Glycan-Interacting Compounds and Methods of Use

Abstract

The present invention provides glycan-interacting antibodies and methods for producing glycan-interacting antibodies useful in the treatment and prevention of human disease, including cancer. Such glycan-interacting antibodies include monoclonal antibodies, derivatives, and fragments thereof as well as compositions and kits comprising them. Further provided are methods of using glycan-interacting antibodies to target cells and treat disease.

1 .- 7 . (canceled) 
     
     
         8 . An isolated antibody, wherein the antibody binds to both AcSTn and GcSTn. 
     
     
         9 . The isolated antibody of  claim 8 , wherein the antibody binds to an unsialyated Tn antigen. 
     
     
         10 . The isolated antibody of  claim 8 , wherein the antibody does not bind to an un-sialylated Tn antigen. 
     
     
         11 . The isolated antibody of  claim 8 , wherein the antibody binds to glycans Neu5Acα2,6GalNAcαO(CH 2 ) 2 CH 2 NH 2 , Neu5Gcα2,6GalNAcαO(CH 2 ) 2 CH 2 NH 2 , Neu5,9Ac2α2,6GalNAcαO(CH 2 ) 2 CH 2 NH 2 , and Neu5Gc9Acα2,6GalNAcαO(CH 2 ) 2 CH 2 NH 2 . 
     
     
         12 . The isolated antibody of  claim 9 , wherein the antibody binds to glycans Neu5Acα2,6GalNAcαO(CH 2 ) 2 CH 2 NH 2 , Neu5Gcα2,6GalNAcαO(CH 2 ) 2 CH 2 NH 2 , Neu5,9Ac2α2,6GalNAcαO(CH 2 ) 2 CH 2 NH 2 , Neu5Gc9Acα2,6GalNAcαO(CH 2 ) 2 CH 2 NH 2 , and GalNAcαO(CH 2 ) 2 CH 2 NH 2 . 
     
     
         13 . The isolated antibody of  claim 10 , wherein the antibody binds to glycans Neu5Acα2,6GalNAcαO(CH 2 ) 2 CH 2 NH 2 , Neu5Gcα2,6GalNAcαO(CH 2 ) 2 CH 2 NH 2 , Neu5,9Ac2α2,6GalNAcαO(CH 2 ) 2 CH 2 NH 2 , and Neu5Gc9Acα2,6GalNAcαO(CH 2 ) 2 CH 2 NH 2 ; and wherein the antibody does not bind to GalNAcαO(CH 2 ) 2 CH 2 NH 2 . 
     
     
         14 . An isolated antibody, wherein the antibody binds to GcSTn and wherein the antibody does not bind to AcSTn. 
     
     
         15 . An isolated antibody that binds to sialyl(α2,6)N-acetylgalactosamine (STn), wherein the antibody comprises a CDR-L1 comprising the amino acid sequence of SEQ ID NO: 108, a CDR-L2 comprising the amino acid sequence of SEQ ID NO: 123, a CDR-L3 comprising the amino acid sequence of SEQ ID NO: 135, a CDR-H1 comprising the amino acid sequence of SEQ ID NO: 81, a CDR-H2 comprising the amino acid sequence of SEQ ID NO: 84, and a CDR-H3 comprising the amino acid sequence of SEQ ID NO: 96. 
     
     
         16 . The isolated antibody of  claim 15 , wherein the antibody is a monoclonal antibody. 
     
     
         17 . The isolated antibody of  claim 16 , wherein the antibody is a humanized antibody. 
     
     
         18 . The isolated antibody of  claim 15 , wherein the antibody comprises a VH comprising the amino acid sequence of SEQ ID NO: 37 and a VL comprising the amino acid sequence of SEQ ID NO: 38. 
     
     
         19 . The isolated antibody of  claim 17 , wherein the antibody comprises a human IgG1, IgG2a, IgG2b, IgG2c, IgG3, or IgG4 constant region. 
     
     
         20 . A pharmaceutical composition comprising the antibody of  claim 15  and at least one pharmaceutically acceptable excipient. 
     
     
         21 . An isolated nucleic acid that encodes the antibody of  claim 15 . 
     
