Bacterial topoisomerase I as a target for discovery of antibacterial compounds

Abstract

Bacterial topoisomerase I is a potential target for discovery of new antibacterial compounds. Mutant topoisomerases identified by SOS induction screening demonstrated that accumulation of the DNA cleavage complex formed by type IA topoisomerases is bactericidal. Characterization of these mutants of Yersinia pestis and Escherichia coli topoisomerase I showed that DNA religation can be inhibited while maintaining DNA cleavage activity by decreasing the binding affinity of Mg(II) ions. This can be accomplished either by mutation of the TOPRIM motif involved directly in Mg(II) binding or by altering the charge distribution of the active site region. Besides being used to elucidate the key elements for the control of the cleavage-religation equilibrium, the SOS-inducing mutants of Y. pestis and E. coli topoisomerase I have also been utilized as models to study the cellular response following the accumulation of bacterial topoisomerase I cleavage complex. Bacterial topoisomerase I is required for preventing hypernegative supercoiling of DNA during transcription. It plays an important role in transcription of stress genes during bacterial stress response. Topoisomerase I targeting poisons may be particularly effective when the bacterial pathogen is responding to host defense, or in the presence of other antibiotics that induce the bacterial stress response.

Figure 1.

Structure of the 67 kDa N-terminal fragment of E. coli topo I (PDB ECL1) and the close-up view of the active site showing the nucleophilic tyrosine Y319 and the residues in the TOPRIM motif and active site region where mutations can result in cell killing due to inhibition of Mg²⁺ binding and DNA religation.

Figure 2.

Structures of compounds shown to inhibit relaxation activity of E. coli topo I. (A) cardiolipin (77). (B) Small molecule leads identified by high-throughput screening (81).