A novel class of broad-spectrum active-site-directed 3C-like protease inhibitors with nanomolar antiviral activity against highly immune-evasive SARS-CoV-2 Omicron subvariants

  • Emerg Microbes Infect. 2023 Dec;12(2):2246594. doi: 10.1080/22221751.2023.2246594.
Jimena Pérez-Vargas  1 ,  Liam J Worrall  2 ,  Andrea D Olmstead  1 ,  Anh-Tien Ton  3 ,  Jaeyong Lee  2  4 ,  Ivan Villanueva  1 ,  Connor A H Thompson  1 ,  Svenja Dudek  1 ,  Siobhan Ennis  5 ,  Jason R Smith  3  6 ,  Tirosh Shapira  1 ,  Joshua De Guzman  1 ,  Shutong Gang  1 ,  Fuqiang Ban  3 ,  Marija Vuckovic  2 ,  Michael Bielecki  6 ,  Suzana Kovacic  6 ,  Calem Kenward  2 ,  Christopher Yee Hong  1 ,  Danielle G Gordon  1 ,  Paul N Levett  7  8 ,  Mel Krajden  7  8 ,  Richard Leduc  9 ,  Pierre-Luc Boudreault  9 ,  Masahiro Niikura  5 ,  Mark Paetzel  4 ,  Robert N Young  6 ,  Artem Cherkasov  3 ,  Natalie C J Strynadka  2 ,  François Jean  1
Affiliations
  • 1. Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, Canada.
  • 2. Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, Canada.
  • 3. Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada.
  • 4. Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada.
  • 5. Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada.
  • 6. Department of Chemistry, Simon Fraser University, Burnaby, Canada.
  • 7. British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada.
  • 8. Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.
  • 9. Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Canada.
PMID: 37555275 DOI: 10.1080/22221751.2023.2246594
Abstract

Antivirals with broad coronavirus activity are important for treating high-risk individuals exposed to the constantly evolving SARS-CoV-2 variants of concern (VOCs) as well as emerging drug-resistant variants. We developed and characterized a novel class of active-site-directed 3-chymotrypsin-like protease (3CLpro) inhibitors (C2-C5a). Our lead direct-acting Antiviral (DAA), C5a, is a non-covalent, non-peptide with a dissociation constant of 170 nM against recombinant SARS-CoV-2 3CLpro. The compounds C2-C5a exhibit broad-spectrum activity against Omicron subvariants (BA.5, BQ.1.1, and XBB.1.5) and seasonal human coronavirus-229E Infection in human cells. Notably, C5a has median effective concentrations of 30-50 nM against BQ.1.1 and XBB.1.5 in two different human cell lines. X-ray crystallography has confirmed the unique binding modes of C2-C5a to the 3CLpro, which can limit virus cross-resistance to emerging Paxlovid-resistant variants. We tested the effect of C5a with two of our newly discovered host-directed antivirals (HDAs): N-0385, a TMPRSS2 inhibitor, and bafilomycin D (BafD), a human vacuolar H+-ATPase [V-ATPase] inhibitor. We demonstrated a synergistic action of C5a in combination with N-0385 and BafD against Omicron BA.5 Infection in human Calu-3 lung cells. Our findings underscore that a SARS-CoV-2 multi-targeted treatment for circulating Omicron subvariants based on DAAs (C5a) and HDAs (N-0385 or BafD) can lead to therapeutic benefits by enhancing treatment efficacy. Furthermore, the high-resolution structures of SARS-CoV-2 3CLpro in complex with C2-C5a will facilitate future rational optimization of our novel broad-spectrum active-site-directed 3C-like Protease Inhibitors.

Keywords
3CLpro inhibitor; SARS-CoV-2 3CLpro; SARS-CoV-2 Omicron subvariants; combination therapy; computer-aided drug design.
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