In Silico Mining of Terpenes from Red-Sea Invertebrates for SARS-CoV-2 Main Protease (Mpro) Inhibitors

Molecules. 2021 Apr 5;26(7):2082. doi: 10.3390/molecules26072082.


Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent for the COVID-19 pandemic, which generated more than 1.82 million deaths in 2020 alone, in addition to 83.8 million infections. Currently, there is no antiviral medication to treat COVID-19. In the search for drug leads, marine-derived metabolites are reported here as prospective SARS-CoV-2 inhibitors. Two hundred and twenty-seven terpene natural products isolated from the biodiverse Red-Sea ecosystem were screened for inhibitor activity against the SARS-CoV-2 main protease (Mpro) using molecular docking and molecular dynamics (MD) simulations combined with molecular mechanics/generalized Born surface area binding energy calculations. On the basis of in silico analyses, six terpenes demonstrated high potency as Mpro inhibitors with ΔGbinding ≤ -40.0 kcal/mol. The stability and binding affinity of the most potent metabolite, erylosides B, were compared to the human immunodeficiency virus protease inhibitor, lopinavir. Erylosides B showed greater binding affinity towards SARS-CoV-2 Mpro than lopinavir over 100 ns with ΔGbinding values of -51.9 vs. -33.6 kcal/mol, respectively. Protein-protein interactions indicate that erylosides B biochemical signaling shares gene components that mediate severe acute respiratory syndrome diseases, including the cytokine- and immune-signaling components BCL2L1, IL2, and PRKC. Pathway enrichment analysis and Boolean network modeling were performed towards a deep dissection and mining of the erylosides B target-function interactions. The current study identifies erylosides B as a promising anti-COVID-19 drug lead that warrants further in vitro and in vivo testing.

Keywords: SARS-CoV-2 main protease; drug discovery; marine natural products; molecular docking; molecular dynamics; virtual drug screening.

MeSH terms

  • Animals
  • Binding Sites
  • COVID-19 / virology
  • COVID-19 Drug Treatment
  • Humans
  • Hydrogen Bonding
  • Invertebrates / chemistry*
  • Invertebrates / metabolism
  • Lopinavir / chemistry
  • Lopinavir / metabolism
  • Molecular Docking Simulation
  • Molecular Dynamics Simulation
  • Protease Inhibitors / chemistry
  • Protease Inhibitors / isolation & purification
  • Protease Inhibitors / therapeutic use
  • Protein Binding
  • SARS-CoV-2 / isolation & purification
  • SARS-CoV-2 / metabolism*
  • Terpenes / chemistry*
  • Terpenes / isolation & purification
  • Terpenes / metabolism
  • Terpenes / therapeutic use
  • Thermodynamics
  • Viral Matrix Proteins / antagonists & inhibitors*
  • Viral Matrix Proteins / metabolism


  • Protease Inhibitors
  • Terpenes
  • Viral Matrix Proteins
  • membrane protein, SARS-CoV-2
  • Lopinavir