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Seven new anthraquinones with rare 2-isopropyldihydrofuran (<b>1</b>–<b>3</b>) and 2,2-dimethylpyrano (<b>4</b>–<b>7</b>) moieties together with thirty-four known compounds were isolated from the extracts of whole <i>Hedyotis diffusa</i> plants. Their structures were elucidated and established by various spectroscopic and spectrometric analytical methods. Among these isolates, selected compounds were examined for their anti-inflammatory activity. The results showed that rare substituted anthraquinones displayed potent inhibitory activity with IC₅₀ values ranging from 0.15 ± 0.01 to 5.52 ± 1.59 µM on the <i>N</i>-formyl-methionyl-leucyl-phenylalanine/cytochalasin B (fMLP/CB)-induced superoxide anion generation and elastase release cellular models. Meanwhile, the proposed drug target of the active anthraquinone was studied by computer modeling. The binding affinity between the anti-inflammatory anthraquinone and elastase was evaluated by molecular docking. These results provided the scientific insight into the medicinal values of <i>Hedyotis diffusa</i> and vision of development as lead compounds.