Anti-pd-l1 antibodies, compositions and articles of manufacture

Abstract

The present application relates to anti-PD-L1 antibodies, nucleic acid encoding the same, therapeutic compositions thereof, and their use enhance T-cell function to upregulate cell-mediated immune responses and for the treatment of T cell dysfunctional disorders, including infection (e.g., acute and chronic) and tumor immunity.

What is claimed is: 
     
         1 . An isolated heavy chain variable region polypeptide comprising an HVR-H1, HVR-H2 and HVR-H3 sequence, wherein:
                     (a)   the HVR-H1 sequence is GFTFSX 1 SWIH   (SEQ ID NO:1);     (b)   the HVR-H2 sequence is AWIX 2 PYGGSX 3 YYADSVKG   (SEQ ID NO:2);     (c)   the HVR-H3 sequence is RHWPGGFDY   (SEQ ID NO:3);                   further wherein: X 1  is D or G; X 2  is S or L; X 3  is T or S.   
     
     
         2 . The polypeptide of  claim 1  wherein X 1  is D; X 2  is S and X 3  is T. 
     
     
         3 . The polypeptide of  claim 1  further comprising variable region heavy chain framework sequences juxtaposed between the HVRs according to the formula: (HC-FR 1)-(HVR-H1)-(HC-FR2)-(HVR-H2)-(HC-FR3)-(HVR-H3)-(HC-FR4). 
     
     
         4 . The polypeptide of  claim 3  wherein the framework sequences are derived from human consensus framework sequences. 
     
     
         5 . The polypeptide of  claim 4  wherein the framework sequences are VH subgroup III consensus framework. 
     
     
         6 . The polypeptide of  claim 5  wherein one or more of the framework sequences is the following:
                 HC-FR1 is EVQLVESGGGLVQPGGSLRLSCAAS   (SEQ ID NO:4)     HC-FR2 is WVRQAPGKGLEWV   (SEQ ID NO:5)     HC-FR3 is RFTISADTSKNTAYLQMNSLRAEDTAVYYCAR   (SEQ 1D NO:6)     HC-FR4 is WGQGTLVTVSA   (SEQ ID NO:7).                  
 
     
     
         7 . The isolated heavy chain polypeptide of  claim 1  in combination with a variable region light chain comprising an HVR-L1, HVR-L2 and HVR-L3, wherein:
                     (a)   the HVR-L1 sequence is RASQX 4 X 5 X 6 TX 7 X 8 A   (SEQ ID NOs:8);     (b)   the HVR-L2 sequence is SASX 9 LX 10 S, and   (SEQ ID NOs:9);     (c)   the HVR-L3 sequence is QQX 11 X 12 X 13 X 14 PX 15 T   (SEQ ID NOs:10);                 
 further wherein: X 4  is D or V; X 5  is V or I; X 6  is S or N; X 7  is A or F; X 8  is V or L; X 9  is F or T; X 10  is Y or A: X 11  is Y, G, F, or S; X 12  is L, Y, F or W; X 13  is Y, N, A, T, G, F or I; X 14  is H, V, P, T or I; X 15  is A, W, R, P or T. 
 
     
     
         8 . The polypeptide of  claim 7  wherein X 4  is D; X 5  is V; X 6  is S; X 7  is A; X 8  is V; X 9  is F; X 10  is Y: X 11  is Y; X 12  is L; X 13  is Y; X 14  is H; X 15  is A. 
     
     
         9 . The polypeptide of  claim 7  further comprising variable region light chain framework sequences juxtaposed between the HVRs according to the formula: (LC-FR1)-(HVR-L1)-(LC-FR2)-(HVR-L2)-(LC-FR3)-(HVR-L3)-(LC-FR4). 
     
     
         10 . The polypeptide of  claim 9  wherein the framework sequences are derived from human consensus framework sequences. 
     
     
         11 . The polypeptide of  claim 10  wherein the framework sequences are VL kappa I consensus framework. 
     
     
         12 . The polypeptide of  claim 11  wherein one or moreof the framework sequences is the following:
                 LC-FR1 is DIQMTQSPSSLSASVGDRVTITC   (SEQ ID NO:11);     LC-FR2 is WYQQKPGKAPKLLIY   (SEQ ID NO:12);     LC-FR3 is GVPSRFSGSGSGTDFTLTISSLQPEDFATYYC   (SEQ ID NO:13);     LC-FR4 is FGQGTKVEIKR   (SEQ ID NO:14).                  
 
