Computational method for designing chemical structures having common functional characteristics

• US 6,219,622 B1
• Filed: 12/16/1997
• Issued: 04/17/2001
• Est. Priority Date: 03/24/1995
• Status: Expired due to Fees

• Current Assignee: University of Guelph
• Original Assignee: University of Guelph
• Inventors: Schmidt, Jonathan M.
• Primary Examiner(s): Horlick, Kenneth R.
• Assistant Examiner(s): Siew, Jeffrey
• Application Number:
  US08/991,430
• Time in Patent Office: 1,218 Days
• Field of Search: 364/496, 364/497, 364/498, 364/499, 364/512, 364/527, 364/550, 435/6, 435/7.1, 536/22.1, 536/23.1, 530/300, 530/388.9, 702/27
• US Class Current: 702/27
• CPC Class Codes: C07K 1/00 General methods for the preparation of peptides , i.e. processes for the organic chemical preparation of peptides or proteins of any length
• CPC Class Codes: G16B 15/00 ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment

Abstract

The present invention related to computational methods for designing chemical structures sharing common, useful, functional properties based on specific combinations of steric configuration and binding affinity. More particularly the present invention provides a method for producing computer-simulated receptors which functionally mimic biological receptors. The simulated receptors are designed to exhibit optimized selective affinity for known target molecules. Chemical structures are then generated and evolved to exhibit selective affinity for the simulated receptors.

Claims

1. A computer implemented method of designing chemical structures having at least one preselected functional characteristic, comprising the steps of:

(a) providing a population of receptors having a preselected fitness coefficient for a set of target molecules sharing at least one quantifiable functional characteristic;

(b) providing a simulated model of a chemical structure, calculating an affinity between the chemical structure and each receptor in a plurality of orientations using an affinity calculation, using the calculated affinity to calculate an affinity fitness score;

(c) altering the chemical structure to produce a variant of the chemical structure and repeating step (b); and

(d) retaining and further altering those variants of the chemical structure whose affinity score is greater than or equal to a preselected affinity score.

2. The method according to claim 1 wherein said affinity calculation includes at least two measures, the first being a proximity measure wherein the proportion of uncharged portions on said simulated receptors being sufficiently close to non-polar regions on said molecular structure to generate effective London dispersion forces is estimated, and the second being the summed strengths of charge-dipole electrostatic force interactions generated between charged portions of said simulated receptor and dipoles present in said molecular structure.

3. The method according to claim 1 wherein said step of calculating the affinity fitness score includes calculating a sum and maximal affinity between the molecular structure and each receptor, the fitness score being calculated as:

Σ

{|calculated maximal affinity −

target maximal affinity|/target maximal affinity}.

4. The method according to claim 1 wherein said step of calculating the affinity fitness score includes calculating a sum and maximal affinity between the molecular structure and each receptor, the fitness score being calculated as:

Σ

{|calculated maximal affinity −

target maximal affinity|/2×

target maximal affinity)+(|calculated sum affinity-target sum affinity|/2×

target sum affinity)}.

5. The method according to claim 1 wherein said functional characteristic is biological toxicity.

6. The method according to claim 1 wherein said functional characteristic is catalytic activity.

7. The method according to claim 1 wherein a representation of each computationally designed chemical structure having a preselected affinity score is output.

8. The method according to claim 1 wherein a representation of said variants whose affinity score is greater than or equal to said preselected affinity score is output.

9. The method according to claim 3 or 4 wherein the preselected fitness score is zero.