Extended tethering approach for rapid identification of ligands

• US 6,919,178 B2
• Filed: 11/21/2001
• Issued: 07/19/2005
• Est. Priority Date: 11/21/2000
• Status: Expired due to Fees

• Current Assignee: Sunesis Pharmaceuticals, Inc. (Viracta Therapeutics, Inc.)
• Original Assignee: Sunesis Pharmaceuticals, Inc. (Viracta Therapeutics, Inc.)
• Inventors: McDowell, Robert, Prescott, John, Erlanson, Daniel A., Braisted, Andrew C.
• Primary Examiner(s): Wang, Andrew
• Assistant Examiner(s): Epperson, Jon D.
• Application Number:
  US09/990,421
• Publication Number:
  US 20020150947A1
• Time in Patent Office: 1,336 Days
• Field of Search: 435 4- 6, 435/7.1, 435DIG 2- 3, 435/22, 435/34
• US Class Current: 435/6.16
• CPC Class Codes: C07B 2200/11 Compounds covalently bound to a solid support
• CPC Class Codes: C07D 333/38 Carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals
• CPC Class Codes: C07D 333/70 attached in position 2
• CPC Class Codes: C07D 401/04 directly linked by a ring-member-to-ring-member bond
• CPC Class Codes: C07D 405/12 linked by a chain containing hetero atoms as chain links
• 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: G01N 2500/04 Screening involving studying the effect of compounds C directly on molecule A (e.g. C are potential ligands for a receptor A, or potential substrates for an enzyme A)
• CPC Class Codes: G01N 33/6845 Methods of identifying protein-protein interactions in protein mixtures

Abstract

The invention concerns a method for rapid identification and characterization of binding partners for a target molecule, and for providing binding partners with improved binding affinity. More specifically, the invention concerns an improved tethering method for the rapid identification of at least two binding partners that bind near one another to a target molecule.

Claims

1. A process comprising the steps of:

(i) contacting a Target Biological Molecule (TBM) having a first and a second site of interest, and containing or modified to contain a nucleophile, selected from the group consisting of thiol, protected thiol, reversible disulfide, hydroxyl, protected hydroxyl, amino, protected amino, carboxyl and protected carboxyl groups, at or near the first site of interest, with a plurality of first organic ligand candidates, said candidates having a functional group reactive with the nucleophile, under conditions such that a reversible covalent bond is formed between the nucleophile and a candidate that has affinity for the first site of interest, to form a TMB-first ligand complex;

(ii) identifying the first ligand from the TBM-first ligand complex;

(iii) designing a derivative of the first ligand identified in (ii) to provide a small molecule extender (SME) having a first functional group reactive with the nucleophile on the TBM and a second functional group reactive with a second ligand having affinity for the second site of interest, wherein said first functional group is capable of forming an irreversible covalent group with the thiol, protected thiol, reversible disulfide bond, hydroxyl, protected hydroxyl, amino, protected amino, carboxyl or protected carboxyl group on said TBM;

(iv) contacting the SME with the TBM to form a TBM-SME complex, and (v) contacting the TBM-SME complex with a plurality of second small organic ligand candidates, said candidates having a functional group reactive with the SME in said TBM-SME complex, wherein a candidate that has affinity for said second site of interest on said TBM forms a reversible covalent bond with said TBM-SME complex, whereby a second ligand is identified.

2. The process of claim 1 wherein the second functional group on said TBM and the functional group on said second ligand candidates in step (v) is a thiol, protected thiol or reversible disulfide group.

3. The process of claim 2 wherein step (v) is conducted under conditions of thiol exchange.

4. The process of claim 3 wherein said conditions are provided by a reducing agent selected from the group consisting of mercaptoethanol, dithiothreitol (DTT), dithioerythreitol (DTE), mercaptopropanoic acid, glutathione, cysteamine, cysteine, tri(carbodiethyl)phosphine (TCEP), and tris(cyanoethyl)phosphine.

