Albany 2013: Book of Abstracts

category image Albany 2013
Conversation 18
June 11-15 2013
©Adenine Press (2012)

A new series of biologically active DNA minor groove binders based on bisbenzimidazole and benzimidazole-pyrrole motives

As we reported earlier, dimeric bisbenzimidazoles DB(n) (Ivanov et al., 2011a) were able to non-covalently bind in the DNA minor groove and displayed inhibitory activity at low concentrations toward three different DNA-dependent enzymes (Susova et al., 2010; Ivanov et al., 2011b; Cherepanova et al., 2011; Tunitskaya et al., 2011). However, these compounds had a substantial drawback: a low solubility in water solutions, which prevent their potential use in vivo as biologically active preparations. Therefore, for the new minor groove binder series, additional groups were added into the molecule structures for the sake of hydrophility and DNA affinity improvement. A DBP(n) series contains piperazine cycle in the oligomethylene linker which connects bisbenzimidazole fragments of molecule together. A DBPy(n) series have a pyrrole and benzimidazole cycles combination in their structure (Figure 1).


Figure 1: Structures of dimeric bisbenzimidazoles of DB(n), DBP(n) and DBPy(n) series.

Compounds DBP(n) (n = 1-4) were studied as inhibitors of calf thymus DNA topoisomerase I (topo-I). All of them inhibited topo-I activity at 1-5 μM concentrations, besides, at concentrations over 5 μM, the inhibitory activities of DBP(n) were few times higher than that of DB(n).

It was found that dimeric bisbenzoimidazoles DBP(1-3) were not mutagenic. They were inactive in the point mutagenesis assessment using the Ames test (with Salmonella Typhimurium bacteria as the tested object) and did not display mutagenic or recombinogenic properties in the Drosophila wing somatic mutation and recombination test (SMART). All the compounds of series were evaluated for cytotoxicity in the MTT test on breast cancer MCF-7, large bowel adenocarcinoma HCT-116, noncancer HEK-293 cell lines and on primary murine fibroblasts. All the tested DBP(n) were not toxic up to concentrations of 100 μM. Contrary the one tested compound from DBPy(n) series - DBPy(4) (n = 4) showed substantial cytotoxicity against cancer HCT-116 and human leukemic K-562 cell lines with an IC50 of 1-2 μM.

Judging by the combination of such criterions as water solubility, topo-I inhibition activity and mutagenicity it would be safe to assume that dimeric bisbenzoimidazoles of DBP(n) series are more perspective minor groove binders than previously synthesized DB(n).

The work was supported by RFBR (Grants 11-04-00589 and 12-04-31599) and by the program of the Presidium of the Russian Academy of Sciences “Molecular and Cellular Biology” and the “Protek” fund.


    A. A. Ivanov, V. I. Salyanov, S. A. Streltsov, N. A. Cherepanova, E. S. Gromova, & A. L. Zhuze. (2011). Synthesis of fluorescent biologicaly active dimeric bisbenzimidazoles – DB(3, 4, 5, 7, 11). Russ J. Bioorgan Chemistry 37, 472-482.

    O. Y. Susova, A. A. Ivanov, S. S. Morales Ruiz, E. A. Lesovaya, A. V. Gromyko, S. A. Streltsov, & A. L. Zhuze. (2010). Minor groove dimeric bisbenzimidazoles inhibit in vitro DNA binding to eukaryotic DNA topoisomerase I. Biochemistry (Moscow) 75, 695-701.

    A. A. Ivanov, S. A. Streltsov, V. I. Salyanov, O. Y. Susova, E. S. Gromova, & A L. Zhuze. (2011). Minor groove ligands based on dimeric bisbenzimidazoles as inhibitors of DNA- dependent enzymes. J Biomol Struct Dyn 28, 1131-1132.

    N. A. Cherepanova, A. A. Ivanov, D. V. Maltseva, A. S. Minero, A. V.Gromyko, S. A. Streltsov, A. L. Zhuze, & E. S. Gromova. (2011). Dimeric bisbenzimidazoles inhibit the DNA methylation catalyzed by the murine Dnmt3a catalytic domain. J Enzyme Inhib Med Chem 26, 295-300.

    V. L. Tunitskaya, A. V. Mukovnya, A. A. Ivanov, A. V. Gromyko, A. V. Ivanov, S. A. Streltsov, A. L. Zhuze & S. N. Kochetkov. (2011). Inhibition of the helicase activity of the HCV NS3 protein by symmetrical dimeric bis-benzimidazoles. Bioorg Med Chem Lett 21, 5331-5335.

Alexander A. Ivanov1*
Olga Yu. Susova1
Victor I. Salyanov2
Kirill I. Kirsanov1
Alexei L. Zhuze2

1Institute of Carcinogenesis Blokhin Cancer Research Center
Russian Academy of Medical Sciences
Kashirskoye Shosse 24
Moscow 115478, Russia
2Engelhardt Institute of Molecular Biology
Russian Academy of Sciences
Vavilova st. 32
Moscow 119991, Russia

Ph: (7495) 324-1114
Fx: (7495) 324-1464