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Blue Biotechnology: Computational Screening of Sarcophyton Cembranoid Diterpenes for SARS-CoV-2 Main Protease Inhibition
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Number of Authors: 162021 (English)In: Marine Drugs, E-ISSN 1660-3397, Vol. 19, no 7, article id 391Article in journal (Refereed) Published
Abstract [en]

The coronavirus pandemic has affected more than 150 million people, while over 3.25 million people have died from the coronavirus disease 2019 (COVID-19). As there are no established therapies for COVID-19 treatment, drugs that inhibit viral replication are a promising target; specifically, the main protease (M-pro) that process CoV-encoded polyproteins serves as an Achilles heel for assembly of replication-transcription machinery as well as down-stream viral replication. In the search for potential antiviral drugs that target M-pro, a series of cembranoid diterpenes from the biologically active soft-coral genus Sarcophyton have been examined as SARS-CoV-2 M-pro inhibitors. Over 360 metabolites from the genus were screened using molecular docking calculations. Promising diterpenes were further characterized by molecular dynamics (MD) simulations based on molecular mechanics-generalized Born surface area (MM-GBSA) binding energy calculations. According to in silico calculations, five cembranoid diterpenes manifested adequate binding affinities as M-pro inhibitors with Delta G(binding) < -33.0 kcal/mol. Binding energy and structural analyses of the most potent Sarcophyton inhibitor, bislatumlide A (340), was compared to darunavir, an HIV protease inhibitor that has been recently subjected to clinical-trial as an anti-COVID-19 drug. In silico analysis indicates that 340 has a higher binding affinity against M-pro than darunavir with Delta G(binding) values of -43.8 and -34.8 kcal/mol, respectively throughout 100 ns MD simulations. Drug-likeness calculations revealed robust bioavailability and protein-protein interactions were identified for 340; biochemical signaling genes included ACE, MAPK14 and ESR1 as identified based on a STRING database. Pathway enrichment analysis combined with reactome mining revealed that 340 has the capability to re-modulate the p38 MAPK pathway hijacked by SARS-CoV-2 and antagonize injurious effects. These findings justify further in vivo and in vitro testing of 340 as an antiviral agent against SARS-CoV-2.

Place, publisher, year, edition, pages
2021. Vol. 19, no 7, article id 391
Keywords [en]
genus Sarcophyton, cembranoid diterpenes metabolites, SARS-CoV-2 main protease, molecular docking, molecular dynamics, reactome
National Category
Infectious Medicine
Identifiers
URN: urn:nbn:se:su:diva-197350DOI: 10.3390/md19070391ISI: 000677354000001PubMedID: 34356816OAI: oai:DiVA.org:su-197350DiVA, id: diva2:1599351
Available from: 2021-09-30 Created: 2021-09-30 Last updated: 2024-07-04Bibliographically approved

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Khalifa, Shaden A. M.Alhumaydhi, Fahad A.

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Ibrahim, Mahmoud A. A.Khalifa, Shaden A. M.Alhumaydhi, Fahad A.
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Department of Molecular Biosciences, The Wenner-Gren Institute
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Marine Drugs
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