Wu Xinyuan, Li Shunyao, Liang Ting, Yu Qing, Zhang Yiwei, Liu Jiaxiang, Li Kaige, Liu Zijian, Cui Mengqing, Zhao Yongchao, Han Xin, Jin Rui, Tan Minjia, Chen Xiao-Hua, Zhao Yujun, Zheng Mingyue, Sun Yi, Zhou Lu, Lu Xiaojie
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.
Angew Chem Int Ed Engl. 2025 Apr 13:e202505581. doi: 10.1002/anie.202505581.
Broadening the application of covalent inhibitors requires the exploration of nucleophilic residues beyond cysteine. The covalent DNA-encoded chemical library (CoDEL) represents an advanced technology for covalent drug discovery. However, its application in lysine-targeting inhibitors remains uncharted territory. Here, we report the utilization of CoDEL selection guided by proteome-wide data to identify lysine-targeting covalent inhibitors. A comprehensive assessment of activity-based protein profiling (ABPP) data on lysine distribution and ligandability reveals potential targets for selective covalent inhibition, including phosphoglycerate mutase 1 (PGAM1), bromodomain (BRD) family proteins, and ubiquitin-conjugating enzyme E2 N (UBE2N). The 10.7-million-member CoDELs, featuring diverse lysine-reactive warheads, enable the discovery of a series of covalent inhibitors, covering photo-covalent, reversible covalent, and irreversible covalent reaction mechanisms. In-depth characterization of binding sites and modes of action provides structural and functional insights. Notably, irreversible covalent inhibitors unveil a novel mechanism for regulating UBE2N-mediated ubiquitination by modulating the conformation of the protein complex. Our work adopts the ABPP-CoDEL strategy, offering an efficient and versatile selection method for the development of covalent inhibitors targeting functional lysines.
拓宽共价抑制剂的应用需要探索除半胱氨酸之外的亲核残基。共价DNA编码化学文库（CoDEL）是共价药物发现的一项先进技术。然而，其在靶向赖氨酸抑制剂方面的应用仍是未知领域。在此，我们报告利用蛋白质组范围数据指导的CoDEL筛选来鉴定靶向赖氨酸的共价抑制剂。基于活性的蛋白质谱分析（ABPP）数据对赖氨酸分布和配体结合能力的全面评估揭示了选择性共价抑制的潜在靶点，包括磷酸甘油酸变位酶1（PGAM1）、溴结构域（BRD）家族蛋白和泛素结合酶E2 N（UBE2N）。拥有多种赖氨酸反应弹头的1070万个成员的CoDEL能够发现一系列共价抑制剂，涵盖光共价、可逆共价和不可逆共价反应机制。对结合位点和作用模式的深入表征提供了结构和功能方面的见解。值得注意的是，不可逆共价抑制剂揭示了一种通过调节蛋白质复合物构象来调控UBE2N介导的泛素化的新机制。我们的工作采用了ABPP-CoDEL策略，为开发靶向功能性赖氨酸的共价抑制剂提供了一种高效且通用的筛选方法。
