Targeting E3 ubiquitin ligases with small molecules

E3泛素连接酶是泛素-蛋白酶体系统（UPS）内的酶，催化泛素向特定底物蛋白的转移。靶向小分子E3连接酶是化学生物学和药物发现的前沿目标，因为它允许：1)与蛋白酶体抑制剂相比，增强了对UPS的选择性干预；2)利用UPS诱导新的靶蛋白降解。例如，E3连接酶配体可以结合到双功能嵌合分子中，这种分子被称为靶向蛋白水解嵌合体（PROTACs），可诱导蛋白质泛素化并随后在细胞内降解。然而，只有少数E3连接酶被成功地靶向小分子，这需要靶向难以靶向的蛋白质表面或蛋白质-蛋白质相互作用(1)。Ciulli实验室致力于开发E3连接酶靶向配体和PROTACs。他们开创了针对von Hippel-Lindau (VHL) E3连接酶的结构导向设计和分子优化。他们确定了强效和选择性的VHL抑制剂VH298作为缺氧信号通路中VHL- hif轴的化学探针。此外，他们还展示了VHL配体如何成功地与多种蛋白质靶向配体结合，从而在细胞和体内产生对多种靶蛋白有活性的PROTACs(2)。Virdee实验室率先开发了用于研究UPS的新型化学试剂和工具，特别关注E3连接酶。一个关键的成就是探针的发展，测量泛素化酶的标志性反式硫代酸活性。这些已被用于深入了解疾病相关的E3调控，并有潜力作为未满足临床需求的疾病的生物标志物。这些技术的应用已经导致鉴定了一类新的具有非赖氨酸泛素化活性的E3连接酶(3)。该项目旨在开发具有生物学和治疗意义的新E3连接酶的新型小分子粘合剂。该项目设计为高度跨学科的，借鉴了Ciulli实验室和Virdee实验室的互补专业知识。该学生将接受Ciulli和Virdee实验室在基础和转化化学和结构生物学的前沿研究方面的多学科领域的优秀培训。References1。张建军，刘建军。中国生物医学工程学报。2015；467:365 - 86.2。刘志强，刘志强。生物工程学报，2019；52:145 - 56.3。鲍康成等。自然2018;556:381-5。

E3 ubiquitin ligases are enzymes within the ubiquitin-proteasome system (UPS) that catalyse the transfer of ubiquitin to specific substrate proteins. Targeting of E3 ligases with small molecules is a frontier goal of chemical biology and drug discovery because it allows: 1) enhanced selective intervention in the UPS, compared for example to proteasome inhibitors; 2) co-opting the UPS to induce the degradation of new target proteins. For example, E3 ligase ligands can be incorporated into bifunctional chimeric molecules, nick-named proteolysis targeting chimeras (PROTACs), that induce protein ubiquitination and subsequent degradation inside the cell. However, only few E3 ligases have been successfully targeted with small molecules, and this requires the targeting of proteins surfaces or protein-protein interactions that are difficult-to-target (1).The Ciulli lab works on developing E3 ligase targeting ligands and PROTACs. They have pioneered the structure-guided design and optimization of molecules targeting the von Hippel-Lindau (VHL) E3 ligase. They qualified potent and selective VHL inhibitor VH298 as a chemical probe of the VHL-HIF axis in the hypoxia signaling pathway. Moreover, they have shown how the VHL ligands can be successfully conjugated to a variety of protein-targeting ligands, yielding PROTACs active against diverse target proteins in cells and in vivo (2).The Virdee lab has pioneered the development of novel chemical reagents and tools for studying the UPS, with a particular focus on E3 ligases. A key achievement is the development of probes that measure the hallmark trans-thiolation activity of ubiquitination enzymes. These have been used to gain insights into disease relevant E3 regulation and have potential as biomarkers for diseases of unmet clinical need. Application of these technologies has led to the identification of a new class of E3 ligase with non-lysine ubiquitination activity (3). This project aims to develop novel small molecule binders for new E3 ligases of biological and therapeutic relevance. The project is designed as highly interdisciplinary, drawing on complementary expertise from both the Ciulli lab and Virdee labs. The student will receive outstanding training in multidisciplinary areas in cutting-edge research in fundamental and translational chemical and structural biology from both the Ciulli and Virdee labs. References1. Bulatov E, Ciulli A. Biochem J 2015; 467:365-86.2. Maniaci C, Ciulli A. Curr Opin Chem Biol 2019; 52:145-56.3. Pao K-C et al. Nature 2018; 556:381-5.