Compositions and Methods for Treating Celiac Sprue Disease

Abstract

The invention provides compositions and methods for treating celiac sprue.

We claim: 
     
         1 . A method for treating celiac sprue, comprising administering to a subject with celiac sprue an amount effective to treat the celiac sprue of one or more polypeptides comprising or consisting of the amino acid sequence of a polypeptide selected from the group consisting of SEQ ID NOS: 75, 74, 76-89, 95, 97-98, 102-111, or processed versions thereof. 
     
     
         2 . The method of  claim 1 , wherein the one or more polypeptides comprise one or more polypeptides comprising or consisting of the amino acid sequence of a polypeptide selected from the group consisting of SEQ ID NOs: 75, 74, 77, 78, 82, 88, 98, 105, 111, or processed versions thereof. 
     
     
         3 . The method of  claim 1  or  2 , wherein the one or more polypeptides comprise a polypeptide with the amino acid sequence of SEQ ID NO: 89. 
     
     
         4 . The method of any one of  claims 1 - 3 , further comprising administering to the subject an amount of one or more further polypeptides comprising an amino acid sequence selected from the group consisting of:
 (A) an amino acid sequence at least 75% identical to the amino acid sequence of SEQ ID NO:35, wherein
 (i) the polypeptide degrades a PQPQLP (SEQ ID NO:34) peptide at pH 4; and 
 (ii) residue 278 is Ser, residue 78 is Glu, and residue 82 is Asp 
   (B) an an amino acid sequence at least 75% identical to the amino acid sequence of SEQ ID NO:1, wherein
 (i) the polypeptide degrades a PQPQLP (SEQ ID NO:34) peptide at pH 4; and 
 (ii) residue 467 is Ser, residue 267 is Glu, and residue 271 is Asp. 
   
     
     
         5 . The method of  claim 4 , wherein the one or more further polypeptides comprise an amino acid sequence at least 85% identical to the amino acid sequence of SEQ ID NO:1 or SEQ ID NO: 35. 
     
     
         6 . The method of  claim 5 , wherein the one or more further polypeptides comprise an amino acid sequence at least 95% identical to the amino acid sequence of SEQ ID NO:1 or SEQ ID NO: 35. 
     
     
         7 . The method of  claim 6 , wherein the one or more further polypeptides comprise the amino acid sequence of SEQ ID NO:1 and/or SEQ ID NO: 35. 
     
     
         8 . The method of any one of  claims 4 - 7 , wherein the one or more further polypeptides comprise the amino acid sequence of any one of SEQ ID NO:2-33 or 36-67. 
     
     
         9 . The method of any one of  claims 4 - 8  wherein the one or more further polypeptides comprises the amino acid sequence of SEQ ID NO:90. 
     
     
         10 . The method of any one of  claims 4 - 9 , therein the one or more polypeptides comprise SEQ ID NO: 75, SEQ ID NO: 89, and/or SEQ ID NO:98, or processed versions thereof 
     
     
         11 . The method of ny one of  claims 4 - 10 , wherein the one or more polypeptides comprise
 SEQ ID NO: 74, 77, and/or 78, or processed versions thereof.   
     
     
         12 . The method of any one of  claims 4 - 10 , wherein the one or more polypeptides comprise SEQ ID NO: 88 and/or SEQ ID NO:111, or processed versions thereof. 
     
     
         13 . The method of any one of  claims 1 - 12 , wherein the polypeptide and, when present, the further polypeptide, are administered orally. 
     
