A Genomic Approach to Discovering Novel Cathepsin Inhibitors from Cyanobacteria

从蓝藻中发现新型组织蛋白酶抑制剂的基因组方法

基本信息

批准号：
10531556
负责人：
Nicole Elizabeth Avalon
金额：
$ 7.16万
依托单位：
UNIVERSITY OF CALIFORNIA, SAN DIEGO
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-12-01 至 2024-11-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10531556
关键词：
Active Sites Anabaena Anabolism Aneurysmal Subarachnoid Hemorrhages Animal Model Antibiotic Resistance Architecture Atlases Behavioral Bioinformatics Biological Assay Biology Bypass Caspase Cathepsin L Cathepsins Cathepsins B Cells Cerebral Ischemia Cerebral hemisphere hemorrhage Cessation of life Chemicals Collection Complex Cyanobacterium Data Docking Drug Targeting Environmental Impact Enzymes FDA approved Fellowship Gene Cluster Gene Expression Genome Genomic Library Genomic approach Genomics Goals In Vitro Injury Institution Ion Channel Ischemia Knock-out Lead Libraries Literature Methods Mining Modeling Molecular Morbidity - disease rate Mus National Research Service Awards Natural Products Neurocognitive Neurocognitive Deficit Neurologic Neurological outcome Neuronal Injury Neurons Oceanography Organism Outcome Pathway interactions Pattern Peptide Hydrolases Peptides Permeability Pharmaceutical Preparations Pharmacologic Substance Pharmacology Phylogeny Plasmids Postdoctoral Fellow Protease Inhibitor Proteins Reporter Ribosomes Scheme Secondary to Source Specificity Structure Techniques Technology Testing Traumatic Brain Injury Tubulin United States United States National Institutes of Health analog behavioral outcome clinical development design drug candidate drug discovery experimental study improved in silico inhibitor innovation interdisciplinary approach interest markov model mortality nanomolar natural product inspired neuroinflammation neuropathology neuroprotection novel novel therapeutics overexpression peptide natural products peptide synthase pharmacophore polyketide synthase polyketides post-doctoral training pre-clinical prevent professor prognostic resistance gene small molecule synergism tandem mass spectrometry tool virtual yeast two hybrid system

项目摘要

Project Abstract Traumatic brain injury (TBI) is a leading cause of morbidity and mortality world-wide and in the United States;1,2 however, there are no FDA-approved medications to ameliorate the devastating consequences of secondary injury caused by complex neuropathological cascades following the initial neuronal insult. Cathepsin B and L represent promising drug targets, as knock-out and inhibition studies of these cysteine proteases in animal models reveal improvement in behavioral and neurocognitive sequelae.3–7 There is a clear need for new therapeutic options to treat secondary injury following TBI, and cathepsin B and L inhibitors have pharmaceutical promise. Over 60% of FDA-approved drugs are derived from or inspired by natural products (NPs).8 Cyanobacteria are known to produce NPs with a range of bioactivity, including activity as protease inhibitors.9,10 NPs are biosynthesized by megaenzymes that are encoded as discrete genomic packages called biosynthetic gene clusters (BGCs).11 We hypothesize that a genomic approach can be used to enhance drug discovery efforts from cyanobacteria for novel cathepsin B and L inhibitors through the three aims outlined below. First, an innovative pharmacophore-based genome mining pipeline will be developed (Aim 1). In this aim, pharmacophores deduced from virtual docking experiments and known cathepsin inhibitors will be used to predict enzymatic domains responsible for the creation of the desired pharmacophore. This retrobiosynthetic prediction will be used to make bioinformatic models to interrogate sequenced cyanobacterial genomes to find candidate BGCs. The BGCs of highest interest will be identified, delineated, and the compounds produced through either cultivation or heterologous expression (Aim 2). Using a full retrobiosynthetic prediction for gallinamide A, a compound that demonstrates nanomolar cathepsin L inhibition, we will search for the BGC within the genomic library at Scripps or in new cyanobacterial collections. Additional BGCs from Aim 1 will be developed in this aim as well. If the BGC is not constitutively expressed or if the BGC is not associated with a cultivatable organism, heterologous expression will be pursued (Aim 3). Compound isolation and molecular networking to analyze and annotate the chemical space of the natural products produced will follow. Compounds will be tested in bioassays to evaluate cathepsin B and L activity on purified enzymes as well as in neuronal and glial cellular studies. The gap between the identified pharmaceutical need and the discovery of novel bioactive molecules can be bridged by the innovative multidisciplinary approach presented in this application. The proposed project will be carried out as part of an NIH F32 NRSA Fellowship at Scripps Institution of Oceanography, UC San Diego, under the co-sponsorship of Professors William Gerwick and Vivian Hook and a team of collaborators that will train the postdoctoral fellow in virtual docking experiments, bioinformatics, heterologous gene expression, and cathepsin-related bioassays.

项目摘要创伤性脑损伤（TBI）是全球发病率和死亡率的主要原因；在美国； 1,2 但是，没有FDA批准的药物可以改善次要的毁灭性后果初始神经元损伤后复杂的神经病理级联反应造成的损伤。组织蛋白酶B和L 代表有希望的药物靶标，是对动物中这些半胱氨酸蛋白酶的敲除和抑制研究模型揭示了行为和神经认知后遗症的改善。3-7显然需要新的 TBI后治疗继发性损伤的治疗选择，组织蛋白酶B和L抑制剂具有药物承诺。超过60％的FDA批准药物来自天然产品或灵感来自天然产品（NP）.8蓝细菌已知会产生具有多种生物活性的NP，包括作为蛋白酶的活性抑制剂。9,10NP是由编码为离散基因组包编码的巨型酶生物合成的生物合成基因簇（BGC）.11我们假设可以使用基因组方法来增强药物通过三个目标概述的新型组织蛋白酶B和L抑制剂的蓝细菌的发现工作以下。首先，将开发基于创新的药效团基因组挖掘管道（AIM 1）。在这个目的，通过虚拟对接实验推导出的药剂团和已知的组织蛋白酶抑制剂将用于预测负责创建所需药效团的酶促结构域。这种转循环合成预测将用于使生物信息学模型询问测序的蓝细菌基因组以找到候选BGC。将确定，划定最高兴趣的BGC，并产生的化合物通过培养或异源表达（目标2）。使用完整的重骨合成预测 Gallinamide A，一种证明纳摩尔组织蛋白酶L抑制的化合物，我们将搜索BGC 在Scripps或新的蓝细菌收集中的基因组库中。 AIM 1的其他BGC将是在此目标中也开发。如果BGC未构成表达，或者BGC与A不相关将追求可培养的生物，异源表达（AIM 3）。化合物分离和分子将随后进行分析和注释生产天然产品的化学空间的网络。化合物将在生物测定中进行测试，以评估纯化酶以及在神经元和神经胶质细胞研究。确定的药物需求与发现之间的差距新颖的生物活性分子可以通过在此提出的创新多学科方法桥接应用。拟议的项目将作为Scripps的NIH F32 NRSA奖学金的一部分进行在威廉·格里克教授的共同赞助下，圣地亚哥分校的海洋学机构， Vivian Hook和一组合作者，将在虚拟对接实验中培训博士后研究员，生物信息学，异源基因表达和与组织蛋白酶相关的生物测定。