WO2017087589A2 - Pd1 and/or lag3 binders - Google Patents
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- WO2017087589A2 WO2017087589A2 PCT/US2016/062394 US2016062394W WO2017087589A2 WO 2017087589 A2 WO2017087589 A2 WO 2017087589A2 US 2016062394 W US2016062394 W US 2016062394W WO 2017087589 A2 WO2017087589 A2 WO 2017087589A2
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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
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- C07K2317/22—Immunoglobulins specific features characterized by taxonomic origin from camelids, e.g. camel, llama or dromedary
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- C07K2317/24—Immunoglobulins specific features characterized by taxonomic origin containing regions, domains or residues from different species, e.g. chimeric, humanized or veneered
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- C07K2317/33—Crossreactivity, e.g. for species or epitope, or lack of said crossreactivity
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- C07K2317/34—Identification of a linear epitope shorter than 20 amino acid residues or of a conformational epitope defined by amino acid residues
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- C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
- C07K2317/565—Complementarity determining region [CDR]
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- C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
- C07K2317/569—Single domain, e.g. dAb, sdAb, VHH, VNAR or nanobody®
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- C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
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- C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
- C07K2317/92—Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value
Definitions
- the present invention relates, in part, to amino acid sequences binding to programmed cell death protein 1 ("PD1"), e.g., human PD1 and lymphocyte activation gene 3 (LAG3).
- PD1 programmed cell death protein 1
- LAG3 lymphocyte activation gene 3
- the present invention relates, in part, to improved heavy-chain immunoglobulin single variable domains (also referred to herein as "ISVs” or “ISVDs”) binding to PD1 and LAG3, as well as to polypeptides and other compounds that comprise such ISVDs.
- ISVs immunoglobulin single variable domains
- PD-1 Programmed death receptor 1
- PD-L1 is an immunoinhibitory receptor that is primarily expressed on activated T and B cells. Interaction with its ligands has been shown to attenuate T- cell responses both in vitro and in vivo. Blockade of the interaction between PD-1 and one of its ligands, PD-L1, has been shown to enhance tumor-specific CD8 + T-cell immunity and may therefore be helpful in clearance of tumor cells by the immune system.
- PD-1 (encoded by the gene Pdcdl) is an Immunoglobulin superfamily member related to CD28, and CTLA-4. PD-1 has been shown to negatively regulate antigen receptor signaling upon engagement of its ligands (PD-L1 and/or PD-L2) The structure of murine PD-1 has been solved as well as the co-crystal structure of mouse PD-1 with human PD-L1 (Zhang, X. et al, Immunity 20: 337-347 (2004); Lin et al., Proc. Natl. Acad. Sci. USA 105: 3011-6 (2008)).
- PD-1 and like family members are type I transmembrane glycoproteins containing an Ig Variable-type (V-type) domain responsible for ligand binding and a cytoplasmic tail that is responsible for the binding of signaling molecules.
- the cytoplasmic tail of PD-1 contains two tyrosine-based signaling motifs, an ITIM (immunoreceptor tyrosine-based inhibition motif) and an ITSM (immunoreceptor tyrosine-based switch motif).
- PD-1 recruits the tyrosine phosphatase SHP-2 to the ITSM motif within its cytoplasmic tail, leading to the dephosphorylation of effector molecules such as CD3 zeta, PKC theta and ZAP70 that are involved in the CD3 T cell signaling cascade.
- effector molecules such as CD3 zeta, PKC theta and ZAP70 that are involved in the CD3 T cell signaling cascade.
- the mechanism by which PD-1 downmodulates T cell responses is similar to, but distinct from that of CTLA-4, as both molecules regulate an overlapping set of signaling proteins (Parry et al, Mol. Cell. Biol. 25: 9543-9553 (2005)).
- PD-1 -mediated inhibition of T-cell signaling is only effective when both activating and inhibitory signals are on the same surface, indicating that the PD-1 signaling mechanism is spatiotemporally determined (Bennett F. et al, J Immunol. 170:711-8 (2003)).
- PD-1 was shown to be expressed on activated lymphocytes (peripheral CD4 + and CD8 + T cells, B cells and monocytes) and has also been shown to be expressed during thymic development on CD4 " CD8 " (double negative) T cells as well as K-T cells.
- the ligands for PD-1 are constitutively expressed or can be induced in a variety of cell types, including non-hematopoietic tissues as well as various tumor types.
- PD- Ll is expressed on B, T, myeloid and dendritic cells (DCs), but also on peripheral cells, like microvascular endothelial cells and non-lymphoid organs like heart, lung etc.
- DCs myeloid and dendritic cells
- PD-L2 is only found on macrophages and DCs.
- the expression pattern of PD-1 ligands is suggestive of a role for PD-1 in maintaining peripheral tolerance and may serve to regulate self-reactive T- and B-cell responses in the periphery.
- Both ligands are type I transmembrane receptors containing both IgV- and IgC-like domains in the extracellular region. Both ligands contain short cytoplasmic regions with no known signaling motifs.
- mice did not identify any drastic immunological phenotype. However aged mice developed spontaneous autoimmune diseases which differ according to the strain onto which the Pdcdl deficiency was backcrossed. These include lupus-like proliferative arthritis (C57BL/6) (Nishimura H. et al, Int. Immunol. 10: 1563-1572 (1998)), fatal cardiomyopathy (BALB/c) (Nishimura H.
- PD-1 has recently been shown to be expressed on a number of mouse and human tumors (and is inducible by IFN gamma on the majority of PD-Ll negative tumor cell lines) and is postulated to mediate immune evasion (Iwai Y. et al., Proc. Natl. Acad. Sci. U.S.A. 99: 12293-12297 (2002); Strome S. E. et al., Cancer Res., 63 : 6501-6505 (2003).
- PD-1 on tumor infiltrating lymphocytes
- PD-Ll on tumor cells
- Such tissues include cancers of the lung, liver, ovary, cervix, skin, colon, glioma, bladder, breast, kidney, esophagus, stomach, oral squamous cell, urothelial cell, and pancreas as well as tumors of the head and neck (Brown J. A. et al., J. Immunol. 170: 1257-1266 (2003); Dong H. et al., Nat. Med. 8: 793-800 (2002); Wintterle et al, Cancer Res. 63 : 7462-7467 (2003); Strome S. E. et al, Cancer Res., 63 : 6501-6505 (2003); Thompson R. H.
- Blockade of the PD-1/PD-L1 interaction could lead to enhanced tumor-specific T-cell immunity and therefore be helpful in clearance of tumor cells by the immune system.
- T. Nomi et al. demonstrated the therapeutic efficacy of PD-1/PD-L1 blockade.
- Administration of either PD-1 or PD-Ll directed antibody significantly inhibited tumor growth.
- Antibody blockade effectively promoted tumor reactive CD8 + T cell infiltration into the tumor resulting in the up-regulation of anti-tumor effectors including IFN gamma, granzyme B and perforin.
- PD-1 blockade can be effectively combined with chemotherapy to yield a synergistic effect.
- antibody blockade of PD-1 or PD-L1 significantly inhibited tumor growth (Tsushima F. et al, Oral Oncol. 42: 268-274 (2006)).
- PD-1 knockout mice PD-L1 expressing myeloma cells grew only in wild-type animals (resulting in tumor growth and associated animal death), but not in PD-1 deficient mice (Iwai Y. et al, Proc. Natl. Acad. Sci. U.S.A. 99: 12293-12297 (2002)).
- Anti-PD-1 antibodies may also be useful in chronic viral infection.
- Memory CD8 + T cells generated after an acute viral infection are highly functional and constitute an important component of protective immunity.
- chronic infections are often characterized by varying degrees of functional impairment (exhaustion) of virus-specific T-cell responses, and this defect is a principal reason for the inability of the host to eliminate the persisting pathogen.
- functional effector T cells are initially generated during the early stages of infection, they gradually lose function during the course of a chronic infection. Barber et al.
- mice infected with a laboratory strain of LCMV developed chronic infection resulting in high levels of virus in the blood and other tissues. These mice initially developed a robust T cell response, but eventually succumbed to the infection upon T cell exhaustion. The authors found that the decline in number and function of the effector T cells in chronically infected mice could be reversed by injecting an antibody that blocked the interaction between PD-1 and PD-L1.
- PD-1 knockout mice exhibit better control of adenovirus infection than wild-type mice (Iwai et al, J. Exp. Med. 198:39-50 (2003)). Also, adoptive transfer of HBV-specific T cells into HBV transgenic animals initiated hepatitis (Isogawa M. et a/., Immunity 23 :53-63 (2005)). The disease state of these animals oscillates as a consequence of antigen recognition in the liver and PD-1 upregulation by liver cells.
- LAG3 (CD223) is a cell surface molecule expressed on activated T cells (Huard et al. Immunogenetics 39:213-217, 1994), NK cells (Triebel et al J Exp Med 171 : 1393- 1405, 1990), B cells (Kisielow et a/. Eur J Immunol 35:2081-2088, 2005), and plasmacytoid dendritic cells (Workman et al. J Immunol 182: 1885-1891, 2009) that plays an important role in the function of these lymphocyte subsets.
- the interaction between LAG3 and its major ligand, Class II MHC is thought to play a role in modulating dendritic cell function (Andreae et al. J Immunol 168:3874-3880, 2002).
- Recent preclinical studies have documented a role for LAG-3 in CD8 T-cell exhaustion (Blackburn et al. Nat Immunol 10:29-37, 2009).
- tumor antigen-specific CD4 + and CD8 + T cells display impaired effector function and an exhausted phenotype characterized by decreased production of pro-inflammatory cytokines and hyporesponsiveness to antigenic re-stimulation. This is mediated by cell extrinsic mechanisms, such as regulatory T-cells (Treg), and cell intrinsic mechanisms, such as inhibitory molecules that are upregulated on exhausted, tumor-infiltrating lymphocytes (TIL). These inhibitory mechanisms represent a daunting barrier to effective antitumor immunity.
- Treg regulatory T-cells
- TIL tumor-infiltrating lymphocytes
- the present invention encompasses a PDl binder (e.g., an immunoglobulin single variable domain (ISVD) or a Nanobody that binds to PDl (e.g., human PDl) comprising the amino acid sequence set forth in SEQ ID NO: 1 or 2; but which comprises a mutation at one or more of positions 1, 1 1, 14, 52a, 73, 74, 83, 89, 100a, 1 10 and 1 12 wherein said positions are numbered according to Kabat (e.g., LI IV, A14P, A74S, K83R, I89L and, optionally, E1D; or
- Kabat e.g., LI IV, A14P, A74S, K83R, I89L and, optionally, E1D; or
- CDR1 that comprises the amino acid sequence: IHAMG (SEQ ID NO: 3) or GSIASIHAMG (SEQ ID NO: 6); CDR2 that comprises the amino acid sequence: VITXSGGITYYADSVKG (SEQ ID NO: 4; wherein X is W or V) or VITXSGGITY (SEQ ID NO: 7; wherein X is W or V); and CDR3 that comprises the amino acid sequence: DKHQSSXYDY (SEQ ID NO: 5, wherein X is W or F) or DKHQSSXYDY (SEQ ID NO: 8, wherein X is W or F).
- the PDl binder (e.g., an ISVD such as a Nanobody) comprises an amino acid residue at position 1 1 that is chosen from L or V; an amino acid residue at position 89 chosen from T, V or L; an amino acid residue at position 1 10 chosen from T, K or Q; and/or an amino acid residue at position 1 12 chosen from S, K or Q.
- the PDl binder (e.g., an ISVD such as a Nanobody) comprises one or more mutations described is a member selected from the group consisting of: 89T; 89L in combination with 1 IV; 89L in combination with 1 10K or 1 10Q; 89L in combination with 1 12K or 1 12Q; 89L in combination with 1 IV and 1 1 OK or
- amino acid at positions 1 1, 89, 1 10 and 1 12 are as any of those set forth in the Table B herein.
- the PDl binder (e.g., an ISVD such as a Nanobody) comprises one or more mutations at a position selected from the group consisting of 1, 14, 41, 74, 83, 87 and 108 and/or one or more humanizing substitutions known per se (for which reference is made to the prior art cited herein, such as WO 08/020079 or WO 09/138519.
- the PD l binder (e.g., an ISVD such as a Nanobody) comprises a C-terminal extension of 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acids.
- the present invention also provides a PDl binder (e.g., an ISVD such as a Nanobody) comprising one or mutations at position 1 1, 89, 1 10 and 1 12 and an amino acid sequence having at least 85% (e.g., 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 99.5, 99.9 or 100%) sequence identity with the amino acid sequence set forth in a member selected from the group consisting of SEQ ID NOs: 9-40 (in which any C-terminal extension that may be present as well as any CDRs are not taken into account for determining the degree of sequence identity).
- a PDl binder e.g., an ISVD such as a Nanobody
- the present invention also provides a multispecific immunoglobulin comprising a PDl binder (e.g., an ISVD such as a Nanobody) that binds to PDl linked to one or more molecules that bind to an epitope that is not the epitope to which the PDl binder binds (e.g., PDl, CTLA4, LAG3, BTLA and/or CD27), e.g., comprising a PDl binding moiety and a CTLA4 binding moiety; a PDl binding moiety and a BTLA binding moiety; a PDl binding moiety and a LAG3 binding moiety; or a PDl binding moiety, a LAG3 binding moiety and a BTLA binding moiety, optionally linked via one or more linkers, e.g., peptide linkers.
- the multispecific immunoglobulin comprising a PDl binder (e.g., an ISVD such as a Nanobody) that bind
- immunoglobulin comprises a first PDl Nanobody linked to one or more molecules selected from the group consisting of an CTLA4 Nanobody, an LAG3 Nanobody, an BTLA Nanobody, an CD27 Nanobody and an PDl Nanobody that binds to the same or a different epitope as that of the first PDl Nanobody; e.g., comprising a PDl binding moiety and a CTLA4 binding moiety; a PD l binding moiety and a BTLA binding moiety; a PDl binding moiety and a LAG3 binding moiety; or a PDl binding moiety, a LAG3 binding moiety and a BTLA binding moiety.
- the present invention includes a polypeptide, ISVD or Nanobody comprising an amino acid sequence that is described herein, e.g., which is selected from SEQ ID NOs: 9-40.
- the present invention also provides a PDl binder of the present invention (e.g., an immunoglobulin single variable domain (ISVD) or multispecific ISVD such as a Nanobody) in association with a further therapeutic agent.
- a PDl binder of the present invention e.g., an immunoglobulin single variable domain (ISVD) or multispecific ISVD such as a Nanobody
- Injection devices and vessels comprising PDl binder (e.g., immunoglobulin single variable domain (ISVD) or multispecific ISVD such as a Nanobody) optionally in association with a further therapeutic agent are provided by the present invention.
