Prolyl-isomerase 1 (Pin1) is a conserved enzyme that regulates cell processes such as cell cycle progression, transcriptional regulation, and apoptosis. However, overexpression of Pin1 is correlated with a higher probability of prostate tumor recurrence. We utilized a molecular docking technique to identify Pin1 inhibitors from a database of natural product and natural product-like compounds. The action of the hit compounds against Pin1 activity was studied using multiple methods, including a fluorometric enzymatic assay, co-immunoprecipitation, western blotting, cell thermal shiftm, and other techniques. We have identified compound1 as a natural-product-like inhibitor of Pin1 activity via structure-based virtual screening and showed that compound1 could target Pin1 and disrupt the interaction between Pin1 and the p65 subunit of NF-B in cells. Furthermore, compound1 reduced nuclear p65 (Thr254) phosphorylation and attenuated NF-B activity in cells. Finally, compound1 induced apoptosis in prostate cancer cells. Compound1 represents a natural product-like Pin1 inhibitor that acts via targeting the Pin1-NF-B interaction.