Anti-pd1 antibodies and their use as therapeutics and diagnostics

Abstract

Provided are antibodies that specifically bind to Programmed Death-1 (PD1, Pdcd-1, or CD279) and inhibit PD1-mediated cellular signaling and activities in immune cells, antibodies binding to a set of amino acid residues required for its ligand binding, and uses of these antibodies to treat or diagnose cancer, infectious diseases or other pathological disorders modulated by PD1-mediated functions.

1 . An antibody antigen binding domain which specifically binds human PD-1, and comprises a complementarity determining region (CDR) having a sequence selected from SEQ ID NOS 11-22, 31-42 and 59-63. 
     
     
         2 . The domain of  claim 1  comprising a heavy chain variable region (Vh) or a light chain variable region (Vk) comprising:
                 a) CDR-H1 (SEQ ID NO: 11, 17, 31, or 37),   d) CDR-L1 (SEQ ID NO: 14, 20, 34, or 40),     b) CDR-H2 (SEQ ID NO: 12, 18, 32, or 38),   e) CDR-L2 (SEQ ID NO: 15, 21, 35, or 41), or     c) CDR-H3 (SEQ ID NO: 13, 18, 33, or 39);   f) CDR-L3 (SEQ ID NO: 16, 22, 36, or 42)                 
 . 
 
     
     
         3 . The domain of  claim 1  comprising a heavy chain variable region (Vh) or a light chain variable region (Vk) comprising:
                     a) mu317   CDR-H1, CDR-H2 and CDR-H3   (SEQ ID NOS: 11-13); or         CDR-L1, CDR-L2 and CDR-L3   (SEQ ID NOS: 14-16);     b) mu326   CDR-H1, CDR-H2 and CDR-H3   (SEQ ID NOS:17-19); or         CDR-L1, CDR-L2 and CDR-L3   (SEQ ID NOS:20-22);     c) 317-4B6   CDR-H1, CDR-H2 and CDR-H3   (SEQ ID NOS:31-33); or         CDR-L1, CDR-L2 and CDR-L3   (SEQ ID NOS:34-36);     d) 326-4A3   CDR-H1, CDR-H2 and CDR-H3   (SEQ ID NOS:37-39); or         CDR-L1, CDR-L2 and CDR-L3   (SEQ ID NOS:40-42);     e) 317-1H   CDR-H1, CDR-H2 and CDR-H3   (SEQ ID NOS: 11, 59, 13); or         CDR-L1, CDR-L2 and CDR-L3   (SEQ ID NOS:14-16);     f) 317-4B2   CDR-H1, CDR-H2 and CDR-H3   (SEQ ID NOS:11, 60, 13); or         CDR-L1, CDR-L2 and CDR-L3   (SEQ ID NOS:61, 15, 16);     g) 317-4B5   CDR-H1, CDR-H2 and CDR-H3   (SEQ ID NOS:11, 60, 13); or         CDR-L1, CDR-L2 and CDR-L3   (SEQ ID NOS:61, 15, 16);     h) 317-4B6   CDR-H1, CDR-H2 and CDR-H3   (SEQ ID NOS:11, 32, 13); or         CDR-L1, CDR-L2 and CDR-L3   (SEQ ID NOS:61, 15, 16);     i) 326-1   CDR-H1, CDR-H2 and CDR-H3   (SEQ ID NOS:17, 62, 19); or         CDR-L1, CDR-L2 and CDR-L3   (SEQ ID NOS:20-22);     j) 326-3B1   CDR-H1, CDR-H2 and CDR-H3   (SEQ ID NOS:17, 62, 19); or         CDR-L1, CDR-L2 and CDR-L3   (SEQ ID NOS:20-22);     k) 326-3G1   CDR-H1, CDR-H2 and CDR-H3   (SEQ ID NOS:17, 62, 19); or         CDR-L1, CDR-L2 and CDR-L3   (SEQ ID NOS:20-22)                                    
 . 
 
     
     
