SMALL MOLECULE PRINTING

• US 20090221433A1
• Filed: 01/03/2007
• Published: 09/03/2009
• Est. Priority Date: 01/03/2006
• Status: Abandoned Application

• Current Assignee: Dana-Farber Cancer Institute, President and Fellows of Harvard College (Harvard Corporation)
• Original Assignee: Dana-Farber Cancer Institute
• Inventors: Barnes, David W., Schreiber, Stuart L., Mazitschek, Ralph, Koehler, Angela N., Bradner, James E.
• Application Number:
  US12/159,481
• Publication Number:
  US 20090221433A1
• Time in Patent Office: Days
• US Class Current: 506/9
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/0072 Organic compounds
• CPC Class Codes: B01J 2219/0074 Biological products
• CPC Class Codes: C40B 30/04 by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
• CPC Class Codes: C40B 40/04 Libraries containing only organic compounds
• CPC Class Codes: C40B 80/00 Linkers or spacers specially adapted for combinatorial chemistry or libraries, e.g. traceless linkers or safety-catch linkers
• CPC Class Codes: G01N 33/50 Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing measuring or testing processes involving enzymes or microorganisms, compositions or test papers therefor; processes for forming such compositions, condition responsive control in microbiological or enzymological processes C12Q
• CPC Class Codes: G01N 33/53 Immunoassay; Biospecific binding assay; Materials therefor
• CPC Class Codes: G01N 33/543 with an insoluble carrier for immobilising immunochemicals
• CPC Class Codes: G01N 33/54353 with ligand attached to the carrier via a chemical coupling agent coatings G01N33/54393
• CPC Class Codes: G01N 33/547 with antigen or antibody attached to the carrier via a bridging agent
• CPC Class Codes: G01N 33/552 Glass or silica
• CPC Class Codes: G01N 33/553 Metal or metal coated
• CPC Class Codes: G01N 33/6803 General methods of protein analysis not limited to specific proteins or families of proteins

Abstract

The present invention provides compositions and methods to facilitate the identification of compounds that are capable of interacting with a biological macromolecule of interest. In one aspect, a composition is provided that comprises an array of one or more types of chemical compounds attached to a solid support using isocyanate or isothiocyanate chemistry, wherein the density of the array of compounds is at least 1000 spots per cm². In general, these inventive arrays are generated by: (1) providing a solid support, wherein said solid support is functionalized with an isocyanate or isothiocyanate moiety capable of interacting with a desired chemical compound to form a covalent attachment; (2) providing one or more solutions of one or more types of compounds to be attached to the solid support; (3) delivering said one or more types of compounds to the solid support; and (4) catalyzing the attachment of the compound to the solid support, whereby an array is formed and the array of compounds has a density of at least 1000 spots per cm². In another aspect, the present invention provides methods for utilizing these arrays to identify small molecule partners for biological macromolecules of interest.

Claims

1. An array comprising:

a plurality of more than one type of chemical compound attached to a solid support through an isocyanate-derived linker or a isothiocyanate-derived linker, wherein the density of said array of compounds comprises at least 100 spots per cm².

2. The array of claim 1, wherein said array of chemical compounds comprises an array of small molecules.

3. The array of claim 1, wherein said array of chemical compounds comprises an array of non-oligomeric chemical compounds.

4. The array of claim 1, wherein said array of chemical compounds comprises an array of non-peptidic and non-oligomeric chemical compounds.

5. The array of claim 1, wherein said array of chemical compounds comprises an array of chemical compounds with a molecular weight less than 2000 g/mol.

6. The array of claim 1, wherein said array of chemical compounds comprises an array of chemical compounds, wherein the chemical compounds are not polynucleotides, peptides, or proteins.

7. The array of claim 1, wherein said array of chemical compounds comprises an array of chemical compounds, wherein the chemical compounds are biomolecules from a cell lysate.

8. The array of claim 1, wherein the chemical compounds include a functional group for attachment selected from the group consisting of primary alcohol, secondary alcohol, phenol, thiol, aniline, hydroxamic acid, primary amides, aliphatic amines, and sulfonamides.

9. The array of claim 1, wherein the chemical compounds include a functional group for attachment selected from the group consisting of primary alcohols, secondary alcohols, phenols, carboxylic acids, hydroxamic acids, thiols, and amines.

10. The array of claim 1, wherein said attachment is characterized in that the resulting linkage is robust enough so that the compounds are (1) not inadvertently cleaved during subsequent manipulation steps and (2) inert so that the functionalities employed do not interfere with subsequent manipulation steps.

11. The array of claim 1, wherein each of said chemical compounds in said array is attached to the solid support through a linkage generated by addition of a nucleophile to an isocyanate or isothiocyanate moiety.

12. The array of claim 11, wherein the addition is catalyzed by vapor.

13. The array of claim 11, wherein the addition is catalyzed by a nucleophile.

14. The array of claim 12, wherein the vapor is pyridine.

15. The array of claim 12, wherein the vapor is a volatile heterocyclic amine.

16. The array of claim 1, wherein the isocyanate-derived linker attaching compound to the support is of the formula:

wherein

L is a substituted or unsubstituted, branched or unbranched, cyclic or acyclic aliphatic or heteroaliphatic linker;

X is N, S, or O; and

R is the chemical compound being attached to the solid support.

