Discovery and Characterization of QPT-1, the Progenitor of a New Class of Bacterial Topoisomerase Inhibitors

Abstract

QPT-1 was discovered in a compound library by high-throughput screening and triage for substances with whole-cell antibacterial activity. This totally synthetic compound is an unusual barbituric acid derivative whose activity resides in the (؊)-enantiomer. QPT-1 had activity against a broad spectrum of pathogenic, antibioticresistant bacteria, was nontoxic to eukaryotic cells, and showed oral efficacy in a murine infection model, all before any medicinal chemistry optimization. Biochemical and genetic characterization showed that the QPT-1 targets the ␤ subunit of bacterial type II topoisomerases via a mechanism of inhibition distinct from the mechanisms of fluoroquinolones and novobiocin. Given these attributes, this compound represents a promising new class of antibacterial agents. The success of this reverse genomics effort demonstrates the utility of exploring strategies that are alternatives to target-based screens in antibacterial drug discovery.

Characterization of the Novel DNA Gyrase Inhibitor AZD0914: Low Resistance Potential and Lack of Cross-Resistance in Neisseria gonorrhoeae

“…Alternatively, given the conservation of this motif, this substitution may impact the stability of the DNA cleavage complex in a fashion similar to that of Glu427, such that any inhibition that depends on efficient DNA cleavage will be impacted (26). Whereas the Asp-to-Asn substitution results in an 8-to 16-fold increase in AZD0914 MIC in N. gonorrhoeae and a 4-fold increase in S. aureus, as well as a 4-fold increase in MIC of the related compound QPT-1 in S. aureus (25), the effect on fluoroquinolone susceptibility is less consistent. The Asp-to-Asn substitution elevates the ciprofloxacin MIC by 4-fold in S. aureus (this work and reference 25) and by 8-fold in E. coli (24).…”

“…All of these S. aureus variants also showed a modest 2-fold increase in the fluoroquinolone MIC (MIC parent , 0.25 g/ml, increasing to 0.5 g/ml). In addition, a related compound, QPT-1, also selected for substitutions at this conserved Asp residue in S. aureus, and an Asp 437 Asn substitution resulted in an elevation of the MICs of QPT-1 and ciprofloxacin by 8-to 16-fold and 2-to 4-fold, respectively (25). The GyrB Lys450 residue forms part of the PL(R/K)GK motif that is conserved in both bacterial and eukaryotic topoisomerases, underlying its key functional role in the catalysis of DNA cleavage (26).…”

Insights into the Mechanism of Inhibition of Novel Bacterial Topoisomerase Inhibitors from Characterization of Resistant Mutants of Staphylococcus aureus

“…It should be noted that D437 is also close to the cleavage region (highlighted by ciprofloxacin and F123 in Fig. 3C), and a D437N change has also been suggested to have a minor effect on the susceptibility of some fluoroquinolone compounds (37), as well as of AZD0914, a novel cleavage complex-mediated inhibitor (38). The other two residues in group 2, K417 and P456, are in close proximity to D437 and are likely to impact the optimal positioning of D437 needed for NBTI binding by charge or steric clashes, respectively.…”

Crystallization and initial crystallographic analysis of covalent DNA-cleavage complexes of Staphyloccocus aureus DNA gyrase with QPT-1, moxifloxacin and etoposide

“…DNA gyrase and topoisomerase IV are the targets of the widely used fluoroquinolone class of antibacterial drugs (Aldred et al, 2014). QPT-1 is the progenitor of a new class of antibacterials (Miller et al, 2008) that we show in an accompanying paper to have the same mode of action as fluoroquinolones but to bind to residues in GyrB rather than GyrA (Chan et al, 2015).…”