Escherichia coli Topoisomerase IV E Subunit and an Inhibitor Binding Mode Revealed by NMR Spectroscopy

Abstract Bacterial topoisomerases are attractive antibacterial drug targets due to their importance in bacterial growth and low homology with other human topoisomerases. Structure-based drug design has been a proven approach of efficiently developing new antibiotics against these targets. Past studies have focused on developing lead compounds against the ATP binding pockets of both DNA gyrase and topoisomerase IV. The detailed understanding of interactions between ligand and target in solution state will provide valuable information toward further developing drugs against topoisomerase IV targets. Herein, we described the detailed characterization of a known potent inhibitor containing a 9H-pyrimido[4,5-b]indole scaffold against the N-terminal domain of topoisomerase IV E subunit from E. coli (eParE). Using a series of biophysical and biochemical experiments, it has been demonstrated that this inhibitor forms a tight complex with eParE. NMR studies revealed the exact protein residues responsible for inhibitor binding. Through the comparative studies between two inhibitors of markedly varied potencies, it is hypothesized that gaining molecular interactions with residues in the alpha 4 and residues close to the loop of beta1-alpha2 and residues in the loop of beta3-beta4 might improve the inhibitor potency.