Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern

Abstract

Severe acute respiratory syndrome coronavirus-2 (SAR-CoV-2) causes coronavirus disease 2019 (COVID19) that is responsible for short and long-term disease, as well as death, in susceptible hosts. The receptor binding domain (RBD) of the SARS-CoV-2 Spike (S) protein binds to cell surface angiotensin converting enzyme type-II (ACE2) to initiate viral attachment and ultimately viral pathogenesis. The SARS-CoV-2 S RBD is a major target of neutralizing antibodies (NAbs) that block RBD - ACE2 interactions. In this report, NAb-RBD binding epitopes in the protein databank were classified as C1, C1D, C2, C3, or C4, using a RBD binding profile (BP), based on NAb-specific RBD buried surface area and used to predict the binding epitopes of a series of uncharacterized NAbs. Naturally occurring SARS-CoV-2 RBD sequence variation was also quantified to predict NAb binding sensitivities to the RBD-variants. NAb and ACE2 binding studies confirmed the NAb classifications and determined whether the RBD variants enhanced ACE2 binding to promote viral infectivity, and/or disrupted NAb binding to evade the host immune response. Of 9 single RBD mutants evaluated, K417T, E484K, and N501Y disrupted binding of 65% of the NAbs evaluated, consistent with the assignment of the SARS-CoV-2 P.1 Japan/Brazil strain as a variant of concern (VoC). RBD variants E484K and N501Y exhibited ACE2 binding equivalent to a Wuhan-1 reference SARS-CoV-2 RBD. While slightly less disruptive to NAb binding, L452R enhanced ACE2 binding affinity. Thus, the L452R mutant, associated with the SARS-CoV-2 California VoC (B.1.427/B.1.429-California), has evolved to enhance ACE2 binding, while simultaneously disrupting C1 and C2 NAb classes. The analysis also identified a non-overlapping antibody pair (1213H7 and 1215D1) that bound to all SARS-CoV-2 RBD variants evaluated, representing an excellent therapeutic option for treatment of SARS-CoV-2 WT and VoC strains.

The Immune Response to SARS-CoV-2 and Variants of Concern

“…C3 neutralising antibodies bound mainly to the outside of the ACE-2 binding site in both conformations. The C4 neutralising antibodies bound to an epitope farther from the ACE-2 binding site, which is only accessible following major conformational change in this area [23]. These findings are in alignment with those of Barnes et al who also reported 4 main classes of neutralising antibodies [24].…”

Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants

“…Furthermore, it was shown that L452R confers viral escape from human leukocyte antigen (HLA)-restricted cellular immunity mediated by cytotoxic T lymphocytes ( 17 ). Finally, it was predicted that mutations in residue L452, which is located in immediate proximity to the RBD-ACE2 interaction interface, result in at least a modestly higher affinity of receptor binding and thus an increased rate of human cell infectivity ( 17 – 19 ). Both the successful immune escape and strengthened virus-cell attachment of L452 mutants might lead to increased transmissibility, infectivity, and/or pathogenicity of nCoV.…”

Broadly-Neutralizing Antibodies Against Emerging SARS-CoV-2 Variants

“…The isolation and characterization of nAbs targeting conserved RBD epitopes that possess dual advantage of breadth across Sarbecoviruses and higher resistance to neutralization escape is necessary to fight this pandemic (79). Due to the conservation at the Class IV epitope, antibodies targeting this site are of interest.…”