Broadening the Scope of Binding Free Energy Calculations Using a Separated Topologies Approach

Binding free energy calculations predict the potencyof compoundsto protein binding sites in a physically rigorous manner and see broadapplication in prioritizing the synthesis of novel drug candidates.Relative binding free energy (RBFE) calculations have emerged as anindustry-standard approach to achieve highly accurate rank-order predictionsof the potency of related compounds; however, this approach requiresthat the ligands share a common scaffold and a common binding mode,restricting the methods' domain of applicability. This is acritical limitation since complex modifications to the ligands, especiallycore hopping, are very common in drug design. Absolute binding freeenergy (ABFE) calculations are an alternate method that can be usedfor ligands that are not congeneric. However, ABFE suffers from aknown problem of long convergence times due to the need to sampleadditional degrees of freedom within each system, such as samplingrearrangements necessary to open and close the binding site. Here,we report on an alternative method for RBFE, called Separated Topologies(SepTop), which overcomes the issues in both of the aforementionedmethods by enabling large scaffold changes between ligands with aconvergence time comparable to traditional RBFE. Instead of only mutatingatoms that vary between two ligands, this approach performs two absolutefree energy calculations at the same time in opposite directions,one for each ligand. Defining the two ligands independently allowsthe comparison of the binding of diverse ligands without the artificialconstraints of identical poses or a suitable atom-atom mapping.This approach also avoids the need to sample the unbound state ofthe protein, making it more efficient than absolute binding free energycalculations. Here, we introduce an implementation of SepTop. We developeda general and efficient protocol for running SepTop, and we demonstratedthe method on four diverse, pharmaceutically relevant systems. Wereport the performance of the method, as well as our practical insightsinto the strengths, weaknesses, and challenges of applying this methodin an industrial drug design setting. We find that the accuracy ofthe approach is sufficiently high to rank order ligands with an accuracycomparable to traditional RBFE calculations while maintaining theadditional flexibility of SepTop.