Core Flipping in Lead Optimization: Rank Ordering using Multisite λ Dynamics

In structure-based drug discovery, reliable structural models of ligands bound to their target receptor are critical for establishing the structure activity relationship of congeneric series. In such a series, substitutions on a common scaffold core might lead to different binding modes, ranging from slight changes of orientations to flipping or inversion of the core structure. Moreover, molecular docking might lead to alternative orientations within the top ranked poses without being able to discriminate which is the most likely. To determine the relative binding affinities between two alternative ligand poses, we propose a methodology based on relative binding free energy calculations using the multisite λ dynamics method. We use a dual-topology approach with distance restraining schemes. We introduced a novel strategy using one-step perturbation to calculate the contributions of the applied restraints. While using FEP/MBAR instead for that purpose led to smaller uncertainties it suffered from convergence issues. We test the validity and predictive power of our approach using two pharmaceutically relevant targets and eight compounds from experimentally characterized congeneric series. For each target, our approach correctly ranks the known X-ray poses to be more favorable than alternative flipped poses. The proposed methodology can be easily extended to rank more than two poses in a single simulation and should also be applicable for the prediction of conformational binding cliffs, ranking fragments, core hopping cases and evaluating different scaffold binding to a common target.