A nonequilibrium alchemical method for drug-receptor absolute binding free energy calculations: the role of restraints

In this paper we further develop a combined Hamiltonian replica exchange / non-equilibrium alchemical method for absolute binding free energies and test its performance on 11 ligands of the BRD4 bromodomain protein. We compare the results obtained with our approach with those obtained with other equilibrium and non-equilibrium alchemical methods showing their relative strengths, weaknesses, and limits. We show how using an enhanced sampling technique, before the alchemical transformations, allows to get accurate estimates of the binding free energies even when starting with sub-optimal initial binding poses (e.g. from docking). We also study the effect of different restraining mechanisms on the final result, and introduce a new "Loose-Tight" restraining algorithm. The method proves to strike a good balance between ease of use, automation, speed, and accuracy for absolute ligand binding free energy calculations and our scripts make it easy to integrate it into pre-existing computational drug discovery pipelines.