The present invention provides assays for the identification of inhibitors of endopeptidase toxins. The assays utilize genetically engineered yeast cells that contain a conditionally expressed endopeptidase toxin. When conditions for expression of the toxin are met, the toxin cleaves a yeast (natural or engineered) peptide product that is required for yeast survival. If the yeast is grown in the presence of an candidate substance that is an inhibitor of the toxin, the yeast survives, thereby providing a rapid and sensitive identification of the inhibitor.