Abstract

Background Ischemic stroke (IS) is a major global cause of disability and death, with its complex pathophysiology posing a significant challenge for effective therapy. Although flavonoids from Ziziphora clinopodioides Flavonoids (ZCF) have demonstrated neuroprotective potential, their comprehensive mechanisms of action remain incompletely understood. Objective The purpose of this study is to systematically elucidate the improvement effect of ZCF on ischemic stroke and its potential mechanism by integrating multi-omics analysis and in vitro and in vivo experimental verification. Methods In this study, the neuroprotective mechanism of ZCF on MCAO/R-treated SD rats and OGD/R-treated PC12 cells was studied by combining transcriptomics, non-targeted metabolomics, and molecular biology verification (Western blot, q-PCR, immunofluorescence, etc.). The key role of FUNDC1 in this pathway was verified by siRNA knockdown. Results ZCF administration significantly improved neurological function, reduced cerebral infarction volume, and reduced neuronal apoptosis. Integrated transcriptomics and metabolomics analysis found that ZCF reversed disease-related changes, and its core effects were the mitophagy and ferroptosis pathways. Mechanistically, ZCF alleviates pathological TDP-43 aggregation, activates FUNDC1-mediated mitophagy, and inhibits ferroptosis. Crucially, siRNA knockdown of FUNDC1 eliminated these protective effects. Conclusion ZCF improves ischemic stroke by enhancing FUNDC1-dependent mitophagy to remove pathological TDP-43, thereby inhibiting the mechanism of ferroptosis.