Gyrase Research Articles

Isolation, vibrational analysis, quantum chemical studies, nature of bonding, and molecular docking studies of triterpenoid isolates from Ganoderma lucidum as potent typhoid fever agent

The bacteria Salmonella Typhi is the source of the dangerous and perhaps fatal disease known as typhoid fever. Typhoid fever treatment is difficult despite the availability of potent medications due to the rise of multi-drug resistance strains. Herein, the extraction, LC-MS and FT-IR spectral characterization, density functional theory (DFT) and molecular docking investigation of 3,15-dihydroxy-11-toxolanost-8,24-dien-26-oic acid (C30H45O5) [MDC_1], Ganoderic acid F (C32H41O9) [MDC_2], and Ganolucidic acid E (C30H43O5) [MDC_3] isolated compounds from G. lucium against Salmonella Typhi enzyme, DNA gyrase B is presented along with the influence of solvation in polar and non-polar solvents. The FT-IR spectral results show that the triterpenoid extract of G. lucidum contains oxygen atoms, which mainly exist in functional groups (such as CO, O–H, C–O) and are consistent with the general molecular structures of triterpenoids. The reactivity parameters in the gas phase show that MDC_1 and MDC_3 have higher energy gaps whereas MD_2 has the lowest energy gap, indicating that it is more reactive than the other complexes. The energy gap of the compounds in solvent also shows a little shift, compared to the energy gap in Ethanol and Heptane, respectively. The results of the molecular docking study revealed several small molecules with strong binding affinities for the protein targets, suggesting that they could be used as potential therapeutics for typhoid fever. Therefore, this study suggests that molecular docking is a powerful tool for identifying novel therapeutics against tropical diseases such as typhoid fever.

Decoding a cryptic mechanism of metronidazole resistance among globally disseminated fluoroquinolone-resistant Clostridioides difficile

Severe outbreaks and deaths have been linked to the emergence and global spread of fluoroquinolone-resistant Clostridioides difficile over the past two decades. At the same time, metronidazole, a nitro-containing antibiotic, has shown decreasing clinical efficacy in treating C. difficile infection (CDI). Most metronidazole-resistant C. difficile exhibit an unusual resistance phenotype that can only be detected in susceptibility tests using molecularly intact heme. Here, we describe the mechanism underlying this trait. We find that most metronidazole-resistant C. difficile strains carry a T-to-G mutation (which we term PnimBG) in the promoter of gene nimB, resulting in constitutive transcription. Silencing or deleting nimB eliminates metronidazole resistance. NimB is related to Nim proteins that are known to confer resistance to nitroimidazoles. We show that NimB is a heme-dependent flavin enzyme that degrades nitroimidazoles to amines lacking antimicrobial activity. Furthermore, occurrence of the PnimBG mutation is associated with a Thr82Ile substitution in DNA gyrase that confers fluoroquinolone resistance in epidemic strains. Our findings suggest that the pandemic of fluoroquinolone-resistant C. difficile occurring over the past few decades has also been characterized by widespread resistance to metronidazole.

Phenotypic and genetic insights into efflux pump mechanism in Mycoplasma anserisalpingitidis.

Mycoplasma anserisalpingitidis is one of the most important waterfowl-pathogenic mycoplasmas. Due to inadequate antibiotic treatment, many strains with high minimal inhibitory concentration (MIC) values for multiple drugs have been isolated lately. Decreased antibiotic susceptibility in several Mycoplasma species are known to be associated with mutations in topoisomerase and ribosomal genes, but other strategies such as active efflux pump mechanisms were also described. The scope of this study was the phenotypic and genetic characterization of the active efflux mechanism in M. anserisalpingitidis. We measured the MIC values in the presence and absence of different efflux pump inhibitors (EPIs), such as carbonyl cyanide m-chlorophenylhydrazine (CCCP), orthovanadate (OV), and reserpine (RSP). Moreover, bioinformatic tools were utilized to detect putative regulatory sequences of membrane transport proteins coding genes, while comparative genome analysis was performed to reveal potential markers of antibiotic resistance. Out of the three examined EPIs, CCCP decreased the MICs at least two-fold below the original MICs (in 23 cases out of 36 strains). In the presence of OV or RSP, MIC value differences could be seen only if modified dilution series (10% decrease steps were used instead of two-fold dilutions) were applied (in 24/36 cases with OV and 9/36 with RSP). During comparative genome analysis, non-synonymous single nucleotide polymorphisms (nsSNPs) were identified in genes encoding ABC membrane transport proteins, which were displayed in higher percentages in M. anserisalpingitidis strains with increased MICs. In terms of other genes, a nsSNP was identified in DNA gyrase subunit A (gyrA) gene which can be related to decreased susceptibility to enrofloxacin. The present study is the first to highlight the importance of efflux pump mechanisms in M. anserisalpingitidis. Considering the observed effects of the EPI CCCP against this bacterium, it can be assumed, that the use of EPIs would increase the efficiency of targeted antibiotic therapy in the future control of this pathogen. However, further research is required to obtain a more comprehensive understanding of efflux pump mechanism in this bacterium.

