Evaluation of protein–ligand affinity prediction using steered molecular dynamics simulations

Abstract

In computational drug design, ranking a series of compound analogs in a manner that is consistent with experimental affinities remains a challenge. In this study, we evaluated the prediction of protein–ligand binding affinities using steered molecular dynamics simulations. First, we investigated the appropriate conditions for accurate predictions in these simulations. A conic harmonic restraint was applied to the system for efficient sampling of work values on the ligand unbinding pathway. We found that pulling velocity significantly influenced affinity predictions, but that the number of collectable trajectories was less influential. We identified the appropriate pulling velocity and collectable trajectories for binding affinity predictions as 1.25 Å/ns and 100, respectively, and these parameters were used to evaluate three target proteins (FK506 binding protein, trypsin, and cyclin-dependent kinase 2). For these proteins using our parameters, the accuracy of affinity prediction was higher and more stable when Jarzynski’s equality was employed compared with the second-order cumulant expansion equation of Jarzynski’s equality. Our results showed that steered molecular dynamics simulations are effective for predicting the rank order of ligands; thus, they are a potential tool for compound selection in hit-to-lead and lead optimization processes.

Keywords:

• protein–ligand interaction
• steered molecular dynamics simulation
• binding affinity
• lead optimization
• drug design

Acknowledgments

The calculations were performed in part on the RIKEN Integrated Cluster of Clusters (RICC) and the HOKUSAI Great Wave system. We are thankful to Dr. T. S. Komatsu and Dr. G. Morimoto for his comments on these results.