Berberine, a bioactive alkaloid derived from traditional Chinese medicine, has been reported to improve reproductive endocrine and metabolic abnormalities in patients with polycystic ovary syndrome (PCOS). Despite clinical and experimental indications of benefit, the precise molecular mechanisms mediating berberine’s effects in PCOS remain incompletely defined. This study applied an integrated strategy combining network pharmacology, multi-omics data mining, in vitro cellular assays and molecular simulations to elucidate how berberine may act on PCOS-related pathways, with emphasis on ferroptosis, ROS, immunity and inflammation.
Differentially expressed genes associated with PCOS were screened from the Gene Expression Omnibus (GEO) database. Known and predicted berberine-targeted genes were retrieved from public databases. These two gene sets were intersected and used to build a protein–protein interaction (PPI) network to reveal potential functional modules and key targets through network pharmacology analysis.
Network pharmacology analysis identified a total of 32 common targets shared between PCOS-associated differential expression and berberine-targeted genes. A PPI network constructed from these intersecting targets was used to explore topological relationships and to prioritize functionally central nodes for further analysis.
Further screening of the PPI network yielded 8 hub genes that together constitute a nuclear receptor–kinase interaction module. Enrichment analysis of these hub genes indicated primary involvement in metabolism-, reproduction- and inflammation-related signaling pathways. The hub genes were reported to be cell-specifically correlated with N6-methyladenosine (m6A) RNA modification, ferroptosis, and immune-inflammatory processes, suggesting multiple regulatory axes through which berberine may influence PCOS pathophysiology.
The authors conducted in vitro cellular assays using KGN (human granulosa-like tumor cell line) and Ishikawa (endometrial) cell models to validate predicted effects. In these assays, berberine treatment produced three principal findings reported in the abstract: suppression of cell proliferation, elevation of intracellular ROS levels, and reduction of intracellular iron concentrations. These cellular phenotypes are consistent with activation or modulation of oxidative stress–linked and iron-dependent pathways such as ferroptosis, and with potential impacts on proliferative and inflammatory signaling relevant to PCOS.
To probe direct ligand–receptor interactions, molecular docking and molecular dynamics simulations were applied. The simulations revealed favorable binding energies of berberine to the modeled target receptors and stable root-mean-square deviation (RMSD) values for the ligand–receptor complexes over simulation time, supporting the plausibility of direct interactions between berberine and the identified targets.
Combining network pharmacology, enrichment analyses, cellular assays and molecular simulations, the study presents a multi-axis model in which berberine targets a nuclear receptor–kinase interaction module and exerts coordinated effects on m6A modification, ferroptosis, ROS accumulation and immune-inflammatory responses. The reported reduction in intracellular iron and increase in ROS in cell models align mechanistically with ferroptosis-related modulation, while hub gene associations implicate nuclear receptor signaling and kinase activity as nodal points linking metabolic, reproductive and inflammatory pathways.
The study concludes that berberine acts via a multi-target, multi-pathway mechanism in PCOS, centering on a nuclear receptor–kinase module and influencing m6A, ferroptosis, ROS and immune inflammation. The work integrates multi-omics computational analysis with experimental validation and molecular simulations to provide a systems-level perspective of berberine’s actions.
Details not reported in the abstract and therefore not available here include the specific identities of the 8 hub genes, exact experimental conditions (concentrations, time points), quantitative results from assays, and complete docking parameters. The abstract states no competing interests.
Overall, the reported evidence supports a model in which berberine modulates oxidative stress, iron handling and immune-inflammatory signaling through interactions with nuclear receptor–kinase networks, offering mechanistic insight into its potential therapeutic effects in PCOS.