Estimation of binding free energies for HIV proteinase inhibitors by molecular dynamics simulations

Absolute binding free energies for three inhibitors of HIV-1 proteinase were estimated from molecular dynamics simulations by a recently reported linear approximation procedure. The results were in fairly good agreement with experimental binding data. Two of the inhibitors were very similar and, for comparison, their relative free energies of binding were also calculated by free energy perturbation methods, giving virtually the same result. Effects of cut-off radii and charge states of the protein model were examined. The effects of pH on binding of one of the inhibitors were predicted.