- PDl binder e.g., immunoglobulin single variable domain (ISVD) or multispecific ISVD such as a Nanobody
- the present invention provides a polynucleotide encoding a PDl binder (e.g.,
- immunoglobulin single variable domain or multispecific ISVD such as a Nanobody
- a vector comprising the polynucleotide or a host cell comprising the polynucleotide or vector.
- the present invention provides a method for making an PDl binder (e.g., immunoglobulin single variable domain (ISVD) or multispecific ISVD such as a Nanobody) comprising introducing a polynucleotide encoding the immunoglobulins into a host cell and culturing the host cell in a medium under conditions favorable to expression of said immunoglobulin from said polynucleotide and, optionally, purifying the immunoglobulin from said host cell and/or said medium.
- PDl binders e.g., an ISVDs such as a Nanobodies
- the present invention also provides a method for preventing PDl from binding to PD-L1 and/or PD-L2 comprising contacting said PDl with a PDl binder (e.g., immunoglobulin single variable domain (ISVD) or multispecific ISVD such as a Nanobody) optionally in association with a further therapeutic agent.
- a PDl binder e.g., immunoglobulin single variable domain (ISVD) or multispecific ISVD such as a Nanobody
- the present invention also provides a method for enhancing an immune response in the body of a subject comprising administering an effective amount of a PDl binder of the present invention (e.g., immunoglobulin single variable domain (ISVD) or multispecific ISVD such as a Nanobody) to the subject optionally in association with a further therapeutic agent.
- a PDl binder of the present invention e.g., immunoglobulin single variable domain (ISVD) or multispecific ISVD such as a Nanobody
- the present invention also provides a method for treating or preventing cancer (e.g., metastatic cancer, a solid tumor, a hematologic cancer, leukemia, lymphoma, osteosarcoma,
- rhabdomyosarcoma neuroblastoma, kidney cancer, leukemia, renal transitional cell cancer, bladder cancer, Wilm's cancer, ovarian cancer, pancreatic cancer, breast cancer, prostate cancer, bone cancer, lung cancer, non-small cell lung cancer, gastric cancer, colorectal cancer, cervical cancer, synovial sarcoma, head and neck cancer, squamous cell carcinoma, multiple myeloma, renal cell cancer, retinoblastoma, hepatoblastoma, hepatocellular carcinoma, melanoma, rhabdoid tumor of the kidney, Ewing's sarcoma, chondrosarcoma, brain cancer, glioblastoma, meningioma, pituitary adenoma, vestibular schwannoma, a primitive neuroectodermal tumor,
- medulloblastoma astrocytoma, anaplastic astrocytoma, oligodendroglioma, ependymoma, choroid plexus papilloma, polycythemia vera, thrombocythemia, idiopathic myelofibrosis, soft tissue sarcoma, thyroid cancer, endometrial cancer, carcinoid cancer or liver cancer, breast cancer or gastric cancer
- an infectious disease bacterial infection, a viral infection or a fungal infection
- PD1 binder e.g., immunoglobulin single variable domain (ISVD) or multispecific ISVD such as a
- Nanobody optionally in association with a further therapeutic agent to the subject.
- the subject is also administered a further therapeutic agent or a therapeutic procedure in association with the PD1 binder.
- the present invent invention provides PD1 binders (e.g., ISVDs such as Nanobodies) that bind to PD1 comprising: CDR1 comprising the amino acid sequence IHAMG (SEQ ID NO: 3) or GSIASIHAMG (SEQ ID NO: 6); CDR2 comprising the amino acid sequence VITXSGGITYYADSVKG (SEQ ID NO: 4; wherein X is W or V) or VITXSGGITY (SEQ ID NO: 7; wherein X is W or V); and CDR3 comprising the amino acid sequence DKHQSSXYDY (SEQ ID NO: 5, wherein X is W or F), which comprise one or more mutations at position 1 1 (e.g., LI IV) and 89 (e.g., I89L) or one or more mutations selected from E1D, LI IV, A14P, W52aV, N73(Q, P or S), A74S, K83R, I89L, WlOOaF with respect to SEQ
- the mutations are E1D, LI IV, A14P, K83R and I89L; or LI IV, A14P, K83R and I89L.
- the mutations are E1D, LI IV, A14P, W52aV, N73(Q, P or S), A74S, K83R, I89L, WlOOaF or LI 1 V,A14P,W52aV, N73(Q, P or S), A74S, K83R, I89L, WlOOaF.
- the PD1 binder comprises the amino acid sequence: DVQLVESGGG WQPGGSLRL SCAASGSIAS IHAMGWFRQA PGKEREFVAV ITWSGGITYY ADSVKGRFTI SRDNSKNTVY LQMNSLRPED TALYYCAGDK HQSSWYDYWG QGTLVTVSS (SEQ ID NO: 57).
- the present invention also provides LAG3 binders that bind to LAG3 comprising CDR1 comprising the amino acid sequence GRTFSDYVMG (SEQ ID NO: 65); CDR2 comprising the amino acid sequence AISESGGRTH (SEQ ID NO: 66); and CDR3 comprising the amino acid sequence TLLWWTSEYAPiKANDYDY (SEQ ID NO: 67), e.g., comprising the amino acid sequence: EVQLVE SGGGWQPGG SLRLSCAASG RTFSDYVMGW FRQAPGKERE FVAAISESGG RTHYADSVKG RFTISRDNSK NTLYLQMNSL RPEDTALYYC ATTLLWWTSE YAPIKANDYD YWGQGTLVTV SS (SEQ ID NO: 64).
- the PDl and LAG3 binders may be in a single molecule such as a PD1/LAG3 binder, which is part of the present invention, that binds to PDl and LAG3 that comprises: a PDl binder comprising: CDR1 comprising the amino acid sequence IHAMG (SEQ ID NO: 3) or GSIASIHAMG (SEQ ID NO: 6); CDR2 comprising the amino acid sequence VITXSGGITYYADSVKG (SEQ ID NO: 4; wherein X is W or V) or VITXSGGITY (SEQ ID NO: 7; wherein X is W or V); and CDR3 comprising the amino acid sequence DKHQSSXYDY (SEQ ID NO: 5, wherein X is W or F); and a LAG3 binder comprising: CDR1 comprising the amino acid sequence GRTFSDYVMG (SEQ ID NO: 65); CDR2 comprising the amino acid sequence AISESGGRTH (SEQ ID NO: 66); and CDR3
- LAG3 binder comprises the amino acid sequence:
- the PD1/LAG3 binder comprises the moieties, e.g., in the order shown:
- the PDl binder 102C12 E1D,L11 V,A14P,A74S,K83R,I89L
- 1PD102C12 E1D, LI IV, A14P, W52aV, N73X (e.g., N73P orN73Q orN73S), A74S, K83R, I89L,
- a peptide linker such as 9GS, 20GS or 35 GS (e.g.,
- LAG3 binder 11B09 or 11B09 LI 1 V,A14P,R41P,N43K,A62S,A74S,K83R,V89L
- a peptide linker such as 9GS, 20GS or 35 GS (e.g.,
- a half-life extender such as ALB 11002; and, optionally, • a C-terminal extension such as an alanine; or
- the PD 1 binder 102C 12 E1D,L1 1V,A14P,A74S,K83R,I89L
- 1PD102C12 E1D, LI IV, A14P, W52aV, N73X (e.g., N73P or N73Q or N73 S), A74S, K83R, I89L, WlOOaF);
- a peptide linker such as 9GS, 20GS or 35 GS (e.g.,
- the PD l binder 102C 12 LI 1 V,A14P,A74S,K83R,I89L
- 1PD102C12 LI IV, A14P, W52aV, N73X (e.g., N73P or N73Q or N73 S), A74S, K83R, I89L, WlOOaF);
- a peptide linker such as 9GS, 20GS or 35 GS (e.g.,
- a peptide linker such as 9GS, 20GS or 35 GS (e.g.,
- a peptide linker such as 9GS, 20GS or 35 GS (e.g.,
- a half-life extender such as ALB 1 1002; and, optionally,
- the half -life extender is, in an embodiment of the invention, a human serum albumin (HSA) binder such as ALB 1 1002.
- HSA binder comprises CDRl comprising the amino acid sequence GFTFS S FGMS (SEQ ID NO: 60); CDR2 comprising the amino acid sequence S I SGSGSDTL (SEQ ID NO: 61); and CDR3 comprising the amino acid sequence GGSLSR (SEQ ID NO: 62), e.g., comprising the amino acid sequence EVQLVESGGG WQPGNSLRL
- the PD1 binder, LAG3 binder, HSA binder and/or PD1/LAG3 binder is in an injection device or vessel optionally in association with a further therapeutic agent. Such a device or vessel is part of the present invention.
- the present invention also provides a polynucleotide encoding any of the binders set forth herein as well as any vector (e.g., plasmid) comprising the polynucleotide as well as any host cell (e.g., CHO or fungal cell such as Pichia, e.g., P. pastoris) comprising the polynucleotide or vector, e.g., ectopic or integrated into one or more host cell chromosomes.
- any vector e.g., plasmid
- host cell e.g., CHO or fungal cell such as Pichia, e.g., P. pastoris
- the present invention also provides a method for making any of the binders set forth herein comprising introducing a polynucleotide encoding the binder into a host cell (e.g., CHO or fungal cell such as Pichia, e.g. , P. pastoris) and culturing the host cell in a medium under conditions favorable to expression of said binder from said polynucleotide and, optionally, purifying the binder from said host cell and/or said medium.
- a host cell e.g., CHO or fungal cell such as Pichia, e.g. , P. pastoris
- the vector or polynucleotide is integrated into one or more host cell chromosomes. Any binder produced by such a method is also part of the present invention.
- the present invention also provides a method for preventing PD1 from binding to PD-L1 and/or PD-L2 or for inhibiting any PD1 activity, e.g., as discussed herein, comprising contacting said PD1 with a PD1 binder of the present invention (e.g., a PD1/LAG3 binder) optionally in association with a further therapeutic agent.
- a PD1 binder of the present invention e.g., a PD1/LAG3 binder
- the present invention also provides a method for preventing LAG3 from binding to MHC class II or for inhibiting any PD1 activity, e.g., as discussed herein comprising contacting said LAG3 with a LAG3 binder of the present invention (e.g., a PD1/LAG3 binder) optionally in association with a further therapeutic agent.
- the present invention also provides a method for enhancing an immune response in the body of a subject (e.g., a human) comprising administering an effective amount of binder of the present invention (e.g., PD1/LAG3 binder) to the subject optionally in association with a further therapeutic agent.
- a subject e.g., a human
- an effective amount of binder of the present invention e.g., PD1/LAG3 binder
- the present invention also provides a method for treating or preventing cancer (e.g., metastatic cancer, a solid tumor or a hematologic cancer) or an infectious disease (e.g., bacterial infection, a viral infection or a fungal infection) in the body of a subject (e.g., a human) comprising administering an effective amount of binder of the present invention (e.g., a PD1/LAG3 binder) optionally in association with a further therapeutic agent to the subject.
- a PD1 and/or LAG3 binder of the present invention e.g., a PD1/LAG3 binder
- a further therapeutic agent e.g., surgical tumorectomy.
- Figure 1 A table listing some of the amino acid positions that will be specifically referred to herein and their numbering according to some alternative numbering systems (such as Aho and IMGT)
- Figure 3 Alignment of 102C12 sequence with that of the SEQ ID NOs: 9-40 (see WO 2008/071447, SEQ ID NO: 348).
- Predominant N-linked glycans for monoclonal antibodies produced in Chinese hamster ovary cells (CHO N-linked glycans) and in engineered yeast cells (engineered yeast N- linked glycans): squares: N-acetylglucosamine (GlcNac); circles: mannose (Man); diamonds: galactose (Gal); triangles: fucose (Fuc).
- FIG. 7 (A-B). Binding of (A) CHO expressing human PD-1 by F023700931,
- ABH0074 + GAM goat anti-mouse secondary antibody used plus mouse antibody ABH0074 that binds to nanobody frameworks.
- Figure 8 (A-B). Binding of (A) CHO expressing human LAG3 by F023700931,
- Figure 9 Blockage of binding between (A) human PD-Ll-Fc and CHO-K1 expressing human PDl by F023700275 or F023700706; (B) human PD-L2-Fc and CHO-K1 expressing human PDl by F023700275 or F023700706; (C) human PD-Ll-Fc and CHO-K1 expressing human PDl by F023700931 ⁇ Pichia or CHO expressed), F023700924 ⁇ Pichia or CHO expressed), F023700933 or F023700962; (D) human PD-L2-Fc and CHO-K1 expressing human PDl by F023700931 ⁇ Pichia or CHO expressed), F023700924 ⁇ Pichia or CHO expressed), F023700933 or F023700962; (E) human PD-Ll-Fc and CHO-K1 expressing human PDl by F023700931, F023700931,
- FIG. 12 A-E. Activation of Jurkat T-cells (expression of luciferase operably linked to
- IL2 promoter in presence of HSA by (A) F023700706 or control Nanobody (IRR00043; two anti-lysozyme nanobodies linked with a 35GS linker that has a C-terminal FLAG3-His6), (B) F023700931 (Pichia or CHO expressed), F023700924 (Pichia or CHO expressed), F023700933, F023700962 or control Nanobody (IRR00085 or IRR00087; RSV binder), (C) F023700924 F023700969, F023700970 or control Nanobody (IRR00043), (D) F023700931, F023701016, F023701017 or control Nanobody (IRR00043), or (E) F023700706, F023701192
- Figure 13 Activation of human peripheral blood monocytes (IL2 production) from donors (A) 91,(B) 985, (C) 907, (D) 91, (E) 985, (F) 907, (G) 91 (with ⁇ SEB), (H) 985 (with 10 nM SEB), (I) 907 ( with 10 nM SEB), (J) 91 (with 25 nM SEB), (K) 985 (with 25 nM SEB), (L) 907 (with 25 nM SEB) with F023700931 (Pichia or CHO expressed), F023700924 (Pichia or CHO expressed), F023700933, F023700962 or control Nanobody; or (M) 91 (N) 985 (O) 907 with F023700931, F023700924 or control Nanobody; or (P) 91, (Q) 985 or (R) 907 with F023700924, F023700969, F02
- Figure 14 (A-F). Mixed lymphocyte assay of CD4 T-cells and dendritic cells from different donors determining (A-C) interferon-gamma production at varying concentrations of Nanobody F023700931 (Pichia or CHO expressed), F023700924 (Pichia or CHO expressed) or F023700933 or a control antibody; (D-F) interferon-gamma production at varying concentrations of Nanobody F023700924, F023700969, F023700970, F023700931 F023701016 or F023701017 or control Nanobody.
