Ensemble-Based Replica Exchange Alchemical Free Energy Methods: The Effect of Protein Mutations on Inhibitor Binding

The accurate prediction of the binding
affinity changes of drugs
caused by protein mutations is a major goal in clinical personalized
medicine. We have developed an ensemble-based free energy approach
called thermodynamic integration with enhanced sampling (TIES), which
yields accurate, precise, and reproducible binding affinities. TIES
has been shown to perform well for predictions of free energy differences
of congeneric ligands to a wide range of target proteins. We have
recently introduced variants of TIES, which incorporate the enhanced
sampling technique REST2 (replica exchange with solute tempering)
and the free energy estimator MBAR (Bennett acceptance ratio). Here
we further extend the TIES methodology to study relative binding affinities
caused by protein mutations when bound to a ligand, a variant which
we call TIES-PM. We apply TIES-PM to fibroblast growth factor receptor
3 (FGFR3) to investigate binding free energy changes upon protein
mutations. The results show that TIES-PM with REST2 successfully captures
a large conformational change and generates correct free energy differences
caused by a gatekeeper mutation located in the binding pocket. Simulations
without REST2 fail to overcome the energy barrier between the conformations,
and hence the results are highly sensitive to the initial structures.
We also discuss situations where REST2 does not improve the accuracy
of predictions.