applied to a Tosoh TSKgel G3000SW column in 300 mM NaCl, 50 mM KH2PO4/K2HPO4, pH 7.5 on an Agilent HPLC 1100 system or to a Superdex 200 column (GE Healthcare) in 2 x PBS on a Dionex HPLC-System. The eluted protein was quantified by UV absorbance and integration of peak areas. BioRad Gel Filtration Standard 151-1901 served as a standard.
Mass spectrometry This section describes the characterization of the multispecific antibodies with VH/VL exchange (VH/VL CrossMabs) with emphasis on their correct assembly. The expected primary structures were analyzed by electrospray ionization mass spectrometry (ESI-MS) of the deglycosylated intact CrossMabs and deglycosylated/plasmin digested or alternatively
deglycosylated/limited LysC digested CrossMabs. The VH/VL CrossMabs were deglycosylated with N-Glycosidase F in a phosphate or Tris buffer at 37°C for up to 17 h at a protein concentration of 1 mg/ml. The plasmin or limited LysC (Roche) digestions were performed with 100 μg deglycosylated VH/VL CrossMabs in a Tris buffer pH 8 at room temperature for 120 hours and at 37°C for 40 min, respectively. Prior to mass spectrometry the samples were desalted via HPLC on a Sephadex G25 column (GE Healthcare). The total mass was determined via ESTMS on a maXis 4G UHR-QTOF MS system (Bruker Daltonik) equipped with a Tri Versa NanoMate source (Advion).
Determination of binding and binding affinity of multispecific antibodies to the respective antigens using surface plasmon resonance (SPR) (BIACORE)
Binding of the generated antibodies to the respective antigens is investigated by surface plasmon resonance using a BIACORE instrument (GE Healthcare Biosciences AB, Uppsala, Sweden). Briefly, for affinity measurements Goat- Anti-Human IgG, JIR 109-005-098 antibodies are immobilized on a CM5 chip via amine coupling for presentation of the antibodies against the respective antigen. Binding is measured in HBS buffer (HBS-P (10 mM HEPES, 150 mM NaCl, 0.005% Tween 20, ph 7.4), 25°C (or alternatively at 37°C). Antigen (R&D Systems or in house purified) was added in various concentrations in solution. Association was measured by an antigen injection of 80 seconds to 3 minutes; dissociation was measured by washing the chip surface with HBS buffer for 3 - 10 minutes and a KD value was estimated using a 1: 1 Langmuir binding model. Negative control data (e.g. buffer curves) are subtracted from sample curves for correction of system intrinsic baseline drift and for noise signal reduction. The respective Biacore Evaluation Software is used for analysis of sensorgrams and for calculation of affinity data.
Example 1 1.1 Preparation of targeted human 4-1BB ligand trimer-containing Fc fusion antigen binding molecules
Different fragments of the DNA sequence encoding part of the ectodomain (amino acids 71-254, 52-254 and 80-254) of human 4-1BB ligand were synthetized according to the P41273 sequence of Uniprot database (SEQ ID NO:42). As components for the assembly of a TNF ligand trimer-containing antigen binding molecule a polypeptide comprising two ectodomains of 4- IBB ligand, separated by (G4S)2 linkers, and fused to the human IgGl-CHl or CL domain, was cloned as depicted in Figure 1A- (human 4-1BB ligand, (G4S)2 connector, human 4-1BB ligand, (G4S)2 connector, human CHI or CL) or as depicted in Figure 1C (human CH3, (G4S)2 connector, human 4- IBB ligand, (G4S)2 connector, human 4-1BB ligand).
A polypeptide comprising one ectodomain of 4- IBB ligand and fused to the human IgGl- CL or CHI domain, was cloned as described in Figure IB (human 4- IBB ligand, (G4S)2 connector, human CL or CHI) or as depicted in Figure ID (human CH3, (G4S)2 connector, human 4-1BB ligand). The polypeptides were subcloned in frame with the human IgGl heavy chain CH2 and CH3 domains with optional peptide linkers, for example for construct 1 the polypeptide encoding the dimeric 4- IBB ligand fused to a human CHI domain was subcloned in frame with the human IgGl heavy chain CH2 and CH3 domains on the knob (Merchant, Zhu et al. 1998) using a linker (G4S)2 of SEQ ID NO: 13 or (GSPGSSSSGS) of SEQ ID NO:57.
The variable region of heavy and light chain DNA sequences encoding a binder specific for fibroblast activation protein (FAP), i.e. 28H1, were subcloned in frame with either the constant heavy chain of the hole (Carter, J. Immunol. Methods (2001), 248, 7-15) or the constant light chain of human IgGl. The generation and preparation of the FAP binders is described in WO 2012/020006 A2, which is incorporated herein by reference.
Table 1 summarizes the characteristics of the constructs produced. The constructs 1 to 10 differ in their geometry, valency for FAP, 4- IBB ligand ectodomain, crossover of the CHI and CL domain (CrossMab technology), mutations in the CHI and CL domains and different peptide linkers in the polypeptide comprising one ectodomain of 4- IBB ligand (monomeric 4-1BBL chain).
Table 1: Characteristics of produced TNF ligand trimer-containing antigen binding molecules (FAP split 4-1BBL trimers)
Construct Valency for FAP 4-1BBL Crossed Charged Linker to
FAP binder ectodomain CH1-CL residues 4-1BBL in domains light chain
1.1 monovalent 28H1 71-254 no no (G4S)2
1.2 monovalent 28H1 71-254 yes yes (G4S)2
(Ligand) (Ligand)
1.3 monovalent 28H1 71-254 yes (FAP yes (G4S)2
Fab) (Ligand)
1.4 monovalent 28H1 71-254 no yes (G4S)2
(Ligand)
1.5 bivalent 28H1 71-254 no no (G4S)2
1.6 monovalent 28H1 71-254 no yes (G4S)1
(Ligand)
1.7 bivalent 28H1 71-254 yes yes (G4S)2
(Ligand) (Ligand)
1.8 bivalent 28H1 71-254 yes (FAP yes (G4S)2
Fab fused to (Ligand)
Ligand)
1.9 monovalent 28H1 52-254 no yes (G4S)2
(Ligand)
1.10 monovalent 28H1 80-254 no yes (G4S)2
(Ligand) In order to avoid mispairing, in most of the constructs one pair of CHI and CL domains was replaced by each other (domain crossover) as described in WO 2009/080253 Al .
To further improve correct pairing, different charged amino acid substitutions were introduced in the crossed or non-crossed CHI and CL domains as charged residues in constructs 2 to 4 and 6 to 10. In the human CL domain the mutations E123R and Q124K were introduced, whereas the mutations K147E and K213E were cloned into the human CHI domain.
For all constructs the knobs into holes heterodimerization technology was used with the S354C/T366W mutations in the CH3 domain of the knob chain and the corresponding
Y349C/T366S/L368A/Y407V mutations in the CH3 domain of the hole chain (Carter, J
Immunol Methods 248, 7-15 (2001)).
The Pro329Gly, Leu234Ala and Leu235Ala mutations have been introduced in the constant region of the knob and hole heavy chains to abrogate binding to Fc gamma receptors according to the method described in International Patent Appl. Publ. No. WO 2012/130831 Al .
For example, in construct 1 the combination of the ligand-Fc knob chain containing the S354C/T366W mutations in the first CH3 domain, with the targeted anti-FAP-Fc hole chain containing the Y349C/T366S/L368A/Y407V mutations in the second CH3 domain allows generation of a heterodimer, which includes an assembled trimeric 4- IBB ligand and a FAP binding Fab (Figure 2, Graph 1.1).
Table 2 shows the cDNA and amino acid sequences of the monovalent FAP-targeted 4- 1BB ligand trimer-containing Fc (kih) fusion antigen binding molecule (Construct 1.1).
Table 2: Sequences of FAP-targeted human 4-lBB ligand trimer containing Fc (kih) fusion molecule Construct 1.1
SEQ ID Description Sequence
NO:
Dimeric hu 4- AGAGAGGGCCCTGAGCTGAGCCCCGATGATCCTGCTGG
66
ACTGCTGGACCTGCGGCAGGGCATGTTTGCTCAGCTGGT
1BBL (71-254) - GGCCCAGAACGTGCTGCTGATCGATGGCCCCCTGTCCTG CH1 Fc knob GTACAGCGATCCTGGACTGGCTGGCGTGTCACTGACAGG
CGGCCTGAGCTACAAAGAGGACACCAAAGAACTGGTGG
chain TGGCCAAGGCCGGCGTGTACTACGTGTTCTTTCAGCTGG
AACTGCGGAGAGTGGTGGCCGGCGAAGGATCTGGCTCT
GTGTCTCTGGCCCTGCATCTGCAGCCTCTGAGAAGCGCT
GCTGGCGCTGCAGCTCTGGCACTGACAGTGGATCTGCCT
CCTGCCAGCTCCGAGGCCCGGAATAGCGCATTTGGGTTT
CAAGGCAGGCTGCTGCACCTGTCTGCCGGCCAGAGGCT
GGGAGTGCATCTGCACACAGAGGCCAGGGCTAGACACG
CCTGGCAGCTGACACAGGGCGCTACAGTGCTGGGCCTG TTCAGAGTGACCCCCGAGATTCCAGCCGGCCTGCCTTCT
CCAAGAAGCGAAGGCGGAGGCGGATCTGGCGGCGGAG
GATCTAGAGAGGGACCCGAACTGTCCCCTGACGATCCA
GCCGGGCTGCTGGATCTGAGACAGGGAATGTTCGCCCA
GCTGGTGGCTCAGAATGTGCTGCTGATTGACGGACCTCT
GAGCTGGTACTCCGACCCAGGGCTGGCAGGGGTGTCCC
TGACTGGGGGACTGTCCTACAAAGAAGATACAAAAGAA
CAGCTGGAACTGAGGCGGGTGGTGGCTGGGGAGGGCTC
AGGATCTGTGTCCCTGGCTCTGCATCTGCAGCCACTGCG
CTCTGCTGCTGGCGCAGCTGCACTGGCTCTGACTGTGGA
CCTGCCACCAGCCTCTAGCGAGGCCAGAAACAGCGCCT
TCGGGTTCCAAGGACGCCTGCTGCATCTGAGCGCCGGAC
AGCGCCTGGGAGTGCATCTGCATACTGAAGCCAGAGCC
CGGCATGCTTGGCAGCTGACTCAGGGGGCAACTGTGCTG
GGACTGTTTCGCGTGACACCTGAGATCCCTGCCGGACTG
CCAAGCCCTAGATCAGAAGGGGGCGGAGGAAGCGGAG
GGGGAGGAAGTGCTAGCACCAAGGGCCCTAGCGTGTTC
CCTCTGGCCCCTAGCAGCAAGAGCACAAGTGGAGGAAC
AGCCGCCCTGGGCTGCCTGGTCAAGGACTACTTCCCCGA
GCCCGTGACCGTGTCCTGGAATTCTGGCGCCCTGACAAG
CGGCGTGCACACATTTCCAGCCGTGCTGCAGAGCAGCG
GCCTGTACTCTCTGAGCAGCGTCGTGACCGTGCCCTCTA
GCTCTCTGGGCACCCAGACCTACATCTGCAACGTGAACC
ACAAGCCCAGCAACACCAAAGTGGACAAGAAGGTGGA
ACCCAAGAGCTGCGACAAGACCCACACCTGTCCCCCTTG
CCCTGCCCCTGAAGCTGCTGGTGGCCCTTCCGTGTTCCT
GTTCCCCCCAAAGCCCAAGGACACCCTGATGATCAGCC
GGACCCCCGAAGTGACCTGCGTGGTGGTCGATGTGTCCC
ACGAGGACCCTGAAGTGAAGTTCAATTGGTACGTGGAC
GGCGTGGAAGTGCACAATGCCAAGACCAAGCCGCGGGA
GGAGCAGTACAACAGCACGTACCGTGTGGTCAGCGTCC
TCACCGTCCTGCACCAGGACTGGCTGAATGGCAAGGAG
TACAAGTGCAAGGTCTCCAACAAAGCCCTCGGCGCCCC
CATCGAGAAAACCATCTCCAAAGCCAAAGGGCAGCCCC
GAGAACCACAGGTGTACACCCTGCCCCCATGCCGGGAT
GAGCTGACCAAGAACCAGGTCAGCCTGTGGTGCCTGGT
CAAAGGCTTCTATCCCAGCGACATCGCCGTGGAGTGGG
AGAGCAATGGGCAGCCGGAGAACAACTACAAGACCACG
CCTCCCGTGCTGGACTCCGACGGCTCCTTCTTCCTCTACA
GCAAGCTCACCGTGGACAAGAGCAGGTGGCAGCAGGGG
AACGTCTTCTCATGCTCCGTGATGCATGAGGCTCTGCAC
AACCACTACACGCAGAAGAGCCTCTCCCTGTCTCCGGGT
AAA
Monomeric hu 4- AGAGAGGGCCCTGAGCTGAGCCCCGATGATCCTGCTGG
ACTGCTGGACCTGCGGCAGGGCATGTTTGCTCAGCTGGT
1BBL (71-254) - GGCCCAGAACGTGCTGCTGATCGATGGCCCCCTGTCCTG CL GTACAGCGATCCTGGACTGGCTGGCGTGTCACTGACAGG
CGGCCTGAGCTACAAAGAGGACACCAAAGAACTGGTGG
TGGCCAAGGCCGGCGTGTACTACGTGTTCTTTCAGCTGG
AACTGCGGAGAGTGGTGGCCGGCGAAGGATCTGGCTCT
GTGTCTCTGGCCCTGCATCTGCAGCCTCTGAGAAGCGCT
GCTGGCGCTGCAGCTCTGGCACTGACAGTGGATCTGCCT
CCTGCCAGCTCCGAGGCCCGGAATAGCGCATTTGGGTTT CAAGGCAGGCTGCTGCACCTGTCTGCCGGCCAGAGGCT
GGGAGTGCATCTGCACACAGAGGCCAGGGCTAGACACG
CCTGGCAGCTGACACAGGGCGCTACAGTGCTGGGCCTG
TTCAGAGTGACCCCCGAGATTCCAGCCGGCCTGCCTTCT
CCAAGAAGCGAAGGCGGAGGCGGATCTGGCGGCGGAG
GATCTCGTACGGTGGCTGCACCATCTGTCTTCATCTTCCC
GCCATCTGATGAGCAGTTGAAATCTGGAACTGCCTCTGT
TGTGTGCCTGCTGAATAACTTCTATCCCAGAGAGGCCAA
AGTACAGTGGAAGGTGGATAACGCCCTCCAATCGGGTA
ACTCCCAGGAGAGTGTCACAGAGCAGGACAGCAAGGAC
AGCACCTACAGCCTCAGCAGCACCCTGACGCTGAGCAA
AGCAGACTACGAGAAACACAAAGTCTACGCCTGCGAAG
TCACCCATCAGGGCCTGAGCTCGCCCGTCACAAAGAGCT
TCAACAGGGGAGAGTGT anti-FAP Fc hole GAAGTGCAGCTGCTGGAATCCGGCGGAGGCCTGGTGCA
GCCTGGCGGATCTCTGAGACTGTCCTGCGCCGCCTCCGG
chain CTTCACCTTCTCCTCCCACGCCATGTCCTGGGTCCGACA
GGCTCCTGGCAAAGGCCTGGAATGGGTGTCCGCCATCTG
GGCCTCCGGCGAGCAGTACTACGCCGACTCTGTGAAGG
GCCGGTTCACCATCTCCCGGGACAACTCCAAGAACACCC
TGTACCTGCAGATGAACTCCCTGCGGGCCGAGGACACC
GCCGTGTACTACTGTGCCAAGGGCTGGCTGGGCAACTTC
GACTACTGGGGACAGGGCACCCTGGTCACCGTGTCCAG
CGCTAGCACCAAGGGCCCCTCCGTGTTCCCCCTGGCCCC
CAGCAGCAAGAGCACCAGCGGCGGCACAGCCGCTCTGG
GCTGCCTGGTCAAGGACTACTTCCCCGAGCCCGTGACCG
TGTCCTGGAACAGCGGAGCCCTGACCTCCGGCGTGCAC
ACCTTCCCCGCCGTGCTGCAGAGTTCTGGCCTGTATAGC
CTGAGCAGCGTGGTCACCGTGCCTTCTAGCAGCCTGGGC
ACCCAGACCTACATCTGCAACGTGAACCACAAGCCCAG
CAACACCAAGGTGGACAAGAAGGTGGAGCCCAAGAGCT
GCGACAAAACTCACACATGCCCACCGTGCCCAGCACCT
GAAGCTGCAGGGGGACCGTCAGTCTTCCTCTTCCCCCCA
AAACCCAAGGACACCCTCATGATCTCCCGGACCCCTGA
GGTCACATGCGTGGTGGTGGACGTGAGCCACGAAGACC
CTGAGGTCAAGTTCAACTGGTACGTGGACGGCGTGGAG
GTGCATAATGCCAAGACAAAGCCGCGGGAGGAGCAGTA
CAACAGCACGTACCGTGTGGTCAGCGTCCTCACCGTCCT
GCACCAGGACTGGCTGAATGGCAAGGAGTACAAGTGCA
AGGTCTCCAACAAAGCCCTCGGCGCCCCCATCGAGAAA
ACCATCTCCAAAGCCAAAGGGCAGCCCCGAGAACCACA
GGTGTGCACCCTGCCCCCATCCCGGGATGAGCTGACCAA
GAACCAGGTCAGCCTCTCGTGCGCAGTCAAAGGCTTCTA
TCCCAGCGACATCGCCGTGGAGTGGGAGAGCAATGGGC
AGCCGGAGAACAACTACAAGACCACGCCTCCCGTGCTG
GACTCCGACGGCTCCTTCTTCCTCGTGAGCAAGCTCACC
GTGGACAAGAGCAGGTGGCAGCAGGGGAACGTCTTCTC
ATGCTCCGTGATGCATGAGGCTCTGCACAACCACTACAC
GCAGAAGAGCCTCTCCCTGTCTCCGGGTAAA anti-FAP light GAGATCGTGCTGACCCAGTCCCCCGGCACCCTGTCTCTG
AGCCCTGGCGAGAGAGCCACCCTGTCCTGCAGAGCCTC
chain CCAGTCCGTGTCCCGGTCCTACCTCGCCTGGTATCAGCA GAAGCCCGGCCAGGCCCCTCGGCTGCTGATCATCGGCG
CCTCTACCAGAGCCACCGGCATCCCTGACCGGTTCTCCG
GCTCTGGCTCCGGCACCGACTTCACCCTGACCATCTCCC
GGCTGGAACCCGAGGACTTCGCCGTGTACTACTGCCAGC
AGGGCCAGGTCATCCCTCCCACCTTTGGCCAGGGCACCA
AGGTGGAAATCAAGCGTACGGTGGCTGCACCATCTGTCT
TCATCTTCCCGCCATCTGATGAGCAGTTGAAATCTGGAA
CTGCCTCTGTTGTGTGCCTGCTGAATAACTTCTATCCCAG
AGAGGCCAAAGTACAGTGGAAGGTGGATAACGCCCTCC
AATCGGGTAACTCCCAGGAGAGTGTCACAGAGCAGGAC
AGCAAGGACAGCACCTACAGCCTCAGCAGCACCCTGAC
GCTGAGCAAAGCAGACTACGAGAAACACAAAGTCTACG
CCTGCGAAGTCACCCATCAGGGCCTGAGCTCGCCCGTCA
CAAAGAGCTTCAACAGGGGAGAGTGT
Dimeric hu 4- REGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWY
SDPGLAGVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELR
1BBL (71-254) - RVVAGEGSGSVSLALHLQPLRSAAGAAALALTVDLPPASS CH1 Fc knob EARNSAFGFQGRLLHLSAGQRLGVHLHTEARARHAWQLT
QGATVLGLFRVTPEIPAGLPSPRSEGGGGSGGGGSREGPEL
chain SPDDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWYSDPGLA
GVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELRRVVAG
EGSGSVSLALHLQPLRSAAGAAALALTVDLPPASSEARNS
AFGFQGRLLHLSAGQRLGVHLHTEARARHAWQLTQGATV
LGLFRVTPEIPAGLPSPRSEGGGGSGGGGSASTKGPSVFPLA
PSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTK
VDKKVEPKSCDKTHTCPPCPAPEAAGGPSVFLFPPKPKDTL
MISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTK
PREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALG
APIEKTISKAKGQPREPQVYTLPPCRDELTKNQVSLWCLVK
GFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLT
VDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK
Monomeric hu 4- REGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWY
SDPGLAGVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELR
1BBL (71-254) - RVVAGEGSGSVSLALHLQPLRSAAGAAALALTVDLPPASS CL1 EARNSAFGFQGRLLHLSAGQRLGVHLHTEARARHAWQLT
QGATVLGLFRVTPEIPAGLPSPRSEGGGGSGGGGSRTVAAP
SVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNA
LQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYA
CEVTHQGLSSPVTKSFNRGEC
EVQLLESGGGLVQPGGSLRLSCAASGFTFSSHAMSWVRQA
anti-FAP(28Hl)
PGKGLEWVSAIWASGEQYYADSVKGRFTISRDNSKNTLYL
Fc hole chain QMNSLRAEDTAVYYCAKGWLGNFDYWGQGTLVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNS
GALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICN
VNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGGPSVF
LFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDG
VEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYK
CKVSNKALGAPIEKTISKAKGQPREPQVCTLPPSRDELTKN
QVSLSCAVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSD
GSFFLVSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKS LSLSPGK
19 anti-FAP (28H1) EIVLTQSPGTLSLSPGERATLSCRASQSVSRSYLAWYQQKP
GQAPRLLIIGASTRATGIPDRFSGSGSGTDFTLTISRLEPEDF
light chain AVYYCQQGQVIPPTFGQGTKVEIKRTVAAPSVFIFPPSDEQ
LKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESV TEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSS PVTKSFNRGEC
Table 3 shows the cDNA and amino acid sequences of acid sequences of the monovalent FAP-targeted 4- IBB ligand trimer-containing Fc (kih) fusion antigen binding molecule
(Construct 1.2) with CH1-CL crossover and charged residues.
Table 3: Sequences of FAP-targeted human 4-lBB ligand trimer containing Fc (kih) fusion molecule Construct 1.2
SEQ ID Description Sequence
NO:
129 Dimeric hu 4- AGAGAGGGCCCTGAGCTGAGCCCCGATGATCCTGCTGG
ACTGCTGGACCTGCGGCAGGGCATGTTTGCTCAGCTGGT
1BBL (71-254) - GGCCCAGAACGTGCTGCTGATCGATGGCCCCCTGTCCTG CL* Fc knob GTACAGCGATCCTGGACTGGCTGGCGTGTCACTGACAGG
CGGCCTGAGCTACAAAGAGGACACCAAAGAACTGGTGG
chain TGGCCAAGGCCGGCGTGTACTACGTGTTCTTTCAGCTGG
AACTGCGGAGAGTGGTGGCCGGCGAAGGATCTGGCTCT
GTGTCTCTGGCCCTGCATCTGCAGCCTCTGAGAAGCGCT
GCTGGCGCTGCAGCTCTGGCACTGACAGTGGATCTGCCT
CCTGCCAGCTCCGAGGCCCGGAATAGCGCATTTGGGTTT
CAAGGCAGGCTGCTGCACCTGTCTGCCGGCCAGAGGCT
GGGAGTGCATCTGCACACAGAGGCCAGGGCTAGACACG
CCTGGCAGCTGACACAGGGCGCTACAGTGCTGGGCCTG
TTCAGAGTGACCCCCGAGATTCCAGCCGGCCTGCCTTCT
CCAAGAAGCGAAGGCGGAGGCGGATCTGGCGGCGGAG
GATCTAGAGAGGGACCCGAACTGTCCCCTGACGATCCA
GCCGGGCTGCTGGATCTGAGACAGGGAATGTTCGCCCA
GCTGGTGGCTCAGAATGTGCTGCTGATTGACGGACCTCT
GAGCTGGTACTCCGACCCAGGGCTGGCAGGGGTGTCCC
TGACTGGGGGACTGTCCTACAAAGAAGATACAAAAGAA
CAGCTGGAACTGAGGCGGGTGGTGGCTGGGGAGGGCTC
AGGATCTGTGTCCCTGGCTCTGCATCTGCAGCCACTGCG
CTCTGCTGCTGGCGCAGCTGCACTGGCTCTGACTGTGGA
CCTGCCACCAGCCTCTAGCGAGGCCAGAAACAGCGCCT
TCGGGTTCCAAGGACGCCTGCTGCATCTGAGCGCCGGAC
AGCGCCTGGGAGTGCATCTGCATACTGAAGCCAGAGCC
CGGCATGCTTGGCAGCTGACTCAGGGGGCAACTGTGCTG
GGACTGTTTCGCGTGACACCTGAGATCCCTGCCGGACTG
CCAAGCCCTAGATCAGAAGGGGGCGGAGGTTCCGGAGG
GGGAGGATCTCGTACGGTGGCTGCACCATCTGTCTTTAT CTTCCCACCCAGCGACCGGAAGCTGAAGTCTGGCACAG
CCAGCGTCGTGTGCCTGCTGAATAACTTCTACCCCCGCG
AGGCCAAGGTGCAGTGGAAGGTGGACAATGCCCTGCAG
AGCGGCAACAGCCAGGAAAGCGTGACCGAGCAGGACA
GCAAGGACTCCACCTACAGCCTGAGCAGCACCCTGACC
CTGAGCAAGGCCGACTACGAGAAGCACAAGGTGTACGC
CTGCGAAGTGACCCACCAGGGCCTGTCTAGCCCCGTGAC
CAAGAGCTTCAACCGGGGCGAGTGCGACAAGACCCACA
CCTGTCCTCCATGCCCTGCCCCTGAAGCTGCTGGCGGCC
CTAGCGTGTTCCTGTTCCCCCCAAAGCCCAAGGACACCC
TGATGATCAGCCGGACCCCTGAAGTGACCTGCGTGGTGG
TGGATGTGTCCCACGAGGACCCTGAAGTGAAGTTCAATT
GGTACGTGGACGGCGTGGAAGTGCACAATGCCAAGACC
AAGCCGCGGGAGGAGCAGTACAACAGCACGTACCGTGT
GGTCAGCGTCCTCACCGTCCTGCACCAGGACTGGCTGAA
TGGCAAGGAGTACAAGTGCAAGGTCTCCAACAAAGCCC
TCGGCGCCCCCATCGAGAAAACCATCTCCAAAGCCAAA
GGGCAGCCCCGAGAACCACAGGTGTACACCCTGCCCCC
ATGCCGGGATGAGCTGACCAAGAACCAGGTCAGCCTGT
GGTGCCTGGTCAAAGGCTTCTATCCCAGCGACATCGCCG
TGGAGTGGGAGAGCAATGGGCAGCCGGAGAACAACTAC
AAGACCACGCCTCCCGTGCTGGACTCCGACGGCTCCTTC
TTCCTCTACAGCAAGCTCACCGTGGACAAGAGCAGGTG
GCAGCAGGGGAACGTCTTCTCATGCTCCGTGATGCATGA
GGCTCTGCACAACCACTACACGCAGAAGAGCCTCTCCCT
GTCTCCGGGTAAA
Monomeric hu 4- AGAGAGGGCCCTGAGCTGAGCCCCGATGATCCTGCTGG
ACTGCTGGACCTGCGGCAGGGCATGTTTGCTCAGCTGGT
1BBL (71-254) - GGCCCAGAACGTGCTGCTGATCGATGGCCCCCTGTCCTG CH1* GTACAGCGATCCTGGACTGGCTGGCGTGTCACTGACAGG
CGGCCTGAGCTACAAAGAGGACACCAAAGAACTGGTGG
TGGCCAAGGCCGGCGTGTACTACGTGTTCTTTCAGCTGG
AACTGCGGAGAGTGGTGGCCGGCGAAGGATCTGGCTCT
GTGTCTCTGGCCCTGCATCTGCAGCCTCTGAGAAGCGCT
GCTGGCGCTGCAGCTCTGGCTCTGACAGTGGATCTGCCT
CCTGCCAGCTCCGAGGCCCGGAATAGCGCATTTGGGTTT
CAAGGCCGGCTGCTGCACCTGTCTGCCGGCCAGAGACT
GGGAGTGCATCTGCACACAGAGGCCAGAGCCAGGCACG
CCTGGCAGCTGACACAGGGCGCTACAGTGCTGGGCCTG
TTCAGAGTGACCCCCGAGATTCCTGCCGGCCTGCCTAGC
CCTAGATCTGAAGGCGGCGGAGGTTCCGGAGGCGGAGG
ATCTGCTAGCACAAAGGGCCCCAGCGTGTTCCCTCTGGC
CCCTAGCAGCAAGAGCACATCTGGCGGAACAGCCGCCC
TGGGCTGCCTGGTGGAAGATTACTTCCCCGAGCCCGTGA
CCGTGTCCTGGAATTCTGGCGCCCTGACAAGCGGCGTGC
ACACCTTTCCAGCCGTGCTGCAGAGCAGCGGCCTGTACT
CTCTGAGCAGCGTCGTGACAGTGCCCAGCAGCTCTCTGG
GCACCCAGACCTACATCTGCAACGTGAACCACAAGCCC
AGCAACACCAAGGTGGACGAGAAGGTGGAACCCAAGTC
CTGC anti-FAP Fc hole See Table 2
chain 69 anti-FAP light See Table 2
chain
115 Dimeric hu 4- REGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWY
SDPGLAGVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELR
1BBL (71-254) - RVVAGEGSGSVSLALHLQPLRSAAGAAALALTVDLPPASS CL* Fc knob EARNSAFGFQGRLLHLSAGQRLGVHLHTEARARHAWQLT
QGATVLGLFRVTPEIPAGLPSPRSEGGGGSGGGGSREGPEL
chain SPDDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWYSDPGLA
GVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELRRVVAG
EGSGSVSLALHLQPLRSAAGAAALALTVDLPPASSEARNS
AFGFQGRLLHLSAGQRLGVHLHTEARARHAWQLTQGATV
LGLFRVTPEIPAGLPSPRSEGGGGSGGGGSRTVAAPSVFIFP
PSDRKLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGN
SQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTH
QGLSSPVTKSFNRGECDKTHTCPPCPAPEAAGGPSVFLFPP
KPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEV
HNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKV
SNKALGAPIEKTISKAKGQPREPQVYTLPPCRDELTKNQVS
LWCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSF
FLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSL
SPGK
116 Monomeric hu 4- REGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWY
SDPGLAGVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELR
1BBL (71-254) - RVVAGEGSGSVSLALHLQPLRSAAGAAALALTVDLPPASS CH1* EARNSAFGFQGRLLHLSAGQRLGVHLHTEARARHAWQLT
QGATVLGLFRVTPEIPAGLPSPRSEGGGGSGGGGSASTKGP
SVFPLAPSSKSTSGGTAALGCLVEDYFPEPVTVSWNSGALT
SGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHK
PSNTKVDEKVEPKSC
18 anti-FAP(28Hl) See Table 2
Fc hole chain
19 anti-FAP (28H1) See Table 2
light chain
Table 4 shows the cDNA and amino acid sequences of the monovalent FAP-targeted 4- 1BB ligand trimer-containing Fc (kih) fusion molecule Construct 1.3 (FAP split trimer with CHl-CL crossover in anti-FAP Fab and charged residues on the 4-lBBL containing chains). Table 4: Sequences of FAP-targeted human 4- IBB ligand trimer containing Fc (kih) fusion molecule Construct 1.3
SEQ ID Description Sequence
NO:
AGAGAGGGCCCTGAGCTGAGCCCCGATGATCCTGCTGG
131 Dimeric hu 4-
ACTGCTGGACCTGCGGCAGGGCATGTTTGCTCAGCTGGT
1BBL (71-254) - GGCCCAGAACGTGCTGCTGATCGATGGCCCCCTGTCCTG CHl* Fc knob GTACAGCGATCCTGGACTGGCTGGCGTGTCACTGACAGG
CGGCCTGAGCTACAAAGAGGACACCAAAGAACTGGTGG
chain TGGCCAAGGCCGGCGTGTACTACGTGTTCTTTCAGCTGG
AACTGCGGAGAGTGGTGGCCGGCGAAGGATCTGGCTCT
GTGTCTCTGGCCCTGCATCTGCAGCCTCTGAGAAGCGCT
GCTGGCGCTGCAGCTCTGGCACTGACAGTGGATCTGCCT
CCTGCCAGCTCCGAGGCCCGGAATAGCGCATTTGGGTTT
CAAGGCAGGCTGCTGCACCTGTCTGCCGGCCAGAGGCT
GGGAGTGCATCTGCACACAGAGGCCAGGGCTAGACACG
CCTGGCAGCTGACACAGGGCGCTACAGTGCTGGGCCTG
TTCAGAGTGACCCCCGAGATTCCAGCCGGCCTGCCTTCT
CCAAGAAGCGAAGGCGGAGGCGGATCTGGCGGCGGAG
GATCTAGAGAGGGACCCGAACTGTCCCCTGACGATCCA
GCCGGGCTGCTGGATCTGAGACAGGGAATGTTCGCCCA
GCTGGTGGCTCAGAATGTGCTGCTGATTGACGGACCTCT
GAGCTGGTACTCCGACCCAGGGCTGGCAGGGGTGTCCC
TGACTGGGGGACTGTCCTACAAAGAAGATACAAAAGAA
CAGCTGGAACTGAGGCGGGTGGTGGCTGGGGAGGGCTC
AGGATCTGTGTCCCTGGCTCTGCATCTGCAGCCACTGCG
CTCTGCTGCTGGCGCAGCTGCACTGGCTCTGACTGTGGA
CCTGCCACCAGCCTCTAGCGAGGCCAGAAACAGCGCCT
TCGGGTTCCAAGGACGCCTGCTGCATCTGAGCGCCGGAC
AGCGCCTGGGAGTGCATCTGCATACTGAAGCCAGAGCC
CGGCATGCTTGGCAGCTGACTCAGGGGGCAACTGTGCTG
GGACTGTTTCGCGTGACACCTGAGATCCCTGCCGGACTG
CCAAGCCCTAGATCAGAAGGGGGCGGAGGAAGCGGAG
GGGGAGGAAGTGCTAGCACCAAGGGCCCCTCCGTGTTC
CCCCTGGCCCCCAGCAGCAAGAGCACCAGCGGCGGCAC
AGCCGCTCTGGGCTGCCTGGTCGAGGACTACTTCCCCGA
GCCCGTGACCGTGTCCTGGAACAGCGGAGCCCTGACCTC
CGGCGTGCACACCTTCCCCGCCGTGCTGCAGAGTTCTGG
CCTGTATAGCCTGAGCAGCGTGGTCACCGTGCCTTCTAG
CAGCCTGGGCACCCAGACCTACATCTGCAACGTGAACC
ACAAGCCCAGCAACACCAAGGTGGACGAGAAGGTGGA
GCCCAAGAGCTGCGACAAAACTCACACATGCCCACCGT
GCCCAGCACCTGAAGCTGCAGGGGGACCGTCAGTCTTC
CTCTTCCCCCCAAAACCCAAGGACACCCTCATGATCTCC
CGGACCCCTGAGGTCACATGCGTGGTGGTGGACGTGAG
CCACGAAGACCCTGAGGTCAAGTTCAACTGGTACGTGG
ACGGCGTGGAGGTGCATAATGCCAAGACAAAGCCGCGG
GAGGAGCAGTACAACAGCACGTACCGTGTGGTCAGCGT
CCTCACCGTCCTGCACCAGGACTGGCTGAATGGCAAGG
AGTACAAGTGCAAGGTCTCCAACAAAGCCCTCGGCGCC CCCATCGAGAAAACCATCTCCAAAGCCAAAGGGCAGCC
CCGAGAACCACAGGTGTACACCCTGCCCCCATGCCGGG
ATGAGCTGACCAAGAACCAGGTCAGCCTGTGGTGCCTG
GTCAAAGGCTTCTATCCCAGCGACATCGCCGTGGAGTGG
GAGAGCAATGGGCAGCCGGAGAACAACTACAAGACCAC
GCCTCCCGTGCTGGACTCCGACGGCTCCTTCTTCCTCTAC
AGCAAGCTCACCGTGGACAAGAGCAGGTGGCAGCAGGG
GAACGTCTTCTCATGCTCCGTGATGCATGAGGCTCTGCA
CAACCACTACACGCAGAAGAGCCTCTCCCTGTCTCCGGG
TAAA
132 Monomeric hu 4- AGAGAGGGCCCTGAGCTGAGCCCCGATGATCCTGCTGG
ACTGCTGGACCTGCGGCAGGGCATGTTTGCTCAGCTGGT
1BBL (71-254) - GGCCCAGAACGTGCTGCTGATCGATGGCCCCCTGTCCTG CL* GTACAGCGATCCTGGACTGGCTGGCGTGTCACTGACAGG
CGGCCTGAGCTACAAAGAGGACACCAAAGAACTGGTGG
TGGCCAAGGCCGGCGTGTACTACGTGTTCTTTCAGCTGG
AACTGCGGAGAGTGGTGGCCGGCGAAGGATCTGGCTCT
GTGTCTCTGGCCCTGCATCTGCAGCCTCTGAGAAGCGCT
GCTGGCGCTGCAGCTCTGGCACTGACAGTGGATCTGCCT
CCTGCCAGCTCCGAGGCCCGGAATAGCGCATTTGGGTTT
CAAGGCAGGCTGCTGCACCTGTCTGCCGGCCAGAGGCT
GGGAGTGCATCTGCACACAGAGGCCAGGGCTAGACACG
CCTGGCAGCTGACACAGGGCGCTACAGTGCTGGGCCTG
TTCAGAGTGACCCCCGAGATTCCAGCCGGCCTGCCTTCT
CCAAGAAGCGAAGGCGGAGGCGGATCTGGCGGCGGAG
GATCTCGTACGGTGGCTGCACCATCTGTCTTCATCTTCCC
GCCATCTGATCGGAAGTTGAAATCTGGAACTGCCTCTGT
TGTGTGCCTGCTGAATAACTTCTATCCCAGAGAGGCCAA
AGTACAGTGGAAGGTGGATAACGCCCTCCAATCGGGTA
ACTCCCAGGAGAGTGTCACAGAGCAGGACAGCAAGGAC
AGCACCTACAGCCTCAGCAGCACCCTGACGCTGAGCAA
AGCAGACTACGAGAAACACAAAGTCTACGCCTGCGAAG
TCACCCATCAGGGCCTGAGCTCGCCCGTCACAAAGAGCT
TCAACAGGGGAGAGTGT
GAAGTGCAGCTGCTGGAATCCGGCGGAGGCCTGGTGCA
133 anti-FAP (VHCL)
GCCTGGCGGATCTCTGAGACTGTCCTGCGCCGCCTCCGG
(28H1) Fc hole CTTCACCTTCTCCTCCCACGCCATGTCCTGGGTCCGACA chain GGCTCCTGGCAAAGGCCTGGAATGGGTGTCCGCCATCTG
GGCCTCCGGCGAGCAGTACTACGCCGACTCTGTGAAGG
GCCGGTTCACCATCTCCCGGGACAACTCCAAGAACACCC
TGTACCTGCAGATGAACTCCCTGCGGGCCGAGGACACC
GCCGTGTACTACTGTGCCAAGGGCTGGCTGGGCAACTTC
GACTACTGGGGACAGGGCACCCTGGTCACCGTGTCCAG
CGCTAGCGTGGCCGCTCCCAGCGTGTTCATCTTCCCACC
CAGCGACGAGCAGCTGAAGTCCGGCACAGCCAGCGTGG
TGTGCCTGCTGAACAACTTCTACCCCCGCGAGGCCAAGG
TGCAGTGGAAGGTGGACAACGCCCTGCAGAGCGGCAAC
AGCCAGGAATCCGTGACCGAGCAGGACAGCAAGGACTC
CACCTACAGCCTGAGCAGCACCCTGACCCTGAGCAAGG
CCGACTACGAGAAGCACAAGGTGTACGCCTGCGAAGTG
ACCCACCAGGGCCTGTCCAGCCCCGTGACCAAGAGCTTC
AACCGGGGCGAGTGCGACAAGACCCACACCTGTCCCCC
TTGCCCTGCCCCTGAAGCTGCTGGTGGCCCTTCCGTGTT CCTGTTCCCCCCAAAGCCCAAGGACACCCTGATGATCAG
CCGGACCCCCGAAGTGACCTGCGTGGTGGTCGATGTGTC
CCACGAGGACCCTGAAGTGAAGTTCAATTGGTACGTGG
ACGGCGTGGAAGTGCACAATGCCAAGACCAAGCCGCGG
GAGGAGCAGTACAACAGCACGTACCGTGTGGTCAGCGT
CCTCACCGTCCTGCACCAGGACTGGCTGAATGGCAAGG
AGTACAAGTGCAAGGTCTCCAACAAAGCCCTCGGCGCC
CCCATCGAGAAAACCATCTCCAAAGCCAAAGGGCAGCC
CCGAGAACCACAGGTGTGCACCCTGCCCCCATCCCGGG
ATGAGCTGACCAAGAACCAGGTCAGCCTCTCGTGCGCA
GTCAAAGGCTTCTATCCCAGCGACATCGCCGTGGAGTGG
GAGAGCAATGGGCAGCCGGAGAACAACTACAAGACCAC
GCCTCCCGTGCTGGACTCCGACGGCTCCTTCTTCCTCGT
GAGCAAGCTCACCGTGGACAAGAGCAGGTGGCAGCAGG
GGAACGTCTTCTCATGCTCCGTGATGCATGAGGCTCTGC
ACAACCACTACACGCAGAAGAGCCTCTCCCTGTCTCCGG
GTAAA
134 anti-FAP GAGATCGTGCTGACCCAGTCTCCCGGCACCCTGAGCCTG
AGCCCTGGCGAGAGAGCCACCCTGAGCTGCAGAGCCAG
(VLCH1) (28H1) CCAGAGCGTGAGCCGGAGCTACCTGGCCTGGTATCAGC light chain AGAAGCCCGGCCAGGCCCCCAGACTGCTGATCATCGGC
GCCAGCACCCGGGCCACCGGCATCCCCGATAGATTCAG
CGGCAGCGGCTCCGGCACCGACTTCACCCTGACCATCAG
CCGGCTGGAACCCGAGGACTTCGCCGTGTACTACTGCCA
GCAGGGCCAGGTGATCCCCCCCACCTTCGGCCAGGGCA
CCAAGGTGGAAATCAAGAGCAGCGCTTCCACCAAAGGC
CCTTCCGTGTTTCCTCTGGCTCCTAGCTCCAAGTCCACCT
CTGGAGGCACCGCTGCTCTCGGATGCCTCGTGAAGGATT
ATTTTCCTGAGCCTGTGACAGTGTCCTGGAATAGCGGAG
CACTGACCTCTGGAGTGCATACTTTCCCCGCTGTGCTGC
AGTCCTCTGGACTGTACAGCCTGAGCAGCGTGGTGACAG
TGCCCAGCAGCAGCCTGGGCACCCAGACCTACATCTGC
AACGTGAACCACAAGCCCAGCAACACCAAGGTGGACAA
GAAGGTGGAACCCAAGTCTTGT
Dimeric hu 4- REGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWY
108
SDPGLAGVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELR
1BBL (71-254) - RVVAGEGSGSVSLALHLQPLRSAAGAAALALTVDLPPASS CHl* Fc knob EARNSAFGFQGRLLHLSAGQRLGVHLHTEARARHAWQLT
QGATVLGLFRVTPEIPAGLPSPRSEGGGGSGGGGSREGPEL
chain SPDDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWYSDPGLA
GVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELRRVVAG
EGSGSVSLALHLQPLRSAAGAAALALTVDLPPASSEARNS
AFGFQGRLLHLSAGQRLGVHLHTEARARHAWQLTQGATV
LGLFRVTPEIPAGLPSPRSEGGGGSGGGGSASTKGPSVFPLA
PSSKSTSGGTAALGCLVEDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKV
DEKVEPKSCDKTHTCPPCPAPEAAGGPSVFLFPPKPKDTLM
ISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKP
REEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALGA
PIEKTISKAKGQPREPQVYTLPPCRDELTKNQVSLWCLVKG
FYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTV
DKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK Monomeric hu 4- REGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWY
109
SDPGLAGVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELR
1BBL (71-254) - RVVAGEGSGSVSLALHLQPLRSAAGAAALALTVDLPPASS CL* EARNSAFGFQGRLLHLSAGQRLGVHLHTEARARHAWQLT
QGATVLGLFRVTPEIPAGLPSPRSEGGGGSGGGGSRTVAAP
SVFIFPPSDRKLKSGTASVVCLLNNFYPREAKVQWKVDNA
LQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYA
CEVTHQGLSSPVTKSFNRGEC anti-FAP (VHCL) EVQLLESGGGLVQPGGSLRLSCAASGFTFSSHAMSWVRQA
135
PGKGLEWVSAIWASGEQYYADSVKGRFTISRDNSKNTLYL
(28H1) Fc hole QMNSLRAEDTAVYYCAKGWLGNFDYWGQGTLVTVSSAS chain VAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWK
VDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKH
KVYACEVTHQGLSSPVTKSFNRGECDKTHTCPPCPAPEAA
GGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFN
WYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWL
NGKEYKCKVSNKALGAPIEKTISKAKGQPREPQVCTLPPSR
DELTKNQVSLSCAVKGFYPSDIAVEWESNGQPENNYKTTP
PVLDSDGSFFLVSKLTVDKSRWQQGNVFSCSVMHEALHN
HYTQKSLSLSPGK
EIVLTQSPGTLSLSPGERATLSCRASQSVSRSYLAWYQQKP
136 anti-FAP
GQAPRLLIIGASTRATGIPDRFSGSGSGTDFTLTISRLEPEDF
(VLCH1) (28H1) AVYYCQQGQVIPPTFGQGTKVEIKSSASTKGPSVFPLAPSS light chain KSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDK
KVEPKSC
Table 5 shows the cDNA and amino acid sequences of the monovalent FAP-targeted 4- 1BB ligand trimer-containing Fc (kih) fusion molecule Construct 1.4 (FAP split trimer with anti- FAP Fab, monomeric 4- IBB ligand fused to CHI-knob chain and charged residues on the 4- 1BBL containing chains).
Table 5: Sequences of FAP-targeted human 4-lBB ligand trimer containing Fc (kih) fusion molecule Construct 1.4
SEQ ID Description Sequence
NO:
137 Monomeric hu 4- AGAGAGGGCCCTGAGCTGAGCCCCGATGATCCTGCTGG
ACTGCTGGACCTGCGGCAGGGCATGTTTGCTCAGCTGGT
1BBL (71-254) - GGCCCAGAACGTGCTGCTGATCGATGGCCCCCTGTCCTG CHl* Fc knob GTACAGCGATCCTGGACTGGCTGGCGTGTCACTGACAGG
CGGCCTGAGCTACAAAGAGGACACCAAAGAACTGGTGG
chain TGGCCAAGGCCGGCGTGTACTACGTGTTCTTTCAGCTGG
AACTGCGGAGAGTGGTGGCCGGCGAAGGATCTGGCTCT
GTGTCTCTGGCCCTGCATCTGCAGCCTCTGAGAAGCGCT
GCTGGCGCTGCAGCTCTGGCTCTGACAGTGGATCTGCCT
CCTGCCAGCTCCGAGGCCCGGAATAGCGCATTTGGGTTT
CAAGGCCGGCTGCTGCACCTGTCTGCCGGCCAGAGACT GGGAGTGCATCTGCACACAGAGGCCAGAGCCAGGCACG
CCTGGCAGCTGACACAGGGCGCTACAGTGCTGGGCCTG
TTCAGAGTGACCCCCGAGATTCCTGCCGGCCTGCCTAGC
CCTAGATCTGAAGGCGGCGGAGGTTCCGGAGGCGGAGG
ATCTGCTAGCACCAAGGGCCCCTCCGTGTTCCCCCTGGC
CCCCAGCAGCAAGAGCACCAGCGGCGGCACAGCCGCTC
TGGGCTGCCTGGTCGAGGACTACTTCCCCGAGCCCGTGA
CCGTGTCCTGGAACAGCGGAGCCCTGACCTCCGGCGTGC
ACACCTTCCCCGCCGTGCTGCAGAGTTCTGGCCTGTATA
GCCTGAGCAGCGTGGTCACCGTGCCTTCTAGCAGCCTGG
GCACCCAGACCTACATCTGCAACGTGAACCACAAGCCC
AGCAACACCAAGGTGGACGAGAAGGTGGAGCCCAAGA
GCTGCGACAAAACTCACACATGCCCACCGTGCCCAGCA
CCTGAAGCTGCAGGGGGACCGTCAGTCTTCCTCTTCCCC
CCAAAACCCAAGGACACCCTCATGATCTCCCGGACCCCT
GAGGTCACATGCGTGGTGGTGGACGTGAGCCACGAAGA
CCCTGAGGTCAAGTTCAACTGGTACGTGGACGGCGTGG
AGGTGCATAATGCCAAGACAAAGCCGCGGGAGGAGCAG
TACAACAGCACGTACCGTGTGGTCAGCGTCCTCACCGTC
CTGCACCAGGACTGGCTGAATGGCAAGGAGTACAAGTG
CAAGGTCTCCAACAAAGCCCTCGGCGCCCCCATCGAGA
AAACCATCTCCAAAGCCAAAGGGCAGCCCCGAGAACCA
CAGGTGTACACCCTGCCCCCATGCCGGGATGAGCTGACC
AAGAACCAGGTCAGCCTGTGGTGCCTGGTCAAAGGCTTC
TATCCCAGCGACATCGCCGTGGAGTGGGAGAGCAATGG
GCAGCCGGAGAACAACTACAAGACCACGCCTCCCGTGC
TGGACTCCGACGGCTCCTTCTTCCTCTACAGCAAGCTCA
CCGTGGACAAGAGCAGGTGGCAGCAGGGGAACGTCTTC
TCATGCTCCGTGATGCATGAGGCTCTGCACAACCACTAC
ACGCAGAAGAGCCTCTCCCTGTCTCCGGGTAAA
Dimeric hu 4- AGAGAGGGCCCTGAGCTGAGCCCCGATGATCCTGCTGG
ACTGCTGGACCTGCGGCAGGGCATGTTTGCTCAGCTGGT
1BBL (71-254) - GGCCCAGAACGTGCTGCTGATCGATGGCCCCCTGTCCTG CL* GTACAGCGATCCTGGACTGGCTGGCGTGTCACTGACAGG
CGGCCTGAGCTACAAAGAGGACACCAAAGAACTGGTGG
TGGCCAAGGCCGGCGTGTACTACGTGTTCTTTCAGCTGG
AACTGCGGAGAGTGGTGGCCGGCGAAGGATCTGGCTCT
GTGTCTCTGGCCCTGCATCTGCAGCCTCTGAGAAGCGCT
GCTGGCGCTGCAGCTCTGGCACTGACAGTGGATCTGCCT
CCTGCCAGCTCCGAGGCCCGGAATAGCGCATTTGGGTTT
CAAGGCAGGCTGCTGCACCTGTCTGCCGGCCAGAGGCT
GGGAGTGCATCTGCACACAGAGGCCAGGGCTAGACACG
CCTGGCAGCTGACACAGGGCGCTACAGTGCTGGGCCTG
TTCAGAGTGACCCCCGAGATTCCAGCCGGCCTGCCTTCT
CCAAGAAGCGAAGGCGGAGGCGGATCTGGCGGCGGAG
GATCTAGAGAGGGACCCGAACTGTCCCCTGACGATCCA
GCCGGGCTGCTGGATCTGAGACAGGGAATGTTCGCCCA
GCTGGTGGCTCAGAATGTGCTGCTGATTGACGGACCTCT
GAGCTGGTACTCCGACCCAGGGCTGGCAGGGGTGTCCC
TGACTGGGGGACTGTCCTACAAAGAAGATACAAAAGAA
CAGCTGGAACTGAGGCGGGTGGTGGCTGGGGAGGGCTC AGGATCTGTGTCCCTGGCTCTGCATCTGCAGCCACTGCG CTCTGCTGCTGGCGCAGCTGCACTGGCTCTGACTGTGGA CCTGCCACCAGCCTCTAGCGAGGCCAGAAACAGCGCCT
TCGGGTTCCAAGGACGCCTGCTGCATCTGAGCGCCGGAC
AGCGCCTGGGAGTGCATCTGCATACTGAAGCCAGAGCC
CGGCATGCTTGGCAGCTGACTCAGGGGGCAACTGTGCTG
GGACTGTTTCGCGTGACACCTGAGATCCCTGCCGGACTG
CCAAGCCCTAGATCAGAAGGGGGCGGAGGTTCCGGAGG
GGGAGGATCTCGTACGGTGGCTGCACCATCTGTCTTCAT
CTTCCCGCCATCTGATCGGAAGTTGAAATCTGGAACTGC
CTCTGTTGTGTGCCTGCTGAATAACTTCTATCCCAGAGA
GGCCAAAGTACAGTGGAAGGTGGATAACGCCCTCCAAT
CGGGTAACTCCCAGGAGAGTGTCACAGAGCAGGACAGC
AAGGACAGCACCTACAGCCTCAGCAGCACCCTGACGCT
GAGCAAAGCAGACTACGAGAAACACAAAGTCTACGCCT
GCGAAGTCACCCATCAGGGCCTGAGCTCGCCCGTCACA
AAGAGCTTCAACAGGGGAGAGTGT anti-FAP (28H1) see Table 2
Fc hole chain anti-FAP (28H1) See Table 2
light chain
Monomelic hu 4- REGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWY
SDPGLAGVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELR
1BBL (71-254) - RVVAGEGSGSVSLALHLQPLRSAAGAAALALTVDLPPASS CL* Fc knob EARNSAFGFQGRLLHLSAGQRLGVHLHTEARARHAWQLT
QGATVLGLFRVTPEIPAGLPSPRSEGGGGSGGGGSREGPEL
chain SPDDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWYSDPGLA
GVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELRRVVAG
EGSGSVSLALHLQPLRSAAGAAALALTVDLPPASSEARNS
AFGFQGRLLHLSAGQRLGVHLHTEARARHAWQLTQGATV
LGLFRVTPEIPAGLPSPRSEGGGGSGGGGSASTKGPSVFPLA
PSSKSTSGGTAALGCLVEDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKV
DEKVEPKSCDKTHTCPPCPAPEAAGGPSVFLFPPKPKDTLM
ISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKP
REEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALGA
PIEKTISKAKGQPREPQVYTLPPCRDELTKNQVSLWCLVKG
FYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTV
DKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK
Dimeric hu 4- REGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWY
SDPGLAGVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELR
1BBL (71-254) - RVVAGEGSGSVSLALHLQPLRSAAGAAALALTVDLPPASS CL* EARNSAFGFQGRLLHLSAGQRLGVHLHTEARARHAWQLT
QGATVLGLFRVTPEIPAGLPSPRSEGGGGSGGGGSREGPEL
SPDDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWYSDPGLA
GVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELRRVVAG
EGSGSVSLALHLQPLRSAAGAAALALTVDLPPASSEARNS
AFGFQGRLLHLSAGQRLGVHLHTEARARHAWQLTQGATV
LGLFRVTPEIPAGLPSPRSEGGGGSGGGGSRTVAAPSVFIFP
PSDRKLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGN
SQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTH QGLS SP VTKSFNRGEC
18 anti-FAP (28H1) see Table 2
Fc hole chain
19 anti-FAP (28H1) see Table 2
light chain
Table 6 shows the cDNA and amino acid sequences of the bivalent FAP-targeted 4- IBB ligand trimer-containing Fc (kih) fusion molecule Construct 1.5 (FAP split trimer with 2 anti- FAP Fabs, dimeric and monomeric 4- IBB ligand fused at the C-terminus of each heavy chain, respectively).
Table 6: Sequences of FAP-targeted human 4-lBB ligand trimer containing Fc (kih) fusion molecule Construct 1.5
SEQ ID Description Sequence
NO:
141 anti-FAP (28H1) GAAGTGCAGCTGCTGGAATCCGGCGGAGGCCTGGTGCA
GCCTGGCGGATCTCTGAGACTGTCCTGCGCCGCCTCCGG
Fc hole chain CTTCACCTTCTCCTCCCACGCCATGTCCTGGGTCCGACA fused to dimeric GGCTCCTGGCAAAGGCCTGGAATGGGTGTCCGCCATCTG
GGCCTCCGGCGAGCAGTACTACGCCGACTCTGTGAAGG
hu 4-lBBL (71- GCCGGTTCACCATCTCCCGGGACAACTCCAAGAACACCC 254) TGTACCTGCAGATGAACTCCCTGCGGGCCGAGGACACC
GCCGTGTACTACTGTGCCAAGGGCTGGCTGGGCAACTTC
GACTACTGGGGACAGGGCACCCTGGTCACCGTGTCCAG
CGCTAGCACCAAGGGCCCCTCCGTGTTCCCCCTGGCCCC
CAGCAGCAAGAGCACCAGCGGCGGCACAGCCGCTCTGG
GCTGCCTGGTCAAGGACTACTTCCCCGAGCCCGTGACCG
TGTCCTGGAACAGCGGAGCCCTGACCTCCGGCGTGCAC
ACCTTCCCCGCCGTGCTGCAGAGTTCTGGCCTGTATAGC
CTGAGCAGCGTGGTCACCGTGCCTTCTAGCAGCCTGGGC
ACCCAGACCTACATCTGCAACGTGAACCACAAGCCCAG
CAACACCAAGGTGGACAAGAAGGTGGAGCCCAAGAGCT
GCGACAAAACTCACACATGCCCACCGTGCCCAGCACCT
GAAGCTGCAGGGGGACCGTCAGTCTTCCTCTTCCCCCCA
AAACCCAAGGACACCCTCATGATCTCCCGGACCCCTGA
GGTCACATGCGTGGTGGTGGACGTGAGCCACGAAGACC
CTGAGGTCAAGTTCAACTGGTACGTGGACGGCGTGGAG
GTGCATAATGCCAAGACAAAGCCGCGGGAGGAGCAGTA
CAACAGCACGTACCGTGTGGTCAGCGTCCTCACCGTCCT
GCACCAGGACTGGCTGAATGGCAAGGAGTACAAGTGCA
AGGTCTCCAACAAAGCCCTCGGCGCCCCCATCGAGAAA
ACCATCTCCAAAGCCAAAGGGCAGCCCCGAGAACCACA
GGTGTGCACCCTGCCCCCATCCCGGGATGAGCTGACCAA GAACCAGGTCAGCCTCTCGTGCGCAGTCAAAGGCTTCTA
TCCCAGCGACATCGCCGTGGAGTGGGAGAGCAATGGGC
AGCCGGAGAACAACTACAAGACCACGCCTCCCGTGCTG
GACTCCGACGGCTCCTTCTTCCTCGTGAGCAAGCTCACC
GTGGACAAGAGCAGGTGGCAGCAGGGGAACGTCTTCTC
ATGCTCCGTGATGCATGAGGCTCTGCACAACCACTACAC
GCAGAAGAGCCTCTCCCTGTCTCCGGGTGGAGGCGGCG
GAAGCGGAGGAGGAGGATCCAGAGAGGGCCCTGAGCTG
AGCCCCGATGATCCTGCTGGACTGCTGGACCTGCGGCAG
GGCATGTTTGCTCAGCTGGTGGCCCAGAACGTGCTGCTG
ATCGATGGCCCCCTGTCCTGGTACAGCGATCCTGGACTG
GCTGGCGTGTCACTGACAGGCGGCCTGAGCTACAAAGA
GGACACCAAAGAACTGGTGGTGGCCAAGGCCGGCGTGT
ACTACGTGTTCTTTCAGCTGGAACTGCGGAGAGTGGTGG
CCGGCGAAGGATCTGGCTCTGTGTCTCTGGCCCTGCATC
TGCAGCCTCTGAGAAGCGCTGCTGGCGCTGCAGCTCTGG
CACTGACAGTGGATCTGCCTCCTGCCAGCTCCGAGGCCC
GGAATAGCGCATTTGGGTTTCAAGGCAGGCTGCTGCACC
TGTCTGCCGGCCAGAGGCTGGGAGTGCATCTGCACACA
GAGGCCAGGGCTAGACACGCCTGGCAGCTGACACAGGG
CGCTACAGTGCTGGGCCTGTTCAGAGTGACCCCCGAGAT
TCCAGCCGGCCTGCCTTCTCCAAGAAGCGAAGGCGGAG
GCGGATCTGGCGGCGGAGGATCTAGAGAGGGACCCGAA
CTGTCCCCTGACGATCCAGCCGGGCTGCTGGATCTGAGA
CAGGGAATGTTCGCCCAGCTGGTGGCTCAGAATGTGCTG
CTGATTGACGGACCTCTGAGCTGGTACTCCGACCCAGGG
CTGGCAGGGGTGTCCCTGACTGGGGGACTGTCCTACAAA
GAAGATACAAAAGAACTGGTGGTGGCTAAAGCTGGGGT
GGCTGGGGAGGGCTCAGGATCTGTGTCCCTGGCTCTGCA
TCTGCAGCCACTGCGCTCTGCTGCTGGCGCAGCTGCACT
GGCTCTGACTGTGGACCTGCCACCAGCCTCTAGCGAGGC
CAGAAACAGCGCCTTCGGGTTCCAAGGACGCCTGCTGC
ATCTGAGCGCCGGACAGCGCCTGGGAGTGCATCTGCAT
ACTGAAGCCAGAGCCCGGCATGCTTGGCAGCTGACTCA
GGGGGCAACTGTGCTGGGACTGTTTCGCGTGACACCTGA
GATCCCTGCCGGACTGCCAAGCCCTAGATCAGAA
GAAGTGCAGCTGCTGGAATCCGGCGGAGGCCTGGTGCA
anti-FAP (28H1)
GCCTGGCGGATCTCTGAGACTGTCCTGCGCCGCCTCCGG
Fc knob chain CTTCACCTTCTCCTCCCACGCCATGTCCTGGGTCCGACA fused to GGCTCCTGGCAAAGGCCTGGAATGGGTGTCCGCCATCTG
GGCCTCCGGCGAGCAGTACTACGCCGACTCTGTGAAGG
monomeric hu 4- GCCGGTTCACCATCTCCCGGGACAACTCCAAGAACACCC 1BBL (71-254) TGTACCTGCAGATGAACTCCCTGCGGGCCGAGGACACC
GCCGTGTACTACTGTGCCAAGGGCTGGCTGGGCAACTTC
GACTACTGGGGACAGGGCACCCTGGTCACCGTGTCCAG
CGCTAGCACCAAGGGCCCATCGGTCTTCCCCCTGGCACC
CTCCTCCAAGAGCACCTCTGGGGGCACAGCGGCCCTGG
GCTGCCTGGTCAAGGACTACTTCCCCGAACCGGTGACGG
TGTCGTGGAACTCAGGCGCCCTGACCAGCGGCGTGCAC
ACCTTCCCGGCTGTCCTACAGTCCTCAGGACTCTACTCC
CTCAGCAGCGTGGTGACCGTGCCCTCCAGCAGCTTGGGC
ACCCAGACCTACATCTGCAACGTGAATCACAAGCCCAG
CAACACCAAGGTGGACAAGAAAGTTGAGCCCAAATCTT GTGACAAAACTCACACATGCCCACCGTGCCCAGCACCT
GAAGCTGCAGGGGGACCGTCAGTCTTCCTCTTCCCCCCA
AAACCCAAGGACACCCTCATGATCTCCCGGACCCCTGA
GGTCACATGCGTGGTGGTGGACGTGAGCCACGAAGACC
CTGAGGTCAAGTTCAACTGGTACGTGGACGGCGTGGAG
GTGCATAATGCCAAGACAAAGCCGCGGGAGGAGCAGTA
CAACAGCACGTACCGTGTGGTCAGCGTCCTCACCGTCCT
GCACCAGGACTGGCTGAATGGCAAGGAGTACAAGTGCA
AGGTCTCCAACAAAGCCCTCGGCGCCCCCATCGAGAAA
ACCATCTCCAAAGCCAAAGGGCAGCCCCGAGAACCACA
GGTGTACACCCTGCCCCCCTGCAGAGATGAGCTGACCA
AGAACCAGGTGTCCCTGTGGTGTCTGGTCAAGGGCTTCT
ACCCCAGCGATATCGCCGTGGAGTGGGAGAGCAACGGC
CAGCCTGAGAACAACTACAAGACCACCCCCCCTGTGCT
GGACAGCGACGGCAGCTTCTTCCTGTACTCCAAACTGAC
CGTGGACAAGAGCCGGTGGCAGCAGGGCAACGTGTTCA
GCTGCAGCGTGATGCACGAGGCCCTGCACAACCACTAC
ACCCAGAAGTCCCTGAGCCTGAGCCCCGGCGGAGGCGG
CGGAAGCGGAGGAGGAGGATCCAGAGAGGGCCCTGAG
CTGAGCCCCGATGATCCTGCTGGACTGCTGGACCTGCGG
CAGGGCATGTTTGCTCAGCTGGTGGCCCAGAACGTGCTG
CTGATCGATGGCCCCCTGTCCTGGTACAGCGATCCTGGA
CTGGCTGGCGTGTCACTGACAGGCGGCCTGAGCTACAA
AGAGGACACCAAAGAACTGGTGGTGGCCAAGGCCGGCG
TGTACTACGTGTTCTTTCAGCTGGAACTGCGGAGAGTGG
TGGCCGGCGAAGGATCTGGCTCTGTGTCTCTGGCCCTGC
ATCTGCAGCCTCTGAGAAGCGCTGCTGGCGCTGCAGCTC
TGGCACTGACAGTGGATCTGCCTCCTGCCAGCTCCGAGG
CCCGGAATAGCGCATTTGGGTTTCAAGGCAGGCTGCTGC
ACCTGTCTGCCGGCCAGAGGCTGGGAGTGCATCTGCAC
ACAGAGGCCAGGGCTAGACACGCCTGGCAGCTGACACA
GGGCGCTACAGTGCTGGGCCTGTTCAGAGTGACCCCCG
AGATTCCAGCCGGCCTGCCTTCTCCAAGAAGCGAA anti-FAP (28H1) see Table 2
light chain
EVQLLESGGGLVQPGGSLRLSCAASGFTFSSHAMSWVRQA
anti-FAP (28H1)
PGKGLEWVSAIWASGEQYYADSVKGRFTISRDNSKNTLYL
Fc hole chain QMNSLRAEDTAVYYCAKGWLGNFDYWGQGTLVTVSSAS fused to dimeric TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNS
GALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICN
hu 4-lBBL (71- VNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGGPSVF 254) LFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDG
VEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYK
CKVSNKALGAPIEKTISKAKGQPREPQVCTLPPSRDELTKN
QVSLSCAVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSD
GSFFLVSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKS
LSLSPGGGGGSGGGGSREGPELSPDDPAGLLDLRQGMFAQ
LVAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYKEDTKELV
VAKAGVYYVFFQLELRRVVAGEGSGSVSLALHLQPLRSAA
GAAALALTVDLPPASSEARNSAFGFQGRLLHLSAGQRLGV
HLHTEARARHAWQLTQGATVLGLFRVTPEIPAGLPSPRSEG
GGGSGGGGSREGPELSPDDPAGLLDLRQGMFAQLVAQNV LLIDGPLSWYSDPGLAGVSLTGGLSYKEDTKELVVAKAGV
YYVFFQLELRRVVAGEGSGSVSLALHLQPLRSAAGAAALA LTVDLPPASSEARNSAFGFQGRLLHLSAGQRLGVHLHTEA RARHAWQLTQGATVLGLFRVTPEIPAGLPSPRSE
122 anti-FAP (28H1) EVQLLESGGGLVQPGGSLRLSCAASGFTFSSHAMSWVRQA
PGKGLEWVSAIWASGEQYYADSVKGRFTISRDNSKNTLYL
Fc knob chain QMNSLRAEDTAVYYCAKGWLGNFDYWGQGTLVTVSSAS fused to TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNS
GALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICN
monomeric hu 4- VNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGGPSVF 1BBL (71-254) LFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDG
VEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYK
CKVSNKALGAPIEKTISKAKGQPREPQVYTLPPCRDELTKN
QVSLWCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSD
GSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKS
LSLSPGGGGGSGGGGSREGPELSPDDPAGLLDLRQGMFAQ
LVAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYKEDTKELV
VAKAGVYYVFFQLELRRVVAGEGSGSVSLALHLQPLRSAA
GAAALALTVDLPPASSEARNSAFGFQGRLLHLSAGQRLGV
HLHTEARARHAWQLTQGATVLGLFRVTPEIPAGLPSPRSE
19 anti-FAP (28H1) see Table 2
light chain
Table 7 shows the cDNA and amino acid sequences of the monovalent FAP-targeted 4- 1BB ligand trimer-containing Fc (kih) fusion molecule Construct 1.6 (FAP split trimer with anti- FAP Fab, monomeric 4- IBB ligand fused to CL* via a (G4S) -linker).
Table 7: Sequences of FAP-targeted human 4-lBB ligand trimer containing Fc (kih) fusion molecule Construct 1.6
SEQ ID Description Sequence
NO:
131 Dimeric hu 4- see Table 4
1BBL (71-254) - CHl* Fc knob
chain
143 Monomeric hu 4- AGAGAGGGCCCTGAGCTGAGCCCCGATGATCCTGCTGG
ACTGCTGGACCTGCGGCAGGGCATGTTTGCTCAGCTGGT
1BBL (71-254) - GGCCCAGAACGTGCTGCTGATCGATGGCCCCCTGTCCTG (G4S)i- CL* GTACAGCGATCCTGGACTGGCTGGCGTGTCACTGACAGG
CGGCCTGAGCTACAAAGAGGACACCAAAGAACTGGTGG
TGGCCAAGGCCGGCGTGTACTACGTGTTCTTTCAGCTGG
AACTGCGGAGAGTGGTGGCCGGCGAAGGATCTGGCTCT GTGTCTCTGGCCCTGCATCTGCAGCCTCTGAGAAGCGCT
GCTGGCGCTGCAGCTCTGGCACTGACAGTGGATCTGCCT
CCTGCCAGCTCCGAGGCCCGGAATAGCGCATTTGGGTTT
CAAGGCAGGCTGCTGCACCTGTCTGCCGGCCAGAGGCT
GGGAGTGCATCTGCACACAGAGGCCAGGGCTAGACACG
CCTGGCAGCTGACACAGGGCGCTACAGTGCTGGGCCTG
TTCAGAGTGACCCCCGAGATTCCAGCCGGCCTGCCTTCT
CCAAGAAGCGAAGGCGGAGGCGGATCTCGTACGGTGGC
TGCACCATCTGTCTTCATCTTCCCGCCATCTGATCGGAA
GTTGAAATCTGGAACTGCCTCTGTTGTGTGCCTGCTGAA
TAACTTCTATCCCAGAGAGGCCAAAGTACAGTGGAAGG
TGGATAACGCCCTCCAATCGGGTAACTCCCAGGAGAGT
GTCACAGAGCAGGACAGCAAGGACAGCACCTACAGCCT
CAGCAGCACCCTGACGCTGAGCAAAGCAGACTACGAGA
AACACAAAGTCTACGCCTGCGAAGTCACCCATCAGGGC
CTGAGCTCGCCCGTCACAAAGAGCTTCAACAGGGGAGA
GTGT
68 anti-FAP (28H1) see Table 2
Fc hole chain
69 anti-FAP (28H1) see Table 2
light chain
108 Dimeric hu 4- see Table 4
1BBL (71-254) - CHl* Fc knob
chain
110 Monomelic hu 4- REGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWY
SDPGLAGVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELR
1BBL (71-254) - RVVAGEGSGSVSLALHLQPLRSAAGAAALALTVDLPPASS (G4S)i- CL* EARNSAFGFQGRLLHLSAGQRLGVHLHTEARARHAWQLT
QGATVLGLFRVTPEIPAGLPSPRSEGGGGSRTVAAPSVFIFP
PSDRKLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGN
SQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTH
QGLS SP VTKSFNRGEC
18 anti-FAP (28H1) see Table 2
Fc hole chain
19 anti-FAP (28H1) see Table 2
light chain
Table 8 shows the cDNA and amino acid sequences of the bivalent FAP-targeted 4- IBB ligand trimer-containing Fc (kih) fusion molecule Construct 7 (FAP split trimer with double anti- FAP on the N-terminus of Fc hole chain and charged residues on crossed CHI and CL fused to 4- IBB ligands).
Table 8: Sequences of FAP-targeted human 4- IBB ligand trimer containing Fc (kih) fusion molecule Construct 1.7
SEQ ID Description Sequence
NO:
129 Dimeric hu 4- see Table 3
1BBL (71-254) - CL* Fc knob
chain
130 Monomeric hu 4- see Table 3
1BBL (71-254) - CH1*
144 [anti-FAP GAAGTGCAGCTGCTGGAATCCGGCGGAGGCCTGGTGCA
GCCTGGCGGATCTCTGAGACTGTCCTGCGCCGCCTCCGG
(28H1)]2 Fc hole CTTCACCTTCTCCTCCCACGCCATGTCCTGGGTCCGACA chain GGCTCCTGGCAAAGGCCTGGAATGGGTGTCCGCCATCTG
GGCCTCCGGCGAGCAGTACTACGCCGACTCTGTGAAGG
GCCGGTTCACCATCTCCCGGGACAACTCCAAGAACACCC
TGTACCTGCAGATGAACTCCCTGCGGGCCGAGGACACC
GCCGTGTACTACTGTGCCAAGGGCTGGCTGGGCAACTTC
GACTACTGGGGACAGGGCACCCTGGTCACCGTGTCCAG
CGCTAGCACAAAGGGACCTAGCGTGTTCCCCCTGGCCCC
CAGCAGCAAGTCTACATCTGGCGGAACAGCCGCCCTGG
GCTGCCTCGTGAAGGACTACTTTCCCGAGCCCGTGACCG
TGTCCTGGAACTCTGGCGCTCTGACAAGCGGCGTGCACA
CCTTTCCAGCCGTGCTGCAGAGCAGCGGCCTGTACTCTC
TGAGCAGCGTCGTGACAGTGCCCAGCAGCTCTCTGGGC
ACCCAGACCTACATCTGCAACGTGAACCACAAGCCCAG
CAACACCAAGGTGGACAAGAAGGTGGAACCCAAGAGCT
GCGACGGCGGAGGGGGATCTGGCGGCGGAGGATCCGAA
GTGCAGCTGCTGGAATCCGGCGGAGGCCTGGTGCAGCC
TGGCGGATCTCTGAGACTGTCCTGCGCCGCCTCCGGCTT
CACCTTCTCCTCCCACGCCATGTCCTGGGTCCGACAGGC
TCCTGGCAAAGGCCTGGAATGGGTGTCCGCCATCTGGGC
CTCCGGCGAGCAGTACTACGCCGACTCTGTGAAGGGCC
GGTTCACCATCTCCCGGGACAACTCCAAGAACACCCTGT
ACCTGCAGATGAACTCCCTGCGGGCCGAGGACACCGCC
GTGTACTACTGTGCCAAGGGCTGGCTGGGCAACTTCGAC
TACTGGGGACAGGGCACCCTGGTCACCGTGTCCAGCGCT
AGCACCAAGGGCCCCTCCGTGTTCCCCCTGGCCCCCAGC
AGCAAGAGCACCAGCGGCGGCACAGCCGCTCTGGGCTG
CCTGGTCAAGGACTACTTCCCCGAGCCCGTGACCGTGTC
CTGGAACAGCGGAGCCCTGACCTCCGGCGTGCACACCTT CCCCGCCGTGCTGCAGAGTTCTGGCCTGTATAGCCTGAG
CAGCGTGGTCACCGTGCCTTCTAGCAGCCTGGGCACCCA
GACCTACATCTGCAACGTGAACCACAAGCCCAGCAACA
CCAAGGTGGACAAGAAGGTGGAGCCCAAGAGCTGCGAC
AAAACTCACACATGCCCACCGTGCCCAGCACCTGAAGC
TGCAGGGGGACCGTCAGTCTTCCTCTTCCCCCCAAAACC
CAAGGACACCCTCATGATCTCCCGGACCCCTGAGGTCAC
ATGCGTGGTGGTGGACGTGAGCCACGAAGACCCTGAGG
TCAAGTTCAACTGGTACGTGGACGGCGTGGAGGTGCAT
AATGCCAAGACAAAGCCGCGGGAGGAGCAGTACAACA
GCACGTACCGTGTGGTCAGCGTCCTCACCGTCCTGCACC
AGGACTGGCTGAATGGCAAGGAGTACAAGTGCAAGGTC
TCCAACAAAGCCCTCGGCGCCCCCATCGAGAAAACCAT
CTCCAAAGCCAAAGGGCAGCCCCGAGAACCACAGGTGT
GCACCCTGCCCCCATCCCGGGATGAGCTGACCAAGAAC
CAGGTCAGCCTCTCGTGCGCAGTCAAAGGCTTCTATCCC
AGCGACATCGCCGTGGAGTGGGAGAGCAATGGGCAGCC
GGAGAACAACTACAAGACCACGCCTCCCGTGCTGGACT
CCGACGGCTCCTTCTTCCTCGTGAGCAAGCTCACCGTGG
ACAAGAGCAGGTGGCAGCAGGGGAACGTCTTCTCATGC
TCCGTGATGCATGAGGCTCTGCACAACCACTACACGCAG
AAGAGCCTCTCCCTGTCTCCGGGTAAA
anti-FAP (28H1) see Table 2
light chain
Dimeric hu 4- see Table 3
1BBL (71-254) - CL* Fc knob
chain
Monomeric hu 4- see Table 3
1BBL (71-254) - CH1*
[anti-FAP EVQLLESGGGLVQPGGSLRLSCAASGFTFSSHAMSWVRQA
PGKGLEWVSAIWASGEQYYADSVKGRFTISRDNSKNTLYL
(28H1)]2 Fc hole QMNSLRAEDTAVYYCAKGWLGNFDYWGQGTLVTVSSAS chain TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNS
GALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICN
VNHKPSNTKVDKKVEPKSCDGGGGSGGGGSEVQLLESGG
GLVQPGGSLRLSCAASGFTFSSHAMSWVRQAPGKGLEWV
SAIWASGEQYYADSVKGRFTISRDNSKNTLYLQMNSLRAE
DTAVYYCAKGWLGNFDYWGQGTLVTVSSASTKGPSVFPL
APSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVH
TFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNT
KVDKKVEPKSCDKTHTCPPCPAPEAAGGPSVFLFPPKPKDT
LMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKT
KPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKAL
GAPIEKTISKAKGQPREPQVCTLPPSRDELTKNQVSLSCAV
KGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLVSKL
TVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK 19 anti-FAP (28H1) see Table 2
light chain
Table 9 shows the cDNA and amino acid sequences of the bivalent FAP-targeted 4- IBB ligand trimer-containing Fc (kih) fusion molecule Construct 1.8 (FAP split trimer with 4- IBB ligands fused to anti-FAP CrossFab, with charged residues, on knob chain).
