Metalloproteinase-binding proteins

Abstract

Disclosed are antibodies that interact with a matrix metalloproteases such as MMP-26. Exemplary antibodies inhibit MMP-26 activity. These antibodies can be used, e.g., to treat or prevent metastatic disorders, hyperproliferative disorders, disorders which are characterized by excessive extracellular matrix degradation, and inflammatory disorders.

1 . A protein comprising a heavy chain immunoglobulin variable domain sequence and a light chain immunoglobulin variable domain sequence, wherein the protein binds to MMP-26 with a K D  of less than 5×10 −7  M and comprises at least one human complementarity determining region or framework region. 
     
     
         2 . The protein of  claim 1  wherein the protein inhibits MMP-26 proteolytic activity. 
     
     
         3 . The protein of  claim 2  wherein the heavy chain variable domain sequence comprises
 (a) a CDR1 that comprises   
       
         
           
                 
                 
               
                     
                   X-Y-X-M-M 
                 
                     
                   or 
                 
                     
                     
                 
                     
                   (A/S/M/Y/W/F/E/Q)-Y-(A/W/F/N/Q)-M-(A/S/M/W/F; 
                 
             
                
                
                
                
               
            
           
         
         (b) a CDR2 that comprises
 R-I-X-(S/P)-S-G-G-X-T-X-Y-A-D-S-V-K-G or 
 (G/S/V/W/R)-I-(G/S/V/Y)-(S/P)-S-G-G-(S/I/F/K/D/H)-T-(L/M/K/D/P)-Y-A-D-S-V-K-G; and/or 
 
         (c) a CDR3 that comprises F-D-I. 
       
     
     
         4 . The protein of  claim 2  wherein the heavy chain variable domain sequence comprises a CDR1 that comprises a sequence of which at least 3 of 5 amino acids are identical to a reference sequence from column 1, a CDR2 that comprises a sequence of which at least 13 of 16 amino acids are identical to a reference sequence from column 2, and a CDR3 of which at least 70% of the amino acids are identical to a reference sequence from column 3 of Table 7. 
     
     
         5 . The protein of  claim 4  wherein the heavy chain variable domain sequence comprises a CDR1 that comprises a sequence of which at least 3 of 5 amino acids are identical to a reference sequence from column 1 in a particular row, a CDR2 that comprises a sequence of which at least 13 of 16 amino acids are identical to a reference sequence from column 2 in the particular row, and a CDR3 of which at least 70% of the amino acids are identical to a reference sequence from column 3 in the particular row, the columns being from Table 7. 
     
     
         6 . The protein of  claim 4  wherein at least 30, 50, 60, 70, 80, 90 or 100% of the CDR amino acid residues that are not identical to residues in the reference sequences from Table 7, Table 8, Table 9, or Table 10 are identical to residues at corresponding positions in a human germline sequence. 
     
     
         7 . The protein of  claim 2  wherein the heavy chain variable domain sequence comprises a CDR1 that comprises a sequence from column 1, a CDR2 that comprises a sequence from column 2, and a CDR3 from that comprises a sequence from column 3 of Table 7, Table 8, Table 9, or Table 10. 
     
     
         8 . The protein of  claim 2  wherein the light chain variable domain sequence is a κ light chain and comprises
 (a) a CDR1 that comprises   
       
         
           
                 
                 
               
                     
                   R-(A/T)-S-Q-(G/S/I)-(I/V)-(S/D/N)-(S/T/R)-Y-L- 
                 
                     
                   (A/N)-X, 
                 
                     
                     
                 
                     
                   R-(A/T)-S-Q-(G/S/I/N)-(I/V)-(G/S/R/D/N)- 
                 
                     
                   (S/T/R/K/D/N)-(S/T/Y/W)-(L/V/Y)-(A/L/N)-A, 
                 
                     
                     
                 
                     
                   R-A-S-Q-(G/S)-I-(S/D)-(S/T)-Y-L-(A/N)-X, 
                 
                     
                     
                 
                     
                   R-A-S-Q-X-I-X-X-Y-L-N-X, 
                 
                     
                   or 
                 
                     
                     
                 
                     
