Qiu Yunrui, Wiewiora Rafal P, Izaguirre Jesus A, Xu Huafeng, Sherman Woody, Tang Weiping, Huang Xuhui
Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.
Data Science Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.
JACS Au. 2024 Sep 24;4(10):3857-3868. doi: 10.1021/jacsau.4c00503. eCollection 2024 Oct 28.
Targeted protein degradation (TPD) is emerging as a promising therapeutic approach for cancer and other diseases, with an increasing number of programs demonstrating its efficacy in human clinical trials. One notable method for TPD is Proteolysis Targeting Chimeras (PROTACs) that selectively degrade a protein of interest (POI) through E3-ligase induced ubiquitination followed by proteasomal degradation. PROTACs utilize a warhead-linker-ligand architecture to bring the POI (bound to the warhead) and the E3 ligase (bound to the ligand) into proximity. The resulting non-native protein-protein interactions (PPIs) formed between the POI and E3 ligase lead to the formation of a stable ternary complex, enhancing cooperativity for TPD. A significant challenge in PROTAC design is the screening of the linkers to induce favorable non-native PPIs between POI and E3 ligase. Here, we present a physics-based computational protocol to predict noncanonical and metastable PPI interfaces between an E3 ligase and a given POI, aiding in the design of linkers to stabilize the ternary complex and enhance degradation. Specifically, we build the non-Markovian dynamic model using the Integrative Generalized Master equation (IGME) method from ∼1.5 ms all-atom molecular dynamics simulations of linker-less encounter complex, to systematically explore the inherent PPIs between the oncogene homologue protein and the von Hippel-Lindau E3 ligase. Our protocol revealed six metastable states each containing a different PPI interface. We selected three of these metastable states containing promising PPIs for linker design. Our selection criterion included thermodynamic and kinetic stabilities of PPIs and the accessibility between the solvent-exposed sites on the warheads and E3 ligand. One selected PPIs closely matches a recent cocrystal PPI interface structure induced by an experimentally designed PROTAC with potent degradation efficacy. We anticipate that our protocol has significant potential for widespread application in predicting metastable POI-ligase interfaces that can enable rational design of PROTACs.
靶向蛋白质降解（TPD）正在成为一种针对癌症和其他疾病的有前景的治疗方法，越来越多的项目在人体临床试验中证明了其有效性。TPD的一种显著方法是蛋白酶靶向嵌合体（PROTACs），它通过E3连接酶诱导的泛素化作用，随后进行蛋白酶体降解，从而选择性地降解目标蛋白（POI）。PROTACs利用弹头-连接子-配体结构，使POI（与弹头结合）和E3连接酶（与配体结合）靠近。POI和E3连接酶之间形成的非天然蛋白质-蛋白质相互作用（PPI）导致形成稳定的三元复合物，增强了TPD的协同性。PROTAC设计中的一个重大挑战是筛选连接子，以诱导POI和E3连接酶之间形成有利的非天然PPI。在此，我们提出一种基于物理的计算方案，以预测E3连接酶和给定POI之间的非经典和亚稳PPI界面，有助于设计连接子来稳定三元复合物并增强降解。具体而言，我们使用整合广义主方程（IGME）方法，从无连接子相遇复合物的约1.5毫秒全原子分子动力学模拟构建非马尔可夫动力学模型，以系统地探索癌基因同源蛋白和冯·希佩尔-林道E3连接酶之间固有的PPI。我们的方案揭示了六个亚稳态，每个亚稳态都包含不同的PPI界面。我们选择了其中三个包含有前景的PPI的亚稳态用于连接子设计。我们的选择标准包括PPI的热力学和动力学稳定性以及弹头和E3配体上溶剂暴露位点之间的可及性。一个选定的PPI与最近由具有强效降解功效的实验设计PROTAC诱导的共晶体PPI界面结构紧密匹配。我们预计我们的方案在预测亚稳POI-连接酶界面方面具有广泛应用的巨大潜力，这可以实现PROTAC的合理设计。
