Structural and thermodynamic analysis of the binding of tRNAphe by the putative anticancer alkaloid chelerythrine: Spectroscopy, calorimetry and molecular docking studies

Abstract

The interaction of the putative anticancer alkaloid chelerythrine with tRNAphe was characterized by spectroscopy, calorimetry and molecular docking studies. The charged iminium form of chelerythrine binds with tRNAphe in a cooperative mode with a binding affinity value of (4.06±0.01)×105M−1. The neutral alkanolamine form does not bind to tRNAphe but in the presence of high concentration of tRNAphe this form gets converted to the iminium form and then binds with tRNAphe. The partial intercalative mode of binding of chelerythrine to the tRNAphe was characterized from the steady state anisotropy, iodide ion-induced fluorescence quenching and viscosity measurements. Chelerythrine binding induced conformational perturbations in tRNAphe as observed from the circular dichroism spectroscopy. The strong binding was also supported by the ethidium bromide displacement assay. The binding was favoured by both enthalpy and entropy contributions. Although the binding was dependent on the [Na+], non-electrostatic forces contributed predominantly to the Gibbs energy change. The negative value of the heat capacity change proposed the involvement of hydrophobic forces in the binding. Molecular docking study was carried out to decipher the details of the recognition of tRNAphe by chelerythrine. The study provided insights about the chelerythrine binding pockets on tRNAphe and marked the necessary interactions for binding of chelerythrine molecule. Partially intercalative mode of the alkaloid binding was supported by docking studies. In total, docking studies corroborated well with our experiential observations. The structural and thermodynamic results of chelerythrine binding to tRNAphe may be helpful to develop new RNA therapeutic agents.