Ensemble docking and molecular dynamics pattern similarity analysis for the discovery of Dengue virus RNA-dependent RNA polymerase inhibitor

Dengue fever, transmitted by Aedes mosquitoes, remains a major public health concern across tropical and subtropical regions. The urgent need for effective antiviral agents has drawn significant attention to the NS5 RNA-dependent RNA polymerase (RdRp), a key enzyme required for viral replication. This study aimed to identify promising RdRp inhibitors using ensemble docking, molecular dynamics (MD) simulations, and MD pattern similarity analysis. A 150-ns MD simulation of both the NS5 RdRp apoprotein and its ligand-bound complex was conducted to assess conformational stability and dynamic behaviour. Ligand binding reduced overall protein flexibility, indicating stabilising interactions suggestive of inhibitory activity. Structural and dynamic features were examined through RMSF, SASA, Rg, and dynamic cross-correlation matrix (DCCM) analyses, which collectively revealed distinct residue correlation patterns upon ligand binding. Clustering of the MD trajectories generated 225 representative conformations, 138 from the apoprotein and 87 from the complex used for ensemble docking of 328 curcuminoid compounds. ADMET analysis further showed that compounds 1CJS and 90 possessed favourable absorption and metabolic properties, with low predicted toxicity. Among all screened ligands, compound 90 demonstrated the strongest binding affinity. Subsequent MD simulations confirmed its stable binding mode and favourable dynamic profile. MD pattern similarity analysis also showed that compound 90 closely mimics the structural and dynamic behaviour of the native ligand GTP, supporting its potential as a potent RdRp inhibitor. Overall, these findings highlight compound 90 as a promising curcuminoid derivative for further development of antiviral agents against the dengue virus.

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