Antibodies and methods for making and using them

Abstract

The invention provides antibodies, including chimeric human antibodies, recombinant antibodies, synthetic anti-bodies, and the nucleic acids encoding them, and methods for making and using these immunoglobulins. The invention provides recombinant and synthetic polypeptide and nucleic acid embodiments of these polypeptides and/or antibodies. The invention also provides polypeptides comprising, or consisting of, consensus human framework regions, or “Independently Consensused Frameworks (ICFs)”, nucleic acids encoding them, and libraries and kits comprising these ICFs and/or antibodies of the invention, individually and in combinatorial libraries and combinations.

What is claimed is: 
     
         1 . An antibody or antigen-binding fragment thereof comprising at least one of the following combinations:
 (1) light chain BD22084 (SEQ ID NO:225) and heavy chain BD20332 (SEQ ID NO:138);   (2) light chain BD22085 (SEQ ID NO:232) and heavy chain BD20335 (SEQ ID NO:143);   (3) light chain BD22086 (SEQ ID NO:227) and heavy chain BD20335 (SEQ ID NO:143);   (4) light chain BD22088 (SEQ ID NO:229) and heavy chain BD20337 (SEQ ID NO:148);   (5) light chain BD22087 (SEQ ID NO:240) and heavy chain BD20335 (SEQ ID NO:143);   (6) light chain BD22089 (SEQ ID NO:243) and heavy chain BD20335 (SEQ ID NO:143);   (7) light chain BD22090 (SEQ ID NO:234) and heavy chain BD20337 (SEQ ID NO:148);   (8) light chain BD22095 (SEQ ID NO:244) and heavy chain BD20337 (SEQ ID NO:148);   (9) light chain BD22091 (SEQ ID NO:242) and heavy chain BD20337 (SEQ ID NO:148);   (10) light chain BD22108 (SEQ ID NO:230) and heavy chain BD20337 (SEQ ID NO:148);   (11) light chain BD22092 (SEQ ID NO:235) and heavy chain BD20338 (SEQ ID NO:149);   (12) light chain BD22094 (SEQ ID NO:231) and heavy chain BD20337 (SEQ ID NO:148);   (13) light chain BD22096 (SEQ ID NO:241) and heavy chain BD20337 (SEQ ID NO:148);   (14) light chain BD22092 (SEQ ID NO:235) and heavy chain BD20337 (SEQ ID NO:148);   (15) light chain BD22102 (SEQ ID NO:248) and heavy chain BD20337 (SEQ ID NO:148);   (16) light chain BD22097 (SEQ ID NO:246) and heavy chain BD20335 (SEQ ID NO:143).   (17) light chain BD22104 (SEQ ID NO:239) and heavy chain BD20337 (SEQ ID NO:148);   (18) light chain BD22085 (SEQ ID NO:232) and heavy chain BD20339 (SEQ ID NO:150);   (19) light chain BD22107 (SEQ ID NO:226) and heavy chain BD20339 (SEQ ID NO:150);   (20) light chain BD22100 (SEQ ID NO:236) and heavy chain BD20335 (SEQ ID NO:143);   (21) light chain BD22103 (SEQ ID NO:228) and heavy chain BD20337 (SEQ ID NO:148);   (22) light chain BD22105 (SEQ ID NO:237) and heavy chain BD20337 (SEQ ID NO:148);   (23) light chain BD22101 (SEQ ID NO:247) and heavy chain BD20335 (SEQ ID NO:143);   (24) light chain BD22106 (SEQ ID NO:245) and heavy chain BD20333 (SEQ ID NO:142);   (25) light chain BD22108 (SEQ ID NO:230) and heavy chain BD20338 (SEQ ID NO:149);   (26) light chain BD22109 (SEQ ID NO:233) and heavy chain BD20341 (SEQ ID NO:154); or   (27) light chain BD22111 (SEQ ID NO:238) and heavy chain BD20336 (SEQ ID NO:144)   and wherein the at least a portion of a light chain, the at least a portion of the heavy chain, or both are derived at least in part from sequences made by the method comprising:   (1) providing an Independently Consensused Framework 1 (ICF1) domain, comprising an amino acid consensus sequence derived from a plurality of amino acid sequences each comprising amino acids derived from at least a portion of a Kabat framework region 1 (KF1) domain, wherein the plurality of amino acid sequences are translated from a germline sequence of an immunoglobulin variable region gene or obtained from a mature immunoglobulin;   (2) providing at least a portion of a complementarity determining region 1 (CDR1) derived from the variable region of a 1F5 antibody;   (3) providing an Independently Consensused Framework 2 (ICF2) domain, comprising an amino acid consensus sequence derived from a plurality of amino acid sequences each comprising amino acids derived from at least a portion of a Kabat framework region 2 (KF2) domain, wherein the plurality of amino acid sequences translated from a germline sequence of an immunoglobulin variable region gene or obtained from a mature immunoglobulin; (4) providing at least a portion of a complementarity determining region 2 (CDR2) derived from the variable region of a 1F5 antibody;   (5) providing an Independently Consensused Framework 3 (ICF3) domain, comprising an amino acid consensus sequence derived from a plurality of amino acid sequences each comprising amino acids derived from at least a portion of a Kabat framework region 3 (KF3) domain, wherein the plurality of amino acid sequences are translated from a germline sequence of an immunoglobulin variable region gene or obtained from a mature immunoglobulin;   (6) providing at least a portion of a complementarity determining region 3 (CDR3) derived from the variable region of a 1F5 antibody; and   (7) optionally providing an Independently Consensused Framework 4 (ICF4) domain, comprising an amino acid consensus sequence derived from a plurality of amino acid sequences each comprising amino acids derived from at least a portion of a Kabat framework region 4 (KF4) domain, wherein the plurality of amino acid sequences are translated from a germline sequence of an immunoglobulin variable region gene or obtained from a mature immunoglobulin; wherein at least one ICF is derived from a genomic nucleic acid sequence,   (8) joining, in a 5′-to-3′ orientation, nucleic acids encoding the ICF1-CDR1-ICF2-CDR2-ICF3-CDR3 and optionally ICF4 domains.   
     
