In Silico Design of Recombinant Plasmid Encoding Ancestral and Consensus Domain III of the E Protein from Dengue Virus Serotype 2

Abstract

The severe adverse effect of current dengue vaccine (Dengvaxia) pushed research to create a safer vaccine. Previous study designed ancestral and consensus amino acid sequences of the third domain of the Envelope protein (EDIII) from DENV2 as a subunit vaccine candidate to minimize variability between vaccine and circulating strains. This study aimed to analyze the 3D structures and design recombinant expression plasmids encoding these sequences for usage in future studies. The 3D structures were visualized and aligned to the wild-type protein. The results indicated that the ancestral [Root Mean Square Deviation (RMSD) 2.31Å, Template-Modelling (TM) score 0.7788] and consensus [RMSD 2.23Å, TM-score 0.7781] proteins were highly similar to the wild-type EDIII. Both sequences were reversely translated and underwent codon optimization. The optimized sequences [ancestral: 0.825 Codon Adaptation Index (CAI), 48.2%GC; consensus: 0.826 CAI, 48.2%GC] were inserted into pET-28a(+) plasmid vector using the enzyme NheI-XhoI to yield the best RNA secondary structures (free energy in MFE structures: -22.50 kcal/mol; Centroid: -19.80 kcal/mol). Although the expression products have N-terminal tags derived from the plasmid, thrombin cleavage will leave a short peptide (GSHMAS) that does not significantly change the conformation of the final protein [RMSD ancestral 2.31Å, consensus 2.23Å; TM-score ancestral 0.7788; consensus 0.7781]. Therefore, recombinant plasmids encoding ancestral and consensus protein of DENV2 were successfully designed and should be utilized in silico, in vitro, and in vivo studies towards dengue vaccine development.