Epitope Mapping of SARS-CoV-2 Antibodies

The epitope regions of CR3022 and S309 were determined using the published structural data in protein data bank (PDB (40 (link)–43 (link))) for the antibody complexed with SARS-CoV-2 viz. PDB id. 6W41 for CR3022 (41 (link)) and PDB id. 6WPS for S309 (42 (link)). All the amino acids in antigens that are within 5Å contact of amino acids of antibodies were considered as epitope residues. The position of the glycosylation site was determined by in-silico mutation of triplets of amino acids in the epitopes to glycosylation sequon – N-X-T (44 (link)) using the FoldX algorithm (43 (link)). Briefly, residues succeeding N-X motif, where X can be any amino acid except Pro, were mutated to either Threonine or Serine or residues preceding X-T, where X can be any amino acid except Pro, were mutated to Asn to generate novel N-X-T/S motifs. The mutations with the least energy cost, as calculated by the Build module of FoldX, were selected for designing M7 and M8.