The complex structure of GRL0617 and SARS-CoV-2 PLpro reveals a hot spot for antiviral drug discovery

• Published in: Nature communications Vol. 12; no. 1; pp. 488 - 12
• Main Authors: Fu, Ziyang, Huang, Bin, Tang, Jinle, Liu, Shuyan, Liu, Ming, Ye, Yuxin, Liu, Zhihong, Xiong, Yuxian, Zhu, Wenning, Cao, Dan, Li, Jihui, Niu, Xiaogang, Zhou, Huan, Zhao, Yong Juan, Zhang, Guoliang, Huang, Hao
• Format: Journal Article
• Language: English
• Published: England Nature Publishing Group 20.01.2021; Nature Publishing Group UK; Nature Portfolio
• Subjects: Antiviral agents; Antiviral Agents - chemistry; Antiviral Agents - pharmacology; C-Terminus; Coronavirus 3C Proteases - chemistry; Coronavirus 3C Proteases - genetics; Coronavirus 3C Proteases - metabolism; COVID-19; COVID-19 - metabolism; COVID-19 - virology; COVID-19 Drug Treatment; Crystal structure; Cysteine proteinase; Cytokines - metabolism; Disease hot spots; Drug Discovery; Drug Interactions; HEK293 Cells; High-Throughput Screening Assays; Humans; Immune response; Immunosuppressive agents; Inflammation; Inhibitors; Inhibitory Concentration 50; Models, Molecular; NMR; Nuclear magnetic resonance; Pandemics; Papain; Protease; Protein Conformation; Proteins; SARS-CoV-2 - drug effects; SARS-CoV-2 - genetics; SARS-CoV-2 - metabolism; Severe acute respiratory syndrome; Severe acute respiratory syndrome coronavirus 2; Structural analysis; Target recognition; Therapeutic targets; Ubiquitin; Ubiquitins - metabolism; Viral diseases; Viruses
• ISSN: 2041-1723; 2041-1723
• 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.