A broad-spectrum macrocyclic peptide inhibitor of the SARS-CoV-2 spike protein
Edited by Brian K. Shoichet, University of California San Francisco, San Francisco, CA; received February 27, 2023; accepted May 16, 2023 by Editorial Board Member Adolfo Garcia-Sastre
Significance
This study reports on the discovery of a macrocyclic peptide that is able to inhibit SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) infection by exploiting a new vulnerable site in the spike glycoprotein. This region is highly conserved across SARS-CoV-2 variants and the subgenus sarbecovirus. Due to the inaccessibility and mutational constraint of this site, it is anticipated to not be susceptible to the development of resistance through antibody selective pressure. In addition to the discovery of a new molecule for the development of potential new peptide or biomolecule therapeutics, the identification of this broadly active conserved site can also stimulate a new direction of drug development, which together may prevent future outbreaks of related viruses.
Abstract
The ongoing COVID-19 pandemic has had great societal and health consequences. Despite the availability of vaccines, infection rates remain high due to immune evasive Omicron sublineages. Broad-spectrum antivirals are needed to safeguard against emerging variants and future pandemics. We used messenger RNA (mRNA) display under a reprogrammed genetic code to find a spike-targeting macrocyclic peptide that inhibits SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) Wuhan strain infection and pseudoviruses containing spike proteins of SARS-CoV-2 variants or related sarbecoviruses. Structural and bioinformatic analyses reveal a conserved binding pocket between the receptor-binding domain, N-terminal domain, and S2 region, distal to the angiotensin-converting enzyme 2 receptor–interaction site. Our data reveal a hitherto unexplored site of vulnerability in sarbecoviruses that peptides and potentially other drug-like molecules can target.
Data, Materials, and Software Availability
High throughput sequencing data for the selections have been deposited in the DataverseNL repository at DOI: https://doi.org/10.34894/WJRHLK (42). The cryo-EM map of the SARS-CoV-2 spike ectodomain in complex with S1B3inL1 has been deposited to the Electron Microscopy Data Bank under the accession code EMD-16144 (43). The corresponding atomic model has been deposited to the Protein Data Bank under the accession code 8BON (44). Compounds generated in this study are available on reasonable request.
Acknowledgments
We thank J. A. W. Kruijtzer for assistance with peptide synthesis, and the Utrecht Sequencing Facility for providing sequencing service and data. We thank C. A. M. de Haan and Y. Lang for advice and technical assistance. This work was partially funded by the Corona Accelerated R&D in Europe (CARE) project. The CARE project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking (JU) under grant agreement No 101005077. The JU receives support from the European Union’s Horizon 2020 Research and Innovation Programme, the European Federation of Pharmaceutical Industries and Associations, the Bill & Melinda Gates Foundation, the Global Health Drug Discovery Institute and the University of Dundee. The content of this publication only reflects the author’s views, and the JU is not responsible for any use that may be made of the information it contains. R.J.P. and C.J.J. received support from Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science. This work made use of the Dutch national e-infrastructure with the support of the SURF Cooperative using grant no. EINF-2453, awarded to D.L.H. V.T. and S.A.K.J. acknowledge general financial support from the department of Chemical Biology and Drug Discovery at Utrecht University. Utrecht Sequencing Facility is subsidized by the University Medical Center Utrecht, Hubrecht Institute, Utrecht University and The Netherlands X-omics Initiative (NWO project 184.034.019). J.S. is funded by the Dutch Research Council NWO Gravitation 2013 BOO, Institute for Chemical Immunology (ICI; 024.002.009).
Author contributions
V.T., D.L.H., F.J.M.v.K., and S.A.K.J. designed research; V.T., D.L.H., O.J.D.-A., M.A.S., C.F., A.A., N.J.M., W.L., M.C., T.D., W.D., and I.D. performed research; V.T., A.N., D.A.A.v.D., S.W.V., M.L., W.D., I.D., B.-J.B., S.G.T., R.J.P., C.J.J., and S.A.K.J. contributed new reagents/analytic tools; V.T., D.L.H., O.J.D.-A., and S.A.K.J. analyzed data; V.T. and M.A.S. visualisation; B.-J.B., J.S., and S.G.T. supervision; R.J.P. and C.J.J. supervision, funding acquisition; F.J.M.v.K. funding acquisition, project administration, supervision; S.A.K.J. visualisation, project administration, supervision; and V.T., D.L.H., O.J.D.-A., M.A.S., C.F., A.N., A.A., N.J.M., I.D., J.S., R.J.P., C.J.J., F.J.M.v.K., and S.A.K.J. wrote the paper.
