Accurate calculation of absolute protein-ligand binding free energies

In the hit identification stage of drug discovery, a diverse chemical space needs to be explored to identify initial hits. Contrary to empirical scoring functions, absolute protein-ligand binding free energy perturbation (AB-FEP) provides a theoretically more rigorous and accurate description of protein ligand binding thermodynamics and could in principle greatly improve the hit rates in virtual screening. In this work, we describe an implementation of an accurate and reliable AB-FEP method in FEP+. We validated the AB-FEP method on eight congeneric compound series binding to eight protein receptors including both neutral and charged ligands. For ligands with net charges, the alchemical ion approach was adopted to avoid artifacts in electrostatic potential energy calculations. The calculated binding free energies were highly correlated with experimental results with the weighted average of R-square of 0.55 for the entire dataset and an overall RMSE of 1.1 kcal/mol when protein reorganization effect upon ligand binding was accounted for. Through AB-FEP calculations using apo versus holo protein structures, we demonstrated that the protein conformational and protonation state changes between the apo and holo proteins are the main physical factors contributing to the protein reorganization free energy manifested by the overestimation of raw AB-FEP calculated binding free energies using the holo structures of the proteins. The highly accurate AB-FEP results demonstrated in this work position it as a useful tool to improve the hit rates in virtual screening, thus facilitate hit discovery.