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Molecules (Basel, Switzerland) Dec 2020Fluoroquinolones (FQs) are arguably among the most successful antibiotics of recent times. They have enjoyed over 30 years of clinical usage and become essential tools... (Review)
Review
Fluoroquinolones (FQs) are arguably among the most successful antibiotics of recent times. They have enjoyed over 30 years of clinical usage and become essential tools in the armoury of clinical treatments. FQs target the bacterial enzymes DNA gyrase and DNA topoisomerase IV, where they stabilise a covalent enzyme-DNA complex in which the DNA is cleaved in both strands. This leads to cell death and turns out to be a very effective way of killing bacteria. However, resistance to FQs is increasingly problematic, and alternative compounds are urgently needed. Here, we review the mechanisms of action of FQs and discuss the potential pathways leading to cell death. We also discuss quinolone resistance and how quinolone treatment can lead to resistance to non-quinolone antibiotics.
Topics: Animals; Anti-Bacterial Agents; Bacteria; Drug Resistance, Microbial; Humans; Quinolones
PubMed: 33271787
DOI: 10.3390/molecules25235662 -
Future Medicinal Chemistry Dec 2023DNA gyrase and urease enzymes are important targets for the treatment of gastroenteritis, appendicitis, tuberculosis, urinary tract infections and Crohn's disease....
DNA gyrase and urease enzymes are important targets for the treatment of gastroenteritis, appendicitis, tuberculosis, urinary tract infections and Crohn's disease. Esterification of norfloxacin was performed to enhance DNA gyrase and urease enzyme inhibition potential. Structure elucidation and chemical characterization were done through spectral (H NMR, Fourier transform IR, C NMR) and carbon, hydrogen, nitrogen and sulfur analysis along with molecular docking. The majority of derivatives exhibited significant results but the derivative showed maximum bactericidal, DPPH scavenging (96%), DNA gyrase and urease enzyme inhibitory activity with IC of 0.15 ± 0.24 and 1.14 ± 0.11 μM respectively which was further supported by molecular docking studies. So, the active derivatives can serve as a lead compound for the treatment of various pathological conditions.
Topics: Molecular Docking Simulation; Norfloxacin; DNA Gyrase; Urease; Anti-Bacterial Agents; Enzyme Inhibitors; Structure-Activity Relationship; Molecular Structure
PubMed: 37997685
DOI: 10.4155/fmc-2023-0225 -
Biomedicines Jan 2023Bacterial DNA gyrase is a type II topoisomerase that can introduce negative supercoils to DNA substrates and is a clinically-relevant target for the development of new... (Review)
Review
Bacterial DNA gyrase is a type II topoisomerase that can introduce negative supercoils to DNA substrates and is a clinically-relevant target for the development of new antibacterials. DNA gyrase is one of the primary targets of quinolones, broad-spectrum antibacterial agents and are used as a first-line drug for various types of infections. However, currently used quinolones are becoming less effective due to drug resistance. Common resistance comes in the form of mutation in enzyme targets, with this type being the most clinically relevant. Additional mechanisms, conducive to quinolone resistance, are arbitrated by chromosomal mutations and/or plasmid-gene uptake that can alter quinolone cellular concentration and interaction with the target, or affect drug metabolism. Significant synthetic strategies have been employed to modify the quinolone scaffold and/or develop novel quinolones to overcome the resistance problem. This review discusses the development of quinolone antibiotics targeting DNA gyrase to overcome bacterial resistance and reduce toxicity. Moreover, structural activity relationship (SAR) data included in this review could be useful for the development of future generations of quinolone antibiotics.
PubMed: 36830908
DOI: 10.3390/biomedicines11020371 -
ELife Jun 2024DNA gyrase, a ubiquitous bacterial enzyme, is a type IIA topoisomerase formed by heterotetramerisation of 2 GyrA subunits and 2 GyrB subunits, to form the active...
DNA gyrase, a ubiquitous bacterial enzyme, is a type IIA topoisomerase formed by heterotetramerisation of 2 GyrA subunits and 2 GyrB subunits, to form the active complex. DNA gyrase can loop DNA around the C-terminal domains (CTDs) of GyrA and pass one DNA duplex through a transient double-strand break (DSB) established in another duplex. This results in the conversion from a positive (+1) to a negative (-1) supercoil, thereby introducing negative supercoiling into the bacterial genome by steps of 2, an activity essential for DNA replication and transcription. The strong protein interface in the GyrA dimer must be broken to allow passage of the transported DNA segment and it is generally assumed that the interface is usually stable and only opens when DNA is transported, to prevent the introduction of deleterious DSBs in the genome. In this paper, we show that DNA gyrase can exchange its DNA-cleaving interfaces between two active heterotetramers. This so-called interface 'swapping' (IS) can occur within a few minutes in solution. We also show that bending of DNA by gyrase is essential for cleavage but not for DNA binding per se and favors IS. Interface swapping is also favored by DNA wrapping and an excess of GyrB. We suggest that proximity, promoted by GyrB oligomerization and binding and wrapping along a length of DNA, between two heterotetramers favors rapid interface swapping. This swapping does not require ATP, occurs in the presence of fluoroquinolones, and raises the possibility of non-homologous recombination solely through gyrase activity. The ability of gyrase to undergo interface swapping explains how gyrase heterodimers, containing a single active-site tyrosine, can carry out double-strand passage reactions and therefore suggests an alternative explanation to the recently proposed 'swivelling' mechanism for DNA gyrase (Gubaev et al., 2016).
