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

描述（由申请人提供）：总体项目目标是开发新的方法来发现“类似药物”的小分子抑制剂，以对抗具有挑战性的蛋白质-蛋白质相互作用（PPI）界面。它验证了一个假设，即适当设计的合成大环可以抑制PPI靶点，同时保持良好的药物样性质。测试系统是细胞内PPI靶点NF-？B基调制剂（NEMO），是？B激酶（IKK）复合物。慢性NF-？B途径存在于人类炎症性疾病和癌症中。抑制NEMO与IKK的相互作用，作为完全消除所有IKK激酶活性的更有针对性的替代方案，代表了一种有希望的减轻炎症的新方法。三个具体目标是：1。执行NEMO的IKK绑定域的虚拟片段屏幕。一种新的算法（FTMAP）将用于PPI目标位点。这些结果将为新的合成无环和大环文库的设计提供信息，用于作为NEMO抑制剂的合成和测试。2. 合成大环和无环抑制剂（来自Aim 1），并在荧光偏振试验中测试它们对NEMO/IKK结合的抑制作用。hit将进行生物化学和结构表征，并通过药物化学进一步优化。所有化合物将在测量ADME特性（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特性的影响将独立于它们对NEMO的活性而确定。3. 利用生化、生物物理、结构和生物学方法表征有希望的命中点和引线（来自目标2），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射线晶体学，药物发现和NF-？B通路生物学。该项目将为针对PPI靶点的药物发现提供理论和方法上的进步。它将阐明在PPI界面上的物理化学和结构起源以及可药物性的标志，并将建立新的基于硅片段的方法和合成大环的效用，作为针对这些靶点的药物样抑制剂的来源。

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.