Designing siRNAs against non-structural genes of all serotypes of Dengue virus using RNAi technology – A computational investigation

Dengue is a viral disease caused by Aedes aegypti and Aedes albopictus mosquitoes, leads to severe health complications, including dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). The disease has intensified in Asian countries such as Bangladesh, India, Myanmar, and Thailand, with regular outbreaks since 2015, partly due to the lack of effective vaccines or treatments against this ferocious virus. Nonstructural (NS) genes of Dengue virus (DENV) are believed to play vital role in viral replication. Targeting the NS genes of existing serotypes of DENV, we aimed to design a potential small interfering RNA (siRNA) that has the capability to silence the NS genes hence, provide a ground strategy for antiviral therapeutics. In this investigation, a comprehensive computational approach encompassing data collection from NCBI database, GC content analysis, conservation prediction across all DENV serotypes, mRNA-siRNA duplex thermodynamic assessment, siRNA efficacy evaluation, molecular modeling and structural refinement, molecular docking were performed. These analyses anticipated three efficient siRNAs (S2, S3 and S11) that could have the capability to silence all the NS protein-coding genes employed by the DENV. Based on additional analysis including molecular dynamic (MD) simulation, principal component analysis (PCA) and free energy landscape (FEL), two siRNAs (S2 and S11) were recommended as potential therapeutics that could effectively degrade viral NS protein-coding genes through the RNAi pathway. However, S2 (Guide: 5′-UGUUUUUCGCCUUUUUCCGUU-3′ and Passenger: 5′- CGGAAAAAGGCGAAAAACACG-3′) molecule is supposed to be appeared the most promising siRNA compared to S11. This study is the foundational contribution enabling chemically synthesized future antiviral drug discovery for combating DENV, especially in the Asian region where frequent outbreaks are common. Nonetheless, in vivo validation and further evaluations are necessary before these siRNAs can be advanced as molecular therapeutics.