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Biology Jan 2024DNA gyrase is essential for the successful replication of circular chromosomes, such as those found in most bacterial species, by relieving topological stressors... (Review)
Review
DNA gyrase is essential for the successful replication of circular chromosomes, such as those found in most bacterial species, by relieving topological stressors associated with unwinding the double-stranded genetic material. This critical central role makes gyrase a valued target for antibacterial approaches, as exemplified by the highly successful fluoroquinolone class of antibiotics. It is reasonable that the activity of gyrase could be intrinsically regulated within cells, thereby helping to coordinate DNA replication with doubling times. Numerous proteins have been identified to exert inhibitory effects on DNA gyrase, although at lower doses, it can appear readily reversible and therefore may have regulatory value. Some of these, such as the small protein toxins found in plasmid-borne addiction modules, can promote cell death by inducing damage to DNA, resulting in an analogous outcome as quinolone antibiotics. Others, however, appear to transiently impact gyrase in a readily reversible and non-damaging mechanism, such as the plasmid-derived Qnr family of DNA-mimetic proteins. The current review examines the origins and known activities of protein inhibitors of gyrase and highlights opportunities to further exert control over bacterial growth by targeting this validated antibacterial target with novel molecular mechanisms. Furthermore, we are gaining new insights into fundamental regulatory strategies of gyrase that may prove important for understanding diverse growth strategies among different bacteria.
PubMed: 38392303
DOI: 10.3390/biology13020084 -
Molecular Diversity Aug 2023A series of N-4 piperazinyl ciprofloxacin derivatives as urea-tethered ciprofloxacin-chalcone hybrids 2a-j and thioacetyl-linked ciprofloxacin-pyrimidine hybrids 5a-i...
A series of N-4 piperazinyl ciprofloxacin derivatives as urea-tethered ciprofloxacin-chalcone hybrids 2a-j and thioacetyl-linked ciprofloxacin-pyrimidine hybrids 5a-i were synthesized. The target compounds were investigated for their antibacterial activity against S. aureus, P. aeruginosa, E. coli, and C. albicans strains, respectively. Ciprofloxacin derivatives 2a-j and 5a-i revealed broad antibacterial activity against either Gram positive or Gram negative strains, with MIC range of 0.06-42.23 µg/mL compared to ciprofloxacin with an MIC range of 0.15-3.25 µg/mL. Among the tested compounds, hybrids 2b, 2c, 5a, 5b, 5h, and 5i exhibited remarkable antibacterial activity with MIC range of 0.06-1.53 µg/mL against the tested bacterial strains. On the other hand, compounds 2c, 2e, 5c, and 5e showed comparable antifungal activity to ketoconazole against candida albicans with MIC range of 2.03-3.89 µg/mL and 2.6 µg/mL, respectively. Further investigations showed that some ciprofloxacin hybrids have inhibitory activity against DNA gyrase as potential molecular target compared to ciprofloxacin with IC range of 0.231 ± 0.01-7.592 ± 0.40 µM and 0.323 ± 0.02 µM, respectively. Docking studies of compounds 2b, 2c, 5b, 5c, 5e, 5h, and 5i on the active site of DNA gyrase (PDB: 2XCT) confirmed their ability to form stable complex with the target enzyme like that of ciprofloxacin.
Topics: Ciprofloxacin; Topoisomerase II Inhibitors; Molecular Docking Simulation; DNA Gyrase; Escherichia coli; Staphylococcus aureus; Anti-Infective Agents; Anti-Bacterial Agents; Microbial Sensitivity Tests; Structure-Activity Relationship; Molecular Structure
PubMed: 36152132
DOI: 10.1007/s11030-022-10528-z -
RSC Advances May 2024This article contributes to the search for new therapeutic agents for treatment of diseases caused by bacterial pathogens. In this study, a new series of compounds...
