Isopentenyl flavonoids were isolated from Daphne giraldii Nitsche and their pharmacological activity was further studied to enrich its chemical composition. Seventeen isopentenyl flavonoids (1a/1b-3a/3b and 4-14), including thirteen undescribed compounds (1a/1b-3a/3b and 4-10), were obtained from D. giraldii under the guidance of HSQC-based DeepSAT. Their structures and configurations were established by comprehensive spectroscopic analysis, ECD, and GFN2NMR methods. Moreover, all compounds were evaluated for potential cytotoxicity against hepatocellular carcinoma HepG2 and Hep3B cell lines. Among them, undescribed compound 3 exhibited potent growth-inhibitory activities against HepG2 and Hep3B cells due to the presence of a unique isopentene group and pyran ring structure, with half-maximal inhibitory concentration values of IC = 17.55 ± 1.65 μM and IC = 1.12 ± 0.08 μM, respectively. Morphological and staining analyses suggested compound 11 induced apoptosis in HepG2 and Hep3B cells, indicating that the isopentene group at the C-8 position was the active group.
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