State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
Laboratory of Structural Biology and Drug Discovery, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
Nat Commun. 2021 Jan 20;12(1):488. doi: 10.1038/s41467-020-20718-8.
SARS-CoV-2 is the pathogen responsible for the COVID-19 pandemic. The SARS-CoV-2 papain-like cysteine protease (PLpro) has been implicated in playing important roles in virus maturation, dysregulation of host inflammation, and antiviral immune responses. The multiple functions of PLpro render it a promising drug target. Therefore, we screened a library of approved drugs and also examined available inhibitors against PLpro. Inhibitor GRL0617 showed a promising in vitro IC of 2.1 μM and an effective antiviral inhibition in cell-based assays. The co-crystal structure of SARS-CoV-2 PLpro in complex with GRL0617 indicates that GRL0617 is a non-covalent inhibitor and it resides in the ubiquitin-specific proteases (USP) domain of PLpro. NMR data indicate that GRL0617 blocks the binding of ISG15 C-terminus to PLpro. Using truncated ISG15 mutants, we show that the C-terminus of ISG15 plays a dominant role in binding PLpro. Structural analysis reveals that the ISG15 C-terminus binding pocket in PLpro contributes a disproportionately large portion of binding energy, thus this pocket is a hot spot for antiviral drug discovery targeting PLpro.
SARS-CoV-2 是导致 COVID-19 大流行的病原体。SARS-CoV-2 的木瓜样半胱氨酸蛋白酶（PLpro）被认为在病毒成熟、宿主炎症失调和抗病毒免疫反应中发挥重要作用。PLpro 的多种功能使其成为有前途的药物靶点。因此，我们筛选了一个已批准药物库，并检查了针对 PLpro 的现有抑制剂。抑制剂 GRL0617 在体外显示出有希望的 IC50 为 2.1 μM，并且在细胞测定中具有有效的抗病毒抑制作用。SARS-CoV-2 PLpro 与 GRL0617 的共晶结构表明，GRL0617 是一种非共价抑制剂，它位于 PLpro 的泛素特异性蛋白酶（USP）结构域中。NMR 数据表明，GRL0617 阻止 ISG15 C 末端与 PLpro 的结合。使用截断的 ISG15 突变体，我们表明 ISG15 的 C 末端在与 PLpro 结合中起主导作用。结构分析表明，PLpro 中的 ISG15 C 末端结合口袋贡献了不成比例大的结合能，因此该口袋是针对 PLpro 的抗病毒药物发现的热点。
