Union Is Strength: Target-Based and Whole-Cell High-Throughput Screens in Antibacterial Discovery

Antimicrobial resistance is one of the greatest global health challenges today. For over 3 decades, antibacterial discovery research and development have been focused on cell-based and target-based high-throughput assays. Target-based screens use diagnostic enzymatic reactions to look for molecules that can bind directly to and inhibit the target. Target-based screens are applied only to proteins that can be successfully expressed and purified and the activity of which can be effectively measured using a biochemical assay. Often the molecules found in these in vitro screens are not active in cells due to poor permeability or efflux. On the other hand, cell-based screens use whole cells and look for growth inhibition. These screens give higher numbers of hits than target-based assays and can simultaneously test many targets of one process or pathway in their physiological context. Both strategies have advantages and disadvantages when used separately. In the past 15 years, our increasing knowledge of bacterial physiology has led to the development of innovative and sophisticated technologies to perform high-throughput screening combining these two strategies and thus minimizing their disadvantages. In this review, we discuss recent examples of high-throughput approaches that used both target-based and whole-cell screening to find new antibacterials, the new insights they have provided, and how this knowledge can be applied to other in vivo-validated targets to develop new antimicrobials.