     
         22 . An isolated host cell that comprises the nucleic acid of  claim 21 . 
     
     
         23 . An isolated host cell that expresses the antibody of  claim 15 . 
     
     
         24 . A method of producing an antibody that binds to sialyl(α2,6)N-acetylgalactosamine (STn), comprising culturing the host cell of  claim 23  under conditions suitable for expressing the antibody. 
     
     
         25 . The method of  claim 24 , further comprising isolating the antibody. 
     
     
         26 . A method of treating cancer comprising administering to a subject with cancer a therapeutically effective amount of the antibody of  claim 15 . 
     
     
         27 . The method of  claim 26 , wherein the cancer is selected from breast cancer, colon cancer, pancreatic cancer, lung cancer, cervical cancer, ovarian cancer, stomach cancer, prostate cancer, and liver cancer. 
     
     
         28 . A method of selecting a subject with cancer for treatment with an anti-STn antibody, comprising contacting a sample from the subject with the antibody of  claim 15 ; and detecting binding of the antibody to STn-expressing cancer cells. 
     
     
         29 . The method of  claim 28 , further comprising administering an anti-STn antibody to the subject. 
     
     
         30 . The method of  claim 28 , wherein the sample is a cell, a tissue, a tissue section, a body fluid, serum, or a combination thereof. 
     
     
         31 . A kit for screening a biological sample for the presence of STn-expressing cancer cells, comprising an antibody of  claim 15 . 
     
     
         32 . An antibody-drug conjugate comprising the antibody of  claim 15  conjugated to a therapeutic agent. 
     
     
         33 . The antibody-drug conjugate of  claim 32 , wherein said therapeutic agent is a cytotoxic agent. 
     
     
         34 . The antibody-drug conjugate of  claim 33 , wherein said cytotoxic agent is monomethyl auristatin E (MMAE) or monomethyl auristatin F (MMAF). 
     
     
         35 . A pharmaceutical composition comprising the antibody-drug conjugate of  claim 32  and at least one pharmaceutically acceptable excipient. 
     
     
         36 . A method of treating cancer comprising administering to a subject with cancer a therapeutically effective amount of the antibody-drug conjugate of  claim 32 . 
     
     
         37 . The method of  claim 36 , wherein the cancer is selected from breast cancer, colon cancer, pancreatic cancer, lung cancer, cervical cancer, ovarian cancer, stomach cancer, prostate cancer, and liver cancer. 
     
     
         38 . A method of killing a STn-expressing cell, comprising contacting the cell with an antibody-drug conjugate of  claim 32 . 
     
     
         39 . A method of making an antibody-drug conjugate, comprising contacting the antibody of  claim 15  with maleimidocaproyl-valine-citruline-p-aminobenzyloxycarbonyl-monomethyl auristatin E (MC-γc-PAB-MMAE). 
     