- A-C interferon-gamma production at varying concentrations of Nanobody F023700931 (Pichia or CHO expressed), F023700924 (Pichia or CHO expressed) or F023700933 or a control antibody
- D-F interferon-gamma production at varying concentrations of Nanobody F023700924, F023700969, F023700970,
- Figure 15 Activation assay of 3A9 T-cells expressing human LAG3 in the presence of HSA and in the presence of (A) F023700656 (11B09 (EID)), F023700842 or control IgG4; (B) F023700931 (Pichia or CHO expressed), F023700924 (Pichia or CHO expressed), F023700933 or F023700962 or control Nanobody (IRR00085 or IRR00087; RSV binders); (C) F023700924, F023700969, F023700970 or control Nanobody; (D) F023700931, F023701016, or F023701017 or control Nanobody.
- EID EID
- F023700842 control IgG4
- B F023700931 (Pichia or CHO expressed), F023700924 (Pichia or CHO expressed), F023700933 or F023700962 or control Nanobody (IRR00085 or IRR00087;
- FIG. 16 (A-B). Activation of Jurkat T-cells expressing human LAG3 and human PD1 and Raji antigen-presenting cells in the presence of (A) F023700931 ⁇ Pichia or CHO expressed), F023700924 (Pichia or CHO expressed), F023700933 or F023700862 [should this be
- F023700892 or control Nanobody or (B) F023700924, F023700969, F023700970, F023700931, F023701016, F023701017, F023700933 or F023700962 or control Nanobody.
- Figure 17 Human T-cell clone activation (interferon-gamma production) in the presence of JY cells expressing human PDL1 in the presence of varying concentrations of (A) F023700931 (Pichia or CHO expressed), F023700924 (Pichia or CHO expressed), F023700933 or F023700962 or control Nanobody; (B) F023700924, F023700969, F023700970, F023700933 or F023700962 or control Nanobody; or (C) F023700931, F023701016, F023701017,
- Figure 19 Serum preAb reactivity to F023700924 and F023700931 and a trivalent control Nanobody T013700112 (lacking mutations to reduce pre-existing antibody binding) by healthy human subject sera at (A) 125 seconds and (B) 360 seconds; by cancer patient sera at (C) 125 seconds or (D) 360 seconds; or by sera of patients suffering from (E) melanoma, (F) non- small cell lung cancer (NSCLC), (G) head & neck cancer, (H) gastric cancer or (I) colorectal cancer.
- NSCLC non- small cell lung cancer
- NSCLC non- small cell lung cancer
- G head & neck cancer
- H gastric cancer
- colorectal cancer colorectal cancer
- the present invention provides ISVDs that comprise mutations which block reactivity of pre-existing antibodies (pre-antibodies) to neo-epitopes within the ISVDs.
- Neoepitopes are epitopes within a protein which are revealed when the protein is mutated (e.g., truncated) or its folding is altered.
- Pre-existing antibodies are antibodies existing in the body of a patient prior to receipt of an ISVD.
- the ISVDs of the present invention are based, in part, in llama antibodies whose C-terminal constant domains have been removed; thus, exposing the neo-epitopes in the C-terminus of the resulting VHH to pre-antibody binding.
- Table H of Buyse & Boutton on page 97 showed comparative data for an ISVD with a V89L mutation alone (with or without C-terminal extension) and the same ISVD with a V89L mutation in combination with an LI IV mutation (again, with or without a C- terminal extension). Also, although generated in two separate experiments, the data shown in Table H for the LI 1 V/V89L combination as compared to the data given in Table B for an LI IV mutation alone (in the same ISVD) showed that the pre-antibody binding reduction that is obtained by the LI 1 V/V89L combination was greater than that for the LI IV mutation alone.
- the CDRs As is well-known in the art, there are multiple conventions to define and describe the CDRs of a VH or VHH fragment, such as the Kabat definition (which is based on sequence variability and is the most commonly used) and the Chothia definition (which is based on the location of the structural loop regions). Reference is for example made to the website www.bioinf.org.u 'ahs/.
- the CDRs according to Kabat may also be mentioned, the CDRs are most preferably defined on the basis of the Abm definition (which is based on Oxford Molecular's AbM antibody modelling software), as this is considered to be an optimal compromise between the Kabat and Chotia definitions.
- CDR determination is according to Kabat, e.g., wherein FR1 of a VHH comprises the amino acid residues at positions 1-30, CDRl of a VHH comprises the amino acid residues at positions 31-35, FR2 of a VHH comprises the amino acids at positions 36-49, CDR2 of a VHH comprises the amino acid residues at positions 50-65, FR3 of a VHH comprises the amino acid residues at positions 66-94, CDR3 of a VHH comprises the amino acid residues at positions 95-102, and FR4 of a VHH comprises the amino acid residues at positions 103-113.
- CDRs are determined according to Kontermann and Diibel (Eds., Antibody Engineering, vol 2, Springer Verlag Heidelberg Berlin, Martin, Chapter 3, pp. 33-51, 2010).
- immunoglobulin single variable domain (also referred to as "ISV” or ISVD”) is generally used to refer to immunoglobulin variable domains (which may be heavy chain or light chain domains, including VH, VHH or VL domains) that can form a functional antigen binding site without interaction with another variable domain ⁇ e.g. without a VH/VL interaction as is required between the VH and VL domains of conventional 4-chain monoclonal antibody).
- ISVDs will be clear to the skilled person and for example include Nanobodies (including a VHH, a humanized VHH and/or a camelized VHs such as camelized human VHs), IgNAR, domains, (single domain) antibodies (such as dAbsTM) that are VH domains or that are derived from a VH domain and (single domain) antibodies (such as dAbsTM) that are VL domains or that are derived from a VL domain.
- ISVDs that are based on and/or derived from heavy chain variable domains (such as VH or VHH domains) are generally preferred. Most preferably, an ISVD will be a Nanobody.
- Nanobody is generally as defined in WO 08/020079 or WO 09/138519, and thus in a specific aspect generally denotes a VHH, a humanized VHH or a camelized VH (such as a camelized human VH) or generally a sequence optimized VHH (such as e.g. optimized for chemical stability and/or solubility, maximum overlap with known human framework regions and maximum expression).
- a sequence optimized VHH such as e.g. optimized for chemical stability and/or solubility, maximum overlap with known human framework regions and maximum expression.
- Nanobody or Nanobodies are registered trademarks of Ablynx N. V. and thus may also be referred to as Nanobody® and/or
- Nanobodies® An example of an ISVD is 102C12 (E1D, LI IV, A14P, A74S, K83R, I89L). Other ISVDs also appear in Tables A and C herein.
- a multispecific binder is a molecule that comprises, for example, a first PDl or LAG3 binding moiety (e.g., an ISVD or a Nanobody) and one or more (e.g., 1, 2, 3, 4, 5) additional binding moieties (e.g., an ISVD or a Nanobody) that bind to an epitope other than that of the first PDl or LAG3 binding moiety (e.g., to CTLA4, CD27 and/or BTLA); e.g., comprising a PDl or LAG3 binding moiety and a CTLA4 binding moiety; a PDl or LAG3 binding moiety and a BTLA binding moiety; one or two PDl binding moieties and one or two LAG3 binding moieties and a human serum albumin binding moiety; or a PDl binding moiety, a LAG3 binding moiety and a BTLA binding moiety.
- a multispecific binder is a molecule that comprises, for example
- a binding moiety or binding domain or binding unit is a molecule such as an ISVD or Nanobody that binds to an antigen.
- a binding moiety or binding domain or binding unit may be part of a larger molecule such as a multivalent or multispecific immunoglobulin that includes more than one moiety, domain or unit and/or that comprises another functional element, such as, for example, a half-life extender (HLE), targeting unit and/or a small molecule such a
- HLE half-life extender
- PEG polyethyleneglycol
- a monovalent PDl or LAG3 binder e.g., ISVD such as a Nanobody
- a bivalent PDl or LAG3 binder comprises two antigen binding domains (e.g., conventional antibodies including bispecific antibodies).
- a multivalent PD l or LAG3 binder comprises more than one antigen-binding domain.
- a monospecific PDl or LAG3 binder binds a single antigen; a bispecific PDl or LAG3 binder binds to two different antigens and a multispecific PDl or LAG3 binder binds to more than one antigen.
- a biparatopic PDl or LAG3 binder is monospecific but binds to two different epitopes of the same antigen.
- a multiparatopic PDl or LAG3 binder binds the same antigen but to more than one epitope in the antigen.
- half-life as used herein relation to a PDl and/or LAG3 binder or ISVD,
- Nanobody, ISVD-based biological, Nanobody -based biological or any other polypeptide referred to herein can generally be defined as described in paragraph o) on page 57 of WO 08/020079 and as mentioned therein refers to the time taken for the serum concentration of the polypeptide to be reduced by 50%, in vivo, for example due to degradation of the polypeptide and/or clearance or sequestration of the polypeptide by natural mechanisms.
- the in vivo half-life of a polypeptide of the invention can be determined in any manner known per se, such as by pharmacokinetic analysis. Suitable techniques will be clear to the person skilled in the art, and may for example generally be as described in paragraph o) on page 57 of WO 08/020079.
- the half-life can be expressed using parameters such as the tl/2-alpha, tl/2-beta and the area under the curve (AUC).
- AUC area under the curve
- Isolated PD1 and/or LAG3 binders e.g., an ISVD such as a Nanobody
- polypeptides, polynucleotides and vectors are at least partially free of other biological molecules from the cells or cell culture from which they are produced.
- biological molecules include nucleic acids, proteins, lipids, carbohydrates, or other material such as cellular debris and growth medium.
- An “isolated” PD1 and/or LAG3 binder may further be at least partially free of expression system components such as biological molecules from a host cell or of the growth medium thereof.
- the term “isolated” is not intended to refer to a complete absence of such biological molecules or to an absence of water, buffers, or salts or to components of a pharmaceutical formulation that includes the antibodies or fragments.
- control sequences refers to polynucleotides necessary for the expression of an operably linked coding sequence in a particular host organism.
- the control sequences that are suitable for prokaryotes include a promoter, optionally an operator sequence, and a ribosome binding site.
- Eukaryotic cells are known to use promoters, polyadenylation signals, and enhancers.
- a nucleic acid or polynucleotide is "operably linked" when it is placed into a functional relationship with another polynucleotide.
- DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotein that participates in the secretion of the polypeptide;
- a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation.
- operably linked means that the DNA sequences being linked are contiguous, and, in the case of a secretory leader, contiguous and in reading phase. However, enhancers do not have to be contiguous. Linking is accomplished by ligation at convenient restriction sites. If such sites do not exist, the synthetic oligonucleotide adaptors or linkers are used in accordance with conventional practice.
- the present invention includes polynucleotides encoding the PD1 and/or LAG3 binders which, optionally, are operably linked to one or more control sequences such as a promoter.
- a "PD1 and/or LAG3" binder refers to a binder that includes a PD 1 binder;
- a PD 1/LAG binder is
- a PD1/LAG3 binder includes a PDl binder and a LAG3 binder.
- the scope of the present invention includes any PDl binder set forth in Figure 18 (A-P) (or any PDl binder comprising CDRl, CDR2 and CDR3 of such a PDl binder), any LAG3 binder set forth in Figure 18 (A-P) (or any LAG3 binder comprising CDRl, CDR2 and CDR3 of such a LAG3 binder) or any PD1/LAG3 binder set forth in Figure 18 (A-P) or any PD1/LAG3 binder comprising CDRl, CDR2 and CDR3 of the PDl binding moiety and/or LAG3 binding moiety thereof.
- Any such binder or CDR may, in an embodiment may be a variant of what is set forth in Figure 18 (A-P), e.g., comprising 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 point mutations ⁇ e.g., conservative substitutions or deletions).
- the basic antibody structural unit comprises a tetramer.
- Each tetramer includes two identical pairs of polypeptide chains, each pair having one "light” (about 25 kDa) and one "heavy” chain (about 50-70 kDa).
- the amino-terminal portion of each chain includes a variable region of about 100 to 110 or more amino acids primarily responsible for antigen recognition.
- the carboxy-terminal portion of the heavy chain may define a constant region primarily responsible for effector function.
- human light chains are classified as kappa and lambda light chains.
- human heavy chains are typically classified as mu, delta, gamma, alpha, or epsilon, and define the antibody's isotype as IgM, IgD, IgG, IgA, and IgE, respectively.
- the variable and constant regions are joined by a "J" region of about 12 or more amino acids, with the heavy chain also including a "D” region of about 10 more amino acids. See generally, Fundamental Immunology Ch. 7 (Paul, W., ed., 2nd ed. Raven Press, N.Y. (1989).
- antigen-binding fragments include, but are not limited to, Fab, Fab', F(ab') 2 , and Fv fragments, and single-chain Fv molecules.
- PDl binder or "PDl ISVD” or “PDl nanobody” refers to a binder or ISVD or Nanobody, respectively, that binds to PDl .
- a similar convention may be applied with respect to molecules that bind to LAG3 or CTLA4 or another antigen.
- E1D Prevent pyroglutamic acid formation in the first amino acid of the construct El LI IV: Decrease pre-antibody binding
- W52aV Prevent oxidation of W52a
- WlOOaF Prevent oxidation of WlOOa
- V89L Decrease pre-antibody binding
- PDl is human PDl .
- human PDl comprises the amino acid sequence:
- LAG3 is human LAG3.
- human LAG3 comprises the amino acid sequence:
- the present invention provides improved PDl binders, for example, improved PDl ISVDs and more in particular improved PDl Nanobodies.
- improved PDl binders provided by the invention are also referred to herein as the "PDl binders of the invention” or "PDl binders”.
- monovalent PDl binders of the present invention will include the amino acid sequence of SEQ ID NO: 1 or 2, but including one or more mutations at position 1, 11, 14, 52a, 73, 74, 83, 89, 100a, 110 or 112 (or at any of the mutational positions set forth herein with regard to PDl binders of the invention).
- multispecific PDl binders for example, that include a LAG3, will include PDl binding moieties including CDR1, CDR2 and CDR3 that are in the PDl binders set forth below in Table A-l and A-2 (e.g., in 102C12 or reference A).
- the PDl binding moiety of the multispecific binder comprises the amino acid of SEQ ID NO: 1 or 2 but including one or more mutations at position 1, 1 1, 14, 52a, 73, 74, 83, 89, 100a, 1 10 or 1 12.
- the present invention provides improved PDl binders, for example, improved PDl ISVDs and more in particular improved PDl Nanobodies.
