Anti-cd39 antibodies, compositions comprising anti-cd39 antibodies and methods of using anti-cd39 antibodies

Abstract

Provided herein are antibodies with binding specificity for CD39 and compositions comprising the antibodies, including pharmaceutical compositions, diagnostic compositions and kits. Also provided are methods of using anti-CD39 antibodies for therapeutic and diagnostic purposes.

1 . An antigen binding protein that binds specifically to a human CD39 (hCD39) and is capable of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or 18 of the following:
 a) inhibiting binding of CD39 to ATP;   b) inhibiting conversion by CD39 of ATP to ADP and/or ADP to AMP;   c) decreasing affinity of CD39 for ATP or ADP;   d) inhibiting or impeding release of ADP or AMP from CD39;   e) impeding or inhibiting CD39 processivity;   f) inhibiting platelet aggregation;   g) decreasing levels of phosphate, ADP, AMP, and/or adenosine and/or increasing levels of ATP;   h) increasing T effector cell function;   i) decreasing the number of regulatory T cells in tissues or in circulation;   j) suppressing regulatory T cells or regulatory T cell activity;   k) increasing B cell function;   l) increasing antigen presenting cell function;   m) inhibiting CD39 function on tumor cells;   n) inhibiting processing of at least one of phospho-antigen from phosphorylated isoprenoid, phosphorylated vitamin B metabolite, and/or phosphorylated riboflavin;   o) decreasing or preventing activation of phospho antigen specific T cells selected from MAIT cells and T6 T cells;   p) inhibiting angiogenesis;   q) increasing proliferation of stimulated CD4+ and CD8+ T cells;   r) increasing stimulated PBMC Secretion of INF-γ, TNF-α, IL-2 and/or IL-1β.   
     
     
         2 . The antigen binding protein of  claim 1 , wherein the antigen binding protein has 1, 2, 3, 4, 5, 6, or 7 of the following characteristics:
 a) is a monoclonal antibody;   b) is a human antibody, a humanized antibody, or a chimeric antibody;   c) is a bispecific antibody, a multi-specific antibody, a diabody, or a multivalent antibody;   d) is of the IgG1, IgG2, IgG3, IgG4, or IgM type;   e) is an antigen-binding antibody:fragment;   f) is a Fab:fragment, a Fab′ fragment, a F(ab′)2 fragment, or an Fv fragment; and/or   g) is a single chain antibody, a single domain antibody, or a nanobody.   
     
     
         3 . A pharmaceutical composition comprising an effective amount of an antibody which binds to hCD39 and has 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 16 of the following of characteristics:
 a) blocks or decreases hydrolysis of ATP to ADP and/or ADP to AMP as determined by at least one of: (i) a decreased phosphate release (Pi), (ii) an increase in ATP levels, and (iii) a decrease of ADP, AMP, and/or adenosine levels,   b) increases T effector cell activity;   c) suppresses regulatory T cell or decreases a regulatory T cell activity;   d) decreases number of regulatory T cells in tissues or in circulation;   e) increases B cell function;   f) increases antigen presenting cell function;   g) inhibits CD39 function on tumor cells;   h) blocks or inhibits processing of at least one of phospho-antigen from a phosphorylated isoprenoid, phosphorylated vitamin B metabolite, and phosphorylated riboflavin;   i) decreases or prevents activation of phospho antigen specific T cells selected from MAIT cells and T6 T cells;   j) inhibits angiogenesis;   k) decreases affinity for ATP and/or ADP;   l) inhibits release of ADP or AMP from CD39;   m) impedes or inhibits CD39 processivity;   n) inhibits platelet aggregation;   o) increases proliferation of stimulated CD4+ and CDS+ T cells;   p) increase stimulated PBMC secretion of INF-7, TNF-α, IL-2, and/or IL-1β.   
     
     
         4 . A pharmaceutical composition comprising the antigen-binding protein of  claim 1 . 
     
     
         5 . The pharmaceutical composition of  claim 4 , further comprising an effective amount of at least one of the following
 a) an anti-PD-I antibody,   b) an anti-PD-LI antibody,   c) an anti-CD73 antibody,   d) an anti-CD38 antibody,   e) an anti-A2A receptor antibody,   f) an anti-A2B receptor antibody,   g) an anti-A2A/A2B dual receptor antibody, or any combination thereof, or   h) a small molecule inhibitor, or a combination thereof.   
     
