LaVerriere, EmilyMeyer, ElisabethKawate, TomohikoGomez, JamesGardner, MichelleCigarroa Kennedy, SofiaWakabayashi, ShokoWatson, ChristopherFitzgerald, MichaelJohnson, EachanOffice, EmmaStanley, MaryAudette, RebeccaBandyopadhyay, NirmalyaBetancourt, NataliaDelano, KaylaDa Silva, IsraelDavis, JoshuaGallo, ChristinaGolas, AaronGuinn, KristineKorn, RebeccaMcConnell, JenniferMoss, CaitlinMurphy, KenanNietupski, RaymondPapavinasasundaram, KadambaPinkham, JessicaPino, PaulaProulx, MeganRuecker, NadineSong, NaomiThompson, MatthewTrujillo, CarolinaMetcalf-Wallach, JoshuaIoerger, ThomasLander, EricHubbard, BrianSerrano-Wu, MichaelEhrt, SabineRubin, EricSassetti, ChristopherSchnappinger, DirkHung, Deborah2019-12-182019-06-19Johnson, 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. Guinn, Sofia Kennedy, Rebecca Korn, Jennifer A McConnell, Caitlin E. Moss, Kenan C Murphy, Raymond M. Nietupski, Kadamba G. Papavinasasundaram, Jessica T. Pinkham, Paula A. Pino, Megan K Proulx, Nadine Ruecker, Naomi Song, Matthew Thompson, Carolina Trujillo, Shoko Wakabayashi, Joshua B Wallach, Christopher Watson, Thomas R. Ioerger, Eric S. Lander, Brian K. Hubbard, Michael H. Serrano-Wu, Sabine Ehrt, Michael Fitzgerald, Eric J. Rubin, Christopher M. Sassetti, Dirk Schnappinger, and Deborah T. Hung. 2019. Large-scale Chemical-genetics Yields New M. Tuberculosis Inhibitor Classes. Nature 571, no. 7763: 72-78.0028-08361476-4687http://nrs.harvard.edu/urn-3:HUL.InstRepos:42066797New antibiotics are needed to combat rising resistance, with new Mycobacterium tuberculosis (Mtb) drugs of highest priority. Conventional whole-cell and biochemical antibiotic screens have failed. 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 engineered strains targeting 474 Mtb essential genes and screened pools of 100-150 strains against activity-enriched and unbiased compounds libraries, probing >8.5-million chemical-genetic interactions. Primary screens identified >10-fold more hits than screening wild-type Mtb alone, with chemical-genetic interactions providing immediate, direct target insight. We identified >40 novel compounds targeting DNA gyrase, cell wall, tryptophan, folate biosynthesis, and RNA polymerase, as well as inhibitors of a novel target EfpA. Chemical optimization yielded EfpA inhibitors with potent wild-type activity, thus demonstrating PROSPECT’s ability to yield inhibitors against novel targets which would have eluded conventional drug discovery.en-USAntitubercular Agents–ClassificationDNA Gyrase–Isolation & PurificationDrug Discovery–PharmacologyDrug Resistance, Microbial–MetabolismFolic Acid–MethodsGene Deletion–BiosynthesisMicrobial Sensitivity Tests–MethodsMolecular Targeted Therapy–CytologyMycobacterium Tuberculosis–Drug EffectsMycolic Acids–EnzymologyReproducibility of Results–GeneticsSmall Molecule Libraries–MetabolismSubstrate Specificity–ClassificationTopoisomerase II Inhibitors–Isolation & PurificationTryptophan–PharmacologyTuberculosis–Isolation & PurificationTuberculosisJournal Article2019-12-1810.1038/s41586-019-1315-z