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Microbiology and Immunology

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

TitleLarge-scale chemical-genetics yields new M. tuberculosis inhibitor classes.
Publication TypeJournal Article
Year of Publication2019
AuthorsJohnson EO, LaVerriere E, Office E, Stanley M, Meyer E, Kawate T, Gomez JE, Audette RE, Bandyopadhyay N, Betancourt N, Delano K, Da Silva I, Davis J, Gallo C, Gardner M, Golas AJ, Guinn KM, Kennedy S, Korn R, McConnell JA, Moss CE, Murphy KC, Nietupski RM, Papavinasasundaram KG, Pinkham JT, Pino PA, Proulx MK, Ruecker N, Song N, Thompson M, Trujillo C, Wakabayashi S, Wallach JB, Watson C, Ioerger TR, Lander ES, Hubbard BK, Serrano-Wu MH, Ehrt S, Fitzgerald M, Rubin EJ, Sassetti CM, Schnappinger D, Hung DT
JournalNature
Volume571
Issue7763
Pagination72-78
Date Published2019 07
ISSN1476-4687
KeywordsAntitubercular Agents, DNA Gyrase, Drug Discovery, Drug Resistance, Microbial, Folic Acid, Gene Deletion, Microbial Sensitivity Tests, Molecular Targeted Therapy, Mycobacterium tuberculosis, Mycolic Acids, Reproducibility of Results, Small Molecule Libraries, Substrate Specificity, Topoisomerase II Inhibitors, Tryptophan, Tuberculosis
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 8.5 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.

DOI10.1038/s41586-019-1315-z
Alternate JournalNature
PubMed ID31217586

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