     
         14 . An isolated polypeptide selected from the group consisting of a polypeptide comprising the amino acid sequence selected from the following group, or processed versions thereof:
 (a) SEQ ID NO: 95, wherein one, two, three, four, five, six, seven, eight, nine, ten, or all eleven of the following are true: (i) AA residue 116 is V or D; (ii) AA residue 255 is S, K, or G; AA residue 284 is D; (iv) AA residue 285 is T; (v) AA residue 286 is A, T, or N; (vi) AA residue 312 is S; (vii) AA residue 347 is N; (viii) AA residue 350 is T or A; (ix) AA residue 351 is N or G; (x) AA residue 354 is D; and (xi) AA residue 361 is S or H;   (b) SEQ ID NO: 75, wherein one, two, three, four, five, six, seven, eight, nine, ten, or all eleven of the following are true: (i) AA residue 106 is D; (ii) AA residue 246 is S, K, or G; (iii) AA residue 275 is D; (iv) AA residue 276 is S; (v) AA residue 277 is A, T, or N; (vi) AA residue 303 is S; (vii) AA residue 338 is S; (viii) AA residue 341 is T or A; (ix) AA residue 342 is N or G; (x) AA residue 345 is Q or D; and (xi) AA residue 352 is S or H;   (c) SEQ ID NO: 76, wherein one, two, three, four, five, six, seven, eight, nine, ten, or all eleven of the following are true: (i) AA residue 120 is D; (ii) AA residue 259 is S, K, or G; (iii) AA residue 288 is D; (iv) AA residue 289 is T; (v) AA residue 290 is A, T, or N; (vi) AA residue 316 is S; (vii) Al residue 351 is S or N; (viii) AA residue 354 is A; (ix) AA residue 355 is N or G; (x) AA residue 358 is D; and (xi) AA residue 365 is S or H;   (d) SEQ ID NO: 78;   (e) SEQ ID NO: 79, wherein one, two, three, four, five, six, seven, eight, nine, ten, or all eleven of the following are true: (i) AA residue 107 is V or D; (ii) AA residue 245 is S, K, or G; (iii) AA residue 274 is D; (iv) AA residue 275 is T; (v) AA residue 276 is A, T, or N; (vi) AA residue 302 is S; (vii) AA residue 337 is S or N; (viii) AA residue 340 is T or A; (ix) AA residue 341 is N or G; (x) AA residue 344 is Q or D; and (xi) AA residue 351 is S or H;   (f) 80, wherein one, two, three, four, five, six, seven, eight, nine, ten, or all eleven of the following are true: (i) IA residue 76 is V or D; (ii) AA residue 206 is S, K, or G; (iii) All residue 235 is D; (iv) IA residue 236 is S; (v) AA residue 237 is A, T, or N; (vi) AA residue 262 is S; (vii) AA residue 297 is S or N; (viii) AA residue 300 is T or A; (ix) AA residue 301 is N or G; (x) AA residue 302 is Q or D; and (xi) AA residue 309 is S or H;   (g) SEQ ID NO: 81, wherein one, two, three, four, five, six, seven, eight, nine, ten, or all eleven of the following are true: (i) AA residue 105 is D; (ii) AA residue 244 is S or K; (iii) AA residue 272 is D; (iv) AA residue 273 is S; (v) AA residue 274 is A, T, or N; (vi) AA residue 299 is S; (vii) AA residue 334 is N; (viii) AA residue 337 is T or A; (ix) AA residue 338 is N or G; (x) AA residue 341 is Q or D; and (xi) AA residue 348 is S or H;   (h) SEQ ID NO: 82, wherein one, two, three, four, five, six, seven, eight, nine, ten, or all eleven of the following are true: (i) AA residue 106 is V or D; (ii) AA residue 244 is S, K, or G; (iii) AA residue 273 is D; (iv) AA residue 274 is T; (v) AA residue 275 is A, T, or N; (vi) AA residue 301 is S; (vii) AA residue 336 is N; (viii) AA residue 339 is T or A; (ix) AA residue 340 is N or G; (x) AA residue 343 is D; and (viii) AA residue 350 is S or H;   (i) SEQ ID NO: 83, wherein one, two, three, four, five, six, seven, eight, nine, ten, or all eleven of the following are true: (i) AA residue 107 is V or D; (ii) AA residue 245 is S, K, or G; (iii) AA residue 274 is D; (iv) AA residue 275 is T; (v) AA residue 276 is A, T, or N; (vi) AA residue 302 is S; (vii) AA residue 337 is N; (viii) AA residue 340 is T or A; (ix) AA residue 341 is N or G; (x) AA residue 344 is Q or D; and (xi) AA residue 351 is S or H;   (j) SEQ NO: 84, wherein one, two, three, four, five, six, seven, eight, nine, ten, or all eleven of the following are true: (i) AA residue 104 is V or D; (ii) AA residue 241 is S, K, or G; (iii) AA residue 270 is D; (iv) AA residue 271 is S; (v) AA residue 272 is D, A, T, or N; (vi) AA residue 398 is S; (vii) AA residue 33 is S; (viii) AA residue 336 is A; (ix) AA residue 337 is N or G; (x) AA residue 340 is D; and (xi) AA residue 347 is S or H;   (k) SEQ ID NO: 85, wherein one, two, three, four, five, six, seven, eight, nine, ten, or all eleven of the following are true: (i) AA residue 104 is D; (ii) AA residue 245 is S, K, or G; (iii) AA residue 274 is D; (iv) AA residue 275 is S; (v) AA residue 276 is A, T, or N; (vi) AA residue 302 is S; (vii) AA residue 337 is S or N; (viii) AA residue 340 is T or A; (ix) AA residue 341 is N or G; (x) AA residue 344 is Q or D; and (xi) AA residue 351 is S or H;   (l) SEQ ID NO: 86, wherein one, Iwo, three, four, five, six, seven, eight, nine, ten, or all eleven of the following are true: (i) AA residue 118 is V or D; (ii) AA residue 250 is K, or G; (iii) AA residue 279 is D; (iv) AA residue 280 is S; (v) AA residue 281 is A, T, or N; (vi) AA residue 307 is S; (vii) AA residue 342 is S or N; (viii) AA residue 345 is A; (ix) AA residue 346 is N or G; (x) AA residue 349 is Q or D; and (xi) AA residue 356 is S or H;   (m) SEQ ID NO: 87, wherein one, two, three, four, live, six, seven, eight, nine, ten, or all eleven of the following are true: (i) AA residue 121 is V or D; (ii) AA residue 253 is S, K, or C; (iii) AA residue 282 is D; (iv) AA residue 283 is S; (v) AA residue 284 is A, T, or N; (vi) AA residue 310 is S; (vii) AA residue 345 is S; (viii) AA residue 348 is T or A; (ix) AA residue 349 is N or G; (x) AA residue 352 is Q or D; and (xi) AA residue 357 is S or H;   (n) SEQ NO: 88, wherein one, two, three, four, five, six, seven, eight, nine, or all ten of the following are true: (i) AA residue 111 is S, K, or C; (ii) AA residue 139 is D; (iii) AA residue 140 is T or S; (iv) AA residue 141 is D, A, T, or N; (v) AA residue 164 is S; (vi) AA residue 199 is S or N; (vii) AA residue 202 is T or A; (viii) AA residue 203 is N or G; (ix) AA residue 204 is Q or D; and (x) AA residue 211 is S or H; and   (o) SEQ ID NO:89.   
     