     
         6 - 8 . (canceled) 
     
     
         9 . The antigen binding protein of  claim 1 , wherein the antigen binding protein has one or more of the following characteristics:
 a) binds to a human CD39 polypeptide or a variant thereof with a KD of less than about 20 nM;   b) binds to a cyno CD39 polypeptide or a variant thereof with a KD of less than about 200 nM;   c) binds to a murine CD39 polypeptide or a variant thereof with a KD of less than about 200 nM; or   d) a combination of at least 2 of a), b), and c).   
     
     
         10 . An antigen binding protein that competes or is capable of competing for binding to human CD39 with a reference antigen binding protein, wherein the reference antigen binding protein is the antigen binding protein of  claim 1 . 
     
     
         11 . An antigen binding protein that binds to or is capable of competing for binding to human CD39 with a reference antigen binding protein, wherein the reference antigen binding protein binds to an epitope at positions 143-158 or 274-277 of SEQ ID NO: 249 on a human CD39 polypeptide, including, but not limited to, D150, El 53, R154 or N99 alone or in combination with D150, ε 153 , R154 or any combination thereof. 
     
     
         12 - 13 . (canceled) 
     
     
         14 . An isolated antibody molecule capable of binding to human CD39 (hCD39), comprising a heavy chain variable region (VH) and a light chain variable region (VL), V H  and/or V L  comprising 1, 2, 3, 4, 5, or 6 of:
 a) a VHCDR1 having the sequence set forth in SEQ ID NOs: 1-45,   b) a VHCDR2 having the sequence set forth in SEQ ID NOs: 46-81,   c) a VHCDR3 having the sequence set forth in SEQ ID NOs: 82-109,   d) a VLCDR1 having the sequence set forth in SEQ ID NOs: 110-124,   e) a VLCDR2 having the sequence set forth in SEQ ID NOs: 125-140, and   f) a VLCDR3 having the sequence set forth in SEQ ID NOs: 141-166.   
     
     
         15 - 20 . (canceled) 
     
     
         21 . A method for treatment of a subject suffering from cancer, a chronic infection, or from an inflammatory disease, comprising the step of administering to the subject a pharmaceutical composition comprising an effective amount of the antigen binding protein of  claim 1 . 
     
     
         22 . The method of  claim 21 , wherein the cancer is a solid cancer. 
     
     
         23 . (canceled) 
     
     
         24 . A method for modulating immune system function in a subject in need thereof, comprising the step of contacting a population of immune cells of the subject with a pharmaceutical composition comprising an effective amount of the antigen binding protein of  claim 1 , under conditions such that the immune system is modulated. 
     
     
         25 . A method for inducing or enhancing an immune response in a subject in need thereof, comprising the step of administering to the subject a pharmaceutical composition comprising an antigen binding protein, wherein the immune response is generated against a tumor antigen. 
     
     
         26 - 29 . (canceled) 
     
     
         30 . The method of  claim 25 , wherein the method further comprises one or more of the following
 a) administering chemotherapy;   b) administering radiation therapy; and/or   c) administering one or more additional therapeutic agents.   
     
     
         31 . The method of  claim 30 , wherein the one or more additional therapeutic agents comprise one or more immunostimulatory agents. 
     
     
         32 . The method of  claim 31 , wherein the one or more immunostimulatory agents comprise an antagonist to an inhibitory receptor of an immune cell. 
     
     
         33 . The method of  claim 32 , wherein the inhibitory receptor is at least one of CTLA-4, PD-1, PD-L1, PD-L2, LAG-3, Tim3, neuritin, BTLA, CECAM-1, CECAM-5, VISTA, LAIR1, CD160, 2B4, TGF-R, and/or Killer cell immunoglobulin-like receptor (KTR). 
     
     
         34 - 45 . (canceled) 
     
     
         46 . A method of screening for a test compound comprising an antigen binding protein of  claim 1  capable of inhibiting an activity of CD39, comprising the steps of:
 contacting a test sample containing CD39 with a test compound; comparing the activity of the test sample to a control sample; 
 whereby a decrease in the activity of CD39 in the test sample compared to the control 
 sample identifies the compound as one that inhibits the activity of CD39. 
 
