Unraveling the coptisine–ctDNA binding mechanism by multispectroscopic, electrochemical and molecular docking methods

Mi, Ran; Bai, Xiao-Ting; Tu, Bao; Hu, Yanjun

doi:10.1039/c5ra08790b

Cited by 31 publications

(28 citation statements)

References 36 publications

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“…(A), the absorption peak of ctDNA at 258 nm decreased gradually accompanied by a blue‐shift of about 2 nm with increasing concentration of 5‐HMF. The transfer of negative charge from 5‐HMF to ctDNA meant that the π–π* transition needed more energy, thus the absorption peak of ctDNA exhibited a mild blue‐shift (2 nm), and the binding between 5‐HMF and ctDNA caused a change of ctDNA structure accompanied by a decrease in the peak intensity . The binding constants ( K a ) between 5‐HMF and ctDNA at 292, 298, 304 and 310 K were determined according to the equation

\begin{matrix} Δ A & = \frac{Δ ϵ}{2} \cdot ([, ((), C_{5 ‐ normalHMF, 0} + C_{ctDNA, 0} + \frac{1}{K_{normala}})) \\ (], \pm \sqrt{{(C_{5 ‐ HMF, 0} + C_{ctDNA, 0} + \frac{1}{K_{a}})}^{2} - 4 C_{5 ‐ normalHMF, 0} C_{ctDNA, 0}}) \end{matrix}

…”

Section: Resultsmentioning

confidence: 74%

“…The transfer of negative charge from 5-HMF to ctDNA meant that the -* transition needed more energy, thus the absorption peak of ctDNA exhibited a mild blue-shift (2 nm), and the binding between 5-HMF and ctDNA caused a change of ctDNA structure accompanied by a decrease in the peak intensity. 32 The binding constants (K a ) between 5-HMF and ctDNA at 292, 298, 304 and 310 K were determined according to the equation 33…”

Section: Analysis Of Binding Constant and Thermodynamic Propertiesmentioning

confidence: 99%

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Exploring the binding interaction of Maillard reaction by‐product 5‐hydroxymethyl‐2‐furaldehyde with calf thymus DNA

Zhou

Zhang

et al. 2019

J Sci Food Agric

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BACKGROUND 5‐Hydroxymethyl‐2‐furaldehyde (5‐HMF), a by‐product of the Maillard reaction, usually present in fried and baked food, may cause potential harm to the human body. Here, the interaction between 5‐HMF and calf thymus DNA (ctDNA) under physiological buffer (pH 7.4) was studied using multi‐spectroscopic methods combined with multivariate curve resolution–alternating least squares (MCR‐ALS) chemometrics and molecular simulation techniques. RESULTS The concentration profiles and pure spectra of the three components (5‐HMF, ctDNA and 5‐HMF–ctDNA complex) were extracted from highly overlapping spectra using MCR‐ALS analysis, which verified the formation of 5‐HMF–ctDNA complex. The binding constant being of the order of 103 L mol−1 at four temperatures (292, 298, 304 and 310 K) indicated a weak affinity in the binding of 5‐HMF to ctDNA. The binding interaction was mainly driven by hydrogen bonds and van der Waals forces. Viscosity analysis, melting assay, ionic strength effect and competitive fluorescence studies ascertained that 5‐HMF bound to ctDNA through groove binding, and it tended to bind to guanine–cytosine rich region of ctDNA which was characterized using Fourier transform infrared spectra and molecular docking. Circular dichroism spectral analysis and DNA cleavage assays indicated that the ctDNA conformation was altered from B to A form and 5‐HMF caused DNA damage at higher concentration. CONCLUSIONS The results suggested that 5‐HMF bound to ctDNA through groove binding and caused DNA damage. This research may contribute to understand the binding mechanism of 5‐HMF to ctDNA and to the assessment of the toxicological effect of 5‐HMF in biological processes. © 2018 Society of Chemical Industry

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\begin{matrix} Δ A & = \frac{Δ ϵ}{2} \cdot ([, ((), C_{5 ‐ normalHMF, 0} + C_{ctDNA, 0} + \frac{1}{K_{normala}})) \\ (], \pm \sqrt{{(C_{5 ‐ HMF, 0} + C_{ctDNA, 0} + \frac{1}{K_{a}})}^{2} - 4 C_{5 ‐ normalHMF, 0} C_{ctDNA, 0}}) \end{matrix}

…”

Section: Resultsmentioning

confidence: 74%

Section: Analysis Of Binding Constant and Thermodynamic Propertiesmentioning

confidence: 99%

Exploring the binding interaction of Maillard reaction by‐product 5‐hydroxymethyl‐2‐furaldehyde with calf thymus DNA

