Mechanism of Cnidii Fructus in the treatment of periodontitis with osteoporosis based on network pharmacology, molecular docking, and molecular dynamics simulation.
10.7518/hxkq.2025.2024275
- Author:
Miaomiao FENG
1
;
Xiaoran XU
1
;
Ningli LI
1
;
Mingzhen YANG
1
;
Yuankun ZHAI
1
Author Information
1. Kaifeng Key Laboratory of Periodontal Tissue Engineering, School of Stomatology, Henan University, Kaifeng 475001, China.
- Publication Type:Journal Article
- Keywords:
Cnidii Fructus;
molecular docking;
molecular dynamics simulation;
network pharmacology;
osteoporosis;
periodontitis
- MeSH:
Molecular Docking Simulation;
Molecular Dynamics Simulation;
Network Pharmacology;
Periodontitis/complications*;
Drugs, Chinese Herbal/chemistry*;
Osteoporosis/complications*;
Humans;
Protein Interaction Maps;
Cnidium/chemistry*
- From:
West China Journal of Stomatology
2025;43(2):249-261
- CountryChina
- Language:Chinese
-
Abstract:
OBJECTIVES:This study aimed to explore the active components, potential targets, and mechanism of Cnidii Fructus in the treatment of periodontitis with osteoprosis through network pharmacology, molecular docking, and molecular dynamics simulation technology.
METHODS:The main chemical constituents and targets of Cnidii Fructus were screened using the TCMSP and SwissTargetPrediction databases, as well as literature reports. Targets of periodontitis and osteoporosis were predicted using different databases. The intersection targets of Cnidii Fructus, periodontitis, and osteoporosis were obtained using Venny 2.1. The protein-protein interaction network was formed on the STRING platform. Cytoscape 3.9.1 was used to construct the active component-intersection target interaction network, perform the topological analysis, and screen key targets and core active components. Furthermore, the Metascape database was used to perform gene ontology (GO) function and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis on the intersection targets. The top five key targets and core active components were selected as receptor proteins and ligand small molecules. Discovery Studio 2019 was used to dock ligands and receptors and visualize the docking results. Molecular dynamics simulation was conducted using Gromacs2022.3 to assess the stability of the interactions between the core active components and the main targets.
RESULTS:A total of 20 potential active ingredients of Cnidii Fructus were screened, and 116 targets of Cnidii Fructus were obtained for treating periodontitis and osteoporosis. GO and KEGG analyses of the 116 targets showed that Cnidii Fructus may play a therapeutic role through the phosphoinositide 3-kinase-protein kinase B (PI3K-Akt) and advanced glycation end products-receptor for advanced glycation end products (AGE-RAGE) signaling pathways. Molecular docking showed that the core constituents were well bound to the main targets. Molecular dynamics simulations confirmed the stability of the Diosmetin-AKT1 complex system.
CONCLUSIONS:The preliminary discovery of the potential molecular pharmacological mechanism of Cnidii Fructus extract in the targeted treatment of periodontitis with osteoporosis through a multi-component, multitarget, and multi-pathway approach can serve as a theoretical foundation for future drug-development research and clinical application.
