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Broadly neutralizing antibody cocktails targeting Nipah virus and Hendra virus fusion glycoproteins

Nature Structural & Molecular Biology volume 28, pages 426–434 (2021)Cite this article

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Abstract

Hendra virus (HeV) and Nipah virus (NiV) are henipaviruses (HNVs) causing respiratory illness and severe encephalitis in humans, with fatality rates of 50–100%. There are no licensed therapeutics or vaccines to protect humans. HeV and NiV use a receptor-binding glycoprotein (G) and a fusion glycoprotein (F) to enter host cells. HNV F and G are the main targets of the humoral immune response, and the presence of neutralizing antibodies is a correlate of protection against NiV and HeV in experimentally infected animals. We describe here two cross-reactive F-specific antibodies, 1F5 and 12B2, that neutralize NiV and HeV through inhibition of membrane fusion. Cryo-electron microscopy structures reveal that 1F5 and 12B2 recognize distinct prefusion-specific, conserved quaternary epitopes and lock F in its prefusion conformation. We provide proof-of-concept for using antibody cocktails for neutralizing NiV and HeV and define a roadmap for developing effective countermeasures against these highly pathogenic viruses.

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Fig. 1: The 12B2 and 1F5 Abs cross-react with NiV F and HeV F and neutralize authentic NiV and HeV by preventing membrane fusion.
Fig. 2: The 12B2 Ab recognizes a conserved quaternary epitope on the NiV F glycoprotein.
Fig. 3: The 1F5 Ab recognizes a conserved quaternary epitope on the HeV glycoprotein.
Fig. 4: Formulation of F-targeted Abs cocktails against NiV and HeV.

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Data availability

The cryo-EM maps and atomic models have been deposited to the Electron Microscopy Data Bank and Protein Data Bank with accession numbers EMD-22884/PDB 7KI4 (NiV F–12B2) and EMD-22885/PDB 7KI6 (HeV F–1F5). Sharing of reagents will proceed through a Materials Transfer Agreement.

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Acknowledgements

This study was supported by the National Institute of Allergy and Infectious Diseases (grant nos. DP1AI158186 and HHSN272201700059C to D.V. and grant nos. AI054715, AI077995 and AI142764 to C.C.B.), the National Institute of General Medical Sciences (grant no. GM120553 to D.V.), an Investigators in the Pathogenesis of Infectious Disease Award from the Burroughs Wellcome Fund (D.V.), a Pew Biomedical Scholars Award (D.V.) and the University of Washington Arnold and Mabel Beckman cryo-EM center. Operations support of the Galveston National Laboratory was supported by NIAID/NIH grant no. UC7AI094660.

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Authors and Affiliations

  1. Department of Biochemistry, University of Washington, Seattle, WA, USA

    Ha V. Dang & David Veesler

  2. Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA

    Robert W. Cross, Viktoriya Borisevich, Chad E. Mire & Thomas W. Geisbert

  3. Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX, USA

    Robert W. Cross, Chad E. Mire & Thomas W. Geisbert

  4. Mapp Biopharmaceutical, Inc., San Diego, CA, USA

    Zachary A. Bornholdt, Brandyn R. West & Larry Zeitlin

  5. Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA

    Yee-Peng Chan, Sofia Cheliout Da Silva, Antony S. Dimitrov, Lianying Yan, Moushimi Amaya & Christopher C. Broder

  6. Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA

    Chanakha K. Navaratnarajah

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Contributions

H.V.D., R.W.C., T.W.G., C.C.B. and D.V. designed the experiments. A.S.D., L.Y. and Y.-P.C. designed and cloned the HeV F and NiV F constructs and produced and isolated 1F5, 5B3 and 12B2 mouse hybridoma and mAbs. H.V.D. expressed and purified the soluble HNV F proteins used in this study. B.R.W., L.Z. and Z.A.B. performed humanization of murine mAbs and produced the humanized mAbs. H.V.D. performed IgG fragmentation and binding assays. H.V.D. conducted the cryo-EM sample preparation, data collection and data processing. H.V.D. and D.V. built and refined the atomic models. R.W.C. carried out the neutralization assays. V.B., C.M. and T.W.G. performed escape mutant analyses. C.K.N. carried out the membrane fusion inhibition assay. M.A. prepared a stable cell line. H.V.D., R.W.C., S.C.D.S., C.C.B. and D.V. analyzed the data. H.V.D. and D.V. prepared the manuscript with input from all authors.

