Benzimidazoles: Selective Inhibitors of Topoisomerase I with Differential Modes of Action.

DNA topoisomerases are unique enzymes that alter the topology of DNA by cleavage and religation mechanisms. Small molecules such as camptothecins and noncamptothecins are reported to inhibit different classes of topoisomerases. Benzimidazole, 2-(3,4-dimethoxyphenyl)-5-[5-(4-methylpiperazin-1-yl)-1 H-benzimidazol-2-yl]-1 H benzimidazole (DMA), a new analogue of Hoechst 33342, was observed as a selective and differential inhibitor of human and Escherichia coli DNA topoisomerase I. In this study, we have concluded that DMA and Hoechst 33342 have differential binding toward human and E. coli topoisomerase I. We also dissected the mechanism of differential binding, as DMA and Hoechst 33342 bind to human topoisomerase I with linear kinetics with reversible binding, whereas the same molecules bind to E. coli topoisomerase I in a nonlinear and irreversible manner, which contributes to higher affinity and comparatively good IC50 values toward E. coli topoisomerase I. Interestingly, DMA and Hoechst 33342 showed inhibition of mutant human topoisomerases I, i.e., A653P, N722S, and T729P, whereas these clinically relevant mutants are resistant to camptothecins.