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Mechanism of Erzhiwan in treating osteoporosis based on molecular docking technology and molecular dynamics simulation

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Abstract

This experiment was a network pharmacology research based on the theoretical system of traditional Chinese medicine. TCMSP database, PubChem database, RCSB database, and SwissTargetPrediction database were used to study the effective chemical constituents of Ligustri lucidi Fructus and Ecliptae Herba in Erzhiwan, a traditional prescription for nourishing the liver and kidney. Then Genecards database, OMIM database, OMIM Gene Map, and Metascape database were used to study the therapeutic targets of osteoporosis. At last, Cytoscape 3.6.0 software, its built-in Bisogenet and CytoNCA, AutoDockTools-1.5.6 software, PYMOL-2.2.0 software, and Gromacs software, by drawing the relationship diagram between chemical components and disease targets, PPI network of disease, semi-flexible molecular docking technology, evaluation and analysis of enrichment pathway, and molecular dynamics simulation, were used to study the therapeutic mechanism of Erzhiwan on osteoporosis. It is found that the intervention and regulation of Erzhiwan on osteoporosis were mainly realized through multiple targets of active ingredients and multiple pathways, which provided support for the continued development of Erzhiwan.

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Data availability

N/A. All data generated or analyzed during this study were included in this published article.

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Funding

This study was supported by the Henan Science and Technology Research Project (212400410206) and the Cadre Teacher Training Program of the Sanquan College of Xinxiang Medical University (SQ2021GGJS06).

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Authors and Affiliations

  1. School of pharmacy, Sanquan College of Xinxiang Medical University, Xinxiang, 453003, China

    Yanling Li, Ziliang Li, Fuqi Hao, Yichi Wang, Wenqian Li, Qingfeng Yan & Huawei Shi

  2. School of pharmacy, Xinxiang Medical University, Xinxiang, 453003, China

    Ziliang Li

  3. Department of Pharmacy, Henan Integrative Medicine Hospital, Zhengzhou, 450004, China

    Tongsheng Ye

  4. Research Institute of Non−Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China

    Weijuan Han

Authors
  1. Yanling Li
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  2. Ziliang Li
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  5. Yichi Wang
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  9. Weijuan Han
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Contributions

Yanling Li and Weijuan Han were responsible for designing the project and obtaining funds; Ziliang Li, Tongsheng Ye, and Fuqi Hao were responsible for data collation and statistical analysis; Yichi Wang and Wenqian Li carried out the molecular dynamics simulation experiments; Qingfeng Yan and Huawei Shi prepared the first draft. All authors had read and approved the final manuscript.

Corresponding author

Correspondence to Weijuan Han.

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Li, Y., Li, Z., Ye, T. et al. Mechanism of Erzhiwan in treating osteoporosis based on molecular docking technology and molecular dynamics simulation. J Mol Model 29, 21 (2023). https://doi.org/10.1007/s00894-022-05418-y

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  • DOI: https://doi.org/10.1007/s00894-022-05418-y

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