An antibody targeting the N-terminal domain of SARS-CoV-2 disrupts the spike trimer
Naveenchandra Suryadevara, Andrea R. Shiakolas, Laura A. VanBlargan, Elad Binshtein, Rita E. Chen, James Brett Case, Kevin J. Kramer, Erica C. Armstrong, Luke Myers, Andrew Trivette, Christopher Gainza, Rachel S. Nargi, Christopher N. Selverian, Edgar Davidson, Benjamin J. Doranz, Summer M. Diaz, Laura S. Handal, Robert H. Carnahan, Michael S. Diamond, Ivelin S. Georgiev, James E. Crowe Jr.
Naveenchandra Suryadevara, Andrea R. Shiakolas, Laura A. VanBlargan, Elad Binshtein, Rita E. Chen, James Brett Case, Kevin J. Kramer, Erica C. Armstrong, Luke Myers, Andrew Trivette, Christopher Gainza, Rachel S. Nargi, Christopher N. Selverian, Edgar Davidson, Benjamin J. Doranz, Summer M. Diaz, Laura S. Handal, Robert H. Carnahan, Michael S. Diamond, Ivelin S. Georgiev, James E. Crowe Jr.
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Research Article Immunology Virology

An antibody targeting the N-terminal domain of SARS-CoV-2 disrupts the spike trimer

Abstract

The protective human antibody response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) focuses on the spike (S) protein, which decorates the virion surface and mediates cell binding and entry. Most SARS-CoV-2 protective antibodies target the receptor-binding domain or a single dominant epitope (“supersite”) on the N-terminal domain (NTD). Using the single B cell technology called linking B cell receptor to antigen specificity through sequencing (LIBRA-Seq), we isolated a large panel of NTD-reactive and SARS-CoV-2–neutralizing antibodies from an individual who had recovered from COVID-19. We found that neutralizing antibodies against the NTD supersite were commonly encoded by the IGHV1-24 gene, forming a genetic cluster representing a public B cell clonotype. However, we also discovered a rare human antibody, COV2-3434, that recognizes a site of vulnerability on the SARS-CoV-2 S protein in the trimer interface (TI) and possesses a distinct class of functional activity. COV2-3434 disrupted the integrity of S protein trimers, inhibited the cell-to-cell spread of the virus in culture, and conferred protection in human angiotensin-converting enzyme 2–transgenic (ACE2-transgenic) mice against the SARS-CoV-2 challenge. This study provides insight into antibody targeting of the S protein TI region, suggesting this region may be a site of virus vulnerability.

Authors

Naveenchandra Suryadevara, Andrea R. Shiakolas, Laura A. VanBlargan, Elad Binshtein, Rita E. Chen, James Brett Case, Kevin J. Kramer, Erica C. Armstrong, Luke Myers, Andrew Trivette, Christopher Gainza, Rachel S. Nargi, Christopher N. Selverian, Edgar Davidson, Benjamin J. Doranz, Summer M. Diaz, Laura S. Handal, Robert H. Carnahan, Michael S. Diamond, Ivelin S. Georgiev, James E. Crowe Jr.

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Figure 5

Structural characterization of the trimer-disrupting antibody COV2-3434.

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Structural characterization of the trimer-disrupting antibody COV2-3434....
(A) Residues identified as important for COV2-3434 binding are highlighted as spheres on the S protein structure: Protein Data Bank (PDB) 7L2C (green ribbons), F43 (magenta), F175 and L176 (cyan), and L226 (orange). Residues critical for COV2-3434 binding were identified from binding screens of an alanine-scanning mutagenesis library of NTD. (B) mAb binding values for COV2-3434, COV2-3439, and control anti-NTD mAb COV2-2305 are shown at SARS-CoV-2 S protein clones identified as critical for MAb binding. mAb reactivities for each mutant are expressed as a percentage of binding to wild-type S protein, with ranges (half of the maximum minus minimum values). Two replicate values were obtained for each experiment. (C) nsEM of SARS-CoV-2 rNTD protein in complex with COV2-3439 and COV2-3434 Fabs. Shown are the top view and side view of superimposed 3D volume COV2-3434 Fab–COV2-3439 Fab–SARS-CoV-2 rNTD complexes as visualized by nsEM aligned to the S protein of SARS-CoV-2 in complex with 4A8 (PDB: 7C2L) Data are from a single experiment (detailed collection statistics are provided in Supplemental Table 3). (D) ELISA binding to SARS-CoV-2 S6Pecto or SARS-CoV-2 S6P-2C was measured by absorbance at 450 nm. The COV2-2130 starting concentration was 200 ng/mL, the COV2-2676 and COV2-3434 starting concentrations were 20 μg/mL, and mAbs were titrated 2-fold. Calculated EC50 values are shown on the graph. Error bars indicate the SD; data represent at least 2 independent experiments performed in technical duplicate. (E) Measurement of serum antibody competition with TI antibody COV2-3434 in individuals before or after SARS-CoV-2 mRNA vaccination. Competition-binding ELISA curves for COV2-3434 with human serum from convalescent or vaccinated donors. Competition-binding experiments were performed for each sample in triplicate and repeated in at least 2 independent experiments. One representative experiment is shown. For all competition-binding curves, data points indicate the mean and error bars indicate the SD. vac., vaccinated; inf., infected.