Biochemical characterization of protease activity of Nsp3 from SARS-CoV-2 and its inhibition by nanobodies

Lee A. Armstrong, Sven M. Lange, Virginia de Cesare, Stephen P. Matthews, Raja Sekar Nirujogi, Isobel Cole, Anthony Hope, Fraser Cunningham, Rachel Toth, Rukmini Mukherjee, Denisa Bojkova, Franz Gruber, David Gray, Paul G. Wyatt, Jindrich Cinatl, Ivan Dikic, Paul Davies, Yogesh Kulathu (Lead / Corresponding author)

Research output: Contribution to journalArticlepeer-review

58 Citations (Scopus)
149 Downloads (Pure)

Abstract

Of the 16 non-structural proteins (Nsps) encoded by SARS CoV-2, Nsp3 is the largest and plays important roles in the viral life cycle. Being a large, multidomain, transmembrane protein, Nsp3 has been the most challenging Nsp to characterize. Encoded within Nsp3 is the papain-like protease domain (PLpro) that cleaves not only the viral polypeptide but also K48-linked polyubiquitin and the ubiquitin-like modifier, ISG15, from host cell proteins. We here compare the interactors of PLpro and Nsp3 and find a largely overlapping interactome. Intriguingly, we find that near full length Nsp3 is a more active protease compared to the minimal catalytic domain of PLpro. Using a MALDI-TOF based assay, we screen 1971 approved clinical compounds and identify five compounds that inhibit PLpro with IC 50 s in the low micromolar range but showed cross reactivity with other human deubiquitinases and had no significant antiviral activity in cellular SARS-CoV-2 infection assays. We therefore looked for alternative methods to block PLpro activity and engineered competitive nanobodies that bind to PLpro at the substrate binding site with nanomolar affinity thus inhibiting the enzyme. Our work highlights the importance of studying Nsp3 and provides tools and valuable insights to investigate Nsp3 biology during the viral infection cycle.
Original languageEnglish
Article numbere0253364
Number of pages25
JournalPLoS ONE
Volume16
Issue number7
DOIs
Publication statusPublished - 16 Jul 2021

ASJC Scopus subject areas

  • General

Fingerprint

Dive into the research topics of 'Biochemical characterization of protease activity of Nsp3 from SARS-CoV-2 and its inhibition by nanobodies'. Together they form a unique fingerprint.

Cite this