Genomics-Accelerated Natural Product Discovery

基因组学-加速天然产物发现

• 批准号: 10391633
• 负责人: Douglas Alan Mitchell
• 金额: $ 1.1万
• 依托单位: UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-15 至 2021-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10391633
• 关键词: Actinobacteria class; Address; Anabolism; Antibiotics; Bacteria; Bacterial Proteins; Bioinformatics; Biological Assay; Biology; Chemicals; Chemistry; Collection; Computer software; Custom; Data; Databases; Dictionary; Doctor of Philosophy; Focus Groups; Genome; Genomics; Health; Human; Ligation; Marriage; Mass Spectrum Analysis; Medicine; Methods; Microbe; Mining; Natural Products; Oximes; Pathway interactions; Peptides; Pharmaceutical Preparations; Pharmacologic Substance; Procedures; Process; Reaction; Reporting; Role; Source; Structure; Talents; Translations; anti-cancer; base; dark matter; design; functional group; genome analysis; improved; interest; novel; programs; screening; small molecule; success

Our group focuses on the discovery, biosynthesis, structure, and function of natural products (NPs), which rep- resent the largest source of chemical matter for small molecule drugs. The most prolific producers of medicinally relevant NPs derive from a group of bacteria known as the actinomycetes. Retrospective genome analysis has repeatedly shown that synthetically talented microbes, including actinomycetes, are capable of synthesizing many more NPs than are currently known. Exploring the undiscovered majority, this so-called NP “dark matter”, holds enormous potential for not only improving human health by expanding our pharmaceutical repertoire but also for advancing the fundamental study of biology given the critical role of NPs as chemical probes. This proposal outlines a chemistry-centric NP discovery strategy designed specifically to address tradi- tional shortcomings. Despite the success of traditional NP discovery methods, the most prevalent, bioassay- guided isolation, suffers from inherent biases that leads to unacceptably high rates of rediscovery. Rather than track a NP by its bioactivity, we have elected to identify NPs by the presence of organic functional groups that can be chemoselectively derivatized without the need for purification. A review of the 250,000 NPs present in the Dictionary of NPs shows that ~50% contain such a functional group. We will detect these groups with pmol sensitivity using mass spectrometry in the context of crude bacterial extracts after reaction with a suitable probe. Importantly, the presence of the functional groups we are targeting can be bioinformatically predicted based on known biosynthetic pathways. We have termed this NP discovery procedure reactivity-based screening (RBS) and have recently reported the discovery of thiopeptides and polyketides by nucleophilic 1,4-addition as well as non-ribosomal peptides (NRPs) by oxime ligation. A custom bioinformatics software program has also been developed by our group to aid in predicting the presence of various targetable organic functional groups. Employing our in-house collection of ~10,000 actinomycetes, many from rare, understudied taxa, we have de- vised this project to consist of three independent but interconnected aims. For Aim I, the focus is on novel thiopeptides, which are extensively posttranslationally modified peptides best known for their ability to block bacterial protein translation. Aim II focuses on the discovery and characterization of novel polyketides while Aim III is directed towards NRPs. Each aim will elucidate NP structure and bioactivity using a multi-tiered strategy. The latter two aims also introduce new probe chemistry beyond the reactions already mentioned. The central hypothesis of this project, for which we have a large amount of supportive data, is that NP discovery can be accelerated through the marriage of genomics prioritization and RBS. We envision this approach to be highly enabling and increase in power as more genomes appear in public databases.

我们的团队专注于天然产物（NPs）的发现，生物合成，结构和功能，这些代表了 是小分子药物的最大化学物质来源。最多产的药用植物 相关的NP来源于一组称为放线菌的细菌。回顾性基因组分析， 反复表明，合成天才的微生物，包括放线菌，能够合成 比目前已知的更多的NP。探索未被发现的大多数，这种所谓的NP“暗物质”， 拥有巨大的潜力，不仅可以通过扩大我们的药物库来改善人类健康， 同时，鉴于纳米粒子作为化学探针的关键作用，也有助于推进生物学的基础研究。 该提案概述了一种以化学为中心的NP发现策略，专门针对传统的NP发现策略， 的缺点。尽管传统的NP发现方法取得了成功，但最流行的生物测定方法- 引导隔离，遭受固有的偏见，导致不可接受的高比率的重新发现。而不是 通过其生物活性追踪NP，我们选择通过存在有机官能团来鉴定NP， 可以化学选择性地衍生而不需要纯化。对250，000个NP的审查， 纳米粒子词典显示约50%含有这样的官能团。我们将用pmol检测这些基团 在与合适的探针反应后，在粗细菌提取物的背景下使用质谱法测定灵敏度。 重要的是，我们靶向的官能团的存在可以基于以下生物信息学预测： 已知的生物合成途径。我们将这种NP发现过程称为基于反应性的筛选（RBS） 并且最近报道了通过亲核1，4-加成以及 非核糖体肽（NRP）通过肟连接。一个定制的生物信息学软件程序也已经被 由我们的小组开发，以帮助预测各种目标有机官能团的存在。 利用我们内部收集的约10，000种放线菌，其中许多来自稀有，未充分研究的分类群，我们已经确定了 该项目由三个独立但相互关联的目标组成。对于Aim I，重点是小说 硫肽，其是广泛的后修饰肽，以其阻断 细菌蛋白质翻译。目的II侧重于新聚酮化合物的发现和表征，而目的 三是针对NRP。每个目标将使用多层次策略阐明NP结构和生物活性。 后两个目标还引入了新的探针化学，超出了已经提到的反应。 这个项目的中心假设，我们有大量的支持数据，是NP的发现， 可以通过基因组学优先级和RBS的结合来加速。我们设想这种方法 随着更多的基因组出现在公共数据库中，它将变得非常有利并增加力量。