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

Abstract

A variety of anticancer and antibacterial drugs target DNA as one of their primary intracellular targets. Understanding ligand−DNA interactions and developing new, promising bioactive molecules for clinical use are greatly aided by elucidating the interaction between small molecules and natural polymeric DNAs. Small molecules′ ability to attach to and inhibit DNA replication and transcription provides 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 this study, 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 bathochromic shifts of fluorescence intensity were observed, suggesting the binding of YH to CT-DNA. The Scatchard plot analysis using the McGhee−von Hipple method revealed noncooperative binding and affinities in the range of 10 5 M −1 . The binding stoichiometry value is 2:1 (2 molecules of YH were span by 1 base pair) and was determined by Job's plot. The thermodynamic parameters suggested exothermic binding, which was favored by negative enthalpy and positive entropy changes from both isothermal titration calorimetry and temperature-dependent fluorescence experiment. Salt-dependent fluorescence suggested that the interaction between the ligand and DNA was governed by nonpolyelectrolytic forces. 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 spectra confirmed minimal perturbation of CT-DNA with YH binding via groove region. Therefore, the groove binding mechanism of interaction was validated by biophysical techniques and in silico, MD approaches. The findings supported here may contribute to the development of new YH therapeutics possessing better efficacy and lesser side effects.

Mechanistic investigation into the binding property of Yohimbe towards natural polymeric DNAs

“…Figure 9 A depicts the relationship between the emission intensities of the Yh to HT DNA complex in the addition and exclusion of urea (F o /F) as a result of urea concentration. A similar result has been obtained of Yh when interacting with calf thymus DNA 34 . Therefore, our result supports the groove binding mode.…”

“…This value indicates that, throughout the range of the investigated concentrations, the 2:1 binding stoichiometry for 2 Yh is spanned by 1 base pair of HT DNA. Similarly, Luikham et al also obtained 2: 1 binding for Yh with calf thymus DNA 34 . The numbers of excluded sites derived from the McGhee–Von Hipple analysis of the fluorescence data and the values of stoichiometry are in close agreement.…”

“…It is viable to monitor the interaction as Yh has a distinctive noticeable absorption spectrum in the 200–300 nm range with two significant peaks at 220 nm and 272 nm, respectively 33 . Similarly, Yh has also shown interactive properties with calf thymus DNA 34 . The electronic transition of the chromophore in both pyrimidines and purines was suggested as the basis of the maximum absorption of HT DNA at 260 nm 35 .…”

Multispectroscopic and Theoretical Investigation on the Binding Interaction of a Neurodegenerative Drug, Lobeline with Human Serum Albumin: Perturbation in Protein Conformation and Hydrophobic–Hydrophilic Surface

“…Fluorescence quenching occurs when ligands interact with fluorophores, leading to a reduction in fluorescence intensity due to alterations in photophysical properties of the fluorophores . This phenomenon can be ascribed to diverse molecular interactions, i.e., molecular rearrangement, excited state reactions, complex formation, dynamic quenching, and energy shift. , Employing fluorescence spectroscopy, HSA was excited at λ exc = 295 nm, focusing on the Trp moieties, resulting in emission spectra with a peak of 344 nm (Figure a). The steady addition of LOB to the HSA solution alters the spectra of emission, marked by a decline in intensity without an evident shift in peak.…”

“…The steady addition of LOB to the HSA solution alters the spectra of emission, marked by a decline in intensity without an evident shift in peak. The binding affinity ( K ) and binding site ( n ) are determined using fluorescence data analyzed with the Scatchard plot method (inset Figure c), the noncooperative binding model by McGhee–von Hippel . The binding constant ( K ) in 10 mM TH buffer at RT was calculated to be 4.3 × 10 5 mol –1 , indicating a moderate binding affinity.…”