Novel fluoroquinolones analogues bearing 4-(arylcarbamoyl)benzyl: design, synthesis, and antibacterial evaluation.

Bacterial resistance to fluoroquinolone has been increasing at an alarming rate worldwide. In an attempt to find more potent anti-bacterial agents, an efficient, straightforward protocol was performed to obtain a large substrate scope of novel ciprofloxacin and sarafloxacin analogues conjugated with 4-(arylcarbamoyl)benzyl 7a-ab. All prepared compounds were evaluated for their anti-bacterial activities against three gram-positive strains (Methicillin resistant staphylococcus aureus (MRSA), Staphylococcus aureus, and Enterococcus faecalis) as well as three gram-negative strains (Pseudomonas aeruginosa, Klebsiella pneumonia, and Escherichia coli) through three standard methods including broth microdilution, agar-disc diffusion, and agar-well diffusion assays. Most of the compounds exhibited great to excellent anti-bacterial potencies against MRSA and S. aureus. Among the targeted compounds, derivative 7n exhibited great antibacterial potency, which was noticeably more potent than parent ciprofloxacin. Subsequently, a molecular docking study was performed for this compound to find out its probable binding mode with the active site of S. aureus DNA gyrase (PDB ID: 2XCT).

Efficient Dye Degradation and Antibacterial Activity of Carbon Dots/Chitosan-Doped La2O3 Nanorods: In Silico Molecular Docking Analysis.

This work demonstrates the degradation of toxic RhB (rhodamine B) dye from polluted water in various pH environments. It assesses the antibacterial action of CDs (carbon dots)/CS (chitosan)-doped La2O3 (lanthanum oxide) NRs (nanorods). CS and CDs have been introduced as dopants to modify the characteristics of La2O3 to achieve efficient outcomes. The influence of doping on the structural, morphological, optical, and elemental properties of synthesized La2O3 NRs was investigated through a number of analytical techniques. The structural analysis of XRD revealed a hexagonal phase. The rod-like structure of pure La2O3 and reduction in the size of NRs upon doping were exhibited by TEM micrographs. From UV-vis spectroscopy, increased absorption upon doping and introduction of redshift that led to reduced bandgap energy were observed. The FTIR spectra indicate the presence of functional groups of pure and integrated samples. The catalytic activity of specimens in basic medium toward dye showed excellent results (94.57%). The inhibition zone of diameter 4.15 mm was evaluated by 6 mL of CDs/CS-doped La2O3 NRs against Escherichia coli once the surface area increased by dopants. In silico experiments were performed for enoyl-[acyl-carrier-protein] reductase (FabI) and DNA gyrase enzymes to assess the potency of CS-doped La2O3 and CDs/CS-doped La2O3 as their inhibitors and to justify their possible mechanism of action.

Assessment of Structural Basis for Thiazolopyridine Derivatives as DNA Gyrase-B Inhibitors.

