美国麻省理工学院和哈佛大学的布罗德研究所Choudhary, Amit团队报道了减少脱靶的蛋白水解靶向嵌合体。相关研究成果于2023年12月18日发表在国际知名学术期刊《自然—化学》。

蛋白质水解靶向嵌合体（PROTACs）是诱导靶蛋白和E3连接酶接近从而触发靶蛋白降解的分子。泊马度胺是PROTACs中广泛使用的E3连接酶招募剂，可以独立降解其他蛋白质，包括锌指（ZF）蛋白，在健康和疾病中发挥重要作用。这种脱靶降解阻碍了基于泊马度胺的PROTACs的治疗适用性，需要制定PROTACs设计规则，最大限度地减少脱靶降解。

该文中，研究人员开发了一个高通量平台，用于解释脱靶降解，并发现已报道的基于泊马度胺的PROTACs诱导了几种ZF蛋白的降解。研究人员制备了一个泊马度胺类似物库，以了解功能化邻苯二甲酰亚胺环的不同位置、氢键以及空间和疏水效应如何影响ZF蛋白降解。在C5位置上适当大小的修饰减少了ZF的脱靶降解，通过靶标参与和蛋白质组学研究验证了这一点。通过应用这些设计原则，研究人员开发了靶向PROTACs的间变性淋巴瘤激酶癌蛋白，具有增强的效力和最小的脱靶降解。

目前的蛋白水解靶向嵌合体可以通过诱导靶蛋白和脱靶蛋白，分别与蜡样蛋白泛素连接酶接近来促进其泛素化和随后的降解。现在，通过开发和部署脱靶分析平台，“撞击蛋白水解靶向嵌合体”可以在降低脱靶的情况下保持脱靶降解功效。

附：英文原文

Title: Proteolysis-targeting chimeras with reduced off-targets

Author: Nguyen, Tuan M., Sreekanth, Vedagopuram, Deb, Arghya, Kokkonda, Praveen, Tiwari, Praveen K., Donovan, Katherine A., Shoba, Veronika, Chaudhary, Santosh K., Mercer, Jaron A. M., Lai, Sophia, Sadagopan, Ananthan, Jan, Max, Fischer, Eric S., Liu, David R., Ebert, Benjamin L., Choudhary, Amit

Issue&Volume: 2023-12-18

Abstract: Proteolysis-targeting chimeras (PROTACs) are molecules that induce proximity between target proteins and E3 ligases triggering target protein degradation. Pomalidomide, a widely used E3 ligase recruiter in PROTACs, can independently degrade other proteins, including zinc-finger (ZF) proteins, with vital roles in health and disease. This off-target degradation hampers the therapeutic applicability of pomalidomide-based PROTACs, requiring development of PROTAC design rules that minimize off-target degradation. Here we developed a high-throughput platform that interrogates off-target degradation and found that reported pomalidomide-based PROTACs induce degradation of several ZF proteins. We generated a library of pomalidomide analogues to understand how functionalizing different positions of the phthalimide ring, hydrogen bonding, and steric and hydrophobic effects impact ZF protein degradation. Modifications of appropriate size on the C5 position reduced off-target ZF degradation, which we validated through target engagement and proteomics studies. By applying these design principles, we developed anaplastic lymphoma kinase oncoprotein-targeting PROTACs with enhanced potency and minimal off-target degradation. Current proteolysis-targeting chimeras can promote the ubiquitination and subsequent degradation of both target and off-target proteins by inducing their respective proximity with the cereblon ubiquitin ligase. Now, by developing and deploying an off-target profiling platform, ‘bumped proteolysis-targeting chimeras’ can maintain on-target degradation efficacy with reduced off-targets.

DOI: 10.1038/s41557-023-01379-8

Source: https://www.nature.com/articles/s41557-023-01379-8