     
         15 . The isolated polypeptide of  claim 14 , selected from the group consisting of the following, or processed versions thereof:
 (i) SEQ 117 NO: 75, wherein one, two, three, four, five, six, seven, eight, nine, ten, or all eleven of the following are true: (i) AA residue 106 is D; (ii) AA residue 246 is S, K, or G; (iii) AA residue 275 is D; (iv) AA residue 276 is S; (v) AA residue 277 is A, T, or N; (vi) AA residue 303 is S; (vii) AA residue 338 is S; (viii) AA residue 341 is T or A; (ix) AA residue 342 is N or G; (x) AA residue 345 is Q or D; and (xi) AA residue 352 is S or H;   (ii) SEQ ID NO: 78;   (iii) SEQ ID NO: 82, wherein one, two, three, four, five, six, seven, eight, nine, ten, or all eleven of the following are true: (1) AA residue 106 is V or D; (ii) AA residue 244 is S, K, or G; (iii) AA residue 273 is D; (iv) AA residue 274 is T; (v) AA residue 275 is A, T, or N; (vi) AA residue 301 is S; (vii) AA residue 336 is N; (viii) AA residue 339 is T or A; (ix) AA residue 340 is N or G; (x) AA residue 343 is D; and (viii) AA residue 350 is S or H;   (iv) SEQ ID NO: 88, wherein one, two, three, four, five, six, seven, eight, nine, or all ten of the following are true: (i) AA residue 111 is S, K, or G; (ii) AA residue 139 is D; (iii) AA residue 140 is T or S; (iv) AA residue 141 is D, A, T, or N; (v) AA residue 164 is S; (vi) AA residue 199 is S or N; (vii) AA residue 202 is T or A; (viii) AA residue 203 is N or G; (ix) AA residue 204 is Q or D; and (x) AA residue 211 is S or H; and   (v) SEQ ID NO:89.   
     
