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Evaluation of the inhibitory potential of bioactive compounds against SARS-CoV-2 by in silico approach

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Abstract

Context

The COVID-19 (coronavirus disease 19) pandemic brought on by the SARS-CoV-2 outbreak (severe acute respiratory syndrome coronavirus 2) has stimulated the exploration of various available chemical compounds that could be used to treat the infection. This has driven numerous researchers to investigate the antiviral potential of several bioactive compounds from medicinal plants due to their reduced adverse effects compared to chemicals. Some of the bioactive compounds used in folklore treatment strategies are reported as effective inhibitors against the proliferative and infective cycles of SARS-CoV-2. The secondary metabolites from plants are generally used to treat various diseases due to their intact medicinal properties. The present study analyzes the inhibitory potential of phytochemicals from medicinal plants like Sphaeranthus indicus, Lantana camara, and Nelumbo nucifera against SARS-CoV-2 by molecular docking.

Methods

Ten druggable protein targets from SARS-CoV-2 are docked against the phytochemicals from the selected medicinal plants. The phytocompounds astragalin, isoquercetin, and 5-hydroxy-7-methoxy-6-c-glycosy flavone were found to have lower binding energy depicting their inhibitive potential compared with the reported inhibitors that are used in the treatment of SARS-CoV-2 infection. The phytocompounds found to have the least binding energy were selected for further analyses. To assess the compounds’ potential as drugs, their ADMET characteristics were also examined. Sphaeranthus indicus, Lantana camara, and Nelumbo nucifera six possible compounds were separately screened for ADME and toxicity characteristics; then, the results were analyzed. To assess the impact of the phytocompound binding on the dynamics of SARS-CoV-2 ribonuclease protein NSP15, microsecond-level all atomistic molecular dynamics simulations were performed, and their dynamics were analyzed. Microsecond-level molecular dynamics simulations of both the ligands complexed with NSP15 revealed that the ligand induces allosteric effects on NSP15, which could lead to destabilization of NSP15 hexameric interface and loss of RNA binding. The low binding energy exhibited by the phytochemicals from Lantana camera, Sphaeranthus indicus, and Nelumbo nucifera against the protein targets of SARS-CoV-2 showed inhibitory potential by the selected molecules. Their predicted interference of the enzymes involved in the molecular mechanisms aiding the proliferation of SARS-CoV-2 indicated the inhibitive ability of the phytochemicals.

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Data availability

The MD simulation trajectories analyzed in this work will be shared upon request.

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Acknowledgements

The authors thank the Kalasalingam Academy of Research and Education, Srivilliputhur, India, for providing with the facilities throughout this work. The authors also thank the financial resources and infrastructural support from Yenepoya (Deemed to be University). The authors also thank the ROMEO-HPC of Université de Reims Champagne-Ardenne, France, for computational resources for the MD simulations.

Funding

Ms. Shalini Mohan, Junior Research Fellow, acknowledges the Department of Biotechnology (DBT), Government of India, for the financial grant offered with the fellowship ID DBT/2022–23/KARE/2059. Dr. Lakshmanan Muthulakshmi acknowledges the Department of Scientific and Industrial Research for the financial grant (DSIR/TDUPW-1101/3/2021-IRD (SC)/-DSIR) and Kalasalingam Academy of Research and Education for seed money grant in the year 2021–2022. Rajas M. Rao acknowledges computational resources from Prof. Manuel Dauchez and ROMEO-HPC, University of Reims Champagne-Ardenne.

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  1. Department of Biotechnology, Biomaterials and Product Development Laboratory, Kalasalingam Academy of Research and Education, Krishnankoil, 626126, India

    J Mariya Sneha Rani, P Akkarshana, V Neelaveni, Shalini Mohan & Lakshmanan Muthulakshmi

  2. Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangaluru, 575018, India

    P. D. Rekha & Rajas M. Rao

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MSRJ, AP, NV and SV did the molecular docking and review of literature. RPD and RMR did the molecular dynamics simulations and analysis. LM compiled the work and edited the manuscript. All the authors wrote, reviewed and approved the final version of the manuscript.

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Rani, J.M.S., Akkarshana, P., Neelaveni, V. et al. Evaluation of the inhibitory potential of bioactive compounds against SARS-CoV-2 by in silico approach. J Mol Model 30, 60 (2024). https://doi.org/10.1007/s00894-024-05858-8

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