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.

我们的小组侧重于天然产物（NP）的发现，生物合成，结构和功能，该发现代表 讨厌小分子药物的最大化学物质来源。医学上最多产的生产者 相关的NP源自一组称为放线菌的细菌。回顾性基因组分析具有 反复表明，包括放线菌在内的合成有才华的微生物能够合成 NP比目前已知的更多。探索未被发现的多数，这个所谓的NP“暗物质”， 不仅通过扩大我们的药物库，还具有改善人类健康的巨大潜力 鉴于NP作为化学问题的关键作用，也可以推进生物学的基本研究。 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 - 统治缺点。尽管传统的NP发现方法取得了成功，但最普遍的生物测定法 - 引导的隔离，遭受继承的偏见，导致重新发现的速率高。而不是 通过其生物活性跟踪NP，我们选择通过存在有机官能团的存在来识别NP 无需纯化而无需化学选择性地衍生化。对存在的25万NP的评论 NPS的字典表明约有50％的功能组。我们将用PMOL检测到这些组 与合适的探针反应后，在粗细菌提取物的背景下，使用质谱法敏感性。 重要的是，我们要靶向的官能团的存在可以根据生物信息预测 已知的生物合成途径。我们已经称此NP发现过程反应性筛选（RB） 并最近报道了通过核φ1,4-的发现发现硫代肽和聚酮化合物以及 通过氧结扎的非核糖体肽（NRP）。自定义的生物信息学软件程序也已经 由我们的小组开发，以帮助预测存在各种目标有机官能团的存在。 使用我们的内部收集约10,000个放线菌，其中许多是从稀有的，被理解的分类单元中的 该项目访问了三个独立但相互联系的目标。为了目标一世，重点是小说 硫代肽，硫代肽是经过广泛的翻译后修饰的辣椒，以阻止其能力而闻名 细菌蛋白翻译。 AIM II专注于新型聚酮化合物的发现和表征 III针对NRP。每个目标都将使用多层策略阐明NP结构和生物活性。 后两个目标还引入了新的探针化学反应，除了已经提到的反应外。 该项目的中心假设，我们有大量支持的数据，是NP Discovery 可以通过基因组学优先级和RB的婚姻来加速。我们设想这种方法 随着更多基因组出现在公共数据库中，高度促进和增加的功率。