WO2017019846A1 - Pd-1-binding molecules and methods use thereof - Google Patents

Pd-1-binding molecules and methods use thereof Download PDF

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Publication number
WO2017019846A1
WO2017019846A1 PCT/US2016/044430 US2016044430W WO2017019846A1 WO 2017019846 A1 WO2017019846 A1 WO 2017019846A1 US 2016044430 W US2016044430 W US 2016044430W WO 2017019846 A1 WO2017019846 A1 WO 2017019846A1
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seq
domain
mab
amino acid
cdr
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PCT/US2016/044430
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English (en)
French (fr)
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WO2017019846A8 (en
Inventor
Kalpana SHAH
Douglas H. Smith
Ross La Motte-Mohs
Leslie S. Johnson
Paul A. Moore
Ezio Bonvini
Scott Koenig
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Macrogenics Inc
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Macrogenics Inc
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Priority to SI201631367T priority Critical patent/SI3328419T1/sl
Priority to CR20180062A priority patent/CR20180062A/es
Priority to CR20200423A priority patent/CR20200423A/es
Priority to MA42542A priority patent/MA42542B1/fr
Priority to IL287916A priority patent/IL287916B2/en
Priority to MX2018001227A priority patent/MX2018001227A/es
Priority to PE2023001364A priority patent/PE20231958A1/es
Priority to IL297090A priority patent/IL297090B2/en
Priority to EP24194716.7A priority patent/EP4450088A3/en
Priority to UAA201801414A priority patent/UA127372C2/uk
Priority to US15/748,458 priority patent/US10577422B2/en
Priority to IL290571A priority patent/IL290571B2/en
Priority to DK16831339.3T priority patent/DK3328419T3/da
Priority to CN201810940625.4A priority patent/CN108976300B/zh
Priority to MYPI2018000111A priority patent/MY188871A/en
Priority to NZ739493A priority patent/NZ739493B2/en
Priority to PL18199685T priority patent/PL3456346T3/pl
Priority to LTEPPCT/US2016/044430T priority patent/LT3328419T/lt
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Priority to MDE20180572T priority patent/MD3328419T2/ro
Priority to SM20210610T priority patent/SMT202100610T1/it
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Priority to PE2023001374A priority patent/PE20240111A1/es
Priority to AU2016298227A priority patent/AU2016298227B9/en
Priority to EP16831339.3A priority patent/EP3328419B1/en
Priority to CN202210614282.9A priority patent/CN114773475B/zh
Priority to CA2993948A priority patent/CA2993948A1/en
Priority to CR20220194A priority patent/CR20220194A/es
Priority to HRP20211645TT priority patent/HRP20211645T1/hr
Priority to ES16831339T priority patent/ES2898511T3/es
Priority to CN201680044392.9A priority patent/CN107847574B/zh
Priority to HK18107602.5A priority patent/HK1248106B/en
Priority to KR1020187005653A priority patent/KR102761886B1/ko
Priority to PL16831339T priority patent/PL3328419T3/pl
Priority to EP18199685.1A priority patent/EP3456346B1/en
Priority to RS20211320A priority patent/RS62568B1/sr
Priority to KR1020257002826A priority patent/KR20250020718A/ko
Priority to KR1020187023163A priority patent/KR102762075B1/ko
Priority to EP21191711.7A priority patent/EP3981792B1/en
Publication of WO2017019846A1 publication Critical patent/WO2017019846A1/en
Priority to ZA2018/00500A priority patent/ZA201800500B/en
Publication of WO2017019846A8 publication Critical patent/WO2017019846A8/en
Priority to CONC2018/0000867A priority patent/CO2018000867A2/es
Priority to IL257216A priority patent/IL257216B/en
Priority to PH12018500232A priority patent/PH12018500232A1/en
Anticipated expiration legal-status Critical
Priority to AU2018214151A priority patent/AU2018214151B2/en
Priority to ZA2018/07856A priority patent/ZA201807856B/en
Priority to AU2020200054A priority patent/AU2020200054B2/en
Priority to US16/752,464 priority patent/US11623959B2/en
Priority to CY20211100853T priority patent/CY1124634T1/el
Priority to CY20211100956T priority patent/CY1124723T1/el
Priority to AU2022200168A priority patent/AU2022200168B2/en
Priority to US18/114,109 priority patent/US20230357404A1/en
Priority to FR24C1033C priority patent/FR24C1033I2/fr
Priority to CY2024026C priority patent/CY2024026I1/el
Priority to LTPA2024525C priority patent/LTPA2024525I1/lt
Priority to FIC20240028C priority patent/FIC20240028I1/fi
Priority to NL301287C priority patent/NL301287I2/nl
Priority to AU2025202334A priority patent/AU2025202334A1/en
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Definitions

  • the present invention is directed to PD-1 binding molecules that comprise the PD- 1 -binding domain of selected anti-PD-1 antibodies capable of binding to both cynomolgus monkey PD-1 and to human PD-1 : PD-1 mAb 1, PD-1 mAb 2, PD-1 mAb 3, PD-1 mAb 4, PD- 1 mAb 5, PD-1 mAb 6, PD-1 mAb 7, PD-1 mAb 8, PD-1 mAb 9, PD-1 mAb 10, PD-1 mAb 11, PD-1 mAb 12, PD-1 mAb 13, PD-1 mAb 14, or PD-1 mAb 15.
  • the invention particularly concerns PD-1 binding molecules that are humanized or chimeric versions of such antibodies, or that comprise PD-1 binding-fragments of such anti-PD-1 antibodies (especially immunocongugates, diabodies, BiTEs, bispecific antibodies, etc.).
  • the invention particularly concerns such PD-1 -binding molecules that are additionally capable of binding an epitope of a molecule involved in regulating an immune check point that is present on the surface of an immune cell.
  • the present invention also pertains to methods of using such PD-l-binding molecules to detect PD-1 or to stimulate an immune response.
  • the present invention also pertains to methods of combination therapy in which a PD-l-binding molecule that comprises one or more PD-l-binding domain(s) of such selected anti-PD-1 antibodies is administered in combination with one or more additional molecules that are effective in stimulating an immune response and/or in combination with one or more additional molecules that specifically bind a cancer antigen.
  • the immune system of humans and other mammals is responsible for providing protection against infection and disease. Such protection is provided both by a humoral immune response and by a cell-mediated immune response.
  • the humoral response results in the production of antibodies and other biomolecules that are capable of recognizing and neutralizing foreign targets (antigens).
  • the cell-mediated immune response involves the activation of macrophages, Natural Killer cells (NK), and antigen specific cytotoxic T-lymphocytes by T-cells, and the release of various cytokines in response to the recognition of an antigen (Dong, C. et al. (2003) "Immune Regulation by Novel Costimulatory Molecules " Immunolog. Res. 28(l):39-48).
  • T-cells The ability of T-cells to optimally mediate an immune response against an antigen requires two distinct signaling interactions (Viglietta, V. et al. (2007) “Modulating Co- Stimulation " Neurotherapeutics 4:666-675; Korman, A.J. et al. (2007) “Checkpoint Blockade in Cancer Immunotherapy " Adv. Immunol. 90:297-339).
  • APC Antigen-Presenting Cells
  • TCR T-Cell Receptor
  • a series of costimulatory and inhibitory signals mediated through interactions between the APC and distinct T-cell surface molecules, triggers first the activation and proliferation of the T-cells and ultimately their inhibition.
  • the first signal confers specificity to the immune response whereas the second signal serves to determine the nature, magnitude and duration of the response.
  • the immune system is tightly controlled by costimulatory and co-inhibitory ligands and receptors. These molecules provide the second signal for T-cell activation and provide a balanced network of positive and negative signals to maximize immune responses against infection while limiting immunity to self (Wang, L. et al. (March 7, 2011) "VISTA, A Novel Mouse Ig Superfamily Ligand That Negatively Regulates T-Cell Responses " J. Exp. Med. 10.1084/jem.20100619: l-16; Lepenies, B. et al. (2008) “The Role Of Negative Costimulators During Parasitic Infections " Endocrine, Metabolic & Immune Disorders - Drug Targets 8:279-288).
  • Binding of B7.1 or of B7.2 to CD28 stimulates T-cell activation; binding of B7.1 or B7.2 to CTLA-4 inhibits such activation (Dong, C. et al. (2003) "Immune Regulation by Novel Costimulatory Molecules " Immunolog. Res. 28(l):39-48; Lindley, P.S. etal. (2009) “The Clinical Utility Of Inhibiting CD28-Mediated Costimulation " Immunol. Rev. 229:307-321; Greenwald, R.J. et al. (2005) "The B7 Family Revisited” Ann. Rev. Immunol. 23 :515-548).
  • CD28 is constitutively expressed on the surface of T-cell s (Gross, J., et al. (1992) "Identification And Distribution Of The Costimulatory Receptor CD28 In The Mouse “ J. Immunol. 149:380-388), whereas CTLA-4 expression is rapidly upregulated following T-cell activation (Linsley, P. et al. (1996) "Intracellular Trafficking Of CTLA4 And Focal Localization Towards Sites Of TCR Engagement " Immunity 4:535-543). Since CTLA-4 is the higher affinity receptor (Sharpe, A.H. et al. (2002) “The B7- CD28 Superfamily " Nature Rev. Immunol. 2: 116-126), binding first initiates T-cell proliferation (via CD28) and then inhibits it (via nascent expression of CTLA-4), thereby dampening the effect when proliferation is no longer needed.
  • B7 Superfamily a set of related B7 molecules (the "B7 Superfamily") (Coyle, A.J. et al. (2001) "The Expanding B7 Superfamily: Increasing Complexity In Costimulatory Signals Regulating T-Cell Function " Nature Immunol. 2(3):203-209; Sharpe, A.H. et al. (2002) "The B7-CD28 Superfamily " Nature Rev. Immunol. 2: 116-126; Greenwald, R.J. et al. (2005) "The B7 Family Revisited " Ann. Rev. Immunol. 23 :515-548; Collins, M. et al.
  • B7.1 CD80
  • B7.2 CD86
  • IVS-L inducible co- stimulator ligand
  • PD-L1 programmed death-1 ligand
  • PD-L2 programmed death-2 ligand
  • B7-H3 B7-H4 and B7-H6
  • PD-1 Programmed Death-1
  • CD279 is an approximately 31 kD type I membrane protein member of the extended CD28/CTLA-4 family of T-cell regulators that broadly negatively regulates immune responses
  • PD-1 is expressed on activated T-cells, B-cells, and monocytes (Agata, Y. et al. (1996) "Expression Of The PD-1 Antigen On The Surface Of Stimulated Mouse T And B Lymphocytes ,” Int. Immunol. 8(5):765-772; Yamazaki, T. et al. (2002) “Expression Of Programmed Death 1 Ligands By Murine T-Cells And APC “ J. Immunol. 169:5538-5545) and at low levels in natural killer (NK) T-cells (Nishimura, H. et al.
  • the extracellular region of PD-1 consists of a single immunoglobulin (Ig)V domain with 23% identity to the equivalent domain in CTLA-4 (Martin-Orozco, N. et al. (2007) "Inhibitory Costimulation And Anti-Tumor Immunity " Semin. Cancer Biol. 17(4):288-298).
  • the extracellular IgV domain is followed by a transmembrane region and an intracellular tail.
  • the intracellular tail contains two phosphorylation sites located in an immunoreceptor tyrosine- based inhibitory motif and an immunoreceptor tyrosine-based switch motif, which suggests that PD-1 negatively regulates TCR signals (Ishida, Y. et al.
  • PD-1 mediates its inhibition of the immune system by binding to B7-H1 and B7-DC (Flies, D.B. et al. (2007) "The New B7s: Playing a Pivotal Role in Tumor Immunity " J. Immunother. 30(3):251-260; United States Patents Nos. 6,803, 192; 7,794,710; United States Patent Application Publication Nos. 2005/0059051; 2009/0055944; 2009/0274666; 2009/0313687; PCT Publication Nos. WO 01/39722; WO 02/086083).
  • B7-H1 and B7-DC are broadly expressed on the surfaces of human and murine tissues, such as heart, placenta, muscle, fetal liver, spleen, lymph nodes, and thymus as well as murine liver, lung, kidney, islets cells of the pancreas and small intestine (Martin-Orozco, N. et al. (2007) “Inhibitory Costimulation And Anti-Tumor Immunity " Semin. Cancer Biol. 17(4):288-298).
  • B7-H1 protein expression has been found in human endothelial cells (Chen, Y. et al. (2005) "Expression ofB7-Hl in Inflammatory Renal Tubular Epithelial Cells " Nephron.
  • the adaptive immune system can be a potent defense mechanism against cancer and disease, it is often hampered by immune suppressive mechanisms in the tumor microenvironment, such as the expression of PD-1. Furthermore, co-inhibitory molecules expressed by tumor cells, immune cells, and stromal cells in the tumor milieu can dominantly attenuate T-cell responses against cancer cells. Thus, a need remains for potent PD-1 -binding molecules. In particular, a need exists for potent PD-1 -binding molecules having a desirable binding kinetic profile and that antagonize the PD-l/PD-Ll axis by blocking the PD-l/PD-Ll interaction, which could provide improved therapeutic value to patients suffering from cancer or other diseases and conditions. The present invention is directed to these and other goals.
  • the present invention is directed to PD-1 binding molecules that comprise the PD- 1 -binding domain of selected anti-PD-1 antibodies capable of binding to both cynomolgus monkey PD-1 and to human PD-1 : PD-1 mAb 1, PD-1 mAb 2, PD-1 mAb 3, PD-1 mAb 4, PD- 1 mAb 5, PD-1 mAb 6, PD-1 mAb 7, PD-1 mAb 8, PD-1 mAb 9, PD-1 mAb 10, PD-1 mAb 11, PD-1 mAb 12, PD-1 mAb 13, PD-1 mAb 14, or PD-1 mAb 15.
  • the invention particularly concerns PD-1 binding molecules that are humanized or chimeric versions of such antibodies, or that comprise PD-1 binding-fragments of such anti-PD-1 antibodies (especially immunocongugates, diabodies, BiTEs, bispecific antibodies, etc.).
  • the invention particularly concerns such PD-1 -binding molecules that are additionally capable of binding an epitope of a molecule involved in regulating an immune check point that is present on the surface of an immune cell.
  • the present invention also pertains to methods of using such PD-l-binding molecules to detect PD-1 or to stimulate an immune response.
  • the present invention also pertains to methods of combination therapy in which a PD-l-binding molecule that comprises one or more PD-l-binding domain(s) of such selected anti-PD-1 antibodies is administered in combination with one or more additional molecules that are effective in stimulating an immune response and/or in combination with one or more additional molecules that specifically bind a cancer antigen.
