A Scalable Platform to Discover Antimicrobials of Ribosomal Origin

项目摘要/摘要 到目前为止，天然产品一直是最丰富的化学物质来源，已被开发成 现代抗菌药和抗真菌药被制药行业采用。然而，尽管迫切需要 新药用于应对令人震惊的耐药性上升，特别是在革兰氏阴性细菌中 病原体，发现天然产物的速度已经降低。在这个R01项目中，我们建议开发 生产新型核糖体天然产物的可扩展平台，即核糖体合成和 翻译后修饰多肽(RIPPS)。在识别出二十多个不同类别的RIPP之后 到目前为止，每年都有几个新的类别被发现，Ripps代表着抗菌剂的一个有希望的补充 以及通过聚酮和非核糖体途径生物合成的抗真菌药物 相比之下，没有得到充分利用。具体来说，我们将整合生物信息学、合成生物学和分析 化学工具为发现开发全自动化、可扩展和高吞吐量(快速)的管道 和来自未鉴定的RIPP生物合成基因簇(BGC)的1000个新RIPP的特征 既有已知的也有未知的。由此产生的新型Ripps将被测试其抗菌和 针对被忽视和热带疾病的抗真菌活动以及其他相关生物学活动 (结核病和疟疾)通过与礼来公司的开放创新药物发现计划合作 (Open Innovation.lilly.com)。该项目是释放RIPPS潜力的第一次大规模尝试 作为新的抗菌和抗真菌药物的来源，基于它们的遗传紧凑性，理想的是 适用于中描述的合成生物学方法和目标。对于这个项目，我们提出了三个 相互关联但可独立实现的具体目标。目标1将从已知类别中发现新的开膛手 使用较低吞吐量的方法。Aim 2将使用 快速流水线。Aim 3将预测和生成尚未报告的类的RIPP，这将 确保各种新颖的天然产品支架。整个项目的成功将改变 自然产品发现，并可能对制药业产生深远影响。

PROJECT SUMMARY/ABSTRACT Natural products have been by far the most prolific source of chemical matter that has been developed into modern antibacterial and antifungal drugs by the pharmaceutical industry. However, despite the pressing need for new drugs to address the alarming rise of drug resistance, especially amongst Gram-negative bacterial pathogens, the rate of discovering natural products has diminished. In this R01 project, we propose to develop a scalable platform to produce novel ribosomal natural products, i.e. ribosomally synthesized and posttranslationally modified peptides (RiPPs). With more than two dozen distinct classes of RiPPs identified thus far, and several new classes being identified each year, RiPPs represent a promising addition to the antibacterial and antifungal drugs biosynthesized by polyketide and non-ribosomal pathways yet they remain vastly underexploited by comparison. Specifically, we will integrate bioinformatics, synthetic biology, and analytical chemistry tools to develop a Fully Automated, Scalable, and high-Throughput (FAST) pipeline for the discovery and characterization of one thousand novel RiPPs from uncharacterized RiPP biosynthetic gene clusters (BGCs) of both known and unknown classes. The resultant novel RiPPs will be assayed for their antibacterial and antifungal activities as well as other related biological activities towards neglected and tropical diseases (tuberculosis and malaria) through a collaboration with Lilly's Open Innovation Drug Discovery Program (openinnovation.lilly.com). This project represents the first large-scale attempt at unlocking the potential of RiPPs as a source of new antibacterial and antifungal drugs, which based on their genetic compactness, are ideally suited for the synthetic biology methods and goals described within. For this project, we propose three interrelated but independently achievable specific aims. Aim 1 will discover novel RiPPs from known classes using lower throughput methods. Aim 2 will scale up the discovery of novel RiPPs from known classes using the FAST pipeline. Aim 3 will predict and produce RiPPs from classes that have not yet been reported, which will ensure a variety of novel natural product scaffolds. Success in the overall project will change the paradigm for natural product discovery and will potentially have a profound impact on the pharmaceutical industry.