Virtually all of the 560 human proteases are stored as inactive proenyzmes and are strictly regulated. We report the identification and characterization of small molecules that directly activate the apoptotic proenzymes, procaspases-3 and -6. Surprisingly, these compounds induce autoproteolytic activation by stabilizing a conformation that is both more active and more susceptible to intermolecular proteolysis. These procaspase activators bypass the normal upstream proapoptotic signaling cascades and induce rapid apoptosis in a variety of cell lines. Systematic biochemical and biophysical analyses identified a cluster of mutations in procaspase-3 that resist small molecule activation both in vitro and in cells. Compounds that induce gain-of-function are rare and the activators reported here will enable direct control of the homodimeric executioner caspases in apoptosis and in cellular differentiation.Activation of proteases trigger a myriad of fate-determining biological events, such as apoptosis and blood clotting, both inside and outside of the cell (1). Proteases are generally stored as inactive proenzymes that are usually activated by upstream proteases or by themselves. These activation events may sometimes involve binding a protein partner or, in rare instances, interaction with a natural small molecule (2) or peptide (3). In the case of autoproteolysis, the proenzyme must achieve not only an active state, but also one in which the sites of proteolysis are exposed. In situ activation of specific proproteases with synthetic small molecules would uncover new molecular principles in zymogen activation and facilitate direct control of these important processes in biology.The executioner procaspases, consisting of procaspases-3, -6 and -7, represent excellent initial candidates for discovery of small molecule protease activators. Caspases are a family of homodimeric cysteine proteases responsible for many of the fate-determining processes in cell biology including apoptosis, innate immune signaling, early stages of stem cell differentiation, and cellular remodeling (4-6). As with most proteases, caspases are synthesized as inactive procaspases, or zymogens, and are activated by upstream proteolysis or autoproteolysis. Previous studies have shown that the mature active caspases are intrinsically dynamic (7,8) and sample both an "on-state" and an "off-state" that structurally resembles the zymogen-like conformation (9,10). Small molecules have been found to trap these two forms of the mature enzyme (11,12). We reasoned that, if the procaspases existed in a similar dynamic equilibrium of off-and on-states, it might be possible to find small molecules that promote autoproteolytic activation via stabilization of an on-state conformation. Executioner procaspases are particularly good targets as they are susceptible to rapid activation by both upstream proteases and self-proteolysis. Thus, any activation would be accentuated in trans by autocatalytic activation. Moreover, these particular caspases are essential...