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Zubair MS, Maulana S, Widodo A, Pitopang R, Arba M, Hariono M. GC-MS, LC-MS/MS, Docking and Molecular Dynamics Approaches to Identify Potential SARS-CoV-2 3-Chymotrypsin-Like Protease Inhibitors from Zingiber officinale Roscoe. Molecules 2021; 26:5230. [PMID: 34500664 PMCID: PMC8434146 DOI: 10.3390/molecules26175230] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/20/2021] [Accepted: 08/25/2021] [Indexed: 02/07/2023] Open
Abstract
This study aims to identify and isolate the secondary metabolites of Zingiber officinale using GC-MS, preparative TLC, and LC-MS/MS methods, to evaluate the inhibitory potency on SARS-CoV-2 3 chymotrypsin-like protease enzyme, as well as to study the molecular interaction and stability by using docking and molecular dynamics simulations. GC-MS analysis suggested for the isolation of terpenoids compounds as major compounds on methanol extract of pseudostems and rhizomes. Isolation and LC-MS/MS analysis identified 5-hydro-7, 8, 2'-trimethoxyflavanone (9), (E)-hexadecyl-ferulate (1), isocyperol (2), N-isobutyl-(2E,4E)-octadecadienamide (3), and nootkatone (4) from the rhizome extract, as well as from the leaves extract with the absence of 9. Three known steroid compounds, i.e., spinasterone (7), spinasterol (8), and 24-methylcholesta-7-en-3β-on (6), were further identified from the pseudostem extract. Molecular docking showed that steroids compounds 7, 8, and 6 have lower predictive binding energies (MMGBSA) than other metabolites with binding energy of -87.91, -78.11, and -68.80 kcal/mole, respectively. Further characterization on the single isolated compound by NMR showed that 6 was identified and possessed 75% inhibitory activity on SARS-CoV-2 3CL protease enzyme that was slightly different with the positive control GC376 (77%). MD simulations showed the complex stability with compound 6 during 100 ns simulation time.
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Affiliation(s)
- Muhammad Sulaiman Zubair
- Department of Pharmacy, Faculty of Science, Tadulako University, Palu 94118, Indonesia; (S.M.); (A.W.)
| | - Saipul Maulana
- Department of Pharmacy, Faculty of Science, Tadulako University, Palu 94118, Indonesia; (S.M.); (A.W.)
| | - Agustinus Widodo
- Department of Pharmacy, Faculty of Science, Tadulako University, Palu 94118, Indonesia; (S.M.); (A.W.)
| | - Ramadanil Pitopang
- Department of Biology, Faculty of Science, Tadulako University, Palu 94118, Indonesia;
| | - Muhammad Arba
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Halu Oleo University, Kendari 93231, Indonesia;
| | - Maywan Hariono
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Sanata Darma University, Yogyakarta 55282, Indonesia
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Ibrahim MAA, Abdelrahman AHM, Atia MAM, Mohamed TA, Moustafa MF, Hakami AR, Khalifa SAM, Alhumaydhi FA, Alrumaihi F, Abidi SH, Allemailem KS, Efferth T, Soliman ME, Paré PW, El-Seedi HR, Hegazy MEF. Blue Biotechnology: Computational Screening of Sarcophyton Cembranoid Diterpenes for SARS-CoV-2 Main Protease Inhibition. Mar Drugs 2021; 19:391. [PMID: 34356816 PMCID: PMC8308023 DOI: 10.3390/md19070391] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 12/29/2022] Open
Abstract
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 (Mpro) 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 Mpro, a series of cembranoid diterpenes from the biologically active soft-coral genus Sarcophyton have been examined as SARS-CoV-2 Mpro 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 Mpro inhibitors with ΔGbinding < -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 Mpro than darunavir with ΔGbinding 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.
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Affiliation(s)
- Mahmoud A. A. Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt;
| | - Alaa H. M. Abdelrahman
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt;
| | - Mohamed A. M. Atia
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza 12619, Egypt;
| | - Tarik A. Mohamed
- Chemistry of Medicinal Plants Department, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt;
| | - Mahmoud F. Moustafa
- Department of Biology, College of Science, King Khalid University, Abha 9004, Saudi Arabia; or
- Department of Botany & Microbiology, Faculty of Science, South Valley University, Qena 83523, Egypt
| | - Abdulrahim R. Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha 61481, Saudi Arabia;
| | - Shaden A. M. Khalifa
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-106 91 Stockholm, Sweden;
| | - Fahad A. Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (F.A.A.); (F.A.); (K.S.A.)
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (F.A.A.); (F.A.); (K.S.A.)
| | - Syed Hani Abidi
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi 74800, Pakistan;
| | - Khaled S. Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (F.A.A.); (F.A.); (K.S.A.)
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany;
| | - Mahmoud E. Soliman
- Molecular Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South Africa;
| | - Paul W. Paré
- Department of Chemistry & Biochemistry, Texas Tech University, Lubbock, TX 79409, USA;
| | - Hesham R. El-Seedi
- Department of Chemistry, Faculty of Science, El-Menoufia University, Shebin El-Kom 32512, Egypt
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
- Pharmacognosy Group, Department of Pharmaceutical Biosciences, Uppsala University, Biomedical Centre, Box 574, 751 23 Uppsala, Sweden
| | - Mohamed-Elamir F. Hegazy
- Chemistry of Medicinal Plants Department, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt;
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany;
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