Claims
- 1. A method for making a combinatorial library of cyclic compounds that have the generic structure:
- 2. The method of claim 1, wherein the side group of X1 or X3 independently can have a C1 to C3 alkyl connecting a cycloalkyl or aryl group.
- 3. The method of claim 2, wherein said cycloalkyl is a substitute.
- 4. The method of claim 2, wherein said aryl is a hetro aryl substituted aryl or X2 substituted.
- 5. The method of claim 1, wherein the side group of X2 incorporates a mono or bicyclic moiety that can be a heterocycle.
- 6. The method of claim 5, wherein said moiety is a substituted mono or bicylic moiety.
- 7. The method of claim 5, wherein X2 provides conformational constraint to the trimer.
- 8. The method of claim 1, wherein S is an molecular spacer of 5 to 25, 5 to 15, or 5 to 10 Å.
- 9. The method of claim 1, wherein S is from an organozinc spacer precursor.
- 10. The method of claim 8, wherein S is selected from glycine, tryptophan, arginine, histidine, phenylalanine, or any other naturally occurring or non-naturally occurring amino acid;
- 11. The method of claim 1, wherein at least one subunit is radiolabelled.
- 12. The method of claim 1, wherein synthesis occurs according to FIGS. [53] 46 and [54] 47.
- 13. A compound having a formula selected from the group consisting of:
- 14. A peptidomimetic of a compound of claim 13.
- 15. A method for inhibiting bacterial growth, comprising contacting a bacterium with a compound of claim 1.
- 16. A method for making a combinatorial library of compounds having the formula,
- 17. The method of claim 16, wherein 3 and 6 are capable of hydrogen bonding with each other.
- 18. The method of claim 17, wherein 1 is a hydroxy acid, wherein R is a linear or branched alkyl or aryl:
- 19. The method of claim 18, wherein 1 is an aromatic hydroxy acid.
- 20. The method of claim 18, wherein 1 is a hydroxy iodide, wherein R is a linear or branched alkyl or aryl:
- 21. The method of claim 18, wherein 2 is a hydroxy amine, wherein R is a linear or branched alkyl or aryl:
- 22. The method of claim 18, wherein 2 is a hydroxy acid, wherein R is a linear or branched alkyl or aryl:
- 23. The method of claim 18, wherein 2 is a hydroxy iodide, wherein R is a linear or branched alkyl or aryl:
- 24. The method of claim 18, wherein 2 is a hydroxy amino acid, wherein R is a linear or branched alkyl or aryl:
- 25. The method of claim 18, wherein 2 is an iodo amino acid, wherein R is a linear or branched alkyl or aryl:
- 26. The method of claim 18, wherein 2 is an iodo hydroxy amino acid, wherein R is a linear or branched alkyl or aryl:
- 27. The method of claim 16, wherein 3 is an amino acid having the following structure, wherein R is a linear or branched alkyl or aryl:
- 28. The method of claim 16, wherein 3 is an iodo acid, wherein R is a linear or branched alkyl or aryl:
- 29. The method of claim 2, wherein 3 is a hydroxyacid, wherein R is a linear or branched alkyl or aryl:
- 30. The method of claim 18, wherein 3 is a aromatic amino acid.
- 31. The method of claim 18, wherein 3 is an aromatic iodo acid.
- 32. The method of claim 18, wherein 3 is a aromatic hydroxy acid.
- 33. The method of claim 18, wherein 3 contains a hydrogen and 6 contains an electronegative atom.
- 34. The method of claim 18, wherein 6 contains a hydrogen and 3 contains an electronegative atom.
- 35. The method of claim 18, wherein 4 is an amino acid.
- 36. The method of claim 35, wherein 4 is an aromatic amino acid.
- 37. The method of claim 35, wherein 4 is a hydroxy acid.
- 38. The method of claim 35, wherein 4 is an iodo acid.
- 39. The method of claim 35, wherein 4 has a hydrophobic moiety.
- 40. The method of claim 39, wherein the hydrophobic moiety is an unsubstituted or substituted alkyl, aryl, napthyl or polycyclic group.
- 41. The method of claim 18, wherein 4 and 5 are capable of pi-stacking.
- 42. The method of claim 18, wherein 5 is an unsubstituted or substituted aryl, napthyl or polycyclic group.
- 43. The method of claim 18, wherein 5 is an amino acid.
- 44. The method of claim 43, wherein 5 is a hydroxy acid.
- 45. The method of claim 43, wherein 5 is a aromatic amino acid.
- 46. The method of claim 43, wherein 5 is a aromatic hydroxy amino acid.
- 47. The method of claim 18, wherein 5 is a hydroxy acid capable of pi-stacking.
- 48. The method of claim 47, wherein 5 is an iodo acid.
- 49. The method of claim 48, wherein 5 is an aromatic iodo acid.
- 50. The method of claim 48, wherein 5 is an iodo acid capable of pi-stacking.
- 51. The method of claim 48, wherein 5 is an L-isomer amino acid.
