A Method for Treating\nSignificant Conformational Changes\nin Alchemical Free Energy Simulations of Protein–Ligand Binding

Relative binding free energy (RBFE) simulation is a rigorous\napproach\nto the calculation of quantitatively accurate binding free energy\nvalues for protein–ligand binding in which a reference binder\nis gradually converted to a target binder through alchemical transformation\nduring the simulation. The success of such simulations relies on being\nable to accurately sample the correct conformational phase space for\neach alchemical state; however, this becomes a challenge when a significant\nconformation change occurs between the reference and target binder–receptor\ncomplexes. Increasing the simulation time and using enhanced sampling\nmethods can be helpful, but effects can be limited, especially when\nthe free energy barrier between conformations is high or when the\ncorrect target complex conformation is difficult to find and maintain.\nCurrent RBFE protocols seed the reference complex structure into every\nalchemical window of the simulation. In our study, we describe an\nimproved protocol in which the reference structure is seeded into\nthe first half of the alchemical windows, and the target structure\nis seeded into the second half of the alchemical windows. By applying\ninformation about the relevant correct end point conformations to\ndifferent simulation windows from the beginning, the need for large\nbarrier crossings or simulation prediction of the correct structures\nduring an alchemical simulation is in many cases obviated. In the\ndiverse cases we examine below, the simulations yielded free energy\npredictions that are satisfactory as compared to experiment and superior\nto running the simulations utilizing the conventional protocol. The\nmethod is straightforward to implement for publicly available FEP\nworkflows.