                   R-A-S-Q-(G/S/I)-(I/V)-(G/S/R/D)-(S/T/R/K/D/N)- 
                 
                     
                   (S/T/Y/W)-(L/V/Y)-(A/L/N)-A; 
                 
             
                
                
                
                
                
                
                
                
                
                
                
                
                
               
            
           
         
         (b) a CDR2 that comprises 
       
       
         
           
                 
               
                   (A/G)-A-S-(S/T/I/K)-L-(E/Q)-(G/S/D), 
                 
                     
                 
                   (A/G/T/Q)-(A/T)-(S/T/F)-(S/T/I/K)-(L/V/R)-(A/E/Q)- 
                 
                   (G/S/T/D/N), 
                 
                   or 
                 
                     
                 
                   A-A-S-X-L-(E/D/N/Q); 
                 
                   and/or 
                 
             
                
                
                
                
                
                
                
                
               
            
           
         
         (c) a CDR3 that comprises 
       
       
         
           
                 
               
                   Q-Q-(S/T/Y)-(Y/N)-S-(S/T)-P-(G/L/P)-(T/I)-T, 
                 
                   or 
                 
                     
                 
                   Q-(R/E/Q)-(A/S/T/Y)-(G/Y/N)-(S/T/I/D)-(S/T/I/Y/F/ 
                 
                   P)-(S/P)-(G/L/Y/F/R/P)-(T/I/F/E)-(T/V)-T. 
                 
             
                
                
                
                
                
               
            
           
         
       
     
     
         9 . The protein of  claim 2  wherein the light chain variable domain sequence is a λ light chain and comprises
 (a) a CDR1 that comprises   
       
         
           
                 
                 
               
                     
                   S-G-X-S-S-X-X-G-S, 
                 
                     
                   or 
                 
                     
                     
                 
                     
                   T-G-T-(S/N)-S-D-(I/V)-G-(A/G)-Y-N-Y-V-S; 
                 
             
                
                
                
                
               
            
           
         
         (b) a CDR2 that comprises 
       
       
         
           
                 
               
                   (R/D/N/E)-(V/D/N)-(G/S/T/D/N)-(K/D/N/E/Q)-R-P-S, 
                 
                   or 
                 
                     
                 
                   (R/E)-(V/D/N)-(T/D/N)-(K/Q)-R-P-S; and/or 
                 
             
                
                
                
                
               
            
           
         
         (c) a CDR3 that comprises 
       
       
         
           
                 
               
                   (A/Q)-(S/T/V)-(Y/W)-(A/D)-(G/S/D)-(S/N)-(L/V/N)- 
                 
                   (S/N)-(G/L)-P-V, 
                 
                   or 
                 
                     
                 
                   W-D-X-S-X-X-X-X-V. 
                 
             
                
                
                
                
                
               
            
           
         
       
     
     
         10 . The protein of  claim 2  wherein the light chain variable domain sequence comprises a CDR1 that comprises a sequence of which at least 9 of 11 amino acids are identical to a reference sequence from column 1, a CDR2 that comprises a sequence of which at least 7 of 9 amino acids are identical to a reference sequence from column 2, and a CDR3 of which at least 70% of the amino acids are identical to a reference sequence from column 3 of Table 8. 
     
     
         11 . The protein of  claim 10  wherein the light chain variable domain sequence comprises a CDR1 that comprises a sequence of which at least 9 of 11 amino acids are identical to a reference sequence from column 1 in a particular row, a CDR2 that comprises a sequence of which at least 7 of 9 amino acids are identical to a reference sequence from column 2 in the particular row, and a CDR3 of which at least 70% of the amino acids are identical to a reference sequence from column 3 in the particular row, the columns being from Table 8. 
     
     
         12 . The protein of  claim 1  wherein the framework regions of the heavy and/or light chain variable domain are at least 70, 80, 90, 92, 95, 97, 98, or 99% identical to a corresponding framework region of a human germline sequence. 
     
     
         13 . The protein of  claim 1  wherein the heavy and/or light chain variable domain are at least 70% identical to a human germline sequence. 
     
     
         14 . The protein of  claim 1  wherein the protein inhibits MMP-26 with a K i  that is at least 20 better than its K i  for another metalloproteinases. 
     
