Molecular mechanism of hesperetin in the treatment of heart failure by network pharmacology, molecular docking and molecular dynamics
10.3760/cma.j.cn121382-20250714-00054
- VernacularTitle:基于网络药理学、分子对接和分子动力学研究橙皮素干预心力衰竭的分子机制
- Author:
Yue LI
1
;
Guiyu LI
;
Xiaoling ZHU
;
Miaoyang LIN
;
Danping XU
Author Information
1. 青海大学医学院中医系，西宁 810001
- Keywords:
Heart failure;
Hesperetin;
Network pharmacology;
Molecular docking;
Molecular dynamics
- From:
International Journal of Biomedical Engineering
2025;48(5):462-472
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To systematically elucidate the molecular mechanism of hesperetin in the treatment of heart failure by network pharmacology, molecular docking, and molecular dynamics, and to clarify its key targets and pathway regulatory networks.Methods:Potential targets of hesperetin were retrieved from the PubChem, Pharmmapper, SwissTargetPrediction, and Similarity ensemble approach databases. Heart failure-related targets were obtained from the OMIM, GeneCards, and TTD databases. Intersection targets were identified using Venny 2.1. A protein-protein interaction (PPI) network of potential targets was constructed using the STRING database and Cytoscape 3.9.0 software. Gene ontology (GO) functional and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analyses of key targets were performed using the Metascape database. Molecular docking was carried out using Autodock vina1.1.2. GROMACS (2024.03) was employed to conduct a 100 ns molecular dynamics simulation on the optimal affinity complex. The thermodynamic stability of the candidate complex during simulation was evaluated by analyzing the root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), and binding free energy. Data were analyzed by an independent sample t test or one-way analysis of variance. Results:A total of 356 related targets of hesperetin and 2 923 related targets of heart failure were screened, with 152 intersection targets identified as potential targets for hesperetin intervention in heart failure. PPI network topological analysis revealed key targets for hesperetin intervention in heart failure, including insulin-like growth factor 1, estrogen receptor 1 (ER1), cysteine aspartic acid specific protease-3, sarcoma proto-oncogene, matrix metalloproteinase 9 (MMP9), MMP2, Janus kinase 2 (JAK2), albumin, heat shock protein 90 alpha family class A member 1, epidermal growth factor receptor, and B-cell lymphoma-2 (Bcl-2). GO functional enrichment analysis indicated that biological processes were mainly enriched in response to hormone stimulation, positive regulation of cell migration, gland development, response to nutritional levels, regulation of system processes, and response to trauma. Molecular functions were primarily enriched in phosphotransferase activity, nuclear receptor activity, endopeptidase activity, kinase binding, heme binding, hormone binding and protease binding. Cellular components were mainly enriched in membrane-related structures such as vesicle cavity, membrane raft, vacuole cavity, receptor complex and extracellular matrix containing collagen. KEGG pathway enrichment analysis showed that these key targets were significantly enriched in lipid and atherosclerosis, diabetic cardiomyopathy, and the hypoxia-inducible factor-1 signaling pathway. Molecular docking results indicated that the binding energy of hesperetin to MMP9 (?46.442 kJ/mol) was significantly lower than that to other key targets. Molecular dynamics simulations revealed that the hesperetin-MMP9 complex maintained structural stability, with an average RMSD of 1.60 ?. The average RMSF values of MMP9 residues (0.83 ?) and ligand atoms (0.68 ?) indicated stable protein conformation and ligand-binding states. The Rg values of MMP9 [(15.04±0.60) ?] and hesperetin [(4.19±0.35) ?] showed minimal fluctuations, further supporting structural compactness. The total binding free energy of the hesperetin-MMP9 complex during the 100 ns simulation was (?142.3±6.3) kJ/mol, with minimal energy fluctuations, confirming that the complex remained structurally stable without significant energy transition throughout the simulation.Conclusions:Hesperetin may bind effectively to targets such as MMP9, JAK2, Bcl-2, and ER1, and form a stable complex with MMP9. It is suggested to influence biological processes related to lipids and signaling pathways such as atherosclerosis, diabetic cardiomyopathy, and hypoxia-inducible factor-1, thereby playing a role in heart failure intervention.
