β-Boswellic Acid Suppresses Migration and Invasion and Attenuates TGF-β1-Induced EMT-Related Changes in PC-3 Prostate Cancer Cells

β-Boswellic acid (BA) has potential antitumor activity, but its effects on migration, invasion, and epithelial–mesenchymal transition (EMT)-related phenotypes in prostate cancer cells remain unclear. In this study, we integrated public transcriptomic data, candidate molecule prediction, machine learning, functional association analysis, and molecular simulations with MTT, wound-healing, Transwell, qPCR, Western blotting, transcriptomic analysis, and data-independent acquisition proteomics to evaluate BA effects on PC-3 cells and explore its potential molecular basis. We identified 22 candidate BA-related molecules and prioritised DPP4, MME, and ABL1 for further analysis. Higher BA concentrations reduced PC-3 cell viability. At the same time, BA suppressed wound closure, migration, and invasion and attenuated TGF-β1-induced EMT-related changes, accompanied by increased E-cadherin and decreased N-cadherin, Snail, and ZEB1 levels. DPP4, MME, and ABL1 also exhibited BA-associated expression changes. Integrated transcriptomic and proteomic analyses suggested that BA-associated molecular alterations involved the cell cycle, DNA replication, cell adhesion, cytoskeletal remodelling, and TGF-β-related processes. In conclusion, BA suppresses migration and invasion in PC-3 cells and attenuates TGF-β1-induced EMT-related changes. Candidate molecules including DPP4, MME, and ABL1, together with the multi-omics findings, provide exploratory clues for further investigation of the potential molecular basis of BA activity.