     
         15 . The protein of  claim 1  wherein the protein reduces cell metastasis in vivo. 
     
     
         16 . The protein of  claim 1  wherein the protein comprises two independent polypeptide chains, a first chain comprising the light chain variable domain sequence and the second chain comprising the heavy chain variable domain sequence, and each chain comprising a constant immunoglobulin domain. 
     
     
         17 . The protein of  claim 1  wherein the protein comprises CL, CH1, CH2, and CH3 domains. 
     
     
         18 . A protein comprising a heavy chain immunoglobulin variable domain sequence and a light chain immunoglobulin variable domain sequence, wherein the protein binds to the MMP-26; and
 (a) at least one of the variable domains is related to a reference antibody selected from the group consisting of a01, b04, b06, b10, c01, c08, d02, d04, d06, d08, D6-orig, a04, a11, c05, c04, c11, c12, d07, A1-orig, H6-orig, a02, a03, a05, a06, a07, a08, a09, a10, a12, b01, b02, b03, b05, b07, b08, b09, b11, b12, c02, c03, c06, c07, c09, c10, d01, d03, d05, and d09,   the relationship being such that at least 80% of the amino acid residues in the variable domain are either (i) identical to a corresponding residue in the reference antibody, (ii) identical to a corresponding residue in a human germline sequence, or both; or   (b) at least one of the variable domains is at least 85% identical to the corresponding variable domain of a reference antibody selected from the group consisting of a01, b04, b06, b10, c01, c08, d02, d04, d06, d08, D6-orig, a04, a11, c05, c04, c11, c12, d07, A1-orig, H6-orig, a02, a03, a05, a06, a07, a08, a09, a10, a12, b01, b02, b03, b05, b07, b08, b09, b11, b12, c02, c03, c06, c07, c09, c10, d01, d03, d05, and d09.   
     
     
         19 . The protein of  claim 18  wherein the human germline sequence is the human germline sequence with which the reference antibody is associated in an example described herein. 
     
     
         20 . The protein of  claim 18  wherein all of the amino acids residues in the variable domain are (i) identical to a corresponding residue in the reference antibody, or (ii) identical to a corresponding residue in the human germline sequence, e.g., with which the reference antibody is associated in an example described herein, or both. 
     
     
         21 . The protein of  claim 18  wherein at least 1, 2, 3, 4, or 5 of the amino acid residues in the variable domain differ from a corresponding residue in the reference antibody, but are identical to a corresponding residue in the human germline sequence. 
     
     
         22 . The protein of  claim 18  wherein, in the framework regions, at least 90% or all of the amino acid residues are identical to a corresponding residue in the human germline sequence. 
     
     
         23 . The protein of  claim 18  wherein at least 1, 2, or 3 of the amino acid residues in the CDR regions of the variable domain differ from a corresponding residue in the reference antibody, but are identical to a corresponding residue in the human germline sequence. 
     
     
         24 . The protein of  claim 18  wherein amino acid residues that are not identical are conserved substitutions relative to a corresponding residue in the reference antibody, or a human germline sequence. 
     
     
         25 . A protein that comprises an antigen binding fragment that binds to MMP-26, wherein the protein binds to a MMP-26 epitope that overlaps with an epitope bound by an antibody selected from the group consisting of a01, b04, b06, b10, c01, c08, d02, d04, d06, d08, D6-orig, a04, a11, c05, c04, c11, c12, d07, A1-orig, H6-orig, a02, a03, a05, a06, a07, a08, a09, a10, a12, b01, b02, b03, b05, b07, b08, b09, b11, b12, c02, c03, c06, c07, c09, c10, d01, d03, d05, and d09 or the protein competes with an antibody selected from the group consisting of a01, b04, b06, b10, c01, c08, d02, d04, d06, d08, D6-orig, a04, a11, c05, c04, c11, c12, d07, A1-orig, H6-orig, a02, a03, a05, a06, a07, a08, a09, a10, a12, b01, b02, b03, b05, b07, b08, b09, b11, b12, c02, c03, c06, c07, c09, c10, d01, d03, d05, and d09, for binding to MMP-26-26. 
     
     
         26 . An isolated nucleic acid comprising a coding sequence that encodes a polypeptide comprising a variable domain sequence of the protein of  claim 1 . 
     
