Identifying Epitope Sites on the Receptor Binding Domain (RBD) of SARS-CoV-2

Abstract COVID-19 and SARS-CoV-2 variants continue to threaten human health and life worldwide. Thousands of structures related to SARS-CoV-2 have been rapidly determined, either by X-ray crystallography or CryoEM and deposited in the Protein Data Bank (PDB) since 2020. Here, we systematically investigated the structures of 302 antibodies and 78 nanobodies in complex with spike protein or the receptor binding domain (RBD) of SARS-CoV-2. We identified 23 common epitopic sites (ES) on the RBD surface and revealed the vital role of the complementarity-determining Region (CDR) loops in recognizing epitopes. The 23 ES are characterized according to the secondary structure feature and accessible surface area. About 75% of the total surface of RBD areas could access by the elicited antibodies, while the CDR3 loops occupied 50% of the contact surface. The analysis of paratope-epitope (antibody-antigen) interaction based on these epitope sites revealed the features of potent neutralizing the virus and the unique usage of amino acids of antibody. The clustering analysis of the antibody biophysical properties and surface area availabilities on the RBD found many binding motifs. Remarkably, most variants of concern (VOC) escape mutations, including Omicron occur within these 23 ES. This analysis not only explains the differential ability of antibodies to recognize epitope sites on the RBD surface but also offers predictive guidelines for understanding the role that accumulated SARS mutations might play in escape from antibodies elicited by immunogens. This structural characterization of the epitope-paratope interactions provides insights for structure-based vaccine design and therapeutic strategies and drugs against the future virus.