Tools for rapid and accurate structure elucidation of natural products

快速准确地解析天然产物结构的工具

• 批准号: 10393432
• 负责人: GARRISON W COTTRELL
• 金额: $ 1.05万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-09-05 至 2025-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10393432
• 关键词: Algorithms; Architecture; Back; Bacteria; Biochemical Pathway; Biological; Chemicals; Classification; Communities; Complex; Consumption; Cyanobacterium; Data; Data Set; Development; FDA approved; Gene Cluster; Goals; Grant; Informatics; Infrastructure; Light; Methods; Methylation; Molecular; Molecular Structure; Natural Product Drug; Natural Products; Organic Chemistry; Pathway interactions; Pharmaceutical Preparations; Physiologic pulse; Prokaryotic Cells; Source; Speed; Stream; Structure; Time; analytical tool; base; convolutional neural network; cost; drug discovery; experimental study; fascinate; genome sequencing; halogenation; innovation; programs; small molecule; social; stereochemistry; tool

Summary from the Application 5 R01 GM107550-08 “Tools for rapid and accurate structure elucidation of natural products” Bacteria are extraordinarily prolific sources of structurally unique and biologically active natural products that derive from a diversity of fascinating biochemical pathways. However, the complete structure elucidation of natural products is often the most time consuming and costly endeavor in natural product drug discovery programs. Compounding this, advancements in genome sequencing have accelerated the identification of unique modular biosynthetic gene clusters in prokaryotes and revealed a wealth of new compounds yet to be isolated and biologically and chemically characterized. Resultantly, there is an urgent and continuing need in this field to connect biosynthetic gene clusters to their respective MS fragmentation signatures in the MS2 molecular networks. The capacity to make such connections will accelerate new compound discovery as well as create associations between gene cluster and biosynthetic pathway, and aid in fast and accurate structure elucidations. Combined with this informatics approach, this proposed continuation project explores innovative methods by which to solve complex molecular structures by enhanced MS and NMR experiments, as well as the development of new algorithms by which to accelerate their analysis. Thus, the overarching goal of this grant is to develop efficient methods that facilitate automated structural classification, structural feature discovery and ultimately efficient structure elucidation of natural products (or any small molecule) and to build an infrastructure that interacts with data input from the community. We will achieve this with the following four specific aims: Aim 1. Integration of MS2 molecular networking with gene cluster networking to rapidly and efficiently locate natural products that have unique molecular architectures; Aim 2. To develop a suite of high sensitivity pulse sequences for natural product structure elucidation; Aim 3. To develop NMR based molecular networking strategies using Deep Convolutional Neural Networks (DCNNs) to facilitate the categorization and structure elucidation of organic compounds; Aim 4. To integrate NMR molecular networking and MS2 -based molecular networking as an efficient structure characterization and elucidation strategy. By achieving these aims we will develop an innovative workflow for finding new compounds and for determining their structures, both quickly and accurately. The connection between gene cluster and molecule will shed light on stereochemistry and potential halogenations and methylations. This information can then be used in combination with more efficient NMR and MS methods to accurately determine structures. These tools will be widely shared, such as through the Global Natural Products Social (GNPS) Molecular Network, to enhance the overall capacity of the natural products and organic chemistry communities to solve complex molecular structures.

申请5 R 01 GM 107550 -08的总结 “快速准确地 天然产物结构解析 细菌是结构独特且具有生物活性的天然产物的非常丰富的来源。 这些产品来自于多种迷人的生物化学途径。然而，完整的 天然产物的结构解析通常是最耗时和昂贵的奋进， 天然产物药物发现计划。更重要的是，基因组的进步 测序加速了独特的模块化生物合成基因簇的鉴定， 原核生物，并揭示了丰富的新化合物尚未分离和生物学， 化学特征因此，在这一领域迫切需要继续 将生物合成基因簇连接到MS 2中它们各自的MS片段化特征 分子网络建立这种连接的能力将加速新化合物的产生。 发现以及创建基因簇和生物合成途径之间的关联，并帮助 快速准确的结构解析。结合这种信息学方法， 拟议的继续项目探索创新的方法，通过它来解决复杂的分子 通过增强的MS和NMR实验，以及新算法的开发， 来加速他们的分析。因此，该补助金的总体目标是开发高效的 有助于自动结构分类、结构特征发现和 最终有效的天然产物（或任何小分子）的结构解析，并建立 与来自社区的数据输入进行交互的基础设施。我们将通过 以下四个具体目标：目标1。MS 2分子网络与基因的整合 集群网络，以快速有效地定位具有独特 分子结构;目标2.开发一套高灵敏度的脉冲序列， 天然产物结构解析;目的3.开发基于NMR的分子网络 使用深度卷积神经网络（DCNN）来促进 有机化合物的分类和结构解析;目的4.为了整合NMR 分子网络和基于MS 2的分子网络作为一种有效的结构 表征和阐明策略。通过实现这些目标，我们将制定一个 创新的工作流程，用于快速发现新化合物并确定其结构， 而且准确基因簇和分子之间的联系将揭示 立体化学和潜在的卤化和甲基化。然后可以使用该信息 与更有效的NMR和MS方法相结合，以准确确定结构。 这些工具将广泛分享，例如通过全球天然产品社会（GNPS） 分子网络，提升天然产物和有机化学的整体能力 来解决复杂的分子结构。