Selective covalent-binding compounds having therapeutic diagnostic and analytical applications

• US 20040121405A1
• Filed: 10/15/2003
• Published: 06/24/2004
• Est. Priority Date: 04/16/2002
• Status: Abandoned Application

• Current Assignee: Semorex, Inc.
• Original Assignee: Semorex, Inc.
• Inventors: Green, Bernard S.
• Application Number:
  US10/474,042
• Publication Number:
  US 20040121405A1
• Time in Patent Office: Days
• US Class Current: 435/7.1
• CPC Class Codes: G01N 2600/00 Assays involving molecular imprinted polymers/polymers created around a molecular template
• CPC Class Codes: G01N 33/531 Production of immunochemical test materials

Abstract

Novel compounds are provided having enhanced affinity for a desired, preselected, target substance (a small molecule; a macromolecule such as a protein, a carbohydrate, a nucleic acid, a cell, a viral particle, etc.) by modification with chemical groups that allow these substances to form strong bonds, such as irreversible covalent bonds, with the desired target substance. These qualities of tight, specific binding are reminiscent of antibody-like affinity; hence the new substances are termed COBALT, an acronym for Covalent-Binding Antibody-Like Trap. The present invention includes a process wherein a target species is chosen and then, by synthetic chemical procedures and modifications, novel substances (COBALTs) are obtained that exhibit selective and covalent binding to the preselected target species. The applications of the COBALTs include diagnostic, analytical, therapeutic and industrial applications.

Claims

1. A compound for specifically binding a target molecular structure, comprising a chemically modified reactive compound that is selective for the target, having an enhanced apparent affinity constant at least double that of the chemically unmodified parent compound.

2. The compound of claim 1, wherein said compound is an antibody mimic having selective affinity for the target structure, said compound modified through chemical activation in order to react chemically with the target molecular structure.

3. The compound of claims 1 or 2, wherein said compound is a molecularly imprinted polymer (MIP), said MIP being modified through chemical activation in order to react with the target molecular structure.

4. The compound of claims 1 or 2, wherein said compound is a molecularly imprinted polymer (MIP), said MIP being modified to include a functional monomer for reacting with an activated target substance.

5. The compound of any of claims 1-4 wherein said MIP is chemically modified so as to react with the target substance to form a covalent bond, wherein said chemical modification includes at least one reactive functional group.

6. The compound of claim 5, wherein said functional group includes at least one of an isocyanate and an isothiocyanate.

7. The compound of claims 5 or 6, wherein said functional group includes at least one of an alpha-halomethyl ether, wherein a halogen moiety may be fluoro, chloro, bromo or iodo;

a beta-haloethyl ether, wherein a halogen moiety may be chloro, bromo or iodo; and

a halomethylaryl, wherein a halogen moiety may be fluoro, chloro, bromo, or iodo.

8. The compound of any of claims 5-7, wherein said functional group includes at least one of 2,5-diketo-N-phenyltriazoline, carboxylic acid chloride, and an activated carboxylic acid.

9. The compound of any of claims 3-8, wherein the target molecular structure is a steroid.

10. The compound of claim 9, wherein said steroid is cholesterol or a bile acid.

11. The compound of claims 1 or 2, wherein said compound is a cyclodextrin.

12. The compound of claims 1 or 2, wherein said compound is a triazine.

13. The compound of claims 1 or 2, wherein said compound is a peptide.

14. The compound of claim 13, wherein said peptide includes at least one of cyclic, linear and modified peptides and derivatives thereof.

15. The compound of any of claims 1-5, wherein the target structure is an organophosphate.

16. The compound of claim 15, wherein said compound includes at least one functional monomer for reacting with said organophosphate.

17. The compound of claims 15 or 16, wherein said compound includes a nucleophile for specifically binding to said organophosphate.

18. The compound of claim 17, wherein said nucleophile is a derivative of at least one of an oxime, a hydroxylamine, a hydrazine, a phenol and a 2-iodosobenzoic acid.

