Selective Inhibition of Escherichia coli RNA and DNA Topoisomerase I by Hoechst 33258 Derived Mono- and Bisbenzimidazoles

A series of Hoechst 33258 based mono-
and bisbenzimidazoles have
been synthesized and their Escherichia coli DNA topoisomerase I inhibition, binding to B-DNA duplex, and antibacterial
activity has been evaluated. Bisbenzimidazoles with alkynyl side chains
display excellent E. coli DNA topoisomerase
I inhibition properties with IC50 values <5.0 μM.
Several bisbenzimidazoles (3, 6, 7, 8) also inhibit RNA topoisomerase activity of E. coli DNA topoisomerase I. Bisbenzimidazoles inhibit
bacterial growth much better than monobenzimidazoles for Gram-positive
strains. The minimum inhibitory concentration (MIC) was much lower
for Gram positive bacteria (Enterococcus spp. and Staphylococcus spp., including
two MRSA strains 0.3–8 μg/mL) than for the majority of
Gram negative bacteria (Pseudomonas aeruginosa, 16–32 μg/mL, Klebsiella pneumoniae > 32 μg/mL). Bisbenzimidazoles showed varied stabilization
of B-DNA duplex (1.2−23.4 °C), and cytotoxicity studies
show similar variation dependent upon the side chain length. Modeling
studies suggest critical interactions between the inhibitor side chain
and amino acids of the active site of DNA topoisomerase I.