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A compound named SD118-xanthocillin X (<strong>1</strong>) (C<sub>18</sub>H<sub>12</sub>N<sub>2</sub>O<sub>2</sub>), isolated from <em>Penicillium</em> <em>commune</em> in a deep-sea sediment sample, has been shown to inhibit the growth of several cancer cell lines <em>in vitro</em>. In the present study, we employed a growth inhibition assay and apoptotic analysis to identify the biological effect and detailed mechanism of SD118-xanthocillin X (<strong>1</strong>) in human hepatocellular carcinoma (HepG2) cells. SD118-xanthocillin X (<strong>1</strong>) demonstrated a concentration-dependent inhibitory effect on the growth of HepG2 cells and caused slight cellular apoptosis and significantly induced autophagy. Autophagy was detected as early as 12 h by the conversion of microtubule-associated protein 1 light chain 3 (LC3-I) to LC3-II, following cleavage and lipid addition to LC3-I. The pharmacological autophagy inhibitor 3-methyladenine largely attenuates the growth inhibition and autophagic effect of SD118-xanthocillin X (<strong>1</strong>) in HepG2 cells. Our data also indicated that the autophagic effect of SD118-xanthocillin X (<strong>1</strong>) occurs via the down-regulation of the MEK/ERK signaling pathway and the up-regulated class III PI3K/Beclin 1 signaling pathway.