Targeting Mycobacterium tuberculosis topoisomerase I by small-molecule inhibitors

Antimicrob Agents Chemother. 2015 Mar;59(3):1549-57. doi: 10.1128/AAC.04516-14. Epub 2014 Dec 22.


We describe inhibition of Mycobacterium tuberculosis topoisomerase I (MttopoI), an essential mycobacterial enzyme, by two related compounds, imipramine and norclomipramine, of which imipramine is clinically used as an antidepressant. These molecules showed growth inhibition of both Mycobacterium smegmatis and M. tuberculosis cells. The mechanism of action of these two molecules was investigated by analyzing the individual steps of the topoisomerase I (topoI) reaction cycle. The compounds stimulated cleavage, thereby perturbing the cleavage-religation equilibrium. Consequently, these molecules inhibited the growth of the cells overexpressing topoI at a low MIC. Docking of the molecules on the MttopoI model suggested that they bind near the metal binding site of the enzyme. The DNA relaxation activity of the metal binding mutants harboring mutations in the DxDxE motif was differentially affected by the molecules, suggesting that the metal coordinating residues contribute to the interaction of the enzyme with the drug. Taken together, the results highlight the potential of these small molecules, which poison the M. tuberculosis and M. smegmatis topoisomerase I, as leads for the development of improved molecules to combat mycobacterial infections. Moreover, targeting metal coordination in topoisomerases might be a general strategy to develop new lead molecules.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Bacterial Proteins / antagonists & inhibitors*
  • Bacterial Proteins / metabolism
  • Binding Sites / genetics
  • DNA / genetics
  • DNA Topoisomerases, Type I / metabolism*
  • DNA, Bacterial / genetics
  • Imipramine / pharmacology
  • Mutation / genetics
  • Mycobacterium smegmatis / drug effects
  • Mycobacterium smegmatis / genetics
  • Mycobacterium smegmatis / metabolism
  • Mycobacterium tuberculosis / drug effects*
  • Mycobacterium tuberculosis / genetics
  • Mycobacterium tuberculosis / metabolism
  • Small Molecule Libraries / pharmacology*
  • Topoisomerase I Inhibitors / pharmacology*
  • Tuberculosis / drug therapy
  • Tuberculosis / microbiology


  • Bacterial Proteins
  • DNA, Bacterial
  • Small Molecule Libraries
  • Topoisomerase I Inhibitors
  • DNA
  • DNA Topoisomerases, Type I
  • Imipramine

Associated data

  • PDB/1ECL
  • PDB/1I7D
  • PDB/1MW8
  • PDB/1MW9
  • PDB/2RGR