A Scalable Platform to Discover Antimicrobials of Ribosomal Origin

项目总结/摘要 天然产物是迄今为止最丰富的化学物质来源， 现代抗细菌和抗真菌药物。然而，尽管迫切需要 新的药物来解决令人担忧的耐药性上升，特别是在革兰氏阴性细菌中， 病原体，发现天然产品的速度已经下降。在R 01项目中，我们建议开发 一个可扩展的平台，以产生新的核糖体天然产物，即核糖体合成的， 后修饰肽（RIPPs）。有二十多个不同类别的RIPP被确定， 到目前为止，每年都有几个新的类别被确定，RIPPs代表了一个有希望的抗菌剂 以及通过聚酮化合物和非核糖体途径生物合成的抗真菌药物， 相比之下，开发不足。具体来说，我们将整合生物信息学，合成生物学和分析生物学。 化学工具来开发全自动、可扩展和高吞吐量（FAST）管道， 和表征来自未表征的RiPP生物合成基因簇（BGC）的一千种新型RiPP 已知和未知的类。将测定所得的新型RIPP的抗菌性和生物相容性。 抗真菌活性以及针对被忽视疾病和热带疾病的其他相关生物活性 （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， （openinnovation.lilly.com）中找到。该项目代表了释放RIPP潜力的首次大规模尝试 作为新的抗细菌和抗真菌药物的来源，基于它们的遗传紧凑性， 适用于合成生物学方法和目标内所述。在这个项目中，我们提出三个 相互关联但独立可实现的具体目标。目标1将从已知类别中发现新的RIPP 使用较低吞吐量的方法。目标2将使用 快速管道。目标3将从尚未报告的类别中预测和产生RIPP，这将 保证了多种新型天然产物支架。整个项目的成功将改变 天然产物的发现，并可能对制药行业产生深远的影响。

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.