A sequenced-based approach for improved small molecule discovery

改进小分子发现的基于测序的方法

• 批准号: 8115914
• 负责人: PAUL R JENSEN
• 金额: $ 37.08万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-08-01 至 2013-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8115914
• 关键词: Actinobacteria class; Anabolism; Antibiotics; Bacteria; Base Sequence; Biological; Biological Factors; Biological Process; Biomedical Research; Carbon; Chemicals; Collection; Communities; DNA Sequence; Data; Databases; Ensure; Fermentation; Fingerprint; Gene Expression Profiling; Genetic; Genome; Genomics; Goals; Housing; Hybrids; Individual; Instruction; Internet; Lead; Light; Macrolides; Marines; Metabolism; Methodology; Methods; Modeling; Molecular; Molecular Bank; Molecular Genetics; Molecular Profiling; Orphan; Pathway interactions; Phylogenetic Analysis; Plague; Probability; Process; Production; Protocols documentation; Research; Research Project Grants; Restriction fragment length polymorphism; Sequence Analysis; Series; Source; Structure; Targeted Research; Techniques; Technology; Testing; Time Study; United States National Institutes of Health; base; comparative genomics; cytotoxicity; drug development; drug discovery; genetic profiling; genome sequencing; improved; liquid chromatography mass spectrometry; method development; microbial; microorganism; novel; public health relevance; repository; scaffold; small molecule; tool

DESCRIPTION (provided by applicant): Recent advances in DNA sequencing technologies and a better understanding of natural product biosynthesis provide newfound opportunities to improve the process by which microbial natural products are discovered. The objectives of this research are to establish a series of methodologies by which strains can be quickly assessed for natural product biosynthesis through the analysis of PCR-generated or genome sequence data. The methods will be developed using a model group of marine bacteria belonging to the genus Salinispora and then applied to a large and diverse collection of marine actinomycetes with the aim of discovering structurally diverse, new chemical entities, which will be provided to the NIH Molecular Libraries Small Molecule Repository (MLSMR). The methods include an initial, rapid molecular "fingerprinting" screen, from which the genetic potential of individual strains can be compared. Sequence-based approaches will then be applied to interpret the biosynthetic richness and novelty of strains with promising fingerprints. These methods will make it possible to predict if the metabolites produced by a strain will be new and how many different compounds in a particular structural class may be produced. Once strains with the greatest genetic potential are identified, detailed chemical studies will be performed. This approach represents a dramatic improvement over traditional paradigms in which large numbers of biosynthetically unknown strains are screened in a limited number of conditions. It will dramatically reduce the isolation of previously discovered compounds, a problem that has long plagued microbial natural product research. This approach provides a culture-independent, genome-level assessment of secondary metabolite biosynthesis as opposed to more traditional methods, which detect only those metabolites produced under a limited set of culture conditions. The methods developed will be broadly applicable to the scientific community and include the creation of a curated sequence database that can be readily downloaded and used to assess genome sequence data for pathways involved in secondary metabolite production. This research has the potential to dramatically increase the rates with which new chemical entities are discovered and made available for biomedical research. PUBLIC HEALTH RELEVANCE: The research presented in this proposal provides a method by which DNA sequence data can be used to dramatically improve the process by which natural products are discovered from microorganisms. It will generate considerable new chemical diversity that can be used for drug discovery research and to study basic biological processes. The methods developed will be made widely available to the research community and thereby have a broad impact on drug discovery and basic biomedical research.

描述（由申请人提供）：DNA测序技术的最新进展和对天然产物生物合成的更好理解为改进微生物天然产物的发现过程提供了新的机会。本研究的目的是建立一系列方法，通过分析 PCR 生成的数据或基因组序列数据，快速评估菌株的天然产物生物合成。这些方法将使用属于盐孢菌属的海洋细菌模型群进行开发，然后应用于大量多样化的海洋放线菌，旨在发现结构多样化的新化学实体，这些实体将提供给美国国立卫生研究院分子图书馆小分子存储库（MLSMR）。这些方法包括初始、快速的分子“指纹”筛选，从中可以比较各个菌株的遗传潜力。然后将应用基于序列的方法来解释具有有希望的指纹的菌株的生物合成丰富性和新颖性。这些方法将能够预测菌株产生的代谢物是否是新的，以及可能产生多少种特定结构类别的不同化合物。一旦鉴定出具有最大遗传潜力的菌株，将进行详细的化学研究。这种方法代表了对传统范例的巨大改进，在传统范例中，在有限的条件下筛选大量生物合成未知的菌株。它将大大减少先前发现的化合物的分离，这是一个长期困扰微生物天然产物研究的问题。这种方法提供了对次生代谢物生物合成的独立于培养物的基因组水平评估，而不是更传统的方法，后者仅检测在一组有限的培养条件下产生的代谢物。开发的方法将广泛适用于科学界，包括创建一个可轻松下载并用于评估涉及次级代谢物产生途径的基因组序列数据的精选序列数据库。这项研究有可能显着提高新化学实体的发现率并可用于生物医学研究。 公共健康相关性：本提案中提出的研究提供了一种方法，通过该方法，DNA 序列数据可用于显着改进从微生物中发现天然产物的过程。它将产生大量新的化学多样性，可用于药物发现研究和研究基本生物过程。开发的方法将广泛供研究界使用，从而对药物发现和基础生物医学研究产生广泛影响。