A Metabologenomics Platform for Large-Scale, High-Throughput Natural Product Discovery

摘要 在微生物基因组中产生天然产物的基因簇的估计远 比已知的天然产物的数量要多，这表明还有大量未开发的分子。 在这些生物体中，它们提供了巨大的潜力，作为新药的先导。不幸的是， 天然产物发现的范例不适合于获得这种丰富的分子， 这在现代社会是不可接受的。因此，在发展中国家的潜力 微生物提供新的天然产品和我们的能力，有效地利用这一潜力。弥合 微生物制药公司正在开发下一代技术， 获得这些化合物的途径以及表征和使用这些化合物的手段。 微生物制药的长期目标是提供一个完整的路线图， 放线菌内的代谢-已知产生最大数量的天然产物-通过进行 代谢基因组筛选10,000种不同的菌株。从这个过程中产生的数据将提供所有 表达的代谢产物及其耦合的生物合成基因簇，而大规模的这一努力将 克服了仅研究少数菌株的方法所面临的“隐藏”基因簇问题。 微生物制药将优化我们的代谢基因组学数据采集平台（Aim 1）， 同时改进我们的相关算法（目标2）。优化平台，以实现快速和 将使用UPLC和高质量准确度质谱法实现可重现的数据采集， 降低成本和提高采购率的目标（目标1a）。这一过程将在50 新的细菌菌株，并将数据纳入已知和新的天然产物数据库（目标1b）。 目标1在第一阶段的成功成果将为实现我们的长期目标奠定重要基础。 未来的目标是廉价有效地筛选10,000株菌株。我们还将实施MS 2网络 功能纳入代谢基因组学数据库（目标2）。 来自所研究的50种菌株的代谢基因组数据的组合，再加上改进的 相关性，将提供过多的新分子，可以以确定性的方式访问。通过 以全新的操作方式进行操作，将出现高价值化合物的稳定流， 它们在复杂的生物系统中的活动已经被大自然磨练了数千年。

ABSTRACT The estimates of natural product producing gene clusters within the genomes of microorganisms are far greater than the number of known natural products, indicating that there is a wealth of untapped molecules within these organisms that offer huge potential as leads for new medicines. Unfortunately, the prevailing paradigms for natural product discovery are ill suited for accessing this bounty of molecules, providing a rate of discovery that is unacceptable in the modern era. There is, therefore, a significant gap between the potential of microorganisms to deliver new natural products and our ability to access this potential effectively. To bridge this gap, Microbial Pharmaceuticals is developing the next-generation technology that will deliver unparalleled access to these compounds and the means by which they can be characterized and put to use. The long-term goal of Microbial Pharmaceuticals is to provide a complete roadmap of secondary metabolism within actinobacteria—known to produce the greatest numbers of natural products—by conducting metabologenomic screening of 10,000 different strains. The data generated from this process will provide all expressed metabolites and their coupled biosynthetic gene clusters, while the large scale of this effort will overcome the “cryptic” gene cluster problem faced by approaches that only investigate a few strains. Microbial Pharmaceuticals will optimize our metabologenomics data acquisition platform (Aim 1) and simultaneously improve upon our correlation algorithms (Aim 2). Optimization of the platform to allow rapid and reproducible data acquisition will be achieved using UPLC and high-mass accuracy mass spectrometry with the goal of decreasing cost and increasing the rate of acquisition (Aim 1a). This process will be piloted on 50 new bacterial strains and the data incorporated into a database of known and new natural products (Aim 1b). The successful outcome of Aim 1 during Phase I will lay the significant groundwork to achieve our long-term future goal of screening 10,000 strains cheaply and efficiently. We will also implement an MS2 networking feature into the metabologenomics database (Aim 2). The combination of metabologenomic data from the 50 strains investigated, coupled to the improved correlations, will provide a plethora of new molecules that may be accessed in a deterministic fashion. By operating in a fundamentally new modus operandi, a steady stream of high value compounds will emerge, which have been honed by nature over millennia for activity in complex biological systems.