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Network pharmacology, molecular docking, and molecular dynamics simulation to elucidate the mechanism of anti-aging action of Tinospora cordifolia

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Abstract

Scientific research has demonstrated that Tinospora cordifolia acts as an anti-aging agent in several experimental models, generating global interest in its underlying molecular mechanisms of this activity. The aim of the study was to identify the possible phytochemical compounds of T. cordifolia that might combat age-related illness through integrating network pharmacology, molecular docking techniques, and molecular dynamics (MD) study to explore their potential mechanisms of action. To carry out this study, several databases were used, including PubChem, KNApSAcK family database, PubMed, SwissADME, Molsoft, SwissTargetPrediction, GeneCards, and OMIM database. For network development and GO enrichment analysis KEGG, ShinyGo 0.77, and the STRING database were used. For better analysis, the networks were also constructed using Cytoscape 3.9.1. The Cytoscape network analyzer tool was used for data analysis, and molecular docking was done via Vina-GPU-2.0. The best compounds and AKT1 were finally subjected to MD simulation for 100 ns. The CytoHubba plugin of Cytoscape identified ten key targets, commonly called hub genes, including AKT1, GAPDH, and TP53, and so on. GO and KEGG pathway enrichment analysis revealed the relevant biological processes, cellular components, and molecular functions involved in treating aging-related disorders. KEGG pathway analysis involved neuroactive ligand–receptor interactions, lipid and atherosclerosis, and cAMP signaling. The docking of 100 T. cordifolia compounds with AKT1 demonstrated good binding affinity, particularly for Amritoside, Sitagliptin, Berberine, and Piperine. Finally, the relative stability of four-hit phytochemicals was validated by MD simulation, which may be the most crucial compound for anti-aging activity. In conclusion, this study used network pharmacology, molecular docking, and MD simulation to identify the compounds in T. cordifolia and proposed a potential mechanism for anti-aging activity. These results suggest future directions for the prevention and treatment of age-related diseases.

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Acknowledgements

The authors would like to thank the Head of the Botany Department, Soban Singh Jeena University, S.S.J. Campus, Almora (Uttarakhand), India, for providing the facility and space for this research work. The authors would also like to acknowledge the Department of Botany, Kumaon Kesari Pt. Badridutt Pandey Government Post Graduate College, Bageshwar, Soban Singh Jeena University, Almora, for providing external support.

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  1. Department of Botany, P.G. College Bageshwar, Bageshwar, Uttarakhand, 263642, India

    Amisha Bisht & Sanjay Kumar

  2. Department of Biotechnology, Kumaun University, Bhimtal, Uttarakhand, India

    Disha Tewari

  3. Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, 263601, India

    Subhash Chandra

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  1. Amisha Bisht
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AB wrote the manuscript and done all the experiments parts. DT analyzed and interpreted the data. SC conceptualized and designed the work. SK and SC supervised the study. The whole manuscript was approved by all authors.

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Correspondence to Sanjay Kumar or Subhash Chandra.

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Bisht, A., Tewari, D., Kumar, S. et al. Network pharmacology, molecular docking, and molecular dynamics simulation to elucidate the mechanism of anti-aging action of Tinospora cordifolia. Mol Divers (2023). https://doi.org/10.1007/s11030-023-10684-w

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