     
     
         13 . An isolated anti-PD-L 1 antibody or antigen binding fragment comprising a heavy chain and a light chain variable region sequence, wherein:
 (a) the heavy chain comprises an HVR-H1, HVR-H2 and HVR-H3, wherein further:
                     (i)   the HVR-H1 sequence is GFTFSX 1 SWIH   (SEQ ID NO:1);     (ii)   the HVR-H2 sequence is AWIX 2 PYGGSX 3 YYADSVKG   (SEQ ID NO:2);     (iii)   the HVR-H3 sequence is RHWPGGFDY, and   (SEQ ID NO:3);                 
   (b) the light chain comprises an HVR-L1, HVR-L2 and HVR-L3, wherein further:
                     (iv)   the HVR-L1 sequence is RASQX 4 X 5 X 6 TX 7 X 8 A   (SEQ ID NOs:8);     (v)   the HVR-L2 sequence is SASX 9 LX 10 S   (SEQ ID NOs:9);     (vi)   the HVR-L3 sequence is QQX 11 X 12 X 13 X 14 PX 15 T   (SEQ ID NOs:10);                 
   wherein: X 1  is D or G; X 2  is S or L; X 3  is T or S; X 4  may be D or V; X 5  may be V or I; X 6  may be S or N; X 7  may be A or F; X 8  may be V or L; X 9  may be F or T; X 10  may be Y or A; X 11  may be Y, G, F, or S; X 12  may be L, Y, F or W; X 13  may be Y, N, A, T, G, F or I: X 14  may be H, V, P, T or 1; X 15  may be A, W, R, P or T.   
     
     
         14 . The antibody or antibody fragment of  claim 13  wherein X 1  is D; X 2  is S and X 3  is T. 
     
     
         15 . The antibody or antibody fragment of  claim 13 , wherein X 4  = D, X 5  = V, X 6  = S, X 7  = A and X 8  = V, X 9  = F, and X 10  = Y, X 11  = Y, X 12  = L, X 13  = Y, X 14  = H and X 15  = A. 
     
     
         16 . The antibody or antibody fragment of  claim 13 , wherein X 1  = D, X 2  = S and X 3  = T, X 4  = D, X 5  = V, X 6  = S, X 7  = A and X 8  = V, X 9  = F, and X 10  = Y, X 11  = Y, X 12  = L, X 13  = Y, X 14  = H and X 15  = A. 
     
     
         17 . The antibody or antibody fragment of any of  claims 13-16  further comprising:
 (a) variable region heavy chain framework sequences juxtaposed between the HVRs according to the formula: (HC-FRl)-(HVR-Hl)-(HC-:FR2)-(HVR-H2)-(HC-FR3)-(HVR-H3)-(HC-FR4), and 
 (b) variable region light chain framework sequences juxtaposed between the HVRs according to the formula: (I.C-FR1)-(HVR-L1)-(LC-FR2)-(HVR-L2)-(LC-FR3)-(HVR-L3)-(LC-FR4). 
 
     
     
         18 . The antibody or antibody fragment of  claim 17  wherein the framework sequences are derived from human consensus framework sequences. 
     
     
         19 . The antibody or antibody fragment of  claim 18  wherein the variable region heavy chain framework sequences are VH subgroup III consensus framework. 
     
     
         20 . The antibody or antibody fragment of  claim 19  wherein one or more of the framework sequences is the following:
                 HC-FR1 is EVQLVESGGGLVQPGGSLRLSCAAS   (SEQ ID NO:4);     HC-FR2 is WVRQAPGKGLEWV   (SEQ ID NO:5);     HC-FR3 is RFTISADTSKNTAYLQMNSLRAEDTAVYYCAR   (SEQ ID NO:6);     HC-FR4 is WGQGTLVTVSA   (SEQ ID NO:7).                  
 
     
     
         21 . The antibody or antibody fragment of  claim 18  wherein the variable region light chain framework sequences are VL kappa I consensus framework. 
     
     
         22 . The antibody or antibody fragment of  claim 21  wherein one or more of the framework sequences is the following:
                 LC-FR1 is DIQMTQSPSSLSASVGDRVTITC   (SEQ ID NO:11);     LC-FR2 is WYQQKPGKAPKLLIY   (SEQ ID NO:12);     LC-FR3 is GVPSRFSGSGSGTDFTLTISSLQPEDFATYYC, and   (SEQ ID NO:13);     LC-FR4 is FGQGTKVEIKR   (SEQ ID NO:14).                  
 
