Prediction of Multiple Peptide Based Vaccine from E1, E2 and Capsid Proteins of Rubella Virus: An In-Silico Approach

Abstract

Rubella is a single strand RNA virus in structure that belongs to Togaviridae family. It causes rubella by respiratory droplet transmission and congenital rubella syndrome if infection to the mother occurs during pregnancy. The current life attenuated vaccine is given as part of MMR vaccine. It has many side effects and contraindicated in pregnancy and immunosuppressed persons. The aim of this study is to determine antigenic peptides from E1, E2, and Capsid proteins that can be used for multiple peptide vaccine design using In-Silico study. A total of 189 sequences of three proteins were obtained from NCBI and subjected to multiple sequence alignments using CLUSTALW tool to determine conserved regions. Immune Epitope Data Base tools were used to determine B cell epitopes, these tools are Bepipred Linear B cell epitopes prediction, surface accessibility and antigenicity prediction. Epitope binding to MHC class I and class II and their population coverage were also determined using IEDB software. The analysis results are as follow, for B cell binding from E1 were (PVCQRHSP, QYHPTAC, and QVPPD), from E2 (AQYPP, PAHP and TTAANSTTAATPATA), and (PPPP, PPQQPQPP and PPHT) from capsid protein. All these peptides have high score in Linear B cell epitopes prediction, surface accessibility and antigenicity prediction. On another hand peptides that reacted to MHC class I were (YFNPGGSYY, FVLLVPWVL and FTNLGTPPL) form E1, E2 and capsid protein respectively. It worth noting that the peptide FVLLVPWVL from E2 protein is also binds to MHC class II with high affinity. All T cell peptides had highest population coverage, and the combined coverage for all peptides in this study was found to be 100%. Using In-Silico studies will ensure less risk of virulence and side effects. Evaluation of antibodies response in animal models is needed to confirm efficacy of these epitopes in inducing protective immune response.