Compositions and methods for treating celiac sprue disease

Abstract

Polypeptides, and methods for their use, are disclosed that have an amino acid sequence at least 75% identical to the amino acid sequence of SEQ ID NO:1, are provided, wherein (a) the polypeptide degrades a PFQPQLPY (SEQ ID NO: 140) peptide and/or a PFPQPQQPF (SEQ ID NO: 68) at pH 4; (b) residue 467 is Ser, residue 267 is Glu, and residue 271 is Asp; and (c) the polypeptide comprises an amino acid change from SEQ ID NO: 1 at one or more residues selected from the group consisting of 221, 262E, 268, 269, 270, 319A, 320, 354E/Q/R/Y, 358S/Q/T, 368F/Q, 399, 402, 406, 424, 449, 461, 463, 105, 171, 172, 173, 174, and 456.

1 . A polypeptide comprising an amino acid sequence at least 90% identical to the amino acid sequence of SEQ ID NO: 1, wherein
 (a) residue 467 is Ser, residue 267 is Glu, and residue 271 is Asp; and   (b) the polypeptide comprises an amino acid change from SEQ ID NO: 1 at one or more residues selected from the group consisting of 221D/N/Q/H, 261S, 262A/D/E/G/L/M/N/Q/R/T, 264A, 268S/T/A, 269L/T, 270A/T/V, 317A/T, 319A, 320M, 354A/D/E/K/N/Q/R/T/Y, 358A/N/S/Q/T, 368A/D/E/F/N/Q/S/T, 399Q, 402S/Q, 406S, 424K, 446S, 449A/E/N/Q, 461R, and 463A/L/M/Q/R/T/V.   
     
     
         2 .- 8 . (canceled) 
     
     
         9 . The polypeptide of  claim 1 , wherein the polypeptide comprises amino acid changes 358S and 463T. 
     
     
         10 . The polypeptide of  claim 9 , further comprising amino acid changes 399Q, and 449Q. 
     
     
         11 . The polypeptide of  claim 10 , further comprising amino acid changes 262E, 269T, and 354Q. 
     
     
         12 . The polypeptide of  claim 11 , further comprising amino acid change 320M. 
     
     
         13 . The polypeptide of  claim 1 , wherein the polypeptide comprises amino acid changes 262E, 269T, 320M, 354Q, 358S, 399Q, 449Q, and 463T. 
     
     
         14 . (canceled) 
     
     
         15 . The polypeptide of  claim 1 , further comprising an amino acid change at one or more amino acid positions selected from the group consisting of 105H, 171R/A/S, 172R/A/S, 173R/S, 174S, and/or 456V. 
     
     
         16 . The polypeptide of  claim 15 , comprising the amino acid changes 171R and 172R. 
     
     
         17 . A polypeptide comprising an amino acid sequence at least 90% identical to the amino acid sequence of SEQ ID NO: 71, wherein
 (a) residue 278 is Ser, residue 78 is Glu, and residue 82 is Asp; and   (b) the polypeptide comprises an amino acid change from SEQ ID NO: 71 at one or more residues selected from the group consisting of 32D/N/Q/H, 72S, 73A/D/E/G/L/M/N/Q/R/T, 75A, 79S/T/A, 80L/T, 81A/T/V, 128A/T, 130A, 131M, 165A/D/E/K/N/Q/R/T/Y, 169A/N/S/Q/T, 179A/D/E/F/N/Q/S/T, 210Q, 213S/Q, 217S, 235K, 257S, 260A/E/N/Q, 267V, 272R, and 274A/L/M/Q/R/T/V.   
     
     
         18 .- 24 . (canceled) 
     
     
         25 . The polypeptide of  claim 17 , wherein the polypeptide comprises amino acid changes 169S and 274T. 
     
     
         26 . The polypeptide of  claim 25 , further comprising amino acid changes 210Q and 260Q. 
     
     
         27 . The polypeptide of  claim 26 , further comprising amino acid changes 73E, 80T and 165Q. 
     
     
         28 .- 30 . (canceled) 
     
     
         31 . The polypeptide of  claim 27 , further comprising amino acid change 131M. 
     
     
         32 . (canceled) 
     
     
         33 . The polypeptide of  claim 17 , wherein the polypeptide comprises amino acid changes 73E, 80T, 131M, 165Q, 169S, 210Q, and 274T. 
     
     
         34 .- 43 . (canceled) 
     
     
         44 . A polypeptide comprising an amino acid sequence at least 99% identical to the amino acid sequence of SEQ ID NO: 59, wherein
 (a) residue 467 is Ser, residue 267 is Glu, and residue 271 is Asp; and   (b) the polypeptide comprises amino acid changes 262E, 269T, 320M, 354Q, 358S, 399Q, 449Q, 463T, 171R and 172R.   
     
     
         45 . The polypeptide of  claim 44 , wherein the polypeptide comprises at least one amino acid deletion from SEQ NO: 59, wherein the polypeptide comprises the amino acid sequence of SEQ NO: 129.