     
     
         23 . The antibody of or antibody fragment of  claim 18  wherein:
 (a) the variable heavy chain framework sequences are the following:
                     (i)   HC-FR1 is EVQLVESGGGLVQPGGSLRLSCAAS   (SEQ ID NO:4);     (ii)   HC-FR2 is WVRQAPGKGLEWV   (SEQ ID NO:5);     (iii)   HC-FR3 is RFTISADTSKNTAYLQMNSLRAEDTAVYYCAR   (SEQ ID NO:6);     (iv)   HC-FR4 is WGQGTLVTVSA; and   (SEQ ID NO:7);                  
 
 (b) the variable light chain framework sequences are the following:
                     (i)   LC-FR1 is DIQMTQSPSSLSASVGDRVTITC   (SEQ ID NO:11);     (ii)   LC-FR2 is WYQQKPGKAPKLLIY   (SEQ ID NO:12);     (iii)   LC-FR3 is GVPSRFSGSGSGTDFTLTISSLQPEDFATYYC   (SEQ ID NO:13);     (iv)   LC-FR4 is FGQGTKVEIKR   (SEQ ID NO:14).                  
 
 
     
     
         24 . The antibody or antibody fragment of  claim 23  further comprising a human constant region. 
     
     
         25 . The antibody or antibody fragment of  claim 24 , wherein the constant region is selected from the group consisting of IgG1, IgG2, IgG3 and IgG4. 
     
     
         26 . The antibody of antibody fragment of  claim 25  wherein the constant region is IgG1. 
     
     
         27 . The antibody or antibody fragment of  claim 23 , further comprising murine constant region. 
     
     
         28 . The antibody or antibody fragment of  claim 27  wherein the constant region is selected from the group consisting of IgG1, IgG2A, IgG2B and IgG3. 
     
     
         29 . The antibody or antibody fragment of  claim 28 , wherein the constant region is IgG2A. 
     
     
         30 . The antibody or antibody fragment of  claim 25  or  28  having reduced or minimal effector function. 
     
     
         31 . The antibody or antibody fragment of  claim 30 , wherein the minimal effector function results from an effector-less Fc mutation. 
     
     
         32 . The antibody or antibody fragment of  claim 31 , wherein the effector-less Fc mutation is N297A. 
     
     
         33 . The antibody or antibody fragment of  claim 31 , wherein the effector-less Fc mutation is D265A/N297A. 
     
     
         34 . The antibody or antibody fragment of  claim 30 , wherein the minimal effector function results from aglycosylation. 
     
     
         35 . An antibody or antigen binding fragment comprising a heavy chain and a light chain variable region sequence, wherein:
 (a) the heavy chain comprises an HVR-H1, HVR-H2 and an HVR-H3, having at least 85% overall sequence identity to GFTFSDSWIH (SEQ ID NO:15), A WISPYGGSTYY ADSVKG (SEQ ID NO: 16) and RHWPGGFDY (SEQ ID NO:3), respectively, and   (b) the light chain comprises an HVR-L1, HVR-L2 and an HVR-L3, having at least 85% overall sequence identity to RASQDVSTAVA (SEQ ID NO: 17), SASFLYS (SEQ ID NO: 18) and QQYLYHPAT (SEQ ID NO: 19), respectively.   
     
     
         36 . The antibody or antibody fragment of  claim 35 , wherein the sequence identity is at least 90%. 
     
     
         37 . The antibody or antibody fragment of  claims 36  further comprising:
 (a) variable region heavy chain (VH) framework sequences juxtaposed between the HVRs according to the formula: (HC-FR1)-(HVR-H1)-(HC-FR2)-(HVR-H2)-(HC-FR3)-(HVR-H3)-(HC-FR4), and 
 (b) variable region light chain (VL) framework sequences juxtaposed between the HVRs according to the formulat: (LCFRI)-(HVR-L l )-(LC-FR2)-(HVR-L2)-(LC-1--R3)-(HVR-L3)-(LC-FR4). 
 
     
     
         38 . The antibody or antibody fragment of  claim 37 , further comprising a VH and VL framework region derived from a human consensus sequence. 
     
     
         39 . The antibody or antibody fragment of  claim 38 , wherein the VH framework sequence is derived from a Kabat subgroup I, II, or III sequence. 
     
     
         40 . The antibody or antibody fragment of  claim 39 , wherein the VH framework sequence is a Kabat subgroup III consensus framework sequence. 
     
     
         41 . The antibody or antibody fragment of  claim 40  wherein the VH framework sequences are the following:
                 HC-FRI, is EVQLVESGGGLVQPGGSLRLSCAAS   (SEQ ID NO:4);     HC-FR2 is WVRQAPGKGLEWV   (SEQ ID NO:5);     HC-FR3 is RFTISADTSKNTAYLQMNSLRAEDTAVYYCAR   (SEQ ID NO:6);     HC-FR4 is WGQGTLVTVSA   (SEQ ID NO:7).                  
 
