Claims
- 1. A method for identifying a target for antibacterial agents, comprising determining the bacterial target of a product of a bacteriophage dp1ORF17, dp1ORF88, or functional fragments thereof.
- 2. The method of claim 1, wherein said determining comprises identifying at least one bacterial protein which binds to said product or said fragment thereof.
- 3. The method of claim 2, wherein said binding is determined using affinity chromatography on a solid matrix.
- 4. The method of claim 1, wherein said determining comprises identifying at least one protein:protein interaction using a genetic screen.
- 5. The method of claim 4, wherein said genetic screen is a yeast two-hybrid screen.
- 6. The method of claim 1, wherein said determining comprises at least one of a co-immunoprecipitation assay and a protein-protein crosslinking assay.
- 7. The method of claim 1, wherein said determining comprises identifying a mutated bacterial coding sequence which protects a bacterium from said product or fragment thereof.
- 8. The method of claim 1, wherein said determining comprises identifying a bacterial coding sequence which protects a bacterium against said product or fragment thereof of a bacteriophage dp1 open reading frame when expressed at high levels in said bacterium.
- 9. The method of claim 1, wherein said determining further comprises identifying a bacterial nucleic acid sequence encoding a polypeptide target of said product or fragment thereof of a bacteriophage dp1 open reading frame.
- 10. The method of claim 9, wherein said nucleic acid sequence is identified by determining at least a fragment of the amino acid sequence of a bacterial protein target, and identifying a bacterial nucleic acid sequence which encodes said protein target.
- 11. The method of claim 1, wherein said bacterial target is from an animal pathogen.
- 12. The method of claim 11, wherein said bacterial target is a gene homologous to a gene from an animal pathogen.
- 13. The method of claim 11, wherein said pathogen is a human pathogen.
- 14. The method of claim 1, wherein said bacterial target is from a plant pathogen.
- 15. The method of claim 1, wherein said bacterial target is a gene homologous to a gene from a plant pathogen.
- 16. The method of claim 1, further comprising determining at least one of a cellular function and biochemical function of said bacteriophage dp1ORF17 or dp1ORF88, or fragment thereof.
- 17. The method of claim 1, wherein said determining the bacterial target comprises identifying a phage open reading frame-specific site of action.
- 18. An isolated, purified, or enriched nucleic acid sequence at least 15 nucleotides in length, wherein said sequence corresponds to at least a fragment of bacteriophage dp1ORF17 or dp1ORF88; wherein said nucleic acid sequence inhibits the growth of a bacterium when expressed therein.
- 19. The nucleic acid sequence of claim 18, wherein said sequence comprises at least 50 nucleotides.
- 20. The nucleic acid sequence of claim 18, wherein said nucleic acid sequence consists essentially of a sequence of dp1ORF17 or dp1ORF88.
- 21. The nucleic acid sequence of claim 20, wherein said nucleic acid sequence encodes a polypeptide which provides a bacterial inhibitory function.
- 22. The nucleic acid sequence of claim 21, wherein said nucleic acid sequence is transcriptionally linked with regulatory sequences enabling induction of expression of said sequence.
- 23. An isolated, purified, or enriched polypeptide comprising at least a fragment S. pneumoniae bacteriophage dp1ORF17 or dp1ORF88, wherein said fragment is at least 5 amino acid residues in length and provides a bacterial inhibitory function.
- 24. The polypeptide of claim 24, wherein said polypeptide comprises a fragment at least 10 amino acid residues in length of a said polypeptide.
- 25. A recombinant vector comprising a nucleic acid sequence at least 24 nucleotides in length encoding a fragment of a bacteriophage dp1ORF17 or dp1ORF88.
- 26. The vector of claim 25, wherein said vector is an expression vector.
- 27. The vector of claim 26, wherein expression of said ORF is inducible.
- 28. A recombinant cell comprising the vector of claim 25.
- 29. The cell of claim 28, wherein said vector is an expression vector and expression of said ORF is inducible.
- 30. A method for identifying a compound active on a bacterial target protein of a bacteriophage dp1ORF17 or dp1ORF88 or a fragment thereof which retains its activity on said bacterial target protein, comprising:
a) contacting said bacterial target protein with a test compound; and b) determining whether said compound binds to or reduces the level of activity of said target protein, wherein binding of said compound with said target protein or a reduction of the level of activity of said protein is indicative that said compound is active on said target.
- 31. The method of claim 30, wherein said contacting is carried out in vitro.
- 32. The method of claim 30, wherein said contacting is carried out in vivo in a cell.
- 33. The method of claim 30, wherein said compound is a small molecule.
- 34. The method of claim 30, wherein said compound is a peptidomimetic compound.
- 35. The method of claim 30, wherein said compound is a fragment of a bacteriophage inhibitor protein.
- 36. The method of claim 30, further comprising determining the site of action of said compound on said target protein.
- 37. A method of screening for potential antibacterial agents, comprising the step of determining whether any of a plurality of compounds is active on a target of a bacteriophage dp1ORF17 or dp1ORF88, or an active fragment thereof
- 38. The method of claim 37, wherein said plurality of compounds are small molecules.
- 39. A method for inhibiting a bacterium, comprising the step of:
contacting said bacterium with a compound active on a target of a bacteriophage dp1ORF17 or dp1ORF88 or an active fragment thereof, wherein said target or the target site is uncharacterized.
- 40. The method of claim 39, wherein said compound is said protein or an active fragment thereof.
- 41. The method of claim 39, wherein said compound is a structural mimetic of said product or active fragment thereof.
- 42. The method of claim 39, wherein said compound is a small molecule.