     
         40 . An isolated antibody that binds to sialyl(α2,6)N-acetylgalactosamine (STn), wherein the antibody comprises:
 a) a CDR-L1 comprising the amino acid sequence of SEQ ID NO: 100, a CDR-L2 comprising the amino acid sequence of SEQ ID NO: 115, a CDR-L3 comprising the amino acid sequence of SEQ ID NO: 127, a CDR-H1 comprising the amino acid sequence of SEQ ID NO: 81, a CDR-H2 comprising the amino acid sequence of SEQ ID NO: 84, and a CDR-H3 comprising the amino acid sequence of SEQ ID NO: 90; 
 b) a CDR-L1 comprising the amino acid sequence of SEQ ID NO: 101, a CDR-L2 comprising the amino acid sequence of SEQ ID NO: 116, a CDR-L3 comprising the amino acid sequence of SEQ ID NO: 128, a CDR-H1 comprising the amino acid sequence of SEQ ID NO: 81, a CDR-H2 comprising the amino acid sequence of SEQ ID NO: 85, and a CDR-H3 comprising the amino acid sequence of SEQ ID NO: 91; 
 c) a CDR-L1 comprising the amino acid sequence of SEQ ID NO: 102, a CDR-L2 comprising the amino acid sequence of SEQ ID NO: 117, a CDR-L3 comprising the amino acid sequence of SEQ ID NO: 129, a CDR-H1 comprising the amino acid sequence of SEQ ID NO: 81, a CDR-H2 comprising the amino acid sequence of SEQ ID NO: 84, and a CDR-H3 comprising the amino acid sequence of SEQ ID NO: 92; 
 d) a CDR-L1 comprising the amino acid sequence of SEQ ID NO: 103, a CDR-L2 comprising the amino acid sequence of SEQ ID NO: 118, a CDR-L3 comprising the amino acid sequence of SEQ ID NO: 130, a CDR-H1 comprising the amino acid sequence of SEQ ID NO: 81, a CDR-H2 comprising the amino acid sequence of SEQ ID NO: 86, and a CDR-H3 comprising the amino acid sequence of SEQ ID NO: 93; 
 e) a CDR-L1 comprising the amino acid sequence of SEQ ID NO: 104, a CDR-L2 comprising the amino acid sequence of SEQ ID NO: 119, a CDR-L3 comprising the amino acid sequence of SEQ ID NO: 131, a CDR-H1 comprising the amino acid sequence of SEQ ID NO: 81, a CDR-H2 comprising the amino acid sequence of SEQ ID NO: 85, and a CDR-H3 comprising the amino acid sequence of SEQ ID NO: 94; 
 f) a CDR-L1 comprising the amino acid sequence of SEQ ID NO: 105, a CDR-L2 comprising the amino acid sequence of SEQ ID NO: 120, a CDR-L3 comprising the amino acid sequence of SEQ ID NO: 132, a CDR-H1 comprising the amino acid sequence of SEQ ID NO: 81, a CDR-H2 comprising the amino acid sequence of SEQ ID NO: 87, and a CDR-H3 comprising the amino acid sequence of SEQ ID NO: 95; 
 g) a CDR-L1 comprising the amino acid sequence of SEQ ID NO: 106, a CDR-L2 comprising the amino acid sequence of SEQ ID NO: 121, a CDR-L3 comprising the amino acid sequence of SEQ ID NO: 133, a CDR-H1 comprising the amino acid sequence of SEQ ID NO: 81, a CDR-H2 comprising the amino acid sequence of SEQ ID NO: 88, a CDR-H3 comprising the amino acid sequence of SEQ ID NO: 96; 
 h) a CDR-L1 comprising the amino acid sequence of SEQ ID NO: 107, a CDR-L2 comprising the amino acid sequence of SEQ ID NO: 122, a CDR-L3 comprising the amino acid sequence of SEQ ID NO: 134, a CDR-H1 comprising the amino acid sequence of SEQ ID NO: 81, a CDR-H2 comprising the amino acid sequence of SEQ ID NO: 85, and a CDR-H3 comprising the amino acid sequence of SEQ ID NO: 97; 
 i) a CDR-L1 comprising the amino acid sequence of SEQ ID NO: 109, a CDR-L2 comprising the amino acid sequence of SEQ ID NO: 124, a CDR-L3 comprising the amino acid sequence of SEQ ID NO: 136, a CDR-H1 comprising the amino acid sequence of SEQ ID NO: 82, a CDR-H2 comprising the amino acid sequence of SEQ ID NO: 89, and a CDR-H3 comprising the amino acid sequence of SEQ ID NO: 98; 
