Resolving the bottleneck in antibiotic discovery

摘要 大多数抗生素产生于Waxman平台，筛选土壤微生物，但这种有限的资源 在60年代后期被过度开采。在没有平台的情况下，化合物的引入比 病原体获得了抗药性，结果是人类健康危机。最近总统的行政命令 “对抗抗生素耐药性细菌”强调了这个问题的重要性。在本计划中，我们将 开发一个有效的发现计划，利用未培养的细菌，以解决瓶颈， 抗菌药物发现 未培养的细菌是未开发的次级代谢物来源，我们开发了方法， 种植它们然后开采来发现抗生素到目前为止，我们从这个来源中发现了25种新化合物， 包括拉索霉素，一种对M. 和替沙菌素，一种新的肽聚糖合成抑制剂，基本上没有耐药性 发展然而，未培养的细菌的真实的潜力仍然没有实现-- 已知的和有毒的化合物一直是主要的瓶颈，即使是这种尚未开发的化学品来源， 多样性我们建议通过引入转录组分析作为一种快速的工具来解决这个问题， 有前途的化合物。影响同一靶点的化合物会产生不同的 聚集在一起的转录图谱这种方法使我们能够将化合物分类为已知的;新的 击中一个已知的目标;新的击中一个新的有价值的目标;击中一个不受欢迎的目标;或一个滋扰 缺乏特异性的化合物。在一项初步研究中，我们确定可以从生产菌株中提取粗提物， 用于在测试生物体中产生转录组谱以鉴定靶标，并推断出存在的转录组谱。 有潜在价值的化合物在拟议的项目中，我们将创建一个转录谱数据库， 已知的抗微生物剂，开发用于转录组分析的有效计算工具，并将询问 转录组的大量提取物和它们的馏分从未培养的细菌。铅分子 将在体外和动物有效性模型中进行验证。该项目的最终结果将是一个新颖的发现 平台、新靶点和药物开发的先导化合物。该项目是金与 刘易斯，PD/PI（NU），抗菌药物发现和耐药性专家; Karen纳尔逊，合作研究者 （JCVI），基因组学，元组学方法和计算生物学专家;和艾米斯波林，共同 研究者（NovoBiotic），从未培养细菌中发现药物的专家。这些专家合作， 为该计划提供初步数据。

Abstract Most antibiotics resulted from the Waxman platform, screening of soil microorganisms, but this limited resource was overmined by the late 60s. In the absence of a platform, compounds are introduced slower than pathogens acquire resistance, and the result is a human health crisis. The recent President's executive order “Combating Antibiotic-Resistant Bacteria” underscores the significance of this problem. In this Program, we will develop an effective discovery program based on exploiting uncultured bacteria to resolve the bottleneck of antimicrobial drug discovery. Uncultured bacteria are an untapped source of secondary metabolites, and we developed methods to grow them and mine for antibiotic discovery. We discovered 25 new compounds from this source so far, including lassomycin, a novel compound with specific activity against the ClpP1P2C1 protease of M. tuberculosis; and teixobactin, a novel inhibitor of peptidoglycan synthesis which is essentially free of resistance development. However, the real potential of uncultured bacteria remains unrealized - the background of knowns and toxic compounds has been the main bottleneck even for this untapped source of chemical diversity. We propose to solve this problem by introducing transcriptome analysis as a rapid tool to identify promising compounds from uncultured bacteria. Compounds affecting the same target produce distinct transcription profiles that cluster together. This approach allows us to classify compounds as known; novel hitting a known target; novel hitting a new valuable target; hitting an undesirable target; or a nuisance compound lacking specificity. In a pilot study, we determined that crude extracts from producing strains can be used to generate transcriptome profiles in a test organism to identify targets, and deduce the presence of a potentially valuable compound. In the proposed project, we will create a database of transcription profiles from known antimicrobials, develop effective computational tools for transcriptome analysis, and will interrogate transcriptomes from a large number of extracts and their fractions from uncultured bacteria. Lead molecules will be validated in vitro and in an animal efficacy model. The end result of the project will be a novel discovery platform, new targets, and lead compounds for drug development. The project is a collaboration between Kim Lewis, PD/PI (NU), an expert in antimicrobial drug discovery and resistance; Karen Nelson, Co-Investigator (JCVI), an expert in genomics, meta-omics approaches and computational biology; and Amy Spoering, Co- Investigator (NovoBiotic), an expert in drug discovery from uncultured bacteria. These experts collaborated on producing preliminary data for this Program.