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.
Highlights
Interventions against variants of severe acute respiratory syndrome coronavirus 2 (SARSCoV-2) are urgently needed
By using camelid immunization with receptor-binding domain (RBD)SARSCoV2 and an advanced proteomic pipeline, we have recently identified thousands of high-affinity receptor binding domain (RBD) Nbs including a repertoire of ultrapotent Nbs[8]
We found that three Nbs (17, 20, and 21) were affected by the double mutant L452R and E484Q, which are the critical RBD mutations recently found in Kappa (B.1.617.1) strain[21]
Summary
Interventions against variants of severe acute respiratory syndrome coronavirus 2 (SARSCoV-2) are urgently needed. Stable and potent nanobodies (Nbs) that target the receptor binding domain (RBD) of SARS-CoV-2 spike are promising therapeutics. It is unknown if Nbs broadly neutralize circulating variants. By using camelid immunization with receptor-binding domain (RBD)SARSCoV2 and an advanced proteomic pipeline, we have recently identified thousands of high-affinity RBD Nbs including a repertoire of ultrapotent Nbs[8]. We assessed the impact of the convergent variants of concern and the critical RBD point mutations on the ultrapotent neutralizing Nbs. Subsequent determination of eight highresolution structures, involving six Nbs bound to either S or RBD, by cryo-EM provided critical insights into the antiviral mechanisms of highly potent neutralizing Nbs. Structural comparisons between neutralizing mAbs and Nbs revealed both similarities and marked differences between the two antibody species
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