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

J Med Chem. 2017 Jun 22;60(12):4904-4922. doi: 10.1021/acs.jmedchem.7b00191. Epub 2017 May 31.


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.

MeSH terms

  • Anti-Bacterial Agents / chemistry
  • Anti-Bacterial Agents / pharmacology*
  • Benzimidazoles / chemistry
  • Benzimidazoles / pharmacology*
  • Bisbenzimidazole / chemistry*
  • Cell Line, Tumor
  • Chemistry Techniques, Synthetic
  • DNA / metabolism
  • Drug Evaluation, Preclinical / methods
  • Drug Screening Assays, Antitumor / methods
  • Escherichia coli / drug effects*
  • Escherichia coli / genetics
  • Escherichia coli Proteins / antagonists & inhibitors
  • Humans
  • Inhibitory Concentration 50
  • Isomerases / antagonists & inhibitors
  • Male
  • Methicillin-Resistant Staphylococcus aureus / drug effects
  • Microbial Sensitivity Tests
  • Molecular Docking Simulation
  • Topoisomerase I Inhibitors / chemistry
  • Topoisomerase I Inhibitors / pharmacology*


  • Anti-Bacterial Agents
  • Benzimidazoles
  • Escherichia coli Proteins
  • Topoisomerase I Inhibitors
  • DNA
  • Isomerases
  • Bisbenzimidazole