Capturing evolved small molecule natural product chemical space

天然小化学品是天然产物，具有广泛的活动范围，具有重要的工业和医药价值。在它们的自然环境中，这些分子已经进化为细胞之间的一种交流形式，并帮助产生它们的有机体的生命。它们的进化状态明显体现在对其生物分子靶标的选择性和对细胞的影响上。生物合成机制导致不同类别的天然产物(如萜类、多酮、非核糖体肽)现在得到了很好的理解，它们的密码已经被破解，从而使遗传指令和最终产物小分子之间的联系得到了重视。天然产物来源的基因组测序的出现打开了大量新的天然产物的缓存，等待发现和评估其工业和制药用途。拟议的研究计划的目的将是设计和实施强大的新工具和战略，使基因组信息能够快速连接到小分子天然产品。拟议的研究计划将寻求开发强大的战略，有选择地识别和捕获这些进化的天然产品，这是一个用于测试的现实。对经过验证的抗生素生产商和许多研究较少的微生物进行的基因组测序对它们的代谢能力产生了深刻的看法。随着微生物基因组测序和下一代测序方法的不断推进，这些在基因组学上可预见的微生物天然产物，或可被称为“未知的”天然产物，正在不断增加。为了有选择地识别这些未知的已知分子，而无需首先重新调查(重新分离)已知的天然产物，将需要尖端策略在发现它们的复杂代谢物中针对它们。技术需要足够敏感，以便在它们以痕量存在时识别它们，并推动这些未知试剂的生产，因为它们的数量正在消失。拟议的计划将创建强大的新平台技术，通过结合现代分析仪器将多种形式的“组学”信息与化学信息和生物信息数据处理策略相结合，选择性地识别聚酮和非核糖体多肽天然产物。该计划将在目前NSERC支持的计划的基础上进行重大改进，该计划已经在开发天然产品信息搜索(ISnap)方面产生了几项创新工作。重要的是，这次更新将集中在这些技术的部署上，以选择性地分离新的具有生物活性的聚酮和非核糖体肽，并考虑到它们所在的化学生态和系统。我想提出一个假设，即之前由生物活性引导活动推动的抗生素发现的早期黄金时代，只揭示了自然进化的抗生素的一小部分。我的实验室将询问导致早期抗生素发现的开创性发现的早期有机体(已知抗生素的生产者)，但我们不会随机评估这些有机体，而是首先使用我的实验室新的CFI LOF基础设施(基因组测序仪和质谱仪)支持的仪器获取它们的基因组序列，然后利用该基因组序列来预测和选择性地挖掘已知的未知天然产品。一旦这些分子被分离出来，我们将询问它们的生物活性，特别是这些未知的已知分子是否对耐药病原菌及其集体活动(协同作用)表现出强大的抗菌活性。

Natural small chemicals, natural products, exhibit a wide spectrum of activity with significant industrial and medicinal value. Within their natural context these molecules have been evolved as a form of communication between cells and to assist the life of the organisms that produce them. Their evolved status is evident in the selectivity to their bio-molecular targets and demonstrated impact on cells. Biosynthetic machinery leading to natural products of different categories (e.g. terpenes, polyketides, nonribosomal peptides) are now well appreciated and their codes have been cracked such that the connection between genetic instruction and end product small molecules is appreciated. The advent of genomic sequencing of natural product sources have opened up a large cache of new natural products that await discovery and evaluation for their industrial and pharmaceutical use. The purpose of the proposed research program will be to design and implement powerful new tools and strategies to enable the rapid connection of genomic information to small molecule natural products. The propose research program will seek to develop powerful strategies to selectively identify and capture these evolved natural products a reality for testing. Genomic sequencing of proven antibiotic producers and numerous poorly studied microorganisms has produced a deep view of their metabolic capability. These genomically-envisioned cohort of microbial natural products, or what can be referred to as ‘unknown known’ natural products, are increasing with the continued advance of microbial genome sequencing with next-generation sequencing approaches. To selectively identify these unknown known molecules, without first re-investigating (re-isolating) the known natural products will demand cutting-edge strategies to target them within the complex metabolomes in which they are found. Technologies will need to be sensitive enough to identify them when they are present in trace amounts and drive the production of these unknown agents with they are revealed in vanishing quantities. The proposed program will create powerful new platform technologies to selectively identify polyketide and nonribosomal peptide natural products by integrating numerous forms of ‘omic’ information with chemoinformatic and bioinformatic data processing strategies in conjunction with modern analytical instruments. The program will build significantly from the current NSERC-supported program that has produced several innovative works in developing an informatic search for natural products (iSNAP). Importantly this renewal will focus on the deployment of these technologies to selectively isolate new bioactive polyketide and nonribosomal peptides that considers the chemical ecology and systems in which they are found. I wish to advance the hypothesis, that the previous early golden age of antibiotic discovery driven by bioactivity guided activities revealed only a small fraction of the antibiotics that have been naturally evolved. My laboratory will interrogate the early organisms (producers of known antibiotics) that lead to the seminal discoveries in early antibiotic discovery, but instead of randomly assessing these organisms we will first obtain genomic sequences of them using instrumentation supported by my laboratories new CFI LOF infrastructure (genomic sequencers and mass spectrometers) and then leverage that genomic sequence to predict and selectively mine for known unknown natural products. Once these molecules are isolated we will then query their biological activities and specifically whether these unknown known molecules exhibit potent antimicrobial activities to drug resistant pathogenic bacteria and their collective activities (synergies).