     
     
         42 . The antibody or antibody fragment of  claim 38 , wherein the VL framework sequence is derived from a Kabat kappa I, II, III or IV subgroup sequence. 
     
     
         43 . The antibody or antibody fragment of  claim 42  wherein the the VL framework sequence is a Kabat kappa I consensus framework sequence. 
     
     
         44 . The antibody or antibody fragment of  claim 43  wherein the VL framework sequences are the following:
                 LC-FR1 is DIQMTQSPSSLSASVGDRVTITC   (SEQ ID NO:11);     LC-FR2 is WYQQKPGKAPKLLIY   (SEQ ID NO:12);     LC-FR3 is GVPSRFSGSGSGTDFTLTISSLQPEDFATYYC   (SEQ ID NO:13);     LC-FR4 is FGQGTKVEIKR   (SEQ ID NO:14).                  
 
     
     
         45 . An isolated anti-PD-Ll antibody or antigen binding fragment comprising a heavy chain and a light chain variable region sequence, wherein:
 (a) the heavy chain sequence has at least 85% sequence identity to the heavy chain sequence: EVQLVESGGGLVQPGGSLRLSCAASGFTFSDSWIHWVRQAPG KGLEWV A WISPYGGSTYY ADSVKGRFTISADTSKNT A YLQMNSLRAEDT A VYYCARRHWPGGFDYWGQGTL VTVSA (SEQ ID NO:20), and   (b) the light chain sequence has at least 85% sequence identity to the light chain sequence: DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGK APKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYLYH PATFGQGTKVEIKR (SEQ ID NO: 21).   
     
     
         46 . The antibody or antigen binding fragment of  claim 45 , wherein the sequence identity is at least 90%. 
     
     
         47 . An isolated anti-PD-Ll antibody or antigen binding fragment comprising a heavy chain and light chain variable region sequence, wherein:
 (a) the heavy chain comprises the sequence: EVQLVESGGGLVQPGGSLRLS CAASGFTFSDSWIHWVRQAPGKGLEWVAWISPYGGSTYYADSVKGRFTI SADTSKNTAYLQMNSLRAEDTAVYYCARRHWPGGFDYWGQGTLVTVS A (SEQ ID NO:20), and   (b) the light chain comprises the sequence: DIQMTQSPSSLSASVGDRVTITC RASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTL TISSLQPEDFATYYCQQYLYI-I PATFGQGTKVEIKR (SEQ ID NO:21).   
     
     
         48 . A composition comprising the anti-PD-Ll antibody or antigen binding fragment of any of  claims 13-47  and at least one pharmaceutically-acceptable carrier. 
     
     
         49 . An isolated nucleic acid encoding the polypeptide of any of  claims 1-11 . 
     
     
         50 . An isolated nucleic acid encoding a light chain or a heavy chain variable sequence of an anti-PD-Ll antibody or antigen binding fragment, wherein:
 (a) the heavy chain further comprises and HVR-EL, HVR-H2 and an HVR-H3 sequence having at least 85% sequence identity to GFTFSDSWIH (SEQ ID NO:15), AWISPYGGSTYYADSVKG (SEQ ID NO: 16) and RHWPGGFDY (SEQ ID NO:3), respectively, or   (b) the light chain further comprises an HVR-L1, HVR-L2 and an HVR-1,3 sequence having at least 85% sequence identity to RASQDVSTAVA (SEQ ID NO: 17), SAS FLYS (SEQ ID NO: 18) and QQYLYHPAT (SEQ ID NO: 19), respectively.   
     
     
         51 . The nucleic acid of  claim 50 , wherein sequence identity is 90%. 
     
     
         52 . The nucleic acid of  claim 50 , wherein the anti-PD-L1 antibody further comprises a VL and a VH framework region derived from a human consensus sequence. 
     
     
         53 . The nucleic acid of  claim 52 , wherein the VH sequence is derived from a Kabat subgroup I, II, or III sequence. 
     
     
         54 . The nucleic acid of  claim 52 , wherein the VL sequence is derived from a Kabat kappa I, II, III or IV subgroup sequence. 
     
     
         55 . The nucleic acid of  claim 50 , wherein the anti-PD-L1 antibody comprises a constant region derived from a murine antibody. 
     
     
         56 . The nucleic acid of  claim 50 , wherein the anti-PD-L1 antibody comprises a constant region derived from a human antibody. 
     
     
         57 . The nucleic acid of  claim 56 , wherein the constant region is IgG1. 
     