 j) a CDR-L1 comprising the amino acid sequence of SEQ ID NO: 110, a CDR-L2 comprising the amino acid sequence of SEQ ID NO: 125, a CDR-L3 comprising the amino acid sequence of SEQ ID NO: 137, a CDR-H1 comprising the amino acid sequence of SEQ ID NO: 83, a CDR-H2 comprising the amino acid sequence of SEQ ID NO: 85, and a CDR-H3 comprising the amino acid sequence of SEQ ID NO: 96; 
 k) a CDR-L1 comprising the amino acid sequence of SEQ ID NO: 110, a CDR-L2 comprising the amino acid sequence of SEQ ID NO: 125, a CDR-L3 comprising the amino acid sequence of SEQ ID NO: 138, a CDR-H1 comprising the amino acid sequence of SEQ ID NO: 83, a CDR-H2 comprising the amino acid sequence of SEQ ID NO: 85, and a CDR-H3 comprising the amino acid sequence of SEQ ID NO: 96; 
 l) a CDR-L1 comprising the amino acid sequence of SEQ ID NO: 103, a CDR-L2 comprising the amino acid sequence of SEQ ID NO: 125, a CDR-L3 comprising the amino acid sequence of SEQ ID NO: 139, a CDR-H1 comprising the amino acid sequence of SEQ ID NO: 81, a CDR-H2 comprising the amino acid sequence of SEQ ID NO: 84, and a CDR-H3 comprising the amino acid sequence of SEQ ID NO: 97; 
 m) a CDR-L1 comprising the amino acid sequence of SEQ ID NO: 100, a CDR-L2 comprising the amino acid sequence of SEQ ID NO: 115, a CDR-L3 comprising the amino acid sequence of SEQ ID NO: 127, a CDR-H1 comprising the amino acid sequence of SEQ ID NO: 81, a CDR-H2 comprising the amino acid sequence of SEQ ID NO: 85, and a CDR-H3 comprising the amino acid sequence of SEQ ID NO: 99; 
 n) a CDR-L1 comprising the amino acid sequence of SEQ ID NO: 111, a CDR-L2 comprising the amino acid sequence of SEQ ID NO: 123, a CDR-L3 comprising the amino acid sequence of SEQ ID NO: 140, a CDR-H1 comprising the amino acid sequence of SEQ ID NO: 81, a CDR-H2 comprising the amino acid sequence of SEQ ID NO: 85, and a CDR-H3 comprising the amino acid sequence of SEQ ID NO: 97; 
 o) a CDR-L1 comprising the amino acid sequence of SEQ ID NO: 112, a CDR-L2 comprising the amino acid sequence of SEQ ID NO: 118, a CDR-L3 comprising the amino acid sequence of SEQ ID NO: 141, a CDR-H1 comprising the amino acid sequence of SEQ ID NO: 83, a CDR-H2 comprising the amino acid sequence of SEQ ID NO: 85, and a CDR-H3 comprising the amino acid sequence of SEQ ID NO: 99; 
 p) a CDR-L1 comprising the amino acid sequence of SEQ ID NO: 100, a CDR-L2 comprising the amino acid sequence of SEQ ID NO: 115, a CDR-L3 comprising the amino acid sequence of SEQ ID NO: 127, a CDR-H1 comprising the amino acid sequence of SEQ ID NO: 81, a CDR-H2 comprising the amino acid sequence of SEQ ID NO: 85, and a CDR-H3 comprising the amino acid sequence of SEQ ID NO: 89; 
 q) a CDR-L1 comprising the amino acid sequence of SEQ ID NO: 100, a CDR-L2 comprising the amino acid sequence of SEQ ID NO: 115, a CDR-L3 comprising the amino acid sequence of SEQ ID NO: 127, a CDR-H1 comprising the amino acid sequence of SEQ ID NO: 81, a CDR-H2 comprising the amino acid sequence of SEQ ID NO: 89, and a CDR-H3 comprising the amino acid sequence of SEQ ID NO: 99; or 
 r) a CDR-L1 comprising the amino acid sequence of SEQ ID NO: 113, a CDR-L2 comprising the amino acid sequence of SEQ ID NO: 115, a CDR-L3 comprising the amino acid sequence of SEQ ID NO: 127, a CDR-H1 comprising the amino acid sequence of SEQ ID NO: 81, a CDR-H2 comprising the amino acid sequence of SEQ ID NO: 89, and a CDR-H3 comprising the amino acid sequence of SEQ ID NO: 99. 
 
