Analyses of activity for factor Xa inhibitors based on Monte Carlo simulations.
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.
Ostrovsky
Dennis
D
Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA.
Udier-Blagović
Marina
M
Jorgensen
William L
WL
D001665:Binding Sites; D015951:Factor Xa / Q000737:chemistry*; D065427:Factor Xa Inhibitors; D006801:Humans; D006860:Hydrogen Bonding; D008024:Ligands; D008958:Models, Molecular; D009010:Monte Carlo Method; D011480:Protease Inhibitors / Q000737:chemistry*; D011725:Pyridines / Q000737:chemistry; D021281:Quantitative Structure-Activity Relationship; D012044:Regression Analysis; D013816:Thermodynamics
D065427:Factor Xa Inhibitors; D008024:Ligands; D011480:Protease Inhibitors; D011725:Pyridines; D015951:Factor Xa