<p>The alarming rise in flaviviruses like Zika virus (ZikV) and dengue virus (DenV) has made them a major global health concern, especially in tropical and subtropical regions where nearly half of the global population is at risk. The urgency for safe and effective antiviral treatment is underscored by the fact that, despite growing research efforts, there are still no FDA-approved drugs available. The methyltransferases of ZikV and DenV, i.e., non-structural protein-5 (NS5), stand out as a highly conserved enzyme that is involved in viral replication and evasion of the host immune system via a capping mechanism, making them a key target for antiflaviviral drug development. In this study, we employed a virtual reality and cheminformatics-assisted pipeline followed by biological validation to identify a potent natural inhibitor of NS5. The systematic computational analysis identified the natural compound ZINC8952607 as a putative inhibitor with high binding affinity towards the methyltransferases of ZikV and DenV. Initial screening and docking analysis reveal that the lead compound strongly binds at the active site of the NS5 protein with a higher affinity. Further, extensive analysis involving molecular dynamics and DFT establishes greater reactivity of the lead compound and its stable complex formation with the NS5 protein. In vitro assay determined the cytotoxicity of the lead molecule with a CC₅₀ value of 3.43 ± 0.17 µM, indicating its reasonable safety as a lead molecule. These findings highlight ZINC8952607 as a potential lead candidate and reinforce the importance of targeting NS5 to develop new antiviral drugs.</p> Graphical abstract <p></p>