     
     
         47 - 49 . (canceled) 
     
     
         50 . An isolated antibody molecule capable of binding to human CD39 (hCD39), comprising a heavy chain and a light chain, the heavy chain comprising one or more molecules having a sequence consisting of one of SEQ ID NO: 255, SEQ ID NO: 257, SEQ ID NO: 259, SEQ ID NO: 261, SEQ ID NO: 263, SEQ ID NO: 265, SEQ ID NO: 267, SEQ ID NO: 269, SEQ ID NO: 271, SEQ ID NO: 273, SEQ ID NO: 275, SEQ ID NO: 277, SEQ ID NO: 279, SEQ ID NO: 281, SEQ ID NO: 283, SEQ ID NO: 285, SEQ ID NO: 287, SEQ ID NO: 289, SEQ ID NO: 291, SEQ ID NO: 293, or SEQ ID NO: 295 and the light chain comprising one or more molecules having a sequence consisting of one of SEQ ID NO: 256, SEQ ID NO: 258, SEQ ID NO: 260, SEQ ID NO: 262, SEQ ID NO: 264, SEQ ID NO: 266, SEQ ID NO: 268, SEQ ID NO: 270, SEQ ID NO: 272, SEQ ID NO: 274, SEQ ID NO: 276, SEQ ID NO: 278, SEQ ID NO: 280, SEQ ID NO: 282, SEQ ID NO: 284, SEQ ID NO: 286, SEQ ID NO: 288, SEQ ID NO: 290, SEQ ID NO: 292, SEQ ID NO: 294, or SEQ ID NO: 296. 
     
     
         51 - 52 . (canceled) 
     
