Mass Spectrometry Reveals That the Antibiotic Simocyclinone D8 Binds to DNA Gyrase in a “Bent-Over” Conformation: Evidence of Positive Cooperativity in Binding

Biochemistry ◽  
2011 ◽  
Vol 50 (17) ◽  
pp. 3432-3440 ◽  
Author(s):  
Marcus J. Edwards ◽  
Mark A. Williams ◽  
Anthony Maxwell ◽  
Adam R. McKay
Keyword(s):  
Mass Spectrometry ◽  
Dna Gyrase ◽  
Positive Cooperativity ◽  
Simocyclinone D8

Defining a minimum pharmacophore for simocyclinone D8 disruption of DNA gyrase binding to DNA

2014 ◽  
Vol 23 (8) ◽  
pp. 3632-3643 ◽  
Author(s):  
Lauren M. Gaskell ◽  
Thuy Nguyen ◽  
Keith C. Ellis
Keyword(s):  
Dna Gyrase ◽  
Simocyclinone D8

Flavone-based analogues inspired by the natural product simocyclinone D8 as DNA gyrase inhibitors

2013 ◽  
Vol 23 (21) ◽  
pp. 5874-5877 ◽  
Author(s):  
Jenson Verghese ◽  
Thuy Nguyen ◽  
Lisa M. Oppegard ◽  
Lauren M. Seivert ◽  
Hiroshi Hiasa ◽  
...  
Keyword(s):  
Natural Product ◽  
Dna Gyrase ◽  
Simocyclinone D8 ◽  
Gyrase Inhibitors

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

2015 ◽  
Vol 59 (11) ◽  
pp. 6689-6695 ◽  
Author(s):  
George A. Jacoby ◽  
Marian A. Corcoran ◽  
David C. Hooper
Keyword(s):  
Protective Effect ◽  
Dna Gyrase ◽  
Molecular Probes ◽  
Protective Activity ◽  
Topoisomerase Iv ◽  
Synthetic Compounds ◽  
Target Dna ◽  
Simocyclinone D8 ◽  
Microcin B17 ◽  
Insight Into

ABSTRACTQnr 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.

scholarly journals E. coli GyrA Tower Domain Interacts with QnrB1 Loop B and Plays an Important Role in QnrB1 Protection from Quinolone Inhibition

2021 ◽  
Author(s):  
Chunhui Chen ◽  
Yin Wang ◽  
Hidemasa Nakaminami ◽  
Eu Suk Kim ◽  
George A. Jacoby ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Amino Acids ◽  
Amino Acid ◽  
Dna Gyrase ◽  
Amino Acid Residues ◽  
Site Specific ◽  
E Coli ◽  
Small Deletion ◽  
Interaction Sites ◽  
Repeat Proteins

The Qnr pentapeptide repeat proteins interact with DNA gyrase and protect it from quinolone inhibition. The two external loops, particularly the larger loop B, of Qnr proteins are essential for quinolone protection of DNA gyrase. The specific QnrB1 interaction sites on DNA gyrase are not known. In this study, we investigated the interaction between GyrA and QnrB1 using site-specific photo crosslinking of QnrB1 loop B combined with mass spectrometry. We found that amino acid residues 286-298 on the Tower domain of GyrA interact with QnrB1 and play a key role in QnrB1 protection of gyrase from quinolone inhibition. Alanine replacement of arginine at residue 293 and a small deletion of amino acids 286-289 of GyrA resulted in a decrease in the QnrB1-mediated increase in quinolone MICs and also abolished the QnrB1 protection of purified DNA gyrase from ciprofloxacin inhibition.

