Antigen binding polypeptides, antigen binding polypeptide complexes and methods of use thereof

Abstract

Disclosed are antigen binding polypeptides and antigen binding polypeptide complexes (e.g., antibodies and antigen binding fragments thereof) having certain structural features. Also disclosed are polynucleotides and vectors encoding such polypeptides and polypeptide complexes; chimeric antigen receptors (CARs), cells, pharmaceutical compositions and kits containing such polypeptides and polypeptide complexes; and methods of using such polypeptides and polypeptide complexes.

1 - 107 . (canceled) 
     
     
         108 . An antigen binding polypeptide complex comprising a first polypeptide and a second polypeptide;
 wherein the first polypeptide has a structure represented by:   VL1-VL2-VH2-VH1-Fc;   VH1-VH2-VL2-VL1-Fc;   VL1-L1-VL2-L2-VH2-L3-VH1-Fc;   VH1-L1-VH2-L2-VL2-L3-VL1-Fc;   VL1-L1-VL2-L2-VH2-L3-VH1-L4-Fc; or   VH1-L1-VH2-L2-VL2-L3-VL1-L4-Fc;   wherein the second polypeptide has a structure represented by:   VL3-VH3-Fc;   VH3-VL3-Fc;   VL3-L5-VH3-Fc; or   VH3-L5-VL3-Fc; and   wherein:   VL1 is a first immunoglobulin light chain variable region;   VL2 is a second immunoglobulin light chain variable region;   VL3 is a third immunoglobulin light chain variable region;   VH1 is a first immunoglobulin heavy chain variable region;   VH2 is a second immunoglobulin heavy chain variable region;   VH3 is a third immunoglobulin heavy chain variable region;   Fc is a region comprising an immunoglobulin heavy chain constant region 2 (CH2), an immunoglobulin heavy chain constant region 3 (CH3), and optionally, an immunoglobulin hinge; and   L1, L2, L3, L4 and L5 are amino acid linkers.   
     
     
         109 . The antigen binding polypeptide complex of  claim 108 ,
 wherein the first polypeptide has a structure represented by:   VL1-VL2-VH2-VH1-CH1-Fc;   VH1-VH2-VL2-VL1-CH1-Fc;   VL1-VL2-VH2-VH1-CL-Fc;   VH1-VH2-VL2-VL1-CL-Fc;   VL1-L1-VL2-L2-VH2-L3-VH1-L4-CH1-Fc;   VH1-L1-VH2-L2-VL2-L3-VL1-L4-CH1-Fc;   VL1-L1-VL2-L2-VH2-L3-VH1-L4-CL-Fc; or   VH1-L1-VH2-L2-VL2-L3-VL1-L4-CL-Fc;   wherein the second polypeptide has a structure represented by:   VL3-VH3-CH1-Fc;   VH3-VL3-CH1-Fc;   VL3-VH3-CL-Fc;   VH3-VL3-CL-Fc;   VL3-L5-VH3-L6-CH1-L7-Fc;   VH3-L5-VL3-L6-CH1-L7-Fc;   VL3-L5-VH3-L6-CL-L7-Fc; or   VH3-L5-VL3-L6-CL-L7-Fc; and   wherein:   CH1 is an immunoglobulin heavy chain constant region 1;   CL is an immunoglobulin light chain constant region; and   L1, L2, L3, L4, L5, L6, and L7 are amino acid linkers.   
     
     
         110 . The antigen binding polypeptide complex of  claim 108 ,
 wherein the second polypeptide has a structure represented by:   VL3-VH3-CH1-CL-Fc;   VH3-VL3-CH1-CL-Fc;   VL3-VH3-CL-CH1-Fc;   VH3-VL3-CL-CH1-Fc;   VL3-L6-VH3-L7-CH1-L8-CL-Fc;   VH3-L6-VL3-L7-CH1-L8-CL-Fc;   VL3-L6-VH3-L7-CL-L8-CH1-Fc;   VH3-L6-VL3-L7-CL-L8-CH1-Fc;   VL3-VH3-L6-CH1-CL-Fc;   VH3-VL3-L6-CH1-CL-Fc;   VL3-VH3-L6-CL-CH1-Fc; or   VH3-VL3-L6-CL-CH1-Fc; and   wherein:   CH1 is an immunoglobulin heavy chain constant region 1;   CL is an immunoglobulin light chain constant region; and   L1, L2, L3, L4, L5, L6, L7 and L8 are amino acid linkers.   
     
