Identification and evaluation of antiviral potential of thymoquinone, a natural compound targeting Chikungunya virus capsid protein

Highlights: • Thymoquinone, a natural compound binds to the hydrophobic pocket of CHIKV CP. • Thymoquinone binding to purified CP was validated by isothermal titration calorimetry and fluorescence spectroscopy. • Cell-based antiviral assay revealed that thymoquinone diminished CHIKV replication with EC50 value of 4.478 μM. • Thymoquinone use as a broad spectrum antiviral against alphavirus has been proposed. Capsid protein (CP) of Chikungunya virus (CHIKV) is a multifunctional protein with a conserved hydrophobic pocket that plays a crucial role in the capsid assembly and virus budding process. This study demonstrates antiviral activity of thymoquinone (TQ), a natural compound targeting the hydrophobic pocket of CP. The binding of TQ to the hydrophobic pocket of CHIKV CP was analysed by structure-based molecular docking, isothermal titration calorimetry and fluorescence spectroscopy. The binding constant K_D obtained for TQ was 27 μM. Additionally, cell-based antiviral studies showed that TQ diminished CHIKV replication with an EC50 value 4.478 μM. Reduction in viral RNA copy number and viral replication as assessed by the qRT-PCR and immunofluorescence assay, confirmed the antiviral potential of TQ. Our study reveals that TQ is an effective antiviral targeting the hydrophobic pocket of CHIKV CP and may serve as the basis for development of a broad-spectrum therapy against alphaviral diseases.