Immunomics Datasets and Tools: To Identify Potential Epitope Segments for Designing Chimeric Vaccine Candidate to Cervix Papilloma

Abstract

Immunomics tools and databases play an important role in the designing of prophylactic or therapeutic vaccines against pathogenic bacteria and viruses. Therefore, we aimed to illustrate the different immunological databases and web servers used to design a chimeric vaccine candidate against human cervix papilloma. Initially, cellular immunity inducing major histocompatibility complex class I and II epitopes from L2 protein of papilloma 58 strain were predicted using the IEDB, NetMHC, and Tepi tools. Then, the overlapped segments from the above analysis were used to calculate efficiency on interferon-gamma and humoral immunity production. In addition, the allergenicity, antigenicity, cross-reactivity with human proteomes, and epitope conservancy of elite segments were determined. The chimeric vaccine candidate (SGD58) was constructed with two different overlapped peptide segments (23⁻36) and (29⁻42), adjuvants (flagellin and RS09), two Th epitopes, and amino acid linkers. The results of homology modeling demonstrated that SGD58 have 88.6% of favored regions based on Ramachandran plot. Protein⁻protein docking with Swarm Dock reveals SGD58 with receptor complex have −54.74 kcal/mol of binding energy with more than 20 interacting residues. Docked complex are stable in 100ns of molecular dynamic simulation. Further, coding sequences of SGD58 also show elevated gene expression in E. coli. In conclusion, SGD58 may prompt vaccine against cervix papilloma. This study provides insight of vaccine design against different pathogenic microbes as well.

Keywords

• cellular immunity
• codon frequency distribution
• HPV58
• minor capsid protein
• TLR agonist
• SGD58
• prophylaxis