     
         111 . The antigen binding polypeptide complex of  claim 108 ,
 wherein the second polypeptide has a structure represented by:   VL3-CL-VH3-CH1-Fc;   VL3-CH1-VH3-CL-Fc;   VH3-CH1-VL3-CL-Fc;   VH3-CL-VL3-CH1-Fc;   VL3-L6-CL-L7-VH3-L8-CH1-Fc;   VL3-L6-CH1-L7-VH3-L8-CL-Fc;   VH3-L6-CH1-L7-VL3-L8-CL-Fc;   VH3-L6-CL-L7-VL3-L8-CH1-Fc;   VL3-CL-L6-VH3-CH1-Fc;   VL3-CH1-L6-VH3-CL-Fc;   VH3-CH1-L6-VL3-CL-Fc; or   VH3-CL-L6-VL3-CH1-Fc; and   wherein:   CH1 is an immunoglobulin heavy chain constant region 1;   CL is an immunoglobulin light chain constant region; and   L1, L2, L3, L4, L5, L6, L7 and L8 are amino acid linkers.   
     
     
         112 . An antigen binding polypeptide complex comprising a first polypeptide, a second polypeptide, and a third polypeptide;
 wherein the first polypeptide has a structure represented by:   VL1-VL2-VH2-VH1-Fc;   VH1-VH2-VL2-VL1-Fc;   VL1-L1-VL2-L2-VH2-L3-VH1-Fc;   VH1-L1-VH2-L2-VL2-L3-VL1-Fc;   VL1-L1-VL2-L2-VH2-L3-VH1-L4-Fc; or   VH1-L1-VH2-L2-VL2-L3-VL1-L4-Fc;   wherein the second polypeptide has a structure represented by:   VL3; or   VL3-L5;   wherein the third polypeptide has a structure represented by:   VH3-Fc; or   VH3-L6-Fc; and   wherein:   VL1 is a first immunoglobulin light chain variable region;   VL2 is a second immunoglobulin light chain variable region;   VL3 is a third immunoglobulin light chain variable region;   VH1 is a first immunoglobulin heavy chain variable region;   VH2 is a second immunoglobulin heavy chain variable region;   VH3 is a third immunoglobulin heavy chain variable region;   Fc is a region comprising an immunoglobulin heavy chain constant region 2 (CH2), an immunoglobulin heavy chain constant region 3 (CH3), and optionally, an immunoglobulin hinge; and   L1, L2, L3, L4, L5 and L6 are amino acid linkers.   
     
     
         113 . The antigen binding polypeptide complex of  claim 112 ,
 wherein the second polypeptide has a structure represented by:   VL3-CH1;   VL3-CL;   VL3-L5-CH1; or   VL3-L5-CL;   wherein the third polypeptide has a structure represented by:   VH3-CH1-Fc;   VH3-CL-Fc;   VH3-L6-Fc;   VH3-L6-CH1-Fc; or   VH3-L6-CL-Fc; and   wherein:   CH1 is an immunoglobulin heavy chain constant region 1; and   CL is an immunoglobulin light chain constant region.   
     
