Chemical Profiling and Mechanistic Insights into Stichopodidae Viscus Extract for Ulcerative Colitis via UPLC-IMS-Q-TOF-HDMSE and Network Pharmacology

Background: The visceral organs of sea cucumbers belonging to the family Stichopodidae, also known as Stichopodidae Viscus (SV), have been traditionally used for the management of gastrointestinal disorders. Experimental evidence has shown that the ethanol extract of SV (SVE) alleviates ulcerative colitis (UC) symptoms in a mouse model. However, the chemical constituents of SVE and the potential molecular targets mediating its effects in UC remain unclear. Methods: In this study, SVE was prepared from Apostichopus japonicus (Selenka). A reliable and sensitive strategy integrating advanced analytical and informatics tools was employed to profile the chemical components of SVE. Analyses were performed using ultra-performance liquid chromatography coupled with ion mobility spectrometry and quadrupole time-of-flight mass spectrometry operating in high-definition MSE (UPLC-IMS-Q-TOF-HDMSE), with data processed using the UNIFI scientific information system. Constituent identification relied on retention time (RT), accurate mass (MS1), experimentally acquired HDMSE (MS2) spectra, and collision cross-section (CCS). Metabolomics-based approaches were further applied to characterize the in vivo exposure profile of SVE components in mouse serum and colon tissue after oral administration. Subsequently, the putative bioactive constituents and their underlying mechanisms of action were investigated using network pharmacology and molecular docking. Results: Based on the integrated identification strategy, a total of 78 compounds, including saponins, phenolic acids, fatty acids, and amino acids, were annotated in SVE, among which 6 compounds were verified using authentic reference standards to ensure unambiguous identification. Subsequently, 35 features in serum and 24 in the colon were found to be significantly altered following a single oral dose of SVE in mice, and were defined as SVE-related differential constituents. After network pharmacology analyses, 129 shared targets were identified between potential targets of SVE-related components in serum and UC-related targets, including PIK3CA, EGFR, and AKT1. Functional enrichment analysis suggested that SVE might exert its effects in UC through modulation of key nodes within the PI3K-Akt and EGFR signaling pathways, as well as lipid- and atherosclerosis-related pathways. Molecular docking results further indicated moderate binding affinities of representative SVE-related differential components toward PIK3CA, AKT1, and EGFR. Conclusions: This study clarifies the chemical basis and potential UC-related mechanisms of SVE, providing a scientific rationale for the development of SV-derived therapeutic candidates for UC.