Preprint / Version 1

Repurposing of phytomedicine-derived bioactive compounds with promising anti-SARS-CoV-2 potential: Molecular docking, MD simulation and drug-likeness/ADMET studies

Authors

  • Mithun Rudrapal aDepartment of Pharmaceutical Chemistry, Rasiklal M. Dhariwal Institute of Pharmaceutical Education and Research, Chinchwad, Pune 411019, Maharashtra, India
  • Shubham Khairnar fMET Institute of Pharmacy, Bhujbal Knowledge City, Adgaon, Nasik 422003, Maharashtra, India
  • Umesh Laddha fMET Institute of Pharmacy, Bhujbal Knowledge City, Adgaon, Nasik 422003, Maharashtra, India
  • Mohammed Alaidarous cDepartment of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia
  • Bader Alshehri cDepartment of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia
  • Saeed Banwas cDepartment of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia
  • Johra Khan cDepartment of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia
  • Dipak Chetia bDepartment of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh 786004, Assam, India
  • Neelutpal Gogoi bDepartment of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh 786004, Assam, India
  • Sanjay Walode aDepartment of Pharmaceutical Chemistry, Rasiklal M. Dhariwal Institute of Pharmaceutical Education and Research, Chinchwad, Pune 411019, Maharashtra, India

Keywords:

SARS-CoV-2 infection, Phytomedicine, Molecular docking, Molecular dynamics, Phytochemicals, Drug repurposing

Abstract

In view of the potential of traditional plant-based remedies (or phytomedicines) in the management of COVID-19, the present investigation was aimed at finding novel anti-SARS-CoV-2 molecules by in silico screening of bioactive phytochemicals (database) using computational methods and drug repurposing approach. A total of 160 compounds belonging to various phytochemical classes (flavonoids, limonoids, saponins, triterpenoids, steroids etc.) were selected (as initial hits) and screened against three specific therapeutic targets (Mpro/3CLpro, PLpro and RdRp) of SARS-CoV-2 by docking, molecular dynamics simulation and drug-likeness/ADMET studies. From our studies, six phytochemicals were identified as notable ant-SARS-CoV-2 agents (best hit molecules) with promising inhibitory effects effective against protease (Mpro and PLpro) and polymerase (RdRp) enzymes. These compounds are namely, ginsenoside Rg2, saikosaponin A, somniferine, betulinic acid, soyasapogenol C and azadirachtin A. On the basis of binding modes and dynamics studies of protein–ligand intercations, ginsenoside Rg2, saikosaponin A, somniferine were found to be the most potent (in silico) inhibitors potentially active against Mpro, PLpro and RdRp, respectively. The present investigation can be directed towards further experimental studies in order to confirm the anti-SARS-CoV-2 efficacy along with toxicities of identified phytomolecules. Keywords: SARS-CoV-2 infection, Phytomedicine, Molecular docking, Molecular dynamics, Phytochemicals, Drug repurposing

Author Biographies

Mohammed Alaidarous, cDepartment of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia

dHealth and Basic Sciences Research Center, Majmaah University, Al Majmaah 11952, Saudi Arabia

Bader Alshehri, cDepartment of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia

dHealth and Basic Sciences Research Center, Majmaah University, Al Majmaah 11952, Saudi Arabia

Saeed Banwas, cDepartment of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia

eDepartment of Biomedical Sciences, Oregon State University, Corvallis, OR 97331, USA

Johra Khan, cDepartment of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia

dHealth and Basic Sciences Research Center, Majmaah University, Al Majmaah 11952, Saudi Arabia

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