Simocyclinone D8, an Inhibitor of DNA Gyrase with a Novel Mode of Action

Abstract

We have characterized the interaction of a new class of antibiotics, simocyclinones, with bacterial DNA gyrase. Even though their structures include an aminocoumarin moiety, a key feature of novobiocin, coumermycin A 1 , and clorobiocin, which also target gyrase, simocyclinones behave strikingly differently from these compounds. Simocyclinone D8 is a potent inhibitor of gyrase supercoiling, with a 50% inhibitory concentration lower than that of novobiocin. However, it does not competitively inhibit the DNA-independent ATPase reaction of GyrB, which is characteristic of other aminocoumarins. Simocyclinone D8 also inhibits DNA relaxation by gyrase but does not stimulate cleavage complex formation, unlike quinolones, the other major class of gyrase inhibitors; instead, it abrogates both Ca 2؉ -and quinolone-induced cleavage complex formation. Binding studies suggest that simocyclinone D8 interacts with the N-terminal domain of GyrA. Taken together, our results demonstrate that simocyclinones inhibit an early step of the gyrase catalytic cycle by preventing binding of the enzyme to DNA. This is a novel mechanism for a gyrase inhibitor and presents new possibilities for antibacterial drug development.DNA topoisomerases are enzymes that control the topology of DNA in cells (5). The enzymes are divided into two types, topoisomerases I and II, depending on whether their reactions involve breakage of one or both strands of the DNA. Overall, the mechanism of action of topoisomerases involves the passage of one segment of DNA through a break in another. This reaction can achieve all the known reactions of topoisomerases: relaxation and supercoiling, catenation and decatenation, and knotting and unknotting. DNA supercoiling activity is unique to gyrase, and as this enzyme is essential in all bacteria but is not found in humans, it is an ideal target for antibacterials (24). The enzyme consists of an A 2 B 2 heterotetramer. The A subunit (GyrA; 97 kDa in Escherichia coli) comprises an N-terminal domain involved in DNA cleavage and religation and a C-terminal DNA-wrapping domain. The B subunit (GyrB; 90 kDa in E. coli) contains the site of ATP hydrolysis at the N-terminal domain (GyrB43); the C-terminal domain interacts with both GyrA and DNA. To introduce supercoils, the enzyme wraps a double-stranded segment around itself, cleaves this DNA (the gate segment) in both strands, passes the wrapped DNA (transported segment) through the break, and then reseals the DNA.DNA gyrase is a proven target for antibacterial agents (24). Two well-studied classes of drugs target the enzyme: the coumarins and the quinolones. Quinolones are synthetic compounds that are widely used in clinical practice (8). Coumarins are naturally occurring products of Streptomyces species which, despite being more potent inhibitors of gyrase in vitro than quinolones, have had limited clinical use due to their low solubility, poor uptake, and eukaryotic cell toxicity (27). Other gyrase inhibitors include the cyclothialidines and the bacterial toxins CcdB and m...

Mechanism of Inhibition of DNA Gyrase by ES‐1273, a Novel DNA Gyrase Inhibitor

“…It has been reported that simocyclinone D8 and GyrI prevent the binding of DNA to DNA gyrase (3,5). However, these compounds inhibit DNA gyrase but not, or only slightly, topo IV.…”

“…Other gyrase inhibitors include cyclothialidine (27), simocyclinone D8 (5), and three proteinaceous inhibitors, CcdB (4), microcin B17 (13), and GyrI (17). Their modes of action have been reported as follows: cyclothialidine inhibits ATPase activity of DNA gyrase B subunit (16), simocyclinone D8 and GyrI prevent the binding of DNA to DNA gyrase (3,5), and CcdB and microcin B17 stabilize DNA gyrase-DNA covalent complexes (1,25).…”

The TetR Family of Regulators

“…Simocyclinone D8 is a structurally complex inhibitor of DNA gyrase (87,88). The final molecule is composed of four parts: an angucyclic polyketide, a D-olivose sugar, a tetraene linker, and an aminocoumarin moiety.…”

Antibiotic Resistance in Bacteria and Its Future for Novel Antibiotic Development

“…The genomics provide many molecular targets to be identified and effectively screened: 5,96) peptide deformylase (PDF), 109) aminoacyl-tRNA synthetase, 110) fatty acid biosynthesis, 111) isoprenoid biosynthesis, 112) lipid A biosynthesis, 113) efflux pump, 114) aromatic amino acid biosynthesis, 96) DNA replication (GyrB subunit inhibitor), 115) protein secretion, 116) cell wall biosynthesis (sortase), 117) proteasome, 118) glyoxylate cycle, 119) and signal networks (two-component systems and quorum sensing pathways). 120,121) 1.…”