Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA.
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.
需要新的抗生素来对抗不断上升的耐药水平，新的结核分枝杆菌 (Mtb) 药物具有最高优先级。然而，传统的全细胞和生化抗生素筛选已经失败。在这里，我们开发了一种称为 PROSPECT（优先筛选扩展化学和目标的菌株）的策略，其中我们针对缺乏必需细菌靶标的菌株池筛选化合物。我们设计了针对 474 个必需 Mtb 基因的菌株，并针对活性富集和无偏化合物库筛选了 100-150 株菌株，探测了超过 850 万个化学遗传相互作用。与单独筛选野生型 Mtb 相比，初级筛选发现的命中数量增加了十倍以上，化学遗传相互作用提供了直接的、直接的目标见解。我们确定了 40 多种针对 DNA 回旋酶、细胞壁、色氨酸、叶酸生物合成和 RNA 聚合酶的化合物，以及针对 Efpa 的抑制剂。化学优化得到了对野生型具有强大活性的 Efpa 抑制剂，从而证明了 PROSPECT 能够产生针对传统药物发现可能会漏掉的目标的抑制剂的能力。