Table 9: Sequences of FAP-targeted human 4- IBB ligand trimer containing Fc (kih) fusion molecule Construct 1.8
SEQ ID Description Sequence
NO:
146 Dimeric hu 4- AGAGAGGGCCCTGAGCTGAGCCCCGATGATCCTGCTGG
ACTGCTGGACCTGCGGCAGGGCATGTTTGCTCAGCTGGT
1BBL (71-254) - GGCCCAGAACGTGCTGCTGATCGATGGCCCCCTGTCCTG FAP (VHCL*) Fc GTACAGCGATCCTGGACTGGCTGGCGTGTCACTGACAGG
CGGCCTGAGCTACAAAGAGGACACCAAAGAACTGGTGG
knob chain TGGCCAAGGCCGGCGTGTACTACGTGTTCTTTCAGCTGG
AACTGCGGAGAGTGGTGGCCGGCGAAGGATCTGGCTCT
GTGTCTCTGGCCCTGCATCTGCAGCCTCTGAGAAGCGCT
GCTGGCGCTGCAGCTCTGGCACTGACAGTGGATCTGCCT
CCTGCCAGCTCCGAGGCCCGGAATAGCGCATTTGGGTTT
CAAGGCAGGCTGCTGCACCTGTCTGCCGGCCAGAGGCT
GGGAGTGCATCTGCACACAGAGGCCAGGGCTAGACACG
CCTGGCAGCTGACACAGGGCGCTACAGTGCTGGGCCTG
TTCAGAGTGACCCCCGAGATTCCAGCCGGCCTGCCTTCT
CCAAGAAGCGAAGGCGGAGGCGGATCTGGCGGCGGAG
GATCTAGAGAGGGACCCGAACTGTCCCCTGACGATCCA
GCCGGGCTGCTGGATCTGAGACAGGGAATGTTCGCCCA
GCTGGTGGCTCAGAATGTGCTGCTGATTGACGGACCTCT
GAGCTGGTACTCCGACCCAGGGCTGGCAGGGGTGTCCC
TGACTGGGGGACTGTCCTACAAAGAAGATACAAAAGAA
CAGCTGGAACTGAGGCGGGTGGTGGCTGGGGAGGGCTC
AGGATCTGTGTCCCTGGCTCTGCATCTGCAGCCACTGCG
CTCTGCTGCTGGCGCAGCTGCACTGGCTCTGACTGTGGA
CCTGCCACCAGCCTCTAGCGAGGCCAGAAACAGCGCCT
TCGGGTTCCAAGGACGCCTGCTGCATCTGAGCGCCGGAC
AGCGCCTGGGAGTGCATCTGCATACTGAAGCCAGAGCC
CGGCATGCTTGGCAGCTGACTCAGGGGGCAACTGTGCTG
GGACTGTTTCGCGTGACACCTGAGATCCCTGCCGGACTG
CCAAGCCCTAGATCAGAAGGGGGCGGAGGTTCCGGAGG
CGGAGGATCTGAGGTGCAGCTGCTGGAATCCGGCGGAG
GCCTGGTGCAGCCTGGCGGATCTCTGAGACTGTCCTGCG
CCGCCTCCGGCTTCACCTTCTCCTCCCACGCCATGTCCTG
GGTCCGACAGGCTCCTGGCAAAGGCCTGGAATGGGTGT
CCGCCATCTGGGCCTCCGGCGAGCAGTACTACGCCGACT
CTGTGAAGGGCCGGTTCACCATCTCCCGGGACAACTCCA AGAACACCCTGTACCTGCAGATGAACTCCCTGCGGGCC
GAGGACACCGCCGTGTACTACTGTGCCAAGGGCTGGCT
GGGCAACTTCGACTACTGGGGCCAGGGCACCCTGGTCA
CCGTGTCCAGCGCTAGCGTGGCTGCACCATCTGTCTTTA
TCTTCCCACCCAGCGACCGGAAGCTGAAGTCTGGCACA
GCCAGCGTCGTGTGCCTGCTGAATAACTTCTACCCCCGC
GAGGCCAAGGTGCAGTGGAAGGTGGACAATGCCCTGCA
GAGCGGCAACAGCCAGGAAAGCGTGACCGAGCAGGAC
AGCAAGGACTCCACCTACAGCCTGAGCAGCACCCTGAC
CCTGAGCAAGGCCGACTACGAGAAGCACAAGGTGTACG
CCTGCGAAGTGACCCACCAGGGCCTGTCTAGCCCCGTGA
CCAAGAGCTTCAACCGGGGCGAGTGCGACAAGACCCAC
ACCTGTCCTCCATGCCCTGCCCCTGAAGCTGCTGGCGGC
CCTAGCGTGTTCCTGTTCCCCCCAAAGCCCAAGGACACC
CTGATGATCAGCCGGACCCCTGAAGTGACCTGCGTGGTG
GTGGATGTGTCCCACGAGGACCCTGAAGTGAAGTTCAAT
TGGTACGTGGACGGCGTGGAAGTGCACAATGCCAAGAC
CAAGCCGCGGGAGGAGCAGTACAACAGCACGTACCGTG
TGGTCAGCGTCCTCACCGTCCTGCACCAGGACTGGCTGA
ATGGCAAGGAGTACAAGTGCAAGGTCTCCAACAAAGCC
CTCGGCGCCCCCATCGAGAAAACCATCTCCAAAGCCAA
AGGGCAGCCCCGAGAACCACAGGTGTACACCCTGCCCC
CATGCCGGGATGAGCTGACCAAGAACCAGGTCAGCCTG
TGGTGCCTGGTCAAAGGCTTCTATCCCAGCGACATCGCC
GTGGAGTGGGAGAGCAATGGGCAGCCGGAGAACAACTA
CAAGACCACGCCTCCCGTGCTGGACTCCGACGGCTCCTT
CTTCCTCTACAGCAAGCTCACCGTGGACAAGAGCAGGT
GGCAGCAGGGGAACGTCTTCTCATGCTCCGTGATGCATG
AGGCTCTGCACAACCACTACACGCAGAAGAGCCTCTCC
CTGTCTCCGGGTAAA
Monomeric hu 4- AGAGAGGGCCCTGAGCTGAGCCCCGATGATCCTGCTGG
ACTGCTGGACCTGCGGCAGGGCATGTTTGCTCAGCTGGT
1BBL (71-254) - GGCCCAGAACGTGCTGCTGATCGATGGCCCCCTGTCCTG FAP (VLCH1*) GTACAGCGATCCTGGACTGGCTGGCGTGTCACTGACAGG
CGGCCTGAGCTACAAAGAGGACACCAAAGAACTGGTGG
TGGCCAAGGCCGGCGTGTACTACGTGTTCTTTCAGCTGG
AACTGCGGAGAGTGGTGGCCGGCGAAGGATCTGGCTCT
GTGTCTCTGGCCCTGCATCTGCAGCCTCTGAGAAGCGCT
GCTGGCGCTGCAGCTCTGGCTCTGACAGTGGATCTGCCT
CCTGCCAGCTCCGAGGCCCGGAATAGCGCATTTGGGTTT
CAAGGCCGGCTGCTGCACCTGTCTGCCGGCCAGAGACT
GGGAGTGCATCTGCACACAGAGGCCAGAGCCAGGCACG
CCTGGCAGCTGACACAGGGCGCTACAGTGCTGGGCCTG
TTCAGAGTGACCCCCGAGATTCCTGCCGGCCTGCCTAGC
CCTAGATCTGAAGGCGGCGGAGGTTCCGGAGGCGGAGG
ATCTGAGATCGTGCTGACCCAGTCTCCCGGCACCCTGAG
CCTGAGCCCTGGCGAGAGAGCCACCCTGAGCTGCAGAG
CCAGCCAGAGCGTGAGCCGGAGCTACCTGGCCTGGTAT
CAGCAGAAGCCCGGCCAGGCCCCCAGACTGCTGATCAT
CGGCGCCAGCACCCGGGCCACCGGCATCCCCGATAGAT
TCAGCGGCAGCGGCTCCGGCACCGACTTCACCCTGACCA
TCAGCCGGCTGGAACCCGAGGACTTCGCCGTGTACTACT
GCCAGCAGGGCCAGGTGATCCCCCCCACCTTCGGCCAG
GGCACCAAGGTGGAAATCAAGTCCTCTGCTAGCACAAA GGGCCCCAGCGTGTTCCCTCTGGCCCCTAGCAGCAAGAG
CACATCTGGCGGAACAGCCGCCCTGGGCTGCCTGGTGG
AAGATTACTTCCCCGAGCCCGTGACCGTGTCCTGGAATT
CTGGCGCCCTGACAAGCGGCGTGCACACCTTTCCAGCCG
TGCTGCAGAGCAGCGGCCTGTACTCTCTGAGCAGCGTCG
TGACAGTGCCCAGCAGCTCTCTGGGCACCCAGACCTACA
TCTGCAACGTGAACCACAAGCCCAGCAACACCAAGGTG
GACGAGAAGGTGGAACCCAAGTCCTGC
anti-FAP (28H1) see Table 2
Fc hole chain anti-FAP (28H1) see Table 2
light chain
Dimeric hu 4- REGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWY
SDPGLAGVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELR
1BBL (71-254) - RVVAGEGSGSVSLALHLQPLRSAAGAAALALTVDLPPASS FAP (VHCL*) Fc EARNSAFGFQGRLLHLSAGQRLGVHLHTEARARHAWQLT
QGATVLGLFRVTPEIPAGLPSPRSEGGGGSGGGGSREGPEL
knob chain SPDDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWYSDPGLA
GVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELRRVVAG
EGSGSVSLALHLQPLRSAAGAAALALTVDLPPASSEARNS
AFGFQGRLLHLSAGQRLGVHLHTEARARHAWQLTQGATV
LGLFRVTPEIPAGLPSPRSEGGGGSGGGGSEVQLLESGGGL
VQPGGSLRLSCAASGFTFSSHAMSWVRQAPGKGLEWVSAI
WASGEQYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDT
AVYYCAKGWLGNFDYWGQGTLVTVSSASVAAPSVFIFPPS
DRKLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQ
ESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQG
LSSPVTKSFNRGECDKTHTCPPCPAPEAAGGPSVFLFPPKPK
DTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNA
KTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNK
ALGAPIEKTISKAKGQPREPQVYTLPPCRDELTKNQVSLWC
LVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYS
KLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK
Monomeric hu 4- REGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWY
SDPGLAGVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELR
1BBL (71-254) - RVVAGEGSGSVSLALHLQPLRSAAGAAALALTVDLPPASS FAP (VLCH1*) EARNSAFGFQGRLLHLSAGQRLGVHLHTEARARHAWQLT
QGATVLGLFRVTPEIPAGLPSPRSEGGGGSGGGGSEIVLTQS
PGTLSLSPGERATLSCRASQSVSRSYLAWYQQKPGQAPRL
LIIGASTRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQ
QGQVIPPTFGQGTKVEIKSSASTKGPSVFPLAPSSKSTSGGT
AALGCLVEDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDEKVEPKSC
anti-FAP (28H1) see Table 2
Fc hole chain anti-FAP (28H1) see Table 2
light chain Table 10 shows the cDNA and amino acid sequences of the monovalent FAP-targeted 4- 1BB ligand (52-254) trimer-containing Fc (kih) fusion molecule Construct 1.9 (FAP split trimer with 4-1BBL ectodomain amino acids 52-254 and charged residues on ligand chains). Table 10: Sequences of FAP-targeted human 4-lBB ligand trimer containing Fc (kih) fusion molecule Construct 1.9
SEQ ID Description Sequence
NO:
150 Dimeric hu 4- CCTTGGGCTGTGTCTGGCGCTAGAGCCTCTCCTGGATCT
GCCGCCAGCCCCAGACTGAGAGAGGGACCTGAGCTGAG
1BBL (52-254) - CCCCGATGATCCTGCCGGACTGCTGGATCTGAGACAGG CHI* Fc knob GCATGTTCGCCCAGCTGGTGGCCCAGAACGTGCTGCTGA
TCGATGGCCCCCTGTCCTGGTACAGCGATCCTGGACTGG
chain CTGGCGTGTCACTGACAGGCGGCCTGAGCTACAAAGAG
GACACCAAAGAACTGGTGGTGGCCAAGGCCGGCGTGTA
CTACGTGTTCTTTCAGCTGGAACTGCGGAGAGTGGTGGC
CGGCGAGGGATCTGGATCTGTGTCTCTGGCCCTGCATCT
GCAGCCCCTGAGAAGCGCTGCTGGCGCTGCAGCTCTGG
CACTGACAGTGGATCTGCCTCCTGCCAGCTCCGAGGCCC
GGAATAGCGCATTTGGGTTTCAAGGCAGACTGCTGCACC
TGTCTGCCGGCCAGAGGCTGGGAGTGCATCTGCACACA
GAGGCCAGGGCTAGACACGCCTGGCAGCTGACACAGGG
CGCTACAGTGCTGGGCCTGTTCAGAGTGACCCCCGAGAT
TCCAGCCGGACTGCCCAGCCCTAGATCTGAAGGCGGCG
GAGGAAGCGGAGGCGGAGGATCCCCTTGGGCTGTGTCT
GGCGCTAGAGCCTCTCCTGGATCTGCCGCCAGCCCCAGA
CTGAGAGAGGGACCTGAGCTGAGCCCCGATGATCCTGC
CGGACTGCTGGACCTGCGGCAGGGAATGTTCGCTCAGCT
GGTGGCTCAGAATGTGCTGCTGATTGACGGACCTCTGTC
CTGGTACTCCGACCCTGGCCTGGCAGGGGTGTCCCTGAC
TGGGGGACTGTCCTACAAAGAAGATACAAAAGAACTGG
TGGAACTGAGGCGGGTGGTGGCTGGGGAGGGCTCAGGA
TCTGTGTCCCTGGCTCTGCATCTGCAGCCTCTGCGCTCTG
CTGCTGGCGCAGCTGCACTGGCTCTGACTGTGGACCTGC
CACCAGCCTCTAGCGAGGCCAGAAACAGCGCCTTCGGG
TTCCAAGGACGGCTGCTGCATCTGAGCGCCGGACAGCG
CCTGGGAGTGCATCTGCATACTGAAGCCAGAGCCCGGC
ATGCTTGGCAGCTGACCCAGGGGGCAACTGTGCTGGGA
CTGTTTCGCGTGACACCTGAGATCCCCGCTGGCCTGCCT
AGCCCAAGAAGTGAAGGGGGAGGCGGATCTGGCGGAG
GGGGATCTGCTAGCACCAAGGGCCCCTCCGTGTTCCCCC
TGGCCCCCAGCAGCAAGAGCACCAGCGGCGGCACAGCC
GCTCTGGGCTGCCTGGTCGAGGACTACTTCCCCGAGCCC
GTGACCGTGTCCTGGAACAGCGGAGCCCTGACCTCCGG
CGTGCACACCTTCCCCGCCGTGCTGCAGAGTTCTGGCCT
GTATAGCCTGAGCAGCGTGGTCACCGTGCCTTCTAGCAG
CCTGGGCACCCAGACCTACATCTGCAACGTGAACCACA AGCCCAGCAACACCAAGGTGGACGAGAAGGTGGAGCCC
AAGAGCTGCGACAAAACTCACACATGCCCACCGTGCCC
AGCACCTGAAGCTGCAGGGGGACCGTCAGTCTTCCTCTT
CCCCCCAAAACCCAAGGACACCCTCATGATCTCCCGGAC
CCCTGAGGTCACATGCGTGGTGGTGGACGTGAGCCACG
AAGACCCTGAGGTCAAGTTCAACTGGTACGTGGACGGC
GTGGAGGTGCATAATGCCAAGACAAAGCCGCGGGAGGA
GCAGTACAACAGCACGTACCGTGTGGTCAGCGTCCTCAC
CGTCCTGCACCAGGACTGGCTGAATGGCAAGGAGTACA
AGTGCAAGGTCTCCAACAAAGCCCTCGGCGCCCCCATC
GAGAAAACCATCTCCAAAGCCAAAGGGCAGCCCCGAGA
ACCACAGGTGTACACCCTGCCCCCATGCCGGGATGAGCT
GACCAAGAACCAGGTCAGCCTGTGGTGCCTGGTCAAAG
GCTTCTATCCCAGCGACATCGCCGTGGAGTGGGAGAGC
AATGGGCAGCCGGAGAACAACTACAAGACCACGCCTCC
CGTGCTGGACTCCGACGGCTCCTTCTTCCTCTACAGCAA
GCTCACCGTGGACAAGAGCAGGTGGCAGCAGGGGAACG
TCTTCTCATGCTCCGTGATGCATGAGGCTCTGCACAACC
ACTACACGCAGAAGAGCCTCTCCCTGTCTCCGGGTAAA
CCTTGGGCTGTGTCTGGCGCTAGAGCCTCTCCTGGATCT
Monomeric hu 4-
GCCGCCAGCCCCAGACTGAGAGAGGGACCTGAGCTGAG
1BBL (52-254) - CCCCGATGATCCTGCCGGACTGCTGGATCTGAGACAGG CL* GCATGTTCGCCCAGCTGGTGGCCCAGAACGTGCTGCTGA
TCGATGGCCCCCTGTCCTGGTACAGCGATCCTGGACTGG
CTGGCGTGTCACTGACAGGCGGCCTGAGCTACAAAGAG
GACACCAAAGAACTGGTGGTGGCCAAGGCCGGCGTGTA
CTACGTGTTCTTTCAGCTGGAACTGCGGAGAGTGGTGGC
CGGCGAGGGATCTGGATCTGTGTCTCTGGCCCTGCATCT
GCAGCCCCTGAGAAGCGCTGCTGGCGCTGCAGCTCTGG
CACTGACAGTGGATCTGCCTCCTGCCAGCTCCGAGGCCC
GGAATAGCGCATTTGGGTTTCAAGGCAGGCTGCTGCACC
TGTCTGCCGGCCAGAGGCTGGGAGTGCATCTGCACACA
GAGGCCAGGGCTAGACACGCCTGGCAGCTGACACAGGG
CGCTACAGTGCTGGGCCTGTTCAGAGTGACCCCCGAGAT
TCCAGCCGGCCTGCCTTCTCCAAGAAGCGAAGGCGGAG
GCGGATCTGGCGGCGGAGGATCTCGTACGGTGGCTGCA
CCATCTGTCTTCATCTTCCCGCCATCTGATCGGAAGTTGA
AATCTGGAACTGCCTCTGTTGTGTGCCTGCTGAATAACT
TCTATCCCAGAGAGGCCAAAGTACAGTGGAAGGTGGAT
AACGCCCTCCAATCGGGTAACTCCCAGGAGAGTGTCAC
AGAGCAGGACAGCAAGGACAGCACCTACAGCCTCAGCA
GCACCCTGACGCTGAGCAAAGCAGACTACGAGAAACAC
AAAGTCTACGCCTGCGAAGTCACCCATCAGGGCCTGAG
CTCGCCCGTCACAAAGAGCTTCAACAGGGGAGAGTGT
anti-FAP (28H1) see Table 2
Fc hole chain anti-FAP (28H1) see Table 2
light chain
PWAVSGARASPGSAASPRLREGPELSPDDPAGLLDLRQGM
Dimeric hu 4- FAQLVAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYKEDTK
1BBL (52-254) - ELVVAKAGVYYVFFQLELRRVVAGEGSGSVSLALHLQPLR CHI* Fc knob SAAGAAALALTVDLPPASSEARNSAFGFQGRLLHLSAGQR
LGVHLHTEARARHAWQLTQGATVLGLFRVTPEIPAGLPSP
chain RSEGGGGSGGGGSPWAVSGARASPGSAASPRLREGPELSP
DDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWYSDPGLAG
VSLTGGLSYKEDTKELVVAKAGVYYVFFQLELRRVVAGE
GSGSVSLALHLQPLRSAAGAAALALTVDLPPASSEARNSAF
GFQGRLLHLSAGQRLGVHLHTEARARHAWQLTQGATVLG
LFRVTPEIPAGLPSPRSEGGGGSGGGGSASTKGPSVFPLAPS
SKSTSGGTAALGCLVEDYFPEPVTVSWNSGALTSGVHTFP
AVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVD
EKVEPKSCDKTHTCPPCPAPEAAGGPSVFLFPPKPKDTLMI
SRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPR
EEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALGAP
IEKTISKAKGQPREPQVYTLPPCRDELTKNQVSLWCLVKGF
YPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVD
KSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK
112 Monomeric hu 4- PWAVSGARASPGSAASPRLREGPELSPDDPAGLLDLRQGM
FAQLVAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYKEDTK
1BBL (52-254) - ELVVAKAGVYYVFFQLELRRVVAGEGSGSVSLALHLQPLR CL* SAAGAAALALTVDLPPASSEARNSAFGFQGRLLHLSAGQR
LGVHLHTEARARHAWQLTQGATVLGLFRVTPEIPAGLPSP
RSEGGGGSGGGGSRTVAAPSVFIFPPSDRKLKSGTASVVCL
LNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYS
LSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
18 anti-FAP (28H1) see Table 2
Fc hole chain
19 anti-FAP (28H1) see Table 2
light chain
Table 11 shows the cDNA and amino acid sequences of the monovalent FAP-targeted 4- 1BB ligand (80-254) trimer-containing Fc (kih) fusion molecule Construct 1.10 (FAP split trimer with 4-1BBL ectodomain amino acids 80-254 and charged residues on ligand chains).
Table 11: Sequences of FAP-targeted human 4- IBB ligand trimer containing Fc (kih) fusion molecule Construct 10
SEQ ID Description Sequence
NO:
152 Dimeric hu 4- GATCCTGCCGGCCTGCTGGATCTGCGGCAGGGAATGTTT
GCCCAGCTGGTGGCCCAGAACGTGCTGCTGATCGATGG
1BBL (80-254) - CCCCCTGAGCTGGTACAGCGATCCTGGACTGGCTGGCGT CHI* Fc knob GTCACTGACAGGCGGCCTGAGCTACAAAGAGGACACCA
AAGAACTGGTGGTGGCCAAGGCCGGCGTGTACTACGTG
chain TTCTTTCAGCTGGAACTGCGGAGAGTGGTGGCCGGCGAA
GGATCTGGCTCTGTGTCTCTGGCCCTGCATCTGCAGCCC
CTGAGAAGCGCTGCTGGCGCTGCAGCTCTGGCACTGAC AGTGGATCTGCCTCCTGCCAGCTCCGAGGCCCGGAATAG
CGCATTTGGGTTTCAAGGCAGACTGCTGCACCTGTCTGC
CGGCCAGAGGCTGGGAGTGCATCTGCACACAGAGGCCA
GGGCTAGACACGCCTGGCAGCTGACACAGGGCGCTACA
GTGCTGGGCCTGTTCAGAGTGACCCCCGAGATTCCAGCC
GGACTGCCCAGCCCTAGATCTGAAGGCGGCGGAGGAAG
CGGAGGCGGAGGATCCGACCCAGCTGGACTGCTGGACC
TGCGGCAGGGAATGTTCGCTCAGCTGGTGGCTCAGAATG
TGCTGCTGATTGACGGACCTCTGTCCTGGTACTCCGACC
CTGGCCTGGCAGGGGTGTCCCTGACTGGGGGACTGTCCT
ACAAAGAAGATACAAAAGAACTGGTGGTGGCTAAAGCT
GGGGTGTACTATGTGTTTTTTCAGCTGGAACTGAGGCGG
GTGGTGGCTGGGGAGGGCTCAGGATCTGTGTCCCTGGCT
CTGCATCTGCAGCCTCTGCGCTCTGCTGCTGGCGCAGCT
GCACTGGCTCTGACTGTGGACCTGCCACCAGCCTCTAGC
GAGGCCAGAAACAGCGCCTTCGGGTTCCAAGGACGGCT
GCTGCATCTGAGCGCCGGACAGCGCCTGGGAGTGCATC
TGCATACTGAAGCCAGAGCCCGGCATGCTTGGCAGCTG
ACCCAGGGGGCAACTGTGCTGGGACTGTTTCGCGTGACA
CCTGAGATCCCCGCTGGCCTGCCTAGCCCAAGAAGTGA
AGGGGGAGGCGGATCTGGCGGAGGGGGATCTGCTAGCA
CCAAGGGCCCCTCCGTGTTCCCCCTGGCCCCCAGCAGCA
AGAGCACCAGCGGCGGCACAGCCGCTCTGGGCTGCCTG
GTCGAGGACTACTTCCCCGAGCCCGTGACCGTGTCCTGG
AACAGCGGAGCCCTGACCTCCGGCGTGCACACCTTCCCC
GCCGTGCTGCAGAGTTCTGGCCTGTATAGCCTGAGCAGC
GTGGTCACCGTGCCTTCTAGCAGCCTGGGCACCCAGACC
TACATCTGCAACGTGAACCACAAGCCCAGCAACACCAA
GGTGGACGAGAAGGTGGAGCCCAAGAGCTGCGACAAAA
CTCACACATGCCCACCGTGCCCAGCACCTGAAGCTGCAG
GGGGACCGTCAGTCTTCCTCTTCCCCCCAAAACCCAAGG
ACACCCTCATGATCTCCCGGACCCCTGAGGTCACATGCG
TGGTGGTGGACGTGAGCCACGAAGACCCTGAGGTCAAG
TTCAACTGGTACGTGGACGGCGTGGAGGTGCATAATGCC
AAGACAAAGCCGCGGGAGGAGCAGTACAACAGCACGT
ACCGTGTGGTCAGCGTCCTCACCGTCCTGCACCAGGACT
GGCTGAATGGCAAGGAGTACAAGTGCAAGGTCTCCAAC
AAAGCCCTCGGCGCCCCCATCGAGAAAACCATCTCCAA
AGCCAAAGGGCAGCCCCGAGAACCACAGGTGTACACCC
TGCCCCCATGCCGGGATGAGCTGACCAAGAACCAGGTC
AGCCTGTGGTGCCTGGTCAAAGGCTTCTATCCCAGCGAC
ATCGCCGTGGAGTGGGAGAGCAATGGGCAGCCGGAGAA
CAACTACAAGACCACGCCTCCCGTGCTGGACTCCGACG
GCTCCTTCTTCCTCTACAGCAAGCTCACCGTGGACAAGA
GCAGGTGGCAGCAGGGGAACGTCTTCTCATGCTCCGTGA
TGCATGAGGCTCTGCACAACCACTACACGCAGAAGAGC
CTCTCCCTGTCTCCGGGTAAA
GATCCTGCCGGCCTGCTGGATCTGCGGCAGGGAATGTTT
Monomeric hu 4-
GCCCAGCTGGTGGCCCAGAACGTGCTGCTGATCGATGG
1BBL (80-254) - CCCCCTGAGCTGGTACAGCGATCCTGGACTGGCTGGCGT CL* GTCACTGACAGGCGGCCTGAGCTACAAAGAGGACACCA
AAGAACTGGTGGTGGCCAAGGCCGGCGTGTACTACGTG
TTCTTTCAGCTGGAACTGCGGAGAGTGGTGGCCGGCGAA
GGATCTGGCTCTGTGTCTCTGGCCCTGCATCTGCAGCCC CTGAGAAGCGCTGCTGGCGCTGCAGCTCTGGCACTGAC
AGTGGATCTGCCTCCTGCCAGCTCCGAGGCCCGGAATAG
CGCATTTGGGTTTCAAGGCAGGCTGCTGCACCTGTCTGC
CGGCCAGAGGCTGGGAGTGCATCTGCACACAGAGGCCA
GGGCTAGACACGCCTGGCAGCTGACACAGGGCGCTACA
GTGCTGGGCCTGTTCAGAGTGACCCCCGAGATTCCAGCC
GGCCTGCCTTCTCCAAGAAGCGAAGGCGGAGGCGGATC
TGGCGGCGGAGGATCTCGTACGGTGGCTGCACCATCTGT
CTTCATCTTCCCGCCATCTGATCGGAAGTTGAAATCTGG
AACTGCCTCTGTTGTGTGCCTGCTGAATAACTTCTATCCC
AGAGAGGCCAAAGTACAGTGGAAGGTGGATAACGCCCT
CCAATCGGGTAACTCCCAGGAGAGTGTCACAGAGCAGG
ACAGCAAGGACAGCACCTACAGCCTCAGCAGCACCCTG
ACGCTGAGCAAAGCAGACTACGAGAAACACAAAGTCTA
CGCCTGCGAAGTCACCCATCAGGGCCTGAGCTCGCCCGT
CACAAAGAGCTTCAACAGGGGAGAGTGT
anti-FAP (28H1) see Table 2
Fc hole chain anti-FAP (28H1) see Table 2
light chain
Dimeric hu 4- DPAGLLDLRQGMFAQLVAQNVLLIDGPLSWYSDPGLAGV
SLTGGLSYKEDTKELVVAKAGVYYVFFQLELRRVVAGEGS
1BBL (80-254) - GSVSLALHLQPLRSAAGAAALALTVDLPPASSEARNSAFGF CHI* Fc knob QGRLLHLSAGQRLGVHLHTEARARHAWQLTQGATVLGLF
RVTPEIPAGLPSPRSEGGGGSGGGGSDPAGLLDLRQGMFA
chain QLVAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYKEDTKEL
VVAKAGVYYVFFQLELRRVVAGEGSGSVSLALHLQPLRSA
AGAAALALTVDLPPASSEARNSAFGFQGRLLHLSAGQRLG
VHLHTEARARHAWQLTQGATVLGLFRVTPEIPAGLPSPRSE
GGGGSGGGGSASTKGPSVFPLAPSSKSTSGGTAALGCLVE
DYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTV
PSSSLGTQTYICNVNHKPSNTKVDEKVEPKSCDKTHTCPPC
PAPEAAGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHED
PEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVL
HQDWLNGKEYKCKVSNKALGAPIEKTISKAKGQPREPQVY
TLPPCRDELTKNQVSLWCLVKGFYPSDIAVEWESNGQPEN
NYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMH
EALHNHYTQKSLSLSPGK
Monomelic hu 4- DPAGLLDLRQGMFAQLVAQNVLLIDGPLSWYSDPGLAGV
SLTGGLSYKEDTKELVVAKAGVYYVFFQLELRRVVAGEGS
1BBL (80-254) - GSVSLALHLQPLRSAAGAAALALTVDLPPASSEARNSAFGF CL* QGRLLHLSAGQRLGVHLHTEARARHAWQLTQGATVLGLF
RVTPEIPAGLPSPRSEGGGGSGGGGSRTVAAPSVFIFPPSDR
KLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQES
VTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLS
SPVTKSFNRGEC
anti-FAP (28H1) see Table 2
Fc hole chain 19 anti-FAP (28H1) see Table 2
light chain
1.2 Production of FAP (28H1) targeted split trimeric 4-1BB ligand Fc fusion constructs
The targeted TNF ligand trimer-containing Fc (kih) fusion antigen binding molecule encoding sequences were cloned into a plasmid vector, which drives expression of the insert from an MPSV promoter and contains a synthetic polyA sequence located at the 3' end of the CDS. In addition, the vector contains an EBV OriP sequence for episomal maintenance of the plasmid.
The targeted TNF ligand trimer-containing Fc (kih) fusion antigen binding molecule was produced by co-transfecting HEK293-EBNA cells with the mammalian expression vectors using polyethylenimine. The cells were transfected with the corresponding expression vectors at a 1: 1:1: 1 ratio (e.g. "vector dimeric ligand-(CHl or CL)- knob chain": "vector monomeric ligand fusion-(CL or CHI)": "vector anti-FAP Fab-hole heavy chain": "vector anti-FAP light chain") for the Constructs 1, 2, 3, 4, 6, 7, 8, 9, 10. For the bivalent Construct 5, a 1: 1: 1 ratio ("vector hole heavy chain": "vector knob heavy chain": "vector anti-FAP light chain") was used.
For production in 500 mL shake flasks, 300 million HEK293 EBNA cells were seeded 24 hours before transfection. For transfection cells were centrifuged for 10 minutes at 210 x g, and the supernatant was replaced by 20 mL pre- warmed CD CHO medium. Expression vectors (200 μg of total DNA) were mixed in 20 mL CD CHO medium. After addition of 540 PEI, the solution was vortexed for 15 seconds and incubated for 10 minutes at room temperature.
Afterwards, cells were mixed with the DNA/PEI solution, transferred to a 500 mL shake flask and incubated for 3 hours at 37 °C in an incubator with a 5% C02 atmosphere. After the incubation, 160 mL of Excell medium supplemented with 6 mM L-Glutamine, 5 g/L PEPSOY and 1.2 mM valproic acid was added and cells were cultured for 24 hours. One day after transfection 12% Feed 7 and Glucose (final concentration 3 g/L) were added. After culturing for 7 days, the supernatant was collected by centrifugation for 30-40 minutes at 400 x g. The solution was sterile filtered (0.22 μιη filter), supplemented with sodium azide to a final concentration of 0.01 % (w/v), and kept at 4 °C.
The targeted TNF ligand trimer-containing Fc (kih) fusion antigen binding molecule was purified from cell culture supernatants by affinity chromatography using Protein A, followed by size exclusion chromatography. For affinity chromatography, the supernatant was loaded on a MabSelect Sure column (CV = 5-15 mL, resin from GE Healthcare) equilibrated with 20 mM sodium phosphate, 20 mM sodium citrate buffer (pH 7.5). Unbound protein was removed by washing with at least 6 column volumes of the same buffer. The bound protein was eluted using either a linear gradient (20 CV) or a step elution (8 CV) with 20 mM sodium citrate, 100 mM Sodium chloride, 100 mM Glycine buffer (pH 3.0). For the linear gradient an additional 4 column volumes step elution was applied.
The pH of collected fractions was adjusted by adding 1/10 (v/v) of 0.5M sodium phosphate, pH 8.0. The protein was concentrated prior to loading on a HiLoad Superdex 200 column (GE Healthcare) equilibrated with 20 mM Histidine, 140 mM sodium chloride, 0.01% (v/v) Tween20 solution of pH 6.0. The protein concentration was determined by measuring the optical density (OD) at 280 nm, using a molar extinction coefficient calculated on the basis of the amino acid sequence.
Purity and molecular weight of the targeted TNF ligand trimer-containing Fc (kih) fusion antigen binding molecule was analyzed by SDS-PAGE in the presence and absence of a reducing agent (5 mM 1,4-dithiotreitol) and staining with Coomassie SimpleBlue™ SafeStain (Invitrogen USA) or or CE-SDS using Caliper LabChip GXII (Perkin Elmer).. The aggregate content of samples was analyzed using a TSKgel G3000 SW XL analytical size-exclusion column (Tosoh) equilibrated in 25 mM K2HP04, 125 mM NaCl, 200 mM L-Arginine Monohydrocloride, 0.02 % (w/v) NaN3, pH 6.7 running buffer at 25°C.
Table 12 summarizes the yield and final monomer content of the FAP-targeted 4-1BBL trimer-containing Fc (kih) fusion antigen binding molecules.
Table 12: Biochemical Analysis of the FAP (28Hl)-targeted 4-1BBL trimer-containing Fc (kih) fusion antigen binding molecules
Monomer
Yield
Construct
[mg/1] [%]
(SEC)
Construct 1.1 12.7 95
Construct 1.2 25.2 97
Construct 1.3 22 92
Construct 1.4 14.2 99
Construct 1.5 14 99
Construct 1.6 12 98
Construct 1.7 3.4 99
Construct 1.8 5.4 98
Construct 1.9 11.2 98
Construct 1.10 19.8 99 1.3 Preparation of targeted murine 4-1BB ligand trimer-containing Fc fusion antigen binding molecules
Similarly to targeted human 4- IBB ligand trimer-containing Fc fusion antigen binding molecules, murine FAP-targeted 4-lBBL trimer-containing Fc fusion antigen binding molecules were prepared.
The DNA sequence encoding part of the ectodomain (amino acids 104-309) of murine 4- 1BB ligand was synthetized according to the Q3U1Z9- 1 sequence of Uniprot database (SEQ ID NO:70). For Construct M. l the cysteines at positions 137, 160 and 246 were mutated to Serine by standard PCR methods, whereas for Construct M.2 the cysteine at position 160 was mutated to Serine (C160S).
The murine ligand was assembled as described for the human 4- lBBL and as depicted in Figure 3A and 3B. The dimeric 4- lBBL, separated by (G4S)2 linkers, was fused to the murine IgGl-CL domain (Figure 3A) and the monomeric 4- lBBL was fused to murine IgGl-CH domain (Figure 3B). The polypeptide encoding the dimeric 4- IBB ligand fused to murine CL domain was subcloned in frame with the murine IgGl heavy chain CH2 and CH3 domains to build the Constructs as depicted in Figure 3C.
For the murine constructs, mutations Lys392Asp and Lys409Asp (DD) were introduced in the heavy chain containing the murine 4-lBBL and mutations Glu356Lys and Asp399Lys (KK) were introduced in the heavy chain containing the anti-FAP Fab to obtain asymmetric molecules (Gunasekaran K. et al, J Biol. Chem., 2010, Jun 18;285(25): 19637-46).
Mutations Asp265Ala and Pro329Gly (DAPG) were introduced in the constant region of the heavy chains to abrogate binding to Fc gamma receptors.
Table 13 shows, respectively, the cDNA and amino acid sequences of the FAP-targeted murine 4- IBB ligand trimer-containing Fc fusion antigen binding molecule Construct M. l .
Table 13: Sequences of FAP-targeted murine Construct M.l
SEQ ID Description Sequence
NO:
71 Dimeric murine AGAACCGAGCCCAGACCCGCCCTGACCATCACCACCAG
4-lBBL (104- CCCTAACCTGGGCACCAGAGAGAACAACGCCGACCAAG
309, TGACCCCCGTGTCCCACATCGGCAGCCCCAATACCACAC
C137,160,246S) - AGCAGGGCAGCCCTGTGTTCGCCAAGCTGCTGGCCAAG
AACCAGGCCAGCCTGAGCAACACCACCCTGAACTGGCA CL Fc DD chain
CAGCCAGGATGGCGCCGGAAGCAGCTATCTGAGCCAGG
GCCTGAGATACGAAGAGGACAAGAAAGAACTGGTGGTG
GACAGCCCTGGCCTGTACTACGTGTTCCTGGAACTGAAG CTGAGCCCCACCTTCACCAACACCGGCCACAAGGTGCA
GGGCTGGGTGTCACTGGTGCTGCAGGCCAAACCCCAGG
TGGACGACTTCGACAACCTGGCCCTGACCGTGGAACTGT
TCCCCAGCAGCATGGAAAACAAGCTGGTGGATCGGAGC
TGGTCCCAGCTTCTGCTGCTGAAGGCCGGACACAGACTG
AGCGTGGGCCTGAGGGCTTATCTGCACGGCGCCCAGGA
CGCCTACAGAGACTGGGAGCTGAGCTACCCCAACACAA
CCAGCTTCGGCCTGTTCCTCGTGAAGCCCGACAACCCTT
GGGAAGGCGGCGGAGGATCTGGCGGAGGCGGATCTAGA
ACAGAGCCTCGGCCTGCCCTGACAATTACCACATCCCCC
AATCTGGGCACCCGGGAAAACAATGCAGATCAAGTGAC
ACCTGTGTCTCATATTGGCTCCCCAAACACTACCCAGCA
GGGCTCCCCCGTGTTTGCTAAACTGCTGGCTAAAAATCA
GGCCTCCCTGTCTAACACAACACTGAACTGGCACTCCCA
GGACGGCGCTGGCAGCTCTTACCTGAGTCAGGGACTGC
GCTATGAGGAAGATAAGAAAGAACTGGTGGTGGATTCC
CCCGGACTGTACTATGTGTTTCTGGAACTGAAACTGTCC
CCTACCTTTACAAATACCGGGCACAAAGTGCAGGGATG
GGTGTCCCTGGTGCTGCAGGCTAAGCCTCAGGTGGACGA
TTTTGATAATCTGGCTCTGACAGTGGAACTGTTTCCTAG
CAGCATGGAAAACAAGCTGGTGGACAGAAGCTGGTCCC
AGCTCCTGCTGCTGAAGGCCGGACACAGACTGAGCGTG
GGCCTGAGAGCCTATCTGCACGGCGCCCAGGACGCCTA
CAGAGACTGGGAGCTGAGCTACCCCAACACAACCAGCT
TCGGCCTGTTCCTCGTGAAGCCCGACAACCCTTGGGAAG
GCGGCGGAGGATCTGGCGGAGGCGGATCCAGAGCTGAT
GCTGCCCCTACCGTGTCCATCTTCCCACCCAGCAGCGAG
CAGCTGACATCTGGGGGAGCTAGCGTCGTGTGCTTCCTG
AACAACTTCTACCCCAAGGACATCAACGTGAAGTGGAA
GATCGACGGCAGCGAGCGGCAGAACGGCGTGCTGAATA
GCTGGACCGACCAGGACAGCAAGGACTCCACCTACAGC
ATGAGCAGCACCCTGACCCTGACCAAGGACGAGTACGA
GCGGCACAACAGCTACACATGCGAGGCCACCCACAAGA
CCAGCACCAGCCCCATCGTGAAGTCCTTCAACCGGAAC
GAGTGCGTGCCCAGAGACTGCGGCTGCAAGCCTTGCAT
CTGCACCGTGCCTGAGGTGTCCAGCGTGTTCATCTTCCC
ACCCAAGCCCAAGGACGTGCTGACCATCACCCTGACAC
CCAAAGTGACCTGCGTGGTGGTGGCCATCAGCAAGGAT
GACCCCGAGGTGCAGTTCAGTTGGTTCGTGGACGACGTG
GAAGTGCACACCGCTCAGACCAAGCCCAGAGAGGAACA
GATCAACAGCACCTTCAGAAGCGTGTCCGAGCTGCCCAT
CATGCACCAGGACTGGCTGAACGGCAAAGAATTCAAGT
GCAGAGTGAACAGCGCCGCCTTTGGCGCCCCTATCGAG
AAAACCATCTCCAAGACCAAGGGCAGACCCAAGGCCCC
CCAGGTGTACACAATCCCCCCACCCAAAGAACAGATGG
CCAAGGACAAGGTGTCCCTGACCTGCATGATCACCAATT
TCTTCCCAGAGGATATCACCGTGGAATGGCAGTGGAAC
GGCCAGCCCGCCGAGAACTACGACAACACCCAGCCTAT
CATGGACACCGACGGCTCCTACTTCGTGTACAGCGACCT
GAACGTGCAGAAGTCCAACTGGGAGGCCGGCAACACCT
TCACCTGTAGCGTGCTGCACGAGGGCCTGCACAACCACC
ACACCGAGAAGTCCCTGTCCCACAGCCCTGGCAAG
Monomeric AGAACCGAGCCCAGACCCGCCCTGACCATCACCACCAG murine 4- 1BBL CCCTAACCTGGGCACCAGAGAGAACAACGCCGACCAAG (104-309, TGACCCCCGTGTCCCACATCGGCAGCCCCAATACCACAC
C137,160,246S) - AGCAGGGCAGCCCTGTGTTCGCCAAGCTGCTGGCCAAG
CL AACCAGGCCAGCCTGAGCAACACCACCCTGAACTGGCA
CAGCCAGGATGGCGCCGGAAGCAGCTATCTGAGCCAGG
GCCTGAGATACGAAGAGGACAAGAAAGAACTGGTGGTG
GACAGCCCTGGCCTGTACTACGTGTTCCTGGAACTGAAG
CTGAGCCCCACCTTCACCAACACCGGCCACAAGGTGCA
GGGCTGGGTGTCACTGGTGCTGCAGGCCAAACCCCAGG
TGGACGACTTCGACAACCTGGCCCTGACCGTGGAACTGT
TCCCCAGCAGCATGGAAAACAAGCTGGTGGATCGGAGC
TGGTCCCAGCTTCTGCTGCTGAAGGCCGGACACAGACTG
AGCGTGGGCCTGAGGGCCTATCTGCATGGCGCCCAGGA
CGCCTACAGAGACTGGGAGCTGAGCTACCCCAACACAA
CCAGCTTCGGCCTGTTCCTCGTGAAGCCCGACAACCCTT
GGGAAGGCGGCGGAGGCTCCGGAGGAGGCGGAAGCGC
TAAGACCACCCCCCCCAGCGTGTACCCTCTGGCCCCTGG
ATCTGCCGCCCAGACCAACAGCATGGTGACCCTGGGCT
GCCTGGTGAAGGGCTACTTCCCCGAGCCTGTGACCGTGA
CCTGGAACAGCGGCAGCCTGAGCAGCGGCGTGCACACC
TTTCCAGCCGTGCTGCAGAGCGACCTGTACACCCTGAGC
AGCTCCGTGACCGTGCCTAGCAGCACCTGGCCCAGCCA
GACAGTGACCTGCAACGTGGCCCACCCTGCCAGCAGCA
CCAAGGTGGACAAGAAAATCGTGCCCCGGGACTGC
anti-FAP (28H1) GAAGTGCAGCTGCTGGAATCCGGCGGAGGCCTGGTGCA Fc KK heavy GCCTGGCGGATCTCTGAGACTGTCCTGCGCCGCCTCCGG chain CTTCACCTTCTCCTCCCACGCCATGTCCTGGGTCCGACA
GGCTCCTGGCAAAGGCCTGGAATGGGTGTCCGCCATCTG
GGCCTCCGGCGAGCAGTACTACGCCGACTCTGTGAAGG
GCCGGTTCACCATCTCCCGGGACAACTCCAAGAACACCC
TGTACCTGCAGATGAACTCCCTGCGGGCCGAGGACACC
GCCGTGTACTACTGTGCCAAGGGCTGGCTGGGCAACTTC
GACTACTGGGGACAGGGCACCCTGGTCACCGTGTCCAG
CGCTAAGACCACCCCCCCTAGCGTGTACCCTCTGGCCCC
TGGATCTGCCGCCCAGACCAACAGCATGGTGACCCTGG
GCTGCCTGGTGAAGGGCTACTTCCCCGAGCCTGTGACCG
TGACCTGGAACAGCGGCAGCCTGAGCAGCGGCGTGCAC
ACCTTTCCAGCCGTGCTGCAGAGCGACCTGTACACCCTG
AGCAGCTCCGTGACCGTGCCTAGCAGCACCTGGCCCAG
CCAGACAGTGACCTGCAACGTGGCCCACCCTGCCAGCA
GCACCAAGGTGGACAAGAAAATCGTGCCCCGGGACTGC
GGCTGCAAGCCCTGCATCTGCACCGTGCCCGAGGTGTCC
AGCGTGTTCATCTTCCCACCCAAGCCCAAGGACGTGCTG
ACCATCACCCTGACCCCCAAAGTGACCTGCGTGGTGGTG
GCCATCAGCAAGGACGACCCCGAGGTGCAGTTCTCTTG
GTTTGTGGACGACGTGGAGGTGCACACAGCCCAGACAA
AGCCCCGGGAGGAACAGATCAACAGCACCTTCAGAAGC
GTGTCCGAGCTGCCCATCATGCACCAGGACTGGCTGAAC
GGCAAAGAATTCAAGTGCAGAGTGAACAGCGCCGCCTT
CGGCGCCCCCATCGAGAAAACCATCAGCAAGACCAAGG
GCAGACCCAAGGCCCCCCAGGTGTACACCATCCCCCCA
CCCAAAAAACAGATGGCCAAGGACAAGGTGTCCCTGAC
GGAGTGGCAGTGGAATGGCCAGCCCGCCGAGAACTACA AGAACACCCAGCCCATCATGAAGACCGACGGCAGCTAC TTCGTGTACAGCAAGCTGAACGTGCAGAAGTCCAACTG
GGAGGCCGGCAACACCTTCACCTGTAGCGTGCTGCACG AGGGCCTGCACAACCACCACACCGAGAAGTCCCTGAGC CACTCCCCCGGCAAG
74 anti-FAP (28H1) GAGATCGTGCTGACCCAGTCCCCCGGCACCCTGTCTCTG light chain AGCCCTGGCGAGAGAGCCACCCTGTCCTGCAGAGCCTC
CCAGTCCGTGTCCCGGTCCTACCTCGCCTGGTATCAGCA
GAAGCCCGGCCAGGCCCCTCGGCTGCTGATCATCGGCG
CCTCTACCAGAGCCACCGGCATCCCTGACCGGTTCTCCG
GCTCTGGCTCCGGCACCGACTTCACCCTGACCATCTCCC
GGCTGGAACCCGAGGACTTCGCCGTGTACTACTGCCAGC
AGGGCCAGGTCATCCCTCCCACCTTTGGCCAGGGCACCA
AGGTGGAAATCAAGCGTGCCGATGCTGCACCAACTGTA
TCGATTTTCCCACCATCCAGTGAGCAGTTAACATCTGGA
GGTGCCTCAGTCGTGTGCTTCTTGAACAACTTCTACCCC
AAAGACATCAATGTCAAGTGGAAGATTGATGGCAGTGA
ACGACAAAATGGCGTCCTGAACAGTTGGACTGATCAGG
ACAGCAAAGACAGCACCTACAGCATGAGCAGCACCCTC
ACGTTGACCAAGGACGAGTATGAACGACATAACAGCTA
TACCTGTGAGGCCACTCACAAGACATCAACTTCACCCAT
TGTCAAGAGCTTCAACAGGAATGAGTGT
75 Dimeric murine RTEPRPALTITTSPNLGTRENNADQVTPVSHIGSPNTTQQGS
4-lBBL (104- PVFAKLLAKNQASLSNTTLNWHSQDGAGSSYLSQGLRYEE
309, DKKELVVDSPGLYYVFLELKLSPTFTNTGHKVQGWVSLVL
C137,160,246S) - QAKPQVDDFDNLALTVELFPSSMENKLVDRSWSQLLLLKA
GHRLSVGLRAYLHGAQDAYRDWELSYPNTTSFGLFLVKP CL Fc DD chain
DNPWEGGGGSGGGGSRTEPRPALTITTSPNLGTRENNADQ
VTPVSHIGSPNTTQQGSPVFAKLLAKNQASLSNTTLNWHS
QDGAGSSYLSQGLRYEEDKKELVVDSPGLYYVFLELKLSP
TFTNTGHKVQGWVSLVLQAKPQVDDFDNLALTVELFPSS
MENKLVDRSWSQLLLLKAGHRLSVGLRAYLHGAQDAYR
DWELSYPNTTSFGLFLVKPDNPWEGGGGSGGGGSRADAA
PTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSE
RQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYT
CEATHKTSTSPIVKSFNRNECVPRDCGCKPCICTVPEVSSVF
IFPPKPKDVLTITLTPKVTCVVVAISKDDPEVQFSWFVDDV
EVHTAQTKPREEQINSTFRSVSELPIMHQDWLNGKEFKCR
VNSAAFGAPIEKTISKTKGRPKAPQVYTIPPPKEQMAKDKV
SLTCMITNFFPEDITVEWQWNGQPAENYDNTQPIMDTDGS
YFVYSDLNVQKSNWEAGNTFTCSVLHEGLHNHHTEKSLS
HSPGK
76 Monomeric RTEPRPALTITTSPNLGTRENNADQVTPVSHIGSPNTTQQGS murine 4- 1BBL PVFAKLLAKNQASLSNTTLNWHSQDGAGSSYLSQGLRYEE (104-309, DKKELVVDSPGLYYVFLELKLSPTFTNTGHKVQGWVSLVL C137,160,246S) - QAKPQVDDFDNLALTVELFPSSMENKLVDRSWSQLLLLKA
GHRLSVGLRAYLHGAQDAYRDWELSYPNTTSFGLFLVKP CL
DNPWEGGGGSGGGGSAKTTPPSVYPLAPGSAAQTNSMVT
LGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTL
SSSVTVPSSTWPSQTVTCNVAHPASSTKVDKKIVPRDC
77 anti-FAP (28H1) EVQLLESGGGLVQPGGSLRLSCAASGFTFSSHAMSWVRQA
Fc KK chain PGKGLEWVSAIWASGEQYYADSVKGRFTISRDNSKNTLYL
QMNSLRAEDTAVYYCAKGWLGNFDYWGQGTLVTVSSAK TTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWN
SGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSQTVTCN
VAHPASSTKVDKKIVPRDCGCKPCICTVPEVSSVFIFPPKPK
DVLTITLTPKVTCVVVAISKDDPEVQFSWFVDDVEVHTAQ
TKPREEQINSTFRSVSELPIMHQDWLNGKEFKCRVNSAAFG
APIEKTISKTKGRPKAPQVYTIPPPKKQMAKDKVSLTCMIT
NFFPEDITVEWQWNGQPAENYKNTQPIMKTDGSYFVYSKL
NVQKSNWEAGNTFTCSVLHEGLHNHHTEKSLSHSPGK
78 anti-FAP (28H1) EIVLTQSPGTLSLSPGERATLSCRASQSVSRSYLAWYQQKP light chain GQAPRLLIIGASTRATGIPDRFSGSGSGTDFTLTISRLEPEDF
AVYYCQQGQVIPPTFGQGTKVEIKRADAAPTVSIFPPSSEQ
LTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWT
DQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPI
VKSFNRNEC
Table 14 shows, respectively, the cDNA and amino acid sequences of the untargeted (DP47) murine 4- IBB ligand trimer-containing Fc fusion antigen binding molecule Control M. l .
Table 14: Sequences of untargeted murine Control M.l
SEQ ID Description Sequence
NO:
71 Dimeric murine See Table 13
4-lBBL (104-
309,
C137,160,246S) - CL Fc DD chain
72 Monomeric See Table 13
murine 4- 1BBL
(104-309,
C137,160,246S) - CH1
154 DP47 Fc KK GAGGTGCAATTGTTGGAGTCTGGGGGAGGCTTGGTACA chain GCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCCGG
ATTCACCTTTAGCAGTTATGCCATGAGCTGGGTCCGCCA
GGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTA
GTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGA
AGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAAC
ACGCTGTATCTGCAGATGAACAGCCTGAGAGCCGAGGA
CACGGCCGTATATTACTGTGCGAAAGGCAGCGGATTTGA
CTACTGGGGCCAAGGAACCCTGGTCACCGTCTCGAGCG
CTAAGACCACCCCCCCTAGCGTGTACCCTCTGGCCCCTG
GATCTGCCGCCCAGACCAACAGCATGGTGACCCTGGGC
TGCCTGGTGAAGGGCTACTTCCCCGAGCCTGTGACCGTG
ACCTGGAACAGCGGCAGCCTGAGCAGCGGCGTGCACAC
CTTTCCAGCCGTGCTGCAGAGCGACCTGTACACCCTGAG
CAGCTCCGTGACCGTGCCTAGCAGCACCTGGCCCAGCCA
GACAGTGACCTGCAACGTGGCCCACCCTGCCAGCAGCA CCAAGGTGGACAAGAAAATCGTGCCCCGGGACTGCGGC
TGCAAGCCCTGCATCTGCACCGTGCCCGAGGTGTCCAGC
GTGTTCATCTTCCCACCCAAGCCCAAGGACGTGCTGACC
ATCACCCTGACCCCCAAAGTGACCTGCGTGGTGGTGGCC
ATCAGCAAGGACGACCCCGAGGTGCAGTTCTCTTGGTTT
GTGGACGACGTGGAGGTGCACACAGCCCAGACAAAGCC
CCGGGAGGAACAGATCAACAGCACCTTCAGAAGCGTGT
CCGAGCTGCCCATCATGCACCAGGACTGGCTGAACGGC
AAAGAATTCAAGTGCAGAGTGAACAGCGCCGCCTTCGG
CGCCCCCATCGAGAAAACCATCAGCAAGACCAAGGGCA
GACCCAAGGCCCCCCAGGTGTACACCATCCCCCCACCCA
AAAAACAGATGGCCAAGGACAAGGTGTCCCTGACCTGC
TGGCAGTGGAATGGCCAGCCCGCCGAGAACTACAAGAA
CACCCAGCCCATCATGAAGACCGACGGCAGCTACTTCGT
GTACAGCAAGCTGAACGTGCAGAAGTCCAACTGGGAGG
CCGGCAACACCTTCACCTGTAGCGTGCTGCACGAGGGCC
TGCACAACCACCACACCGAGAAGTCCCTGAGCCACTCC
CCCGGCAAG
155 DP47 light chain GAAATCGTGTTAACGCAGTCTCCAGGCACCCTGTCTTTG
TCTCCAGGGGAAAGAGCCACCCTCTCTTGCAGGGCCAGT
CAGAGTGTTAGCAGCAGCTACTTAGCCTGGTACCAGCAG
AAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGAGCA
TCCAGCAGGGCCACTGGCATCCCAGACAGGTTCAGTGG
CAGTGGATCCGGGACAGACTTCACTCTCACCATCAGCAG
ACTGGAGCCTGAAGATTTTGCAGTGTATTACTGTCAGCA
GTATGGTAGCTCACCGCTGACGTTCGGCCAGGGGACCA
AAGTGGAAATCAAACGTGCCGATGCTGCACCAACTGTA
TCGATTTTCCCACCATCCAGTGAGCAGTTAACATCTGGA
GGTGCCTCAGTCGTGTGCTTCTTGAACAACTTCTACCCC
AAAGACATCAATGTCAAGTGGAAGATTGATGGCAGTGA
ACGACAAAATGGCGTCCTGAACAGTTGGACTGATCAGG
ACAGCAAAGACAGCACCTACAGCATGAGCAGCACCCTC
ACGTTGACCAAGGACGAGTATGAACGACATAACAGCTA
TACCTGTGAGGCCACTCACAAGACATCAACTTCACCCAT
TGTCAAGAGCTTCAACAGGAATGAGTGT
75 Dimeric murine see Table 13
4-lBBL (104-
309,
C137,160,246S) - CL Fc DD chain
76 Monomeric See Table 13
murine 4- 1BBL
(104-309,
C137,160,246S) - CH1
156 DP47 Fc KK EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQA chain PGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYL
QMNSLRAEDTAVYYCAKGSGFDYWGQGTLVTVSSAKTTP PSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGS LS SGVHTFPA VLQSDL YTLS SS VT VPS STWPS QT VTCNV AH PASSTKVDKKIVPRDCGCKPCICTVPEVSSVFIFPPKPKDVL
TITLTPKVTCVVVAISKDDPEVQFSWFVDDVEVHTAQTKP
REEQINSTFRSVSELPIMHQDWLNGKEFKCRVNSAAFGAPI
EKTISKTKGRPKAPQVYTIPPPKKQMAKDKVSLTCMITNFF
PEDITVEWQWNGQPAENYKNTQPIMKTDGSYFVYSKLNV
QKSNWEAGNTFTCSVLHEGLHNHHTEKSLSHSPGK
157 DP47 light chain EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKP
GQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDF
AVYYCQQYGSSPLTFGQGTKVEIKRADAAPTVSIFPPSSEQ
LTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWT
DQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPI
VKSFNRNEC
Table 15 shows the cDNA and amino acid sequences of the FAP-targeted murine 4- IBB ligand trimer-containing Fc fusion antigen binding molecule Construct M.2.
Table 15: Sequences of FAP-targeted murine Construct M.2
SEQ ID Description Sequence
NO:
158 Dimeric murine AGAACCGAGCCCAGACCCGCCCTGACCATCACCACCAG
4-lBBL (104- CCCTAACCTGGGCACCAGAGAGAACAACGCCGACCAAG 309, C160S) - CL TGACCCCCGTGTCCCACATCGGCTGCCCCAATACCACAC Fc DD chain AGCAGGGCAGCCCTGTGTTCGCCAAGCTGCTGGCCAAG
AACCAGGCCAGCCTGAGCAACACCACCCTGAACTGGCA
CAGCCAGGATGGCGCCGGAAGCAGCTATCTGAGCCAGG
GCCTGAGATACGAAGAGGACAAGAAAGAACTGGTGGTG
GACAGCCCTGGCCTGTACTACGTGTTCCTGGAACTGAAG
CTGAGCCCCACCTTCACCAACACCGGCCACAAGGTGCA
GGGCTGGGTGTCACTGGTGCTGCAGGCCAAACCCCAGG
TGGACGACTTCGACAACCTGGCCCTGACCGTGGAACTGT
TCCCCTGCAGCATGGAAAACAAGCTGGTGGATCGGAGC
TGGTCCCAGCTTCTGCTGCTGAAGGCCGGACACAGACTG
AGCGTGGGCCTGAGGGCTTATCTGCACGGCGCCCAGGA
CGCCTACAGAGACTGGGAGCTGAGCTACCCCAACACAA
CCAGCTTCGGCCTGTTCCTCGTGAAGCCCGACAACCCTT
GGGAAGGCGGCGGAGGCTCCGGAGGAGGCGGATCTAGA
ACAGAGCCTCGGCCTGCCCTGACAATTACCACATCCCCC
AATCTGGGCACCCGGGAAAACAATGCAGATCAAGTGAC
ACCTGTGTCTCATATTGGGTGCCCCAACACTACCCAGCA
GGGGTCCCCAGTGTTTGCTAAACTGCTGGCTAAAAATCA
GGCCTCCCTGTCTAACACAACACTGAATTGGCATAGTCA
GGACGGGGCTGGCAGCAGCTACCTGTCTCAGGGACTGC
GCTATGAGGAAGATAAGAAAGAACTGGTGGTGGATTCC
CCCGGACTGTACTATGTGTTTCTGGAACTGAAACTGTCC
CCTACCTTTACAAATACCGGGCACAAAGTGCAGGGATG
GGTGTCCCTGGTGCTGCAGGCTAAGCCTCAGGTGGACGA
TTTTGATAATCTGGCTCTGACAGTGGAACTGTTTCCTTGC
TCTATGGAAAACAAACTGGTGGACCGCTCTTGGAGCCA
GTTGCTGCTGCTGAAAGCTGGCCACCGGCTGTCTGTGGG ACTGAGAGCATACCTGCATGGGGCACAGGATGCCTACC
GGGATTGGGAACTGTCCTACCCTAACACTACTTCCTTCG
GACTGTTCCTCGTGAAACCTGATAATCCCTGGGAGGGCG
GAGGCGGAAGTGGCGGAGGGGGATCCAGAGCTGATGCT
GCCCCTACCGTGTCCATCTTCCCACCCAGCAGCGAGCAG
CTGACATCTGGGGGAGCTAGCGTCGTGTGCTTCCTGAAC
AACTTCTACCCCAAGGACATCAACGTGAAGTGGAAGAT
CGACGGCAGCGAGCGGCAGAACGGCGTGCTGAATAGCT
GGACCGACCAGGACAGCAAGGACTCCACCTACAGCATG
AGCAGCACCCTGACCCTGACCAAGGACGAGTACGAGCG
GCACAACAGCTACACATGCGAGGCCACCCACAAGACCA
GCACCAGCCCCATCGTGAAGTCCTTCAACCGGAACGAG
TGCGTGCCCAGAGACTGCGGCTGCAAGCCTTGCATCTGC
ACCGTGCCTGAGGTGTCCAGCGTGTTCATCTTCCCACCC
AAGCCCAAGGACGTGCTGACCATCACCCTGACACCCAA
AGTGACCTGCGTGGTGGTGGCCATCAGCAAGGATGACC
CCGAGGTGCAGTTCAGTTGGTTCGTGGACGACGTGGAA
GTGCACACCGCTCAGACCAAGCCCAGAGAGGAACAGAT
CAACAGCACCTTCAGAAGCGTGTCCGAGCTGCCCATCAT
GCACCAGGACTGGCTGAACGGCAAAGAATTCAAGTGCA
GAGTGAACAGCGCCGCCTTTGGCGCCCCTATCGAGAAA
ACCATCTCCAAGACCAAGGGCAGACCCAAGGCCCCCCA
GGTGTACACAATCCCCCCACCCAAAGAACAGATGGCCA
AGGACAAGGTGTCCCTGACCTGCATGATCACCAATTTCT
TCCCAGAGGATATCACCGTGGAATGGCAGTGGAACGGC
CAGCCCGCCGAGAACTACGACAACACCCAGCCTATCAT
GGACACCGACGGCTCCTACTTCGTGTACAGCGACCTGAA
CGTGCAGAAGTCCAACTGGGAGGCCGGCAACACCTTCA
CCTGTAGCGTGCTGCACGAGGGCCTGCACAACCACCAC
ACCGAGAAGTCCCTGTCCCACAGCCCTGGCAAG
Monomeric AGAACCGAGCCCAGACCCGCCCTGACCATCACCACCAG murine 4- 1BBL CCCTAACCTGGGCACCAGAGAGAACAACGCCGACCAAG (104-309, C160S) TGACCCCCGTGTCCCACATCGGCTGCCCCAATACCACAC - CHI AGCAGGGCAGCCCTGTGTTCGCCAAGCTGCTGGCCAAG
AACCAGGCCAGCCTGAGCAACACCACCCTGAACTGGCA
CAGCCAGGATGGCGCCGGAAGCAGCTATCTGAGCCAGG
GCCTGAGATACGAAGAGGACAAGAAAGAACTGGTGGTG
GACAGCCCTGGCCTGTACTACGTGTTCCTGGAACTGAAG
CTGAGCCCCACCTTCACCAACACCGGCCACAAGGTGCA
GGGCTGGGTGTCACTGGTGCTGCAGGCCAAACCCCAGG
TGGACGACTTCGACAACCTGGCCCTGACCGTGGAACTGT
TCCCCTGCAGCATGGAAAACAAGCTGGTGGATCGGAGC
TGGTCCCAGCTTCTGCTGCTGAAGGCCGGACACAGACTG
AGCGTGGGCCTGAGGGCTTATCTGCACGGCGCCCAGGA
CGCCTACAGAGACTGGGAGCTGAGCTACCCCAACACAA
CCAGCTTCGGCCTGTTCCTCGTGAAGCCCGACAACCCTT
GGGAAGGCGGCGGAGGCTCCGGAGGAGGCGGAAGCGC
TAAGACCACCCCCCCCAGCGTGTACCCTCTGGCCCCTGG
ATCTGCCGCCCAGACCAACAGCATGGTGACCCTGGGCT
GCCTGGTGAAGGGCTACTTCCCCGAGCCTGTGACCGTGA
CCTGGAACAGCGGCAGCCTGAGCAGCGGCGTGCACACC
TTTCCAGCCGTGCTGCAGAGCGACCTGTACACCCTGAGC
AGCTCCGTGACCGTGCCTAGCAGCACCTGGCCCAGCCA
GACAGTGACCTGCAACGTGGCCCACCCTGCCAGCAGCA CCAAGGTGGACAAGAAAATCGTGCCCCGGGACTGC
73 anti-FAP (28H1) see Table 13
Fc KK chain
74 anti-FAP (28H1) see Table 13
light chain
160 Dimeric murine RTEPRPALTITTSPNLGTRENNADQVTPVSHIGCPNTTQQGS
4-lBBL (104- PVFAKLLAKNQASLSNTTLNWHSQDGAGSSYLSQGLRYEE 309, C160S) - CL DKKELVVDSPGLYYVFLELKLSPTFTNTGHKVQGWVSLVL Fc DD chain QAKPQVDDFDNLALTVELFPCSMENKLVDRSWSQLLLLK
AGHRLSVGLRAYLHGAQDAYRDWELSYPNTTSFGLFLVK
PDNPWEGGGGSGGGGSRTEPRPALTITTSPNLGTRENNAD
QVTPVSHIGCPNTTQQGSPVFAKLLAKNQASLSNTTLNWH
SQDGAGSSYLSQGLRYEEDKKELVVDSPGLYYVFLELKLS
PTFTNTGHKVQGWVSLVLQAKPQVDDFDNLALTVELFPCS
MENKLVDRSWSQLLLLKAGHRLSVGLRAYLHGAQDAYR
DWELSYPNTTSFGLFLVKPDNPWEGGGGSGGGGSRADAA
PTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSE
RQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYT
CEATHKTSTSPIVKSFNRNECVPRDCGCKPCICTVPEVSSVF
IFPPKPKDVLTITLTPKVTCVVVAISKDDPEVQFSWFVDDV
EVHTAQTKPREEQINSTFRSVSELPIMHQDWLNGKEFKCR
VNSAAFGAPIEKTISKTKGRPKAPQVYTIPPPKEQMAKDKV
SLTCMITNFFPEDITVEWQWNGQPAENYDNTQPIMDTDGS
YFVYSDLNVQKSNWEAGNTFTCSVLHEGLHNHHTEKSLS
HSPGK
161 Monomeric RTEPRPALTITTSPNLGTRENNADQVTPVSHIGCPNTTQQGS murine 4-1BBL PVFAKLLAKNQASLSNTTLNWHSQDGAGSSYLSQGLRYEE (104-309, C160S) DKKELVVDSPGLYYVFLELKLSPTFTNTGHKVQGWVSLVL - CHI QAKPQVDDFDNLALTVELFPCSMENKLVDRSWSQLLLLK
AGHRLSVGLRAYLHGAQDAYRDWELSYPNTTSFGLFLVK
PDNPWEGGGGSGGGGSAKTTPPSVYPLAPGSAAQTNSMV
TLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYT
LSSSVTVPSSTWPSQTVTCNVAHPASSTKVDKKIVPRDC
77 anti-FAP (28H1) see Table 13
Fc KK chain
78 anti-FAP (28H1) see Table 13
light chain
Table 16 shows the cDNA and amino acid sequences of the DP47-untargeted murine 4- 1BB ligand trimer-containing Fc fusion antigen binding molecule Construct Control M.2. Table 16: Sequences of FAP-targeted murine Control M.2
Figure imgf000179_0001
The murine 4- IBB ligand trimer-containing Fc fusion antigen binding molecules were produced and purified as described herein before for the human 4-lBBL constructs. Table 17 summarizes the yield and final monomer content of the FAP-targeted and untargeted murine 4-lBBL trimer-containing Fc fusion antigen binding molecule.
Table 17: Summary of the production of the FAP-targeted and untargeted murine 4-lBBL trimer-containing Fc fusion antigen binding molecules
Monomer
Yield
Construct
[mg/1] [%]
(SEC)
Construct M.l 2.6 95
Control M.2 2.3 96
Construct M.2 8.5 98
Control M.2 8.1 97 1.4 Preparation and purification of untargeted human 4-1BB ligand trimer- containing Fc fusion antigen binding molecules (Control molecules)
The control molecules were prepared as described above for the FAP-targeted Constructs 1 and 2, with the only difference that the anti-FAP binder (VH-VL) was replaced by a germline control, termed DP47, not binding to the antigen. The control is an untargeted monovalent split trimeric human 4- IBB ligand Fc (kih) (Control A, Figure 5A) and for Control B, the construct also contains a CH-CL crossover with charged residues (Figure 5B). The variable region of heavy and light chain DNA sequences of the FAP binder were replaced with those of the germline control (DP47) and subcloned in frame with either the constant heavy chain of the hole or the constant light chain of human IgGl .
The untargeted 4- IBB ligand trimer-containing Fc (kih) fusion antigen binding molecules were produced as described above for the FAP-targeted constructs. The cells were transfected with the corresponding expression vectors at a 1: 1: 1: 1 ratio ("vector dimeric ligand-CHl or CL*- knob chain": "vector monomeric ligand fusion-CL or CHI*": "vector DP47 Fab-hole chain": "vector DP47 light chain").
Table 18 shows, respectively, the cDNA and amino acid sequences of the DP47 -untargeted 4- IBB ligand trimer-containing Fc (kih) fusion antigen binding molecule Control A.
Table 18: Sequences of DP47 untargeted 4-1BB ligand trimer-containing Fc (kih) fusion antigen binding molecule (DP47 split 4-1BBL trimer) Control A
SEQ ID Description Sequence
NO:
66 Dimeric hu 4- See Table 2
1BBL (71-254) - CH1 Fc knob
chain
67 Monomeric hu see Table 2
4-1BBL (71-254)
- CL
79 DP47 Fc hole GAGGTGCAATTGTTGGAGTCTGGGGGAGGCTTGGTACA chain GCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCCGG
ATTCACCTTTAGCAGTTATGCCATGAGCTGGGTCCGCCA
GGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTA
GTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGA
AGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAAC
ACGCTGTATCTGCAGATGAACAGCCTGAGAGCCGAGGA
CACGGCCGTATATTACTGTGCGAAAGGCAGCGGATTTGA
CTACTGGGGCCAAGGAACCCTGGTCACCGTCTCGAGTGC
TAGCACCAAGGGCCCATCGGTCTTCCCCCTGGCACCCTC
CTCCAAGAGCACCTCTGGGGGCACAGCGGCCCTGGGCT
GCCTGGTCAAGGACTACTTCCCCGAACCGGTGACGGTGT CGTGGAACTCAGGCGCCCTGACCAGCGGCGTGCACACC
TTCCCGGCTGTCCTACAGTCCTCAGGACTCTACTCCCTC
AGCAGCGTGGTGACCGTGCCCTCCAGCAGCTTGGGCAC
CCAGACCTACATCTGCAACGTGAATCACAAGCCCAGCA
ACACCAAGGTGGACAAGAAAGTTGAGCCCAAATCTTGT
GACAAAACTCACACATGCCCACCGTGCCCAGCACCTGA
AGCTGCAGGGGGACCGTCAGTCTTCCTCTTCCCCCCAAA
ACCCAAGGACACCCTCATGATCTCCCGGACCCCTGAGGT
CACATGCGTGGTGGTGGACGTGAGCCACGAAGACCCTG
AGGTCAAGTTCAACTGGTACGTGGACGGCGTGGAGGTG
CATAATGCCAAGACAAAGCCGCGGGAGGAGCAGTACAA
CAGCACGTACCGTGTGGTCAGCGTCCTCACCGTCCTGCA
CCAGGACTGGCTGAATGGCAAGGAGTACAAGTGCAAGG
TCTCCAACAAAGCCCTCGGCGCCCCCATCGAGAAAACC
ATCTCCAAAGCCAAAGGGCAGCCCCGAGAACCACAGGT
GTGCACCCTGCCCCCATCCCGGGATGAGCTGACCAAGA
ACCAGGTCAGCCTCTCGTGCGCAGTCAAAGGCTTCTATC
CCAGCGACATCGCCGTGGAGTGGGAGAGCAATGGGCAG
CCGGAGAACAACTACAAGACCACGCCTCCCGTGCTGGA
CTCCGACGGCTCCTTCTTCCTCGTGAGCAAGCTCACCGT
GGACAAGAGCAGGTGGCAGCAGGGGAACGTCTTCTCAT
GCTCCGTGATGCATGAGGCTCTGCACAACCACTACACGC
AGAAGAGCCTCTCCCTGTCTCCGGGTAAA
DP47 light chain GAAATCGTGTTAACGCAGTCTCCAGGCACCCTGTCTTTG
TCTCCAGGGGAAAGAGCCACCCTCTCTTGCAGGGCCAGT
CAGAGTGTTAGCAGCAGCTACTTAGCCTGGTACCAGCAG
AAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGAGCA
TCCAGCAGGGCCACTGGCATCCCAGACAGGTTCAGTGG
CAGTGGATCCGGGACAGACTTCACTCTCACCATCAGCAG
ACTGGAGCCTGAAGATTTTGCAGTGTATTACTGTCAGCA
GTATGGTAGCTCACCGCTGACGTTCGGCCAGGGGACCA
AAGTGGAAATCAAACGTACGGTGGCTGCACCATCTGTCT
TCATCTTCCCGCCATCTGATGAGCAGTTGAAATCTGGAA
CTGCCTCTGTTGTGTGCCTGCTGAATAACTTCTATCCCAG
AGAGGCCAAAGTACAGTGGAAGGTGGATAACGCCCTCC
AATCGGGTAACTCCCAGGAGAGTGTCACAGAGCAGGAC
AGCAAGGACAGCACCTACAGCCTCAGCAGCACCCTGAC
GCTGAGCAAAGCAGACTACGAGAAACACAAAGTCTACG
CCTGCGAAGTCACCCATCAGGGCCTGAGCTCGCCCGTCA
CAAAGAGCTTCAACAGGGGAGAGTGT
Dimeric hu 4- See Table 2
1BBL (71-254) - CH1 Fc knob
chain
Monomeric hu 4- See Table 2
1BBL (71-254) - CL
DP47 Fc hole EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQA chain PGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYL
QMNSLRAEDTAVYYCAKGSGFDYWGQGTLVTVSSASTKG PSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGAL TSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNH KPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGGPSVFLFPP
KPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEV
HNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKV
SNKALGAPIEKTISKAKGQPREPQVCTLPPSRDELTKNQVS
LSCAVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFF
LVSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLS
PGK
82 DP47 light chain EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKP
GQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDF
AVYYCQQYGSSPLTFGQGTKVEIKRTVAAPSVFIFPPSDEQ
LKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESV
TEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSS
PVTKSFNRGEC
Table 19 shows the cDNA and amino acid sequences of the DP47 -untargeted 4- IBB ligand trimer-containing Fc (kih) fusion antigen binding molecule with CHl-CL crossover and charged residues in the 4- IBB ligand containing arms (Control B).
Table 19: Sequences of DP47 untargeted 4-lBB ligand trimer-containing Fc (kih) fusion antigen binding molecule (DP47 split 4-1BBL trimer) Control B
SEQ ID Description Sequence
NO:
96 Dimeric hu 4- see Table 3
1BBL (71-254) - CL* Fc knob
chain
97 Monomeric hu see Table 3
4-1BBL (71-254)
- CHI*
79 DP47 Fc hole see Table 18
chain
80 DP47 light chain see Table 18
98 Dimeric hu 4- see Table 3
1BBL (71-254) - CL* Fc knob
chain
99 Monomeric hu see Table 3
4-1BBL (71-254)
- CHI*
81 DP47 Fc hole see Table 18
chain
82 DP47 light chain see Table 18 Table 20 summarizes the yield and final monomer content of the DP47 untargeted 4- IBB ligand trimer-containing Fc (kih) fusion antigen binding molecules.
Table 20: Production Characteristics of DP47 untargeted 4-1BBL trimer-containing Fc (kih) fusion antigen binding molecules (Control molecules)
Figure imgf000183_0001
Example 2
2.1 Preparation of FAP (4B9) targeted 4-1BB ligand trimer-containing Fc fusion antigen binding molecules
Different fragments of the DNA sequence encoding part of the ectodomain (amino acid 71- 254 and 71-248) of human 4- IBB ligand were synthetized according to the P41273 sequence of Uniprot database (SEQ ID NO:42).
2.1.1 Preparation of monovalent FAP (4B9) targeted 4-1BB ligand (71-254) trimer- containing Fc (kih) fusion antigen binding molecule with crossed CH1-CL domains with charged residues (Construct 2.1) A polypeptide containing two ectodomains of 4-1BB ligand (71-254), separated by (G4S)2 linkers, and fused to the human IgGl-CL domain, was cloned as depicted in Figure 1A: human 4- IBB ligand, (G4S)2 connector, human 4- IBB ligand, (G4S)2 connector, human CL.
A polypeptide containing one ectodomain of 4-1BB ligand (71-254) and fused to the human IgGl-CHl domain, was cloned as described in Figure IB: human 4- IBB ligand, (G4S)2 connector, human CH.
The polypeptide encoding the dimeric 4- IBB ligand fused to human CL domain was subcloned in frame with the human IgGl heavy chain CH2 and CH3 domains on the knob (Merchant, Zhu et al. 1998) using a linker (G4S)2, or alternatively, (GSPGSSSSGS). To improve correct pairing the following mutations have been introduced in the crossed CH-CL. In the dimeric 4- IBB ligand fused to human CL the mutations E123R and Q124K were introduced. In the monomeric 4- IBB ligand fused to human CHI, the mutations K147E and K213E were cloned into the human CHI domain. The variable region of heavy and light chain DNA sequences encoding a binder specific for fibroblast activation protein (FAP), clone 4B9, were subcloned in frame with either the constant heavy chain of the hole or the constant light chain of human IgGl .
The generation and preparation of the FAP binders is described in WO 2012/020006 A2, which is incorporated herein by reference. The Pro329Gly, Leu234Ala and Leu235Ala mutations have been introduced in the constant region of the knob and hole heavy chains to abrogate binding to Fc gamma receptors according to the method described in International Patent Appl. Publ. No. WO 2012/130831.
For all constructs the knobs into hole heterodimerization technology was used with the the S354C/T366W mutations in the knob chain and the corresponding Y349C/T366S/L368A/Y407V mutations in the hole chain.
Combination of the dimeric ligand-Fc knob chain containing the S354C/T366W mutations, the monomeric CHI fusion, the targeted anti-FAP-Fc hole chain containing the
Y349C/T366S/L368A/Y407V mutations and the anti-FAP light chain allows generation of a heterodimer, which includes an assembled trimeric 4- IBB ligand and a FAP binding Fab (Figure 4, Construct 2.1).
Table 21 shows the cDNA and amino acid sequences of the monovalent FAP (4B9)-human 4-1BB ligand (71-254) Fc (kih) fusion antigen binding molecule containing CH1-CL crossover and charged residues (Construct 2.1).
Table 21: Sequences of monovalent FAP(4B9)-targeted human 4-1BB ligand (71-254) containing Fc (kih) fusion molecule Construct 2.1
SEQ ID Description Sequence
NO:
129 Dimeric hu 4- see Table 3
1BBL (71-254) - CL* Fc knob
chain
130 Monomeric hu see Table 3
4-1BBL (71-254)
- CHI* 162 anti-FAP (4B9) GAGGTGCAGCTGCTCGAAAGCGGCGGAGGACTGGTGCA Fc hole chain GCCTGGCGGCAGCCTGAGACTGTCTTGCGCCGCCAGCG
GCTTCACCTTCAGCAGCTACGCCATGAGCTGGGTCCGCC
AGGCCCCTGGCAAGGGACTGGAATGGGTGTCCGCCATC
ATCGGCTCTGGCGCCAGCACCTACTACGCCGACAGCGTG
AAGGGCCGGTTCACCATCAGCCGGGACAACAGCAAGAA
CACCCTGTACCTGCAGATGAACAGCCTGCGGGCCGAGG
ACACCGCCGTGTACTACTGCGCCAAGGGATGGTTCGGC
GGCTTCAACTACTGGGGACAGGGCACCCTGGTCACAGT
GTCCAGCGCTAGCACCAAGGGCCCCTCCGTGTTCCCCCT
GGCCCCCAGCAGCAAGAGCACCAGCGGCGGCACAGCCG
CTCTGGGCTGCCTGGTCAAGGACTACTTCCCCGAGCCCG
TGACCGTGTCCTGGAACAGCGGAGCCCTGACCTCCGGC
GTGCACACCTTCCCCGCCGTGCTGCAGAGTTCTGGCCTG
TATAGCCTGAGCAGCGTGGTCACCGTGCCTTCTAGCAGC
CTGGGCACCCAGACCTACATCTGCAACGTGAACCACAA
GCCCAGCAACACCAAGGTGGACAAGAAGGTGGAGCCCA
AGAGCTGCGACAAAACTCACACATGCCCACCGTGCCCA
GCACCTGAAGCTGCAGGGGGACCGTCAGTCTTCCTCTTC
CCCCCAAAACCCAAGGACACCCTCATGATCTCCCGGACC
CCTGAGGTCACATGCGTGGTGGTGGACGTGAGCCACGA
AGACCCTGAGGTCAAGTTCAACTGGTACGTGGACGGCG
TGGAGGTGCATAATGCCAAGACAAAGCCGCGGGAGGAG
CAGTACAACAGCACGTACCGTGTGGTCAGCGTCCTCACC
GTCCTGCACCAGGACTGGCTGAATGGCAAGGAGTACAA
GTGCAAGGTCTCCAACAAAGCCCTCGGCGCCCCCATCG
AGAAAACCATCTCCAAAGCCAAAGGGCAGCCCCGAGAA
CCACAGGTGTGCACCCTGCCCCCATCCCGGGATGAGCTG
ACCAAGAACCAGGTCAGCCTCTCGTGCGCAGTCAAAGG
CTTCTATCCCAGCGACATCGCCGTGGAGTGGGAGAGCA
ATGGGCAGCCGGAGAACAACTACAAGACCACGCCTCCC
GTGCTGGACTCCGACGGCTCCTTCTTCCTCGTGAGCAAG
CTCACCGTGGACAAGAGCAGGTGGCAGCAGGGGAACGT
CTTCTCATGCTCCGTGATGCATGAGGCTCTGCACAACCA
CTACACGCAGAAGAGCCTCTCCCTGTCTCCGGGTAAA
163 anti-FAP (4B9) GAGATCGTGCTGACCCAGTCCCCCGGCACCCTGTCTCTG light chain AGCCCTGGCGAGAGAGCCACCCTGTCCTGCAGAGCCTC
CCAGTCCGTGACCTCCTCCTACCTCGCCTGGTATCAGCA
GAAGCCCGGCCAGGCCCCTCGGCTGCTGATCAACGTGG
GCAGTCGGAGAGCCACCGGCATCCCTGACCGGTTCTCCG
GCTCTGGCTCCGGCACCGACTTCACCCTGACCATCTCCC
GGCTGGAACCCGAGGACTTCGCCGTGTACTACTGCCAGC
AGGGCATCATGCTGCCCCCCACCTTTGGCCAGGGCACCA
AGGTGGAAATCAAGCGTACGGTGGCTGCACCATCTGTCT
TCATCTTCCCGCCATCTGATGAGCAGTTGAAATCTGGAA
CTGCCTCTGTTGTGTGCCTGCTGAATAACTTCTATCCCAG
AGAGGCCAAAGTACAGTGGAAGGTGGATAACGCCCTCC
AATCGGGTAACTCCCAGGAGAGTGTCACAGAGCAGGAC
AGCAAGGACAGCACCTACAGCCTCAGCAGCACCCTGAC
GCTGAGCAAAGCAGACTACGAGAAACACAAAGTCTACG
CCTGCGAAGTCACCCATCAGGGCCTGAGCTCGCCCGTCA
CAAAGAGCTTCAACAGGGGAGAGTGT
115 Dimeric hu 4- see Table 3 1BBL (71-254) - CL* Fc knob
chain
116 Monomeric hu see Table 3
4-1BBL (71-254)
- CHI*
164 anti-FAP (4B9) EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQA
Fc hole chain PGKGLEWVSAIIGSGASTYYADSVKGRFTISRDNSKNTLYL
QMNSLRAEDTAVYYCAKGWFGGFNYWGQGTLVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNS
GALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICN
VNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGGPSVF
LFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDG
VEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYK
CKVSNKALGAPIEKTISKAKGQPREPQVCTLPPSRDELTKN
QVSLSCAVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSD
GSFFLVSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKS
LSLSPGK
125 anti-FAP (4B9) EIVLTQSPGTLSLSPGERATLSCRASQSVTSSYLAWYQQKP light chain GQAPRLLINVGSRRATGIPDRFSGSGSGTDFTLTISRLEPEDF
AVYYCQQGIMLPPTFGQGTKVEIKRTVAAPSVFIFPPSDEQ
LKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESV
TEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSS
PVTKSFNRGEC
2.1.2 Preparation of monovalent FAP (4B9) targeted 4-lBB ligand (71-254) trimer- containing Fc (kih) fusion antigen binding molecule with crossed CH1-CL domains without charged residues (Construct 2.2) A polypeptide containing two ectodomains of 4-lBB ligand (71-254), separated by (G4S)2 linkers, and fused to the human IgGl-CL domain, was cloned as depicted in Figure 1A: human 4-lBB ligand, (G4S)2 connector, human 4-lBB ligand, (G4S)2 connector, human CL.
A polypeptide containing one ectodomain of 4-lBB ligand (71-254) and fused to the human IgGl-CHl domain, was cloned as described in Figure IB: human 4- IBB ligand, (G4S)2 connector, human CHI.
The polypeptide encoding the dimeric 4- IBB ligand fused to human CL domain was subcloned in frame with the human IgGl heavy chain CH2 and CH3 domains on the knob (Merchant, Zhu et al. 1998) using a linker (G4S)2 or, alternatively (GSPGSSSSGS).
The variable region of heavy and light chain DNA sequences encoding a binder specific for fibroblast activation protein (FAP), clone 4B9, were subcloned in frame with either the constant heavy chain of the hole or the constant light chain of human IgGl . The Pro329Gly, Leu234Ala and Leu235Ala mutations have been introduced in the constant region of the knob and hole heavy chains to abrogate binding to Fc gamma receptors (WO 2012/130831).
Combination of the dimeric ligand-Fc knob chain containing the S354C/T366W mutations, the monomeric CHI fusion, the targeted anti-FAP-Fc hole chain containing the
Y349C/T366S/L368A/Y407V mutations and the anti-FAP light chain allows generation of a heterodimer, which includes an assembled trimeric 4- IBB ligand and a FAP binding Fab (Figure 4, Construct 2.2).
Table 22 shows the cDNA and amino acid sequences of the monovalent FAP (4B9)-human 4- IBB ligand (71-254) Fc (kih) fusion antigen binding molecule containing CHl-CL crossover without charged residues (Construct 2.2).
