Immunoinformatics is an exceptional tool for developing vaccines and characteristic for newly discovered viruses. This method has potential to save money and time. Many researchers used immunoinformatic methodologies to make distinctive T-cell and B-cell epitopes, as well as produce vaccines. We identified and depict T-cell and B-cell epitopes against Omicron (BA.2) using existing immunological information. In this study, we have designed vaccine candidates against Omicron (BA.2), a variant of SARS-CoV-2.
In the present study, we have retrieved the viral protein sequences for envelope protein (E), membrane glycoprotein (M), surface glycoprotein (S), and nucleocapsid phosphoprotein (N) of Omicron (BA.2). The sequence was extracted in the FASTA format having amino acids that codes for different proteins using ViPR database. The physicochemical analysis show that the Omicron (BA.2) surface glycoprotein exhibit the highest extinction coefficient of 151,940 M^-1 cm^-1 and the lowest GRAVY value of -0.072 among the identified viral proteins. Additionally, the selected membrane glycoprotein and surface glycoprotein are highly stable (instability index < 40) and antigenic. The antigenicity of the proteins was determined by the VaxiJen V2.0 server. The extinction coefficient tells us about the measurement of how much light the protein complex absorbs at a particular wavelength [37]. A protein whose instability index is smaller than 40 is predicted as stable [38]. Distinct physicochemical properties, including the number of amino acids, molecular weight, aliphatic index, were resolved by the ProtParam server [18].
There are two major functioning immune cells, B and T lymphocytes whose role is to protect our body against the antigens. When the antigen is detected by an antigen presenting cell (APC; e.g., macrophages and dendritic cells), the antigen is approachable by the MHC class II molecule present on the surface of APCs to helper T cells. Later, the helper T cells having a CD4 + fragment on its surface once stimulated by an APC evoke B cells to yield antibody-producing plasma B cells and memory B cells. Plasma B cells generate several antibodies and memory cells to function in long-term immunological memory. Furthermore, macrophages and CD8 + cytotoxic t cells are also get activated by helper T cells to eventually wipe out the target antigen [39].
The B and T cell epitopes of selected viral proteins were identified by the IEDB server [23], which result in the epitopes based on their antigenicity scores and percentile scores. The top 10 MHC class I and II epitopes were involved for this study. The topology of the specific epitopes was resolved by the TMHMM v2.0 server [26]. In all inflammatory situations such as allergenicity, antigenicity, toxicity, and conservancy test, the T cell epitopes were found to be exceedingly antigenic with a high immune response without toxicity, and showed a conservancy of over 90%. Out of 10 MHC class I and II the eight epitopes were selected based on the given properties, ATSRTLSYYL, VTLADAGFIK, SFRLFARTRS, YQTSNFRVP, ALRLCAYCCN, KTFPPTEPKK, VVFLLVTLAILTALR, NFGDQELIRQGTDYK along with antigenic and non-allergenic B cell epitopes that were selected for additional vaccine candidate study. Cluster analysis of the MHC class I and II that might interact with selected epitopes was performed by MHC cluster 2.0 [29]. The antigenicity is the capability of antigen to bind to or interact with the antibodies as to generate immune response [40]. The allergenicity is the ability of an antigen to induce allergic response in the host [41].
Docking was performed among the selected epitopes and MHC alleles. We see the interaction between the MHC class I epitope and MHC class I allele (HLA-A*11 − 01) and MHC class II epitope and MHC class II allele (HLA-DRB1*04 − 01) correspondingly. The peptide-protein docking is performed to check the capability of epitopes to interact with the MHC molecules. Predocking was performed by UCSF Chimera and then 3D structure prediction of epitopes was performed. The docking was executed by the Patchdock servers and analysed by the Ligplot and HPEPDOCK server.