Tuberculosis (TB) is one of the leading causes of death in the post-COVID- 19 era. It has been observed that there is a devastating condition with a 25-30% increase in TB patients. DNA gyrase B isoform has proved its high potential to be a therapeutically effective target for developing newer and safer anti-TB agents. This study aims to identify minimum structural requirements for the optimization of thiazolopyridine derivatives having DNA gyrase inhibitory activities. Moreover, developed QSAR models could be used to design new thiazolopyridine derivatives and predict their DNA gyrase B inhibitory activity before synthesis. 3D-QSAR and Group-based QSAR (G-QSAR) methodologies were adopted to develop accurate, reliable, and predictive QSAR models. Statistical methods such as kNN-MFA SW-FB and MLR SW-FB were used to correlate dependent parameters with descriptors. Both models were thoroughly validated for internal and external predictive abilities. The 3D-QSAR model significantly correlated steric and electrostatic descriptors with q2 0.7491 and predicted r2 0.7792. The G-QSAR model showed that parameters such as SsOHE-index, slogP, ChiV5chain, and T_C_C_3 were crucial for optimizing thiazolopyridine derivatives as DNA gyrase inhibitors. The 3D-QSAR model was interpreted extensively with respect to 3D field points, and the pattern of fragmentation was studied in the G-QSAR model. The 3D-QSAR and G-QSAR models were found to be highly predictive. These models could be useful for designing potent DNA gyrase B inhibitors before their synthesis.

Development of antisense peptide-peptide nucleic acids against fluoroquinolone-resistant Escherichia coli.

Fluoroquinolones (FQs) are potent and broad-spectrum antibiotics commonly used to treat MDR bacterial infections, but bacterial resistance to FQs has emerged and spread rapidly around the world. The mechanisms for FQ resistance have been revealed, including one or more mutations in FQ target genes such as DNA gyrase (gyrA) and topoisomerase IV (parC). Because therapeutic treatments for FQ-resistant bacterial infections are limited, it is necessary to develop novel antibiotic alternatives to minimize or inhibit FQ-resistant bacteria. To examine the bactericidal effect of antisense peptide-peptide nucleic acids (P-PNAs) that can block the expression of DNA gyrase or topoisomerase IV in FQ-resistant Escherichia coli (FRE). A set of antisense P-PNA conjugates with a bacterial penetration peptide were designed to inhibit the expression of gyrA and parC and were evaluated for their antibacterial activities. Antisense P-PNAs, ASP-gyrA1 and ASP-parC1, targeting the translational initiation sites of their respective target genes significantly inhibited the growth of the FRE isolates. In addition, ASP-gyrA3 and ASP-parC2, which bind to the FRE-specific coding sequence within the gyrA and parC structural genes, respectively, showed selective bactericidal effects against FRE isolates. Our results demonstrate the potential of targeted antisense P-PNAs as antibiotic alternatives against FQ-resistance bacteria.

Identification, Screening and Antibacterial Mechanism Analysis of Novel Antimicrobial Peptides from Sturgeon (Acipenser ruthenus) Spermary.

Fish is an important source of antimicrobial peptides. This study aimed to identify and screen antibacterial peptides with excellent antibacterial activity derived from sturgeon spermary peptides (SSPs) and to analyze their antibacterial activity and mechanism. Liquid chromatography-mass spectrometry/mass spectrometry methods were used to analyze and identify peptide sequences, computational prediction tool and molecular docking methods were used for virtual screening of antimicrobial peptides, and finally, candidate peptides were synthesized by solid-phase synthesis method. The results demonstrate that SSPs have excellent inhibitory activity against Escherichia coli with an inhibitory rate of 76.46%. Most parts of the SSPs were derived from the sturgeon (Acipenser ruthenus) histones, and the coverage of histone H2B was the highest (45%). Two novel peptides (NDEELNKLM and RSSKRRQ) were obtained by in silico prediction tools and molecular docking, which may interact with the DNA gyrase and dihydrofolate reductase of E. coli by forming salt bridges and hydrogen bonds. Compared to the individual peptides, the antibacterial effect was significantly improved by mixing the two peptides in equal proportions. Two novel peptides change the permeability of the E. coli cell membranes and may exert antimicrobial activity by inhibiting the metabolic process of the nucleic acids.

New Benzopyrrole Derivatives: Synthesis and Appraisal of Their Potential as Antimicrobial Agents.

