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


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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 ΔGpred. Additionally, our results demonstrated the highest affinity for molecules carrying substituent groups of–OCH3 and–CH3.

Sobre autores

Mohsen Sargolzaei

Department of Chemistry

Autor responsável pela correspondência
Email: mohsen.sargolzaei@gmail.com
Irã, Shahrood

Mahdi Afshar

Materials Simulation Laboratory, Department of Physics

Email: mohsen.sargolzaei@gmail.com
Irã, Narmak, Tehran, 16345

Hossein Nikoofard

Department of Chemistry

Email: mohsen.sargolzaei@gmail.com
Irã, Shahrood

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