Large-scale chemical-genetics yields new M. tuberculosis inhibitor classes

Nature. 2019 Jul;571(7763):72-78. doi: 10.1038/s41586-019-1315-z. Epub 2019 Jun 19.


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 8.5 million 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.

MeSH terms

  • Antitubercular Agents / classification*
  • Antitubercular Agents / isolation & purification*
  • Antitubercular Agents / pharmacology
  • DNA Gyrase / metabolism
  • Drug Discovery / methods*
  • Drug Resistance, Microbial
  • Folic Acid / biosynthesis
  • Gene Deletion*
  • Microbial Sensitivity Tests / methods*
  • Molecular Targeted Therapy
  • Mycobacterium tuberculosis / cytology
  • Mycobacterium tuberculosis / drug effects*
  • Mycobacterium tuberculosis / enzymology
  • Mycobacterium tuberculosis / genetics*
  • Mycolic Acids / metabolism
  • Reproducibility of Results
  • Small Molecule Libraries / classification
  • Small Molecule Libraries / isolation & purification
  • Small Molecule Libraries / pharmacology*
  • Substrate Specificity
  • Topoisomerase II Inhibitors / isolation & purification
  • Topoisomerase II Inhibitors / pharmacology
  • Tryptophan / biosynthesis
  • Tuberculosis / drug therapy
  • Tuberculosis / microbiology


  • Antitubercular Agents
  • Mycolic Acids
  • Small Molecule Libraries
  • Topoisomerase II Inhibitors
  • Tryptophan
  • Folic Acid
  • DNA Gyrase