A Crystal Structure of the Bifunctional Antibiotic Simocyclinone D8, Bound to DNA Gyrase

Edwards, Marcus J.; Flatman, Ruth; Mitchenall, Lesley A.; Stevenson, C.E.M.; Le, Tung B. K.; Clarke, Thomas A.; McKay, Adam R.; Fiedler, Hans‐Peter; Buttner, Mark J.; Lawson, David M.; Maxwell, Anthony

doi:10.1126/science.1179123

Cited by 82 publications

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“…Simocyclinone D8 is a chlorinated aminocoumarin linked to an angucyclic polyketide via a tetraene linker and a D-olivose sugar produced by Streptomyces antibioticus. Despite its aminocoumarin moiety, it does not inhibit GyrB ATPase activity but rather binds to the GyrA subunit near the QRDR, preventing DNA binding (14,26). No inhibitory activity was evident with a 25-mol simocyclinone D8 disk on a lawn of E. coli J53 Azi r or EW1b, but in vitro, simocyclinone D8 was at least as potent as ciprofloxacin in inhibiting DNA gyrase supercoiling.…”

Section: Resultsmentioning

confidence: 94%

Protective Effect of Qnr on Agents Other than Quinolones That Target DNA Gyrase

Jacoby

Corcoran

Hooper

2015

Antimicrob Agents Chemother

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bQnr is a plasmid-encoded and chromosomally determined protein that protects DNA gyrase and topoisomerase IV from inhibition by quinolones. Despite its prevalence worldwide and existence prior to the discovery of quinolones, its native function is not known. Other synthetic compounds and natural products also target bacterial topoisomerases. A number were studied as molecular probes to gain insight into how Qnr acts. Qnr blocked inhibition by synthetic compounds with somewhat quinolone-like structure that target the GyrA subunit, such as the 2-pyridone ABT-719, the quinazoline-2,4-dione PD 0305970, and the spiropyrimidinetrione pyrazinyl-alkynyl-tetrahydroquinoline (PAT), indicating that Qnr is not strictly quinolone specific, but Qnr did not protect against GyrA-targeting simocyclinone D8 despite evidence that both simocyclinone D8 and Qnr affect DNA binding to gyrase. Qnr did not affect the activity of tricyclic pyrimidoindole or pyrazolopyridones, synthetic inhibitors of the GyrB subunit, or nonsynthetic GyrB inhibitors, such as coumermycin A1, novobiocin, gyramide A, or microcin B17.Thus, in this set of compounds the protective activity of Qnr was confined to those that, like quinolones, trap gyrase on DNA in cleaved complexes. Qnr was discovered as a plasmid-encoded protein that reduces susceptibility to quinolones (1). Quinolones are synthetic compounds that target the essential bacterial enzymes DNA gyrase and topoisomerase IV, homologous tetramers composed of GyrA and GyrB or ParC and ParE subunits, respectively, that introduce negative supercoils or unknot and decatenate the DNA helix with energy from ATP hydrolysis (2).Qnr is a pentapeptide repeat protein that blocks quinolone inhibition of both topoisomerases and binds to each of their subunits as well as to the holoenzymes (3-5). Many bacteria have qnr-like genes on the chromosome, some, especially in aquatic bacteria, closely related to plasmid-determined qnr varieties (6-8). The native function of these proteins, which clearly antedate the clinical use of quinolones, is not known.A number of other agents target topoisomerases. Well-studied natural products include coumermycin A1 (9, 10), gyramide A (11), microcin B17 (12), novobiocin (9, 10), and simocyclinone D8 (13,14). From mutational and other studies the sites of action of many of these agents are known. For example, the primary site of resistance mutations for quinolones in Gram-negative bacteria is a region on the GyrA subunit known as the quinolone resistance-determining region (QRDR) (15), while novobiocin targets ATPase activity of the GyrB subunit (9). Qnr does not protect against novobiocin inhibition of gyrase (16), but the protective effect of Qnr on other natural products is not yet known. Medicinal chemists have synthesized synthetic compounds of various structures intended to act on gyrase at sites different from those directly affected by quinolones, especially the GyrB subunit. Whether Qnr protects gyrase from such compounds has not been investigated. The aim of this study was to...

