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In Silico Mining of Terpenes from Red-Sea Invertebrates for SARS-CoV-2 Main Protease (M-pro) Inhibitors
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Number of Authors: 142021 (English)In: Molecules, ISSN 1431-5157, E-ISSN 1420-3049, Vol. 26, no 7, article id 2082Article in journal (Refereed) Published
Abstract [en]

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 (M-pro) 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 M-pro inhibitors with Delta G(binding) <= -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 M-pro than lopinavir over 100 ns with Delta G(binding) 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.

Place, publisher, year, edition, pages
2021. Vol. 26, no 7, article id 2082
Keywords [en]
drug discovery, marine natural products, molecular docking, molecular dynamics, SARS-CoV-2 main protease, virtual drug screening
National Category
Biological Sciences Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
URN: urn:nbn:se:su:diva-194363DOI: 10.3390/molecules26072082ISI: 000638738200001PubMedID: 33916461OAI: oai:DiVA.org:su-194363DiVA, id: diva2:1570066
Available from: 2021-06-21 Created: 2021-06-21 Last updated: 2023-08-28Bibliographically approved

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Atia, Mohamed A. M.Allemailem, Khaled S.El-Seedi, Hesham R.Hegazy, Mohamed-Elamir F.

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Ibrahim, Mahmoud A. A.Atia, Mohamed A. M.Allemailem, Khaled S.El-Seedi, Hesham R.Hegazy, Mohamed-Elamir F.
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Department of Molecular Biosciences, The Wenner-Gren Institute
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Molecules
Biological SciencesMedical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)

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