     
         114 . An antigen binding polypeptide complex comprising a first polypeptide, a second polypeptide, and a third polypeptide;
 wherein the first polypeptide has a structure represented by:   VL1-VL2-VH2-VH1-Fc;   VH1-VH2-VL2-VL1-Fc;   VL1-L1-VL2-L2-VH2-L3-VH1-Fc;   VH1-L1-VH2-L2-VL2-L3-VL1-Fc;   VL1-L1-VL2-L2-VH2-L3-VH1-L4-Fc; or   VH1-L1-VH2-L2-VL2-L3-VL1-L4-Fc;   wherein the second polypeptide has a structure represented by:   VL3-Fc; or   VL3-L5-Fc;   wherein the third polypeptide has a structure represented by:   VH3; or   VH3-L6; and   wherein:   VL1 is a first immunoglobulin light chain variable region;   VL2 is a second immunoglobulin light chain variable region;   VL3 is a third immunoglobulin light chain variable region;   VH1 is a first immunoglobulin heavy chain variable region;   VH2 is a second immunoglobulin heavy chain variable region;   VH3 is a third immunoglobulin heavy chain variable region;   Fc is a region comprising an immunoglobulin heavy chain constant region 2 (CH2), an immunoglobulin heavy chain constant region 3 (CH3), and optionally, an immunoglobulin hinge; and   L1, L2, L3, L4, L5 and L6 are amino acid linkers.   
     
     
         115 . The antigen binding polypeptide complex of  claim 114 ,
 wherein the second polypeptide has a structure represented by:   VL3-CH1-Fc;   VL3-CL-Fc;   VL3-L5-CH1-Fc; or   VL3-L5-CL-Fc;   wherein the third polypeptide has a structure represented by:   VH3-CH1;   VH3-CL;   VH3-L6-CH1; or   VH3-L6-CL; and   wherein:   CH1 is an immunoglobulin heavy chain constant region 1; and   CL is an immunoglobulin light chain constant region.   
     
     
         116 . The antigen binding polypeptide complex of  claim 108 , wherein VH1, VH2 and VH3 each bind to different antigens, and VL1, VL2 and VL3 each bind to different antigens. 
     
     
         117 . The antigen binding polypeptide complex of  claim 108 , wherein linkers L1, L2, L3, L4 and L5 each comprise an amino acid sequence having at least 95% identity to any one of SEQ ID NOs:1-19 and 665-672. 
     
     
         118 . The antigen binding polypeptide complex of  claim 112 , wherein linkers L1, L2, L3, L4, L5 and L6 each comprise an amino acid sequence having at least 95% identity to any one of SEQ ID NOs:1-19 and 665-672. 
     
     
         119 . The antigen binding polypeptide complex of  claim 114 , wherein linkers L1, L2, L3, L4, L5 and L6 each comprise an amino acid sequence having at least 95% identity to any one of SEQ ID NOs:1-19 and 665-672. 
     
     
         120 . The antigen binding polypeptide complex of  claim 108 , wherein the Fc region comprises at least one knob-into-hole modification. 
     
     
         121 . The antigen binding polypeptide complex of  claim 112 , wherein the Fc region comprises at least one knob-into-hole modification. 
     
     
         122 . The antigen binding polypeptide complex of  claim 114 , wherein the Fc region comprises at least one knob-into-hole modification. 
     
     
         123 . An antibody or antigen binding fragment thereof comprising the antigen binding polypeptide complex of  claim 108 . 
     
     
         124 . The antibody or antigen binding fragment thereof of  claim 123 , wherein the antigen binding fragment is a Fab, scFab, Fab′, F(ab′) 2 , Fv, or scFv. 
     
     
         125 . A polypeptide having at least 95% identity to any one of SEQ ID NOs:78-92. 
     
     
         126 . A polynucleotide having at least 95% identity to any one of SEQ ID NOs:93-107. 
     
     
         127 . A pharmaceutical composition comprising the antigen binding polypeptide complex of  claim 108 , and (ii) a pharmaceutically acceptable carrier. 
     
     
         128 . A pharmaceutical composition comprising (i) a polynucleotide encoding the antigen binding polypeptide complex of  claim 108 , and (ii) a pharmaceutically acceptable carrier. 
     
     
         129 . A method of treating or preventing a cancer, comprising administering to a subject in need thereof a therapeutically effective amount of the antigen binding polypeptide complex of  claim 108 . 
     
     
         130 . A method of treating or preventing a virus infection, comprising administering to a subject in need thereof a therapeutically effective amount of the antigen binding polypeptide complex of  claim 108 .