         4 . The domain of  claim 1  comprising a heavy chain variable region (Vh) and a light chain variable region (Vκ) comprising:
                     a) mu317   CDR-H1, CDR-H2 and CDR-H3   (SEQ ID NOS: 11-13); and         CDR-L1, CDR-L2 and CDR-L3   (SEQ ID NOS: 14-16);     b) mu326   CDR-H1, CDR-H2 and CDR-H3   (SEQ ID NOS:17-19); and         CDR-L1, CDR-L2 and CDR-L3   (SEQ ID NOS:20-22);     c) 317-4B6   CDR-H1, CDR-H2 and CDR-H3   (SEQ ID NOS:31-33); and         CDR-L1, CDR-L2 and CDR-L3   (SEQ ID NOS:34-36);     d) 326-4A3   CDR-H1, CDR-H2 and CDR-H3   (SEQ ID NOS:37-39); and         CDR-L1, CDR-L2 and CDR-L3   (SEQ ID NOS:40-42);     e) 317-1H   CDR-H1, CDR-H2 and CDR-H3   (SEQ ID NOS: 11, 59, 13); and         CDR-L1, CDR-L2 and CDR-L3   (SEQ ID NOS:14-16);     f) 317-4B2   CDR-H1, CDR-H2 and CDR-H3   (SEQ ID NOS:11, 60, 13); and         CDR-L1, CDR-L2 and CDR-L3   (SEQ ID NOS:61, 15, 16);     g) 317-4B5   CDR-H1, CDR-H2 and CDR-H3   (SEQ ID NOS:11, 60, 13); and         CDR-L1, CDR-L2 and CDR-L3   (SEQ ID NOS:61, 15, 16);     h) 317-4B6   CDR-H1, CDR-H2 and CDR-H3   (SEQ ID NOS:11, 32, 13); and         CDR-L1, CDR-L2 and CDR-L3   (SEQ ID NOS:61, 15, 16);     i) 326-1   CDR-H1, CDR-H2 and CDR-H3   (SEQ ID NOS:17, 62, 19); and         CDR-L1, CDR-L2 and CDR-L3   (SEQ ID NOS:20-22);     j) 326-3B1   CDR-H1, CDR-H2 and CDR-H3   (SEQ ID NOS:17, 62, 19); and         CDR-L1, CDR-L2 and CDR-L3   (SEQ ID NOS:20-22);     k) 326-3G1   CDR-H1, CDR-H2 and CDR-H3   (SEQ ID NOS:17, 62, 19); or         CDR-L1, CDR-L2 and CDR-L3   (SEQ ID NOS:20-22)                                    
 . 
 
     
     
         5 . The domain of  claim 1  comprising a heavy chain variable region (Vh) and a light chain variable region (Vk) comprising:
 (a) CDR-H1 (SEQ ID NO 31), CDR-H2 (SEQ ID NO 12, 32, 59 or 60) and CDR-H3 (SEQ ID NO 33), CDR-L1 ( SEQ ID NO 14, 34 or 61), CDR-L2 (SEQ ID NO 35) and CDR-L3 (SEQ ID NO 36); or 
 (b) CDR-H1 (SEQ ID NO 37), CDR-H2 (SEQ ID NO 18, 38 or 62) and CDR-H3 (SEQ ID NO 39), CDR-L1 (SEQ ID NO 40), CDR-L2 (SEQ ID NO 41) and CDR-L3 (SEQ ID NO 42). 
 
     
     
         6 . The domain of  claim 1  comprising a heavy chain variable region (Vh) or a light chain variable region (Vk) comprising:
                 a) mu317 (SEQ ID NOS:4 or 6);   p) 317-3H1 (SEQ ID NOS:69);     b) mu326 (SEQ ID NOS:8 or 10);   q) 317-3I1 (SEQ ID NOS:70);     c) 317-4B6 (SEQ ID NOS:24 or 26);         d) 326-4A3 (SEQ ID NOS:28 or 30);   r) 317-4B1 (SEQ ID NOS:71);     e) 317-4B2 (SEQ ID NOS:43 or 44);   s) 317-4B3 (SEQ ID NOS:72);     f) 317-4B5 (SEQ ID NOS:45 or 46);   t) 317-4B4 (SEQ ID NOS:73);     g) 317-1 (SEQ ID NOS:48 or 50);   u) 317-4A2 (SEQ ID NOS:74);     h) 326-3B1 (SEQ ID NOS:51 or 52);   v) 326-3A1 (SEQ ID NOS:75);     i) 326-3G1 (SEQ ID NOS:53 or 54);   w) 326-3C1 (SEQ ID NOS:76);     j) 326-1 (SEQ ID NOS:56 or 58);   x) 326-3D1 (SEQ ID NOS:77);     k) 317-3A1 (SEQ ID NOS:64);   y) 326-3E1 (SEQ ID NOS:78);     l) 317-3C1 (SEQ ID NOS:65);   z) 326-3F1 (SEQ ID NOS:79);     m) 317-3E1 (SEQ ID NOS:66);   aa) 326-3B N55D (SEQ ID NOS:80);     n) 317-3F1 (SEQ ID NOS:67);   ab) 326-4A1 (SEQ ID NOS: 81); or     o) 317-3G1 (SEQ ID NOS:68);   ac) 326-4A2 (SEQ ID NOS: 82)                             
 . 
 
