Oral Presentation 8th Modern Solid Phase Peptide Synthesis & Its Applications Symposium 2022

Antiviral cyclic peptides targeting the main protease of SARS-CoV-2 (#22)

Sarah E. Fry 1 2 , Jason Johansen-Leete 1 2 , Sven Ullrich 3 , Rebecca Frkic 3 4 , Max J. Bedding 1 2 , Anupriya Aggarwal 5 , Toby Passioura 1 2 6 7 , Mark Larance 7 8 , Stuart Turville 5 , Colin J. Jackson 3 4 , Christoph Nitsche 3 , Richard J. Payne 1 2
  1. School of Chemistry, The University of Sydney, Sydney, NSW, Australia
  2. Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Sydney, NSW, Australia
  3. Research School of Chemistry, Australian National University, Canberra, ACT, Australia
  4. Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Canberra, ACT, Australia
  5. Kirby Institute, Sydney, NSW, Australia
  6. School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
  7. Sydney Analytical, The University of Sydney, Sydney, NSW, Australia
  8. Charles Perkins Centre, The University of Sydney , Sydney , NSW, Australia

Antivirals are crucial for the continued control the COVID-19 pandemic and complement existing vaccine efforts. The SARS-CoV-2 main protease (Mpro) is a highly conserved functional protein that is essential for viral replication and proliferation in the host.1 With an indispensable role in the viral lifecycle and unique specificity, relative to host enzymes, Mpro is a very attractive target for the development of antiviral therapeutics to combat the COVID-19 pandemic.1-3  Indeed, Nirmatrelvir (Pfizer), the first antiviral approved for clinical use that was specifically designed for the SARS-CoV-2 virus, inhibits Mpro.

With a view to developing highly potent and selective antiviral targeting SARS-CoV-2 Mpro we performed Random nonstandard Peptide Integrated Discovery (RaPID) mRNA display against a chemically-cross linked SARS-CoV-2 Mpro dimer. This led to the discovery of several potent thioether-linked cyclic peptide inhibitors of the target in vitro.4-7 Structural analysis of the Mpro complexed with a selenoether analogue of the most potent inhibitor revealed fundamental binding interactions responsible for activity; a glutamine and leucine residue in the S1 and S2 sites respectively, in concert with a binding configuration that straddles both chains of the physiological dimer. The structure-activity relationships that characterise the lead Mpro inhibitor were probed with a series of alanine analogues that further complemented these findings. When assessed in vivo, several of the Mpro inhibitors exhibited antiviral activity against SARS-CoV-2 with EC50 values in the low micromolar range that could be enhanced further with the appendage of a cell-penetrating peptide. Collectively, these cyclic peptide Mpro inhibitors provide a promising foundation for the development of antiviral therapeutics specific to SARS-CoV-2.

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  7. Jason Johansen-Leete, Sven Ullrich, Sarah E. Fry, Rebecca Frkic, Max J. Bedding, Anupriya Aggarwal, Anneliese S. Ashhurst, Kasuni B. Ekanayake, Mithun C. Mahawaththa, Vishnu M. Sasi, Stephanie Luedtke, Daniel J. Ford, Anthony J. O’Donoghue, Toby Passioura, Mark Larance, Gottfried Otting, Stuart Turville, Colin J. Jackson, Christoph Nitsche, Richard J. Payne. Discovery of antiviral cyclic peptides targeting the main protease of SARS-CoV-2 via mRNA display. bioRxiv 2021.08.23.457419; doi: https://doi.org/10.1101/2021.08.23.457419