Understanding the contributions of microbiome-encoded drug metabolizing enzymes

了解微生物组编码的药物代谢酶的贡献

基本信息

批准号：
10626934
负责人：
Andrew L Goodman
金额：
$ 41.88万
依托单位：
YALE UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2019
资助国家：
美国
起止时间：
2019-09-16 至 2025-05-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10626934
关键词：
Address Adverse reactions Applications Grants Bacteria Bile fluid Biological Availability Biological Markers Chemicals Circulation Data Drug Kinetics Engineering Enterohepatic Circulation Enzymes Excretory function Exhibits FDA approved Formulation Gastrointestinal tract structure Genes Genetic Genetic Techniques Gnotobiotic Hepatic Hepatocyte Human Human Genome In Vitro Individual Measurement Measures Mediating Medical Metabolic Biotransformation Metabolism Metagenomics Methods Microsomes Modeling Mus Oral Parents Pharmaceutical Preparations Physiological Process Production Safety Series Serum Surveys System Techniques Testing Time Toxic effect Variant candidate identification commensal bacteria drug candidate drug metabolism experimental study gain of function gut bacteria gut microbes gut microbiome gut microbiota host microbiome in vivo loss of function metabolomics microbial microbiome mouse model pharmacokinetic model physiologically based pharmacokinetics predictive marker repository small molecule tool

项目摘要

Project Summary Drug metabolites can have distinct efficacy and toxicity profiles relative to the parent compound, and interpersonal variation in drug metabolism can determine adverse reactions. Notably, oral drugs that exhibit low bioavailability, are delivered in delayed release formulations, or are excreted through bile can encounter enormous densities of bacteria in the gastrointestinal tract. The gut microbiome carries a collective gene content 150-fold larger than the human genome, encodes a rich repository of enzymes with the potential capacity to metabolize drugs, and varies widely between individuals. The microbiome thus has the potential to impact serum drug and metabolite exposure. However, scalable in vitro systems for identification of active microbial species, enzymes, and candidate drug metabolites are not available. Our understanding of microbiome-mediated drug metabolism is largely limited to anecdotal examples, and it is unknown whether gut microbes encode enzymes that metabolize many drugs. Strategies for determining the quantitative contribution of gut microbial drug metabolism to serum drug and metabolite exposure are also not available. We developed high-throughput approaches that generate metabolomic time-series profiles of the metabolism of hundreds of drugs by hundreds of human gut microbial communities and species, uncover the microbiome- encoded enzymes responsible for these transformations, and identify candidate drug metabolites produced as a result. We also provide evidence that combining gnotobiotics with physiologically-based pharmacokinetic modeling can quantitatively disentangle host and microbial contributions to serum drug metabolite exposure in vivo, using a drug that is converted into a single metabolite by host and microbiome as a proof of concept. In Aim 1 of this proposal, we present a plan to establish the first repertoire of drug-metabolizing enzymes in the human gut microbiome. These results will reveal whether human gut microbes encode enzymes that metabolize many drugs and whether microbiome genes encoding drug-metabolizing enzymes serve as predictive biomarkers of the drug-metabolizing capacity of an individual's microbiome. In Aim 2, we describe a strategy to develop and test generalized host-microbiome pharmacokinetic models that capture host and microbial conversion of a drug into multiple metabolites and include enterohepatic circulation in the model topology. If successful, these aims will establish broadly applicable approaches to identify when and how the microbiome could contribute to the metabolism of drugs and other small molecules.

项目概要相对于母体化合物，药物代谢物可能具有不同的功效和毒性特征，并且药物代谢的人际差异可以决定不良反应。值得注意的是，口服药物表现出生物利用度低，以延迟释放制剂形式递送，或通过胆汁排泄胃肠道内细菌密度巨大。肠道微生物组携带集体基因内容比人类基因组大150倍，编码丰富的酶库，具有潜在的潜力药物代谢能力，个体之间差异很大。因此，微生物组有潜力影响血清药物和代谢物暴露。然而，用于识别活性物质的可扩展体外系统微生物种类、酶和候选药物代谢物不可用。我们的理解微生物组介导的药物代谢在很大程度上仅限于轶事例子，目前尚不清楚肠道是否会影响药物代谢。微生物编码代谢许多药物的酶。确定定量贡献的策略肠道微生物药物代谢对血清药物和代谢物暴露的影响也无法获得。我们开发了高通量方法，可以生成代谢的代谢组学时间序列图谱数百种人类肠道微生物群落和物种的数百种药物，揭示微生物组编码负责这些转化的酶，并确定产生的候选药物代谢物一个结果。我们还提供证据表明，将无菌抗生素与基于生理学的药代动力学相结合建模可以定量地分析宿主和微生物对血清药物代谢物暴露的贡献体内，使用由宿主和微生物组转化为单一代谢物的药物作为概念证明。在本提案的目标 1 中，我们提出了一项计划，旨在建立第一个药物代谢酶库。人类肠道微生物组。这些结果将揭示人类肠道微生物是否编码以下酶：代谢许多药物以及编码药物代谢酶的微生物组基因是否充当个体微生物组药物代谢能力的预测生物标志物。在目标 2 中，我们描述了开发和测试通用宿主微生物组药代动力学模型的策略，该模型捕获宿主和将药物微生物转化为多种代谢物，并在模型中包括肠肝循环拓扑。如果成功，这些目标将建立广泛适用的方法来确定何时以及如何微生物组可能有助于药物和其他小分子的代谢。