- PDl binders of the present invention include polypeptides which are variants of polypeptides comprising the amino acid sequence of SEQ ID NO: 1 or 2 which is mutated at position 1, 1 1, 14, 52a, 73, 74, 83, 89, 100a, 1 10 and/or 1 12.
- the improved PDl binders provided by the invention are also referred to herein as the "PD l binders of the invention” or "PDl binders". These terms encompass any molecule that binds to PDl and includes any of the molecules that bind to PDl which are set forth herein.
- the terms include an ISVD that comprises an amino acid sequence set forth in a member selected from the group consisting of SEQ ID NOs: 9-40 and 57 as well as any conventional antibody or antigen-binding fragment thereof that includes an amino acid sequence set forth in a members selected from the group consisting of SEQ ID NOs: 9-40 and 57; a multispecific
- immunoglobulin such as a bispecific immunoglobulin (e.g., ISVD) that comprises an amino acid sequence set forth in a member selected from the group consisting of SEQ ID NOs: 9-40 and 57, binds to PDl and also binds to another antigen such as a different epitope of PDl, CD27, LAG3, CTLA4, BTLA, TIM3, ICOS, B7-H3, B7-H4, CD137, GITR, PD-L1, PD-L2, ILT1, ILT2
- a bispecific immunoglobulin e.g., ISVD
- KIR3DL1, KTR3DL2, KIR3DL3, NKG2A, NKG2C, NKG2E, IL-10, IL-17, TSLP e.g., comprising a PDl binding moiety and a CTLA4 binding moiety; a PDl binding moiety and a BTLA binding moiety; a PDl binding moiety and a LAG3 binding moiety; or a PDl binding moiety, a LAG3 binding moiety and a BTLA binding moiety.
- a multivalent PDl binder comprises more than one antigen-binding domain, for example more than one ISVD (one or more of which bind to PDl).
- a monospecific PDl binder binds a single antigen (PDl); a bispecific PDl binder binds to two different antigens (one of which is PDl) and a multispecific PD binder binds to more than one antigen (one or more of which is PDl and one or more of which is a different antigen).
- a PDl binder comprises an amino acid sequence selected from SEQ ID NOs: 106-124.
- the invention aims to provide improved PDl binders that are variants of 102C12 and Reference A and that have reduced binding by interfering factors (generally referred to as "pre-existing antibodies") that may be present in the sera from some healthy human subjects as well as from patients. See WO 12/175741, WO 2013/024059 and also for example by Holland et al. (J. Clin. Immunol. 2013, 33(7): 1192-203) as well the PCT application
- the PDl binders of the invention preferably have the same combination of CDRs (i.e. CDRl, CDR2 and CDR3) as are present in 102C12 or in Reference A.
- WO 2008/071447 describes Nanobodies that can bind to PDl and uses thereof.
- SEQ ID NO: 348 of WO 2008/071447 disclosed a PD-1 specific Nanobody called 102C12, the sequence of which is given herein as SEQ ID NO: 1.
- a variant of 102C12 with a humanizing Q108L substitution also referred to herein as "Reference A”
- the present invention includes PDl binders that include a mutation at position 108, e.g., Q108L.
- the present invention includes PDl binders which are variants of 102C12 and PD1/LAG3 binders comprising such variants of 102C12 which are set forth below in Table A-2 below.
- the scope of the present invention includes PDl binders that include CDRl, CDR2 and CDR3 of said varaints set forth below in Table A-2 as well as PD1/LAG3 binders comprising a PDl binding moiety that includes CDRl, CDR2 and CDR3 of said varaints set forth below in Table A-2.
- VITwSGGITYYADSVKG or VITvSGGITYYADSVKG e.g., VITwSGGITYYADSVKG or VITvSGGITYYADSVKG
- VITwSGGITY e.g., VITwSGGITY or VITvSGGITY
- 1PD102C12 E1D, LI IV, DVOLVESGGGWOPGGSLRLSCAASGSIASIHA GWFROAPGKEREFVAVITVS
- 1PD102C12 E1D, LI IV, DVOLVESGGGWOPGGSLRLSCAASGSIASIHA GWFROAPGKEREFVAVITVS
- the present invention includes embodiments wherein a PDl binder comprises one, two or three of the CDRs that are in a PDl binder which is set forth above in Table A-l or A-2 (e.g., SEQ ID NO: 57, 98, 99, 103, 104 or 105) but which comprises 0, 1, 2, 3, 4, or 5 amino acid substitutions, e.g., conservative substitutions, and/or comprises 100, 99, 98, 97, 96 or 95% sequence identity relative to the CDR sequences set forth in Table A-l or A-2 wherein a PDl binder having such CDRs retains the ability to bind to PDl .
- the first amino acid of a PDl binder of the present invention is E.
- the first amino acid of a PDl binder of the present invention is D.
- PD1/LAG3 binders comprising such a PD1/LAG3 binder are part of the present invention.
- the present invention includes any PDl binder comprising the amino acid sequence of SEQ ID NO: 57, 98, 99, 103, 104 or 105 or an amino acid sequence comprising 80% or more (e.g., 85%, 90%, 95%, 96%, 97%, 98% or 99%) amino acid sequence identity (i.e., comparing the full amino acid sequences) wherein the PDl binder retains the ability to bind to PDl and, optionally, includes an HSA binder.
- PD1/LAG3 binders comprising such a PD1/LAG3 binder are part of the present invention.
- a PDl binder described as " 102C12 (EID, LI IV, A14P, A74S, K83R, I89L)" refers to a binder having the sequence of 102C12 (SEQ ID NO: 1) or reference A (SEQ ID NO: 2), but wherein the sequence comprises the mutations EID, LI IV, A14P, A74S, K83R and I89L. This notation is used through out the specification with regard to several different binders.
- 11B09 (LI IV, A14P, R41P, N43K, A62S, A74S, K83R, V89L) refers to a LAG3 binder comprising the amino acid sequence of 11B09 (SEQ ID NO: 64), but wherein the sequence comprises mutations LI IV, A14P, R41P, N43K, A62S, A74S, K83R and V89L.
- residue 1 is an E.
- Mutations may be referred to herein and are designated by their Kabat number as shown above.
- Some preferred, but non-limiting PD1 binders of the invention are 102C12 (E1D
- LI IV, A14P, A74S, K83R, I89L comprise the amino acid sequence set forth in SEQ ID NO: 9-40, 57, 98, 99 or 101-105 or are listed in Figure 2, Figure 3 or Figure 18 (A-P).
- PD1 binders of SEQ ID NOs: 24 to 40, 101 or 102 are examples of PD1 binders of the invention having a C-terminal alanine extension, i.e. an alanine residue at the C-terminal end of the ISVD- sequence (also sometimes referred to as "position 114") compared to the usual C-terminal sequence VTVSS (SEQ ID NO: 52, as present in Reference A).
- This C-terminal alanine extension can prevent the binding of so-called "pre-existing antibodies" (assumed to be IgGs) to a putative epitope that is situated at the C-terminal region of the ISV.
- This epitope is assumed to include, among other residues, the surface-exposed amino acid residues of the C-terminal sequence VTVSS (SEQ ID NO: 52) as well as the amino acid residue at position 14 (and the amino acid residues next/close to the same in the amino acid sequence, such as positions 11, 13 and 15) and may also comprise the amino acid residue at position 83 (and the amino acid residues next/close to the same in the amino acid sequence, such as positions 82, 82a, 82b and 84) and/or the amino acid residue at position 108 (and the amino acid residues next/close to the same in the amino acid sequence, such as position 107).
- one specific objective of the invention is to provide PD1 binders that are improved variants of the PD1 Nanobody referred to herein as "Reference A” and that have reduced binding by so-called “pre-existing antibodies”, and in particular of the kind described in PCT/EP2015/060643 (WO2015/173325)(/.e. those pre-existing antibodies that can bind to an exposed C-terminal region of an ISV even in the presence of a C-terminal extension).
- the invention provides PD1 binders comprising amino acid sequences that are variants of the sequence of SEQ ID NO: 1 or 2 which comprise one or more of the following mutations compared to the sequence of SEQ ID NO: 1 or 2:
- the PD1 binders (e.g., an ISVD such as a Nanobody) provided by the invention comprise a variant of SEQ ID NO: 1 or 2 wherein, in an embodiment of the invention: the amino acid residue at position 1 is selected from E and D;
- amino acid residue at position 1 1 is selected from L and V;
- amino acid residue at position 14 is selected from A and P;
- amino acid residue at position 52a is selected from W and V;
- amino acid residue at position 73 is selected from N, S, P and Q;
- amino acid residue at position 74 is selected from A or S;
- amino acid residue at position 83 is selected from K or R;
- amino acid residue at position 89 is selected from T, V, I or L;
- amino acid residue at position 100a is selected from W and F;
- amino acid residue at position 1 10 is selected from T, K or Q; and/or
- amino acid residue at position 1 12 is selected from S, K or Q;
- the PD1 binder comprises one or more of the following mutations:
- position 1 is D or E, position 1 1 is V, position 14 is P, position 74 is S, position 83 is R; and position 89 is L;
- position 1 is D or E, position 1 1 is V, position 14 is P, position 52a is V; position 73 is S, P or Q; position 74 is S, position 83 is R; position 89 is L; and position 100a is F; c. position 89 is L and position 1 1 is V;
- position 89 is L and position 1 10 is K or Q;
- position 89 is L and position 1 12 is K or Q;
- position 1 is D or E, position 1 1 is V, position 14 is P, position 52a is V; position 73 is S, P or Q; position 74 is S, position 83 is R; position 89 is L; position 100a is F and position 1 10 is K or Q;
- position 1 is D or E, position 1 1 is V, position 14 is P, position 52a is V; position 73 is S, P or Q; position 74 is S, position 83 is R; position 89 is L; position 100a is F and position 1 12 is K or Q;
- position 89 is L and position 1 1 is V and position 1 12 is K or Q;
- position 1 1 is V and position 1 10 is K or Q;
- position 1 1 is V and position 1 12 is K or Q;
- the PD1 binders (e.g., an ISVD such as a Nanobody) of the invention comprise amino acid sequences that are variants of SEQ ID NO: 1 or SEQ ID NO: 2 in which position 89 is T or L, or in which 1 is D or E, 1 1 is V, 14 is P, 74 is S, 83 is R and 89 is L or in which position 1 1 is V and position 89 is L (optionally in suitable combination with a 1 10K or 1 10Q mutation and/or a 1 12K or 1 12Q mutation, and in particular in combination with a 1 10K or 1 10Q mutation) are also part of the present invention.
- the present invention includes amino acid sequences in which position 1 1 is V and position 89 is L, optionally with a 1 1 OK or 1 10Q mutation.
- the PDl binders provided by the invention described herein can bind (and in particular, can specifically bind) to PD-1. In an embodiment of the invention, they can bind to PDl and inhibit binding between PD l and PD-Ll and/or PD-L2.
- the PD l binders of the present invention can bind (and in particular, can specifically bind) to PD-1. In an embodiment of the invention, they can bind to PDl and inhibit binding between PD l and PD-Ll and/or PD-L2.
- the PD l binders of the present invention
- T-cell mediated immune response e.g., by releasing the T-cells from PDl mediated inhibition of proliferation and cytokine production
- Table B lists some non-limiting possible combinations of the amino acid residues that can be present at positions 1 1, 89, 1 10 and 1 12 in the PDl binders of the invention.
- the PD1 binders provided by the invention are further as described in the description, examples and figures herein, i.e. they have CDRs that are as described herein and have an overall degree of sequence identity (as defined herein) with the sequence of SEQ ID NO: 1 or 2 that is as disclosed herein and/or may have a limited number of "amino acid differences" (as described herein) with (one of) these reference sequences.
- the PD1 binders ⁇ e.g., ISVDs such as Nanobodies) of the invention that comprise the amino acid sequence of SEQ ID NO: 1 or 2 and one or more mutations at position 1, 11, 14, 52a, 73, 74, 83, 89, 100a, 110 and/or 112 preferably include the following CDRs (according to the Kabat convention):
- CDR1 (according to Kabat) that is the amino acid sequence IHAMG (SEQ ID NO: 3);
- CDR2 (according to Kabat) that is the amino acid sequence VITXSGGITYYADSVKG (SEQ ID NO: 4; wherein X is W or V);
- the PD1 binders ⁇ e.g., ISVDs such as Nanobodies
- the PD1 binders ⁇ e.g., ISVDs such as Nanobodies
- CDR1, CDR2 and/or CDR3 has 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 substitutions, e.g., conservative substitutions.
- a PD1 binder (e.g., ISVDs such as Nanobodies) of the invention in addition to the CDR1, CDR2 and CDR3 set forth above, preferably also has:
- no more than 7 such as no more than 5, preferably no more than 3, such as only 3, 2 or 1
- amino acid differences with the amino acid sequence of SEQ ID NO: 1 or 2 (in which said amino acid differences, if present, may be present in the frameworks and/or the CDRs but are preferably present only in the frameworks and not in the CDRs; not taking into account any C-terminal extension that may be present and not taking into account the mutations at positions 1, 11, 14, 52a, 73, 74, 83, 89, 100a, 110 and/or 112 required by the specific aspect involved).
- BLAST ALGORITHMS Altschul et al. (2005) FEBS J. 272(20): 5101-5109; Altschul, S.F., et al, (1990) J. Mol. Biol. 215:403-410; Gish, W., et al, (1993) Nature Genet. 3 :266-272; Madden, T.L., et al, (1996) Meth. Enzymol. 266: 131-141; Altschul, S.F., et al, (1997)
- the PD1 binders ⁇ e.g., ISVD such as a Nanobody
- ISVD such as a Nanobody
- the degree of overall sequence identity with respect to SEQ ID NO: 1 or 2 and/or the number and kind of "amino acid differences" that may be present in such a binder of the invention ⁇ i.e. compared to the sequence of SEQ ID NO: 1 or 2) it should be noted that, unless otherwise stated, when it is said that
- an amino acid sequence of the invention has a degree of sequence identity with the sequence of SEQ ID NO: 1 or 2 of at least 85%, preferably at least 90%, more preferably at least 95% (in which the CDRs, any C-terminal extension that may be present, as well as the mutations at positions 1, 11, 14, 52a, 73, 74, 83, 89, 100a, 110 and/or 112 required by the specific aspect involved are not taken into account for determining the degree of sequence identity); and/or when it is said that
- an amino acid sequence of the invention has no more than 7, preferably no more than 5, such as only 3, 2 or 1 "amino acid differences" with the sequence of SEQ ID NO: 1 or 2 (again, not taking into account any C-terminal extension that may be present and not taking into account the mutations at positions 1, 11, 14, 52a, 73, 74, 83, 89, 100a, 110 and/or 112 required by the specific aspect involved),
- this also includes sequences that have no amino acid differences with the sequence of SEQ ID NO: 1 or 2 other than the mutations at positions 1, 11, 14, 52a, 73, 74, 83, 89, 100a, 110 and/or 112 (as required by the specific aspect involved) and any C-terminal extension that may be present.
