Targeted protein degradation via “hijacking” of the ubiquitin-proteasome system using proteolysis targeting chimeras (PROTACs) has evolved into a novel therapeutic modality. The design of PROTACs is challenging; multiple steps involved in PROTAC-induced degradation make it difficult to establish coherent structure-activity relationships. Herein, we characterize PROTAC-mediated ternary complex formation and degradation by employing von Hippel–Lindau protein (VHL) recruiting PROTACs for two different target proteins, SMARCA2 and BRD4. Ternary-complex attributes and degradation activity parameters are evaluated by varying components of the PROTAC’s architecture. Ternary complex binding affinity and cooperativity correlates well with degradation potency and initial rates of degradation. Additionally, we develop a ternary-complex structure modeling workflow to calculate the total buried surface area at the interface, which is in agreement with the measured ternary complex binding affinity. Our findings establish a predictive framework to guide the design of potent degraders.

使用蛋白水解靶向嵌合体（PROTAC）“劫持”泛素蛋白酶体系统来进行靶向蛋白质降解已发展成为一种新型治疗方式。PROTAC 的设计具有挑战性；PROTAC 诱导的降解涉及多个步骤，因此很难建立连贯的结构-活性关系。在此，我们通过使用 von Hippel-Lindau 蛋白 (VHL) 为两种不同的靶蛋白 SMARCA2 和 BRD4 招募 PROTAC 来表征 PROTAC 介导的三元复合物形成和降解。三元复合体属性和降解活动参数通过 PROTAC 架构的不同组件进行评估。三元复合物结合亲和力和协同性与降解效力和初始降解速率密切相关。此外，我们开发了三元复合物结构建模工作流程来计算界面处的总埋藏表面积，这与测量的三元复合物结合亲和力一致。我们的研究结果建立了一个预测框架来指导有效降解剂的设计。