Molecular dynamics (MD) simulations are often considered to be the most rigorous tool available to computational drug discovery. However, there are many subjective choices made by the researcher before each such simulation, thereby impacting the reproducibility of this method. These include: choice of initial coordinates, protonation states and tautomers, cut-off distances, thermostats/barostats and their parameters, constraint algorithms and many others. Recent literature has probed the robustness of MD simulations with respect to many of these choices but large-scale investigations are needed to determine the variance introduced by each of these parameters. In order to perform such a large-scale study, an automated system preparation tool is essential, and in this work we make an extensive use of ProtoCaller, an automatable structure preparation tool in Python. In this presentation we will focus on relative protein-ligand binding free energy calculations and we will investigate the effects of the initial protein crystal structure on the calculated binding free energies. Our study spans twenty-six different ligand-ligand perturbations across three different protein systems with eight crystal structures for each system. We also measure the effect of extended equilibration on these results and compare the variance between repeats on the same crystal structure and simulations using different crystal structures, totalling more than 1200 free energy calculations. The second part of the presentation will consider the impact of side-chain protonation states on binding free energies. Although these can in many cases be reliably predicted either by automated packages or human intuition, this choice is often not obvious and we will investigate the most ambiguous case: the protonation states and rotamers of various histidine residues at different proximities to the binding site. We will conclude by relating the two studies, and discussing the optimal simulation protocol, as well as the risks of false convergence.

Determining the impact of the initial crystal structure and protonation states on binding free energies: A high-throughput study

ACS Spring Meeting 2021

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.