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Phage capsid nanoparticles with defined ligand arrangement block influenza virus entry

Nature Nanotechnology volume 15, pages 373–379 (2020)Cite this article

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Abstract

Multivalent interactions at biological interfaces occur frequently in nature and mediate recognition and interactions in essential physiological processes such as cell-to-cell adhesion. Multivalency is also a key principle that allows tight binding between pathogens and host cells during the initial stages of infection. One promising approach to prevent infection is the design of synthetic or semisynthetic multivalent binders that interfere with pathogen adhesion1,2,3,4. Here, we present a multivalent binder that is based on a spatially defined arrangement of ligands for the viral spike protein haemagglutinin of the influenza A virus. Complementary experimental and theoretical approaches demonstrate that bacteriophage capsids, which carry host cell haemagglutinin ligands in an arrangement matching the geometry of binding sites of the spike protein, can bind to viruses in a defined multivalent mode. These capsids cover the entire virus envelope, thus preventing its binding to the host cell as visualized by cryo-electron tomography. As a consequence, virus infection can be inhibited in vitro, ex vivo and in vivo. Such highly functionalized capsids present an alternative to strategies that target virus entry by spike-inhibiting antibodies5 and peptides6 or that address late steps of the viral replication cycle7.

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Fig. 1: Functionalized Qβ phage capsids as high-affinity IAV binders.
Fig. 2: Cryo-TEM images of A/X31 incubated with diverse Qβ phage capsids.
Fig. 3: Modelling the interaction between Sia binding sites of HA and Sia residues of Qß capsid.
Fig. 4: Inhibitory potential of Qβ[Sia1] against various IAV strains.

Data availability

The data supporting the findings of this study are available within the paper and its Supplementary Information. All relevant data are available from the authors upon reasonable request. Model coordinates of the HA–Sia binding pockets and the Qβ capsid surface are taken from the Protein Data Bank under accession numbers 1HGG and 1QBE, respectively.

Code availability

Custom code is available from the corresponding author (S.L.).

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Acknowledgements

We thank Andrew K. Udit for providing the Qβ(K16M) plasmid and L. Artner for synthetic contributions. This work was supported by the German Research Foundation (DFG, SFB765, SPP1623 and SFB-TR84) and the Germany Ministry of Education and Research (BMBF, RAPID) as well as Charité 3R and the Einstein Foundation Berlin.

Author information

Author notes

  1. These authors contributed equally: Daniel Lauster, Simon Klenk.

Authors and Affiliations

  1. Institut für Chemie und Biochemie, Organische Chemie, Freie Universität Berlin, Berlin, Germany

    Daniel Lauster

  2. Institut für Biologie, Molekulare Biophysik, IRI Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany

    Daniel Lauster & Andreas Herrmann

  3. Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany

    Simon Klenk, Sandra Behren, Lutz Adam & Christian P. R. Hackenberger

  4. Institut für Chemie, Humboldt-Universität zu Berlin, Berlin, Germany

    Simon Klenk, Sandra Behren, Lutz Adam & Christian P. R. Hackenberger

  5. Forschungszentrum für Elektronenmikroskopie und Gerätezentrum BioSupraMol, Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany

    Kai Ludwig & Christoph Böttcher

  6. Institut für Chemie, Biokatalyse, Technische Universität Berlin, Berlin, Germany

    Saba Nojoumi & Nediljko Budisa

  7. Department of Chemistry, University of Manitoba, Winnipeg, Canada

    Saba Nojoumi & Nediljko Budisa

  8. Robert Koch Institut, FG 17 Influenzaviren und weitere Viren des Respirationstraktes, Berlin, Germany

    Marlena Stadtmüller, Sandra Saenger, Stephanie Zimmler & Thorsten Wolff

  9. Medizinische Klinik mit Schwerpunkt Infektiologie und Pneumologie, Charité, Universitätsmedizin Berlin, Partner von Freie Universität Berlin, Humboldt-Universität zu Berlin und Berlin Institute of Health, Berlin, Germany

    Katja Hönzke, Ling Yao, Martin Witzenrath, Leif E. Sander, Andreas C. Hocke & Stefan Hippenstiel

  10. Experimentelle Rheumatologie, Deutsches Rheuma-Forschungszentrum Berlin, ein Leibniz-Institut, Berlin, Germany

    Ute Hoffmann, Markus Bardua & Alf Hamann

  11. Thermo Fisher Scientific, Eindhoven, The Netherlands

    Sacha De Carlo

  12. Chirurgische Klinik, Campus Mitte/Campus Virchow Klinikum, Charité, Universitätsmedizin Berlin, Partner von Freie Universität Berlin, Humboldt-Universität zu Berlin, und Berlin Institute of Health, Berlin, Germany

    Jens Neudecker

  13. Institut für Virologie, Robert von Ostertag-Haus, Zentrum für Infektionsmedizin, Freie Universität Berlin, Berlin, Germany

    Klaus Osterrieder

  14. Fachbereich Physik, Theoretische Biophysik und Physik weicher Materie, Freie Universität Berlin, Berlin, Germany

    Roland R. Netz & Susanne Liese

  15. Department of Mathematics, University of Oslo (UiO), Oslo, Norway

    Susanne Liese

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Contributions

D.L., S.K., S.L., K.L., M.W., L.E.S., A. Hamann, N.B., R.R.N., K.O., A.C.H., S.H., T.W., A. Herrmann and C.P.R.H. designed the study. D.L., S.K, S.N., S.B., M.S., S.S., S.F., K.H., U.H., M.B., L.A. and L.Y. performed the experiments. S.N. performed the capsid expression. K.L., S.D.C. and C.B. performed the electron microscopy and image analyses. J.N. carried out surgical interventions and prepared lung excisions. S.L. performed modelling, simulations and calculations. D.L., S.K., S.L., A. Herrmann, T.W. and C.P.R.H. prepared the manuscript. All authors discussed the results and reviewed the manuscript.

Corresponding authors

Correspondence to Susanne Liese, Andreas Herrmann or Christian P. R. Hackenberger.

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The authors declare no competing interests.

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Peer review information Nature Nanotechnology thanks Andrew Ward and the other, anonymous, reviewers for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–4, experimental section, notes, analytical data and refs. 39–71.

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Supplementary Video 1

Cryo-electron tomography of Qβ[Sia1] bound to A/X31 virus

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Lauster, D., Klenk, S., Ludwig, K. et al. Phage capsid nanoparticles with defined ligand arrangement block influenza virus entry. Nat. Nanotechnol. 15, 373–379 (2020). https://doi.org/10.1038/s41565-020-0660-2

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