Structurally diverse small molecules, including 5-(2-benzofuryl)-4-phenyl-1,2,4-triazole-3-thiol (BETT), have been identified via high-throughput screening as activators of caspase-3 in HeLa cell extracts. However, little is known about their mechanism of action. In this study, we investigate how BETT regulates prothymosin alpha (ProT), a nuclear protein previously shown to play essential roles in apoptosis. We first showed that Apaf-1 is the direct target protein of BETT. We further demonstrated that BETT relieved ProT-mediated inhibition of apoptosome formation by blocking the interaction between Apaf-1 and ProT. Using two-dimensional (1)H-(15)N heteronuclear single-quantum correlation (HSQC) experiments, we were also able to examine the interaction between Apaf-1 and (15)N-labeled ProT alpha. Furthermore, we were able to reconstitute the entire caspase-3 activation pathway using purified ProT, Apaf-1, procaspase-9, procaspase-3, Hsp70, cytochrome c, PHAPI, CAS, and regulatory compounds to mimic stress-induced apoptosis in vitro. Together, these studies would lead to novel and specific methods for the prevention, diagnosis, and treatment of human cancer.