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The metabolism of gentiopicroside in vivo was studied for the first time by LC/MS following picolinoyl derivatization.Incubation of erythrocentaurin, one of the main in vitro metabolites of GPS by intestinal bacteria, with liver microsome indicated that gentiopicroside maybe metabolized to the final metabolite 3, 4-dihydro-5-(hydroxymethyl) isochroman-1-one in vivo.After hydrolyzation with sulfatase, 3, 4-dihydro-5-(hydroxymethyl) isochroman-1-one was successfully detected in rat plasma after oral administration of gentiopicroside by LC/MS following picolinoyl derivatization.4-methoxyphenyl methanol was used as the internal standard to quantify 3, 4-dihydro-5-(hydroxymethyl) isochroman-1-one in rat plasma.The metabolic pathway of gentiopicroside in rats was proposed.The monoterpene compound gentiopicroside was found to be metabolized to dihydroisocoumarin which maybe responsible for the pharmacological effect of gentiopicroside.