Anti-cd71 antibodies, activatable anti-cd71 antibodies, and methods of use thereof

Abstract

The invention relates generally to antibodies that bind CD71, activatable antibodies that specifically bind to CD71 and methods of making and using these anti-CD71 antibodies and anti-CD71 activatable antibodies in a variety of therapeutic, diagnostic and prophylactic indications.

1 .- 88 . (canceled) 
     
     
         89 . A method of treating, alleviating a symptom of, or delaying the progression of a disorder or disease in which diseased cells express CD71 or the disorder or disease is associated with cells expressing CD71, comprising administering to a subject in need thereof a therapeutically effective amount of a conjugated activatable antibody that in an activated state specifically binds to mammalian CD71, wherein the conjugated activatable antibody comprises an activatable antibody conjugated to an agent, wherein the activatable antibody comprises:
 an antibody or an antigen binding fragment thereof (AB) that specifically binds to mammalian CD71, wherein the AB specifically binds human CD71 and cynomolgus monkey CD71, and wherein the AB comprises the VH CDR1 sequence GYTFTSYWMH (SEQ ID NO: 9); the VH CDR2 sequence AIYPGNSETG (SEQ ID NO: 10); the VH CDR3 sequence ENWDPGFAF (SEQ ID NO: 11); the VL CDR1 sequence SASSSVYYMY (SEQ ID NO: 12) or CRASSSVYYMY (SEQ ID NO: 13); the VL CDR2 sequence STSNLAS (SEQ ID NO: 14); and the VL CDR3 sequence QQRRNYPYT (SEQ ID NO: 15);   a masking moiety (MM) coupled to the AB that inhibits the binding of the AB to CD71 when the activatable antibody is in an uncleaved state; and   a cleavable moiety (CM) coupled to the AB, wherein the CM is a polypeptide that functions as a substrate for a protease.   
     
     
         90 .- 92 . (canceled) 
     
     
         93 . The method of  claim 89 , wherein the disorder or disease is a head and neck squamous cell cancer, a non-small cell lung cancer, a non-Hodgkin's lymphoma, an esophageal cancer. 
     
     
         94 .- 97 . (canceled) 
     
     
         98 . The method of  claim 89 , wherein the method comprises administering an additional agent. 
     
     
         99 . The method of  claim 98 , wherein the additional agent is a therapeutic agent. 
     
     
         100 . The method of  claim 89 , wherein the MM has one or more of the characteristics selected from the group consisting of:
 (i) the MM has a dissociation constant for binding to the AB that is greater than the dissociation constant of the AB to CD71;   (ii) the MM does not interfere or compete with the AB for binding to CD71 when the activatable antibody is in a cleaved state;   (iii) the MM is a polypeptide of no more than 40 amino acids in length;   (iv) the MM polypeptide sequence is different from that of human CD71;   (v) the MM polypeptide sequence is no more than 50% identical to any natural binding partner of the AB; and   (vi) the MM comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 16-295 and 297-314.   
     
     
         101 . The method of  claim 89 , wherein the CM comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 356-423, 680-698, 713, 714, and 789-808. 
     
     
         102 . The method of  claim 89 , wherein the antigen binding fragment thereof is selected from the group consisting of a Fab fragment, a F(ab′)2 fragment, a scFv, and a scAb. 
     
     
         103 . The method of  claim 89 , wherein the AB comprises a heavy chain variable region comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 3-5, and a light chain variable region comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 6-8. 
     
     
         104 . The method of  claim 89 , wherein the AB is linked to the CM. 
     
     
         105 . The method of  claim 89 , wherein the AB is linked directly to the CM. 
     
     
         106 . The method of  claim 89 , wherein the AB is linked to the CM via a linking peptide. 
     
     
         107 . The method of  claim 89 , wherein the MM is linked to the CM such that the activatable antibody in an uncleaved state comprises the structural arrangement from N-terminus to C-terminus as follows: MM-CM-AB or AB-CM-MM. 
     
     
         108 . The method of  claim 89 , wherein the activatable antibody comprises a linking peptide between the MM and the CM, a linking peptide between the CM and the AB, or both a linking peptide between the MM and the CM and a linking peptide between the CM and the AB. 
     
     
         109 . The method of  claim 89 , wherein the activatable antibody comprises a first linking peptide (LP1) and a second linking peptide (LP2), and wherein the activatable antibody in the uncleaved state has the structural arrangement from N-terminus to C-terminus as follows: MM-LP1-CM-LP2-AB or AB-LP2-CM-LP1-MM. 
     
     
         110 . The method of  claim 109 , wherein the two linking peptides are not identical to each other. 
     