Table 22: Sequences of monovalent FAP(4B9)-targeted human 4-1BB ligand (71-254) containing Fc (kih) fusion molecule Construct 2.2
SEQ ID Description Sequence
NO:
Dimeric hu 4- AGAGAGGGCCCTGAGCTGAGCCCCGATGATCCTGCTGG
165
ACTGCTGGACCTGCGGCAGGGCATGTTTGCTCAGCTGGT
1BBL (71-254) - GGCCCAGAACGTGCTGCTGATCGATGGCCCCCTGTCCTG CL Fc knob chain GTACAGCGATCCTGGACTGGCTGGCGTGTCACTGACAGG
CGGCCTGAGCTACAAAGAGGACACCAAAGAACTGGTGG
TGGCCAAGGCCGGCGTGTACTACGTGTTCTTTCAGCTGG
AACTGCGGAGAGTGGTGGCCGGCGAAGGATCTGGCTCT
GTGTCTCTGGCCCTGCATCTGCAGCCTCTGAGAAGCGCT
GCTGGCGCTGCAGCTCTGGCACTGACAGTGGATCTGCCT
CCTGCCAGCTCCGAGGCCCGGAATAGCGCATTTGGGTTT
CAAGGCAGGCTGCTGCACCTGTCTGCCGGCCAGAGGCT
GGGAGTGCATCTGCACACAGAGGCCAGGGCTAGACACG
CCTGGCAGCTGACACAGGGCGCTACAGTGCTGGGCCTG
TTCAGAGTGACCCCCGAGATTCCAGCCGGCCTGCCTTCT
CCAAGAAGCGAAGGCGGAGGCGGATCTGGCGGCGGAG
GATCTAGAGAGGGACCCGAACTGTCCCCTGACGATCCA
GCCGGGCTGCTGGATCTGAGACAGGGAATGTTCGCCCA
GCTGGTGGCTCAGAATGTGCTGCTGATTGACGGACCTCT
GAGCTGGTACTCCGACCCAGGGCTGGCAGGGGTGTCCC
TGACTGGGGGACTGTCCTACAAAGAAGATACAAAAGAA
CAGCTGGAACTGAGGCGGGTGGTGGCTGGGGAGGGCTC
AGGATCTGTGTCCCTGGCTCTGCATCTGCAGCCACTGCG
CTCTGCTGCTGGCGCAGCTGCACTGGCTCTGACTGTGGA
CCTGCCACCAGCCTCTAGCGAGGCCAGAAACAGCGCCT
TCGGGTTCCAAGGACGCCTGCTGCATCTGAGCGCCGGAC
AGCGCCTGGGAGTGCATCTGCATACTGAAGCCAGAGCC
CGGCATGCTTGGCAGCTGACTCAGGGGGCAACTGTGCTG
GGACTGTTTCGCGTGACACCTGAGATCCCTGCCGGACTG CCAAGCCCTAGATCAGAAGGGGGCGGAGGTTCCGGAGG GGGAGGATCTCGTACGGTGGCCGCTCCCTCCGTGTTTAT CTTTCCCCCATCCGATGAACAGCTGAAAAGCGGCACCGC
AGCTAAAGTGCAGTGGAAAGTGGATAACGCACTGCAGT
CCGGCAACTCCCAGGAATCTGTGACAGAACAGGACTCC
AAGGACAGCACCTACTCCCTGTCCTCCACCCTGACACTG
TCTAAGGCTGATTATGAGAAACACAAAGTCTACGCCTGC
GAAGTCACCCATCAGGGCCTGAGCTCGCCCGTCACAAA
GAGCTTCAACAGGGGAGAGTGTGACAAGACCCACACCT
GTCCCCCTTGTCCTGCCCCTGAAGCTGCTGGCGGCCCTT
CTGTGTTCCTGTTCCCCCCAAAGCCCAAGGACACCCTGA
TGATCAGCCGGACCCCCGAAGTGACCTGCGTGGTGGTG
GATGTGTCCCACGAGGACCCTGAAGTGAAGTTCAATTGG
TACGTGGACGGCGTGGAAGTGCACAATGCCAAGACCAA
GCCGCGGGAGGAGCAGTACAACAGCACGTACCGTGTGG
TCAGCGTCCTCACCGTCCTGCACCAGGACTGGCTGAATG
GCAAGGAGTACAAGTGCAAGGTCTCCAACAAAGCCCTC
GGCGCCCCCATCGAGAAAACCATCTCCAAAGCCAAAGG
GCAGCCCCGAGAACCACAGGTGTACACCCTGCCCCCAT
GCCGGGATGAGCTGACCAAGAACCAGGTCAGCCTGTGG
TGCCTGGTCAAAGGCTTCTATCCCAGCGACATCGCCGTG
GAGTGGGAGAGCAATGGGCAGCCGGAGAACAACTACAA
GACCACGCCTCCCGTGCTGGACTCCGACGGCTCCTTCTT
CCTCTACAGCAAGCTCACCGTGGACAAGAGCAGGTGGC
AGCAGGGGAACGTCTTCTCATGCTCCGTGATGCATGAGG
CTCTGCACAACCACTACACGCAGAAGAGCCTCTCCCTGT
CTCCGGGTAAA
Monomeric hu 4- AGAGAGGGCCCTGAGCTGAGCCCCGATGATCCTGCTGG
ACTGCTGGACCTGCGGCAGGGCATGTTTGCTCAGCTGGT
1BBL (71-254) - GGCCCAGAACGTGCTGCTGATCGATGGCCCCCTGTCCTG CH1 GTACAGCGATCCTGGACTGGCTGGCGTGTCACTGACAGG
CGGCCTGAGCTACAAAGAGGACACCAAAGAACTGGTGG
TGGCCAAGGCCGGCGTGTACTACGTGTTCTTTCAGCTGG
AACTGCGGAGAGTGGTGGCCGGCGAAGGATCTGGCTCT
GTGTCTCTGGCCCTGCATCTGCAGCCTCTGAGAAGCGCT
GCTGGCGCTGCAGCTCTGGCTCTGACAGTGGATCTGCCT
CCTGCCAGCTCCGAGGCCCGGAATAGCGCATTTGGGTTT
CAAGGCCGGCTGCTGCACCTGTCTGCCGGCCAGAGACT
GGGAGTGCATCTGCACACAGAGGCCAGAGCCAGGCACG
CCTGGCAGCTGACACAGGGCGCTACAGTGCTGGGCCTG
TTCAGAGTGACCCCCGAGATTCCTGCCGGCCTGCCTAGC
CCTAGATCTGAAGGCGGCGGAGGTTCCGGAGGCGGAGG
ATCTGCTAGCACCAAAGGCCCTTCCGTGTTTCCTCTGGC
TCCTAGCTCCAAGTCCACCTCTGGAGGCACCGCTGCTCT
CGGATGCCTCGTGAAGGATTATTTTCCTGAGCCTGTGAC
AGTGTCCTGGAATAGCGGAGCACTGACCTCTGGAGTGC
ATACTTTCCCCGCTGTGCTGCAGTCCTCTGGACTGTACA
GCCTGAGCAGCGTGGTGACAGTGCCCAGCAGCAGCCTG
GGCACCCAGACCTACATCTGCAACGTGAACCACAAGCC
CAGCAACACCAAGGTGGACAAGAAGGTGGAACCCAAGT
CTTGT 162 anti-FAP (4B9) see Table 21
Fc hole chain
163 anti-FAP (4B9) see Table 21
light chain
117 Dimeric hu 4- REGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWY
SDPGLAGVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELR
1BBL (71-254) - RVVAGEGSGSVSLALHLQPLRSAAGAAALALTVDLPPASS CL Fc knob chain EARNSAFGFQGRLLHLSAGQRLGVHLHTEARARHAWQLT
QGATVLGLFRVTPEIPAGLPSPRSEGGGGSGGGGSREGPEL
SPDDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWYSDPGLA
GVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELRRVVAG
EGSGSVSLALHLQPLRSAAGAAALALTVDLPPASSEARNS
AFGFQGRLLHLSAGQRLGVHLHTEARARHAWQLTQGATV
LGLFRVTPEIPAGLPSPRSEGGGGSGGGGSRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGN
SQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTH
QGLSSPVTKSFNRGECDKTHTCPPCPAPEAAGGPSVFLFPP
KPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEV
HNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKV
SNKALGAPIEKTISKAKGQPREPQVYTLPPCRDELTKNQVS
LWCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSF
FLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSL
SPGK
118 Monomeric hu 4- REGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWY
SDPGLAGVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELR
1BBL (71-254) - RVVAGEGSGSVSLALHLQPLRSAAGAAALALTVDLPPASS CH1 EARNSAFGFQGRLLHLSAGQRLGVHLHTEARARHAWQLT
QGATVLGLFRVTPEIPAGLPSPRSEGGGGSGGGGSASTKGP
SVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALT
SGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHK
PSNTKVDKKVEPKSC
164 anti-FAP (4B9) see Table 21
Fc hole chain
125 anti-FAP (4B9) see Table 21
light chain
2.1.3 Preparation of bivalent FAP (4B9) targeted 4-lBB ligand (71-254) trimer- containing Fc (kih) fusion antigen binding molecule with the dimeric and monomeric 4-lBB ligands fused at the C-terminus of each heavy chain (Construct 2.3)
A polypeptide containing two ectodomains of 4-lBB ligand (71-254), separated by (G4S)2 linkers was fused to the C-terminus of human IgGl Fc hole chain, as depicted in Figure 1C: human IgGl Fc hole, (G4S)2 connector, human 4-lBB ligand, (G4S)2 connector, human 4-lBB ligand. A polypeptide containing one ectodomain of 4- IBB ligand (71-254) and fused to the C- terminus of human IgGl Fc knob chain as described in Figure ID: human IgGl Fc knob, (G4S)2 connector, human 4- IBB ligand.
The polypeptide encoding the dimeric 4- IBB ligand was subcloned in frame at the C- terminus of human IgGl heavy chain CH2 and CH3 domains on the hole (Merchant, Zhu et al. 1998) using a (G4S)2 connector. The polypeptide encoding the monomeric 4- IBB ligand was subcloned in frame at the C-terminus of human IgGl heavy chain CH2 and CH3 domains on the knob (Merchant, Zhu et al. 1998) using a (G4S)2 connector.
The variable region of heavy and light chain DNA sequences encoding a binder specific for fibroblast activation protein (FAP), clone 4B9, were subcloned in frame with either the constant heavy chain of the hole, the knob or the constant light chain of human IgGl.
The Pro329Gly, Leu234Ala and Leu235Ala mutations have been introduced in the constant region of the knob and hole heavy chains to abrogate binding to Fc gamma receptors according to the method described in WO 2012/130831. Combination of the anti-FAP hulgGI hole dimeric ligand chain containing the
Y349C/T366S/L368A/Y407V mutations, the anti-FAP hulgGI knob monomeric ligand chain containing the S354C/T366W mutations and the anti-FAP light chain allows generation of a heterodimer, which includes an assembled trimeric 4- IBB ligand and two FAP binding Fabs (Figure 4, Construct 2.3) Table 23 shows the cDNA and amino acid sequences of the bivalent FAP (4B9)-targeted 4-
1BB ligand trimer-containing Fc (kih) fusion molecule Construct 2.3 (FAP split trimer with 2 anti-FAP Fabs, dimeric and monomeric 4- IBB ligand fused at the C-terminus of each heavy chain, respectively).
Table 23: Sequences of bivalent FAP(4B9)-targeted human 4-1BB ligand (71-254) containing Fc (kih) fusion molecule Construct 2.3
SEQ ID Description Sequence
NO:
167 anti-FAP (4B9) GAGGTGCAGCTGCTCGAAAGCGGCGGAGGACTGGTGCA
GCCTGGCGGCAGCCTGAGACTGTCTTGCGCCGCCAGCG
Fc hole chain GCTTCACCTTCAGCAGCTACGCCATGAGCTGGGTCCGCC fused to dimeric AGGCCCCTGGCAAGGGACTGGAATGGGTGTCCGCCATC
ATCGGCTCTGGCGCCAGCACCTACTACGCCGACAGCGTG
hu 4-lBBL (71- AAGGGCCGGTTCACCATCAGCCGGGACAACAGCAAGAA 254) CACCCTGTACCTGCAGATGAACAGCCTGCGGGCCGAGG
ACACCGCCGTGTACTACTGCGCCAAGGGATGGTTCGGC
GGCTTCAACTACTGGGGACAGGGCACCCTGGTCACAGT GTCCAGCGCTAGCACCAAGGGCCCCTCCGTGTTCCCCCT
GGCCCCCAGCAGCAAGAGCACCAGCGGCGGCACAGCCG
CTCTGGGCTGCCTGGTCAAGGACTACTTCCCCGAGCCCG
TGACCGTGTCCTGGAACAGCGGAGCCCTGACCTCCGGC
GTGCACACCTTCCCCGCCGTGCTGCAGAGTTCTGGCCTG
TATAGCCTGAGCAGCGTGGTCACCGTGCCTTCTAGCAGC
CTGGGCACCCAGACCTACATCTGCAACGTGAACCACAA
GCCCAGCAACACCAAGGTGGACAAGAAGGTGGAGCCCA
AGAGCTGCGACAAAACTCACACATGCCCACCGTGCCCA
GCACCTGAAGCTGCAGGGGGACCGTCAGTCTTCCTCTTC
CCCCCAAAACCCAAGGACACCCTCATGATCTCCCGGACC
CCTGAGGTCACATGCGTGGTGGTGGACGTGAGCCACGA
AGACCCTGAGGTCAAGTTCAACTGGTACGTGGACGGCG
TGGAGGTGCATAATGCCAAGACAAAGCCGCGGGAGGAG
CAGTACAACAGCACGTACCGTGTGGTCAGCGTCCTCACC
GTCCTGCACCAGGACTGGCTGAATGGCAAGGAGTACAA
GTGCAAGGTCTCCAACAAAGCCCTCGGCGCCCCCATCG
AGAAAACCATCTCCAAAGCCAAAGGGCAGCCCCGAGAA
CCACAGGTGTGCACCCTGCCCCCATCCCGGGATGAGCTG
ACCAAGAACCAGGTCAGCCTCTCGTGCGCAGTCAAAGG
CTTCTATCCCAGCGACATCGCCGTGGAGTGGGAGAGCA
ATGGGCAGCCGGAGAACAACTACAAGACCACGCCTCCC
GTGCTGGACTCCGACGGCTCCTTCTTCCTCGTGAGCAAG
CTCACCGTGGACAAGAGCAGGTGGCAGCAGGGGAACGT
CTTCTCATGCTCCGTGATGCATGAGGCTCTGCACAACCA
CTACACGCAGAAGAGCCTCTCCCTGTCTCCGGGTGGAGG
CGGCGGAAGCGGAGGAGGAGGATCCAGAGAGGGCCCT
GAGCTGAGCCCCGATGATCCTGCTGGACTGCTGGACCTG
CGGCAGGGCATGTTTGCTCAGCTGGTGGCCCAGAACGTG
CTGCTGATCGATGGCCCCCTGTCCTGGTACAGCGATCCT
GGACTGGCTGGCGTGTCACTGACAGGCGGCCTGAGCTA
CAAAGAGGACACCAAAGAACTGGTGGTGGCCAAGGCCG
GCGTGTACTACGTGTTCTTTCAGCTGGAACTGCGGAGAG
TGGTGGCCGGCGAAGGATCTGGCTCTGTGTCTCTGGCCC
TGCATCTGCAGCCTCTGAGAAGCGCTGCTGGCGCTGCAG
CTCTGGCACTGACAGTGGATCTGCCTCCTGCCAGCTCCG
AGGCCCGGAATAGCGCATTTGGGTTTCAAGGCAGGCTG
CTGCACCTGTCTGCCGGCCAGAGGCTGGGAGTGCATCTG
CACACAGAGGCCAGGGCTAGACACGCCTGGCAGCTGAC
ACAGGGCGCTACAGTGCTGGGCCTGTTCAGAGTGACCC
CCGAGATTCCAGCCGGCCTGCCTTCTCCAAGAAGCGAA
GGCGGAGGCGGATCTGGCGGCGGAGGATCTAGAGAGGG
ACCCGAACTGTCCCCTGACGATCCAGCCGGGCTGCTGGA
TCTGAGACAGGGAATGTTCGCCCAGCTGGTGGCTCAGA
ATGTGCTGCTGATTGACGGACCTCTGAGCTGGTACTCCG
ACCCAGGGCTGGCAGGGGTGTCCCTGACTGGGGGACTG
TCCTACAAAGAAGATACAAAAGAACTGGTGGTGGCTAA
GCGGGTGGTGGCTGGGGAGGGCTCAGGATCTGTGTCCCT
GGCTCTGCATCTGCAGCCACTGCGCTCTGCTGCTGGCGC
AGCTGCACTGGCTCTGACTGTGGACCTGCCACCAGCCTC
TAGCGAGGCCAGAAACAGCGCCTTCGGGTTCCAAGGAC
GCCTGCTGCATCTGAGCGCCGGACAGCGCCTGGGAGTG
CATCTGCATACTGAAGCCAGAGCCCGGCATGCTTGGCA GCTGACTCAGGGGGCAACTGTGCTGGGACTGTTTCGCGT GACACCTGAGATCCCTGCCGGACTGCCAAGCCCTAGATC AGAA
GAGGTGCAGCTGCTCGAAAGCGGCGGAGGACTGGTGCA
anti-FAP (4B9)
GCCTGGCGGCAGCCTGAGACTGTCTTGCGCCGCCAGCG
Fc knob chain GCTTCACCTTCAGCAGCTACGCCATGAGCTGGGTCCGCC fused to AGGCCCCTGGCAAGGGACTGGAATGGGTGTCCGCCATC
ATCGGCTCTGGCGCCAGCACCTACTACGCCGACAGCGTG
monomeric hu 4- AAGGGCCGGTTCACCATCAGCCGGGACAACAGCAAGAA 1BBL (71-254) CACCCTGTACCTGCAGATGAACAGCCTGCGGGCCGAGG
ACACCGCCGTGTACTACTGCGCCAAGGGATGGTTCGGC
GGCTTCAACTACTGGGGACAGGGCACCCTGGTCACAGT
GTCCAGCGCTAGCACCAAGGGCCCATCGGTCTTCCCCCT
GGCACCCTCCTCCAAGAGCACCTCTGGGGGCACAGCGG
CCCTGGGCTGCCTGGTCAAGGACTACTTCCCCGAACCGG
TGACGGTGTCGTGGAACTCAGGCGCCCTGACCAGCGGC
GTGCACACCTTCCCGGCTGTCCTACAGTCCTCAGGACTC
TACTCCCTCAGCAGCGTGGTGACCGTGCCCTCCAGCAGC
TTGGGCACCCAGACCTACATCTGCAACGTGAATCACAA
GCCCAGCAACACCAAGGTGGACAAGAAAGTTGAGCCCA
AATCTTGTGACAAAACTCACACATGCCCACCGTGCCCAG
CACCTGAAGCTGCAGGGGGACCGTCAGTCTTCCTCTTCC
CCCCAAAACCCAAGGACACCCTCATGATCTCCCGGACCC
CTGAGGTCACATGCGTGGTGGTGGACGTGAGCCACGAA
GACCCTGAGGTCAAGTTCAACTGGTACGTGGACGGCGT
GGAGGTGCATAATGCCAAGACAAAGCCGCGGGAGGAGC
AGTACAACAGCACGTACCGTGTGGTCAGCGTCCTCACCG
TCCTGCACCAGGACTGGCTGAATGGCAAGGAGTACAAG
TGCAAGGTCTCCAACAAAGCCCTCGGCGCCCCCATCGA
GAAAACCATCTCCAAAGCCAAAGGGCAGCCCCGAGAAC
CACAGGTGTACACCCTGCCCCCCTGCAGAGATGAGCTG
ACCAAGAACCAGGTGTCCCTGTGGTGTCTGGTCAAGGGC
TTCTACCCCAGCGATATCGCCGTGGAGTGGGAGAGCAA
CGGCCAGCCTGAGAACAACTACAAGACCACCCCCCCTG
TGCTGGACAGCGACGGCAGCTTCTTCCTGTACTCCAAAC
TGACCGTGGACAAGAGCCGGTGGCAGCAGGGCAACGTG
TTCAGCTGCAGCGTGATGCACGAGGCCCTGCACAACCA
CTACACCCAGAAGTCCCTGAGCCTGAGCCCCGGCGGAG
GCGGCGGAAGCGGAGGAGGAGGATCCAGAGAGGGCCC
TGAGCTGAGCCCCGATGATCCTGCTGGACTGCTGGACCT
GCGGCAGGGCATGTTTGCTCAGCTGGTGGCCCAGAACGT
GCTGCTGATCGATGGCCCCCTGTCCTGGTACAGCGATCC
TGGACTGGCTGGCGTGTCACTGACAGGCGGCCTGAGCTA
CAAAGAGGACACCAAAGAACTGGTGGTGGCCAAGGCCG
GCGTGTACTACGTGTTCTTTCAGCTGGAACTGCGGAGAG
TGGTGGCCGGCGAAGGATCTGGCTCTGTGTCTCTGGCCC
TGCATCTGCAGCCTCTGAGAAGCGCTGCTGGCGCTGCAG
CTCTGGCACTGACAGTGGATCTGCCTCCTGCCAGCTCCG
AGGCCCGGAATAGCGCATTTGGGTTTCAAGGCAGGCTG
CTGCACCTGTCTGCCGGCCAGAGGCTGGGAGTGCATCTG
CACACAGAGGCCAGGGCTAGACACGCCTGGCAGCTGAC
ACAGGGCGCTACAGTGCTGGGCCTGTTCAGAGTGACCC CCGAGATTCCAGCCGGCCTGCCTTCTCCAAGAAGCGAA
163 anti-FAP (4B9) see Table 21
light chain
123 anti-FAP (4B9) EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQA
PGKGLEWVSAIIGSGASTYYADSVKGRFTISRDNSKNTLYL
Fc hole chain QMNSLRAEDTAVYYCAKGWFGGFNYWGQGTLVTVSSAS fused to dimeric TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNS
GALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICN
hu 4-lBBL (71- VNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGGPSVF 254) LFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDG
VEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYK
CKVSNKALGAPIEKTISKAKGQPREPQVCTLPPSRDELTKN
QVSLSCAVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSD
GSFFLVSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKS
LSLSPGGGGGSGGGGSREGPELSPDDPAGLLDLRQGMFAQ
LVAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYKEDTKELV
VAKAGVYYVFFQLELRRVVAGEGSGSVSLALHLQPLRSAA
GAAALALTVDLPPASSEARNSAFGFQGRLLHLSAGQRLGV
HLHTEARARHAWQLTQGATVLGLFRVTPEIPAGLPSPRSEG
GGGSGGGGSREGPELSPDDPAGLLDLRQGMFAQLVAQNV
LLIDGPLSWYSDPGLAGVSLTGGLSYKEDTKELVVAKAGV
YYVFFQLELRRVVAGEGSGSVSLALHLQPLRSAAGAAALA
LTVDLPPASSEARNSAFGFQGRLLHLSAGQRLGVHLHTEA
RARHAWQLTQGATVLGLFRVTPEIPAGLPSPRSE
124 anti-FAP (4B9) EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQA
PGKGLEWVSAIIGSGASTYYADSVKGRFTISRDNSKNTLYL
Fc knob chain QMNSLRAEDTAVYYCAKGWFGGFNYWGQGTLVTVSSAS fused to TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNS
GALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICN
monomeric hu 4- VNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGGPSVF 1BBL (71-254) LFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDG
VEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYK
CKVSNKALGAPIEKTISKAKGQPREPQVYTLPPCRDELTKN
QVSLWCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSD
GSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKS
LSLSPGGGGGSGGGGSREGPELSPDDPAGLLDLRQGMFAQ
LVAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYKEDTKELV
VAKAGVYYVFFQLELRRVVAGEGSGSVSLALHLQPLRSAA
GAAALALTVDLPPASSEARNSAFGFQGRLLHLSAGQRLGV
HLHTEARARHAWQLTQGATVLGLFRVTPEIPAGLPSPRSE
125 anti-FAP (4B9) see Table 21
light chain 2.1.4 Preparation of monovalent FAP (4B9) targeted 4-lBB ligand (71-248) trimer- containing Fc (kih) fusion antigen binding molecule with crossed CH1-CL domains with charged residues (Construct 2.4)
A polypeptide containing two ectodomains of 4-lBB ligand (71-248), separated by (G4S)2 linkers, and fused to the human IgGl-CL domain, was cloned as depicted in Figure 1A: human 4- IBB ligand, (G4S)2 connector, human 4- IBB ligand, (G4S)2 connector, human CL. A polypeptide containing one ectodomain of 4-lBB ligand (71-248) and fused to the human IgGl- CH domain, was cloned as described in Figure IB: human 4- IBB ligand, (G4S)2 connector, human CH. The polypeptide encoding the dimeric 4- IBB ligand fused to human CL domain was subcloned in frame with the human IgGl heavy chain CH2 and CH3 domains on the knob (Merchant, Zhu et al. 1998) using a linker (G4S)2 or, alternatively (GSPGSSSSGS). To improve correct pairing the following mutations have been introduced in the crossed CH-CL. In the dimeric 4- IBB ligand fused to human CL, E123R and Q124K. In the monomeric 4- IBB ligand fused to human CHI, K147E and K213E.
The variable region of heavy and light chain DNA sequences encoding a binder specific for fibroblast activation protein (FAP), clone 4B9, were subcloned in frame with either the constant heavy chain of the hole or the constant light chain of human IgGl .
The Pro329Gly, Leu234Ala and Leu235Ala mutations have been introduced in the constant region of the knob and hole heavy chains to abrogate binding to Fc gamma receptors according to the method described in WO 2012/130831.
Combination of the dimeric ligand-Fc knob chain containing the S354C/T366W mutations, the monomeric CHI fusion, the targeted anti-FAP-Fc hole chain containing the
Y349C/T366S/L368A/Y407V mutations and the anti-FAP light chain allows generation of a heterodimer, which includes an assembled trimeric 4- IBB ligand and a FAP binding Fab
(Figure 4, Construct 2.4).
Table 24 shows the cDNA and amino acid sequences of the monovalent FAP (4B9)- human 4-lBB ligand (71-248) Fc (kih) fusion antigen binding molecule containing CH1-CL crossover with charged residues (Construct 2.4). Table 24: Sequences of monovalent FAP(4B9)-targeted human 4-lBB ligand (71-248) containing Fc (kih) fusion molecule Construct 2.4
SEQ ID Description Sequence
NO:
AGAGAGGGCCCTGAGCTGAGCCCCGATGATCCTGCTGG
169 Dimeric hu 4-
ACTGCTGGACCTGCGGCAGGGCATGTTTGCTCAGCTGGT
1BBL (71-248) - GGCCCAGAACGTGCTGCTGATCGATGGCCCCCTGTCCTG CL* Fc knob GTACAGCGATCCTGGACTGGCTGGCGTGTCACTGACAGG
CGGCCTGAGCTACAAAGAGGACACCAAAGAACTGGTGG
chain TGGCCAAGGCCGGCGTGTACTACGTGTTCTTTCAGCTGG
AACTGCGGAGAGTGGTGGCCGGCGAAGGATCTGGCTCT
GTGTCTCTGGCCCTGCATCTGCAGCCTCTGAGATCTGCT
GCTGGCGCCGCTGCTCTGGCACTGACAGTGGATCTGCCT
CCTGCCAGCAGCGAGGCCCGGAATAGCGCATTTGGGTTT
CAAGGCAGGCTGCTGCACCTGTCTGCCGGCCAGAGGCT
GGGAGTGCATCTGCACACAGAGGCCAGGGCTAGACACG
CCTGGCAGCTGACACAGGGCGCTACAGTGCTGGGCCTG
TTCAGAGTGACCCCCGAGATTCCAGCCGGACTGGGAGG
CGGCGGATCTGGCGGCGGAGGATCTAGAGAAGGACCCG
AGCTGTCCCCTGACGATCCAGCCGGGCTGCTGGATCTGA
GACAGGGAATGTTCGCCCAGCTGGTGGCTCAGAATGTG
CTGCTGATTGACGGACCTCTGAGCTGGTACTCCGACCCA
GGGCTGGCAGGGGTGTCCCTGACTGGGGGACTGTCCTAC
AAAGAAGATACAAAAGAACTGGTGGTGGCTAAAGCTGG
GGTGTACTATGTGTTTTTTCAGCTGGAACTGAGGCGGGT
GGTGGCTGGGGAGGGCTCAGGATCTGTGTCCCTGGCTCT
GCATCTGCAGCCACTGCGCTCTGCAGCAGGGGCTGCAG
CACTGGCCCTGACTGTGGACCTGCCCCCAGCTTCTTCCG
AGGCCAGAAACAGCGCCTTCGGGTTCCAAGGACGCCTG
CTGCATCTGAGCGCCGGACAGCGCCTGGGAGTGCATCT
GCATACTGAAGCCAGAGCCCGGCATGCTTGGCAGCTGA
CTCAGGGGGCAACTGTGCTGGGACTGTTTCGCGTGACAC
CTGAGATCCCCGCTGGACTGGGCGGAGGCGGTTCCGGA
GGGGGAGGATCTCGTACGGTGGCTGCACCATCTGTCTTT
ATCTTCCCACCCAGCGACCGGAAGCTGAAGTCTGGCAC
AGCCAGCGTCGTGTGCCTGCTGAATAACTTCTACCCCCG
CGAGGCCAAGGTGCAGTGGAAGGTGGACAATGCCCTGC
AGAGCGGCAACAGCCAGGAAAGCGTGACCGAGCAGGA
CAGCAAGGACTCCACCTACAGCCTGAGCAGCACCCTGA
CCCTGAGCAAGGCCGACTACGAGAAGCACAAGGTGTAC
GCCTGCGAAGTGACCCACCAGGGCCTGTCTAGCCCCGTG
ACCAAGAGCTTCAACCGGGGCGAGTGCGACAAGACCCA
CACCTGTCCTCCATGCCCTGCCCCTGAAGCTGCTGGCGG
CCCTAGCGTGTTCCTGTTCCCCCCAAAGCCCAAGGACAC
CCTGATGATCAGCCGGACCCCTGAAGTGACCTGCGTGGT
GGTGGATGTGTCCCACGAGGACCCTGAAGTGAAGTTCA
ATTGGTACGTGGACGGCGTGGAAGTGCACAATGCCAAG
ACCAAGCCGCGGGAGGAGCAGTACAACAGCACGTACCG
TGTGGTCAGCGTCCTCACCGTCCTGCACCAGGACTGGCT
GAATGGCAAGGAGTACAAGTGCAAGGTCTCCAACAAAG
CCCTCGGCGCCCCCATCGAGAAAACCATCTCCAAAGCC AAAGGGCAGCCCCGAGAACCACAGGTGTACACCCTGCC
CCCATGCCGGGATGAGCTGACCAAGAACCAGGTCAGCC
TGTGGTGCCTGGTCAAAGGCTTCTATCCCAGCGACATCG
CCGTGGAGTGGGAGAGCAATGGGCAGCCGGAGAACAAC
TACAAGACCACGCCTCCCGTGCTGGACTCCGACGGCTCC
TTCTTCCTCTACAGCAAGCTCACCGTGGACAAGAGCAGG
TGGCAGCAGGGGAACGTCTTCTCATGCTCCGTGATGCAT
GAGGCTCTGCACAACCACTACACGCAGAAGAGCCTCTC
CCTGTCTCCGGGTAAA
Monomeric hu 4- AGAGAGGGCCCTGAGCTGAGCCCCGATGATCCTGCTGG
170
ACTGCTGGACCTGCGGCAGGGCATGTTTGCTCAGCTGGT
1BBL (71-248) - GGCCCAGAACGTGCTGCTGATCGATGGCCCCCTGTCCTG CH1* GTACAGCGATCCTGGACTGGCTGGCGTGTCACTGACAGG
CGGCCTGAGCTACAAAGAGGACACCAAAGAACTGGTGG
TGGCCAAGGCCGGCGTGTACTACGTGTTCTTTCAGCTGG
AACTGCGGAGAGTGGTGGCCGGCGAAGGATCTGGCTCT
GTGTCTCTGGCCCTGCATCTGCAGCCTCTGAGATCTGCT
GCTGGCGCCGCTGCTCTGGCACTGACAGTGGATCTGCCT
CCTGCCAGCAGCGAGGCCCGGAATAGCGCATTTGGGTTT
CAAGGCAGGCTGCTGCACCTGTCTGCCGGCCAGAGGCT
GGGAGTGCATCTGCACACAGAGGCCAGGGCTAGACACG
CCTGGCAGCTGACACAGGGCGCTACAGTGCTGGGCCTG
TTCAGAGTGACCCCCGAGATTCCAGCCGGACTGGGAGG
CGGAGGTTCCGGAGGCGGAGGATCTGCTAGCACAAAGG
GCCCCAGCGTGTTCCCTCTGGCCCCTAGCAGCAAGAGCA
CATCTGGCGGAACAGCCGCCCTGGGCTGCCTGGTGGAA
GATTACTTCCCCGAGCCCGTGACCGTGTCCTGGAATTCT
GGCGCCCTGACAAGCGGCGTGCACACCTTTCCAGCCGTG
CTGCAGAGCAGCGGCCTGTACTCTCTGAGCAGCGTCGTG
ACAGTGCCCAGCAGCTCTCTGGGCACCCAGACCTACATC
TGCAACGTGAACCACAAGCCCAGCAACACCAAGGTGGA
CGAGAAGGTGGAACCCAAGTCCTGC
162 anti-FAP (4B9) see Table 21
Fc hole chain
163 anti-FAP (4B9) see Table 21
light chain
119 Dimeric hu 4- REGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWY
SDPGLAGVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELR
1BBL (71-248) - RVVAGEGSGSVSLALHLQPLRSAAGAAALALTVDLPPASS CL* Fc knob EARNSAFGFQGRLLHLSAGQRLGVHLHTEARARHAWQLT
QGATVLGLFRVTPEIPAGLGGGGSGGGGSREGPELSPDDPA
chain GLLDLRQGMFAQLVAQNVLLIDGPLSWYSDPGLAGVSLTG
GLSYKEDTKELVVAKAGVYYVFFQLELRRVVAGEGSGSV
SLALHLQPLRSAAGAAALALTVDLPPASSEARNSAFGFQG
RLLHLSAGQRLGVHLHTEARARHAWQLTQGATVLGLFRV
TPEIPAGLGGGGSGGGGSRTVAAPSVFIFPPSDRKLKSGTAS
VVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKD
STYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR
GECDKTHTCPPCPAPEAAGGPSVFLFPPKPKDTLMISRTPE VTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQY
NSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALGAPIEKTI
SKAKGQPREPQVYTLPPCRDELTKNQVSLWCLVKGFYPSD
IAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSR
WQQGNVFSCSVMHEALHNHYTQKSLSLSPGK
120 Monomeric hu 4- REGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWY
SDPGLAGVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELR
1BBL (71-248) - RVVAGEGSGSVSLALHLQPLRSAAGAAALALTVDLPPASS CH1* EARNSAFGFQGRLLHLSAGQRLGVHLHTEARARHAWQLT
QGATVLGLFRVTPEIPAGLGGGGSGGGGSASTKGPSVFPLA
PSSKSTSGGTAALGCLVEDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKV
DEKVEPKSC
164 anti-FAP (4B9) see Table 21
Fc hole chain
125 anti-FAP (4B9) see Table 21
light chain
2.1.5 Preparation of monovalent FAP (4B9) targeted 4-lBB ligand (71-248) trimer- containing Fc (kih) fusion antigen binding molecule with crossed CH1-CL domains without charged residues (Construct 2.5) A polypeptide containing two ectodomains of 4-lBB ligand (71-248), separated by (G4S)2 linkers, and fused to the human IgGl-CL domain, was cloned as depicted in Figure 1A: human 4- lBB ligand, (G4S)2 connector, human 4-lBB ligand, (G4S)2 connector, human CL. A polypeptide containing one ectodomain of 4-lBB ligand (71-248) and fused to the human IgGl- CH domain, was cloned as described in Figure IB: human 4- IBB ligand, (G4S)2 connector, human CH.
The polypeptide encoding the dimeric 4- IBB ligand fused to human CL domain was subcloned in frame with the human IgGl heavy chain CH2 and CH3 domains on the knob (Merchant, Zhu et al. 1998) using a linker (G4S)2 or, alternatively (GSPGSSSSGS).
The variable region of heavy and light chain DNA sequences encoding a binder specific for fibroblast activation protein (FAP), clone 4B9, were subcloned in frame with either the constant heavy chain of the hole or the constant light chain of human IgGl .
The Pro329Gly, Leu234Ala and Leu235Ala mutations have been introduced in the constant region of the knob and hole heavy chains to abrogate binding to Fc gamma receptors according to the method described in WO 2012/130831. Combination of the dimeric ligand-Fc knob chain containing the S354C/T366W mutations, the monomelic CHI fusion, the targeted anti-FAP-Fc hole chain containing the
Y349C/T366S/L368A/Y407V mutations and the anti-FAP light chain allows generation of a heterodimer, which includes an assembled trimeric 4- IBB ligand and a FAP binding Fab (Figure 4, Construct 2.5)
Table 25 shows the cDNA and amino acid sequences of the monovalent FAP (4B9)-human 4- IBB ligand (71-248) Fc (kih) fusion antigen binding molecule containing CHl-CL crossover without charged residues (Construct 2.5).
Table 25: Sequences of monovalent FAP(4B9)-targeted human 4-1BB ligand (71-248) containing Fc (kih) fusion molecule Construct 2.5
SEQ ID Description Sequence
NO:
171 nucleotide AGAGAGGGCCCTGAGCTGAGCCCCGATGATCCTGCTGG
ACTGCTGGACCTGCGGCAGGGCATGTTTGCTCAGCTGGT
sequence dimeric GGCCCAGAACGTGCTGCTGATCGATGGCCCCCTGTCCTG hu 4-lBBL (71- GTACAGCGATCCTGGACTGGCTGGCGTGTCACTGACAGG
CGGCCTGAGCTACAAAGAGGACACCAAAGAACTGGTGG
248) - CL Fc TGGCCAAGGCCGGCGTGTACTACGTGTTCTTTCAGCTGG knob chain AACTGCGGAGAGTGGTGGCCGGCGAAGGATCTGGCTCT
GTGTCTCTGGCCCTGCATCTGCAGCCTCTGAGATCTGCT
GCTGGCGCCGCTGCTCTGGCACTGACAGTGGATCTGCCT
CCTGCCAGCAGCGAGGCCCGGAATAGCGCATTTGGGTTT
CAAGGCAGGCTGCTGCACCTGTCTGCCGGCCAGAGGCT
GGGAGTGCATCTGCACACAGAGGCCAGGGCTAGACACG
CCTGGCAGCTGACACAGGGCGCTACAGTGCTGGGCCTG
TTCAGAGTGACCCCCGAGATTCCAGCCGGACTGGGAGG
CGGCGGATCTGGCGGCGGAGGATCTAGAGAAGGACCCG
AGCTGTCCCCTGACGATCCAGCCGGGCTGCTGGATCTGA
GACAGGGAATGTTCGCCCAGCTGGTGGCTCAGAATGTG
CTGCTGATTGACGGACCTCTGAGCTGGTACTCCGACCCA
GGGCTGGCAGGGGTGTCCCTGACTGGGGGACTGTCCTAC
AAAGAAGATACAAAAGAACTGGTGGTGGCTAAAGCTGG
GGTGTACTATGTGTTTTTTCAGCTGGAACTGAGGCGGGT
GGTGGCTGGGGAGGGCTCAGGATCTGTGTCCCTGGCTCT
GCATCTGCAGCCACTGCGCTCTGCAGCAGGGGCTGCAG
CACTGGCCCTGACTGTGGACCTGCCCCCAGCTTCTTCCG
AGGCCAGAAACAGCGCCTTCGGGTTCCAAGGACGCCTG
CTGCATCTGAGCGCCGGACAGCGCCTGGGAGTGCATCT
GCATACTGAAGCCAGAGCCCGGCATGCTTGGCAGCTGA
CTCAGGGGGCAACTGTGCTGGGACTGTTTCGCGTGACAC
CTGAGATCCCCGCTGGACTGGGCGGAGGCGGTTCCGGA
GGGGGAGGATCTCGTACGGTGGCCGCTCCCTCCGTGTTT
ATCTTTCCCCCATCCGATGAACAGCTGAAAAGCGGCACC
GCCTCCGTCGTGTGTCTGCTGAACAATTTTTACCCTAGG
GAAGCTAAAGTGCAGTGGAAAGTGGATAACGCACTGCA
GTCCGGCAACTCCCAGGAATCTGTGACAGAACAGGACT CCAAGGACAGCACCTACTCCCTGTCCTCCACCCTGACAC
TGTCTAAGGCTGATTATGAGAAACACAAAGTCTACGCCT
GCGAAGTCACCCATCAGGGCCTGAGCTCGCCCGTCACA
AAGAGCTTCAACAGGGGAGAGTGTGACAAGACCCACAC
CTGTCCCCCTTGTCCTGCCCCTGAAGCTGCTGGCGGCCC
TTCTGTGTTCCTGTTCCCCCCAAAGCCCAAGGACACCCT
GATGATCAGCCGGACCCCCGAAGTGACCTGCGTGGTGG
TGGATGTGTCCCACGAGGACCCTGAAGTGAAGTTCAATT
GGTACGTGGACGGCGTGGAAGTGCACAATGCCAAGACC
AAGCCGCGGGAGGAGCAGTACAACAGCACGTACCGTGT
GGTCAGCGTCCTCACCGTCCTGCACCAGGACTGGCTGAA
TGGCAAGGAGTACAAGTGCAAGGTCTCCAACAAAGCCC
TCGGCGCCCCCATCGAGAAAACCATCTCCAAAGCCAAA
GGGCAGCCCCGAGAACCACAGGTGTACACCCTGCCCCC
ATGCCGGGATGAGCTGACCAAGAACCAGGTCAGCCTGT
GGTGCCTGGTCAAAGGCTTCTATCCCAGCGACATCGCCG
TGGAGTGGGAGAGCAATGGGCAGCCGGAGAACAACTAC
AAGACCACGCCTCCCGTGCTGGACTCCGACGGCTCCTTC
TTCCTCTACAGCAAGCTCACCGTGGACAAGAGCAGGTG
GCAGCAGGGGAACGTCTTCTCATGCTCCGTGATGCATGA
GGCTCTGCACAACCACTACACGCAGAAGAGCCTCTCCCT
GTCTCCGGGTAAA
172 Monomeric hu 4- AGAGAGGGCCCTGAGCTGAGCCCCGATGATCCTGCTGG
ACTGCTGGACCTGCGGCAGGGCATGTTTGCTCAGCTGGT
1BBL (71-248) - GGCCCAGAACGTGCTGCTGATCGATGGCCCCCTGTCCTG CH1 GTACAGCGATCCTGGACTGGCTGGCGTGTCACTGACAGG
CGGCCTGAGCTACAAAGAGGACACCAAAGAACTGGTGG
TGGCCAAGGCCGGCGTGTACTACGTGTTCTTTCAGCTGG
AACTGCGGAGAGTGGTGGCCGGCGAAGGATCTGGCTCT
GTGTCTCTGGCCCTGCATCTGCAGCCTCTGAGATCTGCT
GCTGGCGCCGCTGCTCTGGCACTGACAGTGGATCTGCCT
CCTGCCAGCAGCGAGGCCCGGAATAGCGCATTTGGGTTT
CAAGGCAGGCTGCTGCACCTGTCTGCCGGCCAGAGGCT
GGGAGTGCATCTGCACACAGAGGCCAGGGCTAGACACG
CCTGGCAGCTGACACAGGGCGCTACAGTGCTGGGCCTG
TTCAGAGTGACCCCCGAGATTCCAGCCGGACTGGGAGG
CGGAGGTTCCGGAGGCGGAGGATCTGCTAGCACCAAAG
GCCCTTCCGTGTTTCCTCTGGCTCCTAGCTCCAAGTCCAC
CTCTGGAGGCACCGCTGCTCTCGGATGCCTCGTGAAGGA
TTATTTTCCTGAGCCTGTGACAGTGTCCTGGAATAGCGG
AGCACTGACCTCTGGAGTGCATACTTTCCCCGCTGTGCT
GCAGTCCTCTGGACTGTACAGCCTGAGCAGCGTGGTGAC
AGTGCCCAGCAGCAGCCTGGGCACCCAGACCTACATCT
GCAACGTGAACCACAAGCCCAGCAACACCAAGGTGGAC
AAGAAGGTGGAACCCAAGTCTTGT
162 anti-FAP (4B9) see Table 21
Fc hole chain
163 anti-FAP (4B9) see Table 21
light chain 173 Dimeric hu 4- REGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWY
SDPGLAGVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELR
1BBL (71-248) - RVVAGEGSGSVSLALHLQPLRSAAGAAALALTVDLPPASS CL Fc knob chain EARNSAFGFQGRLLHLSAGQRLGVHLHTEARARHAWQLT
QGATVLGLFRVTPEIPAGLGGGGSGGGGSREGPELSPDDPA
GLLDLRQGMFAQLVAQNVLLIDGPLSWYSDPGLAGVSLTG
GLSYKEDTKELVVAKAGVYYVFFQLELRRVVAGEGSGSV
SLALHLQPLRSAAGAAALALTVDLPPASSEARNSAFGFQG
RLLHLSAGQRLGVHLHTEARARHAWQLTQGATVLGLFRV
TPEIPAGLGGGGSGGGGSRTVAAPSVFIFPPSDEQLKSGTAS
VVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKD
STYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR
GECDKTHTCPPCPAPEAAGGPSVFLFPPKPKDTLMISRTPE
VTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQY
NSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALGAPIEKTI
SKAKGQPREPQVYTLPPCRDELTKNQVSLWCLVKGFYPSD
IAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSR
WQQGNVFSCSVMHEALHNHYTQKSLSLSPGK
174 Monomeric hu 4- REGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWY
SDPGLAGVSLTGGLSYKEDTKELVVAKAGVYYVFFQLELR
1BBL (71-248) - RVVAGEGSGSVSLALHLQPLRSAAGAAALALTVDLPPASS CH1 EARNSAFGFQGRLLHLSAGQRLGVHLHTEARARHAWQLT
QGATVLGLFRVTPEIPAGLGGGGSGGGGSASTKGPSVFPLA
PSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTK
VDKKVEPKSC
164 anti-FAP (4B9) see Table 21
Fc hole chain
125 anti-FAP (4B9) see Table 21
light chain
2.1.6 Preparation of bivalent FAP (4B9) targeted 4-lBB ligand (71-248) trimer- containing Fc (kih) fusion antigen binding molecule with the dimeric and monomeric 4-lBB ligands fused at the C-terminus of each heavy chain (Construct 2.6) A polypeptide containing two ectodomains of 4-lBB ligand (71-248), separated by (G4S)2 linkers was fused to the C-terminus of human IgGl Fc hole chain, as depicted in Figure 1C: human IgGl Fc hole, (G4S)2 connector, human 4-lBB ligand, (G4S)2 connector, human 4-lBB ligand. A polypeptide containing one ectodomain of 4- IBB ligand (71-248) and fused to the C- terminus of human IgGl Fc knob chain as described in Figure ID: human IgGl Fc knob, (G4S)2 connector, human 4- IBB ligand. The polypeptide encoding the dimeric 4- IBB ligand was subcloned in frame at the C- terminus of human IgGl heavy chain CH2 and CH3 domains on the hole (Merchant, Zhu et al. 1998) using a (G4S)2 connector. The polypeptide encoding the monomeric 4- IBB ligand was subcloned in frame at the C-terminus of human IgGl heavy chain CH2 and CH3 domains on the knob (Merchant, Zhu et al. 1998) using a (G4S)2 connector.
The variable region of heavy and light chain DNA sequences encoding a binder specific for fibroblast activation protein (FAP), clone 4B9, were subcloned in frame with either the constant heavy chain of the hole, the knob or the constant light chain of human IgGl.
The Pro329Gly, Leu234Ala and Leu235Ala mutations have been introduced in the constant region of the knob and hole heavy chains to abrogate binding to Fc gamma receptors according to the method described in WO 2012/130831.
Combination of the anti-FAP hulgGI hole dimeric ligand chain containing the
Y349C/T366S/L368A/Y407V mutations, the anti-FAP hulgGI knob monomeric ligand chain containing the S354C/T366W mutations and the anti-FAP light chain allows generation of a heterodimer, which includes an assembled trimeric 4- IBB ligand and two FAP binding Fabs (Figure 4, Construct 2.6).
Table 26 shows the cDNA and amino acid sequences of the bivalent FAP (4B9)-targeted 4- 1BB ligand trimer-containing Fc (kih) fusion molecule Construct 2.6 (FAP split trimer with 2 anti-FAP Fabs, dimeric and monomeric 4- IBB ligand fused at the C-terminus of each heavy chain, respectively).
Table 26: Sequences of bivalent FAP(4B9)-targeted human 4-1BB ligand (71-248) containing Fc (kih) fusion molecule Construct 2.6
SEQ ID Description Sequence
NO:
175 nucleotide GAGGTGCAGCTGCTCGAAAGCGGCGGAGGACTGGTGCA
GCCTGGCGGCAGCCTGAGACTGTCTTGCGCCGCCAGCG
sequence of anti- GCTTCACCTTCAGCAGCTACGCCATGAGCTGGGTCCGCC FAP (4B9) Fc AGGCCCCTGGCAAGGGACTGGAATGGGTGTCCGCCATC
ATCGGCTCTGGCGCCAGCACCTACTACGCCGACAGCGTG
hole chain fused AAGGGCCGGTTCACCATCAGCCGGGACAACAGCAAGAA to dimeric hu 4- CACCCTGTACCTGCAGATGAACAGCCTGCGGGCCGAGG
ACACCGCCGTGTACTACTGCGCCAAGGGATGGTTCGGC
1BBL (71-248)
GGCTTCAACTACTGGGGACAGGGCACCCTGGTCACAGT
GTCCAGCGCTAGCACCAAGGGCCCCTCCGTGTTCCCCCT
GGCCCCCAGCAGCAAGAGCACCAGCGGCGGCACAGCCG
CTCTGGGCTGCCTGGTCAAGGACTACTTCCCCGAGCCCG
TGACCGTGTCCTGGAACAGCGGAGCCCTGACCTCCGGC
GTGCACACCTTCCCCGCCGTGCTGCAGAGTTCTGGCCTG TATAGCCTGAGCAGCGTGGTCACCGTGCCTTCTAGCAGC
CTGGGCACCCAGACCTACATCTGCAACGTGAACCACAA
GCCCAGCAACACCAAGGTGGACAAGAAGGTGGAGCCCA
AGAGCTGCGACAAAACTCACACATGCCCACCGTGCCCA
GCACCTGAAGCTGCAGGGGGACCGTCAGTCTTCCTCTTC
CCCCCAAAACCCAAGGACACCCTCATGATCTCCCGGACC
CCTGAGGTCACATGCGTGGTGGTGGACGTGAGCCACGA
AGACCCTGAGGTCAAGTTCAACTGGTACGTGGACGGCG
TGGAGGTGCATAATGCCAAGACAAAGCCGCGGGAGGAG
CAGTACAACAGCACGTACCGTGTGGTCAGCGTCCTCACC
GTCCTGCACCAGGACTGGCTGAATGGCAAGGAGTACAA
GTGCAAGGTCTCCAACAAAGCCCTCGGCGCCCCCATCG
AGAAAACCATCTCCAAAGCCAAAGGGCAGCCCCGAGAA
CCACAGGTGTGCACCCTGCCCCCATCCCGGGATGAGCTG
ACCAAGAACCAGGTCAGCCTCTCGTGCGCAGTCAAAGG
CTTCTATCCCAGCGACATCGCCGTGGAGTGGGAGAGCA
ATGGGCAGCCGGAGAACAACTACAAGACCACGCCTCCC
GTGCTGGACTCCGACGGCTCCTTCTTCCTCGTGAGCAAG
CTCACCGTGGACAAGAGCAGGTGGCAGCAGGGGAACGT
CTTCTCATGCTCCGTGATGCATGAGGCTCTGCACAACCA
CTACACGCAGAAGAGCCTCTCCCTGTCTCCGGGTGGAGG
CGGCGGAAGCGGAGGAGGAGGATCCAGAGAGGGCCCT
GAGCTGAGCCCCGATGATCCTGCTGGACTGCTGGACCTG
CGGCAGGGCATGTTTGCTCAGCTGGTGGCCCAGAACGTG
CTGCTGATCGATGGCCCCCTGTCCTGGTACAGCGATCCT
GGACTGGCTGGCGTGTCACTGACAGGCGGCCTGAGCTA
CAAAGAGGACACCAAAGAACTGGTGGTGGCCAAGGCCG
GCGTGTACTACGTGTTCTTTCAGCTGGAACTGCGGAGAG
TGGTGGCCGGCGAAGGATCTGGCTCTGTGTCTCTGGCCC
TGCATCTGCAGCCTCTGAGAAGCGCTGCTGGCGCTGCAG
CTCTGGCACTGACAGTGGATCTGCCTCCTGCCAGCTCCG
AGGCCCGGAATAGCGCATTTGGGTTTCAAGGCAGGCTG
CTGCACCTGTCTGCCGGCCAGAGGCTGGGAGTGCATCTG
CACACAGAGGCCAGGGCTAGACACGCCTGGCAGCTGAC
ACAGGGCGCTACAGTGCTGGGCCTGTTCAGAGTGACCC
CCGAGATTCCAGCCGGCCTGGGCGGAGGCGGATCTGGC
GGCGGAGGATCTAGAGAGGGACCCGAACTGTCCCCTGA
CGATCCAGCCGGGCTGCTGGATCTGAGACAGGGAATGT
TCGCCCAGCTGGTGGCTCAGAATGTGCTGCTGATTGACG
GACCTCTGAGCTGGTACTCCGACCCAGGGCTGGCAGGG
GTGTCCCTGACTGGGGGACTGTCCTACAAAGAAGATAC
AAAAGAACTGGTGGTGGCTAAAGCTGGGGTGTACTATG
AGGGCTCAGGATCTGTGTCCCTGGCTCTGCATCTGCAGC
CACTGCGCTCTGCTGCTGGCGCAGCTGCACTGGCTCTGA
CTGTGGACCTGCCACCAGCCTCTAGCGAGGCCAGAAAC
AGCGCCTTCGGGTTCCAAGGACGCCTGCTGCATCTGAGC
GCCGGACAGCGCCTGGGAGTGCATCTGCATACTGAAGC
CAGAGCCCGGCATGCTTGGCAGCTGACTCAGGGGGCAA
CTGTGCTGGGACTGTTTCGCGTGACACCTGAGATCCCTG
CCGGACTG
GAGGTGCAGCTGCTCGAAAGCGGCGGAGGACTGGTGCA
nucleotide
GCCTGGCGGCAGCCTGAGACTGTCTTGCGCCGCCAGCG
sequence anti- GCTTCACCTTCAGCAGCTACGCCATGAGCTGGGTCCGCC
FAP (4B9) Fc
AGGCCCCTGGCAAGGGACTGGAATGGGTGTCCGCCATC
knob chain fused ATCGGCTCTGGCGCCAGCACCTACTACGCCGACAGCGTG to monomelic hu AAGGGCCGGTTCACCATCAGCCGGGACAACAGCAAGAA
CACCCTGTACCTGCAGATGAACAGCCTGCGGGCCGAGG
4-1BBL (71-248) ACACCGCCGTGTACTACTGCGCCAAGGGATGGTTCGGC
GGCTTCAACTACTGGGGACAGGGCACCCTGGTCACAGT
GTCCAGCGCTAGCACCAAGGGCCCATCGGTCTTCCCCCT
GGCACCCTCCTCCAAGAGCACCTCTGGGGGCACAGCGG
CCCTGGGCTGCCTGGTCAAGGACTACTTCCCCGAACCGG
TGACGGTGTCGTGGAACTCAGGCGCCCTGACCAGCGGC
GTGCACACCTTCCCGGCTGTCCTACAGTCCTCAGGACTC
TACTCCCTCAGCAGCGTGGTGACCGTGCCCTCCAGCAGC
TTGGGCACCCAGACCTACATCTGCAACGTGAATCACAA
GCCCAGCAACACCAAGGTGGACAAGAAAGTTGAGCCCA
AATCTTGTGACAAAACTCACACATGCCCACCGTGCCCAG
CACCTGAAGCTGCAGGGGGACCGTCAGTCTTCCTCTTCC
CCCCAAAACCCAAGGACACCCTCATGATCTCCCGGACCC
CTGAGGTCACATGCGTGGTGGTGGACGTGAGCCACGAA
GACCCTGAGGTCAAGTTCAACTGGTACGTGGACGGCGT
GGAGGTGCATAATGCCAAGACAAAGCCGCGGGAGGAGC
AGTACAACAGCACGTACCGTGTGGTCAGCGTCCTCACCG
TCCTGCACCAGGACTGGCTGAATGGCAAGGAGTACAAG
TGCAAGGTCTCCAACAAAGCCCTCGGCGCCCCCATCGA
GAAAACCATCTCCAAAGCCAAAGGGCAGCCCCGAGAAC
CACAGGTGTACACCCTGCCCCCCTGCAGAGATGAGCTG
ACCAAGAACCAGGTGTCCCTGTGGTGTCTGGTCAAGGGC
TTCTACCCCAGCGATATCGCCGTGGAGTGGGAGAGCAA
CGGCCAGCCTGAGAACAACTACAAGACCACCCCCCCTG
TGCTGGACAGCGACGGCAGCTTCTTCCTGTACTCCAAAC
TGACCGTGGACAAGAGCCGGTGGCAGCAGGGCAACGTG
TTCAGCTGCAGCGTGATGCACGAGGCCCTGCACAACCA
CTACACCCAGAAGTCCCTGAGCCTGAGCCCCGGCGGAG
GCGGCGGAAGCGGAGGAGGAGGATCCAGAGAGGGCCC
TGAGCTGAGCCCCGATGATCCTGCTGGACTGCTGGACCT
GCGGCAGGGCATGTTTGCTCAGCTGGTGGCCCAGAACGT
GCTGCTGATCGATGGCCCCCTGTCCTGGTACAGCGATCC
TGGACTGGCTGGCGTGTCACTGACAGGCGGCCTGAGCTA
CAAAGAGGACACCAAAGAACTGGTGGTGGCCAAGGCCG
GCGTGTACTACGTGTTCTTTCAGCTGGAACTGCGGAGAG
TGGTGGCCGGCGAAGGATCTGGCTCTGTGTCTCTGGCCC
TGCATCTGCAGCCTCTGAGAAGCGCTGCTGGCGCTGCAG
CTCTGGCACTGACAGTGGATCTGCCTCCTGCCAGCTCCG
AGGCCCGGAATAGCGCATTTGGGTTTCAAGGCAGGCTG
CTGCACCTGTCTGCCGGCCAGAGGCTGGGAGTGCATCTG
CACACAGAGGCCAGGGCTAGACACGCCTGGCAGCTGAC
ACAGGGCGCTACAGTGCTGGGCCTGTTCAGAGTGACCC
CCGAGATTCCAGCCGGCCTG anti-FAP (4B9) see Table 21
light chain 126 anti-FAP (4B9) EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQA
PGKGLEWVSAIIGSGASTYYADSVKGRFTISRDNSKNTLYL
Fc hole chain QMNSLRAEDTAVYYCAKGWFGGFNYWGQGTLVTVSSAS fused to dimeric TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNS
GALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICN
hu 4-lBBL (71- VNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGGPSVF 248) LFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDG
VEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYK
CKVSNKALGAPIEKTISKAKGQPREPQVCTLPPSRDELTKN
QVSLSCAVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSD
GSFFLVSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKS
LSLSPGGGGGSGGGGSREGPELSPDDPAGLLDLRQGMFAQ
LVAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYKEDTKELV
VAKAGVYYVFFQLELRRVVAGEGSGSVSLALHLQPLRSAA
GAAALALTVDLPPASSEARNSAFGFQGRLLHLSAGQRLGV
HLHTEARARHAWQLTQGATVLGLFRVTPEIPAGLGGGGSG
GGGSREGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGP
LSWYSDPGLAGVSLTGGLSYKEDTKELVVAKAGVYYVFF
QLELRRVVAGEGSGSVSLALHLQPLRSAAGAAALALTVDL
PPASSEARNSAFGFQGRLLHLSAGQRLGVHLHTEARARHA
WQLTQGATVLGLFRVTPEIPAGL
127 anti-FAP (4B9) EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQA
PGKGLEWVSAIIGSGASTYYADSVKGRFTISRDNSKNTLYL
Fc knob chain QMNSLRAEDTAVYYCAKGWFGGFNYWGQGTLVTVSSAS fused to TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNS
GALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICN
monomeric hu 4- VNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGGPSVF 1BBL (71-248) LFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDG
VEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYK
CKVSNKALGAPIEKTISKAKGQPREPQVYTLPPCRDELTKN
QVSLWCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSD
GSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKS
LSLSPGGGGGSGGGGSREGPELSPDDPAGLLDLRQGMFAQ
LVAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYKEDTKELV
VAKAGVYYVFFQLELRRVVAGEGSGSVSLALHLQPLRSAA
GAAALALTVDLPPASSEARNSAFGFQGRLLHLSAGQRLGV
HLHTEARARHA WQLTQGATVLGLFRVTPEIPAGL
125 anti-FAP (4B9) see Table 21
light chain
2.2 Preparation of untargeted human 4- IBB ligand trimer-containing Fc fusion antigen binding molecules (Control molecules)
Further control molecules were prepared as described in Example 1.4 above for Control A and B. A bivalent variant Control C was prepared in analogy to the bivalent Construct 2.3 and 2.6 and a monovalent variant Control E was prepared in analogy to Construct 2.5 (containing a 4- IBB ligand (71-248) trimer), with the only difference that the anti-FAP binder (VH-VL) was replaced by a germline control, termed DP47, not binding to the antigen.
Table 27 shows the cDNA and amino acid sequences of the bivalent DP47-untargeted split trimeric 4- IBB ligand (71-254) Fc (kih) fusion molecule Control C. Table 28 shows the cDNA and amino acid sequences of the monovalent DP47-untargeted split trimeric 4- IBB ligand (71- 248) Fc (kih) fusion molecule Control E.
Table 27: Sequences of bivalent DP47-untargeted human 4-lBB ligand (71-254) containing Fc (kih) fusion molecule Control C
SEQ ID Description Sequence
NO:
177 nucleotide GAGGTGCAATTGTTGGAGTCTGGGGGAGGCTTGGTACA sequence DP47 GCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCCGG Fc hole chain ATTCACCTTTAGCAGTTATGCCATGAGCTGGGTCCGCCA fused to dimeric GGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTA hu 4-lBBL (71- GTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGA
AGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAAC
254)
ACGCTGTATCTGCAGATGAACAGCCTGAGAGCCGAGGA
CACGGCCGTATATTACTGTGCGAAAGGCAGCGGATTTGA
CTACTGGGGCCAAGGAACCCTGGTCACCGTCTCGAGTGC
TAGCACCAAGGGCCCCTCCGTGTTCCCCCTGGCCCCCAG
CAGCAAGAGCACCAGCGGCGGCACAGCCGCTCTGGGCT
GCCTGGTCAAGGACTACTTCCCCGAGCCCGTGACCGTGT
CCTGGAACAGCGGAGCCCTGACCTCCGGCGTGCACACC
TTCCCCGCCGTGCTGCAGAGTTCTGGCCTGTATAGCCTG
AGCAGCGTGGTCACCGTGCCTTCTAGCAGCCTGGGCACC
CAGACCTACATCTGCAACGTGAACCACAAGCCCAGCAA
CACCAAGGTGGACAAGAAGGTGGAGCCCAAGAGCTGCG
ACAAAACTCACACATGCCCACCGTGCCCAGCACCTGAA
GCTGCAGGGGGACCGTCAGTCTTCCTCTTCCCCCCAAAA
CCCAAGGACACCCTCATGATCTCCCGGACCCCTGAGGTC
ACATGCGTGGTGGTGGACGTGAGCCACGAAGACCCTGA
GGTCAAGTTCAACTGGTACGTGGACGGCGTGGAGGTGC
ATAATGCCAAGACAAAGCCGCGGGAGGAGCAGTACAAC
AGCACGTACCGTGTGGTCAGCGTCCTCACCGTCCTGCAC
CAGGACTGGCTGAATGGCAAGGAGTACAAGTGCAAGGT
CTCCAACAAAGCCCTCGGCGCCCCCATCGAGAAAACCA
TCTCCAAAGCCAAAGGGCAGCCCCGAGAACCACAGGTG
TGCACCCTGCCCCCATCCCGGGATGAGCTGACCAAGAA
CCAGGTCAGCCTCTCGTGCGCAGTCAAAGGCTTCTATCC
CAGCGACATCGCCGTGGAGTGGGAGAGCAATGGGCAGC
CGGAGAACAACTACAAGACCACGCCTCCCGTGCTGGAC
TCCGACGGCTCCTTCTTCCTCGTGAGCAAGCTCACCGTG
GACAAGAGCAGGTGGCAGCAGGGGAACGTCTTCTCATG
CTCCGTGATGCATGAGGCTCTGCACAACCACTACACGCA
GAAGAGCCTCTCCCTGTCTCCGGGTGGAGGCGGCGGAA
GCGGAGGAGGAGGATCCAGAGAGGGCCCTGAGCTGAGC
CCCGATGATCCTGCTGGACTGCTGGACCTGCGGCAGGGC
ATGTTTGCTCAGCTGGTGGCCCAGAACGTGCTGCTGATC GATGGCCCCCTGTCCTGGTACAGCGATCCTGGACTGGCT
GGCGTGTCACTGACAGGCGGCCTGAGCTACAAAGAGGA
CACCAAAGAACTGGTGGTGGCCAAGGCCGGCGTGTACT
ACGTGTTCTTTCAGCTGGAACTGCGGAGAGTGGTGGCCG
GCGAAGGATCTGGCTCTGTGTCTCTGGCCCTGCATCTGC
AGCCTCTGAGAAGCGCTGCTGGCGCTGCAGCTCTGGCAC
TGACAGTGGATCTGCCTCCTGCCAGCTCCGAGGCCCGGA
ATAGCGCATTTGGGTTTCAAGGCAGGCTGCTGCACCTGT
CTGCCGGCCAGAGGCTGGGAGTGCATCTGCACACAGAG
GCCAGGGCTAGACACGCCTGGCAGCTGACACAGGGCGC
TACAGTGCTGGGCCTGTTCAGAGTGACCCCCGAGATTCC
AGCCGGCCTGCCTTCTCCAAGAAGCGAAGGCGGAGGCG
GATCTGGCGGCGGAGGATCTAGAGAGGGACCCGAACTG
TCCCCTGACGATCCAGCCGGGCTGCTGGATCTGAGACAG
GGAATGTTCGCCCAGCTGGTGGCTCAGAATGTGCTGCTG
ATTGACGGACCTCTGAGCTGGTACTCCGACCCAGGGCTG
GCAGGGGTGTCCCTGACTGGGGGACTGTCCTACAAAGA
AGATACAAAAGAACTGGTGGTGGCTAAAGCTGGGGTGT
CTGGGGAGGGCTCAGGATCTGTGTCCCTGGCTCTGCATC
TGCAGCCACTGCGCTCTGCTGCTGGCGCAGCTGCACTGG
CTCTGACTGTGGACCTGCCACCAGCCTCTAGCGAGGCCA
GAAACAGCGCCTTCGGGTTCCAAGGACGCCTGCTGCATC
TGAGCGCCGGACAGCGCCTGGGAGTGCATCTGCATACT
GAAGCCAGAGCCCGGCATGCTTGGCAGCTGACTCAGGG
GGCAACTGTGCTGGGACTGTTTCGCGTGACACCTGAGAT
CCCTGCCGGACTGCCAAGCCCTAGATCAGAA
nucleotide GAGGTGCAATTGTTGGAGTCTGGGGGAGGCTTGGTACA sequence DP47 GCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCCGG Fc knob chain ATTCACCTTTAGCAGTTATGCCATGAGCTGGGTCCGCCA fused to GGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTA
GTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGA
monomeric hu 4-
AGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAAC
1BBL (71-254)
ACGCTGTATCTGCAGATGAACAGCCTGAGAGCCGAGGA
CACGGCCGTATATTACTGTGCGAAAGGCAGCGGATTTGA
CTACTGGGGCCAAGGAACCCTGGTCACCGTCTCGAGTGC
TAGCACCAAGGGCCCATCGGTCTTCCCCCTGGCACCCTC
CTCCAAGAGCACCTCTGGGGGCACAGCGGCCCTGGGCT
GCCTGGTCAAGGACTACTTCCCCGAACCGGTGACGGTGT
CGTGGAACTCAGGCGCCCTGACCAGCGGCGTGCACACC
TTCCCGGCTGTCCTACAGTCCTCAGGACTCTACTCCCTC
AGCAGCGTGGTGACCGTGCCCTCCAGCAGCTTGGGCAC
CCAGACCTACATCTGCAACGTGAATCACAAGCCCAGCA
ACACCAAGGTGGACAAGAAAGTTGAGCCCAAATCTTGT
GACAAAACTCACACATGCCCACCGTGCCCAGCACCTGA
AGCTGCAGGGGGACCGTCAGTCTTCCTCTTCCCCCCAAA
ACCCAAGGACACCCTCATGATCTCCCGGACCCCTGAGGT
CACATGCGTGGTGGTGGACGTGAGCCACGAAGACCCTG
AGGTCAAGTTCAACTGGTACGTGGACGGCGTGGAGGTG
CATAATGCCAAGACAAAGCCGCGGGAGGAGCAGTACAA
CAGCACGTACCGTGTGGTCAGCGTCCTCACCGTCCTGCA
CCAGGACTGGCTGAATGGCAAGGAGTACAAGTGCAAGG
TCTCCAACAAAGCCCTCGGCGCCCCCATCGAGAAAACC
ATCTCCAAAGCCAAAGGGCAGCCCCGAGAACCACAGGT GTACACCCTGCCCCCCTGCAGAGATGAGCTGACCAAGA
ACCAGGTGTCCCTGTGGTGTCTGGTCAAGGGCTTCTACC
CCAGCGATATCGCCGTGGAGTGGGAGAGCAACGGCCAG
CCTGAGAACAACTACAAGACCACCCCCCCTGTGCTGGA
CAGCGACGGCAGCTTCTTCCTGTACTCCAAACTGACCGT
GGACAAGAGCCGGTGGCAGCAGGGCAACGTGTTCAGCT
GCAGCGTGATGCACGAGGCCCTGCACAACCACTACACC
CAGAAGTCCCTGAGCCTGAGCCCCGGCGGAGGCGGCGG
AAGCGGAGGAGGAGGATCCAGAGAGGGCCCTGAGCTGA
GCCCCGATGATCCTGCTGGACTGCTGGACCTGCGGCAGG
GCATGTTTGCTCAGCTGGTGGCCCAGAACGTGCTGCTGA
TCGATGGCCCCCTGTCCTGGTACAGCGATCCTGGACTGG
CTGGCGTGTCACTGACAGGCGGCCTGAGCTACAAAGAG
GACACCAAAGAACTGGTGGTGGCCAAGGCCGGCGTGTA
CTACGTGTTCTTTCAGCTGGAACTGCGGAGAGTGGTGGC
CGGCGAAGGATCTGGCTCTGTGTCTCTGGCCCTGCATCT
GCAGCCTCTGAGAAGCGCTGCTGGCGCTGCAGCTCTGGC
ACTGACAGTGGATCTGCCTCCTGCCAGCTCCGAGGCCCG
GAATAGCGCATTTGGGTTTCAAGGCAGGCTGCTGCACCT
GTCTGCCGGCCAGAGGCTGGGAGTGCATCTGCACACAG
AGGCCAGGGCTAGACACGCCTGGCAGCTGACACAGGGC
GCTACAGTGCTGGGCCTGTTCAGAGTGACCCCCGAGATT
CCAGCCGGCCTGCCTTCTCCAAGAAGCGAA
80 nucleotide see Table 18
sequence DP47
light chain
179 DP47 Fc hole EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQA chain fused to PGKGLEWVSAIIGSGASTYYADSVKGRFTISRDNSKNTLYL dimeric hu 4- QMNSLRAEDTAVYYCAKGWFGGFNYWGQGTLVTVSSAS 1BBL (71-254) TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNS
GALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICN
VNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGGPSVF
LFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDG
VEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYK
CKVSNKALGAPIEKTISKAKGQPREPQVCTLPPSRDELTKN
QVSLSCAVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSD
GSFFLVSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKS
LSLSPGGGGGSGGGGSREGPELSPDDPAGLLDLRQGMFAQ
LVAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYKEDTKELV
VAKAGVYYVFFQLELRRVVAGEGSGSVSLALHLQPLRSAA
GAAALALTVDLPPASSEARNSAFGFQGRLLHLSAGQRLGV
HLHTEARARHAWQLTQGATVLGLFRVTPEIPAGLPSPRSEG
GGGSGGGGSREGPELSPDDPAGLLDLRQGMFAQLVAQNV
LLIDGPLSWYSDPGLAGVSLTGGLSYKEDTKELVVAKAGV
YYVFFQLELRRVVAGEGSGSVSLALHLQPLRSAAGAAALA
LTVDLPPASSEARNSAFGFQGRLLHLSAGQRLGVHLHTEA
RARHAWQLTQGATVLGLFRVTPEIPAGLPSPRSE
180 DP47 Fc knob EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQA chain fused to PGKGLEWVSAIIGSGASTYYADSVKGRFTISRDNSKNTLYL monomeric hu 4- QMNSLRAEDTAVYYCAKGWFGGFNYWGQGTLVTVSSAS 1BBL (71-254) TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNS
GALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICN
VNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGGPSVF LFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDG
VEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYK
CKVSNKALGAPIEKTISKAKGQPREPQVYTLPPCRDELTKN
QVSLWCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSD
GSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKS
LSLSPGGGGGSGGGGSREGPELSPDDPAGLLDLRQGMFAQ
LVAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYKEDTKELV
VAKAGVYYVFFQLELRRVVAGEGSGSVSLALHLQPLRSAA
GAAALALTVDLPPASSEARNSAFGFQGRLLHLSAGQRLGV
HLHTEARARHAWQLTQGATVLGLFRVTPEIPAGLPSPRSE
82 DP47 light chain see Table 18
Table 28: Sequences of monovalent untargeted human 4-lBB ligand (71-248) containing Fc (kih) fusion molecule Control E
Figure imgf000208_0001
2.3 Preparation of untargeted human IgGl as Control F
An additional control molecule used in the assays was an untargeted DP47, germline control, human IgGl, containing the Pro329Gly, Leu234Ala and Leu235Ala mutations, to abrogate binding to Fc gamma receptors according to the method described in International Patent Appl. Publ. No. WO 2012/130831). Table 29 shows the cDNA and amino acid sequences of the cDNA and amino acid sequences of the untargeted DP47 huIgGl PGLALA (Control F).
Table 29: Sequences of untargeted DP47 huIgGl (Control F)
SEQ ID Description Sequence
NO:
181 nucleotide GAGGTGCAATTGTTGGAGTCTGGGGGAGGCTTGGTACA
GCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCCGG
sequence DP47 ATTCACCTTTAGCAGTTATGCCATGAGCTGGGTCCGCCA heavy chain (hu GGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTA
GTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGA
IgGl PGLALA) AGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAAC
ACGCTGTATCTGCAGATGAACAGCCTGAGAGCCGAGGA
CACGGCCGTATATTACTGTGCGAAAGGCAGCGGATTTGA
CTACTGGGGCCAAGGAACCCTGGTCACCGTCTCGAGTGC
TAGCACCAAGGGCCCATCGGTCTTCCCCCTGGCACCCTC
CTCCAAGAGCACCTCTGGGGGCACAGCGGCCCTGGGCT
GCCTGGTCAAGGACTACTTCCCCGAACCGGTGACGGTGT
CGTGGAACTCAGGCGCCCTGACCAGCGGCGTGCACACC
TTCCCGGCTGTCCTACAGTCCTCAGGACTCTACTCCCTC
AGCAGCGTGGTGACCGTGCCCTCCAGCAGCTTGGGCAC
CCAGACCTACATCTGCAACGTGAATCACAAGCCCAGCA
ACACCAAGGTGGACAAGAAAGTTGAGCCCAAATCTTGT
GACAAAACTCACACATGCCCACCGTGCCCAGCACCTGA
AGCTGCAGGGGGACCGTCAGTCTTCCTCTTCCCCCCAAA
ACCCAAGGACACCCTCATGATCTCCCGGACCCCTGAGGT
CACATGCGTGGTGGTGGACGTGAGCCACGAAGACCCTG
AGGTCAAGTTCAACTGGTACGTGGACGGCGTGGAGGTG
CATAATGCCAAGACAAAGCCGCGGGAGGAGCAGTACAA
CAGCACGTACCGTGTGGTCAGCGTCCTCACCGTCCTGCA
CCAGGACTGGCTGAATGGCAAGGAGTACAAGTGCAAGG
TCTCCAACAAAGCCCTCGGCGCCCCCATCGAGAAAACC
ATCTCCAAAGCCAAAGGGCAGCCCCGAGAACCACAGGT
GTACACCCTGCCCCCATCCCGGGATGAGCTGACCAAGA
ACCAGGTCAGCCTGACCTGCCTGGTCAAAGGCTTCTATC
CCAGCGACATCGCCGTGGAGTGGGAGAGCAATGGGCAG
CCGGAGAACAACTACAAGACCACGCCTCCCGTGCTGGA
CTCCGACGGCTCCTTCTTCCTCTACAGCAAGCTCACCGT
GGACAAGAGCAGGTGGCAGCAGGGGAACGTCTTCTCAT
GCTCCGTGATGCATGAGGCTCTGCACAACCACTACACGC
AGAAGAGCCTCTCCCTGTCTCCGGGTAAA
80 DP47 light chain see Table 18
182 DP47 heavy chain EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQA
PGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYL
(hu IgGl QMNSLRAEDTAVYYCAKGSGFDYWGQGTLVTVSSASTKG PGLALA) PSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGAL
TSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNH
KPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGGPSVFLFPP KPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEV
HNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKV
SNKALGAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVS
LTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFF
LYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLS
PGK
82 DP47 light chain see Table 18
2.4 Production of monovalent and bivalent FAP (4B9) targeted split trimeric 4- IBB ligand Fc fusion constructs and control molecules
The targeted and untargeted split trimeric 4- IBB ligand Fc (kih) fusion encoding sequences were cloned into a plasmid vector, which drives expression of the insert from an MPSV promoter and contains a synthetic polyA sequence located at the 3' end of the CDS. In addition, the vector contains an EBV OriP sequence for episomal maintenance of the plasmid.
The split trimeric 4- IBB ligand Fc (kih) fusion was produced by co-transfecting HEK293- EBNA cells with the mammalian expression vectors using polyethylenimine. The cells were transfected with the corresponding expression vectors. For Constructs 2.1, 2.2., 2.4 and 2.5 and corresponding control molecules, a 1 : 1 : 1 : 1 ratio (e.g. "vector dimeric ligand-CL- knob chain": "vector monomeric ligand fusion-CHI": "vector anti-FAP Fab-hole chain": "vector anti-FAP light chain") was used. For Constructs 2.3 and 2.6 and its control moelcule, a 1 : 1 : 1 ratio ("vector hulgGI Fc hole dimeric ligand chain": "vector hulgGI Fc knob monomeric ligand chain":
"vector anti-FAP light chain") was taken. Human IgGs, used as control in the assay, were produced as for the bispecific constructs (for transfection only a vector for light and a vector for heavy chain were used.
For production in 500 mL shake flasks, 300 million HEK293 EBNA cells were seeded 24 hours before transfection. For transfection cells were centrifuged for 10 minutes at 210 x g, and the supernatant was replaced by 20mL pre- warmed CD CHO medium. Expression vectors (200 μg of total DNA) were mixed in 20 mL CD CHO medium. After addition of 540 μΐ. PEI, the solution was vortexed for 15 seconds and incubated for 10 minutes at room temperature.
Afterwards, cells were mixed with the DNA/PEI solution, transferred to a 500 mL shake flask and incubated for 3 hours at 37 °C in an incubator with a 5% C02 atmosphere. After the incubation, 160 mL of Excell medium supplemented with 6mM L-Glutamine, 5g/L PEPSOY and 1.2mM valproic acid was added and cells were cultured for 24 hours. One day after transfection 12% Feed 7 and Glucose (final cone. 3g/L) were added. After culturing for 7 days, the supernatant was collected by centrifugation for 30-40 minutes at least 400 x g. The solution was sterile filtered (0.22 μηι filter), supplemented with sodium azide to a final concentration of 0.01 % (w/v), and kept at 4 °C.
The targeted and untargeted TNF ligand trimer-containing Fc (kih) fusion antigen binding molecules and the human IgGl were purified from cell culture supernatants by affinity
chromatography using Protein A, followed by size exclusion chromatography. For affinity chromatography, the supernatant was loaded on a MabSelect Sure column (CV = 5-15 mL, resin from GE Healthcare) equilibrated with Sodium Phosphate (20 mM), Sodium Citrate (20 mM) buffer (pH 7.5). Unbound protein was removed by washing with at least 6 column volumes of the same buffer. The bound protein was eluted using either a linear gradient (20 CV) or a step elution (8 CV) with 20 mM sodium citrate, 100 mM Sodium chloride, 100 mM Glycine buffer (pH 3.0). For the linear gradient an additional 4 column volumes step elution was applied.
The pH of collected fractions was adjusted by adding 1/10 (v/v) of 0.5M sodium phosphate, pH8.0. The protein was concentrated prior to loading on a HiLoad Superdex 200 column (GE Healthcare) equilibrated with 20 mM Histidine, 140 mM sodium chloride, 0.01% (v/v) Tween20 solution of pH 6.0.
The protein concentration was determined by measuring the optical density (OD) at 280 nm, using a molar extinction coefficient calculated on the basis of the amino acid sequence.
Purity and molecular weight of the targeted trimeric 4- IBB ligand Fc (kih) fusion was analyzed by SDS-PAGE in the presence and absence of a reducing agent (5 mM 1,4-dithiotreitol) and staining with Coomassie SimpleBlue™ SafeStain (Invitrogen USA) or CE-SDS using Caliper LabChip GXII (Perkin Elmer). The aggregate content of samples was analyzed using a TSKgel G3000 SW XL analytical size-exclusion column (Tosoh) equilibrated in 25 mM K2HP04, 125 mM NaCl, 200 mM L-Arginine Monohydrocloride, 0.02 % (w/v) NaN3, pH 6.7 running buffer at 25 °C. Table 30 summarizes the yield and final monomer content of the FAP (4B9) targeted and untargeted 4- IBB ligand trimer-containing Fc (kih) fusion antigen binding molecules and control molecules.
Table 30 Biochemical analysis of FAP (4B9) targeted and untargeted 4-1BB ligand trimer- containing Fc (kih) fusion antigen binding molecules and control molecules
Monomer Yield
Construct [%] [mg/1]
(SEC)
Construct 2.1 95 15.8 Construct 2.3 97 11.5
Construct 2.4 97 14.1
Construct 2.5 100 16.5
Control C (bivalent) 98 12.6
Control E (monovalent) 93 4.1
Control F (germline DP47 human IgGl
100 50
PGLALA
Example 3
Preparation, purification and characterization of 4- IBB
DNA sequences encoding the ectodomains of human, mouse or cynomolgus 4- IBB (Table 31) were subcloned in frame with the human IgGl heavy chain CH2 and CH3 domains on the knob (Merchant et al., 1998). An AcTEV protease cleavage site was introduced between an antigen ectodomain and the Fc of human IgGl. An Avi tag for directed biotinylation was introduced at the C-terminus of the antigen-Fc knob. Combination of the antigen-Fc knob chain containing the S354C/T366W mutations, with a Fc hole chain containing the
Y349C/T366S/L368A/Y407V mutations allows generation of a heterodimer which includes a single copy of 4- IBB ectodomain containing chain, thus creating a monomeric form of Fc-linked antigen (Figure 5C). Table 32 shows the cDNA and amino acid sequences of the antigen Fc- fusion constructs.
