The effect of dimeric bisbenzimidazoles on the activity of DNA repair enzymes TDP1, TDP2, PARP1 and PARP2

   Oncological diseases remain a leading cause of pathological mortality worldwide, making the development of anticancer drugs a critical focus in medicinal chemistry. A promising strategy to enhance therapeutic efficacy and reduce chemotherapy-induced toxicity involves the combined inhibition of DNA repair enzymes and topoisomerases. Of particular interest are minor-groove DNA ligands, which exhibit potent inhibition of DNA-dependent enzymes while having low toxicity and mutagenicity. A number of research groups, including ours, are developing inhibitors of DNA repair enzymes that act simultaneously on several targets: tyrosyl-DNA phosphodiesterase 1/2 (TDP1/TDP2), poly(ADP-ribose) polymerase 1 (PARP1)/TDP1, topoisomerase 1 (TOP1)/TDP1. Such bifunctional inhibitors are designed to resolve the problem of tumor cell resistance to known chemotherapy drugs and increase the effectiveness of the latter. In this study, we evaluated the inhibitory activity of 22 minor-groove DNA ligands – bis- and trisbenzimidazoles against four key repair enzymes: TDP1, TDP2, PARP1, and PARP2. Four series of dimeric compounds and their monomeric units were studied. The difference in inhibitory activity of dimeric bisbenzimidazoles depending on the structure of the compound and the enzyme is shown. Our findings reveal distinct structure-activity relationships, with monomeric and dimeric ligands exhibiting potent TDP1 inhibition at micromolar to submicromolar IC50 values (half-maximal inhibitory concentration). Notably, dimeric compounds from the DB2Py(n) and DB3P(n) series demonstrated superior TDP1 inhibition compared to their monomers. In contrast, all tested compounds showed negligible activity against the other three repair enzymes; so, the compounds demonstrate specificity to TDP1. It should be noted that in this work, in the experiments with TDP1 and TDP2, the effect of the tested compounds as narrow-groove ligands binding to DNA was excluded, and their direct effect on the enzyme was investigated. The results of molecular docking suggest the possibility of direct interaction of active compounds with the active center of TDP1. According to the results of modeling, the inhibitors are located in the binding region of the 3’-end of DNA in the active site of TDP1 and could form stable bonds with the catalytically significant TDP1 residues His263 and His493. These interactions probably provide the high inhibitory activity of the compounds observed in biochemical experiments.

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