Topics: DNA Gyrase; Protein Multimerization; DNA, Bacterial; Escherichia coli; DNA
PubMed: 38856655
DOI: 10.7554/eLife.86722 -
The Journal of Biological Chemistry Dec 2023Macromolecular crowding, manifested by high concentrations of proteins and nucleic acids in living cells, significantly influences biological processes such as enzymatic...
Macromolecular crowding, manifested by high concentrations of proteins and nucleic acids in living cells, significantly influences biological processes such as enzymatic reactions. Studying these reactions in vitro, using agents such as polyetthylene glycols (PEGs) and polyvinyl alcohols (PVAs) to mimic intracellular crowding conditions, is essential due to the notable differences from enzyme behaviors observed in diluted aqueous solutions. In this article, we studied Mycobacterium tuberculosis (Mtb) DNA gyrase under macromolecular crowding conditions by incorporating PEGs and PVAs into the DNA supercoiling reactions. We discovered that high concentrations of potassium glutamate, glycine betaine, PEGs, and PVA substantially stimulated the DNA supercoiling activity of Mtb DNA gyrase. Steady-state kinetic studies showed that glycine betaine and PEG400 significantly reduced the K of Mtb DNA gyrase and simultaneously increased the V or k of Mtb DNA gyrase for ATP and the plasmid DNA molecule. Molecular dynamics simulation studies demonstrated that PEG molecules kept the ATP lid of DNA gyrase subunit B in a closed or semiclosed conformation, which prevented ATP molecules from leaving the ATP-binding pocket of DNA gyrase subunit B. The stimulation of the DNA supercoiling activity of Mtb DNA gyrase by these molecular crowding agents likely results from a decrease in water activity and an increase in excluded volume.
Topics: DNA Gyrase; Mycobacterium tuberculosis; Betaine; Kinetics; Adenosine Triphosphate; DNA; DNA, Superhelical
PubMed: 37944619
DOI: 10.1016/j.jbc.2023.105439 -
Infectious Disorders Drug Targets 2020The newly emerging infectious organisms, the global crisis in antibiotic resistance, and the threat of bioterrorism create an urgent need to discover novel antimicrobial... (Review)
Review
The newly emerging infectious organisms, the global crisis in antibiotic resistance, and the threat of bioterrorism create an urgent need to discover novel antimicrobial agents. In order to develop novel antimicrobial agents, the mechanism of infectious disease must be better understood. DNA Gyrase is a bacterial enzyme that plays an important role in the replication of DNA and transcription process. It is not present in higher eukaryotes making it a perfect target for developing new antibacterial agents. This review describes the role of DNA gyrase inhibitors in preventing various diseases. In this review, we outline the synthesis and pharmacological action of various novel DNA gyrase inhibitors. DNA gyrase inhibitors were used to treat tuberculosis, bacterial, fungal infections and malaria. DNA gyrase inhibitors mainly act by preventing the supercoiling of DNA strands..
Topics: Anti-Bacterial Agents; Bacteria; DNA Gyrase; Drug Resistance, Microbial; Humans; Topoisomerase II Inhibitors
PubMed: 33109068
DOI: 10.2174/1871526520666200102110235 -
European Journal of Medicinal Chemistry Aug 2020Antimicrobial resistance is one of the greatest challenges facing the world today. In the United States alone, it is responsible for the death of more than 20,000 people... (Review)
Review
Antimicrobial resistance is one of the greatest challenges facing the world today. In the United States alone, it is responsible for the death of more than 20,000 people each year. DNA gyrase, a well-validated drug target, is involved in bacterial DNA replication, repair and decatenation. Currently, the fluoroquinolone class of antibacterials act via inhibition of the DNA gyrase enzyme. However, their efficacy is hindered by the increasing incidence of antimicrobial resistance. Therefore, in this review, we provide an account regarding the structure of DNA gyrase and quinoline and non-quinolone inhibitors published within the last five years (2015-2019). Further, we also discuss molecular interactions and structure-activity relationship studies of the published inhibitors.
