title: Escherichia coli Topoisomerase IV E Subunit and an Inhibitor Binding Mode Revealed by NMR Spectroscopy.
abstract: Bacterial topoisomerases are attractive antibacterial drug targets because of 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. A detailed understanding of the interactions between ligand and target in a solution state will provide valuable information for further developing drugs against topoisomerase IV targets. Here we describe a detailed characterization of a known potent inhibitor containing a 9H-pyrimido[4,5-b]indole scaffold against the N-terminal domain of the topoisomerase IV E subunit from Escherichia 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 comparative studies of two inhibitors of markedly varied potencies, it is hypothesized that gaining molecular interactions with residues in the α4 and residues close to the loop of β1-α2 and residues in the loop of β3-β4 might improve the inhibitor potency.
authors.affiliation: From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669.
authors.forename: Yan
authors.initials: Y
authors.lastname: Li
authors.affiliation: From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669.
authors.forename: Ying Lei
authors.initials: YL
authors.lastname: Wong
authors.affiliation: From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669.
authors.forename: Fui Mee
authors.initials: FM
authors.lastname: Ng
authors.affiliation: From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669.
authors.forename: Boping
authors.initials: B
authors.lastname: Liu
authors.affiliation: From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669.
authors.forename: Yun Xuan
authors.initials: YX
authors.lastname: Wong
authors.affiliation: From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669.
authors.forename: Zhi Ying
authors.initials: ZY
authors.lastname: Poh
authors.affiliation: From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669.
authors.forename: Shuang
authors.initials: S
authors.lastname: Liu
authors.affiliation: From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669.
authors.forename: Siew Wen
authors.initials: SW
authors.lastname: Then
authors.affiliation: From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669.
authors.forename: Michelle Yueqi
authors.initials: MY
authors.lastname: Lee
authors.affiliation: From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669.
authors.forename: Hui Qi
authors.initials: HQ
authors.lastname: Ng
authors.affiliation: From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669.
authors.forename: Qiwei
authors.initials: Q
authors.lastname: Huang
authors.affiliation: From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669.
authors.forename: Alvin W
authors.initials: AW
authors.lastname: Hung
authors.affiliation: From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669.
authors.forename: Joseph
authors.initials: J
authors.lastname: Cherian
authors.affiliation: From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Hill
authors.affiliation: From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669.
authors.forename: Thomas H
authors.initials: TH
authors.lastname: Keller
authors.affiliation: From the Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos, 03-01, Singapore 138669 cbkang@etc.a-star.edu.sg.
authors.forename: CongBao
authors.initials: C
authors.lastname: Kang
mesh_terms: D027101:DNA Topoisomerase IV / Q000037:antagonists & inhibitors* / Q000737:chemistry*; D004926:Escherichia coli / Q000201:enzymology*; D029968:Escherichia coli Proteins / Q000037:antagonists & inhibitors* / Q000737:chemistry*; D006801:Humans; D007211:Indoles / Q000737:chemistry; D019906:Nuclear Magnetic Resonance, Biomolecular; D000072417:Protein Domains; D017433:Protein Structure, Secondary; D059003:Topoisomerase Inhibitors / Q000737:chemistry*
chemical_list: D029968:Escherichia coli Proteins; D007211:Indoles; D059003:Topoisomerase Inhibitors; D027101:DNA Topoisomerase IV
keywords: DNA gyrase; DNA topoisomerase; NMR; antibiotics; drug discovery