Abstract
New antibiotics are needed to combat rising levels of resistance, with new Mycobacterium tuberculosis (Mtb) drugs having the highest priority. However, conventional whole-cell and biochemical antibiotic screens have failed. Here we develop a strategy termed PROSPECT (primary screening of strains to prioritize expanded chemistry and targets), in which we screen compounds against pools of strains depleted of essential bacterial targets. We engineered strains that target 474 essential Mtb genes and screened pools of 100-150 strains against activity-enriched and unbiased compound libraries, probing more than 8.5million chemical-genetic interactions. Primary screens identified over tenfold more hits than screening wild-type Mtb alone, with chemical-genetic interactions providing immediate, direct target insights. We identified over 40 compounds that target DNA gyrase, the cell wall, tryptophan, folate biosynthesis and RNA polymerase, as well as inhibitors that target EfpA. Chemical optimization yielded EfpA inhibitors with potent wild-type activity, thus demonstrating the ability of PROSPECT to yield inhibitors against targets that would have eluded conventional drug discovery.
Highlights
Johnson, Eachan O, Emily LaVerriere, Emma Office, Mary Stanley, Elisabeth Meyer, Tomohiko Kawate, James E Gomez, Rebecca E Audette, Nirmalya Bandyopadhyay, Natalia Betancourt, Kayla Delano, Israel Da Silva, Joshua Davis, Christina Gallo, Michelle Gardner, Aaron J Golas, Kristine M
We developed a novel strategy termed PROSPECT (PRimary screening Of Strains to Prioritize Expanded Chemistry and Targets) in which we screen compounds against pools of strains depleted for essential bacterial targets
We have developed PROSPECT, a powerful and rapid chemical-genetic interaction profiling strategy, which is able both to discover many new potential compounds for Mycobacterium tuberculosis (Mtb) drug development and to gain insight into their MOA from the primary screening data
Summary
Eachan O, Emily LaVerriere, Emma Office, Mary Stanley, Elisabeth Meyer, Tomohiko Kawate, James E Gomez, Rebecca E Audette, Nirmalya Bandyopadhyay, Natalia Betancourt, Kayla Delano, Israel Da Silva, Joshua Davis, Christina Gallo, Michelle Gardner, Aaron J Golas, Kristine M. Megan K Proulx, Nadine Ruecker, Naomi Song, Matthew Thompson, Carolina Trujillo, Shoko Wakabayashi, Joshua B Wallach, Christopher Watson, Thomas R. Three compounds (Fig. 4d) represent additional novel scaffolds that we validated as acting in the folate pathway based on suppression of their activity with the addition of PABA or folate (Extended Data Fig. 6d) These results demonstrate the scalability and generalizability of this strategy, and the potential to leverage the much higher hit rate and wider target space obtained by performing primary screening with a hypomorph library to provide new chemical scaffolds against novel targets
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