Receptor-Ligand Binding Free Energies from a Consecutive Histograms Monte Carlo Sampling Method.

Abstract

To obtain accurate and converged free energy calculations for ligand binding to biomolecular systems requires validated force fields and extensive sampling of the energy landscape, which requires exhaustive and effective conformational searching methods. Herein, we introduce the consecutive histograms Monte Carlo (CHMC) sampling protocol that generates receptor-ligand binding modes within a series of continuously distributed sampling units ranging from placement near the geometric center of the receptor's binding site to fully unbound states. This protocol employs independent energy-state sampling for calculating the ensemble energy within every predefined location along the receptor-ligand dissociation pathway, without the need to traverse the energy barriers as in molecular dynamic simulations during the dissociation procedure. We applied this method to a set of selected receptor targets with their corresponding ligands providing detailed studies of molecular binding free energy predictions. The results show that the CHMC gives an excellent accounting of the free energy surfaces and binding free energies at a reasonable computational cost.