Table 31: Amino acid numbering of antigen ectodomains (ECD) and their origin
Figure imgf000212_0001
Table 32: cDNA and Amino acid sequences of monomeric antigen Fc(kih) fusion molecules
SEQ ID Antigen Sequence
NO:
86 Nucleotide GACAAAACTCACACATGCCCACCGTGCCCAGCACCTGA
ACTCCTGGGGGGACCGTCAGTCTTCCTCTTCCCCCCAAA
sequence ACCCAAGGACACCCTCATGATCTCCCGGACCCCTGAGGT
CACATGCGTGGTGGTGGACGTGAGCCACGAAGACCCTG Fc hole chain AGGTCAAGTTCAACTGGTACGTGGACGGCGTGGAGGTG
CATAATGCCAAGACAAAGCCGCGGGAGGAGCAGTACAA
CAGCACGTACCGTGTGGTCAGCGTCCTCACCGTCCTGCA
CCAGGACTGGCTGAATGGCAAGGAGTACAAGTGCAAGG
TCTCCAACAAAGCCCTCCCAGCCCCCATCGAGAAAACC
ATCTCCAAAGCCAAAGGGCAGCCCCGAGAACCACAGGT
GTGCACCCTGCCCCCATCCCGGGATGAGCTGACCAAGA
ACCAGGTCAGCCTCTCGTGCGCAGTCAAAGGCTTCTATC
CCAGCGACATCGCCGTGGAGTGGGAGAGCAATGGGCAG
CCGGAGAACAACTACAAGACCACGCCTCCCGTGCTGGA
CTCCGACGGCTCCTTCTTCCTCGTGAGCAAGCTCACCGT
GGACAAGAGCAGGTGGCAGCAGGGGAACGTCTTCTCAT
GCTCCGTGATGCATGAGGCTCTGCACAACCACTACACGC
AGAAGAGCCTCTCCCTGTCTCCGGGTAAA
87 Nucleotide CTGCAGGACCCCTGCAGCAACTGCCCTGCCGGCACCTTC
TGCGACAACAACCGGAACCAGATCTGCAGCCCCTGCCC
sequence CCCCAACAGCTTCAGCTCTGCCGGCGGACAGCGGACCT human 4- IBB GCGACATCTGCAGACAGTGCAAGGGCGTGTTCAGAACC
CGGAAAGAGTGCAGCAGCACCAGCAACGCCGAGTGCGA
antigen Fc knob CTGCACCCCCGGCTTCCATTGTCTGGGAGCCGGCTGCAG chain CATGTGCGAGCAGGACTGCAAGCAGGGCCAGGAACTGA
CCAAGAAGGGCTGCAAGGACTGCTGCTTCGGCACCTTC
AACGACCAGAAGCGGGGCATCTGCCGGCCCTGGACCAA
CTGTAGCCTGGACGGCAAGAGCGTGCTGGTCAACGGCA
CCAAAGAACGGGACGTCGTGTGCGGCCCCAGCCCTGCT
GATCTGTCTCCTGGGGCCAGCAGCGTGACCCCTCCTGCC
CCTGCCAGAGAGCCTGGCCACTCTCCTCAGGTCGACGAA
CAGTTATATTTTCAGGGCGGCTCACCCAAATCTGCAGAC
AAAACTCACACATGCCCACCGTGCCCAGCACCTGAACTC
CTGGGGGGACCGTCAGTCTTCCTCTTCCCCCCAAAACCC
AAGGACACCCTCATGATCTCCCGGACCCCTGAGGTCACA
TGCGTGGTGGTGGACGTGAGCCACGAAGACCCTGAGGT
CAAGTTCAACTGGTACGTGGACGGCGTGGAGGTGCATA
ATGCCAAGACAAAGCCGCGGGAGGAGCAGTACAACAGC
ACGTACCGTGTGGTCAGCGTCCTCACCGTCCTGCACCAG
GACTGGCTGAATGGCAAGGAGTACAAGTGCAAGGTCTC
CAACAAAGCCCTCCCAGCCCCCATCGAGAAAACCATCT
CCAAAGCCAAAGGGCAGCCCCGAGAACCACAGGTGTAC
ACCCTGCCCCCATGCCGGGATGAGCTGACCAAGAACCA
GGTCAGCCTGTGGTGCCTGGTCAAAGGCTTCTATCCCAG
CGACATCGCCGTGGAGTGGGAGAGCAATGGGCAGCCGG
AGAACAACTACAAGACCACGCCTCCCGTGCTGGACTCC
GACGGCTCCTTCTTCCTCTACAGCAAGCTCACCGTGGAC
AAGAGCAGGTGGCAGCAGGGGAACGTCTTCTCATGCTC
CGTGATGCATGAGGCTCTGCACAACCACTACACGCAGA
AGAGCCTCTCCCTGTCTCCGGGTAAATCCGGAGGCCTGA
ACGACATCTTCGAGGCCCAGAAGATTGAATGGCACGAG
cleotide TTGCAGGATCTGTGTAGTAACTGCCCAGCTGGTACATTC
88 Nu
TGTGATAATAACAGGAGTCAGATTTGCAGTCCCTGTCCT
sequence CCAAATAGTTTCTCCAGCGCAGGTGGACAAAGGACCTGT cynomolgus 4- GACATATGCAGGCAGTGTAAAGGTGTTTTCAAGACCAG
GAAGGAGTGTTCCTCCACCAGCAATGCAGAGTGTGACT
1BB antigen GCATTTCAGGGTATCACTGCCTGGGGGCAGAGTGCAGC
ATGTGTGAACAGGATTGTAAACAAGGTCAAGAATTGAC AAAAAAAGGTTGTAAAGACTGTTGCTTTGGGACATTTAA
Fc knob chain
TGACCAGAAACGTGGCATCTGTCGCCCCTGGACAAACT
GTTCTTTGGATGGAAAGTCTGTGCTTGTGAATGGGACGA
AGGAGAGGGACGTGGTCTGCGGACCATCTCCAGCCGAC
CTCTCTCCAGGAGCATCCTCTGCGACCCCGCCTGCCCCT
GCGAGAGAGCCAGGACACTCTCCGCAGGTCGACGAACA
GTTATATTTTCAGGGCGGCTCACCCAAATCTGCAGACAA
AACTCACACATGCCCACCGTGCCCAGCACCTGAACTCCT
GGGGGGACCGTCAGTCTTCCTCTTCCCCCCAAAACCCAA
GGACACCCTCATGATCTCCCGGACCCCTGAGGTCACATG
CGTGGTGGTGGACGTGAGCCACGAAGACCCTGAGGTCA
AGTTCAACTGGTACGTGGACGGCGTGGAGGTGCATAAT
GCCAAGACAAAGCCGCGGGAGGAGCAGTACAACAGCA
CGTACCGTGTGGTCAGCGTCCTCACCGTCCTGCACCAGG
ACTGGCTGAATGGCAAGGAGTACAAGTGCAAGGTCTCC
AACAAAGCCCTCCCAGCCCCCATCGAGAAAACCATCTC
CAAAGCCAAAGGGCAGCCCCGAGAACCACAGGTGTACA
CCCTGCCCCCATGCCGGGATGAGCTGACCAAGAACCAG
GTCAGCCTGTGGTGCCTGGTCAAAGGCTTCTATCCCAGC
GACATCGCCGTGGAGTGGGAGAGCAATGGGCAGCCGGA
GAACAACTACAAGACCACGCCTCCCGTGCTGGACTCCG
ACGGCTCCTTCTTCCTCTACAGCAAGCTCACCGTGGACA
AGAGCAGGTGGCAGCAGGGGAACGTCTTCTCATGCTCC
GTGATGCATGAGGCTCTGCACAACCACTACACGCAGAA
GAGCCTCTCCCTGTCTCCGGGTAAATCCGGAGGCCTGAA
CGACATCTTCGAGGCCCAGAAGATTGAATGGCACGAG
GTGCAGAACAGCTGCGACAACTGCCAGCCCGGCACCTT
murine 4- IBB
CTGCCGGAAGTACAACCCCGTGTGCAAGAGCTGCCCCC
antigen Fc knob CCAGCACCTTCAGCAGCATCGGCGGCCAGCCCAACTGC chain AACATCTGCAGAGTGTGCGCCGGCTACTTCCGGTTCAAG
AAGTTCTGCAGCAGCACCCACAACGCCGAGTGCGAGTG
CATCGAGGGCTTCCACTGCCTGGGCCCCCAGTGCACCAG
ATGCGAGAAGGACTGCAGACCCGGCCAGGAACTGACCA
AGCAGGGCTGTAAGACCTGCAGCCTGGGCACCTTCAAC
GACCAGAACGGGACCGGCGTGTGCCGGCCTTGGACCAA
TTGCAGCCTGGACGGGAGAAGCGTGCTGAAAACCGGCA
CCACCGAGAAGGACGTCGTGTGCGGCCCTCCCGTGGTGT
CCTTCAGCCCTAGCACCACCATCAGCGTGACCCCTGAAG
GCGGCCCTGGCGGACACTCTCTGCAGGTCCTGGTCGACG
AACAGTTATATTTTCAGGGCGGCTCACCCAAATCTGCAG
ACAAAACTCACACATGCCCACCGTGCCCAGCACCTGAA
CTCCTGGGGGGACCGTCAGTCTTCCTCTTCCCCCCAAAA
CCCAAGGACACCCTCATGATCTCCCGGACCCCTGAGGTC
ACATGCGTGGTGGTGGACGTGAGCCACGAAGACCCTGA
GGTCAAGTTCAACTGGTACGTGGACGGCGTGGAGGTGC
ATAATGCCAAGACAAAGCCGCGGGAGGAGCAGTACAAC
AGCACGTACCGTGTGGTCAGCGTCCTCACCGTCCTGCAC
CAGGACTGGCTGAATGGCAAGGAGTACAAGTGCAAGGT
CTCCAACAAAGCCCTCCCAGCCCCCATCGAGAAAACCA
TCTCCAAAGCCAAAGGGCAGCCCCGAGAACCACAGGTG
TACACCCTGCCCCCATGCCGGGATGAGCTGACCAAGAA
CCAGGTCAGCCTGTGGTGCCTGGTCAAAGGCTTCTATCC
CAGCGACATCGCCGTGGAGTGGGAGAGCAATGGGCAGC
CGGAGAACAACTACAAGACCACGCCTCCCGTGCTGGAC TCCGACGGCTCCTTCTTCCTCTACAGCAAGCTCACCGTG
GACAAGAGCAGGTGGCAGCAGGGGAACGTCTTCTCATG
CTCCGTGATGCATGAGGCTCTGCACAACCACTACACGCA
GAAGAGCCTCTCCCTGTCTCCGGGTAAATCCGGAGGCCT
GAACGACATCTTCGAGGCCCAGAAGATTGAATGGCACG
AG
90 Fc hole chain DKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCV
VVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYR VVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKG QPREPQVCTLPPSRDELTKNQVSLSCAVKGFYPSDIAVEWE SNGQPENNYKTTPPVLDSDGSFFLVSKLTVDKSRWQQGNV FSCSVMHEALHNHYTQKSLSLSPGK
91 human 4- IBB LQDPCSNCPAGTFCDNNRNQICSPCPPNSFSSAGGQRTCDI
CRQCKGVFRTRKECSSTSNAECDCTPGFHCLGAGCSMCEQ
antigen Fc knob DCKQGQELTKKGCKDCCFGTFNDQKRGICRPWTNCSLDG chain KSVLVNGTKERDVVCGPSPADLSPGASSVTPPAPAREPGHS
PQVDEQLYFQGGSPKSADKTHTCPPCPAPELLGGPSVFLFP
PKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVE
VHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCK
VSNKALPAPIEKTISKAKGQPREPQVYTLPPCRDELTKNQV
SLWCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGS
FFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLS
LSPGKSGGLNDIFEAQKIEWHE
92 cynomolgus 4- LQDLCSNCPAGTFCDNNRSQICSPCPPNSFSSAGGQRTCDIC
RQCKGVFKTRKECSSTSNAECDCISGYHCLGAECSMCEQD
1BB antigen CKQGQELTKKGCKDCCFGTFNDQKRGICRPWTNCSLDGK Fc knob chain SVLVNGTKERDVVCGPSPADLSPGASSATPPAPAREPGHSP
QVDEQLYFQGGSPKSADKTHTCPPCPAPELLGGPSVFLFPP
KPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEV
HNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKV
SNKALPAPIEKTISKAKGQPREPQVYTLPPCRDELTKNQVS
LWCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSF
FLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSL
SPGKSGGLNDIFEAQKIEWHE
93 murine 4- IBB VQNSCDNCQPGTFCRKYNPVCKSCPPSTFSSIGGQPNCNIC
RVCAGYFRFKKFCSSTHNAECECIEGFHCLGPQCTRCEKDC
antigen Fc knob RPGQELTKQGCKTCSLGTFNDQNGTGVCRPWTNCSLDGR chain SVLKTGTTEKDVVCGPPVVSFSPSTTISVTPEGGPGGHSLQ
VLVDEQLYFQGGSPKSADKTHTCPPCPAPELLGGPSVFLFP
PKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVE
VHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCK
VSNKALPAPIEKTISKAKGQPREPQVYTLPPCRDELTKNQV
SLWCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGS
FFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLS
LSPGKSGGLNDIFEAQKIEWHE
All 4-lBB-Fc-fusion molecule encoding sequences were cloned into a plasmid vector, which drives expression of the insert from an MPSV promoter and contains a synthetic polyA signal sequence located at the 3' end of the CDS. In addition, the vector contains an EBV OriP sequence for episomal maintenance of the plasmid. For preparation of the biotinylated monomeric antigen/Fc fusion molecules, exponentially growing suspension HEK293 EBNA cells were co-transfected with three vectors encoding the two components of fusion protein (knob and hole chains) as well as BirA, an enzyme necessary for the biotinylation reaction. The corresponding vectors were used at a 2 : 1 : 0.05 ratio
("antigen ECD-AcTEV- Fc knob" : "Fc hole" : "BirA").
For protein production in 500 ml shake flasks, 400 million HEK293 EBNA cells were seeded 24 hours before transfection. For transfection cells were centrifuged for 5 minutes at 210 g, and the supernatant was replaced by pre- warmed CD CHO medium. Expression vectors were resuspended in 20 mL of CD CHO medium containing 200 μg of vector DNA. After addition of 540 μΐ^ of polyethylenimine (PEI), the solution was vortexed for 15 seconds and incubated for 10 minutes at room temperature. Afterwards, cells were mixed with the DNA/PEI solution, transferred to a 500 mL shake flask and incubated for 3 hours at 37°C in an incubator with a 5 % C02 atmosphere. After the incubation, 160 mL of F17 medium was added and cells were cultured for 24 hours. The production medium was supplemented with 5μΜ kifunensine. One day after transfection, 1 mM valproic acid and 7 % Feed 1 with supplements were added to the culture. After 7 days of culturing, the cell supernatant was collected by spinning down cells for 15 min at 210 g. The solution was sterile filtered (0.22 μιη filter), supplemented with sodium azide to a final concentration of 0.01 % (w/v), and kept at 4°C.
Secreted proteins were purified from cell culture supernatants by affinity chromatography using Protein A, followed by size exclusion chromatography. For affinity chromatography, the supernatant was loaded on a HiTrap ProteinA HP column (CV = 5 mL, GE Healthcare) equilibrated with 40 mL 20 mM sodium phosphate, 20 mM sodium citrate pH 7.5. Unbound protein was removed by washing with at least 10 column volumes of 20 mM sodium phosphate, 20 mM sodium citrate, 0.5 M sodium chloride containing buffer (pH 7.5). The bound protein was eluted using a linear pH-gradient of sodium chloride (from 0 to 500 mM) created over 20 column volumes of20 mM sodium citrate, 0.01 % (v/v) Tween-20, pH 3.0 . The column was then washed with 10 column volumes of 20 mM sodium citrate, 500 mM sodium chloride, 0.01 % (v/v) Tween-20, pH 3.0.
The pH of collected fractions was adjusted by adding 1/40 (v/v) of 2M Tris, pH8.0. The protein was concentrated and filtered prior to loading on a HiLoad Superdex 200 column (GE Healthcare) equilibrated with 2mM MOPS, 150 mM sodium chloride, 0.02 % (w/v) sodium azide solution of pH 7.4.
For affinity determination to the human receptor, the ectodomain of human 4- IBB was also subcloned in frame with an avi (GLNDIFEAQKIEWHE) and a hexahistidine tag. Protein production was performed as described above for the Fc-fusion protein. Secreted proteins were purified from cell culture supernatants by chelating chromatography, followed by size exclusion chromatography. The first chromatographic step was performed on a NiNTA Superflow Cartridge (5ml, Qiagen) equilibrated in 20 mM sodium phosphate, 500 nM sodium chloride, pH7.4. Elution was performed by applying a gradient over 12 column volume from 5 % to 45 % of elution buffer (20 mM sodium phosphate, 500 nM sodium chloride, 500 mM
Imidazole, pH7.4). The protein was concentrated and filtered prior to loading on a HiLoad Superdex 75 column (GE Healthcare) equilibrated with 2 mM MOPS, 150 mM sodium chloride, 0.02 % (w/v) sodium azide solution of pH 7.4 (Table 33).
Table 33: Sequences of monomeric human 4- IBB His molecule
Figure imgf000217_0001
Example 4
Biochemical characterization of FAP- targeted 4- IBB ligand trimer-containing Fc fusion antigen binding molecule by surface plasmon resonance
The binding of FAP-targeted 4- IBB ligand trimer-containing Fc (kih) fusion antigen binding molecules to recombinant 4- IBB was assessed by surface plasmon resonance (SPR). All SPR experiments were performed on a Biacore T 100 at 25 °C with HBS-EP as a running buffer (0.01 M HEPES pH 7.4, 0.15 M NaCl, 3 mM EDTA, 0.005 % Surfactant P20, Biacore,
Freiburg/Germany) . The avidity of the interaction between the FAP-targeted or untargeted 4- IBB ligand trimer- containing Fc (kih) fusion antigen binding molecules and recombinant 4- IBB (human, cyno and murine) was determined as described below. The data demonstrated that both targeted 4- IBB ligand trimer-containing Fc (kih) fusion antigen binding molecules as well as untargeted DP47 4- IBB ligand trimer-containing Fc (kih) fusion antigen binding molecules bind with comparable avidities to human and cynomolgus 4- IBB but negligibly to the mouse homolog.
Recombinant biotinylated human, cynomolgus and murine 4- IBB Fc(kih) fusion molecules were directly coupled on a SA chip using the standard coupling instruction (Biacore, Freiburg/Germany). The immobilization level was about 30 RU. FAP-targeted 4-1BB ligand trimer-containing Fc (kih) fusion antigen binding molecules, or the DP47 untargeted controls, were passed at a concentration range from 0.39 to 200 nM with a flow of 30 μΐνηιίηυίεβ through the flow cells over 120 seconds. The dissociation was monitored for 180 seconds. Bulk refractive index differences were corrected for by subtracting the response obtained on a reference empty flow cell. For affinity measurement, direct coupling of around 7200 resonance units (RU) of an anti- human Fc specific antibody was performed on a CM5 chip at pH 5.0 using the standard amine coupling kit (GE Healthcare). FAP-targeted or untargeted 4- IBB ligand trimer-containing Fc (kih) fusion antigen binding molecules, at 50 nM were captured with a flow rate of 30 μΐ/min for 60 sec on flow cell 2. A dilution series (1.95 to 1000 nM) of human 4-lBB-avi-His was passed on both flow cells at 30 μΐ/min for 180 sec to record the association phase. The dissociation phase was monitored for 180 s and triggered by switching from the sample solution to HBS-EP. The chip surface was regenerated after every cycle using a double injection of 60 sec 10 mM Glycine-HCl pH 2.1. Bulk refractive index differences were corrected for by subtracting the response obtained on reference flow cell 1. For the interaction between the 4- IBB ligand trimer- containing Fc (kih) fusion antigen binding molecules and hu4-lBB avi His, the affinity constants were derived from the rate constants by fitting to a 1 : 1 Langmuir binding curve using the Biaeval software (GE Healthcare).
Table 34: Fittings to 1: 1 Langmuir binding and Affinity constants
Ligand Analyte ka (1/Ms) kd (1/s) KD (M)
FAP split 4-1BBL hu4-lBB
trimer
(Construct 1.1) 4.8E+04 2.6E-02 5.5E-07
DP47 split 4-1BBL hu4-lBB
trimer (Control A) 6.2E+04 3.3E-02 5.2E-07 Example 5
Functional characterization of the targeted 4- IBB ligand trimer-containing Fc fusion antigen binding molecules
5.1. Binding on naive versus activated human PMBCs of the FAP-targeted 4-1BB ligand trimer-containing Fc (kih) fusion antigen binding molecules
Buffy coats were obtained from the Zurich blood donation center. To isolate fresh peripheral blood mononuclear cells (PBMCs) the buffy coat was diluted with the same volume of DPBS (Gibco by Life Technologies, Cat. No. 14190 326). 50 mL polypropylene centrifuge tubes (TPP, Cat.-No. 91050) were supplied with 15 mL Histopaque 1077 (SIGMA Life Science, Cat.-No. 10771, polysucrose and sodium diatrizoate, adjusted to a density of 1.077 g/mL) and the diluted buffy coat solution was layered above the Histopaque 1077. The tubes were centrifuged for 30 min at 400 x g. PBMCs were then collected from the interface, washed three times with DPBS and resuspended in T cell medium consisting of RPMI 1640 medium (Gibco by Life Technology, Cat. No. 42401-042) supplied with 10 % Fetal Bovine Serum (FBS, Gibco by Life Technology, Cat. No. 16000-044, Lot 941273, gamma-irradiated, mycoplasma-free and heat inactivated at 56 °C for 35 min), 1 % (v/v) GlutaMAX-I (GIBCO by Life Technologies, Cat. No. 35050 038), 1 mM Sodium Pyruvate (SIGMA, Cat. No. S8636), 1 % (v/v) MEM nonessential amino acids (SIGMA, Cat.-No. M7145) and 50 μΜ β-Mercaptoethanol (SIGMA, M3148). PBMCs were used directly after isolation or stimulated to induce 4- IBB expression at the cell surface of T and NK cells by culturing for 4 days in T cell medium supplemented with 200 U/mL Proleukin (Novartis Pharma Schweiz AG, CHCLB-P-476-700- 10340) and 2 μg/mL PHA-L (SIGMA Cat.-No. L2769) in a 6-well tissue culture plate and then 1 day in a 6-well tissue culture plate coated with 10 ug/mL anti-human CD3 (clone OKT3, BioLegend, Cat.-No. 317315) and 2 μg/mL anti-human CD28 (clone CD28.2, BioLegend, Cat.-No.: 302928) in T cell medium at 37 °C and 5% C02.
To determine binding of 4-1BBL trimer-containing Fc fusion antigen binding molecules to human PBMCs, 0.1 x 106 naive or activated PBMCs were added to each well of a round-bottom suspension cell 96-well plates (Greiner bio-one, cellstar, Cat. No. 650185). Plates were centrifuged 4 minutes with 400 x g and at 4 °C. Supernatant was discarded. Afterwards cells were stained in 100 μίΛνεΙΙ DPBS containing 1: 1000 diluted LIVE/DEAD Fixable Blue Dead Cell Stain Kit, for UV excitation (Life Technologies, Molecular Probes, L-23105) or Fixable Viability Dye eF660 (eBioscience 65-0864-18) or LIVE/DEAD Fixable Green Dead Cell Stain Kit (Life Technologies, Molecular Probes, L-23101) for 30 minutes at 4 °C in the dark. If DAPI was used as Live/Death stain, this staining step was skipped. Cells were washed once with 200 cold FACS buffer (DPBS supplied with 2 % (v/v) FBS, 5 mM EDTA pH8 (Amresco, Cat. No. E177) and 7.5 mM sodium azide (Sigma-Aldrich S2002).
Next, 50 μΐ/ννεΐΐ of 4 °C cold FACS buffer containing different titrated concentrations of 4-1BBL trimer-containing Fc fusion antigen binding molecules were added and cells were incubated for 120 minutes at 4 °C, washed four times with 200 μΐ/ννεΐΐ 4 °C FACS buffer and resuspended. Cells were further stained with 50 μΐ/ννεΐΐ of 4 °C cold FACS buffer containing 0.67 μg/mL anti-human CD3-PerCP-Cy5.5 (clone UCHT1, mouse IgGlK, BioLegend, Cat.-No. 300430) or 0.16 μΐ. anti-human CD3-PE/Cy7 (clone SP34-2, mouse IgGl K, BD Pharmingen, Cat.-No. 557749, Lot 33324597), 0.67 μg/mL anti-human CD45-AF488 (clone HI30, mouse IgGlK, BioLegend, Cat.-No. 304017) or 0.12 μg/mL anti-human CD56-FITC (clone NCAM16.2, mouse IgG2bK, BD Pharmingen, Cat.-No. 345811) or 1 μΐ, anti-human CD56-APC (clone B159, mouse IgGl K, BD Pharmingen, Cat.-No. 555518, Lot 3098894), 0.25 μg/mL anti-human CD4- BV421 (clone RPA-T4, mouse IgGlK, BioLegend, Cat.-No. 300532) or 0.23 μg/mL anti-human CD4-BV421 (clone OKT4, mouse IgG2bK, BioLegend, Cat.-No. 317434), 0.25 μΐ, anti-human CD8a-APC (clone RPA-T8, mouse IgGlK, BD Pharmingen, Cat.-No. 555369) or 0.67 μΐ, anti- human CD8a-APC/Cy7 (clone RPA-T8, mouse IgGlK, BioLegend, Cat.-No. 301016) or 0.83 ng/mL anti-human CD8a-BV711 (clone RPA-T8, mouse IgGlK, BD Pharmingen, Cat.-No.
301044) and 5 μg/mL PE-conjugated AffiniPure anti-human IgG Fcy-fragment- specific goat IgG F(ab )2 fragment (Jackson ImmunoResearch, Cat. No. 109 116 098 or 109 116 170). Cells were washed twice with FACS-buffer. If cells were stained with fixable viability dyes, they were fixed with 50 μίΛνεΙΙ DPBS containing 1 % formaldehyde (Sigma, HT501320-9.5L). Cells were resuspended in FACS buffer and acquired the next or the same day using a 5-laser LSR-Fortessa (BD Bioscience with DIVA software) or 3-laser Miltenyi Quant Analyzer 10 (Mitenyi Biotec) and Flow Jo (FlowJo X 10.0.7). If DAPI staining was used to detect dead cells, they were resuspended in 80 μίΛνεΙΙ FACS buffer containing 0.2 μg/mL DAPI (Santa Cruz Biotec, Cat. No. Sc-3598) and acquired the same day using a 5-laser LSR-Fortessa (BD Bioscience with DIVA software).
As shown in Figure 6, both FAP-targeted or untargeted 4- IBB ligand trimer-containing Fc fusion antigen binding molecules did not bind to resting human CD4+ T cells and showed no detectable binding to resting CD8+ T cells and NK cells. In contrast, both constructs bound strongly to activated NK, CD8+ or CD4+ T cells, although the latter showed approximately 10 fold lower intensity of specific fluorescence as compared to the NK cells and 20 fold decreased intensity of specific fluorescence as compared to CD8+ T cells.
Figures 7 A and 7B show the binding of Constructs 1.1 to 1.10 as prepared in Example 1 on 4-lBB-expressing activated human CD3+ CD8+ T cells and 4-lBB-expressing activated human CD3+ CD4+ T cells, respectively. Table 35 shows the EC50 values as measured for Constructs 1.1 to 1.10.
Table 35: Binding on activated human CD3+ CD8+ T cells and CD3+ CD4+ T cells
Figure imgf000221_0001
Figures 8A and 8B show the binding of Constructs 2.1, 2.3, 2.4, 2.5 and 2.6 as prepared in
Example 2 on CD4+ and CD8+ from fresh human blood and on activated 4- IBB -expressing CD4+ T cells and CD 8 + T cells, respectively. Gates were set on living CD45+ CD3+ CD4+ or CD45+ CD3+ CD8+ T cells and MFI of PE-conjugated AffiniPure anti-human IgG IgG Fcy- fragment- specific goat F(ab )2 fragment were blotted against the titrated concentration of targeted split trimeric 4- IBB ligand Fc fusion variants. Table 36 shows the EC50 values as measured for Constructs 2.1, 2.3, 2.4, 2.5 and 2.6.
Table 36: Binding on activated 4-lBB-expressing CD4+ T cells and CD8 + T cells
Construct EC50 [nM] EC50 [nM]
4-lBB+CD8+ 4-lBB+CD4+
Control B 0.36 0.42
Control C 0.39 0.41
Control E 0.57 0.76
2.1 0.21 0.24
2.3 0.44 0.3
2.4 0.3 0.38 2.5 0.35 0.68
2.6 0.33 0.24
5.2 Binding of FAP- targeted 4- IBB ligand trimer-containing Fc fusion antigen binding molecule to activated mouse splenocytes
Mouse spleens were collected in 3 mL PBS and a single cell suspension was generated using gentle MACS tubes (Miltenyi Biotec Cat.-No. 130-096-334) and gentleMACS Octo Dissociator (Miltenyi Biotec). Afterwards splenocytes were filtered through a 30 μηι Pre- Separation Filters (Miltenyi Biotec Cat.-No. 130-041-407) and centrifuged for 7 min at 350 x g and 4°C. Supernatant was aspirated and cells were resuspended in RPMI 1640 medium supplied with 10 % (v/v) FBS, 1 % (v/v) GlutaMAX-I, 1 mM Sodium-Pyruvate, 1 % (v/v) MEM non- essential amino acids, 50 μΜ β-Mercaptoethanol and 10 % Penicillin-Streptomycin (SIGMA, Cat.-No. P4333). 106 cells/mL were cultured for 2 days in a 6- well tissue culture plate coated with 10 μg/mL anti-mouse CD3s Armenian Hamster IgG (clone 145-2C11, BioLegend, Cat.-No. 100331) and 2 μg/mL anti-mouse CD28 Syrian Hamster IgG (clone 37.51, BioLegend, Cat.-No. 102102). Activated mouse splenocytes were harvested, washed in DPBS, counted and 0.1 x 106 cells were transferred to each well of a 96 U-bottom non-tissue culture treated well plate.
Supernatant was removed and cells were stained in 100 uL/well DPBS containing 1:5000 diluted Fixable Viability Dye eF660 (Bioscience, Cat-No. 65-0864-18) for 30 min at 4°C. Cells were washed with PBS and stained in 50 uL FACS buffer containing different concentration of FAP- targeted 4- IBB ligand trimer-containing Fc fusion antigen binding molecules (FAP split 4-lBBL trimer), untargeted 4- IBB ligand trimer-containing Fc fusion antigen binding molecules (DP47 split 4-lBBL trimer) or anti-mouse CD137 human IgGl P329G LALA mAb (clone Lob.12.3, BioXcell Catalog#: BE0169). Cells were incubated for 120 min at 4°C. Cells were washed four times with FACS buffer and stained in 50 μίΛνεΙΙ FACS buffer containing 10 μg/mL purified anti-mouse CD16/CD32 rat IgG-Fc-Block (BD Pharmingen, Cat.-No. 553142 clone 2.4G2), 5 μg/mL anti-mouse CD8b rat IgG2bK-FITC (BioLegend, Cat.-No. 126606, clone YTS 156.7.7), 0.67 μg/mL anti-mouse CD3 rat IgG2bK-APC-Cy7 (BioLegend, Cat.-No. 100222, clone 17A2), 0.67 μg/mL anti-mouse CD4 rat IgG2bK-PE-Cy7 (BioLegend, Cat.-No. 100422, clone GK1.5), 2 μg/mL anti-mouse NK1.1 Mouse (C3H x BALB/c) IgG2aK-PerCp-Cy5.5 (BioLegend, Cat.-No. 108728, clone PK136) and 10 μg/mL PE-conjugated AffiniPure polyclonal F(ab )2 Fragment goat anti-human IgG, Fey fragment specific, minimal cross -reactive to bovine mouse and rabbit serum proteins (Jackson ImmunoResearch, Cat.-No. 109-116-170) for 30 min at 4°C. Cells were washed twice with 200 μίΛνεΙΙ cold FACS buffer. Cells were fixed with 50 μίΛνεΙΙ DPBS containing 1 % formaldehyde. Cells were resuspended in FACS-buffer and acquired the next day using a 5-laser LSR-Fortessa (BD Bioscience with DIVA software).
As shown in Figure 9, FAP-targeted hu4-lBB ligand trimer-containing Fc fusion antigen binding molecules (FAP split hu4-lBBL trimer) and untargeted hu4-lBB ligand trimer- containing Fc fusion antigen binding molecules (DP47 split hu4-lBBL trimer) do not bind to mouse 4- IBB. Therefore activity cannot be tested in immune competent mice. For in vivo mode of action studies either humanized mouse models in immune incompetent mice or surrogates containing mouse 4-1BBL trimers as shown in Figure 3 have to be used.
5.3 Binding to FAP-expressing tumor cells For binding assays on FAP expressing cells, the human melanoma cell line MV-3 (see
Ruiter et al., Int. J. Cancer 1991, 48(1), 85-91), WM-266-4 (ATTC CRL-1676) or NIH/3T3- huFAP clone 39 cell line were used. To generate the latter cell line, NIH/3T3 cells were transfected with human FAP (NIH/3T3-huFAP clone 39). The cells were generated by transfection of mouse embryonic fibroblast NIH/3T3 cells (ATCC CRL-1658) with the expression pETR4921 plasmid encoding human FAP under a CMV promoter. Cells were maintained in the presence of 1.5 μg/mL puromycin (InvivoGen, Cat.-No.: ant-pr-5). 0.1 x 106 of FAP expressing tumor cells were added to each well of a round-bottom suspension cell 96- well plates (Greiner bio-one, cellstar, Cat.-No. 650185). Cells were washed once with 200 μΙ_, DPBS and pellets were resuspended. 100
Figure imgf000223_0001
of 4 °C cold DPBS buffer containing 1:5000 diluted Fixable Viability Dye eFluor 450 (eBioscience, Cat.-No. 65-0863-18) or Fixable Viability Dye eFluor 660 (eBioscience, Cat.-No. 65-0864-18) were added and plates were incubated for 30 minutes at 4 °C. Cells were washed once with 200 μΙ_, 4 °C cold DPBS buffer and resuspended in 50 μίΛνβΙΙ of 4 °C cold FACS buffer (DPBS supplied with 2 % (v/v) FBS, 5 mM EDTA pH 8 (Amresco, Cat.-No. E177) and 7.5 mM Sodium azide (Sigma- Aldrich S2002) containing different concentrations of titrated 4-1BBL trimer-containing Fc fusion antigen binding molecules, followed by incubation for 1 hour at 4 °C. After washing four times with with 200 μΐ/ννεΐΐ, cells were stained with 50
Figure imgf000223_0002
of 4 °C cold FACS buffer containing 30 μg/mL FITC-conjugated AffiniPure anti-human IgG Fey- fragment- specific goat F(ab )2 fragment (Jackson ImmunoResearch, Cat.-No. 109-096-098) or 5 μg/mL PE-conjugated AffiniPure anti- human IgG Fgy-fragment- specific goat F(ab )2 fragment (Jackson ImmunoResearch, Cat. No. 109-116-098 or 109-116-170) for 30 minutes at 4°C. Cells were washed twice with 200 μΐ. 4 °C FACS buffer and then resuspended in 50
Figure imgf000223_0003
DPBS containing 1 % formaldehyde. The same or the next day cells were resuspended in 100 μΙ_, FACS-buffer and acquired using 5-laser LSR-Fortessa (BD Bioscience with DIVA software) or 3-laser Miltenyi Quant Analyzer 10 (Mitenyi Biotec) and Flow Jo (FlowJo X 10.0.7). As shown in Figure 10, the FAP-targeted 4- IBB ligand trimer-containing Fc(kih) fusion antigen binding molecule (FAP split 4-1BBL trimer) Construct 1.1, but not the untargeted, DP47-Fab-containing construct (DP47 split 4-1BBL trimer) Control A, efficiently bound to human fibroblast activation protein (FAP)-expressing melanoma (10A) MV-3 cells or (10B) WM-266-4 cells.
Figure 11A shows the binding of Constructs 1.1 to 1.10 as prepared in Example 1 to human-FAP expressing human melanoma MV-3 cells and in Figure 1 IB the binding of
Construct 1.1., 1.2, 1.3 and 1.5 to human FAP expressing NIH/3T3-huFAP clone 39 transfected mouse embryonic fibroblast cells is presented. Table 37 shows the EC50 values as measured for Constructs 1.1 to 1.10.
Table 37: Binding to human FAP-expressing tumor cells
Figure imgf000224_0001
Figure 12 shows the binding of different FAP (4B9)-targeted or untargeted split trimeric human 4- IBB ligand Fc (kih) constructs to human-FAP expressing human melanoma MV-3 cells (Figure 12A) and WM-266-4 cells (Figure 12B). The constructs 2.1, 2.3, 2.4, 2.5 and 2.6 were prepared as described in Example 2 and Controls were prepared as described herein before. Gates were set on living tumor cells and MFI of PE-conjugated AffiniPure anti-human IgG Fcy- fragment- specific goat F(ab )2 fragment were blotted against the titrated concentration of targeted split trimeric 4-1BB ligand Fc fusion constructs. Table 38 shows the EC50 values as measured. Table 38: Binding to human FAP-expressing tumor cells
Figure imgf000225_0001
5.4 Functional characterization of the murine targeted 4-1BB ligand trimer- containing Fc (kih) fusion antigen binding molecules 5.4.1 Binding to activated mouse splenocytes
Mouse spleens were collected in 3 mL PBS and a single cell suspension was generated using gentle MACS tubes (Miltenyi Biotec Cat.-No. 130-096-334) and gentleMACS Octo Dissociator (Miltenyi Biotec). Afterwards splenocytes were filtered through 30 μηι Pre- Separation Filters (Miltenyi Biotec Cat.-No. 130-041-407) and centrifuged for 7 min at 350 x g and 4°C. Supernatant was aspirated and cells were resuspended in RPMI 1640 medium supplied with 10 % (v/v) FBS, 1 % (v/v) GlutaMAX-I, 1 mM Sodium-Pyruvate, 1 % (v/v) MEM nonessential amino acids, 50 μΜ β-Mercaptoethanol .
For binding on fresh mouse splenocytes cells were used directly. To induce mouse 4- IBB expression on T cells, mouse splenocytes were activated as following: 106 cells/mL were cultured for 2 days in a 6- well tissue culture plate coated with 10 μg/mL anti-mouse CD3s Armenian Hamster IgG (clone 145-2C11, BioLegend, Cat.-No. 100331) and 2 μg/mL anti- mouse CD28 Syrian Hamster IgG (clone 37.51, BioLegend, Cat.-No. 102102).
Fresh mouse splenocytes or activated mouse splenocytes were collected, washed in DPBS (Gibco life technologies, Cat.-No. 14190-136), counted and 0.1 x 106 cells were transferred to each well of a 96 U-bottom non-tissue culture treated well plate (Greiner bio-one, cell star, Cat.-No. 650185). Supernatant was removed and cells were stained in 100 uL/well 4 °C cold DPBS containing 1: 1000 diluted LIVE/DEAD Fixable Aqua Dead Cell Stain Kit (Life Technologies, L34957) for 30 min at 4°C. Cells were washed with cold DPBS and stained in 50 uL/well cold FACS buffer (DPBS supplied with 2 % (v/v) FBS, 5 mM EDTA pH8 (Amresco, Cat. No. E177) and 7.5 mM Sodium azide (Sigma-Aldrich S2002)) containing different concentration of mouse 4- IBB ligand trimer-containing Fc(kih) fusion molecules or mouse IgGl K Isotype control (BioLegend, Cat.-No. 400153, clone MOPC-21). Cells were incubated for 120 min at 4°C, washed four times with cold DPBS and stained in 50 μίΛνεΙΙ cold FACS buffer containing 30 μg/mL FITC-conjugated anti-mouse IgG Fc-gamma-specific goat IgG F(ab )2 (Jackson Immunoresearch, Cat.-No. 115-096-071) for 30 min at 4°C. Afterwards cells were washed twice with cold DPBS and stained with 50 μΐ/ννεΐΐ FACS buffer supplied with 10 μg/mL purified anti-mouse CD16/CD32 rat IgG-Fc-Block (BD Pharmingen, Cat.-No. 553142 clone 2.4G2), 0.67 μg/mL anti-mouse CD8a-APC-Cy7 (BioLegend, Cat.-No. 100714, clone 53-6.7), 0.67 μg/mL anti-mouse CD3£-PerCP-Cy5.5 (BioLegend, Cat.-No. 100328, clone 145-2C11), 0.67 μg/mL anti-mouse CD4 rat IgG2bK-PE-Cy7 (BioLegend, Cat.-No. 100422, clone GK1.5) for 30 min at 4°C. Cells were washed twice with 200 μίΛνεΙΙ cold DPBS, fixed with 50 μίΛνεΙΙ DPBS containing 1 % Formaldehyde and resuspended in FACS-buffer. Cells were acquired using 3-laser MACSQuant Analyzer 10 (Miltenyi Biotech) and Flow Jo vlO.0.7 (FlowJo LLC). Gates were set on CD3+ CD8+ or CD3+ CD4+ T cells and the median florescence intensity (MFI) of FITC-conjugated anti-mouse IgG Fc-gamma-specific goat IgG F(ab )2 was analyzed and normalized by the subtraction of the MFI of the blank control (no addition of mouse 4- IBB ligand trimer-containing Fc(kih) fusion molecule) . The MFI was blotted against the
concentration of used mouse 4- IBB ligand trimer-containing Fc(kih) fusion molecules to display the binding to mouse 4- IBB cell-bound molecule.
As can be seen in Figure 13, the murine 4-1BBL Constructs M.l and M.2 as well as corresponding control molecules Control M.l and Control M.2 bind with a quite similar affinity to mouse 4-1BB. Table 39 shows the EC50 values as measured for Constructs M.l and M.2 and the control molecules.
Table 39: Binding on activated 4-lBB-expressing CD4+ T cells and CD8 + T cells
Figure imgf000226_0001
5.4.2 Binding on FAP-expressing tumor cells
For binding assays on FAP expressing cells, the human melanoma cell line MV-3 (see Ruiter et al., Int. J. Cancer 1991, 48(1), 85-91) and WM-266-4 (ATTC CRL-1676) were used (anti-FAP specific clone 28H1 is mouse/human-crossreactive). 0.1 x 106 of FAP expressing tumor cells were added to each well of a round-bottom suspension cell 96-well plates (Greiner bio-one, cellstar, Cat.-No. 650185). Cells were washed once with 200 μΐ^ cold DPBS and pellets were resuspended in 100 μΐ/ννεΐΐ of 4 °C cold DPBS buffer containing 1: 1000 diluted
LIVE/DEAD Fixable Aqua Dead Cell Stain Kit (Life Technologies, L34957) and incubated for 30 min at 4°C. Cells were washed once with 200 μΐ^ cold DPBS buffer and resuspended in 50 of cold FACS buffer (DPBS supplied with 2 % (v/v) FBS, 5 mM EDTA pH8 (Amresco, Cat. No. E177) and 7.5 mM Sodium azide (Sigma- Aldrich S2002)) containing murine 4- IBB ligand trimer-containing Fc(kih) fusion molecules at a series of concentrations followed by incubation for 1 hour at 4 °C. After washing four times with 200 DPBS/well, cells were stained with 50 μίΛνεΙΙ of 4 °C cold FACS buffer containing 30 μg/mL FITC-conjugated anti- mouse IgG Fc-gamma-specific goat IgG F(ab )2 (Jackson Immunoresearch, Cat.-No. 115-096- 071) for 30 min at 4 °C. Cells were washed twice with 200 L well cold DPBS buffer, fixed with 50 μίΛνεΙΙ DPBS containing 1 % Formaldehyde and resuspended in FACS-buffer. Cells were acquired using 3-laser MACSQuant Analyzer 10 (Miltenyi Biotech) and Flow Jo vlO.0.7 (FlowJo LLC). Gates were set on living cells and the median florescence intensity (MFI) of FITC-conjugated anti-mouse IgG Fc-gamma-specific goat IgG F(ab )2 was analyzed and normalized by the subtraction of the MFI of the blank control (no addition of mouse 4-1BB ligand trimer-containing Fc(kih) fusion molecule). The MFI was blotted against the
concentration of used murine 4- IBB ligand trimer-containing Fc(kih) fusion molecules to display the binding to murine 4- IBB cell-bound molecule. As expected, the murine 4-1BBL constructs M.l and M.2 bind with a quite similar affinity to FAP whereas the control molecules do not bind.
Figure 14 shows the binding of the FAP-targeted or untargeted split trimeric murine 4- IBB ligand Fc (kih) Constructs M.l and M.2 to human-FAP expressing human melanoma MV-3 cells (Figure 14A) and WM-266-4 cells (Figure 14B). Table 40 shows the EC50 values as measured.
Table 40: Binding to human FAP-expressing tumor cells
Construct EC50 [nM] EC50 [nM]
FAP+ MV-3 FAP+ WM-266-4
M. l 7.26 5.14
M.2 6.9 5.63 Example 6
Biological activity of the targeted 4-lBB ligand trimer-containing Fc fusion antigen binding molecules
6.1. NF-κΒ activation in HeLa cells expressing human 4-lBB Generation of HeLa cells expressing human 4- IBB and NF-KB-luciferase
The cervix carcinoma cell line HeLa (ATCC CCL-2) was transduced with a plasmid based on the expression vector pETR10829, which contains the sequence of human 4- IBB (Uniprot accession Q07011) under control of a CMV-promoter and a puromycin resistance gene. Cells were cultured in DMEM medium supplemented with 10 % (v/v) FBS, 1 % (v/v) GlutaMAX-I and 3 μg/mL Puromycin.
4-lBB-transduced HeLa cells were tested for 4- IBB expression by flow cytometry:
0.2xl06 living cells were resuspended in 100 μL· FACS buffer containing 0.1 μg PerCP/Cy5.5 conjugated anti-human 4-lBB mouse IgGlK clone 4B4-1 (BioLegend Cat.-No.309814) or its isotype control (PerCP/Cy5.5 conjugated mouse IgGlK isotype control antibody clone MOPC-21, BioLegend Cat.-No.400150) and incubated for 30 minutes at 4 °C. Cells were washed twice with FACS buffer, resuspended in 300 μΐ^ FACS buffer containing 0.06 μg DAPI (Santa Cruz Biotec, Cat. No. Sc-3598) and acquired using a 5-laser LSR-Fortessa (BD Bioscience, DIVA software). Limited dilutions were performed to generate single clones as described: human-4-lBB- transduced HeLa cells were resuspended in medium to a density of 10, 5 and 2.5 cells/ml and 200 μΐ of cell suspensions were transferred to round bottom tissue-culture treated 96-well plates (6 plates/cell concentration, TPP Cat.-No. 92697). Single clones were harvested, expanded and tested for 4-lBB expression as described above. The clone with the highest expression of 4-lBB (clone 5) was chosen for subsequent transfection with the NF-KB-luciferase expression-vector 5495p Tranlucent HygB. The vector confers transfected cells both with resistance to
Hygromycin B and capacity to express luciferase under control of NF-kB-response element
(back bone vector Panomics, Cat.-No. LR0051 with introduced HyB resistence). Human-4-lBB HeLa clone 5 cells were cultured to 70 % confluence. 50 μg (40 μί) linearized (restriction enzymes Asel and Sail) 5495p Tranlucent HygB expression vector were added to a sterile 0.4 cm Gene Pulser/MicroPulser Cuvette (Biorad, Cat.-No, 165-2081). 2.5x106 human-4-lBB HeLa clone 5 cells in 400 μΐ supplement-free DMEM medium were added and mixed carefully with the plasmid solution. Transfection of cells was performed using a Gene Pulser Xcell total system (Biorad, Cat-No. 165-2660) under the following settings: exponential pulse, capacitance 500 μΡ, voltage 160 V, resistance∞. Immediately after the pulse transfected cells were transferred to a 75 cm2 tissue culture flask (TPP, Cat.-No. 90075) with 15 mL 37°C warm DMEM medium supplied with 10 % (v/v) FBS and 1 % (v/v) GlutaMAX-I. Next day, culture medium containing 3 μg/mL Puromycin and 200 μg/mL Hygromycin B (Roche, Cat.-No. 10843555001) was added. Surviving cells were expanded and limited dilution was performed as described above to generate single clones.
Clones were tested for 4- IBB expression as described above and for NF-KB-Luciferase activity as following: Clones were harvested in selection medium and counted using a Cell Counter Vi-cell xr 2.03 (Beckman Coulter, Cat.-No. 731050). Cells were set to a cell density of 0.33xl06 cells/mL and 150 μL· of this cell suspension were transferred to each well of a sterile white 96-well flat bottom tissue culture plate with lid (greiner bio-one, Cat.-No. 655083) and - as a control - to normal 96-well flat bottom tissue culture plate (TPP Cat.-No. 92096) to test survival and cell density the next day. Cells were incubated at 37 °C and 5 % C02 overnight. The next day 50 μΐ^ of medium containing different concentrations of recombinant human tumor necrosis factor alpha (rhTNF-cc, PeproTech, Cat.-No. 300-01 A) were added to each well of a 96- well plate resulting in final concentration of rhTNF-cc of 100, 50, 25, 12.5, 6.25 and 0 ng/well. Cells were incubated for 6 hours at 37 °C and 5 % C02 and then washed three times with 200 μίΛνεΙΙ DPBS. Reporter Lysis Buffer (Promega, Cat-No: E3971) was added to each well (40 μΐ) and the plates were stored over night at -20 °C. The next day frozen cell plates and Detection Buffer (Luciferase 1000 Assay System, Promega, Cat.-No. E4550) were thawed to room temperature. 100 uL of detection buffer were added to each well and the plate was measured as fast as possible using a SpectraMax M5/M5e microplate reader and the SoftMax Pro Software (Molecular Devices). Measured units of released light for 500 ms/well (URLs) above control (no rhTNF-cc added) were taken as luciferase activity. The NF-KB-luc-4-lBB-HeLa clone 26 exhibiting the highest luciferase activity and a considerable level of 4-lBB-expression and was chosen for further use.
NF-κΒ activation in Hela cells expressing human 4- IBB co-cultured with FAP-expressing tumor cells
NF-KB-luciferase human-4-lBB HeLa cells were harvested and resuspended in DMEM medium supplied with 10 % (v/v) FBS and 1 % (v/v) GlutaMAX-I to a concentration of 0.2 x 106 cells/ml. 100 μΐ (2 x 104 cells) of this cell suspension were transferred to each well of a sterile white 96-well flat bottom tissue culture plate with lid (greiner bio-one, Cat. No. 655083) and the plate were incubated at 37 °C and 5 % C02 overnight. The next day 50 μΐ^ of medium containing titrated concentrations of FAP-targeted 4- IBB ligand trimer-containing Fc fusion antigen binding molecules (FAP split 4-1BBL trimer) or DP47-untargeted 4- IBB ligand trimer- containing Fc fusion antigen binding molecules (DP47 split 4-1BBL trimer) were added. FAP- expressing tumor cells (MV3, WM-266-4 or NIH/3T3-huFAP clone 39) were resuspended in DMEM medium supplied with 10 % (v/v) FBS and 1 % (v/v) GlutaMAX-I to a concentration of 2 x 106 cells/ml. Suspension of FAP-expressing tumor cell (50 μΐ, final ratio 1:5) or only medium were added to each well and plates were incubated for 6 hours at 37 °C and 5 % C02. Cells were washed two times with 200
Figure imgf000230_0001
DPBS. 40 μΐ freshly prepared Reporter Lysis Buffer (Promega, Cat-No: E3971) were added to each well and the plate were stored over night at -20 °C. The next day frozen cell plate and Detection Buffer (Luciferase 1000 Assay System,
Promega, Cat. No. E4550) were thawed at room temperature. 100 μΐ^ of detection buffer were added to each well and luciferase activity was measured as fast as possible using a SpectraMax M5/M5e microplate reader and a SoftMax Pro Software (Molecular Devices) counting light emission in URL (units of released light for 0.5s/well) or Victor3 1420 multilabel counter plate reader (Perkin Elmer) and the Perkin Elmer 2030 Manager Software counting light emission as counts per seconds (CPS) and blotted against the concentration of tested constructs.
FAP-targeted 4- IBB ligand trimer-containing Fc fusion antigen binding molecule (FAP split 4-lBBL trimer) triggered activation of the NFKB signaling pathway in the reporter cell line in the presence of FAP-expressing tumor cells. In contrast, the untargeted variant of the same molecule failed to trigger such an effect at any of the tested concentrations (Figure 16). This activity of targeted 4-lBBL was strictly dependent on the expression of FAP at the cell surface of tumor cells as no NF-kB activation could be detected upon culturing of the NF-kB reporter cell line with FAP-negative tumor cells even in the presence of FAP-targeted 4- IBB ligand trimer-containing Fc fusion antigen binding molecule. The activities as measured for Constructs 1.1 to 1.10 are shown in Figure 17 and the data as measured for Constructs 2.1, 2.4 and 2.5 are presented in Figure 18.
6.2. NFKB activation in HEK T293 cells expressing cynomolgus monkey 4- IBB
Generation of HEK T293 cells expressing cvnomolgus monkey 4-1BB and NFKB- luciferase For the production of viral-like particles (VLP) the Human Embryonic Kidney (HEK)
T293/17 (ATCC CRL-11268) was transfected using Lipofectamine® LTX Reagent with PLUS™ Reagent (Life Technologies, Cat.-No. 15338100) with the vector pETR14372 encoding a NFKB-luciferase-IRIS-GFP reporter gene cassette (NFKB-IUC-GFP) accordingly to the manufacture's protocol. 6 hours later DMEM supplied with 10% FBS medium replacement was performed and VLP were harvested 4 days later. Fresh HEK 293T cells were transduced at a confluency of 70-80 % with the produced pETR14372-VLP and 4 μg/mL polybrene. Cells were cultured for 24 h and a medium exchange was performed. The transduced HEK T293/17 cells were harvested and a limited dilution of 1 cell/well was performed to screen for stable single clones. The single clones were stimulated with 25 ng/mL TNF-cc (PeproTech Inc. Cat.-No. 300- 01 A) in the medium and were screened for a positive GFP signal over time using the Incuyte Zoom Fluorescence Microscope System (Essen Bioscience). After GFP signal recording cells were tested for lucif erase activity using the Nano Glo Lucif erase Kit (Pro mega, Nl 120) accordingly to the manufacture's protocol. Luciferase activity was measured using Victor3 1420 multilabel counter plate reader (Perkin Elmer) and the Perkin Elmer 2030 Manager Software. Light emission was counted in counts per seconds (CPS) for 0.5 sec/well. The clone 61 showed the highest expression of GFP and Luciferase after TNF-cc activation and was further used for the reporter cell line generation.
As described above, new VLP were produced using the vector pETR14879 encoding cynomolgus monkey 4- IBB and a puromycine resistance and the HEK 293T NFKB-fluc-GFP clone 61 cell line was transduced at a confluency of 70-80% with the produced pETR14879-VLP and 4 μg/mL polybrene. Cells were cultured for 24 h and a medium exchange was performed. Four days after transduction the cells were stained with PE-conjugated anti-human cynomolgus- crossreactive 4-1BB antibody (mouse IgGlK, clone MOPC-21, BioLegend, Cat.-No. 309804) in DPBS containing 1% FBS, were sorted by FACS (ARIA, BD) and seeded with 5 cells/well in DMEM supplied with 10% FBS medium containing 1 μg/mL Puromycine (InvivoGen, Cat.-No. ant-pr). Growing clones were tested as described for GFP and Luciferase activity after TNF-cc stimulation and for high cynomolgus monkey 4- IBB expression by flow cytometry. Double positive clones were chosen and tested for Luficerase activity in the presence of monovalent FAP-targeted Construct 2.1 or Control B and FAP-expressing MV-3 or WM-266-4 cells. HEK T293/17-NF-KB-luc-GFP-cy4-lBB expressing Clone 61-13 was chosen to be used for all further experiments.
NFKB activation of HEK T293/17 reporter cells expressing cynomolgus monkey 4- IBB co-cultured with FAP-expressing tumor cells
HEK T293/17-NFKB-luc-GFP-cy4-lBB expressing Clone 61-13 cells were harvested and resuspended in DMEM medium supplied with 10 % (v/v) FBS and 1 % (v/v) GlutaMAX-I to a concentration of 0.2 x 106 cells/mL. 100 μΐ (2 x 104 cells) of this cell suspension were transferred to each well of a sterile white 96-well flat bottom tissue culture plate with lid (greiner bio-one, Cat. No. 655083) and the plate were incubated at 37 °C and 5 % C02 overnight. The next day 50 μϊ^ of medium containing different titrated concentrations of FAP-targeted or untargeted 4- IBB ligand trimer-containing Fc fusion antigen binding molecules were added. FAP-expressing tumor cells (MV3 and WM-266-4) were resuspended in medium to a concentration of 2 x 106 cells/ml. Suspension of FAP-expressing tumor cell (50 μΐ) was added to each well and plates were incubated for 6 hours at 37 °C and 5 % C02. The principle of the assay is shown in Figure 19. After incubation cells were washed three times with 200 μίΛνεΙΙ DPBS. 40 μΐ freshly prepared Reporter Lysis Buffer (Promega, Cat-No: E3971) were added to each well and plates were stored over night at -20 °C. The next day frozen cell plates and detection buffer (Luciferase 1000 Assay System, Promega, Cat. No. E4550) were thawed to room temperature. 100 μΐ^ of detection buffer were added to each well and luciferase activity was measured as fast as possible using
SpectraMax M5/M5e (Molecular Devices) microplate reader (500 ms integration time, no filter collecting all wavelength). Light emission was counted in units of released light (URL) for 0.5 sec/well and blotted against the concentration of tested FAP-targeted or untargeted 4- IBB ligand trimer-containing Fc fusion antigen binding molecules. The results for Constructs of Example 2 are shown in Figure 20.
6.3 Antigen-specific CD8+ T cell-based assay
Isolation and culture of antigen-specific CD8 T cells Fresh blood was obtained from a HLA-A2+ CMV-infected volunteer. PBMCs were isolated as described above. CD8 T cells were purified from PBMCs using a negative selection human CD8 T cell isolation Kit according to manufacturer's recommendations (Miltenyi Biotec, Cat. No. 130-094-156). Ten million of isolated CD8 T cells were resuspended in 1 mL sterile DPBS supplemented with 1 % (v/v) FBS along with 50 of PE-labeled HLA-A2-pentamer containing the CMV-derived NLVPMVATV peptide (Prolmmune, Cat. No. F008-2B) and incubated for 10 min at room temperature. Cells were washed twice with 3 mL sterile DPBS supplied with 1 % (v/v) FBS. Cells were resuspended in 1 mL cells DPBS supplied with 1 % (v/v) FBS containing 1 μg/mL anti-human CD8-FITC (clone LT8, Abeam, Cat. No. Ab28010) and incubated for 30 minutes at 4°C. Cells were washed twice, resupended to a concentration of 5xl06 cells/mL in DPBS supplied with 1 % (v/v) FBS, and filtrated through a 30 μιη pre- separation nylon-net cell strainer (Miltenyi Biotec, Cat. No. 130-041-407). NLV-peptide- specific CD8+ T cells were isolated by FACS sorting using an ARIA cell sorter (BD Bioscience with DIVA software) with the following settings: 100 μιη nozzle and purity sort mask. Sorted cells were collected in a 15 ml polypropylene centrifuge tube (TPP, Cat. No. 91015) containing 5 ml RPMI 1640 medium supplied with 10 % (v/v) FBS, 1 % (v/v) GlutaMAX-I and 400 U/mL Proleukin. Sorted cells were centrifuged for 7 minutes at 350 x g at room temperature and resuspended in same medium to a concentration of 0.53 x 106 cells/mL. 100 μίΛνεΙΙ of this cell suspension were added to each well of a previously prepared feeder plate.
PHA-L-activated irradiated allogeneic feeder cells were prepared from PBMCs as previously described (Levitsky et al., 1998) and distributed to 96 well culture plates at 2xl05 feeder cells per well.
After one day of culturing 100 μΐ^ medium/well were removed from well containing sorted CD8+ T-cells and replaced by new RPMI 1640 medium supplemented with 10 % (v/v) FBS and 1 % (v/v) GlutaMAX-I and 400 U/mL Proleukin, this was repeated during culture on a regular basis (every 2-4 days). As soon as cells start to proliferate, they were transferred to 24- well flat- bottom tissue culture plate (TPP, 92024). Cells were expanded/split and reactivated with new feeder cell preparation on a regular basis.
Activation assay of antigen-specific CD8+ T cells
MV3 cells were harvested and washed with DPBS and 2 x 10 cells were resuspended in 250 μΐ. C diluent of the PKH-26 Red Fluorescence Cell linker Kit (Sigma, Cat.-No. PKH26GL). 1 μΐ^ PKH26-Red- stain solution was diluted with 250 μΐ^ C diluent and added to the suspension of MV3 cells which were then incubated for 5 min at room temperature in the dark. This was followed by addition of 0.5 mL FBS and cells were incubated for 1 minute and washed once with T cell medium consisting of RPMI 1640 medium supplemented with 10 % (v/v) FBS, 1 % (v/v) GlutaMAX-I, 1 mM Sodium- Pyruvate, 1 % (v/v) MEM non-essential amino acids and 50 μΜ β-Mercaptoethanol. 1 x 106 MV3 cells/mL were resuspended in T cell medium and separated into three tubes. Synthetic NLVPMVATV peptide (obtained from thinkpeptides) was added to a final concentration of 1x10" M or 1x10" M and cells were incubated for 90 min. MV3 cells were washed once with T cell medium and resuspended to a density of 0.5 x 106 cells/mL, distributed (100
Figure imgf000233_0001
to a 96- well round bottom cell- suspension plate (Greiner bio- one, cellstar, Cat.-No. 650185) and incubated over night at 37 °C and 5 % C02. The principle of the assay is shown in Figure 21.
The next day, 50 μΐ/ννεΐΐ T cell medium containing different titrated concentrations of targeted 4- IBB ligand trimer-containing Fc fusion antigen binding molecules were added. NLV- specific CD8 T cells were harvested, CFDA-SE (5(6)-Carboxyfluoresceindiacetate-N- succinimidylester, SIGMA-Aldrich, Cat.-No. 21888-25MG-F) was added to a final concentration of 40 nM and cells were incubated under rotation for 15 min at 37 °C. Labeling was stopped by adding FBS, cells were washed and resuspended in T cell medium to a final concentration of 0.125 x 106 cells/mL. 50 μL· of this CFSE-labeled CD8 T cell suspension were added to each well (final E:T ratio = 1:8). Cell plates were incubated for 24 h, 50 μΐ/ννεΐΐ were removed and 50 μί T cell medium containing 2.64 μΙ τιΙ. Golgi stop (Protein Transport Inhibitor containing Monesin, BD Bioscience, Cat.-No. 554724) were added to each well (final concentration 0.66
Figure imgf000233_0002
DPBS and stained with 100 L well 4 °C DPBS containing 1 :5000 diluted Fixable Viability Dye-eF450 (eBioscience, Cat.-No. 65-0864) for 30 minutes at 4°C. Cell plates were washed with 200
DPBS followed by staining with fluorescent dye-conjugated antibodies: anti-human CD137-PerCP/Cy5.5 (clone 4B4-1, mouse IgGlK, BioLegend, Cat.-No. 309814), anti-human CD8-BV605 (clone RPA-T8, mouse IgGlK, BioLegend, Cat.-No. 301012) or 0.67 μg/mL anti- human CD8a-APC/Cy7 (clone RPA-T8, mouse IgGlK, BioLegend, Cat.-No. 301016) and anti- human CD25 PE/Cy7 (clone BC96, mouse IgGlK, BioLegend, Cat.-No. 302612). After incubation for 30 min at 4°C, cells were washed twice with 200 μίΛνεΙΙ FACS buffer, resuspended in 50
Figure imgf000234_0001
freshly prepared FoxP3 Fix/Perm buffer (eBioscience Cat.-No. 00- 5123 and 00-5223) and incubated for 30 min at 4 °C. Plates were washed twice with 200 μΐ ννεΐΐ Perm-Buffer (DPBS supplied with 2 % (v/v) FBS, 1 % (w/v) saponin (Sigma Life Science, S7900) and 1 % (w/v) sodium azide (Sigma- Aldrich, S2002) and stained with 50 L well Perm- Buffer (eBioscience, Cat.-No. 00-8333-56) containing 0.25 μg/mL anti-human IFNy-APC (clone B27, mouse IgGlK, BioLegend, Cat.-No. 506510) or 0.33 μg/mL anti-human IFNy-BV510 (clone 4S.B3, mouse IgGlK, BioLegend, Cat.-No.502543). Plates were incubated for 1 h at 4 °C and washed twice with 200 μίΛνεΙΙ Perm-Buffer. For fixation, 50 μίΛνεΙΙ DPBS containing 1 % formaldehyde were added. The same or the next day, cells were resuspended in 100
Figure imgf000234_0002
FACS buffer and acquired using a 5-laser Fortessa flow cytometer (BD Bioscience with DIVA software) or 3-laser Miltenyi Quant Analyzer 10 (Miltenyi Biotec) and Flow Jo (FlowJo X 10.0.7).
As shown in Figures 22 and 23 for Constructs 1.1 to 1.10 and in Figures 24 and 25 for Constructs 2.1, 2.3 and 2.4, antigen- specific CD8+ T cells, but not unstimulated controls, exhibited increased levels of surface 4-1BB expression in the presence of FAP-targeted 4-1BB ligand trimer-containing Fc fusion antigen binding molecule (FAP split 4-1BBL trimer). This effect of 4-1BBL was dose dependent and required FAP-targeting as addition of the untargeted control molecule did not affect the level of 4- IBB expression. Furthermore, T-cells activated at the higher peptide concentration (1x10 -"8 M) showed sustained secretion of INFyin the presence of FAP-targeted 4- IBB ligand trimer-containing Fc fusion antigen binding molecule (FAP split 4-1BBL trimer). Collectively, these data demonstrate that the antigen-targeted 4-1BB ligand trimer-containing Fc fusion antigen binding molecule modulates the surface phenotype and responsiveness of antigen specific T-cells in a targeting dependent manner.
6.4 Comparison of cell-targeted and untargeted mouse 4-1BBL Fc fusion antigen binding molecules
Targeted and untargeted mouse 4- IBB ligand trimer-containing Fc fusion antigen binding molecules (FAP split mouse 4-1BBL trimer and DP47 split mouse 4-1BBL trimer) were prepared as described in Example 1.3.
To compare the bioactivity of cell-targeted and untargeted mouse 4- IBB ligand trimer- containing Fc fusion antigen binding molecules, Proliferation Dye eFlour670- labeled
(eBioscience, Cat.-No.65-0840-90) or CellTrace Violet Cell Proliferation dye-labeled (Cell tracer, Cat.-No. C34557) fresh mouse splenocytes were cocultured for 3-4 days in 96 well tissue culture U-bottom plates (TTP, Cat.-No. 92097) with adherent 50 Gy irradiated NIH/3T3-huFAP clone 39 cells (generation see 5.3) in RPMI 1640 medium (Gibco, Cat.-No. 42401-042) supplied with 10 % (v/v) FBS, 1 % (v/v) GlutaMAX-I, 1 mM Sodium-Pyruvate, 1 % (v/v) MEM non- essential amino acids and 50 μΜ β-Mercaptoethanolin the presence of 0.5 μg/mL anti-mouse CD3 Syrian hamster IgG (clone 145-2C11, BD, Cat.-No. 553057) and the indicated drug candidate molecule added at a range of concentrations (Figure 26). After three or four days, cells were washed with FACS buffer and stained for 30 min at 4°C in 25 uL FACS buffer/well containing anti-mouse CD8 ratIgG2a-B V711 (BioLegend, Cat.-No. 100747, clone 53-6.7,) and anti-mouse CD4 ratIgG2a-BV421 (BioLegend, Cat.-No. 100544, clone RM4-5) and 0.67 μg/mL anti-mouse CD137 (4-1BB) Syrian hamster IgG-PE (BioLegend, Cat.-No. 106106, clone 17B5) and anti-mouse CD25-PErCP-Cy5.5 ratIgG2b (BioLegend, Cat.-No. 1019112). Cells were washed and incubated for 1 h at room temperature in prepared Fix/Perm Buffer (Foxp3 /
Transcription Factor Staining Buffer Set, eBioscience, Cat.-Ni. 00-5523-00). Cells were washed twice with freshly prepared Perm buffer and co- stained with 25 μίΛνεΙΙ Perm-buffer containing fluorescently-labeled antibodies against the cytotoxic lineage transcription factor Eomes, i.e. anti-mouse Eomes ratIgG2a-AlexaFluor488 (eBioscience, Cat.-No. 534875, clone Danl lmag) and - if CD137 was not stained - against the cytotoxic effector molecule granzyme B, i.e. anti- mouse ratIgG2a granzyme B-PE (eBioscience, Cat.-No. 128822, clone 16G6) for 1 h at room temperature. Cells were then washed twice, resuspended in FACS buffer and acquired using laser Fortessa flow cytometer (BD Bioscience with DIVA software) or the 3-laser MACSQuant Analyzer 10 (Miltenyi Biotech) and Flow Jo vlO.0.7 (FlowJo LLC). Gates were set on living CD8+ T cells and CD4+ T cells and the frequency of proliferating cells was determined as well as the expression levels of CD25, Eomes and granzyme B or CD137. The proliferation frequency and frequencys and MFIs of activation markers were blotted against the concentration of used mouse 4- IBB ligand trimer-containing Fc(kih) fusion molecules to display the functional activity. As can be seen in Figure 27, an increase in proliferating CD8+ T cells could be observed for Constructs M.1 and M.2. 6.5 Liver changes in mice treated with anti-murine 4-1BB antibody Lob 12.3
(muIgGl Wt) or with Construct M.2
C57BL/6 mice bearing MC38-muFAP (murine colorectal cancer model) s.c. were treated once per week for 3 weeks with agonistic anti-murine 4- IBB antibodies targeted to FAP
(Efficacy Study 020-GA1401: "Experiment to show efficacy of 4-1BB targeted therapy in combination with a-PD-Ll in MC38-muFAP s.c. model in C57B6 mice."). Antibodies used were Lob 12.3 muIgGl Wt (with "wildtype" Fc, clone Lob 12.3 from BioXcell Catalog*: BE0169) or Construct M.2 with DAPG mutation (inactive Fc). The two antibodies were administered once weekly for three consecutive weeks. Four animals/group were sacrificed 7 days after last treatment and livers examined microscopically. Liver changes were observed only in animals receiving Lob 12.3 muIgGl Wt, consisting in foci of hepatocellular degeneration with accumulation of F4/80 positive macrophages and a lower amount of mixed population of inflammatory cells (mainly lymphocytes) frequently showing a vasocentric distribution. Occasionally single cell necrosis of hepatocytes, and perivascular mononuclear cell infiltrates in portal spaces were noted. No treatment related findings were observed in the liver of animals receiving Construct M.2 (Table 41). Table 41: Incidence of Histopathogical Findings (n=4/group)
Figure imgf000236_0001
Hepatitis, attributed to crosslinking by FcyRs in the liver, has been observed in patients treated with Urelumab BMS-663513 (Ascierto P. A. et al. 2010) and in mouse using the mouse surrogate. The absence of liver findings in animals treated with an antibody with inactive Fc support this hypothesis.
6.6 Determination of pharmacokinetic parameters of human 4- IBB ligand trimer- containing Fc fusion antigen binding molecules
In order to test if the human 4- IBB ligand trimer-containing Fc fusion antigen binding molecules of the invention are suitable for pharmaceutical use, the pharmacokinetic parameters (PK data) such as clearance, volume of distribution or elimination half-time (ti/2) in mice were determined. Thus, the following experiments were carried out:
Experiment A: Single dose PK of Construct 1.2 and Control B in healthy NOG mice
NOG female mice at an average age of 8 to 10 weeks at start of experiment (purchased from Taconic, SOPF facility) were maintained under specific-pathogen-free condition with daily cycles of 12 h light /12 h darkness according to committed guidelines (GV-Solas; Felasa;
TierschG). Experimental study protocol was reviewed and approved by local government (P 2011128). After arrival animals were maintained for one week to get accustomed to new environment and for observation. Continuous health monitoring was carried out on regular basis.
A single dose pharmacokinetic study (SDPK) was performed to evaluate exposure of Construct 1.2 and Control B. An i.v. bolus administration of 2.5 mg/kg was administered to
NOG mice and blood samples were taken at selected time points for pharmacokinetic evaluation. Mouse serum samples were analyzed by ELISA. Biotinylated human 4- IBB, test samples, Digoxygenin labelled anti-huCHl antibody and anti-Digoxygenin detection antibody (POD) were added stepwise to a 96-well streptavidin-coated microtiter plate and incubated after every step for lh at roomtemperature. The plate was washed three times after each step to remove unbound substances. Finally, the peroxidase-bound complex was visualized by adding ABTS substrate solution to form a colored reaction product. The reaction product intensity which was photometrically determined at 405 nm (with reference wavelength at 490 nm) is proportional to the analyte concentration in the serum sample. The calibration range of the standard curve for the constructs was 0.156 to 10 ng/ml, where 3 ng/ml is the lower limit of quantification (LLOQ). Figure 28A shows the decrease in concentration over the time as observed in this experiment.
Experiment B: Single dose PK of Constructs 2.1, 2.3, Control B and Control C in tumor bearing NOG mice humaniced with stem cells A single dose pharmacokinetic study (SDPK) was performed to evaluate exposure of
Construct 2.1, 2.3, Control B and Control C. NSG female mice transferred with human stem cells were delivered by Jackson Laboratories. Mice were maintained under specific -pathogen- free condition with daily cycles of 12 h light /12 h darkness according to committed guidelines (GV-Solas; Felasa; TierschG). Experimental study protocol was reviewed and approved by local government (ZH 193 -2014). After arrival animals were maintained for one week to get accustomed to new environment and for observation. Continuous health monitoring was carried out on regular basis.
Human MKN45 cells (human gastric carcinoma) were originally obtained from ATCC and after expansion deposited in the Glycart internal cell bank. Cells were cultured in DMEM containing 10% FCS. Cells were cultured at 37 °C in a water- saturated atmosphere at 5 % C02. In vitro passage 9 was used for subcutaneous injection, at a viability of 97%. Human fibroblasts NIH-3T3 were engineered at Roche Nutley to express human FAP. Clone 39 was used at an in vitro passage number 12 and at a viability of 98%. 50 microliters cell suspension (1x106 MKN45 cells + 1x106 3T3-huFAP) mixed with 50 microliters Matrigel were injected subcutaneously in the flank of anaesthetized mice. An i.v. bolus administration of 10 mg/kg was administered to humaniced mice when tumor reached an average size of 190 mm . Blood samples were taken at selected time points for pharmacokinetic evaluation. Mouse serum samples were analyzed by ELISA. Biotinylated human 4- IBB, test samples, Digoxygenin labelled anti-huCHl antibody and anti-Digoxygenin detection antibody (POD) were added stepwise to a 96-well streptavidin-coated microtiter plate and incubated after every step for lh at room temperature. The plate was washed three times after each step to remove unbound substances. Finally, the peroxidase-bound complex is visualized by adding ABTS substrate solution to form a colored reaction product. The reaction product intensity which was photometrically determined at 405 nm (with reference wavelength at 490 nm) is proportional to the analyte concentration in the serum sample. The calibration range of the standard curve for the constructs was 0.156 to 10 ng/ml, where 3 ng/ml is the lower limit of quantification (LLOQ). Figure 28B shows the decrease in concentration of the constructs over the time as observed in this experiment.
Experiment C: Single dose PK of Construct 2.1 and 2.3 in healthy NOG mice
NOG female mice at an average ager of 8-10 weeks at start of experiment (purchased from Taconic, SOPF facility) were maintained under specific -pathogen-free condition with daily cycles of 12 h light /12 h darkness according to committed guidelines (GV-Solas; Felasa;
TierschG). Experimental study protocol was reviewed and approved by local government (P 2011128). After arrival animals were maintained for one week to get accustomed to new environment and for observation. Continuous health monitoring was carried out on regular basis. A single dose pharmacokinetic study (SDPK) was performed to evaluate exposure of
Construct 2.1 and 2.3. An i.v. bolus administration of 2.5 mg/kg was administered to NOG mice and blood samples were taken at selected time points for pharmacokinetic evaluation. Mouse serum samples were analyzed by ELISA. Biotinylated human 4- IBB, test samples, Digoxygenin labelled anti-huCHl antibody and anti-Digoxygenin detection antibody (POD) were added stepwise to a 96-well streptavidin-coated microtiter plate and incubated after every step for lh at roomtemperature. The plate is washed three times after each step to remove unbound substances. Finally, the peroxidase-bound complex is visualized by adding ABTS substrate solution to form a colored reaction product. The reaction product intensity, which is photometrically determined at 405 nm (with reference wavelength at 490 nm), is proportional to the analyte concentration in the serum sample. The calibration range of the standard curve for the constructs was 0.156 to 10 ng/ml, where 3 ng/ml is the lower limit of quantification (LLOQ). Figure 28C shows the observed decrease in concentration over the time.
The tested constructs 2.1 and 2.3 are stable enough in the body and possess PK parameters in a suitable range for pharmaceutical development. It can also be concluded from the results that construct 2.1 is slightly more stable.
6.7 FAP prevalence in human tumors
The prevalence of FAP in human tumors was evaluated as described in WO 2014/161845 to get an understanding on possible clinical use of FAP-targeted constructs.
Rat anti-human Seprase antibody (IgG2a, clone D8) from Vitatex (MABS1001) was used to immunostain 2,5 μιη FFPET sections from various tumour indications on the Ventana
Benchmark XT. Sections were subjected to standard CC1 treatment followed by antibody incubation for 60' at 37°C at a concentration of 5 μg/mL in Dako antibody diluent (S3022) and positive staining was detected using the Ultraview DAB detection system (Ventana #760-4456). Matched isotype antibody from Abeam (ab 18450) was used as the negative control. FAP+ stromal infiltrate was present in human tumors of different indications including head and neck squamous cell carcinoma (HNSCC), breast cancer, colorectal cancer (CRC), pancreatic cancer (PAC), gastric cancer, non- small-cell lung carcinoma (NSCLC) and Mesothelioma marking potentially interesting clinical indications for a FAP-targeted constructs (Table 42).
Table 42: FAP prevalence in human tumors
Figure imgf000239_0001
Example 7
7.1 Preparation of CD19 (8B8-018) targeted 4-1BB ligand trimer-containing Fc fusion antigen binding molecules
7.1.1 Preparation, purification and characterization of CD 19 antigen Fc fusion for phage display campaign
In order to express and purify the human and cynomolgus CD 19 ectodomain in a monomeric state (human CD19 see SEQ ID NO:31), the respective DNA fragment was fused to a human IgGl Fc gene segment containing the "knob" mutations (human: SEQ ID NO: 186; cynomolgus: SEQ ID NO: 188) and was transfected with an "Fc-hole" (SEQ ID NO: 86) counterpart (Merchant et al., 1998). An IgA cleavage site (PTPPTP) was introduced between an antigen ectodomain and the Fc knob chain. An Avi tag for directed biotinylation was introduced at the C-terminus of the antigen-Fc knob chain and mutations H435R and Y436F were
introduced in the Fc hole for purification purposes (Jendeberg L. et al, J. Immunological methods, 1997). Combination of the antigen-Fc knob chain containing the S354C/T366W mutations (human: SEQ ID NO: 187; cynomolgus: SEQ ID NO: 189), with a Fc hole chain containing the Y349C/T366S/L368A/ Y407V mutations (SEQ ID NO: 90) allows generation of a heterodimeric Fc fusion fragment which includes a single copy of the CD 19 ectodomain (in analogy to the 4- 1BB construct in Figure 5C). Table 43 lists the cDNA and amino acid sequences of the antigen Fc-fusion construct.
Table 43: cDNA and Amino acid sequences of monomeric human and cynomolgus CD 19 antigen Fc(kih) fusion molecule
SEQ ID NO: Antigen Sequence
86 Nucleotide see Table 32
sequence
Fc hole chain
186 Nucleotide CCCGAGGAACCCCTGGTCGTGAAGGTGGAAGAGGGCGACAAT
GCCGTGCTGCAGTGCCTGAAGGGCACCTCCGATGGCCCTACC
sequence CAGCAGCTGACCTGGTCCAGAGAGAGCCCCCTGAAGCCCT TC human CD 19 CTGAAGCTGTCTCTGGGCCTGCCTGGCCTGGGCATCCATATG antigen Fc AGGCCTCTGGCCATCTGGCTGT TCATCT TCAACGTGTCCCAG
CAGATGGGCGGCT TCTACCTGTGTCAGCCTGGCCCCCCATCT
knob chain GAGAAGGCT TGGCAGCCTGGCTGGACCGTGAACGTGGAAGGA avi tag TCCGGCGAGCTGT TCCGGTGGAACGTGTCCGATCTGGGCGGC
CTGGGATGCGGCCTGAAGAACAGATCTAGCGAGGGCCCCAGC AGCCCCAGCGGCAAACTGATGAGCCCCAAGCTGTACGTGTGG GCCAAGGACAGACCCGAGATCTGGGAGGGCGAGCCTCCT TGC CTGCCCCCTAGAGACAGCCTGAACCAGAGCCTGAGCCAGGAC CTGACAATGGCCCCTGGCAGCACACTGTGGCTGAGCTGTGGC
GTGCCACCCGACTCTGTGTCTAGAGGCCCTCTGAGCTGGACC CACGTGCACCCTAAGGGCCCTAAGAGCCTGCTGAGCCTGGAA CTGAAGGACGACAGGCCCGCCAGAGATATGTGGGTCATGGAA ACCGGCCTGCTGCTGCCTAGAGCCACAGCCCAGGATGCCGGC AAGTACTACTGCCACAGAGGCAACCTGACCATGAGCTTCCAC CTGGAAATCACCGCCAGACCCGTGCTGTGGCACTGGCTGCTG AGAACAGGCGGCTGGAAGGTCGACGCTAGCGGTGGTAGTCCG ACACCTCCGACACCCGGGGGTGGTTCTGCAGACAAAACTCAC ACATGCCCACCGTGCCCAGCACCTGAAGCCGCAGGGGGACCG TCAGTCTTCCTCTTCCCCCCAAAACCCAAGGACACCCTCATG ATCTCCCGGACCCCTGAGGTCACATGCGTGGTGGTGGACGTG AGCCACGAAGACCCTGAGGTCAAGTTCAACTGGTACGTGGAC GGCGTGGAGGTGCATAATGCCAAGACAAAGCCGCGGGAGGAG CAGTACAACAGCACGTACCGTGTGGTCAGCGTCCTCACCGTC CTGCACCAGGACTGGCTGAATGGCAAGGAGTACAAGTGCAAG GTCTCCAACAAAGCCCTCGGAGCCCCCATCGAGAAAACCATC TCCAAAGCCAAAGGGCAGCCCCGAGAACCACAGGTGTACACC CTGCCCCCATGCCGGGATGAGCTGACCAAGAACCAGGTCAGC CTGTGGTGCCTGGTCAAAGGCTTCTATCCCAGCGACATCGCC GTGGAGTGGGAGAGCAATGGGCAGCCGGAGAACAACTACAAG ACCACGCCTCCCGTGCTGGACTCCGACGGCTCCTTCTTCCTC TACAGCAAGCTCACCGTGGACAAGAGCAGGTGGCAGCAGGGG AACGTCTTCTCATGCTCCGTGATGCATGAGGCTCTGCACAAC CACTACACGCAGAAGAGCCTCTCCCTGTCTCCGGGTAAATCC GGAGGCCTGAACGACATCTTCGAGGCCCAGAAGATTGAATGG CACGAG
90 Polypeptide see Table 32
sequence Fc
hole chain
187 Polypeptide PEEPLVVKVEEGDNAVLQCLKGTSDGPTQQLTWSRESPLKPF
LKLSLGLPGLGIHMRPLAIWLFIFNVSQQMGGFYLCQPGPPS
sequence EKAWQPGWTVNVEGSGELFRWNVSDLGGLGCGLKNRSSEGPS human CD 19 SPSGKLMSPKLYVWAKDRPEIWEGEPPCLPPRDSLNQSLSQD antigen Fc LTMAPGSTLWLSCGVPPDSVSRGPLSWTHVHPKGPKSLLSLE
LKDDRPARDMWVMETGLLLPRATAQDAGKYYCHRGNLTMSFH
knob chain LEITARPVLWHWLLRTGGWKVDASGGSPTPPTPGGGSADKTH avi tag TCPPCPAPEAAGGPSVFLFPPKPKDTLMISRTPEVTCVVVDV
SHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTV LHQDWLNGKEYKCKVSNKALGAP IEKTI SKAKGQPREPQVYT LPPCRDELTKNQVSLWCLVKGFYPSDIAVEWESNGQPENNYK TTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHN HYTQKSLSLSPGKSGGLNDIFEAQKIEWHE
188 Nucleotide CCCCAGGAACCCCTGGTCGTGAAGGTGGAAGAGGGCGACAAT
GCCGTGCTCCAGTGCCTGGAAGGCACCTCCGATGGCCCTACA
sequence CAGCAGCTCGTGTGGTGCAGAGACAGCCCCTTCGAGCCCTTC cynomolgus CTGAACCTGTCTCTGGGCCTGCCTGGCATGGGCATCAGAATG CD 19 antigen GGCCCTCTGGGCATCTGGCTGCTGATCTTCAACGTGTCCAAC
CAGACCGGCGGCTTCTACCTGTGTCAGCCTGGCCTGCCAAGC Fc knob GAGAAGGCTTGGCAGCCTGGATGGACCGTGTCCGTGGAAGGA TCTGGCGAGCTGTTCCGGTGGAACGTGTCCGATCTGGGCGGC
chain avi tag CTGGGATGCGGCCTGAAGAACAGAAGCAGCGAGGGCCCTAGC
AGCCCCAGCGGCAAGCTGAATAGCAGCCAGCTGTACGTGTGG GCCAAGGACAGACCCGAGATGTGGGAGGGCGAGCCTGTGTGT GGCCCCCCTAGAGATAGCCTGAACCAGAGCCTGAGCCAGGAC CTGACAATGGCCCCTGGCAGCACACTGTGGCTGAGCTGTGGC GTGCCACCCGACTCTGTGTCCAGAGGCCCTCTGAGCTGGACA CACGTGCGGCCAAAGGGCCCTAAGAGCAGCCTGCTGAGCCTG GAACTGAAGGACGACCGGCCCGACCGGGATATGTGGGTGGTG GATACAGGCCTGCTGCTGACCAGAGCCACAGCCCAGGATGCC GGCAAGTACTACTGCCACAGAGGCAACTGGACCAAGAGCTTT TACCTGGAAATCACCGCCAGACCCGCCCTGTGGCACTGGCTG CTGAGAATCGGAGGCTGGAAGGTCGACGCTAGCGGTGGTAGT CCGACACCTCCGACACCCGGGGGTGGTTCTGCAGACAAAACT CACACATGCCCACCGTGCCCAGCACCTGAAGCCGCAGGGGGA CCGTCAGTCTTCCTCTTCCCCCCAAAACCCAAGGACACCCTC ATGATCTCCCGGACCCCTGAGGTCACATGCGTGGTGGTGGAC GTGAGCCACGAAGACCCTGAGGTCAAGTTCAACTGGTACGTG GACGGCGTGGAGGTGCATAATGCCAAGACAAAGCCGCGGGAG GAGCAGTACAACAGCACGTACCGTGTGGTCAGCGTCCTCACC GTCCTGCACCAGGACTGGCTGAATGGCAAGGAGTACAAGTGC AAGGTCTCCAACAAAGCCCTCGGAGCCCCCATCGAGAAAACC ATCTCCAAAGCCAAAGGGCAGCCCCGAGAACCACAGGTGTAC ACCCTGCCCCCATGCCGGGATGAGCTGACCAAGAACCAGGTC AGCCTGTGGTGCCTGGTCAAAGGCTTCTATCCCAGCGACATC GCCGTGGAGTGGGAGAGCAATGGGCAGCCGGAGAACAACTAC AAGACCACGCCTCCCGTGCTGGACTCCGACGGCTCCTTCTTC CTCTACAGCAAGCTCACCGTGGACAAGAGCAGGTGGCAGCAG GGGAACGTCTTCTCATGCTCCGTGATGCATGAGGCTCTGCAC AACCACTACACGCAGAAGAGCCTCTCCCTGTCTCCGGGTAAA TCCGGAGGCCTGAACGACATCTTCGAGGCCCAGAAGATTGAA TGGCACGAG
Polypeptide PQEPLVVKVEEGDNAVLQCLEGTSDGPTQQLVWCRDSPFEPF
LNLSLGLPGMGIRMGPLGIWLLIFNVSNQTGGFYLCQPGLPS
sequence EKAWQPGWTVSVEGSGELFRWNVSDLGGLGCGLKNRSSEGPS cynomolgus SPSGKLNSSQLYVWAKDRPEMWEGEPVCGPPRDSLNQSLSQD CD 19 antigen LTMAPGSTLWLSCGVPPDSVSRGPLSWTHVRPKGPKSSLLSL
ELKDDRPDRDMWVVDTGLLLTRATAQDAGKYYCHRGNWTKSF
Fc knob YLEITARPALWHWLLRIGGWKVDASGGSPTPPTPGGGSADKT chain avi tag HTCPPCPAPEAAGGPSVFLFPPKPKDTLMI SRTPEVTCVVVD
VSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLT VLHQDWLNGKEYKCKVSNKALGAP IEKTI SKAKGQPREPQVY TLPPCRDELTKNQVSLWCLVKGFYPSDIAVEWESNGQPENNY KTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALH NHYTQKSLSLSPGKSGGLNDIFEAQKIEWHE For the production of the monomeric antigen/Fc fusion molecules, exponentially growing suspension CHO cells were co-transfected with two plasmids encoding the two components of fusion protein (knob and hole chains) using standard methods.