This article contributes to the search for new therapeutic agents for treatment of diseases caused by bacterial pathogens. In this study, a new series of compounds incorporating numerous bioactive moieties such as quinazolin-2,4-dione, acylthiourea linkage, and/or five membered nitrogen heterocycles (pyrazole and oxazole) 2-5a-c was described to identify new antibacterial drug candidates inhibition of DNA gyrase enzyme. The precursor -['-(2-cyano-acetyl)-hydrazinocarbothioyl]-4-(2,4-dioxo-1,4-dihydro-2-quinazolin-3-yl)-benzamide 2 was prepared by treatment of compound 1 with ammonium thiocyanate and cyanoacetic acid hydrazide through multicomponent reaction (MCR). In addition, compounds 3a-d and 4a-b were synthesized by treatment of 2 with aromatic aldehydes and/or ketones through Knoevenagel reaction, affording high purity products in satisfactory yields. Moreover, new heterocyclic moieties such as pyrazole and/or oxazole attached to quinazolin-2,4-dione core 5a-c were synthesized by treatment of 3c with different nucleophilic reagents like hydrazine, phenyl hydrazine and hydroxyl amine, respectively. Subsequently, the obtained products were structurally characterized by IR, H-, C-NMR, and MS analyses. The minimum inhibitory concentration (MIC) and antibacterial potency of all compounds were estimated against two G-ve ( and ), and two G+ve bacteria ( and ). Encouragingly, compound 3c demonstrated the best antibacterial activity against all the strains of the tested pathogenic bacteria at low concentrations compared with the standard drug, Ciprofloxacin. Electron withdrawing groups such as -NO and -Cl enhance the antibacterial activity. Next, a molecular docking study between the synthesized derivatives and the target enzyme, DNA gyrase enzyme (PDB: 2xct) was undertaken to investigate intermolecular interactions between the compounds and target enzyme.
PubMed: 38808238
DOI: 10.1039/d4ra02960g -
Frontiers in Chemistry 2022A series of small-molecule fluoroquinolones were synthesized, characterized by HRMS and NMR spectroscopy, and screened for their antibacterial activity against MRSA, ,...
A series of small-molecule fluoroquinolones were synthesized, characterized by HRMS and NMR spectroscopy, and screened for their antibacterial activity against MRSA, , and as model G/G pathogens. Compounds , , and were more potent than the reference drug balofloxacin against MRSA and (MIC values of 0.0195 and 0.039 μg/ml for , 0.039 and 0.078 μg/ml for each of and , respectively). Analysis of the time-dependent antibacterial effect of compound toward MRSA showed that in the early logarithmic growth phase, bactericidal effects occurred, while in the late logarithmic growth phase, bacterial inhibition occurred because of concentration effects and possibly the development of drug resistance. Compound exhibited low toxicity toward normal mammalian cell lines 3T3 and L-02 and tumor cell lines A549, H520, BEL-7402, and MCF-7. The compound was not hemolytic. Atomic force microscopy (AFM) revealed that compound could effectively destroy the membrane and wall of MRSA cells, resulting in the outflow of the cellular contents. Docking studies indicated the good binding profile of these compounds toward DNA gyrase and topoisomerase IV. ADMET's prediction showed that most of the synthesized compounds followed Lipinski's "rule of five" and possessed good drug-like properties. Our data suggested that compound exhibited potent anti-MRSA activity and is worthy of further investigation.
PubMed: 36059868
DOI: 10.3389/fchem.2022.963442 -
RSC Advances Aug 2023The extracellular matrix (ECM) undergoes constant physiochemical change. User-programmable biomaterials afford exciting opportunities to study such dynamic processes ....
The extracellular matrix (ECM) undergoes constant physiochemical change. User-programmable biomaterials afford exciting opportunities to study such dynamic processes . Herein, we introduce a protein-polymer hydrogel whose stiffness can be pharmacologically and reversibly regulated with conventional antibiotics. Specifically, a coumermycin-mediated homodimerization of gel-tethered DNA gyrase subunit B (GyrB) creates physical crosslinking and a rheological increase in hydrogel mechanics, while competitive displacement of coumermycin with novobiocin returns the material to its softened state. These unique platforms could potentially be modulated and are expected to prove useful in elucidating the effects of ECM-presented mechanical signals on cell function.