A series of twenty compounds (23-42) were synthesized and characterized by spectral studies in order to explore newer antimicrobial compounds. The majority of the synthesized compounds reported significant antimicrobial properties against various pathogenic bacterial and fungal strains with the help of tube dilution method. Significant activities (MIC ranging from 3.9 to 15.62 μg/ml) have been shown against Gram-negative and Gram-positive bacteria with. In contrast, moderate to outstanding antibacterial activity was reported versus Gram-negative bacteria such as E. coli and P. aeruginosa along with Gram-positive bacteria such as S. aureus and B. subtilis. While antifungal activity was moderate to excellent against two fungus strains (Candida tropicalis, Candida glabrata). Compounds 25 and 34 had the utmost activity versus Gram-positive and Gram-negative bacteria too. The antifungal activity of compound 35 was comparable to that of standard. In-silico Molecular docking evaluations were performed for antibacterial and antifungal activities against the target DNA gyrase A (PDB: 1AB4) and 14 alpha-sterol demethylase enzyme (PDB: 1EA1), respectively. The dock score for typicals compounds for antibacterial and antifungal activity were -4.733 and -9.4, respectively. The three-dimensional QSAR examination was carried out by multiple linear regression (SA-MLR) with good predictive power (r2=0.9105, q2=0.8011). Establishment of several interactions between the ligand 25 and 34 and the active site of residue of both receptors, enable the ligand 25 and 34 to be fit well in the pocket of the active site, as seen in Molecular dynamics simulations analysis. Thus, data suggest that these ligands could be further explored as potential precursors to develop antimicrobial drugs.

Molecular Docking and ADME Profiles of β-Carboline Analogues as Potential Antibiotic Agents Targeting DNA Gyrase

Molecular Docking and ADME Profiles of β-Carboline Analogues as Potential Antibiotic Agents Targeting DNA Gyrase

Exploring the 5-Substituted 2-Aminobenzothiazole-Based DNA Gyrase B Inhibitors Active against ESKAPE Pathogens.

We present a new series of 2-aminobenzothiazole-based DNA gyrase B inhibitors with promising activity against ESKAPE bacterial pathogens. Based on the binding information extracted from the cocrystal structure of DNA gyrase B inhibitor A, in complex with Escherichia coli GyrB24, we expanded the chemical space of the benzothiazole-based series to the C5 position of the benzothiazole ring. In particular, compound E showed low nanomolar inhibition of DNA gyrase (IC50 < 10 nM) and broad-spectrum antibacterial activity against pathogens belonging to the ESKAPE group, with the minimum inhibitory concentration < 0.03 μg/mL for most Gram-positive strains and 4-16 μg/mL against Gram-negative E. coli, Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae. To understand the binding mode of the synthesized inhibitors, a combination of docking calculations, molecular dynamics (MD) simulations, and MD-derived structure-based pharmacophore modeling was performed. The computational analysis has revealed that the substitution at position C5 can be used to modify the physicochemical properties and antibacterial spectrum and enhance the inhibitory potency of the compounds. Additionally, a discussion of challenges associated with the synthesis of 5-substituted 2-aminobenzothiazoles is presented.

Synthesis, antibacterial screening and computational studies of quinazoline-4 (3H)-one-triazole conjugates

A novel series of quinazoline-4 (3H)-one-tagged triazole conjugates were synthesised using the copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) methodology. All synthesized compounds were structurally elucidated with the help of 2D-NMR (HMBC, HSQC, COSY) techniques and other spectral evidence. The in vitro antibacterial activities of these compounds were evaluated and compared with commercial drugs ciprofloxacin, ampicillin, and levofloxacin. Four compounds (4a, 4d, 4g, and 4i) of the series exhibited potent activity and selectivity against the gram-negative bacterial strains. Amongst these, 4i emerged as the most active conjugate with almost 12-fold superior activity to ampicillin against Klebsiella pneumoniae (gram-negative), one of the most challenging multidrug-resistant strains worldwide. Structure-activity relationship (SAR) analysis further revealed that the incorporation of a triazole ring incredibly increased the antibacterial activity of quinazoline Schiff bases towards the gram-negative bacteria. Moreover, the para-positioning of strong electron-donating (–OCH3) and electron-withdrawing (-NO2) groups at the phenyl ring of the triazole ring positively influenced the antibacterial activity, whereas the meta-substitution generally decreased the antibacterial activity of the conjugates. Furthermore, molecular docking studies were conducted to explore the binding characteristics of these compounds in the binding site of DNA gyrase (Staphylocouccus aureus).

