Lawn assay for compounds that affect enzyme activity or bind to target molecules

• US 5,856,083 A
• Filed: 11/03/1995
• Issued: 01/05/1999
• Est. Priority Date: 05/06/1994
• Status: Expired due to Fees

• Current Assignee: Pharmacopeia LLC (Ligand Pharmaceuticals, Inc.)
• Original Assignee: Pharmacopeia, Inc.
• Inventors: Chelsky, Daniel, Burbaum, Jonathan J.
• Primary Examiner(s): DUFFY, PATRICIA ANN
• Application Number:
  US08/553,056
• Time in Patent Office: 1,159 Days
• Field of Search: 435/4, 435/6, 435/7.1, 435/7.2, 435/7.21, 435/7.8, 435/174, 435/176, 435/177, 435/178, 435/968, 435/969, 435/182, 435/7.7, 436/518, 436/524, 436/528, 436/537, 436/164, 436/169, 436/170, 436/172, 436/529, 436/535
• US Class Current: 435/4
• CPC Class Codes: C07B 2200/11 Compounds covalently bound to a solid support
• CPC Class Codes: C07C 205/59 the carbon skeleton being further substituted by singly-bound oxygen atoms
• CPC Class Codes: C07D 311/08 not hydrogenated in the hetero ring
• CPC Class Codes: C07D 311/22 with oxygen or sulfur atoms directly attached in position 4
• CPC Class Codes: C07D 311/96 spiro-condensed with carbocyclic rings or ring systems
• CPC Class Codes: C07D 491/10 Spiro-condensed systems
• CPC Class Codes: C07D 493/10 Spiro-condensed systems
• CPC Class Codes: C07D 495/10 Spiro-condensed systems
• CPC Class Codes: C12Q 1/00 Measuring or testing processes involving enzymes, nucleic acids or microorganisms measuring or testing apparatus with condition measuring or sensing means, e.g. colony counters, C12M1/34; Compositions therefor; Processes of preparing such compositions
• CPC Class Codes: C40B 40/00 Libraries per se, e.g. arrays, mixtures
• CPC Class Codes: G01N 33/573 for enzymes or isoenzymes

Abstract

A lawn assay is described for determining compounds that affect enzyme activity or that bind to target molecules. Compounds to be screened are cleaved, and diffused from solid supports into a colloidal matrix. Enzymatic catalysis or binding to target molecules by the compounds is carried out in the matrix. Active compounds are found by monitoring a photometrically detectable change in a substrate, coenzyme, or cofactor involved in the enzymatic reaction, or in a labeled ligand bound to the target molecule, that produces a zone of activity associated with the compounds.

Claims

1. A lawn assay for identifying compounds that affect an enzymatic reaction, said assay comprising the steps of:

a) providing an enzyme;

b) further providing a substrate for the enzyme and optionally a coenzyme for said enzyme;

c) providing a plurality of solid supports, wherein each support comprises multiple copies of a compound attached thereto by a cleavable linker, said compound to be screened for its effect on said enzymatic reaction;

d) contacting said solid supports with a first colloidal matrix and cleaving at least a portion of said multiple copies from said supports, either before or after said contacting, so that said compound diffuses into said matrix;

e) carrying out said enzymatic reaction; and

f) monitoring a photometrically detectable change in said substrate, or said coenzyme to determine a zone of activity in said matrix associated with one or more of said supports to idientify one or more compounds that affect said enzymatic reaction, wherein said enzyme is dispersed in said first colloidal matrix, and wherein said substrate is dispersed in a second colloidal matrix, and optionally wherein said coenzyme is dispersed in said first or second matrix, and wherein said step of carrying out said enzymatic reaction comprises, following said step of contacting said solid supports to said first colloidal matrix, and following said cleaving of at least a portion of said multiple copies from said solid supports, contacting said second matrix with said first matrix to allow said substrate to diffuse into said first colloidal matrix.

2. The lawn assay of claim 1 comprising an assay for an enzyme inhibitor.

3. The lawn assay of claim 1 wherein said substrate is selected from the group consisting of a fluorogenic substrate and a fluorescent substrate.

4. The lawn assay of claim 1 wherein said step of contacting comprises embedding said solid supports in said colloidal matrix.

