System to detect small molecule/peptide interaction

• US 5,846,722 A
• Filed: 10/16/1996
• Issued: 12/08/1998
• Est. Priority Date: 10/16/1996
• Status: Expired due to Fees

• Current Assignee: Telik, Inc. (MabVax Therapeutics Holdings, Inc.)
• Original Assignee: Terrapin Technologies, Inc.
• Inventors: Kauvar, Lawrence M., Napolitano, Eugene W.
• Primary Examiner(s): Ketter, James
• Assistant Examiner(s): SANDALS, WILLIAM O
• Application Number:
  US08/731,613
• Time in Patent Office: 783 Days
• Field of Search: 435/69.1, 435/91.1, 435/254.2, 435/325, 435/6, 435/69.7, 530/350, 536/23.4, 536/24.1
• US Class Current: 435/6.14
• CPC Class Codes: C07K 2319/22 containing a Strep-tag
• CPC Class Codes: C07K 2319/81 containing a Zn-finger domain for DNA binding
• CPC Class Codes: C12N 15/62 DNA sequences coding for fusion proteins
• CPC Class Codes: C12Q 1/6897 involving reporter genes operably linked to promoters
• 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 33/6845 Methods of identifying protein-protein interactions in protein mixtures

Abstract

Improved methods for determining interactions between peptides or proteins and small molecules are disclosed. The invention methods can be used to screen libraries of either the small molecules or the proteins. In general, the methods comprise contacting an agent/ligand complex consisting essentially of an agent to be tested for binding to a target protein coupled to a ligand capable of binding a proteinaceous ligand-binding domain with a first fusion protein comprising said target protein and a first complementary portion of a segregable protein; and a second fusion protein comprising a proteinaceous ligand-binding domain and a second complementary portion of said segregable protein; and detecting whether the first complementary portion and second complementary portion are brought into proximity.

Claims

1. A method to determine whether an agent and a target protein interact, said method comprising the steps of:

contacting an agent/ligand complex comprising a small molecule agent to be tested for binding to a target protein coupled to a ligand that binds a proteinaceous ligand-binding domain with

a first fusion protein comprising said target protein and a first complementary portion of a segregable protein; and

a second fusion protein comprising a proteinaceous ligand-binding domain and a second complementary portion of said segregable protein; and

detecting whether the first complementary portion and second complementary portion are brought into proximity.

2. The method of claim 1 wherein the first and second complementary portions of the segregable protein are subunits of a dimer of Raf-1 serine/threonine kinase.

3. The method of claim 1 wherein the first and second complementary portions of the segregable protein are the Raf-1 serine/threonine kinase and the cytoplasmic domain of the human interferon γ

receptor (H.sub.γ

R).

4. The method of claim 1 wherein the first and second complementary portions of the segregable protein are portions of β

-galactosidase.

5. The method of claim 1 wherein the first and second complementary portions of the segregable protein are portions of a transcription activator.

6. The method of claim 1 wherein the target protein is a known receptor and the agent is a member of a library of small molecules.

7. The method of claim 1 wherein the agent is a substance of known biological activity and the target protein is a member of a library of target proteins.

8. The method of claim 1 wherein the target protein is a member of a panel of target proteins.

9. The method of claim 1 wherein the first complementary portion and second complementary portion of the segregable protein are the cytoplasmic domains of a signaling receptor.

10. The method of claim 9 wherein the signaling receptor is a T lymphocyte antigen receptor.

11. A recombinant host cell in vitro modified to contain:

i) a target protein expression unit which comprises a nucleotide sequence encoding a fusion protein comprising a target protein and a first complementary portion of a segregable active protein; and

ii) a ligand binding domain expression unit which comprises a nucleotide sequence encoding a fusion protein comprising a ligand-binding domain and a second complementary portion of said segregable active protein which is modified to contain an agent/ligand complex comprising a small molecule agent to be tested for binding to said target protein coupled to a ligand which binds said proteinaceous ligand-binding domain.

12. The host cell of claim 11 wherein the first complementary portion and second complementary portion are cytoplasmic regions of a signaling receptor.

