Unraveling the unbinding pathways of SARS-CoV-2 Papain-like proteinase known inhibitors by Supervised Molecular Dynamics simulation

PLoS One. 2021 May 19;16(5):e0251910. doi: 10.1371/journal.pone.0251910. eCollection 2021.

Abstract

The COVID-19 disease has infected and killed countless people all over the world since its emergence at the end of 2019. No specific therapy for COVID-19 is not currently available, and urgent treatment solutions are needed. Recent studies have found several potential molecular targets, and one of the most critical proteins of the SARS-CoV-2 virus work machine is the Papain-like protease (Plpro). Potential inhibitors are available, and their X-ray crystallographic structures in complex with this enzyme have been determined recently. However, their activities against this enzyme are insufficient and need to be characterized and improved to be of clinical values. Therefore, in this work, by utilizing the Supervised Molecular Dynamics (SuMD) simulation method, we achieved multiple unbinding events of Plpro inhibitors, GRL0617, and its derivates, and captured and understood the details of the unbinding pathway. We found that residues of the BL2 loop, such as Tyr268 and Gln269, play major roles in the unbinding pathways, but the most important contributing factor is the natural movements and behavior of the BL2 loop, which can control the entire process. We believe that the details found in this study can be used to refine and optimize potential inhibitors like GRL0617 and design more efficacious inhibitors as a treatment for the SARS-CoV-2 virus.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antiviral Agents / chemistry
  • Antiviral Agents / pharmacology
  • Binding Sites / drug effects
  • COVID-19 / enzymology
  • COVID-19 Drug Treatment*
  • Coronavirus Papain-Like Proteases / antagonists & inhibitors*
  • Coronavirus Papain-Like Proteases / chemistry
  • Coronavirus Papain-Like Proteases / metabolism
  • Crystallography, X-Ray
  • Humans
  • Molecular Dynamics Simulation
  • Papain / metabolism
  • Protease Inhibitors / chemistry
  • Protease Inhibitors / pharmacology*
  • Protein Binding / drug effects
  • SARS-CoV-2 / drug effects
  • SARS-CoV-2 / enzymology*

Substances

  • Antiviral Agents
  • Protease Inhibitors
  • Coronavirus Papain-Like Proteases
  • Papain

Grants and funding

This investigation was supported by the grant number 99-213-1 from Golestan University, Gorgan, Iran.