A New Crystal Structure of the Bifunctional Antibiotic Simocyclinone D8 Bound to DNA Gyrase Gives Fresh Insight into the Mechanism of Inhibition

Hearnshaw, S.J.; Edwards, Marcus J.; Stevenson, Clare E. M.; Lawson, David M.; Maxwell, Anthony

doi:10.1016/j.jmb.2014.02.017

Cited by 36 publications

(39 citation statements)

References 36 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: 95%

“…The toxin also inhibits gyrase by stabilizing the cleavage complex but differs from quinolones in the site of resistance mutations. Lack of protection against simocyclinone D8 is intriguing because this agent binds to the N-terminal domain of GyrA, like quinolones, with mutations at such GyrA residues as 81, 83, 84, and 87 providing resistance to both agents (14). Furthermore, simocyclinone blocks DNA binding such that if Qnr functions as a DNA mimic, competition between Qnr and simocylinone would be expected.…”

Section: Discussionmentioning

confidence: 99%

“…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.…”

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confidence: 99%

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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: 95%

Section: Discussionmentioning

confidence: 99%

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

Jacoby

Corcoran

Hooper

2015

Antimicrob Agents Chemother

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“…In the present investigation, the functionally important residues in the GyrA protein structure were retrieved by means of available literature evidences [44]. The literature also indicates that conservation score and pharmacophore information is certainly helpful in the screening of binding site residues [45].…”

Section: Binding Site Analysismentioning

confidence: 99%

Investigation of Nalidixic Acid Resistance Mechanism in Salmonella enterica Using Molecular Simulation Techniques

Preethi

Shanthi

Ramanathan

2015

Appl Biochem Biotechnol

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The emergence of nalidixic acid-resistant strains of Salmonella typhimurium remains to be a major public health problem. In particular, the substitution of Asn in place of Asp at the 87 loci in the GyrA of S. typhimurium was experimentally stated for nalidixic acid resistance. However, the data on the possible mechanism of nalidixic acid resistance are limited. In this study, I-Mutant2.0 and DUET program were employed to explore the impact of mutation on the stability of GyrA protein. Subsequently, molecular simulation techniques were employed to provide detailed information on the nalidixic acid-resistant associates with the D87N mutation in the GyrA of S. typhimurium. The binding free energy data depicts that nalidixic acid forms stable complex only with native-type GyrA than mutant (D87N) type GyrA protein. Moreover, our results theoretically suggest that hydrogen bonding formed by the Arg91 is certainly responsible for the GyrA of S. typhimurium drug selectivity. It is hoped that these evidences are immensely important for the development of new antibiotic and to overcome the nalidixic acid resistance in the near future.

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“…The non-classical aminocoumarin, simocyclinone D8 (Figure 1), lacks the 7-aminosugar moiety and inhibits bacterial DNA gyrase through simultaneous binding to two alternate binding pockets via interactions with the coumarin moiety and a terminal angucyclinone group. Simocyclinone D8 thus has a unique mechanism of action, despite structural similarities to the standard aminocoumarins [8][9][10]. Similarly, differences in the binding sites between the fluoroquinolone antibiotics (e.g.…”

Section: Introductionmentioning

confidence: 99%

Versatility of 7-Substituted Coumarin Molecules as Antimycobacterial Agents, Neuronal Enzyme Inhibitors and Neuroprotective Agents

Kapp

Visser

Sampson

et al. 2017

Preprint

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An in vitro medium-throughput screen using M. tuberculosis H37Rv was employed to screen an in-house library of structurally diverse compounds for antimycobacterial activity. From this initial screen, eleven 7-substituted coumarin derivatives with confirmed monoamine oxidase-B and cholinesterase inhibitory activities, demonstrated growth inhibition of more than 50% at a 50 µM concentration. This prompted further exploration of all the 7-substituted coumarins in our library, nineteen in total, as potential antimycobacterial agents. Four derivatives showed promising antimycobacterial activity with MIC99 values of 8.31 -29.70 µM and 44.15 -57.17 µM on M. tuberculosis H37Rv in independent assays using Gaste-Fe and 7H9 + OADC media, respectively. These compounds were found to bind to albumin which may explain the variations in MIC between the two assays. Preliminary antimycobacterial evaluation of moxifloxacin resistant M. tuberculosis show that these compounds are able to maintain their activity in fluoroquinolone resistant mycobacteria. Analysis of structure activity relationships for antimycobacterial versus neuronal enzyme inhibitory activity indicate that structural modification on position 4 and/or 7 of the coumarin scaffold may be utilized to improve selectivity towards either inhibition of neuronal enzymes or antimycobacterial effect. Cytotoxicity evaluations of the compounds indicate moderate cytotoxicity with slight selectivity towards mycobacteria. Further neuroprotective assays on SH-SY5Y human neuroblastoma cells indicate significant neuroprotection for selected compounds irrespective of their neuronal enzyme inhibitory properties. These coumarin molecules are thus interesting lead compounds that may provide insight into the design of new antimicrobacterial and/or neuroprotective agents.

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A New Crystal Structure of the Bifunctional Antibiotic Simocyclinone D8 Bound to DNA Gyrase Gives Fresh Insight into the Mechanism of Inhibition

Cited by 36 publications

References 36 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

Investigation of Nalidixic Acid Resistance Mechanism in Salmonella enterica Using Molecular Simulation Techniques

Versatility of 7-Substituted Coumarin Molecules as Antimycobacterial Agents, Neuronal Enzyme Inhibitors and Neuroprotective Agents

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