Binding and Unbinding Pathways of Peptide Substrates on the SARS-CoV-2 3CL Protease

Abstract

Based on many crystal structures of ligand complexes, much study has been devoted to understanding the molecular recognition of SARS-CoV-2 3C-like protease (3CL pro ), a potent drug target for COVID-19. In this research, to extend this present static view, we examined the kinetic process of binding/ unbinding of an eight-residue substrate peptide to/from 3CL pro by evaluating the path ensemble with the weighted ensemble simulation. The path ensemble showed the mechanism of how a highly flexible peptide folded into the bound form. At the early stage, the dominant motion was the diffusion on the protein surface showing a broad distribution, whose center was led into the cleft of the chymotrypsin fold. We observed a definite sequential formation of the hydrogen bonds at the later stage occurring in the cleft, initiated between Glu166 (3CL pro ) and P3_Val (peptide), followed by binding to the oxyanion hole and completed by the sequencespecific recognition at P1_Gln.

Revolutionizing peptide‐based drug discovery: Advances in the post‐AlphaFold era

“…In those instances, it would be preferable to carry out simulations that are unbiased. Techniques such as Weighted Ensemble (WE) methods, [91][92][93][94] adaptive sampling 95 and Markov State Models, 96,97 or milestoning 98 are ideal for starting multiple independent simulations within a framework that allows to reconstruct the ensemble generated from the individual trajectories. These methods allow to obtain rates well beyond what would be possible to simulate directly-for example the use of MSMs to study of the PMI peptide to MDM2-PMI predicted association rates beyond the seconds timescale.…”