Virtual reality sampled pathways guide free energy calculation of protein-ligand binding

We describe a novel two-step approach for combining cloud-mounted interactive molecular dynamics in virtual reality (iMD-VR) with free energy sampling (FES) approaches to quantitatively explore the dynamics of biological processes at the molecular level. The combined approach we refer to as the iMD-VR-FES protocol. Stage one involves using a state-of-the-art iMD-VR framework to quickly sample a diverse range of protein-ligand unbinding pathways, benefitting from the sophistication of human spatial and chemical intuition. Stage two involves using the iMD-VR-sampled pathways as initial guesses for defining a path-based reaction coordinate from which we can obtain a corresponding free energy profile using FES methods. To investigate the performance of the method, we apply iMR-VR-FES to investigate the unbinding of a benzamidine ligand from a trypsin protein. Unbinding free energies calculated using iMD-VR-FES show good internal consistency, and broadly agree with previous literature values. Moreover, the resulting free energy profiles can distinguish energetic differences corresponding to various protein-ligand conformations (e.g., helping to identifying favorable vs. unfavorable pathways) and also enable identification of metastable states along the unbinding pathways. The two-step iMD-VR-FES approach offers an intuitive way for researchers to test various hypotheses of dynamical and conformational change, in order to quickly obtain both qualitative and quantitative insight.