A Relative Binding Free Energy Framework for Structurally Dissimilar Molecules

Relative binding free energy (RBFE) calculations, widely used to predict the potencies of congeneric small molecules binding to a protein receptor, can greatly increase the efficiency of the hit-to-lead and lead optimization stages of the drug discovery process. Traditional RBFE methods, however, cannot be easily applied to small molecules lacking a common core or binding mode, precluding their use in a challenging but crucial component of many drug discovery campaigns. In principle, an absolute binding free energy (ABFE) method can be applied to such molecules, but ABFE often suffers from high computational cost and poor statistical convergence due to the large amount of additional sampling required when compared to RBFE. Here, we introduce core-hopping binding free energy (CBFE) calculations, a computationally efficient framework for the accurate determination of relative binding free energies between small molecules with different cores, leveraging several recently developed techniques such as Alchemical Enhanced Sampling (ACES) with optimized transformation pathways and flexible λ-spacing, as well as λ-dependent Boresch restraints. We benchmark the performance of CBFE across 4 protein systems consisting of 56 small molecules, and find that the results are consistent with RBFE for a congeneric series of ligands and offer considerable improvement in computational cost and precision relative to ABFE results for a series of small molecules with diverse cores and binding modes. All CBFE-related developments are fully implemented in the GPU-accelerated AMBER free energy module (pmemd.cuda) and are available as part of the latest official AMBER release.