On Free Energy Calculations in Drug Discovery

This Account discusses recent progress and challenges in binding free energy computations, focusing on two classes of enhanced sampling techniques: alchemical transformations and path-based methods. Binding free energy is a crucial metric in drug discovery, as it measures the affinity of a ligand for its target receptor. Free energy and affinity guide the ranking and selection of potential drug candidates. The theoretical foundations of free energy calculations were established several decades ago, but their efficient application to drug-target binding remains a grand challenge in computational drug design. The main obstacles stem from sampling issues (as binding is a rare event), force field accuracy limitations, and simulation convergence. Alchemical transformations are now the most used methods for computing binding free energies in the pharmaceutical industry. However, while they efficiently calculate energy differences, the application of these methods is often limited to relative binding free energy calculations. Absolute and accurate (error < 1 kcal/mol) binding free energy predictions remain one of the great challenges for computational chemists and physicists. Another limitation of alchemical methods is that they lack the ability to provide mechanistic or kinetic insights into the binding process, crucial for optimizing lead compounds and designing novel therapies. Path-based methods offer, in principle, the possibility to accurately estimate absolute binding free energy while also providing insights into binding pathways and interactions.