PubMed: 37588975
DOI: 10.1039/d3ra04046a -
Nucleic Acids Research Feb 2020Negative supercoiling by DNA gyrase is essential for maintaining chromosomal compaction, transcriptional programming, and genetic integrity in bacteria. Questions remain...
Negative supercoiling by DNA gyrase is essential for maintaining chromosomal compaction, transcriptional programming, and genetic integrity in bacteria. Questions remain as to how gyrases from different species have evolved profound differences in their kinetics, efficiency, and extent of negative supercoiling. To explore this issue, we analyzed homology-directed mutations in the C-terminal, DNA-wrapping domain of the GyrA subunit of Escherichia coli gyrase (the 'CTD'). The addition or removal of select, conserved basic residues markedly impacts both nucleotide-dependent DNA wrapping and supercoiling by the enzyme. Weakening CTD-DNA interactions slows supercoiling, impairs DNA-dependent ATP hydrolysis, and limits the extent of DNA supercoiling, while simultaneously enhancing decatenation and supercoil relaxation. Conversely, strengthening DNA wrapping does not result in a more extensively supercoiled DNA product, but partially uncouples ATP turnover from strand passage, manifesting in futile cycling. Our findings indicate that the catalytic cycle of E. coli gyrase operates at high thermodynamic efficiency, and that the stability of DNA wrapping by the CTD provides one limit to DNA supercoil introduction, beyond which strand passage competes with ATP-dependent supercoil relaxation. These results highlight a means by which gyrase can evolve distinct homeostatic supercoiling setpoints in a species-specific manner.
Topics: Adenosine Triphosphate; Catalysis; Chromosomes, Bacterial; DNA Gyrase; DNA, Bacterial; DNA, Superhelical; Escherichia coli; Models, Molecular; Mutation; Nucleic Acid Conformation; Protein Binding; Protein Domains
PubMed: 31950157
DOI: 10.1093/nar/gkz1230 -
Antimicrobial Agents and Chemotherapy Dec 2022CUO246, a novel DNA gyrase/topoisomerase IV inhibitor, is active against a broad range of Gram-positive, fastidious Gram-negative, and atypical bacterial pathogens and...
CUO246, a novel DNA gyrase/topoisomerase IV inhibitor, is active against a broad range of Gram-positive, fastidious Gram-negative, and atypical bacterial pathogens and retains activity against quinolone-resistant strains in circulation. The frequency of selection for single step mutants of wild-type S. aureus with reduced susceptibility to CUO246 was <4.64 × 10 at 4× and 8× MIC and remained low when using an isogenic QRDR mutant (<5.24 × 10 at 4× and 8× MIC). Biochemical assays indicated that CUO246 had potent inhibitory activity against both DNA gyrase (GyrAB) and topoisomerase IV (ParCE). Furthermore, CUO246 showed rapid bactericidal activity in time-kill assays and potent efficacy against S. aureus in a neutropenic murine thigh infection model. These results suggest that CUO246 may be useful in treating infections by various causative agents of acute skin and skin structure infections, respiratory tract infections, and sexually transmitted infections.
Topics: Animals; Mice; DNA Gyrase; DNA Topoisomerase IV; Topoisomerase II Inhibitors; DNA, Bacterial; Staphylococcus aureus; Microbial Sensitivity Tests; Anti-Bacterial Agents
PubMed: 36448795
DOI: 10.1128/aac.00921-22 -
ACS Omega Sep 2022Type II topoisomerases like DNA gyrase initiate ATP-dependent negative supercoils in bacterial DNA. It is critical in all of the bacteria but is missing from eukaryotes,...
