Zerfas Breanna L, Liu Yingpeng, Che Jianwei, Donovan Katherine A, Hatcher John M, Huerta Fidel, Metivier Rebecca J, Nowak Radosław P, Ragosta Leah, Tsang Tiffany, Fischer Eric S, Jones Lyn H
Center for Protein Degradation, Dana-Farber Cancer Institute Boston MA USA
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School Boston MA USA.
RSC Med Chem. 2025 Mar 18. doi: 10.1039/d5md00028a.
IRE1α is an ER protein involved in the unfolded protein response (UPR) and dysregulation of the ER stress pathway has been implicated in several diseases. Inhibitors of the cytoplasmic endonuclease or kinase domains of the enzyme have limited utility and targeted degradation would address additional scaffolding functions of the protein. Here, we describe the design and development of IRE1α proteolysis targeting chimeras (PROTACs) based on a lysine-reactive salicylaldehyde RNase inhibitor, and present the structure-activity relationships (SARs) that delivered the first highly selective degraders of a native ER-membrane associated protein. Medicinal chemistry optimization exploited ternary complex computational modelling to inform design, HiBiT-SpyTag IRE1α degradation and NanoBRET cereblon occupancy cell-based assays to generate SARs, and mass spectrometry-based proteomics to assess broad selectivity in an unbiased manner. Merging IRE1α and CRBN ligand chemotypes provided the truncated chimera CPD-2828 with physicochemical properties more akin to an oral molecular glue degrader than a traditional PROTAC.
IRE1α是一种参与未折叠蛋白反应（UPR）的内质网（ER）蛋白，内质网应激途径的失调与多种疾病有关。该酶细胞质核酸内切酶或激酶结构域的抑制剂效用有限，靶向降解将解决该蛋白的其他支架功能。在此，我们描述了基于赖氨酸反应性水杨醛核糖核酸酶抑制剂的IRE1α蛋白酶靶向嵌合体（PROTAC）的设计与开发，并展示了结构-活性关系（SAR），这些关系产生了首个对天然内质网相关膜蛋白具有高度选择性的降解剂。药物化学优化利用三元复合物计算模型指导设计，基于HiBiT-SpyTag的IRE1α降解和基于NanoBRET的大脑神经酰胺酶（cereblon）占据细胞检测来生成SAR，并利用基于质谱的蛋白质组学以无偏倚的方式评估广泛选择性。将IRE1α和CRBN配体化学类型合并，得到了截短嵌合体CPD-2828，其物理化学性质更类似于口服分子胶降解剂而非传统PROTAC。
