Hk1-binding proteins

Abstract

The invention features hK1 binding polypeptides as well as compositions comprising such polypeptides and methods of making and using such polypeptides.

1 .- 33 . (canceled) 
     
     
         34 . A method of treating or delaying the onset or recurrence of a condition involving airway inflammation, wherein the condition is selected from the group consisting of chronic obstructive pulmonary disease (COPD), rhinitis and sinusitis, the method comprising:
 administering an antibody that comprises an immunoglobulin heavy chain (HC) variable domain sequence and an immunoglobulin light chain (LC) variable domain sequence, wherein the HC variable domain sequence and the LC variable domain sequence form an antigen binding site that binds to hK1 and inhibits enzymatic activity of hK1 (SEQ ID NO: 1021) with a Ki of less than 10 nM, said HC variable domain sequence having:
 a CDR1 that comprises an amino acid sequence: Xaa1-Tyr-Xaa2-Met-Xaa3 (SEQ ID NO:31), wherein Xaa1 is selected from Lys and His; Xaa2 is selected from Lys, Val and Ser; Xaa3 is selected from Val, Ile and Thr; 
 a CDR2 that comprises an amino acid sequence: Xaa1-Ile-Tyr-Pro-Ser-Gly-Gly-Xaa2-Thr-Xaa3-Tyr-Ala-Asp-Ser-Val-Lys-Gly (SEQ ID NO: 32), wherein Xaa1 is selected from Ser, Trp, and Arg; Xaa2 is selected from Ile, Asn, and Arg; Xaa3 is selected from Ala, Ile, and Gly; and 
 a CDR3 that comprises the sequence DITPGGGSGFRLPKNYYYYGMDV (SEQ ID NO: 12), VGVWYGMDV (SEQ ID NO: 114), OR DSGGYYYGMDV (SEQ ID NO: 156); 
   and said LC variable domain sequence having:
 a CDR1 that comprises an amino acid sequence: Arg-Ala-Ser-Gln-Ser-Xaa1-Ser-Ser-Xaa2-Xaa3-Xaa4-Xaa5 (SEQ ID NO: 284), wherein Xaa1 is selected from Ile and Val; Xaa2 is selected from Tyr and Ser; Xaa3 is selected from Leu and Tyr; Xaa4 is selected from Asn, Ala, and Leu; and Xaa5 is Ala or is absent; 
 a CDR2 that comprises an amino acid sequence: Xaa1-Ala-Ser-Xaa2-Xaa3-Xaa4 (SEQ ID NO:314), wherein Xaa1 is selected from Ala, Asp, and Gly; Xaa2 is selected from Ser and Asn; Xaa3 is selected from Leu and Arg; Xaa4 is selected from Gln, Ala, Ser and Thr; and 
 a CDR3 that comprises the sequence QQSYSTPLT (SEQ ID NO:9), QQRSNWPSPIA (SEQ ID NO:111), OR QQYGSSLT (SEQ ID NO: 153) 
   to a subject in an amount effective to treat or delay the onset or recurrence of the condition involving airway inflammation.   
     
     
         35 . The method of  claim 34 , wherein the antibody is administered by subcutaneous injection. 
     
     
         36 . The method of  claim 34 , wherein the antibody is administered by inhalation. 
     
     
         37 . The method of  claim 36 , wherein the antibody is administered using an inhaler. 
     
     
         38 . The method of  claim 34 , wherein the antibody comprises the CDR regions of SEQ ID NOS:7-12. 
     
     
         39 . The method of  claim 34 , wherein the antibody comprises the heavy and light chain variable domain sequences that are identical to corresponding variable domain sequences of SEQ ID NOs:1240 and 1159. 
     
     
         40 . The method of  claim 34 , wherein the antibody is a humanized antibody. 
     
     
         41 . The method of  claim 34 , wherein the antibody is a full-length IgG antibody. 
     
     
         42 . The method of  claim 34 , wherein the antibody is an antigen binding fragment of an antibody, and does not include an Fc domain. 
     
     
         43 . The method of  claim 34 , wherein the antibody comprises a human FR1, FR2, FR3, and FR4 in the heavy chain variable domain sequence and a human FR1, FR2, FR3, and FR4 in the light chain variable domain sequence. 
     
     
         44 . A kit comprising:
 (a) an antibody that comprises an immunoglobulin heavy chain (HC) variable domain sequence and an immunoglobulin light chain (LC) variable domain sequence, wherein the HC variable domain sequence and the LC variable domain sequence form an antigen binding site that binds to hK1 and inhibits enzymatic activity of hK1 (SEQ ID NO: 1021) with a Ki of less than 10 nM, said HC variable domain sequence having:
 a CDR1 that comprises an amino acid sequence: Xaa1-Tyr-Xaa2-Met-Xaa3 (SEQ ID NO:31), wherein Xaa1 is selected from Lys and His; Xaa2 is selected from Lys, Val and Ser; Xaa3 is selected from Val, Ile and Thr; 
 a CDR2 that comprises an amino acid sequence: Xaa1-Ile-Tyr-Pro-Ser-Gly-Gly-Xaa2-Thr-Xaa3-Tyr-Ala-Asp-Ser-Val-Lys-Gly (SEQ ID NO: 32), wherein Xaa1 is selected from Ser, Trp, and Arg; Xaa2 is selected from Ile, Asn, and Arg; Xaa3 is selected from Ala, Ile, and Gly; and 
 a CDR3 that comprises the 
  sequence DITPGGGSGFRLPKNYYYYGMDV (SEQ ID NO: 12), VGVWYGMDV (SEQ ID NO: 114), OR DSGGYYYGMDV (SEQ ID NO: 156); 
   and said LC variable domain sequence having:
 a CDR1 that comprises an amino acid sequence: Arg-Ala-Ser-Gln-Ser-Xaa1-Ser-Ser-Xaa2-Xaa3-Xaa4-Xaa5 (SEQ ID NO: 284), wherein Xaa1 is selected from Ile and Val; Xaa2 is selected from Tyr and Ser; Xaa3 is selected from Leu and Tyr; Xaa4 is selected from Asn, Ala, and Leu; and Xaa5 is Ala or is absent; 
 a CDR2 that comprises an amino acid sequence: Xaa1-Ala-Ser-Xaa2-Xaa3-Xaa4 (SEQ ID NO:314), wherein Xaa1 is selected from Ala, Asp, and Gly; Xaa2 is selected from Ser and Asn; Xaa3 is selected from Leu and Arg; Xaa4 is selected from Gln, Ala, Ser and Thr; and 
 a CDR3 that comprises the sequence QQSYSTPLT (SEQ ID NO:9), QQRSNWPSPIA (SEQ ID NO:111), OR QQYGSSLT (SEQ ID NO: 153); and 
   (b) instructions for use.   
     
