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Vol. 37 No. 7 (2025): Vol 37 Issue 7, 2025

Copyright (c) 2025 Ramesh Ch. Deka, Ambalika Phonglo, Dikshita Dowerah, Srutishree Sarma, Najima Ahmed

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This work is licensed under a Creative Commons Attribution 4.0 International License.

Targeting SARS-CoV-2 Spike Protein with Regional Ethnomedicinal Plant-derived Phytocompounds: A Comprehensive Molecular Docking, ADMET and MD Simulation Study

https://doi.org/10.14233/ajchem.2025.33728
Ambalika Phonglo
CMML-Catalysis and Molecular Modelling Lab, Department of Chemical Sciences, Tezpur University, Napaam-784028, India; Department of Chemistry, Anandaram Dhekial Phookan College, Haibargaon-782002, India
https://orcid.org/0009-0009-1708-6924
Dikshita Dowerah
Department of Chemistry, Arunachal University of Studies, Namsai-792103, India
https://orcid.org/0000-0002-4985-8513
Srutishree Sarma
CMML-Catalysis and Molecular Modelling Lab, Department of Chemical Sciences, Tezpur University, Napaam-784028, India
https://orcid.org/0009-0007-8161-7131
Najima Ahmed
CMML-Catalysis and Molecular Modelling Lab, Department of Chemical Sciences, Tezpur University, Napaam-784028, India; Center for Multidisciplinary Research, Tezpur University, Napaam-784028, India
https://orcid.org/0009-0009-5931-8869
Ramesh Ch. Deka
CMML-Catalysis and Molecular Modelling Lab, Department of Chemical Sciences, Tezpur University, Napaam-784028, India
https://orcid.org/0000-0003-4352-2661

Corresponding Author(s) : Ramesh Ch. Deka

ramesh@tezu.ernet.in

Asian Journal of Chemistry, Vol. 37 No. 7 (2025): Vol 37 Issue 7, 2025

Abstract

The achievement of efficient vaccine development for the SARS-CoV-2 virus marks a significant milestone, ultimately controlling the COVID-19 pandemic. However, the studies to find small molecules with potential SARS-CoV-2 inhibitory properties remained significant as there are not many treatment alternatives available. In this study, we studied biologically active phytocompounds present in regional ethnomedicinal plants like Lindera neesiana, Litsea cubeba and Zanthoxylum armatum DC using various computational techniques such as molecular docking, drug-likeness, ADMET study, MD simulation, etc. The SARS-CoV-2 spike protein’s RBD (PDB ID: 6m0j) has been docked with 107 phytocompounds. Top 5 phytocompounds with the best docking scores were further screened for their drug-likeness and ADMET properties. Following that, 100 ns MD simulations including PCA analysis were performed, providing additional evidence of the stability of the studied protein-ligand complexes. Binding free energies were also evaluated using the MM-GBSA method, which revealed spathulenol to exhibit the most favourable energy signifying its strong binding affinity and stability within the RBD of the spike protein. This in-silico study identifies the specific phytocompounds present in L. neesiana, L. cubeba and Z. armatum DC as a potential inhibitor of SARS-CoV-2 spike protein.

Keywords

SARS-CoV-2 ADMET Docking studies MD simulation PCA analysis MM-GBSA
(1)
Phonglo, A.; Dowerah, D.; Sarma, S.; Ahmed, N.; Deka, R. C. Targeting SARS-CoV-2 Spike Protein With Regional Ethnomedicinal Plant-Derived Phytocompounds: A Comprehensive Molecular Docking, ADMET and MD Simulation Study. ajc 2025, 37, 1761-1777.
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