- the PD1 binders of the invention comprising the amino acid sequence of SEQ ID NO: 1 or 2, but with at least one amino acid mutation at positon 1, 11, 14, 52a, 73, 74, 83, 89, 100a, 110 and/or 112, may have 100% sequence identity with SEQ ID NO: 1 or 2 (including a CDR1, CDR2 and CDR3 thereof optionally comprising a W52aV and/or WlOOaF mutation, but not taking into account the mutation(s) or combination of mutations at positions 1, 11, 14, 52a, 73, 74, 83, 89, 100a, 110 and/or 112 disclosed herein and/or any C-terminal extension that may be present) and/or may have no amino acid differences with SEQ ID NO: 1 or 2 (i.e. other than the mutation(s) or combination of mutations at positions 1, 11, 14, 52a, 73, 74, 83, 89, 100a, 110 and/or 112 disclosed herein and any C
- these amino acid differences may be present in the CDRs and/or in the framework regions, but they are preferably present only in the framework regions (as defined by the Abm convention, i.e. not in the CDRs as defined according to the Abm convention), i.e. such that the PD1 binders of the invention have the same CDRs (defined according to the Abm convention) as are present in SEQ ID NO: 1, 2, 9-40, 57, 98, 99, 101, 102, 103, 104 or 105.
- a PD1 binder of the invention according to any aspect of the invention has one or more amino acid differences with the sequence of SEQ ID NO: 1 or 2 (besides the mutations at positions 1, 11, 14, 52a, 73, 74, 83, 89, 100a, 110 and/or 112 that are required by the specific aspect involved), then some specific, but non-limiting examples of such mutations/amino acid differences that may be present (i.e.
- the PD-1 binders of the invention when they are present at and/or form the N-terminal part of the polypeptide in which they are present, then they preferably contain a D at position 1 (i.e. an E1D mutation compared to Reference A).
- a preferred but non-limiting example of such an N-terminal PD-1 binder is given as SEQ ID NOs: 24 or 57.
- the invention relates to a polypeptide (which is as further described herein) that has a PD-1 binder (which is as further described herein) at its N-terminal end, wherein said PD-1 binder has a D at position 1, and is for example SEQ ID NOs: 24, 25, 57 or 101-105.
- a PD-1 binder of the invention when used in monovalent format, it preferably has both a C-terminal extension X(n) as described herein and a D at position 1.
- a preferred but non-limiting example of such a monovalent PD-1 binder is given as SEQ ID NO: 40.
- the invention relates to a monovalent PD-1 binder of the invention (which is as further described herein) that has a D at position 1 and a C-terminal extension X(n) (which is preferably a single Ala residue).
- said monovalent PD-1 binder is SEQ ID NO: 40, 101 or 102.
- SEQ ID NOs: 23, 24, 39, 40 and 57 are examples of PD-1 binders of the invention having amino acid differences with SEQ ID NO: 1 or 2 such as A14P, A74S and/or K83R (in addition, as indicated in the previous paragraphs, SEQ ID NOs: 24 and 40 and 57 also have a E1D mutation).
- SEQ ID NOs: 24 and 40 and 57 also have a E1D mutation.
- the invention relates to PD-1 binders of the invention (i.e.
- the PD1 binders of the invention when they are used in a monovalent format and/or when they are present at and/or form the C-terminal end of the polypeptide in which they are present (or when they otherwise have an "exposed" C-terminal end in such polypeptide by which is generally meant that the C-terminal end of the ISVD is not associated with or linked to a constant domain (such as a CHI domain)); (see WO 12/175741 and PCT/EP2015/060643 (WO2015/173325)), preferably also have a C-terminal extension of the formula (X) n , in which n is 1 to 10, preferably 1 to 5, such as 1, 2, 3, 4 or 5 (and preferably 1 or 2, such as 1); and each X is an (preferably naturally occurring) amino acid residue that is independently chosen from naturally occurring amino acid residues (although according to preferred one aspect, it does not comprise any cysteine residues), and preferably independently chosen from the group consisting of alanine (A), glycine
- any C-terminal extension present in a PD1 binder of the invention does not contain a (free) cysteine residue (unless said cysteine residue is used or intended for further functionalization, for example for PEGylation).
- C-terminal extensions are the following amino acid sequences: A, AA, AAA, G, GG, GGG, AG, GA, AAG, AGG, AGA, GGA, GAA or GAG.
- the C-terminal amino acid residues of framework 4 can, in an embodiment of the invention be as set forth in SEQ ID NO: 1, 2, 9-40, 57, 100, 101, 103, 104, 105, 106 or 107 but wherein the 5 C-terminal residues can be substituted as follows:
- VTVKS SEQ ID NO: 42
- VTVQS SEQ ID NO: 42
- VKVSS SEQ ID NO: 44
- VQVSS SEQ ID NO: 45
- VTVKSX 11
- VTVQSX(n) (SEQ ID NO: 47), VKVSSX(n) (SEQ ID NO: 48) or VQVSSX ⁇ (SEQ ID NO: 49), such as VTVKSA (SEQ ID NO: 50), VTVQSA (SEQ ID NO: 51), VKVSSA (SEQ ID ): 52) or VQVSSA (SEQ ID NO: 53).
- the C-terminal amino acid residues of framework 4 can, in an embodiment of the invention be as set forth in SEQ ID NO: 1, 2, 9-40, 57, 98, 99, 101, 102, 103, 104 or 105 but wherein the 5 C-terminal residues can be substituted as follows: (i) when no C-terminal extension is present: VTVSS (SEQ ID NO: 54) (as in the sequence of SEQ ID NO: 1 or 2); or
- VTVSSX (n) (SEQ ID NO: 55) such as
- VTVSSA (SEQ ID NO: 56).
- X and n are as defined herein for the C-terminal extensions.
- PDl binders of the invention are given in SEQ ID NOs: 9-40, 57, 98, 99, 101, 102, 103, 104 or 105 and each of these sequences forms a further aspect of the invention.
- the PDl binders of SEQ ID NOs: 9-24, 57, 98, 99, 103, 104 and 105 do not have a C-terminal extension
- the PDl binders of SEQ ID NOs: 25-40, 101 and 102 contain a C-terminal alanine (which is a preferred but non-limiting example of a C- terminal extension as described herein).
- Examples of PDl binders of the present invention comprise the amino acid sequence set forth in SEQ ID NO: 23, 24, 39 , 40, 57, 98, 99, 101, 102, 103, 104 or 105.
- a PDl binder e.g., an ISVD such as a
- Nanobody comprises:
- CDR1 (according to Kabat) that is the amino acid sequence IHAMG (SEQ ID NO: 3);
- CDR2 (according to Kabat) that is the amino acid sequence VITXSGGITYYADSVKG (SEQ ID NO: 4; wherein X is W or V);
- amino acid differences as defined herein, and not taking into account any of the mutations set forth herein at position(s) 1, 1 1, 14, 52a, 73, 74, 83, 89, 100a, 1 10 and/or 1 12 that may be present and not taking into account any C-terminal extension that may be present) with the amino acid sequence of SEQ ID NO: 1 or 2 (in which said amino acid differences, if present, may be present in the frameworks and/or the CDRs but are preferably present only in the frameworks and not in the CDRs);
- n 1 to 10
- X is an (preferably naturally occurring) amino acid residue that is independently chosen, and preferably independently chosen from the group consisting of alanine (A), glycine (G), valine (V), leucine (L) or isoleucine (I);
- amino acid residue at position 1 is E or D;
- amino acid residue at position 11 is L or V;
- amino acid residue at position 14 is A or P;
- amino acid residue at position 52a is W or V;
- amino acid residue at position 73 is N, S, P or Q;
- amino acid residue at position 74 is A or S
- amino acid residue at position 83 is K or R
- amino acid residue at position 89 is T, V, I or L;
- amino acid residue at position 100a is W or F;
- amino acid residue at position 110 is T, K or Q;
- amino acid residue at position 112 is S, K or Q;
- the PD1 binder comprises one or more of the following mutations:
- (ix) position 100a is F; for example, comprising a set of mutations as follows:
- position 1 is D or E, position 1 1 is V, position 14 is P, position 74 is S, position 83 is R and position 89 is L;
- position 1 is D or E, position 1 1 is V, position 14 is P, position 52a is V; position 73 is S, P or Q; position 74 is S, position 83 is R, position 89 is L and position 100a is F; c. position 1 is D or E, position 1 1 is V, position 14 is P, position 74 is S, position 83 is R and position 89 is L;
- position 89 is L and position 1 10 is K or Q;
- position 89 is L and position 1 12 is K or Q;
- position 89 is L and position 1 1 is V and position 1 10 is K or Q;
- position 1 1 is V and position 1 10 is K or Q; or
- position 1 1 is V and position 1 12 is K or Q.
- the invention relates to a PD1 binder (e.g., an ISVD such as a
- Nanobody having:
- a degree of sequence identity with the amino acid sequence of SEQ ID NO: 1 or 2 in which any C-terminal extension that may be present as well as the CDRs thereof , optionally comprising a W52aV and/or WlOOaF mutation, are not taken into account for determining the degree of sequence identity
- the degree of sequence identity of at least 85%, preferably at least 90%, more preferably at least 95% (e.g., 100%)) (in which the CDRs, any C-terminal extension that may be present, as well as the mutations at positions 1, 11, 14, 52a, 73, 74, 83, 89, 100a, 110 and/or 112 required by the specific aspect involved are not taken into account for determining the degree of sequence identity);
- amino acid differences as defined herein, and not taking into account any of the mutations set forth herein at position(s) 1, 11, 14, 52a, 73, 74, 83, 89, 100a, 110 and/or 112 that may be present and not taking into account any C-terminal extension that may be present) with the amino acid sequence of SEQ ID NO: 1 or 2 (in which said amino acid differences, if present, may be present in the frameworks and/or the CDRs but are preferably present only in the frameworks and not in the CDRs);
- n 1 to 10 - a C-terminal extension (X) n , in which n is 1 to 10, preferably 1 to 5, such as 1, 2, 3, 4 or 5 (and preferably 1 or 2, such as 1); and each X is an (preferably naturally occurring) amino acid residue that is independently chosen, and preferably independently chosen from the group consisting of alanine (A), glycine (G), valine (V), leucine (L) or isoleucine (I);
- A alanine
- G glycine
- V valine
- L leucine
- I isoleucine
- PD1 binder e.g., an ISVD such as a Nanobody
- PD1 binder comprises, in an embodiment of the invention, one or more of the following amino acid residues (i.e. mutations compared to the amino acid sequence of SEQ ID NO: 1 or 2) at the positions mentioned (numbering according to Kabat):
- the PDl binder e.g., an ISVD such as a Nanobody
- the PDl binder preferably has a C-terminal extension X(n), which C-terminal extension may be as described herein for the PDl binders of the invention and/or as described in WO 12/175741 or PCT/EP2015/060643 (WO2015/173325).
- PDl binders e.g., an ISVD such as a Nanobody
- SEQ ID NOs: 9-40 57, 98, 99, 101, 102, 103, 104 and 105 and each of these amino acid sequences individually forms a further aspect of the invention.
- the invention includes PD l binders comprising amino acid sequences of SEQ ID NO: 1 or 2 but wherein position 89 is T; or in which position 1 is E or D, position 1 1 is V, position 14 is P, position 52a is V, position 73 is P, S or Q, position 74 is S, position 83 is R, position 89 is L and/or positon 100a is F; or in which position 1 1 is V and position 89 is L (optionally in suitable combination with a 1 10K or 1 10Q mutation and/or a 1 12K or 1 12Q mutation, and in particular in combination with a 1 10K or 1 10Q mutation).
- the amino acid sequences in which position 1 1 is V and position 89 is L, optionally with a 1 10K or 1 10Q mutation.
- the invention relates to a PD1 binder (e.g., an
- immunoglobulin single variable domain such as a Nanobody having:
- CDR1 (according to Kabat) that is the amino acid sequence IHAMG (SEQ ID NO: 3);
- CDR2 (according to Kabat) that is the amino acid sequence VITXSGGITYYADSVKG (SEQ ID NO: 4; wherein X is W or V);
- a degree of sequence identity with the amino acid sequence of SEQ ID NO: 1 or 2 (in which any C-terminal extension that may be present as well as the CDRs thereof, optionally comprising a W52aV and/or WlOOaF mutation, are not taken into account for determining the degree of sequence identity) of at least 85%, preferably at least 90%, more preferably at least
- amino acid differences as defined herein, and not taking into account any of the mutations set forth herein at position(s) 1, 1 1, 14, 52a, 73, 74, 83, 89, 100a, 1 10 and/or 1 12 that may be present and not taking into account any C-terminal extension that may be present) with the amino acid sequence of SEQ ID NO: 1 or 2 (in which said amino acid differences, if present, may be present in the frameworks and/or the CDRs but are preferably present only in the frameworks and not in the CDRs);
- n 1 to 10
- X is an (preferably naturally occurring) amino acid residue that is independently chosen, and preferably independently chosen from the group consisting of alanine (A), glycine (G), valine (V), leucine (L) or isoleucine (I);
- amino acid at position 73 is N, S, P or Q;
- amino acid residue at position 1 10 is T, K or Q (and is preferably T);
- amino acid residue at position 1 12 is S, K or Q (and is preferably S).
- the invention relates to a PD1 binder (e.g., an
- immunoglobulin single variable domain such as a Nanobody having:
- CDR1 (according to Kabat) that is the amino acid sequence IHAMG (SEQ ID NO: 3);
- CDR2 (according to Kabat) that is the amino acid sequence VITXSGGITYYADSVKG (SEQ ID NO: 4; wherein X is W or V);
- a degree of sequence identity with the amino acid sequence of SEQ ID NO: 1 or 2 in which any C-terminal extension that may be present as well as the CDRs thereof, optionally comprising a W52aV and/or WlOOaF mutation, are not taken into account for determining the degree of sequence identity) of at least 85%, preferably at least 90%, more preferably at least 95%) (e.g., 100%)) (in which the CDRs, any C-terminal extension that may be present, as well as the mutations at positions 1, 1 1, 14, 52a, 73, 74, 83, 89, 100a, 1 10 and/or 1 12 required by the specific aspect involved are not taken into account for determining the degree of sequence identity);
- amino acid differences as defined herein, and not taking into account any of the mutations set forth herein at position(s) 1, 11, 14, 52a, 73, 74, 83, 89, 100a, 110 and/or 112 that may be present and not taking into account any C-terminal extension that may be present) with the amino acid sequence of SEQ ID NO: 1 or 2 (in which said amino acid differences, if present, may be present in the frameworks and/or the CDRs but are preferably present only in the frameworks and not in the CDRs);
- n 1 to 10
- X is an (preferably naturally occurring) amino acid residue that is independently chosen, and preferably independently chosen from the group consisting of alanine (A), glycine (G), valine (V), leucine (L) or isoleucine (I);
- amino acid at position 73 is S, P, N or Q;
- the amino acid residue at position 110 is T, K or Q (and is preferably T); or
- amino acid residue at position 112 is S, K or Q (and is preferably S).
