Submitted: 10 Oct 2020
Revision: 19 Jan 2021
Accepted: 02 Jun 2021
ePublished: 14 Jun 2021
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Int J Phytocos Nat Ingred. 2021;8(1): 5.
doi: 10.15171/ijpni.2021.05
  Abstract View: 112
  PDF Download: 54

Original Research

Evaluation of some plant-derived natural ingredients against SARS-CoV-2: An in-silico approach

Athira M Menon 1, Priyanka Kumari 2, Chetna Nagoda 3, Shalini Tekriwal 4, Abhishek Kumar 5, Sunil Dutta Purohit 6, Tikam Chand Dakal 1*

1 Genome & Computational Biology Lab, Department of Biotechnology, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
2 Department of Bioscience and Biotechnology, Banasthali Vidyapith, Tonk, Rajasthan, India
3 Center for Converging Technologies, Rajasthan University, Jaipur, India
4 Department of Biotechnology, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
5 Institute of Bioinformatics, Bangalore, Karnataka, India
6 Society for Promotion of Science Education and Research (SPSER), Udaipur, India

Abstract

Background: The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), infected by a new strain of human coronavirus, has engulfed the whole globe with its vicious potential to eradicate humankind. The pandemic has emerged from the Wuhan provinces of China with high transmissibility. Researchers are rushing to discover vaccines and drugs for the disease, which is not known yet. In this study, we have focused on the in-silico screening of phytochemicals occurring naturally in plant extracts that could possibly interact with receptor binding motif (RBM) of spike protein and thereby inhibit virus-cell interaction.
Materials and Methods: In this study, we have taken 100 phytochemicals that have been studied in various viral interactions and have shown antiviral properties. Initially, these compounds were analyzed on the basis of their physicochemical and pharmacokinetic properties, biological activities, possible target interactions, similar compounds in humans, and gene regulations using bioinformatic tools, namely Swiss-ADME, PASS (prediction of activity spectra for substances), SwissTargetPrediction, similar ensemble approach (SEA) search server, DIEGP-pred, respectively and were filtered out on the basis of immunobiological activities and expression of genes involved in cytokine storm regulation and immunostimulation. Further, they were docked with the receptor-binding domain (RBD) of spike protein in the SARS-CoV-2 using SwissDock and analyzed by UCSF Chimera.
Results: A hundred phytochemicals were analyzed on the basis of their physicochemical, pharmacokinetics, biological activities, and gene expression. Out of which 20 compounds were found to be fit all the criteria and were docked with the receptor binding domain (RBD) of the spike protein of SARS-CoV-2. Although almost every one of them showed binding with RBD, two phytochemicals, namely, orientin and apigenin, naturally found in Ocimum sanctum and chamomile, were found to bind with RBM and interacted with amino acid sequences that are mainly involved in RBM-ACE2 (angiotensin-converting enzyme 2) interaction.
Conclusions: We have got phytochemicals that interact directly in the receptor-binding motif of the spike protein. These phytochemicals were also screened for their pharmacokinetics and physiochemical activities, which make sure that the compound holds efficient drug-like properties. This could be a robust test of an iterative framework of inhibiting virus-receptor interaction with the help of phytochemicals.

Keywords: Phytochemicals, SARS-CoV-2, Pharmacokinetics, Molecular Docking
Please cite this paper as: Menon AM, Kumari P, Nagoda C, Tekriwal S, Kumar A, Purohit SD, et al. Evaluation of some plant-derived natural ingredients against SARS-CoV-2: An in-silico approach. Int J Phytocos Nat Ingred. 2021;8:5. doi:10.15171/ijpni.2021.05.
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