In silico studies on phytochemicals to combat the emerging COVID-19 infection |
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| Institution: | 1. Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 Cultural West Road, Shandong Province 250012, PR China;2. Department of Chemistry, Government College of Engineering, Keonjhar, Odisha 758002, India;3. Department of Chemistry, School of Applied Sciences, Centurion University of Technology and Management, Odisha, India;4. Department of Chemistry, C. V. Raman Global University, Bidyanagar, Mahura, Janla, Bhubaneswar, Odisha 752054, India;5. Biotechnology Department, Faculty of Science and Technology, Shendi University, Shendi, Nher Anile, Sudan;6. Division of Chemistry and Biotechnology, Dongguk University, 123 Dongdae-ro, Gyeongju, Republic of Korea;7. Department of Pharmacology and Toxicology, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt;8. Department of Chemistry, College of Science, King Saud University, PO BOX 2455, Riyadh 11451, Saudi Arabia;9. Natural Products Research Laboratory, Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK;10. Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India |
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| Abstract: | The current COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and its variants, remains a serious health hazard globally. The SARS-CoV-2 Mpro and spike proteins, as well as the human ACE2 receptor, have previously been reported as good targets for the development of new drug leads to combat COVID-19. Various ligands, including synthetic and plant-derived small molecules, can interact with the aforementioned proteins. In this study, we investigated the interaction of eight phytochemicals, from selected medicinal plants (Aegle marmelos, Azadirachta indica, and Ocimum sanctum) commonly used in Indian traditional medicine, with SARS-CoV-2 Mpro (PDBID: 6LU7), SARS-CoV-2S spike protein (PDB ID: 6M0J) and the human ACE2 receptor (PDB ID: 6M18). All compounds were subjected to density functional theory (DFT) and frontier molecular orbitals (FMO) analysis to determine their geometry, and key electronic and energetic properties. Upon examining the interactions of the phytochemicals with the human ACE2 receptor and the SARS-CoV-2 Mpro, spike protein targets, two compounds (C-5 and C-8) were identified as the best binding ligands. These were further examined in MD simulation studies to determine the stability of the ligand–protein interactions. QSAR, pharmacokinetic and drug-likeness properties studies revealed that C-5 may be the best candidate to serve as a template for the design and development of new drugs to combat COVID-19. |
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| Keywords: | COVID-19 DFT Molecular docking Molecular dynamics simulation Pharmacokinetic study QSAR |
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