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

• US 6,335,155 B1
• Filed: 06/26/1998
• Issued: 01/01/2002
• Est. Priority Date: 06/26/1998
• Status: Expired due to Term

• 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): Ponnaluri, Padmashri
• Application Number:
  US09/105,372
• Time in Patent Office: 1,285 Days
• Field of Search: 435/4, 435/5, 435/7.1, 435/7.5, 435/74, 435/7.6, 435/DIG.2, 435/DIG.3, 435/DIG.22, 435/DIG.34, 436/173
• 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 high-throughput, solution-based method for rapid identification of a small, non-oligomeric, soluble, synthetic organic ligand, wherein said ligand is less than 500 daltons in size, and binds to a site of interest on a biological target molecule, said method comprising:

(a) obtaining a biological target molecule that comprises a site of interest, wherein said biological target molecule comprises or has been modified to comprise at said site of interest a first —

SH group, masked —

SH group, or activated —

SH group;

(a) combining said biological target molecule with one or more members of a library of small, non-oligomeric, soluble, synthetic organic ligand candidates, wherein said ligand candidates are less than 500 daltons in size, comprise a second —

SH group, masked —

SH group, or activated —

SH group, and both said biological target molecule and said members of a library are in aqueous solution, under conditions of thiol-disulfide exchange, and wherein at least one member of said library binds to said site of interest by a disulfide bond, to form a target molecule/organic ligand conjugate; and

(c) detecting the formation of said target molecule/organic ligand conjugate and identifying the ligand present in said conjugate by subjecting said conjugate directly, without prior fragmentation and without liberation of said ligand from said conjugate, to mass spectrometry analysis.

2. The method according to claim 1, wherein said conditions of thiol-disulfide exchange are provided by the addition of a reducing agent.

3. The method of claim 2 wherein said reducing agent is dithiothreitol or mercaptoethanol.

4. The method according to claim 1, wherein said biological target molecule is a protein.

5. The method according to claim 4, wherein said protein is selected from the group consisting of an enzyme, a hormone, a transcription factor, a receptor, a ligand for a receptor, a growth factor and an immunoglobulin.

6. The method according to claim 1, wherein said biological target molecule comprises said first —

SH group, masked —

SH group, or activated —

SH group without prior modification of said biological target molecule.

7. The method according to claim 1 wherein said biological target molecule has been modified to comprise said first —

SH group, masked —

SH group, or activated —

SH group.

8. The method according to claim 7, wherein said biological target molecule has been modified by bonding to said biological target molecule at the site of interest a compound that comprises said first —

SH group, masked —

SH group, or activated —

SH group.

9. The method of claim 4 wherein said protein comprises or has been modified to comprise no more than 5 free —

SH groups.

10. The method of claim 9 wherein said protein comprises or has been modified to comprise no more than 2 free —

SH groups.

11. The method of claim 10 wherein said protein comprises or has been modified to comprise one free —

SH group.

12. The method of claim 1 wherein said small, synthetic organic ligand candidates are less than 250 daltons in size.

13. The method of claim 1 wherein said small, synthetic organic ligand candidates are present in said aqueous solution in a concentration from 0.1 μ

M to 50 mM.

14. The method of claim 13 wherein said concentration is 0.01 μ

M to 10 mM.