Preservative effects of composite biopreservatives on goat meat during chilled storage: Insights into meat quality, high-throughput sequencing and molecular docking

To investigate the preservative effect of composite biopreservatives on goat meat during chilled storage, three biopreservatives (chitosan, tea polyphenols and grape seed extract) were selected. Meat samples were soaked in composite biopreservatives at previously optimized concentrations, prior to storage at 4 °C for 12 days. Meat quality parameters including pH, TBARS, TVB-N, color, sensory index and total viable count were evaluated. 16S rDNA high-throughput sequencing combined with bioinformatics was used to assess the changes in the bacterial community, while molecular docking permitted the investigation of molecular interaction between gyrase, catechins, and anthocyanins. Treatment by composite biopreservatives contributed to the stability and maintenance of meat quality, notably by significantly reducing TBARS and maintaining meat color and sensory scores. Pseudomonadales, Bacillales and Flavobacteriales were effectively inhibited as the main spoilage bacteria in goat meat during chilled storage. Molecular docking revealed that catechins and anthocyanins could bind to DNA gyrase by hydrogen bonds and hydrophobic interactions, thus inhibiting DNA synthesis and bacterial growth. Hence, the composite biopreseratives exerted a preservative impact on the chilled goat meat.

Novel indole derivatives of dihydropyrimidinone: Synthesis, characterization, molecular docking and antimicrobial activity

The enaminone was reacted with substituted aldehyde and urea in glacial acetic acid. The indole derivatives of dihydropyrimidinone were obtained in good yield. Spectroscopic methods were employed to confirm and characterize the structures of all novel synthesized compounds. All the compounds were screened for antimicrobial activity against Gram-positive, Gram-negative, and Candida albicans. Most of the synthesized compounds were active against all tested trains. Enaminone was found to be highly active against all strains except P. aeruginosa and S. typhi. Enaminone presented (MIC = 64 µg/mL) against S. pneumonia, (MIC = 16 µg/mL) against B. anthracis, and (MIC = 32 µg/mL) against S. aureus as compared to positive control erythromycin (MIC = 8 µg/mL), gentamycin (MIC = 2 µg/mL) and ciprofloxacin (MIC = 4 g/L) respectively. A molecular docking study was performed at the active site of E. coli DNA gyrase, K. pneumonia DNA gyrase, and topoisomerase IV. The results showed that the compound with phenyl substitution exhibited an inhibition zone of 18 mm against E. coli and presented the highest binding energy S = -9.83 kcal/mol. It showed three π−bonds with (DA20, and DT15), aromatic rings in the molecule, and the carboxyl groups of the urea ring chelated Mg2+. Compound with 4-nitrophenyl exhibited an inhibition zone of 13.6 mm against K. pneumoniae. It also presented the highest binding energy S = -9.55 kcal/mol. LYS444 and DC315 were predicted to form an H-bond donor with hydrogen in phenyl and urea rings. All the compounds followed Lipinski's rule of five without any violation.

Evolution of YacG to safeguard DNA gyrase from external perturbation

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.

Chrysin based pyrimidine-piperazine hybrids: design, synthesis, in vitro antimicrobial and in silico E. coli topoisomerase II DNA gyrase efficacy.

Ten chrysin-based pyrimidine-piperazine hybrids have been evaluated in vitro for antimicrobial activity against eleven bacterial and two fungal strains. All compounds 5a-j exhibited moderate to good inhibition, with MIC values ranging from 6.25 to 250µg/ml. At 6.25µg/ml and 12.5µg/ml MIC values, respectively, compounds 5b and 5h demonstrated the most promising potency against E. coli, outperforming ampicillin, chloramphenicol, and ciprofloxacin. None of the substances had the same level of action as norfloxacin. 5a, 5d, 5g, 5h, and 5i have exhibited superior antifungal efficacy than Griseofulvin against C. albicans with 250µg/ml MIC. All the compounds were also individually docked into the E. coli DNA gyrase ATP binding site (PDB ID: 1KZN) and CYP51 inhibitor (PDB ID: 5V5Z). The most active compound, 5h and 5g displayed a Glide docking score of - 5.97kcal/mol and - 10.99kcal/mol against DNA gyrase and 14α-demethylase enzyme CYP51 respectively. Potent compounds 5b, 5h, and 5g may be used to design new, innovative antimicrobial agents, according to in vitro, ADMET, and in silico biological efficacy analyses.

