Designing ferritin nanocage based vaccine candidates for SARS-CoV-2 by in silico engineering of its HLA I and HLA II epitope peptides

New variants of SARS-CoV-2 are continuously being reported. To curtail the spread of this virus, it is essential to find an efficient and potent vaccine. Here, we report in silico designing of a protein (ferritin: FR) nanocage fused with multiple epitopes identified using the immuno-informatics approach and high-throughput screening. Employing computational approaches, we identified potential epitopes from membrane, nucleocapsid, and envelope proteins of SARS-CoV-2 and docked them on the selected human leukocyte antigen Class I and II receptors, then the stability of the complexes was assessed using molecular dynamics simulation studies. We have engineered chimeric ferritin nanocage, chm66FR, with the nested peptide of 10 epitopes by replacing the loop region at the 66(th) position of the nanocage, then its stability was confirmed using metadynamics simulation. Further, we used the homotrimeric '6-helical bundle' of the spike protein to engineer the chimeric 6HB (chm6HB). The chm6HB is, engineered with three epitope peptides, mounted on the N-terminal trimeric interface of the chm66FR to generate the chm6HB-chm66FR, which contains 15 epitope peptides. Chimeric FR nanocages and the chm6HB could be potential vaccine candidates against strains of SARS-CoV-2. These multivalent and multiple epitopes protein nanocages and scaffolds could mount both humoral and T-cell mediated immune responses against SARS-CoV-2. Communicated by Ramaswamy H. Sarma