     
         58 . The nucleic acid of  claim 57 , having reduced or minimal effector function. 
     
     
         59 . The nucleic acid of  claim 58 , wherein the minimal effector function results from an effector-less Fc mutation. 
     
     
         60 . The nucleic acid of  claim 59 , wherein the effector-less Fc mutation is N297A. 
     
     
         61 . A vector comprising the nucleic acid of any of  claims 49-60 . 
     
     
         62 . A host cell comprising the vector of  claim 61 . 
     
     
         63 . The host cell of  claim 62  which is eukaryotic. 
     
     
         64 . The host cell of  claim 63  which is mammalian. 
     
     
         65 . The host cell of  claim 64  which is a Chinese Hamster Ovary (CHO) cell. 
     
     
         66 . The host cell of  claim 62  which is prokaryotic. 
     
     
         67 . The host cell of  claim 66  which is  E.   Coli . 
     
     
         68 . A process for making an anti-PD-L1 antibody comprising culturing the host cell of any of  claims 62-67  under conditions suitable for the expression of the vector encoding the anti-PD-Ll antibody or antigen binding fragment, and recovering the antibody or fragment. 
     
     
         69 . An article of manufacture comprising the composition of  claim 48  and at least one BNCA molecule. 
     
     
         70 . An article of manufacture comprising the composition of  claim 48  and at least one chemotherapeutic agent. 
     
     
         71 . The article of manufacture according to  claim 70 , wherein the chemotherapeutic agent is gemcitabine. 
     
     
         72 . An article of manufacture comprising the composition of  claim 48  and at least one agonist to a positive costimulatory molecule. 
     
     
         73 . The article of manufacture according to  claim 72 , further comprising a BNCA antagonist. 
     
     
         74 . An article of manufacture comprising the composition of  claim 48  and at least one antibiotic. 
     
     
         75 . The article of manufacture according to  claim 74 , wherein the antibiotic is an anti-viral agent. 
     
     
         76 . The article of manufacture according to  claim 75 , wherein anti-viral agent is a reverse transcriptase inhibitor. 
     
     
         77 . The article of manufacture according to  claim 76 , wherein the reverse transcriptase inhibitor is a polymerase inhibitor. 
     
     
         78 . The article of manufacture according to  claim 75 , wherein the anti-viral agent is a protease inhibitor. 
     
     
         79 . An article of manufacture comprising the composition of  claim 48  and at least one vaccine. 
     
     
         80 . A method of enhacing T-cell function comprising administration of an effective amount of the composition of  claim 48  to a dysfunctional T-cell. 
     
     
         81 . A method of treating a T-cell dysfunctional disorder comprising administering a therapeutically effective amount of the composition of  claim 48  to a patient suffering from a T-cell dysfunctional disorder. 
     
     
         82 . The method of  claim 81 , wherein the T-cell dysfunctional disorder is infection. 
     
     
         83 . The method of  claim 82 , wherein the infection is chronic. 
     
     
         84 . The method of  claim 81 , wherein the T-cell dysfunctional disorder is tumor immunity. 
     
     
         85 . The method of  claim 83 , therein the chronic infection is persistent. 
     
     
         86 . The method of  claim 83 , wherein the chronic infection is latent. 
     
     
         87 . The method of  claim 83 , wherein the chronic infection is slow. 
     
     
         88 . The method of  claim 82  wherein the infection results from a pathogen selected from the group consisting of bacteria, virus, fungi and protozoan. 
     
     
         89 . The method of  claim 88  wherein the pathogen is a bacteria and the method further comprises the administration of an anti-bacterial agent. 
     
     
         90 . The method of  claim 88 , wherein the pathogen is virus and the method further comprises the administration of an anti-viral agent. 
     
     
         91 . The method of  claim 88 , wherein the pathogen is a fungi and the method further comprises the administration of an anti-fungal agent. 
     
     
         92 . The method of  claim 88 , wherein the pathogen is a protozoan and the method further comprising the administration of an anti-protozoan agent. 
     
     
         93 . The method of  claim 88 , further comprising the administration of a vaccine. 
     
     
         94 . The method of  claim 84 , wherein the method futher comprising the application of a treatment regimen selected from the group consisting of: radiation therapy, chemotherapy, targeted therapy, immunotherapy, hormonal therapy, angiogenesis inhibiton and palliative care. 
     
     
         95 . The method of  claim 84 , wherein the tumor immunity results from a cancer selected from the group consisting of: breast, lung, colon, ovarian, melanoma, bladder, kidney, liver, salivary, stomach, gliomas, thyroid, thymic, epithelial, head and neck cancers, gastric and pancreatic cancer.