Competing interests
I.D. is an employee of Thermo Fisher Scientific. V.T., D.L.H., F.J.M.v.K., and S.A.K.J. are named inventors on a patent application that has been filed on 15 July 2022 entitled: Antiviral cyclic compounds (EP22185235; patent applicants: Universiteit Utrecht Holdings B.V. on behalf of Utrecht University). The other authors declare no competing interests.
Supporting Information
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Information & Authors
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Published in
Cover image: Pictured is an eastern honeybee (Apis cerana). Nonno Hasegawa et al. traced the geographic spread of deformed wing virus (DWV) strains A and B in western honeybees (Apis mellifera). DWV-A likely originated in East Asia and expanded globally after varroa mites, which transmit the virus, switched from parasitizing eastern honeybees to western honeybees in the mid-20th century. DWV-B was acquired by western honeybees more recently, likely outside Asia. The results reveal how globalization facilitates the spillover of viruses from one species to another. See the article by Hasegawa et al., e2301258120. Image credit: Tetsuya Shimizu (photographer).
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Copyright
Copyright © 2023 the Author(s). Published by PNAS. This article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).
Data, Materials, and Software Availability
High throughput sequencing data for the selections have been deposited in the DataverseNL repository at DOI: https://doi.org/10.34894/WJRHLK (42). The cryo-EM map of the SARS-CoV-2 spike ectodomain in complex with S1B3inL1 has been deposited to the Electron Microscopy Data Bank under the accession code EMD-16144 (43). The corresponding atomic model has been deposited to the Protein Data Bank under the accession code 8BON (44). Compounds generated in this study are available on reasonable request.
Submission history
Received: February 27, 2023
Accepted: May 16, 2023
Published online: June 20, 2023
Published in issue: June 27, 2023
Keywords
Acknowledgments
We thank J. A. W. Kruijtzer for assistance with peptide synthesis, and the Utrecht Sequencing Facility for providing sequencing service and data. We thank C. A. M. de Haan and Y. Lang for advice and technical assistance. This work was partially funded by the Corona Accelerated R&D in Europe (CARE) project. The CARE project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking (JU) under grant agreement No 101005077. The JU receives support from the European Union’s Horizon 2020 Research and Innovation Programme, the European Federation of Pharmaceutical Industries and Associations, the Bill & Melinda Gates Foundation, the Global Health Drug Discovery Institute and the University of Dundee. The content of this publication only reflects the author’s views, and the JU is not responsible for any use that may be made of the information it contains. R.J.P. and C.J.J. received support from Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science. This work made use of the Dutch national e-infrastructure with the support of the SURF Cooperative using grant no. EINF-2453, awarded to D.L.H. V.T. and S.A.K.J. acknowledge general financial support from the department of Chemical Biology and Drug Discovery at Utrecht University. Utrecht Sequencing Facility is subsidized by the University Medical Center Utrecht, Hubrecht Institute, Utrecht University and The Netherlands X-omics Initiative (NWO project 184.034.019). J.S. is funded by the Dutch Research Council NWO Gravitation 2013 BOO, Institute for Chemical Immunology (ICI; 024.002.009).
Author Contributions
V.T., D.L.H., F.J.M.v.K., and S.A.K.J. designed research; V.T., D.L.H., O.J.D.-A., M.A.S., C.F., A.A., N.J.M., W.L., M.C., T.D., W.D., and I.D. performed research; V.T., A.N., D.A.A.v.D., S.W.V., M.L., W.D., I.D., B.-J.B., S.G.T., R.J.P., C.J.J., and S.A.K.J. contributed new reagents/analytic tools; V.T., D.L.H., O.J.D.-A., and S.A.K.J. analyzed data; V.T. and M.A.S. visualisation; B.-J.B., J.S., and S.G.T. supervision; R.J.P. and C.J.J. supervision, funding acquisition; F.J.M.v.K. funding acquisition, project administration, supervision; S.A.K.J. visualisation, project administration, supervision; and V.T., D.L.H., O.J.D.-A., M.A.S., C.F., A.N., A.A., N.J.M., I.D., J.S., R.J.P., C.J.J., F.J.M.v.K., and S.A.K.J. wrote the paper.
Competing Interests
I.D. is an employee of Thermo Fisher Scientific. V.T., D.L.H., F.J.M.v.K., and S.A.K.J. are named inventors on a patent application that has been filed on 15 July 2022 entitled: Antiviral cyclic compounds (EP22185235; patent applicants: Universiteit Utrecht Holdings B.V. on behalf of Utrecht University). The other authors declare no competing interests.
Notes
This article is a PNAS Direct Submission. B.K.S. is a guest editor invited by the Editorial Board.
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