Design of Macrocyclic Inhibitors of the NEMO/IKKa/b Protein-Protein Interaction

描述(由申请人提供)：该项目的总体目标是开发新的方法来发现“类药物”小分子抑制剂，以对抗具有挑战性的蛋白质-蛋白质相互作用(PPI)界面。它验证了这样一个假设，即适当设计的合成大环可以抑制PPI靶标，同时保持良好的药物性质。测试系统是针对细胞内PPI的核因子-B必需调节剂(NEMO)，它是B蛋白激酶(IKK)抑制剂复合体的组成部分。在人类炎症性疾病和癌症中发现了核因子-βB途径的慢性高活性。抑制NEMO与IKK的相互作用，作为完全消融所有IKK激酶活性的更有针对性的替代方案，代表了一种有前途的抗炎新方法。具体的三个目的是：1.进行Nemo的ikk结合结构域的虚拟片段筛选。一种新的算法(FTMAP)将用于PPI目标站点。这些结果将为设计新的合成非环和大环文库提供参考，用于合成和测试NEMO抑制剂。2.合成大环和非环抑制剂(来自AIM 1)，并在荧光偏振分析中测试它们对NEMO/IKK结合的抑制作用。HITS将在生化和结构上进行表征，并通过药物化学进一步优化。所有化合物都将在测定ADME性质(例如，溶解度、细胞渗透性和肝微粒体稳定性)的分析中进行评估。因此，不同的大环设计对这些关键药物性质的影响将独立于它们对NEMO的活性来确定。3.使用生化、生物物理、结构和生物学方法表征有希望的命中和引线(来自目标2)，以阐明它们与NEMO相互作用的性质，确定它们与靶标产生的结合能的来源，并评估它们作为生物探针和/或药物引线的效用。项目团队在项目的各个方面都拥有强大的专业知识和高度相关的经验，包括计算化学、大环合成、X射线结晶学、药物发现和核因子-B途径生物学。该项目将在针对PPI目标的药物发现方面提供理论和方法上的进步。它将阐明PPI界面上的物理化学和结构起源以及可药性的特征，并将确立新型在基于硅胶片段的方法和合成大环中的用途，作为针对这些靶点的类药物抑制剂的来源。 公共卫生相关性：该项目的目标是针对一类特别具有挑战性的药物靶标--蛋白质-蛋白质相互作用--与小分子(即合成有机)药物。它的目的是抑制核因子-？B信号通路的一个组成部分--核因子-？B基本调节器(NEMO)，后者在炎症疾病和癌症等人类病理中被错误调节。抑制这一途径代表着开发有效药物的一种很有前途的新方法，因此，与公共卫生高度相关。

DESCRIPTION (provided by applicant): The overall project goal is to develop new approaches for discovering "drug-like" small molecule inhibitors against challenging protein-protein interaction (PPI) interfaces. It tests the hypothesis that appropriately designed synthetic macrocycles can inhibit PPI targets while maintaining good drug-like properties. The test system is the intracellular PPI target NF-?B essential modulator (NEMO), a component of the inhibitor of ?B kinase (IKK) complex. Chronic hyperactivity of the NF-?B pathway is found in human inflammatory diseases and cancers. Inhibiting the interaction of NEMO with IKK, as a more targeted alternative to completely ablating all IKK kinase activity, represents a promising new approach for attenuating inflammation. The three Specific Aims are: 1. Perform a virtual fragment screen of the IKK binding domain of NEMO. A novel algorithm (FTMAP) will be used against the PPI target sites. The results will inform the design of novel synthetic acyclic and macrocyclic libraries for synthesis and testing as NEMO inhibitors. 2. Synthesize macrocycles and acyclic inhibitors (from Aim 1), and test them for inhibition of NEMO/IKK binding in a fluorescence polarization assay. Hits will be characterized biochemically and structurally and further optimized through medicinal chemistry. All the compounds will be assessed in assays that measure ADME properties (e.g., solubility, cell permeability and liver microsome stability). The consequences of different macrocyclic designs for these key pharmaceutical properties will thus be determined independently of their activity against NEMO. 3. Characterize promising hits and leads (from Aim 2) using biochemical, biophysical, structural and biological approaches, to elucidate the nature of their interactions with NEMO, determine the origins of the binding energy they generate with the target, and assess their utility as biological probes and/or drug leads. The project team encompasses strong expertise and highly relevant experience across every aspect of the project, including computational chemistry, macrocycle synthesis, X-ray crystallography, drug discovery, and NF-?B pathway biology. The project will provide theoretical and methodological advances in drug discovery against PPI targets. It will elucidate the physicochemical and structural origins and hallmarks of druggability at a PPI interface, and will establish the utility of novel in silico fragment-based approaches and synthetic macrocycles as sources for drug-like inhibitors against such targets. PUBLIC HEALTH RELEVANCE: The goal of this project is to target a particularly challenging class of drug targets, - protein-protein interactions - with small molecule (i.e., synthetic organic) drugs. It aims to inhibit NF-?B Essential Modulator (NEMO), a component of the NF-?B signaling pathway, which is misregulated in human pathologies such as inflammatory disease and cancer. Inhibiting this pathway represents a promising new approach for the development of effective drugs and, consequently, is highly relevant to public health.