17. The array of claim 1, wherein the isothiocyanate-derived linker attaching compound to the support is of the formula:

wherein

L is a substituted or unsubstituted, branched or unbranched, cyclic or acyclic aliphatic or heteroaliphatic linker;

X is N, S, or O; and

R is the chemical compound being attached to the solid support.

18. The array of claim 1, wherein the isocyanate-derived linker attaching compound to the support is of the formula:

wherein

n is an integer between 1 and 12, inclusive;

X is O, S, or N; and

R is an attached compound.

19. The array of claim 1, wherein the isocyanate-derived linker attaching compound to the support is of the formula:

wherein

L is a substituted or unsubstituted, branched or unbranched, cyclic or acyclic aliphatic or heteroaliphatic linker;

n is an integer between 1 and 12, inclusive;

X is N, S, or O; and

R is the chemical compounds being attached to the solid support.

20. The array of claim 1, wherein the isocyanate-derived linker attaching compound to the support is of the formula:

wherein

each occurrence of n is independently an integer between 1 and 20, inclusive;

m is an integer between 1 and 20, inclusive;

X is N, S, or O; and

R is the chemical compounds being attached to the solid support.

21. The array of claim 1, wherein the isothiocyanate-derived linker attaching compound to glass slide is of the formula:

wherein

X is O, S, or N; and

R is an attached compound.

22. The array of claim 1, wherein the linker attaching compound to the solid support is shown below:

wherein n is an integer between 1 and 12, inclusive;

m is an integer between 1 and 200, inclusive;

X is O, S, or N; and

R is an attached compound.

23. The array of claim 1, wherein the linker attaching compound to the solid support is of the formula:

wherein n is an integer between 1 and 200, inclusive; and

R is an attached compound.

24. The array of claim 1, wherein the solid support is glass.

25. The array of claim 1, wherein the solid support is derivatized glass.

26. The array of claim 1, wherein the solid support is silylated glass.

27. The array of claim 1, wherein the solid support is γ

-aminopropylsilylated glass.

28. The array of claim 1, wherein the solid support is a polymer.

29. The array of claim 1, wherein the solid support is metal.

30. The array of claim 1, wherein the solid support is a metal-coated surface.

31. The array of claim 1, wherein the solid support is a gold-coated surface.

32. The array of claim 1, wherein the density of said array is at least 1000 spots per cm².

33. The array of claim 1, wherein the density of said array is at least 2500 spots per cm².

34. The array of claim 1, wherein the density of said array is at least 5000 spots per cm².

43. A method of identifying small molecule partners for biological macromolecules of interest comprising steps of:

providing the array of claim 1, wherein said array comprises an array of small molecules attached to a support through an isocyanate-derived linker or an isothiocyanate-derived linker, and wherein said array of small molecules has a density of at least 100 spots per cm²;

contacting said array with one or more types of biological macromolecules of interest; and

determining the binding of specific small molecule-biological macromolecule partners.

44. A method of identifying small molecule partners for a gene product comprising:

providing the array of claim 1, wherein said array comprises an array of small molecules attached to a support through an isocyanate-derived linker or an isothiocyanate-derived linker, and wherein said array of small molecules has a density of at least 100 spots per cm²;

contacting said array with a library of biomolecules; and

determining the binding of specific recombinant proteins with a small molecule partner.

45. The method of claim 44, wherein the library of biomolecules is a library of proteins.

46. The method of claim 44, wherein the library of biomolecules is a library of recombinant proteins.

47. The method of claim 44, wherein the library of biomolecules is a cell lysate.

35. An array comprising:

a plurality of one or more types of chemical compounds attached to a solid support through an isocyanate-derived linker or an isothiocyanate-derived linker, wherein the density of said array of compounds comprises at least 100 spots per cm².

36. A method for forming an array of chemical compounds, the method comprising steps of:

providing a solid support, wherein said solid support is functionalized with a weakly electrophilic moiety capable of interacting with more than one type of chemical compound to form a covalent linkage;

providing one or more solutions of more than one type of chemical compounds to be attached to the solid support;

delivering said one or more solutions of said more than one type of chemical compounds to the solid support, whereby each of said chemical compounds is attached to the solid support through a covalent interaction, and whereby said array of compounds has a density of at least 100 spots per cm²; and

exposing the solid support to a base in vapor form under conditions sufficient to catalyze covalent attachment of the compounds to the support.

37. The method of claim 36, wherein the weakly electrophilic moiety is an isocyanate moiety.

38. The method of claim 36, wherein the weakly electrophilic moiety is an isothiocyanate moiety.

39. The method of claim 36, wherein the base is pyridine.

40. The method of claim 36, wherein the conditions sufficient to catalyze covalent attachment of the compounds to the support comprises performing the attachment in a water-free environment.

41. The method of claim 36, wherein the conditions sufficient to catalyze covalent attachment of the compounds to the support comprises performing the attachment in an inert atmosphere.

42. The method of claim 36, wherein the inert atmosphere is an argon or nitrogen atmosphere.

48. A solid support comprising a solid support derivatized with isocyanate moieties.

49. The solid support of claim 48, wherein the isocyanate moieties are of the formula:

wherein L is a substituted or unsubstituted, branched or unbranched, cyclic or acyclic aliphatic or heteroaliphatic linker.

50. A solid support comprising a solid support derivatized with isothiocyanate moieties.

51. The solid support of claim 50, wherein the isothiocyanate moieties are of the formula:

wherein L is a substituted or unsubstituted, branched or unbranched, cyclic or acyclic aliphatic or heteroaliphatic linker.