Analysis of the Neutralizing Activity of Antibodies Targeting Open or Closed SARS-CoV-2 Spike Protein Conformations

Abstract

SARS-CoV-2 infection elicits a polyclonal neutralizing antibody (nAb) response that primarily targets the spike protein, but it is still unclear which nAbs are immunodominant and what distinguishes them from subdominant nAbs. This information would however be crucial to predict the evolutionary trajectory of the virus and design future vaccines. To shed light on this issue, we gathered 83 structures of nAbs in complex with spike protein domains. We analyzed in silico the ability of these nAbs to bind the full spike protein trimer in open and closed conformations, and predicted the change in binding affinity of the most frequently observed spike protein variants in the circulating strains. This led us to define four nAb classes with distinct variant escape fractions. By comparing these fractions with those measured from plasma of infected patients, we showed that the class of nAbs that most contributes to the immune response is able to bind the spike protein in its closed conformation. Although this class of nAbs only partially inhibits the spike protein binding to the host’s angiotensin converting enzyme 2 (ACE2), it has been suggested to lock the closed pre-fusion spike protein conformation and therefore prevent its transition to an open state. Furthermore, comparison of our predictions with mRNA-1273 vaccinated patient plasma measurements suggests that spike proteins contained in vaccines elicit a different nAb class than the one elicited by natural SARS-CoV-2 infection and suggests the design of highly stable closed-form spike proteins as next-generation vaccine immunogens.

Critical review of conformational B-cell epitope prediction methods

“…• Antigens can undergo conformational changes where some regions get masked and become unavailable for antibody binding. The spike protein trimer of SARS-CoV-2 is an example of this: it occurs in open and closed conformations characterized by differences in solvent accessibility and epitopes [57].…”

“…In order to evaluate the ability of the benchmarked methods to predict the known epitopes in the spike protein, we gathered 83 spike protein-antibody complexes resolved by X-ray crystallography or cryo-electron microscopy and deposited in the PDB [5] (see [57,58] for the list of PDB ids). We extracted 83 epitopes from these complexes; 75 of them are localized on the RBD of the spike protein, while the remaining eight target its N-terminal domain (NTD).…”

Dissection of Antibody Responses of Gam-COVID-Vac-Vaccinated Subjects Suggests Involvement of Epitopes Outside RBD in SARS-CoV-2 Neutralization

“…remains unchanged in terms of amino acid sequence, in contrast to, for example, peptide 32 ( , (accessed on 28 November 2022)). Notably, monoclonal antibodies with virus-neutralizing ability targeting the N-terminal domain (NTD) region of which peptide 12 is a part thereof have been described [ 31 ], and it was reported that also other vaccines can induce an antibody response directed against this region [ 18 , 19 , 20 , 32 ], indicating that the region defined by peptide 12 may be important for inducing neutralizing antibodies.…”

Importance, Applications and Features of Assays Measuring SARS-CoV-2 Neutralizing Antibodies

“…Thus MIAs can only measure whether antibodies can prevent the interaction of RBD and ACE2. In this context, it must be mentioned that epitopes located outside RBD in the S protein may also play a role in virus-neutralization [ 45 , 46 , 47 , 48 , 49 , 53 , 126 , 127 ]. It is thus possible that certain subjects lacking antibodies blocking the RBD–ACE2 interaction may still contain NAbs.…”