- 52. The method of claim 18, wherein 5 has an aromatic ring and the ring is oriented toward 4.
- 53. The method of claim 18, wherein 6 is a natural or non-natural amino acid.
- 54. The method of claim 53, wherein 6 is an iodo acid.
- 55. The method of claim 53, wherein 6 is a hydroxy acid.
- 56. The method of claim 18, wherein 6 provides a (type-VI) beta-turn element into the compound.
- 57. The method of claim 39, wherein the beta-turn element is a type-VI beta-turn element.
- 58. The method of claim 18, wherein 7 is a natural or non-natural amino acid.
- 59. The method of claim 58, wherein 7 is an iodo acid.
- 60. The method of claim 58, wherein 7 is a hydroxy acid.
- 61. The method of claim 18, wherein 7 has a linear or branched alkyl chain, or a large aromatic or hydrophobic group.
- 62. The method of claim 61, wherein said alkyl chain is substituted.
- 63. The method of claim 16, wherein 1-2 is a combination of contiguous subunits.
- 64. The method of claim 16, wherein X3-X4-X5 is a combination of contiguous subunits.
- 65. The method of claim 16, wherein 6-7 is a combination of contiguous subunits.
- 66. The method of claim 18, wherein the bond between 5 and 6 is a ketone.
- 67. The method of claim 16, wherein synthesis occurs according to FIGS. [62] 55 and [63] 56.
- 68. The method of claim 18, wherein at least one subunit is radiolabelled.
- 69. A method for inhibiting bacterial growth, comprising contacting a bacterium with a compound of claim 16.
- 70. A method for making a combinatorial library of compounds that have the generic structure
- 71. The method of claim 70, wherein the library does not include unmodifed or naturally occurring Class A Synergimycin.
- 72. The method of claim 70, wherein R of 8, 9, 10, 11, 12 or 13 is a side group of a naturally or nonnatural amino acid.
- 73. The method of claim 70, wherein the side group of 11 contains one of or a combination of a C1 to C8 alkyl, cycloalkyl or aryl.
- 74. The method of claim 70, wherein 8, 9, 10, 11, 12 or 13 are independently a hydroxy acid, an aromatic hydroxy acid, a hydroxy iodide, a hydroxy amine, a hydroxy amino acid, an iodo amino acid or an iodo hydroxy amino acid.
- 75. The method of claim 70, wherein 8 is a hydryoxy acid, hydroxy ester or hydroxy aldehyde.
- 76. The method of claim 70, wherein 9 is an iodo acid or hydroxy acid.
- 77. The method of claim 70, wherein 10 is a hydroxy acid or iodo acid.
- 78. The method of claim 70, wherein 11 is a haloalkyl, halo aryl or hydrophobic halogen group.
- 79. The method of claim 70, wherein 12 is a hydroxy acid, hydroxy ester, hydroxy aldehyde, iodo acid, iodo ester or iodo aldehyde.
- 80. The method of claim 70, wherein 13 is a halo amine, hydroxy acid or iodo acid.
- 81. The method of claim 70, wherein macrocyclization occurs according to FIGS. [43] 36 or [45] 38.
- 82. The method of claim 70, wherein at least one subunit is radiolabelled.
- 83. A method for making a peptidomimetic of target molecule A-B, wherein the bond between A and B is an amide or ester, comprising the steps of
(a) obtaining a modified A, wherein A contains an acid chloride or aldehyde; (b) obtaining a modified B, wherein B contains halide; (c) coupling the modified A to the modified B using an organozinc reaction, resulting in a carbon-carbon bond; thereby making a mimetic of A-B.
- 84. The method of claim 83, wherein the method is performed a plurality of cycles on a target molecule etc. to obtain a mimetic of said target molecule.
- 85. The method of claim 83, wherein an amino acid derivative is converted into an organozinc reagent.
- 86. The method of claim 83, wherein the target molecule has a peptide bond between A and B.
- 87. The method of claim 83, wherein the peptide is cyclic.
- 88. The method of claim 83, wherein the target peptide is a synergimycin.
- 89. The method of claim 83, wherein the target peptide is a Holliday Junction-trapping compound.
- 90. The method of claim 83, wherein the organozinc reaction couples the organozinc reagent to an acid chloride, replacing an amide or ester with a ketone.
- 91. The method of claim 83, wherein the organozinc reaction couples the organozinc reagent to an aldehyde, replacing an amide or ester with a chiral alcohol.
- 92. The method of claim 83, wherein the organozinc reaction is performed in liquid or solid phase.
Parent Case Info
[0001] This application claims benefit of the filing date of U.S. Provisional Application No. 60/369,420, filed Apr. 1, 2002, and which is incorporated herein by reference.
[0002] This invention was made with government support under solicited grant RFA-GM-01-006, awarded by the National Institutes of Health. The government has certain rights in the invention.
Provisional Applications (1)
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Number |
Date |
Country |
|
60369420 |
Apr 2002 |
US |