Kazi Nafizul Haque, Klink Nikolas, Gallant Kai, Kipka Gian-Marvin, Gersch Malte
Chemical Genomics Center, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany.
Nat Struct Mol Biol. 2025 May 5. doi: 10.1038/s41594-025-01534-4.
The mitochondrial deubiquitinase ubiquitin-specific protease (USP) 30 negatively regulates PINK1-parkin-driven mitophagy. Whether enhanced mitochondrial quality control through inhibition of USP30 can protect dopaminergic neurons is currently being explored in a clinical trial for Parkinson's disease. However, the molecular basis for specific inhibition of USP30 by small molecules has remained elusive. Here we report the crystal structure of human USP30 in complex with a specific inhibitor, enabled by chimeric protein engineering. Our study uncovers how the inhibitor extends into a cryptic pocket facilitated by a compound-induced conformation of the USP30 switching loop. Our work underscores the potential of exploring induced pockets and conformational dynamics to obtain deubiquitinase inhibitors and identifies residues facilitating specific inhibition of USP30. More broadly, we delineate a conceptual framework for specific USP deubiquitinase inhibition based on a common ligandability hotspot in the Leu73 ubiquitin binding site and on diverse compound extensions. Collectively, our work establishes a generalizable chimeric protein-engineering strategy to aid deubiquitinase crystallization and enables structure-based drug design with relevance to neurodegeneration.
线粒体去泛素酶泛素特异性蛋白酶（USP）30对由PINK1-帕金驱动的线粒体自噬起负调控作用。目前，一项针对帕金森病的临床试验正在探索通过抑制USP30来增强线粒体质量控制是否能够保护多巴胺能神经元。然而，小分子特异性抑制USP30的分子基础仍不清楚。在此，我们报告了通过嵌合蛋白工程获得的与一种特异性抑制剂结合的人USP30的晶体结构。我们的研究揭示了抑制剂是如何通过USP30开关环的化合物诱导构象延伸到一个隐蔽口袋中的。我们的工作强调了探索诱导口袋和构象动力学以获得去泛素酶抑制剂的潜力，并确定了促进对USP30特异性抑制的残基。更广泛地说，我们基于亮氨酸73泛素结合位点的一个共同可配体热点和不同的化合物延伸，描绘了一个特异性USP去泛素酶抑制的概念框架。总体而言，我们的工作建立了一种可推广的嵌合蛋白工程策略来辅助去泛素酶结晶，并实现了与神经退行性疾病相关的基于结构的药物设计。
