Peganum harmala L. is a medicinal plant, and its seeds have been used to treat gastrointestinal cancer and malaria for a long time in North-Western China. In the present study, we aimed to probe the potential molecular targets and pharmacological mechanisms of Peganum harmala L. seeds (PHS) on hepatocellular carcinoma (HCC) using network analysis and molecular docking. First, the chemical ingredients of PHS were obtained from TCMID and BATMAN-TCM databases, and the effective ingredients were screened by SwissADME. Furthermore, the target information of the effective ingredients was acquired from PharmMapper and SwissTargetPrediction databases. Secondly, HCC-related targets were obtained from Liverome, DisGeNET, and GeneCards databases. The intersection with the PHS was obtained. The "compounds-targets" was drawn using Cytoscape software, and PPI network diagrams were drawn using their intersection targets. GO analysis and KEGG enrichment analysis were carried out using the DAVID database. Finally, molecular docking was conducted between protein receptors and the active components using AutoDockTools. Our results showed 105 intersection targets of PHS with HCC. Moreover, 10 core targets included ALB, AKT1, EGFR, CASP3, SRC, ESR1, MAPK3, MMP9, ANXA5, and MAPK1. Besides, 404 GO functional annotations were obtained, including 287 biological processes, 37 cell compositions, and 80 molecular functions. In addition, 110 signaling molecules and pathways, including chemical oncogene receptors, PI3K-Akt pathway, HCC, and hepatitis B, were identified. The molecular docking results showed that the binding energies of the 10 core targets and the 12 active components were all less than –5 kcal/mol. In conclusion, this study expounded on the "component-target-pathway" interaction mechanism of PHS for the treatment of HCC, and it also provided a scientific basis for the clinical application of PHS.
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