A new class of antibacterials, the imidazopyrazinones, reveal structural transitions involved in DNA gyrase poisoning and mechanisms of resistance
- Resource Type
- Authors
- Thomas Germe; Judit Vörös; Frederic Jeannot; Thomas Taillier; Robert A Stavenger; Eric Bacqué; Anthony Maxwell; Benjamin D Bax
- Source
- 'Nucleic Acids Research ', vol: 46, pages: 4114-4128 (2018)
Nucleic Acids Research
- Subject
- Models, Molecular
0301 basic medicine
0303 health sciences
Nucleic Acid Enzymes
030106 microbiology
DNA
02 engineering and technology
021001 nanoscience & nanotechnology
Anti-Bacterial Agents
03 medical and health sciences
Adenosine Triphosphate
030104 developmental biology
Ciprofloxacin
DNA Gyrase
Pyrazines
Drug Resistance, Bacterial
Mutation
Genetics
Topoisomerase II Inhibitors
Magnesium
DNA Cleavage
Corrigendum
0210 nano-technology
Fluoroquinolones
030304 developmental biology
- Language
- ISSN
- 1362-4962
0305-1048
Imidazopyrazinones (IPYs) are a new class of compounds that target bacterial topoisomerases as a basis for their antibacterial activity. We have characterized the mechanism of these compounds through structural/mechanistic studies showing they bind and stabilize a cleavage complex between DNA gyrase and DNA (‘poisoning’) in an analogous fashion to fluoroquinolones, but without the requirement for the water–metal–ion bridge. Biochemical experiments and structural studies of cleavage complexes of IPYs compared with an uncleaved gyrase–DNA complex, reveal conformational transitions coupled to DNA cleavage at the DNA gate. These involve movement at the GyrA interface and tilting of the TOPRIM domains toward the scissile phosphate coupled to capture of the catalytic metal ion. Our experiments show that these structural transitions are involved generally in poisoning of gyrase by therapeutic compounds and resemble those undergone by the enzyme during its adenosine triphosphate-coupled strand-passage cycle. In addition to resistance mutations affecting residues that directly interact with the compounds, we characterized a mutant (D82N) that inhibits formation of the cleavage complex by the unpoisoned enzyme. The D82N mutant appears to act by stabilizing the binary conformation of DNA gyrase with uncleaved DNA without direct interaction with the compounds. This provides general insight into the resistance mechanisms to antibiotics targeting bacterial type II topoisomerases.