Topics: Anti-Bacterial Agents; Bacteria; DNA Gyrase; Microbial Sensitivity Tests; Molecular Structure; Topoisomerase II Inhibitors
PubMed: 32460040
DOI: 10.1016/j.ejmech.2020.112326 -
Journal of Medicinal Chemistry May 2022New antibiotics with either a novel mode of action or novel mode of inhibition are urgently needed to overcome the threat of drug-resistant tuberculosis (TB). The...
New antibiotics with either a novel mode of action or novel mode of inhibition are urgently needed to overcome the threat of drug-resistant tuberculosis (TB). The present study profiles new spiropyrimidinetriones (SPTs), DNA gyrase inhibitors having activity against drug-resistant (), the causative agent of TB. While the clinical candidate zoliflodacin has progressed to phase 3 trials for the treatment of gonorrhea, compounds herein demonstrated higher inhibitory potency against DNA gyrase (e.g., compound with IC = 2.0) and lower minimum inhibitor concentrations (0.49 μM for ). Notably, and analogues showed selective activity relative to representative Gram-positive and Gram-negative bacteria. DNA gyrase inhibition was shown to involve stabilization of double-cleaved DNA, while on-target activity was supported by hypersensitivity against a gyrA hypomorph. Finally, a docking model for SPTs with DNA gyrase was developed, and a structural hypothesis was built for structure-activity relationship expansion.
Topics: Anti-Bacterial Agents; Antitubercular Agents; DNA Gyrase; Gram-Negative Bacteria; Gram-Positive Bacteria; Microbial Sensitivity Tests; Mycobacterium tuberculosis; Topoisomerase II Inhibitors
PubMed: 35500229
DOI: 10.1021/acs.jmedchem.2c00266 -
Molecular Microbiology Jun 2023DNA gyrase, the sole negative supercoiling type II topoisomerase, is composed of two subunits, GyrA and GyrB, encoded by the gyrA and gyrB genes, respectively, that form...
DNA gyrase, the sole negative supercoiling type II topoisomerase, is composed of two subunits, GyrA and GyrB, encoded by the gyrA and gyrB genes, respectively, that form a quaternary complex of A B . In this study, we have investigated the assembly of mycobacterial DNA gyrase from its individual subunits, a step prerequisite for its activity. Using analytical size-exclusion chromatography, we show that GyrA from Mycobacterium tuberculosis and Mycobacterium smegmatis forms tetramers (A ) in solution unlike in Escherichia coli and other bacteria where GyrA exists as a dimer. GyrB, however, persists as a monomer, resembling the pattern found in E. coli. GyrB in both mycobacterial species interacts with GyrA and triggers the dissociation of the GyrA tetramer to facilitate the formation of catalytically active A B . Despite oligomerisation, the GyrA tetramer retained its DNA binding ability, and DNA binding had no effect on GyrA's oligomeric state in both species. Moreover, the presence of DNA facilitated the assembly of holoenzyme in the case of M. smegmatis by stabilising the GyrA B tetramer but with little effect in M. tuberculosis. Thus, in addition to the distinct organisation and regulation of the gyr locus in mycobacteria, the enzyme assembly also follows a different pattern.
Topics: DNA Gyrase; Escherichia coli; Mycobacterium tuberculosis; Mycobacterium smegmatis; DNA, Superhelical
PubMed: 37190861
DOI: 10.1111/mmi.15068 -
Nucleic Acids Research Jun 2021Type IIA topoisomerases catalyze a variety of different reactions: eukaryotic topoisomerase II relaxes DNA in an ATP-dependent reaction, whereas the bacterial... (Review)
Review
Type IIA topoisomerases catalyze a variety of different reactions: eukaryotic topoisomerase II relaxes DNA in an ATP-dependent reaction, whereas the bacterial representatives gyrase and topoisomerase IV (Topo IV) preferentially introduce negative supercoils into DNA (gyrase) or decatenate DNA (Topo IV). Gyrase and Topo IV perform separate, dedicated tasks during replication: gyrase removes positive supercoils in front, Topo IV removes pre-catenanes behind the replication fork. Despite their well-separated cellular functions, gyrase and Topo IV have an overlapping activity spectrum: gyrase is also able to catalyze DNA decatenation, although less efficiently than Topo IV. The balance between supercoiling and decatenation activities is different for gyrases from different organisms. Both enzymes consist of a conserved topoisomerase core and structurally divergent C-terminal domains (CTDs). Deletion of the entire CTD, mutation of a conserved motif and even by just a single point mutation within the CTD converts gyrase into a Topo IV-like enzyme, implicating the CTDs as the major determinant for function. Here, we summarize the structural and mechanistic features that make a type IIA topoisomerase a gyrase or a Topo IV, and discuss the implications for type IIA topoisomerase evolution.
Topics: Bacteria; DNA; DNA Gyrase; DNA Topoisomerase IV; DNA Topoisomerases, Type II; Evolution, Molecular; Protein Conformation; Protein Domains
PubMed: 33905522
DOI: 10.1093/nar/gkab270