     
         45 . The kit of  claim 44 , further comprising a diagnostic reagent for detecting hK1 in vivo. 
     
     
         46 . The kit of  claim 44 , further comprising a diagnostic reagent for detecting hK1 in vitro. 
     
     
         47 . The kit of  claim 45 , wherein the diagnostic reagent is an MRI detectable label. 
     
     
         48 . The kit of  claim 46 , wherein the antibody is immobilized on a solid support. 
     
     
         49 . The kit of  claim 48 , wherein the solid support is a bead or an array. 
     
     
         50 . The kit of  claim 44 , further comprising a therapeutic reagent for treatment of a subject having a condition involving airway inflammation. 
     
     
         51 . The kit of  claim 44 , further comprising at least one additional buffer or reagent. 
     
     
         52 . A nucleic acid sequence(s) encoding:
 an antibody that comprises an immunoglobulin heavy chain (HC) variable domain sequence and an immunoglobulin light chain (LC) variable domain sequence, wherein the HC variable domain sequence and the LC variable domain sequence form an antigen binding site that binds to hK1 and inhibits enzymatic activity of hK1 (SEQ ID NO: 1021) with a Ki of less than 10 nM, said HC variable domain sequence having:
 a CDR1 that comprises an amino acid sequence: Xaa1-Tyr-Xaa2-Met-Xaa3 (SEQ ID NO:31), wherein Xaa1 is selected from Lys and His; Xaa2 is selected from Lys, Val and Ser; Xaa3 is selected from Val, Ile and Thr; 
 a CDR2 that comprises an amino acid sequence: Xaa1-Ile-Tyr-Pro-Ser-Gly-Gly-Xaa2-Thr-Xaa3-Tyr-Ala-Asp-Ser-Val-Lys-Gly (SEQ ID NO: 32), wherein Xaa1 is selected from Ser, Trp, and Arg; Xaa2 is selected from Ile, Asn, and Arg; Xaa3 is selected from Ala, Ile, and Gly; and 
 a CDR3 that comprises the 
  sequence DITPGGGSGFRLPKNYYYYGMDV (SEQ ID NO: 12), VGVWYGMDV (SEQ ID NO: 114), OR DSGGYYYGMDV (SEQ ID NO: 156); 
   and said LC variable domain sequence having:
 a CDR1 that comprises an amino acid sequence: Arg-Ala-Ser-Gln-Ser-Xaa1-Ser-Ser-Xaa2-Xaa3-Xaa4-Xaa5 (SEQ ID NO: 284), wherein Xaa1 is selected from Ile and Val; Xaa2 is selected from Tyr and Ser; Xaa3 is selected from Leu and Tyr; Xaa4 is selected from Asn, Ala, and Leu; and Xaa5 is Ala or is absent; 
 a CDR2 that comprises an amino acid sequence: Xaa1-Ala-Ser-Xaa2-Xaa3-Xaa4 (SEQ ID NO:314), wherein Xaa1 is selected from Ala, Asp, and Gly; Xaa2 is selected from Ser and Asn; Xaa3 is selected from Leu and Arg; Xaa4 is selected from Gln, Ala, Ser and Thr; and 
 a CDR3 that comprises the sequence QQSYSTPLT (SEQ ID NO:9), QQRSNWPSPIA (SEQ ID NO:111), OR QQYGSSLT (SEQ ID NO: 153). 
   
     
     
         53 . The nucleic acid sequence(s) of  claim 52 , wherein the nucleic acid sequences are expressed in yeast. 
     
     
         54 . The nucleic acid sequence(s) of  claim 53 , wherein the yeast is  Pichia, Hanseula , or  Saccharomyces.    
     
     
         55 . The nucleic acid sequence(s) of  claim 54 , wherein the yeast is  Pichia pastoris.    
     
     
         56 . The nucleic acid sequence(s) of  claim 52 , wherein the nucleic acid sequences further encode a vector. 
     
     
         57 . The nucleic acid sequence(s) of  claim 56 , wherein the vector comprises a nucleic acid sequence encoding a selectable marker. 
     
     
         58 . The nucleic acid sequence(s) of  claim 52 , wherein the nucleic acid sequence encodes a fusion polypeptide. 
     
     
         59 . The nucleic acid sequence(s) of  claim 52 , wherein the nucleic acid sequences are germline sequences. 
     
     
         60 . The nucleic acid sequence(s) of  claim 56 , wherein the vector further comprises a tissue-specific promoter. 
     
     
         61 . A yeast cell comprising the nucleic acid sequence(s) of  claim 52 .