Ukr.Biochem.J. 2012; Volume 84, Issue 5, Sep-Oct, pp. 38-47

Novel hybrid inhibitors of the phage T7 RNA polymerase: synthesis, docking and screening in vitro

V. G. Kostina, L. G. Palchykovska, M. O. Platonov,
О. V. Vasylchenko, N. A. Lysenko, I. V. Alexeeva

Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv,
e-mail: L.

A number of new hybrid heteroaromatic compounds, consisting of tricyclic fragments (acridone, thioxanthone and phenazine) and bicyclic fragments (benzimidazole, benzothiazole and benzoxa­zole) were synthesized using the method, developed by the authors. As a result of screening against the transcription model system of the phage T7 DNA-dependent RNA polymerase three effective inhibitors of the RNA syntheses with the IC50 value­ of 8.9, 5.7 and 19.8 µM were detected. To cast light on the mode of interaction between the synthesized compounds and the target, the molecular docking was applied to the model pocket of the phage Т7 RNA polymerase transcription complex. It was established that these ligands form networks of H-bonds with residues of the pocket conservative amino acids and π-interaction with the Mg2+ ion. A planar geometry of the hybrid molecules, realized due to the intramolecular H-bonds, proved to be an important structural feature, which correlates with an efficacious inhibitory activity.

Keywords: , , , , , , ,

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