Virtual screening of bioactive anti-SARS-CoV natural products and identification of 3β,12-diacetoxyabieta-6,8,11,13-tetraene as a potential inhibitor of SARS-CoV-2 virus and its infection related pathways by MD simulation and network pharmacology

Huq AKMM 1 , Roney M 1 , Imran S 2 , Khan SU 3 , Uddin MN 4 , Htar TT 5 Show all authors , Baig AA 6 , Bhuiyan MA 7 , Zakaria ZA 8 , Aluwi MFFM 1 , Tajuddin SN 1

Affiliations 

  • 1 Bio Aromatic Research Centre, Universiti Malaysia Pahang, Kuantan, Pahang, Malaysia
  • 2 Atta-ur-Rahman Institute for Natural Product Discovery (AuRIns), Universiti Teknologi MARA Cawangan Selangor Kampus Puncak Alam, Puncak Alam, Selangor, Malaysia
  • 3 Product & Process Innovation Department, Qarshi Brands (Pvt) Ltd, Haripur, KPK, Pakistan
  • 4 Institute of Food Science and Technology, Bangladesh Council of Scientific and Industrial Research, Dhaka, Bangladesh
  • 5 School of Pharmacy, Monash University Malaysia, Subang Jaya, Selangor, Malaysia
  • 6 Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu, Terengannu, Malaysia
  • 7 School of Medicine, Department of Pharmacy, University of Asia Pacific, Dhaka, Bangladesh
  • 8 Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, Sabah, Malaysia
J Biomol Struct Dyn, 2023;41(23):13923-13936.
PMID: 36786766 DOI: 10.1080/07391102.2023.2176926

Abstract

Since the first prevalence of COVID-19 in 2019, it still remains the most devastating pandemic throughout the world. The current research aimed to find potential natural products to inhibit the novel coronavirus and associated infection by MD simulation and network pharmacology approach. Molecular docking was performed for 39 natural products having potent anti-SARS-CoV activity. Five natural products showed high binding interaction with the viral main protease for the SARS-CoV-2 virus, where 3β,12-diacetoxyabieta-6,8,11,13 tetraene showed stable binding in MD simulation until 100 ns. Both 3β,12-diacetoxyabieta-6,8,11,13 tetraene and tomentin A targeted 11 common genes that are related to COVID-19 and interact with each other. Gene ontology development analysis further showed that all these 11 genes are attached to various biological processes. The KEGG pathway analysis also showed that the proteins that are targeted by 3β,12-diacetoxyabieta-6,8,11,13 tetraene and tomentin A are associated with multiple pathways related to COVID-19 infection. Furthermore, the ADMET and MDS studies reveals 3β,12-diacetoxyabieta-6,8,11,13 as the best-suited compound for oral drug delivery.Communicated by Ramaswamy H. Sarma.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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