     
         16 . The isolated polypeptide of  claim 14  or  15 , mprising the amino acid sequence of SEQ ID NO: 89, or a processed version thereof. 
     
     
         17 . The isolated polypeptide of  claim 14 , comprising the amino acid sequence of SEQ ID NO:78, or a processed version thereof. 
     
     
         18 . A nucleic acid encoding the polypeptide of any one of  claims 14 - 17 . 
     
     
         19 . A nucleic acid expression vector comprising the isolated nucleic acid of  claim 18 . 
     
     
         20 . A recombinant host cell comprising e nucleic acid expression vector of  claim 19 . 
     
     
         21 . A composition, comprising
 (a) one or more polypeptides comprising the amino acid sequence of a polypeptide selected from the group consisting of SEQ ID NOs: 74-89, 95, 97-99, and 102-111, or processed versions thereof; and   (b) one or more further polypeptides comprising an amino acid sequence selected from the group consisting of:
 (A) an amino acid sequence at least 75% identical to the arnrno acid sequence of SEQ D NO:35, wherein 
 (i) the polypeptide degrades a PQPQLP (SEQ ID NO:34) peptide at pH 4; and 
 (ii) residue 278 is Ser, residue 78 is Glu, and residue 82 is Asp 
 (B) an an amino acid sequence at least 75% identical to the amino acid sequence of SEQ ID NO:1, wherein 
 (i) the polypeptide degrades a PQPQLP (SEQ ID NO:34) peptide at pH 4; and 
 (ii) residue 467 is Ser, residue 267 is Glu, and residue 271 is Asp. 
   
     
     
         22 . The composition of  claim 21 , wherein the one or more polypeptides comprise SEQ ID NO: 75, STQ ID NO: 89, and/or SEQ ID NO:98, or processed versions thereof. 
     
     
         23 . The composition of  claim 21 , wherein the one or more polypeptides comprise SEQ ID NO: 74, 77, and/or 78, or processed versions thereof. 
     
     
         24 . The composition of  claim 21 , wherein the one or more polypeptides comprise SEQ ID NO: 88 and/or SEQ ID NO:111, or processed versions thereof. 
     
     
         25 . The composition of any one of  claims 21 - 24 , wherein the one or more further polypeptides comprise the amino acid sequence of SEQ ID NO:1 and/or SEQ ID NO: 35. 
     
     
         26 . The composition of any one of  claims 21 - 25 , wherein the one or more further polypeptides comprise the amino acid sequence of any one of SEQ ID NO:2-33 or 36-67. 
     
     
         27 . The composition of any one of  claims 21 - 26  wherein the one or more further polypeptides comprises the amino acid sequence of SEQ ID NO:90, or a processed version thereof. 
     
     
         28 . A pharmaceutical composition, comprising the isolated polypeptide of any one of  claims 14 - 17  or the composition of any one of  claims 21 - 27 , and a pharmaceutically acceptable carrier. 
     
     
         29 . The pharmaceutical composition of  claim 28 , wherein the composition is formulated for oral delivery.