Secreted protein was purified from cell culture supernatant by affinity chromatography using Protein A, followed by size exclusion chromatography. For affinity chromatography, the supernatant was loaded on a MabSelect Sure column volume (CV) = 5-15 mL, resin from GE Healthcare) equilibrated with Sodium Phosphate (20 mM), Sodium Citrate (20 mM), 0.5M sodium chloride buffer (pH 7.5). Unbound protein was removed by washing with at least 6 column volumes of the same buffer. The bound protein was eluted using a linear gradient; step 1, 10 CV from 0 to 60% elution buffer (20 mM sodium citrate, 500 mM Sodium chloride buffer (pH 2.5)); step 2, 2 CV from 60 to 100% elution buffer. For the linear gradient an additional 2 column volumes step elution with 100% elution buffer was applied.
The pH of collected fractions was adjusted by adding 1/40 (v/v) of 2M Tris, pH8.0. The protein was concentrated and filtered prior to loading on a HiLoad Superdex 200 column (GE Healthcare) equilibrated with 2mM MOPS, 150 mM sodium chloride, 0.02 % (w/v) sodium azide solution of pH 7.4.
Table 44 summarizes the yield and final monomer content of monomeric human and cynomolgus CD 19 antigen Fc(kih) fusion protein.
Table 44 - Biochemical analysis of monomeric human and cynomolgus CD 19 antigen Fc(kih) fusion protein
Figure imgf000243_0001
Part of the purified antigen was in vitro biotinylated using the BirA biotin-protein ligase standard reaction kit (Avidity, Cat. # BirA500) according to the manufacturer's instructions. The biotinylation degree for the human CD19-containing fusion was 94 %, for the respective cynomolgus CD 19 construct 100%. The biotinylated protein was then used for selection, screening and characterization of affinity-matured 8B8-derived clones devoid of the de- amidation hotspots N27d and N28. 7.1.2 Generation of anti-CD19 clone 8B8-018
7.1.2.1 Immunization and generation of mouse anti-human CD19 antibodies
(hybridomas)
Balb/c mice were immunized six times and boosted with CD19-transfected HEK293 cells (mean receptor density 35,000 per cell). The immune response was monitored by testing serum samples with a CD19-cell-ELISA on human CD19-transfected NIH-3T3 cells. Spleen cells from mice with sufficient titers of anti-human CD 19 antibody were used for immortalization by fusion with mouse myeloma cell line P3X63 Ag8.653. Three fusions were carried out and hybridoma supernatants screened by cell-ELISA on human CD19-transfected NIH-3T3 cells and FACS binding assay using Daudi (CD 19+) and CD 19- cells for anti-human CD 19 specific antibodies (see Example 1 of WO 2011/147834).
7.1.2.2 Hybridoma screening and cell biological functional evaluation of anti-CD19 antibody
Cell-ELISA for screening antibodies against human CD 19
A cell ELISA was applied for screening of hybridomas, and to identify those hybridomas that secrete antibodies against human-CD 19. NIH3T3 cells transfected with human-CD 19 were used as positive cells; non-transfected NIH3T3 cells were used as negative control cells. For the assessment of the positive hybridomas the OD ratio between transfected and non-transfected NIH3T3 cells was quantified.
- Culture Medium: DMEM high glucose (4.5 mg/ml), 10 % FCS, Na-Pyruvate, NEAA, Glutamine
Antibodies positive control: anti CD 19 monoclonal antibody (IgGl) Pharmingen Cat# 555409 c = 1 mg/ml
- Detection antibody: Goat anti-Mouse IgG (H+L) HRP Conjugate Bio-Rad Cat# 170- 06516
- Dilution 1: 2000 in lx ELISA Blocking Reagent
Other reagents: Fibronectin Roche Cat# 838039 c = 1 mg/ml
Glutardialdehyde: 25 % stock solution // Grade Agar Scientific #R102 final concentration: 0.05 % in PBS
- ELISA Blocking Reagent: lOx stock solution // Roche Cat# 1112589
- TMB substrate: Roche Cat# 11432559
- Stop Solution: 1 M H2S04
- BioRad Cat# 170-6516 Dilution 1 : 2000 in lx ELISA Blocking Reagent Day 1:
Fibronectin coating: 5 μg/cm2 in PBS; 96well plate = 32 cm2; 160 μg/plate in 6 ml
- PBS, 50 μΐ/well
incubate 45 min at RT, aspirate coating solution
- Seed 1.25 x 104 cells/well in 50 μΐ culture medium in a 96well plate
incubate 40 hours at 37 °C
add to upper half of the plate: NIH3T3 cells expressing CD19
add to lower half of the plate: non-transfected NIH3T3 cells
Day 3:
- Addition of positive control antibody or samples (supernatant or mouse serum) in 50 μΐ culture medium
- incubate for 2 h at 4 °C
Remove medium, fix cells with 100 μΐ Glutardialdehyde (0.05 % in PBS)
- Wash two times with 200 μΐ PBS
- Addition of detection antibody 1:2000, 50 μΐ/well
incubate 2 h at RT
wash three times with 200 μΐ PBS
- add 50 μΐ TMB, incubate for 30 min. at RT,
stop by addition of 25 μΐ 1 M H2S04; read extinction at 450nm/620nm
- Calculation of results: ratio OD NIH3T3 CD 19 : OD NIH3T3 non-transfected
The selected antibody demonstrated specific binding to CD 19 transfected NIH3T3 cells as compared to untransfected NIH3T3 cells (see Example 2 of WO 2011/147834).
7.1.2.3 Humanization of anti-CD19 antibody
The CD 19 binding specificity of the murine antibody was transferred onto a human acceptor framework to eliminate potential immunogenicity issues arising from sequence stretches that the human body will recognize as foreign. This was done by engrafting the entire complementary determining regions (CDR) of the murine (donor) antibody onto a human (acceptor) antibody framework, and is called CDR-grafting or antibody humanization.
The murine amino acid sequence was aligned with a collection of human germ- line antibody V genes, and sorted according to sequence identity and homology. Before selecting one particular acceptor sequence, the so-called canonical loop structures of the donor antibody have to be determined (Morea, V., et al., Methods, Vol 20, Issue 3 (2000) 267-279). These canonical loop structures are determined by the type of residues present at the so-called canonical positions. These positions lie (partially) outside of the CDR regions, and have to be kept functionally equivalent in the final construct in order to retain the CDR conformation of the parental (donor) antibody. The human germ-line sequence VBASE_VH1_1 was chosen as the acceptor for the heavy chain and sequence VBASE_VK2_5 was chosen for the light chain.
7.1.2.4 Removal of deamidation hotspots
It has been found that the wild- type humanized anti-human CD 19 antibody has three deamidation hotspots in the HVR-L1: NSNGNT (SEQ ID NO: 190). Additionally it has been found that in the HVR-H2 a further deamidation hotspot is present: KFNG (SEQ ID NO: 191). To address the deamidation hotspot in the HVR-H2 an N (Asn) to Q (Gin) point mutation at position 64 (numbering according to Kabat) has been introduced. Thus, the antibody as reported herein has a HVR-H2 comprising the amino acid sequence TEKFQGRVTM (SEQ ID NO: 192).
To address the deamidation hotspots in the light chain and to obtain a humanized anti- human CD 19 antibody with improved deamidation stability individual mutations at Kabat position 27d, 27e, 28 and 29 and a double mutation at positions 27e and 28 (numbering according to Kabat) were introduced. In total 9 variants (var.l to var.9) of the wild-type humanized antibody (var.O) have been generated (see Table 45).
Table 45: Variants of humanized wild-type CD 19 antibody
Kabat 2222 Kabat 6
po s it i on 77 8 9 po s it i on 4
LC : de HC :
var . 0 : wt QSLENSNGNTYLNW TEKFNGKATM
var . 1 : N27 dH QSLEHSNGNTYLNW TEKFQGRVTM
var . 2 : N27 dQ QSLEQSNGNTYLNW TEKFQGRVTM
var . 3 : S 27 eA QSLENANGNTYLNW TEKFQGRVTM
var . 4 : S 27 eV QSLENV GNTYLNW TEKFQGRVTM
var . 5 : S 27 eP QSLENPNGNTYLNW TEKFQGRVTM
var . 6 : N2 8 Q QSLENSQGNTYLNW TEKFQGRVTM
var . 7 : G2 9A QSLENSNANTYLNW TEKFQGRVTM
var . 8 : G2 9V QSLENSNV TYLNW TEKFQGRVTM
var . 9 : S 27 eP /N2 3 S QSLENPSGNTYLNW TEKFQGRVTM variant→ 0 1 2 3 4 5 6 7 8 9 ^parameter
KD (BIAcore)
5 250 136 2 1 6 54 4 16 45
[nM]
tl/2
- 0.1 1.1 105.2 191.5 43.6 4.4 51.5 17.6 4
[min] variant→ 0 1 2 3 4 5 6 7 8 9
^parameter
human CD 19
binding after
pH 7.4 46 0 75 84 85 95 91 72 83 83 incubation
[ ]
human CD 19
binding after
pH 6.0 90 0 95 95 97 99 97 86 91 87 incubation
[ ]
SEC main
peak after
> 95 > 95 > 95 > 95 > 95 > 95 > 95 > 95 > 95 incubation
[ ]
It has been found that with a single mutation at position 27e according to Kabat from S (serine) to P (proline) all deamidation hotspots in the HVR-L1 can be addressed. This is a mutation not of the deamidation prone N (asparagine) residue but of a neighboring residue. Thus, the antibody as reported herein has a HVR-L1 comprising the amino acid sequence
LENPNGNT (SEQ ID NO: 193). In one embodiment the humanized anti-human CD 19 antibody comprises a HVR-L1 that has the amino acid sequence LENPSGNT (SEQ ID NO: 194).
Additionally these antibodies maintain the cross-reactivity to cynomolgus CD19 as shown in the following Table 46.
Figure imgf000247_0001
The wild- type humanized anti-human CD 19 antibody (var.O) shows after purification approx. 7.5 % deamidation. After storage for two weeks at pH 7.4 the amount of deamidated antibody is increased to approx. 18.5 %. The variant antibody with an S27eP mutation (var.5) shows approx. 2% deamidation and 2% succinimide formation after purification. During storagf at pH 7.4 for two weeks only approx. 7.5 % deamidated antibody is present. Var. 5 is named clone 8B8-018 and was elected for the preparation of CD19-targeted TNF family ligand trimer- containing antigen binding molecules. 7.1.3 Preparation of monovalent CD19(8B8-018) targeted 4-lBB ligand (71-254) trimer-containing Fc (kih) fusion antigen binding molecule with crossed CH1-CL domains with charged residues (Construct 3.1)
A polypeptide containing two ectodomains of 4-lBB ligand (71-254), separated by (G4S)2 linkers, and fused to the human IgGl-CL domain, was cloned as depicted in Figure 29A: human 4-lBB ligand, (G4S)2 connector, human 4-lBB ligand, (G4S)2 connector, human CL. A polypeptide containing one ectodomain of 4-lBB ligand (71-254) and fused to the human IgGl- CH domain, was cloned as described in Figure 29B: human 4- IBB ligand, (G4S)2 connector, human CH. The polypeptide encoding the dimeric 4- IBB ligand fused to human CL domain was subcloned in frame with the human IgGl heavy chain CH2 and CH3 domains on the knob (Merchant, Zhu et al. 1998). To improve correct pairing the following mutations have been introduced in the crossed CH-CL. In the dimeric 4- IBB ligand fused to human CL, E123R and Q124K. In the monomeric 4- IBB ligand fused to human CHI, K147E and K213E. The variable region of heavy and light chain DNA sequences encoding a binder specific for CD 19, clone 8B8-018, were subcloned in frame with either the constant heavy chain of the hole or the constant light chain of human IgGl. The Pro329Gly, Leu234Ala and Leu235Ala mutations have been introduced in the constant region of the knob and hole heavy chains to abrogate binding to Fc gamma receptors according to the method described in WO 2012/130831. Combination of the dimeric ligand-Fc knob chain containing the S354C/T366W mutations, the monomeric CHI fusion, the targeted anti-CD 19-Fc hole chain containing the
Y349C/T366S/L368A/Y407V mutations and the anti-CD 19 light chain allows generation of a heterodimer, which includes an assembled trimeric 4-lBB ligand and a CD19 binding Fab
(Figure 30, Construct 3.1). Table 47 shows the cDNA and amino acid sequences of the monovalent CD19(8B8-018) targeted split trimeric 4- IBB ligand (71-254) Fc (kih) fusion antigen binding molecule with crossed CH-CL and charged residues (construct 3.1).
Table 47: cDNA and amino acid sequences of monovalent CD19 (8B8-018) targeted split trimeric 4-lBB ligand (71-254) Fc (kih) fusion containing CH-CL cross with charged residues (construct 3.1). * for charged residues
SEQ ID Description Sequence
NO:
129 Nucleotide see Table 3
sequence Dimeric
hu 4-lBBL (71- 254) - CL* Fc
knob chain
130 Nucleotide see Table 3
sequence
Monomelic hu
4-1BBL (71-254)
- CHI*
203 Nucleotide CAGGTCCAGCTGGTGCAGTCCGGCGCCGAGGTCAAGAA sequence anti- ACCCGGGGCTTCTGTGAAGGTTTCATGCAAGGCAAGCG CD19(8B8-018) GATACACCTTCACCGACTATATCATGCATTGGGTCAGGC Fc hole chain AGGCCCCTGGCCAAGGTCTCGAATGGATGGGCTACATTA
ACCCATATAATGATGGCTCCAAATACACCGAGAAGTTTC
AGGGAAGAGTCACTATGACATCTGACACCAGTATCAGC
ACTGCTTACATGGAGCTGTCCCGCCTTCGGTCTGATGAC
ACCGCAGTGTATTACTGTGCCAGGGGCACATATTACTAC
GGCTCAGCTCTGTTCGACTATTGGGGGCAGGGAACCACA
GTAACCGTGAGCTCCGCTAGCACCAAGGGCCCCTCCGTG
TTCCCCCTGGCCCCCAGCAGCAAGAGCACCAGCGGCGG
CACAGCCGCTCTGGGCTGCCTGGTCAAGGACTACTTCCC
CGAGCCCGTGACCGTGTCCTGGAACAGCGGAGCCCTGA
CCTCCGGCGTGCACACCTTCCCCGCCGTGCTGCAGAGTT
CTGGCCTGTATAGCCTGAGCAGCGTGGTCACCGTGCCTT
CTAGCAGCCTGGGCACCCAGACCTACATCTGCAACGTG
AACCACAAGCCCAGCAACACCAAGGTGGACAAGAAGGT
GGAGCCCAAGAGCTGCGACAAAACTCACACATGCCCAC
CGTGCCCAGCACCTGAAGCTGCAGGGGGACCGTCAGTC
TTCCTCTTCCCCCCAAAACCCAAGGACACCCTCATGATC
TCCCGGACCCCTGAGGTCACATGCGTGGTGGTGGACGTG
AGCCACGAAGACCCTGAGGTCAAGTTCAACTGGTACGT
GGACGGCGTGGAGGTGCATAATGCCAAGACAAAGCCGC
GGGAGGAGCAGTACAACAGCACGTACCGTGTGGTCAGC
GTCCTCACCGTCCTGCACCAGGACTGGCTGAATGGCAAG
GAGTACAAGTGCAAGGTCTCCAACAAAGCCCTCGGCGC
CCCCATCGAGAAAACCATCTCCAAAGCCAAAGGGCAGC
CCCGAGAACCACAGGTGTGCACCCTGCCCCCATCCCGG
GATGAGCTGACCAAGAACCAGGTCAGCCTCTCGTGCGC
AGTCAAAGGCTTCTATCCCAGCGACATCGCCGTGGAGTG
GGAGAGCAATGGGCAGCCGGAGAACAACTACAAGACC
ACGCCTCCCGTGCTGGACTCCGACGGCTCCTTCTTCCTC
GTGAGCAAGCTCACCGTGGACAAGAGCAGGTGGCAGCA
GGGGAACGTCTTCTCATGCTCCGTGATGCATGAGGCTCT
GCACAACCACTACACGCAGAAGAGCCTCTCCCTGTCTCC
GGGTAAA
204 Nucleotide GACATCGTCATGACCCAGACACCCCTGTCCCTCTCTGTG sequence anti- ACCCCTGGCCAGCCAGCCTCAATTAGCTGCAAGTCCTCT CD19(8B8-018) CAAAGTCTGGAGAACCCCAATGGGAACACTTACCTTAAT light chain TGGTATCTGCAGAAACCCGGACAATCCCCTCAACTCCTG
ATCTACAGGGTCTCTAAGAGATTCTCAGGCGTGCCAGAT
CGCTTTAGCGGTTCCGGGTCTGGCACAGACTTCACCTTG
AAGATTAGTCGGGTTGAAGCTGAGGATGTGGGAGTCTA
TTACTGTCTGCAGCTCACTCATGTGCCCTACACCTTTGGT
CAGGGCACAAAACTGGAGATCAAGCGGACCGTGGCCGC TCCCTCCGTGTTCATCTTCCCACCCTCCGACGAGCAGCT
GAAGTCCGGCACCGCCAGCGTGGTGTGCCTGCTGAACA
ACTTCTACCCCCGCGAGGCCAAGGTGCAGTGGAAGGTG
GACAACGCCCTGCAGTCCGGCAACTCCCAGGAATCCGT
GACCGAGCAGGACTCCAAGGACAGCACCTACTCCCTGT
CCTCCACCCTGACCCTGTCCAAGGCCGACTACGAGAAGC
ACAAGGTGTACGCCTGCGAAGTGACCCACCAGGGCCTG
TCCAGCCCCGTGACCAAGTCCTTCAACCGGGGCGAGTGC
115 Dimeric hu 4- see Table 3
1BBL (71-254) - CL* Fc knob
chain
116 Monomeric hu see Table 3
4-1BBL (71-254)
- CHI*
205 anti-CD19(8B8- QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMHWVRQ
018) Fc hole APGQGLEWMGYINPYNDGSKYTEKFQGRVTMTSDTSISTA chain YMELSRLRSDDTAVYYCARGTYYYGSALFDYWGQGTTVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVT
VSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQ
TYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAG
GPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNW
YVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLN
GKEYKCKVSNKALGAPIEKTISKAKGQPREPQVCTLPPSRD
ELTKNQVSLSCAVKGFYPSDIAVEWESNGQPENNYKTTPP
VLDSDGSFFLVSKLTVDKSRWQQGNVFSCSVMHEALHNH
YTQKSLSLSPGK
206 anti-CD19(8B8- DIVMTQTPLSLSVTPGQPASISCKSSQSLENPNGNTYLNWY
018) light chain LQKPGQSPQLLIYRVSKRFSGVPDRFSGSGSGTDFTLKISRV
EAEDVGVYYCLQLTHVPYTFGQGTKLEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGN
SQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTH
QGLS SP VTKSFNRGEC
7.1.4 Preparation of monovalent CD19(8B8-018) targeted 4-1BB ligand (71-254) trimer-containing Fc (kih) fusion antigen binding molecule with crossed CH1-CL domains without charged residues (Construct 3.2) A polypeptide containing two ectodomains of 4-1BB ligand (71-254), separated by (G4S)2 linkers, and fused to the human IgGl-CL domain, was cloned in analogy as depicted in Figure (29 A), but without amino acid mutations in the CL domain: human 4- IBB ligand, (G4S)2 connector, human 4- IBB ligand, (G4S)2 connector, human CL. A polypeptide containing one ectodomain of 4- IBB ligand (71-254) and fused to the human IgGl-CHl domain, was cloned in analogy as depicted in Figure (29B), but without amino acid mutations in the CHI domain: human 4-1BB ligand, (G4S)2 connector, human CHI. The variable region of heavy and light chain DNA sequences encoding a binder specific for CD19, clone 8B8-018, were subcloned in frame with either the constant heavy chain of the hole or the constant light chain of human IgGl.
The Pro329Gly, Leu234Ala and Leu235Ala mutations have been introduced in the constant region of the knob and hole heavy chains to abrogate binding to Fc gamma receptors according to the method described in WO 2012/130831. Combination of the dimeric ligand-Fc knob chain containing the S354C/T366W mutations, the monomeric CHI fusion, the targeted anti-CD 19-Fc hole chain containing the Y349C/T366S/L368A/Y407V mutations and the anti- CD 19 light chain allows generation of a heterodimer, which includes an assembled trimeric 4- IBB ligand and a CD19-binding Fab (Figure 30, Construct 3.2).
Table 48 shows the cDNA and amino acid sequences of the monovalent CD19(8B8-018) targeted split trimeric 4- IBB ligand (71-254) Fc (kih) fusion antigen binding molecule containing crossed CH-CL cross without charged residues (construct 3.2).
Table 48: cDNA and amino acid sequences of monovalent CD19(8B8-018) targeted split trimeric 4-1BB ligand (71-254) Fc (kih) fusion containing CH-CL cross without charged residues (construct 3.2).
SEQ ID Description Sequence
NO:
165 Nucleotide see Table 22
sequence dimeric
ligand (71-254)- CL Fc knob chain
166 Nucleotide see Table 22
sequence
monomeric hu
4-1BBL (71-254)
- CHI
203 Nucleotide see Table 47
sequence anti- CD19(8B8-018)
Fc hole chain
204 Nucleotide see Table 47
sequence anti- CD19(8B8-018)
light chain
117 Dimeric ligand see Table 22
(71-254) - CL Fc
knob chain
118 Monomeric see Table 22
ligand (71-254) - CHI
205 anti-CD19(8B8- see Table 47
018) Fc hole
chain
206 anti-CD19(8B8- see Table 47
018) light chain
7.1.5 Preparation of bivalent CD19(8B8-018) targeted 4-lBB ligand (71-254) trimer- containing Fc (kih) fusion antigen binding (Construct 3.3)
A polypeptide containing two ectodomains of 4-lBB ligand (71-254), separated by (G4S)2 linkers was fused to the C-terminus of human IgGl Fc hole chain, as depicted in Figure 29C: human IgGl Fc hole, (G4S)2 connector, human 4-lBB ligand, (G4S)2 connector, human 4-lBB ligand. A polypeptide containing one ectodomain of 4- IBB ligand (71-254) and fused to the C- terminus of human IgGl Fc knob chain as described in Figure 29D: human IgGl Fc knob, (G4S)2 connector, human 4- IBB ligand. The variable region of heavy and light chain DNA sequences encoding a binder specific for CD19, clone 8B8-018, were subcloned in frame with either the constant heavy chain of the hole, the knob or the constant light chain of human IgGl . The Pro329Gly, Leu234Ala and Leu235Ala mutations have been introduced in the constant region of the knob and hole heavy chains to abrogate binding to Fc gamma receptors according to the method described in WO 2012/130831. Combination of the anti-CD19 hulgGI hole dimeric ligand chain containing the Y349C/T366S/L368A/Y407V mutations, the anti-CD19 hulgGI knob monomeric ligand chain containing the S354C/T366W mutations and the anti-CD 19 light chain allows generation of a heterodimer, which includes an assembled trimeric 4-lBB ligand and two CD19 binding Fabs (Figure 30, construct 3.3). Table 49 shows the cDNA and amino acid sequences of the bivalent CD19(8B8-018) targeted split trimeric 4- IBB ligand (71-254) Fc (kih) fusion antigen binding molecule (construct 3.3).
Table 49: Base pair sequences of bivalent CD19(8B8-018) targeted split trimeric 4-lBB ligand Fc (kih) PGLALA fusion (construct 3.3)
SEQ ID Description Sequence
NO:
207 Nucleotide CAGGTCCAGCTGGTGCAGTCCGGCGCCGAGGTCAAGAA sequence anti- ACCCGGGGCTTCTGTGAAGGTTTCATGCAAGGCAAGCG CD19(8B8-018) GATACACCTTCACCGACTATATCATGCATTGGGTCAGGC Fc hole dimeric AGGCCCCTGGCCAAGGTCTCGAATGGATGGGCTACATTA
ACCCATATAATGATGGCTCCAAATACACCGAGAAGTTTC ligand chain | AGGGAAGAGTCACTATGACATCTGACACCAGTATCAGC
ACTGCTTACATGGAGCTGTCCCGCCTTCGGTCTGATGAC ACCGCAGTGTATTACTGTGCCAGGGGCACATATTACTAC GGCTCAGCTCTGTTCGACTATTGGGGGCAGGGAACCACA GTAACCGTGAGCTCCGCTAGCACCAAGGGCCCCTCCGTG TTCCCCCTGGCCCCCAGCAGCAAGAGCACCAGCGGCGG CACAGCCGCTCTGGGCTGCCTGGTCAAGGACTACTTCCC CGAGCCCGTGACCGTGTCCTGGAACAGCGGAGCCCTGA CCTCCGGCGTGCACACCTTCCCCGCCGTGCTGCAGAGTT CTGGCCTGTATAGCCTGAGCAGCGTGGTCACCGTGCCTT CTAGCAGCCTGGGCACCCAGACCTACATCTGCAACGTG AACCACAAGCCCAGCAACACCAAGGTGGACAAGAAGGT GGAGCCCAAGAGCTGCGACAAAACTCACACATGCCCAC CGTGCCCAGCACCTGAAGCTGCAGGGGGACCGTCAGTC TTCCTCTTCCCCCCAAAACCCAAGGACACCCTCATGATC TCCCGGACCCCTGAGGTCACATGCGTGGTGGTGGACGTG AGCCACGAAGACCCTGAGGTCAAGTTCAACTGGTACGT GGACGGCGTGGAGGTGCATAATGCCAAGACAAAGCCGC GGGAGGAGCAGTACAACAGCACGTACCGTGTGGTCAGC GTCCTCACCGTCCTGCACCAGGACTGGCTGAATGGCAAG GAGTACAAGTGCAAGGTCTCCAACAAAGCCCTCGGCGC CCCCATCGAGAAAACCATCTCCAAAGCCAAAGGGCAGC CCCGAGAACCACAGGTGTGCACCCTGCCCCCATCCCGG GATGAGCTGACCAAGAACCAGGTCAGCCTCTCGTGCGC AGTCAAAGGCTTCTATCCCAGCGACATCGCCGTGGAGTG GGAGAGCAATGGGCAGCCGGAGAACAACTACAAGACC ACGCCTCCCGTGCTGGACTCCGACGGCTCCTTCTTCCTC GTGAGCAAGCTCACCGTGGACAAGAGCAGGTGGCAGCA GGGGAACGTCTTCTCATGCTCCGTGATGCATGAGGCTCT GCACAACCACTACACGCAGAAGAGCCTCTCCCTGTCTCC GGGTGGAGGCGGCGGAAGCGGAGGAGGAGGATCCAGA GAGGGCCCTGAGCTGAGCCCCGATGATCCTGCTGGACT GCTGGACCTGCGGCAGGGCATGTTTGCTCAGCTGGTGGC CCAGAACGTGCTGCTGATCGATGGCCCCCTGTCCTGGTA CAGCGATCCTGGACTGGCTGGCGTGTCACTGACAGGCG GCCTGAGCTACAAAGAGGACACCAAAGAACTGGTGGTG GCCAAGGCCGGCGTGTACTACGTGTTCTTTCAGCTGGAA CTGCGGAGAGTGGTGGCCGGCGAAGGATCTGGCTCTGT GTCTCTGGCCCTGCATCTGCAGCCTCTGAGAAGCGCTGC TGGCGCTGCAGCTCTGGCACTGACAGTGGATCTGCCTCC TGCCAGCTCCGAGGCCCGGAATAGCGCATTTGGGTTTCA AGGCAGGCTGCTGCACCTGTCTGCCGGCCAGAGGCTGG GAGTGCATCTGCACACAGAGGCCAGGGCTAGACACGCC TGGCAGCTGACACAGGGCGCTACAGTGCTGGGCCTGTTC AGAGTGACCCCCGAGATTCCAGCCGGCCTGCCTTCTCCA AGAAGCGAAGGCGGAGGCGGATCTGGCGGCGGAGGATC TAGAGAGGGACCCGAACTGTCCCCTGACGATCCAGCCG GGCTGCTGGATCTGAGACAGGGAATGTTCGCCCAGCTG GTGGCTCAGAATGTGCTGCTGATTGACGGACCTCTGAGC TGGTACTCCGACCCAGGGCTGGCAGGGGTGTCCCTGACT GGGGGACTGTCCTACAAAGAAGATACAAAAGAACTGGT GGTGGCTAAAGCTGGGGTGTACTATGTGTTTTTTCAGCT GGAACTGAGGCGGGTGGTGGCTGGGGAGGGCTCAGGAT CTGTGTCCCTGGCTCTGCATCTGCAGCCACTGCGCTCTG CTGCTGGCGCAGCTGCACTGGCTCTGACTGTGGACCTGC
CACCAGCCTCTAGCGAGGCCAGAAACAGCGCCTTCGGG
TTCCAAGGACGCCTGCTGCATCTGAGCGCCGGACAGCG
CCTGGGAGTGCATCTGCATACTGAAGCCAGAGCCCGGC
ATGCTTGGCAGCTGACTCAGGGGGCAACTGTGCTGGGA
CTGTTTCGCGTGACACCTGAGATCCCTGCCGGACTGCCA
AGCCCTAGATCAGAA
Nucleotide CAGGTCCAGCTGGTGCAGTCCGGCGCCGAGGTCAAGAA sequence anti- ACCCGGGGCTTCTGTGAAGGTTTCATGCAAGGCAAGCG CD19(8B8-018) GATACACCTTCACCGACTATATCATGCATTGGGTCAGGC Fc knob AGGCCCCTGGCCAAGGTCTCGAATGGATGGGCTACATTA
ACCCATATAATGATGGCTCCAAATACACCGAGAAGTTTC
monomeric ligand
AGGGAAGAGTCACTATGACATCTGACACCAGTATCAGC
ACTGCTTACATGGAGCTGTCCCGCCTTCGGTCTGATGAC
ACCGCAGTGTATTACTGTGCCAGGGGCACATATTACTAC
GGCTCAGCTCTGTTCGACTATTGGGGGCAGGGAACCACA
GTAACCGTGAGCTCCGCTAGCACCAAGGGCCCATCGGT
CTTCCCCCTGGCACCCTCCTCCAAGAGCACCTCTGGGGG
CACAGCGGCCCTGGGCTGCCTGGTCAAGGACTACTTCCC
CGAACCGGTGACGGTGTCGTGGAACTCAGGCGCCCTGA
CCAGCGGCGTGCACACCTTCCCGGCTGTCCTACAGTCCT
CAGGACTCTACTCCCTCAGCAGCGTGGTGACCGTGCCCT
CCAGCAGCTTGGGCACCCAGACCTACATCTGCAACGTG
AATCACAAGCCCAGCAACACCAAGGTGGACAAGAAAGT
TGAGCCCAAATCTTGTGACAAAACTCACACATGCCCACC
GTGCCCAGCACCTGAAGCTGCAGGGGGACCGTCAGTCT
TCCTCTTCCCCCCAAAACCCAAGGACACCCTCATGATCT
CCCGGACCCCTGAGGTCACATGCGTGGTGGTGGACGTG
AGCCACGAAGACCCTGAGGTCAAGTTCAACTGGTACGT
GGACGGCGTGGAGGTGCATAATGCCAAGACAAAGCCGC
GGGAGGAGCAGTACAACAGCACGTACCGTGTGGTCAGC
GTCCTCACCGTCCTGCACCAGGACTGGCTGAATGGCAAG
GAGTACAAGTGCAAGGTCTCCAACAAAGCCCTCGGCGC
CCCCATCGAGAAAACCATCTCCAAAGCCAAAGGGCAGC
CCCGAGAACCACAGGTGTACACCCTGCCCCCCTGCAGA
GATGAGCTGACCAAGAACCAGGTGTCCCTGTGGTGTCTG
GTCAAGGGCTTCTACCCCAGCGATATCGCCGTGGAGTGG
GAGAGCAACGGCCAGCCTGAGAACAACTACAAGACCAC
CCCCCCTGTGCTGGACAGCGACGGCAGCTTCTTCCTGTA
CTCCAAACTGACCGTGGACAAGAGCCGGTGGCAGCAGG
GCAACGTGTTCAGCTGCAGCGTGATGCACGAGGCCCTG
CACAACCACTACACCCAGAAGTCCCTGAGCCTGAGCCC
CGGCGGAGGCGGCGGAAGCGGAGGAGGAGGATCCAGA
GAGGGCCCTGAGCTGAGCCCCGATGATCCTGCTGGACT
GCTGGACCTGCGGCAGGGCATGTTTGCTCAGCTGGTGGC
CCAGAACGTGCTGCTGATCGATGGCCCCCTGTCCTGGTA
CAGCGATCCTGGACTGGCTGGCGTGTCACTGACAGGCG
GCCTGAGCTACAAAGAGGACACCAAAGAACTGGTGGTG
GCCAAGGCCGGCGTGTACTACGTGTTCTTTCAGCTGGAA
CTGCGGAGAGTGGTGGCCGGCGAAGGATCTGGCTCTGT
GTCTCTGGCCCTGCATCTGCAGCCTCTGAGAAGCGCTGC
TGGCGCTGCAGCTCTGGCACTGACAGTGGATCTGCCTCC
TGCCAGCTCCGAGGCCCGGAATAGCGCATTTGGGTTTCA
AGGCAGGCTGCTGCACCTGTCTGCCGGCCAGAGGCTGG GAGTGCATCTGCACACAGAGGCCAGGGCTAGACACGCC
TGGCAGCTGACACAGGGCGCTACAGTGCTGGGCCTGTTC AGAGTGACCCCCGAGATTCCAGCCGGCCTGCCTTCTCCA AGAAGCGAA
204 Nucleotide see Table 47
sequence anti- CD19(8B8-018)
light chain
209 anti-CD19(8B8- QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMHWVRQ
018) Fc hole APGQGLEWMGYINPYNDGSKYTEKFQGRVTMTSDTSISTA dimeric ligand YMELSRLRSDDTAVYYCARGTYYYGSALFDYWGQGTTVT chain VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVT
VSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQ
TYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAG
GPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNW
YVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLN
GKEYKCKVSNKALGAPIEKTISKAKGQPREPQVCTLPPSRD
ELTKNQVSLSCAVKGFYPSDIAVEWESNGQPENNYKTTPP
VLDSDGSFFLVSKLTVDKSRWQQGNVFSCSVMHEALHNH
YTQKSLSLSPGGGGGSGGGGSREGPELSPDDPAGLLDLRQ
GMFAQLVAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYKED
TKELVVAKAGVYYVFFQLELRRVVAGEGSGSVSLALHLQP
LRSAAGAAALALTVDLPPASSEARNSAFGFQGRLLHLSAG
QRLGVHLHTEARARHAWQLTQGATVLGLFRVTPEIPAGLP
SPRSEGGGGSGGGGSREGPELSPDDPAGLLDLRQGMFAQL
VAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYKEDTKELVV
AKAGVYYVFFQLELRRVVAGEGSGSVSLALHLQPLRSAAG
AAALALTVDLPPASSEARNSAFGFQGRLLHLSAGQRLGVH
LHTEARARHAWQLTQGATVLGLFRVTPEIPAGLPSPRSE
210 anti-CD19(8B8- QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMHWVRQ
018) Fc knob APGQGLEWMGYINPYNDGSKYTEKFQGRVTMTSDTSISTA monomeric ligand YMELSRLRSDDTAVYYCARGTYYYGSALFDYWGQGTTVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVT
VSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQ
TYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAG
GPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNW
YVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLN
GKEYKCKVSNKALGAPIEKTISKAKGQPREPQVYTLPPCRD
ELTKNQVSLWCLVKGFYPSDIAVEWESNGQPENNYKTTPP
VLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNH
YTQKSLSLSPGGGGGSGGGGSREGPELSPDDPAGLLDLRQ
GMFAQLVAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYKED
TKELVVAKAGVYYVFFQLELRRVVAGEGSGSVSLALHLQP
LRSAAGAAALALTVDLPPASSEARNSAFGFQGRLLHLSAG
QRLGVHLHTEARARHAWQLTQGATVLGLFRVTPEIPAGLP
SPRSE
206 anti-CD19(8B8- see Table 47
018) light chain 7.1.6 Preparation of monovalent CD19(8B8-018) targeted 4-1BB ligand (71-248) trimer-containing Fc (kih) fusion antigen binding molecule with crossed CH1-CL domains with charged residues (Construct 3.4)
A polypeptide containing two ectodomains of 4-1BB ligand (71-248), separated by (G4S)2 linkers, and fused to the human IgGl-CL domain, was cloned in analogy to the one depicted in Figure 29A: human 4- IBB ligand, (G4S)2 connector, human 4- IBB ligand, (G4S)2 connector, human CL. A polypeptide containing one ectodomain of 4- IBB ligand (71-248) and fused to the human IgGl-CH domain, was cloned in nalogy to the one described in Figure 29B: human 4- 1BB ligand, (G4S)2 connector, human CH. The polypeptide encoding the dimeric 4- IBB ligand fused to human CL domain was subcloned in frame with the human IgGl heavy chain CH2 and CH3 domains on the knob (Merchant, Zhu et al. 1998). To improve correct pairing the following mutations have been introduced in the crossed CH-CL. In the dimeric 4- IBB ligand fused to human CL, E123R and Q124K. In the monomeric 4- IBB ligand fused to human CHI, K147E and K213E. The variable region of heavy and light chain DNA sequences encoding a binder specific for CD19, clone 8B8-018, were subcloned in frame with either the constant heavy chain of the hole or the constant light chain of human IgGl. The Pro329Gly, Leu234Ala and Leu235Ala mutations have been introduced in the constant region of the knob and hole heavy chains to abrogate binding to Fc gamma receptors according to the method described in WO
2012/130831. Combination of the dimeric ligand-Fc knob chain containing the S354C/T366W mutations, the monomeric CHI fusion, the targeted anti-CD 19-Fc hole chain containing the Y349C/T366S/L368A/Y407V mutations and the anti-CD 19 light chain allows generation of a heterodimer, which includes an assembled trimeric 4-1BB ligand and a CD19 binding Fab
(Figure 30, construct 3.4). Table 50 shows the cDNA and amino acid sequences of the monovalent CD19(8B8-018) targeted split trimeric 4- IBB ligand (71-248) Fc (kih) fusion antigen binding molecule with crossed CH-CL and charged residues (construct 3.4).
Table 50: cDNA and amino acid sequences of monovalent CD19(8B8-018) targeted split trimeric 4-1BB ligand (71-248) Fc (kih) fusion containing CH-CL cross with charged residues (construct 3.4). * charged residues
SEQ ID Description Sequence
NO:
169 Nucleotide see Table 24
sequence dimeric
ligand (71-248) - CL* Fc knob chain
170 Nucleotide see Table 24
sequence
monomeric hu
4-1BBL (71-248)
- CHI*
203 Nucleotide see Table 47
sequence anti- CD19(8B8-018)
Fc hole chain
204 Nucleotide see Table 47
sequence anti- CD19(8B8-018)
light chain
119 Dimeric ligand see Table 24
(71-248) - CL*
Fc knob chain
120 Monomeric see Table 24
ligand (71-248)- CH1*
205 anti-CD19(8B8- see Table 47
018) Fc hole
chain
206 anti-CD19(8B8- see Table 47
018) light chain
7.1.7 Preparation of monovalent CD19(8B8-018) targeted 4-1BB ligand (71-248) trimer-containing Fc (kih) fusion antigen binding molecule with crossed CH1-CL domains without charged residues (Construct 3.5) A polypeptide containing two ectodomains of 4-1BB ligand (71-248), separated by (G4S)2 linkers, and fused to the human IgGl-CL domain, was cloned in analogy as depicted in Figure (29 A), but without amino acid mutations in the CL domain: human 4- IBB ligand, (G4S)2 connector, human 4- IBB ligand, (G4S)2 connector, human CL. A polypeptide containing one ectodomain of 4- IBB ligand (71-248) and fused to the human IgGl-CHl domain, was cloned in analogy as depicted in Figure (29B), but without amino acid mutations in the CHI domain:
human 4-1BB ligand, (G4S)2 connector, human CHI.
The variable region of heavy and light chain DNA sequences encoding a binder specific for CD19, clone 8B8-018, were subcloned in frame with either the constant heavy chain of the hole or the constant light chain of human IgGl. The Pro329Gly, Leu234Ala and Leu235Ala mutations have been introduced in the constant region of the knob and hole heavy chains to abrogate binding to Fc gamma receptors according to the method described in WO 2012/130831. Combination of the dimeric ligand-Fc knob chain containing the S354C/T366W mutations, the monomeric CHI fusion, the targeted anti-CD 19-Fc hole chain containing the
Y349C/T366S/L368A/Y407V mutations and the anti-CD 19 light chain allows generation of a heterodimer, which includes an assembled trimeric 4-1BB ligand and a CD19-binding Fab (Figure 30, Construct 3.5).
Table 51 shows the cDNA and amino acid sequences of the monovalent CD19(8B8-018) targeted split trimeric 4- IBB ligand (71-248) Fc (kih) fusion antigen binding molecule containing crossed CH-CL cross without charged residues (construct 3.5).
Table 51: cDNA and amino acid sequences of monovalent CD19(8B8-018) targeted split trimeric 4-1BB ligand (71-248) Fc (kih) fusion containing CH-CL cross without charged residues (construct 3.5).
SEQ ID Description Sequence
NO:
171 Nucleotide see Table 25
sequence dimeric
ligand (71-248) - CL Fc knob chain
172 Nucleotide see Table 25
sequence
monomeric ligand
(71-248)-CHl
203 Nucleotide see Table 47
sequence anti- CD19(8B8-018)
Fc hole chain
204 Nucleotide see Table 47
sequence anti- CD19(8B8-018)
light chain
173 Dimeric ligand see Table 25
(71-248) - CL Fc
knob chain
174 Monomeric see Table 25
ligand (71-248)- CH1
205 anti-CD19(8B8- see Table 47
018) Fc hole
chain
206 anti-CD19(8B8- see Table 47
018) light chain 7.1.8 Preparation of bivalent CD19(8B8-018) targeted 4-lBB ligand (71-248) trimer- containing Fc (kih) fusion antigen binding (Construct 3.6)
A polypeptide containing two ectodomains of 4-lBB ligand (71-248), separated by (G4S)2 linkers was fused to the C-terminus of human IgGl Fc hole chain, as depicted in Figure 29C: human IgGl Fc hole, (G4S)2 connector, human 4-lBB ligand, (G4S)2 connector, human 4-lBB ligand. A polypeptide containing one ectodomain of 4- IBB ligand (71-254) and fused to the C- terminus of human IgGl Fc knob chain as described in Figure 29D: human IgGl Fc knob, (G4S)2 connector, human 4- IBB ligand.
The variable region of heavy and light chain DNA sequences encoding a binder specific for CD19, clone 8B8-018, were subcloned in frame with either the constant heavy chain of the hole, the knob or the constant light chain of human IgGl. The Pro329Gly, Leu234Ala and Leu235Ala mutations have been introduced in the constant region of the knob and hole heavy chains to abrogate binding to Fc gamma receptors according to the method described in WO 2012/130831. Combination of the anti-CD19 hulgGI hole dimeric ligand chain containing the Y349C/T366S/L368A/Y407V mutations, the anti-CD19 hulgGI knob monomeric ligand chain containing the S354C/T366W mutations and the anti-CD 19 light chain allows generation of a heterodimer, which includes an assembled trimeric 4-lBB ligand and two CD19 binding Fabs (Figure 30, construct 3.6).
Table 52 shows the cDNA and amino acid sequences of the bivalent CD19(8B8-018) targeted split trimeric 4- IBB ligand (71-248) Fc (kih) fusion antigen binding molecule (construct 3.6).
Table 52: cDNA and amino acid sequences of bivalent CD19(8B8-018) targeted split trimeric 4-lBB ligand (71-248) Fc (kih) fusion (construct 3.6)
SEQ ID Description Sequence
NO:
211 Nucleotide CAGGTCCAGCTGGTGCAGTCCGGCGCCGAGGTCAAGAA sequence anti- ACCCGGGGCTTCTGTGAAGGTTTCATGCAAGGCAAGCG CD19(8B8-018) GATACACCTTCACCGACTATATCATGCATTGGGTCAGGC Fc hole dimeric AGGCCCCTGGCCAAGGTCTCGAATGGATGGGCTACATTA ligand (71-248) ACCCATATAATGATGGCTCCAAATACACCGAGAAGTTTC
AGGGAAGAGTCACTATGACATCTGACACCAGTATCAGC
chain
ACTGCTTACATGGAGCTGTCCCGCCTTCGGTCTGATGAC
ACCGCAGTGTATTACTGTGCCAGGGGCACATATTACTAC
GGCTCAGCTCTGTTCGACTATTGGGGGCAGGGAACCACA
GTAACCGTGAGCTCCGCTAGCACCAAGGGCCCCTCCGTG
TTCCCCCTGGCCCCCAGCAGCAAGAGCACCAGCGGCGG
CACAGCCGCTCTGGGCTGCCTGGTCAAGGACTACTTCCC
CGAGCCCGTGACCGTGTCCTGGAACAGCGGAGCCCTGA
CCTCCGGCGTGCACACCTTCCCCGCCGTGCTGCAGAGTT
CTGGCCTGTATAGCCTGAGCAGCGTGGTCACCGTGCCTT CTAGCAGCCTGGGCACCCAGACCTACATCTGCAACGTG
AACCACAAGCCCAGCAACACCAAGGTGGACAAGAAGGT
GGAGCCCAAGAGCTGCGACAAAACTCACACATGCCCAC
CGTGCCCAGCACCTGAAGCTGCAGGGGGACCGTCAGTC
TTCCTCTTCCCCCCAAAACCCAAGGACACCCTCATGATC
TCCCGGACCCCTGAGGTCACATGCGTGGTGGTGGACGTG
AGCCACGAAGACCCTGAGGTCAAGTTCAACTGGTACGT
GGACGGCGTGGAGGTGCATAATGCCAAGACAAAGCCGC
GGGAGGAGCAGTACAACAGCACGTACCGTGTGGTCAGC
GTCCTCACCGTCCTGCACCAGGACTGGCTGAATGGCAAG
GAGTACAAGTGCAAGGTCTCCAACAAAGCCCTCGGCGC
CCCCATCGAGAAAACCATCTCCAAAGCCAAAGGGCAGC
CCCGAGAACCACAGGTGTGCACCCTGCCCCCATCCCGG
GATGAGCTGACCAAGAACCAGGTCAGCCTCTCGTGCGC
AGTCAAAGGCTTCTATCCCAGCGACATCGCCGTGGAGTG
GGAGAGCAATGGGCAGCCGGAGAACAACTACAAGACC
ACGCCTCCCGTGCTGGACTCCGACGGCTCCTTCTTCCTC
GTGAGCAAGCTCACCGTGGACAAGAGCAGGTGGCAGCA
GGGGAACGTCTTCTCATGCTCCGTGATGCATGAGGCTCT
GCACAACCACTACACGCAGAAGAGCCTCTCCCTGTCTCC
GGGTGGAGGCGGCGGAAGCGGAGGAGGAGGATCCAGA
GAGGGCCCTGAGCTGAGCCCTGATGATCCTGCCGGACT
GCTGGACCTGCGGCAGGGAATGTTTGCCCAGCTGGTGGC
CCAGAACGTGCTGCTGATCGATGGCCCCCTGTCCTGGTA
CAGCGATCCTGGACTGGCTGGCGTGTCACTGACAGGCG
GCCTGAGCTACAAAGAGGACACCAAAGAACTGGTGGTG
GCCAAGGCCGGCGTGTACTACGTGTTCTTTCAGCTGGAA
CTGCGGAGAGTGGTGGCCGGCGAAGGATCTGGCTCTGT
GTCTCTGGCCCTGCATCTGCAGCCTCTGAGATCTGCTGC
TGGCGCCGCTGCTCTGGCACTGACAGTGGATCTGCCTCC
TGCCAGCAGCGAGGCCCGGAATAGCGCATTTGGGTTTCA
AGGCAGGCTGCTGCACCTGTCTGCCGGCCAGAGGCTGG
GAGTGCATCTGCACACAGAGGCCAGGGCTAGACACGCC
TGGCAGCTGACACAGGGCGCTACAGTGCTGGGCCTGTTC
AGAGTGACCCCCGAGATTCCAGCAGGCCTGGGAGGCGG
CGGATCTGGCGGCGGAGGATCTAGAGAAGGACCCGAGC
TGTCCCCCGACGATCCCGCTGGGCTGCTGGATCTGAGAC
AGGGCATGTTCGCTCAGCTGGTGGCTCAGAATGTGCTGC
TGATTGACGGACCTCTGAGCTGGTACTCCGACCCAGGGC
TGGCAGGGGTGTCCCTGACTGGGGGACTGTCCTACAAA
GAAGATACAAAAGAACTGGTGGTGGCTAAAGCTGGGGT
GGCTGGGGAGGGCTCAGGATCTGTGTCCCTGGCTCTGCA
TCTGCAGCCACTGCGCTCTGCAGCAGGGGCTGCAGCACT
GGCCCTGACTGTGGACCTGCCCCCAGCTTCTTCCGAGGC
CAGAAACAGCGCCTTCGGGTTCCAAGGACGCCTGCTGC
ATCTGAGCGCCGGACAGCGCCTGGGAGTGCATCTGCAT
ACTGAAGCCAGAGCCCGGCATGCTTGGCAGCTGACTCA
GGGGGCAACTGTGCTGGGACTGTTTCGCGTGACACCTGA
GATCCCAGCCGGGCTC
Nucleotide CAGGTCCAGCTGGTGCAGTCCGGCGCCGAGGTCAAGAA sequence anti- ACCCGGGGCTTCTGTGAAGGTTTCATGCAAGGCAAGCG CD19(8B8-018) GATACACCTTCACCGACTATATCATGCATTGGGTCAGGC
AGGCCCCTGGCCAAGGTCTCGAATGGATGGGCTACATTA Fc knob ACCCATATAATGATGGCTCCAAATACACCGAGAAGTTTC monomeric (71- AGGGAAGAGTCACTATGACATCTGACACCAGTATCAGC 248) ligand ACTGCTTACATGGAGCTGTCCCGCCTTCGGTCTGATGAC
ACCGCAGTGTATTACTGTGCCAGGGGCACATATTACTAC
GGCTCAGCTCTGTTCGACTATTGGGGGCAGGGAACCACA
GTAACCGTGAGCTCCGCTAGCACCAAGGGCCCATCGGT
CTTCCCCCTGGCACCCTCCTCCAAGAGCACCTCTGGGGG
CACAGCGGCCCTGGGCTGCCTGGTCAAGGACTACTTCCC
CGAACCGGTGACGGTGTCGTGGAACTCAGGCGCCCTGA
CCAGCGGCGTGCACACCTTCCCGGCTGTCCTACAGTCCT
CAGGACTCTACTCCCTCAGCAGCGTGGTGACCGTGCCCT
CCAGCAGCTTGGGCACCCAGACCTACATCTGCAACGTG
AATCACAAGCCCAGCAACACCAAGGTGGACAAGAAAGT
TGAGCCCAAATCTTGTGACAAAACTCACACATGCCCACC
GTGCCCAGCACCTGAAGCTGCAGGGGGACCGTCAGTCT
TCCTCTTCCCCCCAAAACCCAAGGACACCCTCATGATCT
CCCGGACCCCTGAGGTCACATGCGTGGTGGTGGACGTG
AGCCACGAAGACCCTGAGGTCAAGTTCAACTGGTACGT
GGACGGCGTGGAGGTGCATAATGCCAAGACAAAGCCGC
GGGAGGAGCAGTACAACAGCACGTACCGTGTGGTCAGC
GTCCTCACCGTCCTGCACCAGGACTGGCTGAATGGCAAG
GAGTACAAGTGCAAGGTCTCCAACAAAGCCCTCGGCGC
CCCCATCGAGAAAACCATCTCCAAAGCCAAAGGGCAGC
CCCGAGAACCACAGGTGTACACCCTGCCCCCCTGCAGA
GATGAGCTGACCAAGAACCAGGTGTCCCTGTGGTGTCTG
GTCAAGGGCTTCTACCCCAGCGATATCGCCGTGGAGTGG
GAGAGCAACGGCCAGCCTGAGAACAACTACAAGACCAC
CCCCCCTGTGCTGGACAGCGACGGCAGCTTCTTCCTGTA
CTCCAAACTGACCGTGGACAAGAGCCGGTGGCAGCAGG
GCAACGTGTTCAGCTGCAGCGTGATGCACGAGGCCCTG
CACAACCACTACACCCAGAAGTCCCTGAGCCTGAGCCC
CGGCGGAGGCGGCGGAAGCGGAGGAGGAGGATCCAGA
GAGGGCCCTGAGCTGAGCCCTGATGATCCTGCCGGACT
GCTGGACCTGCGGCAGGGAATGTTTGCCCAGCTGGTGGC
CCAGAACGTGCTGCTGATCGATGGCCCCCTGTCCTGGTA
CAGCGATCCTGGACTGGCTGGCGTGTCACTGACAGGCG
GCCTGAGCTACAAAGAGGACACCAAAGAACTGGTGGTG
GCCAAGGCCGGCGTGTACTACGTGTTCTTTCAGCTGGAA
CTGCGGAGAGTGGTGGCCGGCGAAGGATCTGGCTCTGT
GTCTCTGGCCCTGCATCTGCAGCCTCTGAGATCTGCTGC
TGGCGCCGCTGCTCTGGCACTGACAGTGGATCTGCCTCC
TGCCAGCAGCGAGGCCCGGAATAGCGCATTTGGGTTTCA
AGGCAGGCTGCTGCACCTGTCTGCCGGCCAGAGGCTGG
GAGTGCATCTGCACACAGAGGCCAGGGCTAGACACGCC
TGGCAGCTGACACAGGGCGCTACAGTGCTGGGCCTGTTC
AGAGTGACCCCCGAGATTCCTGCCGGGCTC
204 Nucleotide see Table 47
sequence anti- CD19(8B8-018)
light chain
213 anti-CD19(8B8- QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMHWVRQ
018) Fc hole APGQGLEWMGYINPYNDGSKYTEKFQGRVTMTSDTSISTA dimeric ligand YMELSRLRSDDTAVYYCARGTYYYGSALFDYWGQGTTVT (71-248) chain VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVT
VSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQ
TYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAG
GPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNW
YVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLN
GKEYKCKVSNKALGAPIEKTISKAKGQPREPQVCTLPPSRD
ELTKNQVSLSCAVKGFYPSDIAVEWESNGQPENNYKTTPP
VLDSDGSFFLVSKLTVDKSRWQQGNVFSCSVMHEALHNH
YTQKSLSLSPGGGGGSGGGGSREGPELSPDDPAGLLDLRQ
GMFAQLVAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYKED
TKELVVAKAGVYYVFFQLELRRVVAGEGSGSVSLALHLQP
LRSAAGAAALALTVDLPPASSEARNSAFGFQGRLLHLSAG
QRLGVHLHTEARARHAWQLTQGATVLGLFRVTPEIPAGLG
GGGSGGGGSREGPELSPDDPAGLLDLRQGMFAQLVAQNV
LLIDGPLSWYSDPGLAGVSLTGGLSYKEDTKELVVAKAGV
YYVFFQLELRRVVAGEGSGSVSLALHLQPLRSAAGAAALA
LTVDLPPASSEARNSAFGFQGRLLHLSAGQRLGVHLHTEA
RARHAWQLTQGATVLGLFRVTPEIPAGL
214 anti-CD19(8B8- QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMHWVRQ
018) Fc knob APGQGLEWMGYINPYNDGSKYTEKFQGRVTMTSDTSISTA monomeric (71- YMELSRLRSDDTAVYYCARGTYYYGSALFDYWGQGTTVT 248) ligand VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVT
VSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQ
TYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAG
GPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNW
YVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLN
GKEYKCKVSNKALGAPIEKTISKAKGQPREPQVYTLPPCRD
ELTKNQVSLWCLVKGFYPSDIAVEWESNGQPENNYKTTPP
VLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNH
YTQKSLSLSPGGGGGSGGGGSREGPELSPDDPAGLLDLRQ
GMFAQLVAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYKED
TKELVVAKAGVYYVFFQLELRRVVAGEGSGSVSLALHLQP
LRSAAGAAALALTVDLPPASSEARNSAFGFQGRLLHLSAG
QRLGVHLHTEARARHAWQLTQGATVLGLFRVTPEIPAGL
206 anti-CD19(8B8- see Table 47
018) light chain
7.2 Preparation of CD19 (8B8-derived affinity matured) targeted 4-1BB ligand trimer-containing Fc fusion antigen binding molecules and corresponding control molecules 7.2.1 Generation of 8B8-derived affinity-matured anti-CD19 binders devoid of hotspots
7.2.1.1 Selection of affinity matured CD19-specific antibodies
De-amidation of the asparagine residues at positions 27d and 28, located in CDRl of the light chain of the humanized clone 8B8, leads to a significant reduction in the biological activity. Therefore, 2 phage display libraries were generated in which a) both asparagine residues at positions 27d and 28 were eliminated and b) additional CDRs of heavy and light chain were randomized in order to select for 8B8 variants with an improved affinity.
7.2.1.2 Generation of 8B8 affinity maturation libraries devoid of LCDR1 hotspots Generation of affinity-matured 8B8-derived antibodies without the de-amidation sites
N27d and N28, located in LCDR1, was carried out by phage display using standard protocols (Silacci et al, 2005). In a first step, the VL and VH DNA sequences of the humanized parental clone 8B8 (SEQ ID NO: 215 and SEQ ID NO: 216) were cloned into our phagemid which was then used as a template for randomization. In a next step, two libraries were generated for the selection of favourable clones by phage display. In order to eliminate the above-mentioned hotspot positions, a LCDR1 randomization primer (SEQ ID NO: 217) that only allowed amino acids S T Q E at positions 27d and 28 was used for both libraries. Maturation library 1 was randomized in CDRl and 2 of both the light and the heavy chain, while maturation library 2 was randomized in CDRl and 3 of the light chain and in CDR3 of the heavy chain. The randomized positions in the respective CDR regions are shown in Figure 31A. For the generation of the maturation library 1, randomized in CDRl and 2 of both the light and the heavy chain, three fragments were assembled by "splicing by overlapping extension" (SOE) PCR and cloned into the phage vector (Figure 31B). The following primer combinations were used to generate the library fragments: fragment 1 (LMB3 (SEQ ID NO: 222) and CD19 LI reverse random (SEQ ID NO: 217), fragment 2 (CD19 L2 forward random (SEQ ID NO: 218) and CD19 HI reverse random (SEQ ID NO: 219), and fragment 3 (CD 19 H2 forward random (SEQ ID NO: 220) and CD19 H3 reverse constant (SEQ ID NO: 221) (Table 53). After assembly of sufficient amounts of full length randomized fragment, it was digested with NcoVNhel alongside with identically treated acceptor phagemid vector. A 3-fold molar excess of library insert was ligated with 10 μg of phagemid vector. Purified ligations were used for 20 transformations resulting in 2 x 10 exp9 transformants. Phagemid particles displaying the 8B8 affinity maturation library were rescued and purified by PEG/NaCl purification to be used for selections.
The generation of the second library, randomized in CDRl and 3 of the light chain and in CDR3 of the heavy chain, was done similarly. The following primer combinations were used to generate the library fragments: fragment 1 (LMB3 (SEQ ID NO: 222) and CD19 LI reverse random (SEQ ID NO: 217), fragment 2 (CD19 LI forward constant (SEQ ID NO 223) and CD19 L3 reverse random (SEQ ID NO 224), and fragment 3 (CD 19 L3 forward constant (SEQ ID NO: 225) and CD19 H3 reverse random (SEQ ID NO: 226) (Table 54). After assembly of sufficient amounts of full length randomized fragment, it was digested with NcoVKpnl alongside with identically treated acceptor phagemid vector. A 3-fold molar excess of library insert was ligated with 20ug of phagemid vector. Purified ligations were used for 40 transformations resulting in 2 x 10 exp9 transforaiants. Phagemid particles displaying the 8B8 affinity maturation library were rescued and purified by PEG/NaCl purification to be used for selections.
Table 53: Primers for 8B8 affinity maturation and hotspot removal library L1_L2 / H1_H2
SEQ ID Name Sequence
217 CD19 L1 CAG CTG CGG GCT CTG ACC CGG TTT CTG GAG ATA
reverse CCA GTT CAG 1 CGT 2 GCC 3 GGA 4 TTC CAG AGA TTG random GCT GGA TTT GCA AGA AAT G
1: 40% Y, 6% A/S/T/G/P/D/N/E/Q/V, 2: 40% N, 6%
A/S/T/Y/G/P/D/E/Q/V, 3: 25% S/T/Q/E, 4: 25% S/T/Q/E
218 CD19 L2 CTC CAG AAA CCG GGT CAG AGC CCG CAG CTG CTG
forward ATC TAC 5 GTA TCT 6 CGC 7 8 GGC GTT 9 GAT CGT TTC random AGC GGT TCT GGA TCC GGC ACC
5: 30% R, 20% E, 5% A/S/T/Y/G/P/D/N/Q/V. 6: 30% K, 20% S, 5% A/N/T/Y/G/P/D/E/Q/V, 7: 40% F, 5%
A/S/T/Y/G/P/D/E/Q/V/I/L, 8: 40% S, 6.6%
A/T/Y/G/P/D/E/Q/V, 9: 50% P, 50% L
219 CD19 H1 CAT CCA CTC CAG ACC CTG GCC CGG GGC CTG ACG
reverse AAC CCA 10 CAT 11 12 13 14 GAA 15 GTA ACC AGA TGC random TTT GCA GCT CAC TTT AAC GGA AGC
10: 52% H, 4% G/A/S/P/T/N/Y/D/E/Q/V/I,ll: 30% I, 15% Y, 5% G/A/S/T/P/N/H/D/E/Q/V,12: 52% Y, 4%
G/A/S/P/T/N/H/D/E/Q/V/1,13: 30% D, 15% G, 5%
A/S/P/Y/N/H/D/E/Q/V/I, 14: 52% T, 4%
G/A/S/P/Y/N/H/D/E/Q/V/I, 15: 52% T, 4%
G/A/S/P/Y/N/H/D/E/Q/V/I
220 CD19 H2 CAG GCC CCG GGC CAG GGT CTG GAG TGG ATG GGC
forward 16 ATT 17 CCA 18 19 20 21 TCC 22 TAT ACC 23 AAA TTC random CAG GGC CGC GTC ACG ATG ACC
16: 45% Y, 5% A/S/P/T/N/H/D/E/Q/V/I, 17: 52% N, 4%
G/A/S/P/Y/T/H/D/E/Q/V/I, 18: 40% Y, 5%
G/A/S/P/T/N/H/D/E/Q/V/I, 19: 30% N, 15% S, 5%
G/A/T/P/Y/H/D/E/Q/V/I, 20: 30% D, 15% G, 5%
A/S/T/P/Y/N/H/E/Q/V/I, 21: 52% G, 4%
N/A/S/P/Y/T/H/D/E/Q/V/I, 22: 30% K, 15% N, 4%
G/A/S/P/Y/T/H/D/E/Q/V/I, 23: 30% E, 15% Q, 5%
G/A/S/T/P/Y/N/H/D/V/I
221 CD19 H3 CGTCACCGGTTCGGGGAAGTAGTCCTTGACCAG
reverse
constant
222 LMB3 CAGGAAACAGCTATGACCATGATTAC Table 54: Primers for 8B8 affinity maturation and hotspot removal library L1_L3 / H3
Figure imgf000265_0001
7.2.1.3 Selection of affinity matured 8B8-derived clones devoid of LCDR1 hotspots N27d and N28
For the selection of affinity-matured clones devoid of the LCDRlhotspots N27d and N28, two selection approaches by phage display were performed:
In the first approach, the selection was executed on human CD19-Fc fusion protein using both phage display libraries. Panning rounds were performed in solution according to the following pattern: 1. binding of ~ 10 12 phagemid particles to 30nM biotinylated CD19-Fc protein for 0.5 h in a total volume of lml, 2. capture of biotinylated CD19-Fc protein and specifically bound phage particles by addition of 5.4 x 10 streptavidin-coated magnetic beads for 10 min, 3. washing of beads using 5x lml PBS/Tween20 and 5x lml PBS, 4. elution of phage particles by addition of lml lOOmM TEA for 10 min and neutralization by adding 500ul 1M Tris/HCl pH 7.4, 5. re-infection of exponentially growing E. coli TGI bacteria, and 6.infection with helperphage VCSM13 and subsequent PEG/NaCl precipitation of phagemid particles to be used in subsequent selection rounds. Selections were carried out over 3 rounds using decreasing antigen concentrations (30xlO"9M, 10xlO"9M, and 3xlO"9M). In round 2 and 3, capture of antigen:phage complexes was performed using neutravidin plates instead of streptavidin beads. Neutravidin plates were washed with 5x PBS/Tween20 and 5x PBS. In round 3, the neutravidin plate was incubated overnight in 2 liters PBS for an "off-rate" selection before phage was eluted from the plate. Furthermore, cynomolgus CD19-Fc protein was used in round 2 in order to enrich cross -reactive binders.
In the second selection approach, the phage panning was executed on cells transiently expressing either the human or cynomolgus CD 19 ECD on the cell surface. For the transient transfection of HEK cells, expression plasmids were generated that harbor the DNA sequences (from 5' to 3') for the following protein segments: A Flag tag, a SNAP tag, the CD 19 ECD of either human or cynomolgus origin, and the transmembrane region of the Platelet-derived growth factor receptor (PDGFR) (SEQ ID NOs: 227 and 228). The expression of the respective proteins (SEQ ID NOs: 229 and 230) on the cell surface was confirmed by flow cytometry using an anti- Flag antibody for detection. Both libraries were exposed in the first selection round to cells either expressing the human or cynomolgus CD19 ECD-containing protein fusion. For the subsequent panning rounds, the species of the CD 19 ECD was alternated accordingly. Cells transiently transfected with an irrelevant membrane protein were used for pre-clearing. Panning rounds were performed according to the following pattern:
1. Transfection of HEK cells with constructs expressing either CD 19 ECD or an irrelevant transmembrane protein according to the standard procedure described before,
2. Incubation of the cells for total 48h at 37°C in an incubator with a 5% C02 atmosphere, 3. Isolation of cells by centrifugation (3 min at 250xg) and re-suspension of lxlOE7 CD19 ECD- positive cells and lxlOE7 negative cells in PBS/5% BSA, respectively,
3. Pre-clearing of unspecific phage by incubating the phage library with 1x107 CD19-negative cells for 60 min at 4°C using a gently rotating tube rotator,
4. Centrifugation of cells at 250xg for 3min and transfer of supernatant into a fresh tube and addition of lxlOE7 CD19-positive cells and incubation for 60 min at 4 °C by gentle rotation on a tube rotator,
5. Washing of cells by centrifugation for 1 min at 250xg, aspiration of the supernatant, and re- suspension in 1 ml PBS (8 times), 6. Phage elution with 1 ml lOOmM TEA, incubation for 5 min at RT, and neutralization of the eluate with 500 ul 1M Tris-HCl, pH7.6,
7. re-infection of exponentially growing E. coli TGI bacteria, and
8. infection with helperphage VCSM13 and subsequent PEG/NaCl precipitation of phagemid particles to be used in subsequent selection rounds. Selections were carried out over 3 rounds.
For both selection approaches, specific binders were identified by ELISA as follows: 100 ul of 30 nM biotinylated CD19-Fc protein per well were coated on neutravidin plates. Fab- containing bacterial supernatants were added and binding Fabs were detected via their Flag-tags using an anti-Flag/HRP secondary antibody. Clones that were ELISA-positive on recombinant human CD 19 were further tested in a cell-based ELISA using cells that were transiently transfected with the human CD 19 ECD- containing expression plasmid (SEQ ID NO: 227). This analysis was performed as follows: 48 h after transfection, HEK cells were harvested and centrifuged at 250xg for 5 min. Cells were then re suspended in ice-cold PBS BSA 2% to 4 x 106 cells/ml and incubated for 20 min on ice to block unspecific binding sites. 4 xlO5 cells in lOOul were distributed to each well of a 96 well plate and centrifuged at 250xg and 4°C for 3 min. Supernatant was aspirated off and 50ul bacterial supernatant containing soluble Fab fragments was diluted with 50ul ice-cold PBS/BSA 2%, added to the plate, mixed with the cells and incubated for 1 h at 4 C. Afterwards, cells were washed 3 times with ice cold PBS before lOOul PBS BSA 2% per well containing a 1:2000 dilution of anti-Fab-HRP antibody were added. After an incubation time of 1 h, cells were washed again 3 times with ice-cold PBS. For the development, lOOul "1-step ultra TMB-ELISA" substrate was added per well. After an incubation time of 10 minutes, supernatant was transferred to a new 96-well plate containing 40ul H2S04 1M per well and absorbance was measured 450 nM. Clones exhibiting significant signals over background were subjected to a kinetic screening experiment by SPR-analysis using ProteOn XPR36.
7.2.1.4 Identification of affinity-matured 8B8-derived variants by SPR
In order to further characterize the ELISA-positive clones, the off-rate was measured by surface plasmon resonance and compared with the parental humanized clone 8B8.
For this experiment, 7000 RU of polyclonal anti-human Fab antibody were immobilized on all 6 channels of a GLM chip by Amine coupling (NaAcetate pH4.5, 25 μΐ/min, 240s) (vertical orientation). Each antibody-containing bacterial supernatant was filtered and 2-fold diluted with PBS, and then injected for 360s at 25 μΐ/minute to achieve immobilization levels of between 100 and 400 response units (RU) in vertical orientation. Injection of monomeric CD19-Fc: For one- shot kinetics measurements, injection direction was changed to horizontal orientation, three-fold dilution series of purified monomeric CD19-Fc (varying concentration ranges between 150 and 6 nM) were injected simultaneously at 50 μΐ/min along separate channels 1-4, with association times of 180 s, and dissociation times of 300 s. A human IgG Fc fragment (150nM) was injected in channel 5 as a negative control for specific binding to monomeric CD19-Fc Buffer (PBST) was injected along the sixth channel to provide an "in-line" blank for referencing. Regeneration was performed by two pulses of lOmM glycine pH 1.5 and 50mM NaOH for 30s at 90ul/min (horizontal orientation). Dissociation rate constants (koff) were calculated using a simple one-to- one Langmuir binding model in ProteOn Manager v3.1 software by simultaneously fitting the sensorgrams. Clones expressing Fabs with the slowest dissociation rate constants were identified (Table 55). Of note, the dissociation rate constants of clones 5A07 and 5B08 could not be determined due to inadequate fitting. Nevertheless, both clones were selected because results obtained suggested a very slow dissociation. The variable domains of the corresponding phagemids were sequenced. Importantly, both asparagine residue in LCDR1 (position 27d and 28) were replaced by a serine or a threonine, demonstrating that both de-amidation sites were removed. An alignment is shown in Figure 32. The CDRs of the best clones are listed in Table 56 (variable regions of the light chain) and Table 57 (variable regions of the heavy chain) (clone 5H09: (SEQ ID NO:231-236); clone 7H07: (SEQ ID NO:237-242); clone 2B03: (SEQ ID NO: 243-248); clone 2B11: (SEQ ID NO:249-254); clone 5A07: (SEQ ID NO:255-260); clone 5B08: (SEQ ID NO:261-266); clone 5D08: (SEQ ID NO:267-272).
Table 55: Dissociation constants of selected clones obtained in screening analysis with bacterial supernatant clone Dissociation constant kd (1/s)
Parental 8B8 3.01E-4
5H09 2.58E-4
7H07 5.75E-5
2B03 3.24E-5
2B11 4.37E-6
5A07 n.d.
5B08 n.d.
5D08 1.95E-4 Table 56: CDR sequences of the selected 8B8 light chains
Figure imgf000269_0001
Table 57: CDR sequences of the selected 8B8 heavy chains
Figure imgf000269_0002
7.2.2 Characterization of affinity-matured 8B8-derived antibodies
7.2.2.1 Cloning of variable antibody domains into expression vectors
The variable regions of heavy and light chain DNA sequences of the selected anti-CD 19 binders were subcloned in frame with either the constant heavy chain or the constant light chain of human IgGl. In the heavy chain, Pro329Gly, Leu234Ala and Leu235Ala mutations have been introduced in order to abrogate binding to Fc gamma receptors according to the method described in International Patent Appl. Publ. No. WO 2012/130831 Al. The cDNA and amino acid sequences of the anti-CD 19 IgGs are shown in Table 58 and Table 59, respectively. All antibody-encoding sequences were cloned into an expression vector, which drives transcription of the insert with a chimeric MPSV promoter and contains a synthetic polyA signal sequence located at the 3' end of the CDS. In addition, the vector contains an EBV OriP sequence for episomal maintenance of the plasmid.