     
         53 . An isolated antibody molecule capable of binding to human CD39 (hCD39), comprising a heavy chain variable region (V H ) and a light chain variable region (V L ), V H  and/or V L  comprising 1, 2, 3, 4, 5, or 6 of:
 a) a VHCDR1 sequence comprising:
 (i) a Kabat CDRH1 sequence defined by the consensus sequence S-Y-Δ 3 -M-Δ 5  (SEQ ID NOS: 25-29 and 44-45), where Δ 3  is E, F, Q, or Y and Δ 5  is H or Y; 
 (ii) a Kabat CDR-H1 sequence defined by the consensus sequence θ 1 -θ 2 -θ 3 -I-S (SEQ ID NOS: 30-37), where θ 1  is A, H, K, L, S, or W; θ 2  is L, M, N, or T; and θ 3  is A or P; 
 (iii) a Kabat CDR-H1 sequence defined by the consensus sequence η 1 -Y-η 3 -I-S SEQ ID NOS: 38-41), where η 1  is S, K, N, or R and η 3  is A or G; 
 (iv) a Chothia CDR-H1 sequence defined by the consensus sequence G-Y-T-F-Ω 5 -S-Y (SEQ ID NOS: 1-2 and 4-6), where Ω 5  is T, K, Q, F, or V; 
 (v) a Chothia CDR-H1 sequence defined by the consensus sequence G-G-T-F-ν 5 -ν 6 -Y (SEQ ID NOS: 17-22 and 24), where ν 5  is S, G, or E and ν 6  is S, K, R, or S; or 
 (vi) a Chothia CDR-H1 consensus sequence defined by the consensus sequence G-G-T-F-κ 5 -κ 6 -κ 7  (SEQ ID NOS: 7-16), where κ 5  is S, Q, P, or A; κ 6  is S, K, H, L, A, or W; and κ 7  is Y, L, T, N, or M, 
   b) a VHCDR2 sequence comprising:
 (i) a Kabat CDR-H2 sequence defined by the consensus sequence ε 1 -I-N-P-ε 5 -ε 6 -G-S-T-ε 10 -Y-A-Q-K-F-Q-G (SEQ ID NOS: 63-66 and 68), where Fi is K, S, R, or V; ε 1  is L, R, or S; ε 6  is G or V; and ε 10  is S or W; 
 (ii) a Kabat CDR-H2 sequence defined by the consensus sequence G-I-α 3 -α 4 -α 5 -α 6 -G-T-A-N-Y-A-Q-K-F-Q-G (SEQ ID NOS: 69-72), where as is I or L or is absent; α 4  is P or is absent; and as is I, G, or R; and α 6  is A, F, or G; 
 (iii) a Kabat CDR-H2 sequence defined by the consensus sequence β 1 -I-I-P-β 5 -β 6 -G-β 8 -A-N-Y-A-Q-K-F-G-Q (SEQ ID NOS: 74 and 76-79), where β 1  is S or G; β 5  is I, E, S, or T; β 6  is F, I, or S; and β 8  is I or T; 
 (iv) a Chothia CDR-H2 sequence defined by the consensus sequence N-P-ε 5 -ε 6 -G-S-T (SEQ ID NOS: 46-48), where ε 5  is L, R, or S and Fe is G or V; 
 (v) a Chothia CDR-H2 sequence defined by the consensus sequence α 3 -α 4 -α 5 -α 6 -G-T-A (SEQ ID NOS: 51-54), where as is I or L or is absent; α 4  is P or is absent; and as is I, G, or R; and α 6  is A, F, or G; or 
 (vi) a Chothia CDR-H2 sequence defined by the consensus sequence I-P-β 5 -β 6 -G-β 8 -A (SEQ ID NOS: 56-60), where β 5  is I, E, S, or T; β 6  is F, I, or S; and β 8  is I or T, 
   c) a VHCDR3 sequence comprising:
 (i) a CDR-H3 sequence defined by the consensus sequence G-K-R-E-G-G-T-E-Y-L-R-   12  (SEQ ID NOS: 82-86), where    12  is H, K, S, N, or V; 
 (ii) a CDR-H3 sequence defined by the consensus sequence E-S-G-ϕ 4 -Y-R-D-H-R-L-ϕ 1 -V (SEQ ID NOS: 94-96), where ϕ 4  is G or T and ii is D or G; or 
 (iii) a CDR-H3 sequence defined by the consensus sequence G-G-A-K-Y-A-   7 -   8 -   9 -G-M-D-V (SEQ ID NOS: 87-93), where    7  is S, V, G, or R;    8  is T, Q, K, G, or R; and    9  is Y, H, L, or W, 
   d) a VLCDRI sequence comprising:
 (i) a CDR-L1 sequence defined by the consensus sequence ϕ 1 -A-S-ϕ 4 -ϕ 8 -V-ϕ 7 -ϕ 8 -ϕ 9 -Y-L-A (SEQ ID NOS: 1101-114), where ϕ 1  is E, K, or R; ϕ 4  is Q or E; ϕ 5  is S or Y; ϕ 7  is S or A; ϕ 8  is S or Y; and ϕ 9  is D or S; 
 (ii) a CDR-L1 sequence defined by the consensus sequence σ 1 -A-S-Q-σ 5 -σ 6 -σ 7 -σ 8 -σ 9 -L-σ 11  (SEQ ID NOS: 118 and 120-123), where σ 1  is Q or Rl; σ 5  is D or S; σ 6  is I or V; σ 7  is G or S; σ 8  is N, R, or S; σ 9  is N, Y, or W; and σ 11  is A or N; or 
 (iii) a CDR-L1 sequence defined by the consensus sequence K-S-S-Γ 4 -S-V-L-Γ 8 -S-Γ 10 -N-N-K-N-Y-L-A (SEQ ID NOS: 115-117), where Γ 4  is Q, R or K; Γ 8  is F or Y; and Γ 10  is S or N, 
   e) a VLCDR2 sequence comprising:
 (i) a CDR-L2 sequence defined by the consensus sequence ψ 1 -A-S-ψ 4 -R-ψ 6 -ψ 7  (SEQ ID NOS: 125-136), where ψ 1  is G or Y, ψ 4  is S or N; ψ 6  is A or H; and ψ 7  is T, Y, or N; 
 (ii) a CDR-L2 sequence defined by the consensus sequence D-A-S-χ-A-T (SEQ ID NOS: 138 and 139), where £ 4  is N or K; or 
 (iii) a CDR-L2 sequence defined by the consensus sequence W-A-S-T-R-σ 6 -S(SEQ ID NOS: 131 and 133-134), where σ 6  is A, E, or Q, and 
   f) a VLCDR3 sequence comprising:
 (i) a CDR-L3 sequence defined by the consensus sequence Q-Q-Y-π 4 -π 5 -π 6 -π 7  (SEQ ID NOS: 141-147), where π 4  is G, H, or Y; π 5  is S, N, F, G, or R; π 6  is S, Y, A, G, or R; and π 7  is P, I, or L; 
 (ii) a CDR-L3 sequence defined by consensus sequence Q-Q-λ 3 -λ 4 -λ 5 -λ 6 -P-T (SEQ ID NOS: 148-150), where λ 3  is R, F, H, S, L, D, Y, or V; λ 4  is S, V, T, G, L, Y, or N; a, λ 5  is N, L, F, K, or V; and λ 6  is W, F, Y, or L; 
 (iii) a CDR-L3 sequence defined by the consensus sequence Q-Q-Y-ρ 3 -ρ 4 -W-P-L-T (SEQ ID NOS: 151 and 152), where ρ 3  is Nor L and ρ 4  is Nor L; or 
 (iv) a CDR-L3 sequence defined by the consensus sequence Q-Q-ω 3 -ω 4 -ω 5 -ω 6 -P-ω 8 -T (SEQ ID NOS: 153-156), where ω 3  is Y or F; ω 4  is Y or W; ω 5  is S, L, T, or F; ω 6  is T, Y, or F; and ω 8  is L or P.