- the PD1 binders e.g., an ISVD such as a
- Nanobody of the invention comprise one or more of the following amino acid residues (i.e. mutations compared to the sequence of SEQ ID NO: 1 or 2) at the positions mentioned
- - 1 IV in combination with 14P, 52aV, 73S or 73Q or 73P, 74S, 83R, 89L and/or lOOaF and, optionally, ID;
- the PD1 binders e.g., an ISVD such as a Nanobody
- the PD1 binders comprise one or more of the following amino acid residues (i.e. mutations compared to the sequence of SEQ ID NO: 1 or 2) at the positions mentioned
- the PD1 binders e.g., an ISVD such as a Nanobody
- the PD1 binders comprise one or more of the following amino acid residues (i.e. mutations compared to the sequence of SEQ ID NO: 1 or 2) at the positions mentioned
- the PD1 binders e.g., an ISVD such as a
- Nanobody of the invention comprise one or more of the following amino acid residues (i.e. mutations compared to the sequence of SEQ ID NO: 1 or 2) at the positions mentioned (numbering according to Kabat):
- the PD1 binders (e.g., an ISVD such as a Nanobody) of the invention comprise a T at position 89 and have CDRs that are the same as the CDRs that are present in the sequence of SEQ ID NO: 9-40, 57, 98, 99, 101, 102, 103, 104 or 105 (e.g., according to Kabat) and have an overall degree of sequence identity with the amino acid sequence of SEQ ID NO: 1 or 2 that are as described herein.
- CDRs that are the same as the CDRs that are present in the sequence of SEQ ID NO: 9-40, 57, 98, 99, 101, 102, 103, 104 or 105 (e.g., according to Kabat) and have an overall degree of sequence identity with the amino acid sequence of SEQ ID NO: 1 or 2 that are as described herein.
- the PD1 binders (e.g., an ISVD such as a Nanobody) of the invention comprise a V at position 1 1 and an L at position 89 and have CDRs that are the same as the CDRs that are present in the sequence of SEQ ID NO: 9-40, 57, 100, 101, 102 103, 104 or 105 (e.g., according to Kabat) and have an overall degree of sequence identity with the amino acid sequence of SEQ ID NO: 1 or 2 that are as described herein.
- an ISVD such as a Nanobody
- the PD1 binders e.g., an ISVD such as a Nanobody
- the PD1 binders are preferably further such that they contain a suitable combination of an A14P mutation, an A74S mutation and/or a K83R mutation, and preferably a suitable combination of any two of these mutations, such as all three of these mutations (e.g., E1D (optionally), LI IV, A14P, W52aV, N73 S or N73Q or N73P, A74S, K83R, I89L and WlOOaF).
- E1D optionally
- the N-terminal binding moiety preferably has an E1D mutation.
- the invention relates to a PDl binder (e.g., an immunoglobulin single variable domain (ISVD) such as a Nanobody) having:
- ISVD immunoglobulin single variable domain
- a degree of sequence identity with the amino acid sequence of SEQ ID NO: 1 or 2 in which any C-terminal extension that may be present as well as the CDRs, optionally comprising a W52aV and/or WlOOaF mutation, are not taken into account for determining the degree of sequence identity
- the degree of sequence identity of at least 85%, preferably at least 90%, more preferably at least 95% (e.g., 100%)
- the CDRs, any C-terminal extension that may be present, as well as the mutations at positions 1, 1 1, 14, 52a, 73, 74, 83, 89, 100a, 1 10 and/or 1 12 required by the specific aspect involved are not taken into account for determining the degree of sequence identity
- amino acid differences as defined herein, and not taking into account any of the mutations set forth herein at position(s) 1, 1 1, 14, 52a, 73, 74, 83, 89, 100a, 1 10 and/or 1 12 that may be present and not taking into account any C-terminal extension that may be present) with the amino acid sequence of SEQ ID NO: 1 or 2 (in which said amino acid differences, if present, may be present in the frameworks and/or the CDRs but are preferably present only in the frameworks and not in the CDRs);
- a C-terminal extension (X) n in which n is 1 to 10, preferably 1 to 5, such as 1, 2, 3, 4 or 5 (and preferably 1 or 2, such as 1); and each X is an (preferably naturally occurring) amino acid residue that is independently chosen, and preferably independently chosen from the group consisting of alanine (A), glycine (G), valine (V), leucine (L) or isoleucine (I); wherein, in an embodiment of the invention:
- amino acid at position 73 is N, S, P or Q;
- amino acid at position 89 is V, I, T or L;
- the amino acid residue at position 110 is T, K or Q (and is preferably T);
- amino acid residue at position 112 is S, K or Q (and is preferably S)
- the PDl binder comprises one or more of the following mutations:
- position 89 is L and position 1 10 is K or Q;
- position 89 is L and position 1 12 is K or Q;
- position 89 is L and position 1 1 is V and position 1 10 is K or Q;
- position 89 is L and position 1 1 is V and position 1 12 is K or Q;
- position 1 1 is V and position 1 10 is K or Q; or
- position 1 1 is V and position 1 12 is K or Q.
- the invention relates to a PD1 binder (e.g., an immunoglobulin single variable domain (ISVD) such as a Nanobody) having:
- ISVD immunoglobulin single variable domain
- a degree of sequence identity with the amino acid sequence of SEQ ID NO: 1 or 2 in which any C-terminal extension that may be present as well as the CDRs, optionally comprising a W52aV and/or WlOOaF mutation, are not taken into account for determining the degree of sequence identity
- a degree of sequence identity with the amino acid sequence of SEQ ID NO: 1 or 2 (in which any C-terminal extension that may be present as well as the CDRs, optionally comprising a W52aV and/or WlOOaF mutation, are not taken into account for determining the degree of sequence identity) of at least 85%, preferably at least 90%, more preferably at least 95% (e.g., 100%)) (in which the CDRs, any C-terminal extension that may be present, as well as the mutations at positions 1, 11, 14, 52a, 73, 74, 83, 89, 100a, 110 and/or 112 required by the specific aspect involved are not taken into account for determining the degree of sequence identity);
- no more than 7 such as no more than 5, preferably no more than 3, such as only 3, 2 or 1
- amino acid differences (as defined herein, and not taking into account any of the mutations set forth herein at position(s) 1, 11, 14, 52a, 73, 74, 83, 89, 100a, 110 and/or 112 that may be present and not taking into account any C-terminal extension that may be present) with the amino acid sequence of SEQ ID NO: 1 or 2 (in which said amino acid differences, if present, may be present in the frameworks and/or the CDRs but are preferably present only in the frameworks and not in the CDRs);
- n 1 to 10
- X is an (preferably naturally occurring) amino acid residue that is independently chosen, and preferably independently chosen from the group consisting of alanine (A), glycine (G), valine (V), leucine (L) or isoleucine (I);
- immunoglobulin single variable domain comprises one or more of the following amino acid residues (i.e. mutations compared to the amino acid sequence of SEQ ID NO: 1 or 2) at the positions mentioned (numbering according to Kabat):
- the PD1 binding moiety preferably has a C- terminal extension X(n), which C-terminal extension may be as described herein for the PD1 binders of the invention and/or as described in WO 12/175741 or PCT/EP2015/060643
- PD1 binders e.g., an ISVD such as a Nanobody
- SEQ ID NOs: 9 to 40 57, 98, 99, 101, 102, 103, 104 or 105 and each of these amino acid sequences individually forms a further aspect of the invention.
- the amino acid sequence at position 1 1 is V and position 89 is L, optionally with a 1 10K or 1 10Q mutation.
- the invention relates to a PD1 binder (e.g., an
- immunoglobulin single variable domain such as a Nanobody having:
- W52aV and/or WlOOaF mutation are not taken into account for determining the degree of sequence identity) of at least 85%, preferably at least 90%, more preferably at least 95% (e.g., 100%) (in which the CDRs, any C-terminal extension that may be present, as well as the mutations at positions 1, 1 1, 14, 52a, 73, 74, 83, 89, 100a, 1 10 and/or 1 12 required by the specific aspect involved are not taken into account for determining the degree of sequence identity);
- amino acid differences as defined herein, and not taking into account any of the mutations set forth herein at position(s) 1, 1 1, 14, 52a, 73, 74, 83, 89, 100a, 1 10 and/or 1 12 that may be present and not taking into account any C-terminal extension that may be present) with the amino acid sequence of SEQ ID NO: 1 or 2 (in which said amino acid differences, if present, may be present in the frameworks and/or the CDRs but are preferably present only in the frameworks and not in the CDRs);
- a C-terminal extension (X) n in which n is 1 to 10, preferably 1 to 5, such as 1, 2, 3, 4 or 5 (and preferably 1 or 2, such as 1); and each X is an (preferably naturally occurring) amino acid residue that is independently chosen, and preferably independently chosen from the group consisting of alanine (A), glycine (G), valine (V), leucine (L) or isoleucine (I);
- amino acid residue at position 1 is E or D;
- amino acid residue at position 1 1 is L or V;
- amino acid residue at position 14 is A or P;
- amino acid residue at position 52a is W or V;
- amino acid residue at position 73 is S, P, N or Q;
- amino acid residue at position 74 is A or S
- amino acid residue at position 83 is K or R
- amino acid residue at position 89 is T, L or I;
- amino acid residue at position 100a is W or F;
- amino acid residue at position 1 10 is T, K or Q (and is preferably T);
- amino acid residue at position 1 12 is S, K or Q (and in preferably S).
- the invention relates to a PD1 binder (e.g., an
- immunoglobulin single variable domain such as a Nanobody having:
- a degree of sequence identity with the amino acid sequence of SEQ ID NO: 1 or 2 in which any C-terminal extension that may be present as well as the CDRs, optionally comprising a W52aV and/or WlOOaF mutation, are not taken into account for determining the degree of sequence identity
- the degree of sequence identity of at least 85%, preferably at least 90%, more preferably at least 95% (e.g., 100%)
- the CDRs, any C-terminal extension that may be present, as well as the mutations at positions 1, 1 1, 14, 52a, 73, 74, 83, 89, 100a, 1 10 and/or 1 12 required by the specific aspect involved are not taken into account for determining the degree of sequence identity
- amino acid differences as defined herein, and not taking into account any of the mutations set forth herein at position(s) 1, 11, 14, 52a, 73, 74, 83, 89, 100a, 110 and/or 112 that may be present and not taking into account any C-terminal extension that may be present) with the amino acid sequence of SEQ ID NO: 1 or 2 (in which said amino acid differences, if present, may be present in the frameworks and/or the CDRs but are preferably present only in the frameworks and not in the CDRs);
- n 1 to 10
- X is an (preferably naturally occurring) amino acid residue that is independently chosen, and preferably independently chosen from the group consisting of alanine (A), glycine (G), valine (V), leucine (L) or isoleucine (I);
- amino acid residue at position 1 is E or D;
- amino acid residue at position 11 is V;
- amino acid residue at position 14 is P;
- amino acid residue at position 52a is V;
- amino acid residue at position 73 is S, P or Q;
- amino acid residue at position 74 is S
- amino acid residue at position 83 is R
- amino acid residue at position 89 is L
- amino acid residue at position 100a is F
- amino acid residue at position 110 is T, K or Q; or
- amino acid residue at position 112 is S, K or Q.
- the PD1 binders e.g., an ISVD such as a Nanobody
- the PD1 binders comprise one of the following sets of mutations (i.e. mutations compared to the sequence of SEQ ID NO: 1 or 2) at the positions mentioned (numbering according to Kabat): 1 IV in combination with 89L;
- the PD1 binders e.g., an ISVD such as a Nanobody
- the PD1 binders comprise one of the following sets of mutations (i.e. mutations compared to the sequence of SEQ ID NO: 1 or 2) at the positions mentioned (numbering according to Kabat):
- the PD1 binders e.g., an ISVD such as a Nanobody
- the PD1 binders comprise one of the following sets of mutations (i.e. mutations compared to the sequence of SEQ ID NO: 1 or 2) at the positions mentioned (numbering according to Kabat):
- the PD1 binders e.g., an ISVD such as a Nanobody
- the PD1 binders comprise one or more of the following sets of mutations (i.e.
- the PD1 binders (e.g., an ISVD such as a Nanobody) of the invention comprise a T or L at position 89 and have CDRs that are the same as the CDRs that are present in the sequence of SEQ ID NO: 1, 2, 9-40, 57, 98, 99, 101, 102, 103, 104 or 105 (e.g., according to Abm) and have an overall degree of sequence identity with the amino acid sequence of SEQ ID NO: 1 or 2 that are as described herein.
- an ISVD such as a Nanobody
- the PD1 binders (e.g., an ISVD such as a Nanobody) of the invention comprise a V at position 1 1 and an L at position 89 and have CDRs that are the same as the CDRs that are present in the sequence of SEQ ID NO: 1, 2, 9-40, 57, 98, 99, 101, 102, 103, 104 or 105 (e.g., according to Abm) and have an overall degree of sequence identity with the amino acid sequence of SEQ ID NO: 1 or 2 that are as described herein.
- an ISVD such as a Nanobody
- the PD-1 binders of the invention are preferably further such that they contain a suitable combination of an E1D mutation, an LI IV mutation, an A14P mutation, a W52aV mutation, an N73 S or N73Q or N73P mutation, an A74S mutation, a K83R mutation, an I89L mutation and/or a WlOOaF mutation, and preferably a suitable combination of any two of these mutations, such as all of these mutations.
- a PD-1 binder is monovalent or wherein the PD1 binding moiety thereof is present at the N-terminal end of a polypeptide, it preferably also has an E1D mutation.
- the invention relates to an immunoglobulin single variable domain that comprises or consists essentially of an amino acid sequence chosen from one of the following amino acid sequences: SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 1 1, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, or SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO:
- the invention relates to an immunoglobulin single variable domain that is or essentially consists of an amino acid sequence chosen from one of the following amino acid sequences: SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 57, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 104 and SEQ ID NO: 105.
