Exploring the mechanism of Eucommiae Cortex- Epimedii Folium herbal pair in the treatment of osteoporosis by network pharmacology, molecular docking and molecular dynamics
10.3760/cma.j.cn121382-20240507-00409
- VernacularTitle:基于网络药理学、分子对接和分子动力学研究杜仲-淫羊藿药对治疗骨质疏松的作用机制
- Author:
Minjuan WANG
1
;
Ting WANG
;
Xifeng ZHAI
;
Yang LI
;
Lei CAO
;
Jiawei HU
Author Information
1. 陕西省疾病预防控制中心理化检验所，西安 710054
- Keywords:
Network pharmacology;
Molecular docking;
Molecular dynamics;
Eucommiae Cortex;
Epimedii Folium;
Osteoporosis
- From:
International Journal of Biomedical Engineering
2024;47(4):364-374
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To explore the mechanism of Eucommiae Cortex- Epimedii Folium herbal pair in the treatment of osteoporosis through network pharmacology, molecular docking, and molecular dynamics methods. Methods:Search the traditional Chinese medicine systems pharmacology database and analysis platform (TCMSP) and relevant literature to screen the active compounds of Eucommiae Cortex- Epimedii Folium herbal pair. Using TargetNet, SwissTargetPrediction, and STITCH databases to predict the target of active compounds. GeneCards, OMIM, TTD and DisGeNET databases were used to screen the related targets of osteoporosis, and the intersection targets were obtained by Venny 2.1.0 online tool. Using STRING database for protein-protein interaction (PPI) network analysis. Construct a network diagram using Cytoscape 3.8.2 software and perform network feature analysis to determine key targets and core compounds. Using R 3.6.3 software for gene ontology (GO) functional annotation and Kyoto Encyclopedia of genes and genomes (KEGG) signaling pathway analysis. Apply SYBYL-X 2.1.1 software to perform molecular docking between core compounds and key targets, and use GROMACS 2021.6 software for molecular dynamics simulation. Results:Totally 47 active compounds, 329 targets related to compounds, 4 604 targets related to osteoporosis, and 210 intersecting targets of Eucommiae Cortex- Epimedii Folium herbal pair were selected. Network feature analysis showed that luteolin, quercetin, kaempferol, caffeic acid, chryseriol, and pinoresinol were core compounds, while protein kinase B1(Akt1), interleukin-6 (IL-6), steroid receptor coactivator (Src), cysteinyl aspartate specific proteinase-3 (CASP3), epidermal growth factor receptor (EGFR), estrogen receptor 1 (ESR1), prostaglandin-endoperoxide synthase 2 (PTGS2), mitogen-activated protein kinase 8 (MAPK8), and JUN were key targets. GO analysis showed that biological process (BP) mainly involve cellular hormone metabolism, intracellular receptor signaling pathways, oxidative stress responses, hormone metabolism processes, etc. Cell component (CC) mainly involved membrane rafts, membrane microregions, membrane regions, transcription factor complexes, etc. Molecular function (MF) mainly involved nuclear receptor activity, transcription factor activity, steroid hormone receptors, hormone binding, etc. KEGG analysis showed that the signaling pathways of Eucommiae Cortex- Epimedii Folium herbal pair in the treatment of osteoporosis mainly included osteoclast differentiation, PI3K-Akt signaling pathway, and MAPK signaling pathway. Molecular docking showed that the core compounds could accurately bind to the active sites of key target proteins, and molecular dynamics analysis further verified the binding stability between the core compounds and key target proteins. Conclusions:The combination of Eucommiae Cortex- Epimedii Folium herbal pair has the characteristics of multiple components, targets, and pathways in the treatment of osteoporosis, laying a theoretical foundation for its clinical use.
