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.

项目总结/摘要 来自土壤中的链霉菌的天然产物一直是药物的丰富来源，包括 抗微生物剂和抗癌剂。不幸的是，发现新的生物活性天然产物， 由于已知分子的重新发现，使用传统技术的链霉菌通常不成功。 基因组测序表明，链霉菌能够产生更多的（可能是数百个 数千个）分子。然而，生物合成 负责生产这些新型天然产物的机制通常是神秘的（即转录失活）。 链霉菌与其他微生物的共培养诱导产生在真菌中未观察到的天然产物。 单一栽培然而，控制这种诱导的信号知之甚少。仍然存在重大差距 从隐蔽的生物合成基因簇中发现新的生物活性天然产物的策略。我们 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里，我们的目标是确定能够诱导天然产物的小分子。 生产（即化学诱导剂，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）。低水平的某些抗生素已被发现， 诱导产生一些天然产物。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）研究不同抗生素在各种远距离环境中作为化学诱导剂的能力。 2）确定化学诱导剂的作用机理。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 和其他人以更有针对性的方式激活天然产品的生产，并最终增加 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 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 (e.g.蛋白质-蛋白质相互作用）。第二个项目的目标是：1）开发一个生物信息学 鉴定编码多种环状多肽产生的隐蔽非核糖体肽合成酶基因的方法 2）化学合成数百种预测的环肽的文库，3）使用文库 研究多肽细胞膜通透性的调节规律; 4）筛选文库中的抗生素， 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， 是研究环肽膜渗透性的有用工具，并可能具有有趣的生物活性。