Table 58: cDNA and amino acid sequences of anti-CD19 clone 8B8 in P329GLALA human IgGl format
SEQ Clone Sequence
ID and
NO: Chain
GATGCTGTGATGACCCAAACTCCACTCTCCCTGCCTGTCAGTCTTGGA
GATCAAGCCTCCATCTCTTGCAGGTCTAGTCAGAGCCTTGAAAACAGT
AATGGAAACACCTATTTGAACTGGTACCTCCAGAAACCAGGCCAGTC
TCCACAACTCCTGATCTACAGGGTTTCCAAACGATTTTCTGGGGTCCT
AGACAGGTTCAGTGGTAGTGGATCAGGGACAGATTTCACACTGAAAA
8B8 TCAGCAGAGTGGAGGCTGAGGATTTGGGAGTTTATTTCTGCCTACAA Parental CTTACACATGTCCCGTACACGTTCGGAGGGGGGACCAAGCTGGAAAT
273
light AAAACGTACGGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATG chain AGCAGTTGAAA TCTGGAA CTGCCTCTGTTGTGTGCCTGCTGAA TAA CTTCT
ATCCCAGAGAGGCCAAAGTACAGTGGAAGGTGGATAACGCCCTCCAATCG
GGTAACTCCCAGGAGAGTGTCACAGAGCAGGACAGCAAGGACAGCACCT
ACAGCCTCAGCAGCACCCTGACGCTGAGCAAAGCAGACTACGAGAAACAC
AAAGTCTACGCCTGCGAAGTCACCCATCAGGGCCTGAGCTCGCCCGTCAC
AAAGAGCTTCAACAGGGGAGAGTGT
GAGGTCCAGCTGCAGCAGTCTGGACCTGAGCTGGTAAAGCCTGGGGC
TTCAGTGAAGATGGCCTGCAAGGCTTCTGGATACACATTCACTGACTA
TATTATGCACTGGGTGAAGCAGAAGACTGGGCAGGGCCTTGAGTGGA
TTGGATATATTAATCCTTACAATGATGGTTCTAAGTACACTGAGAAGT
TCAACGGCAAGGCCACACTGACTTCAGACAAATCTTCCATCACAGCC
TACATGGAGCTCAGCAGCCTGACCTCTGAGGACTCTGCGGTCTATTAC
TGTGCAAGAGGGACCTATTATTATGGTAGCGCCCTCTTTGACTACTGG
GGCCAAGGCACCACTCTCACAGTCTCCTCGGCrAGCA CCAAGGGCCCA
TCGGTCTTCCCCCTGGCACCCTCCTCCAAGAGCACCTCTGGGGGCACAGC
GGCCCTGGGCTGCCTGGTCAAGGACTACTTCCCCGAACCGGTGACGGTG
TCGTGGAACTCAGGCGCCCTGACCAGCGGCGTGCACACCTTCCCGGCTG
8B8 TCCTACAGTCCTCAGGACTCTACTCCCTCAGCAGCGTGGTGACCGTGCCC parental TCCAGCAGCTTGGGCA CCCAGA CCTA CA TCTGCAA CGTGAA TCA CAAGCC
274
heavy CAGCAACACCAAGGTGGACAAGAAAGTTGAGCCCAAATCTTGTGACAAAA chain CTCACACATGCCCACCGTGCCCAGCACCTGAAGCTGCAGGGGGACCGTC
AGTCTTCCTCTTCCCCCCAAAACCCAAGGACACCCTCATGATCTCCCGGAC
CCCTGAGGTCACATGCGTGGTGGTGGACGTGAGCCACGAAGACCCTGAG
GTCAAGTTCAACTGGTACGTGGACGGCGTGGAGGTGCATAATGCCAAGAC
AAAGCCGCGGGAGGAGCAGTACAACAGCACGTACCGTGTGGTCAGCGTC
CTCACCGTCCTGCACCAGGACTGGCTGAATGGCAAGGAGTACAAGTGCAA
GGTCTCCAACAAAGCCCTCGGCGCCCCCATCGAGAAAACCATCTCCAAAG
CCAAAGGGCAGCCCCGAGAACCACAGGTGTACACCCTGCCCCCATCCCG
GGATGAGCTGACCAAGAACCAGGTCAGCCTGACCTGCCTGGTCAAAGGCT
TCTATCCCAGCGACATCGCCGTGGAGTGGGAGAGCAATGGGCAGCCGGA
GAA CAA CTA CAAGA CCA CGCCTCCCGTGCTGGA CTCCGA CGGCTC CTTCT
TCCTCTACAGCAAGCTCACCGTGGACAAGAGCAGGTGGCAGCAGGGGAA CGTCTTCTCA TGCTCCGTGA TGCA TGAGGCTCTGCA CAA CCA CPA CA CGCA GAAGAGCCTCTCCCTGTCTCCGGGTAAA
8B8 DAVMTQTPLSLPVSLGDQASISCRSSQSLENSNGNTYLNWYLQKPGQSP
QLLIYRVSKRFSGVLDRFSGSGSGTDFTLKISRVEAEDLGVYFCLQLTHVP
Parental
275 YTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASWCLLNNFYPREAKVQW light
KVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGL
chain SSPVTKSFNRGEC
EVQLQQSGPELVKPGASVKMACKASGYTFTDYIMHWVKQKTGQGLEWI
GYINPYNDGSKYTEKFNGKATLTSDKSSITAYMELSSLTSEDSAVYYCAR
8B8 GTYYYGSALFOYWGQGTT TVSSASTKGPSVFPLAPSSKSTSGGTAALGCL
VKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSWTVPSSSLGTQTYIC
parental
276 NVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGGPSVFLFPPKPKDTL heavy
MISRTPEVTCVWDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRW
chain SVLTVLHQDWLNGKEYKCKVSNKALGAPIEKTISKAKGQPREPQVYTLPPSRD
ELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSK
LTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK
Table 59: cDNA and amino acid sequences of affinity matured anti-CD19 clones in P329GLALA human IgGl format
SEQ Clone Sequence
ID and
NO: Chain
GATATTGTCATGACTCAAACTCCACTGTCTCTGTCCGTGACCCCGGGT
CAGCCAGCGAGCATTTCTTGCAAATCCAGCCAATCTCTGGAAACCTCC
ACCGGCACCACGTACCTGAACTGGTATCTCCAGAAACCGGGTCAGAG
CCCGCAGCTGCTGATCTACCGTGTATCTAAGCGCTTCTCCGGCGTTCC
TGATCGTTTCAGCGGTTCTGGATCCGGCACCGACTTTACTCTGAAAAT
CAGCCGTGTGGAAGCTGAAGACGTTGGCGTCTACTATTGTCTGCAGCT
2B 11
GCTGGAAGATCCATACACCTTCGGTCAAGGAACGAAACTGGAAATTA
277 light
AACGTACGGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGATG
chain AGCAGTTGAAATCTGGAACTGCCTCTGTTGTGTGCCTGCTGAATAACT
TCTATCCCAGAGAGGCCAAAGTACAGTGGAAGGTGGATAACGCCCTC
CAATCGGGTAACTCCCAGGAGAGTGTCACAGAGCAGGACAGCAAGG
ACAGCACCTACAGCCTCAGCAGCACCCTGACGCTGAGCAAAGCAGAC
TACGAGAAACACAAAGTCTACGCCTGCGAAGTCACCCATCAGGGCCT
GAGCTCGCCCGTCACAAAGAGCTTCAACAGGGGAGAGTGT
CAGGTGCAATTGGTTCAATCTGGTGCTGAAGTAAAAAAACCGGGCGC
TTCCGTTAAAGTGAGCTGCAAAGCATCTGGTTACACCTTCACTGACTA
TATCATGCACTGGGTTCGTCAGGCCCCGGGCCAGGGTCTGGAGTGGA
TGGGCTACATTAACCCATACAACGACGGTTCCAAATATACCGAGAAA
TTCCAGGGCCGCGTCACGATGACCAGCGACACTTCTATCTCCACCGCG
TACATGGAACTGTCTAGACTGCGTTCTGACGACACCGCTGTTTACTAT
2B 11 TGTGCACGCGGTACCTACTACTACGGTCCACAGCTGTTTGATTACTGG
278 heavy GGCCAAGGTACCACGGTGACCGTAAGCTCTGCTAGCACCAAGGGCCC chain ATCGGTCTTCCCCCTGGCACCCTCCTCCAAGAGCACCTCTGGGGGCAC
AGCGGCCCTGGGCTGCCTGGTCAAGGACTACTTCCCCGAACCGGTGA
CGGTGTCGTGGAACTCAGGCGCCCTGACCAGCGGCGTGCACACCTTC
CCGGCTGTCCTACAGTCCTCAGGACTCTACTCCCTCAGCAGCGTGGTG
ACCGTGCCCTCCAGCAGCTTGGGCACCCAGACCTACATCTGCAACGT
GAATCACAAGCCCAGCAACACCAAGGTGGACAAGAAAGTTGAGCCC
AAATCTTGTGACAAAACTCACACATGCCCACCGTGCCCAGCACCTGA AGCTGCAGGGGGACCGTCAGTCTTCCTCTTCCCCCCAAAACCCAAGG
ACACCCTCATGATCTCCCGGACCCCTGAGGTCACATGCGTGGTGGTG
GACGTGAGCCACGAAGACCCTGAGGTCAAGTTCAACTGGTACGTGGA
CGGCGTGGAGGTGCATAATGCCAAGACAAAGCCGCGGGAGGAGCAG
TACAACAGCACGTACCGTGTGGTCAGCGTCCTCACCGTCCTGCACCA
GGACTGGCTGAATGGCAAGGAGTACAAGTGCAAGGTCTCCAACAAA
GCCCTCGGCGCCCCCATCGAGAAAACCATCTCCAAAGCCAAAGGGCA
GCCCCGAGAACCACAGGTGTACACCCTGCCCCCATCCCGGGATGAGC
TGACCAAGAACCAGGTCAGCCTGACCTGCCTGGTCAAAGGCTTCTAT
CCCAGCGACATCGCCGTGGAGTGGGAGAGCAATGGGCAGCCGGAGA
ACAACTACAAGACCACGCCTCCCGTGCTGGACTCCGACGGCTCCTTCT
TCCTCTACAGCAAGCTCACCGTGGACAAGAGCAGGTGGCAGCAGGGG
AACGTCTTCTCATGCTCCGTGATGCATGAGGCTCTGCACAACCACTAC
ACGCAGAAGAGCCTCTCCCTGTCTCCGGGTAAA
DIVMTQTPLSLSVTPGQPASISCKSSQSLETSTGTTYLNWYLQKPGQSPQL
2B 11 LIYRVSKRFSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCLQLLEDPY
279 light TFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKV chain QWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYAC
EVTHQGLSSPVTKSFNRGEC
QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMHWVRQAPGQGLEW
MGYINPYNDGSKYTEKFQGRVTMTSDTSISTAYMELSRLRSDDTAVYYC
ARGTYYYGPQLFDYWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAA
2B 11 LGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSS
SLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGGPSVF
280 heavy
LFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKT
chain KPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALGAPIEKTISK
AKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPE
NNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHY
TQKSLSLSPGK
GATATTGTTATGACTCAAACTCCACTGTCTCTGTCCGTGACCCCGGGT
CAGCCAGCGAGCATTTCTTGCAAATCCAGCCAATCTCTGGAAACCTCC
ACCGGCAACACGTACCTGAACTGGTATCTCCAGAAACCGGGTCAGAG
CCCGCAGCTGCTGATCTACCGTGTATCTAAGCGCTTCTCCGGCGTTCC
TGATCGTTTCAGCGGTTCTGGATCCGGCACCGACTTTACTCTGAAAAT
CAGCCGTGTGGAAGCTGAAGACGTTGGCGTCTACTATTGTCTGCAGG
7H07
CAACCCATATCCCATACACCTTCGGTCAAGGAACTAAACTGGAAATT
281 light
AAACGTACGGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGAT
chain GAGCAGTTGAAATCTGGAACTGCCTCTGTTGTGTGCCTGCTGAATAAC
TTCTATCCCAGAGAGGCCAAAGTACAGTGGAAGGTGGATAACGCCCT
CCAATCGGGTAACTCCCAGGAGAGTGTCACAGAGCAGGACAGCAAG
GACAGCACCTACAGCCTCAGCAGCACCCTGACGCTGAGCAAAGCAGA
CTACGAGAAACACAAAGTCTACGCCTGCGAAGTCACCCATCAGGGCC
TGAGCTCGCCCGTCACAAAGAGCTTCAACAGGGGAGAGTGT
CAGGTGCAATTGGTTCAATCTGGTGCTGAAGTAAAAAAACCGGGCGC
TTCCGTTAAAGTGAGCTGCAAAGCATCTGGTTACACCTTCACTGACTA
TATCATGCACTGGGTTCGTCAGGCCCCGGGCCAGGGTCTGGAGTGGA
TGGGCTACATTAACCCATACAACGACGGTTCCAAATATACCGAGAAA
7H07 TTCCAGGGCCGCGTCACGATGACCAGCGACACTTCTATCTCCACCGCG
282 heavy TACATGGAACTGTCTAGACTGCGTTCTGACGACACCGCTGTTTACTAT chain TGTGCACGCGGTACCTACTACTACGGTTCTGAACTGTTTGATTACTGG
GGCCAAGGTACCACGGTGACCGTAAGCTCTGCTAGCACCAAGGGCCC
ATCGGTCTTCCCCCTGGCACCCTCCTCCAAGAGCACCTCTGGGGGCAC
AGCGGCCCTGGGCTGCCTGGTCAAGGACTACTTCCCCGAACCGGTGA
CGGTGTCGTGGAACTCAGGCGCCCTGACCAGCGGCGTGCACACCTTC CCGGCTGTCCTACAGTCCTCAGGACTCTACTCCCTCAGCAGCGTGGTG
ACCGTGCCCTCCAGCAGCTTGGGCACCCAGACCTACATCTGCAACGT
GAATCACAAGCCCAGCAACACCAAGGTGGACAAGAAAGTTGAGCCC
AAATCTTGTGACAAAACTCACACATGCCCACCGTGCCCAGCACCTGA
AGCTGCAGGGGGACCGTCAGTCTTCCTCTTCCCCCCAAAACCCAAGG
ACACCCTCATGATCTCCCGGACCCCTGAGGTCACATGCGTGGTGGTG
GACGTGAGCCACGAAGACCCTGAGGTCAAGTTCAACTGGTACGTGGA
CGGCGTGGAGGTGCATAATGCCAAGACAAAGCCGCGGGAGGAGCAG
TACAACAGCACGTACCGTGTGGTCAGCGTCCTCACCGTCCTGCACCA
GGACTGGCTGAATGGCAAGGAGTACAAGTGCAAGGTCTCCAACAAA
GCCCTCGGCGCCCCCATCGAGAAAACCATCTCCAAAGCCAAAGGGCA
GCCCCGAGAACCACAGGTGTACACCCTGCCCCCATCCCGGGATGAGC
TGACCAAGAACCAGGTCAGCCTGACCTGCCTGGTCAAAGGCTTCTAT
CCCAGCGACATCGCCGTGGAGTGGGAGAGCAATGGGCAGCCGGAGA
ACAACTACAAGACCACGCCTCCCGTGCTGGACTCCGACGGCTCCTTCT
TCCTCTACAGCAAGCTCACCGTGGACAAGAGCAGGTGGCAGCAGGGG
AACGTCTTCTCATGCTCCGTGATGCATGAGGCTCTGCACAACCACTAC
ACGCAGAAGAGCCTCTCCCTGTCTCCGGGTAAA
DIVMTQTPLSLSVTPGQPASISCKSSQSLETSTGNTYLNWYLQKPGQSPQL
7H07 LIYRVSKRFSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCLQATHIPYT
283 light FGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQ chain WKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACE
VTHQGLSSPVTKSFNRGEC
QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMHWVRQAPGQGLEW
MGYINPYNDGSKYTEKFQGRVTMTSDTSISTAYMELSRLRSDDTAVYYC
ARGTYYYGSELFDYWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAA
LGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSS
7H07
SLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGGPSVF
284 heavy
LFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKT
chain KPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALGAPIEKTISK
AKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPE
NNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHY
TQKSLSLSPGK
GATATTGTTATGACTCAAACTCCACTGTCTCTGTCCGTGACCCCGGGT
CAGCCAGCGAGCATTTCTTGCAAATCCAGCCAATCTCTGGAAACCTC
CACCGGCAACACGTACCTGAACTGGTATCTCCAGAAACCGGGTCAGA
GCCCGCAGCTGCTGATCTACCGTGTATCTAAGCGCTTCTCCGGCGTTC
CTGATCGTTTCAGCGGTTCTGGATCCGGCACCGACTTTACTCTGAAAA
TCAGCCGTGTGGAAGCTGAAGACGTTGGCGTCTACTATTGTCTGCAG
2B03
TTGACCCACGTTCCGTACACCTTCGGTCAAGGAANNAAACTGGAAAT
285 light
TAAACGTACGGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGA
chain TGAGCAGTTGAAATCTGGAACTGCCTCTGTTGTGTGCCTGCTGAATAA
CTTCTATCCCAGAGAGGCCAAAGTACAGTGGAAGGTGGATAACGCCC
TCCAATCGGGTAACTCCCAGGAGAGTGTCACAGAGCAGGACAGCAA
GGACAGCACCTACAGCCTCAGCAGCACCCTGACGCTGAGCAAAGCA
GACTACGAGAAACACAAAGTCTACGCCTGCGAAGTCACCCATCAGGG
CCTGAGCTCGCCCGTCACAAAGAGCTTCAACAGGGGAGAGTGT
CAGGTGCAATTGGTTCAATCTGGTGCTGAAGTAAAAAAACCGGGCGC
TTCCGTTAAAGTGAGCTGCAAAGCATCTGGTTACACCTTCACTGACTA
2B03 TATCACGCACTGGGTTCGTCAGGCCCCGGGCCAGGGTCTGGAGTGGA
286 heavy TGGGCTACATTAACCCATACAACGACGGTTCCAAATATACCGAGAAA chain TTCCAGGGCCGCGTCACGATGACCAGCGACACTTCTATCTCCACCGC
GTACATGGAACTGTCTAGACTGCGTTCTGACGACACCGCTGTTTACTA
TTGTGCACGCGGTACCTACTACTACGGTCCAGATCTGTTTGATTACTG GGGCCAAGGTACCACGGTGACCGTAAGCTCTGCTAGCACCAAGGGCC
CATCGGTCTTCCCCCTGGCACCCTCCTCCAAGAGCACCTCTGGGGGCA
CAGCGGCCCTGGGCTGCCTGGTCAAGGACTACTTCCCCGAACCGGTG
ACGGTGTCGTGGAACTCAGGCGCCCTGACCAGCGGCGTGCACACCTT
CCCGGCTGTCCTACAGTCCTCAGGACTCTACTCCCTCAGCAGCGTGGT
GACCGTGCCCTCCAGCAGCTTGGGCACCCAGACCTACATCTGCAACG
TGAATCACAAGCCCAGCAACACCAAGGTGGACAAGAAAGTTGAGCC
CAAATCTTGTGACAAAACTCACACATGCCCACCGTGCCCAGCACCTG
AAGCTGCAGGGGGACCGTCAGTCTTCCTCTTCCCCCCAAAACCCAAG
GACACCCTCATGATCTCCCGGACCCCTGAGGTCACATGCGTGGTGGT
GGACGTGAGCCACGAAGACCCTGAGGTCAAGTTCAACTGGTACGTGG
ACGGCGTGGAGGTGCATAATGCCAAGACAAAGCCGCGGGAGGAGCA
GTACAACAGCACGTACCGTGTGGTCAGCGTCCTCACCGTCCTGCACC
AGGACTGGCTGAATGGCAAGGAGTACAAGTGCAAGGTCTCCAACAA
AGCCCTCGGCGCCCCCATCGAGAAAACCATCTCCAAAGCCAAAGGGC
AGCCCCGAGAACCACAGGTGTACACCCTGCCCCCATCCCGGGATGAG
CTGACCAAGAACCAGGTCAGCCTGACCTGCCTGGTCAAAGGCTTCTA
TCCCAGCGACATCGCCGTGGAGTGGGAGAGCAATGGGCAGCCGGAG
AACAACTACAAGACCACGCCTCCCGTGCTGGACTCCGACGGCTCCTT
CTTCCTCTACAGCAAGCTCACCGTGGACAAGAGCAGGTGGCAGCAGG
GGAACGTCTTCTCATGCTCCGTGATGCATGAGGCTCTGCACAACCACT
ACACGCAGAAGAGCCTCTCCCTGTCTCCGGGTAAA
DIVMTQTPLSLSVTPGQPASISCKSSQSLETSTGNTYLNWYLQKPGQSPQ
2B03 LLIYR VS KRFS GVPDRFS GSGS GTDFTLKISR VE AED VGV Y YCLQLTH VP
287 light YTFGQGXKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAK chain VQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYA
CEVTHQGLSSPVTKSFNRGEC
QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYITHWVRQAPGQGLEW
MGYINPYNDGSKYTEKFQGRVTMTSDTSISTAYMELSRLRSDDTAVYYC
ARGTYYYGPDLFDYWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAA
LGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSS
2B03
SLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGGPSV
288 heavy
FLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKT
chain KPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALGAPIEKTISK
AKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQP
ENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNH
YTQKSLSLSPGK
GATATTGTTATGACTCAAACTCCACTGTCTCTGTCCGTGACCCCGGGT
CAGCCAGCGAGCATTTCTTGCAAATCCAGCCAATCTCTGGAAACCTC
CACCGGCAACACGTACCTGAACTGGTATCTCCAGAAACCGGGTCAGA
GCCCGCAGCTGCTGATCTACCGTGTATCTAAGCGCTTCTCCGGCGTTC
CTGATCGTTTCAGCGGTTCTGGATCCGGCACCGACTTTACTCTGAAAA
5A07 TCAGCCGTGTGGAAGCTGAAGACGTTGGCGTCTACTATTGTCTGCAG
CCAGGTCATTACCCAGGTACCTTCGGTCAAGGAACTAAACTGGAAAT
289 light
TAAACGTACGGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGA
chain TGAGCAGTTGAAATCTGGAACTGCCTCTGTTGTGTGCCTGCTGAATAA
CTTCTATCCCAGAGAGGCCAAAGTACAGTGGAAGGTGGATAACGCCC
TCCAATCGGGTAACTCCCAGGAGAGTGTCACAGAGCAGGACAGCAA
GGACAGCACCTACAGCCTCAGCAGCACCCTGACGCTGAGCAAAGCA
GACTACGAGAAACACAAAGTCTACGCCTGCGAAGTCACCCATCAGGG
CCTGAGCTCGCCCGTCACAAAGAGCTTCAACAGGGGAGAGTGT
5A07 CAGGTGCAATTGGTTCAATCTGGTGCTGAAGTAAAAAAACCGGGCGC
290 heavy TTCCGTTAAAGTGAGCTGCAAAGCATCTGGTTACACCTTCACTGACTA chain TATCATGCACTGGGTTCGTCAGGCCCCGGGCCAGGGTCTGGAGTGGA TGGGCTACATTAACCCATACAACGACGGTTCCAAATATACCGAGAAA
TTCCAGGGCCGCGTCACGATGACCAGCGACACTTCTATCTCCACCGC
GTACATGGAACTGTCTAGACTGCGTTCTGACGACACCGCTGTTTACTA
TTGTGCACGCGGTACTTACTACTACGGTTCCGCCCTCTTTGATTACTG
GGGCCAAGGTACCACGGTGACCGTAAGCTCTGCTAGCACCAAGGGCC
CATCGGTCTTCCCCCTGGCACCCTCCTCCAAGAGCACCTCTGGGGGCA
CAGCGGCCCTGGGCTGCCTGGTCAAGGACTACTTCCCCGAACCGGTG
ACGGTGTCGTGGAACTCAGGCGCCCTGACCAGCGGCGTGCACACCTT
CCCGGCTGTCCTACAGTCCTCAGGACTCTACTCCCTCAGCAGCGTGGT
GACCGTGCCCTCCAGCAGCTTGGGCACCCAGACCTACATCTGCAACG
TGAATCACAAGCCCAGCAACACCAAGGTGGACAAGAAAGTTGAGCC
CAAATCTTGTGACAAAACTCACACATGCCCACCGTGCCCAGCACCTG
AAGCTGCAGGGGGACCGTCAGTCTTCCTCTTCCCCCCAAAACCCAAG
GACACCCTCATGATCTCCCGGACCCCTGAGGTCACATGCGTGGTGGT
GGACGTGAGCCACGAAGACCCTGAGGTCAAGTTCAACTGGTACGTGG
ACGGCGTGGAGGTGCATAATGCCAAGACAAAGCCGCGGGAGGAGCA
GTACAACAGCACGTACCGTGTGGTCAGCGTCCTCACCGTCCTGCACC
AGGACTGGCTGAATGGCAAGGAGTACAAGTGCAAGGTCTCCAACAA
AGCCCTCGGCGCCCCCATCGAGAAAACCATCTCCAAAGCCAAAGGGC
AGCCCCGAGAACCACAGGTGTACACCCTGCCCCCATCCCGGGATGAG
CTGACCAAGAACCAGGTCAGCCTGACCTGCCTGGTCAAAGGCTTCTA
TCCCAGCGACATCGCCGTGGAGTGGGAGAGCAATGGGCAGCCGGAG
AACAACTACAAGACCACGCCTCCCGTGCTGGACTCCGACGGCTCCTT
CTTCCTCTACAGCAAGCTCACCGTGGACAAGAGCAGGTGGCAGCAGG
GGAACGTCTTCTCATGCTCCGTGATGCATGAGGCTCTGCACAACCACT
ACACGCAGAAGAGCCTCTCCCTGTCTCCGGGTAAA
DIVMTQTPLSLSVTPGQPASISCKSSQSLETSTGNTYLNWYLQKPGQSPQ
5A07 LLIYR VS KRFS GVPDRFS GSGS GTDFTLKISR VE AED VGV Y YCLQPGH YP
291 light GTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAK chain VQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYA
CEVTHQGLSSPVTKSFNRGEC
QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMHWVRQAPGQGLEW
MGYINPYNDGSKYTEKFQGRVTMTSDTSISTAYMELSRLRSDDTAVYYC
ARGTYYYGSALFDYWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAA
LGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSS
5A07
SLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGGPSV
292 heavy
FLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKT
chain KPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALGAPIEKTISK
AKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQP
ENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNH
YTQKSLSLSPGK
GATATTGTTATGACTCAAACTCCACTGTCTCTGTCCGTGACCCCGGGT
CAGCCAGCGAGCATTTCTTGCAAATCCAGCCAATCTCTGGAAACCTC
CACCGGCAACACGTACCTGAACTGGTATCTCCAGAAACCGGGTCAGA
GCCCGCAGCTGCTGATCTACCGTGTATCTAAGCGCTTCTCCGGCGTTC
CTGATCGTTTCAGCGGTTCTGGATCCGGCACCGACTTTACTCTGAAAA
5D08 TCAGCCGTGTGGAAGCTGAAGACGTTGGCGTCTACTATTGTCTGCAG
293 light CTGACCCATGAACCATACACCTTCGGTCAAGGAACTAAACTGGAAAT chain TAAACGTACGGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGA
TGAGCAGTTGAAATCTGGAACTGCCTCTGTTGTGTGCCTGCTGAATAA
CTTCTATCCCAGAGAGGCCAAAGTACAGTGGAAGGTGGATAACGCCC
TCCAATCGGGTAACTCCCAGGAGAGTGTCACAGAGCAGGACAGCAA
GGACAGCACCTACAGCCTCAGCAGCACCCTGACGCTGAGCAAAGCA
GACTACGAGAAACACAAAGTCTACGCCTGCGAAGTCACCCATCAGGG CCTGAGCTCGCCCGTCACAAAGAGCTTCAACAGGGGAGAGTGT
CAGGTGCAATTGGTTCAATCTGGTGCTGAAGTAAAAAAACCGGGCGC
TTCCGTTAAAGTGAGCTGCAAAGCATCTGGTTACACCTTCACTGACTA
TATCATGCACTGGGTTCGTCAGGCCCCGGGCCAGGGTCTGGAGTGGA
TGGGCTACATTAACCCATACAACGACGGTTCCAAATATACCGAGAAA
TTCCAGGGCCGCGTCACGATGACCAGCGACACTTCTATCTCCACCGC
GTACATGGAACTGTCTAGACTGCGTTCTGACGACACCGCTGTTTACTA
TTGTGCACGCGGTACCTACTACTACGGTTCTGAACTGTTTGATTACTG
GGGCCAAGGTACCACGGTGACCGTAAGCTCTGCTAGCACCAAGGGCC
CATCGGTCTTCCCCCTGGCACCCTCCTCCAAGAGCACCTCTGGGGGCA
CAGCGGCCCTGGGCTGCCTGGTCAAGGACTACTTCCCCGAACCGGTG
ACGGTGTCGTGGAACTCAGGCGCCCTGACCAGCGGCGTGCACACCTT
CCCGGCTGTCCTACAGTCCTCAGGACTCTACTCCCTCAGCAGCGTGGT
GACCGTGCCCTCCAGCAGCTTGGGCACCCAGACCTACATCTGCAACG
5D08 TGAATCACAAGCCCAGCAACACCAAGGTGGACAAGAAAGTTGAGCC
294 heavy CAAATCTTGTGACAAAACTCACACATGCCCACCGTGCCCAGCACCTG chain AAGCTGCAGGGGGACCGTCAGTCTTCCTCTTCCCCCCAAAACCCAAG
GACACCCTCATGATCTCCCGGACCCCTGAGGTCACATGCGTGGTGGT
GGACGTGAGCCACGAAGACCCTGAGGTCAAGTTCAACTGGTACGTGG
ACGGCGTGGAGGTGCATAATGCCAAGACAAAGCCGCGGGAGGAGCA
GTACAACAGCACGTACCGTGTGGTCAGCGTCCTCACCGTCCTGCACC
AGGACTGGCTGAATGGCAAGGAGTACAAGTGCAAGGTCTCCAACAA
AGCCCTCGGCGCCCCCATCGAGAAAACCATCTCCAAAGCCAAAGGGC
AGCCCCGAGAACCACAGGTGTACACCCTGCCCCCATCCCGGGATGAG
CTGACCAAGAACCAGGTCAGCCTGACCTGCCTGGTCAAAGGCTTCTA
TCCCAGCGACATCGCCGTGGAGTGGGAGAGCAATGGGCAGCCGGAG
AACAACTACAAGACCACGCCTCCCGTGCTGGACTCCGACGGCTCCTT
CTTCCTCTACAGCAAGCTCACCGTGGACAAGAGCAGGTGGCAGCAGG
GGAACGTCTTCTCATGCTCCGTGATGCATGAGGCTCTGCACAACCACT
ACACGCAGAAGAGCCTCTCCCTGTCTCCGGGTAAA
DIVMTQTPLSLSVTPGQPASISCKSSQSLETSTGNTYLNWYLQKPGQSPQ
5D08 LLIYR VS KRFS GVPDRFS GSGS GTDFTLKISR VE AED VGV Y YCLQLTHEP
295 light YTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAK chain VQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYA
CEVTHQGLSSPVTKSFNRGEC
QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMHWVRQAPGQGLEW
MGYINPYNDGSKYTEKFQGRVTMTSDTSISTAYMELSRLRSDDTAVYYC
ARGTYYYGSELFDYWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAA
LGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSS
5D08
SLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGGPSV
296 heavy
FLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKT
chain KPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALGAPIEKTISK
AKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQP
ENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNH
YTQKSLSLSPGK
GATATTGTTATGACTCAAACTCCACTGTCTCTGTCCGTGACCCCGGGT
CAGCCAGCGAGCATTTCTTGCAAATCCAGCCAATCTCTGGAAACCTC
CACCGGCAACACGTACCTGAACTGGTATCTCCAGAAACCGGGTCAGA
5B08 GCCCGCAGCTGCTGATCTACCGTGTATCTAAGCGCTTCTCCGGCGTTC
297 light CTGATCGTTTCAGCGGTTCTGGATCCGGCACCGACTTTACTCTGAAAA chain TCAGCCGTGTGGAAGCTGAAGACGTTGGCGTCTACTATTGTCTGCAG
CTGGATTCTTACCCAAACACCTTCGGTCAAGGAACTAAACTGGAAAT
TAAACGTACGGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGA
TGAGCAGTTGAAATCTGGAACTGCCTCTGTTGTGTGCCTGCTGAATAA CTTCTATCCCAGAGAGGCCAAAGTACAGTGGAAGGTGGATAACGCCC
TCCAATCGGGTAACTCCCAGGAGAGTGTCACAGAGCAGGACAGCAA
GGACAGCACCTACAGCCTCAGCAGCACCCTGACGCTGAGCAAAGCA
GACTACGAGAAACACAAAGTCTACGCCTGCGAAGTCACCCATCAGGG
CCTGAGCTCGCCCGTCACAAAGAGCTTCAACAGGGGAGAGTGT
CAGGTGCAATTGGTTCAATCTGGTGCTGAAGTAAAAAAACCGGGCGC
TTCCGTTAAAGTGAGCTGCAAAGCATCTGGTTACACCTTCACTGACTA
TATCATGCACTGGGTTCGTCAGGCCCCGGGCCAGGGTCTGGAGTGGA
TGGGCTACATTAACCCATACAACGACGGTTCCAAATATACCGAGAAA
TTCCAGGGCCGCGTCACGATGACCAGCGACACTTCTATCTCCACCGC
GTACATGGAACTGTCTAGACTGCGTTCTGACGACACCGCTGTTTACTA
TTGTGCACGCGGTACCTACTACTACGGTCCACAGCTGTTTGATTACTG
GGGCCAAGGTACCACGGTGACCGTAAGCTCTGCTAGCACCAAGGGCC
CATCGGTCTTCCCCCTGGCACCCTCCTCCAAGAGCACCTCTGGGGGCA
CAGCGGCCCTGGGCTGCCTGGTCAAGGACTACTTCCCCGAACCGGTG
ACGGTGTCGTGGAACTCAGGCGCCCTGACCAGCGGCGTGCACACCTT
CCCGGCTGTCCTACAGTCCTCAGGACTCTACTCCCTCAGCAGCGTGGT
GACCGTGCCCTCCAGCAGCTTGGGCACCCAGACCTACATCTGCAACG
5B08 TGAATCACAAGCCCAGCAACACCAAGGTGGACAAGAAAGTTGAGCC
298 heavy CAAATCTTGTGACAAAACTCACACATGCCCACCGTGCCCAGCACCTG chain AAGCTGCAGGGGGACCGTCAGTCTTCCTCTTCCCCCCAAAACCCAAG
GACACCCTCATGATCTCCCGGACCCCTGAGGTCACATGCGTGGTGGT
GGACGTGAGCCACGAAGACCCTGAGGTCAAGTTCAACTGGTACGTGG
ACGGCGTGGAGGTGCATAATGCCAAGACAAAGCCGCGGGAGGAGCA
GTACAACAGCACGTACCGTGTGGTCAGCGTCCTCACCGTCCTGCACC
AGGACTGGCTGAATGGCAAGGAGTACAAGTGCAAGGTCTCCAACAA
AGCCCTCGGCGCCCCCATCGAGAAAACCATCTCCAAAGCCAAAGGGC
AGCCCCGAGAACCACAGGTGTACACCCTGCCCCCATCCCGGGATGAG
CTGACCAAGAACCAGGTCAGCCTGACCTGCCTGGTCAAAGGCTTCTA
TCCCAGCGACATCGCCGTGGAGTGGGAGAGCAATGGGCAGCCGGAG
AACAACTACAAGACCACGCCTCCCGTGCTGGACTCCGACGGCTCCTT
CTTCCTCTACAGCAAGCTCACCGTGGACAAGAGCAGGTGGCAGCAGG
GGAACGTCTTCTCATGCTCCGTGATGCATGAGGCTCTGCACAACCACT
ACACGCAGAAGAGCCTCTCCCTGTCTCCGGGTAAA
DIVMTQTPLSLSVTPGQPASISCKSSQSLETSTGNTYLNWYLQKPGQSPQ
5B08 LLIYRVSKRFSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCLQLDSYP
299 light NTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAK chain VQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYA
CEVTHQGLSSPVTKSFNRGEC
QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMHWVRQAPGQGLEW
MGYINPYNDGSKYTEKFQGRVTMTSDTSISTAYMELSRLRSDDTAVYYC
ARGTYYYGPQLFDYWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAA
LGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSS
5B08
SLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGGPSV
300 heavy
FLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKT
chain KPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALGAPIEKTISK
AKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQP
ENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNH
YTQKSLSLSPGK
GATATTGTTATGACTCAAACTCCACTGTCTCTGTCCGTGACCCCGGGT
5H09 CAGCCAGCGAGCATTTCTTGCAAATCCAGCCAATCTCTGGAATCTTCC
301 light ACCGGCAACACGTACCTGAACTGGTATCTCCAGAAACCGGGTCAGAG chain CCCGCAGCTGCTGATCTACCGTGTATCTAAGCGCTTCTCCGGCGTTCC
TGATCGTTTCAGCGGTTCTGGATCCGGCACCGACTTTACTCTGAAAAT CAGCCGTGTGGAAGCTGAAGACGTTGGCGTCTACTATTGTCTGCAGC
TGATCGATTACCCAGTTACCTTCGGTCAAGGAACTAAACTGGAAATT
AAACGTACGGTGGCTGCACCATCTGTCTTCATCTTCCCGCCATCTGAT
GAGCAGTTGAAATCTGGAACTGCCTCTGTTGTGTGCCTGCTGAATAA
CTTCTATCCCAGAGAGGCCAAAGTACAGTGGAAGGTGGATAACGCCC
TCCAATCGGGTAACTCCCAGGAGAGTGTCACAGAGCAGGACAGCAA
GGACAGCACCTACAGCCTCAGCAGCACCCTGACGCTGAGCAAAGCA
GACTACGAGAAACACAAAGTCTACGCCTGCGAAGTCACCCATCAGGG
CCTGAGCTCGCCCGTCACAAAGAGCTTCAACAGGGGAGAGTGT
CAGGTGCAATTGGTTCAATCTGGTGCTGAAGTAAAAAAACCGGGCGC
TTCCGTTAAAGTGAGCTGCAAAGCATCTGGTTACACCTTCACTGACTA
TATCATGCACTGGGTTCGTCAGGCCCCGGGCCAGGGTCTGGAGTGGA
TGGGCTACATTAACCCATACAACGACGGTTCCAAATATACCGAGAAA
TTCCAGGGCCGCGTCACGATGACCAGCGACACTTCTATCTCCACCGC
GTACATGGAACTGTCTAGACTGCGTTCTGACGACACCGCTGTTTACTA
TTGTGCACGCGGTACCTACTACTACGGTTCTGCACTGTTTGATTACTG
GGGCCAAGGTACCACGGTGACCGTAAGCTCTGCTAGCACCAAGGGCC
CATCGGTCTTCCCCCTGGCACCCTCCTCCAAGAGCACCTCTGGGGGCA
CAGCGGCCCTGGGCTGCCTGGTCAAGGACTACTTCCCCGAACCGGTG
ACGGTGTCGTGGAACTCAGGCGCCCTGACCAGCGGCGTGCACACCTT
CCCGGCTGTCCTACAGTCCTCAGGACTCTACTCCCTCAGCAGCGTGGT
GACCGTGCCCTCCAGCAGCTTGGGCACCCAGACCTACATCTGCAACG
5H09 TGAATCACAAGCCCAGCAACACCAAGGTGGACAAGAAAGTTGAGCC
302 heavy CAAATCTTGTGACAAAACTCACACATGCCCACCGTGCCCAGCACCTG chain AAGCTGCAGGGGGACCGTCAGTCTTCCTCTTCCCCCCAAAACCCAAG
GACACCCTCATGATCTCCCGGACCCCTGAGGTCACATGCGTGGTGGT
GGACGTGAGCCACGAAGACCCTGAGGTCAAGTTCAACTGGTACGTGG
ACGGCGTGGAGGTGCATAATGCCAAGACAAAGCCGCGGGAGGAGCA
GTACAACAGCACGTACCGTGTGGTCAGCGTCCTCACCGTCCTGCACC
AGGACTGGCTGAATGGCAAGGAGTACAAGTGCAAGGTCTCCAACAA
AGCCCTCGGCGCCCCCATCGAGAAAACCATCTCCAAAGCCAAAGGGC
AGCCCCGAGAACCACAGGTGTACACCCTGCCCCCATCCCGGGATGAG
CTGACCAAGAACCAGGTCAGCCTGACCTGCCTGGTCAAAGGCTTCTA
TCCCAGCGACATCGCCGTGGAGTGGGAGAGCAATGGGCAGCCGGAG
AACAACTACAAGACCACGCCTCCCGTGCTGGACTCCGACGGCTCCTT
CTTCCTCTACAGCAAGCTCACCGTGGACAAGAGCAGGTGGCAGCAGG
GGAACGTCTTCTCATGCTCCGTGATGCATGAGGCTCTGCACAACCACT
ACACGCAGAAGAGCCTCTCCCTGTCTCCGGGTAAA
DIVMTQTPLSLSVTPGQPASISCKSSQSLESSTGNTYLNWYLQKPGQSPQ
5H09 LLIYR VS KRFS GVPDRFS GSGS GTDFTLKISR VE AED VGV Y YCLQLID YP
303 light VTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAK chain VQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYA
CEVTHQGLSSPVTKSFNRGEC
QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMHWVRQAPGQGLEW
MGYINPYNDGSKYTEKFQGRVTMTSDTSISTAYMELSRLRSDDTAVYYC
ARGTYYYGSALFDYWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAA
LGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSS
5H09
SLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGGPSV
304 heavy
FLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKT
chain KPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALGAPIEKTISK
AKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQP
ENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNH
YTQKSLSLSPGK 7.2.2.2 Affinity determination of selected antibodies by SPR
For the exact determination of the affinities by SPR, the selected anti-CD 19 antibodies were produced by co-transfecting HEK293-EBNA cells with the mammalian expression vectors using polyethylenimine. The cells were transfected with the corresponding expression vectors in a 1: 1 ratio ("vector heavy chain": "vector light chain") according to the standard procedure. 7 days after transfection, the antibody titer in the supernatant was measured and all titers were equilibrated to 10 μg/ml.
The Affinity (KD) of the parental antibody 8B8 as well as it derivatives was measured by SPR using a ProteOn XPR36 instrument (Biorad) at 25°C. 7000 RU of polyclonal anti-human Fab antibody were immobilized on all 6 channels of a GLM chip by Amine coupling (NaAcetate pH4.5, 25ul/min, 240s) (vertical orientation). Each antibody-containing HEK supernatant was filtered, diluted with PBST (10 mM phosphate, 150 mM sodium chloride pH 7.4, 0.005% Tween 20) to a concentration of lOug/ml, and then injected at a for 360s at 25 μΐ/minute to achieve immobilization levels between 500 and 800 response units (RU) in vertical orientation. Injection of monomeric CD19-Fc: For one-shot kinetics measurements, injection direction was changed to horizontal orientation, three-fold dilution series of purified monomeric CD19-Fc (varying concentration ranges between 150 and 6 nM) were injected simultaneously at 50μ1/ηιίη along separate channels 1-4, with association times of 180s, and dissociation times of 300s. A human IgG Fc fragment (150nM) was injected in channel 5 as a negative control for specific binding to monomeric CD19-Fc . Buffer (PBST) was injected along the sixth channel to provide an "inline" blank for referencing. An overview of the respective sensorgrams is shown in Figure 33. Regeneration was performed by two pulses of lOmM glycine pH 1.5 and 50mM NaOH for 30s at 90ul/min (vertical orientation). Association rate constants (kon) and dissociation rate constants (koff) were calculated using a simple one-to-one Langmuir binding model in ProteOn Manager v3.1 software by simultaneously fitting the association and dissociation sensorgrams. The equilibrium dissociation constant (KD) was calculated as the ratio koff/kon. A summary of the kinetic and thermodynamic data is shown in Table 60. The dissociation constant of all affinity- matured clones was improved compared to their parental clone 8B8.
Table 60: Summary of the kinetic and thermodynamic data for the interaction between anti-CD19 hulgGI and human CD19 clone ka (1/Ms) kd (1/s) KD (M)
Parental 8B8 5.66E+4 1.34E-4 2.36E-9
5H09 7.91E+4 1.50E-5 1.89E-10
7H07 7.45E+4 5.57E-5 7.47E-10 clone ka (1/Ms) kd (1/s) KD (M)
2B03 6.02E+4 5.00E-5 8.31E-10
2B11 6.34E+4 3.14E-5 4.95E-10
5A07 6.98E+4 3.07E-5 4.40E-10
5B08 6.81E+4 5.26E-5 7.72E-10
5D08 8.88E+4 8.44E-5 9.51E-10
7.2.2.3 Preparation and purification of anti-CD19 IgGl P329G LALA
The selected anti-CD 19 antibodies were produced by co-transfecting HEK293-EBNA cells with the mammalian expression vectors using polyethylenimine. The cells were transfected with the corresponding expression vectors in a 1: 1 ratio ("vector heavy chain": "vector light chain").
For the production in 500 mL shake flasks, 400 million HEK293 EBNA cells were seeded 24 hours before transfection. Before the transfection, cells were centrifuged for 5 minutes at 210 x g, and the supernatant was replaced by pre- warmed CD CHO medium. Expression vectors (200 μg of total DNA) were mixed in 20 mL CD CHO medium. After addition of 540 PEI, the solution was vortexed for 15 seconds and incubated for 10 minutes at room temperature. Afterwards, cells were mixed with the DNA/PEI solution, transferred to a 500 mL shake flask and incubated for 3 hours at 37°C in an incubator with a 5% C02 atmosphere. After the incubation, 160 mL of F17 medium was added and cells were cultured for 24 hours. One day after transfection 1 mM valproic acid and 7% Feed with supplements were added. After culturing for 7 days, the supernatant was collected by centrifugation for 15 minutes at 210 x g. The solution was sterile filtered (0.22 μιη filter), supplemented with sodium azide to a final concentration of 0.01 % (w/v), and kept at 4 °C.
Purification of antibody molecules from cell culture supernatants was carried out by affinity chromatography using Protein A as described above for purification of antigen Fc fusions. The protein was concentrated and filtered prior to loading on a HiLoad Superdex 200 column (GE Healthcare) equilibrated with 20mM Histidine, 140mM NaCl solution of pH 6.0.
The protein concentration of purified antibodies was determined by measuring the OD at 280 nm, using the molar extinction coefficient calculated on the basis of the amino acid sequence. Purity and molecular weight of the antibodies were analyzed by CE-SDS in the presence and absence of a reducing agent (Invitrogen, USA) using a LabChipGXII (Caliper). The aggregate content of antibody samples was analyzed using a TSKgel G3000 SW XL analytical size- exclusion column (Tosoh) equilibrated in a 25 mM K2HP04, 125 mM NaCl, 200mM L-Arginine Monohydrocloride, 0.02 % (w/v) NaN3, pH 6.7 running buffer at 25°C (Table 61). Table 61: Biochemical analysis of anti-CD19 P329G LALA IgGl clones
Figure imgf000281_0001
For the preparation of bispecific constructs clone 2B11 was chosen because it lacks the three deamidation hotspots. The DNA sequence encoding part of the ectodomain (amino acid 71-254 and 71-248) of human 4-lBB ligand was synthetized according to the P41273 sequence of Uniprot database.
7.2.3 Preparation of monovalent CD19 (8B8-2B11) targeted 4-lBB ligand (71-254) trimer-containing Fc (kih) fusion antigen binding molecule with crossed CH1-CL domains with charged residues (Construct 4.1) The construct 4.1 was prepared as described for construct 3.1 (Figure 30), but using the variable region of heavy and light chain DNA sequences encoding a binder specific for CD 19, clone 8B8-2B11.
Table 62 shows the cDNA and amino acid sequences of the monovalent CD19(8B8-2B11) targeted split trimeric 4- IBB ligand (71-254) Fc (kih) fusion antigen binding molecule with crossed CH-CL and charged residues (construct 4.1).
Table 62: cDNA and amino acid sequences of monovalent CD19(8B8-2B11) targeted split trimeric 4-lBB ligand (71-254) Fc (kih) fusion containing CH-CL cross with charged residues (construct 4.1). * for charged residues
SEQ ID Description Sequence
NO:
129 Nucleotide see Table 3
sequence Dimeric
hu 4-lBBL (71- 254) - CL* Fc
knob chain
130 Nucleotide see Table 3
sequence
Monomeric hu 4-1BBL (71-254)
- CHI*
305 Nucleotide CAGGTGCAATTGGTTCAATCTGGTGCTGAAGTAAAAAA sequence anti- ACCGGGCGCTTCCGTTAAAGTGAGCTGCAAAGCATCTGG CD19(8B8-2B 11) TTACACCTTCACTGACTATATCATGCACTGGGTTCGTCA Fc hole chain GGCCCCGGGCCAGGGTCTGGAGTGGATGGGCTACATTA
ACCCATACAACGACGGTTCCAAATATACCGAGAAATTC
CAGGGCCGCGTCACGATGACCAGCGACACTTCTATCTCC
ACCGCGTACATGGAACTGTCTAGACTGCGTTCTGACGAC
ACCGCTGTTTACTATTGTGCACGCGGTACCTACTACTAC
GGTCCACAGCTGTTTGATTACTGGGGCCAAGGTACCACG
GTGACCGTAAGCTCTGCTAGCACCAAGGGCCCCTCCGTG
TTCCCCCTGGCCCCCAGCAGCAAGAGCACCAGCGGCGG
CACAGCCGCTCTGGGCTGCCTGGTCAAGGACTACTTCCC
CGAGCCCGTGACCGTGTCCTGGAACAGCGGAGCCCTGA
CCTCCGGCGTGCACACCTTCCCCGCCGTGCTGCAGAGTT
CTGGCCTGTATAGCCTGAGCAGCGTGGTCACCGTGCCTT
CTAGCAGCCTGGGCACCCAGACCTACATCTGCAACGTG
AACCACAAGCCCAGCAACACCAAGGTGGACAAGAAGGT
GGAGCCCAAGAGCTGCGACAAAACTCACACATGCCCAC
CGTGCCCAGCACCTGAAGCTGCAGGGGGACCGTCAGTC
TTCCTCTTCCCCCCAAAACCCAAGGACACCCTCATGATC
TCCCGGACCCCTGAGGTCACATGCGTGGTGGTGGACGTG
AGCCACGAAGACCCTGAGGTCAAGTTCAACTGGTACGT
GGACGGCGTGGAGGTGCATAATGCCAAGACAAAGCCGC
GGGAGGAGCAGTACAACAGCACGTACCGTGTGGTCAGC
GTCCTCACCGTCCTGCACCAGGACTGGCTGAATGGCAAG
GAGTACAAGTGCAAGGTCTCCAACAAAGCCCTCGGCGC
CCCCATCGAGAAAACCATCTCCAAAGCCAAAGGGCAGC
CCCGAGAACCACAGGTGTGCACCCTGCCCCCATCCCGG
GATGAGCTGACCAAGAACCAGGTCAGCCTCTCGTGCGC
AGTCAAAGGCTTCTATCCCAGCGACATCGCCGTGGAGTG
GGAGAGCAATGGGCAGCCGGAGAACAACTACAAGACC
ACGCCTCCCGTGCTGGACTCCGACGGCTCCTTCTTCCTC
GTGAGCAAGCTCACCGTGGACAAGAGCAGGTGGCAGCA
GGGGAACGTCTTCTCATGCTCCGTGATGCATGAGGCTCT
GCACAACCACTACACGCAGAAGAGCCTCTCCCTGTCTCC
GGGTAAA
277 Nucleotide see Table 59
sequence anti- CD19(8B8-2B 11)
light chain
115 Dimeric hu 4- see Table 3
1BBL (71-254) - CL* Fc knob
chain
116 Monomelic hu see Table 3
4-1BBL (71-254)
- CHI*
306 anti-CD19(8B8- QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMHWVRQ
APGQGLEWMGYINPYNDGSKYTEKFQGRVTMTSDTSISTA 2B11) Fc hole YMELSRLRSDDTAVYYCARGTYYYGPQLFDYWGQGTTVT chain VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVT
VSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQ
TYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAG
GPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNW
YVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLN
GKEYKCKVSNKALGAPIEKTISKAKGQPREPQVCTLPPSRD
ELTKNQVSLSCAVKGFYPSDIAVEWESNGQPENNYKTTPP
VLDSDGSFFLVSKLTVDKSRWQQGNVFSCSVMHEALHNH
YTQKSLSLSPGK
206 anti-CD19(8B8- see Table 59
2bl l) light chain
7.2.4 Preparation of monovalent CD19(8B8-2B11) targeted 4-lBB ligand (71-254) trimer-containing Fc (kih) fusion antigen binding molecule with crossed CH1-CL domains without charged residues (Construct 4.2) The construct 4.2 was prepared as described for construct 3.2 (Figure 30), but using the variable region of heavy and light chain DNA sequences encoding a binder specific for CD 19, clone 8B8-2B11.
Table 63 shows the cDNA and amino acid sequences of the monovalent CD19(8B8-2B11) targeted split trimeric 4- IBB ligand (71-254) Fc (kih) fusion antigen binding molecule containing crossed CH-CL cross without charged residues (construct 4.2).
Table 63: cDNA and amino acid sequences of monovalent CD19(8B8-2B11) targeted split trimeric 4-lBB ligand (71-254) Fc (kih) fusion containing CH-CL cross without charged residues (construct 4.2).
SEQ ID Description Sequence
NO:
165 Nucleotide see Table 22
sequence dimeric
ligand (71-254)- CL Fc knob chain
166 Nucleotide see Table 22
sequence
monomeric hu
4-1BBL (71-254)
- CHI
305 Nucleotide see Table 62
sequence anti- CD19(8B8-2B11)
Fc hole chain 277 Nucleotide see Table 59
sequence anti- CD19(8B8-2B11)
light chain
117 Dimeric ligand see Table 22
(71-254) - CL Fc
knob chain
118 Monomeric see Table 22
ligand (71-254) - CH1
306 anti-CD19(8B8- see Table 62
2B11) Fc hole
chain
279 anti-CD19(8B8- see Table 59
018) light chain
7.2.5 Preparation of bivalent CD19(8B8-2B11) targeted 4-1BB ligand (71-254) trimer- containing Fc (kih) fusion antigen binding (Construct 4.3)
The construct 4.3 was prepared as described for construct 3.3 (Figure 30), but using the variable region of heavy and light chain DNA sequences encoding a binder specific for CD 19, clone 8B8-2B11.
Table 64 shows the cDNA and amino acid sequences of the bivalent CD19 (8B8-2B11) targeted split trimeric 4- IBB ligand (71-254) Fc (kih) fusion antigen binding molecule (construct 4.3).
Table 64: cDNA and amino acid sequences of bivalent CD19(8B8-2B11) targeted split trimeric 4- IBB ligand Fc (kih) PGLALA fusion (construct 4.3)
SEQ ID Description Sequence
NO:
307 Nucleotide CAGGTGCAATTGGTTCAATCTGGTGCTGAAGTAAAAAA sequence anti- ACCGGGCGCTTCCGTTAAAGTGAGCTGCAAAGCATCTGG CD19(8B8-2B11) TTACACCTTCACTGACTATATCATGCACTGGGTTCGTCA Fc hole dimeric GGCCCCGGGCCAGGGTCTGGAGTGGATGGGCTACATTA ligand chain ACCCATACAACGACGGTTCCAAATATACCGAGAAATTC
CAGGGCCGCGTCACGATGACCAGCGACACTTCTATCTCC
ACCGCGTACATGGAACTGTCTAGACTGCGTTCTGACGAC
ACCGCTGTTTACTATTGTGCACGCGGTACCTACTACTAC
GGTCCACAGCTGTTTGATTACTGGGGCCAAGGTACCACG
GTGACCGT AAGCTCTGCTAGCACCAAGGGCCCCTCCGTGT
TCCCCCTGGCCCCCAGCAGCAAGAGCACCAGCGGCGGCAC
AGCCGCTCTGGGCTGCCTGGTCAAGGACTACTTCCCCGAG
CCCGTGACCGTGTCCTGGAACAGCGGAGCCCTGACCTCCG
GCGTGCA CA CCTTCCCCGCCGTGCTGCA GAGTTCTGGCCT GTATAGCCTGAGCAGCGTGGTCACCGTGCCTTCTAGCAGCC
TGGGCACCCAGACCTACATCTGCAACGTGAACCACAAGCCC
AGCAACACCAAGGTGGACAAGAAGGTGGAGCCCAAGAGCT
GCGACAAAACTCACACATGCCCACCGTGCCCAGCACCTGAA
GCTGCAGGGGGACCGTCAGTCTTCCTCTTCCCCCCAAAACC
CAAGGACACCCTCATGATCTCCCGGACCCCTGAGGTCACAT
GCGTGGTGGTGGACGTGAGCCACGAAGACCCTGAGGTCAA
GTTCAA CTGGTA CGTGGA CGGCGTGGAGGTGCA TAA TGCCA
AGACAAAGCCGCGGGAGGAGCAGTACAACAGCACGTACCG
TGTGGTCAGCGTCCTCACCGTCCTGCACCAGGACTGGCTGA
ATGGCAAGGAGTACAAGTGCAAGGTCTCCAACAAAGCCCTC
GGCGCCCCCATCGAGAAAACCATCTCCAAAGCCAAAGGGC
AGCCCCGAGAACCACAGGTGTGCACCCTGCCCCCATCCCG
GGATGAGCTGACCAAGAACCAGGTCAGCCTCTCGTGCGCA
GTCAAAGGCTTCTATCCCAGCGACATCGCCGTGGAGTGGGA
GAGCAATGGGCAGCCGGAGAACAACTACAAGACCACGCCT
CCCGTGCTGGACTCCGACGGCTCCTTCTTCCTCGTGAGCAA
GCTCACCGTGGACAAGAGCAGGTGGCAGCAGGGGAACGTC
TTCTCA TGCTCCGTGA TGCA TGAGGCTCTGCA CAA CCA CTA
CACGCAGAAGAGCCTCTCCCTGTCTCCGGGTGGAGGCGGC
GGAAGCGGAGGAGGAGGATCCAGAGAGGGCCCTGAGCTG
AGCCCCGATGATCCTGCTGGACTGCTGGACCTGCGGCAGG
GCA TGTTTGCTCAGCTGGTGGCCCAGAA CGTGCTGCTGA TC
GATGGCCCCCTGTCCTGGTACAGCGATCCTGGACTGGCTG
GCGTGTCACTGACAGGCGGCCTGAGCTACAAAGAGGACAC
CAAAGAACTGGTGGTGGCCAAGGCCGGCGTGTACTACGTG
TTCTTTCAGCTGGAACTGCGGAGAGTGGTGGCCGGCGAAG
GATCTGGCTCTGTGTCTCTGGCCCTGCATCTGCAGCCTCTG
AGAAGCGCTGCTGGCGCTGCAGCTCTGGCACTGACAGTGG
ATCTGCCTCCTGCCAGCTCCGAGGCCCGGAATAGCGCATTT
GGGTTTCAAGGCAGGCTGCTGCACCTGTCTGCCGGCCAGA
GGCTGGGAGTGCATCTGCACACAGAGGCCAGGGCTAGACA
CGCCTGGCAGCTGACACAGGGCGCTACAGTGCTGGGCCTG
TTCAGAGTGACCCCCGAGATTCCAGCCGGCCTGCCTTCTCC
AAGAAGCGAAGGCGGAGGCGGATCTGGCGGCGGAGGATC
TAGAGAGGGACCCGAACTGTCCCCTGACGATCCAGCCGGG
CTGCTGGATCTGAGACAGGGAATGTTCGCCCAGCTGGTGG
CTCAGAA TGTGCTGCTGA TTGA CGGA CCTCTGAGCTGGTA C
TCCGACCCAGGGCTGGCAGGGGTGTCCCTGACTGGGGGAC
TGTCCTACAAAGAAGATACAAAAGAACTGGTGGTGGCTAAA
GGTGGTGGCTGGGGAGGGCTCAGGATCTGTGTCCCTGGCT
CTGCATCTGCAGCCACTGCGCTCTGCTGCTGGCGCAGCTG
CACTGGCTCTGACTGTGGACCTGCCACCAGCCTCTAGCGAG
GCCAGAAACAGCGCCTTCGGGTTCCAAGGACGCCTGCTGC
ATCTGAGCGCCGGACAGCGCCTGGGAGTGCATCTGCATAC
TGAAGCCAGAGCCCGGCATGCTTGGCAGCTGACTCAGGGG
GCAA CTGTGCTGGGA CTGTTTCGCGTGA CA CCTGAGA TCCC
TGCCGGACTGCCAAGCCCTAGATCAGAA
Nucleotide CAGGTGCAATTGGTTCAATCTGGTGCTGAAGTAAAAAA sequence anti- ACCGGGCGCTTCCGTTAAAGTGAGCTGCAAAGCATCTGG CD19(8B8-2B 11) TTACACCTTCACTGACTATATCATGCACTGGGTTCGTCA Fc knob GGCCCCGGGCCAGGGTCTGGAGTGGATGGGCTACATTA
ACCCATACAACGACGGTTCCAAATATACCGAGAAATTC monomeric ligand CAGGGCCGCGTCACGATGACCAGCGACACTTCTATCTCC
ACCGCGTACATGGAACTGTCTAGACTGCGTTCTGACGAC
ACCGCTGTTTACTATTGTGCACGCGGTACCTACTACTAC
GGTCCACAGCTGTTTGATTACTGGGGCCAAGGTACCACG
GTGACCGT AAGCT TGCTAGCACCAAGGGCCCATCGGTCT
TCCCCCTGGCACCCTCCTCCAAGAGCACCTCTGGGGGCAC
AGCGGCCCTGGGCTGCCTGGTCAAGGA CTA CTTCCCCGAA
CCGGTGACGGTGTCGTGGAACTCAGGCGCCCTGACCAGCG
GCGTGCACACCTTCCCGGCTGTCCTACAGTCCTCAGGACTC
TACTCCCTCAGCAGCGTGGTGACCGTGCCCTCCAGCAGCTT
GGGCACCCAGACCTACATCTGCAACGTGAATCACAAGCCCA
GCAACACCAAGGTGGACAAGAAAGTTGAGCCCAAATCTTGT
GACAAAACTCACACATGCCCACCGTGCCCAGCACCTGAAGC
TGCAGGGGGACCGTCAGTCTTCCTCTTCCCCCCAAAACCCA
AGGACACCCTCATGATCTCCCGGACCCCTGAGGTCACATGC
GTGGTGGTGGACGTGAGCCACGAAGACCCTGAGGTCAAGT
TCAACTGGTACGTGGACGGCGTGGAGGTGCATAATGCCAA
GACAAAGCCGCGGGAGGAGCAGTACAACAGCACGTACCGT
GTGGTCAGCGTCCTCACCGTCCTGCACCAGGACTGGCTGA
ATGGCAAGGAGTACAAGTGCAAGGTCTCCAACAAAGCCCTC
GGCGCCCCCATCGAGAAAACCATCTCCAAAGCCAAAGGGC
AGCCCCGAGAACCACAGGTGTACACCCTGCCCCCCTGCAG
AGATGAGCTGACCAAGAACCAGGTGTCCCTGTGGTGTCTGG
TCAAGGGCTTCTACCCCAGCGATATCGCCGTGGAGTGGGA
GAGCAACGGCCAGCCTGAGAACAACTACAAGACCACCCCC
CCTGTGCTGGACAGCGACGGCAGCTTCTTCCTGTACTCCAA
ACTGACCGTGGACAAGAGCCGGTGGCAGCAGGGCAACGTG
TTCAGCTGCAGCGTGA TGCA CGAGGCCCTGCA CAA CCA CTA
CACCCAGAAGTCCCTGAGCCTGAGCCCCGGCGGAGGCGG
CGGAAGCGGAGGAGGAGGATCCAGAGAGGGCCCTGAGCT
GAGCCCCGATGATCCTGCTGGACTGCTGGACCTGCGGCAG
GGCATGTTTGCTCAGCTGGTGGCCCAGAACGTGCTGCTGAT
CGATGGCCCCCTGTCCTGGTACAGCGATCCTGGACTGGCT
GGCGTGTCACTGACAGGCGGCCTGAGCTACAAAGAGGACA
CCAAAGAACTGGTGGTGGCCAAGGCCGGCGTGTACTACGT
GTTCTTTCAGCTGGAACTGCGGAGAGTGGTGGCCGGCGAA
GGATCTGGCTCTGTGTCTCTGGCCCTGCATCTGCAGCCTCT
GAGAAGCGCTGCTGGCGCTGCAGCTCTGGCACTGACAGTG
GATCTGCCTCCTGCCAGCTCCGAGGCCCGGAATAGCGCATT
TGGGTTTCAAGGCAGGCTGCTGCACCTGTCTGCCGGCCAG
AGGCTGGGAGTGCATCTGCACACAGAGGCCAGGGCTAGAC
ACGCCTGGCAGCTGACACAGGGCGCTACAGTGCTGGGCCT
GTTCAGAGTGACCCCCGAGATTCCAGCCGGCCTGCCTTCTC
CAAGAAGCGAA
277 Nucleotide see Table 59
sequence anti- CD19(8B8-018)
light chain
309 anti-CD19(8B8- QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMHWVRQ
2B11) Fc hole APGQGLEWMGYINPYNDGSKYTEKFQGRVTMTSDTSISTA dimeric ligand YMELSRLRSDDTAVYYCARGTYYYGPQLFDYWGQGTTVT chain YSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSW
NSGALTSGVHTFPAVLQSSGLYSLSSWTVPSSSLGTQTYICNVN HKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGGPSVFLFPP
KPKDTLMISRTPEVTCVWDVSHEDPEVKFNWYVDGVEVHNA
KTKPREEQYNSTYRWSVLTVLHQDWLNGKEYKCKVSNKALG
APIEKTISKAKGQPREPQVCTLPPSRDELTKNQVSLSCAVKGFY
PSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLVSKLTVDKSR
WQQGNVFSCSVMHEALHNHYTQKSLSLSPGGGGGSGGGGSR
EGPELSPDDPAGLLDLR QGMFA QLVA QNVLLIDGPLSWYSDP
GLAGVSLTGGLSYKEDTKELWAKAGVYYVFFQLELRRWAGE
GSGSVSLALHLQPLRSAAGAAALALTVDLPPASSEARNSAFGFQ
GRLLHLSAGQRLGVHLHTEARARHAWQLTQGATVLGLFRVTP
EIPAGLPSPRSEGGGGSGGGGSREGPELSPDDPAGLLDLRQG
MFAQLVAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYKEDTKEL
WAKAGVYYVFFQLELRRWAGEGSGSVSLALHLQPLRSAAGA
AALALTVDLPPASSEARNSAFGFQGRLLHLSAGQRLGVHLHTE
ARARHAWQLTQGATVLGLFRVTPEIPAGLPSPRSE
310 anti-CD19(8B8- QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMHWVRQ
2B11) Fc knob APGQGLEWMGYINPYNDGSKYTEKFQGRVTMTSDTSISTA monomeric ligand YMELSRLRSDDTAVYYCARGTYYYGPQLFDYWGQGTTVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSW
NSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVN
HKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGGPSVFLFPP
KPKDTLMISRTPEVTCVWDVSHEDPEVKFNWYVDGVEVHNA
KTKPREEQYNSTYRWSVLTVLHQDWLNGKEYKCKVSNKALG
APIEKTISKAKGQPREPQVYTLPPCRDELTKNQVSLWCLVKGF
YPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKS
RWQQGNVFSCSVMHEALHNHYTQKSLSLSPGGGGGSGGGGS
REGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWYSD
PGLAGVSLTGGLSYKEDTKELWAKAGVYYVFFQLELRRWAG
EGSGSVSLALHLQPLRSAAGAAALALTVDLPPASSEARNSAFGF
QGRLLHLSAGQRLGVHLHTEARARHAWQLTQGATVLGLFRVT
PEIPAGLPSPRSE
279 anti-CD19(8B8- see Table 59
018) light chain
7.2.6 Preparation of monovalent CD19(8B8-2B11) targeted 4-1BB ligand (71-248) trimer-containing Fc (kih) fusion antigen binding molecule with crossed CH1-CL domains with charged residues (Construct 4.4) The construct 4.4 was prepared as described for construct 3.4 (Figure 30), but using the variable region of heavy and light chain DNA sequences encoding a binder specific for CD 19, clone 8B8-2B 11.
Table 65 shows the cDNA and amino acid sequences of the monovalent CD19(8B8-2B 11) targeted split trimeric 4- IBB ligand (71-248) Fc (kih) fusion antigen binding molecule with crossed CH-CL and charged residues (construct 4.4). Table 65: cDNA and amino acid sequences of monovalent CD19(8B8-2B11) targeted split trimeric 4-lBB ligand (71-248) Fc (kih) fusion containing CH-CL cross with charged residues (construct 4.4). * charged residues
Figure imgf000288_0001
7.2.7 Preparation of monovalent CD19(8B8-2B11) targeted 4-lBB ligand (71-248) trimer-containing Fc (kih) fusion antigen binding molecule with crossed CH1-CL domains without charged residues (Construct 4.5)
The construct 4.5 was prepared as described for construct 3.5 (Figure 30), but using the variable region of heavy and light chain DNA sequences encoding a binder specific for CD 19, clone 8B8-2B11. Table 66 shows the cDNA and amino acid sequences of the monovalent CD19(8B8-2B11) targeted split trimeric 4- IBB ligand (71-248) Fc (kih) fusion antigen binding molecule containing crossed CH-CL cross without charged residues (construct 4.5).
Table 66: cDNA and amino acid sequences of monovalent CD19(8B8-2B11) targeted split trimeric 4-lBB ligand (71-248) Fc (kih) fusion containing CH-CL cross without charged residues (construct 4.5).
Figure imgf000289_0001
7.2.8 Preparation of bivalent CD19(8B8-2B11) targeted 4-lBB ligand (71-248) trimer- containing Fc (kih) fusion antigen binding (Construct 4.6) The construct 4.6 was prepared as described for construct 3.6 (Figure 30), but using the variable region of heavy and light chain DNA sequences encoding a binder specific for CD 19, clone 8B8-2B11. Table 67 shows the cDNA and amino acid sequences of the bivalent CD19(8B8-2B11) targeted split trimeric 4- IBB ligand (71-248) Fc (kih) fusion antigen binding molecule (construct 3.6).
Table 67: cDNA and amino acid sequences of bivalent CD19(8B8-2B11) targeted split trimeric 4-1BB ligand (71-248) Fc (kih) fusion (construct 4.6)
SEQ ID Description Sequence
NO:
311 Nucleotide CAGGTGCAATTGGTTCAATCTGGTGCTGAAGTAAAAAA sequence anti- ACCGGGCGCTTCCGTTAAAGTGAGCTGCAAAGCATCTGG CD19(8B8-2B11) TTACACCTTCACTGACTATATCATGCACTGGGTTCGTCA Fc hole dimeric GGCCCCGGGCCAGGGTCTGGAGTGGATGGGCTACATTA ligand (71-248) ACCCATACAACGACGGTTCCAAATATACCGAGAAATTC
CAGGGCCGCGTCACGATGACCAGCGACACTTCTATCTCC
chain
ACCGCGTACATGGAACTGTCTAGACTGCGTTCTGACGAC
ACCGCTGTTTACTATTGTGCACGCGGTACCTACTACTAC
GGTCCACAGCTGTTTGATTACTGGGGCCAAGGTACCACG
GTGACCGT AAGCT TGCTAGCACCAAGGGCCCCTCCGTGT
TCCCCCTGGCCCCCAGCAGCAAGAGCACCAGCGGCGGCAC
AGCCGCTCTGGGCTGCCTGGTCAAGGACTACTTCCCCGAG
CCCGTGACCGTGTCCTGGAACAGCGGAGCCCTGACCTCCG
GCGTGCA CA CCTTCCCCGCCGTGCTGCA GAGTTCTGGCCT
GTATAGCCTGAGCAGCGTGGTCACCGTGCCTTCTAGCAGCC
TGGGCACCCAGACCTACATCTGCAACGTGAACCACAAGCCC
AGCAACACCAAGGTGGACAAGAAGGTGGAGCCCAAGAGCT
GCGACAAAACTCACACATGCCCACCGTGCCCAGCACCTGAA
GCTGCAGGGGGACCGTCAGTCTTCCTCTTCCCCCCAAAACC
CAAGGACACCCTCATGATCTCCCGGACCCCTGAGGTCACAT
GCGTGGTGGTGGACGTGAGCCACGAAGACCCTGAGGTCAA
GTTCAA CTGGTA CGTGGA CGGCGTGGAGGTGCA TAA TGCCA
AGACAAAGCCGCGGGAGGAGCAGTACAACAGCACGTACCG
TGTGGTCAGCGTCCTCACCGTCCTGCACCAGGACTGGCTGA
ATGGCAAGGAGTACAAGTGCAAGGTCTCCAACAAAGCCCTC
GGCGCCCCCATCGAGAAAACCATCTCCAAAGCCAAAGGGC
AGCCCCGAGAACCACAGGTGTGCACCCTGCCCCCATCCCG
GGATGAGCTGACCAAGAACCAGGTCAGCCTCTCGTGCGCA
GTCAAAGGCTTCTATCCCAGCGACATCGCCGTGGAGTGGGA
GAGCAATGGGCAGCCGGAGAACAACTACAAGACCACGCCT
CCCGTGCTGGACTCCGACGGCTCCTTCTTCCTCGTGAGCAA
GCTCACCGTGGACAAGAGCAGGTGGCAGCAGGGGAACGTC
TTCTCA TGCTCCGTGA TGCA TGAGGCTCTGCA CAA CCA CTA
CACGCAGAAGAGCCTCTCCCTGTCTCCGGGTGGAGGCGGC
GGAAGCGGAGGAGGAGGATCCAGAGAGGGCCCTGAGCTG
AGCCCTGATGATCCTGCCGGACTGCTGGACCTGCGGCAGG
GAA TGTTTGCCCAGCTGGTGGCCCAGAA CGTGCTGCTGA TC
GATGGCCCCCTGTCCTGGTACAGCGATCCTGGACTGGCTG
GCGTGTCACTGACAGGCGGCCTGAGCTACAAAGAGGACAC
CAAAGAACTGGTGGTGGCCAAGGCCGGCGTGTACTACGTG
TTCTTTCAGCTGGAACTGCGGAGAGTGGTGGCCGGCGAAG
GATCTGGCTCTGTGTCTCTGGCCCTGCATCTGCAGCCTCTG
AGATCTGCTGCTGGCGCCGCTGCTCTGGCACTGACAGTGG ATCTGCCTCCTGCCAGCAGCGAGGCCCGGAATAGCGCATTT
GGGTTTCAAGGCAGGCTGCTGCACCTGTCTGCCGGCCAGA
GGCTGGGAGTGCATCTGCACACAGAGGCCAGGGCTAGACA
CGCCTGGCAGCTGACACAGGGCGCTACAGTGCTGGGCCTG
TTCAGAGTGACCCCCGAGATTCCAGCAGGCCTGGGAGGCG
GCGGATCTGGCGGCGGAGGATCTAGAGAAGGACCCGAGCT
GTCCCCCGACGATCCCGCTGGGCTGCTGGATCTGAGACAG
GGCATGTTCGCTCAGCTGGTGGCTCAGAATGTGCTGCTGAT
TGACGGACCTCTGAGCTGGTACTCCGACCCAGGGCTGGCA
GGGGTGTCCCTGACTGGGGGACTGTCCTACAAAGAAGATAC
AAAAGAACTGGTGGTGGCTAAAGCTGGGGTGTACTATGTGT
CTCAGGATCTGTGTCCCTGGCTCTGCATCTGCAGCCACTGC
GCTCTGCAGCAGGGGCTGCAGCACTGGCCCTGACTGTGGA
CCTGCCCCCAGCTTCTTCCGAGGCCAGAAACAGCGCCTTCG
GGTTCCAAGGACGCCTGCTGCATCTGAGCGCCGGACAGCG
CCTGGGAGTGCATCTGCATACTGAAGCCAGAGCCCGGCAT
GCTTGGCAGCTGA CTCA GGGGGCAA CTGTGCTGGGA CTGT
TTCGCGTGA CA CCTGAGA TCCCAGCCGGGCTC
Nucleotide CAGGTGCAATTGGTTCAATCTGGTGCTGAAGTAAAAAA sequence anti- ACCGGGCGCTTCCGTTAAAGTGAGCTGCAAAGCATCTGG CD19(8B8-2B 11) TTACACCTTCACTGACTATATCATGCACTGGGTTCGTCA Fc knob GGCCCCGGGCCAGGGTCTGGAGTGGATGGGCTACATTA
ACCCATACAACGACGGTTCCAAATATACCGAGAAATTC
monomeric (71-
CAGGGCCGCGTCACGATGACCAGCGACACTTCTATCTCC
248) ligand
ACCGCGTACATGGAACTGTCTAGACTGCGTTCTGACGAC
ACCGCTGTTTACTATTGTGCACGCGGTACCTACTACTAC
GGTCCACAGCTGTTTGATTACTGGGGCCAAGGTACCACG
GTGACCGT AAGCT TGCTAGCACCAAGGGCCCATCGGTCT
TCCCCCTGGCACCCTCCTCCAAGAGCACCTCTGGGGGCAC
AGCGGCCCTGGGCTGCCTGGTCAAGGA CTA CTTCCCCGAA
CCGGTGACGGTGTCGTGGAACTCAGGCGCCCTGACCAGCG
GCGTGCACACCTTCCCGGCTGTCCTACAGTCCTCAGGACTC
TACTCCCTCAGCAGCGTGGTGACCGTGCCCTCCAGCAGCTT
GGGCACCCAGACCTACATCTGCAACGTGAATCACAAGCCCA
GCAACACCAAGGTGGACAAGAAAGTTGAGCCCAAATCTTGT
GACAAAACTCACACATGCCCACCGTGCCCAGCACCTGAAGC
TGCAGGGGGACCGTCAGTCTTCCTCTTCCCCCCAAAACCCA
AGGACACCCTCATGATCTCCCGGACCCCTGAGGTCACATGC
GTGGTGGTGGACGTGAGCCACGAAGACCCTGAGGTCAAGT
TCAACTGGTACGTGGACGGCGTGGAGGTGCATAATGCCAA
GACAAAGCCGCGGGAGGAGCAGTACAACAGCACGTACCGT
GTGGTCAGCGTCCTCACCGTCCTGCACCAGGACTGGCTGA
ATGGCAAGGAGTACAAGTGCAAGGTCTCCAACAAAGCCCTC
GGCGCCCCCATCGAGAAAACCATCTCCAAAGCCAAAGGGC
AGCCCCGAGAACCACAGGTGTACACCCTGCCCCCCTGCAG
AGATGAGCTGACCAAGAACCAGGTGTCCCTGTGGTGTCTGG
TCAAGGGCTTCTACCCCAGCGATATCGCCGTGGAGTGGGA
GAGCAACGGCCAGCCTGAGAACAACTACAAGACCACCCCC
CCTGTGCTGGACAGCGACGGCAGCTTCTTCCTGTACTCCAA
ACTGACCGTGGACAAGAGCCGGTGGCAGCAGGGCAACGTG
TTCAGCTGCAGCGTGA TGCA CGAGGCCCTGCA CAA CCA CTA
CACCCAGAAGTCCCTGAGCCTGAGCCCCGGCGGAGGCGG
CGGAAGCGGAGGAGGAGGATCCAGAGAGGGCCCTGAGCT GAGCCCTGATGATCCTGCCGGACTGCTGGACCTGCGGCAG
GGAATGTTTGCCCAGCTGGTGGCCCAGAACGTGCTGCTGAT
CGATGGCCCCCTGTCCTGGTACAGCGATCCTGGACTGGCT
GGCGTGTCACTGACAGGCGGCCTGAGCTACAAAGAGGACA
CCAAAGAACTGGTGGTGGCCAAGGCCGGCGTGTACTACGT
GTTCTTTCAGCTGGAACTGCGGAGAGTGGTGGCCGGCGAA
GGATCTGGCTCTGTGTCTCTGGCCCTGCATCTGCAGCCTCT
GAGATCTGCTGCTGGCGCCGCTGCTCTGGCACTGACAGTG
GATCTGCCTCCTGCCAGCAGCGAGGCCCGGAATAGCGCAT
TTGGGTTTCAAGGCAGGCTGCTGCACCTGTCTGCCGGCCA
GAGGCTGGGAGTGCATCTGCACACAGAGGCCAGGGCTAGA
CACGCCTGGCAGCTGACACAGGGCGCTACAGTGCTGGGCC
TGTTCAGAGTGACCCCCGAGATTCCTGCCGGGCTC
277 Nucleotide see Table 59
sequence anti- CD19(8B8-2B 11)
light chain
313 anti-CD19(8B8- QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMHWVRQ
2B11) Fc hole APGQGLEWMGYINPYNDGSKYTEKFQGRVTMTSDTSISTA dimeric ligand YMELSRLRSDDTAVYYCARGTYYYGPQLFDYWGQGTTVT (71-248) chain YSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSW
NSGALTSGVHTFPAVLQSSGLYSLSSWTVPSSSLGTQTYICNVN
HKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGGPSVFLFPP
KPKDTLMISRTPEVTCVWDVSHEDPEVKFNWYVDGVEVHNA
KTKPREEQYNSTYRWSVLTVLHQDWLNGKEYKCKVSNKALG
APIEKTISKAKGQPREPQVCTLPPSRDELTKNQVSLSCAVKGFY
PSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLVSKLTVDKSR
WQQGNVFSCSVMHEALHNHYTQKSLSLSPGGGGGSGGGGSR
EGPELSPDDPAGLLDLR QGMFA QLVA QNVLLIDGPLSWYSDP
GLAGVSLTGGLSYKEDTKELWAKAGVYYVFFQLELRRWAGE
GSGSVSLALHLQPLRSAAGAAALALTVDLPPASSEARNSAFGFQ
GRLLHLSAGQRLGVHLHTEARARHAWQLTQGATVLGLFRVTP
EIPAGLGGGGSGGGGSREGPELSPDDPAGLLDLRQGMFAQL
VAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYKEDTKELWAKA
GVYYVFFQLELRRWAGEGSGSVSLALHLQPLRSAAGAAALALT
VDLPPASSEARNSAFGFQGRLLHLSAGQRLGVHLHTEARARHA
WQLTQGATVLGLFRVTPEIPAGL
314 anti-CD19(8B8- QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMHWVRQ
2B11) Fc knob APGQGLEWMGYINPYNDGSKYTEKFQGRVTMTSDTSISTA monomeric (71- YMELSRLRSDDTAVYYCARGTYYYGPQLFDYWGQGTTVT 248) ligand VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSW
NSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVN
HKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGGPSVFLFPP
KPKDTLMISRTPEVTCVWDVSHEDPEVKFNWYVDGVEVHNA
KTKPREEQYNSTYRWSVLTVLHQDWLNGKEYKCKVSNKALG
APIEKTISKAKGQPREPQVYTLPPCRDELTKNQVSLWCLVKGF
YPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKS
RWQQGNVFSCSVMHEALHNHYTQKSLSLSPGGGGGSGGGGS
REGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWYSD
PGLAGVSLTGGLSYKEDTKELWAKAGVYYVFFQLELRRWAG
EGSGSVSLALHLQPLRSAAGAAALALTVDLPPASSEARNSAFGF
QGRLLHLSAGQRLGVHLHTEARARHAWQLTQGATVLGLFRVT PEIPAGL
279 anti-CD19(8B8- see Table 59
018) light chain
7.3 Preparation of untargeted split trimeric 4- IBB ligand Fc fusion and human IgG as control molecules
7.3.1 Preparation of untargeted human 4-1BB ligand trimer-containing Fc fusion antigen binding molecules (Control molecules)
These control molecules were prepared as described above for the CD 19 targeted construct 3.1 (termed control B), 3.3 (termed control C), 3.4 (termed control D) and 3.5 (termed control E) with the only difference that the anti-CD 19 binder (VH-VL) was replaced by a germline control, termed DP47, not binding to the antigen (see Figure 30). Table 68 shows, respectively, the cDNA and amino acid sequences of the monovalent
DP47 -untargeted split trimeric 4- IBB ligand (71-254) Fc (kih) fusion containing crossed CH-CL with charged residues, control B.
Table 69 shows, respectively, the cDNA and amino acid sequences of the bivalent DP47- untargeted split trimeric 4- IBB ligand (71-254) Fc (kih) fusion, control C. Table 70 shows, respectively, the cDNA and amino acid sequences of the monovalent
DP47 -untargeted split trimeric 4- IBB ligand (71-248) Fc (kih) fusion containing CH-CL cross with charged residues, control D.
Table 71 shows, respectively, the cDNA and amino acid sequences of the monovalent DP47 -untargeted split trimeric 4- IBB ligand (71-248) Fc (kih) fusion without charged residues in the CH-CL cross, control E.
Table 68: cDNA and amino acid sequences of monovalent DP47 untargeted split trimeric human 4-1BB ligand (71-254) Fc (kih) fusion with CH-CL cross and with charged residues (control B). * charges residues
SEQ ID Description Sequence
NO:
96 nucleotide sequence dimeric hu 4- 1BBL see Table 3
(71-254) - CL* Fc knob chain
97 nucleotide sequence monomeric hu see Table 3
4-1BBL (71-254) - CHI*
79 nucleotide sequence DP47 Fc hole chain see Table 18
80 nucleotide sequence DP47 light chain see Table 18
98 Dimeric hu 4-1BBL (71-254) - CL* Fc see Table 3 knob chain
99 Monomelic hu see Table 3
4-1BBL (71-254) - CHI*
81 DP47 Fc hole chain see Table 18
82 DP47 light chain see Table 18
Table 69: cDNA and amino acid sequences of bivalent DP47 untargeted split trimeric human 4-lBB ligand (71-254) Fc (kih) fusion (control C).
SEQ ID Description Sequence
NO:
177 nucleotide sequence DP47 Fc hole chain see Table 27
fused to dimeric hu 4-1BBL (71-254)
178 nucleotide sequence DP47 Fc knob chain see Table 27
fused to monomeric hu 4-1BBL (71-254)
80 nucleotide sequence DP47 light chain see Table 18
179 DP47 Fc hole chain fused to dimeric hu 4- see Table 27
1BBL (71-254)
180 DP47 Fc knob chain fused to monomeric see Table 27
hu 4-lBBL (71-254)
82 DP47 light chain see Table 18
Table 70: cDNA and amino acid sequences of monovalent DP47 untargeted split trimeric human 4-lBB ligand (71-248) Fc (kih) fusion with CH-CL cross and with charged residues (control D). * charged residues
SEQ ID Description Sequence
NO:
169 nucleotide sequence dimeric hu 4-1BBL see Table 24
(71-248) - CL* Fc knob chain
170 nucleotide sequence monomeric hu see Table 24
4-1BBL (71-248) - CHI*
79 nucleotide sequence DP47 Fc hole chain see Table 18
80 nucleotide sequence DP47 light chain see Table 18
119 Dimeric hu 4-1BBL (71-254) - CL* Fc see Table 24
knob chain
120 Monomeric hu see Table 24
4-1BBL (71-254) - CHI*
81 DP47 Fc hole chain see Table 18
82 DP47 light chain see Table 18 Table 71: cDNA and amino acid sequences of monovalent DP47 untargeted split trimeric human 4-lBB ligand (71-248) Fc (kih) fusion with CH-CL cross and without charged residues (control E).
Figure imgf000295_0001
7.3.2 Antibodies as Control Molecules
Two control human IgGl containing PGLALA were prepared.
Table 72 shows the cDNA and amino acid sequences of the anti-CD 19 hulgGI PGLALA (clone 8B8-018), i.e. control G.
Table 73 shows the cDNA and amino acid sequences of germline control DP47 hulgGI PGLALA (control F).
Table 72: cDNA and amino acid sequences of anti-CD19(8B8-018) hulgGI PGLALA (control G)
SEQ ID Description Sequence
NO:
315 nucleotide sequence CAGGTCCAGCTGGTGCAGTCCGGCGCCGAGGT
CD19(8B8-018) heavy CAAGAAACCCGGGGCTTCTGTGAAGGTTTCAT chain (hulgGI PGLALA) GCAAGGCAAGCGGATACACCTTCACCGACTAT
ATCATGCATTGGGTCAGGCAGGCCCCTGGCCA
AGGTCTCGAATGGATGGGCTACATTAACCCAT
ATAATGATGGCTCCAAATACACCGAGAAGTTT
CAGGGAAGAGTCACTATGACATCTGACACCAG
TATCAGCACTGCTTACATGGAGCTGTCCCGCC
TTCGGTCTGATGACACCGCAGTGTATTACTGT GCCAGGGGCACATATTACTACGGCTCAGCTCT
GTTCGACTATTGGGGGCAGGGAACCACAGTAA
CCGTGAGCTCCGCAAGTACTAAGGGCCCATCG
GTCTTCCCCCTGGCACCCTCCTCCAAGAGCAC
CTCTGGGGGCACAGCGGCCCTGGGCTGCCTGG
TCAAGGACTACTTCCCCGAACCGGTGACGGTG
TCGTGGAACTCAGGCGCCCTGACCAGCGGCGT
GCACACCTTCCCGGCTGTCCTACAGTCCTCAG
GACTCTACTCCCTCAGCAGCGTGGTGACCGTG
CCCTCCAGCAGCTTGGGCACCCAGACCTACAT
CTGCAACGTGAATCACAAGCCCAGCAACACCA
AGGTGGACAAGAAAGTTGAGCCCAAATCTTGT
GACAAAACTCACACATGCCCACCGTGCCCAGC
ACCTGAAGCAGCTGGGGGACCGTCAGTCTTCC
TCTTCCCCCCAAAACCCAAGGACACCCTCATG
ATCTCCCGGACCCCTGAGGTCACATGCGTGGT
GGTGGACGTGAGCCACGAAGACCCTGAGGTC
AAGTTCAACTGGTACGTGGACGGCGTGGAGGT
GCATAATGCCAAGACAAAGCCGCGGGAGGAG
CAGTACAACAGCACGTACCGTGTGGTCAGCGT
CCTCACCGTCCTGCACCAGGACTGGCTGAATG
GCAAGGAGTACAAGTGCAAGGTCTCCAACAA
AGCCCTCGGAGCCCCCATCGAGAAAACCATCT
CCAAAGCCAAAGGGCAGCCCCGAGAACCACA
GGTGTACACCCTGCCCCCATCCCGGGATGAGC
TGACCAAGAACCAGGTCAGCCTGACCTGCCTG
GTCAAAGGCTTCTATCCCAGCGACATCGCCGT
GGAGTGGGAGAGCAATGGGCAGCCGGAGAAC
AACTACAAGACCACGCCTCCCGTGCTGGACTC
CGACGGCTCCTTCTTCCTCTACAGCAAGCTCAC
CGTGGACAAGAGCAGGTGGCAGCAGGGGAAC
GTCTTCTCATGCTCCGTGATGCATGAGGCTCTG
CACAACCACTACACGCAGAAGAGCCTCTCCCT
GTCCCCGGGCAAA
204 nucleotide sequence see Table 47
CD19(8B8-018) light
chain
316 CD19(8B8-018) heavy QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYI chain (hulgGI PGLALA) MHWVRQAPGQGLEWMGYINPYNDGSKYTEKF
QGRVTMTSDTSISTAYMELSRLRSDDTAVYYCA
RGTYYYGSALFDYWGQGTTVTVSSASTKGPSVF
PLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNS
GALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLG
TQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCP
PCPAPEAAGGPSVFLFPPKPKDTLMISRTPEVTCV
VVDVSHEDPEVKFNWYVDGVEVHNAKTKPREE
QYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNK
ALGAPIEKTISKAKGQPREPQVYTLPPSRDELTK
NQVSLTCLVKGFYPSDIAVEWESNGQPENNYKT
TPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCS
VMHEALHNHYTQKSLSLSPGK
206 CD19(8B8-018) light see Table 47
Figure imgf000297_0001
Table 73: cDNA and amino acid sequences of germline control DP47 hulgGI PGLALA (control F)
Figure imgf000297_0002
7.4 Production of CD19-targeted split trimeric 4-1BB ligand Fc fusion antigen binding molecules and their control molecules
The targeted and untargeted split trimeric 4- IBB ligand Fc (kih) fusion antigen binding molecule encoding sequences were cloned into a plasmid vector, which drives expression of the insert from an MPSV promoter and contains a synthetic polyA sequence located at the 3' end of the CDS. In addition, the vector contains an EBV OriP sequence for episomal maintenance of the plasmid.