  • the invention provides an anti-human PD-1 -binding molecule that comprises the three Heavy Chain CDR Domains, CDRHI , CDRH2 and CDRH3 and the three Light Chain CDR Domains, CDRL I , CDRL2, and CDR L 3, wherein:
  • Heavy Chain CDRs of PD-1 mAb 1 and respectively have the amino acid sequences: SEQ ID NO:71, SEQ ID NO:72, and SEQ ID NO:73;
  • CDRL I Domain CDRL2 Domain
  • CDRL3 Domain are the Light Chain CDRs of PD-1 mAb 1, and respectively have the amino acid sequences: SEQ ID NO:76, SEQ ID NO:77, and SEQ ID NO:78; or
  • Heavy Chain CDRs of PD-1 mAb 2 and respectively have the amino acid sequences: SEQ ID NO:85, SEQ ID NO:86, and SEQ ID NO:87; and
  • CDRLI Domain CDRL2 Domain
  • CDRL3 Domain are the Light Chain CDRs of PD-1 mAb 2, and, respectively have the amino acid sequences: SEQ ID NO:90, SEQ ID NO:91, and SEQ ID NO:92; or
  • Heavy Chain CDRs of PD-1 mAb 3 have the amino acid sequences: SEQ ID NO:99, SEQ ID NO: 100, and SEQ ID NO:101; and
  • CDRL I Domain CDRL2 Domain
  • CDRL3 Domain are the Light Chain CDRs of PD-1 mAb 3, and, respectively have the amino acid sequences: SEQ ID NO:104, SEQ ID NO:105, and SEQ ID NO:106; or
  • Heavy Chain CDRs of PD-1 mAb 4 and respectively have the amino acid sequences: SEQ ID NO:109, SEQ ID NO:110, and SEQ ID NO:lll; and
  • CDRL I Domain, CDRL2 Domain, and CDRL3 Domain are the Light Chain CDRs of PD-1 mAb 4, and, respectively have the amino acid sequences: SEQ ID NO:114, SEQ ID NO:115, and SEQ ID NO:116; the CDRHI Domain, CDRH2 Domain, and CDRH3 Domain are the Heavy Chain CDRs of PD-1 mAb 5, and respectively have the amino acid sequences: SEQ ID NO:119, SEQ ID NO:120, and SEQ ID NO: 121; and
  • CDRL I Domain, CDRL2 Domain, and CDRL3 Domain are the Light Chain CDRs of PD-1 mAb 5, and, respectively have the amino acid sequences: SEQ ID NO:124, SEQ ID NO:125, and SEQ ID NO:126; the CDRHI Domain, CDRH2 Domain, and CDRH3 Domain are the Heavy Chain CDRs of PD-1 mAb 6, and respectively have the amino acid sequences: SEQ ID NO:129, SEQ ID NO:130, and SEQ ID NO: 131; and
  • CDRL I Domain, CDRL2 Domain, and CDRL3 Domain are the Light Chain CDRs of PD-1 mAb 6, and, respectively have the amino acid sequences: SEQ ID NO:134, SEQ ID NO:135, and SEQ ID NO:136; the CDRHI Domain, CDRH2 Domain, and CDRH3 Domain are the Heavy Chain CDRs of PD-1 mAb 7, and respectively have the amino acid sequences: SEQ ID NO:139, SEQ ID NO:140, and SEQ ID NO:141; and
  • CDRL I Domain, CDRL2 Domain, and CDRL3 Domain are the Light Chain CDRs of PD-1 mAb 7, and, respectively have the amino acid sequences: SEQ ID NO:144, SEQ ID NO:145, and SEQ ID NO:146; the CDRHI Domain, CDRH2 Domain, and CDRH3 Domain are the Heavy Chain CDRs of PD-1 mAb 8, and respectively have the amino acid sequences: SEQ ID NO:161, SEQ ID NO:162, and SEQ ID NO: 163; and
  • CDRL I Domain, CDRL2 Domain, and CDRL3 Domain are the Light Chain CDRs of PD-1 mAb 8, and, respectively have the amino acid sequences: SEQ ID NO:166, SEQ ID NO:167, and SEQ ID NO:168; the CDRHI Domain, CDRH2 Domain, and CDRH3 Domain are the Heavy Chain CDRs of PD-1 mAb 9, and respectively have the amino acid sequences: SEQ ID NO:171, SEQ ID NO:172, and SEQ ID NO: 173; and
  • CDRL I Domain, CDRL2 Domain, and CDRL3 Domain are the Light Chain CDRs of PD-1 mAb 9, and, respectively have the amino acid sequences: SEQ ID NO:176, SEQ ID NO:177, and SEQ ID NO:178; the CDRHI Domain, CDRH2 Domain, and CDRH3 Domain are the Heavy Chain CDRs of PD-1 mAb 10, and respectively have the amino acid sequences: SEQ ID NO:192, SEQ ID NO:193, and SEQ ID NO: 194; and
  • CDRL I Domain, CDRL2 Domain, and CDRL3 Domain are the Light Chain CDRs of PD-1 mAb 10, and, respectively have the amino acid sequences: SEQ ID NO:197, SEQ ID NO:198, and SEQ ID NO:199; the CDRHI Domain, CDRH2 Domain, and CDRH3 Domain are the Heavy Chain CDRs of PD-1 mAb 11, and respectively have the amino acid sequences: SEQ ID NO:202, SEQ ID NO:203, and SEQ ID NO:204; and
  • CDRL I Domain, CDRL2 Domain, and CDRL3 Domain are the Light Chain CDRs of PD-1 mAb 11, and, respectively have the amino acid sequences: SEQ ID NO:207, SEQ ID NO:208, and SEQ ID NO:209; the CDRHI Domain, CDRH2 Domain, and CDRH3 Domain are the Heavy Chain CDRs of PD-1 mAb 12, and respectively have the amino acid sequences: SEQ ID NO:212, SEQ ID NO:213, and SEQ ID NO:214; and
  • CDRL I Domain, CDRL2 Domain, and CDRL3 Domain are the Light Chain CDRs of PD-1 mAb 12, and, respectively have the amino acid sequences: SEQ ID NO:217, SEQ ID NO:218, and SEQ ID NO:219 the CDRHI Domain, CDRH2 Domain, and CDRH3 Domain are the Heavy Chain CDRs of PD-1 mAb 13, and respectively have the amino acid sequences: SEQ ID NO:222, SEQ ID NO:223, and SEQ ID NO:224; and
  • CDRL I Domain, CDRL2 Domain, and CDRL3 Domain are the Light Chain CDRs of PD-1 mAb 13, and, respectively have the amino acid sequences: SEQ ID NO:227, SEQ ID NO:228, and SEQ ID NO:229; the CDRHI Domain, CDRH2 Domain, and CDRH3 Domain are the Heavy Chain CDRs of PD-1 mAb 14, and respectively have the amino acid sequences: SEQ ID NO:232, SEQ ID NO:233, and SEQ ID NO:234; and
  • CDRL I Domain, CDRL2 Domain, and CDRL3 Domain are the Light Chain CDRs of PD-1 mAb 14, and, respectively have the amino acid sequences: SEQ ID NO:237, SEQ ID NO:238, and SEQ ID NO:239; the CDRHI Domain, CDRH2 Domain, and CDRH3 Domain are the Heavy Chain CDRs of PD-1 mAb 15, and respectively have the amino acid sequences: SEQ ID NO:242, SEQ ID NO:243, and SEQ ID NO:244; and
  • CDRL I Domain, CDRL2 Domain, and CDRL3 Domain are the Light Chain CDRs of PD-1 mAb 15, and, respectively have the amino acid sequences: SEQ ID NO:247, SEQ ID NO:248, and SEQ ID NO:249;
  • the CDRHI Domain, CDRH2 Domain, and CDRH3 Domain are the Heavy Chain CDRs of hPD-1 mAb 7(1.2), and respectively have the amino acid sequences: SEQ ID NO:139, SEQ ID NO:140, and SEQ ID NO: 141;
  • CDRL I Domain, CDRL2 Domain, and CDRL3 Domain are the Light Chain CDRs of hPD-1 mAb 7(1.2), and, respectively have the amino acid sequences: SEQ ID NO:157, SEQ ID NO:145, and SEQ ID NO:146; the CDRHI Domain, CDRH2 Domain, and CDRH3 Domain are the Heavy Chain CDRs of hPD-1 mAb 7(1.3), and respectively have the amino acid sequences: SEQ ID NO:139, SEQ ID NO:140, and SEQ ID NO: 141; and
  • CDRL I Domain CDRL2 Domain
  • CDRL3 Domain are the Light Chain CDRs of hPD- 1 mAb 7(1.3), and, respectively have the amino acid sequences: SEQ ID NO:157, SEQ ID NO:158, and SEQ ID NO:145;
  • CDRL I Domain CDRL2 Domain
  • CDRL3 Domain are the Light Chain CDRs of hPD- 1 mAb 9(2.2), and, respectively have the amino acid sequences: SEQ ID NO:188, SEQ ID NO:189, and SEQ ID NO:178
  • the invention further concerns the embodiments of all such anti-human PD- 1 - binding molecules wherein the molecule is an antibody, and especially wherein the molecule is a chimeric antibody or a humanized antibody.
  • the invention further concerns the embodiments of such anti-human PD- 1 -binding molecules wherein the Heavy Chain Variable Domain has the amino acid sequence of SEQ ID NO:79, SEQ ID NO:93, SEQ ID NO:147, SEQ ID NO:149, SEQ ID NO:179, SEQ ID NO: 181, or SEQ ID NO:250
  • the invention further concerns the embodiments of such anti-human PD- 1 -binding molecules wherein the Light Chain Variable Domain has the amino acid sequence of SEQ ID NO:81, SEQ ID NO:95, SEQ ID NO:151, SEQ ID NO:153, SEQ ID NO:155, SEQ ID NO:184, SEQ ID NO:186, or SEQ ID NO:251
  • the invention further concerns the embodiment wherein the anti -human PD- 1 - binding molecule is a bispecific binding molecule, capable of simultaneously binding to human PD- 1 and to a second epitope, and particularly concerns the embodiment wherein the second epitope is an epitope of a molecule involved in regulating an immune check point present on the surface of an immune cell (especially wherein the second epitope is an epitope of B7-H3, B7-H4, BTLA, CD40, CD40L, CD47, CD70, CD80, CD86, CD94, CD 137, CD137L, CD226, CTLA-4, Galectin-9, GITR, GITRL, HHLA2, ICOS, ICOSL, KIR, LAG-3, LIGHT, MHC class I or II, KG2a, NKG2d, OX40, OX40L, PD1H, PD-1, PD-L1, PD-L2, PVR, SIRPa, TCR, TIGIT, TIM-3
  • the invention further concerns the embodiments wherein the anti-human PD-1- binding molecule is a bispecific molecule comprising a LAG-3 epitope-binding site, particularly wherein the LAG-3 epitope-binding site comprises:
  • Variable Heavy Chain of LAG-3 mAb 1 having the amino acid sequences: SEQ ID NO:42, SEQ ID NO:43, and SEQ ID NO:44, respectively;
  • Variable Heavy Chain of hLAG-3 mAb 1 VH1 having the amino acid sequences: SEQ ID NO:42, SEQ ID NO:43, and SEQ ID NO:44, respectively;
  • Variable Heavy Chain of LAG-3 mAb 6 having the amino acid sequences: SEQ ID NO:57, SEQ ID NO:58, and SEQ ID NO:59, respectively;
  • Variable Heavy Chain of hLAG-3 mAb 6 VH1 having the amino acid sequences: SEQ ID NO:57, SEQ ID NO:58, and SEQ ID NO:59, respectively;
  • the invention further concerns the embodiment of such anti-human PD-1 -binding molecules wherein the molecule is a diabody, and especially, wherein the diabody is a covalently bonded complex that comprises two, or three, or four, or five polypeptide chains.
  • the invention further concerns the embodiment of such anti-human PD-1 -binding molecules wherein the molecule is a trivalent binding molecule, and especially wherein the trivalent binding molecule is a covalently bonded complex that comprises three, four, five or more than five polypeptide chains.
  • the invention additionally concerns the embodiment of such anti- human PD-1 -binding molecules in which the molecule comprises an Fc Region.
  • the invention additionally concerns the embodiment of such anti-human PD-1 -binding molecules in which the molecule comprises an Albumin-Binding Domain, and especially a deimmunized Albumin- Binding Domain.
  • the invention further concerns the embodiments of all such anti-human PD-1- binding molecules wherein the molecule comprises an Fc Region, and wherein the Fc Region is a variant Fc Region that comprises one or more amino acid modifications that reduces the affinity of the variant Fc Region for an FcyR and/or enhances the serum half-life, and more particularly, wherein the modifications comprise at least one amino acid substitution selected from the group consisting of:
  • the invention further concerns the embodiments in which any of the above- described PD-l-binding molecules is used to stimulate a T-cell mediate immune response.
  • the invention additionally concerns the embodiments in which any of the above-described PD-l- binding molecules is used in the treatment of a disease or condition associated with a suppressed immune system, especially cancer or an infection.
  • the invention particularly concerns such use in the treatment or diagnosis or prognosis of cancer, wherein the cancer is characterized by the presence of a cancer cell selected from the group consisting of a cell of: an adrenal gland tumor, an AIDS-associated cancer, an alveolar soft part sarcoma, an astrocytic tumor, bladder cancer, bone cancer, a brain and spinal cord cancer, a metastatic brain tumor, a breast cancer, a carotid body tumors, a cervical cancer, a chondrosarcoma, a chordoma, a chromophobe renal cell carcinoma, a clear cell carcinoma, a colon cancer, a colorectal cancer, a cutaneous benign fibrous histiocytoma, a desmoplastic small round cell tumor, an ependymoma, a Ewing's tumor, an extraskeletal myxoid chondrosarcoma, a fibrogenesis imperfecta ossium, a fibrous dysplasia of the group consisting
  • the invention particularly concerns such use in the treatment or diagnosis or prognosis of cancer, wherein the cancer is colorectal cancer, hepatocellular carcinoma, glioma, kidney cancer, breast cancer, multiple myeloma, bladder cancer, neuroblastoma; sarcoma, non- Hodgkin's lymphoma, non-small cell lung cancer, ovarian cancer, pancreatic cancer, a rectal cancer, acute myeloid leukemia (AML), chronic myelogenous leukemia (CML), acute B lymphoblastic leukemia (B-ALL), chronic lymphocytic leukemia (CLL), hairy cell leukemia (HCL), blastic plasmacytoid dendritic cell neoplasm (BPDCN), non-Hodgkin's lymphomas (NHL), including mantel cell leukemia (MCL), and small lymphocytic lymphoma (SLL), Hodgkin's lymphoma, systemic mastocytosis, or
  • the invention further concerns the embodiments in which any of the above- described PD-l-binding molecules is detectably labeled and is used in the detection of PD-1.
  • Figure 1 provides a schematic of a representative covalently bonded diabody having two epitope-binding sites composed of two polypeptide chains, each having an E-coil or K-coil Heterodimer-Promoting Domain.
  • a cysteine residue may be present in a linker and/or in the Heterodimer-Promoting Domain as shown in Figure 3B.
  • VL and VH Domains that recognize the same epitope are shown using the same shading or fill pattern.
  • Figure 2 provides a schematic of a representative covalently bonded diabody molecule having two epitope-binding sites composed of two polypeptide chains, each having a CH2 and CH3 Domain, such that the associated chains form all or part of an Fc Region. VL and VH Domains that recognize the same epitope are shown using the same shading or fill pattern.
  • Figures 3A-3C provide schematics showing representative tetravalent diabodies having four epitope-binding sites composed of two pairs of polypeptide chains (i.e., four polypeptide chains in all).
  • One polypeptide of each pair possesses a CH2 and CH3 Domain, such that the associated chains form all or part of an Fc Region.
  • VL and VH Domains that recognize the same epitope are shown using the same shading or fill pattern.
  • the two pairs of polypeptide chains may be same.
  • the resulting molecule possesses four epitope-binding sites and is bispecific and bivalent with respect to each bound epitope.
  • the resulting molecule possesses four epitope-binding sites and is monospecific and tetravalent with respect to a single epitope.
  • the two pairs of polypeptides may be different.
  • the resulting molecule possesses four epitope-binding sites and is tetraspecific and monovalent with respect to each bound epitope.
  • Figure 3A shows an Fc diabody which contains a peptide Heterodimer-Promoting Domain comprising a cysteine residue.
  • Figure 3B shows an Fc Region-containing diabody, which contains E-coil and K-coil Heterodimer-Promoting Domains comprising a cysteine residue and a linker (with an optional cysteine residue).
  • Figure 3C shows an Fc-Region-Containing diabody, which contains antibody CHI and CL domains.
  • Figures 4A and 4B provide schematics of a representative covalently bonded diabody molecule having two epitope-binding sites composed of three polypeptide chains. Two of the polypeptide chains possess a CH2 and CH3 Domain, such that the associated chains form all or part of an Fc Region.
  • the polypeptide chains comprising the VL and VH Domain further comprise a Heterodimer-Promoting Domain. VL and VH Domains that recognize the same epitope are shown using the same shading or fill pattern.
  • Figure 5 provides the schematics of a representative covalently bonded diabody molecule having four epitope-binding sites composed of five polypeptide chains. Two of the polypeptide chains possess a CH2 and CH3 Domain, such that the associated chains form an Fc Region that comprises all or part of an Fc Region.
  • the polypeptide chains comprising the linked VL and VH Domains further comprise a Heterodimer-Promoting Domain. VL and VH Domains that recognize the same epitope are shown using the same shading or fill pattern.
  • Figures 6A-6F provide schematics of representative Fc Region-containing trivalent binding molecules having three epitope-binding sites.
  • Figures 6A and 6B respectively, illustrate schematically the domains of trivalent binding molecules comprising two diabody- type binding domains and a Fab-type binding domain having different domain orientations in which the diabody-type binding domains are N-terminal or C-terminal to an Fc Region.
  • the molecules in Figures 6A and 6B comprise four chains.
  • Figures 6C and 6D respectively, illustrate schematically the domains of trivalent binding molecules comprising two diabody- type binding domains N-terminal to an Fc Region, and a Fab-type binding domain in which the light chain and heavy chain are inked via a polypeptide spacer, or an scFv-type binding domain.
  • the trivalent binding molecules in Figures 6E and 6F respectively illustrate schematically the domains of trivalent binding molecules comprising two diabody-type binding domains C- terminal to an Fc Region, and a linked Fab-type binding domain, or an scFv-type binding domain in which the diabody-type binding domains are.
  • the trivalent binding molecules in Figures 6C-6F comprise three chains. VL and VH Domains that recognize the same epitope are shown using the same shading or fill pattern.
  • Figures 7A-7D shows that the anti-PD-1 antibodies PD-1 mAb 1-15 bind to human PD-1. Binding curves for binding to shPD-l-His are shown in Figure 7A (PD-1 mAb 1, PD- 1 mAb 2, PD-1 mAb 4 and PD-1 mAb 9), Figure 7B (PD-1 mAb 5, PD-1 mAb 6, and PD-1 mAb 7), and Figure 7C (PD-1 mAb 3, PD-1 mAb 8, PD-1 mAb 10, PD-1 mAb 11, PD-1 mAb 12, PD-1 mAb 13, PD-1 mAb 14, and PD-1 mAb 15).
  • Figure 7A PD-1 mAb 1, PD- 1 mAb 2, PD-1 mAb 4 and PD-1 mAb 9
  • Figure 7B PD-1 mAb 5, PD-1 mAb 6, and PD-1 mAb 7
  • Figure 7C PD-1 mAb 3, PD-1 mAb 8, PD-1
  • Binding curves for binding to shPD-1- human Fc are shown in Figure 7D (PD-1 mAb 3, PD-1 mAb 8, PD-1 mAb 10, PD-1 mAb 11, PD-1 mAb 12, PD-1 mAb 13, PD-1 mAb 14, and PD-1 mAb 15).
  • Figures 8A-8C shows that the anti-PD-1 antibodies PD-1 mAb 1-15 bind to cynomolgus monkey PD-1. Binding curves for binding to scynoPD-l-hFc are shown in Figure 8A (PD-1 mAb 1, PD-1 mAb 2, PD-1 mAb 4, PD-1 mAb 5, PD-1 mAb 6, PD-1 mAb 7), Figure 8B (PD-1 mAb 9), and Figure 8C (PD-1 mAb 3, PD-1 mAb 8, PD-1 mAb 10, PD-1 mAb 11, PD-1 mAb 12, PD-1 mAb 13, PD-1 mAb 14, and PD-1 mAb 15).
  • Figures 9A-9D show the ability of the anti-PD-1 antibodies PD-1 mAb 1-15 to block the binding of human PD-Ll to human PD-1. Inhibition curves are shown in Figure 9A (PD-1 mAb 1, PD-1 mAb 2, PD-1 mAb 3, PD-1 mAb 15, and PD-1 mAb A), Figure 9B (PD- 1 mAb 4), Figure 9C (PD-1 mAb 5, PD-1 mAb 6, PD-1 mAb 7, and PD-1 mAb A), and Figure 9D (PD-1 mAb 3, PD-1 mAb 8, PD-1 mAb 10, PD-1 mAb 11, PD-1 mAb 12, PD-1 mAb 13, PD-1 mAb 14, PD-1 mAb 15, and PD-1 mAb A).
  • Figures 10A-10B show the tissue specificity of the anti -human PD-1 antibody PD- 1 mAb 7.
  • Figure 10A shows histological stains of normal colon (Panels i and vii), liver (Panels ii and viii), lung (Panels iii and ix), pancreas (Panels iv and x), kidney (Panels v and xi) and heart (Panels vi and xii) tissue.
  • Figure 10A, Panels i-vi show the results of tissue incubated with labeled PD-1 mAb 7 (0.313 ⁇ g/mL).
  • Figure 10A Panels vii-xii show the results of tissue incubated with labeled isotype control mAb (0.314 ⁇ g/mL).
  • Figure 10B shows histological stains of skin (Panels i and iv), tonsils (Panels ii and v), and NSO cells expressing PD-1 (Panels iii and vi).
  • Figure 10B Panels i-iii show the results of tissue incubated with labeled PD-1 mAb 7 (0.313 ⁇ g/mL).
  • Figure 11 shows the binding profiles of humanized anti-human PD-1 antibodies hPD-1 mAb 2, hPD-1 mAb 7(1.1), hPD-1 mAb 7(1.2), hPD-1 mAb 9(1.1), and the reference anti-PD-1 antibodies PD-1 mAb A and PD-1 mAb B having IgGl (AA) or IgG4 (P) for binding to cell surface PD-1.