5. The process of claim 4 wherein said second ligand candidates in step (v) are members of a library.

6. The process of claim 5 wherein the library member having the highest affinity for said second site of interest on the TBM forms a disulfide bond with the TBM-SME complex.

7. The process of claim 1 comprising identifying said second ligand having affinity for said second site of interest on the TBM.

8. The process of claim 7 wherein said second ligand is identified by mass spectrometry (MS).

9. The process of claim 7 wherein said second ligand is identified by means of a detectable tag.

10. The process of claim 7, further comprising the step of synthesizing a molecule comprising said first and second ligands covalently linked to one another.

11. The process of claim 10 wherein said covalent linkage is provided by a disulfide bond.

12. The process of claim 11 wherein said molecule consists essentially of said first and second ligands, covalently linked through a disulfide bond.

13. The process of claim 12 further comprising the step of synthesizing derivatives of said molecule.

14. The process of claim 13 wherein the disulfide bond covalently linking the first and second ligands is replaced with a different covalent linkage.

15. A process comprising:

(i) providing a Target Biological Molecule (TBM) containing or modified to contain a reactive nucleophile near a first site of interest on the TBM;

(ii) contacting the TBM from (i) with a small molecule extender having a group reactive with the nucleophile on the TBM and having a free thiol or protected thiol;

(iii) adjusting the conditions of contacting in step (ii) to cause a covalent bond to be formed between the nucleophile on the TBM and the group on the small molecule extender thereby forming a covalent complex comprising the TBM and the small molecule extender, the complex displaying a free thiol or protected thiol near a second site of interest on the TBM;

(iv) contacting the complex from (iii) with a library of small organic molecules each molecule having a free thiol or exchangeable disulfide linking group, under conditions of thiol exchange wherein the library member having the highest affinity for the second site of interest on the TBM forms a disulfide bond with the complex; and

(v) identifying the library member from (iv).

16. The process of claim 15 further comprising the step of synthesizing a molecule consisting essentially of the small molecule extender having the electrophile group from step (ii) covalently linked through the disulfide with the library member identified in step (i).

17. The process of claim 16 further comprising the step of synthesizing a derivative of the molecule.

18. The process of claim 17 wherein the derivative contains a different group reactive with the nucleophile.

19. The process of claim 17 wherein the disulfide group covalently linking the small molecule extender with the library member identified in step (i) is replaced with a different group.

20. The process of claim 15 further comprising synthesizing a molecule consisting essentially of the small molecule extender without the group reactive with the nucleophile covalently linked through the disulfide with the library member identified in step (v).

21. The process of claim 20 further comprising replacing the disulfide, covalently linking the small molecule extender without the group reactive with the nucleophile with the library member identified in step (c), with a different group.

22. The process of claim 15 wherein the reactive nucleophile is a thiol.

23. The process of claim 22 further comprising, after step (i),

(a) contacting the TBM with a library of small organic molecules, each molecule having an exchangeable disulfide linking group, under conditions of thiol exchange wherein the library member having the highest affinity for the first site of interest forms a disulfide bond with the TBM;

(b) identifying the library member from (i); and

(c) forming a derivative of the library member in (ii) that is the small molecule extender having a group reactive with the nucleophile and having a thiol or protected thiol of step (b).

24. The process of claim 23 further comprising adding a disulfide reducing agent selected from the group consisting of mercaptoethanol, dithiothreitol (DTT), dithioerythreitol (DTE), mercaptopropanoic acid, glutathione, cysteamine cysteine, tri(carboxyethyl)phosphine (TCEP), and tris(cyanoethyl)phosphine.

25. The process of claim 15 wherein the identifying step comprises mass spectrum analysis.

26. The process of claim 23 wherein the identifying step comprises mass spectrum analysis.

27. The process of claim 23 wherein each molecule in the library of small organic molecules having an exchangeable disulfide linking group contains a cysteamine moiety.