Russian Journal of Bioorganic Chemistry

, Volume 43, Issue 4, pp 435–442 | Cite as

Molecular dynamics simulation study of binding affinity of thieno[2,3-b]benzo[1,8]naphthyridine derivatives to DNA

  • Mohsen SargolzaeiEmail author
  • Mahdi Afshar
  • Hossein Nikoofard


DNA binding position and binding affinity of drugs are important information that helps medicinal chemists in synthesis of new drugs. We used molecular docking and molecular dynamics simulation to reveal binding strength of thieno[2,3-b]benzo[1,8]naphthyridine derivatives to DNA. Molecular docking showed that molecules with more steric hindrance select groove position in DNA structure. Other molecules are intercalated between base pairs of GC and AT. Restrained electrostatic potential (RESP) charges, root mean square deviation (RMSD), and total potential analyses were performed. RMSD and total potential analyses showed that all simulations have stability for MMGBSA analysis. Binding affinity of all drugs was derived via MMGBSA analysis. Thermodynamics analysis showed that binding affinity of groove binding drugs is less than that of intercalating ones. Also, it was found that a linear relationship exists between RESP charges and ΔG pred. Additionally, our results demonstrated the highest affinity for molecules carrying substituent groups of–OCH3 and–CH3.


molecular dynamics docking calfthymus DNA Gibbs free energy of binding 


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Copyright information

© Pleiades Publishing, Ltd. 2017

Authors and Affiliations

  • Mohsen Sargolzaei
    • 1
    Email author
  • Mahdi Afshar
    • 2
  • Hossein Nikoofard
    • 1
  1. 1.Department of ChemistryShahrood University of TechnologyShahroodIran
  2. 2.Materials Simulation Laboratory, Department of PhysicsIran University of Science and TechnologyNarmak, TehranIran

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