  • Figures 12A-12B show the ability of humanized anti-PD antibodies hPD-1 mAb 2, hPD-1 mAb 7(1.1), hPD-1 mAb 7(1.2), hPD-1 mAb 9(1.1), and the reference anti-PD-1 antibodies PD-1 mAb A and PD-1 mAb B, having IgGl (AA) or IgG4 (P) to block the binding of soluble human PD-L1 ( Figure 12A) and soluble human PD-L2 ( Figure 12B) to cell surface human PD-1.
  • IgGl AA
  • IgG4 IgG4
  • Figure 13 shows the ability of humanized anti-PD antibodies hPD-1 mAb 2, hPD-1 mAb 7(1.1), hPD-1 mAb 7(1.2), hPD-1 mAb 9(1.1), and the reference anti-PD-1 antibodies PD-1 mAb A and PD-1 mAb B, having IgGl (AA) or IgG4 (P) to antagonize the PD-l/PD- Ll axis by blocking the PD-1/PD-L1 interaction and preventing down-regulation of T-cell responses in a Jurkat-luc-NFAT / CHO-PD-L1 luciferase reporter assay.
  • IgGl AA
  • IgG4 IgG4
  • Figure 14 shows that PD-1 mAb 2, PD-1 mAb 7, PD-1 mAb 9 and PD-1 mAb 15 are able to stimulate cytokine production to levels comparable or higher than the referenced anti-PD-1 antibodies (PD-1 mAb A and PD-1 mAb B) and that treatment with PD-1 mAb 2, PD-1 mAb 7, PD-1 mAb 9 and PD-1 mAb 15 in combination with LAG-3 mAb 1 provided the largest enhancement of cytokine release.
  • SEB Staphylococcal enterotoxin B
  • Figures 15A-15B show the ability of humanized anti-PD antibodies hPD-1 mAb 2, hPD-1 mAb 7(1.2), hPD-1 mAb 9(1.1), and the reference anti-PD-1 antibodies PD-1 mAb A and PD-1 mAb B, having IgGl (AA) or IgG4 (P) to stimulate cytokine production.
  • IFNy Figure 15A
  • T Fa Figure 15B
  • FIGS 16A-16B show that the PD-1 x LAG-3 bispecific diabody constructs DART A, DART D, DART E, DART F, DART G and DART H, are able to stimulate cytokine production to levels comparable or higher than that observed upon the administration of the combination of an anti-PD-1 mAb + an anti-LAG-3 mAb (PD-1 mAb A + LAG-3 mAb A), and that the PD-1 x LAG-3 bispecific diabody constructs DART A, DART D, DART E, DART F and DART G provided the largest enhancement of cytokine release.
  • FIGS 17A-17B show that the PD-1 x LAG-3 bispecific diabody constructs DART A, DART B and DART C are able to stimulate cytokine production to levels higher than that observed upon the administration of the combination of an anti-PD-1 mAb + an anti -LAG-3 mAb (PD-1 mAb A + LAG-3 mAb A).
  • IFNy secretion profiles of PBMCs from two representative donors, stimulated with a high concentration of SEB (85 ng/mL) treated with PD-1 x LAG-3 bispecific diabodies, or anti-PD-1 and anti -LAG-3 antibodies alone and in combination are plotted.
  • the results using PBMCs from two representative donors are shown in Figure 17A and Figure 17B
  • FIGS 18A-18B show that the PD-1 x LAG-3 bispecific diabody constructs DART A, DART B and DART C are able to stimulate cytokine production to levels higher than that observed upon the administration of the combination of an anti-PD-1 mAb + an anti -LAG-3 mAb (PD-1 mAb A + LAG-3 mAb A).
  • IFNy secretion profiles of PBMCs from two representative donors, stimulated with a middle concentration of SEB (0.5 ng/mL) treated with PD-1 x LAG-3 bispecific diabodies, or anti-PD-1 and anti -LAG-3 antibodies alone and in combination are plotted.
  • the results using PBMCs from two representative donors are shown in Figure 18A and Figure 18B.
  • FIG. 19 shows that the PD-1 x LAG-3 bispecific diabody constructs DART D and DART H are able to stimulate cytokine production to levels comparable or higher than that observed upon the administration of the combination of an anti-PD-1 mAb + an anti -LAG-3 mAb (PD-1 mAb A + LAG-3 mAb A), and that DART D provided the largest enhancement of cytokine release.
  • IL-2 secretion profiles of PBMCs from a representative donor stimulated with a high concentration of SEB (85 ng/mL) treated with PD-1 x LAG-3 bispecific diabodies, or anti-PD-1 and anti -LAG-3 antibodies alone and in combination are plotted.
  • Figure 20 shows that the PD-1 x LAG-3 bispecific diabody constructs DART B and DART I are able to stimulate cytokine production to levels higher than that observed upon the administration of the combination of an anti-PD-1 mAb + an anti -LAG-3 mAb (PD-1 mAb A + LAG-3 mAb A, hPD-1 mAb 7(1.2) + hLAG-3 mAb 1(1.4), hPD-1 mAb 7(1.2) + hLAG-3 mAb 6(1.1)).
  • IFNy secretion profiles of PBMCs from a representative donor, stimulated with a middle concentration of SEB (0.5 ng/mL) treated with PD-1 x LAG-3 bispecific diabodies, or anti-PD-1 and anti -LAG-3 antibodies alone and in combination are plotted.
  • Figures 21A-21D show that the that the PD-1 x LAG-3 bispecific diabody DART I is able to stimulate cytokine production to levels higher than that observed upon the administration of the combination of an anti-PD-1 mAb + an anti -LAG-3 mAb (PD-1 mAb A + LAG-3 mAb A).
  • IFNy ( Figures 21A and 21C) and IL-2 ( Figures 21B and 21D) secretion profiles of CD4 memory cells from two representative donors, stimulated with tetanus toxoid (5 ⁇ g/mL) treated with the PD-1 x LAG-3 bispecific diabody DART-I, anti-PD-1 and anti- LAG-3 antibodies in combination, or an isotype control are plotted.
  • the results at day 7 using CD4 memory T cells from two representative donors are shown in Figures 21A-B and Figures 21C-D
  • Figure 22 shows that the the pharmacokinetics of the PD-1 x LAG-3 bispecific molecule, DART I are comparable to those of the anti-PD-1 antibody, PD-1 mAb A IgG4 (P) in cynomolgus monkey.
  • the lines indicate the mean serum concentration of DART I (solid) and PD-1 mAb A (dashed).
  • the individual values for the male (filled) and female (open) monkeys are plotted for DART I (triangles) and PD-1 mAb A (circles).
  • Figures 23A-23C show serum antibody concentrations and percentage of bound PD-1 on the surface of CD4+ or CD8+ T cells over time in animals following treatment with different anti-PD-1 antibodies.
  • the percentage of bound PD 1 on the surface of CD4+ or CD8+ T cells following anti-PD 1 mAb treatment is plotted on the right y-axes; symbols represent % bound PD 1 on T cells for each individual animal and dashed lines represent the mean values.
  • Serum mAb concentrations are plotted on the left y-axes; symbols represent serum levels for each individual animal and solid lines represent nonlinear fits of the data.
  • the present invention is directed to PD-1 -binding molecules that comprise the PD- 1 -binding domain of selectedanti-PD-1 antibodies capable of binding to both cynomolgus monkey PD-1 and to human PD-1 : PD-1 mAb 1, PD-1 mAb 2, PD-1 mAb 3, PD-1 mAb 4, PD- 1 mAb 5, PD-1 mAb 6, PD-1 mAb 7, PD-1 mAb 8, PD-1 mAb 9, PD-1 mAb 10, PD-1 mAb 11, PD-1 mAb 12, PD-1 mAb 13, PD-1 mAb 14, or PD-1 mAb 15.
  • the invention particularly concerns PD-l-binding molecules that are humanized or chimeric versions of such antibodies, or that comprise PD-l-binding fragments of such anti-PD-1 antibodies (especially immunocongugates, diabodies (including but not limited to DART-A, DART-B, DART-C, DART-D, DART-E, DART-F, DART-G, DART-H, DART-I, and DART-J), BiTEs, bispecific antibodies, etc.).
  • the invention particularly concerns such PD-l-binding molecules that are additionally capable of binding an epitope of a molecule involved in regulating an immune check point that is present on the surface of an immune cell.
  • the present invention also pertains to methods of using such PD-l-binding molecules to detect PD-1 or to stimulate an immune response.
  • the present invention also pertains to methods of combination therapy in which a PD-l-binding molecule that comprises one or more PD-l-binding domain(s) of such selected anti-PD-1 antibodies is administered in combination with one or more additional molecules that are effective in stimulating an immune response and/or in combination with one or more additional molecules that specifically bind a cancer antigen.
  • the antibodies of the present invention are immunoglobulin molecules capable of specific binding to a target, such as a carbohydrate, polynucleotide, lipid, polypeptide, etc., through at least one antigen recognition site, located in the Variable Domain of the immunoglobulin molecule.
  • a target such as a carbohydrate, polynucleotide, lipid, polypeptide, etc.
  • antibody refers to monoclonal antibodies, multispecific antibodies, human antibodies, humanized antibodies, synthetic antibodies, chimeric antibodies, polyclonal antibodies, camelized antibodies, single- chain Fvs (scFv), single-chain antibodies, Fab fragments, F(ab') fragments, disulfide-linked bispecific Fvs (sdFv), intrabodies, and epitope-binding fragments of any of the above.
  • antibodies include immunoglobulin molecules and immunologically active fragments of immunoglobulin molecules, i.e., molecules that contain an antigen-binding site.
  • Immunoglobulin molecules can be of any type ⁇ e.g., IgG, IgE, IgM, IgD, IgA and IgY), class ⁇ e.g., IgGi, IgG 2 , IgG 3 , IgG 4 , IgAi and IgA 2 ) or subclass.
  • IgGi IgG 2 , IgG 3 , IgG 4 , IgAi and IgA 2
  • Antibodies are capable of immunospecifically binding to a polypeptide or protein or a non-protein molecule due to the presence on such molecule of a particular domain or moiety or conformation (an "epitope").
  • An epitope-containing molecule may have immunogenic activity, such that it elicits an antibody production response in an animal; such molecules are termed "antigens").
  • antigens immunogenic activity
  • the last few decades have seen a revival of interest in the therapeutic potential of antibodies, and antibodies have become one of the leading classes of biotechnology-derived drugs (Chan, C.E. etal. (2009) “The Use Of Antibodies In The Treatment Of Infectious Diseases," Singapore Med. J. 50(7):663-666). Over 200 antibody-based drugs have been approved for use or are under development.
  • the term "monoclonal antibody” refers to a homogeneous antibody population wherein the monoclonal antibody is comprised of amino acids (naturally occurring and non- naturally occurring) that are involved in the selective binding of an antigen. Monoclonal antibodies are highly specific, being directed against a single epitope (or antigenic site).
  • monoclonal antibody encompasses not only intact monoclonal antibodies and full- length monoclonal antibodies, but also fragments thereof (such as Fab, Fab', F(ab') 2 Fv), single- chain (scFv), mutants thereof, fusion proteins comprising an antibody portion, humanized monoclonal antibodies, chimeric monoclonal antibodies, and any other modified configuration of the immunoglobulin molecule that comprises an antigen recognition site of the required specificity and the ability to bind to an antigen. It is not intended to be limited as regards to the source of the antibody or the manner in which it is made (e.g., by hybridoma, phage selection, recombinant expression, transgenic animals, etc.).
  • the term includes whole immunoglobulins as well as the fragments etc. described above under the definition of "antibody.”
  • Methods of making monoclonal antibodies are known in the art. One method which may be employed is the method of Kohl er, G. et al. (1975) "Continuous Cultures Of Fused Cells Secreting Antibody Of Predefined Specificity," Nature 256:495-497 or a modification thereof.
  • monoclonal antibodies are developed in mice, rats or rabbits.
  • the antibodies are produced by immunizing an animal with an immunogenic amount of cells, cell extracts, or protein preparations that contain the desired epitope.
  • the immunogen can be, but is not limited to, primary cells, cultured cell lines, cancerous cells, proteins, peptides, nucleic acids, or tissue.
  • Cells used for immunization may be cultured for a period of time (e.g. , at least 24 hours) prior to their use as an immunogen.
  • Cells may be used as immunogens by themselves or in combination with a non-denaturing adjuvant, such as Ribi (see, e.g., Jennings, V.M. (1995) "Review of Selected Adjuvants Used in Antibody Production," ILAR J. 37(3): 119- 125).
  • a non-denaturing adjuvant such as Ribi (see, e.g., Jennings, V.M. (1995) "Review of Selected Adjuvants Used in Antibody Production," ILAR J. 37(3): 119- 125).
  • Ribi non-denaturing adjuvant
  • cells should be kept intact and preferably viable when used as immunogens. Intact cells may allow antigens to be better detected than ruptured cells by the immunized animal.
  • the immunogen may be administered multiple times at periodic intervals such as, bi-weekly, or weekly, or may be administered in such a way as to maintain viability in the animal (e.g., in a tissue recombinant).
  • existing monoclonal antibodies and any other equivalent antibodies that are immunospecific for a desired pathogenic epitope can be sequenced and produced recombinantly by any means known in the art.
  • such an antibody is sequenced and the polynucleotide sequence is then cloned into a vector for expression or propagation.
  • the sequence encoding the antibody of interest may be maintained in a vector in a host cell and the host cell can then be expanded and frozen for future use.
  • the polynucleotide sequence of such antibodies may be used for genetic manipulation to generate the monospecific or multispecific (e.g., bispecific, trispecific and tetraspecific) molecules of the invention as well as an affinity optimized, a chimeric antibody, a humanized antibody, and/or a caninized antibody, to improve the affinity, or other characteristics of the antibody.
  • the general principle in humanizing an antibody involves retaining the basic sequence of the antigen-binding portion of the antibody, while swapping the non-human remainder of the antibody with human antibody sequences.
  • Natural antibodies are composed of two Light Chains complexed with two Heavy Chains. Each light chain contains a Variable Domain (VL) and a Constant Domain (CL). Each heavy chain contains a Variable Domain (VH), three Constant Domains (CHI, CH2 and CH3), and a hinge domain located between the CHI and CH2 Domains.
  • the basic structural unit of naturally occurring immunoglobulins e.g., IgG
  • the amino-terminal (“N-terminal") portion of each chain includes a Variable Domain of about 100 to 1 10 or more amino acids primarily responsible for antigen recognition.
  • the carboxy-terminal ("C-terminal") portion of each chain defines a constant region, with light chains having a single Constant Domain and heavy chains usually having three Constant Domains and a Hinge Domain.
  • the structure of the light chains of an IgG molecule is n-VL-CL-c and the structure of the IgG heavy chains is n-VH-CHl-H-CH2-CH3- c (where H is the hinge domain, and n and c represent, respectively, the N-terminus and the C- terminus of the polypeptide).
  • the Variable Domains of an IgG molecule consist of the complementarity determining regions (CDR), which contain the residues in contact with epitope, and non-CDR segments, referred to as framework segments (FR), which in general maintain the structure and determine the positioning of the CDR loops so as to permit such contacting (although certain framework residues may also contact antigen).
  • CDR complementarity determining regions
  • FR framework segments
  • the VL and VH Domains have the structure n-FRl-CDRl-FR2-CDR2-FR3-CDR3-FR4-c.
  • Polypeptides that are (or may serve as) the first, second and third CDR of an antibody Light Chain are herein respectively designated CDRLI Domain, CDRL2 Domain, and CDRL3 Domain.
  • polypeptides that are (or may serve as) the first, second and third CDR of an antibody heavy chain are herein respectively designated CDRHI Domain, CDRH2 Domain, and CDRH3 Domain.
  • CDRLI Domain, CDRL2 Domain, CDRL3 Domain, CDRHI Domain, CDRH2 Domain, and CDRH3 Domain are directed to polypeptides that when incorporated into a protein cause that protein to be able to bind to a specific epitope regardless of whether such protein is an antibody having light and heavy chains or a diabody or a single-chain binding molecule (e.g. , an scFv, a BiTe, etc.), or is another type of protein.
  • epitope-binding fragment means a fragment of an antibody capable of immunospecifically binding to an epitope
  • epitope-binding site refers to that portion of a molecule comprising an epitope-binding fragment that is responsible for epitope binding.
  • An epitope-binding site may contain 1, 2, 3, 4, 5 or all 6 of the CDR Domains of such antibody and, although capable of immunospecifically binding to such epitope, may exhibit an immunospecificity, affinity or selectivity toward such epitope that differs from that of such antibody.
  • an epitope-binding fragment will contain all 6 of the CDR Domains of such antibody.
  • An epitope-binding fragment of an antibody may be a single polypeptide chain (e.g., an scFv), or may comprise two or more polypeptide chains, each having an amino terminus and a carboxy terminus (e.g., a diabody, a Fab fragment, an F(ab') 2 fragment, etc.).
  • the invention particularly encompasses single-chain Variable Domain fragments ("scFv") of the anti-PD-1 antibodies of this invention and multispecific binding molecules comprising the same.
  • Single-chain Variable Domain fragments are made by linking Light and/or Heavy chain Variable Domain by using a short linking peptide.
  • Bird et al. (1988) (“Single-Chain Antigen-Binding Proteins," Science 242:423-426) describes example of linking peptides which bridge approximately 3.5 nm between the carboxy terminus of one Variable Domain and the amino terminus of the other Variable Domain. Linkers of other sequences have been designed and used (Bird et al.
  • Linkers can in turn be modified for additional functions, such as attachment of drugs or attachment to solid supports.
  • the single-chain variants can be produced either recombinantly or synthetically.
  • an automated synthesizer can be used for synthetic production of scFv.
  • a suitable plasmid containing polynucleotide that encodes the scFv can be introduced into a suitable host cell, either eukaryotic, such as yeast, plant, insect or mammalian cells, or prokaryotic, such as E. coli.
  • Polynucleotides encoding the scFv of interest can be made by routine manipulations such as ligation of polynucleotides.
  • the resultant scFv can be isolated using standard protein purification techniques known in the art.
  • the invention also particularly encompasses humanized variants of the anti-PD-1 antibodies of the invention and multispecific binding molecules comprising the same.
  • humanized antibody refers to a chimeric molecule, generally prepared using recombinant techniques, having an antigen-binding site of an immunoglobulin from a non- human species and a remaining immunoglobulin structure of the molecule that is based upon the structure and /or sequence of a human immunoglobulin.
