Ka. Rossi et al., APPLICATION OF THE FREE-ENERGY PERTURBATION METHOD TO HUMAN CARBONIC-ANHYDRASE-II INHIBITORS, Journal of medicinal chemistry, 38(12), 1995, pp. 2061-2069
An analysis of the free energy perturbation (FEP) method is presented
that attempts to evaluate the efficacy of the FEP method in the drug d
iscovery process. To accomplish this we have evaluated whether the FEP
technique can accurately predict energetic and structural quantities
relating to the inhibition of human carbonic anhydrase II (HCAII) by s
ulfonamides. Three well-characterized (both structurally and energetic
ally) sulfonamide inhibitors of HCAII were examined in this study, 1a,
1b, and 1c. Results from FEP simulations on these compounds indicate
that the FEP method can predict energetic trends reasonably well; howe
ver, the FEP method was less successful in reproducing detailed struct
ural data. In particular, an expected movement of His-64 when inhibito
r 1c was bound did not occur. We conclude that the FEP method can be u
sed to determine relative free energies of binding but cannot be relie
d upon to reproduce subtle geometric changes.