Putative Inhibitors of SARS-CoV-2 Main Protease from A Library of Marine Natural Products: A Virtual Screening and Molecular Modeling Study

Mar Drugs. 2020 Apr 23;18(4):225. doi: 10.3390/md18040225.


The current emergency due to the worldwide spread of the COVID-19 caused by the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a great concern for global public health. Already in the past, the outbreak of severe acute respiratory syndrome (SARS) in 2003 and Middle Eastern respiratory syndrome (MERS) in 2012 demonstrates the potential of coronaviruses to cross-species borders and further underlines the importance of identifying new-targeted drugs. An ideal antiviral agent should target essential proteins involved in the lifecycle of SARS-CoV. Currently, some HIV protease inhibitors (i.e., Lopinavir) are proposed for the treatment of COVID-19, although their effectiveness has not yet been assessed. The main protease (Mpr) provides a highly validated pharmacological target for the discovery and design of inhibitors. We identified potent Mpr inhibitors employing computational techniques that entail the screening of a Marine Natural Product (MNP) library. MNP library was screened by a hyphenated pharmacophore model, and molecular docking approaches. Molecular dynamics and re-docking further confirmed the results obtained by structure-based techniques and allowed this study to highlight some crucial aspects. Seventeen potential SARS-CoV-2 Mpr inhibitors have been identified among the natural substances of marine origin. As these compounds were extensively validated by a consensus approach and by molecular dynamics, the likelihood that at least one of these compounds could be bioactive is excellent.

Keywords: COVID-19; SARS-CoV-2; docking; marine natural product; virtual screening.

MeSH terms

  • Antiviral Agents / chemistry
  • Antiviral Agents / pharmacology*
  • Antiviral Agents / therapeutic use
  • Betacoronavirus / drug effects
  • Betacoronavirus / enzymology*
  • Biological Products / chemistry
  • Biological Products / pharmacology
  • Biological Products / therapeutic use
  • COVID-19
  • COVID-19 Drug Treatment
  • Coronavirus 3C Proteases
  • Coronavirus Infections* / drug therapy
  • Coronavirus Infections* / virology
  • Cysteine Endopeptidases
  • Databases, Chemical
  • Humans
  • Models, Molecular
  • Molecular Docking Simulation
  • Pandemics*
  • Pneumonia, Viral* / drug therapy
  • Pneumonia, Viral* / virology
  • Protease Inhibitors / chemistry
  • Protease Inhibitors / pharmacology*
  • Protease Inhibitors / therapeutic use
  • SARS-CoV-2
  • Viral Nonstructural Proteins / antagonists & inhibitors*


  • Antiviral Agents
  • Biological Products
  • Protease Inhibitors
  • Viral Nonstructural Proteins
  • Cysteine Endopeptidases
  • Coronavirus 3C Proteases