  • the anti-human PD-1 antibodies of the present invention include humanized, chimeric or caninized variants of antibodies PD-1 mAb 1, PD-1 mAb 2, PD-1 mAb 3, PD-1 mAb 4, PD-1 mAb 5, PD-1 mAb 6, PD-1 mAb 7, PD-1 mAb 8, PD-1 mAb 9, PD-1 mAb 10, PD-1 mAb 11, PD-1 mAb 12, PD-1 mAb 13, PD- 1 mAb 14, or PD-1 mAb 15.
  • the polynucleotide sequence of the variable domains of such antibodies may be used for genetic manipulation to generate such derivatives and to improve the affinity, or other characteristics of such antibodies.
  • the general principle in humanizing an antibody involves retaining the basic sequence of the antigen-binding portion of the antibody, while swapping the non-human remainder of the antibody with human antibody sequences.
  • the antigen-binding site may comprise either a complete Variable Domain fused to a Constant Domain or only the complementarity determining regions (CDRs) of such Variable Domain grafted to appropriate framework regions.
  • Antigen-binding sites may be wild-type or modified by one or more amino acid substitutions. This eliminates the constant region as an immunogen in human individuals, but the possibility of an immune response to the foreign variable domain remains (LoBuglio, A.F. et al. (1989) "Mouse/Human Chimeric Monoclonal Antibody In Man: Kinetics And Immune Response," Proc. Natl. Acad. Sci. (U.S.A.) 86:4220- 4224).
  • variable domains of both heavy and light chains contain three complementarity determining regions (CDRs) which vary in response to the antigens in question and determine binding capability, flanked by four framework regions (FRs) which are relatively conserved in a given species and which putatively provide a scaffolding for the CDRs.
  • CDRs complementarity determining regions
  • FRs framework regions
  • humanized antibodies preserve all CDR sequences (for example, a humanized mouse antibody which contains all six CDRs from the mouse antibodies). In other embodiments, humanized antibodies have one or more CDRs (one, two, three, four, five, or six) which differ in sequence relative to the original antibody.
  • a number of "humanized” antibody molecules comprising an antigen-binding site derived from a non-human immunoglobulin have been described, including chimeric antibodies having rodent or modified rodent Variable Domain and their associated complementarity determining regions (CDRs) fused to human Constant Domains (see, for example, Winter et al. (1991) "Man-made Antibodies " Nature 349:293-299; Lobuglio et al. (1989) 'Mouse/Human Chimeric Monoclonal Antibody In Man: Kinetics And Immune Response," Proc. Natl. Acad. Sci. (U.S.A.) 86:4220-4224 (1989), Shaw et al.
  • CDRs complementarity determining regions
  • Fey Receptors Fey Receptors
  • the CH2 and CH3 Domains of the two heavy chains interact to form the Fc Region, which is a domain that is recognized by cellular Fc Receptors, including but not limited to Fc gamma Receptors (FcyRs).
  • Fc Region is used to define a C-terminal region of an IgG heavy chain.
  • the amino acid sequence of the CH2-CH3 Domain of an exemplary human IgGl is (SEQ ID NO:l):
  • X is a lysine (K) or is absent.
  • amino acid sequence of the CH2-CH3 Domain of an exemplary human IgG2 is (SEQ ID NO:2):
  • X is a lysine (K) or is absent.
  • amino acid sequence of the CH2-CH3 Domain of an exemplary human IgG3 is (SEQ ID NO:3):
  • ALHNRFTQKS LSLSPGX as numbered by the EU index as set forth in Kabat, wherein, X is a lysine (K) or is absent.
  • amino acid sequence of the CH2-CH3 Domain of an exemplary human IgG4 is (SEQ ID NO:4):
  • ALHNHYTQKS LSLSLGX as numbered by the EU index as set forth in Kabat, wherein, X is a lysine (K) or is absent.
  • the numbering of the residues in the constant region of an IgG heavy chain is that of the EU index as in Kabat et al, Sequences of Proteins of Immunological Interest. 5 th Ed. Public Health Service, H1, MD (1991) ("Kabat”), expressly incorporated herein by references.
  • EU index as in Kabat refers to the numbering of the human IgGl EU antibody. Amino acids from the Variable Domains of the mature heavy and light chains of immunoglobulins are designated by the position of an amino acid in the chain.
  • Kabat described numerous amino acid sequences for antibodies, identified an amino acid consensus sequence for each subgroup, and assigned a residue number to each amino acid, and the CDRs are identified as defined by Kabat (it will be understood that CDRHI as defined by Chothia, C. & Lesk, A. M. ((1987) "Canonical structures for the hypervariable regions of immunoglobulins " . J. Mol. Biol. 196:901-917) begins five residues earlier).
  • Rabat's numbering scheme is extendible to antibodies not included in his compendium by aligning the antibody in question with one of the consensus sequences in Kabat by reference to conserved amino acids.
  • Gm Polymorphic forms of human immunoglobulins have been well-characterized. At present, 18 Gm allotypes are known: Glm (1, 2, 3, 17) or Glm (a, x, f, z), G2m (23) or G2m (n), G3m (5, 6, 10, 11, 13, 14, 15, 16, 21, 24, 26, 27, 28) or G3m (bl, c3, b3, bO, b3, b4, s, t, gl, c5, u, v, g5) (Lefranc, et al, "The Human IgG Subclasses: Molecular Analysis Of Structure, Function And Regulation. ' " Pergamon, Oxford, pp. 43-78 (1990); Lefranc, G.
  • the antibodies of the present invention may be incorporate any allotype, isoallotype, or haplotype of any immunoglobulin gene, and are not limited to the allotype, isoallotype or haplotype of the sequences provided herein.
  • the C-terminal amino acid residue (bolded above) of the CH3 Domain may be post-translationally removed. Accordingly, the C-terminal residue of the CH3 Domain is an optional amino acid residue in the PD-1 -binding molecules of the invention.
  • PD-1 -binding molecules lacking the C-terminal residue of the CH3 Domain.
  • constructs comprising the C-terminal lysine residue of the CH3 Domain.
  • Activating and inhibitory signals are transduced through the ligation of an Fc region to a cellular Fc gamma Receptor (FcyR).
  • FcyR Fc gamma Receptor
  • the ability of such ligation to result in diametrically opposing functions results from structural differences among the different FcyRs.
  • Two distinct domains within the cytoplasmic signaling domains of the receptor called immunoreceptor tyrosine-based activation motifs (ITAMs) and immunoreceptor tyrosine-based inhibitory motifs (ITEVIS) account for the different responses.
  • ITAMs immunoreceptor tyrosine-based activation motifs
  • ITEVIS immunoreceptor tyrosine-based inhibitory motifs
  • ITAM-containing FcyR complexes include FcyRI, FcyRIIA, FcyRIIIA, whereas ITEVI- containing complexes only include FcyRIIB.
  • Human neutrophils express the FcyRIIA gene.
  • FcyRIIA clustering via immune complexes or specific antibody cross-linking serves to aggregate ITAMs along with receptor-associated kinases which facilitate ITAM phosphorylation.
  • ITAM phosphorylation serves as a docking site for Syk kinase, activation of which results in activation of downstream substrates ⁇ e.g., PLK). Cellular activation leads to release of proinflammatory mediators.
  • the FcyRIIB gene is expressed on B lymphocytes; its extracellular domain is 96% identical to FcyRIIA and binds IgG complexes in an indistinguishable manner.
  • the presence of an ITIM in the cytoplasmic domain of FcyRIIB defines this inhibitory subclass of FcyR. Recently the molecular basis of this inhibition was established.
  • the ITIM in FcyRIIB When co-ligated along with an activating FcyR, the ITIM in FcyRIIB becomes phosphorylated and attracts the SH2 domain of the inositol polyphosphate 5 '-phosphatase (SHIP), which hydrolyzes phosphoinositol messengers released as a consequence of ITAM- containing FcyR- mediated tyrosine kinase activation, consequently preventing the influx of intracellular Ca ++ .
  • SHIP inositol polyphosphate 5 '-phosphatase
  • cross-linking of FcyRIIB dampens the activating response to FcyR ligation and inhibits cellular responsiveness. B-cell activation, B-cell proliferation and antibody secretion is thus aborted.
  • an antibody to bind an epitope of an antigen depends upon the presence and amino acid sequence of the antibody's VL and VH Domains. Interaction of an antibody light chain and an antibody heavy chain and, in particular, interaction of its VL and VH Domains forms one of the two epitope-binding sites of a natural antibody. Natural antibodies are capable of binding to only one epitope species (i.e., they are monospecific), although they can bind multiple copies of that species (i.e., exhibiting bivalency or multivalency).
  • the binding domains of the present invention bind to epitopes in an "immunospecific" manner.
  • an antibody, diabody or other epitope-binding molecule is said to "immunospecifically” bind a region of another molecule (i.e., an epitope) if it reacts or associates more frequently, more rapidly, with greater duration and/or with greater affinity with that epitope relative to alternative epitopes.
  • an antibody that immunospecifically binds to a viral epitope is an antibody that binds this viral epitope with greater affinity, avidity, more readily, and/or with greater duration than it immunospecifically binds to other viral epitopes or non-viral epitopes.
  • an antibody or moiety or epitope that immunospecifically binds to a first target may or may not specifically or preferentially bind to a second target.
  • immunospecific binding does not necessarily require (although it can include) exclusive binding.
  • reference to binding means "specific” binding. Two molecules are said to be capable of binding to one another in a “physiospecific” manner, if such binding exhibits the specificity with which receptors bind to their respective ligands.
  • antibodies can be enhanced by generating multispecific antibody-based molecules that can simultaneously bind two separate and distinct antigens (or different epitopes of the same antigen) and/or by generating antibody-based molecule having higher valency (i.e., more than two binding sites) for the same epitope and/or antigen.
  • WO 2013/174873, WO 2011/133886 and WO 2010/136172 disclose that the use of linkers may cause problems in therapeutic settings, and teaches a trispecific antibody in which the CL and CHI Domains are switched from their respective natural positions and the VL and VH Domains have been diversified (WO 2008/027236; WO 2010/108127) to allow them to bind to more than one antigen.
  • the molecules disclosed in these documents trade binding specificity for the ability to bind additional antigen species.
  • PCT Publications Nos. WO 2013/163427 and WO 2013/119903 disclose modifying the CH2 Domain to contain a fusion protein adduct comprising a binding domain. The document notes that the CH2 Domain likely plays only a minimal role in mediating effector function.
  • PCT Publications Nos. WO 2010/028797, WO2010028796 and WO 2010/028795 disclose recombinant antibodies whose Fc Regions have been replaced with additional VL and VH Domains, so as to form trivalent binding molecules.
  • PCT Publications Nos. WO 2003/025018 and WO2003012069 disclose recombinant diabodies whose individual chains contain scFv Domains.
  • PCT Publications No. WO 2013/006544 discloses multivalent Fab molecules that are synthesized as a single polypeptide chain and then subjected to proteolysis to yield heterodimeric structures. Thus, the molecules disclosed in these documents trade all or some of the capability of mediating effector function for the ability to bind additional antigen species.
  • the art has additionally noted the capability to produce diabodies that differ from such natural antibodies in being capable of binding two or more different epitope species (i.e., exhibiting bispecificity or multispecificity in addition to bivalency or multivalency) (see, e.g., Holliger et al. (1993) '"Diabodies ': Small Bivalent And Bispecific Antibody Fragments, ' " Proc. Natl. Acad. Sci. (U.S.A.) 90:6444-6448; US 2004/0058400 (Hollinger et al); US 2004/0220388 / WO 02/02781 (Mertens et al.); Alt et al. (1999) FEBS Lett.
  • a diabody is based on the antibody derivative known as a single-chain Variable Domain fragment (scFv).
  • scFv Single-chain Variable Domain fragment
  • Such molecules are made by linking Light and/ or Heavy chain Variable Domains by using a short linking peptide.
  • Bird et al. (1988) (“Single -Chain Antigen-Binding Proteins," Science 242:423-426) describes example of linking peptides which bridge approximately 3.5 nm between the carboxy terminus of one Variable Domain and the amino terminus of the other Variable Domain.
  • Linkers of other sequences have been designed and used (Bird et al. (1988) "Single-Chain Antigen-Binding Proteins," Science 242:423-426).
  • Linkers can in turn be modified for additional functions, such as attachment of drugs or attachment to solid supports.
  • the single-chain variants can be produced either recombinantly or synthetically.
  • an automated synthesizer can be used for synthetic production of scFv.
  • a suitable plasmid containing polynucleotide that encodes the scFv can be introduced into a suitable host cell, either eukaryotic, such as yeast, plant, insect or mammalian cells, or prokaryotic, such as E. coli.
  • Polynucleotides encoding the scFv of interest can be made by routine manipulations such as ligation of polynucleotides.
  • the resultant scFv can be isolated using standard protein purification techniques known in the art.
  • non-monospecific diabodies provides a significant advantage over antibodies, including but not limited to, the capacity to co-ligate and co-localize cells that express different epitopes.
  • Bispecific diabodies thus have wide-ranging applications including therapy and immunodiagnosis. Bispecificity allows for great flexibility in the design and engineering of the diabody in various applications, providing enhanced avidity to multimeric antigens, the cross-linking of differing antigens, and directed targeting to specific cell types relying on the presence of both target antigens.
  • diabody molecules known in the art Due to their increased valency, low dissociation rates and rapid clearance from the circulation (for diabodies of small size, at or below -50 kDa), diabody molecules known in the art have also shown particular use in the field of tumor imaging (Fitzgerald et al. (1997) “Improved Tumour Targeting By Disulphide Stabilized Diabodies Expressed In Pichia pastoris, " Protein Eng. 10: 1221).
  • bispecific diabodies can be used to co-ligate receptors on the surface of different cells or on a single cell. Co-ligation of different cells and/or receptors is useful to modulation effector functions and/or immune cell signaling.
  • Multispecific molecules ⁇ e.g., bispecific diabodies) comprising epitope-binding sites may be directed to a surface determinant of any immune cell such as B7-H3 (CD276), B7-H4 (VTCN1), BTLA (CD272), CD3, CD8, CD16, CD27, CD32, CD40, CD40L, CD47, CD64, CD70 (CD27L), CD80 (B7-1), CD86 (B7-2), CD94 (KLRD1), CD137 (4-1BB), CD137L (4-1BBL), CD226, CTLA-4 (CD152), Galectin-9, GITR, GITRL, HHLA2, ICOS (CD278), ICOSL (CD275), Killer Activation Receptor (KIR), L
  • epitope-binding sites directed to a cell surface receptor that is involved in regulating an immune checkpoint are useful in the generation of bispecific or multispecific binding molecules which antagonize or block the inhibitory signaling of immune checkpoint molecules and thereby stimulate, upregulate or enhance, immune responses in a subject.
  • Molecules involved in regulating immune checkpoints include, but are not limited to B7-H3, B7-H4, BTLA, CD40, CD40L, CD47, CD70, CD80, CD86, CD94, CD 137, CD137L, CD226, CTLA-4, Galectin-9, GITR, GITRL, HHLA2, ICOS, ICOSL, KIR, LAG-3, LIGHT, MHC class I or II, NKG2a, NKG2d, OX40, OX40L, PD1H, PD-1, PD-L1, PD-L2, PVR, SIRPa, TCR, TIGIT, TIM-3 and/or VISTA.
  • bispecific diabodies composed of non- covalently associated polypeptides are unstable and readily dissociate into non-functional monomers (see, e.g., Lu, D. et al. (2005) "A Fully Human Recombinant IgG-Tike Bispecific Antibody To Both The Epidermal Growth Factor Receptor And The Insulin-Tike Growth Factor Receptor For Enhanced Antitumor Activity;' J. Biol. Chem. 280(20): 19665-19672).
  • DART® Dual Affinity Re- Targeting Reagents
  • Such diabodies comprise two or more covalently complexed polypeptides and involve engineering one or more cysteine residues into each of the employed polypeptide species that permit disulfide bonds to form and thereby covalently bond two polypeptide chains.
  • cysteine residues For example, the addition of a cysteine residue to the C-terminus of such constructs has been shown to allow disulfide bonding between the polypeptide chains, stabilizing the resulting heterodimer without interfering with the binding characteristics of the bivalent molecule.
  • the first polypeptide comprises (in the N-terminal to C-terminal direction): (i) a First Domain that comprises a binding region of a Light Chain Variable Domain of a first immunoglobulin (VLl), (ii) a Second Domain that comprises a binding region of a Heavy Chain Variable Domain of a second immunoglobulin (VH2), and (iii) a Third Domain that contains a cysteine residue (or a cysteine-containing domain) and a Heterodimer-Promoting Domain that serves to promote heterodimerization with the second polypeptide of the diabody and to covalently bond the diabody' s first and second polypeptides to one another.
  • the second polypeptide contains (in the N-terminal to C-terminal direction): (i) a First Domain that comprises a binding region of a Light Chain Variable Domain of the second immunoglobulin (VL2), (ii) a Second Domain that comprises a binding region of a Heavy Chain Variable Domain of the first immunoglobulin (VH1), and (iii) a Third Domain that contains a cysteine residue (or a cysteine-containing domain) and a complementary Heterodimer-Promoting Domain that complexes with the Heterodimer-Promoting Domain of the first polypeptide chain in order to promote heterodimerization with the first polypeptide chain.
  • the cysteine residue (or a cysteine-containing domain) of the third domain of the second polypeptide chain serves to promote the covalent bonding of the second polypeptide chain to the first polypeptide chain of the diabody.
  • Such molecules are stable, potent and have the ability to simultaneously bind two or more antigens.
  • the Third Domains of the first and second polypeptides each contain a cysteine residue, which serves to bind the polypeptides together via a disulfide bond.
  • Figure 1 provides a schematic of such a diabody, which utilizes E-coil/K- coil Heterodimer-Promoting domains and a cysteine containing linker for covalent bonding.
  • one or both of the polypeptides may additionally possesses the sequence of a CH2-CH3 Domain, such that complexing between the two diabody polypeptides forms an Fc Region that is capable of binding to the Fc receptor of cells (such as B lymphocytes, dendritic cells, natural killer cells, macrophages, neutrophils, eosinophils, basophils and mast cells).
  • the CH2 and/or CH3 Domains of such polypeptide chains need not be identical in sequence, and advantageously are modified to foster complexing between the two polypeptide chains. [0079] Many variations of such molecules have been described (see, e.g., United States Patent Publications No.
  • Fc Region-containing DART® diabodies may comprise two pairs of polypeptide chains.
  • the first polypeptide chain comprises (in the N-terminal to C-terminal direction): (i) a First Domain that comprises a binding region of a Light Chain Variable Domain of a first immunoglobulin (VLl), (ii) a Second Domain that comprises a binding region of a Heavy Chain Variable Domain of a second immunoglobulin (VH2), (iii) a Third Domain that contains a cysteine residue (or a cysteine-containing domain) and a serves to promote heterodimerization with the second polypeptide of the diabody and to covalently bond the diabody's first and second polypeptides to one another, and (iv) a CH2-CH3 Domain.
