Mining the cultured and uncultured biosphere for new drugs

挖掘培养和未培养的生物圈来寻找新药物

• 批准号: 10678668
• 负责人: Jason Christopher Kwan
• 金额: $ 37.54万
• 依托单位: UNIVERSITY OF WISCONSIN-MADISON
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-01 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10678668
• 关键词: Amino Acid Sequence; Anabolism; Animals; Antibiotics; Bacteria; Bacterial Genome; Bacterial Infections; Chemicals; Curiosities; Data; Directed Molecular Evolution; Environment; Evolution; Genome; Growth; Insecta; Knowledge; Laboratories; Malignant Neoplasms; Marine Invertebrates; Methods; Mining; Mycoses; Natural Source; Nature; Pathway interactions; Pharmaceutical Preparations; Research; Resistance; Sequence Analysis; Techniques; Work; drug candidate; drug discovery; drug isolation; improved; novel therapeutics; programs; small molecule; symbiont

PROJECT SUMMARY/ABSTRACT This research program focuses on a fundamental barrier in the discovery of new drug molecules from the environment, known as the supply problem. There is no shortage of new bioactive molecules in the environment that we can use as drugs, because such molecules have been evolving for billions of years within trillions of microniches. In this program, we will (1) use both sequence analysis and directed evolution to devise ways of making promising molecules from uncultured bacteria in laboratory-grown strains, and (2) improve the discovery rate of new molecules from isolated culturable bacterial strains by determining the shared ways that their small molecule pathways are regulated, and exploiting that knowledge to turn on these pathways. 1) It is estimated that 1 trillion species of bacteria exist. The number of species that have been grown in the lab is minuscule by comparison, but that minuscule portion has given us most of the classes of antibiotics currently known as well as many other drugs. We know that we are missing an incredible amount of chemical diversity in the uncultured biosphere because we can observe the biosynthetic pathways for small molecules through culture-independent sequencing. Often these are found in the genomes of bacterial symbionts that live within another animal, such a marine invertebrate or insect. Currently, this sequence data is simply an academic curiosity because it is incredibly challenging to move pathways from uncultured symbionts to laboratory strains which might be separated by more than a billion years of evolution. We will continue to uncover important small molecule pathways in symbionts, but we will also work towards the supply of these compounds through two strategies. In the first we will devise new techniques to search for related pathways in the genomes of free- living bacteria, that might have been previously missed due to incomplete genome assembly. In the second strategy, we will use evolution to optimize protein sequences for the new host, mimicking how pathways have been horizontally transferred between different bacteria for billions of years. 2) When bacterial strains are isolated for drug discovery, most of the small molecule pathways they possess are not expressed under standard culture conditions, and we have to rely on the small subset that are produced in the lab. This is because most pathways are tightly controlled so that they are expressed under specific environmental conditions. Many small molecules made by bacteria are thought to inhibit the growth of rival species, and therefore conditional expression maximizes their impact while reducing the chance that resistance will develop. While small molecule pathways are passed between species through horizontal transfer, they become integrated into the pre-existing regulatory network of a new host. We propose to identify the global regulatory mechanisms for small molecules in a specific group of bacteria, using techniques that are generalizable, and manipulate them to produce small molecules previously inaccessible in the lab. This will overcome a major roadblock in drug discovery, allowing the full exploitation of biosynthesis in isolated strains.

项目摘要/摘要 这项研究计划集中在发现新药分子的根本障碍上。 环境，被称为供应问题。新的生物活性分子在地球上并不缺乏。 我们可以用作药物的环境，因为这样的分子在体内已经进化了数十亿年 数以万亿计的微米。在这个节目中，我们将(1)使用序列分析和定向进化来设计 从实验室培养的菌株中未培养的细菌中制造有希望的分子的方法，以及(2)改进 从分离的可培养细菌菌株中发现新分子的速度 它们的小分子途径是受调控的，并利用这一知识来启动这些途径。 1)据估计，有1万亿种细菌存在。已在实验室中培育的物种数量 与之相比微不足道，但这一微小的部分已经为我们提供了目前大多数类别的抗生素 和许多其他药物一样为人所知。我们知道我们丢失了令人难以置信的化学多样性 未培养的生物圈，因为我们可以通过 与文化无关的测序。这些通常在细菌共生体的基因组中发现，这些共生体生活在 另一种动物，如海洋无脊椎动物或昆虫。目前，这一序列数据只是学术上的 好奇心，因为将途径从未培养的共生体转移到实验室菌株是非常具有挑战性的 它们之间可能有超过十亿年的进化相隔。我们将继续发现重要的小 共生体中的分子途径，但我们也将通过两个途径来提供这些化合物 战略。首先，我们将设计新的技术来搜索自由基因基因组中的相关途径。 活的细菌，这可能是以前由于基因组组装不完整而错过的。在第二个 策略，我们将使用进化来优化新宿主的蛋白质序列，模仿路径如何 在不同的细菌之间水平转移了数十亿年。 2)当细菌菌株被分离用于药物发现时，它们拥有的大多数小分子途径 不是在标准培养条件下表达的，我们必须依赖于 在实验室里生产的。这是因为大多数通路都受到严格控制，因此它们在 特定的环境条件。细菌制造的许多小分子被认为能抑制细菌的生长。 竞争物种，因此条件表达最大限度地发挥其影响，同时减少 抵抗力将会增强。而小分子路径在物种之间通过水平 转让后，它们将整合到新主机的先前存在的监管网络中。我们建议确定 对特定细菌组中小分子的全球调控机制，使用的技术是 可以推广，并操纵它们来生产以前在实验室无法获得的小分子。这将是 克服药物发现的主要障碍，允许充分利用分离菌株的生物合成。