# US 5,703,792 A · Three dimensional measurement of molecular diversity

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- Number: US 5,703,792 A
- Document ID: US5703792A
- Status: Granted
- Kind: A
- Application number: 08/357,580
- Filed: 1994-12-13
- Granted: 1997-12-30
- Earliest claimed: 1993-05-21
- Assignees: Arris Pharmaceutical Corporation
- Inventors: David Chapman
- Web page: https://patentgrep.com/patent/US5703792A

## CPC

- G16B 35/20: Screening of libraries
- 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}
- G16B 35/00: ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
- G16C 20/60: In silico combinatorial chemistry
- G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- C07K: PEPTIDES (peptides in foodstuffs A23; obtaining protein compositions for foodstuffs, working-up proteins for foodstuffs A23J; preparations for medicinal purposes A61K; peptides containing beta-lactam rings C07D; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, C07D; ergot alkaloids of the cyclic peptide type C07D519/02; macromolecular compounds having statistically distributed amino acid units in their molecules, i.e. when the preparation does not provide for a specific; but for a random sequence of the amino acid units, homopolyamides and block copolyamides derived from amino acids C08G69/00; macromolecular products derived from proteins C08H1/00; preparation of glue or gelatine C09H; single cell proteins, enzymes C12N; genetic engineering processes for obtaining peptides C12N15/00; compositions for measuring or testing processes involving enzymes C12Q; investigation or analysis of biological material G01N33/00)
- G16C: COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE

## Abstract

A method and system for selecting molecules or molecular parts for screening. A base set of molecules on which chemical tests are to be performed is defined, and once defined, the base set may be extended by selecting molecules which are determined to maximize the diversity of the extended set. Diversity of a set of molecules is measured by reference to steric, electrostatic, and hydrogen bonding features of the set of 3D conformational shapes which each molecule in the set may take on. Each molecule is assigned a measure of incremental (added) diversity with respect to the base set of molecules on which chemical tests are to be performed. To do this, for each new molecule, a set of conformations is defined, and for each conformation, a measure of dissimilarity from each conformation of those molecules in the base set is defined. The molecule's measure of added diversity is responsive to a closest match between the any conformation of that molecule and any conformation of any molecule already in the base set. This measure of dissimilarity is determined by means of a continuous function minimization technique, such as gradient descent or simulated annealing. The base set may then be extended with the molecule whose measure of added diversity is greatest.

## Claims

### Claim 1

A system for selecting molecules or molecular parts for screening, comprising
a processor having a memory, said memory comprising a candidate universe of molecules and a base set of molecules;
means for directing said processor to define, for each molecule in said candidate universe, a measure of added diversity relative to said base set; and
means for directing said processor to select a molecule from said candidate universe for addition to said base set, responsive to said measure of added diversity.

### Claim 2 (depends on 1)

A system as in claim 1, comprising
a display device coupled to said processor;
means for presenting a description of said selected molecule on said display device;
means for Soliciting input from an operator regarding whether said selected molecule should be added to said base set; and
means for determining, responsive to said input, whether or not to add said selected molecule to said base set.

### Claim 3 (depends on 1)

A system as in claim 1, comprising
means for defining an interconformational diversity of a molecule in said candidate universe.

### Claim 4 (depends on 1)

A system as in claim 1, comprising
means for determining a conformation of a molecule in said memory;
means for directing said processor to determine a measure of dissimilarity between a first conformation and a second conformation;
wherein said measure of added diversity for a first molecule is responsive to said measure of dissimilarity between conformations of said first molecule and conformations of a molecule in said base set.

### Claim 5 (depends on 4)

A system as in claim 4, wherein said means for directing said processor to determine a measure of dissimilarity between a first conformation and a second conformation comprises
means for aligning said first conformation and said second conformation;
means for defining a first selected subset of atoms for said first conformation and a second selected subset of atoms for said second conformation;
means for determining, for each atom in said first selected subset, a smoothed distance from an associated atom in said second selected subset; and
means for defining a combination of said smoothed distances.

### Claim 6 (depends on 5)

A system as in claim 5, wherein said first selected subset and said second selected subset comprise one of: all atoms, uncharged hydrogen donors, uncharged hydrogen acceptors, positively formally charged groups of atoms, negatively formally charged groups of atoms.

### Claim 7 (depends on 5)

A system as in claim 5, wherein said first selected subset and said second selected subset comprise one of: relatively electronegative atoms, relatively large atoms, relatively lipophilic atoms, relatively polarizable groups of atoms.

### Claim 8 (depends on 5)

A system as in claim 5, wherein said means for aligning comprises means for directing said processor to perform a continuous function minimization technique.

### Claim 9 (depends on 4)

A system as in claim 4, wherein said means for directing said processor to determine a measure of dissimilarity between a first conformation and a second conformation is responsive to a measure of non-overlap for selected subsets of atoms for an alignment of said first conformation and said second conformation.

### Claim 10 (depends on 1)

A system as in claim 1, comprising
means for inhibiting said means for directing said processor to select a molecule from said candidate universe for addition to said base set, said means for inhibiting being responsive to at least one of: a measure of size of said base set, said measure of added diversity for said selected molecule, a measure of total diversity for said base set, a measure of computation time expended by said processor.

### Claim 11 (depends on 1)

A system as in claim 1, wherein said base set is a null base set.

### Claim 12 (depends on 1)

A system as in claim 1, wherein said means for directing said processor to define, for each molecule in said candidate universe, a measure of added diversity relative to said base set, is responsive to a statistically selected sample subset of conformations of said each molecule.

### Claim 13 (depends on 1)

A system as in claim 1, wherein said means for directing said processor to select a molecule from said candidate universe for addition to said base set comprises an list of molecules in said candidate universe, sorted by a measure of estimated added diversity relative to said base set.

### Claim 14 (depends on 1)

A system as in claim 1, wherein said means for directing said processor to select a molecule from said candidate universe for addition to said base set is responsive to one of: topological similarity to molecules in the base set, known toxic features of the candidate molecule, interactive approval or disapproval by an operator or coroutine.