     
         111 . The method of  claim 109 , wherein each of LP1 and LP2 is a peptide of about 1 to 20 amino acids in length. 
     
     
         112 . The method of  claim 89 , wherein the activatable antibody has one or more of the characteristics selected from the group consisting of:
 (a) the activatable antibody comprises the heavy chain sequence of SEQ ID NO: 325 or 699 and a light chain comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 327, 329, 331, 333, 335, 337, 650, 652, 654, 656, 658, 660, 670-673, 701-712, and 721-788;   (b) the activatable antibody comprises a combination of amino acid sequences, wherein the combination of amino acid sequences is selected from a single row in Table D, wherein for a given combination,
 (i) the heavy chain of the AB comprises the amino acid sequences of the VH CDR sequences corresponding to the given combination in the single row listed in Table D, 
 (ii) the light chain of the AB comprises the amino acid sequences of the VL CDR sequences corresponding to the given combination in the single row listed in Table D, 
 (iii) the MM comprises the amino acid sequence of the mask sequence (MM) corresponding to the given combination in the single row listed in Table D, and 
 (iv) the CM comprises the amino acid sequence of the substrate sequence (CM) corresponding to the given combination in the single row listed in Table D; 
   (c) the activatable antibody comprises a combination of amino acid sequences, wherein for a given combination of amino acid sequences,
 (i) the heavy chain of the AB comprises the amino acid sequences of the VH sequence or VH CDR sequences selected from the group consisting of: the VH sequence or VH CDR sequences listed in the corresponding column of Table E, 
 (ii) the light chain of the AB comprises the amino acid sequences of the VL sequence or VL CDR sequences selected from the group consisting of: the VL sequence or VL CDR sequences listed in the corresponding column of Table E, 
 (iii) the MM comprises the amino acid sequence of the mask sequence (MM) selected from the group consisting of: the MM sequences listed in the corresponding column of Table E, and 
 (iv) the CM comprises the amino acid sequence of the substrate sequence (CM) selected from the group consisting of: the CM sequences listed in the corresponding column of Table E; and 
   (d) the activatable antibody comprises a heavy chain variable region comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 3-5, and a light chain variable region comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 6-8, 809-836, and 841-908.   
     
     
         113 . The method of  claim 89 , wherein the MM is linked to the CM. 
     
     
         114 . The method of  claim 89 , wherein the MM is linked directly to the CM. 
     
     
         115 . The method of  claim 89 , wherein the MM is linked to the CM via a linking peptide. 
     
     
         116 . The method of  claim 89 , wherein the agent is conjugated to the AB via a linker. 
     
     
         117 . A method of treating, alleviating a symptom of, or delaying the progression of a disorder or disease in which diseased cells express CD71 or the disorder or disease is associated with cells expressing CD71, comprising administering to a subject in need thereof a therapeutically effective amount of a conjugated activatable antibody, the conjugated activatable antibody comprising:
 an antibody or an antigen binding fragment thereof (AB) that specifically binds to human CD71 and cynomolgus monkey CD71, wherein the AB comprises the VH CDR1 sequence GYTFTSYWMH (SEQ ID NO: 9); the VH CDR2 sequence AIYPGNSETG (SEQ ID NO: 10); the VH CDR3 sequence ENWDPGFAF (SEQ ID NO: 11); the VL CDR1 sequence SASSSVYYMY (SEQ ID NO: 12) or CRASSSVYYMY (SEQ ID NO: 13); the VL CDR2 sequence STSNLAS (SEQ ID NO: 14); and the VL CDR3 sequence QQRRNYPYT (SEQ ID NO: 15);   a masking moiety (MM) comprising the amino acid sequence of SEQ ID NO: 309 coupled to the AB such that the MM inhibits the binding of the AB to CD71 when the activatable antibody is in an uncleaved state;   a cleavable moiety (CM) comprising the amino acid sequence of SEQ ID NO: 688 coupled to the AB; and   a vc-MMAE moiety conjugated to the AB;   wherein the MM is linked to the CM such that the activatable antibody in an uncleaved state comprises a structural arrangement from N-terminus to C-terminus of MM-CM-AB or AB-CM-MM.   
     
     
         118 . The method of  claim 117 , wherein the activatable antibody comprises a first linking peptide (LP1) and a second linking peptide (LP2), and wherein the activatable antibody in the uncleaved state has the structural arrangement from N-terminus to C-terminus as follows: MM-LP1-CM-LP2-AB or AB-LP2-CM-LP1-MM. 
     
     
         119 . The method of  claim 118 , wherein the two linking peptides are not identical to each other. 
     
     
         120 . The method of  claim 118 , wherein each of LP1 and LP2 is a peptide of about 1 to 20 amino acids in length.