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  3. The interaction mechanism of candidone with calf thymus DNA: A multi-spectroscopic and MD simulation study

The interaction mechanism of candidone with calf thymus DNA: A multi-spectroscopic and MD simulation study

  • Int J Biol Macromol. 2023 Apr 30:235:123713. doi: 10.1016/j.ijbiomac.2023.123713.
Mahvash Farajzadeh Dehkordi 1,  Sadegh Farhadian 2,  Fatemeh Hashemi-Shahraki 3,  Babak Rahmani 4,  Sina Darzi 5,  Gholamreza Dehghan 6
Affiliations

Affiliations

  • 1 Department of Molecular Medicine, Qazvin University of Medical Sciences, Qazvin, Iran; Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran.
  • 2 Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran. Electronic address: [email protected].
  • 3 Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
  • 4 Department of Molecular Medicine, Qazvin University of Medical Sciences, Qazvin, Iran; Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran. Electronic address: [email protected].
  • 5 Health Products Safety Research Center, Qazvin University of Medical Sciences, Qazvin, Iran.
  • 6 Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran.
PMID: 36801300 DOI: 10.1016/j.ijbiomac.2023.123713
Abstract

In this investigation, the effects of candidone on the structure and conformation of DNA were evaluated by spectroscopic methods, molecular dynamics simulation, and molecular docking studies. Fluorescence emission peaks, ultraviolet-visible spectra, and molecular docking exhibited the complex formation between candidone and DNA in a groove-binding mode. Fluorescence spectroscopy results also showed a static quenching mechanism of DNA in the presence of candidone. Moreover, thermodynamic parameters demonstrated that candidone spontaneously bound to DNA with a high binding affinity. The hydrophobic interactions were the dominant forces over the binding process. Based on the Fourier transform infrared data candidone tended to attach to the A-T base pairs of the minor grooves of DNA. The thermal denaturation and circular dichroism measurements displayed that candidone caused a slight change in the DNA structure, which was confirmed by the molecular dynamics simulation results. According to the obtained findings from the molecular dynamic simulation, the structural flexibility and dynamics of DNA were altered to a more extended structure.

Keywords

Calf thymus DNA; Candidone; Minor groove binding; Molecular dynamic simulation; Spectroscopy methods.

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