Mining Cryptic Biosynthetic Gene Clusters for Novel Bioactive Compounds

挖掘新型生物活性化合物的隐秘生物合成基因簇

• 批准号: 10027775
• 负责人: Elizabeth Ivy Parkinson
• 金额: $ 37.05万
• 依托单位: PURDUE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-07-01 至 2025-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10027775
• 关键词: Antibiotics; Antineoplastic Agents; Bacteria; Bioinformatics; Cell Membrane Permeability; Chemicals; Coculture Techniques; Communities; Cyclic Peptides; DNA analysis; Distant; FDA approved; Family; Gene Cluster; Genes; Genetic Transcription; Goals; Human; Laboratories; Libraries; Medicine; Methods; Mining; Natural Products; Organic Synthesis; Peptides; Pharmaceutical Preparations; Production; Regulation; Signal Transduction; Soil; Source; Streptomyces; Techniques; Work; anticancer activity; antimicrobial drug; bioactive natural products; genome sequencing; microorganism; novel; peptide synthase; protein protein interaction; small molecule; tool

PROJECT SUMMARY/ABSTRACT Natural products from the soil-dwelling bacteria Streptomyces have been a rich source of medicines, including antimicrobials and anticancer agents. Unfortunately, discovery of novel bioactive natural products from Streptomyces using traditional techniques is often unsuccessful due to the re-discovery of known molecules. Genome sequencing suggests that Streptomyces are capable of making many more (likely hundreds-of thousands more) molecules than those typically observed in the laboratory. However, the biosynthetic machinery responsible for producing these novel natural products is often cryptic (i.e. transcriptionally inactive). Co-culture of Streptomyces with other microorganisms induces production of natural products not observed in monocultures. However, the signals that control this induction are poorly understood. A significant gap remains in the strategies available to discover new bioactive natural products from cryptic biosynthetic gene clusters. Our long-term goal is to develop strategies to overcome this gap, thus maximizing the natural product potential from Streptomyces. Over the next five years, we aim to identify small molecules capable of inducing natural product production (i.e. chemical elicitors, Project 1) as well as utilizing state-of-the-art bioinformatics to predict and directly chemically synthesize natural products (Project 2). Low levels of certain antibiotics have been found to induce production of a few natural products. The generality of this effect remains unknown, as does the mechanism by which these compounds induce production of natural products. The objectives for the first project are to 1) Study the ability of mechanistically distinct antibiotics to act as chemical elicitors in a variety of distantly related Streptomyces strains and 2) Determine the mechanisms of the chemical elicitors. This work will provide a greater understanding of antibiotic regulation of natural product production, which will allow both our laboratory and others to activate production of natural products in a more targeted manner and ultimately increase the number of bioactive natural products that we as a community can discover. In the second project, we are directly chemically synthesizing cyclic peptide natural products that are bioinformatically predicted from non-ribosomal peptide synthetase biosynthetic gene clusters. Cyclic peptides are an important family of natural products, including many FDA-approved drugs. Their large size and rigidity allows them to target challenging-to-hit targets (e.g. protein-protein interactions). The objectives for the second project are to 1) Develop a bioinformatics method to identify cryptic non-ribosomal peptide synthetase genes that encode production of diverse cyclic peptides, 2) Chemically synthesize a library of several hundred of the predicted cyclic peptides, 3) Use the library to study the rules that regulate peptide cell-membrane permeability and 4) Screen the library for antibiotic and anticancer activity. This work will provide access to hundreds of previously inaccessible natural products that will be useful tools for the study of cyclic peptide membrane permeability and will likely have interesting bioactivities.

项目摘要/摘要 来自土壤细菌链霉菌的天然产物是一种丰富的药物来源，包括 抗菌剂和抗癌剂。不幸的是，新的生物活性天然产物的发现 由于已知分子的重新发现，使用传统技术的链霉菌往往不成功。 基因组测序表明，链霉菌能够制造更多的(可能是数百- 比通常在实验室中观察到的分子多数千个)。然而，生物合成的 负责生产这些新的天然产物的机器通常是隐晦的(即转录不活跃)。 链霉菌与其他微生物共培养诱导天然产物的产生 单一培养。然而，控制这种诱导的信号却知之甚少。仍然存在着巨大的差距 在现有的策略中，从隐蔽的生物合成基因簇中发现新的生物活性天然产物。我们的 长期目标是制定战略来克服这一差距，从而最大限度地发挥自然产品的潜力 链霉菌。在接下来的五年里，我们的目标是识别能够诱导天然产物的小分子 生产(即化学激发子，项目1)以及利用最先进的生物信息学来预测和 直接化学合成天然产物(项目2)。已发现低水平的某些抗生素会导致 诱导一些天然产品的生产。这种效果的一般性尚不清楚， 这些化合物诱导天然产物产生的机制。第一个项目的目标 是为了研究机械上不同的抗生素作为化学激发剂在各种遥远的 2)确定了化学激发子的作用机制。这项工作将提供 更好地了解抗生素对天然产品生产的监管，这将使我们的实验室 和其他国家以更有针对性的方式激活天然产品的生产，最终增加 我们作为一个社区可以发现的生物活性天然产品的数量。在第二个项目中，我们直接 从非核糖体中化学合成生物信息学预测的环肽天然产物 多肽合成酶生物合成基因簇。环肽是一类重要的天然产物， 包括许多FDA批准的药物。它们的大小和僵硬使它们能够瞄准具有挑战性的目标 (例如，蛋白质-蛋白质相互作用)。第二个项目的目标是1)开发一种生物信息学 一种识别编码不同环状病毒产物的隐蔽非核糖体肽合成酶基因的方法 多肽，2)化学合成数百个预测环肽的文库，3)使用该文库 研究多肽细胞膜通透性的调节规律；4)筛选抗生素和 抗癌活性。这项工作将提供数百种以前无法获得的天然产品，这些产品将 将成为研究环肽膜通透性的有用工具，并可能具有有趣的生物活性。