In silico studies on phytochemicals to combat the emerging COVID-19 infection

Mohnad Abdalla, Ranjan K. Mohapatra, Ashish K. Sarangi, Pranab K. Mohapatra, Wafa Ali Eltayb, Mahboob Alam, Amr Ahmed El-Arabey, Mohammad Azam, Saud I. Al-Resayes, Veronique Seidel, Kuldeep Dhama

Research output: Contribution to journalArticlepeer-review

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.
Original languageEnglish
Article number101367
Number of pages16
JournalJournal of the Saudi Chemical Society
Volume25
Issue number12
Early online date19 Oct 2021
DOIs
Publication statusE-pub ahead of print - 19 Oct 2021

Keywords

  • COVID-19
  • DFT
  • molecular docking
  • molecular dynamics simulation
  • pharmacokinetic study
  • QSAR

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