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To study the antibacterial mechanism of palmatine based on network pharmacology, molecular docking, and molecular dynamics.
The drug targets of palmatine were predicted through the Swiss Target Prediction website, and the potential antibacterial targets of palmatine were obtained by mapping them with the antibacterial targets retrieved from GeneCards and OMIM databases. Protein-protein interaction network was constructed using STRING database and Cytoscape software and key targets were screened. The DAVID database was used to carry out Gene Ontology（GO） functional analysis and Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway enrichment analysis of potential targets, and visual processing was performed to build the “Component-Target-Pathway” network of palmatine. The binding of palmatine to key targets was validated through molecular docking and molecular dynamics simulations. In vitro antibacterial experiments were conducted to verify the antibacterial activity of palmatine.
A total of 28 critical anti-bacterial targets of palmatine were screened and enriched to 199 GO entries and 105 related pathways. “Ingredients-Target-Pathway”network showed that MAPK8, RAC1, and STAT3 were key anti-bacterial targets.The molecular docking results indicated that palmatine had an excellent binding effect with key targets MAPK8 and RAC1. Molecular dynamics studies found that there were hydrogen bonds and hydrophobic interactions between palmatine and proteins, enabling stable binding of palmatine to target proteins. In vitro antibacterial experiments showed that palmatine had strong inhibitory activity against Staphylococcus aureus and Candida albicans, and it had synergistic effects when combined with positive drugs.
Palmatine may exert its antibacterial effects by inhibiting the gene expression of MAPK8 and RAC1 through endocrine resistance and signaling pathways such as PI3K-Akt and FoxO.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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