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ACS Omega Apr 2024Bacterial type II topoisomerases are well-characterized and clinically important targets for antibacterial chemotherapy. Novel bacterial topoisomerase inhibitors (NBTIs)...
Dynamic Profiling and Binding Affinity Prediction of NBTI Antibacterials against DNA Gyrase Enzyme by Multidimensional Machine Learning and Molecular Dynamics Simulations.
Bacterial type II topoisomerases are well-characterized and clinically important targets for antibacterial chemotherapy. Novel bacterial topoisomerase inhibitors (NBTIs) are a newly disclosed class of antibacterials. Prediction of their binding affinity to these enzymes would be beneficial for design/optimization of new NBTIs. Utilizing NBTI experimental data, we constructed two comprehensive multidimensional DNA gyrase surrogate models for ( = 0.791) and ( = 0.806). Both models accurately predicted the ICs of 26 NBTIs from our recent studies. To investigate the NBTI's dynamic profile and binding to both targets, 10 selected NBTIs underwent molecular dynamics (MD) simulations. The analysis of MD production trajectories confirmed key hydrogen-bonding and hydrophobic contacts that NBTIs establish in both enzymes. Moreover, the binding free energies of selected NBTIs were computed by the linear interaction energy (LIE) method employing an in-house derived set of fitting parameters (α = 0.16, β = 0.029, γ = 0.0, and intercept = -1.72), which are successfully applicable to DNA gyrase of Gram-positive/Gram-negative pathogens. Both methods offer accurate predictions of the binding free energies of NBTIs against and DNA gyrase. We are confident that this integrated modeling approach could be valuable in the design and optimization of efficient NBTIs for combating resistant bacterial pathogens.
PubMed: 38680300
DOI: 10.1021/acsomega.4c00036 -
Antibiotics (Basel, Switzerland) Apr 2024, (GAS), and (GBS) are bacteria that can cause a range of infections, some of them life-threatening. This review examines the spread of antibiotic resistance and its... (Review)
Review
, (GAS), and (GBS) are bacteria that can cause a range of infections, some of them life-threatening. This review examines the spread of antibiotic resistance and its mechanisms against antibiotics for streptococcal infections. Data on high-level penicillin-resistant invasive pneumococci have been found in Brazil (42.8%) and Japan (77%). The resistance is caused by mutations in genes that encode penicillin-binding proteins. Similarly, GAS and GBS strains reported from Asia, the USA, and Africa have undergone similar transformations in PBPs. Resistance to major alternatives of penicillins, macrolides, and lincosamides has become widespread among pneumococci and streptococci, especially in Asia (70-95%). The combination of several types with (B) is associated with the development of high-level macrolide resistance in GAS. Major mechanisms are ribosomal target modifications encoded by genes, ribosomal alterations, and active efflux pumps that regulate antibiotic entry due to A/E and D genes. Tetracycline resistance for streptococci in different countries varied from 22.4% in the USA to 83.7/100% in China, due to genes. Combined tetracycline/macrolide resistance is usually linked with the insertion of into the transposon carrying . New quinolone resistance is increasing by between 11.5 and 47.9% in Asia and Europe. The mechanism of quinolone resistance is based on mutations in /, determinants for DNA gyrase, or / encoding topoisomerase IV. The results for antibiotic resistance are alarming, and urgently call for increased monitoring of this problem and precautionary measures for control to prevent the spread of resistant mutant strains.
PubMed: 38667036
DOI: 10.3390/antibiotics13040360 -
Journal of Molecular Biology May 2024DNA mismatch repair endonuclease MutL is a member of GHKL ATPase superfamily. Mutations of MutL homologs are causative of a hereditary cancer, Lynch syndrome. We...