  • the second polypeptide contains (in the N-terminal to C-terminal direction): (i) a First Domain that comprises a binding region of a Light Chain Variable Domain of the second immunoglobulin (VL2), (ii) a Second Domain that comprises a binding region of a Heavy Chain Variable Domain of the first immunoglobulin (VHl), and (iii) ) a Third Domain that contains a cysteine residue (or a cysteine-containing domain) and a Heterodimer-Promoting Domain that promotes heterodimerization with the first polypeptide chain.
  • VL2 Light Chain Variable Domain of the second immunoglobulin
  • VHl Heavy Chain Variable Domain of the first immunoglobulin
  • a Third Domain that contains a cysteine residue (or a cysteine-containing domain) and a Heterodimer-Promoting Domain that promotes heterodimerization with the first polypeptide chain.
  • two first polypeptides complex with each other to form an F
  • Other Fc-Region-containing DART® diabodies may comprise three polypeptide chains.
  • the first polypeptide of such DART® diabodies contains three domains: (i) a VL1- containing Domain, (ii) a VH2-containing Domain and (iii) a Domain containing a CH2-CH3 sequence.
  • the second polypeptide of such DART® diabodies contains: (i) a VL2-containing Domain, (ii) a VHl -containing Domain and (iii) a Domain that promotes heterodimerization and covalent bonding with the diabody ' s first polypeptide chain.
  • the third polypeptide of such DART® diabodies comprises a CH2-CH3 sequence.
  • the first and second polypeptide chains of such DART® diabodies associate together to form a VLl /VHl binding site that is capable of binding to the epitope, as well as a VL2/VH2 binding site that is capable of binding to the second epitope.
  • Such more complex DART® molecules also possess cysteine- containing domains which function to form a covalently bonded complex.
  • the first and second polypeptides are bonded to one another through a disulfide bond involving cysteine residues in their respective Third Domains.
  • the first and third polypeptide chains complex with one another to form an Fc Region that is stabilized via a disulfide bond.
  • Figures 4A-4B provide schematics of such diabodies comprising three polypeptide chains.
  • Still other Fc-Region-containing DART® diabodies may comprise five polypeptide chains which may comprise the binding regions from the Light and Heavy Chain Variable Domains of up to three different immunoglobulins (referred to as VLl/VHl, VL2/VH2 and VL3/VH3).
  • the first polypeptide chain of such diabodies may contain: (i) a VH1- containing domain, (ii) a CHI -containing domain, and (iii) a Domain containing a CH2-CH3 sequence.
  • the second and fifth polypeptide chains of such diabodies may contain: (i) a VLl- containing domain, and (ii) a CL-containing domain.
  • the third polypeptide chain of such diabodies may contain: (i) a VH1 -containing domain, (ii) a CHI -containing domain, (iii) a Domain containing a CH2-CH3 sequence, (iv) a VL2 -containing Domain, (v) a VH3- containing Domain and (vi) a Heterodimer-Promoting Domain, where the Heterodimer- Promoting Domains promote the dimerization of the third chain with the fourth chain.
  • the fourth polypeptide of such diabodies may contain: (i) a VL3 -containing Domain, (ii) a VH2- containing Domain and (iii) a Domain that promotes heterodimerization and covalent bonding with the diabody's third polypeptide chain.
  • the first and third polypeptides complex with each other to form an Fc Region.
  • Such more complex DART® molecules also possess cysteine-containing domains which function to form a covalently bonded complex, such that each polypeptide chain is bonded to at least one addition polypeptide chain through a disulfide bond involving cysteine residues.
  • such domains are ordered in the N-terminal to C-terminal direction.
  • Figure 5 provides schematics of such diabodies comprising five polypeptide chains.
  • the preferred PD-l-binding molecules of the present invention include antibodies, diabodies, BiTEs, etc. and are capable of binding to a continuous or discontinuous ⁇ e.g., conformational) portion (epitope) of human PD-1 (CD279).
  • the PD-l-binding molecules of the present invention will preferably also exhibit the ability to bind to PD-1 molecules of one or more non-human species, in particular, primate species (and especially a primate species, such as cynomolgus monkey).
  • a representative human PD-1 polypeptide NCBI Sequence
  • NP 005009.2 including a 20 amino acid residue signal sequence (shown underlined) and the
  • amino acid residue mature protein has the amino acid sequence (SEQ ID NO:68):
  • the anti-human PD- 1 -binding molecules of the invention are characterized by any (one or more) of the following criteria:
  • non-human primate PD-1 e.g., PD-1 of cynomolgus
  • (9) inhibits (i.e., blocks or interferes with) the binding/the inhibitory activity) of PD-1 ligand (PD-L1/PD-L2) to PD-1;
  • the term "antigen specific T-cell response" refers to responses by a T- cell that result from stimulation of the T-cell with the antigen for which the T-cell is specific.
  • responses by a T-cell upon antigen specific stimulation include proliferation and cytokine production (e.g., TNF-a, IFN- ⁇ production).
  • SEB Staphylococcus aureus Enterotoxin type B antigen
  • the preferred anti-human PD-1 -binding molecules of the present invention possess the VH and/or VL Domains of murine anti-human PD-1 monoclonal antibodies "PD-1 mAb 1," “PD-1 mAb 2,” “PD-1 mAb 3,””PD-1 mAb 4," "PD-1 mAb 5,” “PD-1 mAb 6,” “PD-1 mAb 7,” “PD-1 mAb 8,” "PD-1 mAb 9,” “PD-1 mAb 10,” “PD-1 mAb 11,” “PD-1 mAb 12,” “PD-1 mAb 13,” “PD-1 mAb 14,” or “PD-1 mAb 15,” and more preferably possess 1, 2 or all 3 of the CDRHS of the VH Domain and/or 1, 2 or all 3 of the CDRLS of the VL Domain of such anti-human PD-1 monoclonal antibodies.
  • Such preferred anti -human PD-1 -binding molecules include bispecific (or multispecific) antibodies, chimeric or humanized antibodies, BiTes
  • the invention particularly relates to PD-1 -binding molecules comprising a PD-1 binding domain that possess:
  • PD-1 mAb 1 that binds, or competes for binding with, the same epitope as PD-1 mAb 1, PD-1 mAb 2, PD- 1 mAb 3, PD-1 mAb 4, PD-1 mAb 5, PD-1 mAb 6, PD-1 mAb 7, PD-1 mAb 8, PD-1 mAb 9, PD-1 mAb 10, PD-1 mAb 11, PD-1 mAb 12, PD-1 mAb 13, PD-1 mAb 14, or PD-1 mAb 15.
  • An exemplary polynucleotide that encodes the VH Domain of PD-1 mAb 1 is SEQ ID NO: 1
  • An exemplary polynucleotide that encodes the VL Domain of PD-1 mAb 1 is SEQ ID NO: 1
  • the above-described murine anti-human PD-1 antibody PD-1 mAb 1 was humanized and further deimmunized when antigenic epitopes were identified in order to demonstrate the capability of humanizing an anti -human PD-1 antibody so as to decrease its antigenicity upon administration to a human recipient.
  • the humanization yielded one humanized VH Domain, designated herein as "hPD-1 mAb 1 VHl,” and one humanized VL Domain designated herein as "hPD-1 mAb 1 VL1.” Accordingly, an antibody comprising the humanized VL Domains paired with the humanized VH Domain is referred to as "hPD-1 mAb 1.”
  • An exemplary polynucleotide that encodes hPD-1 mAb 1 VHl is SEQ ID NO:80
  • An exemplary polynucleotide that encodes hPD-1 mAb 1 VLl is SEQ ID NO:82
  • CDR H 3 of PD-1 mAb 2 (SEQ ID NO:87): LSDYFDY [0099]
  • An exemplary polynucleotide that encodes the VH Domain of PD-1 mAb 2 is SEQ ID NO:87.
  • An exemplary polynucleotide that encodes the VL Domain of PD-1 mAb 2 is SEQ ID NO: 1
  • the above-described murine anti-human PD-1 antibody PD-1 mAb 2 was humanized and further deimmunized when antigenic epitopes were identified in order to demonstrate the capability of humanizing an anti -human PD-1 antibody so as to decrease its antigenicity upon administration to a human recipient.
  • the humanization yielded one humanized VH Domain, designated herein as "hPD-1 mAb 2 VHl,” and one humanized VL Domains designated herein as "hPD-1 mAb 1 VL1.” Accordingly, any antibody comprising the humanized VL Domains paired with the humanized VH Domain is referred to as "hPD-1 mAb 2.”
  • An exemplary polynucleotide that encodes hPD-1 mAb 2 VHl is SEQ ID NO:94
  • An exemplary polynucleotide that encodes hPD-1 mAb 2 VLl is SEQ ID NO:96
  • An exemplary polynucleotide that encodes the VH Domain of PD-1 mAb 3 is SEQ ID NO: 1
  • An exemplary polynucleotide that encodes the VL Domain of PD-1 mAb 3 is SEQ ID NO: 1
  • An exemplary polynucleotide that encodes the VL Domain of PD-1 mAb 4 is SEQ ID NO: 1
  • An exemplary polynucleotide that encodes the VH Domain of PD-1 mAb 5 is SEQ ID NO: 1
  • An exemplary polynucleotide that encodes the VL Domain of PD-1 mAb 5 is SEQ ID NO: 1
  • An exemplary polynucleotide that encodes the VH Domain of PD-1 mAb 6 is SEQ ID NO: 1
  • An exemplary polynucleotide that encodes the VL Domain of PD-1 mAb 6 is SEQ ID NO: 1
  • An exemplary polynucleotide that encodes the VH Domain of PD-1 mAb 7 is SEQ ID NO: 1
  • CDR L 3 of PD-1 mAb 7 (SEQ ID NO: 146): QQSKEVPYT [00126]
  • An exemplary polynucleotide that encodes the VL Domain of PD-1 mAb 7 is SEQ ID NO: 1466
  • the above-described murine anti-human PD-1 antibody PD-1 mAb 7 was humanized and further deimmunized when antigenic epitopes were identified in order to demonstrate the capability of humanizing an anti -human PD-1 antibody so as to decrease its antigenicity upon administration to a human recipient.
  • the humanization yielded two humanized VH Domains, designated herein as “hPD-1 mAb 7 VHl,” and “hPD-1 mAb 7 VH2,” and three humanized VL Domains designated herein as “hPD-1 mAb 7 VL1,” “hPD- 1 mAb 7 VL2,” and “hPD-1 mAb 7 VL3.” Any of the humanized VL Domains may be paired with either of the humanized VH Domains.
  • any antibody comprising one of the humanized VL Domains paired with the humanized VH Domain is referred to generically as "hPD-1 mAb 7," and particular combinations of humanized VH/VL Domains are referred to by reference to the specific VH/VL Domains, for example a humanized antibody comprising hPD-1 mAb 7 VHl and hPD-1 mAb 1 VL2 is specifically referred to as “hPD-1 mAb 7(1.2)."
  • An exemplary polynucleotide that encodes hPD-1 mAb 7 VHl is SEQ ID NO: 148
  • An exemplary polynucleotide that encodes hPD-1 mAb 7 VH2 is SEQ ID NO: 150
  • An exemplary polynucleotide that encodes hPD-1 mAb 7 VLl is SEQ ID NO: 152
  • An exemplary polynucleotide that encodes hPD- 1 mAb 7 VL2 is SEQ ID NO: 154
  • An exemplary polynucleotide that encodes hPD- 1 mAb 7 VL3 is SEQ ID NO: 156
  • the CDRLI of the VL Domain of both hPD- 1 mAb 7 VL2 and hPD-1 mAb 7 VL3 comprises an asparagine to serine amino acid substitution and has the amino acid sequence: RASESVDNYGMSFMN ((SEQ ID NO: 157), the substituted serine is shown underlined). It is contemplated that a similar substitution may be incorporated into any of the PD- 1 mAb 7 CDRLI Domains described above.
  • the CDR L 2 of the VL Domain of hPD- 1 mAb 7 VL3 comprises a glutamine to arginine amino acid substitution and has the amino acid sequence: AASNRGS ((SEQ ID NO: 158), the substituted arginine is shown underlined). It is contemplated that a similar substitution may be incorporated into any of the PD- 1 mAb 7 CDRL2 Domains described above.
  • An exemplary polynucleotide that encodes the VH Domain of PD-1 mAb 8 is SEQ ID NO: 1
  • ggccacattg actgtagaca agtcctccac cacagcctac atggagctcc gcagcctgac atctgaggac tctgcagtct attactgtgc gagcgatttt
  • An exemplary polynucleotide that encodes the VL Domain of PD-1 mAb 8 is SEQ ID NO: 1
  • An exemplary polynucleotide that encodes the VH Domain of PD-1 mAb 9 is SEQ ID NO: 1
  • CDR L 2 of PD-1 mAb 9 (SEQ ID NO: 177): NAKTLAA
  • An exemplary polynucleotide that encodes the VL Domain of PD-1 mAb 9 is SEQ ID NO: 1
  • the above-described murine anti-human PD-1 antibody PD-1 mAb 9 was humanized and further deimmunized when antigenic epitopes were identified in order to demonstrate the capability of humanizing an anti -human PD-1 antibody so as to decrease its antigenicity upon administration to a human recipient.
  • the humanization yielded two humanized VH Domains, designated herein as "hPD-1 mAb 9 VHl,” and “hPD-1 mAb 9 VH2,” and two humanized VL Domains designated herein as "hPD-1 mAb 9 VL1," and "hPD-1 mAb 9 VL2.” Any of the humanized VL Domains may be paired with the humanized VH Domains.
  • any antibody comprising one of the humanized VL Domains paired with the humanized VH Domain is referred to generically as "hPD-1 mAb 9," and particular combinations of humanized VH/VL Domains are referred to by reference to the specific VH/VL Domains, for example a humanized antibody comprising hPD-1 mAb 9 VHl and hPD- 1 mAb 9 VL2 is specifically referred to as “hPD-1 mAb 9(1.2)."
  • An exemplary polynucleotide that encodes hPD-1 mAb 9 VHl is SEQ ID NO: 180
  • An exemplary polynucleotide that encodes hPD-1 mAb 9 VH2 is SEQ ID NO: 182
  • the CDRHI of the VH Domain of hPD- 1 mAb 9 VH2 comprises a serine to glycine amino acid substitution and has the amino acid sequence: SYLVG ((SEQ ID NO: 183), the substituted glycine is shown underlined). It is contemplated that a similar substitution may be incorporated into any of the PD-1 mAb 9 CDRHI Domains described above.
  • An exemplary polynucleotide that encodes hPD- 1 mAb 9 VLl is SEQ ID NO: 185
  • An exemplary polynucleotide that encodes hPD-1 mAb 9 VL2 is SEQ ID NO: 187
  • the CDRLI of the VL Domain of hPD-1 mAb 9 VL2 comprises a serine to asparagine amino acid substitution and has the amino acid sequence: RASENIYNYLA (SEQ ID NO: 188), the substituted asparagine is shown underlined). It is contemplated that a similar substitution may be incorporated into any of the PD-1 mAb 9 CDRLI Domains described above.
  • the CDR L 2 of the VL Domain of hPD-1 mAb 9 VL2 comprises an asparagine to aspartate amino acid substitution and has the amino acid sequence: DAKTLAA ((SEQ ID NO: 189), the substituted aspartate is shown underlined). It is contemplated that a similar substitution may be incorporated into any of the PD-1 mAb 7 CDRL2 Domains described above.
  • CDR H 3 of PD-1 mAb 10 (SEQ ID NO: 194) QELAFDY [00161]
  • An exemplary polynucleotide that encodes the VH Domain of PD-1 mAb 10 is SEQ ID NO: 194.
  • An exemplary polynucleotide that encodes the VL Domain of PD-1 mAb 10 is SEQ ID NO: 1
  • CDR H 3 of PD-1 mAb 11 (SEQ ID NO:204): GTYSYFDV [00165]
  • An exemplary polynucleotide that encodes the VH Domain of PD-1 mAb 11 is SEQ ID NO:204
  • An exemplary polynucleotide that encodes the VL Domain of PD-1 mAb 11 is SEQ ID NO: 1
  • CDR H 3 of PD-1 mAb 12 (SEQ ID NO:214): ERITTWEGAYWYFDV [00169]
  • An exemplary polynucleotide that encodes the VH Domain of PD-1 mAb 12 is SEQ ID NO:214
  • An exemplary polynucleotide that encodes the VL Domain of PD-1 mAb 12 is SEQ ID NO: 1
  • An exemplary polynucleotide that encodes the VH Domain of PD-1 mAb 13 is SEQ ID NO: 1
  • CDRLI of PD-1 mAb 13 (SEQ ID NO:227): LASQTIGTWLA
  • An exemplary polynucleotide that encodes the VH Domain of PD- 1 mAb 14 is SEQ ID NO: 1
  • An exemplary polynucleotide that encodes the VL Domain of PD-1 mAb 14 is SEQ ID NO: 1
  • CDRLI of PD-1 mAb 15 (SEQ ID NO:247): LASQTIGTWLA
  • An exemplary polynucleotide that encodes the VL Domain of PD-1 mAb 15 is SEQ ID NO: 1
  • the above-described murine anti-human PD-1 antibody PD-1 mAb 15 was humanized and further deimmunized when antigenic epitopes were identified in order to demonstrate the capability of humanizing an anti -human PD-1 antibody so as to decrease its antigenicity upon administration to a human recipient.
  • the humanization yielded one humanized VH Domain, designated herein as "hPD-1 mAb 2 VHl,” and one humanized VL Domains designated herein as "hPD-1 mAb 1 VL1.”
  • An antibody comprising the humanized VL Domain paired with the humanized VH Domain is referred to as "hPD-1 mAb 15.”
  • An exemplary polynucleotide that encodes hPD-1 mAb 15 VHl is SEQ ID NO:251
  • An exemplary polynucleotide that encodes hPD-1 mAb 15 VL1 is SEQ ID NO:253
  • FcyRI CD64
  • FcyRIIA CD32A
  • FcyRIII CD 16
  • FcyRIIB CD32B
  • FcRn neonatal Fc Receptor
  • Modification of the Fc Region normally leads to an altered phenotype, for example altered serum half-life, altered stability, altered susceptibility to cellular enzymes or altered effector function. It may be desirable to modify an antibody or other binding molecule of the present invention with respect to effector function, for example, so as to enhance the effectiveness of such molecule in treating cancer. Reduction or elimination of effector function is desirable in certain cases, for example in the case of antibodies whose mechanism of action involves blocking or antagonism, but not killing of the cells bearing a target antigen.
