In Silico Recombinant Plasmid Design of Ancestral and Consensus Sequences of Domain III Envelope Protein from Dengue Virus Type 4

Abstract

Dengue is a disease caused by dengue virus or known as DENV, which currently has 4 antigenically different serotypes: DENV1, DENV2, DENV3, and DENV4. It is possible for a single person to be infected with two or more different serotypes during their lifetime, the increase in the number of times a person is infected the more severe the reactions will be. A previous study found that domain III envelope protein (EDIII) is a promising vaccine candidate as it produces the desired immunogenic reaction and is safer to use. Therefore, this study aims to optimize the designed ancestral and consensus sequence from the previous study to design a suitable vaccine candidate. Based on the RMSD score (ANC: 2.1, CONS: 2.2) and TM-Score (ANC: 0.85, CONS: 0.85) it was concluded that the ancestral and consensus sequence showed a high degree of structural similarity with the wildtype protein (PB ID). The sequences were then optimized for E. coli strain B, resulting in a CAI score of 0.782 for consensus and 0.807 for ancestral sequence. Construction of recombinant plasmid has been conducted in silico. Ancestral and consensus sequence for EDIII of DENV4 were inserted into pET28a using NcoI and XhoI restriction enzyme with additional amino acid (methionine and lysine) which gave the best secondary mRNA structure with accessible RBS and start codon with the MFE of -19.59 kcal/mol (ANC) and -13.70 kcal/mol (CONS).