Exploring Echinacea angustifolia for anti-viral compounds against Zika virus RNA-dependent RNA polymerase: a computational study

Abstract

Abstract The Zika virus (ZIKV), a member of the Flaviviridae family, has caused multiple widespread outbreaks, posing significant challenges to global health. This study explores the potential of compounds from Echinacea angustifolia (E. angustifolia) to inhibit the activity of ZIKV’s RNA-dependent RNA polymerase (RDRP), a key enzyme in the viral replication process and an ideal candidate for antiviral therapy. Utilizing computational techniques, we conducted a thorough virtual examination using the MTi-OpenScreen tool to identify potential RDRP inhibitors among E. angustifolia compounds. The top four compounds were further examined through re-docking procedures. To assess the robustness and effectiveness of these interactions, we performed molecular dynamics simulations along with calculations of the binding free energy and PCA analysis. This investigation highlighted four naturally occurring compounds, viz., Echinacoside, Rutin, Echinacin, and Cynaroside, demonstrating a notable affinity for binding to the allosteric site of ZIKV RDRP. These compounds showed strong hydrogen bond formation with crucial residues of the RDRP and presented favorable binding free energies. Our research sheds light on the viability of these E. angustifolia compounds as ZIKV RDRP inhibitors, laying a foundation for further experimental research in developing novel antiviral treatments against ZIKV infections.