13. The host cell of claim 11 wherein said ligand is biotin and said ligand binding domain is a biotin binding peptide.

14. The host cell of claim 11, wherein the expression units (i) and (ii) and the agent/ligand complex are introduced into said host cell using a method selected from the group consisting of lipofection, eletroporation, and chemical transformation with lithium acetate.

15. The host cell of claim 11 wherein the expression of said target protein expression unit and said ligand-binding domain expression unit are controlled by constitutive promoters.

16. The host cell of claim 11 which is further modified to contain a detectable marker expression unit which comprises an inducible promoter operably linked to a nucleotide sequence encoding a detectable marker, wherein the expression of said detectable maker is regulated by said inducible promoter responsive to the association of said first and second complementary portions.

17. The host cell of claim 16 wherein the first and second complementary portions are portions of a transcription activator, one of said portions consisting of the DNA binding domain and the second portion consisting of the RNA polymerase activation domain.

18. The host cell of claim 17 wherein said detectable marker is selected from the group consisting of beta-galactosidase, a gene encoding a protein that complements a nutritional auxotrophy, green flourescent protein, and a selectable marker.

19. The host cell of claim 18 wherein said DNA binding domain and RNA polymerase activation domain are subunits of a protein selected from the group consisting of the Gal4, GCN4 and ADR1 proteins.

20. The host cell of claim 11 wherein said host cell is a yeast cell.

21. The host cell of claim 20 wherein said yeast cell contains a mutation that reduces the activity of the MDR pump.

22. The host cell of claim 21 wherein said mutation is the sterile-6 mutation.

23. A population of the host cells of claim 11 wherein said population comprises at least two host cells that express target proteins with different amino acid sequences.

24. The population of claim 23 wherein the target proteins are products of expression of a cDNA library.

25. A method to determine whether a small molecule agent and a target protein interact, said method comprising the steps of:

a) incubating a recombinant host cell in vitro which contains

i) a detectable marker expression unit which comprises an inducible promoter operably linked to a nucleotide sequence encoding a detectable marker, wherein the expression of said detectable maker is regulated by said inducible promoter;

ii) a target protein expression unit which comprises a nucleotide sequence encoding a fusion protein comprising a target protein and a first portion of a transcription activator protein selected from the group consisting of a DNA binding domain and an RNA polymerase activation domain;

iii) a ligand binding domain expression unit which comprises a nucleotide sequence encoding a fusion protein comprising a ligand binding domain and a second portion of a transcription activator protein selected from the group consisting of a DNA binding domain and an RNA polymerase activation domain, whichever is not employed in (ii); and

iv) a small molecule agent/ligand complex wherein said ligand binds to said ligand-binding domain;

under conditions in which said expression units (ii) and (iii) are expressed;

b) detecting whether said detectable marker is expressed; and

c) determining the level of binding of said agent to said target protein by the level of expression of said detectable marker.

26. The method of claim 25 wherein said ligand binding domain is a biotin binding domain and the ligand of said agent/ligand complex is biotin.

27. The method of claim 25 wherein said host cell is a yeast cell.

28. The method of claim 25 wherein the expression units and the test agent/ligand complex are introduced into said host cell using a method selected from the group consisting of lipofection, eletroporation and permeabilization using Penetratin-1.

29. The method of claim 25 wherein the expression units (a)(i), (a)(ii) and (a)(iii) are introduced into said host prior to the introduction of the agent/ligand complex (a)(iv).

30. The method of claim 25 wherein the expression of said target protein expression unit and said ligand-binding domain expression unit are controlled by constitutive promoters.

31. The method of claim 25 wherein said detectable marker is selected from the group consisting of beta-galactosidase, a gene encoding a protein which complements a nutritional auxotrophy, and a selectable marker.

32. The method of claim 25 wherein said DNA binding domain and said RNA polymerase activation domain are subunits of a protein selected from the group consisting of the Gal4, GCN4 and ADR1 proteins.

33. The method of claim 25 wherein the target peptide is a known receptor and the agent is a member of a library of small molecules.

34. The method of claim 25 wherein the agent is a substance of known biological activity and the target protein is a member of a library of target proteins.

35. The method of claim 25 wherein the target protein is a member of a panel of target proteins.

36. The method of claim 27 wherein said yeast contains a mutation that reduces the activity of the MDR pump.

37. The method of claim 31 wherein said mutation is the sterile-6 mutation.