  • Increased effector function is generally desirable when directed to undesirable cells, such as tumor and foreign cells, where the FcyRs are expressed at low levels, for example, tumor-specific B cells with low levels of FcyRIIB (e.g., non-Hodgkins lymphoma, CLL, and Burkitt's lymphoma).
  • FcyRIIB e.g., non-Hodgkins lymphoma, CLL, and Burkitt's lymphoma.
  • molecules of the invention with conferred or altered effector function activity are useful for the treatment and/or prevention of a disease, disorder or infection where an enhanced efficacy of effector function activity is desired.
  • the PD-l-binding molecules of the present invention comprise an Fc Region that possesses one or more modifications (e.g., substitutions, deletions, or insertions) to the sequence of amino acids of a wild-type Fc Region (e.g., SEQ ID NO:l), which reduce the affinity and avidity of the Fc Region and, thus, the molecule of the invention, for one or more FcyR receptors.
  • the molecules of the invention comprise an Fc Region that possesses one or more modifications to the amino acids of the wild- type Fc Region, which increase the affinity and avidity of the Fc Region and, thus, the molecule of the invention, for one or more FcyR receptors.
  • the molecules comprise a variant Fc Region wherein said variant confers or mediates increased antibody dependent cell mediated cytotoxicity (ADCC) activity and/or an increased binding to FcyRIIA, relative to a molecule comprising no Fc Region or comprising a wild-type Fc Region.
  • ADCC antibody dependent cell mediated cytotoxicity
  • the molecules comprise a variant Fc Region wherein said variant confers or mediates decreased ADCC activity (or other effector function) and/or an increased binding to FcyRIIB, relative to a molecule comprising no Fc Region or comprising a wild-type Fc Region.
  • the invention encompasses PD-1 -binding molecules comprising a variant Fc Region, which variant Fc Region does not show a detectable binding to any FcyR, relative to a comparable molecule comprising the wild-type Fc Region.
  • the invention encompasses PD-1 -binding molecules comprising a variant Fc Region, which variant Fc Region only binds a single FcyR, preferably one of FcyRIIA, FcyRIIB, or FcyRIIIA.
  • any such increased affinity and/or avidity is preferably assessed by measuring in vitro the extent of detectable binding to the FcyR or FcyR-related activity in cells that express low levels of the FcyR when binding activity of the parent molecule (without the modified Fc Region) cannot be detected in the cells, or in cells which express non-FcyR receptor target antigens at a density of 30,000 to 20,000 molecules/cell, at a density of 20,000 to 10,000 molecules/cell, at a density of 10,000 to 5,000 molecules/cell, at a density of 5,000 to 1,000 molecules/cell, at a density of 1,000 to 200 molecules/cell or at a density of 200 molecules/cell or less (but at least 10, 50, 100 or 150 molecules/cell).
  • the PD-l-binding molecules of the present invention may comprise a variant Fc Region having altered affinities for an activating and/or inhibitory Fey receptor.
  • the PD-l-binding molecule comprises a variant Fc Region that has increased affinity for FcyRIIB and decreased affinity for FcyRIIIA and/or FcyRIIA, relative to a comparable molecule with a wild-type Fc Region.
  • the PD-l-binding molecule of the present invention comprise a variant Fc Region, which has decreased affinity for FcyRIIB and increased affinity for FcyRIIIA and/or FcyRIIA, relative to a comparable molecule with a wild-type Fc Region.
  • the PD-l-binding molecules of the present invention comprise a variant Fc Region that has decreased affinity for FcyRIIB and decreased affinity for FcyRIIIA and/or FcyRIIA, relative to a comparable molecule with a wild-type Fc Region.
  • the PD-l-binding molecules of the present invention comprise a variant Fc Region, which has unchanged affinity for FcyRIIB and decreased (or increased) affinity for FcyRIIIA and/or FcyRIIA, relative to a comparable molecule with a wild-type Fc Region.
  • the PD-l-binding molecules of the present invention comprise a variant Fc Region having an altered affinity for FcyRIIIA and/or FcyRIIA such that the immunoglobulin has an enhanced effector function.
  • effector cell functions include antibody dependent cell mediated cytotoxicity, antibody dependent phagocytosis, phagocytosis, opsonization, opsonophagocytosis, cell binding, rosetting, C lq binding, and complement dependent cell mediated cytotoxicity.
  • the alteration in affinity or effector function is at least 2- fold, preferably at least 4-fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8-fold, at least 9-fold, at least 10-fold, at least 50-fold, or at least 100-fold, relative to a comparable molecule comprising a wild-type Fc Region.
  • the variant Fc Region immunospecifically binds one or more FcRs with at least 65%, preferably at least 70%, 75%, 80%, 85%, 90%, 95%, 100%, 125%, 150%, 175%, 200%, 225%, or 250% greater affinity relative to a molecule comprising a wild-type Fc Region.
  • Such measurements can be in vivo or in vitro assays, and in a preferred embodiment are in vitro assays such as ELISA or surface plasmon resonance assays.
  • the PD-l-binding molecules of the present invention comprise a variant Fc Region wherein said variant agonizes at least one activity of an FcyR receptor, or antagonizes at least one activity of an FcyR receptor.
  • the molecules comprise a variant that antagonizes one or more activities of FcyRIIB, for example, B-cell receptor-mediated signaling, activation of B-cells, B-cell proliferation, antibody production, intracellular calcium influx of B cells, cell cycle progression, FcyRIIB- mediated inhibition of FcsRI signaling, phosphorylation of FcyRIIB, SHIP recruitment, SHIP phosphorylation and association with She, or activity of one or more downstream molecules (e.g., MAP kinase, JNK, p38, or Akt) in the FcyRIIB signal transduction pathway.
  • FcyRIIB for example, B-cell receptor-mediated signaling, activation of B-cells, B-cell proliferation, antibody production, intracellular calcium influx of B cells, cell cycle progression, FcyRIIB- mediated inhibition of FcsRI signaling, phosphorylation of FcyRIIB, SHIP recruitment, SHIP phosphorylation and association with She, or activity of one
  • the PD-l-binding molecules of the present invention comprise a variant that agonizes one or more activities of FcsRI, for example, mast cell activation, calcium mobilization, degranulation, cytokine production, or serotonin release.
  • the molecules comprise an Fc Region comprising regions from two or more IgG isotypes (e.g., IgGl, IgG2, IgG3 and IgG4).
  • an Fc Region is said to be of a particular IgG isotype if its amino acid sequence is most homologous to that isotype relative to other IgG isotypes.
  • the various IgG isotypes exhibit differing physical and functional properties including serum half-life, complement fixation, FcyR binding affinities and effector function activities (e.g., ADCC, CDC, etc.) due to differences in the amino acid sequences of their hinge and/or Fc Regions, for example as described in Flesch and Neppert (1999) J. Clin. Lab. Anal. 14: 141-156; Chappel et al. (1993) J. Biol. Chem. 33 :25124-25131; Chappel et al. (1991) Proc. Natl. Acad. Sci. (U.S.A.) 88:9036-9040; or Briiggemann et al. (1987) J. Exp.
  • This type of variant Fc Region may be used alone, or in combination with an amino acid modification, to affect Fc-mediated effector function and/or binding activity.
  • the amino acid modification and IgG hinge/Fc Region may display similar functionality ⁇ e.g., increased affinity for FcyRIIA) and may act additively or, more preferably, synergistically to modify the effector functionality in the molecule of the invention, relative to a molecule of the invention comprising a wild-type Fc Region.
  • the amino acid modification and IgG Fc Region may display opposite functionality ⁇ e.g., increased and decreased affinity for FcyRIIA, respectively) and may act to selectively temper or reduce a specific functionality in the molecule of the invention, relative to a molecule of the invention not comprising an Fc Region or comprising a wild-type Fc Region of the same isotype.
  • the PD-1 -binding molecules of the present invention comprise a variant Fc Region, wherein said variant Fc Region comprises at least one amino acid modification relative to a wild-type Fc Region, such that said molecule has an altered affinity for an FcR, provided that said variant Fc Region does not have a substitution at positions that make a direct contact with FcyR based on crystallographic and structural analysis of Fc-FcR interactions such as those disclosed by Sondermann et al. (2000) Nature 406:267- 73.
  • the molecules of the invention comprise variant Fc Regions comprise modification of at least one residue that does not make a direct contact with an FcyR based on structural and crystallographic analysis, e.g., is not within the Fc-FcyR binding site.
  • Variant Fc Regions are well known in the art, and any known variant Fc Region may be used in the present invention to confer or modify the effector function exhibited by a molecule of the invention comprising an Fc Region (or portion thereof) as functionally assayed, e.g., in an NK dependent or macrophage dependent assay.
  • Fc Region variants identified as altering effector function are disclosed in PCT Publications No. WO 04/063351; WO 06/088494; WO 07/024249; WO 06/113665; WO 07/021841; WO 07/106707; and WO 2008/140603, and any suitable variant disclosed therein may be used in the present molecules.
  • the PD-l-binding molecules of the present invention comprise a variant Fc Region, having one or more amino acid modifications in one or more regions, which modification(s) alter (relative to a wild-type Fc Region) the Ratio of Affinities of the variant Fc Region to an activating FcyR (such as FcyRIIA or FcyRIIIA) relative to an inhibiting FcyR (such as FcyRIIB):
  • PD-l-binding molecules of the present invention that possess a variant Fc Region (relative to the wild-type Fc Region) in which the variant Fc Region has a Ratio of Affinities greater than 1.
  • Such molecules have particular use in providing a therapeutic or prophylactic treatment of a disease, disorder, or infection, or the amelioration of a symptom thereof, where an enhanced efficacy of effector cell function (e.g., ADCC) mediated by FcyR is desired, e.g., cancer or infectious disease.
  • a variant Fc Region having a Ratio of Affinities less than 1 mediates decreased efficacy of effector cell function.
  • Table 1 lists exemplary single, double, triple, quadruple and quintuple mutations by whether their Ratio of Affinities is greater than or less than 1.
  • any amino acid modifications e.g., substitutions
  • any amino acid modifications e.g., substitutions
  • any amino acid modifications e.g., substitutions
  • any amino acid modifications at any of positions 255, 256, 258, 267, 268, 269, 270, 272, 276, 278, 280, 283, 285, 286, 289, 290, 292, 293, 294, 295, 296, 298, 300, 301, 303, 305, 307, 309, 312, 320, 322, 326, 329, 330, 332, 331, 333, 334, 335, 337, 338, 339, 340, 359, 360, 373, 376, 416, 419, 430, 434, 435, 437, 438 or 439.
  • the variant Fc Region has any of the following residues: A256, N268, Q272, D286, Q286, S286, A290, S290, A298, M301, A312, E320, M320, Q320, R320, E322, A326, D326, E326, N326, S326, K330, T339, A333, A334, E334, H334, L334, M334, Q334, V334, K335, Q335, A359, A360 or A430.
  • any amino acid modifications e.g., substitutions
  • any amino acid modifications e.g., substitutions
  • any amino acid modifications e.g., substitutions
  • any amino acid modifications e.g., substitutions
  • any amino acid modifications e.g., substitutions
  • any amino acid modifications e.g., substitutions
  • any of the following residues A255, A256, A258, A267, A268, N268, A272, Q272, A276, A280, A283, A285, A286, D286, Q286, S286, A290, S290, M301, E320, M320, Q320, R320, E322, A326, D326, E326, S326, K330, A331, Q335, A337 or A430.
  • Preferred variants include one or more modifications at any of positions: 228, 230, 231, 232, 233, 234, 235, 239, 240, 241, 243, 244, 245, 247, 262, 263, 264, 265, 266, 271, 273, 275, 281, 284, 291, 296, 297, 298, 299, 302, 304, 305, 313, 323, 325, 326, 328, 330 or 332.
  • Particularly preferred variants include one or more modifications selected from groups A-AI:
  • Still more particularly preferred variants include one or more modifications selected from Groups 1-105:
  • a PD-1 -binding molecule of the invention will comprise a variant Fc Region having at least one modification in the Fc Region.
  • the variant Fc Region comprises at least one substitution selected from the group consisting of L235V, F243L, R292P, Y300L, V305I, and P396L.
  • the variant Fc Region comprises:
  • the variant Fc Region comprises substitutions of:
  • a PD-1 -binding molecule of the invention comprises a variant Fc Region that exhibits decreased (or substantially no) binding to FcyRIA (CD64), FcyRIIA (CD32A), FcyRIIB (CD32B), FcyRIIIA (CD 16a) or FcyRIIIB (CD 16b) (relative to the binding exhibited by the wild-type IgGl Fc Region (SEQ ID NO:l)).
  • a PD-1- binding molecule of the invention will comprise a variant Fc Region that exhibits reduced (or substantially no) binding to an FcyR (e.g., FcyRIIIA) and reduced (or substantially no) ADCC effector function.
  • the variant Fc Region comprises at least one substitution selected from the group consisting of L234A, L235A, D265A,N297Q, and N297G.
  • the variant Fc Region comprises the substitution of L234A; L235A; L234A and L235A; D265A; N297Q, or N297G.
  • a preferred IgGl sequence for the CH2 and CH3 Domains of the PD-l-binding molecules of the invention will have the L234A/L235A substitutions (SEQ ID NO:5):
  • X is a lysine (K) or is absent.
  • a PD-l-binding molecule of the invention comprises an Fc Region which inherently exhibits decreased (or substantially no) binding to FcyRIIIA (CD 16a) and/or reduced effector function (relative to the binding exhibited by the wild-type IgGl Fc Region (SEQ ID NO:l)).
  • a PD-l-binding molecule of the present invention comprises an IgG2 Fc Region (SEQ ID NO:2) or an IgG4 Fc Region (SEQ ID:NO:4).
  • the instant invention also encompasses the introduction of a stabilizing mutation, such as the IgG4 hinge region S228P substitution (see, e.g., SEQ ID NO:13: ESKYGPPCPPCP, (Lu et al, (2008) "The Effect Of A Point Mutation On The Stability Of Igg4 As Monitored By Analytical Ultracentrifugation " J. Pharmaceutical Sciences 97:960-969) to reduce the incidence of strand exchange.
  • a stabilizing mutation such as the IgG4 hinge region S228P substitution (see, e.g., SEQ ID NO:13: ESKYGPPCPPCP, (Lu et al, (2008) "The Effect Of A Point Mutation On The Stability Of Igg4 As Monitored By Analytical Ultracentrifugation " J. Pharmaceutical Sciences 97:960-969) to reduce the incidence of strand exchange.
  • the invention encompasses the use of any variant Fc Region known in the art, such as those disclosed in Jefferis, B.J. et al (2002) "Interaction Sites On Human IgG-Fc For FcgammaR: Current Models " Immunol. Lett. 82:57-65; Presta, L.G. etal. (2002) “Engineering Therapeutic Antibodies For Improved Function " Biochem. Soc. Trans. 30:487-90; Idusogie, E.E. et al. (2001) "Engineered Antibodies With Increased Activity To recruit Complement " J. Immunol. 166:2571-75; Shields, R.L. et al.
  • the molecules of the invention further comprise one or more glycosylation sites, so that one or more carbohydrate moieties are covalently attached to the molecule.
  • the molecules of the invention with one or more glycosylation sites and/or one or more modifications in the Fc Region confer or have an enhanced antibody mediated effector function, e.g., enhanced ADCC activity, compared to the unmodified antibody.
  • the invention further comprises molecules comprising one or more modifications of amino acids that are directly or indirectly known to interact with a carbohydrate moiety of the Fc Region, including but not limited to amino acids at positions 241, 243, 244, 245, 245, 249, 256, 258, 260, 262, 264, 265, 296, 299, and 301.
  • Amino acids that directly or indirectly interact with a carbohydrate moiety of an Fc Region are known in the art, see, e.g., Jefferis et al, 1995 Immunology Letters, 44: 111-7, which is incorporated herein by reference in its entirety.
  • the invention encompasses molecules that have been modified by introducing one or more glycosylation sites into one or more sites of the molecules, preferably without altering the functionality of the molecules, e.g., binding activity to target antigen or FcyR.
  • Glycosylation sites may be introduced into the variable and/or constant region of the molecules of the invention.
  • "glycosylation sites” include any specific amino acid sequence in an antibody to which an oligosaccharide ⁇ i.e., carbohydrates containing two or more simple sugars linked together) will specifically and covalently attach. Oligosaccharide side chains are typically linked to the backbone of an antibody via either N-or O-linkages.
  • N-linked glycosylation refers to the attachment of an oligosaccharide moiety to the side chain of an asparagine residue.
  • O-linked glycosylation refers to the attachment of an oligosaccharide moiety to a hydroxyamino acid, e.g., serine, threonine.
  • the molecules of the invention may comprise one or more glycosylation sites, including N-linked and O-linked glycosylation sites. Any glycosylation site for N-linked or O-linked glycosylation known in the art may be used in accordance with the instant invention.
  • An exemplary N-linked glycosylation site that is useful in accordance with the methods of the present invention is the amino acid sequence: Asn-X-Thr/Ser, wherein X may be any amino acid and Thr/Ser indicates a threonine or a serine.
  • a site or sites may be introduced into a molecule of the invention using methods well known in the art to which this invention pertains (see for example, IN VITRO MUTAGENESIS, RECOMBINANT DNA: A SHORT COURSE, J. D. Watson, et al. W.H. Freeman and Company, New York, 1983, chapter 8, pp. 106-116, which is incorporated herein by reference in its entirety.
  • An exemplary method for introducing a glycosylation site into a molecule of the invention may comprise: modifying or mutating an amino acid sequence of the molecule so that the desired Asn-X-Thr/Ser sequence is obtained.
  • the invention encompasses methods of modifying the carbohydrate content of a molecule of the invention by adding or deleting a glycosylation site.
  • Methods for modifying the carbohydrate content of antibodies (and molecules comprising antibody domains, e.g., Fc Region) are well known in the art and encompassed within the invention, see, e.g., U.S. Patent No. 6,218,149; EP 0 359 096 B l; U.S. Publication No. US 2002/0028486; WO 03/035835; U.S. Publication No. 2003/0115614; U.S. Patent No. 6,218,149; U.S. Patent No.
  • the invention encompasses methods of modifying the carbohydrate content of a molecule of the invention by deleting one or more endogenous carbohydrate moieties of the molecule.
  • the invention encompasses shifting the glycosylation site of the Fc Region of an antibody, by modifying positions adjacent to 297.
  • the invention encompasses modifying position 296 so that position 296 and not position 297 is glycosylated.