     
         27 . The nucleic acid of  claim 26  that further comprises a second coding sequence that encodes a polypeptide comprising an immunoglobulin light chain variable domain. 
     
     
         28 . The nucleic acid of  claim 26  that further comprises a second coding sequence that encodes a polypeptide comprising an immunoglobulin heavy chain variable domain. 
     
     
         29 . A host cell that produces the protein of  claim 1 , the cell comprising a first nucleic acid encoding a polypeptide comprising a heavy chain variable domain sequence of the protein and a second nucleic acid encoding a polypeptide comprising a light chain domain sequence of the protein. 
     
     
         30 . A host cell that contains a first nucleic acid encoding a polypeptide comprising a heavy chain variable region and a second nucleic acid encoding a polypeptide comprising a light chain variable region, wherein the heavy chain variable region comprises an amino acid sequence at least 85% identical to an amino acid sequence of a heavy chain immunoglobulin variable domain sequence described herein, and the light chain variable region comprises an amino acid sequence at least 85% identical to a light chain immunoglobulin variable domain sequence described herein. 
     
     
         31 . A method of providing a MMP-26-binding antibody, the method comprising:
 providing the host cell of  claim 29 ; and
 expressing said first and second nucleic acids in the host cell under conditions that allow assembly of said light and heavy chain variable regions to form an antigen binding protein that interacts with MMP-26. 
   
     
     
         32 . A method of treating or preventing a neoplastic disorder, the method comprising:
 administering the protein of  claim 1  to a subject in an amount effective to treat or prevent a neoplastic disorder in the subject.   
     
     
         33 . The method of  claim 32  wherein the subject has, is predisposed to, or is diagnosed with a malignant cancer or metastatic disorder. 
     
     
         34 . The method of  claim 32  wherein the neoplastic disorder is associated with breast, prostate, or lung cancer. 
     
     
         35 . A method of treating or preventing an inflammatory disorder, the method comprising:
 administering the protein of  claim 1  to a subject in an amount effective to treat or prevent an inflammatory disorder in the subject.   
     
     
         36 . The method of  claim 35  wherein the inflammatory disorder is selected from the group consisting of: rheumatoid arthritis, lupus, restenosis, graft v. host response, or multiple sclerosis. 
     
     
         37 . A method of treating or preventing a disorder characterized by excessive or undesired MMP-26 activity, the method comprising:
 administering the protein of  claim 1  to a subject in an amount effective to treat or prevent a disorder characterized by excessive or undesired MMP-26 activity in the subject.   
     
     
         38 . The method of  claim 37  wherein the disorder is periodontitis, rheumatoid arthritis, or osteoarthritis. 
     
     
         39 . A method of modulating MMP-26 activity, the method comprising:
 providing an MMP-26-binding protein of  claim 1 ; and   contacting the protein to MMP-26, in vitro or in vivo, in an amount sufficient to modulate MMP-26 activity.   
     
     
         40 . The method of  claim 39  wherein the protein is contacted to MMP-26 in the vicinity of a neoplastic cell. 
     
     
         41 . A method for detecting the presence of a MMP-26 protein, in a sample, in vitro, the method comprising:
 (i) contacting the sample with an MMP-26-binding protein according to  claim 1 , under conditions that allow interaction of the MMP-26-binding protein and the MMP-26 protein to occur; and   (ii) detecting interaction between the MMP-26-binding protein, and the sample.   
     
     
         42 . The method of  claim 41  wherein at least one of the MMP-26 binding protein or the MMP-26 is immobilized. 
     
     
         43 . A method for detecting the presence of MMP-26 in vivo, the method comprising:
 (i) administering to a subject an MMP-26-binding protein, under conditions that allow interaction of the MMP-26-binding protein and the MMP-26 protein to occur; and   (ii) detecting location of the MMP-26-binding protein in the subject or formation of a complex between the MMP-26-binding protein and MMP-26 in the subject.   
     
     
         44 . The method of  claim 43  wherein the detecting comprises imaging the subject. 
     
     
         45 . The method of  claim 43  wherein the MMP-26-binding protein is labeled with an MRI detectable label.