Zhou

Zhang

et al. 2019

J Sci Food Agric

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“…Molecular docking technique is one of the promising tools by placing a small molecule of drugs into the binding sites of the targeted macromolecules for rational drug designing and discovery. If the binding free energy is low, the potential of binding is more between the desired compound and the receptor (target).…”

Section: Resultsmentioning

confidence: 99%

Biological contour, molecular docking and antiproliferative studies of DNA targeted histidine based transition metal(II) complexes: Invention and its depiction

Arunadevi¹,

Raman²

2018

Applied Organom Chemis

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A novel series of histidine derived transition metal complexes were synthesized and characterized by multispectral techniques such as UV-Vis., FT IR, EPR, NMR, ESI-mass analysis and other physico-chemical methods like elemental analysis, molar conductivity, magnetic susceptibility. The synthesized compounds were attempted for their biological prospective. The biological studies involved are DNA interaction (binding and damage), antimicrobial, antioxidant, antiproliferative and molecular docking. DNA interaction studies were carried out with the help of UV-Vis absorption titration, viscosity measurement and cyclic voltammetric techniques which revealed that the synthesized compounds could interact with CT-DNA through intercalative binding mode. A gel electrophoresis assay demonstrated the ability of complexes to cleave the supercoiled pUC18 DNA. The antioxidant property shows that the metal complexes have preferable ability to scavenge hydroxyl radical than the ligand.Moreover, the antimicrobial assay indicates that these complexes are good antimicrobial agents against various pathogens. Furthermore, the in vitro antiproliferative activities of the complexes were examined on HeLa, Hep G2 and NIH 3 T3 cell lines using an MTT assay. The morphological changes were investigated using Hoechst 33258 staining apoptosis assay. In addition, molecular docking studies were executed to considerate the nature of binding of the synthesized complexes with protein and DNA.

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“…[18] For dynamic quenching, the process increased temperatures and produce a faster diffusion leading to a larger dynamic quenching constant, however, higher temperatures result in dissociation of weakly bound complexes decreasing the quenching constant in the static quenching process. [18,19] To study this mechanism, we investigated the fluorescence quenching of cefalexin/cefixime to BSA at different temperatures (T = 292, 298, 304, and 310 K), using the Stern − Volmer equation.…”

Section: Fluorescence Spectroscopy Characteristicsmentioning

confidence: 99%

Probing the interaction of cephalosporin with bovine serum albumin: A structural and comparative perspective

Cheng

Yang

et al. 2017

Luminescence

Self Cite

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Cephalosporins belong the largest class of antibiotics used in the treatment of a wide range of infectious diseases caused by susceptible organisms. In the present study, we chose two typical antibiotics cefalexin/cefixime based on their structure, and investigated the interaction of cephalexin/cefixime with bovine serum albumin (BSA) using UV-vis absorption spectra, fluorescence spectroscopy, circular dichroism (CD) spectroscopy and molecular modeling approaches. Spectroscopic experiments revealed the formation of a BSA − cefalexin/cefixime complex. The binding parameters calculated using a modified Stern − Volmer method and the Scatchard method reached 10 3 -10 4 L·mol −1 . Thermodynamic parameter studies revealed that binding characteristics by negative enthalpy and positive entropy changes, and electrostatic interactions play a major role. Site marker competitive displacement experiments and molecular modeling approaches demonstrated that cefalexin and cefixime bind with appropriate affinity to site I (subdomain IIA) of BSA. Furthermore, synchronous fluorescence spectra, CD spectra and molecular modeling results indicated that the secondary structure of BSA was changed in the presence of cefalexin and cefixime. Additionally, the effects of metal ions on the BSA − cefalexin/cefixime system were also assessed.

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Unraveling the coptisine–ctDNA binding mechanism by multispectroscopic, electrochemical and molecular docking methods

Abstract: This study provides evidences of coptisine–DNA intercalation, which may help to develop new efficient, safe probes for the fluorometric detection of DNA instead of traditional toxic and carcinogenic probes.

Cited by 31 publications

References 36 publications

Exploring the binding interaction of Maillard reaction by‐product 5‐hydroxymethyl‐2‐furaldehyde with calf thymus DNA

Exploring the binding interaction of Maillard reaction by‐product 5‐hydroxymethyl‐2‐furaldehyde with calf thymus DNA

Biological contour, molecular docking and antiproliferative studies of DNA targeted histidine based transition metal(II) complexes: Invention and its depiction

Probing the interaction of cephalosporin with bovine serum albumin: A structural and comparative perspective

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