Mapping epistatic interactions in molecular evolution of antibiotic resistance

绘制抗生素耐药性分子进化中的上位相互作用

• 批准号: 10361439
• 负责人: Erdal Toprak
• 金额: $ 37.27万
• 依托单位: UT SOUTHWESTERN MEDICAL CENTER
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-04-09 至 2023-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10361439
• 关键词: Affinity; Algorithms; Alleles; Anti-Bacterial Agents; Antibiotic Resistance; Antibiotics; Antimalarials; Automobile Driving; Bacteria; Basic Science; Biochemical; Biological Assay; Cells; Cellular Metabolic Process; Chemicals; Clinical; Clinical Sciences; Competitive Binding; Computational Biology; Computer Analysis; DNA Gyrase; DNA-Directed RNA Polymerase; Data; Dihydrofolate Reductase; Dihydrofolate Reductase Inhibitor; Dose; Drug Targeting; Enzymes; Escherichia coli; Evolution; Fatty Acids; Folic Acid; Free Energy; Genes; Genetic; Genetic Epistasis; Glutamates; Goals; Health; Human; Hybrids; Hydrogen Bonding; In Vitro; Laboratories; Lead; Libraries; Ligase; Maps; Measurement; Methods; Molecular; Molecular Evolution; Morbidity - disease rate; Mutation; NMR Spectroscopy; Names; Nuclear Magnetic Resonance; Pathway interactions; Pharmaceutical Preparations; Phenotype; Plasma; Point Mutation; Population; Procedures; Proteins; Public Health; Reproducibility; Resistance; Role; Sampling; Tail; Testing; Trimethoprim; Trimethoprim Resistance; Urine; Variant; anti-cancer; bacterial resistance; base; clinically relevant; combinatorial; computerized tools; cost; deep sequencing; design; dihydrofolate; drug-sensitive; exhaustion; experimental study; fitness; improved; molecular dynamics; mutant; next generation sequencing; novel; novel therapeutics; pathogenic bacteria; preservation; resistance mechanism; synthetic construct; tool

PROJECT SUMMARY Evolution of antibiotic resistance is a global public health problem. How evolution renders antibiotic molecules ineffective by altering antibiotic targets is an interesting phenomenon from both clinical and basic science perspectives. In pathogenic bacteria, there is only a handful of drug target enzymes such as DNA gyrases, RNA polymerases, fatty acid synthetases, and enzymes involved in folic acid synthesis. Therefore, a mechanistic understanding of resistance-conferring mutations in these enzymes is clinically critical for designing new drugs or drug variants that can inhibit resistant bacteria. In this project, we propose to study evolution of the Escherichia coli dihydrofolate reductase (DHFR) enzyme and map epistatic interactions between DHFR mutations. DHFR is a ubiquitous enzyme with an essential role in the folic acid synthesis pathway and is used as a drug target in antibacterial, anticancer, and antimalarial therapies. In bacteria, an antibiotic named trimethoprim competitively binds to DHFR and blocks its catalytic activity. Therefore, DHFR mutations that either confer resistance or compensate for reduced catalytic activity of resistant DHFR mutants are selected for bacterial survival. We will use laboratory evolution experiments to identify functional DHFR mutations and reproducible genetic trajectories leading to elevated trimethoprim resistance. We will characterize these mutations by using in vitro biochemical assays and deep-sequencing based fitness measurements for calculating epistatic interactions between DHFR mutations. We will use molecular dynamics along with other computational tools and nuclear magnetic resonance (NMR) spectroscopy to reveal structural changes responsible for resistance and epistatic interactions. The combination of these approaches presents a unique opportunity to quantitatively evaluate evolutionary paths leading to trimethoprim resistance and create a discovery pipeline for studying protein evolution. By creating a deeper understanding for the evolutionary dynamics of an important drug target enzyme, our proposal will develop experimental and computational tools for studying protein evolution with the ultimate goal of improving human health. Indeed, our preliminary analyses suggest that we will be able to design and test novel trimethoprim derivatives that can selectively inhibit DHFR mutants that carry the L28R replacement, a common and synergistic DHFR mutation. We propose to synthesize trimethoprim-Dihydrofolate hybrid molecules that will possess the salient structural features of both DHF and trimethoprim molecules selectively inhibit DHFR mutants with the L28R replacement. We will evolve pan sensitive E. coli strains in the morbidostat in order to quantify the efficacy of the mutant specific trimethoprim derivatives in impeding resistance evolution and accordingly develop new strategies for better use of it.

项目摘要 抗生素耐药性的演变是一个全球性的公共卫生问题。进化如何使抗生素 通过改变抗生素靶点而无效的分子是临床和基础研究中的一个有趣现象。 科学观点。在致病菌中，只有极少数的药物靶向酶如DNA 促旋酶、RNA聚合酶、脂肪酸合成酶和参与叶酸合成的酶。因此 对这些酶的耐药突变机制的理解在临床上至关重要， 设计新的药物或药物变体，可以抑制耐药细菌。 在这个项目中，我们打算研究大肠杆菌二氢叶酸还原酶（DHFR）的进化 酶和地图之间的DHFR突变上位相互作用。DHFR是一种普遍存在的酶， 在叶酸合成途径中发挥重要作用，并用作抗菌、抗癌和抗肿瘤的药物靶点 抗疟疾疗法。在细菌中，一种名为甲氧苄啶的抗生素竞争性地与DHFR结合， 催化活性因此，DHFR突变，无论是赋予耐药性或补偿减少的催化 选择抗性DHFR突变体的活性用于细菌存活。 我们将使用实验室进化实验来鉴定功能性DHFR突变和可重复性。 导致甲氧苄啶耐药性升高的遗传轨迹。我们将通过使用 用于计算上位性的体外生物化学测定和基于深度测序的适合度测量 DHFR突变之间的相互作用。我们将使用分子动力学沿着与其他计算工具 和核磁共振（NMR）光谱，以揭示负责电阻的结构变化 和上位相互作用。这些方法的结合提供了一个独特的机会， 评估导致甲氧苄啶耐药性的进化路径，并为研究建立发现管道 蛋白质进化通过对一个重要药物靶点的进化动力学有更深入的了解， 酶，我们的建议将开发实验和计算工具，用于研究蛋白质进化与 改善人类健康的最终目标。事实上，我们的初步分析表明，我们将能够 设计和测试新型甲氧苄啶衍生物，可以选择性抑制携带L28 R的DHFR突变体 替代，一种常见的协同DHFR突变。我们建议合成甲氧苄啶-二氢叶酸 具有DHF和甲氧苄啶分子的显著结构特征的混合分子 选择性抑制具有L28 R置换的DHFR突变体。我们将进化出对泛敏感的E。大肠杆菌菌株 为了定量突变体特异性甲氧苄啶衍生物在阻碍 抗性进化，并相应地开发新的策略以更好地利用它。