DNA mismatch repair endonuclease MutL is a member of GHKL ATPase superfamily. Mutations of MutL homologs are causative of a hereditary cancer, Lynch syndrome. We characterized MutL homologs from human and a hyperthermophile, Aquifex aeolicus, (aqMutL) to reveal the catalytic mechanism for the ATPase activity. Although involvement of a basic residue had not been conceived in the catalytic mechanism, analysis of the pH dependence of the aqMutL ATPase activity revealed that the reaction is catalyzed by a residue with an alkaline pK. Analyses of mutant aqMutLs showed that Lys79 is the catalytic residue, and the corresponding residues were confirmed to be critical for activities of human MutL homologs, on the basis of which a catalytic mechanism for MutL ATPase is proposed. These and other results described here would contribute to evaluating the pathogenicity of Lynch syndrome-associated missense mutations. Furthermore, it was confirmed that the catalytic lysine residue is conserved among DNA gyrases and microrchidia ATPases, other members of GHKL ATPases, indicating that the catalytic mechanism proposed here is applicable to these members of the superfamily.
Topics: Humans; Adenosine Triphosphatases; Amino Acid Sequence; Catalysis; Catalytic Domain; Conserved Sequence; Hydrogen-Ion Concentration; Lysine; MutL Proteins; Transcription Factors; DNA Gyrase; DNA-Binding Proteins
PubMed: 38641238
DOI: 10.1016/j.jmb.2024.168575 -
Biotechnology and Applied Biochemistry Apr 2024Most of the Escherichia coli turned into serious pathogens or developed antibiotic resistance, mainly due to their ability to show different phenotypic traits. In order...
In vitro antibacterial activity of antibiotics and plant essential oils against Escherichia coli MTCC443 supported through the molecular docking and pharmacokinetics study.
Most of the Escherichia coli turned into serious pathogens or developed antibiotic resistance, mainly due to their ability to show different phenotypic traits. In order to overcome the resistance to these antibiotics, the use of essential oils (EOs) is of great significance against highly pathogenic microorganisms. This study has been made to compare the in vitro antibacterial activity and further validated the same through the molecular docking study of 13 antibiotics such as ciprofloxacin, chloramphenicol, erythromycin, ampicillin, cefotaxime, rifampicin, kanamycin, vancomycin, streptomycin, penicillin, nalidixic acid, trimethoprim, and polymyxin, and 10 EOs such as garlic, tulsi, neem, clove, thyme, peppermint, coriander, tea, lavender, and eucalyptus against the target protein (DNA gyrase) of E. coli MTCC443. E. coli Microbial Type Culture Collection 443 was found to be highly sensitive to ciprofloxacin (zone of inhibition [ZOI], 2.5 cm ±0.1) and chloramphenicol (ZOI, 1.8 cm ±0.1), whereas garlic oil (ZOI, 5.5 cm ±0.1) and coriander oil (ZOI, 4.4 cm ±0.1) were found comparatively most effective. Further, the in silico investigation observed the same; ciprofloxacin (binding affinity: -7.2 kcal/mol) and chloramphenicol (binding affinity: -6.6 kcal/mol). Penicillin (binding affinity: -4.2 kcal/mol) and polymyxin (binding affinity: -0.3 kcal/mol) were found to be least effective against the tested microbe, whereas vancomycin (binding affinity: +0.8 kcal/mol) had no effect on it. Garlic (binding affinity: -7.8 kcal/mol), coriander (binding affinity: -6.8 kcal/mol), peppermint (binding affinity: -6.2 kcal/mol), and neem (binding affinity: -6.2 kcal/mol) oil exhibited the potent antibacterial activity against E. coli MTCC443, whereas thyme (binding affinity: -6.1 kcal/mol), tea tree (binding affinity: -4.9 kcal/mol), and tulsi (binding affinity: -3.8 kcal/mol) oil were observed moderately effective. Eucalyptus (binding affinity: -2.9 kcal/mol) and lavender (binding affinity: -2.8 kcal/mol) oil were found to be the least effective among all the oils tested. The pharmacokinetics and networking were performed to the pharmacology of the potential compounds.
PubMed: 38627930
DOI: 10.1002/bab.2583 -
Helicobacter 2024The current standard treatment for Helicobacter pylori infection, which involves a combination of two broad-spectrum antibiotics, faces significant challenges due to its...
