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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is viewed as a global health emergency since its first appearance in China in late 2019. SARS-CoV-2 was responsible for over 600 million confirmed cases and over 6.5 million deaths worldwide. Direct inhibitors are important along with vaccination as countermeasures to stop the spread of coronavirus disease. The 3-chymotrypsin-like protease (3CLpro) of SARS-CoV-2 virus is important for replication of the virus, which makes it an important target for inhibition. In this study, we utilise molecular docking and molecular dynamics to screen a list of compounds that have potential to inhibit the 3CLpro. After optimisation and rescore of all the docked compounds, zanamivir was found to have the best binding affinity towards 3CLpro. The MMPBSA analysis of molecular dynamics trajectories also shows that zanamivir have the best binding affinity towards 3CLpro. Hydrogen bond analysis further reveals that zanamivir established extra hydrogen bond interactions with 3CLpro, which other tested compounds do not have.

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Augmented Discovery of Potential Inhibitors of SARS-CoV-2 3CL Protease

  • 会议论文

  • 发表日期：

    2025年

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  • Tan Ke Han,
  • Rozana Othman,
  • Nurshamimi Nor Rashid

摘要

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is viewed as a global health emergency since its first appearance in China in late 2019. SARS-CoV-2 was responsible for over 600 million confirmed cases and over 6.5 million deaths worldwide. Direct inhibitors are important along with vaccination as countermeasures to stop the spread of coronavirus disease. The 3-chymotrypsin-like protease (3CLpro) of SARS-CoV-2 virus is important for replication of the virus, which makes it an important target for inhibition. In this study, we utilise molecular docking and molecular dynamics to screen a list of compounds that have potential to inhibit the 3CLpro. After optimisation and rescore of all the docked compounds, zanamivir was found to have the best binding affinity towards 3CLpro. The MMPBSA analysis of molecular dynamics trajectories also shows that zanamivir have the best binding affinity towards 3CLpro. Hydrogen bond analysis further reveals that zanamivir established extra hydrogen bond interactions with 3CLpro, which other tested compounds do not have.