Page 84 - GPD-3-4

Gene & Protein in Disease

ORIGINAL RESEARCH ARTICLE
Can Epimedii herba treat periodontitis? A

prediction based on network pharmacology,
molecular docking, and dynamics analysis

Junhan Wan 1,2,3 , Wenwen Wang 1,2 , Ningli Li 1,2 , Mingzhen Yang 1,2 ,
Yingjie Zhu 4 , and Yuankun Zhai 1,2,5 *
1 School of Stomatology, Henan University, Kaifeng, Henan, China
2 Kaifeng Key Laboratory of Periodontal Tissue Engineering, Kaifeng, Henan, China

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
*Corresponding author: performed. Molecular docking between the screened chemical components of EH and
Yuankun Zhai key targets was performed using Discovery Studio 2019. The binding stability between
(zhaiyuankun@henu.edu.cn)
components and target proteins was confirmed using molecular dynamics simulations.
Citation: Wan J, Wang W, Li N, The binding stability between components and target proteins was confirmed using
Yang M, Zhu Y, Zhai Y. Can
Epimedii herba treat periodontitis? molecular dynamics simulations. Through network pharmacological analysis, 23
A prediction based on network active compounds of EH were identified, including kaempferol and icariin. Based on
pharmacology, molecular GeneCards, GEO, and other databases, 3291 periodontitis-related genes were obtained.
docking, and dynamics analysis.
Gene Protein Dis. 2024;3(4):4427. Venn diagram analysis revealed 137 intersection targets of EH and periodontitis, and
doi: 10.36922/gpd.4427 Protein kinase B (AKT1) and Tumor necrosis factor (TNF) were identified as the key
Received: August 2, 2024 targets of EH for periodontitis treatment. GO and KEGG analyses revealed that the
Accepted: October 22, 2024 primary pathways mediating the therapeutic effects of EH were related to cancer, lipid,
Published Online: November 18, and atherosclerosis. Molecular docking showed that 8-isopentenyl-kaempferol had the
2024 best binding ability to ESR1, which was confirmed by dynamics simulations. This study
Copyright: © 2024 Author(s). demonstrated that EH can be used for periodontitis treatment, and the corresponding
This is an Open-Access article targets and potential mechanisms were investigated based on network pharmacology,
distributed under the terms of the
Creative Commons Attribution molecular docking, and dynamics simulation analysis. Notably, 8-isopentenyl-
License, permitting distribution, kaempferol exhibited good binding affinity and stability to ESR1, which may partially
and reproduction in any medium, explain the molecular mechanisms of EH for treating periodontitis. Hence, EH can be a
provided the original work is
properly cited. novel choice for the clinical treatment of periodontitis in the future.
Publisher’s Note: AccScience
Publishing remains neutral with Keywords: Epimedii herba; Periodontitis; Network pharmacology; Molecular docking;
regard to jurisdictional claims in
published maps and institutional Molecular dynamics; 8-Isopentenyl-kaempferol
affiliations.

Volume 3 Issue 4 (2024) 1 doi: 10.36922/gpd.4427