Characterization of the binding of paylean and DNA by fluorescence, UV spectroscopy and molecular docking techniques

Zhou, Huifeng; Bi, Shuyun; Wang, Yu; Zhao, Tingting

doi:10.1002/bio.3066

Cited by 11 publications

(4 citation statements)

References 43 publications

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“…Based on this principle, experimental scientists try to use a variety of ways to measure the amount of energy exchanged by molecular vibration with the outside world to probe the behavior of the molecular vibration. Various spectroscopic techniques were invented owing to these efforts, such as infrared (IR) spectroscopy, ultraviolet spectroscopy, Raman spectroscopy, photon fluorescence spectroscopy, cold ion spectroscopy, , etc. Because it is hardly possible to conduct a comprehensive study on the molecular vibrational behavior only using a single spectroscopic device in most cases, it is always a tough task for experimental study of the vibrational properties even for many well-known molecules.…”

Section: Introductionmentioning

confidence: 99%

Efficiently Calculating Anharmonic Frequencies of Molecular Vibration by Molecular Dynamics Trajectory Analysis

Wang

2019

ACS Omega

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Two efficient methods, the Eckart frame algorithm and the multiorder derivative algorithm, for vibrational frequency calculation directly based on the raw data of atomic trajectory from the state-of-the-art first-principles molecular dynamics simulation are presented. The Eckart frame approach is robust to retrieve the full set of anharmonic fundamental frequencies of any molecule from the atomic trajectory for a sufficiently long molecular dynamics simulation at a temperature close to 0 K. In addition to the fundamental vibrational frequencies, the multiorder derivative approach is universal for the calculations of vibrational frequencies based on the molecular dynamics result in a wide range of temperatures. The accuracy, efficiency, and applicability of these two methods are demonstrated through several successful examples in calculating the anharmonic fundamental vibrational frequencies of methane, ethylene, water, and cyclobutadiene.

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Section: Introductionmentioning

confidence: 99%

Efficiently Calculating Anharmonic Frequencies of Molecular Vibration by Molecular Dynamics Trajectory Analysis

Wang

2019

ACS Omega

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“…Spectroanalytical techniques are powerful tools in determining the method of DNA interaction and binding strength of many compounds. These include UV-visible absorption titration [12,14] , isothermal titration calorimetry [15] , fluorescence spectroscopy [11,12,14] , circular dichroism spectroscopy [12] , molecular docking studies [10,14] , cyclic voltammetry [10] , differential pulse voltammetry [10] , hydrodynamic measurement [12] , atomic force spectroscopy [16] , resonance Rayleigh scattering technique [17] and nuclear magnetic resonance. [18] In this study, due to their diverse medicinal applications, quinoline derivatives as heterocyclic N,S-donor ligands and their square planar Pd(II) complexes were synthesized and characterized.…”

Section: Introductionmentioning

confidence: 99%

“…Spectroanalytical techniques are powerful tools in determining the method of DNA interaction and binding strength of many compounds. These include UV–visible absorption titration, isothermal titration calorimetry, fluorescence spectroscopy, circular dichroism spectroscopy, molecular docking studies, cyclic voltammetry, differential pulse voltammetry, hydrodynamic measurement, atomic force spectroscopy, resonance Rayleigh scattering technique and nuclear magnetic resonance …”

Section: Introductionmentioning

confidence: 99%

Fluorescence and absorption studies of DNA–Pd(II) complex interaction: Synthesis, spectroanalytical investigations and biological activities

et al. 2019

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Novel palladium(II) complexes (7a–7e) of substituted quinoline derivatives were synthesized. The complexes were characterized using various techniques such as thermogravimetric analysis (TGA), elemental analysis, conductance measurement, mass, absorption, infra‐red (IR), 1H NMR, 13C NMR and energy‐dispersive X‐ray spectroscopy (EDX). Complexes for herring sperm DNA (HS DNA) binding were explored and absorption titration and the binding constant (Kb) as well as Gibb's free energy were evaluated. Complex 7d exhibited the highest binding constant, therefore the thermodynamic parameters of 7d at different temperatures were evaluated. To support the results of the absorption titration, fluorescence titration, viscosity measurement and molecular docking studies were performed. The fluorescence quenching data as evaluated from Stern–Volmer equation were used to calculate KSV, Kf and the number of binding sites. The results of all these studies were in good agreement with the absorption study. DNA electrophoretic mobility was performed to explore the possible application of metal complexes as artificial metallonucleases. The antibacterial activity of the complexes was accessed against different pathogenic bacteria and cytotoxicity was measured using brine shrimp and S. pombe.

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“…If the electrostatic interaction played a leading role in the binding of protein to ligands, with the concentration of salt in the system. With the increased of the interaction intensity between protein and ligand, the interaction intensity between protein and ligand decreased gradually [22] . This also indicated that when ∆H<0, ∆S>0 could not directly judge the main force between MEL-AMS system was electrostatic force.…”

Section: Type Of Interaction Force Of Mel-ams Systemmentioning

confidence: 99%

Spectroscopic study on the mechanism of meloxicam and α-amylase

Cheng

Liu

Zhang

2019

J Pharm Biopharm Res

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In order to explore the mechanism of action of meloxicam and α-amylase. The interaction between the rheumatoid arthritis drug meloxicam and α-amylase was studied by fluorescence spectroscopy, synchronous fluorescence spectroscopy and molecular docking under the experimental conditions of pH=6.80. The results showed that meloxicam was able to effectively quench the endogenous fluorescence of α-amylase in a static quenching form a 1:1 complex and change the conformation of α-amylase. Thermodynamic results indicated that the main type of meloxicam and α-amylase system was hydrophobic interaction. Molecular docking indicated that the binding system had hydrogen bonds in addition to hydrophobic interaction and meloxicam was surrounded by the active amino acid residues Trp13 and Trp263 of α-amylase, which changed the microenvironment of amino acid residues at the active center of α-amylase. By establishing the binding model, it can be seen that the protein binding rate W(B) of meloxicam to-amylase was 2.76%-41.79% under the experimental conditions. The results showed that the binding of meloxicam to-amylase had an effect on the number of free-amylase. The drug binding rate W(Q) of the system was 2.76%-1.67%, which indicated that the combination of α-amylase and meloxicam would not affect the efficacy of meloxicam.

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Characterization of the binding of paylean and DNA by fluorescence, UV spectroscopy and molecular docking techniques

Cited by 11 publications

References 43 publications

Efficiently Calculating Anharmonic Frequencies of Molecular Vibration by Molecular Dynamics Trajectory Analysis

Efficiently Calculating Anharmonic Frequencies of Molecular Vibration by Molecular Dynamics Trajectory Analysis

Fluorescence and absorption studies of DNA–Pd(II) complex interaction: Synthesis, spectroanalytical investigations and biological activities

Spectroscopic study on the mechanism of meloxicam and α-amylase

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