Institute for Pharmaceutical Chemistry, Department of Biochemistry, Chemistry and Pharmacy, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt, Germany.
Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Straße 15, 60438, Frankfurt, Germany.
Nat Commun. 2024 Nov 25;15(1):10204. doi: 10.1038/s41467-024-54409-5.
Recent successes in developing small molecule degraders that act through the ubiquitin system have spurred efforts to extend this technology to other mechanisms, including the autophagosomal-lysosomal pathway. Therefore, reports of autophagosome tethering compounds (ATTECs) have received considerable attention from the drug development community. ATTECs are based on the recruitment of targets to LC3/GABARAP, a family of ubiquitin-like proteins that presumably bind to the autophagosome membrane and tether cargo-loaded autophagy receptors into the autophagosome. In this work, we rigorously tested the target engagement of the reported ATTECs to validate the existing LC3/GABARAP ligands. Surprisingly, we were unable to detect interaction with their designated target LC3 using a diversity of biophysical methods. Intrigued by the idea of developing ATTECs, we evaluated the ligandability of LC3/GABARAP by in silico docking and large-scale crystallographic fragment screening. Data based on approximately 1000 crystal structures revealed that most fragments bound to the HP2 but not to the HP1 pocket within the LIR docking site, suggesting a favorable ligandability of HP2. Through this study, we identified diverse validated LC3/GABARAP ligands and fragments as starting points for chemical probe and ATTEC development.
近年来，小分子降解剂通过泛素系统作用的开发取得了一些成功，这促使人们努力将该技术扩展到其他机制，包括自噬体-溶酶体途径。因此，自噬体连接化合物（ATTEC）的报道引起了药物开发界的广泛关注。ATTEC 基于将靶标募集到 LC3/GABARAP，LC3/GABARAP 是一类假定与自噬体膜结合并将货物装载的自噬体受体连接到自噬体的泛素样蛋白家族。在这项工作中，我们严格测试了报道的 ATTEC 的靶标结合，以验证现有的 LC3/GABARAP 配体。令人惊讶的是，我们无法使用多种生物物理方法检测到与它们指定的靶标 LC3 的相互作用。受开发 ATTEC 想法的启发，我们通过计算机对接和大规模晶体筛选片段评估了 LC3/GABARAP 的配体能力。基于大约 1000 个晶体结构的数据表明，大多数片段结合到 HP2 而不是 LIR 对接位点的 HP1 口袋，这表明 HP2 的配体能力良好。通过这项研究，我们确定了多种经验证的 LC3/GABARAP 配体和片段作为化学探针和 ATTEC 开发的起点。
