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: 10241319
• 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/10241319
• 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; Nature; Pathway interactions; Pharmaceutical Preparations; Research; Resistance; Sequence Analysis; Source; Techniques; Work; drug candidate; drug discovery; 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.

项目概要/摘要 该研究计划的重点是发现新药物分子的基本障碍 环境，即供给问题。体内不乏新的生物活性分子 我们可以将其用作药物的环境，因为这些分子已经进化了数十亿年 数万亿个微利基市场。在这个程序中，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前途的分子的方法，以及（2）改进 通过确定从分离的可培养细菌菌株中发现新分子的共享方式 它们的小分子途径受到调节，并利用这些知识来打开这些途径。 1) 据估计，存在1万亿种细菌。实验室培育的物种数量 相比之下是微乎其微的，但这微不足道的部分却为我们提供了目前大多数类别的抗生素 以及许多其他药物一样已知。我们知道我们缺少大量的化学多样性 未培养的生物圈，因为我们可以通过以下方式观察小分子的生物合成途径 不依赖于培养物的测序。这些通常存在于生活在其中的细菌共生体的基因组中。 另一种动物，例如海洋无脊椎动物或昆虫。目前，这个序列数据还只是学术性的 好奇心，因为将路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 它们之间可能相隔超过十亿年的进化。我们将继续发现重要的小 共生体中的分子途径，但我们还将努力通过两个途径供应这些化合物 策略。首先，我们将设计新技术来搜索自由基因组中的相关途径 活细菌，以前可能由于基因组组装不完整而被遗漏。在第二个 策略，我们将利用进化来优化新宿主的蛋白质序列，模仿途径如何 数十亿年来在不同细菌之间水平转移。 2) 当分离细菌菌株用于药物发现时，它们拥有的大多数小分子途径 在标准培养条件下不表达，我们必须依赖于 在实验室生产。这是因为大多数途径都受到严格控制，因此它们在以下条件下表达： 具体的环境条件。人们认为细菌产生的许多小分子可以抑制细菌的生长 竞争物种，因此条件表达可以最大限度地发挥其影响，同时减少 抵抗力将会发展。虽然小分子途径通过水平方向在物种之间传递 转移后，它们被整合到新宿主预先存在的监管网络中。我们建议确定 特定细菌群中小分子的全局调节机制，使用的技术 可推广，并操纵它们产生以前在实验室中无法获得的小分子。这将 克服了药物发现的主要障碍，允许充分利用分离菌株的生物合成。