Molecular and structural insights into dengue virus non-structural proteins from pakistani clinical isolates for the identification of novel antiviral targets

Dengue virus (DENV) remains a global health threat, with Pakistan experiencing recurrent outbreaks, yet non-structural genes (NS1, NS2A, NS5) critical for viral replication and pathogenesis remain understudied in local strains. In this study, 150 NS1-positive serum samples (2022-2024) were analyzed via nested PCR, Sanger sequencing, and phylogenetic tools (MEGA11), revealing DENV-2 as the dominant serotype (85 % of samples), with NS5 showing 97 % homology to Indian/Swat strains, while NS1 and NS2A exhibited sequence variation in functional domains. In silico modeling and docking studies identified RK-0404,678 as a strong binder to NS5 (-6.4 kcal/mol) and Galidesivir to NS5 (-7.2 kcal/mol), suggesting their potential as antiviral candidates. These findings highlight DENV-2 dominance in Pakistan and identify conserved regions in NS5 as promising drug targets, though further experimental validation is warranted.