- amino acid residues of a PD1 binder are numbered according to the general numbering for VHs given by Kabat et al. ("Sequence of proteins of immunological interest", US Public Health Services, NIH
- the total number of amino acid residues in each of the CDRs may vary and may not correspond to the total number of amino acid residues indicated by the Kabat numbering (that is, one or more positions according to the Kabat numbering may not be occupied in the actual sequence, or the actual sequence may contain more amino acid residues than the number allowed for by the Kabat numbering).
- the numbering according to Kabat may or may not correspond to the actual numbering of the amino acid residues in the actual sequence.
- position 1 according to the Kabat numbering corresponds to the start of FRl and vice versa
- position 36 according to the Kabat numbering corresponds to the start of FR2 and vice versa
- position 66 according to the Kabat numbering corresponds to the start of FR3 and vice versa
- position 103 according to the Kabat numbering corresponds to the start of FR4 and vice versa.
- the invention relates to polypeptides or other chemical entities that comprise or essentially consist of at least one (such as one, two or three) PDl binding moieties described herein.
- PDl binders e.g., an ISVD such as a Nanobody
- PDl binders can be fused to one or more other amino acid sequences, chemical entities or moieties.
- These other amino acid sequences, chemical entities or moieties can confer one or more desired properties to the resulting PDl binders of the invention and/or can alter the properties of the resulting PDl binders of the invention in a desired manner, for example to provide the resulting PDl binders of the invention with a desired biological and/or therapeutic activity (for example, to provide the resulting PDl binders of the invention with affinity and preferably potency against another therapeutically relevant target such that the resulting polypeptide becomes "bispecific" with respect to PDl and that other therapeutically relevant target such as CTLA4, LAG3, BTLA or CD27), to provide a desired half-life and/or to otherwise modify or improve pharmacokinetic and/or
- linkers such as a 9GS, 15GS or 35GS linker (any combination of 9, 15, 20 or 35 G and S amino acids such as, for example, GGGGSGGGS (9GS linker; SEQ ID NO: 125), GGGGS GGGGS GGGGS GGGGS (20GS linker; SEQ ID NO: 100) or
- GGGGSGGGGSGGGGSGGGGSGGGGSGGGGSGGGGS (35GS linker; SEQ ID NO: 58)) or (GGGS)n wherein n is 1, 2, 3 ,4, 5, 6, 7, 8, 9 or 10); and/or
- a PDl binder e.g., an ISVD such as a Nanobody
- a PDl binder e.g., an ISVD such as a Nanobody
- a PDl binder e.g., an ISVD such as a Nanobody
- a different epitope of PDl CD27, LAG3, CTLA4, BTLA, TIM3, ICOS, B7-H3, B7-H4, CD137, GITR, PD-L1, PD-L2, ILT1, ILT2 CEACAM1, CEACAM5, TIM3, TIGIT, VISTA, ILT3, ILT4, ILT5, ILT6, ILT7, ILT8, CD40, OX40, CD 137, KIR2DL1, KIR2DL2, KIR2DL3, KIR2DL4, KIR2DL5A, KIR2DL5B, KIR3DL1, KIR3DL2, KIR3DL3, KG2A,
- a PDl binder e.g
- binding domains or binding units that target the PD1 binder e.g., an ISVD such as a Nanobody
- a desired cell, tissue or organ such as a cancer cell
- binding domains or binding units that provide for increased specificity against PD1 (usually, these will be able to bind to PD1 but will generally by themselves essentially not be functional against PD1); and/or
- a binding domain, binding unit or other chemical entity that allows for the PD1 binder e.g., an ISVD such as a Nanobody
- an ISVD such as a Nanobody
- a desired cell for example, an internalizing anti-EGFR Nanobody as described in WO 05/044858
- a moiety that improves half-life such as a suitable poly ethylenegly col group (i.e. PEGylation) or an amino acid sequence that provides for increased half-life such as human serum albumin or a suitable fragment thereof (i.e. albumin fusion) or for example a serum albumin binding peptide as described in WO 2008/068280; and/or
- a payload such as a cytotoxic payload
- detectable label or tag such as a radiolabel or fluorescent label
- a tag that can help with immobilization, detection and/or purification of the PD1 binder e.g., an ISVD such as a Nanobody
- a HIS e.g., HHHHHH; SEQ ID NO: 93 or
- a tag that can be functionalized such as a C-terminal GGC or GGGC tag;
- PD1 binders e.g., an ISVD such as a Nanobody
- ISVD such as a Nanobody
- PD1 binder e.g., an ISVD such as a Nanobody
- a (preferably human) antibody such as an Fc part or a functional fragment thereof or one or more constant domains
- a Camelid heavy-chain only antibody such as one or more constant domains
- the present invention provides improved LAG3 binders, for example, improved anti- LAG3 ISVDs and more in particular improved LAG3 Nanobodies, e.g., 11B09 (LI IV, A14P, R41P, N43K, A62S, A74S, K83R, V89L); F0237611B09
- improved LAG3 binders for example, improved anti- LAG3 ISVDs and more in particular improved LAG3 Nanobodies, e.g., 11B09 (LI IV, A14P, R41P, N43K, A62S, A74S, K83R, V89L); F0237611B09
- LAG3 binders are any of the molecules described herein that bind to LAG3 (e.g., an ISVD such as a Nanobody) as well as any multivalent or multispecific binder (e.g., PD1/LAG3 binder) which includes such a molecule that is fused to another binder.
- LAG3 e.g., an ISVD such as a Nanobody
- any multivalent or multispecific binder e.g., PD1/LAG3 binder
- a LAG3 binder may include a LAG3 binding moiety fused to a moiety that binds to PDl, CD27, CTLA4, HSA, BTLA, TEVI3, ICOS, B7-H3, B7-H4, CD137, GITR, PD-L1, PD-L2, ILT1, ILT2 CEACAM1, CEACAM5, TIM3, TIGIT, VISTA, ILT3, ILT4, ILT5, ILT6, ILT7, ILT8, CD40, OX40, CD137, KIR2DL1, KIR2DL2, KIR2DL3, KIR2DL4, KTR2DL5A, KTR2DL5B, KTR3DL1, KIR3DL2, KTR3DL3, NKG2A, KG2C,
- LAG3 binder may be referred to as a LAG3 binding moiety if it is part of a larger molecule, e.g., a multivalent molecule, wherein the LAG3 binding moiety is fused to another binding moiety, such as F023700924 or F023700931.
- LAG3 binders of the present invention include polypeptides which are variants of polypeptides comprising the amino acid sequence of SEQ ID NO: 63 but which is mutated at position 1, 11, 14, 41 43, 62, 74, 83 and/or 89.
- the LAG3 binders of the invention preferably have the same combination of CDRs (i.e. CDR1, CDR2 and CDR3) as are present in 11B09 or in a binder comprising the sequence of 11B09 (SEQ ID NO: 63). See Table B-l .
- the present invention also includes LAG3 binders which are variants of 11B09 which comprise an amino acid sequence as set forth below in Table B-2 below.
- the scope of the present invention includes LAG3 binders that include CDR1, CDR2 and CDR3 of said varaints set forth below in Table B-2.
- the present invention includes PD1/LAG3 binders comprising a LAG3 binding moiety that includes CDRl, CDR2 and CDR3 or the amino acid sequence of 11B09 or of one of its varaints set forth below in Table B-2.
- Bivalent SO (sequence DVQLVESGGGWQPGGSLRLSCAASGRTFSDYVMGWFRQAPGKEREFVA optimized) 611B09 + ALB 11002 AISESGGRTHYADSVKGRFTI SRDNSKNTLYLQMNSLRPEDTALYYCAT
- the present invention includes embodiments wherein the LAG3 binder of the invention (e.g., in a PD1/LAG3 binder) includes one, two or three of the CDRs of a LAG3 binder set forth above in Table B-l or B-2 (e.g., SEQ ID NO: 63, 64, 95, 96 or 97) wherein each comprises 0, 1, 2, 3, 4, or 5 amino acid substitutions, e.g., conservative substitutions, and/or comprises 100, 99, 98, 97, 96 or 95% sequence identity relative to the CDR sequences set forth in Table B-l or B-2 wherein the LAG3 binder of the invention having such CDRs retains the ability to bind to LAG3.
- the first amino acid of a LAG3 binder of the present invention is E.
- the first amino acid of a LAG3 binder of the present invention is E or D.
- the present invention includes the LAG3 binder F023700656 (11B09 (EID); SEQ ID NO: 63 (EID)).
- residue 1 is a D.
- the present invention includes any LAG3 binder comprising the amino acid sequence of SEQ ID NO: 63, 64 or 127 (or having the LAG3 binder moiety of SEQ ID NO: 96 or 97) (as well as LAG3 binders having an EID or DIE mutation) or an amino acid sequence comprising 80% or more (e.g., 85%, 90%, 95%, 96%, 97%, 98% or 99%) amino acid sequence identity (i.e., comparing the full amino acid sequences) wherein the LAG3 binder retains the ability to bind to LAG3 and, optionally, includes an HSA binder.
- LAG3 binder comprising the amino acid sequence of SEQ ID NO: 63, 64 or 127 (or having the LAG3 binder moiety of SEQ ID NO: 96 or 97) (as well as LAG3 binders having an EID or DIE mutation) or an amino acid sequence comprising 80% or more (e.g., 85%, 90%, 95%, 9
- LAG3 binders such as LAG3 ISVDs (e.g., a Nanobodies), having CDRl, CDR2 and CDR3 of a binder comprising the amino acid sequence set forth in SEQ ID NO: 63, 64, 96, 97 or 127 (or a variant thereof as described herein), e.g., comprising the following CDRs:
- a degree of sequence identity with the amino acid sequence of SEQ ID NO: 63, 64, 96, 97 or 127 (in which any C-terminal extension that may be present as well as the CDRs are not taken into account for determining the degree of sequence identity) of at least 85%, preferably at least 90%, more preferably at least 95% (in which the CDRs, any C-terminal extension that may be present, as well as the mutations at positions 1, 11, 14, 41 43, 62, 74, 76, 83, 89, 100 and/or 105 are not taken into account for determining the degree of sequence identity);
- amino acid differences as defined herein, and not taking into account any of the mutations set forth herein at position(s) 1, 11, 14, 41 43, 62, 74, 76, 83, 89, 100 and/or 105 that may be present and not taking into account any C-terminal extension that may be present) with the amino acid sequence of SEQ ID NO: 63, 64, 96, 97 or 127 (in which said amino acid differences, if present, may be present in the frameworks and/or the CDRs but are preferably present only in the frameworks and not in the CDRs);
- a C-terminal extension as discussed herein, e.g., (X) n , in which n is 1 to 10, preferably 1 to 5, such as 1, 2, 3, 4 or 5 (and preferably 1 or 2, such as 1); and each X is an (preferably naturally occurring) amino acid residue that is independently chosen, and preferably independently chosen from the group consisting of alanine (A), glycine (G), valine (V), leucine (L) or isoleucine (I).
- the present invention also includes LAG3 binders fused to one or more half-life extenders, such as an ISVD that binds human serum albumin, e.g., ALB 11002.
- the present invention includes PD1 binders and LAG3 binders that may be fused in a single multivalent, multispecific molecule that binds to PD1 and LAG3 (a PD1/LAG3 binder) and, in an embodiment of the invention, such binders are linked to one or more half-life extenders that increases the half-life of the binders in the body of a subject.
- the half-life extender is an ISVD (e.g, a Nanobody) that specifically binds to human serum albumin (HSA), e.g., ALB 11002.
- the multispecific binder is F023700899; F023700931; F023701016; F023701017; F023700924; F023700969; F023700970; F023701163; F023701168; F023701173; F02370117 F023701176; 8; F023701161; F023701166; F023701171; F023701176; F023701162; F023701167; F023701172; or
- the PD1/LAG3 binder comprises
- a PD1 binder comprising CDR1, CDR2 and CDR3 of any of the PD1 binders set forth in Table A-l or A-2, optionally, each independently comprising 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acid substitutions (e.g., conservative mutations) or:
- a CDR1 comprising the amino acid sequence IHAMG (SEQ ID NO: 3) or GSIASIHAMG (SEQ ID NO: 6);
- a CDR2 comprising the amino acid sequence VITXSGGITYYADSVKG (SEQ ID NO: 4; wherein X is W or V, e.g., W) or VITXSGGITY (SEQ ID NO: 7; wherein X is W or V, e.g., W); and
- a CDR3 comprising the amino acid sequence DKHQSSXYDY (SEQ ID NO: 5, wherein X is W or F, e.g., W);
- LAG3 binder comprising CDR1, CDR2 and CDR3 of any of the LAG3 binders set forth in Table B-l or B-2, optionally, each independently comprising 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acid substitutions (e.g., conservative mutations) or :
- a CDR1 comprising the amino acid sequence GRTFSDYVMG (SEQ ID NO: 65);
- a CDR2 comprising the amino acid sequence AISESGGRTH (SEQ ID NO: 66);
- a CDR3 comprising the amino acid sequence TLLWWTSEYAPIKANDYDY (SEQ ID NO: 67), and, optionally, a half-life extender and/or a C-terminal extender, for example, an HSA binder as set forth herein and/or, optionally a C-terminal extender such as Alanine.
- the PDl binder is as set forth above under "PDl Binders”, e.g., comprising the amino acid sequence of SEQ ID NO: 57, 98, 99, 103, 104 or 105 (optionally wherein residue 1 is E or D).
- the LAG3 binder is as set forth above under "LAG3 Binders”, e.g., comprising the amino acid sequence of SEQ ID NO: 63, 64 or 95 (optionally wherein residue 1 is E or D).
- Multispecific binders may include a PDl and LAG3 and, optionally, an HSA binder as well as one or more binders that bind to an additional antigen such as, CD27, CTLA4, BTLA, TTM3, ICOS, B7-H3, B7-H4, CD137, GITR, PD-L1, PD-L2, ILT1, ILT2 CEACAM1,
- the PDl and/or LAG3 binders contain one or more further binding domains or binding units (e.g. a further essentially non-functional binding domain or binding unit against PDl and/or LAG3 that provides for increased specificity against PDl and/or LAG3, a binding domain or binding unit against a therapeutic target other than PDl and/or LAG3 (e.g., CTLA4, BTLA or CD27), a binding domain or binding unit against a target such as human serum albumin that provides for increased half-life, and/or a binding domain or binding unit that targets the PDl and/or LAG3 binder to a specific cell, tissue or organ and/or that allows for the PDl and/or LAG3 binder to be internalized into a cell), these other binding domains or binding units preferably comprise one or more ISVDs (e.g., Nanobodies), and more preferably are all ISVDs.