Type II topoisomerases like DNA gyrase initiate ATP-dependent negative supercoils in bacterial DNA. It is critical in all of the bacteria but is missing from eukaryotes, making it a striking target for antibacterials. Ciprofloxacin is a clinically approved drug, but its clinical effectiveness is affected by the emergence of resistance in both Gram-positive and Gram-negative bacteria. Thus, it is vital to identify novel compounds that can efficiently inhibit DNA gyrase, and quantitative structure-activity relationship (QSAR) modeling is a quick and economical means to do so. A QSAR-based virtual screening approach was applied to identify new gyrase inhibitors using an -generated combinatorial library of 29828 compounds from seven ciprofloxacin scaffold structures. QSAR was built using a data set of 271 compounds, which were identified as positive and negative inhibitors from existing data reported in studies. The best QSAR model was developed using the 5-fold cross-validation Neural Network in Orange, and it was based on five PaDEL descriptors with an accuracy and sensitivity of 83%. As a result of screening of an -built combinatorial library with the best-developed QSAR model, 675 compounds were identified as potential inhibitors of DNA gyrase. These inhibitors were further docked with DNA gyrase using AutoDock to compare the binding mode and score of the selected/screened compounds, and 615 compounds exhibited a docking score comparable to or lower than that of ciprofloxacin. Out of these, the top five analogues 902b, 9699f, 4419f, 5538f, and 898b reported in our study have binding scores of -13.81, -12.95, -12.52, -12.43, and -12.41 kcal/mol, respectively. The MD simulations of these five analogues for 100 ns supported the interaction stability of analogues with DNA gyrase. Ninety-one per cent of the analogues screened by the QSAR model displayed better binding energy than ciprofloxacin, demonstrating the efficacy of the generated model. The NN-QSAR model proposed in this manuscript can be downloaded from https://github.com/ritu225/NN-QSAR_model.git.
PubMed: 36120069
DOI: 10.1021/acsomega.2c04310 -
Proceedings of the National Academy of... Mar 2021DNA gyrase, a type II topoisomerase, introduces negative supercoils into DNA using ATP hydrolysis. The highly effective gyrase-targeted drugs, fluoroquinolones (FQs),...
DNA gyrase, a type II topoisomerase, introduces negative supercoils into DNA using ATP hydrolysis. The highly effective gyrase-targeted drugs, fluoroquinolones (FQs), interrupt gyrase by stabilizing a DNA-cleavage complex, a transient intermediate in the supercoiling cycle, leading to double-stranded DNA breaks. MfpA, a pentapeptide-repeat protein in mycobacteria, protects gyrase from FQs, but its molecular mechanism remains unknown. Here, we show that MfpA (MsMfpA) inhibits negative supercoiling by gyrase (Msgyrase) in the absence of FQs, while in their presence, MsMfpA decreases FQ-induced DNA cleavage, protecting the enzyme from these drugs. MsMfpA stimulates the ATPase activity of Msgyrase by directly interacting with the ATPase domain (MsGyrB47), which was confirmed through X-ray crystallography of the MsMfpA-MsGyrB47 complex, and mutational analysis, demonstrating that MsMfpA mimics a T (transported) DNA segment. These data reveal the molecular mechanism whereby MfpA modulates the activity of gyrase and may provide a general molecular basis for the action of other pentapeptide-repeat proteins.
Topics: Adenosine Triphosphatases; Bacterial Proteins; Crystallography, X-Ray; DNA Cleavage; DNA Gyrase; Molecular Mimicry; Monomeric GTP-Binding Proteins; Mycobacterium; Protein Conformation
PubMed: 33836580
DOI: 10.1073/pnas.2016705118 -
Antibiotics (Basel, Switzerland) Jan 2022DNA 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...
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 (- and -) as DNA gyrase inhibitors. The synthesized compounds were screened for their activity (antibacterial and DNA gyrase inhibition) against ciprofloxacin-resistant and clinical isolates having mutations (deletion and substitution) in QRDR region of DNA gyrase. The target compound () that exhibited the most potent activity against ciprofloxacin Gram-negative clinical isolates was selected to screen its inhibitory activity against DNA gyrase displayed IC of 12.03 µM. In addition, a docking study was performed with inhibitor (), 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 () to DNA gyrase is mediated and modulated by divalent Mg 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.
PubMed: 35052930
DOI: 10.3390/antibiotics11010053