The split trimeric 4- IBB ligand Fc (kih) fusion antigen binding molecule was produced by co-transfecting HEK293-EBNA cells with the mammalian expression vectors using
polyethylenimine. The cells were transfected with the corresponding expression vectors. For variants 1,2,4,5 and it's control B, D and E, at a 1: 1: 1: 1 ratio ("vector dimeric ligand-CL- knob chain": "vector monomeric ligand fusion-CHI": "vector anti-CD19 Fab-hole chain": "vector anti-CD19 light chain"). For variant 3, 6 and it's control C, at a 1: 1: 1 ratio ("vector hulgGI Fc hole dimeric ligand chain": "vector hulgGI Fc knob monomeric ligand chain": "vector anti- CD^ light chain"). Human IgGs, used as control in the assay, were produced as for the bispecific construct (for transfection only a vector for light and a vector for heavy chain were used at a 1: 1 ratio).
For production in 500 mL shake flasks, 300 million HEK293 EBNA cells were seeded 24 hours before transfection. For transfection cells were centrifuged for 10 minutes at 210 x g, and the supernatant was replaced by 20mL pre- warmed CD CHO medium. Expression vectors (200 μg of total DNA) were mixed in 20 mL CD CHO medium. After addition of 540 PEI, the solution was vortexed for 15 seconds and incubated for 10 minutes at room temperature. Afterwards, cells were mixed with the DNA/PEI solution, transferred to a 500 mL shake flask and incubated for 3 hours at 37 °C in an incubator with a 5% C02 atmosphere. After the incubation, 160 mL of Excell medium supplemented with 6 mM L-Glutamine, 5g/L PEPSOY and 1.2mM valproic acid was added and cells were cultured for 24 hours. One day after transfection 12% Feed (amino acid and glucose) were added. After culturing for 7 days, the supernatant was collected by centrifugation for 30-40 minutes at least 400 x g. The solution was sterile filtered (0.22 μπι filter), supplemented with sodium azide to a final concentration of 0.01 % (w/v), and kept at 4 °C.
The split trimeric 4- IBB ligand Fc (kih) fusion antigen binding molecule, as well as the IgG, was purified from cell culture supernatants by affinity chromatography using Protein A, followed by size exclusion chromatography. For affinity chromatography, the supernatant was loaded on a MabSelect Sure column (CV = 5-15 mL, resin from GE Healthcare) equilibrated with sodium phosphate (20 mM), sodium sitrate (20 mM) buffer (pH 7.5). Unbound protein was removed by washing with at least 6 column volumes of the same buffer. The bound protein was eluted using either a linear gradient (20 CV) or a step elution (8 CV) with 20 mM sodium citrate, 100 mM sodium chloride, 100 mM glycine buffer (pH 3.0). For the linear gradient an additional 4 column volumes step elution was applied.
The pH of collected fractions was adjusted by adding 1/10 (v/v) of 0.5M sodium phosphate, pH8.0. The protein was concentrated prior to loading on a HiLoad Superdex 200 column (GE Healthcare) equilibrated with 20 mM histidine, 140 mM sodium chloride, 0.01% (v/v) Tween20 solution of pH 6.0.
The protein concentration was determined by measuring the optical density (OD) at 280 nm, using a molar extinction coefficient calculated on the basis of the amino acid sequence.
Purity and molecular weight of the targeted trimeric 4- IBB ligand Fc (kih) fusion was analyzed by SDS-PAGE in the presence and absence of a reducing agent (5 mM 1,4-dithiotreitol) and staining with Coomassie SimpleBlue™ SafeStain (Invitrogen USA). The aggregate content of samples was analyzed using a TSKgel G3000 SW XL analytical size-exclusion column (Tosoh) equilibrated in 25 mM K2HP04, 125 mM NaCl, 200 mM L-arginine monohydrochloride, 0.02 % (w/v) NaN3, pH 6.7 running buffer at 25°C. Table 74 summarizes the yield and final monomer content of the CD 19 targeted split trimeric 4- IBB ligand Fc (kih) fusion antigen molecules. Table 74: Biochemical analysis of CD19 targeted split trimeric 4-lBB ligand Fc (kih) fusion antigen binding molecules
Figure imgf000299_0001
Table 75 summarizes the yield and final monomer content of the DP47 untargeted split trimeric 4- IBB ligand Fc (kih) fusion, both monovalent (control B, D and E) and bivalent (control C).
Table 75: Biochemical analysis of DP47 untargeted split trimeric 4- IBB ligand Fc (kih) fusion
Monomer Yield
Construct [ ] [mg/1]
(SEC)
monovalent DP47 -untargeted split trimeric human 4- IBB
ligand (71-254) Fc (kih) fusion 99 15.4
(control B)
bivalent DP47 untargeted split trimeric human 4- IBB ligand
(71-254) Fc (kih) fusion 98 12.6
(control C)
monovalent DP47 -untargeted split trimeric human 4- IBB
ligand (71-254) Fc (kih) fusion 99.5 25.9
(control D) monovalent DP47-untargeted split trimeric human 4- IBB
ligand (71-254) Fc (kih) fusion 93.3 4.1
(control E)
Table 76 summarizes the yield and final monomer content of anti-CD19 (8B8-018) and germline DP47 human IgGl PGLALA (control F).
Table 76: Biochemical analysis of control human IgGl PGLALA
Figure imgf000300_0001
Example 8
Functional characterization of the CD19 targeted 4-lBB ligand trimer-containing Fc fusion antigen binding molecules
8.1. Surface plasmon resonance (affinity) Binding of CD 19 targeted split trimeric 4- IBB ligand Fc fusion antigen binding molecules
(constructs 3.4 and 3.6) to the recombinant 4-lBB Fc(kih) and CD19 was assessed by surface plasmon resonance (SPR). All SPR experiments were performed on a Biacore T200 at 25 °C with HBS-EP as running buffer (0.01 M HEPES pH 7.4, 0.15 M NaCl, 3 mM EDTA, 0.005% Surfactant P20, Biacore, Freiburg/Germany). Interaction with human and cvnomolgus 4- IBB
Anti-human Fab antibody (Biacore, Freiburg/Germany) was directly coupled on a CM5 chip at pH 5.0 using the standard amine coupling kit (Biacore, Freiburg/Germany). The immobilization level was approximately 8000 RU. The CD 19 targeted split trimeric 4- IBB ligand Fc fusions were captured for 60 seconds at 2 and 5 nM (control D was also injected). Recombinant human or cynomolgus 4-lBB avi His was passed at a concentration range from 2.7 to 2000 nM (3-fold dilution) with a flow of 30 μί/ηιίηυίεβ through the flow cells over 120 seconds. The dissociation was monitored for 180 seconds. Bulk refractive index differences were corrected for by subtracting the response obtained on reference flow cell. Here, the antigens were flown over a surface with immobilized anti-human Fab antibody but on which HBS-EP has been injected rather than the antibodies. Interaction with human CD 19
Anti-human Fab antibody (Biacore, Freiburg/Germany) was directly coupled on a CM5 chip at pH 5.0 using the standard amine coupling kit (Biacore, Freiburg/Germany). The immobilization level was approximately 8000 RU. The CD 19 targeted split trimeric 4- IBB ligand Fc fusions, or the control antibody (anti-CD19(8B8-018) hulgGI PGLALA) were captured for 60 seconds at 20 nM. Recombinant human CD19-Fc(kih) was passed at a concentration range from 7.8 to 500 nM (2-fold dilution) with a flow of 30 μΐνηιίηυίεβ through the flow cells over 120 seconds. The dissociation was monitored for 120/1800 seconds. Bulk refractive index differences were corrected for by subtracting the response obtained on reference flow cell. Here, the antigens were flown over a surface with immobilized anti-human Fab antibody but on which HBS-EP has been injected rather than the antibodies.
Kinetic constants were derived using the Biacore T200 Evaluation Software (vAA, Biacore AB, Uppsala/Sweden), to fit rate equations for 1: 1 Langmuir binding by numerical integration.
The bispecific constructs 3.4, 3.6 and control D bind similarly to 4-1BB. Table 77 shows the average with standard deviation (in parenthesis) from the two experiments (using the construct capture solution either at 2 nM or 5 nM). The bispecific constructs 3.4 and 3.6 bind human CD 19 with a similar affinity as the IgG. Affinity constants for the interaction were determined by fitting to a 1: 1 Langmuir binding. For measurements with hu4-lBB and cy4-lBB, average and standard deviation (in parenthesis) are shown (two experiments with 2 or 5 nM capture solution).
Table 77: Binding of CD19 targeted split trimeric 4-1BB ligand Fc fusion to recombinant human (hu) 4-1BB, cynomolgus (cy) 4-1BB and human (hu) CD19.
Antigen ka (l/Ms) kd (1/s) KD (M) monovalent CD19(8B8- hu 4- 7.2E+04 2.5E-02 3.4E-07
018) targeted split trimeric 1BB (5.9E+03) (1.0E-05) (2.8E-08) 4-1BB ligand (71-248) Fc
(kih) fusion containing CH- cy 4- 1.2E+05 1.3E-02 1.1E-07
CL cross with charged 1BB (8.6E+03) (1.8E-04) (9.9E-09) residues
hu CD19 2.77E+04 2.67E-04 9.64E-09
(construct 3.4)
bivalent CD19(8B8-018) hu 4- 6.9E+04 2.4E-02 3.5E-07 targeted split trimeric 4- 1BB (1.7E+03) (1.5E-04) (1.1E-08) 1BB ligand (71-248) Fc cy 4- 1.1E+05 1.4E-02 1.3E-07
(kih) fusion 1BB (7.7E+03) (3.1E-04) (1.3E-08)
hu CD19 2.55E+04 2.69E-04 1.06E-08
(construct 3.6) monovalent DP47
untargeted split trimeric hu 4- 7.3E+04 2.6E-02 3.5E-07 human 4- IBB ligand (71- 1BB (3.9E+03) (6.3E-04) (l.OE-08) 248) Fc (kih) fusion with
CH-CL cross and with
charged residues cy 4- 1.2E+05 1.4E-02 1.2E-07
1BB (1.9E+03) (1.0E-04) (2.9E-09)
(control D)
anti-CD19(8B8-018)
hu CD19 2.12E+04 2.61E-04 1.23E-08 hulgGI PGLALA
8.2. Surface plasmon resonance (simultaneous binding)
The capacity of binding simultaneously human 4-1BB Fc(kih) and human CD19 was assessed by surface plasmon resonance (SPR). All SPR experiments were performed on a Biacore T200 at 25 °C with HBS-EP as running buffer (0.01 M HEPES pH 7.4, 0.15 M NaCl, 3 mM EDTA, 0.005% Surfactant P20, Biacore, Freiburg/Germany). Biotinylated human 4-1BB Fc(kih) was directly coupled to a flow cell of a streptavidin (SA) sensor chip. Immobilization levels up to 250 resonance units (RU) were used.
The CD19 targeted trimeric split 4-lBBL constructs (constructs 3.1, 3.3, 3.4, 3.5, 3.6, 4.4) were passed at a concentration range of 200 nM with a flow of 30 μΕ/ηιίηυίε through the flow cells over 90 seconds and dissociation was set to zero sec. Human CD19 was injected as second analyte with a flow of 30 μΕ/ηιίηυίε through the flow cells over 90 seconds at a concentration of 500 nM (Figure 34A). The dissociation was monitored for 120 sec. Bulk refractive index differences were corrected for by subtracting the response obtained in a reference flow cell, where no protein was immobilized.
As can be seen in the graphs of Figure 35, all bispecific constructs could bind
simultaneously human 4- IBB and human CD 19.
Example 9
Functional characterization of the CD-19 targeted 4-1BB ligand trimer-containing Fc fusion antigen binding molecules
9.1. Binding on activated human PMBCs of the CD19-targeted 4-1BB ligand trimer- containing Fc (kih) fusion antigen binding molecules
To determine binding of 4-lBBL trimer-containing Fc fusion antigen binding molecules to human PBMCs, different titrated concentrations of the CD19-targeted 4-lBBL trimer-containing Fc fusion antigen binding molecules were used in the assay as described in Example 5.2. Figures 36A and 36B show the binding of Constructs 3.1, 3.3, 3.4, 3.5 and 3.6 as prepared in Example 7 on activated 4-lBB-expressing CD4+ T cells and CD8 + T cells, respectively. Gates were set on living CD45+ CD3+ CD4+ or CD45+ CD3+ CD8+ T cells and MFI of PE- conjugated AffiniPure anti-human IgG IgG Fcy-fragment-specific goat F(ab )2 fragment were blotted against the titrated concentration of targeted split trimeric 4- IBB ligand Fc fusion variants. Table 78 shows the EC50 values as measured for Constructs 3.1, 3.3. 3.4, 3.5 and 3.6 and control molecules.
Table 78: Binding on activated 4-lBB-expressing CD4+ T cells and CD8 + T cells
Figure imgf000303_0001
9.2 Binding to CD19-expressing tumor cells
For binding assays on CD19-expressing tumor cells, the following human CD 19- expressing lymphoma cell lines were used: diffuse large non-Hodgkin B cell lymphoma (B-NHL) cell line SU-DHL-8 (DSMZ ACC573), acute B cell precursor lymphoid leukemia cell line Nalm6 (DSMZ ACC-128), diffuse large cell lymphoblast lymphoma cell line Toledo (ATCC CRL-2631) and diffuse large B cell lymphoma cell line OCI-Lyl 8 (DSMZ ACC-699). The assays were preformed as described for the FAP-expressing MV-3 and WM-266-4 tumor cell lines in Example 5.3.
Gates were set on living tumor cells and MFI of PE-conjugated AffiniPure anti-human IgG IgG Fcy-fragment- specific goat F(ab )2 fragment were blotted against the titrated concentration of targeted split trimeric 4- IBB ligand Fc fusion constructs.
Figure 37A shows the binding of Constructs 3.1, 3.3, 3.4, 3.5 and 3.6 as prepared in Example 7.1 to diffuse large non-Hodgkin B cell lymphoma (B-NHL) cell line SU-DHL-8 and in Figure 37B the binding of Constructs 3.1, 3.3, 3.4, 3.5 and 3.6 to acute B cell precursor lymphoid leukemia cell line Nalm6 is presented. Figure 37C shows the binding of Constructs 3.1, 3.3, 3.4, 3.5 and 3.6 to diffuse large cell lymphoblast lymphoma cell line Toledo and Figure 37D shows the binding of Constructs 3.1, 3.3, 3.4, 3.5 and 3.6 to diffuse large B cell lymphoma cell line OCTLyl8. Table 79 shows the EC50 values as measured for Constructs 3.1, 3.3, 3.4, 3.5 and 3.6 and control molecules.
Table 79: Binding to CD19-expressing tumor cells
Figure imgf000304_0001
Example 10 Biological activity of the CD19-targeted 4-lBB ligand trimer-containing Fc fusion antigen binding molecules
10.1. NF-κΒ activation in HeLa cells expressing human 4-lBB
HeLa cells expressing human 4- IBB and NF-KB-luciferase were generated as described in Example 6.1. NF-κΒ activation in Hela cells expressing human 4-lBB co-cultured with CD19- expressing tumor cells
NF-KB-luciferase human-4-lBB HeLa cells were harvested and resuspended in DMEM medium supplied with 10 % (v/v) FBS and 1 % (v/v) GlutaMAX-I to a concentration of 0.2 x 106 cells/ml. 100 μΐ (2 x 104 cells) of this cell suspension were transferred to each well of a sterile white 96-well flat bottom tissue culture plate with lid (greiner bio-one, Cat. No. 655083) and the plate were incubated at 37 °C and 5 % C02 overnight. The next day 50 μΐ^ of medium containing titrated concentrations of CD19-targeted 4-lBB ligand trimer-containing Fc fusion antigen binding molecules (CD19 split 4-lBBL trimer) or DP47-untargeted 4-lBB ligand trimer- containing Fc fusion antigen binding molecules (DP47 split 4-lBBL trimer) were added. CD 19- expressing B cell lymphoma cell lines (diffuse large non-Hodgkin B cell lymphoma (B-NHL) cell line SU-DHL-8 (DSMZ ACC573) and human non-Hodgkin s B cell lymphoma cell line Pfeiffer (ATCC CRL-2632)) were resuspended in DMEM medium supplied with 10 % (v/v) FBS and 1 % (v/v) GlutaMAX-I to a concentration of 2 x 106 cells/ml. Suspension of CD19-expressing B cell lymphoma cell (50 μΐ, final ratio 1:5) or only medium were added to each well and plates were incubated for 6 hours at 37 °C and 5 % C02. Cells were washed two times with 200
Figure imgf000305_0001
DPBS. 40 μΐ freshly prepared Reporter Lysis Buffer (Promega, Cat-No: E3971) were added to each well and the plate were stored over night at -20 °C. The next day frozen cell plate and Detection Buffer (Luciferase 1000 Assay System, Promega, Cat. No. E4550) were thawed at room temperature. 100 μΐ^ of detection buffer were added to each well and luciferase activity was measured as fast as possible using a SpectraMax M5/M5e microplate reader and a SoftMax Pro Software (Molecular Devices) counting light emission in URL (units of released light for 0.5s/well) or Victor3 1420 multilabel counter plate reader (Perkin Elmer) and the Perkin Elmer 2030 Manager Software counting light emission as counts per seconds (CPS) and blotted against the concentration of tested constructs.
CD19-targeted 4-1BB ligand trimer-containing Fc fusion antigen binding molecules Constructs 3.1 and 3.3 triggered activation of the NF-kB signaling pathway in the reporter cell line in the presence of CD19-expressing B cell lymphoma cells. In contrast, the untargeted control molecules failed to trigger such an effect at any of the tested concentrations (Figure 38).
Example 11
11.1 Preparation of CEA (T84.66-LCHA) targeted 4-1BB ligand trimer-containing Fc fusion antigen binding molecules
11.1.1 Humanization of anti-CEA clone T84.66 Novel humanized variants of the murine antibody T84.66 (Wagener et al., J Immunol 130,
2308 (1983), Neumaier et al., J Immunol 135, 3604 (1985)) were developed by grafting of the CDRs onto human germline framework acceptor sequences.
Humanization of an antibody from non-human origin consists essentially of transplanting the CDR residues from the non-human antibody (donor) onto the framework of a human
(acceptor) antibody. Normally the acceptor framework is selected by aligning the sequence of the donor to a collection of potential acceptor sequences and choosing one that has either reasonable homology to the donor, or shows similar amino acids at some positions critical for structure and activity. In the present case, the search for the antibody acceptor framework was performed by aligning the mouse T84.66 protein (NCBI Acc No: CAA36980 for the heavy chain (SEQ ID NO:317), and CAA36979 (SEQ ID NO:318) for the light chain) sequence to a collection of human germ-line sequences and picking that human sequence that showed high sequence identity. Here, the sequence IGHVl-69*08 from the IMGT database was chosen as the heavy chain framework acceptor sequence (IMGT Acc No. Z14309, SEQ ID NO:319), and the IGKV3-11*01 sequence (IMGT Acc No. X01668, SEQ ID NO:320) was chosen to be the framework acceptor for the light chain. Onto these two acceptor frameworks, the three complementary determining regions (CDRs) of the mouse heavy and light variable domains were grafted. Since the framework 4 (FR4) region is not part of the variable region of the germ line V gene, the alignment for that position was done individually. The JH4 sequence was chosen for the heavy chain, and the JK2 sequence was chosen for the light chain. 11.1.2 Binding of different humanized variants of T84.66 IgG to cells
The binding of different humanized variants of T84.66 IgG was tested on CEA-expressing human gastric adenocarcinoma cells (MKN45, DSMZ ACC 409).
Cells were harvested, counted, checked for viability and re- suspended at 2xl06 cells/ml in FACS buffer (100 μΐ PBS 0.1% BSA). 100 μΐ of cell suspension (containing 0.2xl06 cells) were incubated in round-bottom 96-well plate for 30 min at 4°C with increasing concentrations of the CEA IgG (4 ng/ml- 60 μg/ml), washed twice with cold PBS 0.1% BSA, re-incubated for further 30 min at 4°C with the PE-conjugated AffiniPure F(ab')2 Fragment goat anti-human IgG Fcg Fragment Specific secondary antibody (Jackson Immuno Research Lab PE #109-116-170), washed twice with cold PBS 0.1% BSA and immediately analyzed by FACS using a FACS CantoII (Software FACS Diva). Binding curves and EC50 values were obtained and calculated using GraphPadPrism5.
Figure 39 shows the different binding pattern of selected humanized variants of the T84.66 IgG to human CEA, expressed on MKN45 cells. Based on the calculated EC50 binding values (Table 80), the humanized variant 1 was selected for further evaluation.
Table 80: Binding of different humanized variants of T84.66 IgGs to cells (EC50 values, based on binding curves shown in Figure 39, calculated by Graph Pad Prism).
Figure imgf000307_0001
Humanized variant 1 is termed in the following T84.66-LCHA. The amino acid sequences of its CDRs and of the VH and VL as well as the aminoacid sequences of the VH and VL domain of the parental chimeric T84.66 clone are shown in Table 81.
Table 81: Amino acid sequences of the variable domains of CEA clone T84.66-LCHA and its parental antibody T84.66
Description Sequence SEQ ID
NO:
CEA CDR-H1 DTYMH 321
CEA CDR-H2 RIDPANGNSKYVPKFQG 322
CEA CDR-H3 FGYYVSDYAMAY 323
CEA CDR-L1 RAGESVDIFGVGFLH 324
CEA CDR-L2 RASNRAT 325
CEA CDR-L3 QQTNEDPYT 326
Parental CEA EVQLQQSGAELVEPGASVKLSCTASGFNIKDTYMHWVKQRPEQ 327 binder VH GLEWIGRIDPANGNSKYVPKFQGKATITADTSSNTAYLQLTSLTS
EDTAVYYCAPFGYYVSDYAMAYWGQGTSVTVSS
Parental CEA DIVLTQSPASLAVSLGQRATMSCRAGESVDIFGVGFLHWYQQKP 328 binder VL GQPPKLLIYRASNLESGIPVRFSGTGSRTDFTLIIDPVEADDVATY
YCQQTNEDPYTFGGGTKLEIK
Humanized QVQLVQSGAEVKKPGSSVKVSCKASGFNIKDTYMHWVRQAPGQ 329
GLEWMGRIDPANGNSKYVPKFQGRVTITADTSTSTAYMELSSLR CEA binder SEDTAVYYCAPFGYYVSDYAMAYWGQGTLVTVSS
CEA (T84.66- LCHA) VH
Humanized EIVLTQSPATLSLSPGERATLSCRAGESVDIFGVGFLHWYQQKPG 330 CEA binder QAPRLLIYRASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYY
CEA (T84.66- CQQTNEDPYTFGQGTKLEIK
LCHA) VL
11.2 Preparation of CEA (T84.66-LCHA) targeted 4-1BB ligand trimer-containing Fc fusion antigen binding molecules
Different fragments of the DNA sequence encoding part of the ectodomain (amino acid 71- 254 and 71-248) of human 4- IBB ligand were synthetized according to the P41273 sequence of Uniprot database (SEQ ID NO:42).
11.2.1 Preparation of monovalent CEA (T84.66-LCHA) targeted 4-1BB ligand (71- 254) trimer-containing Fc (kih) fusion antigen binding molecule with crossed CH1- CL domains with charged residues (Construct 5.1)
A polypeptide containing two ectodomains of 4-1BB ligand (71-254), separated by (G4S)2 linkers, and fused to the human IgGl-CL domain, was cloned as depicted in Figure 29A: human 4-1BB ligand, (G4S)2 connector, human 4-1BB ligand, (G4S)2 connector, human CL. A polypeptide containing one ectodomain of 4-1BB ligand (71-254) and fused to the human IgGl- CH domain, was cloned as described in Figure 29B: human 4- IBB ligand, (G4S)2 connector, human CH.
To improve correct pairing the following mutations have been introduced in the crossed CH-CL. In the dimeric 4- IBB ligand fused to human CL, E123R and Q124K. In the monomeric 4-1BB ligand fused to human CHI, K147E and K213E.
The variable region of heavy and light chain DNA sequences encoding a binder specific for CEA, clone T84.66-LCHA, were subcloned in frame with either the constant heavy chain of the hole or the constant light chain of human IgGl . The Pro329Gly, Leu234Ala and Leu235Ala mutations have been introduced in the constant region of the knob and hole heavy chains to abrogate binding to Fc gamma receptors according to the method described in WO 2012/130831.
Combination of the dimeric ligand-Fc knob chain containing the S354C/T366W mutations, the monomeric CHI fusion, the targeted anti-CEA-Fc hole chain containing the
Y349C/T366S/L368A/Y407V mutations and the anti-CEA light chain allows generation of a heterodimer, which includes an assembled trimeric 4- IBB ligand and a CEA binding Fab
(Figure 40, Construct 5.1). Table 82 shows the cDNA and amino acid sequences of the monovalent CEA (T84.66- LCHA) targeted split trimeric 4- IBB ligand (71-254) Fc (kih) fusion antigen binding molecule with crossed CH-CL and charged residues (construct 5.1).
Table 82: cDNA and amino acid sequences of monovalent CEA(T84.66-LCHA) targeted split trimeric 4-lBB ligand (71-254) Fc (kih) fusion containing CH-CL cross with charged residues (construct 5.1). * for charged residues
SEQ ID Description Sequence
NO:
129 Nucleotide see Table 3
sequence Dimeric
hu 4-lBBL (71- 254) - CL* Fc
knob chain
130 Nucleotide see Table 3
sequence
Monomeric hu
4-1BBL (71-254)
- CHI*
331 Nucleotide CAGGTGCAGCTGGTGCAGTCTGGCGCCGAAGTGAAGAA sequence anti- ACCCGGCAGCAGCGTGAAGGTGTCCTGCAAGGCCAGCG CEA(T84.66- GCTTCAACATCAAGGACACCTACATGCACTGGGTGCGCC LCHA) Fc hole AGGCCCCTGGACAGGGACTGGAATGGATGGGCAGAATC chain GACCCCGCCAACGGCAACAGCAAATACGTGCCCAAGTT
CCAGGGCAGAGTGACCATCACCGCCGACACCAGCACCT
CCACCGCCTACATGGAACTGAGCAGCCTGCGGAGCGAG
GACACCGCCGTGTACTACTGTGCCCCCTTCGGCTACTAC
GTGTCCGACTACGCCATGGCCTATTGGGGCCAGGGCAC
ACTCGTGACCGTGTCCTCTGCTAGCACCAAGGGCCCCTC
CGTGTTCCCCCTGGCCCCCAGCAGCAAGAGCACCAGCG
GCGGCACAGCCGCTCTGGGCTGCCTGGTCAAGGACTACT
TCCCCGAGCCCGTGACCGTGTCCTGGAACAGCGGAGCC
CTGACCTCCGGCGTGCACACCTTCCCCGCCGTGCTGCAG
AGTTCTGGCCTGTATAGCCTGAGCAGCGTGGTCACCGTG
CCTTCTAGCAGCCTGGGCACCCAGACCTACATCTGCAAC
GTGAACCACAAGCCCAGCAACACCAAGGTGGACAAGAA
GGTGGAGCCCAAGAGCTGCGACAAAACTCACACATGCC
CACCGTGCCCAGCACCTGAAGCTGCAGGGGGACCGTCA
GTCTTCCTCTTCCCCCCAAAACCCAAGGACACCCTCATG
ATCTCCCGGACCCCTGAGGTCACATGCGTGGTGGTGGAC
GTGAGCCACGAAGACCCTGAGGTCAAGTTCAACTGGTA
CGTGGACGGCGTGGAGGTGCATAATGCCAAGACAAAGC
CGCGGGAGGAGCAGTACAACAGCACGTACCGTGTGGTC
AGCGTCCTCACCGTCCTGCACCAGGACTGGCTGAATGGC
AAGGAGTACAAGTGCAAGGTCTCCAACAAAGCCCTCGG
CGCCCCCATCGAGAAAACCATCTCCAAAGCCAAAGGGC
AGCCCCGAGAACCACAGGTGTGCACCCTGCCCCCATCCC
GGGATGAGCTGACCAAGAACCAGGTCAGCCTCTCGTGC
GCAGTCAAAGGCTTCTATCCCAGCGACATCGCCGTGGA GTGGGAGAGCAATGGGCAGCCGGAGAACAACTACAAGA
CCACGCCTCCCGTGCTGGACTCCGACGGCTCCTTCTTCC
TCGTGAGCAAGCTCACCGTGGACAAGAGCAGGTGGCAG
CAGGGGAACGTCTTCTCATGCTCCGTGATGCATGAGGCT
CTGCACAACCACTACACGCAGAAGAGCCTCTCCCTGTCT
CCGGGTAAA
332 Nucleotide GAGATCGTGCTGACCCAGAGCCCTGCCACCCTGTCACTG sequence anti- TCTCCAGGCGAGAGAGCCACCCTGAGCTGTAGAGCCGG CEA(T84.66- CGAGAGCGTGGACATCTTCGGCGTGGGATTTCTGCACTG LCHA) light GTATCAGCAGAAGCCCGGCCAGGCCCCCAGACTGCTGA
TCTACAGAGCCAGCAACCGGGCCACAGGCATCCCCGCC
chain
AGATTTTCTGGCTCTGGCAGCGGCACCGACTTCACCCTG
ACAATCAGCAGCCTGGAACCCGAGGACTTCGCCGTGTA
CTACTGCCAGCAGACCAACGAGGACCCCTACACCTTTGG
CCAGGGCACCAAGCTGGAAATCAAGCGTACGGTGGCTG
CACCATCTGTCTTCATCTTCCCGCCATCTGATGAGCAGTT
GAAATCTGGAACTGCCTCTGTTGTGTGCCTGCTGAATAA
CTTCTATCCCAGAGAGGCCAAAGTACAGTGGAAGGTGG
ATAACGCCCTCCAATCGGGTAACTCCCAGGAGAGTGTC
ACAGAGCAGGACAGCAAGGACAGCACCTACAGCCTCAG
CAGCACCCTGACGCTGAGCAAAGCAGACTACGAGAAAC
ACAAAGTCTACGCCTGCGAAGTCACCCATCAGGGCCTG
AGCTCGCCCGTCACAAAGAGCTTCAACAGGGGAGAGTG
T
115 Dimeric hu 4- see Table 3
1BBL (71-254) - CL* Fc knob
chain
116 Monomeric hu see Table 3
4-1BBL (71-254)
- CHI*
333 anti- CEA QVQLVQSGAEVKKPGSSVKVSCKASGFNIKDTYMHWVRQ
(T84.66-LCHA) APGQGLEWMGRIDPANGNSKYVPKFQGRVTITADTSTSTA Fc hole chain YMELSSLRSEDTAVYYCAPFGYYVSDYAMAYWGQGTLV
TVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPV
TVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGT
QTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAA
GGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFN
W
YVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLN
GKEYKCKVSNKALGAPIEKTISKAKGQPREPQVCTLPPSRD
ELTKNQVSLSCAVKGFYPSDIAVEWESNGQPENNYKTTPP
VLDSDGSFFLVSKLTVDKSRWQQGNVFSCSVMHEALHNH
YTQKSLSLSPGK
334 anti- CEA EIVLTQSPATLSLSPGERATLSCRAGESVDIFGVGFLHWYQ
(T84.66-LCHA) QKPGQ APRLLIYR ASNR ATGIPARFS GS GSGTDFTLTIS SLEP light chain EDFAVYYCQQTNEDPYTFGQGTKLEIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQ
ESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQG
LSSPVTKSFNRGEC 11.2.2 Preparation of monovalent CEA (T84.66-LCHA) targeted 4-1BB ligand (71- 254) trimer-containing Fc (kih) fusion antigen binding molecule with crossed CH1- CL domains without charged residues (Construct 5.2) A polypeptide containing two ectodomains of 4-1BB ligand (71-254), separated by (G4S)2 linkers, and fused to the human IgGl-CL domain, was cloned in analogy as depicted in Figure (29 A), but without amino acid mutations in the CL domain: human 4- IBB ligand, (G4S)2 connector, human 4- IBB ligand, (G4S)2 connector, human CL. A polypeptide containing one ectodomain of 4- IBB ligand (71-254) and fused to the human IgGl-CHl domain, was cloned in analogy as depicted in Figure (29B), but without amino acid mutations in the CHI domain: human 4-1BB ligand, (G4S)2 connector, human CHI.
The variable region of heavy and light chain DNA sequences encoding a binder specific for CEA, clone T84.66-LCHA, were subcloned in frame with either the constant heavy chain of the hole or the constant light chain of human IgGl . The Pro329Gly, Leu234Ala and Leu235Ala mutations have been introduced in the constant region of the knob and hole heavy chains to abrogate binding to Fc gamma receptors according to the method described in WO 2012/130831. Combination of the dimeric ligand-Fc knob chain containing the S354C/T366W mutations, the monomeric CHI fusion, the targeted anti-CEA-Fc hole chain containing the Y349C/T366S/L368A/Y407V mutations and the anti- CEA light chain allows generation of a heterodimer, which includes an assembled trimeric 4- 1BB ligand and a CEA-binding Fab (Figure 40, Construct 5.2).
Table 83 shows the cDNA and amino acid sequences of the monovalent CEA (T84.66- LCHA) targeted split trimeric 4- IBB ligand (71-254) Fc (kih) fusion antigen binding molecule containing crossed CH-CL cross without charged residues (construct 5.2).
Table 83: cDNA and amino acid sequences of monovalent CEA (T84.66-LCHA) targeted split trimeric 4-1BB ligand (71-254) Fc (kih) fusion containing CH-CL cross without charged residues (construct 5.2)
SEQ ID Description Sequence
NO:
165 Nucleotide sequence dimeric see Table 22
ligand (71-254)- CL Fc knob
chain
166 Nucleotide sequence monomeric see Table 22
hu 4-lBBL (71-254) - CHI
331 Nucleotide sequence anti- CEA see Table 82 (T84.66-LCHA) Fc hole chain
332 Nucleotide sequence anti- CEA see Table 82
(T84.66-LCHA) light chain
117 Dimeric ligand (71-254) - CL Fc see Table 22
knob chain
118 Monomeric ligand (71-254) -CHI see Table 22
333 anti- CEA (T84.66-LCHA) Fc see Table 82
hole chain
334 anti- CEA (T84.66-LCHA) light see Table 82
chain
11.2.3 Preparation of bivalent CEA(T84.66-LCHA) targeted 4-lBB ligand (71-254) trimer-containing Fc (kih) fusion antigen binding (Construct 5.3)
A polypeptide containing two ectodomains of 4-lBB ligand (71-254), separated by (G4S)2 linkers was fused to the C-terminus of human IgGl Fc hole chain, as depicted in Figure 29C: human IgGl Fc hole, (G4S)2 connector, human 4-lBB ligand, (G4S)2 connector, human 4-lBB ligand. A polypeptide containing one ectodomain of 4- IBB ligand (71-254) and fused to the C- terminus of human IgGl Fc knob chain as described in Figure 29D: human IgGl Fc knob, (G4S)2 connector, human 4- IBB ligand. The variable region of heavy and light chain DNA sequences encoding a binder specific for CEA, clone T84.66-LCHA, were subcloned in frame with either the constant heavy chain of the hole, the knob or the constant light chain of human IgGl. The Pro329Gly, Leu234Ala and Leu235Ala mutations have been introduced in the constant region of the knob and hole heavy chains to abrogate binding to Fc gamma receptors according to the method described in WO 2012/130831. Combination of the anti-CEA hulgGI hole dimeric ligand chain containing the Y349C/T366S/L368A/Y407V mutations, the anti-CEA hulgGI knob monomeric ligand chain containing the S354C/T366W mutations and the anti-CEA light chain allows generation of a heterodimer, which includes an assembled trimeric 4- IBB ligand and two CEA binding Fabs (Figure 40, construct 5.3). Table 84 shows the cDNA and amino acid sequences of the bivalent CEA(T84.66-LCHA) targeted split trimeric 4- IBB ligand (71-254) Fc (kih) fusion antigen binding molecule (construct 5.3). Table 84: cDNA and amino acid sequences of bivalent CEA(T84.66-LCHA) targeted split trimeric 4-lBB ligand (71-254) Fc (kih) PGLALA fusion (construct 5.3)
SEQ ID Description Sequence
NO:
335 Nucleotide CAGGTGCAGCTGGTGCAGTCTGGCGCCGAAGTGAAGAA sequence anti- ACCCGGCAGCAGCGTGAAGGTGTCCTGCAAGGCCAGCG CEA(T84.66- GCTTCAACATCAAGGACACCTACATGCACTGGGTGCGCC LCHA) Fc hole AGGCCCCTGGACAGGGACTGGAATGGATGGGCAGAATC
GACCCCGCCAACGGCAACAGCAAATACGTGCCCAAGTT
dimeric 4- 1BBL
CCAGGGCAGAGTGACCATCACCGCCGACACCAGCACCT
(71-254) chain
CCACCGCCTACATGGAACTGAGCAGCCTGCGGAGCGAG
GACACCGCCGTGTACTACTGTGCCCCCTTCGGCTACTAC
GTGTCCGACTACGCCATGGCCTATTGGGGCCAGGGCAC
A TCGTGACCGTGTC T TGCTAGCACCAAGGGCCCCTCC
GTGTTCCCCCTGGCCCCCAGCAGCAAGAGCACCAGCGGCG
GCACAGCCGCTCTGGGCTGCCTGGTCAAGGACTACTTCCC
CGAGCCCGTGACCGTGTCCTGGAACAGCGGAGCCCTGACC
TCCGGCGTGCACACCTTCCCCGCCGTGCTGCAGAGTTCTG
GCCTGTATAGCCTGAGCAGCGTGGTCACCGTGCCTTCTAGC
AGCCTGGGCACCCAGACCTACATCTGCAACGTGAACCACAA
GCCCAGCAACACCAAGGTGGACAAGAAGGTGGAGCCCAAG
AGCTGCGACAAAACTCACACATGCCCACCGTGCCCAGCACC
TGAAGCTGCAGGGGGACCGTCAGTCTTCCTCTTCCCCCCAA
AACCCAAGGACACCCTCATGATCTCCCGGACCCCTGAGGTC
ACATGCGTGGTGGTGGACGTGAGCCACGAAGACCCTGAGG
TCAAGTTCAACTGGTACGTGGACGGCGTGGAGGTGCATAAT
GCCAAGACAAAGCCGCGGGAGGAGCAGTACAACAGCACGT
ACCGTGTGGTCAGCGTCCTCACCGTCCTGCACCAGGACTG
GCTGAATGGCAAGGAGTACAAGTGCAAGGTCTCCAACAAAG
CCCTCGGCGCCCCCATCGAGAAAACCATCTCCAAAGCCAAA
GGGCAGCCCCGAGAACCACAGGTGTGCACCCTGCCCCCAT
CCCGGGATGAGCTGACCAAGAACCAGGTCAGCCTCTCGTG
CGCAGTCAAAGGCTTCTATCCCAGCGACATCGCCGTGGAGT
GGGAGAGCAATGGGCAGCCGGAGAACAACTACAAGACCAC
GCCTCCCGTGCTGGACTCCGACGGCTCCTTCTTCCTCGTGA
GCAAGCTCACCGTGGACAAGAGCAGGTGGCAGCAGGGGAA
CGTCTTCTCA TGCTCCGTGA TGCA TGAGGCTCTGCA CAA CC
ACTACACGCAGAAGAGCCTCTCCCTGTCTCCGGGTGGAGG
CGGCGGAAGCGGAGGAGGAGGATCCAGAGAGGGCCCTGA
GCTGAGCCCCGATGATCCTGCTGGACTGCTGGACCTGCGG
CAGGGCA TGTTTGCTCA GCTGGTGGCCCAGAA CGTGCTGCT
GATCGATGGCCCCCTGTCCTGGTACAGCGATCCTGGACTG
GCTGGCGTGTCACTGACAGGCGGCCTGAGCTACAAAGAGG
ACACCAAAGAACTGGTGGTGGCCAAGGCCGGCGTGTACTA
CGTGTTCTTTCAGCTGGAACTGCGGAGAGTGGTGGCCGGC
GAAGGATCTGGCTCTGTGTCTCTGGCCCTGCATCTGCAGCC
TCTGAGAAGCGCTGCTGGCGCTGCAGCTCTGGCACTGACA
GTGGATCTGCCTCCTGCCAGCTCCGAGGCCCGGAATAGCG
CATTTGGGTTTCAAGGCAGGCTGCTGCACCTGTCTGCCGGC
CAGAGGCTGGGAGTGCATCTGCACACAGAGGCCAGGGCTA
GACACGCCTGGCAGCTGACACAGGGCGCTACAGTGCTGGG
CCTGTTCAGAGTGACCCCCGAGATTCCAGCCGGCCTGCCTT CTCCAAGAAGCGAAGGCGGAGGCGGATCTGGCGGCGGAG
GATCTAGAGAGGGACCCGAACTGTCCCCTGACGATCCAGC
CGGGCTGCTGGATCTGAGACAGGGAATGTTCGCCCAGCTG
GTGGCTCAGAATGTGCTGCTGATTGACGGACCTCTGAGCTG
GTACTCCGACCCAGGGCTGGCAGGGGTGTCCCTGACTGGG
GGACTGTCCTACAAAGAAGATACAAAAGAACTGGTGGTGGC
GCGGGTGGTGGCTGGGGAGGGCTCAGGATCTGTGTCCCTG
GCTCTGCATCTGCAGCCACTGCGCTCTGCTGCTGGCGCAG
CTGCACTGGCTCTGACTGTGGACCTGCCACCAGCCTCTAGC
GAGGCCAGAAACAGCGCCTTCGGGTTCCAAGGACGCCTGC
TGCATCTGAGCGCCGGACAGCGCCTGGGAGTGCATCTGCA
TACTGAAGCCAGAGCCCGGCATGCTTGGCAGCTGACTCAG
GGGGCAA CTGTGCTGGGA CTGTTTCGCGTGA CA CCTGAGA T
CCCTGCCGGACTGCCAAGCCCTAGATCAGAA
Nucleotide CAGGTGCAGCTGGTGCAGTCTGGCGCCGAAGTGAAGAA sequence anti- ACCCGGCAGCAGCGTGAAGGTGTCCTGCAAGGCCAGCG CEA(T84.66- GCTTCAACATCAAGGACACCTACATGCACTGGGTGCGCC LCHA) Fc knob AGGCCCCTGGACAGGGACTGGAATGGATGGGCAGAATC
GACCCCGCCAACGGCAACAGCAAATACGTGCCCAAGTT
monomeric 41-
CCAGGGCAGAGTGACCATCACCGCCGACACCAGCACCT BBL (71-254)
CCACCGCCTACATGGAACTGAGCAGCCTGCGGAGCGAG
GACACCGCCGTGTACTACTGTGCCCCCTTCGGCTACTAC
GTGTCCGACTACGCCATGGCCTATTGGGGCCAGGGCAC
A TCGTGACCGTGTC T TGCTAGCACCAAGGGCCCATCG
GTCTTCCCCCTGGCACCCTCCTCCAAGAGCACCTCTGGGG
GCACAGCGGCCCTGGGCTGCCTGGTCAAGGACTACTTCCC
CGAACCGGTGACGGTGTCGTGGAACTCAGGCGCCCTGACC
AGCGGCGTGCACACCTTCCCGGCTGTCCTACAGTCCTCAG
GACTCTACTCCCTCAGCAGCGTGGTGACCGTGCCCTCCAGC
AGCTTGGGCA CCCAGA CCTA CA TCTGCAA CGTGAA TCA CAA
GCCCAGCAACACCAAGGTGGACAAGAAAGTTGAGCCCAAAT
CTTGTGA CAAAA CTCA CA CA TGCCCA CCGTGCCCAGCA CCT
GAAGCTGCAGGGGGACCGTCAGTCTTCCTCTTCCCCCCAAA
ACCCAAGGACACCCTCATGATCTCCCGGACCCCTGAGGTCA
CATGCGTGGTGGTGGACGTGAGCCACGAAGACCCTGAGGT
CAAGTTCAA CTGGTA CGTGGA CGGCGTGGAGGTGCA TAA TG
CCAAGACAAAGCCGCGGGAGGAGCAGTACAACAGCACGTA
CCGTGTGGTCAGCGTCCTCACCGTCCTGCACCAGGACTGG
CTGAATGGCAAGGAGTACAAGTGCAAGGTCTCCAACAAAGC
CCTCGGCGCCCCCATCGAGAAAACCATCTCCAAAGCCAAAG
GGCAGCCCCGAGAACCACAGGTGTACACCCTGCCCCCCTG
CAGAGATGAGCTGACCAAGAACCAGGTGTCCCTGTGGTGTC
TGGTCAAGGGCTTCTACCCCAGCGATATCGCCGTGGAGTG
GGAGAGCAACGGCCAGCCTGAGAACAACTACAAGACCACC
CCCCCTGTGCTGGA CAGCGA CGGCAGCTTCTTCCTGTA CTC
CAAACTGACCGTGGACAAGAGCCGGTGGCAGCAGGGCAAC
GTGTTCAGCTGCAGCGTGA TGCA CGAGGCCCTGCA CAA CC
ACTACACCCAGAAGTCCCTGAGCCTGAGCCCCGGCGGAGG
CGGCGGAAGCGGAGGAGGAGGATCCAGAGAGGGCCCTGA
GCTGAGCCCCGATGATCCTGCTGGACTGCTGGACCTGCGG
CAGGGCA TGTTTGCTCA GCTGGTGGCCCAGAA CGTGCTGCT
GATCGATGGCCCCCTGTCCTGGTACAGCGATCCTGGACTG
GCTGGCGTGTCACTGACAGGCGGCCTGAGCTACAAAGAGG ACACCAAAGAACTGGTGGTGGCCAAGGCCGGCGTGTACTA
CGTGTTCTTTCAGCTGGAACTGCGGAGAGTGGTGGCCGGC
GAAGGATCTGGCTCTGTGTCTCTGGCCCTGCATCTGCAGCC
TCTGAGAAGCGCTGCTGGCGCTGCAGCTCTGGCACTGACA
GTGGATCTGCCTCCTGCCAGCTCCGAGGCCCGGAATAGCG
CATTTGGGTTTCAAGGCAGGCTGCTGCACCTGTCTGCCGGC
CAGAGGCTGGGAGTGCATCTGCACACAGAGGCCAGGGCTA
GACACGCCTGGCAGCTGACACAGGGCGCTACAGTGCTGGG
CCTGTTCAGAGTGACCCCCGAGATTCCAGCCGGCCTGCCTT
CTCCAAGAAGCGAA
332 Nucleotide see Table 82
sequence anti- CEA(T84.66- LCHA) light
chain
337 anti- QVQLVQSGAEVKKPGSSVKVSCKASGFNIKDTYMHWVRQ
CEA(T84.66- APGQGLEWMGRIDPANGNSKYVPKFQGRVTITADTSTSTA LCHA) Fc hole YMELSSLRSEDTAVYYCAPFGYYVSDYAMAYWGQGTLV dimeric 41-BBL TVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVS (71-254) chain WNSGALTSGVHTFPAVLQSSGLYSLSSWTVPSSSLGTQTYICNV
NHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGGPSVFLFP
PKPKDTLMISRTPEVTCVWDVSHEDPEVKFNWYVDGVEVHN
AKTKPREEQYNSTYRWSVLTVLHQDWLNGKEYKCKVSNKAL
GAPIEKTISKAKGQPREPQVCTLPPSRDELTKNQVSLSCAVKG
FYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLVSKLTVDK
SRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGGGGGSGGGG
SREGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWYS
DPGLAGVSLTGGLSYKEDTKELWAKAGVYYVFFQLELRRWA
GEGSGSVSLALHLQPLRSAAGAAALALTVDLPPASSEARNSAFG
FQGRLLHLSAGQRLGVHLHTEARARHAWQLTQGATVLGLFRV
TPEIPAGLPSPRSEGGGGSGGGGSREGPELSPDDPAGLLDLR
QGMFAQLVAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYKEDT
KELWAKAGVYYVFFQLELRRWAGEGSGSVSLALHLQPLRSA
AGAAALALTVDLPPASSEARNSAFGFQGRLLHLSAGQRLGVHL
HTEARARHAWQLTQGATVLGLFRVTPEIPAGLPSPRSE
338 anti- QVQLVQSGAEVKKPGSSVKVSCKASGFNIKDTYMHWVRQ
CEA(T84.66- APGQGLEWMGRIDPANGNSKYVPKFQGRVTITADTSTSTA LCHA) Fc knob YMELSSLRSEDTAVYYCAPFGYYVSDYAMAYWGQGTLV monomeric 4- TVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVS 1BBL (71-254) WNSGALTSGVHTFPAVLQSSGLYSLSSWTVPSSSLGTQTYICNV
NHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGGPSVFLFP
chain
PKPKDTLMISRTPEVTCVWDVSHEDPEVKFNWYVDGVEVHN
AKTKPREEQYNSTYRWSVLTVLHQDWLNGKEYKCKVSNKAL
GAPIEKTISKAKGQPREPQVYTLPPCRDELTKNQVSLWCLVKG
FYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDK
SRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGGGGGSGGGG
SREGPELSPDDPAGLLDLRQGMFAQLVAQNVLLIDGPLSWYS
DPGLAGVSLTGGLSYKEDTKELWAKAGVYYVFFQLELRRWA
GEGSGSVSLALHLQPLRSAAGAAALALTVDLPPASSEARNSAFG
FQGRLLHLSAGQRLGVHLHTEARARHAWQLTQGATVLGLFRV
TPEIPAGLPSPRSE 334 anti- see Table 82
CEA(T84.66-
LCHA) light
chain
11.2.4 Preparation of monovalent CEA(T84.66-LCHA) targeted 4-1BB ligand (71-248) trimer-containing Fc (kih) fusion antigen binding molecule with crossed CH1-CL domains with charged residues (Construct 5.4) A polypeptide containing two ectodomains of 4-1BB ligand (71-248), separated by (G4S)2 linkers, and fused to the human IgGl-CL domain, was cloned in analogy to the one depicted in Figure 29A: human 4- IBB ligand, (G4S)2 connector, human 4- IBB ligand, (G4S)2 connector, human CL. A polypeptide containing one ectodomain of 4- IBB ligand (71-248) and fused to the human IgGl-CH domain, was cloned in analogy to the one described in Figure 29B: human 4- IBB ligand, (G4S)2 connector, human CH.
The polypeptide encoding the dimeric 4- IBB ligand fused to human CL domain was subcloned in frame with the human IgGl heavy chain CH2 and CH3 domains on the knob (Merchant, Zhu et al. 1998). To improve correct pairing the following mutations have been introduced in the crossed CH-CL. In the dimeric 4- IBB ligand fused to human CL, E123R and Q124K. In the monomeric 4- IBB ligand fused to human CHI, K147E and K213E.
The variable region of heavy and light chain DNA sequences encoding a binder specific for CEA, clone T84.66-LCHA, were subcloned in frame with either the constant heavy chain of the hole or the constant light chain of human IgGl . The Pro329Gly, Leu234Ala and Leu235Ala mutations have been introduced in the constant region of the knob and hole heavy chains to abrogate binding to Fc gamma receptors according to the method described in WO
2012/130831. Combination of the dimeric ligand-Fc knob chain containing the S354C/T366W mutations, the monomeric CHI fusion, the targeted anti-CD 19-Fc hole chain containing the Y349C/T366S/L368A/Y407V mutations and the anti-CD 19 light chain allows generation of a heterodimer, which includes an assembled trimeric 4- IBB ligand and a CEA binding Fab
(Figure 40, construct 5.4).
Table 85 shows the cDNA and amino acid sequences of the monovalent CEA(T84.66- LCHA) targeted split trimeric 4- IBB ligand (71-248) Fc (kih) fusion antigen binding molecule with crossed CH-CL and charged residues (construct 5.4). Table 85: cDNA and amino acid sequences of monovalent CEA(T84.66-LCHA) targeted split trimeric 4-1BB ligand (71-248) Fc (kih) fusion containing CH-CL cross with charged residues (construct 5.4). * charged residues
Figure imgf000317_0001
11.2.5 Preparation of monovalent CEA(T84.66-LCHA) targeted 4-1BB ligand (71-248) trimer-containing Fc (kih) fusion antigen binding molecule with crossed CH1-CL domains without charged residues (Construct 5.5)
A polypeptide containing two ectodomains of 4-1BB ligand (71-248), separated by (G4S)2 linkers, and fused to the human IgGl-CL domain, was cloned in analogy as depicted in Figure (29 A), but without amino acid mutations in the CL domain: human 4-1BB ligand, (G4S)2 connector, human 4- IBB ligand, (G4S)2 connector, human CL. A polypeptide containing one ectodomain of 4- IBB ligand (71-248) and fused to the human IgGl-CHl domain, was cloned in analogy as depicted in Figure (29B), but without amino acid mutations in the CHI domain:
human 4-1BB ligand, (G4S)2 connector, human CHI. The variable region of heavy and light chain DNA sequences encoding a binder specific for CEA, clone T84.66-LCHA, were subcloned in frame with either the constant heavy chain of the hole or the constant light chain of human IgGl . The Pro329Gly, Leu234Ala and Leu235Ala mutations have been introduced in the constant region of the knob and hole heavy chains to abrogate binding to Fc gamma receptors according to the method described in WO 2012/130831. Combination of the dimeric ligand-Fc knob chain containing the S354C/T366W mutations, the monomeric CHI fusion, the targeted anti-CEA-Fc hole chain containing the Y349C/T366S/L368A/Y407V mutations and the anti-CEA light chain allows generation of a heterodimer, which includes an assembled trimeric 4-lBB ligand and a CD19-binding Fab (Figure 40, Construct 5.5).
Table 86 shows the cDNA and amino acid sequences of the monovalent CEA(T84.66- LCHA) targeted split trimeric 4- IBB ligand (71-248) Fc (kih) fusion antigen binding molecule containing crossed CH-CL cross without charged residues (construct 5.5).
Table 86: cDNA and amino acid sequences of monovalent CEA(T84.66-LCHA) targeted split trimeric 4-lBB ligand (71-248) Fc (kih) fusion containing CH-CL cross without charged residues (construct 5.5).
Figure imgf000318_0001
11.2.6 Preparation of bivalent CEA(T84.66-LCHA) targeted 4-lBB ligand (71-248) trimer-containing Fc (kih) fusion antigen binding (Construct 5.6)
A polypeptide containing two ectodomains of 4-lBB ligand (71-248), separated by (G4S)2 linkers was fused to the C-terminus of human IgGl Fc hole chain, as depicted in Figure 29C: human IgGl Fc hole, (G4S)2 connector, human 4-lBB ligand, (G4S)2 connector, human 4-lBB ligand. A polypeptide containing one ectodomain of 4- IBB ligand (71-254) and fused to the C- terminus of human IgGl Fc knob chain as described in Figure 29D: human IgGl Fc knob, (G4S)2 connector, human 4- IBB ligand.
The variable region of heavy and light chain DNA sequences encoding a binder specific for CEA, clone T84.66-LCHA, were subcloned in frame with either the constant heavy chain of the hole, the knob or the constant light chain of human IgGl. The Pro329Gly, Leu234Ala and Leu235Ala mutations have been introduced in the constant region of the knob and hole heavy chains to abrogate binding to Fc gamma receptors according to the method described in WO 2012/130831. Combination of the anti-CEA hulgGI hole dimeric ligand chain containing the Y349C/T366S/L368A/Y407V mutations, the anti-CEA hulgGI knob monomeric ligand chain containing the S354C/T366W mutations and the anti-CEA light chain allows generation of a heterodimer, which includes an assembled trimeric 4- IBB ligand and two CEA binding Fabs (Figure 40, construct 5.6).
Table 87 shows the cDNA and amino acid sequences of the bivalent CEA(T84.66-LCHA) targeted split trimeric 4- IBB ligand (71-248) Fc (kih) fusion antigen binding molecule (construct 5.6).
Table 87: cDNA and amino acid sequences of bivalent CEA (T84.66-LCHA) targeted split trimeric 4-1BB ligand (71-248) Fc (kih) fusion (construct 5.6)
SEQ ID Description Sequence
NO:
339 Nucleotide CAGGTGCAGCTGGTGCAGTCTGGCGCCGAAGTGAAGAA sequence anti- ACCCGGCAGCAGCGTGAAGGTGTCCTGCAAGGCCAGCG CEA (T84.66- GCTTCAACATCAAGGACACCTACATGCACTGGGTGCGCC LCHA) Fc hole AGGCCCCTGGACAGGGACTGGAATGGATGGGCAGAATC dimeric 4-1BBL GACCCCGCCAACGGCAACAGCAAATACGTGCCCAAGTT
CCAGGGCAGAGTGACCATCACCGCCGACACCAGCACCT
(71-248) chain
CCACCGCCTACATGGAACTGAGCAGCCTGCGGAGCGAG
GACACCGCCGTGTACTACTGTGCCCCCTTCGGCTACTAC
GTGTCCGACTACGCCATGGCCTATTGGGGCCAGGGCAC
ACTCGTGACCGTGTCCTCTGCTAGCACCAAGGGCCCCTC
CGTGTTCCCCCTGGCCCCCAGCAGCAAGAGCACCAGCG
GCGGCACAGCCGCTCTGGGCTGCCTGGTCAAGGACTACT
TCCCCGAGCCCGTGACCGTGTCCTGGAACAGCGGAGCC
CTGACCTCCGGCGTGCACACCTTCCCCGCCGTGCTGCAG
AGTTCTGGCCTGTATAGCCTGAGCAGCGTGGTCACCGTG
CCTTCTAGCAGCCTGGGCACCCAGACCTACATCTGCAAC
GTGAACCACAAGCCCAGCAACACCAAGGTGGACAAGAA
GGTGGAGCCCAAGAGCTGCGACAAAACTCACACATGCC
CACCGTGCCCAGCACCTGAAGCTGCAGGGGGACCGTCA
GTCTTCCTCTTCCCCCCAAAACCCAAGGACACCCTCATG
ATCTCCCGGACCCCTGAGGTCACATGCGTGGTGGTGGAC
GTGAGCCACGAAGACCCTGAGGTCAAGTTCAACTGGTA
CGTGGACGGCGTGGAGGTGCATAATGCCAAGACAAAGC
CGCGGGAGGAGCAGTACAACAGCACGTACCGTGTGGTC
AGCGTCCTCACCGTCCTGCACCAGGACTGGCTGAATGGC
AAGGAGTACAAGTGCAAGGTCTCCAACAAAGCCCTCGG CGCCCCCATCGAGAAAACCATCTCCAAAGCCAAAGGGC
AGCCCCGAGAACCACAGGTGTGCACCCTGCCCCCATCCC
GGGATGAGCTGACCAAGAACCAGGTCAGCCTCTCGTGC
GCAGTCAAAGGCTTCTATCCCAGCGACATCGCCGTGGA
GTGGGAGAGCAATGGGCAGCCGGAGAACAACTACAAGA
CCACGCCTCCCGTGCTGGACTCCGACGGCTCCTTCTTCC
TCGTGAGCAAGCTCACCGTGGACAAGAGCAGGTGGCAG
CAGGGGAACGTCTTCTCATGCTCCGTGATGCATGAGGCT
CTGCACAACCACTACACGCAGAAGAGCCTCTCCCTGTCT
CCGGGTGGAGGCGGCGGAAGCGGAGGAGGAGGATCCA
GAGAGGGCCCTGAGCTGAGCCCTGATGATCCTGCCGGA
CTGCTGGACCTGCGGCAGGGAATGTTTGCCCAGCTGGTG
GCCCAGAACGTGCTGCTGATCGATGGCCCCCTGTCCTGG
TACAGCGATCCTGGACTGGCTGGCGTGTCACTGACAGGC
GGCCTGAGCTACAAAGAGGACACCAAAGAACTGGTGGT
GGCCAAGGCCGGCGTGTACTACGTGTTCTTTCAGCTGGA
ACTGCGGAGAGTGGTGGCCGGCGAAGGATCTGGCTCTG
TGTCTCTGGCCCTGCATCTGCAGCCTCTGAGATCTGCTG
CTGGCGCCGCTGCTCTGGCACTGACAGTGGATCTGCCTC
CTGCCAGCAGCGAGGCCCGGAATAGCGCATTTGGGTTTC
AAGGCAGGCTGCTGCACCTGTCTGCCGGCCAGAGGCTG
GGAGTGCATCTGCACACAGAGGCCAGGGCTAGACACGC
CTGGCAGCTGACACAGGGCGCTACAGTGCTGGGCCTGTT
CAGAGTGACCCCCGAGATTCCAGCAGGCCTGGGAGGCG
GCGGATCTGGCGGCGGAGGATCTAGAGAAGGACCCGAG
CTGTCCCCCGACGATCCCGCTGGGCTGCTGGATCTGAGA
CAGGGCATGTTCGCTCAGCTGGTGGCTCAGAATGTGCTG
CTGATTGACGGACCTCTGAGCTGGTACTCCGACCCAGGG
CTGGCAGGGGTGTCCCTGACTGGGGGACTGTCCTACAAA
GAAGATACAAAAGAACTGGTGGTGGCTAAAGCTGGGGT
GGCTGGGGAGGGCTCAGGATCTGTGTCCCTGGCTCTGCA
TCTGCAGCCACTGCGCTCTGCAGCAGGGGCTGCAGCACT
GGCCCTGACTGTGGACCTGCCCCCAGCTTCTTCCGAGGC
CAGAAACAGCGCCTTCGGGTTCCAAGGACGCCTGCTGC
ATCTGAGCGCCGGACAGCGCCTGGGAGTGCATCTGCAT
ACTGAAGCCAGAGCCCGGCATGCTTGGCAGCTGACTCA
GGGGGCAACTGTGCTGGGACTGTTTCGCGTGACACCTGA
GATCCCAGCCGGGCTC
Nucleotide CAGGTGCAGCTGGTGCAGTCTGGCGCCGAAGTGAAGAA sequence anti- ACCCGGCAGCAGCGTGAAGGTGTCCTGCAAGGCCAGCG CEA (T84.66- GCTTCAACATCAAGGACACCTACATGCACTGGGTGCGCC LCHA) Fc knob AGGCCCCTGGACAGGGACTGGAATGGATGGGCAGAATC
GACCCCGCCAACGGCAACAGCAAATACGTGCCCAAGTT
monomeric (71-
CCAGGGCAGAGTGACCATCACCGCCGACACCAGCACCT
248) 4- 1BBL
CCACCGCCTACATGGAACTGAGCAGCCTGCGGAGCGAG
chain GACACCGCCGTGTACTACTGTGCCCCCTTCGGCTACTAC
GTGTCCGACTACGCCATGGCCTATTGGGGCCAGGGCAC
ACTCGTGACCGTGTCCTCTGCTAGCACCAAGGGCCCATC
GGTCTTCCCCCTGGCACCCTCCTCCAAGAGCACCTCTGG
GGGCACAGCGGCCCTGGGCTGCCTGGTCAAGGACTACT
TCCCCGAACCGGTGACGGTGTCGTGGAACTCAGGCGCC
CTGACCAGCGGCGTGCACACCTTCCCGGCTGTCCTACAG
TCCTCAGGACTCTACTCCCTCAGCAGCGTGGTGACCGTG CCCTCCAGCAGCTTGGGCACCCAGACCTACATCTGCAAC
GTGAATCACAAGCCCAGCAACACCAAGGTGGACAAGAA
AGTTGAGCCCAAATCTTGTGACAAAACTCACACATGCCC
ACCGTGCCCAGCACCTGAAGCTGCAGGGGGACCGTCAG
TCTTCCTCTTCCCCCCAAAACCCAAGGACACCCTCATGA
TCTCCCGGACCCCTGAGGTCACATGCGTGGTGGTGGACG
TGAGCCACGAAGACCCTGAGGTCAAGTTCAACTGGTAC
GTGGACGGCGTGGAGGTGCATAATGCCAAGACAAAGCC
GCGGGAGGAGCAGTACAACAGCACGTACCGTGTGGTCA
GCGTCCTCACCGTCCTGCACCAGGACTGGCTGAATGGCA
AGGAGTACAAGTGCAAGGTCTCCAACAAAGCCCTCGGC
GCCCCCATCGAGAAAACCATCTCCAAAGCCAAAGGGCA
GCCCCGAGAACCACAGGTGTACACCCTGCCCCCCTGCA
GAGATGAGCTGACCAAGAACCAGGTGTCCCTGTGGTGT
CTGGTCAAGGGCTTCTACCCCAGCGATATCGCCGTGGAG
TGGGAGAGCAACGGCCAGCCTGAGAACAACTACAAGAC
CACCCCCCCTGTGCTGGACAGCGACGGCAGCTTCTTCCT
GTACTCCAAACTGACCGTGGACAAGAGCCGGTGGCAGC
AGGGCAACGTGTTCAGCTGCAGCGTGATGCACGAGGCC
CTGCACAACCACTACACCCAGAAGTCCCTGAGCCTGAG
CCCCGGCGGAGGCGGCGGAAGCGGAGGAGGAGGATCC
AGAGAGGGCCCTGAGCTGAGCCCTGATGATCCTGCCGG
ACTGCTGGACCTGCGGCAGGGAATGTTTGCCCAGCTGGT
GGCCCAGAACGTGCTGCTGATCGATGGCCCCCTGTCCTG
GTACAGCGATCCTGGACTGGCTGGCGTGTCACTGACAGG
CGGCCTGAGCTACAAAGAGGACACCAAAGAACTGGTGG
TGGCCAAGGCCGGCGTGTACTACGTGTTCTTTCAGCTGG
AACTGCGGAGAGTGGTGGCCGGCGAAGGATCTGGCTCT
GTGTCTCTGGCCCTGCATCTGCAGCCTCTGAGATCTGCT
GCTGGCGCCGCTGCTCTGGCACTGACAGTGGATCTGCCT
CCTGCCAGCAGCGAGGCCCGGAATAGCGCATTTGGGTTT
CAAGGCAGGCTGCTGCACCTGTCTGCCGGCCAGAGGCT
GGGAGTGCATCTGCACACAGAGGCCAGGGCTAGACACG
CCTGGCAGCTGACACAGGGCGCTACAGTGCTGGGCCTG
TTCAGAGTGACCCCCGAGATTCCTGCCGGGCTC
332 Nucleotide see Table 82
sequence anti- CEA (T84.66- LCHA) light
chain
341 anti- CEA QVQLVQSGAEVKKPGSSVKVSCKASGFNIKDTYMHWVRQ
(T84.66-LCHA) APGQGLEWMGRIDPANGNSKYVPKFQGRVTITADTSTSTA Fc hole dimeric 4- YMELSSLRSEDTAVYYCAPFGYYVSDYAMAYWGQGTLV 1BBL (71-248) TVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPV
TVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGT
chain
QTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAA
GGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFN
WYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWL
NGKEYKCKVSNKALGAPIEKTISKAKGQPREPQVCTLPPSR
DELTKNQVSLSCAVKGFYPSDIAVEWESNGQPENNYKTTP
PVLDSDGSFFLVSKLTVDKSRWQQGNVFSCSVMHEALHN
HYTQKSLSLSPGGGGGSGGGGSREGPELSPDDPAGLLDLR
QGMFAQLVAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYKE DTKELVVAKAGVYYVFFQLELRRVVAGEGSGSVSLALHL
QPLRSAAGAAALALTVDLPPASSEARNSAFGFQGRLLHLS
AGQRLGVHLHTEARARHAWQLTQGATVLGLFRVTPEIPA
GLGGGGSGGGGSREGPELSPDDPAGLLDLRQGMFAQLVA
QNVLLIDGPLSWYSDPGLAGVSLTGGLSYKEDTKELVVAK
AGVYYVFFQLELRRVVAGEGSGSVSLALHLQPLRSAAGAA
ALALTVDLPPASSEARNSAFGFQGRLLHLSAGQRLGVHLH
TEARARHAWQLTQGATVLGLFRVTPEIPAGL
342 anti- CEA QVQLVQSGAEVKKPGSSVKVSCKASGFNIKDTYMHWVRQ
(T84.66-LCHA) APGQGLEWMGRIDPANGNSKYVPKFQGRVTITADTSTSTA Fc knob YMELSSLRSEDTAVYYCAPFGYYVSDYAMAYWGQGTLV monomeric (71- TVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPV
TVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGT
248) 4- 1BBL
QTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAA
chain
GGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFN
WYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWL
NGKEYKCKVSNKALGAPIEKTISKAKGQPREPQVYTLPPCR
DELTKNQVSLWCLVKGFYPSDIAVEWESNGQPENNYKTTP
PVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHN
HYTQKSLSLSPGGGGGSGGGGSREGPELSPDDPAGLLDLR
QGMFAQLVAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYKE
DTKELVVAKAGVYYVFFQLELRRVVAGEGSGSVSLALHL
QPLRSAAGAAALALTVDLPPASSEARNSAFGFQGRLLHLS
AGQRLGVHLHTEARARHAWQLTQGATVLGLFRVTPEIPA
GL
334 anti-CD19(8B8- see Table 82
018) light chain
11.2.7 Preparation of monovalent CEA(T84.66) targeted 4-1BB ligand (71-254) trimer-containing Fc (kih) fusion antigen binding molecule with crossed CH1-CL domains with charged residues (Construct 5.7) A polypeptide containing two ectodomains of 4-1BB ligand (71-254), separated by (G4S)2 linkers, and fused to the human IgGl-CL domain, was cloned as depicted in Figure 29A: human 4- 1BB ligand, (G4S)2 connector, human 4-1BB ligand, (G4S)2 connector, human CL. A polypeptide containing one ectodomain of 4-1BB ligand (71-254) and fused to the human IgGl- CH domain, was cloned as described in Figure 29B: human 4- IBB ligand, (G4S)2 connector, human CH.
To improve correct pairing the following mutations have been introduced in the crossed CH-CL. In the dimeric 4- IBB ligand fused to human CL, E123R and Q124K. In the monomeric 4-1BB ligand fused to human CHI, K147E and K213E.
The variable region of heavy and light chain DNA sequences encoding a binder specific for CEA, clone T84.66, were subcloned in frame with either the constant heavy chain of the hole or the constant light chain of human IgGl . The Pro329Gly, Leu234Ala and Leu235Ala mutations have been introduced in the constant region of the knob and hole heavy chains to abrogate binding to Fc gamma receptors according to the method described in WO 2012/130831.
Combination of the dimeric ligand-Fc knob chain containing the S354C/T366W mutations, the monomeric CHI fusion, the targeted anti-CD 19-Fc hole chain containing the
Y349C/T366S/L368A/Y407V mutations and the anti-CD 19 light chain allows generation of a heterodimer, which includes an assembled trimeric 4- IBB ligand and a CEA binding Fab.
Construct 5.7 corresponds to Construct 5.1 as shown in Figure 40.
Table 88 shows the cDNA and amino acid sequences of the monovalent CEA(T84.66) targeted split trimeric 4- IBB ligand (71-254) Fc (kih) fusion antigen binding molecule with crossed CH-CL and charged residues (construct 5.7).
Table 88: cDNA and amino acid sequences of monovalent CEA(T84.66) targeted split trimeric 4-lBB ligand (71-254) Fc (kih) fusion containing crossed CH-CL with charged residues (construct 5.7). * for charged residues
SEQ ID Description Sequence
NO:
129 Nucleotide see Table 3
sequence Dimeric
hu 4-lBBL (71- 254) - CL* Fc
knob chain
130 Nucleotide see Table 3
sequence
Monomeric hu
4-1BBL (71-254)
- CHI*
343 Nucleotide GAGGTGCAGCTGCAGCAGTCTGGCGCCGAACTGGTGGA sequence anti- ACCTGGCGCCTCTGTGAAGCTGAGCTGTACCGCCAGCGG CEA(T84.66) Fc CTTCAACATCAAGGACACCTACATGCACTGGGTCAAGC hole chain AGCGGCCTGAGCAGGGCCTGGAATGGATCGGCAGAATC
GACCCCGCCAACGGCAACAGCAAATACGTGCCCAAGTT
CCAGGGCAAGGCCACCATCACCGCCGACACCAGCAGCA
ACACAGCCTACCTGCAGCTGACCAGCCTGACCTCCGAG
GACACCGCCGTGTACTACTGCGCCCCCTTCGGCTACTAC
GTGTCCGACTACGCCATGGCCTATTGGGGCCAGGGCAC
AAGCGTGACCGTGTCCTCTGCTAGCACCAAGGGCCCCTC
CGTGTTCCCCCTGGCCCCCAGCAGCAAGAGCACCAGCG
GCGGCACAGCCGCTCTGGGCTGCCTGGTCAAGGACTACT
TCCCCGAGCCCGTGACCGTGTCCTGGAACAGCGGAGCC
CTGACCTCCGGCGTGCACACCTTCCCCGCCGTGCTGCAG
AGTTCTGGCCTGTATAGCCTGAGCAGCGTGGTCACCGTG
CCTTCTAGCAGCCTGGGCACCCAGACCTACATCTGCAAC
GTGAACCACAAGCCCAGCAACACCAAGGTGGACAAGAA
GGTGGAGCCCAAGAGCTGCGACAAAACTCACACATGCC CACCGTGCCCAGCACCTGAAGCTGCAGGGGGACCGTCA
GTCTTCCTCTTCCCCCCAAAACCCAAGGACACCCTCATG
ATCTCCCGGACCCCTGAGGTCACATGCGTGGTGGTGGAC
GTGAGCCACGAAGACCCTGAGGTCAAGTTCAACTGGTA
CGTGGACGGCGTGGAGGTGCATAATGCCAAGACAAAGC
CGCGGGAGGAGCAGTACAACAGCACGTACCGTGTGGTC
AGCGTCCTCACCGTCCTGCACCAGGACTGGCTGAATGGC
AAGGAGTACAAGTGCAAGGTCTCCAACAAAGCCCTCGG
CGCCCCCATCGAGAAAACCATCTCCAAAGCCAAAGGGC
AGCCCCGAGAACCACAGGTGTGCACCCTGCCCCCATCCC
GGGATGAGCTGACCAAGAACCAGGTCAGCCTCTCGTGC
GCAGTCAAAGGCTTCTATCCCAGCGACATCGCCGTGGA
GTGGGAGAGCAATGGGCAGCCGGAGAACAACTACAAGA
CCACGCCTCCCGTGCTGGACTCCGACGGCTCCTTCTTCC
TCGTGAGCAAGCTCACCGTGGACAAGAGCAGGTGGCAG
CAGGGGAACGTCTTCTCATGCTCCGTGATGCATGAGGCT
CTGCACAACCACTACACGCAGAAGAGCCTCTCCCTGTCT
CCGGGTAAA
344 Nucleotide GACATCGTGCTGACCCAGAGCCCTGCCTCTCTGGCCGTG sequence anti- TCTCTGGGACAGAGGGCCACCATGTCTTGCAGAGCCGG CEA(T84.66) CGAGAGCGTGGACATCTTCGGCGTGGGATTTCTGCACTG light chain GTATCAGCAGAAGCCCGGCCAGCCCCCCAAGCTGCTGA
TCTACAGAGCCAGCAACCTGGAAAGCGGCATCCCCGTG
CGGTTTAGCGGCACCGGCAGCAGAACCGACTTCACCCT
GATCATCGACCCCGTGGAAGCCGACGACGTGGCCACCT
ACTACTGCCAGCAGACCAACGAGGACCCCTACACCTTTG
GCGGAGGCACCAAGCTGGAAATCAAGCGTACGGTGGCT
GCACCATCTGTCTTCATCTTCCCGCCATCTGATGAGCAG
TTGAAATCTGGAACTGCCTCTGTTGTGTGCCTGCTGAAT
AACTTCTATCCCAGAGAGGCCAAAGTACAGTGGAAGGT
GGATAACGCCCTCCAATCGGGTAACTCCCAGGAGAGTG
TCACAGAGCAGGACAGCAAGGACAGCACCTACAGCCTC
AGCAGCACCCTGACGCTGAGCAAAGCAGACTACGAGAA
ACACAAAGTCTACGCCTGCGAAGTCACCCATCAGGGCC
TGAGCTCGCCCGTCACAAAGAGCTTCAACAGGGGAGAG
TGT
115 Dimeric hu 4- see Table 3
1BBL (71-254) - CL* Fc knob
chain
116 Monomeric hu see Table 3
4-1BBL (71-254)
- CHI*
345 anti- CEA EVQLQQSGAELVEPGASVKLSCTASGFNIKDTYMHWVKQ
(T84.66) Fc hole RPEQGLEWIGRIDPANGNSKYVPKFQGKATITADTSSNTAY chain LQLTSLTSEDTAVYYCAPFGYYVSDYAMAYWGQGTSVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTV
SWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQT
YICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGG
PSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWY
VDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNG
KEYKCKVSNKALGAPIEKTISKAKGQPREPQVCTLPPSRDE LTKNQVSLSCAVKGFYPSDIAVEWESNGQPENNYKTTPPV
LDSDGSFFLVSKLTVDKSRWQQGNVFSCSVMHEALHNHY TQKSLSLSPGK
346 anti- CEA DIVLTQSPASLAVSLGQRATMSCRAGESVDIFGVGFLHWY
(T84.66) light QQKPGQPPKLLIYRASNLESGIPVRFSGTGSRTDFTLIIDPVE chain ADDVATYYCQQTNEDPYTFGGGTKLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNS
QESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQ
GLS SP VTKSFNRGEC
11.2.8 Preparation of bivalent CEA(T84.66) targeted 4-1BB ligand (71-254) trimer- containing Fc (kih) fusion antigen binding molecule (Construct 5.8)
A polypeptide containing two ectodomains of 4-1BB ligand (71-254), separated by (G4S)2 linkers was fused to the C-terminus of human IgGl Fc hole chain, as depicted in Figure 29C: human IgGl Fc hole, (G4S)2 connector, human 4-1BB ligand, (G4S)2 connector, human 4-1BB ligand. A polypeptide containing one ectodomain of 4- IBB ligand (71-254) and fused to the C- terminus of human IgGl Fc knob chain as described in Figure 29D: human IgGl Fc knob, (G4S)2 connector, human 4- IBB ligand. The variable region of heavy and light chain DNA sequences encoding a binder specific for CEA, clone T84.66, were subcloned in frame with either the constant heavy chain of the hole, the knob or the constant light chain of human IgGl. The Pro329Gly, Leu234Ala and Leu235Ala mutations have been introduced in the constant region of the knob and hole heavy chains to abrogate binding to Fc gamma receptors according to the method described in WO 2012/130831. Combination of the anti-CEA hulgGI hole dimeric ligand chain containing the
Y349C/T366S/L368A/Y407V mutations, the anti-CEA hulgGI knob monomeric ligand chain containing the S354C/T366W mutations and the anti-CEA light chain allows generation of a heterodimer, which includes an assembled trimeric 4- IBB ligand and two CEA binding Fabs. Construct 5.8 corresponds to Construct 5.3 as shown in Figure 40. Table 89 shows the cDNA and amino acid sequences of the bivalent CEA(T84.66) targeted split trimeric 4- IBB ligand (71-254) Fc (kih) fusion antigen binding molecule (construct 5.8).
