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Chlorogenic acid (5-CQA),neochlorogenic acid (3-CQA),and cryptochlorogenic acid (4-CQA),usually simultaneously exist in many traditional Chinese medicines (TCMs).However,insufficient attentions have been paid to the comparative metabolism study on these three isomeric constituents with similar effects on anti-inflammation until now.In this study,a novel strategy was established to perform comparative analysis of their metabolic fates in rats and elucidate the pharmacological mechanism of anti-inflammation.Firstly,diagnostic product ions (DPIs) deduced from the representative reference standards were adopted to rapidly screen and characterize the metabolites in rat plasma,urine and faeces using UHPLC-Q-TOF MS.Subsequently,Network pharmacology was utilized to elucidate their anti-inflammatory mechanism.Consequently,a total of 73 metabolites were detected and characterized,including 50,47 and 43 metabolites for 5-CQA,4-CQA and 3-CQA,orderly.Moreover,the network pharmacology study indicated that these three isomeric constituents and their major metabolites with similar in vivo metabolic pathways exerted anti-inflammatory effects through co-owned 20 biological processes,which involved 10 major signal pathways and 159 potential targets.Our study shed light on the similarities and differences of the metabolic profiling and anti-inflammatory activity among these three isomeric constituents and set an example for the further researches on the active mechanism of isomeric constituents existing in TCMs based on comparative metabolism study.