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Journal of Applied Microbiology Dec 2023The present study aims to determine the antimicrobial potential of Virgibacillus salairus (MML1918) against human pathogens and its in-vitro and in-silico properties.
AIM
The present study aims to determine the antimicrobial potential of Virgibacillus salairus (MML1918) against human pathogens and its in-vitro and in-silico properties.
METHODS AND RESULTS
In this present study, totally 63 halophilic bacterial cultures were obtained and cultivated in nutrient broth medium containing 8% NaCl and the metabolites, were extracted using ethyl acetate and screened for their antimicrobial property by cell viability assay against 12 pathogenic bacteria and fungi, among 63 halophilic bacteria the Vir. salaries (MML1918) found to be the best producer for secondary metabolites production against clinical pathogens. The optimization of growth for important physiochemical parameters was characterized and applied for different production media and based on its highest activity as 17.5 ± .07 mm zone of inhibition (ZOI) for Bacillus cereus followed by 17.5 ± 00 mm ZOI for Staphylococcus aureus, the production medium ATCC1097 was chosen for mass production. The mass production of secondary metabolites from Vir. salaries MML1918 was carried out in a fermenter under controlled conditions and crude metabolites was extracted and condensed. The antimicrobial activity of crude metabolites showed B. cereus (19.3 ± 0.5 mm ZOI), Staph. aureus, and Candida albicans (18.3 ± 0.5 mm ZOI) as the highest ZOI in production media for halophilic bacteria ATCC1097. Further, the gas chromatography-mass spectrometry analysis showed 24 compounds present in crude metabolites. Among the 24 compounds, four molecules were found to be important based on molecule percentage in crude and structural similarity. The molecular docking studies show that the selected four molecules effectively bind with the active region DNA gyrase B.
CONCLUSION
Virgibacillus salarius (MML1918) effectively showed antimicrobial activity against several pathogenic organisms and can be employed as a suitable candidate for producing novel antimicrobial agents.
Topics: Humans; Virgibacillus; Anti-Bacterial Agents; DNA Gyrase; Molecular Docking Simulation; Microbial Sensitivity Tests; Anti-Infective Agents; Bacillus cereus; Staphylococcus aureus; DNA
PubMed: 38031334
DOI: 10.1093/jambio/lxad286 -
Pharmaceuticals (Basel, Switzerland) Aug 2021DNA gyrase is an important target for the development of novel antibiotics. Although ATP-competitive DNA gyrase (GyrB) inhibitors are a well-studied class of...
DNA gyrase is an important target for the development of novel antibiotics. Although ATP-competitive DNA gyrase (GyrB) inhibitors are a well-studied class of antibacterial agents, there is currently no representative used in therapy, largely due to unwanted off-target activities. Selectivity of GyrB inhibitors against closely related human ATP-binding enzymes should be evaluated early in development to avoid off-target binding to homologous binding domains. To address this challenge, we developed selective 3D-pharmacophore models for GyrB, human topoisomerase IIα (TopoII), and the Hsp90 N-terminal domain (NTD) to be used in in silico activity profiling paradigms to identify molecules selective for GyrB over TopoII and Hsp90, as starting points for hit expansion and lead optimization. The models were used to profile highly active GyrB, TopoII, and Hsp90 inhibitors. Selected compounds were tested in in vitro assays. GyrB inhibitors and were inactive against TopoII and Hsp90, while and , potent Hsp90 inhibitors, displayed no inhibition of GyrB and TopoII, and TopoII inhibitors and were inactive at GyrB and Hsp90. The results provide a proof of concept for the use of target activity profiling methods to identify selective starting points for hit and lead identification.
PubMed: 34451886
DOI: 10.3390/ph14080789 -
Structure (London, England : 1993) May 2020Most biological processes involve formation of transient complexes where binding of a ligand allosterically modulates function. The ccd toxin-antitoxin system is...
Most biological processes involve formation of transient complexes where binding of a ligand allosterically modulates function. The ccd toxin-antitoxin system is involved in plasmid maintenance and bacterial persistence. The CcdA antitoxin accelerates dissociation of CcdB from its complex with DNA gyrase, binds and neutralizes CcdB, but the mechanistic details are unclear. Using a series of experimental and computational approaches, we demonstrate the formation of transient ternary and quaternary CcdA:CcdB:gyrase complexes and delineate the molecular steps involved in the rejuvenation process. Binding of region 61-72 of CcdA to CcdB induces the vital structural and dynamic changes required to facilitate dissociation from gyrase, region 50-60 enhances the dissociation process through additional allosteric effects, and segment 37-49 prevents gyrase rebinding. This study provides insights into molecular mechanisms responsible for recovery of CcdB-poisoned cells from a persister-like state. Similar methodology can be used to characterize other important transient, macromolecular complexes.