- ISVDs e.g., Nanobodies
- these one or more further binding domains or binding units can be one or more Nanobodies (including a VHH, a humanized VHH and/or a camelized VHs such as camelized human VHs), a (single domain) antibody is a VH domain or that is derived from a VH domain, a dAb that is or essentially consists of a VH domain or that is derived from a VH domain, or even a (single) domain antibody or a dAb that is or essentially consists of VL domain.
- these one or more binding domains or binding units when present, may comprise one or more Nanobodies, and more in particular are all Nanobodies.
- the ISVD (e.g., Nanobody) that binds a target other than PDl and/or LAG3 binds to another target such as HSA, CTLA-4, BTLA or CD27.
- a PD1 and/or LAG3 binder e.g., an ISVD such as a Nanobody
- the invention has an ISVD (e.g., Nanobody) at its C-terminal end (e.g., which C-terminal ISVD binds to PD1 and/or LAG3 or may for example be, if present in the polypeptide, a further essentially nonfunctional ISVD against PD1 and/or LAG3 that provides for increased specificity against PD1 and/or LAG3, an ISVD against a therapeutic target other than PD1 and/or LAG3, an ISVD against a target such as human serum albumin that provides for increased half-life, or an ISVD that targets the PD1 and/or LAG3 binder to
- C-terminal ISVD preferably has a C-terminal extension X(n) (e.g., -Ala), which C-terminal extension may be as described herein for the PD1 and/or LAG3 binders of the invention and/or as described in WO 12/175741 or PCT/EP2015/060643 (WO2015/173325).
- X(n) e.g., -Ala
- any further ISVDs e.g., Nanobodies
- any further ISVDs which one or more further ISVDs may, as mentioned, be a further essentially non-functional ISVD against PD1 and/or LAG3 that provides for increased specificity against PD1 and/or LAG3, an ISVD against a therapeutic target other than PD1 and/or LAG3, an ISVD against a target such as human serum albumin that provides for increased half-life, and/or an ISVD that targets the polypeptide of the invention to a specific cell, tissue or organ and/or that allows for the polypeptide of the invention to be internalized into a cell), and where such further ISVDs are Nanobodies or are ISVDs that are, or that essentially consist of and/or that are derived from VH sequences, then according to a preferred aspect of the invention said one or more (and preferably
- the PD1 and/or LAG3 binder When a PD1 and/or LAG3 binder is to have an increased half-life (i.e. compared to a monovalent binder of the invention that lacks a half-life extender such as ALB 11002), the PD1 and/or LAG3 binder preferably contains at least one (e.g., one) ISVD (e.g., a Nanobody) that provides for such increased half-life (e.g., ALB 11002).
- ISVD e.g., a Nanobody
- Such an ISVD is, in an embodiment of the invention, directed against a suitable serum protein such as transferrin or against (human) serum albumin.
- such an ISVD or Nanobody may be a (single) domain antibody or dAb against human serum albumin as described in for example EP 2 139 918, WO 201 1/006915, WO 2012/175400, WO 2014/111550 and may in particular be a serum albumin binding
- Nanobody as described in WO 2004/041865, WO 2006/122787, WO 2012/175400 or
- Particularly preferred serum albumin binding ISVDs are the Nanobody Alb-1 (see WO 2006/122787) or its humanized variants such as Alb-8 (WO 2006/122787, SEQ ID NO: 62), Alb-23 (WO 2012/175400, SEQ ID NO: 1) and other humanized (and preferably also sequence-optimized) variants of Alb-1 and/or variants of Alb-8 or Alb-23 (or more generally ISVDs that have essentially the same CDRs as Alb-1, Alb-8 and Alb-23).
- HSA binders any of the molecules, such as those described herein, that bind to HSA (e.g., an ISVD such as a Nanobody) as well as any multivalent or multispecific binder which includes such a molecule that is fused to another binder.
- HSA e.g., an ISVD such as a Nanobody
- An individual HSA binder may be referred to as a HSA binding moiety if it is part of a larger molecule, e.g., a multivalent molecule, wherein the HSA binding moiety is fused to another binding moiety.
- the half-life extender is an ISVD (e.g., Nanobody) that binds to human serum albumin, e.g. , ALB 11002 as summarized below in Table C.
- ISVD e.g., Nanobody
- the HSA binders of the invention preferably have the same combination of CDRs (i.e. CDR1, CDR2 and CDR3) as are present in ALB 11002 or comnprising the sequence of ALB 11002 (SEQ ID NO: 59). See Table C.
- the present invention also includes HSA binders which are variants of ALB 11002 which comprise an amino acid sequence as set forth below in Table C below.
- the scope of the present invention includes HSA binders that include CDR1, CDR2 and CDR3 of said varaints set forth below in Table C.
- the present invention includes PD1/LAG3 binders comprising an HSA binding moiety that includes CDRl, CDR2 and CDR3 or the amino acid sequence of ALB 11002 or of one of its varaints set forth below in Table C.
- ALB 11002 lacks the C-terminal Alanine.
- the HSA binder comprises the amino acid sequence set forth in SEQ ID NO: 59 but which comprises an E1D, VI 1L and/or an L93V mutation, e.g., comprising the amino acid sequence:
- the first amino acid of a HSA binder of the present invention is E. In an embodiment of the invention, the first amino acid of a HSA binder of the present invention is D.
- the present invention includes embodiments wherein one, two or three of the CDRs of a HSA binder each comprises 0, 1, 2, 3, 4, or 5 amino acid substitutions, e.g., conservative substitutions, and/or comprises 99, 98, 97, 96 or 95% sequence identity relative to the CDR sequences set forth in Table C, wherein the HSA binder having such CDRs retain the ability to bind to HSA.
- the half-life extender is an HSA ISVD (e.g., a
- Nanobody comprising:
- a degree of sequence identity with the amino acid sequence of SEQ ID NO: 59 (in which any C-terminal extension that may be present as well as the CDRs are not taken into account for determining the degree of sequence identity) of at least 85%, preferably at least 90%, more preferably at least 95% (in which the CDRs, any C-terminal extension that may be present are not taken into account for determining the degree of sequence identity);
- amino acid differences (not taking into account any C-terminal extension that may be present) with the amino acid sequence of SEQ ID NO: 59 (in which said amino acid differences, if present, may be present in the frameworks and/or the CDRs but are preferably present only in the frameworks and not in the CDRs);
- n 1 to 10
- X is an (preferably naturally occurring) amino acid residue that is independently chosen, and preferably independently chosen from the group consisting of alanine (A), glycine (G), valine (V), leucine (L) or isoleucine (I).
- Such a human serum albumin binding ISVD when present, may contain within its sequence one or more framework mutations that reduce binding by pre-existing antibodies.
- a serum albumin binding ISVD when such a serum albumin binding ISVD is a Nanobody or a (single) domain antibody that is, essentially consist of and/or is derived from a VH domain, the serum albumin binding ISVD may contain (a suitable combination of) amino acid residues/mutations at positions 1 1, 89, 1 10 and/or 1 12 that are as described in PCT/EP2015/060643 (WO2015/173325) and/or that essentially are as described herein for the PD1 binders of the invention.
- PCT/EP2015/060643 (WO2015/173325) describes a number of variants of Alb-1, Alb-8 and Alb- 23 that contain amino acid residues/mutations at positions 11, 89, 110 and/or 112 that reduce binding by pre-existing antibodies that can be used in the polypeptides of the invention.
- the serum albumin binding ISVD (and as a result, the PDl and/or LAG3 binder of the invention) preferably has a C-terminal extension X(n), which C- terminal extension may be as described herein for the PDl and/or LAG3 binders of the invention and/or as described in WO 12/175741 or PCT/EP2015/060643 (WO2015/173325).
- the C-terminal extension may be a single Alanine residue. It also preferably has mutations that reduce the binding of pre-existing antibodies, like (a suitable combination of) the amino acid residues/mutations at positions 11, 89, 110 and/or 112 described in PCT/EP2015/060643
- the resulting PDl and/or LAG3 binder of the invention when a PDl and/or LAG3 binder of the invention has increased half-life (e.g. through the presence of a half-life increasing ISVD (e.g., Nanobody) or any other suitable way of increasing half-life), the resulting PDl and/or LAG3 binder of the invention preferably has a half- life (as defined herein) that is at least 2 times, preferably at least 5 times, for example at least 10 times or more than 20 times, greater than the half-life of a PDl and/or LAG3 binder of the invention lacking the a half-life extender (as measured in either in man and/or a suitable animal model, such as mouse or cynomolgus monkey).
- a half-life extender as measured in either in man and/or a suitable animal model, such as mouse or cynomolgus monkey.
- a PDl and/or LAG3 binder of the invention preferably has a half-life (as defined herein) in human subjects of at least 1 day, preferably at least 3 days, more preferably at least 7 days, such as at least 10 days.
- PDl binders and LAG3 binders that are based on one or more ISVDs (e.g., Nanobodies) can have different "formats", i.e. essentially be monovalent, bivalent or trivalent, can be monospecific, bispecific, trispecific etc., and can be biparatopic (as defined herein and in for example WO2009/68625).
- a PDl binder or LAG3 binder of the invention can be: monovalent, i.e. comprising a single PDl or LAG3 binding moiety (e.g., an ISVD such as a Nanobody).
- a PDl binder or LAG3 binder of the invention when used in monovalent format, preferably has a C-terminal extension X(n) as further described herein.
- a PDl binder or LAG3 binder of the invention may also be half-life extended;
- such a PDl binder or LAG3 binder of the invention comprises two or more ISVDs (e-g-, Nanobodies) against PDl or against LAG3, respectively, which may be the same or different; and when different, may be directed against the same epitope of PDl or LAG3, or against different epitopes on PDl or LAG3 (in the latter case, so as to provide a biparatopic or multiparatopic PDl binder or LAG3 binder of the invention).
- ISVDs e-g-, Nanobodies
- Such a PDl binder or LAG3 binder of the invention may also be half-life extended;
- such a PDl binder of the invention will be directed against PDl and at least one other target such as, for example, CTLA-4, LAG-3, BTLA and/or CD27; e.g., comprising a PDl binding moiety and a CTLA4 binding moiety; a PDl binding moiety and a BTLA binding moiety; a PDl binding moiety and a LAG3 binding moiety (i.e., a PD1/LAG3 binder); or a PDl binding moiety, a LAG3 binding moiety and a
- said other target may for example be another therapeutically relevant target (i.e. other than PDl) so as to provide a PDl binder of the invention that is bispecific with regards to PDl and said other therapeutic target.
- Said other target may also be a target that provides for increased half-life (such as human serum albumin), so as to provide a PDl binder of the invention that has increased half-life.
- such other target may allow also for the PDl binder of the invention to be targeted to specific cells, tissues or organs or may allow for the PDl binder of the invention to be internalized into a cell. It is also possible to combine these approaches/ISVDs, for example to provide a PDl binder of the invention that is bispecific for PDl and for at least one other therapeutically relevant target and that is half-life extended.
- these PDl binders and LAG3 binders include one or more ISVDs (e.g., Nanobodies) other than a PDl binding moiety or LAG3 binding moiety
- at least one and preferably all of these other ISVDs will contain within its sequence one or more framework mutations that reduce binding by pre-existing antibodies (such as, in particular, a combination of amino acid residues/mutations at positions 1, 11, 14, 52a, 73, 74, 83, 89, 100a, 110 and/or 112 that is as described herein for the PDl binders and LAG3 binders of the invention and/or as generally described in PCT/EP2015/060643 (WO2015/173325)).
- ISVDs e.g., Nanobodies
- PDl binders or LAG3 binders of the invention when such PDl binders or LAG3 binders of the invention have a PDl binding moiety or LAG3 binding moiety, respectively, at their C-terminal end, then said C-terminal PDl binding moiety or LAG3 binding moiety (and as a result, the PDl binder or LAG3 binder of the invention) will preferably have a C-terminal extension X(n) as described herein.
- LAG3 binders of the invention when such PDl binders LAG3 binders of the invention have another ISVD at their C-terminal end ⁇ i.e.
- the PDl binder or LAG3 binder of the invention will preferably has a C-terminal extension X(n) as described herein and/or will contain within its sequence one or more framework mutations that reduce binding by pre-existing antibodies (again, as further described herein and in PCT/EP2015/060643 (WO2015/173325)).
- a PDl binder or LAG3 binder ⁇ e.g., an ISVD such as a Nanobody
- a PDl binder or LAG3 binder of the invention is intended for topical use ⁇ i.e. on the skin or in the eye) or is for example meant to have a (localized) therapeutic action somewhere in for example the GI tract ⁇ i.e. after oral administration or administration by suppository) or in the lungs ⁇ i.e. after administration by inhalation) or is otherwise meant to be directly applied to its intended place of action (for example, by direct injection)
- a PDl binder or LAG3 binder of the invention will usually not require half-life extension.
- a prolonged half-life for treatment of certain acute conditions or indications, it may be preferable not to have a prolonged half-life.
- PDl binders and or LAG3 binder of the invention are schematically represented in Table D-la and D-lb below, and each of these forms a further aspect of the invention.
- suitable polypeptides of the invention without half-life extension will be clear to the skilled person based on the disclosure herein.
- Table D-la Schematic Representation of Some PDl and/or LAG3 Binders of the Invention Without a Half-Life Extending ISVD.
Abstract
Description
Claims
Priority Applications (24)
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CR20180278A CR20180278A (en) | 2015-11-18 | 2016-11-17 | PD1 AND / OR LAG3 BINDERS |
CN201680079323.1A CN108473585B (en) | 2015-11-18 | 2016-11-17 | PD1 and/or LAG3 binding agents |
JP2018525608A JP6817302B2 (en) | 2015-11-18 | 2016-11-17 | PD1 and / or LAG3 binding material |
MYPI2018000773A MY189018A (en) | 2015-11-18 | 2016-11-17 | Pd1 and/or lag3 binders |
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EA201891165A EA201891165A1 (en) | 2015-11-18 | 2016-11-17 | MOLECULES BINDING PD1 AND / OR LAG3 |
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AU2016355570A AU2016355570B2 (en) | 2015-11-18 | 2016-11-17 | PD1 and/or LAG3 binders |
BR112018010084A BR112018010084A2 (en) | 2015-11-18 | 2016-11-17 | pd1 and / or lag3 binders |
EP16805655.4A EP3377531A2 (en) | 2015-11-18 | 2016-11-17 | Pd1 and/or lag3 binders |
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PH12018501080A PH12018501080A1 (en) | 2015-11-18 | 2018-05-18 | Pd1 and/or lag3 binders |
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DO2021000005A DOP2021000005A (en) | 2015-11-18 | 2021-01-08 | BINDING PROTEINS TO PD1 AND / OR LAG3 |
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