AccScience Publishing / GPD / Volume 3 / Issue 4 / DOI: 10.36922/gpd.4427
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ORIGINAL RESEARCH ARTICLE

Can Epimedii herba treat periodontitis? A prediction based on network pharmacology, molecular docking, and dynamics analysis

Junhan Wan1,2,3 ,  Wenwen Wang1,2 ,  Ningli Li1,2 ,  Mingzhen Yang1,2 ,  Yingjie Zhu4 ,  Yuankun Zhai1,2,5*
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1 School of Stomatology, Henan University, Kaifeng, Henan, China
2 Kaifeng Key Laboratory of Periodontal Tissue Engineering, Kaifeng, Henan, China
3 School and Hospital of Stomatology Medical University, Shenyang, Liaoning, China
4 Medical Center of Hip, Luoyang Orthopedic-Traumatological Hospital, Luoyang, Henan, China
5 Henan International Joint Laboratory for Nuclear Protein Regulation, Kaifeng, Henan, China
GPD 2024, 3(4), 4427 https://doi.org/10.36922/gpd.4427
Submitted: 2 August 2024 | Accepted: 22 October 2024 | Published: 18 November 2024
© 2024 by the Author(s). This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution 4.0 International License ( https://creativecommons.org/licenses/by/4.0/ )
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Abstract

Epimedii herba (EH) showed numerous activities and has the potential to treat periodontitis. However, the pharmacological mechanism has not been exhaustively elucidated. This study predicted the specific targets and mechanisms of EH to prevent and treat periodontitis. A traditional Chinese medicine system pharmacology database and analysis platform was used to screen key compounds of EH and their corresponding targets. Therapeutic Target Database and Comparative Toxicogenomics Database were used to identify targets related to periodontitis. Intersection targets were observed using a Venn diagram. The key components and corresponding protein targets of EH were searched. The intersection targets were obtained and then they were imported into the STRING database to construct a PPI network. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed. Molecular docking between the screened chemical components of EH and key targets was performed using Discovery Studio 2019. The binding stability between components and target proteins was confirmed using molecular dynamics simulations. The binding stability between components and target proteins was confirmed using molecular dynamics simulations. Through network pharmacological analysis, 23 active compounds of EH were identified, including kaempferol and icariin. Based on GeneCards, GEO, and other databases, 3291 periodontitis-related genes were obtained. Venn diagram analysis revealed 137 intersection targets of EH and periodontitis, and Protein kinase B (AKT1) and Tumor necrosis factor (TNF) were identified as the key targets of EH for periodontitis treatment. GO and KEGG analyses revealed that the primary pathways mediating the therapeutic effects of EH were related to cancer, lipid, and atherosclerosis. Molecular docking showed that 8-isopentenyl-kaempferol had the best binding ability to ESR1, which was confirmed by dynamics simulations. This study demonstrated that EH can be used for periodontitis treatment, and the corresponding targets and potential mechanisms were investigated based on network pharmacology, molecular docking, and dynamics simulation analysis. Notably, 8-isopentenyl-kaempferol exhibited good binding affinity and stability to ESR1, which may partially explain the molecular mechanisms of EH for treating periodontitis. Hence, EH can be a novel choice for the clinical treatment of periodontitis in the future.

Keywords
Epimedii herba
Periodontitis
Network pharmacology
Molecular docking
Molecular dynamics
8-Isopentenyl-kaempferol
Funding
This work was supported by grants from the Foundation of Science and Technology Department of Henan Province, China (no. 212102310103); Natural Science Foundation of Education Department of Henan Province, China (no. 21A320004); Foundation of the National Health Commission of Henan Province, China (no. Wjlx2020017); Foundation of the Educational Administration Department of Henan University, China (no. HDXJJG2020-83); and Foundation of Science & Technology Department of Kaifeng City, Henan Province, China (no. 2203015).
Conflict of interest
Yuankun Zhai is an Editorial Board Member of this journal but was not in any way involved in the editorial and peer-review process conducted for this paper, directly or indirectly. Separately, other authors declared that they have no known competing financial interests or personal relationships that could have influenced the work reported in this paper.
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