Comparative study of two cephalosporin antibiotics binding to calf thymus DNA by multispectroscopy, electrochemistry, and molecular docking

Huang, Sheng Chao; Cheng, Li Yang; Yang, Jing; Hu, Yan

doi:10.1002/bio.3696

Cited by 8 publications

(4 citation statements)

References 37 publications

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“…AutoDock 1.5.6 software was used to dock small molecules/ligands into target DNA with spatial conformational matching, energetic matching, and microenvironmental aligning. [87][88][89][90] The scoring algorithm was utilized to examine and acquire the best docking findings that could represent intermolecular interaction coherently. [91] We used PDB identifiers 5M68 for AT duplex DNA and 1D16 for GC duplex DNA to choose two oligonucleotides with similar GC content.…”

Section: Molecular Dockingmentioning

confidence: 99%

Deciphering binding affinity, energetics, and base specificity of plant alkaloid Harmane with AT and GC hairpin duplex DNA

2022

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Insights into binding efficacy and thermodynamic aspects of small molecules are important for rational drug designing and development. Here, the interaction of Harmane (Har), a very important bioactive indole alkaloid, with AT and GC hairpin duplexÀDNAs has been reported using various biophysical tools. Detailed molecular mechanism with special emphasis on binding nature, base specificity, and thermodynamics have been elucidated via probing nucleic acids with varying base compositions. Har bound to both the DNA strands exhibited hypochromic effect in absorbance whereas bathochromic and hypochromic effects in fluorescence spectra.The binding constants estimated were in the order of 10 5 M À1 (higher for GC sequence compared with AT) with 1:1 stoichiometry. Noncooperative binding mode has been observed via intercalation in both the cases. The thermodynamic profile was obtained from temperature-dependent fluorescence experiments. Both Har-AT and Har-GC complexations were exothermic in nature associated with positive entropy and negative enthalpy changes. Salt-dependent studies revealed that the binding interaction was governed by nonpolyelectrolytic and hydrophobic interaction forces. The ligand-induced structural perturbation of the DNA structures was evident from the circular dichroism data. Molecular modelling data indicated towards the involvement of hydrophobic forces and hydrogen bonding.

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Section: Molecular Dockingmentioning

confidence: 99%

Deciphering binding affinity, energetics, and base specificity of plant alkaloid Harmane with AT and GC hairpin duplex DNA

2022

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“…The effect of DNP on the MB–DNA/Hoechst 33258–DNA complex was observed by measuring fluorescence intensity. [ 27 ] DNP concentrations of the solution increased from 0 to 6 × 10 −3 mol·L −1 . A displacement assay for Hoechst 33258 was recorded in the fluorescence emission spectra range (410–570 nm) with an excitation wavelength at 352 nm.…”

Section: Methodsmentioning

confidence: 99%

Exploring the binding mode of donepezil with calf thymus DNA using spectroscopic and molecular docking methods

et al. 2020

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Donepezil (DNP) is one of approved drugs to treat Alzheimer's disease (AD). However, the potential effect of DNP on DNA is still unclear. Therefore, the interaction of DNP with calf thymus DNA (DNA) was studied in vitro using spectroscopic and molecular docking methods. Steady‐state and transient fluorescence experiments showed that there was a clear binding interaction between DNP and DNA, resulting from DNP fluorescence being quenched using DNA. DNP and DNA have one binding site between them, and the binding constant (Kb) was 0.78 × 104 L·mol−1 at 298 K. In this binding process, hydrophobic force was the main interaction force, because enthalpy change (ΔH) and entropy change (ΔS) of DNP–DNA were 67.92 kJ·mol−1 and 302.96 J·mol−1·K−1, respectively. DNP bound to DNA in a groove‐binding mode, which was verified using a competition displacement study and other typical spectroscopic methods. Fourier transform infrared (FTIR) spectrum results showed that DNP interacted with guanine (G) and cytosine (C) bases of DNA. The molecular docking results further supported the results of spectroscopic experiments, and suggested that both Pi‐Sigma force and Pi‐Alkyl force were the major hydrophobic force functioning between DNP and DNA.

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“…Therefore, the interaction of drug and DNA has become a hotspot for researchers in recent years. [ 8–10 ]…”

Section: Introductionmentioning

confidence: 99%

“…Therefore, the interaction of drug and DNA has become a hotspot for researchers in recent years. [8][9][10] This encouraged us to utilize multispectroscopy methods coupled with molecular modelling to elucidate the binding mode and binding mechanism of tiamulin with DNA. The comprehensive conformation analysis of DNA is useful for understanding biological complications and the genomics of disease mechanisms.…”

mentioning

confidence: 99%

Exploring the intercalation binding of tiamulin with DNA using multispectroscopy and a molecular modelling approach

Wang

et al. 2022

Luminescence

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The binding of tiamulin with calf thymus DNA was systematically investigated using multispectroscopy and molecular modelling techniques. For DNA, once tiamulin was added, viscosity (η) and melting temperature (Tm) both exhibited an uptrend. The fluorescence performance of the tiamulin–DNA complex did not change with the ionic strength changes. The binding constant (Ka) of tiamulin for single‐stranded DNA (ssDNA, 1.48 × 104 M−1) was obviously higher than that for double‐stranded DNA (dsDNA, 9.51 × 103 M−1) at 291 K. The helix structure became looser and the base stack force became stronger for DNA due to the presence of tiamulin as seen from circular dichroic (CD) spectra. The intercalation binding mode of tiamulin with DNA was disclosed. Molecular modelling also revealed tiamulin inserting into the base pairs with the lowest binding free energy of −18.73 kJ mol−1 using van der Waals forces as well as hydrogen bonds.

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Comparative study of two cephalosporin antibiotics binding to calf thymus DNA by multispectroscopy, electrochemistry, and molecular docking

Cited by 8 publications

References 37 publications

Deciphering binding affinity, energetics, and base specificity of plant alkaloid Harmane with AT and GC hairpin duplex DNA

Deciphering binding affinity, energetics, and base specificity of plant alkaloid Harmane with AT and GC hairpin duplex DNA

Exploring the binding mode of donepezil with calf thymus DNA using spectroscopic and molecular docking methods

Exploring the intercalation binding of tiamulin with DNA using multispectroscopy and a molecular modelling approach

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