Binding affinity scoring function penalizing compounds which make unfavorable hydrophobic contacts with localized water molecules in the receptor active site

• US 8,510,058 B2
• Filed: 04/04/2011
• Issued: 08/13/2013
• Est. Priority Date: 04/04/2011
• Status: Active Grant

• Current Assignee: Schrodinger, Inc.
• Original Assignee: Schrödinger, LLC (Schrodinger, Inc.)
• Inventors: Friesner, Richard A., Murphy, Robert
• Primary Examiner(s): BORIN, MICHAEL L
• Application Number:
  US13/079,725
• Publication Number:
  US 20120252683A1
• Time in Patent Office: 862 Days
• Field of Search: None
• US Class Current: 702/19
• 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
• CPC Class Codes: G16B 15/30 Drug targeting using structural data; Docking or binding prediction
• CPC Class Codes: G16C 20/50 Molecular design, e.g. of drugs

Abstract

A method of scoring binding affinity of a proposed ligand molecule for a receptor molecule using a computer and computer data bases, which accounts for the increase in energy required where docking disrupts water molecules that are localized at ligand hydration sites. The method uses computer-stored data representing a predicted ligand-receptor structure (preferably one that is validated). The computerized scoring analysis includes determining whether the receptor includes one or more hydration sites occupied by localized water, and, if so, assessing a penalty if docking the ligand into the receptor results in unfavorable interaction of the ligand with a localized water molecule remaining at the receptor hydration site (i.e. after docking).

Claims

1. A method of scoring binding affinity of a proposed ligand molecule for a receptor molecule using a sufficiently programmed computer for the following steps:

a. obtaining computer stored data representing a predicted ligand-receptor structure,

b. determining whether the receptor alone, without a docked ligand, includes one or more hydration sites occupied by localized water, and, if so,

c. determining if after docking a receptor-localized water interacts with a hydrophobic ligand atom, and if the docking of the ligand into the receptor results in unfavorable interaction of the ligand with a localized water molecule occupying a receptor hydration site,

d. determining whether one or more of the exceptions conditions i.-iv. is present;

i. the hydrophobic ligand atom has a net positively charged ligand atom positioned a distance of 4 atoms or fewer from the hydrophobic ligand atom, where the distance is determined by bond connectivity of the atoms in the ligand;

ii. the hydrophobic ligand atom that is part of a ligand —

CH3 group, or a ligand atom within 3 atoms of a —

CH3 group, where the localized water borders the edge of a hydrophobic pocket giving it access to surrounding water;

iii. the localized receptor water is positioned within 5 Å

of a positively charged ligand atom;

iv. the localized receptor water has hydrogen bonds to the ligand;

e. applying a penalty to scoring function of binding affinity if

     1) the localized receptor water interacts with a hydrophobic ligand atom as determined in step c, and

     2) none of the exception conditions i. iv. is present.

2. The method of claim 1 in which the localized receptor hydration sites are determined by computerized sampling of receptor sites for hydration followed by computerized assignment of water occupancies for the various sampled sites.

3. The method of claim 1 comprising using a computer programmed to assess a penalty only if localized water within a hydration site interacts with a hydrophobic ligand atom at a distance of 5 Å

or less.

4. The method of claim 3 comprising using a computer programmed to determine whether exception condition b. i is present and not assessing the penalty if condition b.i. is present.

5. The method of claim 3 in which Cl, Br or both are not considered hydrophobic ligand atoms.

6. The method of claim 3 comprising using a computer programmed to determine whether exception condition b. ii. is present and not assessing the penalty if condition b.ii. is present.

7. The method of claim 1 comprising using a computer programmed to determine whether exception condition b. iii. is present and not assessing the penalty if condition b.iii. is present.

8. The method of claim 1 comprising using a computer programmed to determine whether exception condition b. iv. is present and not assessing the penalty if condition b.iv. is present.

9. The method of claim 1 in which receptor sites with a localized water are determined to be waters that are predicted to have an occupancy in the reference frame of the protein of >

1.5×

the bulk water occupancy.

10. The method of claim 2 in which molecular dynamics simulations are used to determine water occupancy.

11. The method of claim 10 in which an active-site solvation analysis is used to identify localized water sites.

12. The method of claim 1 in which a penalty is applied to the binding affinity score of the ligand when the free energy of displacement of a water molecule from the receptor site into bulk waters is determined to be more favorable than a specified cutoff value.

13. The method of claim 1 in which a penalty is applied to the binding affinity score of the ligand by a method comprising estimating the energetic favorability of the water molecule in the hydration site from the hydrophobicity of the site or from specific interactions with receptor groups.

14. The method of claim 13 in which estimating the energetic favorability of the hydration site includes calculation selected from the group consisting of molecular dynamics simulations, Monte Carlo simulations, exhaustive enumeration of geometries of the water molecule within the site, and optimization (via for example energy minimization) of the position of the water molecule within the site.

15. The method of claim 12 in which the cutoff value is at least 0 kcal/mole.

16. The method of claim 12 in which free energies of displacement of a water molecule from the receptor site into bulk water is determined by molecular dynamics simulation followed by the application of modified inhomogeneous solvation theory to assign displacement free energies.