Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity
Authors and Affiliations
Authors and Affiliations
Donghyuk Shin1,2,3, Rukmini Mukherjee1,2, Diana Grewe2, Denisa Bojkova4, Kheewoong Baek5, Anshu Bhattacharya1,2, Laura Schulz6, Marek Widera4, Ahmad Reza Mehdipour6, Georg Tascher1, Paul P. Geurink7, Alexander Wilhelm4,11, Gerbrand J. van der Heden van Noort7, Huib Ovaa7,13, Stefan Müller1, Klaus-Peter Knobeloch8, Krishnaraj Rajalingam9, Brenda A. Schulman5, Jindrich Cinatl4, Gerhard Hummer6,10, Sandra Ciesek4,11,12 & Ivan Dikic1,2,3,12,*
1Institute of Biochemistry II, Faculty of Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany. 2Buchmann Institute for Molecular Life Sciences, Goethe University, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany. 3Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany. 4Institute of Medical Virology, University Hospital Frankfurt, Frankfurt am Main, Germany. 5Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany. 6Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany. 7Oncode Institute and Department of Chemical Immunology, Leiden University Medical Centre, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands. 8Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany. 9Cell Biology Unit, University Medical Center of the Johannes Gutenberg University Mainz, 55131, Mainz, Germany. 10Institute of Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany. 11Institute of Pharmaceutical Biology, Goethe-University, Frankfurt/Main, Germany. 12Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch Translational Medicine and Pharmacology, Frankfurt, Germany. 13Deceased.
The papain-like protease PLpro is an essential coronavirus enzyme required for processing viral polyproteins to generate a functional replicase complex and enable viral spread1,2. PLpro is also implicated in cleaving proteinaceous post-translational modifications on host proteins as an evasion mechanism against host anti-viral immune responses3–5. Here, we provide biochemical, structural and functional characterization of the SARS-CoV-2 PLpro (SCoV2-PLpro) and outline differences to SARS-CoV PLpro (SCoV-PLpro) in controlling host interferon (IFN) and NF-κB pathways. While SCoV2-PLpro and SCoV-PLpro share 83% sequence identity, they exhibit different host substrate preferences. In particular, SCoV2-PLpro preferentially cleaves the ubiquitin-like protein ISG15, whereas SCoV-PLpro predominantly targets ubiquitin chains. The crystal structure of SCoV2-PLpro in complex with ISG15 reveals distinctive interactions with the amino-terminal ubiquitin-like domain of ISG15, highlighting this high affinity and specificity. Furthermore, upon infection, SCoV2-PLpro contributes to the cleavage of ISG15 from interferon responsive factor 3 (IRF3) and attenuates type I interferon responses. Importantly, inhibition of SCoV2-PLpro with GRL-0617 impairs the virus-induced cytopathogenic effect, fosters the anti-viral interferon pathway and reduces viral replication in infected cells. These results highlight a dual therapeutic strategy in which targeting of SCoV2-PLpro can suppress SARS-CoV-2 infection and promote anti-viral immunity.