  • Effector function can also be modified by techniques such as by introducing one or more cysteine residues into the Fc Region, thereby allowing interchain disulfide bond formation in this region to occur, resulting in the generation of a homodimeric antibody that may have improved internalization capability and/or increased complement-mediated cell killing and ADCC (Caron, P.C. et a/. (1992) "Engineered Humanized Dimeric Forms OfIgG Are More Effective Antibodies;' J. Exp. Med. 176: 1191-1195; Shopes, B. (1992) 11 A Genetically Engineered Human IgG Mutant With Enhanced Cytolytic Activity;' J. Immunol. 148(9):2918-2922.
  • Homodimeric antibodies with enhanced antitumor activity may also be prepared using heterobifunctional cross-linkers as described in Wolff, E.A. et al. (1993) "Monoclonal Antibody Homodimers: Enhanced Antitumor Activity In Nude Mice " Cancer Research 53 :2560-2565.
  • an antibody can be engineered which has dual Fc Regions and may thereby have enhanced complement lysis and ADCC capabilities (Stevenson, G.T. et al. (1989) "A Chimeric Antibody With Dual Fc Regions (bisFabFc) Prepared By Manipulations At The IgG Hinge " Anti-Cancer Drug Design 3 :219-230).
  • the serum half-life of the molecules of the present invention comprising Fc Regions may be increased by increasing the binding affinity of the Fc Region for FcRn.
  • the term "half- life" as used herein means a pharmacokinetic property of a molecule that is a measure of the mean survival time of the molecules following their administration.
  • Half-life can be expressed as the time required to eliminate fifty percent (50%) of a known quantity of the molecule from a subject's body ⁇ e.g., human patient or other mammal) or a specific compartment thereof, for example, as measured in serum, i.e., circulating half-life, or in other tissues.
  • an increase in half-life results in an increase in mean residence time (MRT) in circulation for the molecule administered.
  • MRT mean residence time
  • the PD-1 -binding molecules of the present invention comprise a variant Fc Region, wherein said variant Fc Region comprises at least one amino acid modification relative to a wild-type Fc Region, such that said molecule has an increased half-life (relative to a wild-type Fc Region).
  • the PD-l-binding molecules of the present invention comprise a variant Fc Region, wherein said variant Fc Region comprises a half-live extending amino acid substitution at one or more positions selected from the group consisting of 238, 250, 252, 254, 256, 257, 256, 265, 272, 286, 288, 303, 305, 307, 308, 309, 311, 312, 317, 340, 356, 360, 362, 376, 378, 380, 382, 413, 424, 428, 433, 434, 435, and 436 .
  • said variant Fc Region comprises a half-live extending amino acid substitution at one or more positions selected from the group consisting of 238, 250, 252, 254, 256, 257, 256, 265, 272, 286, 288, 303, 305, 307, 308, 309, 311, 312, 317, 340, 356, 360, 362, 376, 378, 380, 382, 413, 424, 428, 433, 434, 435, and 4
  • Numerous specific mutations capable of increasing the half-life of an Fc Region-containing molecule are known in the art and include, for example M252Y, S254T, T256E, and combinations thereof. For example, see the mutations described in U.S. Patent Nos. 6,277,375, 7,083,784; 7,217,797, 8,088,376; U.S. Publication Nos. 2002/0147311; 2007/0148164; and International Publication Nos. WO 98/23289; WO 2009/058492; and WO 2010/033279, which are herein incorporated by reference in their entireties.
  • Fc Region-containing molecules with enhanced half-life also include those with substitutions at two or more of Fc Region residues 250, 252, 254, 256, 257, 288, 307, 308, 309, 311, 378, 428, 433, 434, 435 and 436.
  • two or more substitutions selected from: T250Q, M252Y, S254T, T256E, K288D, T307Q, V308P, A378V, M428L, N434A, H435K, and Y436I.
  • the variant Fc Region comprises substitutions of:
  • the instant invention further encompasses variant Fc Regions comprising:
  • One embodiment of the present invention relates to bispecific binding molecules that are capable of binding to a "first epitope” and a "second epitope,” wherein the first epitope is an epitope of human PD-1 and the second epitope is the same or a different epitope of PD-1, or is an epitope of another molecule that is present on the surface of an immune cell (such as a T lymphocyte) and is involved in regulating an immune checkpoint.
  • an immune cell such as a T lymphocyte
  • the second epitope is an epitope of B7-H3, B7-H4, BTLA, CD3, CD8, CD16, CD27, CD32, CD40, CD40L, CD47, CD64, CD70, CD80, CD86, CD94, CD137, CD137L, CD226, CTLA-4, Galectin-9, GITR, GITRL, HHLA2, ICOS, ICOSL, KIR, LAG-3, LIGHT, MHC class I or II, KG2a, KG2d, OX40, OX40L, PDIH, PD-1, PD-Ll, PD-L2, PVR, SIRPa, TCR, TIGIT, TEVI-3 or VISTA.
  • the second epitope not an epitope of PD-1.
  • the second epitope is CD137, CTLA-4, LAG-3, OX40, TIGIT, or TEVI-3.
  • a bispecific molecule comprises more than two epitope binding sites. Such bispecific molecules may bind two or more different epitopes of LAG-3 and at least one epitope of a molecule that is not LAG-3.
  • the instant invention encompasses bispecific antibodies capable of simultaneously binding to PD-1 and the second epitope (e.g.
  • the bispecific antibody capable of simultaneously binding to PD-1 and the second epitope is produced using any of the methods described in PCT Publication Nos.
  • One embodiment of the present invention relates to bispecific diabodies that comprise, and most preferably are composed of, a first polypeptide chain and a second polypeptide chain, whose sequences permit the polypeptide chains to covalently bind to each other to form a covalently associated diabody that is capable of simultaneously binding to a first epitope and a second epitope, such epitopes not being identical to one another.
  • Such bispecific diabodies thus comprise "VL1" / "VH1" domains that are capable of binding to the first epitope and "VL2" / " VH2" domains that are capable of binding to the second epitope.
  • VL1 and VH1 denote respectively, the Variable Light Chain Domain and Variable Heavy Chain Domain that bind the "first" epitope of such bispecific diabody.
  • VL2 and VH2 denote respectively, the Variable Light Chain Domain and Variable Heavy Chain Domain that bind the "second" epitope of such bispecific diabody. It is irrelevant whether a particular epitope is designated as the first vs. the second epitope; such notation having relevance only with respect to the presence and orientation of domains of the polypeptide chains of the binding moleucles of the present invention.
  • one of such epitopes is an epitope of PD-1 and the other of such epitopes is not an epitope of PD-1 (for example, an epitope of B7-H3, B7-H4, BTLA, CD40, CD80, CD86, CD137, CTLA-4, ICOS, KIR, LAG-3, MHC class I or II, OX40, PD-L1, TCR, TIM-3, etc.).
  • the VL Domain of the first polypeptide chain interacts with the VH Domain of the second polypeptide chain to form a first functional antigen-binding site that is specific for a first antigen (i.e., either PD-1 or an antigen that contains the second epitope).
  • a first antigen i.e., either PD-1 or an antigen that contains the second epitope
  • the VL Domain of the second polypeptide chain interacts with the VH Domain of the first polypeptide chain in order to form a second functional antigen-binding site that is specific for a second antigen (i.e., either an antigen that contains the second epitope or PD-1).
  • the selection of the VL and VH Domains of the first and second polypeptide chains is coordinated, such that the two polypeptide chains of the diabody collectively comprise VL and VH Domains capable of binding to both an epitope of PD-1 and to the second epitope (i.e., they comprise VLPD-I/VHPD-I and VL2/VH2, wherein PD-1 is the "first" epitope, or VL1/VH1 and VLPD- l/VHpD-i, wherein PD-1 is the "second" epitope).
  • the first polypeptide chain of an embodiment of such bispecific diabodies comprises, in the N-terminal to C-terminal direction, an N-terminus, the VLl Domain of a monoclonal antibody capable of binding to either the first or second epitope (i.e., either VLPD- l or VLEpitope 2), a first intervening spacer peptide (Linker 1), a VH2 Domain of a monoclonal antibody capable of binding to either the second epitope (if such first polypeptide chain contains VLPD-I) or the first epitope (if such first polypeptide chain contains VLEpitope 2), a second intervening spacer peptide (Linker 2) optionally containing a cysteine residue, a Heterodimer-Promoting Domain and a C-terminus ( Figure 1).
  • the second polypeptide chain of this embodiment of bispecific diabodies comprises, in the N-terminal to C-terminal direction, an N-terminus, a VL2 Domain of a monoclonal antibody capable of binding to either PD-1 or the second epitope (i.e., either VLPD -1 Or VLEpitope 2, and being the VL Domain not selected for inclusion in the first polypeptide chain of the diabody), an intervening linker peptide (Linker 1), a VHl Domain of a monoclonal antibody capable of binding to either the second epitope (if such second polypeptide chain contains VLPD-I) or to PD-1 (if such second polypeptide chain contains VLEpitope 2), a second intervening spacer peptide (Linker 2) optionally containing a cysteine residue, a Heterodimer-Promoting Domain, and a C-terminus ( Figure 1).
  • Linker 1 an intervening linker peptide
  • Linker 2 optionally containing a cyst
  • the length of the intervening linker peptide (e.g., Linker 1) that separates such VL and VH Domains is selected to substantially or completely prevent the VL and VH Domains of the polypeptide chain from binding to one another.
  • the VL and VH Domains of the first polypeptide chain are substantially or completely incapable of binding to one another.
  • the VL and VH Domains of the second polypeptide chain are substantially or completely incapable of binding to one another.
  • a preferred intervening spacer peptide (Linker 1) has the sequence (SEQ ID NO:14): GGGS GGGG.
  • the length and composition of the second intervening linker peptide (Linker 2) is selected based on the choice of heterodimer-promoting domains. Typically, the second intervening linker peptide (Linker 2) will comprise 3-20 amino acid residues. In particular, where the heterodimer-promoting domains do not comprise a cysteine residue a cysteine- containing second intervening linker peptide (Linker 2) is utilized. A cysteine-containing second intervening spacer peptide (Linker 2) will contain 1, 2, 3 or more cysteines. A preferred cysteine-containing spacer peptide (Linker 2) has the sequence is SEQ ID NO: 15: GGCGGG.
  • Linker 2 does not comprise a cysteine (e.g., GGG , GGGS (SEQ ID NO:29), LGGGS G (SEQ ID NO:261), GGGS GGGS GGG (SEQ ID NO:262), AS TKG (SEQ ID NO:30), LE PKS S (SEQ ID NO:33), APS S S (SEQ ID NO:34), etc.) and a Cysteine-Containing Heterodimer-Promoting Domain, as described below is used.
  • a cysteine- containing Linker 2 and a cysteine-containing Heterodimer-Promoting Domain are used.
  • the Heterodimer-Promoting Domains may be GVE PKS C (SEQ ID NO: 16) or VE PKS C ( SEQ ID NO: 17) or AE PKS C (SEQ ID NO: 18) on one polypeptide chain and GFNRGEC (SEQ ID NO: 19) or FNRGEC (SEQ ID NO: 20) on the other polypeptide chain (US2007/0004909).
  • the Heterodimer-Promoting Domains of such diabodies are formed from one, two, three or four tandemly repeated coil domains of opposing charge that comprise a sequence of at least six, at least seven or at least eight amino acid residues such that the Heterodimer-Promoting Domain possesses a net charge
  • Helix-stabilized Fv (hsFv) Antibody Fragments Substituting the Constant Domains of a Fab Fragment for a Heterodimeric Coiled-coil Domain," J. Molec. Biol. 312:221-228; Arndt, K.M. et al. (2002) “Comparison of In Vivo Selection and Rational Design of Heterodimeric Coiled Coils," Structure 10: 1235-1248; Boucher, C. et al. (2010) “Protein Detection By Western Blot Via Coiled-Coil Interactions," Analytical Biochemistry 399: 138-140; Cachia, P.J. et al.
  • Such repeated coil domains may be exact repeats or may have substitutions.
  • the coil domain of the Heterodimer-Promoting Domain of the first polypeptide chain may comprise a sequence of eight amino acid residues selected to confer a negative charge to such Heterodimer-Promoting Domain
  • the coil domain of the Heterodimer-Promoting Domain of the second polypeptide chain may comprise a sequence of eight amino acid residues selected to confer a positive charge to such Heterodimer-Promoting Domain. It is immaterial which coil is provided to the first or second polypeptide chains, provided that a coil of opposite charge is used for the other polypeptide chain.
  • the positively charged amino acid may be lysine, arginine, histidine, etc. and/or the negatively charged amino acid may be glutamic acid, aspartic acid, etc.
  • the positively charged amino acid is preferably lysine and/or the negatively charged amino acid is preferably glutamic acid. It is possible for only a single Heterodimer- Promoting Domain to be employed (since such domain will inhibit homodimerization and thereby promote heterodimerization), however, it is preferred for both the first and second polypeptide chains of the diabodies of the present invention to contain Heterodimer-Promoting Domains.
  • one of the Heterodimer-Promoting Domains will comprise four tandem "E-coil” helical domains (SEQ ID NO:21: E VAALE K - E VAALE K - EVAALEK-EVAALEK), whose glutamate residues will form a negative charge at pH 7, while the other of the Heterodimer-Promoting Domains will comprise four tandem "K-coil” domains (SEQ ID NO:22: KVAAL KE - KVAAL KE - KVAAL KE - KVAAL KE - KVAAL KE ), whose lysine residues will form a positive charge at pH 7.
  • Heterodimer-Promoting Domain in which one of the four tandem "E-coil" helical domains of SEQ ID NO:21 has been modified to contain a cysteine residue: EVAACEK- E VAALE K - E VAALE K - E VAALE K (SEQ ID NO:23).
  • Heterodimer-Promoting Domain in which one of the four tandem "K-coil" helical domains of SEQ ID NO:22 has been modified to contain a cysteine residue: KVAACKE - KVAALKE - KVAALKE -KVAALKE (SEQ ID NO:24).
  • a diabody in order to improve the in vivo pharmacokinetic properties of diabodies, may be modified to contain a polypeptide portion of a serum- binding protein at one or more of the termini of the diabody. Most preferably, such polypeptide portion of a serum-binding protein will be installed at the C-terminus of the diabody.
  • Albumin is the most abundant protein in plasma and has a half-life of 19 days in humans. Albumin possesses several small molecule binding sites that permit it to non-covalently bind to other proteins and thereby extend their serum half-lives.
  • the Albumin-Binding Domain 3 (ABD3) of protein G of Streptococcus strain G148 consists of 46 amino acid residues forming a stable three-helix bundle and has broad albumin-binding specificity (Johansson, M.U. et al. (2002) “Structure, Specificity, And Mode Of Interaction For Bacterial Albumin-Binding Modules " J. Biol. Chem. 277(10):8114-8120.
  • a particularly preferred polypeptide portion of a serum- binding protein for improving the in vivo pharmacokinetic properties of a diabody is the Albumin-Binding Domain (ABD) from streptococcal protein G, and more preferably, the Albumin-Binding Domain 3 (ABD3) of protein G of Streptococcus dysgalactiae strain G148 (SEQ ID NO:25): LAEAKVLANR ELDKYGVS DY YKNL I DNAKS AEGVKAL I DE I LAALP .
  • deimmunized variants of SEQ ID NO:25 have the ability to attenuate or eliminate MHC class II binding. Based on combinational mutation results, the following combinations of substitutions are considered to be preferred substitutions for forming such a deimmunized ABD: 66D/70S +71A; 66S/70S +71A; 66S/70S +79A; 64A/65A/71A; 64A/65A/71A+66S; 64A/65A/71A+66D; 64A/65A/71A+66E; 64A/65A/79A+66S; 64A/65A/79A+66D; 64A/65A/79A+66E.
  • Variant ABDs having the modifications L64A, I65A and D79A or the modifications N66S, T70S and D79A.
  • Variant deimmunized ABD having the amino acid sequence:
  • the first polypeptide chain of such a diabody having an ABD contains a peptide linker preferably positioned C-terminally to the E- coil (or K-coil) Domain of such polypeptide chain so as to intervene between the E-coil (or K- coil) Domain and the ABD (which is preferably a deimmunized ABD).
  • a preferred sequence for such a peptide linker is SEQ ID NO:29: GGGS.
  • One embodiment of the present invention relates to bispecific diabodies comprising an Fc Region capable of simultaneously binding to PD-1 and a second epitope (e.g. B7-H3, B7-H4, BTLA, CD40, CD80, CD86, CD137, CTLA-4, ICOS, KIR, LAG-3, MHC class I or II, OX40, PD-1, PD-Ll, TCR, TIM-3, etc.).
  • a second epitope e.g. B7-H3, B7-H4, BTLA, CD40, CD80, CD86, CD137, CTLA-4, ICOS, KIR, LAG-3, MHC class I or II, OX40, PD-1, PD-Ll, TCR, TIM-3, etc.
  • the addition of an IgG CH2-CH3 Domain to one or both of the diabody polypeptide chains, such that the complexing of the diabody chains results in the formation of an Fc Region, increases the biological half-life and/or
  • CHI Domain a peptide having the amino acid sequence GVE PKS C (SEQ ID NO: 16) VE PKS C ( SEQ ID NO: 17), or AE PKS C (SEQ ID NO: 18), derived from the hinge domain of a human IgG
  • the CL Domain one may employ the C-terminal 6 amino acids of the human kappa light chain, GFNRGEC (SEQ ID NO: 19) or FNRGEC (SEQ ID NO:20).
  • GFNRGEC SEQ ID NO: 19
  • FNRGEC SEQ ID NO:20
  • a peptide comprising tandem coil domains of opposing charge such as the "E-coil” helical domains (SEQ ID NO:21: E VAALE K - E VAALE K - E VAALE K - E VAALE K o r SEQ ID NO:23: EVAACE K-EVAALEK-EVAALEK-EVAALEK); and the "K-coil” domains (SEQ ID NO:22: KVAALKE -KVAALKE -KVAALKE -KVAALKE or SEQ ID NO:24: KVAACKE - KVAALKE - KVAALKE - KVAALKE ) .
  • a representative coil domain containing four-chain diabody is shown in Figure 3B.
  • the Fc Region-containing diabody molecules of the present invention generally include additional intervening linker peptides (Linkers). Typically, the additional Linkers will comprise 3-20 amino acid residues. Additional or alternative linkers that may be employed in the Fc Region-containing diabody molecules of the present invention include: GGGS (SEQ ID NO:29), LGGGS G (SEQ ID NO:261), GGGS GGGS GGG (SEQ ID NO:262), AS T KG (SEQ ID NO:30), DKTHTCPPCP (SEQ ID NO:31), E PKS CDKTHTCPPCP (SEQ ID NO:32), LE PKS S (SEQ ID NO:33), APS S S (SEQ ID NO:34), and APS S S PME (SEQ ID NO:35), LE PKSADKTHTCPPC SEQ ID NO:36), GGC, and GGG.