5. The lawn assay of claim 4 wherein said cleaving occurs after said supports are embedded in said colloidal matrix.

6. The lawn assay of claim 1 wherein said cleavable linker is photocleavable, and said cleaving is carried out by exposure to UV light.

7. The lawn assay of claim 1 comprising cleaving said compounds from said supports prior to said step of contacting said solid supports with said first matrix.

8. The lawn assay of claim 1 wherein said solid supports comprise a library of compounds to be screened.

9. A lawn assay for identifying compounds that affect an enzymatic reaction said assay comprising the steps of:

a) providing an enzyme, and a coenzyme for said enzyme;

b) further providing a substrate for the enzyme;

c) providing a plurality of solid supports, wherein each individual support has multiple copies of a compound attached thereto by a cleavable linker, said compound to be screened for its effect on said enzymatic reaction;

d) contacting said solid supports with a first colloidal matrix and cleaving at least a portion of said multiple copies from said supports, either before or after said contacting, so that said copies of said compound diffuses into said matrix;

e) carrying out said enzymatic reaction; and

f) photometrically determining a change in absorbance in said coenzyme that results from said enzymatic reaction to determine a zone of activity in said matrix associated with one or more of said supports to identify one or more compounds that affect said enzymatic reaction.

10. A lawn assay according to claim 9 wherein said coenzyme is selected from the group consisting of NADP, NADPH, NAD, and NADH.

11. A lawn assay for identifying compounds that affect enzymatic activity comprising the steps of:

a) providing a first colloidal matrix containing an enzyme and a plurality of solid supports, said solid supports comprising a library of compounds to be screened for their affect on said enzyme'"'"'s activity, each of said supports having multiple copies of one of said compounds attached thereto through a cleavable linker;

b) providing a substrate for said enzyme and optionally a coenzyme for said enzyme;

c) cleaving at least a portion of said compounds from the solid supports;

d) contacting said substrate with said matrix; and

e) carrying out said enzymatic reaction and observing a detectable signal from said substrate, from a reaction product, or from said coenzyme involved in said reaction to determine one or more zones of activity caused by an effect on said enzyme activity by one or more of said compounds to identify one or more compounds that affect said enzymatic reaction;

wherein said substrate is dispersed in a second matrix, wherein step d) comprises contacting said second matrix with said first matrix to allow said substrate to diffuse into said first matrix.

12. The lawn assay of claim 11 comprising an assay for an enzyme inhibitor.

13. The lawn assay of claim 12 wherein said cleavable linker is photocleavable, and said cleaving is carried out by exposure to UV light.

14. The lawn assay of claim 13 wherein said substrate is selected from the group consisting of a fluorogenic substrate and a fluorescent substrate.

15. The lawn assay of claim 13 which comprises determining a change in absorbency in said coenzyme.

16. The lawn assay according to claim 15 wherein said coenzyme is selected from the group consisting of NADP, NADPH, NAD, and NADH.

17. The lawn assay of claim 11 wherein said activity is affected by inhibition of an interaction between a protein which inhibits said enzyme activity and said enzyme, further wherein said protein is contacted with said enzyme to inhibit said enzymatic reaction.

18. The method of claim 11 wherein said colloidal matrix is selected from the group consisting of silica gel, agar, agarose, pectin, polyacrylamide, gelatin, starch, gellan gum and cross-linked dextran.

19. The method of claim 18 wherein said colloidal matrix is low melting agarose in an amount of from 0.5-2.0%, wt/vol.

20. A lawn assay for identifying compounds that are enzyme inhibitors comprising:

a) providing a first layer which is a colloidal matrix containing enzyme, which matrix has embedded therein a mono-layer of solid supports, wherein each individual support has a compound attached through a photocleavable linker, said compound to be screened for inhibitory activity;

b) providing a second layer which is a colloidal matrix and which contains a substrate that can be monitored photometrically during its enzymatic conversion to product;

c) cleaving the linker to release said compound by exposure to UV light;

d) contacting said first layer with said second layer; and

e) detecting zones of inhibition of enzymatic activity in said first layer produced thereby to identify one or more compounds that are enzyme inhibitors.

21. The lawn assay of claim 20 wherein said solid supports are selected from the group consisting of beads, pellets, disks, fibers, and gels.

22. The lawn assay of claim 20 wherein said solid supports are polystyrene beads.