BACKGROUND
The current standard treatment for Helicobacter pylori infection, which involves a combination of two broad-spectrum antibiotics, faces significant challenges due to its detrimental impact on the gut microbiota and the emergence of drug-resistant strains. This underscores the urgent requirement for the development of novel anti-H. pylori drugs. Zoliflodacin, a novel bacterial gyrase inhibitor, is currently undergoing global phase III clinical trials for treating uncomplicated Neisseria gonorrhoeae. However, there is no available data regarding its activity against H. pylori.
MATERIALS AND METHODS
We evaluated the in vitro activity of zoliflodacin against H. pylori clinical isolates (n = 123) with diverse multidrug resistance. We performed DNA gyrase supercoiling and microscale thermophoresis assays to identify the target of zoliflodacin in H. pylori. We analyzed 2262 H. pylori whole genome sequences to identify Asp424Asn and Lys445Asn mutations in DNA gyrase subunit B (GyrB) that are associated with zoliflodacin resistance.
RESULTS
Zoliflodacin exhibits potent activity against all tested isolates, with minimal inhibitory concentration (MIC) values ranging from 0.008 to 1 μg/mL (MIC: 0.125 μg/mL; MIC: 0.25 μg/mL). Importantly, there was no evidence of cross-resistance to any of the four first-line antibiotics commonly used against H. pylori. We identified GyrB as the primary target of zoliflodacin, with Asp424Asn or Lys445Asn substitutions conferring resistance. Screening of 2262 available H. pylori genomes for the two mutations revealed only one clinical isolate carrying Asp424Asn substitution.
CONCLUSION
These findings support the potential of zoliflodacin as a promising candidate for H. pylori treatment, warranting further development and evaluation.
Topics: Humans; Anti-Bacterial Agents; Barbiturates; DNA Gyrase; Drug Resistance, Bacterial; Helicobacter Infections; Helicobacter pylori; Isoxazoles; Microbial Sensitivity Tests; Morpholines; Oxazolidinones; Spiro Compounds; Clinical Trials, Phase III as Topic
PubMed: 38627919
DOI: 10.1111/hel.13075 -
International Journal of Molecular... Mar 2024With the rapid emergence of drug-resistant strains of (Mtb), various levels of resistance against existing anti-tuberculosis (TB) drugs have developed. Consequently,...
With the rapid emergence of drug-resistant strains of (Mtb), various levels of resistance against existing anti-tuberculosis (TB) drugs have developed. Consequently, the identification of new anti-TB targets and drugs is critically urgent. DNA gyrase subunit B (GyrB) has been identified as a potential anti-TB target, with novobiocin and SPR719 proposed as inhibitors targeting GyrB. Therefore, elucidating the molecular interactions between GyrB and its inhibitors is crucial for the discovery and design of efficient GyrB inhibitors for combating multidrug-resistant TB. In this study, we revealed the detailed binding mechanisms and dissociation processes of the representative inhibitors, novobiocin and SPR719, with GyrB using classical molecular dynamics (MD) simulations, tau-random acceleration molecular dynamics (τ-RAMD) simulations, and steered molecular dynamics (SMD) simulations. Our simulation results demonstrate that both electrostatic and van der Waals interactions contribute favorably to the inhibitors' binding to GyrB, with Asn52, Asp79, Arg82, Lys108, Tyr114, and Arg141 being key residues for the inhibitors' attachment to GyrB. The τ-RAMD simulations indicate that the inhibitors primarily dissociate from the ATP channel. The SMD simulation results reveal that both inhibitors follow a similar dissociation mechanism, requiring the overcoming of hydrophobic interactions and hydrogen bonding interactions formed with the ATP active site. The binding and dissociation mechanisms of GyrB with inhibitors novobiocin and SPR719 obtained in our work will provide new insights for the development of promising GyrB inhibitors.
