Is Ring Breaking Feasible in Relative Binding Free Energy Calculations?

Our interest is relative binding free energy (RBFE) Calculations based on molecular k simulations. These are promising tools for lead optimization in drug discovery, computing changes in binding free energy due to modifications of a lead compound. However, in the alchemical' framework for RUE calculations, sorbe types of mutations have the potential to introduce error into the computed binding free energies. Here we explore the magninide of this error in several different model binding calculations. We find that some of the calculations involving ring breaking have significant errors, and these errors are especially large in bridged ring systems. Since the error is a function of ligand strain, which is impredictablein advance, we believe that ring breaking should be avoided when possible.