Methods for rapidly identifying small organic molecule ligands for binding to biological target molecules

• US 6,811,966 B2
• Filed: 01/11/2002
• Issued: 11/02/2004
• Est. Priority Date: 06/26/1998
• Status: Expired due to Fees

• Current Assignee: Sunesis Pharmaceuticals, Inc. (Viracta Therapeutics, Inc.)
• Original Assignee: Sunesis Pharmaceuticals, Inc. (Viracta Therapeutics, Inc.)
• Inventors: Wells, Jim, Erlanson, Dan, Braisted, Andrew C.
• Primary Examiner(s): Page, Thurman K.
• Assistant Examiner(s): Epperson, Jon D.
• Application Number:
  US10/043,833
• Publication Number:
  US 20030104471A1
• Time in Patent Office: 1,026 Days
• Field of Search: 435/4, 435/5, 435/6, 435/7.1, 435/7.5, 435/DIG.2, 435/DIG.3, 435/DIG.34, 435/DIG.22
• US Class Current: 435/4
• CPC Class Codes: G01N 33/53 Immunoassay; Biospecific binding assay; Materials therefor
• CPC Class Codes: G01N 33/566 using specific carrier or receptor proteins as ligand binding reagents where possible specific carrier or receptor proteins are classified with their target compounds
• CPC Class Codes: Y10T 436/24 Nuclear magnetic resonance, electron spin resonance or other spin effects or mass spectrometry

Abstract

The present invention is directed to novel methods for rapidly and unambiguously identifying small organic molecule ligands for binding to biological target molecules. Small organic molecule ligands identified according to the methods of the present invention may find use, for example, as novel therapeutic drug lead compounds, enzyme inhibitors, labeling compounds, diagnostic reagents, affinity reagents for protein purification, and the like. Also presented are novel methods for identifying high affinity binding ligands for a biological target molecule of interest, wherein those methods comprise linking two or more small organic molecule ligands previously identified as being capable of binding to the biological target molecule of interest. Biological target molecules include, for example, polypeptides, nucleic acids, carbohydrates, nucleoproteins, glycoproteins, glycolipids and lipoproteins.

Claims

1. A process comprising

(a) screening a library of small organic compounds, less than about 2000 daltons in size, with a target protein-ligand conjugate formed by the covalent bonding of a target protein comprising a first reactive functionality with a ligand that (1) comprises less than about 20 carbon atoms;

(2) has affinity for interacting with a particular site on the target protein, (3) comprises a second reactive functionality and (4) comprises a free chemically reactive group, wherein the second reactive functionality of the ligand reacts with the first reactive functionality of the target protein to form a first covalent bond such that the ligand in the target protein-ligand conjugate contains a free chemically reactive group, in aqueous solution, under conditions wherein at least one member of the library forms a second covalent bond with said free chemically reactive group in the target protein-ligand conjugate, and

(b) determining the identity of a small organic compound that binds covalently to the free chemically reactive group of the target protein-ligand conjugate.

2. The process of claim 1 wherein the second covalent bond is a disulfide bond.

3. The process of claim 1 wherein the free chemically reactive group is a thiol.

4. The process of claim 1 wherein each member of the library of small organic compounds comprises thiols or disulfides.

5. The process of claim 4 wherein each member of the library further contains a group selected from amides, secondary amides, disulfides and carbamates.

6. The process of claim 1 wherein the identifying step comprises using mass spectrometry.

7. The process of claim 6 wherein mass spectrometry is used to measure the mass of complex formed by the small organic compound covalently bound to the target protein-ligand conjugate.

8. The process of claim 7 wherein the complex is first fragmented prior to subjecting it to mass spectrometry.

9. The process of claim 8 comprising liberating or releasing the small organic compound from the complex prior to subjecting the small organic molecule to mass spectrometry.

10. The process of claim 9 wherein the liberating step comprises treating the conjugate with an agent that disrupts the disulfide bond through which the small organic compound forms a complex with the target protein-ligand conjugate.

11. The process of claim 10 wherein the agent is selected from borohydride or a phosphine.

12. The process of claim 10 further comprising coupling the liberated small organic compound to a labeled probe that facilitates identification of the compound by mass spectrometry.

13. The process of claim 1 wherein the target protein is selected from enzymes, proteases, kinases, phosphatases (dephosphorylases), cytokine receptors, hormones, interleukins, tyrosine kinase receptors, TNF, mdm2, chemokines and their receptors, signal transduction molecules and transcription factors.

14. The process of claim 11 wherein said agent is tris-(2-carboxyethyl)-phosphine (TECP).

15. The process of claim 1 wherein the first reactive functionality is an -SH group, masked -SH group, or activated -SH group.

16. The process of claim 15 wherein said -SH group, masked -SH group, or activated -SH group is associated with a cysteine residue of said target protein.