Gyrase inhibitors and intracellular DNA supercoiling

1986 ◽  
Vol 14 (2) ◽  
pp. 499-501 ◽  
Author(s):  
ROBERT J. FRANCO ◽  
KARL DRLICA
Keyword(s):  
Dna Supercoiling ◽  
Gyrase Inhibitors

scholarly journals Biological Activities of Novel Gyrase Inhibitors of the Aminocoumarin Class

2008 ◽  
Vol 52 (6) ◽  
pp. 1982-1990 ◽  
Author(s):  
Christine Anderle ◽  
Martin Stieger ◽  
Matthew Burrell ◽  
Stefan Reinelt ◽  
Anthony Maxwell ◽  
...  
Keyword(s):  
Reporter Gene ◽  
Rank Order ◽  
Biological Activities ◽  
Dna Supercoiling ◽  
Binding Energies ◽  
In Vitro Assays ◽  
Gene Assay ◽  
Gyrase Inhibitors

ABSTRACT Thirty-one aminocoumarin antibiotics derived from mutasynthesis experiments were investigated for their biological activities. Their inhibitory activities toward Escherichia coli DNA gyrase were determined in two different in vitro assays: an ATPase assay and a DNA supercoiling assay. The assays gave a similar rank order of the activities of the compounds tested, although the absolute 50% inhibitory concentrations (IC50s) obtained in each assay were different. To confirm that the compounds also acted as gyrase inhibitors in vivo, reporter gene assays were carried out with E. coli by using gyrA and sulA promoter fusions with the luxCDABE operon. A strong induction of both promoters was observed for those compounds that showed gyrase inhibitory activity in the biochemical assays. Compounds carrying analogs of the prenylated benzoyl moiety (ring A) of clorobiocin that were structurally very different showed high levels of activity both in the biochemical assay and in the reporter gene assay, indicating that the structure of this moiety can be varied considerably without a loss of affinity for bacterial gyrase. The experimentally determined IC50s were compared to the binding energies calculated in silico, which indicated that a shift of the pyrrole carboxylic acid moiety from the O-3″ to the O-2″ position of the deoxysugar moiety has a significant impact on the binding mode of the compounds. The aminocoumarin compounds were also investigated for their MICs against different bacterial pathogens. Several compounds showed high levels of activity against staphylococci, including a methicillin-resistant Staphylococcus aureus strain. However, they showed only poor activities against gram-negative strains.

scholarly journals Discovery of Novel DNA Gyrase Inhibitors by High-Throughput Virtual Screening

2007 ◽  
Vol 51 (10) ◽  
pp. 3688-3698 ◽  
Author(s):  
David A. Ostrov ◽  
José A. Hernández Prada ◽  
Patrick E. Corsino ◽  
Kathryn A. Finton ◽  
Nhan Le ◽  
...  
Keyword(s):  
Small Molecules ◽  
Dna Gyrase ◽  
Binding Pocket ◽  
Small Region ◽  
Dna Supercoiling ◽  
Resistant Bacteria ◽  
Topoisomerase Iv ◽  
Antimicrobial Drugs ◽  
Drug Resistant Bacteria ◽  
Gyrase Inhibitors

ABSTRACT The bacterial type II topoisomerases DNA gyrase and topoisomerase IV are validated targets for clinically useful quinolone antimicrobial drugs. A significant limitation to widely utilized quinolone inhibitors is the emergence of drug-resistant bacteria due to an altered DNA gyrase. To address this problem, we have used structure-based molecular docking to identify novel drug-like small molecules that target sites distinct from those targeted by quinolone inhibitors. A chemical ligand database containing approximately 140,000 small molecules (molecular weight, <500) was molecularly docked onto two sites of Escherichia coli DNA gyrase targeting (i) a previously unexplored structural pocket formed at the dimer interface of subunit A and (ii) a small region of the ATP binding pocket on subunit B overlapping the site targeted by coumarin and cyclothialidine drugs. This approach identified several small-molecule compounds that inhibited the DNA supercoiling activity of purified E. coli DNA gyrase. These compounds are structurally unrelated to previously identified gyrase inhibitors and represent potential scaffolds for the optimization of novel antibacterial agents that act on fluoroquinolone-resistant strains.

scholarly journals Structural Maintenance of Chromosomes Protein of Bacillussubtilis Affects Supercoiling In Vivo

2002 ◽  
Vol 184 (19) ◽  
pp. 5317-5322 ◽  
Author(s):  
Janet C. Lindow ◽  
Robert A. Britton ◽  
Alan D. Grossman
Keyword(s):  
Topoisomerase I ◽  
Dna Gyrase ◽  
Dna Supercoiling ◽  
Null Mutant ◽  
Wild Type ◽  
Mutant Plasmid ◽  
Chromatid Cohesion ◽  
Structural Maintenance Of Chromosomes ◽  
Gyrase Inhibitors