Corresponding author

Correspondence to David Veesler.

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Competing interests

Z.A.B., B.R.W. and L.Z. are employees and shareholders in Mapp Biopharmaceutical Inc., and L.Z. is a co-owner of Mapp Biopharmaceutical, Inc. D.V. is a consultant for Vir Biotechnology Inc. The Veesler laboratory has received an unrelated sponsored research agreement from Vir Biotechnology Inc. The other authors declare no competing interests.

Additional information

Peer review information Nature Structural & Molecular Biology thanks Dimiter Dimitrov and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available. Beth Moorefield was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 Cryo-EM characterization of NiV F in complex with the 12B2 Fab fragment.

a, Representative micrograph. Scale bar, 100 nm. b, Reference-free 2D class averages. Scale bar, 100 Å. c, Gold-standard (black) and map-model (red) Fourier shell correlation curves. Dotted line indicates the 0.143 and 0.5 thresholds. d, Two orthogonal views of the cryo-EM map colored by local resolution estimated using cryoSPARC. e, Cryo-EM data processing flow chart. Selected groups of particles at different steps are boxed. NUR: Non-Uniform refinement.

Extended Data Fig. 2 Binding of the 12B2 Fab fragment to immobilized NiV F S69A ectodomain (N67 glycan mutant) analyzed by biolayer interferometry.

Raw data are colored according to the key and fitted curves are displayed as black dashed lines. The vertical dotted lines correspond to the transition between the association and dissociation phases.

Extended Data Fig. 3 CryoEM characterization of HeV F in complex with the 1F5 Fab fragment.

a, Representative micrograph. Scale bar, 100 nm. b, Reference-free 2D class averages. Scale bar, 100 Å. c, Gold-standard (black) and map-model (red) Fourier shell correlation curves. Dotted line indicates the 0.143 and 0.5 thresholds. d, Two orthogonal views of the cryo-EM map colored by local resolution estimated using cryoSPARC. e, Cryo-EM data processing flow chart. Selected groups of particles at different steps are boxed. NUR: Non-Uniform refinement.

Extended Data Fig. 4 EM characterization of the negatively stained ternary complex of NiV F/12B2/5B3 and NiV F/12B2/1F5.

a,c, A representative micrograph and 2D class averages of NiV F/12B2/5B3 complex (a) and NiV F/12B2/1F5 complex (c) from the corresponding negative staining dataset of NiV F incubated with excess of 12B2/1F5 Fabs or 12B2/5B3 Fabs (See Materials & Methods). Micrograph scale bar: 100 nm; 2D class average scale bar: 100Å. b,d, Three-dimensional reconstructions of the ternary complex of NiV F/12B2/5B3 (b) and NiV F/12B2/1F5 (d), representing a complex with the highest stoichiometry of Fabs:NiV F from the corresponding negative staining dataset.

Extended Data Fig. 5 Comparison of the footprints of the 12B2 and the 1F5 antibody on prefusion F and postfusion F and among HNV F proteins.

a, b, Molecular surface representation of the NiV F prefusion trimer (a) and the homology model of NiV F postfusion (b) showing the 12B2 footprint in orange. c-d, Molecular surface representation of the HeV F prefusion trimer (c) and the homology model of NiV F postfusion (d) showing the 1F5 footprint in purple. The homology model of NiV F postfusion in (b) and (d) was obtained by threading the NiV F sequence onto the human parainfluenza postfusion F structure23 (PDB: 1ZTM). e, Sequence alignment of HNV F glycoproteins (NiV, HeV, GhV: Ghana bat virus; CedV: Cedar virus; MojVF: Mojiang virus). Residues on HNV F constituting the 12B2 or 1F5 epitope are denoted with an orange or purple asterisk, respectively.

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Dang, H.V., Cross, R.W., Borisevich, V. et al. Broadly neutralizing antibody cocktails targeting Nipah virus and Hendra virus fusion glycoproteins. Nat Struct Mol Biol 28, 426–434 (2021). https://doi.org/10.1038/s41594-021-00584-8

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