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（NP）的发现、生物合成、结构和功能，代表 是小分子药物的最大化学物质来源。最多产的药用生产商 相关的纳米颗粒源自一组称为放线菌的细菌。回顾性基因组分析已 反复证明，具有合成天赋的微生物，包括放线菌，能够合成 NP 比目前已知的要多得多。探索未被发现的大多数，即所谓的 NP“暗物质”， 不仅通过扩大我们的药物库来改善人类健康，而且具有巨大的潜力 鉴于纳米粒子作为化学探针的关键作用，也促进了生物学的基础研究。 该提案概述了一种以化学为中心的纳米颗粒发现策略，专门用于解决传统的纳米颗粒发现问题。 的缺点。尽管传统的纳米粒子发现方法取得了成功，但最流行的生物测定法 引导隔离存在固有偏差，导致重新发现率高得令人无法接受。而不是 通过生物活性追踪纳米颗粒，我们选择通过有机官能团的存在来识别纳米颗粒，这些有机官能团 可以化学选择性衍生化，无需纯化。对 250,000 个 NP 的审查 NP 字典显示~50% 含有这样的官能团。我们将用 pmol 检测这些基团 与合适的探针反应后，在粗细菌提取物中使用质谱法测定灵敏度。 重要的是，我们所针对的功能基团的存在可以基于生物信息学进行预测 已知的生物合成途径。我们将这种 NP 发现程序称为基于反应性的筛选 (RBS) 最近报道了通过亲核1,4-加成以及硫肽和聚酮化合物的发现 通过肟连接制备非核糖体肽（NRP）。定制的生物信息学软件程序也已经 由我们小组开发，用于帮助预测各种可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（其中许多来自稀有的、尚未研究的分类群），我们已经 认为该项目由三个独立但相互关联的目标组成。 《Aim I》的重点是小说 硫肽，是经过广泛翻译后修饰的肽，以其阻断能力而闻名 细菌蛋白质翻译。 Aim II 专注于新型聚酮化合物的发现和表征，而 Aim III 针对 NRP。每个目标都将使用多层策略来阐明纳米粒子的结构和生物活性。 后两个目标还引入了除了已经提到的反应之外的新探针化学。 这个项目的中心假设是 NP 的发现，我们有大量的数据支持该假设 可以通过基因组优先顺序和 RBS 的结合来加速。我们设想这种方法 随着越来越多的基因组出现在公共数据库中，变得高度可用并增强力量。