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.
Highlights
A robust humoral immune response to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is essential to control viral infection [1, 2]
The receptor binding domain (RBD) consists of a scaffold, conserved among different coronaviruses, and a variable receptor binding module (RBM), which positions amino acids for contact with ACE2 [42]
The goal of this study was to use SARS-CoV-2 neutralizing antibodies (NAbs)/RBD structural information found in the protein databank and SARS-CoV-2 S RBD sequence variation data from the GISAID, to characterize a series of NAbs for potential use as therapeutics against SARS-CoV-2
Summary
A robust humoral immune response to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is essential to control viral infection [1, 2]. The “down” conformation of RBD “hides” the ACE2 binding site in the closed trimeric arrangement to, at least partially, protect the RBD, which is essential for virus cell attachment, from the host’s immune response. Three-dimensional structural studies have played a large role in our understanding of SARS-CoV-2 S RBD-specific NAb epitopes (Table 1). The C1 class is defined by NAbs that bind within the RBD ACE2 binding site, essentially mimicking ACE2 binding, and only bind to RBD when it is in the up conformation. C3 NAbs bind largely outside the ACE2 binding site of RBD in both up and down conformations, while a fourth class (C4) binds farther from the ACE2 binding site and the epitope is only accessible once SARS-CoV-2 S undergoes large conformational changes [30].
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
