Proteolysis Targeting Chimeras (PROTACs) are an emerging therapeutic modality and chemical biology tools for Targeted Protein Degradation (TPD). PROTACs contain a ligand targeting the protein of interest, a ligand recruiting an E3 ligase and a linker connecting these two ligands. There are over 600 E3 ligases known so far, but only a handful have been exploited for TPD applications. A key reason for this is the scarcity of ligands binding various E3 ligases and the paucity of structural data available, which complicates ligand design across the family. In this study, we aim to progress PROTAC discovery by proposing a shortlist of E3 ligases that can be prioritized for covalent targeting by performing systematic structural ligandability analysis on a chemoproteomic dataset of potentially reactive cysteines across hundreds of E3 ligases. One of the goals of this study is to apply AlphaFold (AF) models for ligandability evaluations, as for a vast majority of these ligases an experimental structure is not available in the protein data bank (PDB). Using a combination of pocket features, AF model quality and additional aspects, we propose a shortlist of E3 ligases and corresponding cysteines that can be prioritized to potentially discover covalent ligands and expand the PROTAC toolbox.

中文翻译：

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AlphaFold 模型在评估 E3 连接酶中可配体半胱氨酸中的应用

蛋白水解靶向嵌合体 (PROTAC) 是一种新兴的靶向蛋白质降解 (TPD) 治疗方式和化学生物学工具。 PROTAC 包含一个靶向目标蛋白的配体、一个招募 E3 连接酶的配体以及一个连接这两个配体的接头。迄今为止，已知有超过 600 种 E3 连接酶，但只有少数被用于 TPD 应用。造成这种情况的一个关键原因是缺乏结合各种 E3 连接酶的配体以及缺乏可用的结构数据，这使得整个家族的配体设计变得复杂。在这项研究中，我们的目标是通过对数百种 E3 连接酶的潜在反应性半胱氨酸的化学蛋白质组数据集进行系统的结构配体性分析，提出一份可优先用于共价靶向的 E3 连接酶候选清单，从而推进 PROTAC 的发现。本研究的目标之一是应用 AlphaFold (AF) 模型进行配体性评估，因为对于绝大多数这些连接酶，蛋白质数据库 (PDB) 中没有提供实验结构。结合口袋特征、AF 模型质量和其他方面，我们提出了 E3 连接酶和相应半胱氨酸的候选清单，可以优先考虑潜在地发现共价配体并扩展 PROTAC 工具箱。