Lipid probes and uses thereof

Patent metadata

Field	Value
Publication number	US-10859585-B2
Application number	US-201816235096-A
Country	US
Kind code	B2
Filing date	Dec 28, 2018
Priority date	Mar 27, 2015
Publication date	Dec 8, 2020
Grant date	Dec 8, 2020

Abstract

Disclosed herein are methods, compositions, probes, assays and kits for identifying a lipid binding protein as a drug binding target. Also disclosed herein are methods, compositions, and probes for mapping a ligand binding site on a lipid binding protein, identification of lipid binding proteins, generating drug-lipid binding protein profiles, high throughput drug screening, and identification of drugs as potential lipid binding protein ligands.

First claim

What is claimed is:

1. A process of generating a lipid probe-protein composition, comprising:
contacting a sample comprising a protein with a lipid probe; and
treating the sample and the lipid probe by a photoreactive means to generate the lipid probe-protein composition, wherein the treating time is from about 5 minutes to about 1 hour; and
wherein the lipid probe is a lipid probe of Formula (I):

wherein:
A is C 16 -C 20 alkyl or C 16 -C 20 alkenyl;
D is —NH 2 , —NHR 7 , or —OR 8 ;
R 7 is C 1 -C 4 alkyl, (C 1 -C 5 alkyl)OH, or (C 1 -C 5 )SO 3 M;
R 8 is (CH 2 OH)n;
M is monovalent or divalent cation;
n is 1, 2, or 3;

PG is a photoreactive group; and
AH is an affinity handle; and

wherein PG is attached to A or D and AH is attached to A or D.

2. The process of claim 1 , wherein the treating time is about 10 minutes.

3. The process of claim 1 , wherein the photoreactive group comprises azides, benzophenone, diazo compounds, diazirines, diazonium salts, or diaryl ketones.

4. The process of claim 1 , wherein the affinity handle comprises a carbodiimide, N-hydroxysuccinimide (NHS) ester, imidoester, pentafluorophenyl ester, hydroxymethyl phosphine, maleimide, haloacetyl, pyridyl disulfide, thiosulfonate, vinylsulfone, hydrazide, alkoxyamine, alkyne, azide, or isocyanate group.

5. The process of claim 1 , wherein the protein is an enzyme, a transporter, a receptor, an adaptor, a channel protein, or a chaperone.

6. The process of claim 1 , wherein the protein is encoded by a gene of Table 3, a protein encoded by a gene of Table 4, or a protein encoded by a gene of Table 5.

7. The process of claim 1 , wherein the photoreactive means comprises ultraviolet light.

8. The process of claim 1 , wherein the treating occurs at a temperature of from about 0° C. to about 40° C.

9. The process of claim 1 , wherein the treating occurs at a temperature of about 4° C.

10. A lipid probe-protein composition generated by the process of claim 2 .

11. A process of generating a lipid probe-protein composition, comprising:
contacting a sample comprising a protein with a lipid probe, wherein the lipid probe is selected from lipid probes 1, 3-10, 12-15, 17-21 and 23 of Table 1; and
treating the sample and the lipid probe by a photoreactive means to generate the lipid probe-protein composition, wherein the treating time is from about 5 minutes to about 1 hour.

12. The process of claim 11 , wherein the treating time is about 10 minutes.

13. The process of claim 11 , wherein the photoreactive group comprises azides, benzophenone, diazo compounds, diazirines, diazonium salts, or diaryl ketones.

14. The process of claim 11 , wherein the affinity handle comprises a carbodiimide, N-hydroxysuccinimide (NHS) ester, imidoester, pentafluorophenyl ester, hydroxymethyl phosphine, maleimide, haloacetyl, pyridyl disulfide, thiosulfonate, vinylsulfone, hydrazide, alkoxyamine, alkyne, azide, or isocyanate group.

15. The process of claim 11 , wherein the protein is an enzyme, a transporter, a receptor, an adaptor, a channel protein, or a chaperone.

16. The process of claim 11 , wherein the protein is encoded by a gene of Table 3, a protein encoded by a gene of Table 4, or a protein encoded by a gene of Table 5.

17. The process of claim 11 , wherein the photoreactive means comprises ultraviolet light.

18. The process of claim 11 , wherein the treating occurs at a temperature of from about 0° C. to about 40° C.

19. The process of claim 11 , wherein the treating occurs at a temperature of about 4° C.

20. A lipid probe-protein composition generated by the process of claim 11 .

Assignees

• Scripps Research Inst

Inventors

• Cravatt Benjamin F
• Niphakis Micah J
• Lum Kenneth
• Correia Bruno
• Cognetta Armand
• Hulce Jonathan

Classifications

• G01N2500/04

  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 title

• G01N33/92 Primary

  involving lipids, e.g. cholesterol {, lipoproteins, or their receptors (steroid hormones G01N33/743)} · CPC title

• G01N33/6842

  Proteomic analysis of subsets of protein mixtures with reduced complexity, e.g. membrane proteins, phosphoproteins, organelle proteins · CPC title

• G01N2570/00

  Omics, e.g. proteomics, glycomics or lipidomics; Methods of analysis focusing on the entire complement of classes of biological molecules or subsets thereof, i.e. focusing on proteomes, glycomes or lipidomes · CPC title