Topics: Bacterial Proteins; Bacterial Toxins; Binding Sites; Cysteine; DNA Gyrase; Fluorescence Resonance Energy Transfer; Models, Molecular; Multiprotein Complexes; Mutation; Surface Plasmon Resonance
PubMed: 32294467
DOI: 10.1016/j.str.2020.03.006 -
Mini Reviews in Medicinal Chemistry 2024Antibiotic or antimicrobial resistance is an urgent global public health threat that occurs when bacterial or fungal infections do not respond to the drug regimen... (Review)
Review
Antibiotic or antimicrobial resistance is an urgent global public health threat that occurs when bacterial or fungal infections do not respond to the drug regimen designed to treat these infections. As a result, these microbes are not evaded and continue to grow. Antibiotic resistance against natural and already-known antibiotics like Ciprofloxacin and Novobiocin can be overcome by developing an agent that can act in different ways. The success of agents like Zodiflodacin and Zenoxacin in clinical trials against DNA gyrase inhibitors that act on different sites of DNA gyrase has resulted in further exploration of this target. However, due to the emergence of bacterial resistance against these targets, there is a great need to design agents that can overcome this resistance and act with greater efficacy. This review provides information on the synthetic and natural DNA gyrase inhibitors that have been developed recently and their promising potential for combating antimicrobial resistance. The review also presents information on molecules that are in clinical trials and their current status. It also analysed the SAR studies and mechanisms of action of enlisted agents.
Topics: Topoisomerase II Inhibitors; DNA Gyrase; Humans; Anti-Bacterial Agents; Bacteria; Microbial Sensitivity Tests; Structure-Activity Relationship
PubMed: 37909434
DOI: 10.2174/0113895575264264230921080718 -
The FEBS Journal Mar 2023Toxin-antitoxin (TA) systems consist of a toxin inhibiting essential cellular functions (such as DNA, RNA and protein synthesis), and its cognate antitoxin neutralizing...
Toxin-antitoxin (TA) systems consist of a toxin inhibiting essential cellular functions (such as DNA, RNA and protein synthesis), and its cognate antitoxin neutralizing the toxicity. Recently, we identified a TA system termed TsbA/TsbT in the Staphylococcus aureus genome. The induction of the tsbT gene in Escherichia coli halted both DNA and RNA synthesis, reduced supercoiled plasmid and resulted in increasingly relaxed DNA. These results suggested that DNA gyrase was the target of TsbT. In addition, TsbT inhibited both E. coli and S. aureus DNA gyrase activity and induced linearization of plasmid DNA in vitro. Taken together, these results demonstrate that the TsbT toxin targets DNA gyrase in vivo. Site-directed mutagenesis experiments showed that the E27 and D37 residues in TsbT are critical for toxicity. Secondary structure prediction combining the analysis of vacuum-ultraviolet circular-dichroism spectroscopy and neural network method demonstrated that the 22nd-32nd residues of TsbT form an α-helix structure, and that the E27 residue is located around the centre of the α-helix segment. These findings give new insights not only into S. aureus TA systems, but also into bacterial toxins targeting DNA topoisomerases.
Topics: Escherichia coli; Bacterial Proteins; Staphylococcus aureus; DNA Gyrase; Toxin-Antitoxin Systems; Antitoxins; RNA
PubMed: 36148483
DOI: 10.1111/febs.16634 -
Research in Microbiology 2023Cells have evolved strategies to safeguard their genome integrity. We describe a mechanism to counter double strand breaks in the chromosome that involves the protection...
Cells have evolved strategies to safeguard their genome integrity. We describe a mechanism to counter double strand breaks in the chromosome that involves the protection of an essential housekeeping enzyme from external agents. YacG is a DNA gyrase inhibitory protein from Escherichia coli that protects the bacterium from the cytotoxic effects of catalytic inhibitors as well as cleavage-complex stabilizers of DNA gyrase. By virtue of blocking the primary DNA binding site of the enzyme, YacG prevents the accumulation of double strand breaks induced by gyrase poisons. It also enables the bacterium to resist the growth-inhibitory property of novobiocin. Gyrase poison-induced oxidative stress upregulates YacG production, probably as a cellular response to counter DNA damage. YacG-mediated protection of the genome is specific for gyrase targeting agents as the protection is not observed from the action of general DNA damaging agents. YacG also intensifies the transcription stress induced by rifampicin substantiating the importance of gyrase activity during transcription. Although essential for bacterial survival, DNA gyrase often gets entrapped by external inhibitors and poisons, resulting in cell death. The existence of YacG to specifically protect an essential housekeeping enzyme might be a strategy adopted by bacteria for competitive fitness advantage.
PubMed: 37343614
DOI: 10.1016/j.resmic.2023.104093 -
Bioorganic Chemistry Jan 2020Bacterial DNA gyrase is an important target for the development of novel antibacterial drugs, which are urgently needed because of high level of antibiotic resistance...
Bacterial DNA gyrase is an important target for the development of novel antibacterial drugs, which are urgently needed because of high level of antibiotic resistance worldwide. We designed and synthesized new 4,5,6,7-tetrahydrobenzo[d]thiazole-based DNA gyrase B inhibitors and their conjugates with siderophore mimics, which were introduced to increase the uptake of inhibitors into the bacterial cytoplasm. The most potent conjugate 34 had an IC of 58 nM against Escherichia coli DNA gyrase and displayed MIC of 14 µg/mL against E. coli ΔtolC strain. Only minor improvements in the antibacterial activities against wild-type E. coli in low-iron conditions were seen for DNA gyrase inhibitor - siderophore mimic conjugates.
