Unveiling the antiviral potential of Plant compounds from the Meliaceae family against the Zika virus through QSAR modeling and MD simulation analysis

Abstract

Zika virus (ZIKV) is a flavivirus transmitted by mosquitoes, causing neurological disorders and congenital malformations. RNA-dependent RNA polymerase (RdRp) is one of its essential enzymes and a promising drug target for antiviral therapy due to its involvement in the growth and multiplication of the virus. In this study, we conducted a QSAR-based chemical library screening from the Meliaceae family to identify potential RdRp inhibitors. The QSAR model was built using the known inhibitors of RdRp NS5 of ZIKV and their biological activity (EC50), along with the structural and chemical characteristics of the compounds. The top two hit compounds were selected from QSAR screening for further analysis using molecular docking to evaluate their binding energies and intermolecular interactions with RdRp, including the critical residue Trp⁴⁸⁵. Furthermore, molecular dynamics (MD) simulations were performed to evaluate their binding stability and flexibility upon binding to RdRp. The MD results showed that the selected compounds formed stable complexes with RdRp, and their binding interactions were similar to those observed for the native ligand. The binding energies of the top two hits (-8.6 and −7.7 kcal/mole) were comparable to those of previously reported ZIKV RdRp inhibitors (-8.9 kcal/mole). The compound IMPHY009135 showed the strongest binding affinity with RdRp, forming multiple hydrogen bonds and hydrophobic interactions with key residues. However, compound IMPHY009276 showed the most stable and consistent RMSD, which was similar to the native ligand. Our findings suggest that IMPHY009135 and IMPHY009276 are potential lead compounds for developing novel antiviral agents against ZIKV.

Communicated by Ramaswamy H. Sarma

Keywords:

• Zika virus
• RdRp
• virtual screening
• docking
• molecular dynamics simulation

Disclosure statement

The authors declare no conflict of interest.

Authors’ contributions

Conceptualization, D.S., A.M.A., S.P.P., and M.A.K.; Data curation, D.S., and S.P.P.; Formal analysis, D.S., A.M.A., and S.P.P., Investigation, D.S., A.M.A., and M.A.K.; Methodology, D.S., A.M.A., S.P.P., and M.A.K; Supervision, A.M.A., and M.A.K.; Validation, D.S., A.M.A., S.P.P., and M.A.K.; Visualization, D.S., A.M.A., S.P.P., and M.A.K., Writing—original draft, D.S.; Writing—review & editing, D.S., A.M.A., S.P.P., and M.A.K.

Additional information

Funding

This work was funded by the researchers supporting project number (RSP2023R261) King Saud University, Riyadh, Saudi Arabia.