The root of Isatis indigotica is used as a traditional Chinese medicine (termed Isatidis Radix) due to its antiviral effects. We examined compounds isolated from Isatidis Radix and elucidated the structures of three new natural alkaloids, and we examined the possible mechanisms or active targets of indole alkaloids occurring in blood of rats treated by gavage. Three new natural products were isolated from Radix Isatidis for the first time, including 1-methoxy-2-indoleacetonitrile, 1-hydroxy-3-indoleacetonitrile, 8-Methoxy-1, 2-dihydroquinoline, and 4 compounds isolated from this medicinal material for the first time. Their structures were elucidated using nuclear magnetic resonance. The components of Isatidis Radix were analysed using liquid chromatography tandem mass spectrometry, and 33 compounds were detected in plasma of treated rats; 24 of these compounds were indole alkaloids, and they included the newly identified compounds. Molecular docking and in vitro antithrombin activity tests showed HA inhibition activity of indoleacetonitriles.
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