Beta-lactamases with improved properties for therapy
This invention relates to, in part, compositions of beta-lactamases and methods of using these enzymes in, for example, gastrointestinal tract (GI tract) disorders such as C. difficile infection (CDI).
1. A beta-lactamase comprising an amino acid sequence having at least 95% sequence identity with SEQ ID NO: 1 and having a polar and neutral hydrophilic residue other than alanine (A) at position 238 according to Ambler classification.
2. The beta-lactamase of claim 1 , further comprising a polar and positively charged hydrophilic residue other than glycine (G) at position 156 according to Ambler classification.
3. The beta-lactamase of claim 1 , further comprising a polar and neutral hydrophilic residue other than aspartate (D) at position 276 according to Ambler classification.
4. The beta-lactamase of claim 3 , further comprising an aromatic hydrophobic residue other than phenylalanine (F) at position 33 according to Ambler classification.
5. The beta-lactamase of claim 1 , wherein the polar and neutral hydrophilic residue is selected from asparagine (N), glutamine (Q), serine (S), threonine (T), proline (P), and cysteine (C).
6. The beta-lactamase of claim 2 , wherein the polar and positively charged hydrophilic residue is selected from arginine (R), and lysine (K).
7. The beta-lactamase of claim 3 , wherein the polar and neutral hydrophilic residue is selected from asparagine (N), glutamine (Q), serine (S), threonine (T), proline (P), and cysteine (C).
8. The beta-lactamase of claim 4 , wherein the aromatic hydrophobic residue is selected from tryptophan (W), and tyrosine (Y).
9. The beta-lactamase of claim 1 , wherein the beta-lactamase hydrolyzes one or more of penicillins and cephalosporins.
10. The beta-lactamase of claim 9 , wherein the penicillin is ampicillin.
11. The beta-lactamase of claim 9 , wherein the cephalosporin is selected from ceftriaxone, cefotaxime, cefozolin, cefoperazone, cefepime, cefuroxime, and ceftazidime.
12. The beta-lactamase of claim 1 , wherein the beta-lactamase has improved catalytic efficiency against cephalosporins as compared to SEQ ID NO: 1.
13. The beta-lactamase of claim 12 , wherein the beta-lactamase has about a 10 fold to about a 1000 fold improved catalytic efficiency against a cephalosporin as compared to SEQ ID NO: 1.
14. The beta-lactamase of claim 13 , wherein the cephalosporin is selected from ceftriaxone, cefotaxime, cefozolin, cefoperazone, cefepime, cefuroxime, and ceftazidime.
15. The beta-lactamase of claim 1 , wherein the beta-lactamase is active in the GI tract.
16. The beta-lactamase of claim 15 , wherein the beta-lactamase is stable in the small intestine, optionally selected from one or more of the duodenum, jejunum, and ileum.
17. A polynucleotide comprising a polynucleotide sequence encoding the beta-lactamase of claim 1 .
18. A host cell comprising the polynucleotide of claim 17 .
19. A pharmaceutical composition, comprising the beta-lactamase of claim 1 and a pharmaceutically acceptable carrier or excipient.
20. The pharmaceutical composition of claim 19 , wherein the composition is formulated for oral administration, optionally selected from a tablet, multi-particulate sprinkle, and a multi-particulate capsule.
21. A method for preventing an antibiotic-induced adverse effect in the gastrointestinal (GI) tract, comprising administering an effective amount of a beta-lactamase to a patient in need thereof, wherein the beta-lactamase comprises an amino acid sequence having at least 95% sequence identity with SEQ ID NO: 1 and having a polar and neutral hydrophilic residue other than alanine (A) at position 238 according to Ambler classification.
22. The method of claim 21 , further comprising a polar and positively charged hydrophilic residue other than glycine (G) at position 156 according to Ambler classification.
23. The method of claim 21 , further comprising a polar and neutral hydrophilic residue other than aspartate (D) at position 276 according to Ambler classification.
24. The method of claim 23 , further comprising an aromatic hydrophobic residue other than phenylalanine (F) at position 33 according to Ambler classification.
25. The method of claim 21 , wherein the polar and neutral hydrophilic residue is selected from asparagine (N), glutamine (Q), serine (S), threonine (T), proline (P), and cysteine (C).
26. The method of claim 22 , wherein the polar and positively charged hydrophilic residue is selected from arginine (R), and lysine (K).
27. The method of claim 23 , wherein the polar and neutral hydrophilic residue is selected from asparagine (N), glutamine (Q), serine (S), threonine (T), proline (P), and cysteine (C).
28. The method of claim 24 , wherein the aromatic hydrophobic residue is selected from tryptophan (W), and tyrosine (Y).
29. The method of claim 21 , wherein the subject is being administered or will be administered an antibiotic.
30. The method of claim 21 , wherein the antibiotic-induced adverse effect is C. difficile infection (CDI) and/or a C. difficile -associated disease.
31. The method of claim 30 , wherein the C. difficile -associated disease is antibiotic-associated diarrhea (AAD).