Background: Pulsatillae radix (PR), a medicinal root plant and a well-known Chinese herbal remedy, is primarily used for its heat-clearing, detoxifying, blood-cooling, and antiinflammatory properties. This study aimed to investigate the underlying mechanisms by which PR exerts therapeutic effects on ulcerative colitis (UC) through an integrated approach, combining ultra-high performance liquid chromatography with quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF-MS/MS), network pharmacology, and molecular docking.

Methods: The constituents of PR were systematically analyzed using UHPLC-Q-TOF-MS/MS. Potential targets of active components were identified via the SwissTargetPrediction and PharmMapper databases, while UC-related disease targets were retrieved from GeneCard, OMIM, and other relevant databases. Overlapping targets between PR and UC were determined using Venn analysis. Cytoscape software facilitated the construction of the compound-disease-target network. The STRING database was employed to generate a protein-protein interaction (PPI) network for the intersecting targets, and core targets were identified using the CytoNCA plugin. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted using the DAVID platform. Lastly, molecular docking of key components with target proteins was carried out using PyMOL.

Results: A total of 27 active compounds, 237 drug targets, and 4622 disease targets were identified. Intersection analysis revealed 141 shared targets, while the PPI network identified 10 hub targets. GO and KEGG enrichment analyses indicated that the hub targets were primarily associated with phosphorylation, cytoplasmic functions, nuclear receptor activity, as well as pathways related to the advanced glycation end products-receptor for advanced glycation end products (AGE-RAGE) signaling, T cell receptor (TCR) signaling, lipid and cholesterol metabolism, and various cancer-related pathways. Molecular docking experiments demonstrated that (+)- pinoresinol, cichoric acid, β-ecdysone, pulsatilla saponin D, 23-HBA, and AB4 exhibited stable binding to PIK3R1, TLR4, and ESR1, with AB4 forming the most stable complex with ESR1.

Conclusions: This study established a rapid and effective UHPLC-Q-TOF-MS/MS method for characterizing the main chemical components of PR. Using network pharmacology and molecular docking, the active components and potential mechanisms of PR involved in the UC treatment were investigated, providing a foundation for future experimental studies on pharmacodynamics and the underlying mechanisms.