UbiQ is proud to have been part of a major collaboration reported recently by Rut et al. in Science Advances (2020, 6, eabd4596) describing the activity profiling and crystal structures of inhibitor bound SARS-CoV-2 PLpro. 

The viral papain-like cysteine protease (PLpro, NSP3) is essential for SARS-CoV-2 replication and represents a promising target for the development of antiviral drugs. Here, we used a combinatorial substrate library and performed comprehensive activity profiling of SARS-CoV-2 PLpro. On the scaffold of the best hits from positional scanning, fluorogenic substrates and irreversible inhibitors were designed with a high degree of selectivity for SARS PLpro. Crystal structures of two of these inhibitors in complex with SARS-CoV-2 PLpro revealed their inhibitory mechanisms, providing a molecular basis for the observed substrate specificity profiles. Last, we demonstrate that SARS-CoV-2 PLpro harbors deISGylating activity similar to SARSCoV-1 PLpro but its ability to hydrolyze K48-linked ubiquitin chains is diminished, which our sequence and structure analysis provides a basis for. Overall, our work reveals the molecular rules governing PLpro substrate specificity and provides a framework for development of inhibitors with potential therapeutic value or drug repurposing.

Figure 1. Nonnatural amino acid-containing inhibitors VIR250 and VIR251 and their crystal structures in complex with SARS-CoV-2 PLpro.

1. Wroclaw University of Science and Technology, Poland.
2. Medical University of South Carolina, Charleston, USA. 
3. University of Texas Health Science Center at San Antonio, San Antonio, USA.
4. New York University School of Medicine, New York, USA.
5. Sanford Burnham Prebys Medical Discovery Institute, La Jolla, USA.
6. UbiQ Bio B.V., Amsterdam, The Netherlands.
7. Independent Consultant.

(*) These authors contributed equally to this work. (†) Corresponding author. (‡) Present address: Arvinas Inc., New Haven, USA.