Analyses of activity for factor Xa inhibitors based on Monte Carlo simulations

J Med Chem. 2003 Dec 18;46(26):5691-9. doi: 10.1021/jm030288d.

Abstract

Monte Carlo/Extended Linear Response (MC/ELR) simulations have been conducted on 60 inhibitors of human factor Xa to determine the important interactions associated with their activity. A variety of physicochemical descriptors were configurationally averaged during the course of the simulations of each inhibitor bound to factor Xa and free in water. A regression equation was then derived; it reproduces the experimental inhibition data with a correlation coefficient, r(2), of 0.74, an rms error of 0.67 kcal/mol, and an average unsigned error of 0.60 kcal/mol using only two physically reasonable descriptors. The two factors that emerged as important in determining inhibitory potential are (1) favorable van der Waals interactions between protein and ligand and (2) direct hydrogen bonding between the inhibitor and protein. The conclusions were supported with structural analyses and results of MC/free energy perturbation (FEP) calculations.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Binding Sites
  • Factor Xa / chemistry*
  • Factor Xa Inhibitors
  • Humans
  • Hydrogen Bonding
  • Ligands
  • Models, Molecular
  • Monte Carlo Method
  • Protease Inhibitors / chemistry*
  • Pyridines / chemistry
  • Quantitative Structure-Activity Relationship
  • Regression Analysis
  • Thermodynamics

Substances

  • Factor Xa Inhibitors
  • Ligands
  • Protease Inhibitors
  • Pyridines
  • Factor Xa