     
     
         7 . The domain of  claim 1  comprising a heavy chain variable region (Vh) and a light chain variable region (Vk) comprising:
                 a) mu317 (SEQ ID NOS:4 and 6);   p) 317-3H1 (SEQ ID NOS:69 and 26);     b) mu326 (SEQ ID NOS:8 and 10);   q) 317-3I1 (SEQ ID NOS:70 and 26);     c) 317-4B6 (SEQ ID NOS:24 and 26);         d) 326-4A3 (SEQ ID NOS:28 and 30);   r) 317-4B1 (SEQ ID NOS:71 and 26);     e) 317-4B2 (SEQ ID NOS:43 and 44);   s) 317-4B3 (SEQ ID NOS:72 and 26);     f) 317-4B5 (SEQ ID NOS:45 and 46);   t) 317-4B4 (SEQ ID NOS:73 and 26);     g) 317-1 (SEQ ID NOS:48 and 50);   u) 317-4A2 (SEQ ID NOS:74 and 26);     h) 326-3B1 (SEQ ID NOS:51 and 52);   v) 326-3A1 (SEQ ID NOS:75 and 30);     i) 326-3G1 (SEQ ID NOS:53 and 54);   w) 326-3C1 (SEQ ID NOS:76 and 30);     j) 326-1 (SEQ ID NOS:56 and 58);   x) 326-3D1 (SEQ ID NOS:77 and 30);     k) 317-3A1 (SEQ ID NOS:64 and 26);   y) 326-3E1 (SEQ ID NOS:78 and 30);     l) 317-3C1 (SEQ ID NOS:65 and 26);   z) 326-3F1 (SEQ ID NOS:79 and 30);     m) 317-3E1 (SEQ ID NOS:66 and 26);   aa) 326-3B N55D (SEQ ID NOS:80 and 30);     n) 317-3F1 (SEQ ID NOS:67 and 26);   ab) 326-4A1 (SEQ ID NOS:28 and 81); or     o) 317-G1 (SEQ ID NOS:68 and 26);   ac) 326-4A2 (SEQ ID NOS:28 and 82)                             
 . 
 
     
     
         8 . The domain of  claim 1  comprising a heavy chain variable region (Vh) and a light chain variable region (Vk) comprising:
 c) hu317-4B6 (SEQ ID NOS:24 and 26); or 
 d) hu326-4A3 (SEQ ID NOS:28 and 30). 
 
     
     
         9 . A domain of  claim 1  which specifically binds PD1 residues:
 (a) K45 and I93 (AA numbering based on 2008 PNAS, 105:10483; equivalent to K58 and I106 in SEQ ID NO 2); or 
 (b) I93, L95 and P97(AA numbering based on 2008 PNAS, 105:10483; equivalent to I106, L108 and P110 in SEQ ID NO 2). 
 
     
     
         10 . The domain of  claim 1  which induces IL-2 release in HuT78/PD-1 cells co-cultured with HEK293/OS8/PD-L1 cells or with EK293/OS8/PD-L2 cells, and/or inhibits of IL-2 secretion in HuT78/P3Z cells co-cultured with HEK293/PD-L1 cells or with HEK293/PD-L2 cells. 
     
     
         11 . A monoclonal IgG antibody comprising a domain of  claim 1 . 
     
     
         12 . A monoclonal IgG antibody comprising a domain of  claim 7 . 
     
     
         13 . A monoclonal IgG antibody comprising a domain of  claim 8 . 
     
     
         14 . An IgG antibody comprising a domain of  claim 7  and an IgG4 heavy chain effector or constant domain comprising SEQ ID NO 87 or 88. 
     
     
         15 . An IgG antibody comprising a domain of  claim 8  and an IgG4 heavy chain effector or constant domain comprising SEQ ID NO 87 or 88. 
     
     
         16 . A method of using a domain of  claim 1  comprising the step of administering the domain to a person determined to have cancer or a viral infection or to otherwise be in need of PD-1 antagonism. 
     
     
         17 . An antibody IgG4 heavy chain effector or constant domain comprising any of SEQ ID NO:83-88. 
     
     
         18 . A polynucleotide encoding a domain of  claim 1 . 
     
     
         19 . A fusion protein comprising:
 (a) a single chain variable fragment (scFv) of an anti-human CD3 mAb OKT3 fused to the C-terminal domain (113-220) of mouse CD8α (SEQ ID NO:89); or   (b) the extracellular and transmembrane domains of human PD-1 fused to the cytoplasmic domain of human CD3ζ chain (SEQ ID NO: 90).   
     
     
         20 . A method of using the fusion protein of  claim 19 , comprising assaying, screening or selecting anti-PD-1 antibodies with a cell line expressing the fusion protein.