19. The compound of any of claims 1-5, wherein said compound comprises a plurality of boronic acid functions.

20. The compound of any of claims 1-5, wherein said compound comprises a plurality of aldehyde functions.

21. The compound of claims 19 or 20, wherein said functions perform specific and tight binding to carbohydrates.

22. The compound of claim 1, wherein said compound is an antibody or derivative thereof being chemically modified to react covalently with the target molecular structure.

23. The compound of any of claims 1-22, for binding to and specifically reacting with a site on the target molecular structure, apart from the active site of the target molecular structure.

24. A combinatorial library of compounds, each containing a chemically reactive group, screened for selectivity and chemical reaction with the molecular structure as a target, for creating the compound of any of claims 1-23.

25. The compound of any of claims 1-23 for use in at least one of diagnostics, combinatorial screening genomic, proteomic, and glycomic applications.

26. The compound of claim 25, wherein said combinatorial screening includes combinatorial screening for drug discovery.

27. The compound of any of claims 1-23 for use in at least one of an environmental detection, environmental removal of chemical weapons or environmental hazards and protection from chemical weapons or environmental hazards.

28. The use of compounds from any of claims 1-23 as a therapeutic compound.

29. The use of compounds of any of claims 1-23 for drugs or extracorporeal treatment.

55. The compound of claim 11, wherein said cyclodextrin is an alpha-, beta-, or gamma-cyclodextrin.

56. The compound of claim 55, wherein said cyclodextrin includes one or more amino groups for replacing one or more of the hydroxyl groups.

57. The compound of claims 55 or 56, wherein one or more hydroxyl or amino groups is linked directly to at least one of an arylcarboxylic acid group, and an arylalkylcarboxylic acid group, through an amide or ester bond.

58. The compound of any of claims 55-57, wherein one or more of the hydroxyl or amino groups is linked directly to at least one of an aryl group or arylmethyl group, wherein aryl includes at least one of phenyl and substituted phenyl, pyridyl and substituted pyridyl, naphthyl and substituted naphthyl groups.

63. The compound of claim 12 wherein said triazine is a derivatives of 2,4,6-trichloro-1,3,5-triazine (cyanuric chloride) wherein one or more of the chloro groups are replaced by an alcohol group, a phenol group or an amine group.

30. A method for creating a compound for specifically binding a target molecular structure, the compound comprising a selective and chemically reactive compound with an enhanced apparent affinity constant, the method comprising:

providing a combinatorial library of compounds containing chemically reactive groups;

screening said combinatorial library for a compound having a selective chemical reaction with the target molecular structure; and

creating the compound for specifically binding the target molecular structure from at least said compound of said combinatorial library.

31. The method of claim 30, wherein said compounds in said combinatorial library include a plurality of monomers and the compound for specifically binding the target molecular structure is a polymer.

32. The method of claims 30 or 31, wherein the compound for specifically binding the target molecular structure is a MIP (molecularly imprinted polymer).

33. The method of claim 30, wherein the compound is a cyclodextrin.

34. The method of claim 30, wherein the compound is a triazine.

35. The method of claim 30, wherein the compound is a peptide.

36. The method of claim 35, wherein said peptide includes at least one of cyclic, linear and modified peptides and derivatives thereof.

37. The method of any of claims 30-36, wherein the compound features at least one functional group, said at least one functional group reacting with the target molecular structure.

59. The compound of claim 33, wherein said cyclodextrin is an alpha-, beta-, or gamma-cyclodextrin.

60. The compound of claim 59, wherein said cyclodextrin includes one or more amino groups for replacing one or more of the hydroxyl groups.

61. The compound of claims 59 or 60, wherein one or more hydroxyl or amino groups is linked directly to at least one of an arylcarboxylic acid group, and an arylalkylcarboxylic acid group, through an amide or ester bond.

62. The compound of any of claims 59-61, wherein one or more of the hydroxyl or amino groups is linked directly to at least one of an aryl group or arylmethyl group, wherein aryl includes at least one of phenyl and substituted phenyl, pyridyl and substituted pyridyl, naphthyl and substituted naphthyl groups.