Topics: Mycobacterium tuberculosis; Novobiocin; Thermodynamics; Antitubercular Agents; Molecular Dynamics Simulation; Adenosine Triphosphate
PubMed: 38612573
DOI: 10.3390/ijms25073764 -
Molecules (Basel, Switzerland) Mar 2024Carbothioamides , were generated in high yield by reacting furan imidazolyl ketone with -arylthiosemicarbazide in EtOH with a catalytic amount of conc. HCl. The...
Carbothioamides , were generated in high yield by reacting furan imidazolyl ketone with -arylthiosemicarbazide in EtOH with a catalytic amount of conc. HCl. The reaction of carbothioamides , with hydrazonyl chlorides - in EtOH with triethylamine at reflux produced 1,3-thiazole derivatives -. In a different approach, the 1,3-thiazole derivatives and were produced by reacting and with chloroacetone to afford and , respectively, followed by diazotization with 4-methylbenzenediazonium chloride. The thiourea derivatives and then reacted with ethyl chloroacetate in ethanol with AcONa at reflux to give the thiazolidinone derivatives and . The produced compounds were tested for antioxidant and antibacterial properties. Using phosphomolybdate, promising thiazoles and showed the best antioxidant activities at 1962.48 and 2007.67 µgAAE/g dry samples, respectively. Thiazoles and had the highest antibacterial activity against and with 28, 25 and 27, 28 mm, respectively. Thiazoles and had the best activity against with 26 mm and 37 mm, respectively. Thiazole had the highest activity against , surpassing cyclohexamide. Most compounds demonstrated lower MIC values than neomycin against , and . A molecular docking study examined how antimicrobial compounds interact with DNA gyrase B crystal structures. The study found that all of the compounds had good binding energy to the enzymes and reacted similarly to the native inhibitor with the target DNA gyrase B enzymes' key amino acids.
Topics: Antioxidants; Molecular Docking Simulation; DNA Gyrase; Escherichia coli; Staphylococcus aureus; Anti-Bacterial Agents; Imidazoles; Candida albicans; Thiazoles
PubMed: 38611769
DOI: 10.3390/molecules29071491 -
European Journal of Medicinal Chemistry Apr 2024The emergence of serious bacterial resistance towards clinical oxacins poses a considerable threat to global public health, necessitating the development of novel...
The emergence of serious bacterial resistance towards clinical oxacins poses a considerable threat to global public health, necessitating the development of novel structural antibacterial agents. Seven types of novel indolylacryloyl-derived oxacins (IDOs) were designed and synthesized for the first time from commercial 3,4-difluoroaniline via an eight-step procedure. The synthesized compounds were characterized by modern spectroscopic techniques. All target molecules were evaluated for antimicrobial activities. Most of the prepared IDOs showed a broad antibacterial spectrum and strong activities against the tested strains, especially ethoxycarbonyl IDO 10d (0.25-0.5 μg/mL) and hydroxyethyl IDO 10e (0.25-1 μg/mL) exhibited much superior antibacterial efficacies to reference drug norfloxacin. These highly active IDOs also displayed low hemolysis, cytotoxicity and resistance, as well as rapid bactericidal capacity. Further investigations indicated that ethoxycarbonyl IDO 10d and hydroxyethyl IDO 10e could effectively reduce the exopolysaccharide content and eradicate the formed biofilm, which might delay the development of drug resistance. Preliminary exploration of the antibacterial mechanism revealed that active IDOs could not only destroy membrane integrity, resulting in changes in membrane permeability, but also promote the accumulation of reactive oxygen species, leading to the production of malondialdehyde and decreased bacterial metabolism. Moreover, they exhibited the capability to bind with DNA and DNA gyrase, forming supramolecular complexes through various noncovalent interactions, thereby inhibiting DNA replication and causing bacterial death. All the above results suggested that the newly developed indolylacryloyl-derived oxacins should hold great promise as potential multitargeting broad-spectrum antibacterial candidates to overcome drug resistance.
