Insight into the Interaction and Inhibition of NS3 ATPase of Dengue Virus with 3'-Azido-3'-deoxythymidine:...

The NS3 protein of dengue virus (DENV) is highly conserved and plays a vital role in replication, and thus it is considered as a potential antiviral target. The current study was carried out to observe interactions between the NS3 protein of DENV-4 and 3'-azido-3'-deoxythymidine (AZT-TP) using biophysical studies and ATPase inhibition assays, and further complemented it with in silico approaches. Fluorescence and time-resolved studies showed significant static quenching of NS3 fluorophores. Surface plasmon resonance (SPR) studies showed strong binding affinity with a significant pharmacodynamics rate, i.e., higher kinetic rate of association (k _a) and lower dissociation rate constant (K_d). Isothermal titration calorimetry (ITC) measurements revealed strong and spontaneous binding between NS3 and AZT-TP with feasible thermodynamic parameters. The ATPase inhibition assay showed a decrease in NS3 ATPase activities in a dose-dependent manner, indicating the inhibitory potential of AZT-TP. Molecular docking showed significant binding (-8.0 kcal/mol) with the conserved residues involved in NS3 helicase/ATPase activities. Molecular dynamics (MD) simulation studies showed no major conformational changes in the NS3 and AZT-TP complex, and it was well-anchored at its binding position with nearly a linear trajectory up to 200 ns. Total Gibbs free energy and contribution of different interactions calculated using MMPB-(GB)-SA complemented the biophysical and docking results. The study suggests that there might be a direct binding between AZT-TP and residues involved in the ATPase activities and thus provides promising data to explore the future prospects of AZT-TP as an NS3 inhibitor for antiviral development.