Rational approach toward COVID-19 main protease inhibitors via molecular docking, molecular dynamics simulation and free energy calculation

Sci Rep. 2020 Oct 19;10(1):17716. doi: 10.1038/s41598-020-74468-0.

Abstract

In the rapidly evolving coronavirus disease (COVID-19) pandemic, repurposing existing drugs and evaluating commercially available inhibitors against druggable targets of the virus could be an effective strategy to accelerate the drug discovery process. The 3C-Like proteinase (3CLpro) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been identified as an important drug target due to its role in viral replication. The lack of a potent 3CLpro inhibitor and the availability of the X-ray crystal structure of 3CLpro (PDB-ID 6LU7) motivated us to perform computational studies to identify commercially available potential inhibitors. A combination of modeling studies was performed to identify potential 3CLpro inhibitors from the protease inhibitor database MEROPS ( https://www.ebi.ac.uk/merops/index.shtml ). Binding energy evaluation identified key residues for inhibitor design. We found 15 potential 3CLpro inhibitors with higher binding affinity than that of an α-ketoamide inhibitor determined via X-ray structure. Among them, saquinavir and three other investigational drugs aclarubicin, TMC-310911, and faldaprevir could be suggested as potential 3CLpro inhibitors. We recommend further experimental investigation of these compounds.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aclarubicin / chemistry
  • Aclarubicin / metabolism
  • Aminoisobutyric Acids
  • Betacoronavirus / enzymology*
  • Betacoronavirus / isolation & purification
  • Binding Sites
  • COVID-19
  • Coronavirus 3C Proteases
  • Coronavirus Infections / pathology
  • Coronavirus Infections / virology
  • Cysteine Endopeptidases / metabolism
  • Databases, Factual
  • Humans
  • Hydrogen Bonding
  • Leucine / analogs & derivatives
  • Molecular Docking Simulation*
  • Molecular Dynamics Simulation*
  • Oligopeptides / chemistry
  • Oligopeptides / metabolism
  • Pandemics
  • Pneumonia, Viral / pathology
  • Pneumonia, Viral / virology
  • Proline / analogs & derivatives
  • Protease Inhibitors / chemistry*
  • Protease Inhibitors / metabolism
  • Quinolines
  • SARS-CoV-2
  • Thermodynamics
  • Thiazoles / chemistry
  • Thiazoles / metabolism
  • Viral Nonstructural Proteins / antagonists & inhibitors*
  • Viral Nonstructural Proteins / metabolism

Substances

  • Aminoisobutyric Acids
  • Oligopeptides
  • Protease Inhibitors
  • Quinolines
  • Thiazoles
  • Viral Nonstructural Proteins
  • Aclarubicin
  • faldaprevir
  • Proline
  • Cysteine Endopeptidases
  • Coronavirus 3C Proteases
  • Leucine