Evaluation of antiviral activity of piperazine against Chikungunya virus targeting hydrophobic pocket of alphavirus capsid protein

•Three-dimensional structure of capsid protein (CP) of Aura virus in complex with piperazine determined at 2.2 Å resolution.•Piperazine binds to the hydrophobic pocket of Aura virus CP (AVCP).•Molecular docking studies confirmed the binding of piperazine to the hydrophobic pocket of Chikungunya virus CP (CVCP).•Piperazine reduces CHIKV load in Vero cells as assessed by immunofluorescence and plaque reduction assay.•Current study suggests the potential of piperazine and piperazine based derivatives as anti-alphaviral drugs.

Small heterocyclic molecules such as piperazine are potential pharmacotherapeutic agents and binding of these molecules to the hydrophobic pocket of capsid protein (CP) offers a new perspective for therapeutic intervention. Here, we report the crystal structure of CP from Aura virus (AVCP) in complex with piperazine at 2.2 Å resolution. Piperazine binds to the conserved hydrophobic pocket of CP where dioxane based antivirals bind. Comparative structural studies of the piperazine-bound AVCP structure with the apo, active and dioxane-bound AVCP structures provide insights into the conformational variations in the pocket. Additionally, the molecular docking studies showed that piperazine binds into the hydrophobic pocket of Chikungunya virus CP (CVCP) with more affinity than with AVCP. Furthermore, the antiviral activity of piperazine against Chikungunya virus (CHIKV) was investigated by plaque reduction and immunofluorescence assays. The AVCP-piperazine complex may serve as a lead scaffold for structure-based design of piperazine derivatives as alphaviral inhibitors. The antiviral properties of piperazine provide its usefulness for further investigations towards the development of piperazine based anti-alphaviral drugs.