64. The method of claim 34 wherein said triazine includes a derivative of 2,4,6-trichloro-1,3,5-triazine (cyanuric chloride) and wherein one or more of the chloro groups are replaced by an alcohol group, a phenol group or an amine group.

38. A method for creating a compound for specifically binding a target molecular structure, the method comprising:

preparing an MIP for binding to the target molecular structure; and

converting at least a portion of said MIP to an active functional group for forming a covalent bond with the target molecular structure upon binding of said MIP to the target molecular structure, thereby forming the compound for binding the target molecular structure.

39. The method of claim 38, wherein preparing said MIP further comprises:

selecting at least one functional group of the target molecular structure;

preparing a complementary functional group for said MIP to bind to said at least one functional group; and

polymerizing a plurality of monomers containing said complementary functional group to form a polymer, wherein said polymer is said MIP.

40. The method of claim 38, wherein preparing said MIP further comprises:

selecting at least one functional group of the target molecular structure;

preparing a derivative of said target molecular structure as a functional monomer; and

polymerizing a plurality of monomers containing said functional monomer to form a polymer, wherein said polymer is said MIP.

41. The method of claim 39, wherein preparing said MIP further comprises:

hydrolyzing at least one bond of said polymer to release said target molecular structure.

42. The method of claims 40 or 41, wherein the target molecular structure is a steroid or a bile acid, and wherein said functional group of the target molecular structure is R—

OH and said functional monomer includes at least one of an ester R—

O—

CO—

R′

or carbamate R—

O—

C(═

O)—

NH—

R′

derivative of said target alcohol ROH, wherein said R′

group has a vinyl, polymerizable function.

43. The method of claim 42, wherein said steroid is cholesterol.

44. The method of claim 42, wherein said bile acid includes at least one of deoxycholic acid, chenodeoxycholic acid or lithocholic acid.

45. The method of claim 42, wherein said active functional group is an acid chloride, Cl—

C(═

O)-polymer functional group, for reacting with a target molecular structure containing a hydroxyl group or an amino group.

46. The method of claim 42, wherein said active functional group is an isocyanate, O═

C═

N-polymer, or isothiocyanate, S═

C═

N-polymer for reacting with a target molecular structure containing a hydroxyl group or an amino group.

47. A method for creating a compound for specifically binding a chemically activated target molecular structure, the method comprising:

preparing an MIP for binding to the target molecular structure; and

converting at least a portion of said MIP to a functional group for forming a covalent bond with the target molecular structure upon binding of said MIP to the activated target molecular structure.

48. The method of claim 47, wherein preparing said MIP further comprises:

selecting at least one reactive functional group of the activated target molecular structure;

preparing a derivative of said target molecular structure which can be polymerized (a functional monomer); and

polymerizing a plurality of monomers containing said functional monomer to form a polymer, wherein said polymer is said MIP.

49. The method of claim 48, wherein preparing said MIP further comprises:

hydrolyzing at least one bond of said polymer to release said target molecular structure and leave at least one functional group in said MIP cavity for reacting with said activated target molecular structure.

50. The method of claims 48 or 49, wherein the activated target molecular structure is an organophosphate and wherein said functional monomer includes at least one of a 4-vinylbenzaldehyde oxime ester of the phosphate or phosphonate.

51. The method of claim 50, wherein preparing said MIP further comprises:

hydrolyzing at least one bond of said polymer to release said functional group of the target molecular structure.

52. The method of claims 50 or 51, wherein the target molecular structure includes at least one of cholesterol and bile acid and wherein said functional group of the target molecular structure is R—

OH and said complementary functional group includes at least one of an ester R—

O—

CO—

R′

or carbamate R—

O—

C(═

O)—

NH—

R′

derivative of said target alcohol ROH, wherein said R′

group has a vinyl, polymerizable function.

53. The method of claim 52, wherein said active functional group is an acid chloride, Cl—

C(═

O)-polymer functional group for carbamate polymers.

54. The method of claim 52, wherein said bile acid includes at least one of deoxycholic acid, chenodeoxycholic acid or lithocholic acid.