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

2009 ◽  
Vol 54 (1) ◽  
pp. 213-220 ◽  
Author(s):  
C. Sissi ◽  
E. Vazquez ◽  
A. Chemello ◽  
L. A. Mitchenall ◽  
A. Maxwell ◽  
...  
Keyword(s):  
Dna Gyrase ◽  
Coumarin Derivative ◽  
Streptomyces Antibioticus ◽  
B Subunit ◽  
Terminal Domain ◽  
Antiproliferative Agent ◽  
Gyrase A ◽  
A Subunit ◽  
The Individual ◽  
Simocyclinone D8

ABSTRACT 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 (A2B2) 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.

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

2005 ◽  
Vol 49 (3) ◽  
pp. 1093-1100 ◽  
Author(s):  
Ruth H. Flatman ◽  
Alison J. Howells ◽  
Lutz Heide ◽  
Hans-Peter Fiedler ◽  
Anthony Maxwell
Keyword(s):  
Complex Formation ◽  
Dna Gyrase ◽  
Antibacterial Drug ◽  
Binding Studies ◽  
Bacterial Dna ◽  
New Class ◽  
Atpase Reaction ◽  
Cleavage Complex ◽  
Simocyclinone D8 ◽  
Gyrase Inhibitors

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 A1, 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 Ca2+- 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.

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

2014 ◽  
Vol 426 (10) ◽  
pp. 2023-2033 ◽  
Author(s):  
Stephen J. Hearnshaw ◽  
Marcus J. Edwards ◽  
Clare E. Stevenson ◽  
David M. Lawson ◽  
Anthony Maxwell
Keyword(s):  
Crystal Structure ◽  
Dna Gyrase ◽  
Mechanism Of Inhibition ◽  
Simocyclinone D8 ◽  
Fresh Insight ◽  
Insight Into

scholarly journals A natural product inspired fragment-based approach towards the development of novel anti-bacterial agents

MedChemComm ◽  
2016 ◽  
Vol 7 (7) ◽  
pp. 1387-1391 ◽  
Author(s):  
Michael J. Austin ◽  
Stephen J. Hearnshaw ◽  
Lesley A. Mitchenall ◽  
Paul J. McDermott ◽  
Lesley A. Howell ◽  
...  
Keyword(s):  
Natural Product ◽  
Dna Gyrase ◽  
Simocyclinone D8

Simocyclinone D8 served as a natural product inspiration for the synthesis of a new DNA gyrase inhibitor.

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

Science ◽  
2009 ◽  
Vol 326 (5958) ◽  
pp. 1415-1418 ◽  
Author(s):  
M. J. Edwards ◽  
R. H. Flatman ◽  
L. A. Mitchenall ◽  
C. E.M. Stevenson ◽  
T. B.K. Le ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Dna Gyrase ◽  
Simocyclinone D8

How SIMS microscopy can be used in medicine

1992 ◽  
Vol 50 (2) ◽  
pp. 1602-1603
Author(s):  
Philippe Fragu
Keyword(s):  
Mass Spectrometry ◽  
Biomedical Applications ◽  
Secondary Ion Mass Spectrometry ◽  
Chemical Elements ◽  
Biological Applications ◽  
The Past ◽  
Potential Source ◽  
Secondary Ion ◽  
Chemical Integrity ◽  
Scientific Endeavour

The identification, localization and quantification of intracellular chemical elements is an area of scientific endeavour which has not ceased to develop over the past 30 years. Secondary Ion Mass Spectrometry (SIMS) microscopy is widely used for elemental localization problems in geochemistry, metallurgy and electronics. Although the first commercial instruments were available in 1968, biological applications have been gradual as investigators have systematically examined the potential source of artefacts inherent in the method and sought to develop strategies for the analysis of soft biological material with a lateral resolution equivalent to that of the light microscope. In 1992, the prospects offered by this technique are even more encouraging as prototypes of new ion probes appear capable of achieving the ultimate goal, namely the quantitative analysis of micron and submicron regions. The purpose of this review is to underline the requirements for biomedical applications of SIMS microscopy.Sample preparation methodology should preserve both the structural and the chemical integrity of the tissue.

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