Antiviral cyclic peptides targeting the main protease of SARS-CoV-2

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

doi:10.1039/d1sc06750h

Antiviral cyclic peptides targeting the main protease of SARS-CoV-2

Chem Sci. 2022 Feb 28;13(13):3826-3836. doi: 10.1039/d1sc06750h. eCollection 2022 Mar 30.

Authors

Jason Johansen-Leete^{1

2}, Sven Ullrich³, Sarah E Fry^{1

2}, Rebecca Frkic^{3

4}, Max J Bedding^{1

2}, Anupriya Aggarwal⁵, Anneliese S Ashhurst^{1

2

6}, Kasuni B Ekanayake^{3

4}, Mithun C Mahawaththa^{3

4}, Vishnu M Sasi^{3

4}, Stephanie Luedtke⁷, Daniel J Ford^{1

2}, Anthony J O'Donoghue⁷, Toby Passioura^{1

2

8

9}, Mark Larance^{9

10}, Gottfried Otting^{3

4}, Stuart Turville⁵, Colin J Jackson^{3

4}, Christoph Nitsche³, Richard J Payne^{1

2}

Affiliations

¹ School of Chemistry, The University of Sydney Sydney NSW 2006 Australia richard.payne@sydney.edu.au.
² Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney Sydney NSW 2006 Australia.
³ Research School of Chemistry, Australian National University Canberra ACT 2601 Australia christoph.nitsche@anu.edu.au.
⁴ Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University Canberra ACT 2601 Australia.
⁵ Kirby Institute Sydney NSW 2052 Australia.
⁶ School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia.
⁷ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr. La Jolla CA 92093 USA.
⁸ School of Life and Environmental Sciences, The University of Sydney Sydney NSW 2006 Australia.
⁹ Sydney Analytical, The University of Sydney Sydney NSW 2006 Australia.
¹⁰ Charles Perkins Centre, The University of Sydney Sydney NSW 2006 Australia.

Abstract

Antivirals that specifically target SARS-CoV-2 are needed to control the COVID-19 pandemic. The main protease (M^pro) is essential for SARS-CoV-2 replication and is an attractive target for antiviral development. Here we report the use of the Random nonstandard Peptide Integrated Discovery (RaPID) mRNA display on a chemically cross-linked SARS-CoV-2 M^pro dimer, which yielded several high-affinity thioether-linked cyclic peptide inhibitors of the protease. Structural analysis of M^pro complexed with a selenoether analogue of the highest-affinity peptide revealed key binding interactions, including glutamine and leucine residues in sites S1 and S2, respectively, and a binding epitope straddling both protein chains in the physiological dimer. Several of these M^pro peptide inhibitors possessed antiviral activity against SARS-CoV-2 in vitro with EC₅₀ values in the low micromolar range. These cyclic peptides serve as a foundation for the development of much needed antivirals that specifically target SARS-CoV-2.