Study of GJKBW against RA based on the Chinmedomics combined LIP-MS molecular fishing technology: a new strategy for discovering the therapeutic material basis

Rheumatoid arthritis (RA) is a major chronic autoimmune disease. Current conventional drugs face significant challenges, including severe side effects, high recurrence rates, and unsuitability for long-term use. In contrast, traditional Chinese medicine (TCM) has garnered increasing attention due to its multi-target regulatory advantages. Guan Jie Ke Be Wan (GJKBW) demonstrates notable therapeutic efficacy, but its therapeutic material basis and mechanisms of action remain unclear, which limits its precise clinical application and therapeutic optimization. Based on this, this study adopted Chinmedomics combined with Limited Proteolysis-coupled Mass Spectrometry (LIP-MS) molecular fishing technology to screen the key metabolic pathways in RA and analyze the relevant protein targets in these pathways. Key protein targets were extracted to identify the potential therapeutic material basis of GJKBW. LIP-MS and molecular dynamics analysis were employed to validate the reliability of its specific binding to the target proteins, and finalized the results and related mechanisms. Finally, the linoleic acid metabolic pathway was identified as a key pathway in RA. It was discovered that that GJKBW exerted its therapeutic effects by targeting key proteins such as FADS2, PLA2G4A, and PLA2G15 to regulate linoleic acid metabolism. This regulation subsequently influenced the downstream metabolism of arachidonic acid, ultimately leading to the inhibition of the expression of related inflammatory factors. Isobergapten and Wogonin are identified as the therapeutic material basis for GJKBW within this mechanism of action. This study provides a novel paradigm for the “quantity-effect” correlation research of TCM formulas, incorporating “bioinformatics prediction-multi-omics validation-LIP-MS screening-molecular dynamics analysis”. • The LA metabolic pathway was a key pathway in the treatment of RA by GJKBW. • GJKBW regulates LA metabolism by targeting key proteins such as FADS2, PLA2G4A, and PLA2G15. • Isobergapten and Wogonin were identified as the therapeutic material basis of GJKBW in regulating LA metabolism. • An analytical method for therapeutic material basis was established based on Chinmedomics with LIP-MS molecular fishing technology in treating RA.