Abstract
Interventions against variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are urgently needed. Stable and potent nanobodies (Nbs) that target the receptor binding domain (RBD) of SARS-CoV-2 spike are promising therapeutics. However, it is unknown if Nbs broadly neutralize circulating variants. We found that RBD Nbs are highly resistant to variants of concern (VOCs). High-resolution cryoelectron microscopy determination of eight Nb-bound structures reveals multiple potent neutralizing epitopes clustered into three classes: Class I targets ACE2-binding sites and disrupts host receptor binding. Class II binds highly conserved epitopes and retains activity against VOCs and RBDSARS-CoV. Cass III recognizes unique epitopes that are likely inaccessible to antibodies. Systematic comparisons of neutralizing antibodies and Nbs provided insights into how Nbs target the spike to achieve high-affinity and broadly neutralizing activity. Structure-function analysis of Nbs indicates a variety of antiviral mechanisms. Our study may guide the rational design of pan-coronavirus vaccines and therapeutics.
© 2021. The Author(s).
Publication types
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Research Support, N.I.H., Extramural
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Research Support, Non-U.S. Gov't
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Research Support, U.S. Gov't, Non-P.H.S.
MeSH terms
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Angiotensin-Converting Enzyme 2 / chemistry
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Angiotensin-Converting Enzyme 2 / metabolism
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Antibodies, Monoclonal / chemistry
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Antibodies, Monoclonal / immunology
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Antibodies, Monoclonal / metabolism
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Binding Sites
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Broadly Neutralizing Antibodies / chemistry
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Broadly Neutralizing Antibodies / classification
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Broadly Neutralizing Antibodies / immunology*
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Broadly Neutralizing Antibodies / metabolism
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COVID-19 / prevention & control
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COVID-19 Drug Treatment
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Epitopes / chemistry
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Epitopes / immunology*
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Epitopes / metabolism
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Humans
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Models, Molecular
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Mutation
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Protein Binding
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SARS-CoV-2 / genetics
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SARS-CoV-2 / immunology*
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Single-Domain Antibodies / chemistry
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Single-Domain Antibodies / classification
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Single-Domain Antibodies / immunology*
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Single-Domain Antibodies / metabolism
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Spike Glycoprotein, Coronavirus / chemistry
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Spike Glycoprotein, Coronavirus / genetics
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Spike Glycoprotein, Coronavirus / immunology
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Spike Glycoprotein, Coronavirus / metabolism
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Structure-Activity Relationship
Substances
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Antibodies, Monoclonal
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Broadly Neutralizing Antibodies
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Epitopes
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Single-Domain Antibodies
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Spike Glycoprotein, Coronavirus
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spike protein, SARS-CoV-2
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ACE2 protein, human
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Angiotensin-Converting Enzyme 2