Table 89: cDNA and amino acid sequences of bivalent CEA(T84.66) targeted split trimeric 4-1BB ligand (71-254) Fc (kih) PGLALA fusion (construct 5.8)
SEQ ID Description Sequence
NO:
347 Nucleotide GAGGTGCAGCTGCAGCAGTCTGGCGCCGAACTGGTGGA sequence anti- ACCTGGCGCCTCTGTGAAGCTGAGCTGTACCGCCAGCGG CEA(T84.66) Fc CTTCAACATCAAGGACACCTACATGCACTGGGTCAAGC
AGCGGCCTGAGCAGGGCCTGGAATGGATCGGCAGAATC hole dimeric 4- GACCCCGCCAACGGCAACAGCAAATACGTGCCCAAGTT 1BBL (71-254) CCAGGGCAAGGCCACCATCACCGCCGACACCAGCAGCA chain ACACAGCCTACCTGCAGCTGACCAGCCTGACCTCCGAG
GACACCGCCGTGTACTACTGCGCCCCCTTCGGCTACTAC GTGTCCGACTACGCCATGGCCTATTGGGGCCAGGGCAC AAGCGTGACCGTGTCCTCTGCTAGCACCAAGGGCCCCTC CGTGTTCCCCCTGGCCCCCAGCAGCAAGAGCACCAGCG GCGGCACAGCCGCTCTGGGCTGCCTGGTCAAGGACTACT TCCCCGAGCCCGTGACCGTGTCCTGGAACAGCGGAGCC CTGACCTCCGGCGTGCACACCTTCCCCGCCGTGCTGCAG AGTTCTGGCCTGTATAGCCTGAGCAGCGTGGTCACCGTG CCTTCTAGCAGCCTGGGCACCCAGACCTACATCTGCAAC GTGAACCACAAGCCCAGCAACACCAAGGTGGACAAGAA GGTGGAGCCCAAGAGCTGCGACAAAACTCACACATGCC CACCGTGCCCAGCACCTGAAGCTGCAGGGGGACCGTCA GTCTTCCTCTTCCCCCCAAAACCCAAGGACACCCTCATG ATCTCCCGGACCCCTGAGGTCACATGCGTGGTGGTGGAC GTGAGCCACGAAGACCCTGAGGTCAAGTTCAACTGGTA CGTGGACGGCGTGGAGGTGCATAATGCCAAGACAAAGC CGCGGGAGGAGCAGTACAACAGCACGTACCGTGTGGTC AGCGTCCTCACCGTCCTGCACCAGGACTGGCTGAATGGC AAGGAGTACAAGTGCAAGGTCTCCAACAAAGCCCTCGG CGCCCCCATCGAGAAAACCATCTCCAAAGCCAAAGGGC AGCCCCGAGAACCACAGGTGTGCACCCTGCCCCCATCCC GGGATGAGCTGACCAAGAACCAGGTCAGCCTCTCGTGC GCAGTCAAAGGCTTCTATCCCAGCGACATCGCCGTGGA GTGGGAGAGCAATGGGCAGCCGGAGAACAACTACAAGA CCACGCCTCCCGTGCTGGACTCCGACGGCTCCTTCTTCC TCGTGAGCAAGCTCACCGTGGACAAGAGCAGGTGGCAG CAGGGGAACGTCTTCTCATGCTCCGTGATGCATGAGGCT CTGCACAACCACTACACGCAGAAGAGCCTCTCCCTGTCT CCGGGTGGAGGCGGCGGAAGCGGAGGAGGAGGATCCA GAGAGGGCCCTGAGCTGAGCCCCGATGATCCTGCTGGA CTGCTGGACCTGCGGCAGGGCATGTTTGCTCAGCTGGTG GCCCAGAACGTGCTGCTGATCGATGGCCCCCTGTCCTGG TACAGCGATCCTGGACTGGCTGGCGTGTCACTGACAGGC GGCCTGAGCTACAAAGAGGACACCAAAGAACTGGTGGT GGCCAAGGCCGGCGTGTACTACGTGTTCTTTCAGCTGGA ACTGCGGAGAGTGGTGGCCGGCGAAGGATCTGGCTCTG TGTCTCTGGCCCTGCATCTGCAGCCTCTGAGAAGCGCTG CTGGCGCTGCAGCTCTGGCACTGACAGTGGATCTGCCTC CTGCCAGCTCCGAGGCCCGGAATAGCGCATTTGGGTTTC AAGGCAGGCTGCTGCACCTGTCTGCCGGCCAGAGGCTG GGAGTGCATCTGCACACAGAGGCCAGGGCTAGACACGC CTGGCAGCTGACACAGGGCGCTACAGTGCTGGGCCTGTT CAGAGTGACCCCCGAGATTCCAGCCGGCCTGCCTTCTCC AAGAAGCGAAGGCGGAGGCGGATCTGGCGGCGGAGGA TCTAGAGAGGGACCCGAACTGTCCCCTGACGATCCAGC CGGGCTGCTGGATCTGAGACAGGGAATGTTCGCCCAGCT GGTGGCTCAGAATGTGCTGCTGATTGACGGACCTCTGAG CTGGTACTCCGACCCAGGGCTGGCAGGGGTGTCCCTGAC TGGGGGACTGTCCTACAAAGAAGATACAAAAGAACTGG
TGGAACTGAGGCGGGTGGTGGCTGGGGAGGGCTCAGGA TCTGTGTCCCTGGCTCTGCATCTGCAGCCACTGCGCTCT
GCTGCTGGCGCAGCTGCACTGGCTCTGACTGTGGACCTG
CCACCAGCCTCTAGCGAGGCCAGAAACAGCGCCTTCGG
GTTCCAAGGACGCCTGCTGCATCTGAGCGCCGGACAGC
GCCTGGGAGTGCATCTGCATACTGAAGCCAGAGCCCGG
CATGCTTGGCAGCTGACTCAGGGGGCAACTGTGCTGGG
ACTGTTTCGCGTGACACCTGAGATCCCTGCCGGACTGCC
AAGCCCTAGATCAGAA
Nucleotide GAGGTGCAGCTGCAGCAGTCTGGCGCCGAACTGGTGGA sequence anti- ACCTGGCGCCTCTGTGAAGCTGAGCTGTACCGCCAGCGG CEA(T84.66) Fc CTTCAACATCAAGGACACCTACATGCACTGGGTCAAGC knob monomelic AGCGGCCTGAGCAGGGCCTGGAATGGATCGGCAGAATC
GACCCCGCCAACGGCAACAGCAAATACGTGCCCAAGTT
4-1BBL (72-254)
CCAGGGCAAGGCCACCATCACCGCCGACACCAGCAGCA
chain
ACACAGCCTACCTGCAGCTGACCAGCCTGACCTCCGAG
GACACCGCCGTGTACTACTGCGCCCCCTTCGGCTACTAC
GTGTCCGACTACGCCATGGCCTATTGGGGCCAGGGCAC
AAGCGTGACCGTGTCCTCTGCTAGCACCAAGGGCCCATC
GGTCTTCCCCCTGGCACCCTCCTCCAAGAGCACCTCTGG
GGGCACAGCGGCCCTGGGCTGCCTGGTCAAGGACTACT
TCCCCGAACCGGTGACGGTGTCGTGGAACTCAGGCGCC
CTGACCAGCGGCGTGCACACCTTCCCGGCTGTCCTACAG
TCCTCAGGACTCTACTCCCTCAGCAGCGTGGTGACCGTG
CCCTCCAGCAGCTTGGGCACCCAGACCTACATCTGCAAC
GTGAATCACAAGCCCAGCAACACCAAGGTGGACAAGAA
AGTTGAGCCCAAATCTTGTGACAAAACTCACACATGCCC
ACCGTGCCCAGCACCTGAAGCTGCAGGGGGACCGTCAG
TCTTCCTCTTCCCCCCAAAACCCAAGGACACCCTCATGA
TCTCCCGGACCCCTGAGGTCACATGCGTGGTGGTGGACG
TGAGCCACGAAGACCCTGAGGTCAAGTTCAACTGGTAC
GTGGACGGCGTGGAGGTGCATAATGCCAAGACAAAGCC
GCGGGAGGAGCAGTACAACAGCACGTACCGTGTGGTCA
GCGTCCTCACCGTCCTGCACCAGGACTGGCTGAATGGCA
AGGAGTACAAGTGCAAGGTCTCCAACAAAGCCCTCGGC
GCCCCCATCGAGAAAACCATCTCCAAAGCCAAAGGGCA
GCCCCGAGAACCACAGGTGTACACCCTGCCCCCCTGCA
GAGATGAGCTGACCAAGAACCAGGTGTCCCTGTGGTGT
CTGGTCAAGGGCTTCTACCCCAGCGATATCGCCGTGGAG
TGGGAGAGCAACGGCCAGCCTGAGAACAACTACAAGAC
CACCCCCCCTGTGCTGGACAGCGACGGCAGCTTCTTCCT
GTACTCCAAACTGACCGTGGACAAGAGCCGGTGGCAGC
AGGGCAACGTGTTCAGCTGCAGCGTGATGCACGAGGCC
CTGCACAACCACTACACCCAGAAGTCCCTGAGCCTGAG
CCCCGGCGGAGGCGGCGGAAGCGGAGGAGGAGGATCC
AGAGAGGGCCCTGAGCTGAGCCCCGATGATCCTGCTGG
ACTGCTGGACCTGCGGCAGGGCATGTTTGCTCAGCTGGT
GGCCCAGAACGTGCTGCTGATCGATGGCCCCCTGTCCTG
GTACAGCGATCCTGGACTGGCTGGCGTGTCACTGACAGG
CGGCCTGAGCTACAAAGAGGACACCAAAGAACTGGTGG
TGGCCAAGGCCGGCGTGTACTACGTGTTCTTTCAGCTGG
AACTGCGGAGAGTGGTGGCCGGCGAAGGATCTGGCTCT
GTGTCTCTGGCCCTGCATCTGCAGCCTCTGAGAAGCGCT
GCTGGCGCTGCAGCTCTGGCACTGACAGTGGATCTGCCT
CCTGCCAGCTCCGAGGCCCGGAATAGCGCATTTGGGTTT CAAGGCAGGCTGCTGCACCTGTCTGCCGGCCAGAGGCT
GGGAGTGCATCTGCACACAGAGGCCAGGGCTAGACACG
CCTGGCAGCTGACACAGGGCGCTACAGTGCTGGGCCTG
TTCAGAGTGACCCCCGAGATTCCAGCCGGCCTGCCTTCT
CCAAGAAGCGAA
344 Nucleotide see Table 88
sequence anti- CEA(T84.66)
light chain
349 anti- EVQLQQSGAELVEPGASVKLSCTASGFNIKDTYMHWVKQ
CEA(T84.66) Fc RPEQGLEWIGRIDPANGNSKYVPKFQGKATITADTSSNTAY hole dimeric 4- LQLTSLTSEDTAVYYCAPFGYYVSDYAMAYWGQGTSVTV 1BBL(71-254) SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTV
SWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQT
chain
YICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGG
PSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWY
VDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNG
KEYKCKVSNKALGAPIEKTISKAKGQPREPQVCTLPPSRDE
LTKNQVSLSCAVKGFYPSDIAVEWESNGQPENNYKTTPPV
LDSDGSFFLVSKLTVDKSRWQQGNVFSCSVMHEALHNHY
TQKSLSLSPGGGGGSGGGGSREGPELSPDDPAGLLDLRQG
MFAQLVAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYKEDT
KELVVAKAGVYYVFFQLELRRVVAGEGSGSVSLALHLQPL
RSAAGAAALALTVDLPPASSEARNSAFGFQGRLLHLSAGQ
RLGVHLHTEARARHAWQLTQGATVLGLFRVTPEIPAGLPS
PRSEGGGGSGGGGSREGPELSPDDPAGLLDLRQGMFAQLV
AQNVLLIDGPLSWYSDPGLAGVSLTGGLSYKEDTKELVVA
KAGVYYVFFQLELRRVVAGEGSGSVSLALHLQPLRSAAGA
AALALTVDLPPASSEARNSAFGFQGRLLHLSAGQRLGVHL
HTEARARHAWQLTQGATVLGLFRVTPEIPAGLPSPRSE
350 anti- EVQLQQSGAELVEPGASVKLSCTASGFNIKDTYMHWVKQ
CEA(T84.66) Fc RPEQGLEWIGRIDPANGNSKYVPKFQGKATITADTSSNTAY knob monomelic LQLTSLTSEDTAVYYCAPFGYYVSDYAMAYWGQGTSVTV 4-1BBL (71-254) SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTV
SWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQT
chain
YICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPEAAGG
PSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWY
VDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNG
KEYKCKVSNKALGAPIEKTISKAKGQPREPQVYTLPPCRDE
LTKNQVSLWCLVKGFYPSDIAVEWESNGQPENNYKTTPPV
LDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHY
TQKSLSLSPGGGGGSGGGGSREGPELSPDDPAGLLDLRQG
MFAQLVAQNVLLIDGPLSWYSDPGLAGVSLTGGLSYKEDT
KELVVAKAGVYYVFFQLELRRVVAGEGSGSVSLALHLQPL
RSAAGAAALALTVDLPPASSEARNSAFGFQGRLLHLSAGQ
RLGVHLHTEARARHAWQLTQGATVLGLFRVTPEIPAGLPS
PRSE
346 anti- see Table 88
CEA(T84.66)
light chain 11.3 Preparation of untargeted split trimeric 4-1BB ligand Fc fusion molecules and human IgG as control molecules
11.3.1 Preparation of untargeted human 4-1BB ligand trimer-containing Fc fusion antigen binding molecules (Control molecules) These control molecules were prepared as described above for the CEA targeted construct
3.1 (termed control B), 3.3 (termed control C), 3.4 (termed control D) and 3.5 (termed control E) with the only difference that the anti-CD 19 binder (VH-VL) was replaced by a germline control, termed DP47, not binding to the antigen (see Figure 40). The cDNA and amino acid sequences of control B, the monovalent DP47 -untargeted split trimeric 4-1BB ligand (71-254) Fc (kih) fusion containing crossed CH-CL with charged residues, are shown in Table 68 above (see Example 7.3.1). Table 69 shows the cDNA and amino acid sequences of the bivalent DP47- untargeted split trimeric 4- IBB ligand (71-254) Fc (kih) fusion, control C. Table 70 shows the cDNA and amino acid sequences of the monovalent DP47 -untargeted split trimeric 4- IBB ligand (71-248) Fc (kih) fusion containing CH-CL cross with charged residues, control D. Table 71 shows the cDNA and amino acid sequences of the monovalent DP47 -untargeted split trimeric 4- 1BB ligand (71-248) Fc (kih) fusion without charged residues in the CH-CL cross, control E.
11.3.2 Antibodies as control molecules
An additional control used in the assays, termed control F, was an untargeted DP47, germline control, human IgGl, containing the Pro329Gly, Leu234Ala and Leu235Ala mutations, to abrogate binding to Fc gamma receptors. The cDNA and amino acid sequences of control F can be found in Table 73 above.
11.4 Production of CEA- targeted split trimeric 4-1BB ligand Fc fusion antigen binding molecules and their control molecules
The targeted and untargeted split trimeric 4- IBB ligand Fc (kih) fusion antigen binding molecule encoding sequences were cloned into a plasmid vector, which drives expression of the insert from an MPSV promoter and contains a synthetic polyA sequence located at the 3' end of the CDS. In addition, the vector contains an EBV OriP sequence for episomal maintenance of the plasmid.
The split trimeric 4- IBB ligand Fc (kih) fusion was produced by co-transfecting HEK293- EBNA cells with the mammalian expression vectors using polyethylenimine. The cells were transfected with the corresponding expression vectors. For variants 1,2,4,5 and it's control B, D and E, at a 1: 1: 1: 1 ratio ("vector dimeric ligand-CL- knob chain": "vector monomeric ligand fusion-CHI": "vector anti-CEA Fab-hole chain": "vector anti-CEA light chain"). For variant 3, 6 and it's control C, at a 1: 1: 1 ratio ("vector huIgGl Fc hole dimeric ligand chain": "vector hulgGI Fc knob monomeric ligand chain": "vector anti-CEA light chain"). Human IgGs, used as control in the assay, were produced as for the bispecific construct (for transfection only a vector for light and a vector for heavy chain were used at a 1: 1 ratio). For production in 500 mL shake flasks, 300 million HEK293 EBNA cells were seeded 24 hours before transfection. For transfection cells were centrifuged for 10 minutes at 210 x g, and the supernatant was replaced by 20mL pre- warmed CD CHO medium. Expression vectors (200 μg of total DNA) were mixed in 20 mL CD CHO medium. After addition of 540 PEI, the solution was vortexed for 15 seconds and incubated for 10 minutes at room temperature.
Afterwards, cells were mixed with the DNA/PEI solution, transferred to a 500 mL shake flask and incubated for 3 hours at 37°C in an incubator with a 5% C02 atmosphere. After the incubation, 160 mL of Excell medium supplemented with 6mM L-Glutamine, 5g/L PEPSOY and 1.2 mM valproic acid was added and cells were cultured for 24 hours. One day after transfection 12% Feed (amino acid and glucose) were added. After culturing for 7 days, the supernatant was collected by centrifugation for 30-40 minutes at least 400 x g. The solution was sterile filtered (0.22 μιη filter), supplemented with sodium azide to a final concentration of 0.01 % (w/v), and kept at 4 °C.
The split trimeric 4- IBB ligand Fc (kih) fusion, as well as the IgG, was purified from cell culture supernatants by affinity chromatography using Protein A, followed by size exclusion chromatography. For affinity chromatography, the supernatant was loaded on a MabSelect Sure column (CV = 5-15 mL, resin from GE Healthcare) equilibrated with Sodium Phosphate (20 mM), Sodium Citrate (20 mM) buffer (pH 7.5). Unbound protein was removed by washing with at least 6 column volumes of the same buffer. The bound protein was eluted using either a linear gradient (20 CV) or a step elution (8 CV) with 20 mM sodium citrate, 100 mM Sodium chloride, 100 mM Glycine buffer (pH 3.0). For the linear gradient an additional 4 column volumes step elution was applied.
The pH of collected fractions was adjusted by adding 1/10 (v/v) of 0.5M sodium phosphate, pH8.0. The protein was concentrated prior to loading on a HiLoad Superdex 200 column (GE Healthcare) equilibrated with 20 mM Histidine, 140 mM sodium chloride, 0.01% (v/v) Tween20 solution of pH 6.0.
The protein concentration was determined by measuring the optical density (OD) at 280 nm, using a molar extinction coefficient calculated on the basis of the amino acid sequence.
Purity and molecular weight of the targeted trimeric 4- IBB ligand Fc (kih) fusion antigen binding molecule was analyzed by SDS-PAGE in the presence and absence of a reducing agent (5 mM 1,4-dithiotreitol) and staining with Coomassie SimpleBlue™ SafeStain (Invitrogen USA) or CE-SDS using Caliper LabChip GXII (Perkin Elmer). The aggregate content of samples was analyzed using a TSKgel G3000 SW XL analytical size-exclusion column (Tosoh) equilibrated in 25 mM K2HP04, 125 mM NaCl, 200 mM L-Arginine Monohydrocloride, 0.02 % (w/v) NaN3, pH 6.7 running buffer at 25 °C. Table 90 summarizes the yield and final monomer content of the CEA targeted split trimeric 4- IBB ligand Fc (kih) fusion antigen binding molecules.
Table 90: Biochemical analysis of CEA targeted split trimeric 4-lBB ligand Fc (kih) fusion.
Figure imgf000331_0001
Table 91 summarizes the yield and final monomer content of the DP47 untargeted split trimeric 4-lBB ligand Fc (kih) fusion molecules, both monovalent (control B, D and E) and bivalent (control C), and of the germline DP47 human IgGl PGLALA (control F).
Table 91: Biochemical analysis of DP47 untargeted split trimeric 4- IBB ligand Fc (kih) fusion
Monomer
Yield
Construct [ ] [mg/1]
(SEC)
monovalent DP47 -untargeted split trimeric human 4- IBB
99 15.4 ligand (71-254) Fc (kih) fusion (control B)
bivalent DP47 untargeted split trimeric human 4- IBB ligand
98 12.6 (71-254) Fc (kih) fusion (control C)
monovalent DP47 -untargeted split trimeric human 4- IBB
99.5 25.9 ligand (71-254) Fc (kih) fusion (control D)
monovalent DP47 -untargeted split trimeric human 4- IBB
93.3 4.1 ligand (71-254) Fc (kih) fusion (control E)
germline DP47 human IgGl PGLALA 100 50 Example 12
Functional characterization of the CEA targeted 4- IBB ligand trimer-containing Fc fusion antigen binding molecules
12.1 Surface plasmon resonance (simultaneous binding) Production of hu NA3B3A2 as antigen for CEA targeted trimeric split 4-1BBL constructs
The antigen used to assess binding by SPR to CEA was a hybrid molecule composed of A3 and B3 domains from human CEACAM5 (CEA) and N and A2 domains from human
CEACAMl (BGPl) similarly to what has been described for NAB A (Durbin H. et al, Proc Natl Acad Sci U S A. 1994 May 10;91(10):4313-7). The antigen is termed here NA3B3A2 and a schematic description can be found in Figure 41 A.
Table 92 shows the nucleotide and amino acid sequences of hu NA3B3A2-avi-His.
Table 92: Nucleotide and amino acid sequences of hu NA3B3A2-avi-His
SEQ ID Antigen Sequence
NO:
351 nucleotide CAGCTGACCACCGAGTCCATGCCCTTCAACGTGGCCG
AGGGCAAAGAGGTGCTGCTGCTGGTCCACAACCTGCC
sequence hu CCAGCAGCTGTTCGGCTACAGCTGGTACAAGGGCGAG NA3B3A2-avi CGGGTGGACGGCAACCGGCAGATCGTGGGCTACGCCA
TCGGCACCCAGCAGGCCACACCCGGCCCTGCCAATAG
His CGGCAGAGAGACAATCTACCCCAACGCCAGCCTGCTG
ATCCAGAACGTGACCCAGAACGACACCGGCTTCTACA
CACTCCAAGTCATCAAGAGCGACCTGGTCAACGAGGA
AGCCACCGGCCAGTTCCACGTGTACCCCGAGCTGCCC
AAGCCCAGCATCAGCAGCAACAACAGCAAGCCCGTGG
AAGATAAGGACGCCGTGGCCTTTACCTGCGAGCCCGA
GGCCCAGAACACCACCTACCTGTGGTGGGTCAACGGC
CAGAGCCTGCCCGTGTCCCCCAGACTCCAGCTGAGCA
ACGGCAACAGAACCCTGACCCTGTTCAACGTGACCCG
GAATGACGCCAGAGCCTACGTGTGCGGCATCCAGAAC
AGCGTGTCCGCCAACCGCAGCGACCCCGTGACCCTGG
ATGTGCTGTACGGCCCCGACACCCCCATCATCAGCCCC
CCTGACAGCAGCTACCTGAGCGGCGCCAACCTGAACC
TGAGCTGCCACAGCGCCAGCAACCCCAGCCCTCAGTA
CAGCTGGCGGATCAACGGCATCCCCCAGCAGCACACC
CAGGTGCTGTTTATCGCCAAGATCACCCCCAACAACA
ACGGCACCTACGCCTGCTTCGTGTCCAACCTGGCCACC
GGCCGGAACAACAGCATCGTGAAGTCCATCACCGTGT
CCGCCTCCCTGAGCCCCGTGGTGGCCAAGCCTCAGAT
CAAGGCCAGCAAGACCACCGTGACCGGCGACAAGGA
CAGCGTGAACCTGACCTGCTCCACCAACGATACCGGC
ATCAGCATCCGGTGGTTCTTCAAGAATCAGTCCCTGCC CAGCAGCGAGCGGATGAAGCTGAGCCAGGGCAACAT
CACCCTGTCCATCAACCCCGTGAAAAGAGAGGACGCC
GGCACCTATTGGTGCGAGGTGTTCAACCCCATCAGCA
AGAACCAGAGCGACCCCATCATGCTGAACGTGAACTA
CAACGCCCTGCCCCAAGAAAACCTGATCAATGTTGAT
CTGGAAGTGCTGTTCCAGGGCCCAGGCAGCGGCCTGA
ACGACATCTTCGAAGCCCAGAAAATCGAGTGGCACGA
GGCCAGAGCCCACCACCACCATCACCAC
352 human QLTTESMPFNVAEGKEVLLLVHNLPQQLFGYSWYKGER
VDGNRQIVGYAIGTQQATPGPANSGRETIYPNASLLIQNV
NA3B3A2-avi- TQNDTGFYTLQVIKSDLVNEEATGQFHVYPELPKPSISSN His NSKPVEDKDAVAFTCEPEAQNTTYLWWVNGQSLPVSPR
LQLSNGNRTLTLFNVTRNDARAYVCGIQNSVSANRSDPV
TLDVLYGPDTPIISPPDSSYLSGANLNLSCHSASNPSPQYS
WRINGIPQQHTQVLFIAKITPNNNGTYACFVSNLATGRN
NSIVKSITVSASLSPVVAKPQIKASKTTVTGDKDSVNLTC
STNDTGISIRWFFKNQSLPSSERMKLSQGNITLSINPVKRE
DAGTYWCEVFNPISKNQSDPIMLNVNYNALPQENLINVD
LEVLFQGPGSGLNDIFEAQKIEWHEARAHHHHHH
Protein production was performed as described above for the Fc-fusion protein (Example 7.1.1). Secreted proteins were purified from cell culture supernatants by chelating
chromatography, followed by size exclusion chromatography. The first chromatographic step was performed on a NiNTA Superflow Cartridge (5ml, Qiagen) equilibrated in 20 mM sodium phosphate, 500 nM sodium chloride, pH7.4. Elution was performed by applying a gradient over 12 column volume from 5% to 45% of elution buffer (20 mM sodium phosphate, 500 nM sodium chloride, 500 mM Imidazole, pH7.4).
The protein was concentrated and filtered prior to loading on a HiLoad Superdex 75 column (GE Healthcare) equilibrated with 20 mM Histidine, 140 mM NaCl, 0.01% Tween-20 pH 6.0. Table 93 summarizes the yield and final monomer content of human NA3B3A2-avi-His.
Table 93: Biochemical analysis of human NA3B3 A2-avi-His
Figure imgf000333_0001
The capacity of binding simultaneously human 4- IBB Fc (kih) and human NA3B3A2 was assessed by surface plasmon resonance (SPR). All SPR experiments were performed on a Biacore T200 at 25 °C with HBS-EP as running buffer (0.01 M HEPES pH 7.4, 0.15 M NaCl, 3 mM EDTA, 0.005% Surfactant P20, Biacore, Freiburg/Germany). Biotinylated human 4-lBB Fc (kih) was directly coupled to a flow cell of a strep tavidin (SA) sensor chip. Immobilization levels up to 250 resonance units (RU) were used. The CEA targeted trimeric split 4-lBBL constructs (constructs 5.4, 5.6, 5.7 and 5.8) were passed at a concentration range of 200 nM with a flow of 30 μΕ/ηιίηυίε through the flow cells over 90 seconds and dissociation was set to zero seconds. Human NA3B3A2 was injected as second analyte with a flow of 30 μΕ/ηιίηυίε through the flow cells over 90 seconds at a concentration of 500 nM (Figure 41B). The dissociation was monitored for 120 seconds. Bulk refractive index differences were corrected for by subtracting the response obtained in a reference flow cell, where no protein was immobilized.
As can be seen in the graphs of Figure 42, all bispecific constructs could bind
simultaneously human 4- IBB and human NA3B3A2. 12.2. Binding on activated human PMBCs of the CEA-targeted 4-1BB ligand trimer- containing Fc (kih) fusion antigen binding molecules
To determine binding of 4-lBBL trimer-containing Fc fusion antigen binding molecules to human PBMCs, different titrated concentrations of the CEA-targeted 4-lBBL trimer-containing Fc fusion antigen binding molecules were used in the assay as described in Example 5.2. Figure 43 shows the binding of Constructs 5.4, 5.6, 5.7 and 5.8 as prepared in Example 11 on activated 4-lBB-expressing CD4+ T cells and CD8 + T cells, respectively. Gates were set on living CD45+ CD3+ CD4+ or CD45+ CD3+ CD8+ T cells and MFI of PE-conjugated
AffiniPure anti-human IgG IgG Fey- fragment- specific goat F(ab )2 fragment were blotted against the titrated concentration of targeted split trimeric 4- IBB ligand Fc fusion variants. Table 94 shows the EC50 values as measured for Constructs 5.4, 5.6, 5.7 and 5.8 and control molecules.
Table 94: Binding on activated 4-lBB-expressing CD4+ T cells and CD8 + T cells
Construct EC50 [nM] EC50 [nM]
4-lBB+CD8+ 4-lBB+CD4+
Control B 0.05 0.26
Control C 0.02 0.30
Control D 0.04 0.28
Control E 0.13 1.22
5.4 0.13 0.35
5.6 0.06 0.34
5.7 0.0004 0.36
5.8 0.17 0.38 12.2 Binding to CEA-expressing tumor cells
For binding assays on CEA-expressing tumor cells, the following human CEA-expressing lymphoma cell lines were used: CEA-expressing tumor cell lines human gastric cancer cell line MKN-45 (ATCC TCP- 1008) and human colorectal adenocarcinoma cell line LSI 80 (ATCC CL- 187). The assays were preformed as described for the FAP-expressing MV-3 and WM-266-4 tumor cell lines in Example 5.3.
Gates were set on living tumor cells and MFI of PE-conjugated AffiniPure anti-human IgG IgG Fcy-fragment-specific goat F(ab )2 fragment were blotted against the titrated concentration of targeted split trimeric 4- IBB ligand Fc fusion constructs. Figure 44 shows the binding of Constructs 5.7 as prepared in Example 11.2.7 to human-
CEA expressing human gastric cell line MKN-45 (left) and human colorectal adenocarcinoma cells line LSI 80 (right). Table 95 shows the EC50 values as measured for human-CEA expressing human gastric cell line MKN-45.
Table 95: Binding to CEA-expressing tumor cells
Figure imgf000335_0001
Example 13
Biological activity of the CEA-targeted 4-1BB ligand trimer-containing Fc fusion antigen binding molecules
13.1. NF-κΒ activation in HeLa cells expressing human 4-1BB HeLa cells expressing human 4- IBB and NF-KB-lucif erase were generated as described in
Example 6.1.
NF-κΒ activation in Hela cells expressing human 4- IBB co-cultured with human CEA- expressing tumor cells
NF-KB-luciferase human-4-lBB HeLa cells were harvested and resuspended in DMEM medium supplied with 10 % (v/v) FBS and 1 % (v/v) GlutaMAX-I to a concentration of 0.2 x 106 cells/ml. 100 μΐ (2 x 104 cells) of this cell suspension were transferred to each well of a sterile white 96-well flat bottom tissue culture plate with lid (greiner bio-one, Cat. No. 655083) and the plate were incubated at 37 °C and 5 % C02 overnight. The next day 50 μΐ^ of medium containing titrated concentrations of CEA-targeted 4- IBB ligand trimer-containing Fc fusion antigen binding molecules (CEA split 4-lBBL trimer) or DP47-untargeted 4- IBB ligand trimer- containing Fc fusion antigen binding molecules (DP47 split 4-lBBL trimer) were added. CEA- expressing tumor cell lines human gastric cancer cell line MKN-45 (ATCC TCP- 1008) was resuspended in DMEM medium supplied with 10 % (v/v) FBS and 1 % (v/v) GlutaMAX-I to a concentration of 2 x 106 cells/ml.
Suspension of CEA-expressing B cell lymphoma cell (50 μΐ, final ratio 1:5) or only medium were added to each well and plates were incubated for 6 hours at 37 °C and 5 % C02. Cells were washed two times with 200 μίΛνεΙΙ DPBS. 40 μΐ freshly prepared Reporter Lysis Buffer (Promega, Cat-No: E3971) were added to each well and the plate were stored over night at -20 °C. The next day frozen cell plate and Detection Buffer (Luciferase 1000 Assay System, Promega, Cat. No. E4550) were thawed at room temperature. 100 μΐ^ of detection buffer were added to each well and luciferase activity was measured as fast as possible using a SpectraMax M5/M5e microplate reader and a SoftMax Pro Software (Molecular Devices) counting light emission in URL (units of released light for 0.5s/well) or Victor3 1420 multilabel counter plate reader (Perkin Elmer) and the Perkin Elmer 2030 Manager Software counting light emission as counts per seconds (CPS) and blotted against the concentration of tested constructs.
CEA-targeted 4- IBB ligand trimer-containing Fc fusion antigen binding molecules Constructs 5.7 and 5.8 triggered activation of the NF-kB signaling pathway in the reporter cell line in the presence of human gastric cancer cell line MKN-45 cells. In contrast, the untargeted control molecules failed to trigger such an effect at any of the tested concentrations (Figure 45). Table 96 shows the corresponding EC50 values.
Table 96: Binding to CEA-expressing tumor cells
Construct EC50 [nM] EC50 [nM]
MKN-45 MKN45
no tumor cells
5.4 3.1 0.34
5.6 2.05 0.21
5.7 0.85 0.05
5.8 1.52 0.45 Example 14
14.1 Preparation of FAP targeted OX40 ligand trimer-containing Fc fusion antigen binding molecules
The DNA sequence encoding part of the ectodomain (amino acids 51-183) of human OX40 ligand was synthetized according to the P23510 sequence of Uniprot database. To decrease heterogeneity of human Ox40 ligand due to glycosylation asparagine residues at position 90 and 114 were mutated to aspartic acid by site-directed mutagenesis (according to Compaan D.M., Hymowitz S.G., Structure (2006) 14(8), 1321-30).
A polypeptide containing two ectodomains of OX40 ligand, separated by (G4S)2 linkers, and fused to the human IgGl-CL domain, was cloned as depicted in Figure 46A: human OX40 ligand, (G4S)2 connector, human OX40 ligand, (G4S)2 connector, human CL.
A polypeptide containing one ectodomain of OX40 ligand and fused to the human IgGl- CH domain, was cloned as described in Figure 46B: human OX40 ligand, (G4S)2 connector, human CH. To improve correct pairing the following mutations have been introduced in the crossed
CH-CL. In the dimeric 4- IBB ligand fused to human CL, E123R and Q124K. In the monomeric 4-1BB ligand fused to human CHI, K147E and K213E.
The generation and preparation of the FAP binders is described in WO 2012/020006 A2, which is incorporated herein by reference. The variable region of heavy and light chain DNA sequences encoding a binder specific for FAP, clone 28H11, were subcloned in frame with either the constant heavy chain of the hole or the constant light chain of human IgGl. The Pro329Gly, Leu234Ala and Leu235Ala mutations have been introduced in the constant region of the knob and hole heavy chains to abrogate binding to Fc gamma receptors according to the method described in WO 2012/130831. Combination of the dimeric ligand-Fc knob chain containing the S354C/T366W mutations, the monomeric CHI fusion, the targeted anti-FAP-Fc hole chain containing the
Y349C/T366S/L368A/Y407V mutations and the anti-FAP light chain allows generation of a heterodimer, which includes an assembled trimeric OX40 ligand and a FAP binding Fab (Figure 46C, Construct 6.1). Table 97 shows the cDNA and amino acid sequences of the monovalent CEA (T84.66-
LCHA) targeted split trimeric OX40 ligand (51-183) Fc (kih) fusion antigen binding molecule with crossed CH-CL and charged residues (construct 6.1). Table 97: cDNA and amino acid sequences of monovalent FAP(28H1) targeted split trimeric OX40 ligand Fc (kih) fusion containing CH-CL cross with charged residues (construct 6.1). * for charged residues
SEQ ID Description Sequence
NO:
353 Nucleotide CAGGTGTCCCACAGATACCCCAGAATCCAGAGCATCAA sequence Dimeric GGTGCAGTTCACCGAGTACAAGAAAGAGAAGGGCTTCA hu OX40L (51- TCCTGACCAGCCAGAAAGAGGACGAGATCATGAAGGTG 183) - CL* Fc CAGGACAACAGCGTGATCATCAACTGCGACGGCTTCTA
CCTGATCAGCCTGAAGGGCTACTTCAGCCAGGAAGTGG
knob chain
ACATCAGCCTGCACTACCAGAAGGACGAGGAACCCCTG
TTCCAGCTGAAGAAAGTGCGGAGCGTGAACAGCCTGAT
GGTGGCCAGCCTGACCTACAAGGACAAGGTGTACCTGA
ACGTGACCACCGACAACACCAGCCTGGACGACTTCCAC
GTGAACGGCGGCGAGCTGATCCTGATTCACCAGAACCC
CGGCGAGTTCTGCGTGCTGGGAGGCGGAGGATCTGGCG
GAGGCGGATCTCAGGTGTCACACCGCTACCCCCGGATTC
AGTCCATTAAGGTGCAGTTTACAGAGTATAAGAAAGAA
AAAGGCTTTATTCTGACTTCCCAGAAAGAAGATGAGATT
ATGAAGGTGCAGGATAATTCTGTGATCATCAATTGTGAC
GGCTTCTACCTGATCAGCCTGAAGGGCTACTTCAGCCAG
GAAGTGGACATCAGCCTGCACTACCAGAAGGACGAGGA
ACCCCTGTTCCAGCTGAAGAAAGTGCGGAGCGTGAACA
GCCTGATGGTGGCCAGCCTGACCTACAAGGACAAGGTG
TACCTGAACGTGACCACCGACAACACCAGCCTGGACGA
CTTCCACGTGAACGGCGGCGAGCTGATCCTGATCCACCA
GAACCCTGGCGAGTTCTGCGTGCTGGGAGGCGGAGGCT
CCGGAGGGGGAGGATCTCGTACGGTGGCTGCACCATCT
GTCTTTATCTTCCCACCCAGCGACCGGAAGCTGAAGTCT
GGCACAGCCAGCGTCGTGTGCCTGCTGAATAACTTCTAC
CCCCGCGAGGCCAAGGTGCAGTGGAAGGTGGACAATGC
CCTGCAGAGCGGCAACAGCCAGGAAAGCGTGACCGAGC
AGGACAGCAAGGACTCCACCTACAGCCTGAGCAGCACC
CTGACCCTGAGCAAGGCCGACTACGAGAAGCACAAGGT
GTACGCCTGCGAAGTGACCCACCAGGGCCTGTCTAGCCC
CGTGACCAAGAGCTTCAACCGGGGCGAGTGCGACAAGA
CCCACACCTGTCCTCCATGCCCTGCCCCTGAAGCTGCTG
GCGGCCCTAGCGTGTTCCTGTTCCCCCCAAAGCCCAAGG
ACACCCTGATGATCAGCCGGACCCCTGAAGTGACCTGC
GTGGTGGTGGATGTGTCCCACGAGGACCCTGAAGTGAA
GTTCAATTGGTACGTGGACGGCGTGGAAGTGCACAATG
CCAAGACCAAGCCGCGGGAGGAGCAGTACAACAGCACG
TACCGTGTGGTCAGCGTCCTCACCGTCCTGCACCAGGAC
TGGCTGAATGGCAAGGAGTACAAGTGCAAGGTCTCCAA
CAAAGCCCTCGGCGCCCCCATCGAGAAAACCATCTCCA
AAGCCAAAGGGCAGCCCCGAGAACCACAGGTGTACACC
CTGCCCCCATGCCGGGATGAGCTGACCAAGAACCAGGT
CAGCCTGTGGTGCCTGGTCAAAGGCTTCTATCCCAGCGA
CATCGCCGTGGAGTGGGAGAGCAATGGGCAGCCGGAGA
ACAACTACAAGACCACGCCTCCCGTGCTGGACTCCGAC GGCTCCTTCTTCCTCTACAGCAAGCTCACCGTGGACAAG AGCAGGTGGCAGCAGGGGAACGTCTTCTCATGCTCCGTG ATGCATGAGGCTCTGCACAACCACTACACGCAGAAGAG CCTCTCCCTGTCTCCGGGTAAA
Nucleotide CAGGTGTCCCACAGATACCCCAGAATCCAGAGCATCAA sequence GGTGCAGTTCACCGAGTACAAGAAAGAGAAGGGCTTCA Monomelic hu TCCTGACCAGCCAGAAAGAGGACGAGATCATGAAGGTG OX40L (51-183) CAGGACAACAGCGTGATCATCAACTGCGACGGCTTCTA - CHI* CCTGATCAGCCTGAAGGGCTACTTCAGCCAGGAAGTGG
ACATCAGCCTGCACTACCAGAAGGACGAGGAACCCCTG
TTCCAGCTGAAGAAAGTGCGGAGCGTGAACAGCCTGAT
GGTGGCCAGCCTGACCTACAAGGACAAGGTGTACCTGA
ACGTGACCACCGACAACACCAGCCTGGACGACTTCCAC
GTGAACGGCGGCGAGCTGATCCTGATTCACCAGAACCC
CGGCGAGTTCTGCGTGCTGGGAGGCGGAGGTTCCGGAG
GCGGAGGATCTGCTAGCACAAAGGGCCCCAGCGTGTTC
CCTCTGGCCCCTAGCAGCAAGAGCACATCTGGCGGAAC
AGCCGCCCTGGGCTGCCTGGTGGAAGATTACTTCCCCGA
GCCCGTGACCGTGTCCTGGAATTCTGGCGCCCTGACAAG
CGGCGTGCACACCTTTCCAGCCGTGCTGCAGAGCAGCG
GCCTGTACTCTCTGAGCAGCGTCGTGACAGTGCCCAGCA
GCTCTCTGGGCACCCAGACCTACATCTGCAACGTGAACC
ACAAGCCCAGCAACACCAAGGTGGACGAGAAGGTGGA
ACCCAAGTCCTGC
Nucleotide see Table 2
sequence anti- FAP(28H1) Fc
hole chain
Nucleotide see Table 2
sequence anti- FAP(28H1) light
chain
Dimeric hu QVSHRYPRIQSIKVQFTEYKKEKGFILTSQKEDEIMKVQDN OX40L (51-183) SVIINCDGFYLISLKGYFSQEVDISLHYQKDEEPLFQLKKVR - CL* Fc knob SVNSLMVASLTYKDKVYLNVTTDNTSLDDFHVNGGELILI chain HQNPGEFCVLGGGGSGGGGSQVSHRYPRIQSIKVQFTEYK
KEKGFILTSQKEDEIMKVQDNSVIINCDGFYLISLKGYFSQE
VDISLHYQKDEEPLFQLKKVRSVNSLMVASLTYKDKVYLN
VTTDNTSLDDFHVNGGELILIHQNPGEFCVLGGGGSGGGG
SRTVAAPSVFIFPPSDRKLKSGTASVVCLLNNFYPREAKVQ
WKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYE
KHKVYACEVTHQGLSSPVTKSFNRGECDKTHTCPPCPAPE
AAGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVK
FNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQD
WLNGKEYKCKVSNKALGAPIEKTISKAKGQPREPQVYTLP
PCRDELTKNQVSLWCLVKGFYPSDIAVEWESNGQPENNYK
TTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEAL
HNHYTQKSLSLSPGK
Monomeric hu QVSHRYPRIQSIKVQFTEYKKEKGFILTSQKEDEIMKVQDN OX40L (51-183) SVIINCDGFYLISLKGYFSQEVDISLHYQKDEEPLFQLKKVR
SVNSLMVASLTYKDKVYLNVTTDNTSLDDFHVNGGELILI - CHI* HQNPGEFCVLGGGGSGGGGSASTKGPSVFPLAPSSKSTSGG
TAALGCLVEDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDEKVEPKS
C
18 anti- FAP(28H1) see Table 2
Fc hole chain
19 anti- FAP(28H1) see Table 2
light chain
14.2 Preparation of untargeted human IgGl as Control F
A control molecule used in the assays, termed control F (Figure 46D), was an untargeted DP47, germline control, human IgGl, containing the Pro329Gly, Leu234Ala and Leu235Ala mutations, to abrogate binding to Fc gamma receptors according to the method described in International Patent Appl. Publ. No. WO 2012/130831). Its preparation is described in Example 2.3, Table 29 shows the cDNA and amino acid sequences of the cDNA and amino acid sequences of the untargeted DP47 hulgGI PGLALA (Control F).
14.3 Production of FAP- targeted split trimeric OX40 ligand Fc fusion antigen binding molecules and their control molecules
The targeted and untargeted split trimeric OX40 ligand Fc (kih) fusion encoding sequences were cloned into a plasmid vector, which drives expression of the insert from an MPSV promoter and contains a synthetic polyA sequence located at the 3' end of the CDS. In addition, the vector contains an EBV OriP sequence for episomal maintenance of the plasmid. The split trimeric Ox40 ligand Fc (kih) fusion was produced by co-transfecting HEK293-
EBNA cells with the mammalian expression vectors using polyethylenimine. The cells were transfected with the corresponding expression vectors. For variants 1,2,4,5 and it's control B, D and E, at a 1: 1: 1: 1 ratio ("vector dimeric ligand-CL- knob chain": "vector monomeric ligand fusion-CHI": "vector anti- FAP Fab-hole chain": "vector anti-FAP light chain"). For variant 3, 6 and it's control C, at a 1: 1: 1 ratio ("vector hulgGI Fc hole dimeric ligand chain": "vector hulgGI Fc knob monomeric ligand chain": "vector anti-FAP light chain"). Human IgGs, used as control in the assay, were produced as for the bispecific construct (for transfection only a vector for light and a vector for heavy chain were used at a 1: 1 ratio).
For production in 500 mL shake flasks, 300 million HEK293 EBNA cells were seeded 24 hours before transfection. For transfection cells were centrifuged for 10 minutes at 210 x g, and the supernatant was replaced by 20mL pre- warmed CD CHO medium. Expression vectors (200 μg of total DNA) were mixed in 20 mL CD CHO medium. After addition of 540 PEI, the solution was vortexed for 15 seconds and incubated for 10 minutes at room temperature.
Afterwards, cells were mixed with the DNA/PEI solution, transferred to a 500 mL shake flask and incubated for 3 hours at 37°C in an incubator with a 5% C02 atmosphere. After the incubation, 160 mL of Excell medium supplemented with 6mM L-Glutamine, 5g/L PEPSOY and 1.2mM valproic acid was added and cells were cultured for 24 hours. One day after transfection 12% Feed (amino acid and glucose) were added. After culturing for 7 days, the supernatant was collected by centrifugation for 30-40 minutes at least 400 x g. The solution was sterile filtered (0.22 μιη filter), supplemented with sodium azide to a final concentration of 0.01 % (w/v), and kept at 4°C. The split trimeric OX40 ligand Fc (kih) fusion antigen binding molecule, as well as the
IgG, was purified from cell culture supernatants by affinity chromatography using Protein A, followed by size exclusion chromatography. For affinity chromatography, the supernatant was loaded on a MabSelect Sure column (CV = 5-15 mL, resin from GE Healthcare) equilibrated with Sodium Phosphate (20 mM), Sodium Citrate (20 mM) buffer (pH 7.5). Unbound protein was removed by washing with at least 6 column volumes of the same buffer. The bound protein was eluted using either a linear gradient (20 CV) or a step elution (8 CV) with 20 mM sodium citrate, 100 mM Sodium chloride, 100 mM Glycine buffer (pH 3.0). For the linear gradient an additional 4 column volumes step elution was applied.
The pH of collected fractions was adjusted by adding 1/10 (v/v) of 0.5M sodium phosphate, pH8.0. The protein was concentrated prior to loading on a HiLoad Superdex 200 column (GE Healthcare) equilibrated with 20 mM Histidine, 140 mM sodium chloride, 0.01% (v/v) Tween20 solution of pH 6.0.
The protein concentration was determined by measuring the optical density (OD) at 280 nm, using a molar extinction coefficient calculated on the basis of the amino acid sequence.
Purity and molecular weight of the targeted trimeric 4- IBB ligand Fc (kih) fusion was analyzed by SDS-PAGE in the presence and absence of a reducing agent (5 mM 1,4-dithiotreitol) and staining with Coomassie SimpleBlue™ SafeStain (Invitrogen USA) or CE-SDS using Caliper LabChip GXII (Perkin Elmer). The aggregate content of samples was analyzed using a TSKgel G3000 SW XL analytical size-exclusion column (Tosoh) equilibrated in 25 mM K2HP04, 125 mM NaCl, 200 mM L-Arginine Monohydrocloride, 0.02 % (w/v) NaN3, pH 6.7 running buffer at 25°C.
Table 98 summarizes the yield and final monomer content of the FAP targeted split trimeric Ox40 ligand Fc (kih) fusion antigen binding molecule, and of the germline DP47 human IgGl PGLALA (control F). Table 98: Biochemical analysis of CEA targeted split trimeric 4-lBB ligand Fc (kih) fusion.
Figure imgf000342_0003
Example 15
Functional characterization of the targeted OX40 ligand trimer-containing Fc fusion antigen binding molecule
15.1 Binding to human FAP-expressing tumor cells
The binding to cell surface FAP was tested using WM-266-4 cells (ATCC CRL-1676). 0.5 x 105 WM-266-4 cells were added to each well of a round-bottom suspension cell 96- well plates (greiner bio-one, cellstar, Cat. No. 650185). Cells were stained for 120 minutes at 4°C in the dark in 50 μίΛνβϋ 4 °C cold FACS buffer (DPBS (Gibco by Life Technologies, Cat. No. 14190 326) w/ BSA (0.1 % v/w, Sigma- Aldrich, Cat. No. A9418) containing titrated anti -Ox40 antibody construct. After three times washing with excess FACS buffer, cells were stained for 45 minutes at 4°C in the dark in 25
Figure imgf000342_0001
4 °C cold FACS buffer containing Fluorescein isothiocyanate (FITC)-conjugated AffiniPure anti-human IgG Fcy-fragment- specific goat IgG F(ab )2 fragment (Jackson ImmunoResearch, Cat. No. 109 096 098).
Plates were finally resuspended in 90
Figure imgf000342_0002
FACS-buffer containing 0.2 μg/mL DAPI (Santa Cruz Biotec, Cat. No. Sc-3598) and acquired the same day using 5-laser LSR-Fortessa (BD Bioscience with DIVA software).
As shown in Figure 47A, the monovalent FAP(28H1) targeted split trimeric Ox40 ligand Fc (kih) fusion antigen binding molecule (FAP-OX40L) but not the negative control F efficiently bound to human FAP-expressing target cells. EC50 values of binding to FAP positive WM-266- 4 was [6.9 nM],
15.2 Binding to OX40 and FAP negative tumor cells
The lack of binding to OX40 negative FAP negative tumor cells was tested using A549 NucLight™ Red Cells (Essenbioscience, Cat. No. 4491) expressing the NucLight Red fluorescent protein restricted to the nucleus to allow separation from unlabeled human FAP positive WM266-4 cells. Parental A549 (ATCC CCL-185) were transduced with the Essen CellPlayer NucLight Red Lentivirus (Essenbioscience, Cat. No. 4476; EFl , puromycin) at an MOI of 3 (TU/cell) in the presence of 8 μg/ml polybrene following the standard Essen protocol.
A mixture of 5 x 104 unlabeled WM266-4 cells and unlabeled A549 NucLight™ Red Cells in FACS buffer were added to each well of a round-bottom suspension cell 96-well plates and binding assay was performed as described in section 15.1.
As shown in Figure 47B, FAP-OX40L did not bind to OX40 negative FAP negative human tumor cells.
15.3 Binding to human OX40 expressing cells: naive and activated human peripheral mononuclear blood leukocytes (PBMCs) Buffy coats were obtained from the Zurich blood donation center. To isolate fresh peripheral blood mononuclear cells (PBMCs) the buffy coat was diluted with the same volume of DPBS (Gibco by Life Technologies, Cat. No. 14190 326). 50 mL polypropylene centrifuge tubes (TPP, Cat.-No. 91050) were supplied with 15 mL Histopaque 1077 (SIGMA Life Science, Cat.-No. 10771, polysucrose and sodium diatrizoate, adjusted to a density of 1.077 g/mL) and the buffy coat solution was layered above the Histopaque 1077. The tubes were centrifuged for 30 min at 400 x g, room temperature and with low acceleration and no break. Afterwards the PBMCs were collected from the interface, washed three times with DPBS and resuspended in T cell medium consisting of RPMI 1640 medium (Gibco by Life Technology, Cat. No. 42401-042) supplied with 10 % Fetal Bovine Serum (FBS, Gibco by Life Technology, Cat. No. 16000-044, Lot 941273, gamma-irradiated, mycoplasma-free and heat inactivated at 56 °C for 35 min), 1 % (v/v) GlutaMAX I (GIBCO by Life Technologies, Cat. No. 35050 038), 1 mM Sodium-Pyruvat (SIGMA, Cat. No. S8636), 1 % (v/v) MEM non-essential amino acids (SIGMA, Cat.-No. M7145) and 50 μΜ β-Mercaptoethanol (SIGMA, M3148).
PBMCs were used directly after isolation (binding on resting human PBMCs) or they were stimulated to receive a strong human Ox40 expression on the cell surface of T cells (binding on activated human PBMCs). Therefore naive PBMCs were cultured for four days in T cell medium supplied with 200 U/mL Proleukin (Novartis) and 2 ug/mL PHA-L (Sigma- Aldrich, L2769-10) in 6-well tissue culture plate and then over night on pre-coated 6-well tissue culture plates [4 ug/mL] anti-human CD3 (clone OKT3, eBioscience, Ca.No. 16-0037-85) and [2 ug/mL] anti- human CD28 (clone CD28.2, eBioscience, Cat No.16-0289-85] in T cell medium supplied with 200 U/mL Proleukin at 37 °C and 5% C02.
For detection of Ox40 naive human PBMC and activated human PBMC were mixed. To enable distinction of naive from activated human PBMC naive cells were labeled prior to the binding assay using the eFluor670 cell proliferation dye (eBioscience, Cat.-No.65-0840-85). For labeling cells were harvested, washed with pre-warmed (37°C) DPBS and adjusted to a cell density of 1 x 10 cells/mL in DPBS. eFluor670 cell proliferation dye (eBioscience, Cat- No.65-0840-85 ) was added to the suspension of naive human PBMC at a final concentration of 2.5 mM and a final cell density of 0.5 x 10 cells/mL in DPBS. Cells were then incubated for 10 min at room temperature in the dark. To stop labeling reaction 4 mL heat inactivated FBS were added and cells were washed three times with T cell medium. A two to one mixture of 1 x 105 resting eFluor670 labeled human PBMC and 0.5 x 105 unlabeled activated human PBMC were then added to each well of a round-bottom suspension cell 96-well plates (greiner bio-one, cellstar, Cat. No. 650185). Cells were stained for 120 minutes at 4°C in the dark in 50 μίΛνβϋ 4 °C cold FACS buffer containing titrated anti -Ox40 antibody constructs. After three times washing with excess FACS buffer, cells were stained for 45 minutes at 4°C in the dark in 25
Figure imgf000344_0001
4 °C cold FACS buffer containing a mixture of fluorescently labeled anti-human CD4 (clone RPA-T4, mouse IgGl k, BioLegend, Cat.-No. 300532), anti-human CD8 (clone RPa-T8, mouse IgGlk, BioLegend, Cat- No. 3010441) and Fluorescein isothiocyanate (FITC)-conjugated AffiniPure anti-human IgG Fcy-fragment- specific goat IgG F(ab )2 fragment (Jackson ImmunoResearch, Cat.-No.
109-096-098).
Plates were finally resuspended in 90
Figure imgf000344_0002
FACS-buffer containing 0.2 μg/mL DAPI (Santa Cruz Biotec, Cat. No. Sc-3598) and acquired the same day using 5-laser LSR-Fortessa (BD Bioscience with DIVA software).
As shown in Figures 48A and 48 B, FAP-OX40L did not bind to resting human CD4+ T- cells or CD8+ T-cells, which are negative for OX40. In contrast, FAP-OX40L bound to activated CD8+ or CD4+ T-cells, which do express OX40. Binding to CD4+ T-cells was much stronger than that to CD8+ T cells. Activated human CD8+ T cells do express only a fraction of the OX40 levels detected on activated CD4+ T cells. Expression levels for OX40 are depending on kinetic and strength of stimulation and conditions were here optimized for OX40 expression on CD4+ T cells but not for CD8+ T cells. Thus, only little OX40 expression was induced on CD8 T cells. The EC 50 value of binding to OX40 positive CD4+ or CD8+ T cells was [0.15 nM].
15.4 NFKB activation in HeLa cells expressing human OX40 and reporter gene NFKB-luciferase
Agonstic binding of Ox40 to its ligand induces downstream signaling via activation of nuclear factor kappa B (NFKB) (A. D. Weinberg et al., J. Leukoc. Biol. 2004, 75(6), 962-972). The recombinant reporter cell line HeLa_hOx40_NFkB_Lucl was generated to express human Ox40 on its surface. Additionally, it harbors a reporter plasmid containing the luciferase gene under the control of an NFKB-sensitive enhancer segment. Ox40 triggering induces dose- dependent activation of NFKB, which translocates in the nucleus, where it binds on the NFKB sensitive enhancer of the reporter plasmid to increase expression of the luciferase protein.
Luciferase catalyzes luciferin-oxidation resulting in oxyluciferin which emits light. This can be quantified by a luminometer. Thus, the capacity of the various anti-Ox40 molecules to induce NFKB activation in HeLa_hOx40_NFkB_Lucl reporter cells was analyzed as a measure for bioactivity.
Adherent HeLa_hOx40_NFkB_Lucl cells were harvested using cell dissociation buffer (Invitrogen, Cat.-No. 13151-014) for 10 minutes at 37 °C. Cells were washed once with DPBS and were adjusted to a cell density of 1.33xl05 in assay media comprising of MEM (Invitrogen, Cat.-No. 22561-021), 10 % (v/v) heat-inactivated FBS, 1 mM Sodium-Pyruvat and 1% (v/v) non-essential amino acids. Cells were seeded in a density of 0.2* 105 cells per well in a sterile white 96-well flat bottom tissue culture plate with lid (greiner bio-one, Cat. No. 655083) and kept over night at 37 °C and 5% C02 in an incubator (Hera Cell 150).
The next day, HeLa_hOx40_NFkB_Lucl were stimulated for 5 hours by adding assay medium containing titrated FAP-Ox40L or negative control F. For testing the effect of hyper- crosslinking on anti-Ox40 antibodies, 25 μΐ/ννεΐΐ of medium containing secondary antibody anti- human IgG Fey- fragment- specific goat IgG F(ab )2 fragment (Jackson ImmunoResearch, 109- 006-098) were added in a 1:2 ratio (2 times more secondary antibody than the primary antibody). After incubation, supernatant was aspirated and plates washed two times with DPBS.
Quantification of light emission was done using the luciferase 100 assay system and the reporter lysis buffer (both Promega, Cat.-No. E4550 and Cat-No: E3971) according to manufacturer instructions. Briefly, cells were lysed for 10 minutes at -20 °C by addition of 30 uL per well lx lysis buffer. Cells were thawed for 20 minutes at 37 °C before 90 uL per well provided luciferase assay reagent was added. Light emission was quantified immediately with a SpectraMax
M5/M5e microplate reader (Molecular Devices, USA) using 500ms integration time, without any filter to collect all wavelengths. Emitted relative light units (URL) were corrected by basal luminescence of HeLa_hOx40_NFkB_Lucl cells and were blotted against the logarithmic primary antibody concentration using Prism4 (GraphPad Software, USA). Curves were fitted using the inbuilt sigmoidal dose response. As shown in Figure 49, a limited, dose dependent NFkB activation was induced already by addition of FAP-Ox40L (left side) to the reporter cell line. Hyper-crosslinking of FAP-Ox40L by anti-human IgG specific secondary antibodies increased the induction of NFKB-mediated luciferase-activation in a concentration-dependent manner (right side).
Consequently, we tested the NFkB activating capacity of FAP-Ox40L with hyper- crosslinking of the constructs by FAP+ tumor cell lines. Tested tumor cell line was NIH/3T3-huFAP clone 39. NIH/3T3-huFAP clone 39 was generated by the transfection of the mouse embryonic fibroblast NIH/3T3 cell line (ATCC CRL- 1658) with the expression vector pETR4921 to express huFAP under 1.5 μg/mL Puromycin selection. The surface expression of FAP was quantified using the Quifikit (Dako Cat. No.
K0078) according to manufactures instructions. The primary antibody used to detect cell surface FAP expression was the human/ mouse crossreactive clone Fl 1-24 (mouse IgGl, Calbiochem, Ca. No. OP188). The surface expression on NIH/3T3-huFAP clone 39 was app. 90000 huFAP per cell.
As described herein before, adherent HeLa_hOx40_NFkB_Lucl cells were cultured over night at a cell density of 0.2* 105 cells per well and were stimulated for 5 hours with assay medium containing titrated FAP-Ox40L. To test the effect of hyper-crosslinking by cell surface FAP binding 25 μΐ/ννεΐΐ of medium containing FAP+ tumor cells NIH/3T3-huFAP clone 39 were co-cultured in a 3 to 1 ratio (three times as much FAP+ tumor cells than reporter cells per well). Activated NFKB was quantified by measuring light emission using luciferase 100 assay system and the reporter lysis buffer (both Promega, Cat.-No. E4550 and Cat-No: E3971.
As shown in Figure 50A, the presence of FAP-expressing tumor cells strongly increased induction of NFKB-mediated luciferase-activation when FAP-Ox40L was added. Area under the curve of the respective blotted dose-response curves was quantified as a marker for the agonistic capacity of each construct. As shown in Figure 50A, the presence of cell surface presented FAP ensured higher cross-linking and thus a better agonistic effect of FAP-Ox40L then addition of an Fc specific secondary antibody.
15.5 OX40 mediated costimulation of suboptimally TCR triggered resting human PBMC and hypercrosslinking by cell surface FAP
It was shown in Example 15.4 that addition of FAP+ tumor cells can strongly increase the NFkB activity induced by FAP targeted OX40L in a human Ox40 positive reporter cell lines by providing strong oligomerization of OX40 receptors. Likewise, we tested FAP-OX40L constructs in the presence of NIH/3T3-huFAP clone 39 cells for their ability to rescue suboptimal TCR stimulation of resting human PBMC cells.
Human PBMC preparations contain (1) resting Ox40 negative CD4+ and CD8+ T cells and (2) antigen presenting cells with various Fc-γ receptor molecules on their cell surface e.g. B cells and monocytes. Anti-human CD3 antibody of human IgGl isotype can bind with its Fc part to the present Fc-γ receptor molecules and mediate a prolonged TCR activation on resting Ox40 negative CD4+ and CD8+ T cells. These cells then start to express Ox40 within several hours. Functional agonistic compounds against Ox40 can signal via the Ox40 receptor present on activated CD8+ and CD4+ T cells and support TCR-mediated stimulation. Resting CFSE-labeled human PBMC were stimulated for five days with a suboptimal concentration of anti-CD3 antibody in the presence of irradiated FAP+ NIH/3T3-huFAP clone 39 cells and titrated FAP-Ox40L. Effects on T-cell survival and proliferation were analyzed through monitoring of total cell counts and CFSE dilution in living cells by flow cytometry.
Mouse embryonic fibroblast NIH/3T3-huFAP clone 39 cells (see Example 15.4) were harvested using cell dissociation buffer (Invitrogen, Cat.-No. 13151-014) for 10 minutes at 37 °C. Cells were washed once with DPBS. NIH/3T3-huFAP clone 39 cells were cultured at a density of 0.2* 105 cells per well in T cell media in a sterile 96-well round bottom adhesion tissue culture plate (TPP, Cat. No. 92097) over night at 37 °C and 5% C02 in an incubator (Hera Cell 150). The next day they were irradiated in an xRay irradiator using a dose of 4500 RAD to prevent later overgrowth of human PBMC by the tumor cell line.
Human PBMCs were isolated by ficoll density centrifugation as described in Example 15.3. Cells were then labeled with CFSE at a cell density of lxl 06 cells/ mL with CFDA-SE (Sigma- Aldrich, Cat.-No. 2188) at a final concentration of [50 nM] for 10 minutes at 37 °C. Thereafter, cells were washed twice with excess DPBS containing FBS (10% v/v). Labeled cells were rested in T-cell media at 37 °C for 30 minutes. Thereafter, non-converted CFDA-SE was removed by two additional washing steps with DPBS. CFSE labeled resting human PBMC were added to each well at a density of 0.5* 105 cells per well. Anti-human CD3 antibody (clone V9, human IgGl, described in Rodrigues et a!., Int J Cancer Sup pi 7, 45-50 (1992) and US patent No.
6,054,297) at a final concentration of [20 nM] and FAP-OX40L were added at the indicated concentrations. Cells were activated for five days at 37 °C and 5% C02 in an incubator (Hera Cell 150). Then, Cells were surface- stained with fluorescent dye-conjugated antibodies anti- human CD4 (clone RPA-T4, BioLegend, Cat.-No. 300532) and CD8 (clone RPa-T8, BioLegend, Cat.-No. 3010441) for 20 min at 4°C. After a washing step with FACS buffer, cells were resuspended in 85 μίΛνεΙΙ FACS buffer and acquired using a 5-laser Fortessa flow cytometer (BD Bioscience with DIVA software).
As shown in Figure 51, hyper-crosslinking of FAP-OX40L constructs by the present NIH/3T3-huFAP clone 39 cells strongly promoted proliferation (see "Events" graphs on the top) and survival (see "proliferation" graphs on the bottom) in TCR stimulated human CD4 and CD8 T cells. In line with a lower expression of OX40 on human CD8+ T cells the agonistic effect of FAP-OX40L was less strong on CD8+ T cells than on CD4+ T cells.
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Claims

Claims
A TNF family ligand trimer-containing antigen binding molecule comprising
(a) at least one moiety capable of specific binding to a target cell antigen and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond, wherein the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or a fragment thereof that are connected to each other by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof.
The TNF family ligand trimer-containing antigen binding molecule of claim 1, further comprising
(c) an Fc domain composed of a first and a second subunit capable of stable association.
The TNF family ligand trimer-containing antigen binding molecule of claims 1 or 2, comprising
(a) at least one moiety capable of specific binding to a target cell antigen and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond, wherein the antigen binding molecule is characterized in that
(i) the first polypeptide contains a CHI or CL domain and the second polypeptide contains a CL or CHI domain, respectively, wherein the second polypeptide is linked to the first polypeptide by a disulfide bond between the CHI and CL domain, and wherein the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the CHI or CL domain by a peptide linker and wherein the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to the CL or CHI domain of said polypeptide, or
(ii) the first polypeptide contains a CH3 domain and the second polypeptide contains a CH3 domain, respectively, and wherein the first polypeptide comprises two
ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the C-terminus of the CH3 domain by a peptide linker and wherein the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to C-terminus of the CH3 domain of said polypeptide, or
(iii) the first polypeptide contains a VH-CL or a VL-CH1 domain and the second
polypeptide contains a VL-CH1 domain or a VH-CL domain, respectively, wherein the second polypeptide is linked to the first polypeptide by a disulfide bond between the CH1 and CL domain, and wherein the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to to VH or VL by a peptide linker and wherein the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to VL or VH of said polypeptide.
4. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to
3, wherein the TNF ligand family member costimulates human T-cell activation.
5. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to
4, wherein the TNF ligand family member is selected from 4-1BBL and OX40L. 6. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to
5, wherein the TNF ligand family member is 4-1BBL.
7. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to
6, wherein the ectodomain of a TNF ligand family member comprises the amino acid sequence selected from the group consisting of SEQ ID NO: l, SEQ ID NO: 2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:96, SEQ ID NO: 373, SEQ ID NO:374 and SEQ ID
NO:375, particularly the amino acid sequence of SEQ ID NO: l or SEQ ID NO:96.
8. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to
7, wherein the ectodomain of a TNF ligand family member comprises the amino acid sequence of SEQ ID NO:96. 9. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to
8, comprising
(a) at least one moiety capable of specific binding to a target cell antigen and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond, wherein the antigen binding molecule is characterized in that the first polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO:5, SEQ ID
NO:97, SEQ ID NO:98 and SEQ ID NO:99 and in that the second polypeptide comprises the amino acid sequence selected from the group consisting of SEQ ID NO: l, SEQ ID NO:96, SEQ ID NO:3 and SEQ ID NO:4.
10. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 9, comprising
(a) at least one moiety capable of specific binding to a target cell antigen, and (b) a first polypeptide containing a CHI or CL domain and a second polypeptide containing a CL or CHI domain, respectively, wherein the second polypeptide is linked to the first polypeptide by a disulfide bond between the CHI and CL domain,
and wherein the antigen binding molecule is characterized in that the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the CHI or CL domain by a peptide linker and in that the second polypeptide comprises only one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to the CL or CHI domain of said
polypeptide. 11. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to
10, wherein the moiety capable of specific binding to a target cell antigen is selected from the group consisting of an antibody fragment, a Fab molecule, a crossover Fab molecule, a single chain Fab molecule, a Fv molecule, a scFv molecule, a single domain antibody, an aVH and a scaffold antigen binding protein. 12. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to
11, wherein the molecule comprises one moiety capable of specific binding to a target cell antigen.
13. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to
12, wherein the moiety capable of specific binding to a target cell antigen is a Fab molecule capable of specific binding to a target cell antigen.
14. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to
13, wherein the target cell antigen is selected from the group consisting of Fibroblast Activation Protein (FAP), Melanoma- associated Chondroitin Sulfate Proteoglycan (MCSP), Epidermal Growth Factor Receptor (EGFR), Carcinoembryonic Antigen (CEA), CD19, CD20 and CD33.
15. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to
14, wherein the target cell antigen is Fibroblast Activation Protein (FAP).
16. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to
15, wherein the moiety capable of specific binding to FAP comprises a VH domain comprising (i) CDR-H1 comprising the amino acid sequence of SEQ ID NO:7 or SEQ ID
NO: 100, (ii) CDR-H2 comprising the amino acid sequence of SEQ ID NO:8 or SEQ ID NO: 101, and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO:9 or SEQ ID NO: 102, and a VL domain comprising (iv) CDR-L1 comprising the amino acid sequence of SEQ ID NO: 10 or SEQ ID NO: 103, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO: 11 or SEQ ID NO: 104, and (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO: 12 or SEQ ID NO: 105. 17. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 16, wherein the moiety capable of specific binding to FAP comprises a variable heavy chain comprising an amino acid sequence of SEQ ID NO: 16 and a variable light chain comprising an amino acid sequence of SEQ ID NO: 17 or wherein the moiety capable of specific binding to FAP comprises a variable heavy chain comprising an amino acid sequence of SEQ ID NO: 106 and a variable light chain comprising an amino acid sequence of SEQ ID NO: 107.
18. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 2 to
17, wherein the Fc domain is an IgG, particularly an IgGl Fc domain or an IgG4 Fc domain.
19. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 2 to
18, wherein the Fc domain is an IgGl Fc domain comprising the amino acid substitutions at positions 234 and 235 (EU numbering) and/or 329 (EU numbering).
20. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 19, wherein the antigen binding molecule comprises
a first heavy chain and a first light chain, both comprising a Fab molecule capable of specific binding to a target cell antigen,
a first peptide comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker fused at its C-terminus by a second peptide linker to a second heavy or light chain,
and a second peptide comprising one ectodomain of said TNF ligand family member fused at its C-terminus by a third peptide linker to a second light or heavy chain, respectively. 21. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 20, wherein the first peptide comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C-terminus by a second peptide linker to a CHI domain that is part of a heavy chain,
and the second peptide comprising one ectodomain of said TNF ligand family member or a fragment thereof is fused at its C-terminus by a third peptide linker to a CL domain that is part of a light chain.
22. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 20, wherein the first peptide comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C-terminus by a second peptide linker to a CL domain that is part of a heavy chain,
and the second peptide comprising one ectodomain of said TNF ligand family member or a fragment thereof is fused at its C-terminus by a third peptide linker to a CHI domain that is part of a light chain.
The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 20, wherein the first peptide comprising two ectodomains of a TNF ligand family member or fragments thereof connected to each other by a first peptide linker is fused at its C-terminus by a second peptide linker to a VH domain that is part of a heavy chain,
and the second peptide comprising one ectodomain of said TNF ligand family member or a fragment thereof is fused at its C-terminus by a third peptide linker to a VL domain that is part of a light chain. 24. The TNF family ligand trimer-containing antigen binding molecule of claims 21 to 23, wherein in the CL domain adjacent to the TNF ligand family member the amino acid at position 123 (EU numbering) has been replaced by arginine (R) and the amino acid at position 124 (EU numbering) has been substituted by lysine (K), and wherein in the CHI domain adjacent to the TNF ligand family member the amino acids at position 147 (EU numbering) and at position 213 (EU numbering) have been substituted by glutamic acid (E).
25. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 24, wherein the antigen binding molecule comprises
(a) a first heavy chain and a first light chain, both comprising a Fab molecule capable of specific binding to a target cell antigen,
(b) a second heavy chain comprising an amino acid sequence selected from the group consisting of SEQ ID NO:5, SEQ ID NO:97, SEQ ID NO:98 and SEQ ID NO:99, and a second light chain comprising an amino acid sequence selected from the group consisting of SEQ ID NO: l, SEQ ID NO:96, SEQ ID NO:3 and SEQ ID NO:4.
26. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 24, wherein the antigen binding molecule comprises
(a) a first heavy chain and a first light chain, both comprising a Fab molecule capable of specific binding to a target cell antigen,
(b) a second heavy chain comprising an amino acid sequence selected from the group consisting of SEQ ID NO:5, SEQ ID NO:97, SEQ ID NO:98 and SEQ ID NO:99, and a second light chain comprising an amino acid sequence selected from the group consisting of SEQ ID NO: l, SEQ ID NO:96, SEQ ID NO:3 and SEQ ID NO:4.
27. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 21, wherein the antigen binding molecule comprises
(i) a first heavy chain comprising the VH domain comprising the amino acid sequence of
SEQ ID NO: 16 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO: 17 or
a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO: 106 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO: 107,
(ii) a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 14, SEQ ID NO: 108, SEQ ID NO: 111 and SEQ ID NO: 113, and
(iii) a second light chain comprising the amino acid sequence of SEQ ID NO: 15, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 112 and SEQ ID NO: 114. 28. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 20 and 22, wherein the antigen binding molecule comprises
(i) a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO: 16 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO: 17 or
a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ
ID NO: 106 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO: 107,
(ii) a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 115, SEQ ID NO: 117, SEQ ID NO: 119 and SEQ ID NO: 173, and (iii) a second light chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 116, SEQ ID NO: 118, SEQ ID NO: 120 and SEQ ID NO: 174.
29. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 19, comprising
(a) at least one moiety capable of specific binding to a target cell antigen, and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond, wherein the antigen binding molecule is characterized in that the first polypeptide contains a CH3 domain and the second polypeptide contains a CH3 domain, respectively, and wherein the first polypeptide comprises two ectodomains of a TNF ligand family member or fragments thereof that are connected to each other and to the C-terminus of the CH3 domain by a peptide linker and wherein the second polypeptide comprises one ectodomain of said TNF ligand family member or a fragment thereof connected via a peptide linker to C- terminus of the CH3 domain of said polypeptide.
30. The TNF family ligand trimer-containing antigen binding molecule of claim 29, comprising two moieties capable of specific binding to a target cell antigen. 31. The TNF family ligand trimer-containing antigen binding molecule of claim 29, wherein the antigen binding molecule comprises
(i) a first heavy chain comprising the amino acid sequence of SEQ ID NO: 121, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 122, and two light chains comprising the amino acid sequence of SEQ ID NO: 19, or
(ii) a first heavy chain comprising the amino acid sequence of SEQ ID NO: 123, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 124, and two light chains comprising the amino acid sequence of SEQ ID NO: 125, or
(iii) a first heavy chain comprising the amino acid sequence of SEQ ID NO: 126, a second heavy chain comprising the amino acid sequence of SEQ ID NO: 127, and two light chains comprising the amino acid sequence of SEQ ID NO: 125.
32. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 14, 18 to 26 and 29 to 30, wherein the target cell antigen is CD19.
33. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 14, 18 to 26, 29 to 30 and 32, wherein the moiety capable of specific binding to CD 19 comprises a VH domain comprising (i) CDR-H1 comprising the amino acid sequence of
SEQ ID NO: 195 or SEQ ID NO:252, (ii) CDR-H2 comprising the amino acid sequence of SEQ ID NO: 196 or SEQ ID NO:253, and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO: 197 or SEQ ID NO:254, and a VL domain comprising (iv) CDR-L1 comprising the amino acid sequence of SEQ ID NO: 198 or SEQ ID NO:249, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO: 199 or SEQ ID NO:250, and (vi) CDR-
L3 comprising the amino acid sequence of SEQ ID NO:200 or SEQ ID NO:251.
34. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 14, 18 to 26, 29 to 30, 32 and 33, wherein the moiety capable of specific binding to CD19 comprises a variable heavy chain comprising an amino acid sequence of SEQ ID NO:201 and a variable light chain comprising an amino acid sequence of SEQ ID NO:202 or wherein the moiety capable of specific binding to FAP comprises a variable heavy chain comprising an amino acid sequence of SEQ ID NO:357 and a variable light chain comprising an amino acid sequence of SEQ ID NO:358.
35. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 14, 18 to 26 and 32 to34, wherein the antigen binding molecule comprises
(i) a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO:201 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO:202 or
a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO:357 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO:358,
(ii) a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 14, SEQ ID NO: 108, SEQ ID NO: 111 and SEQ ID NO: 113, and
(iii) a second light chain comprising the amino acid sequence of SEQ ID NO: 15, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 112 and SEQ ID NO: 114.
36. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 14, 18 to 26 and 32 to 35, wherein the antigen binding molecule comprises
(i) a first heavy chain comprising the VH domain comprising the amino acid sequence of
SEQ ID NO:201 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO:202 or
a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO:357 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO:358,
(ii) a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 115, SEQ ID NO: 117, SEQ ID NO: 119 and SEQ ID NO: 173, and
(iii) a second light chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 116, SEQ ID NO: 118, SEQ ID NO: 120 and SEQ ID NO: 174. 37. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 14, 29, 30 and 32 to 34, wherein the antigen binding molecule comprises
(i) a first heavy chain comprising the amino acid sequence of SEQ ID NO:209, a second heavy chain comprising the amino acid sequence of SEQ ID NO:210, and two light chains comprising the amino acid sequence of SEQ ID NO:206, or
(ii) a first heavy chain comprising the amino acid sequence of SEQ ID NO:213, a second heavy chain comprising the amino acid sequence of SEQ ID NO:214, and two light chains comprising the amino acid sequence of SEQ ID NO:206, or
(iii) a first heavy chain comprising the amino acid sequence of SEQ ID NO:309, a second heavy chain comprising the amino acid sequence of SEQ ID NO:310, and two light chains comprising the amino acid sequence of SEQ ID NO:279, or
(iv) a first heavy chain comprising the amino acid sequence of SEQ ID NO:313, a second heavy chain comprising the amino acid sequence of SEQ ID NO:314, and two light chains comprising the amino acid sequence of SEQ ID NO:279.
38. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 14, 18 to 26 and 29 to 30, wherein the target cell antigen is CEA.
39. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 14, 18 to 26, 29 to 30 and 38, wherein the moiety capable of specific binding to CEA comprises a VH domain comprising (i) CDR-H1 comprising the amino acid sequence of SEQ ID NO:321, (ii) CDR-H2 comprising the amino acid sequence of SEQ ID NO:322, and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO:323, and a VL domain comprising (iv) CDR-L1 comprising the amino acid sequence of SEQ ID NO:324, (v) CDR- L2 comprising the amino acid sequence of SEQ ID NO:325, and (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO:326.
40. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 14, 18 to 26, 29 to 30, 38 and 39, wherein the moiety capable of specific binding to CEA comprises a variable heavy chain comprising an amino acid sequence of SEQ ID NO:329 and a variable light chain comprising an amino acid sequence of SEQ ID NO:330.
41. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 14, 18 to 26 and 38 to 40, wherein the antigen binding molecule comprises
(i) a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO:329 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO:330,
(ii) a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 14, SEQ ID NO: 108, SEQ ID NO: 111 and SEQ ID NO: 113, and
(iii) a second light chain comprising the amino acid sequence of SEQ ID NO: 15, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 112 and SEQ ID NO: 114.
42. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 14, 18 to 26 and 38 to 41, wherein the antigen binding molecule comprises
(i) a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO:329 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO:330,
(ii) a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 115, SEQ ID NO: 117, SEQ ID NO: 119 and SEQ ID NO: 173, and (iii) a second light chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 116, SEQ ID NO: 118, SEQ ID NO: 120 and SEQ ID NO: 174.
43. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 14, 29, 30 and 38 to 40, wherein the antigen binding molecule comprises
(i) a first heavy chain comprising the amino acid sequence of SEQ ID NO:337, a second heavy chain comprising the amino acid sequence of SEQ ID NO:338, and two light chains comprising the amino acid sequence of SEQ ID NO:334, or
(ii) a first heavy chain comprising the amino acid sequence of SEQ ID NO:341, a second heavy chain comprising the amino acid sequence of SEQ ID NO:342, and two light chains comprising the amino acid sequence of SEQ ID NO:334.
44. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 5, 10 to 24, 29, 30, 32 to 34 and 38 to 40, wherein the TNF ligand family member is OX40L.
45. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 5, 10 to 24, 29, 30, 32 to 34, 38 to 40 and 44, wherein the ectodomain of a TNF ligand family member comprises the amino acid sequence of SEQ ID NO:53 or SEQ ID NO:54, particularly the amino acid sequence of SEQ ID NO:53.
46. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 5, 10 to 24, 29, 30, 32 to 34, 38 to 40, 44 and 45, comprising
(a) at least one moiety capable of specific binding to a target cell antigen and
(b) a first and a second polypeptide that are linked to each other by a disulfide bond, wherein the antigen binding molecule is characterized in that the first polypeptide comprises the amino acid sequence of SEQ ID NO:371 or SEQ ID:372 and in that the second polypeptide comprises the amino acid sequence of SEQ ID NO:53 or SEQ ID NO:54.
47. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 5, 10 to 24, 29, 30 and 44 to 46, wherein the target cell antigen is Fibroblast Activation
Protein (FAP) and the moiety capable of specific binding to FAP comprises a VH domain comprising (i) CDR-H1 comprising the amino acid sequence of SEQ ID NO:7 or SEQ ID NO: 100, (ii) CDR-H2 comprising the amino acid sequence of SEQ ID NO:8 or SEQ ID NO: 101, and (iii) CDR-H3 comprising the amino acid sequence of SEQ ID NO:9 or SEQ ID NO: 102, and a VL domain comprising (iv) CDR-L1 comprising the amino acid sequence of
SEQ ID NO: 10 or SEQ ID NO: 103, (v) CDR-L2 comprising the amino acid sequence of SEQ ID NO: 11 or SEQ ID NO: 104, and (vi) CDR-L3 comprising the amino acid sequence of SEQ ID NO: 12 or SEQ ID NO: 105.
48. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 5, 10 to 24, 29, 30 and 44 to 47, wherein the antigen binding molecule comprises
(i) a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO: 16 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO: 17 or
a first heavy chain comprising the VH domain comprising the amino acid sequence of SEQ ID NO: 106 and a first light chain comprising the VL domain comprising the amino acid sequence of SEQ ID NO: 107,
(ii) a second heavy chain comprising the amino acid sequence selected from the group consisting of SEQ ID NO:355, and
(iii) a second light chain comprising the amino acid sequence of SEQ ID NO:356.
49. An isolated polynucleotide encoding the TNF family ligand trimer-containing antigen
binding molecule of any one of claims 1 to 48.
50. A vector, particularly an expression vector, comprising the isolated polynucleotide of claim 49.
51. A host cell comprising the isolated polynucleotide of claim 49 or the vector of claim 50.
52. A method for producing the TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 48, comprising the steps of
(i) culturing the host cell of claim 51 under conditions suitable for expression of the antigen binding molecule, and
(ii) recovering the antigen binding molecule.
53. A pharmaceutical composition comprising the TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 48 and at least one pharmaceutically acceptable excipient.
54. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 48, or the pharmaceutical composition of claim 53, for use as a medicament.
55. The TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 48, or the pharmaceutical composition of claim 53, for use in the treatment of cancer.
56. Use of the TNF family ligand trimer-containing antigen binding molecule of any one of claims 1 to 48 for the manufacture of a medicament for the treatment of cancer. A method of treating a disease in an individual, comprising administering to said individual a therapeutically effective amount of a composition comprising a TNF family ligand trimer- containing antigen binding molecule of any one of claims 1 to 48 in a pharmaceutically acceptable form.
The method of claim 57, wherein said disease is cancer.
***
PCT/EP2015/076528 2014-11-14 2015-11-13 Antigen binding molecules comprising a tnf family ligand trimer WO2016075278A1 (en)

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EP15797922.0A EP3224275B1 (en) 2014-11-14 2015-11-13 Antigen binding molecules comprising a tnf family ligand trimer
CN202110472897.8A CN113372434B (en) 2014-11-14 2015-11-13 Antigen binding molecules comprising trimers of TNF family ligands
SG11201703597TA SG11201703597TA (en) 2014-11-14 2015-11-13 Antigen binding molecules comprising a tnf family ligand trimer
CN202210001707.9A CN114634570A (en) 2014-11-14 2015-11-13 Antigen binding molecules comprising TNF family ligand trimers
UAA201705791A UA125577C2 (en) 2014-11-14 2015-11-13 Antigen binding molecules comprising a tnf family ligand trimer
NZ730933A NZ730933A (en) 2014-11-14 2015-11-13 Antigen binding molecules comprising a tnf family ligand trimer
MYPI2017701668A MY191428A (en) 2014-11-14 2015-11-13 Antigen binding molecules comprising a tnf family ligand trimer
KR1020177016136A KR102588377B1 (en) 2014-11-14 2015-11-13 Antigen binding molecules comprising a tnf family lignad trimer
JP2017525959A JP6873901B2 (en) 2014-11-14 2015-11-13 Antigen-binding molecule containing TNF family ligand trimer
MA40882A MA40882B1 (en) 2014-11-14 2015-11-13 Antigen binding molecules comprising a trimer of ligand of the tnf family
AU2015345024A AU2015345024B2 (en) 2014-11-14 2015-11-13 Antigen binding molecules comprising a TNF family ligand trimer
PL15797922T PL3224275T3 (en) 2014-11-14 2015-11-13 Antigen binding molecules comprising a tnf family ligand trimer
IL282922A IL282922B (en) 2014-11-14 2015-11-13 Antigen binding molecules comprising a tnf family ligand trimer
MX2020012798A MX2020012798A (en) 2014-11-14 2015-11-13 Antigen binding molecules comprising a tnf family ligand trimer.
RS20200473A RS60201B1 (en) 2014-11-14 2015-11-13 Antigen binding molecules comprising a tnf family ligand trimer
BR112017009006-6A BR112017009006A2 (en) 2014-11-14 2015-11-13 binding molecule, isolated polynucleotide, vector, host cell, binding molecule production method, pharmaceutical composition, use of the binding molecule, and method of treating a disease in an individual
EP18207248.8A EP3489256B1 (en) 2014-11-14 2015-11-13 Antigen binding molecules comprising a tnf family ligand trimer
CA2963718A CA2963718A1 (en) 2014-11-14 2015-11-13 Antigen binding molecules comprising a tnf family ligand trimer
EP20158607.0A EP3738609A1 (en) 2014-11-14 2015-11-13 Antigen binding molecules comprising a tnf family ligand trimer
CN201580073211.0A CN108064237B (en) 2014-11-14 2015-11-13 Antigen binding molecules comprising TNF family ligand trimers
SI201531194T SI3224275T1 (en) 2014-11-14 2015-11-13 Antigen binding molecules comprising a tnf family ligand trimer
KR1020237034293A KR20230146133A (en) 2014-11-14 2015-11-13 Antigen binding molecules comprising a tnf family lignad trimer
PE2022001462A PE20221909A1 (en) 2014-11-14 2015-11-13 ANTIGEN-BINDING MOLECULES COMPRISING A LIGAND TRIMER OF THE TNF FAMILY
LTEP15797922.0T LT3224275T (en) 2014-11-14 2015-11-13 Antigen binding molecules comprising a tnf family ligand trimer
MX2017006250A MX2017006250A (en) 2014-11-14 2015-11-13 Antigen binding molecules comprising a tnf family ligand trimer.
CR20170194A CR20170194A (en) 2014-11-14 2015-11-13 ANTIGEN UNION MOLECULES UNDERSTANDING A TNF FAMILY BINDING TRIMMER
PL18207248T PL3489256T3 (en) 2014-11-14 2015-11-13 Antigen binding molecules comprising a tnf family ligand trimer
DK15797922.0T DK3224275T3 (en) 2014-11-14 2015-11-13 Antigen-binding molecules comprising a TNF family ligand trimer
ES15797922T ES2788979T3 (en) 2014-11-14 2015-11-13 Antigen-binding molecules comprising a ligand trimer of the TNF family
EA201791057A EA037557B1 (en) 2014-11-14 2015-11-13 Antigen binding molecules comprising a tnf family ligand trimer
US15/067,024 US10392445B2 (en) 2014-11-14 2016-03-10 Tumor necrosis factor (TNF) family ligand trimer-containing antigen-binding molecules
IL251317A IL251317B (en) 2014-11-14 2017-03-21 Antigen binding molecules comprising a tnf family ligand trimer
CONC2017/0003212A CO2017003212A2 (en) 2014-11-14 2017-03-31 Antigen-binding molecules comprising a ligand trimer of the tnf family
PH12017500892A PH12017500892A1 (en) 2014-11-14 2017-05-12 Antigen binding molecules comprising a tnf family ligand trimer
HK18114659.3A HK1255482A1 (en) 2014-11-14 2018-11-16 Antigen binding molecules comprising a tnf family ligand trimer
US16/522,391 US11306154B2 (en) 2014-11-14 2019-07-25 Methods of treating cancer by administering antigen-binding molecules comprising a TNF family ligand trimer
US16/522,412 US11267903B2 (en) 2014-11-14 2019-07-25 Antigen-binding molecules comprising a tumor necrosis factor (TNF) family ligand trimer
HRP20200679TT HRP20200679T1 (en) 2014-11-14 2020-04-28 Antigen binding molecules comprising a tnf family ligand trimer
AU2020264337A AU2020264337B2 (en) 2014-11-14 2020-11-05 Antigen binding molecules comprising a TNF family ligand trimer
US17/580,980 US20220259327A1 (en) 2014-11-14 2022-01-21 Antigen binding molecules comprising a tnf family ligand trimer
US17/580,970 US20220259326A1 (en) 2014-11-14 2022-01-21 Antigen binding molecules comprising a tnf family ligand trimer
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