Low-cost drug discovery with engineered E. coli reveals an anti-mycobacterial activity of benazepril

Whole-cell screening for Mycobacterium tuberculosis (Mtb) inhibitors is complicated by the pathogens slow growth and biocontainment requirements. Here we present a synthetic biology framework for assaying Mtb drug targets in engineered E. coli. We construct Target Essential Surrogate E. coli (TESEC) in which an essential metabolic enzyme is deleted and replaced with an Mtb-derived functional analog, linking bacterial growth to the activity of the target enzyme. High throughput screening of a TESEC model for Mtb alanine racemase (ALR) revealed benazepril as a targeted inhibitor. In vitro biochemical assays indicated a noncompetitive mechanism unlike that of clinical ALR inhibitors. This is the first report of an antimicrobial activity in an approved Angiotensin Converting Enzyme (ACE) inhibitor and may explain clinical data associating use of ACE inhibitors with reduced Mtb infection risk. We establish the scalability of TESEC for drug discovery by characterizing TESEC strains for four additional targets. SIGNIFICANCE STATEMENTThe challenge of discovering new antibiotics is both scientific and economic. No simple test can determine if a given molecule will be safe and effective in real human patients. Many drug candidates must therefore be advanced for each new antibiotic that reaches the market - a risky and expensive process. In this work we use synthetic biology to engineer the common laboratory model bacterium E. coli as a tool for early stage antibiotic discovery. As a proof of concept we expressed a known tuberculosis drug target and found a novel inhibitor: benazepril. Many other drug targets could be screened similarly using the system that we describe. Because E. coli can be grown safely and cheaply, this approach may help to reduce costs and make drug discovery more accessible.