SARS-Cov-2 Delta Variant Decreases Nanobody Binding and ACE2 Blocking Effectivity

The Delta variant spreads more rapidly than previous variants of SARS-CoV-2. This variant comprises several mutations on the receptor-binding domain (RBD_Delta) of its spike (S) glycoprotein, which binds to the peptidase domain (PD) of angiotensin-converting enzyme 2 (ACE2) receptors in host cells. The RBD-PD interaction has been targeted by antibodies and nanobodies to prevent viral infection, but their effectiveness against the Delta variant remains unclear. Here, we investigated RBD_Delta-PD interactions in the presence and absence of nanobodies H11-H4, H11-D4, and Ty1 by performing 21.8 µs of all-atom molecular dynamics (MD) simulations. Unbiased simulations revealed that Delta variant mutations strengthen RBD binding to ACE2 by increasing the hydrophobic interactions and salt bridge formation, but weaken interactions with H11-H4, H11-D4, and Ty1. Among these nanobodies H11-H4 and H11-D4 bind RBD without overlapping ACE2. They were unable to dislocate ACE2 from RBD_Delta when bound side by side with ACE2 on RBD. Steered MD simulations at comparable loading rates to atomic force microscopy (AFM) experiments estimated lower rupture forces of the nanobodies from RBD_Delta compared to ACE2. Our results suggest that existing nanobodies are less effective to inhibit RBD_Delta-PD interactions and a new generation of nanobodies will be needed to neutralize the Delta variant.