Genetic and structural basis for recognition of SARS-CoV-2 spike protein by a two-antibody cocktail

Abstract

The SARS-CoV-2 pandemic has led to an urgent need to understand the molecular basis for immune recognition of SARS-CoV-2 spike (S) glycoprotein antigenic sites. To define the genetic and structural basis for SARS-CoV-2 neutralization, we determined the structures of two human monoclonal antibodies COV2-2196 and COV2-21301, which form the basis of the investigational antibody cocktail AZD7442, in complex with the receptor binding domain (RBD) of SARS-CoV-2. COV2-2196 forms an “aromatic cage” at the heavy/light chain interface using germline-encoded residues in complementarity determining regions (CDRs) 2 and 3 of the heavy chain and CDRs 1 and 3 of the light chain. These structural features explain why highly similar antibodies (public clonotypes) have been isolated from multiple individuals1–4. The structure of COV2-2130 reveals that an unusually long LCDR1 and HCDR3 make interactions with the opposite face of the RBD from that of COV2-2196. Using deep mutational scanning and neutralization escape selection experiments, we comprehensively mapped the critical residues of both antibodies and identified positions of concern for possible viral escape. Nonetheless, both COV2-2196 and COV2130 showed strong neutralizing activity against SARS-CoV-2 strain with recent variations of concern including E484K, N501Y, and D614G substitutions. These studies reveal germline-encoded antibody features enabling recognition of the RBD and demonstrate the activity of a cocktail like AZD7442 in preventing escape from emerging variant viruses.

A public vaccine-induced human antibody protects against SARS-CoV-2 and emerging variants

“…S2E12 heavy chain amino acid residues that engage the RBD are identical to those in 2C08, suggesting that 2C08 likely engages the RBD in a manner similar to that of the structurally characterized S2E12. Furthermore, we identified two additional human mAbs, 253H55L and COV2-2196, that share genetic and functional features with 2C08 and have nearly identical antibody-RBD interactions as those of S2E12 ( 22 , 36 ) ( Fig. 3C, Fig.…”

“…It remains to be determined what fraction of the antibody responses induced by SARS-CoV-2 vaccines in humans are comprised of 2C08-type antibodies that are public, potently neutralizing, and so far, minimally impacted by the mutations found in the variants of concern. It is important to note that at least one 2C08-like mAb, COV2-2196, is currently being developed for clinical use ( 36 ).…”

Mutational escape from the polyclonal antibody response to SARS-CoV-2 infection is largely shaped by a single class of antibodies

“…Class 1 and 2 antibodies compete with ACE2 for RBD binding and have some overlap in their structural footprints particularly at ACE2 contact sites at the "top" of the receptor-binding ridge. Class 3 antibodies bind the opposite side of the receptor-binding motif (including the 443-450 2 have previously determined escape maps 30,33,35,36 , including class 4 antibodies, which bind to the RBD outside the receptor-binding motif and are generally less potently neutralizing 17,19,26,31 . Antibodies with similar escape mutations are located close to one another in the multidimensional scaling projection, and antibodies with very distinct escape mutations are far apart ( Figure 1C ).…”

“…Escape maps for class 1, 2, or 3 antibodies we have profiled here or in previous studies, related to Figure 1C . All escape maps were previously generated 30,33,35,36 except for C105, C144, C002, C121, C135, and C110 which are new to this study.…”

SARS-CoV-2 Spike receptor-binding domain with a G485R mutation in complex with human ACE2

“…Mutations at E484 and/or F486 arose as escape substitutions multiple times when a SARS-CoV-2 virus was tested against a panel of neutralising monoclonal antibodies against the SARS-CoV-2 RBD (Liu et al , 2021). The structure of the Spike-RBD in complex with two monoclonal antibodies in an investigational antibody cocktail have recently been published (Dong et al , 2021). These structures reveal that Spike RBD residues 485-487 are surrounded by a hydrophobic pocket formed by the monoclonal antibody COV2-2196, revealing the importance of these residues in antibody binding.…”