     
     
         41 . The isolated antibody of  claim 40 , wherein the antibody is a monoclonal antibody. 
     
     
         42 . The isolated antibody of  claim 40 , wherein the antibody is a humanized antibody. 
     
     
         43 . The isolated antibody of  claim 40 , wherein the antibody comprises:
 a) a VH comprising the amino acid sequence of SEQ ID NO: 31 and a VL comprising the amino acid sequence of SEQ ID NO: 32;   b) a VH comprising the amino acid sequence of SEQ ID NO: 27 and a VL comprising the amino acid sequence of SEQ ID NO: 28;   c) a VH comprising the amino acid sequence of SEQ ID NO: 29 and a VL comprising the amino acid sequence of SEQ ID NO: 30;   d) a VH comprising the amino acid sequence of SEQ ID NO: 21 and a VL comprising the amino acid sequence of SEQ ID NO: 22;   e) a VH comprising the amino acid sequence of SEQ ID NO: 23 and a VL comprising the amino acid sequence of SEQ ID NO: 24   f) a VH comprising the amino acid sequence of SEQ ID NO: 19 and a VL comprising the amino acid sequence of SEQ ID NO: 20;   g) a VH comprising the amino acid sequence of SEQ ID NO: 35 and a VL comprising the amino acid sequence of SEQ ID NO: 36;   h) a VH comprising the amino acid sequence of SEQ ID NO: 51 and a VL comprising the amino acid sequence of SEQ ID NO: 52;   i) a VH comprising the amino acid sequence of SEQ ID NO: 25 and a VL comprising the amino acid sequence of SEQ ID NO: 26;   j) a VH comprising the amino acid sequence of SEQ ID NO: 48 and a VL comprising the amino acid sequence of SEQ ID NO: 49;   k) a VH comprising the amino acid sequence of SEQ ID NO: 48 and a VL comprising the amino acid sequence of SEQ ID NO: 50;   l) a VH comprising the amino acid sequence of SEQ ID NO: 15 and a VL comprising the amino acid sequence of SEQ ID NO: 16;   m) a VH comprising the amino acid sequence of SEQ ID NO: 47 and a VL comprising the amino acid sequence of SEQ ID NO: 32;   n) a VH comprising the amino acid sequence of SEQ ID NO: 39 and a VL comprising the amino acid sequence of SEQ ID NO: 40;   o) a VH comprising the amino acid sequence of SEQ ID NO: 39 and a VL comprising the amino acid sequence of SEQ ID NO: 40;   p) a VH comprising the amino acid sequence of SEQ ID NO: 44 and a VL comprising the amino acid sequence of SEQ ID NO: 45;   q) a VH comprising the amino acid sequence of SEQ ID NO: 42 and a VL comprising the amino acid sequence of SEQ ID NO: 32; or   r) a VH comprising the amino acid sequence of SEQ ID NO: 46 and a VL comprising the amino acid sequence of SEQ ID NO: 32.   
     
     
         44 . An isolated nucleic acid that encodes the antibody of  claim 40 . 
     
     
         45 . An isolated host cell comprising the isolated nucleic acid of  claim 44 . 
     
     
         46 . A method of producing an antibody that binds to sialyl(α2,6)N-acetylgalactosamine (STn), comprising culturing the host cell of  claim 45  under conditions suitable for expressing the antibody. 
     
     
         47 . A method of treating cancer comprising administering to a subject with cancer a therapeutically effective amount of the antibody of  claim 40 . 
     
     
         48 . A method of selecting a subject with cancer for treatment with an anti-STn antibody, comprising contacting a sample from the subject with the antibody of  claim 40 ; and detecting binding of the antibody to STn-expressing cancer cells. 
     
     
         49 . An antibody-drug conjugate comprising the antibody of  claim 40  conjugated to a therapeutic agent. 
     
     
         50 . The antibody-drug conjugate of  claim 49 , wherein said therapeutic agent is a cytotoxic agent. 
     
     
         51 . The antibody-drug conjugate of  claim 50 , wherein said cytotoxic agent is monomethyl auristatin E (MMAE) or monomethyl auristatin F (MMAF). 
     
     
         52 . A method of treating cancer comprising administering to a subject with cancer a therapeutically effective amount of the antibody-drug conjugate of  claim 49 . 
     
     
         53 . A method of killing a STn-expressing cell, comprising contacting the cell with an antibody-drug conjugate of  claim 49 . 
     
     
         54 . A method of making an antibody-drug conjugate, comprising contacting the antibody of  claim 40  with maleimidocaproyl-valine-citruline-p-aminobenzyloxycarbonyl-monomethyl auristatin E (MC-γc-PAB-MMAE).