ABSTRACT Structural maintenance of chromosomes (SMC) proteins are found in nearly all organisms. Members of this protein family are involved in chromosome condensation and sister chromatid cohesion. Bacillus subtilis SMC protein (BsSMC) plays a role in chromosome organization and partitioning. To better understand the function of BsSMC, we studied the effects of an smc null mutation on DNA supercoiling in vivo. We found that an smc null mutant was hypersensitive to the DNA gyrase inhibitors coumermycin A1 and norfloxacin. Furthermore, depleting cells of topoisomerase I substantially suppressed the partitioning defect of an smc null mutant. Plasmid DNA isolated from an smc null mutant was more negatively supercoiled than that from wild-type cells. In vivo cross-linking experiments indicated that BsSMC was bound to the plasmid. Our results indicate that BsSMC affects supercoiling in vivo, most likely by constraining positive supercoils, an activity which contributes to chromosome compaction and organization.

scholarly journals Towards Conformation-Sensitive Inhibition of Gyrase: Implications of Mechanistic Insight for the Identification and Improvement of Inhibitors

Molecules ◽  
2021 ◽  
Vol 26 (5) ◽  
pp. 1234
Author(s):  
Dagmar Klostermeier
Keyword(s):  
Conformational Changes ◽  
Bacterial Infections ◽  
Dna Supercoiling ◽  
Full Potential ◽  
Resistance Mutations ◽  
Allosteric Inhibitors ◽  
Strand Breaks ◽  
Medical Need ◽  
Negative Supercoiling ◽  
Gyrase Inhibitors

Gyrase is a bacterial type IIA topoisomerase that catalyzes negative supercoiling of DNA. The enzyme is essential in bacteria and is a validated drug target in the treatment of bacterial infections. Inhibition of gyrase activity is achieved by competitive inhibitors that interfere with ATP- or DNA-binding, or by gyrase poisons that stabilize cleavage complexes of gyrase covalently bound to the DNA, leading to double-strand breaks and cell death. Many of the current inhibitors suffer from severe side effects, while others rapidly lose their antibiotic activity due to resistance mutations, generating an unmet medical need for novel, improved gyrase inhibitors. DNA supercoiling by gyrase is associated with a series of nucleotide- and DNA-induced conformational changes, yet the full potential of interfering with these conformational changes as a strategy to identify novel, improved gyrase inhibitors has not been explored so far. This review highlights recent insights into the mechanism of DNA supercoiling by gyrase and illustrates the implications for the identification and development of conformation-sensitive and allosteric inhibitors.

scholarly journals Experimental and Molecular Docking Studies of Cyclic Diphenyl Phosphonates as DNA Gyrase Inhibitors for Fluoroquinolone-Resistant Pathogens

Antibiotics ◽  
2022 ◽  
Vol 11 (1) ◽  
pp. 53
Author(s):  
Neveen M. Saleh ◽  
Yasmine S. Moemen ◽  
Sara H. Mohamed ◽  
Ghady Fathy ◽  
Abdullah A. S. Ahmed ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Dna Gyrase ◽  
Docking Study ◽  
Dna Supercoiling ◽  
Docking Studies ◽  
Clinical Isolates ◽  
Detectable Effect ◽  
Topoisomerase Iv ◽  
Molecular Docking Studies ◽  
Gyrase Inhibitors

DNA gyrase and topoisomerase IV are proven to be validated targets in the design of novel antibacterial drugs. In this study, we report the antibacterial evaluation and molecular docking studies of previously synthesized two series of cyclic diphenylphosphonates (1a–e and 2a–e) as DNA gyrase inhibitors. The synthesized compounds were screened for their activity (antibacterial and DNA gyrase inhibition) against ciprofloxacin-resistant E.coli and Klebsiella pneumoniae clinical isolates having mutations (deletion and substitution) in QRDR region of DNA gyrase. The target compound (2a) that exhibited the most potent activity against ciprofloxacin Gram-negative clinical isolates was selected to screen its inhibitory activity against DNA gyrase displayed IC50 of 12.03 µM. In addition, a docking study was performed with inhibitor (2a), to illustrate its binding mode in the active site of DNA gyrase and the results were compatible with the observed inhibitory potency. Furthermore, the docking study revealed that the binding of inhibitor (2a) to DNA gyrase is mediated and modulated by divalent Mg2+ at good binding energy (–9.08 Kcal/mol). Moreover, structure-activity relationships (SARs) demonstrated that the combination of hydrazinyl moiety in conjunction with the cyclic diphenylphosphonate based scaffold resulted in an optimized molecule that inhibited the bacterial DNA gyrase by its detectable effect in vitro on gyrase-catalyzed DNA supercoiling activity.

