Structural Insight into Groove Binding of Yohimbine with Calf Thymus DNA: A Spectroscopic, Calorimetric, and Computational Approach

A variety of anticancer and antibacterial drugs targetDNA as oneof their primary intracellular targets. Understanding ligand-DNAinteractions and developing new, promising bioactive molecules forclinical use are greatly aided by elucidating the interaction betweensmall molecules and natural polymeric DNAs. Small molecules ' ability to attach to and inhibit DNA replication and transcriptionprovides more information on how drugs impact the expression of genes.Yohimbine has been broadly studied in pharmacological properties,while its binding mode to DNA has not been explicated so far. In thisstudy, an attempt was made to explore the interaction between Yohimbine(YH) and calf thymus (CT-DNA) by using varying thermodynamics and in silico approaches. Minor hypochromic and bathochromicshifts of fluorescence intensity were observed, suggesting the bindingof YH to CT-DNA. The Scatchard plot analysis using the McGhee-vonHipple method revealed noncooperative binding and affinities in therange of 10(5) M-1. The binding stoichiometryvalue is 2:1 (2 molecules of YH were span by 1 base pair) and wasdetermined by Job's plot. The thermodynamic parameters suggestedexothermic binding, which was favored by negative enthalpy and positiveentropy changes from both isothermal titration calorimetry and temperature-dependentfluorescence experiment. Salt-dependent fluorescence suggested thatthe interaction between the ligand and DNA was governed by nonpolyelectrolyticforces. Kinetics experiment confirmed the static type of quenching.The results of iodide quenching, urea denaturation assay, dye displacement,DNA melting, and in silico molecular docking (MD)suggested groove binding of YH to CT-DNA. Circular dichroism spectraconfirmed minimal perturbation of CT-DNA with YH binding via grooveregion. Therefore, the groove binding mechanism of interaction wasvalidated by biophysical techniques and in silico, MD approaches. The findings supported here may contribute to thedevelopment of new YH therapeutics possessing better efficacy andlesser side effects.

Automated summary

A study was conducted to explore the interaction between Yohimbine (YH) and calf thymus DNA (CT-DNA). The results showed that YH can bind to CT-DNA, and the binding is of the static quenching type.