Broad ultra-potent neutralization of SARS-CoV-2 variants by monoclonal antibodies specific to the tip of RBD

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) continue to wreak havoc across the globe. Higher transmissibility and immunologic resistance of VOCs bring unprecedented challenges to epidemic extinguishment. Here we describe a monoclonal antibody, 2G1, that neutralizes all current VOCs and has surprising tolerance to mutations adjacent to or within its interaction epitope. Cryo-electron microscopy structure showed that 2G1 bound to the tip of receptor binding domain (RBD) of spike protein with small contact interface but strong hydrophobic effect, which resulted in nanomolar to sub-nanomolar affinities to spike proteins. The epitope of 2G1 on RBD partially overlaps with ACE2 interface, which gives 2G1 ability to block interaction between RBD and ACE2. The narrow binding epitope but high affinity bestow outstanding therapeutic efficacy upon 2G1 that neutralized VOCs with sub-nanomolar IC50 in vitro. In SARS-CoV-2 and Beta- and Delta- variant-challenged transgenic mice and rhesus macaque models, 2G1 protected animals from clinical illness and eliminated viral burden, without serious impact to animal safety. Mutagenesis experiments suggest that 2G1 could be potentially capable of dealing with emerging SARS-CoV-2 variants in future. This report characterized the therapeutic antibodies specific to the tip of spike against SARS-CoV-2 variants and highlights the potential clinical applications as well as for developing vaccine and cocktail therapy.

Comprehensive Evaluation of ACE2-Fc Combination with Neutralization Antibody on Broad Protection against SARS-CoV-2 and Its Variants

“…We projected these escape mutations on RBD (Figure 4C) and found that the escape mutations of 5B2 (N370S, N440K, V503M), 9B10 (A475V, E484K), 3A4 (F490L) and 8G9 (N354D, D389N, E484K) were not within the 4 Å distance from ACE2 (Figure 4E) (structure based on PDB ID: 6M17), so these mutations did not affect ACE2-Fc binding and neutralization. But for escape mutation of 2G1 (F486I), although F486I mutation totally lost four π-π stacking interactions with 2G1 (Figure 4F) (structure in our previous study [21]), it also lost one π-π stacking interaction with Y83 of ACE2 (Figure 4G). However, there was still a hydrophobic interaction between I486 of RBD and L79 or M82 of ACE2 (Figure 4G).…”

“…Next, we evaluate the SARS-CoV-2 neutralizing antibodies from convalescent patients developed by our Laboratory 17 to understand whether they might be escaped by Delta or Omicron variants using the pseudovirus assay (Figure 1E). Eleven mAbs interacting with diverse epitopes on the RBD were evaluated (Figure 1F).…”

“…The sequence of ACE2-Fc the same as the sequence of mACE2-Ig 2 (catalytic activity reduced variant) was synthesized and cloned into pcDNA3.4 to express in ExpiCHO™ Expression System (ThermoFisher). Antibodies were attained according to the methods described in our previous report 17 . In brief, PBMC was isolated from convalescent patients and then RBD specific memory B cells were sorted out by FACS.…”

“…ACE2-293T cells were established as described in our previous study [21]. In brief, lentivirus bearing ACE2 gene was transduced to 293T cells to attain ACE2-293T cell pool, which was subsequently sorted out the 1% highest ACE2 expression cells with FACS Aria III instrument (BD).…”

Efficient Neutralization of SARS-CoV-2 Omicron and Other VOCs by a Broad Spectrum Antibody 8G3

“…Using an B cell antibody repertoire from early stage COVID-19 convalescents 8 , we compared dozens of candidate molecules in neutralizing activity against pseudo-typed SARS-CoV-2 WA1/2020 and Omicron viruses. We found that most of the antibodies that performed well against the WA1/2020 virus nearly lost their neutralization against Omicron; only a few antibodies retained full or partial activity (Fig.…”