DNA Minor Groove Binding-Directed Poisoning of Human DNA Topoisomerase I by Terbenzimidazoles

Abstract

We have employed a broad range of spectroscopic, calorimetric, DNA cleavage, and DNA winding/unwinding measurements to characterize the DNA binding and topoisomerase I (TOP1) poisoning properties of three terbenzimidazole analogues, 5-phenylterbenzimidazole (5PTB), terbenzimidazole (TB), and 5-(naphthyl[2,3-d]imidazo-2-yl)bibenzimidazole (5NIBB), which differ with respect to the substitutions at their C5 and/or C6 positions. Our results reveal the following significant features. (i) The overall extent to which the three terbenzimidazole analogues poison human TOP1 follows the hierarchy 5PTB > TB >> 5NIBB. (ii) The impact of the three terbenzimidazole analogues on the superhelical state of plasmid DNA depends on the [total ligand] to [base pair] ratio (rbp), having no effect on DNA superhelicity at rbp ratios < or = 0.1, while weakly unwinding DNA at rbp ratios > 0.1. This weak DNA unwinding activity exhibited by the three terbenzimidazoles does not appear to be correlated with the abilities of these compounds to poison TOP1. (iii) Upon complexation with both poly(dA).poly(dT) and salmon testes DNA, the three terbenzimidazole analogues exhibit flow linear dichroism properties characteristic of a minor groove-directed mode of binding to these host DNA duplexes. (iv) The apparent minor groove binding affinities of the three terbenzimidazole analogues for the d(GA4T4C)2 duplex follow a qualitatively similar hierarchy to that noted above for ligand-induced poisoning of human TOP1-namely, 5PTB > TB > 5NIBB. In the aggregate, our results suggest that DNA minor groove binding, but not DNA unwinding, is important in the poisoning of TOP1 by terbenzimidazoles.

Molecular Characterization of Recombinant Pneumocystis carinii Topoisomerase I: Differential Interactions with Human Topoisomerase I Poisons and Pentamidine

“…Both the bisbenzimidazole Ho33342 and the terbenzimidazole QS-II-48 are potent human topoisomerase I poisons (12,59,69). Both also strongly stimulate DNA cleavage by P. carinii topoisomerase I (Fig.…”

“…With the exception of CPT derivatives and the several antiCandida drugs characterized by Fostel and coworkers, the topoisomerase I poisons discussed above are cationic drugs that bind in the minor groove of DNA (12,46,69). The correlation between minor-groove binding and topoisomerase I poisoning activity has been noted with terbenzimidazoles (69) and other drug classes (11,12,59), although it is clear that strong minorgroove binding behavior is not the sole determinant for topoisomerase I poisoning activity, as several well-known minorgroove binding agents, including berenil and netropsin, show little or no activity as topoisomerase I poisons (reviewed in reference 46).…”

“…It is known, however, that pentamidine binds tightly to the minor groove of AϩT-rich DNA (20). Because a number of minor-groove binding agents are topoisomerase I poisons (11,12,69), it has been suggested that topoisomerase I is the molecular target of pentamidine. At concentrations ranging from 0 to 400 M, pentamidine does not inhibit the P. carinii topoisomerase I-mediated relaxation of supercoiled DNA ( Fig.…”

Novel and Specific Inhibitors of a Poxvirus Type I Topoisomerase

“…8), indicating that this minor groove binding group is not essential for vTopo inhibition. Finally, biand terbenzimidazoles have been shown to be DNA minor groove binders acting by stabilizing the covalent complex between hTopo and DNA via a long range conformational change rather than direct intercalation at the cleavage site, as with camptothecin (Xu et al, 1998). The ribonuclease assay readily detected the mono-and bibenzimidazole library compounds shown in Fig.…”

Isodiospyrin as a novel human DNA topoisomerase I inhibitor

“…4A), further suggesting different modes of htopo I inhibition by these two agents. [21,[36][37][38][39][40][41][42]. Most if not all of these htopo I poisons are DNA intercalators, suggesting that the intercalative mode of DNA binding may underlie a major htopo I poisoning mechanism [37,40,41,43].…”