Targeting protein-protein interactions as drug targets

将蛋白质-蛋白质相互作用作为药物靶点

• 批准号: 10306398
• 负责人: Michael D. Burkart
• 金额: $ 19.75万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-12-01 至 2024-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10306398
• 关键词: Acyl Carrier Protein; Anabolism; Anti-Bacterial Agents; Antibiotics; Bacteria; Bacterial Infections; Benchmarking; Binding; Biotin; Cell Wall; Clinic; Complex; Computer Assisted; Computer Models; Computer software; Computing Methodologies; Crystallization; Data; Development; Docking; Drug Targeting; Effectiveness; Enzymes; Escherichia coli; Escherichia coli Infections; Fatty Acids; Fatty-acid synthase; Future; Goals; Hemolysin; Homeostasis; Infection; Kinetics; Knowledge; Lead; Lipid A; Lung; Mechanics; Mediating; Metabolism; Methods; Modeling; Multiple Partners; Mutagenesis; Mycobacterium tuberculosis; Mycolic Acid; Outcome Study; Pathology; Pathway interactions; Production; Proteins; Protocols documentation; Renaissance; Resistance; Resolution; Roentgen Rays; Role; Series; Structure; System; Testing; Therapeutic; Thioctic Acid; Titrations; Tuberculosis; Very Long Chain Fatty Acid; Virulence; Work; X-Ray Crystallography; base; cofactor; computerized tools; drug development; drug discovery; experience; experimental study; fatty acid biosynthesis; fatty acid synthase II; high reward; high risk; human disease; in silico; microbial; molecular dynamics; molecular recognition; mortality; mycobacterial; next generation; novel; novel strategies; novel therapeutics; programs; protein complex; protein function; protein protein interaction; protein structure; simulation; small molecule inhibitor

7. Project Summary. This proposal describes a program to identify drug targets for tuberculosis and Escherichia coli infections through the combination of computational and experimental methods to elucidate targets within mycobacterial and bacterial fatty acid synthesis. In Escherichia coli, the pathway involves 27 discrete interactions between AcpP and its partner proteins. In tuberculosis, the FAS-II pathway is involved the production of mycolic acids, which serve a pivotal role in the virulence of Mycobacterium tuberculosis (Mtb). As both pathways require an acyl carrier protein (ACP) to deliver growing fatty acyl substrates and intermediates to associated partner proteins (PPs), protein-protein interactions within the AcpP.PP complex are an essential for effective substrate processivity. Resolution of the structures of these assemblies and the interactions responsible for their formation will not only further our knowledge of the mechanisms by which these proteins function and are regulated but will also enable structure-based drug discovery work. In order to elucidate these structures, we will leverage our knowledge of the Escherichia coli AcpP.PP interfaces to identify a computational docking protocol that produces novel Mtb AcpP.PP structures. Our computational methodology will be optimized by evaluating its effectiveness in recapitulating known structures of E. coli AcPP.PP complexes resolved via NMR and X-ray crystallography studies. This computational protocol, once tested, will be used to predict both AcpP.PP and AcpM.PP complexes. The structures of the resulting complexes will then be validated using NMR titration and mutagenesis experiments. The resulting models will be refined using molecular dynamics simulations, which yield a dynamical understanding protein structure that will inform computer-aided drug discovery efforts.

7. 项目概要。该提案描述了一项确定结核病药物靶点的计划 通过计算和实验相结合的方法来阐明大肠杆菌感染 分枝杆菌和细菌脂肪酸合成中的靶点。在大肠杆菌中，该途径涉及 27 AcpP 及其伙伴蛋白之间离散的相互作用。在结核病中，FAS-II 通路涉及 产生分枝酸，其在结核分枝杆菌 (Mtb) 的毒力中发挥关键作用。作为 两种途径都需要酰基载体蛋白 (ACP) 来输送生长的脂肪酰基底物和中间体 对于相关伴侣蛋白 (PP)，AcpP.PP 复合物内的蛋白质-蛋白质相互作用是必不可少的 以获得有效的基材加工能力。解析这些组件的结构和相互作用 负责它们的形成不仅将进一步加深我们对这些蛋白质的机制的了解 功能并受到监管，但也将使基于结构的药物发现工作成为可能。为了阐明这些 结构，我们将利用我们对大肠杆菌 AcpP.PP 接口的知识来识别 产生新型 Mtb AcpP.PP 结构的计算对接协议。我们的计算方法 将通过评估其重现大肠杆菌 AcPP.PP 已知结构的有效性来进行优化 通过 NMR 和 X 射线晶体学研究解析了配合物。该计算协议一旦经过测试，将 用于预测 AcpP.PP 和 AcpM.PP 复合体。所得复合物的结构将随后 使用核磁共振滴定和诱变实验进行验证。所得模型将使用以下方法进行细化 分子动力学模拟，产生对蛋白质结构的动态理解，从而提供信息 计算机辅助药物发现工作。

项目成果

Masked cerulenin enables a dual-site selective protein crosslink.

• DOI: 10.1039/d3sc02864j
• 发表时间: 2023-10-11
• 期刊: CHEMICAL SCIENCE
• 影响因子: 8.4
• 作者: Jiang, Ziran;Chen, Aochiu;Chen, Jeffrey;Sekhon, Arman;Louie, Gordon V.;Noel, Joseph P.;La Clair, James J.;Burkart, Michael D.
• 通讯作者: Burkart, Michael D.