In Silico Design and Construction of an RBD Immunogen Against the Adherence of SARS Cov_2

The contagious SARS virus CoV_2 spread rapidly around the world. The virus has infected more than 550 million people worldwide and killed about 7 million to date. Regarding the mechanism of infection, the receptor-binding domain (RBD) of the Spike protein plays an important role in the virus entry into the host cell. In this study, with a bioinformatics approach the cassette design, codon compatibility, protein stability and finally the structural accuracy (through examining the protein expression) were investigated. To increase the probability of RBD cassette expression, the gene codons and various parameters were optimized and the thermodynamic analysis of mRNA structure were performed to increase stability. The structure of the third protein was also predicted and the quality of the structures was evaluated. The linear and conformational B-cell epitopes were determined. The recombinant RBD protein showed the highest antigen index. The compatibility index of the recombinant protein codon increased to 0.96. The third predicted structure based on the I_TASSER server showed good quality. Thermodynamic analysis of the mRNA structure showed that the predicted structure is stable. The conformational and linear B-cell epitopes were observed in all three domains of the recombinant protein. Finally, the recombinant protein was expressed in a bacterial host. Immunoinformatics and expression results showed that the designed recombinant construct has a high antigenicity and production potential and can be considered as an immunogenic candidate against SARS CoV_2 virus in the future studies.