scholarly journals nifH Promoter Activity Is Regulated by DNA Supercoiling in Sinorhizobium meliloti

2005 ◽  
Vol 37 (4) ◽  
pp. 221-226 ◽  
Author(s):  
Yan-Jie Liu ◽  
Biao Hu ◽  
Jia-Bi Zhu ◽  
Shan-Jiong Shen ◽  
Guan-Qiao Yu
Keyword(s):  
Gene Expression ◽  
Promoter Activity ◽  
Sinorhizobium Meliloti ◽  
Dna Gyrase ◽  
Dna Supercoiling ◽  
Wild Type ◽  
Promoter Activation ◽  
The Status ◽  
Negative Supercoiling ◽  
Gyrase Inhibitors

AbstractIn prokaryotes, DNA supercoiling regulates the expression of many genes; for example, the expression of Klebsiella pneumoniae nifLA operon depends on DNA negative supercoiling in anaerobically grown cells, which indicates that DNA supercoiling might play a role in gene regulation of the anaerobic response. Since the expression of the nifH promoter in Sinorhizobium meliloti is not repressed by oxygen, it is proposed that the status of DNA supercoiling may not affect the expression of the nifH promoter. We tested this hypothesis by analyzing nifH promoter activity in wild-type and gyr Escherichia coli in the presence and absence of DNA gyrase inhibitors. Our results show that gene expression driven by the S. meliloti nifH promoter requires the presence of active DNA gyrase. Because DNA gyrase increases the number of negative superhelical turns in DNA in the presence of ATP, our data indicate that negative supercoiling is also important for nifH promoter activity. Our study also shows that the DNA supercoiling-dependent S. meliloti nifH promoter activity is related to the trans-acting factors NtrC and NifA that activate it. DNA supercoiling appeared to have a stronger effect on NtrC-activated nifH promoter activity than on NifA-activated promoter activity. Collectively, these results from the S. meliloti nifH promoter model system seem to indicate that, in addition to regulating gene expression during anaerobic signaling, DNA supercoiling may also provide a favorable topology for trans-acting factor binding and promoter activation regardless of oxygen status.

scholarly journals Functional interactions between gyrase subunits are optimized in a species-specific manner

2020 ◽  
Vol 295 (8) ◽  
pp. 2299-2312
Author(s):  
Daniela Weidlich ◽  
Dagmar Klostermeier
Keyword(s):  
Atp Hydrolysis ◽  
Dna Supercoiling ◽  
Structural Features ◽  
Subunit Interaction ◽  
Dna Topoisomerase ◽  
Bacterial Dna ◽  
E Coli ◽  
Functional Interactions ◽  
Species Specific ◽  
Gyrase Inhibitors

DNA gyrase is a bacterial DNA topoisomerase that catalyzes ATP-dependent negative DNA supercoiling and DNA decatenation. The enzyme is a heterotetramer comprising two GyrA and two GyrB subunits. Its overall architecture is conserved, but species-specific elements in the two subunits are thought to optimize subunit interaction and enzyme function. Toward understanding the roles of these different elements, we compared the activities of Bacillus subtilis, Escherichia coli, and Mycobacterium tuberculosis gyrases and of heterologous enzymes reconstituted from subunits of two different species. We show that B. subtilis and E. coli gyrases are proficient DNA-stimulated ATPases and efficiently supercoil and decatenate DNA. In contrast, M. tuberculosis gyrase hydrolyzes ATP only slowly and is a poor supercoiling enzyme and decatenase. The heterologous enzymes are generally less active than their homologous counterparts. The only exception is a gyrase reconstituted from mycobacterial GyrA and B. subtilis GyrB, which exceeds the activity of M. tuberculosis gyrase and reaches the activity of the B. subtilis gyrase, indicating that the activities of enzymes containing mycobacterial GyrB are limited by ATP hydrolysis. The activity pattern of heterologous gyrases is in agreement with structural features present: B. subtilis gyrase is a minimal enzyme, and its subunits can functionally interact with subunits from other bacteria. In contrast, the specific insertions in E. coli and mycobacterial gyrase subunits appear to prevent efficient functional interactions with heterologous subunits. Understanding the molecular details of gyrase adaptations to the specific physiological requirements of the respective organism might aid in the development of species-specific gyrase inhibitors.

New 1,4-dihydro[1,8]naphthyridine derivatives as DNA gyrase inhibitors

2017 ◽  
Vol 27 (5) ◽  
pp. 1162-1168 ◽  
Author(s):  
Hülya Karaca Gençer ◽  
Serkan Levent ◽  
Ulviye Acar Çevik ◽  
Yusuf Özkay ◽  
Sinem Ilgın
Keyword(s):  
Dna Gyrase ◽  
Gyrase Inhibitors
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