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Section: Resultsmentioning

confidence: 94%

Protective Effect of Qnr on Agents Other than Quinolones That Target DNA Gyrase

Jacoby

Corcoran

Hooper

2015

Antimicrob Agents Chemother

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“…The available data indicate that DNA gyrase is the biological target of SD8 (6,7,26). To monitor this interaction, we performed CD measurements using the reconstituted protein.…”

Section: Resultsmentioning

confidence: 99%

“…In particular, SD8 has been shown to be even more effective than novobiocin at inhibiting gyrase-catalyzed supercoiling (7). Its mechanism of action is thought to involve the prevention of DNA binding by gyrase, and the structure of the N-terminal domain of GyrA (GyrA59) with SD8 bound has recently been solved (6). This novel mode of action suggests that SD8 is a potential new lead molecule for drug design.…”

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confidence: 99%

Mapping Simocyclinone D8 Interaction with DNA Gyrase: Evidence for a New Binding Site on GyrB

Sissi

Vázquez

Chemello

et al. 2010

Antimicrob Agents Chemother

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Simocyclinone D8, a coumarin derivative isolated from Streptomyces antibioticus Tü 6040, represents an interesting new antiproliferative agent. It was originally suggested that this drug recognizes the GyrA subunit and interferes with the gyrase catalytic cycle by preventing its binding to DNA. To further characterize the mode of action of this antibiotic, we investigated its binding to the reconstituted DNA gyrase (A 2 B 2 ) as well as to its GyrA and GyrB subunits and the individual domains of these proteins, by performing protein melting and proteolytic digestion studies as well as inhibition assays. Two binding sites were identified, one (anticipated) in the N-terminal domain of GyrA (GyrA59) and the other (unexpected) at the C-terminal domain of GyrB (GyrB47). Stabilization of the A subunit appears to be considerably more effective than stabilization of the B subunit. Our data suggest that these two distinct sites could cooperate in the reconstituted enzyme.Resistance to antibiotics is a constantly increasing clinical concern, particularly in hospitals and other health care settings (16,22). In fact, antibiotic-resistant pathogens cause serious infections for which there are limited therapeutic interventions and that are often life threatening. Hence, the discovery and development of new, effective antibacterial drugs that possibly exhibit new mechanisms of action represent challenging and urgent goals. Possible successful approaches include (i) the exploitation of new drug targets in the pathogen and (ii) the identification of drugs that act at a novel site(s) of known targets (35). In either case, detailed information on the molecular mechanism(s) of drug action is required to rationally develop new effective agents.In this connection, a major target for antimicrobial intervention is DNA gyrase (19). This enzyme is a prokaryotic type II topoisomerase that modulates the topological state of DNA through cleaving and resealing steps (24, 31). Besides performing reactions such as decatenation, unknotting, and relaxation common to the type II family members, DNA gyrase is also able to introduce negative supercoils, a reaction coupled to ATP hydrolysis (9, 10). DNA gyrase works as a tetramer (A 2 B 2 ) formed by two A subunits (GyrA) and two B subunits (GyrB) (28). The catalytic tyrosine covalently linked to DNA in the cleavage complex is located in the N-terminal domain of GyrA (GyrA59). The C-terminal domain of GyrA (GyrA33) facilitates the wrapping of DNA around the enzyme. GyrB contains the ATP-binding and hydrolysis site in its N-terminal domain (GyrB43), whereas its C-terminal portion (GyrB47) is involved in DNA and GyrA binding.A number of drugs are effective in impairing the activity of DNA gyrase (Fig. 1), among which the fluoroquinolones are the therapeutically most relevant (3, 5). As suggested by biological and chemico-physical studies, they act at the cleavage site by trapping the cleavage complex and interacting principally with GyrA but also with GyrB and DNA (12,27,34,37). Recently, the structur...

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“…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.…”

Section: Tfrs Regulating Self-resistance In Antibiotic-producing Orgamentioning

confidence: 99%

The TetR Family of Regulators

Cuthbertson

Nodwell

2013

Microbiol Mol Biol Rev

480

512

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SUMMARY The most common prokaryotic signal transduction mechanisms are the one-component systems in which a single polypeptide contains both a sensory domain and a DNA-binding domain. Among the >20 classes of one-component systems, the TetR family of regulators (TFRs) are widely associated with antibiotic resistance and the regulation of genes encoding small-molecule exporters. However, TFRs play a much broader role, controlling genes involved in metabolism, antibiotic production, quorum sensing, and many other aspects of prokaryotic physiology. There are several well-established model systems for understanding these important proteins, and structural studies have begun to unveil the mechanisms by which they bind DNA and recognize small-molecule ligands. The sequences for more than 200,000 TFRs are available in the public databases, and genomics studies are identifying their target genes. Three-dimensional structures have been solved for close to 200 TFRs. Comparison of these structures reveals a common overall architecture of nine conserved α helices. The most important open question concerning TFR biology is the nature and diversity of their ligands and how these relate to the biochemical processes under their control.

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A Crystal Structure of the Bifunctional Antibiotic Simocyclinone D8, Bound to DNA Gyrase

Abstract: A Crystal Structure of the Bifunctional Antibiotic www.sciencemag.org (this information is current as of December 4, 2009 ):The following resources related to this article are available online at

Cited by 82 publications

References 24 publications

Protective Effect of Qnr on Agents Other than Quinolones That Target DNA Gyrase

Protective Effect of Qnr on Agents Other than Quinolones That Target DNA Gyrase

Mapping Simocyclinone D8 Interaction with DNA Gyrase: Evidence for a New Binding Site on GyrB

The TetR Family of Regulators

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