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: 10204056
• 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/10204056
• 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.

项目概要/摘要 来自土壤细菌链霉菌的天然产物是丰富的药物来源，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 由于重新发现已知分子，使用传统技术的链霉菌常常不成功。 基因组测序表明，链霉菌能够产生更多（可能是数百种） 比实验室中通常观察到的分子多出数千个）。然而，生物合成 负责生产这些新型天然产物的机器通常是神秘的（即转录不活跃）。 链霉菌与其他微生物的共培养可诱导产生天然产物，而这些天然产物在 单一栽培。然而，人们对控制这种诱导的信号知之甚少。仍存在显着差距 从神秘的生物合成基因簇中发现新的生物活性天然产物的可用策略。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天然产品的潜力 链霉菌。在接下来的五年中，我们的目标是识别能够诱导天然产物的小分子 生产（即化学诱导子，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）。研究发现某些抗生素的含量较低 诱导一些天然产物的产生。这种效应的普遍性仍然未知， 这些化合物诱导天然产物产生的机制。第一个项目的目标 1) 研究机械上不同的抗生素在多种远距离药物中作为化学诱导子的能力 相关链霉菌菌株和 2) 确定化学激发子的机制。这项工作将提供 更好地了解天然产物生产的抗生素调节，这将使我们的实验室 等以更有针对性的方式激活天然产物的生产，并最终增加 我们作为一个社区可以发现许多具有生物活性的天然产品。在第二个项目中，我们直接 化学合成从非核糖体生物信息学预测的环肽天然产物 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。它们的大尺寸和刚性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) 开发生物信息学 鉴定编码多种环状产物的隐秘非核糖体肽合成酶基因的方法 肽，2) 化学合成包含数百个预测环肽的库，3) 使用该库 研究调节肽细胞膜通透性的规则，4) 筛选抗生素和抗生素库 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 成为研究环肽膜渗透性的有用工具，并且可能具有有趣的生物活性。