Topics: Anti-Bacterial Agents; Bacteria; Drug Design; Microbial Sensitivity Tests; Molecular Mimicry; Siderophores; Thiazoles; Topoisomerase II Inhibitors
PubMed: 31911309
DOI: 10.1016/j.bioorg.2019.103550 -
Journal of Applied Microbiology Sep 2022This study was conducted to evaluate 35 natural flavonoids for their in vitro susceptibility against E. coli (ATCC 25922), Ps. aeruginosa (ATCC 27853), B. subtilis (ATCC...
AIMS
This study was conducted to evaluate 35 natural flavonoids for their in vitro susceptibility against E. coli (ATCC 25922), Ps. aeruginosa (ATCC 27853), B. subtilis (ATCC 530) and Staph. aureus (ATCC 6538) in search of a potential broad-spectrum antibiotic.
METHODS AND RESULTS
Glabridin, a natural isoflavonoid isolated from Glycyrrhiza glabra L., was identified to be highly active with a MIC of 8-16 μg ml against Staph. aureus, B. subtilis and E. coli. By the results of the docking simulation, we located the potential targets of glabridin as DNA gyrase and dihydrofolate reductase (DHFR). The subsequent DNA gyrase inhibition assays (glabridin: IC = 0.8516 μmol L , ciprofloxacin: IC = 0.04697 μmol L ), DHFR inhibition assays (glabridin: inhibition ratio = 29%, methotrexate: inhibition ratio = 45% under 100 μmol L treatment) and TUNEL confirmed that glabridin acted as DNA gyrase inhibitor and DHFR mild inhibitor, exerting bactericidal activity by blocking bacterial nucleic acid synthesis. CCK-8 and in silico calculations were also conducted to verify the low cytotoxicity and acceptable druggability of glabridin.
CONCLUSION
These findings suggest that glabridin represents the prototypical member of an exciting structural class of natural antimicrobial agents.
SIGNIFICANCE AND IMPACT OF THE STUDY
This study reports a novel mechanism of bactericidal activity of glabridin against Staph. aureus.
Topics: Anti-Bacterial Agents; DNA Gyrase; Escherichia coli; Flavonoids; Glycyrrhiza; Microbial Sensitivity Tests; Staphylococcus aureus
PubMed: 35801665
DOI: 10.1111/jam.15705 -
Journal of Medicinal Chemistry May 2021Herein, we describe the discovery and optimization of a novel series that inhibits bacterial DNA gyrase and topoisomerase IV binding to, and stabilization of, DNA...
Herein, we describe the discovery and optimization of a novel series that inhibits bacterial DNA gyrase and topoisomerase IV binding to, and stabilization of, DNA cleavage complexes. Optimization of this series led to the identification of compound , which has potent activity against Gram-positive bacteria, a favorable safety profile, and excellent pharmacokinetic properties. Compound was found to be efficacious against fluoroquinolone-sensitive infection in a mouse thigh model at lower doses than moxifloxacin. An X-ray crystal structure of the ternary complex formed by topoisomerase IV from , compound , and cleaved DNA indicates that this compound does not engage in a water-metal ion bridge interaction and forms no direct contacts with residues in the quinolone resistance determining region (QRDR). This suggests a structural basis for the reduced impact of QRDR mutations on antibacterial activity of compared to fluoroquinolones.
Topics: Animals; Anti-Bacterial Agents; DNA Gyrase; DNA Topoisomerase IV; Drug Design; Drug Resistance, Bacterial; Fluoroquinolones; Mice; Staphylococcus aureus; Topoisomerase II Inhibitors
PubMed: 33929852
DOI: 10.1021/acs.jmedchem.1c00375 -
Future Medicinal Chemistry Feb 2020DNA gyrase and topoisomerase IV are essential bacterial enzymes, and in the fight against bacterial resistance, they are important targets for the development of novel...
DNA gyrase and topoisomerase IV are essential bacterial enzymes, and in the fight against bacterial resistance, they are important targets for the development of novel antibacterial drugs. Building from our first generation of 4,5,6,7-tetrahydrobenzo[]thiazole-based DNA gyrase inhibitors, we designed and prepared an optimized series of analogs that show improved inhibition of DNA gyrase and topoisomerase IV from and , with IC values in the nanomolar range. Importantly, these inhibitors also show improved antibacterial activity against Gram-positive strains. The most promising inhibitor, , is active against , and wild-type and resistant strains, with minimum inhibitory concentrations between 4 and 8 μg/ml, which represents good starting point for development of novel antibacterials.
Topics: Anti-Bacterial Agents; Benzothiazoles; DNA Gyrase; Dose-Response Relationship, Drug; Gram-Positive Bacteria; Humans; Microbial Sensitivity Tests; Models, Molecular; Molecular Structure; Structure-Activity Relationship; Topoisomerase II Inhibitors
PubMed: 32043377
DOI: 10.4155/fmc-2019-0127