Accessing and expanding microbial chemical diversity by synthetic biology and new enzymology

项目摘要/摘要 天然产物是新药先导的有效来源，但新发现率很低 生物活性化合物的有限获取正在挑战目前基于天然产物的药物开发 和发展。国际和平研究所研究计划的总体目标是获取和扩大化学多样性 微生物通过使用创新策略，从而推进天然产品的研究。中环 这项工作的假设是，微生物基因组可以被利用来探索天然产品和类似物。 从数千个微生物基因组中挖掘生物合成基因簇的生物信息学区分了 微生物是大量新的治疗相关化合物的重要来源。然而， 目前的发现过程只能获得这些化合物中的一小部分，这突显了紧迫的 需要新的战略。酶作为生物催化剂在学术和科学领域是公认的化学合成替代品 工业背景。微生物天然产物的生物合成富含不同功能的酶。 从微生物中发现新的酶学可以促进结构复杂的天然产物的合成 以及通过化学方法或生物学方法(例如合成生物学)的类似物。为了实现这一目标并 检验假设，这一建议的研究方向1将重点放在生产蓝藻天然产物上 使用多个合成生物底盘。蓝藻在结构和功能上都是一个丰富的来源 多种天然产物，但几乎所有的蓝藻化合物都只能通过从 收集了现场样本。研究方向1可以导致对蓝藻的强有力的、彻底的探索 直接从基因组中分离出菌株。本提案的研究方向2将发现并表征 来自微生物BCS的合成重要酶，有助于获得和扩大化学多样性 天然产品。在方向1中发现的新酶也将在方向2中表征，并可以 然后在方向1中用于生产天然和非天然化合物，证明了成本的提高 效率。方向2的特别关注将是发现和表征新型硝化酶。一起， 国际和平研究所研究计划的这两个方向可以提供创新战略，使有效 利用看似无限的微生物化学多样性来发现和开发新药 并允许开发新的化学工艺。这些研究还可以促进 因此，天然产物研究从小规模的追求转向基于基因组的高通量努力 潜在地引发了天然产品和药物研究的范式转变。

Project Summary/Abstract Natural products form a validated and preeminent source of new drug leads, but the low rate of new discoveries and the limited access of bioactive compounds are challenging current natural products-based drug discovery and development. The overall goal of the PI’s research program is to access and expand chemical diversity of microbes by the use of innovative strategies, thereby advancing natural products research. The central hypothesis of this work is that microbial genomes can be exploited to explore natural products and analogs. Bioinformatics mining of biosynthetic gene clusters from thousands of microbial genomes have distinguished microbes as the prominent source of an immense number of new therapeutically relevant compounds. However, current discovery process is able to access only a small fraction of these compounds, underlining the urgent need of new strategies. Enzymes as biocatalysts are proven alternatives for chemical synthesis in academic and industrial settings. The biosynthesis of microbial natural products is enriched with functionally diverse enzymes. Discovery of new enzymology from microbes can advance the synthesis of structural complex natural products and analogs via chemical methods or biological approaches (e.g., synthetic biology). To achieve the goal and test the hypothesis, research direction 1 of this proposal will focus on producing cyanobacterial natural products using multiple synthetic biology chassis. Cyanobacteria are a prolific source of structurally and functionally diverse natural products, but almost all cyanobacterial compounds are accessed only through the isolation from collected field samples. The research direction 1 can lead to the robust, thorough exploration of cyanobacterial strains directly from the genomes. Research direction 2 of this proposal will discover and characterize synthetically significant enzymes from microbial BCs, aiding the access and expansion of chemical diversity of natural products. The new enzymes discovered in direction 1 will also be characterized in direction 2 and can then be used in direction 1 to produce natural and unnatural compounds, demonstrating the improved cost efficiency. Specific attention in direction 2 will be to discover and characterize novel nitration enzymes. Together, these two directions of the PI’s research program can afford innovative strategies that enable effective exploitation of the seemingly limitless chemical diversity of microbes for discovery and development of new drugs and allow the development of new chemical processes. These studies can also boost the transformation of natural products research from small-scale pursuits to a genome-based high-throughput endeavor, therefore potentially triggering a paradigm shift in natural products and drug research.