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A Drug Repurposing Approach to Identify Therapeutics by Screening Pathogen Box Exploiting SARS-CoV-2 Main Protease.

Rashmi Tyagi1, Anubrat Paul1, V Samuel Raj1

  • 1Center for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Sonepat, 131 029, Haryana, India.

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Researchers screened 400 compounds against the SARS-CoV-2 main protease (Mpro). MMV1782211 showed strong binding and stable interaction, indicating potential as a COVID-19 therapeutic.

Keywords:
ADMETCOVID-19molecular dockingmolecular dynamics simulationsvirtual screening

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Area of Science:

  • Computational drug discovery
  • Virology
  • Medicinal chemistry

Background:

  • Coronavirus disease-19 (COVID-19), caused by SARS-CoV-2, poses a significant global health threat with limited therapeutic options.
  • The SARS-CoV-2 main protease (Mpro) is crucial for viral replication, making it a promising drug target.
  • The rapid evolution of SARS-CoV-2 necessitates the continuous development of novel antiviral agents.

Purpose of the Study:

  • To identify potential novel inhibitors of the SARS-CoV-2 main protease (Mpro) through in-silico screening.
  • To evaluate the binding affinity and interaction stability of candidate compounds with the Mpro target.
  • To discover new therapeutic leads for combating COVID-19.

Main Methods:

  • In-silico screening of 400 diverse bioactive compounds against the SARS-CoV-2 Mpro.
  • Molecular docking and superimposition to analyze interactions within the Mpro catalytic domain.
  • Molecular dynamics simulations and MM/PBSA free energy calculations to assess complex stability and binding energy.

Main Results:

  • Ten compounds exhibited higher binding affinity to Mpro than the reference inhibitor (N3), possessing favorable physicochemical properties.
  • Three compounds, MMV1782211, MMV1782220, and MMV1578574, demonstrated active interaction with the Mpro catalytic domain.
  • MMV1782211 showed the most stable interaction and highest binding free energy (-115.8 kJ/mol) with Mpro, confirmed by molecular dynamics and MM/PBSA calculations.

Conclusions:

  • The in-silico analysis identified MMV1782211 as a potent candidate molecule targeting the SARS-CoV-2 Mpro.
  • MMV1782211 warrants further investigation through in-vitro and in-vivo studies for its potential as a COVID-19 therapeutic.
  • This study highlights the efficacy of computational approaches in discovering novel antiviral drug leads.