Topics: Anti-Bacterial Agents; Norfloxacin; Bacteria; Cell Membrane Permeability; DNA; Microbial Sensitivity Tests
PubMed: 38608408
DOI: 10.1016/j.ejmech.2024.116392 -
ACS Infectious Diseases Apr 2024Antimicrobial resistance is a global threat to human health. Therefore, efforts have been made to develop new antibacterial agents that address this critical medical...
Antimicrobial resistance is a global threat to human health. Therefore, efforts have been made to develop new antibacterial agents that address this critical medical issue. Gepotidacin is a novel, bactericidal, first-in-class triazaacenaphthylene antibacterial in clinical development. Recently, phase III clinical trials for gepotidacin treatment of uncomplicated urinary tract infections caused by uropathogens, including , were stopped for demonstrated efficacy. Because of the clinical promise of gepotidacin, it is important to understand how the compound interacts with its cellular targets, gyrase and topoisomerase IV, from . Consequently, we determined how gyrase and topoisomerase IV mutations in amino acid residues that are involved in gepotidacin interactions affect the susceptibility of cells to the compound and characterized the effects of gepotidacin on the activities of purified wild-type and mutant gyrase and topoisomerase IV. Gepotidacin displayed well-balanced dual-targeting of gyrase and topoisomerase IV in cells, which was reflected in a similar inhibition of the catalytic activities of these enzymes by the compound. Gepotidacin induced gyrase/topoisomerase IV-mediated single-stranded, but not double-stranded, DNA breaks. Mutations in GyrA and ParC amino acid residues that interact with gepotidacin altered the activity of the compound against the enzymes and, when present in both gyrase and topoisomerase IV, reduced the antibacterial activity of gepotidacin against this mutant strain. Our studies provide insights regarding the well-balanced dual-targeting of gyrase and topoisomerase IV by gepotidacin in .
Topics: Acenaphthenes; Amino Acids; Anti-Bacterial Agents; DNA Gyrase; DNA Topoisomerase IV; Escherichia coli; Heterocyclic Compounds, 3-Ring
PubMed: 38606465
DOI: 10.1021/acsinfecdis.3c00346 -
ACS Infectious Diseases Apr 2024Fluoroquinolones make up a critically important class of antibacterials administered worldwide to treat human infections. However, their clinical utility has been...
Fluoroquinolones make up a critically important class of antibacterials administered worldwide to treat human infections. However, their clinical utility has been curtailed by target-mediated resistance, which is caused by mutations in the fluoroquinolone targets, gyrase and topoisomerase IV. An important pathogen that has been affected by this resistance is , the causative agent of gonorrhea. Over 82 million new cases of this sexually transmitted infection were reported globally in 2020. Despite the impact of fluoroquinolone resistance on gonorrhea treatment, little is known about the interactions of this drug class with its targets in this bacterium. Therefore, we investigated the effects of the fluoroquinolone ciprofloxacin on the catalytic and DNA cleavage activities of wild-type gyrase and topoisomerase IV and the corresponding enzymes that harbor mutations associated with cellular and clinical resistance to fluoroquinolones. Results indicate that ciprofloxacin interacts with both gyrase (its primary target) and topoisomerase IV (its secondary target) through a water-metal ion bridge that has been described in other species. Moreover, mutations in amino acid residues that anchor this bridge diminish the susceptibility of the enzymes for the drug, leading to fluoroquinolone resistance. Results further suggest that ciprofloxacin primarily induces its cytotoxic effects by enhancing gyrase-mediated DNA cleavage as opposed to inhibiting the DNA supercoiling activity of the enzyme. In conclusion, this work links the effects of ciprofloxacin on wild-type and resistant gyrase to results reported for cellular and clinical studies and provides a mechanistic explanation for the targeting and resistance of fluoroquinolones in .
Topics: Humans; Ciprofloxacin; Fluoroquinolones; DNA Topoisomerase IV; Neisseria gonorrhoeae; Gonorrhea; DNA Gyrase; Microbial Sensitivity Tests
PubMed: 38606464
DOI: 10.1021/acsinfecdis.4c00041