     
         2 . The antigen binding antibody fragment of  claim 1 , wherein the antibody fragment is an Fab fragment, an Fab′ fragment, an F(ab′) 2  fragment, a single-chain antibody, an Fv fragment, an scFv fragment, an antibody mimetic, an Fd fragment, or an Fd′ fragment. 
     
     
         3 . The antigen binding antibody fragment of  claim 2 , wherein the antibody fragment is fused to an Fc. 
     
     
         4 . A recombinant, synthetic or isolated antibody having a structure comprising at least one variable region combination of  claim 1 . 
     
     
         5 . A chimeric antibody or antigen binding fragment thereof comprising at least one variable region combination of  claim 1 . 
     
     
         6 . A chimeric antigen binding antibody fragment of  claim 5 , wherein the chimeric antibody fragment is a chimeric Fab, a chimeric Fab′, a chimeric F(ab′) 2 , a chimeric single-chain antibody, a chimeric Fv, a chimeric scFv, an antibody mimetic, a chimeric Fd, or a chimeric Fd′. 
     
     
         7 . A pharmaceutical composition or formulation comprising: (a) an antibody or antigen binding fragment thereof of  claim 1 . 
     
     
         8 . The pharmaceutical composition or formulation of  claim 9 , further comprising a pharmaceutically acceptable carrier or excipient. 
     
     
         9 . An antibody or antigen binding fragment thereof that specifically binds to a CD20 antigen and comprises a heavy chain variable region comprising (a) an ICF1 comprising an amino acid sequence of SEQ ID NOs:6 or 7; (b) a CDR1 comprising an amino acid sequence of SEQ ID NO:151; (c) an ICF2 comprising an amino acid sequence of SEQ ID NOs:9, 10, or 11; (d) a CDR2 comprising an amino acid sequence of SEQ ID NO:152; (e) an ICF3 comprising an amino acid sequence of SEQ ID NOS:13, 17, 19, or 20; (f) a CDR3 comprising an amino acid sequence of SEQ ID NO:153; and/or (g) an ICF4 comprising an amino acid sequence of SEQ ID NO:21. 
     
     
         10 . The antibody or antigen binding fragment thereof of  claim 9  wherein said heavy chain variable region comprises: (a) an ICF1 comprising an amino acid sequence of SEQ ID NO:7; (b) a CDR1 comprising an amino acid sequence of SEQ ID NO:151; (c) an ICF2 comprising an amino acid sequence of SEQ ID NO:10; (d) a CDR2 comprising an amino acid sequence of SEQ ID NO:152; (e) an ICF3 comprising an amino acid sequence of SEQ ID NO:19; (f) a CDR3 comprising an amino acid sequence of SEQ ID NO:153; and (g) an ICF4 comprising an amino acid sequence of SEQ ID NO:21. 
     
     
         11 . An antibody or antigen binding fragment thereof that specifically binds to a CD20 antigen and comprises a light chain variable region comprising (a) an ICF1 comprising an amino acid sequence of SEQ ID NOS:43-49; (b) a CDR1 comprising an amino acid sequence of SEQ ID NO:163; (c) an ICF2 comprising an amino acid sequence of SEQ ID NOs:58-61; (d) a CDR2 comprising an amino acid sequence of SEQ ID NO:164; (e) an ICF3 comprising an amino acid sequence of SEQ ID NOs:67-71, 73, or 74; (f) a CDR3 comprising an amino acid sequence of SEQ ID NO:165; and/or (g) an ICF4 comprising the amino acid sequence of SEQ ID NO:83. 
     
     
         12 . The antibody or antigen binding fragment thereof of  claim 11  wherein said light chain variable region comprises: (a) an ICF1 comprising an amino acid sequence of SEQ ID NO:43; (b) a CDR1 comprising an amino acid sequence of SEQ ID NO:163; (c) an ICF2 comprising an amino acid sequence of SEQ ID NO:61; (d) a CDR2 comprising an amino acid sequence of SEQ ID NO:164; (e) an ICF3 comprising an amino acid sequence of SEQ ID NO:73; (f) a CDR3 comprising an amino acid sequence of SEQ ID NO:165; and (g) an ICF4 comprising the amino acid sequence of SEQ ID NO:83.