Characterization of DNA Gyrase Activity and Elucidation of the Impact of Amino Acid Substitution in GyrA on Fluoroquinolone Resistance in Mycobacterium avium.

Mycobacterium avium, a member of the M. avium complex (MAC), is the major pathogen contributing to nontuberculous mycobacteria (NTM) infections worldwide. Fluoroquinolones (FQs) are recommended for the treatment of macrolide-resistant MACs. The association of FQ resistance and mutations in the quinolone resistance-determining region (QRDR) of gyrA of M. avium is not yet clearly understood, as many FQ-resistant clinical M. avium isolates do not have such mutations. This study aimed to elucidate the role of amino acid substitution in the QRDR of M. avium GyrA in the development of FQ resistance. We found four clinical M. avium subsp. hominissuis isolates with Asp-to-Gly change at position 95 (Asp95Gly) and Asp95Tyr mutations in gyrA that were highly resistant to FQs and had 2- to 32-fold-higher MICs than the wild-type (WT) isolates. To clarify the contribution of amino acid substitutions to FQ resistance, we produced recombinant WT GyrA, GyrB, and four GyrA mutant proteins (Ala91Val, Asp95Ala, Asp95Gly, and Asp95Tyr) to elucidate their potential role in FQ resistance, using them to perform FQ-inhibited DNA supercoiling assays. While all the mutant GyrAs contributed to the higher (1.3- to 35.6-fold) FQ 50% inhibitory concentration (IC50) than the WT, Asp95Tyr was the most resistant mutant, with an IC50 15- to 35.6-higher than that of the WT, followed by the Asp95Gly mutant, with an IC50 12.5- to 17.6-fold higher than that of the WT, indicating that these amino acid substitutions significantly reduced the inhibitory activity of FQs. Our results showed that amino acid substitutions in the gyrA of M. avium contribute to FQ resistance. IMPORTANCE The emergence of fluoroquinolone (FQ) resistance has further compounded the control of emerging Mycobacterium avium-associated nontuberculous mycobacteria infections worldwide. For M. avium, the association of FQ resistance and mutations in the quinolone resistance-determining region (QRDR) of gyrA is not yet clearly understood. Here, we report that four clinical M. avium isolates with a mutation in the QRDR of gyrA were highly resistant to FQs. We further clarified the impact of mutations in the QRDR of GyrA proteins by performing in vitro FQ-inhibited DNA supercoiling assays. These results confirmed that, like in Mycobacterium tuberculosis, mutations in the QRDR of gyrA also strongly contribute to FQ resistance in M. avium. Since many FQ-resistant M. avium isolates do have these mutations, the detailed molecular mechanism of FQ resistance in M. avium needs further exploration.

Bacillus velezensis FX-6 suppresses the infection of Botrytis cinerea and increases the biomass of tomato plants.

Botrytis cinerea causing tomato gray mold is a major cause of economic loss in tomato production. It is urgent and necessary to seek an effective and environmentally friendly control strategy to control tomato grey mold disease. In this study, Bacillus velezensis FX-6 isolated from the rhizosphere of plants displayed significant inhibitory ability against B. cinerea and could promote tomato plant growth. FX-6 could effectively inhibit the growth of Botrytis cinerea mycelium in vitro and in vivo, and the inhibitory rate in vitro could reach 78.63%. According to morphological observations and phylogenetic trees based on sequences of the 16S rDNA and gyrA (DNA gyrase subunit A) genes, the strain FX-6 was identified as Bacillus velezensis. In addition, B. velezensis FX-6 showed antagonistic activity against seven phytopathogens, this indicated that FX-6 had broad-spectrum biocontrol activity. We also found that FX-6 fermentation broth had the strongest antagonistic activity against B. cinerea when the culture time was 72 hours, and the inhibition rate was 76.27%. The growth promotion test revealed that strain FX-6 significantly promoted tomato seed germination and seedling growth. Further deeply study on growth-promoting mechanism indicated that the FX-6 produced IAA and siderophore, and had ACC deaminase activity. The trait of significant biological control activity and growth promoting effect on tomato imply that B. velezensis FX-6 has the potential to be used as a biocontrol agent for tomato gray mold management.

