Deep Learning Structural Models Sufficiently Accurate for Free Energy Calculations? Application of FEP+ to AlphaFold2 Predicted Structures

Abstract

The availability of AlphaFold2 has led to great excitement in the scientific community - particularly among drug hunters - due to the ability of the algorithm to predict protein structures with high accuracy. However, beyond globally accurate protein structure prediction, it remains to be determined whether ligand binding sites are predicted with sufficient accuracy in these structures to be useful in supporting computationally driven drug discovery programs. We explored this question by performing free energy perturbation (FEP) calculations on a set of well-studied protein-ligand complexes, where AlphaFold2 predictions were performed by removing all templates with >30% identity to the target protein from the training set. We observed that in most cases, the {Delta}{Delta}G values for ligand transformations calculated with FEP, using these prospective AlphaFold2 structures, were comparable in accuracy to the corresponding calculations previously carried out using X-ray structures. We conclude that under the right circumstances, AlphaFold2 modeled structures are accurate enough to be used by physics-based methods such as FEP, in typical lead optimization stages of a drug discovery program.