- 43. The method of claim 39, wherein said contacting is performed in vitro.
- 44. The method of claim 39, wherein said contacting is performed in vivo in an animal.
- 45. The method of claim 44, wherein said animal is a human.
- 46. The method of claim 39, wherein said contacting is carried out in vivo in a plant.
- 47. The method of claim 39, wherein said bacterium is pathogenic.
- 48. A method for treating a bacterial infection in an animal suffering from an infection, comprising administering to said animal a therapeutically effective amount of a compound active on a target of a bacteriophage dp1ORF17 or dp1ORF88, or an active fragment thereof, in a bacterium involved in said infection,
- 49. The method of claim 48, wherein said compound is a small molecule.
- 50. The method of claim 48, wherein said compound is a peptidomimetic compound.
- 51. The method of claim 48, wherein said compound is a fragment of a bacteriophage inhibitor protein.
- 52. The method of claim 48, wherein said animal is a mammal.
- 53. The method of claim 52, wherein said mammal is a human.
- 54. A method for propylactically treating an animal at risk of an infection, comprising administering to said animal a prophylactically effective amount of a compound active on a target of a bacteriophage dp1ORF17 or dp1ORF88, or an active fragment thereof,
- 55. The method of claim 54, wherein said compound is a small molecule.
- 56. The method of claim 54, wherein said compound is a peptidomimetic compound.
- 57. The method of claim 54, wherein said compound is a fragment of a bacteriophage inhibitor protein.
- 58. The method of claim 54, wherein said animal is a mammal.
- 59. The method of claim 58, wherein said mammal is a human.
- 60. An antibacterial agent active on a target of a bacteriophage dp1ORF17 or dp1ORF88, or an active fragment thereof.
- 61. The agent of claim 60, wherein said agent is a pepetidomimetic of said bacteriophage product.
- 62. The agent of claim 60, wherein said agent is a small molecule.
- 63. The agent of claim 60, wherein said agent is a fragment of said bacteriophage product.
- 64. The agent of claim 60, wherein said agent is active at a phage-specific site on said target.
- 65. A method of making an antibacterial agent, comprising:
a) identifying a target of a bacteriophage dp1ORF17 or dp1ORF88 or an active fragment thereof; b) screening a plurality of test compounds to identify a compound active on said target; and c) synthesizing said compound in an amount sufficient to provide a therapeutic effect when administered to an organism infected by a bacterium naturally producing said target.
- 66. The method of claim 65, wherein said compound is a small molecule.
- 67. The method of claim 65, wherein said compound is a peptidomimetic compound.
- 68. The method of claim 65, wherein said compound is a fragment or derivative of said bacteriophage open reading frame product.
- 69. An antibody which binds to a bacteriophage dp1ORF17 or dp1ORF88 or a fragment thereof which retains its ability to ellicit an immunologic response in an animal.
- 70. The antibody of claim 69, wherein said antibody binds a protein which corresponds to said bacteriophage product or fragment thereof.
- 71. The method of claim 30, wherein said target is uncharacterized.
- 72. The antibacterial agent of claim 60, wherein said target is an uncharacterized target or said agent is active at a phage open reading frame-specific site on said target.
- 73. An isolated, purified or enriched nucleic acid sequence encoding a polypeptide selected from the group consisting of:
a) a nucleotide sequence encoding dp1ORF17 or dp1ORF88; b) a sequence at least 70% identical to a); c) a complement of a) or b); and d) a sequence which hybridizes to a), b) or c) under high stringency conditions.
- 74. The nucleic acid sequence of claim 73, wherein b) is at least 75% identical to a).
- 75. The nucleic acid sequence of claim 73, wherein b) is at least 80% identical to a).
- 76. The nucleic acid sequence of claim 73, wherein said nucleic acid comprises a nucleotide sequence encoding dp1ORF17 or dp1ORF88.
- 77. The nucleic acid sequence of claim 76, wherein said nucleotide sequence is SEQ ID NO:1 or 2.
- 78. A recombinant vector comprising the nucleic acid sequence of claim 73.
- 79. A cell comprising the vector of claim 28.
- 80. An isolated, purified or enriched polypeptide comprising a sequence selected from the group consisting of:
a) an amino acid sequence of dp1ORF17 or dp1ORF88; b) an amino acid sequence having at least 40% identity to the sequence of a); and c) an active fragment of a) or b), wherein said active fragment retains its bacterial inhibitory function.
- 81. The polypeptide of claim 80, wherein said amino acid sequence is at least 50% identical to a).
- 82. The polypeptide of claim 81, wherein said amino acid sequence is at least 65% identical to a).
- 83. A method for identifying an antibacterial agent, comprising identifying an active fragment of the product of a bacteria-inhibiting ORF of a bacteriophage of claim 80.
- 84. The method of claim 83, further comprising constructing a synthetic peptidomimetic molecule, wherein the structure of said molecule corresponds to the structure of said active fragment.
CROSS-REFERENCE TO RELATED PATENT APPLICATIONS
[0001] This application is a continuation-in-part of U.S. application Ser. No. 09/676,412, filed Sep. 29, 2000, which claims the benefit of U.S. Provisional application No. 60/157,218, filed Sep. 30, 1999, all of which are hereby incorporated by reference in its entireties, including drawings.
Provisional Applications (1)
|
Number |
Date |
Country |
|
60157218 |
Sep 1999 |
US |
Continuation in Parts (1)
|
Number |
Date |
Country |
Parent |
09676412 |
Sep 2000 |
US |
Child |
10097111 |
Jul 2002 |
US |