4-Thiazolidinone Based 5-Arylidene Hybrids: Design, Synthesis, Antimicrobial Activity, and Molecular Docking Studies

In recent years, the most pressing challenge in drug development has been the fight against bacterial drug resistance. Microbes have developed resistance against the present classes of antibiotics, necessitating the development of new antibiotics capable of replacing less effective drugs commercially accessible in the market. In order to achieve this, a straightforward technique for the synthesis of 4-thiazolidinone-based pyrazole-pyridine hybrids was designed (5a–o). The hybrids were characterized using spectroscopic techniques and tested for antimicrobial efficacy against a variety of bacterial and fungal species. The MIC value of compounds 5d, 5f, 5j, 5 l, 5 m, and 5o against tested bacterial strains was 62.5 μg/mL. Compound 5i showed a MIC value of 250 μg/mL against Candida albicans, which is twice the activity of the standard drug. Furthermore, to rationalize the antimicrobial finding and to gain an insight into the plausible mechanism of action, molecular docking study was performed against microbial DNA gyrase. A very significant correlation obtained between the in silico binding affinity and the antimicrobial activity could set an excellent platform for structure based drug design.

Prophage Gifsy-1 Induction in Salmonella enterica Serovar Typhimurium Reduces Persister Cell Formation after Ciprofloxacin Exposure.

Persister cells are drug-tolerant bacteria capable of surviving antibiotic treatment despite the absence of heritable resistance mechanisms. It is generally thought that persister cells survive antibiotic exposure through the implementation of stress responses and/or energy-sparing strategies. Exposure to DNA gyrase-targeting antibiotics could be particularly detrimental for bacteria that carry prophages integrated in their genomes. Gyrase inhibitors are known to induce prophages to switch from their dormant lysogenic state into the lytic cycle, causing the lysis of their bacterial host. However, the influence of resident prophages on the formation of persister cells has only been recently appreciated. Here, we evaluated the effect of endogenous prophage carriage on the generation of bacterial persistence during Salmonella enterica serovar Typhimurium exposure to both gyrase-targeting antibiotics and other classes of bactericidal antibiotics. Results from the analysis of strain variants harboring different prophage combinations revealed that prophages play a major role in limiting the formation of persister cells during exposure to DNA-damaging antibiotics. In particular, we present evidence that prophage Gifsy-1 (and its encoded lysis proteins) are major factors limiting persister cell formation upon ciprofloxacin exposure. Resident prophages also appear to have a significant impact on the initial drug susceptibility, resulting in an alteration of the characteristic biphasic killing curve of persister cells into a triphasic curve. In contrast, a prophage-free derivative of S. Typhimurium showed no difference in the killing kinetics for β-lactam or aminoglycoside antibiotics. Our study demonstrates that induction of prophages increased the susceptibility toward DNA gyrase inhibitors in S. Typhimurium, suggesting that prophages have the potential for enhancing antibiotic efficacy. IMPORTANCE Bacterial infections resulting from antibiotic treatment failure can often be traced to nonresistant persister cells. Moreover, intermittent or single treatment of persister cells with β-lactam antibiotics or fluoroquinolones can lead to the formation of drug-resistant bacteria and to the emergence of multiresistant strains. It is therefore important to have a better understanding of the mechanisms that impact persister formation. Our results indicate that prophage-associated bacterial killing significantly reduces persister cell formation in lysogenic cells exposed to DNA-gyrase-targeting drugs. This suggests that therapies based on gyrase inhibitors should be favored over alternative strategies when dealing with lysogenic pathogens.