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Front. Mol. Biosci. | doi: 10.3389/fmolb.2021.637122

In Silico Screening of Natural Phytoconstituents Towards Identification of Potential Lead Compounds to Treat COVID-19 Provisionally accepted The final, formatted version of the article will be published soon. Notify me

Muthumanickam Sankar1,  Boomi Pandi1*, Nachiyappan Mutharasan1,  Balajee Ramachandran1, Vidhyavathi Ramasamy1, Poorani Gurumallesh Prabu2,  Shanmugaraj Gowrishankar3, Yao Wang4,  Biruntha Muniyandi5,  Subaskumar Rathinasamy6,  Balakumar Chandrasekaran7*,  Mohammad F. Bayan7, Ravikumar Sundaram8, Jeyakanthan Jeyaraman1, Gurumallesh Prabu Halliah9 and  Solomon King10
  • 1Department of Bioinformatics, Alagappa University, India
  • 2Kumaraguru College of Technology, India
  • 3Department of Biotechnology, Alagappa University, India
  • 4Anyang Institute of Technology, China
  • 5Department of Animal Health and Management, School of Biological Sciences, Alagappa University, India
  • 6Sri Ramakrishna Mission Vidyalaya College of Arts and Science, India
  • 7Faculty of Pharmacy, Philadelphia University, Jordan
  • 8Department of Biomedical Sciences, School of Biological Sciences, Alagappa University, India
  • 9Department of Industrial Chemistry, Alagappa University, India
  • 10Bioscience Research Foundation (BRF), India

The COVID-19 is one of the families of Coronavirus that can easily assail to humans. As of now, 10 million people are infected and above 2 million people died from COVID-19 globally. Over the past one year, several researchers have been made essential advances in discovering potential drugs. Till now, no efficient drugs are available in the market. The present study aims to identify the potent phytocompounds from different medicinal plants (Zingiberoffinale, Cuminum cyminum, PiperNigrum, Curcuma Longa and Allium Sativum). Totally 227 phytocompounds are identified and it was screened against S-ACE2 and Mpro through the Structure-Based Virtual Screening approaches. Based on the binding affinity score, 30 active phytocompounds are selected. The binding affinity for Beta-sitosterol and Beta-Elemene against S-ACE2 has shown -12.0 and -10.9 kcal/mol respectively. Meanwhile, the binding affinity for the Beta-sitosterol and Beta chlorogenin against Mpro is found to be -9.7 and -8.4 kcal/mol respectively. Further, the selected compounds are proceed with Molecular Dynamics Simulation, Prime MM-GBSA and ADME/T properties to understand the stability, interaction, conformational changes, Binding Free Energy and pharmaceutical relevant parameters. Moreover, the hotspot residues such as Lys31 and Lys353 for S-ACE2 and catalytic dyad His41 and Cys145 for Mpro are actively involved in the inhibition of viral entry. From the analyses, we anticipate that this work could be valuable to ongoing novel drug discovery with potential treatment for COVID-19.

Keywords: COVID-19, main protease, Molecular Dynamics Simulation, Natural medicinal plants, S-ACE2, Structure-based virtual screening

Received: 02 Dec 2020; Accepted: 16 Apr 2021.

Copyright: © 2021 Sankar, Pandi, Mutharasan, Ramachandran, Ramasamy, Gurumallesh Prabu, Gowrishankar, Wang, Muniyandi, Rathinasamy, Chandrasekaran, Bayan, Sundaram, Jeyaraman, Halliah and King. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
Dr. Boomi Pandi, Department of Bioinformatics, Alagappa University, Karaikudi, 630 004, Tamil Nadu, India,
Mx. Balakumar Chandrasekaran, Faculty of Pharmacy, Philadelphia University, Amman, 19392, Amman, Jordan,