  • Linkers will comprise 3-20 amino acid residues. Additional or alternative linkers that may be employed in the Fc Region-containing diabody molecules of the present invention include
  • SEQ ID NO:33 may be used in lieu of GGG or GGC for ease of cloning. Additionally, the amino acids GGG, or SEQ ID NO:33 may be immediately followed by SEQ ID NO:31 to form the alternate linkers: GGGDKTHTCPPCP (SEQ ID NO:263); and LE PKS S DKTHTCPPCP (SEQ ID NO:37).
  • Fc Region-containing diabody molecule of the present invention may incorporate an IgG hinge region in addition to or in place of a linker.
  • Exemplary hinge regions include: EPKSCDKTHTCPPCP (SEQ ID NO:32) from IgGl, ERKCCVECPPCP (SEQ ID NO:ll) from IgG2, ESKYGPPCPSCP (SEQ ID NO:12) from IgG4, and ESKYGPPCPPCP (SEQ ID NO: 13) an IgG4 hinge variant comprising a stabilizing substitute to reduce strand exchange.
  • diabodies of the invention may comprise four different chains.
  • the first and third polypeptide chains of such a diabody contain three domains: (i) a VL1 -containing Domain, (ii) a VH2-containing Domain, (iii) Heterodimer- Promoting Domain and (iv) a Domain containing a CH2-CH3 sequence.
  • the second and fourth polypeptide chains contain: (i) a VL2-containing Domain, (ii) a VHl -containing Domain and (iii) a Heterodimer-Promoting Domain, where the Heterodimer-Promoting Domains promote the dimerization of the first/third polypeptide chains with the second/fourth polypeptide chains.
  • the VL and/or VH Domains of the third and fourth polypeptide chains, and VL and/or VH Domains of the first and second polypeptide chains may be the same or different so as to permit tetravalent binding that is either monospecific, bispecific or tetraspecific.
  • VL3 and VH3 denote respectively, the Variable Light Chain Domain and Variable Heavy Chain Domain that bind the "third" epitope of such diabody.
  • VL4 and VH4 denote respectively, the Variable Light Chain Domain and Variable Heavy Chain Domain that bind the "fourth" epitope of such diabody.
  • Table 2 The general structure of the polypeptide chains of a representative four-chain Fc Region-containing diabodies of invention is provided in Table 2:
  • diabodies of the present invention are bispecific, tetravalent (i.e., possess four epitope-binding sites), Fc-containing diabodies ( Figures 3A-3C) that are composed of four total polypeptide chains.
  • the bispecific, tetravalent, Fc-containing diabodies of the invention comprise two epitope-binding sites immunospecific for PD-1 (which may be capable of binding to the same epitope of PD-1 or to different epitopes of PD-1), and two epitope-binding sites specific for a second epitope (e.g., B7-H3, B7-H4, BTLA, CD40, CD80, CD86, CD137, CTLA-4, ICOS, KIR, LAG-3 MHC class I or II, OX40, PD-L1, TCR, TEVI-3, etc.).
  • two epitope-binding sites immunospecific for PD-1 which may be capable of binding to the same epitope of PD-1 or to different epitopes of PD-1
  • two epitope-binding sites specific for a second epitope e.g., B7-H3, B7-H4, BTLA, CD40, CD80, CD86, CD137, CTLA-4, ICOS
  • the bispecific Fc Region-containing diabodies may comprise three polypeptide chains.
  • the first polypeptide of such a diabody contains three domains: (i) a VL1 -containing Domain, (ii) a VH2-containing Domain and (iii) a Domain containing a CH2-CH3 sequence.
  • the second polypeptide of such diabodies contains: (i) a VL2-containing Domain, (ii) a VH1 -containing Domain and (iii) a Domain that promotes heterodimerization and covalent bonding with the diabody's first polypeptide chain.
  • the third polypeptide of such diabodies comprises a CH2-CH3 sequence.
  • the first and second polypeptide chains of such diabodies associate together to form a VLl/VHl binding site that is capable of binding to the first epitope, as well as a VL2/VH2 binding site that is capable of binding to the second epitope.
  • the first and second polypeptides are bonded to one another through a disulfide bond involving cysteine residues in their respective Third Domains.
  • the first and third polypeptide chains complex with one another to form an Fc Region that is stabilized via a disulfide bond.
  • Such diabodies have enhanced potency.
  • Figures 4A and 4B illustrate the structures of such diabodies.
  • Such Fc-Region-containing bispecific diabodies may have either of two orientations (Table 3):
  • diabodies of the present invention are bispecific, bivalent (i.e., possess two epitope-binding sites), Fc-containing diabodies ( Figures 4A-4B) that are composed of three total polypeptide chains.
  • the bispecific, bivalent Fc-containing diabodies of the invention comprise one epitope-binding site immunospecific for PD-1, and one epitope- binding site specific for a second epitope (e.g., B7-H3, B7-H4, BTLA, CD40, CD80, CD86, CD137, CTLA-4, ICOS, KIR, LAG- 3 MHC class I or II, OX40, PD-L1, TCR, TIM-3, etc.).
  • the bispecific Fc Region-containing diabodies may comprise a total of five polypeptide chains.
  • two of said five polypeptide chains have the same amino acid sequence.
  • the first polypeptide chain of such diabodies contains: (i) a VH1 -containing domain, (ii) a CHI -containing domain, and (iii) a Domain containing a CH2-CH3 sequence.
  • the first polypeptide chain may be the heavy chain of an antibody that contains a VH1 and a heavy chain constant region.
  • the second and fifth polypeptide chains of such diabodies contain: (i) a VL1 -containing domain, and (ii) a CL- containing domain.
  • the second and/or fifth polypeptide chains of such diabodies may be light chains of an antibody that contains a VL1 complementary to the VH1 of the first/third polypeptide chain.
  • the first, second and/or fifth polypeptide chains may be isolated from naturally occurring antibodies. Alternatively, they may be constructed recombinantly.
  • the third polypeptide chain of such diabodies contains: (i) a VH1 -containing domain, (ii) a CH1- containing domain, (iii) a Domain containing a CH2-CH3 sequence, (iv) a VL2-containing Domain, (v) a VH3 -containing Domain and (vi) a Heterodimer-Promoting Domain, where the Heterodimer-Promoting Domains promote the dimerization of the third chain with the fourth chain.
  • the fourth polypeptide of such diabodies contains: (i) a VL3 -containing Domain, (ii) a VH2-containing Domain and (iii) a Domain that promotes heterodimerization and covalent bonding with the diabody's third polypeptide chain.
  • the first and second, and the third and fifth, polypeptide chains of such diabodies associate together to form two VL1/VH1 binding sites capable of binding a first epitope.
  • the third and fourth polypeptide chains of such diabodies associate together to form a VL2/VH2 binding site that is capable of binding to a second epitope, as well as a VL3/VH3 binding site that is capable of binding to a third epitope.
  • the first and third polypeptides are bonded to one another through a disulfide bond involving cysteine residues in their respective constant regions.
  • the first and third polypeptide chains complex with one another to form an Fc Region.
  • Such diabodies have enhanced potency.
  • FIG. 5 illustrates the structure of such diabodies.
  • the VLl/VHl, VL2/VH2, and VL3/VH3 Domains may be the same or different so as to permit binding that is monospecific, bispecific or trispecific.
  • these domains are preferably selected so as to bind PD-1 and a second epitope (e.g., B7-H3, B7-H4, BTLA, CD40, CD80, CD86, CD137, CTLA- 4, ICOS, KIR, LAG- 3 MHC class I or II, OX40, PD-L1, TCR, TIM-3, etc.).
  • a second epitope e.g., B7-H3, B7-H4, BTLA, CD40, CD80, CD86, CD137, CTLA- 4, ICOS, KIR, LAG- 3 MHC class I or II, OX40, PD-L1, TCR, TIM-3, etc.
  • VL and VH Domains of the polypeptide chains are selected so as to form VL/VH binding sites specific for a desired epitope.
  • the VL/VH binding sites formed by the association of the polypeptide chains may be the same or different so as to permit tetravalent binding that is monospecific, bispecific, tnspecific or tetraspecific.
  • VL and VH Domains may be selected such that a bispecific diabody may comprise two binding sites for a first epitope and two binding sites for a second epitope, or three binding sites for a first epitope and one binding site for a second epitope, or two binding sites for a first epitope, one binding site for a second epitope and one binding site for a third epitope (as depicted in Figure 5).
  • the general structure of the polypeptide chains of representative five-chain Fc Region- containing diabodies of invention is provided in Table 4:
  • diabodies of the present invention are bispecific, tetravalent (i.e., possess four epitope-binding sites), Fc-containing diabodies that are composed of five total polypeptide chains having two binding sites for a first epitope and two binding sites for a second epitope.
  • the bispecific, tetravalent, Fc-containing diabodies of the invention comprise two epitope-binding sites immunospecific for PD-1 (which may be capable of binding to the same epitope of PD-1 or to different epitopes of PD-1), and two epitope-binding sites specific for a second epitope (e.g., B7-H3, B7-H4, BTLA, CD40, CD80, CD86, CD137, CTLA-4, ICOS, KIR, LAG-3 MHC class I or II, OX40, PD-L1, TCR, TIM-3, etc.).
  • two epitope-binding sites immunospecific for PD-1 which may be capable of binding to the same epitope of PD-1 or to different epitopes of PD-1
  • two epitope-binding sites specific for a second epitope e.g., B7-H3, B7-H4, BTLA, CD40, CD80, CD86, CD137, CTLA-4, ICOS,
  • the bispecific, tetravalent, Fc-containing diabodies of the invention comprise three epitope-binding sites immunospecific for PD-1 which may be capable of binding to the same epitope of PD-1 or to different epitopes of PD-1), and one epitope-binding sites specific for a second epitope (e.g., B7-H3, B7-H4, BTLA, CD40, CD80, CD86, CD137, CTLA-4, ICOS, KIR, LAG-3 MHC class I or II, OX40, PD-L1, TCR, TIM-3, etc.).
  • a second epitope e.g., B7-H3, B7-H4, BTLA, CD40, CD80, CD86, CD137, CTLA-4, ICOS, KIR, LAG-3 MHC class I or II, OX40, PD-L1, TCR, TIM-3, etc.
  • the bispecific, tetravalent, Fc-containing diabodies of the invention comprise one epitope-binding sites immunospecific for PD-1, and three epitope- binding sites specific for a second epitope (e.g., B7-H3, B7-H4, BTLA, CD40, CD80, CD86, CD137, CTLA-4, ICOS, KIR, LAG-3 MHC class I or II, OX40, PD-L1, TCR, TIM-3, etc.).
  • a second epitope e.g., B7-H3, B7-H4, BTLA, CD40, CD80, CD86, CD137, CTLA-4, ICOS, KIR, LAG-3 MHC class I or II, OX40, PD-L1, TCR, TIM-3, etc.
  • a further embodiment of the present invention relates to bispecific, trivalent binding molecules, comprising an Fc Region, and being capable of simultaneously binding to a first epitope, a second epitope and a third epitope, wherein at least one of such epitopes is not identical to another.
  • Such bispecific diabodies thus comprise "VL1" / "VH1" domains that are capable of binding to the first epitope, "VL2” / "VH2" domains that are capable of binding to the second epitope and "VL3" / "VH3” domains that are capable of binding to the third epitope.
  • one or two of such epitopes is an epitope of PD-1 and another (or the other) of such epitopes is not an epitope of PD-1 (for example, an epitope of B7-H3, B7-H4, BTLA, CD40, CD80, CD86, CD137, CTLA-4, ICOS, KIR, LAG-3, MHC class I or II, OX40, PD-1, PD-L1, TCR, TIM-3, etc.).
  • Such bispecific trivalent binding molecules comprise three epitope- binding sites, two of which are diabody-type binding domains, which provide binding Site A and binding Site B, and one of which is a non-diabody-type binding domain, which provides binding Site C (see, e.g., Figures 6A-6F, and PCT Application No: PCT/US 15/33081; and PCT/US15/33076).
  • the trivalent binding molecules of the present invention will comprise four different polypeptide chains (see Figures 6A-6B), however, the molecules may comprise fewer or greater numbers of polypeptide chains, for example by fusing such polypeptide chains to one another (e.g., via a peptide bond) or by dividing such polypeptide chains to form additional polypeptide chains, or by associating fewer or additional polypeptide chains via disulfide bonds.
  • Figures 6B-6F illustrate this aspect of the present invention by schematically depicting such molecules having three polypeptide chains.
  • the trivalent binding molecules of the present invention may have alternative orientations in which the diabody-type binding domains are N-terminal ( Figures 6A, 6C and 6D) or C-terminal ( Figures 6B, 6E and 6F) to an Fc Region.
  • the first polypeptide chain of such trivalent binding molecules of the present invention contains: (i) a VLl-containing Domain, (ii) a VH2- containing Domain, (iii) a Heterodimer-Promoting Domain, and (iv) a Domain containing a CH2-CH3 sequence.
  • the VL1 and VL2 Domains are located N-terminal or C-terminal to the CH2-CH3 -containing domain as presented in Table 5 ( Figures 6A and 6B).
  • the second polypeptide chain of such embodiments contains: (i) a VL2-containing Domain, (ii) a VH1- containing Domain, and (iii) a Heterodimer-Promoting Domain.
  • the third polypeptide chain of such embodiments contains: (i) a VH3 -containing Domain, (ii) a CHI -containing Domain and (iii) a Domain containing a CH2-CH3 sequence.
  • the third polypeptide chain may be the heavy chain of an antibody that contains a VH3 and a heavy chain constant region.
  • the fourth polypeptide of such embodiments contains: (i) a VL3 -containing Domain and (ii) a CL- containing Domain.
  • the fourth polypeptide chains may be a light chain of an antibody that contains a VL3 complementary to the VH3 of the third polypeptide chain.
  • the third or fourth polypeptide chains may be isolated from naturally occurring antibodies. Alternatively, they may be constructed recombinantly, synthetically or by other means.
  • the Variable Light Chain Domain of the first and second polypeptide chains are separated from the Variable Heavy Chain Domains of such polypeptide chains by an intervening spacer linker having a length that is too short to permit their VL1/VH2 (or their VL2/VH1) domains to associate together to form epitope-binding site capable of binding to either the first or second epitope.
  • a preferred intervening spacer peptide (Linker 1) for this purpose has the sequence (SEQ ID NO:14): GGGSGGGG.
  • Other Domains of the trivalent binding molecules may be separated by one or more intervening spacer peptides, optionally comprising a cysteine residue.
  • Exemplary linkers useful for the generation of trivalent binding molecules are provided herein and are also provided in PCT Application Nos: PCT/US15/33081; and PCT/US15/33076.
  • the first and second polypeptide chains of such trivalent binding molecules associate together to form a VLl/VHl binding site capable of binding a first epitope, as well as a VL2/VH2 binding site that is capable of binding to a second epitope.
  • the third and fourth polypeptide chains of such trivalent binding molecules associate together to form a VL3/VH3 binding site that is capable of binding to a third epitope.
  • the VLl/VHl, VL2/VH2, and VL3/VH3 Domains may be the same or different so as to permit binding that is monospecific, bispecific or trispecific.
  • the trivalent binding molecules of the present invention may comprise three polypeptides.
  • Trivalent binding molecules comprising three polypeptide chains may be obtained by linking the domains of the fourth polypeptide N-terminal to the VH3- containing Domain of the third polypeptide.
  • a third polypeptide chain of a trivalent binding molecule of the invention containing the following three domains is utilized: (i) a VL3 -containing Domain, (ii) a VH3 -containing Domain, and (iii) a Domain containing a CH2-CH3 sequence, wherein the VL3 and VH3 are spaced apart from one another by an intervening spacer peptide that is sufficiently long (at least 9 or more amino acid residues) so as to allow the association of these domains to form an epitope-binding site.
  • VLl/VHl, VL2/VH2, and VL3/VH3 Domains may be the same or different so as to permit binding that is monospecific, bispecific or trispecific.
  • these domains are preferably selected so as to bind PD-1 and a second epitope (or a second and third epitope) (preferably, such epitopes are epitopes of B7- H3, B7-H4, BTLA, CD40, CD80, CD86, CD137, CTLA-4, ICOS, KIR, LAG-3 MHC class I or II, OX40, PD-L1, TCR, TIM-3, etc.).
  • the VL and VH Domains may be selected such that a trivalent binding molecule comprises two binding sites for a first epitope and one binding sites for a second epitope, or one binding site for a first epitope and two binding sites for a second epitope, or one binding site for a first epitope, one binding site for a second epitope and one binding site for a third epitope.
  • the general structure of the polypeptide chains of representative trivalent binding molecules of invention is provided in Figures 6A-6F and in Table 5: Table 5

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SI201631367T SI3328419T1 (sl) 2015-07-30 2016-07-28 PD-1-vezavne molekule in postopki uporabe le-teh
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MA58293B1 (fr) 2024-11-29
FIC20240028I1 (fi) 2024-08-05
EP3981792A1 (en) 2022-04-13
CY1124634T1 (el) 2022-07-22
NL301287I2 (nl) 2024-08-21
HUS2400028I1 (hu) 2024-08-28
HUE068868T2 (hu) 2025-02-28
JO3736B1 (ar) 2021-01-31
SMT202100527T1 (it) 2021-11-12
TW202229357A (zh) 2022-08-01
MX2018001227A (es) 2018-03-26
PE20240111A1 (es) 2024-01-22
PL3456346T3 (pl) 2021-12-20
AU2016298227B2 (en) 2019-10-03
HRP20211645T1 (hr) 2022-02-04
PL3328419T3 (pl) 2021-12-27
CN107847574B (zh) 2023-05-23
MD3981792T2 (ro) 2025-02-28
DK3981792T3 (da) 2024-09-02
AU2016298227B9 (en) 2019-10-31
LT3981792T (lt) 2024-11-11
GEP20227438B (en) 2022-11-10
MA42542B1 (fr) 2021-09-30
UA127372C2 (uk) 2023-08-02
HUE056201T2 (hu) 2022-02-28
SG10201906059VA (en) 2019-08-27
ES2898511T3 (es) 2022-03-07
HRP20241289T1 (hr) 2024-12-20
IL290571B2 (en) 2023-03-01
CN116333138A (zh) 2023-06-27
PE20231958A1 (es) 2023-12-06
FR24C1033I2 (fr) 2025-05-23
SMT202400381T1 (it) 2024-11-15

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