Concentration-dependent mode of binding of drug oxatomide with DNA: multi-spectroscopic, voltammetric and metadynamics simulation analysis

Ponkarpagam, S.; Mahalakshmi, G.; Vennila, K.N.; Elango, Kuppanagounder P.

doi:10.1080/07391102.2021.1911860

Cited by 19 publications

(7 citation statements)

References 33 publications

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“…According to reports, when small molecules interact with DNA via intercalation mode, lengthening of the DNA chain occurs, which in turn increases the viscosity, whereas groove binding causes bending of the DNA helix rather than lengthening, which offers very minor or even no change in the viscosity. 53 By considering these facts, viscosity experiments were carried out using an Ubbelohde viscometer at a fixed temperature of 25 °C (0.01), where the flow time was used to determine the viscosity of DNA with increasing concentration of ligand 7g. The solution's relative viscosity was calculated by using the viscosity equation (eq 4) shown below…”

Section: ■ Results and Discussionmentioning

confidence: 99%

Visible Light-Prompted Regioselective Synthesis of Novel 5-Aroyl/hetaroyl-2′,4-dimethyl-2,4′-bithiazoles as DNA- and BSA-Targeting Agents

Aggarwal,

Jain,

Dubey

et al. 2023

Biomacromolecules

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Organic transformations mediated by visible light have gained popularity in recent years as they are green, renewable, inexpensive, and clean and yield excellent products. The present study describes cyclo-condensation of 2-methylthiazole-4-carbothioamide with differently substituted α-bromo-1,3-diketones achieved by utilizing a white light-emitting diode (LED) (9W) to accomplish the regioselective synthesis of novel 5-aroyl/hetaroyl-2′,4-dimethyl-2,4′-bithiazole derivatives as DNA/bovine serum albumin (BSA)-targeting agents. The structure characterization of the exact regioisomer was achieved unequivocally by heteronuclear two-dimensional nuclear magnetic resonance (2D-NMR) spectroscopy [1H–13C] HMBC; [1H–13C] HMQC; and [1H–15N] HMBC. In silico toxicity studies indicated that the synthesized compounds exhibit low toxicity risks and adhere to the rules of oral bioavailability without any exception. Computational molecular modeling of the bithiazole derivatives with the dodecamer sequence of the DNA duplex and BSA identified 5-(4-chlorobenzoyl)-2′,4-dimethyl-2,4′-bithiazole 7g as the most suitable derivative that can interact effectively with these biomolecules. Furthermore, theoretical results concurred with the ex vivo binding mode of the 7g with calf thymus DNA (ct-DNA) and BSA through a variety of spectroscopic techniques, viz., ultraviolet–visible (UV–visible), circular dichroism (CD), steady-state fluorescence, and competitive displacement assay, along with viscosity measurements.

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Section: ■ Results and Discussionmentioning

confidence: 99%

Visible Light-Prompted Regioselective Synthesis of Novel 5-Aroyl/hetaroyl-2′,4-dimethyl-2,4′-bithiazoles as DNA- and BSA-Targeting Agents

Aggarwal,

Jain,

Dubey

et al. 2023

Biomacromolecules

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“…These observations indicated that L2 binds to CT-DNA through the intercalation mode. [35][36][37][38] 2.2.7. KI quenching study.…”

Section: Dna Binding Studiesmentioning

confidence: 99%

N,N′,N′′-Trisubstituted guanidine derivatives as DNA-intercalators: synthesis, crystal structures and biophysical investigations

Durga Priyadharshini,

Sathishkumar,

Bensingh

et al. 2023

New J. Chem.

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“…However, the fluorescence intensity of EtBr increases appreciably when it settles between base pairs as a result of interaction with DNA. [31] Therefore, in competitive experiments of small molecules with intercalative binding mode with the EtBr-DNA complex, it is expected that the small molecule will push EtBr from DNA bases, resulting in a substantial reduction in fluorescence intensity of EtBr-DNA complex and quenching. The severity of the decrease in the fluorescence intensity of the EB-DNA system is related to the degree of mixing of the small molecule into the DNA.…”

Section: Competitive Binding Assaymentioning

confidence: 99%

DNA‐Binding Studies of Ofloxacin Using a Series of Spectroscopic, Electrochemical Techniques and in Silico Approaches

Çeşme¹,

Özaltay²

2022

ChemistrySelect

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Ofloxacin (OFL), a quinolone antibiotic, shows a bactericidal effect by inhibiting the DNA gyrase enzyme in bacteria. In addition to its use in various infections has a wide range of benefits from urinary system disorders to pneumonia and bronchitis. DNA is the main molecular target for many small molecules of therapeutic importance. In this article, the interaction between OFL and fsDNA (fish sperm DNA) is reported using a combination of biophysical (spectroscopic and electrochemical) and in silico techniques (molecular docking and molecular dynamics). The interaction and complex formation were studied using UV-visible and steady-state fluorescence spectroscopy. Ethidium bromide (EtBr), Rhodamine B (RB) competitive displacement, potassium iodide quenching, and ionic strength assays confirmed the binding mode between OFL and DNA via minor groove binding. Thermodynamic parameters at various temperatures supported the enthalpically driven, exothermic, and spontaneous reaction between OFL and fsDNA. It was found that hydrogen bond interaction and van der Waals forces play a dominant role in forming the complex form. DNA melting experiments corroborated these findings. In-silico molecular docking and molecular dynamics simulation studies revealed the interaction mode, major stabilizing forces, and the nucleotide sequences OFL binds and dock into the GC-rich region of the DNA minor groove, confirming the in vitro experiment results.

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Concentration-dependent mode of binding of drug oxatomide with DNA: multi-spectroscopic, voltammetric and metadynamics simulation analysis

Cited by 19 publications

References 33 publications

Visible Light-Prompted Regioselective Synthesis of Novel 5-Aroyl/hetaroyl-2′,4-dimethyl-2,4′-bithiazoles as DNA- and BSA-Targeting Agents

Visible Light-Prompted Regioselective Synthesis of Novel 5-Aroyl/hetaroyl-2′,4-dimethyl-2,4′-bithiazoles as DNA- and BSA-Targeting Agents

N,N′,N′′-Trisubstituted guanidine derivatives as DNA-intercalators: synthesis, crystal structures and biophysical investigations

DNA‐Binding Studies of Ofloxacin Using a Series of Spectroscopic, Electrochemical Techniques and in Silico Approaches

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