DNA Gyrase Inhibitors Research Articles

DNA Gyrase Inhibitors Increase the Frequency of Bacteriophage-like RcGTA-Mediated Gene Transfer in Rhodobacter capsulatus.

Rhodobacter capsulatus produces a bacteriophage-like particle called the gene transfer agent (RcGTA) that mediates horizontal gene transfer. RcGTA particles transfer random ~4.5-kb fragments of genomic DNA that integrate into recipient genomes by allelic replacement. This work addresses the effect of sub-inhibitory concentrations of antibiotics on gene transfer by RcGTA. A transduction assay was developed to test the effects of various substances on gene transfer. Using this assay, low concentrations of DNA gyrase inhibitors were found to increase the frequency of gene transfer. Novobiocin was studied in more detail, and it was found that this antibiotic did not influence the production or release of RcGTA but instead appeared to act on the recipient cells. The target of novobiocin in other species has been shown to be the GyrB subunit of DNA gyrase (a heterotetramer of 2GyrA and 2GyrB). R. capsulatus encodes GyrA and GyrB homologues, and a GyrB overexpression plasmid was created and found to confer resistance to novobiocin. The presence of the overexpression plasmid in recipient cells greatly diminished the novobiocin-mediated increase in gene transfer, confirming that this effect is due to the binding of novobiocin by GyrB. The results of this work show that antibiotics affect gene transfer in R. capsulatus and may be relevant to microbial genetic exchange in natural ecosystems.

Phenylhydrazone linked 1,2,3-triazole hybrids: synthesis, antimicrobial evaluation and docking studies as dual inhibitors of DNA gyrase and lanosterol 14-α demethylase

Phenylhydrazone linked 1,2,3-triazole hybrids: synthesis, antimicrobial evaluation and docking studies as dual inhibitors of DNA gyrase and lanosterol 14-α demethylase

Potent Inhibition of Bacterial DNA Gyrase by Digallic Acid and Other Gallate Derivatives.

Bacterial DNA gyrase, an essential enzyme, is a validated target for discovering and developing new antibiotics. Here we screened a pool of polyphenols and discovered that digallic acid is a potent DNA gyrase inhibitor. We also found that several food additives based on gallate, such as dodecyl gallate, potently inhibit bacterial DNA gyrase. Interestingly, the IC50 of these gallate derivatives against DNA gyrase is correlated with the length of hydrocarbon chain connecting to the gallate. These new bacterial DNA gyrase inhibitors are ATP competitive inhibitors of DNA gyrase. Our results also show that digallic acid and certain gallate derivatives potently inhibit E. coli DNA topoisomerase IV. Several gallate derivatives have strong antimicrobial activities against Staphylococcus aureus and methicillin-resistant Staphylococcus aureus (MRSA). This study provides a solid foundation for the design and synthesis of gallate-based DNA gyrase inhibitors that may be used to combat antibacterial resistance.

Discovery of oxazoline-triazole based hybrid molecules as DNA gyrase inhibitors: A new class of potential Anti-tubercular agents

A library of novel oxazoline-triazole hybrid analogues (6a-6 g and 7a-7 m)was designed using a molecular hybridization approach and synthesized from commercially available ethyl 2/3/4-hydroxybenzoate. The synthesized compounds were characterized by modern art instrumentation, including IR and NMR (1H, 13C). All the final compounds were evaluated for their in-vitro antibacterial (S. aureus, B. subtilis, E. coli and P. aeruginosa), antifungal (C. neoformans, C. albicans and A. niger) and anti-tubercular (Mycobacterium tuberculosis H37Rv, MDR and XDR strains) activities. Among the series, compound 7a-7i exhibited excellent activity (MIC = 1.6 µM) against H37Rv strain of M.tuberculosis. However, antibacterial screening data (in vitro) revealed a moderate inhibition for 6e-6 g and 7f-7 h against gram-positive bacteria (Bacillus subtilis) and 7a-7i against gram-negative bacteria with a MIC value of 25 µg/ml. While moderate activity was observed against fungal (C. neoformns and C. albicans) strains with MIC value of 25–200 µg/mL. Additionally, five compounds (7a, 7d-7f and 7 h) were further evaluated for their in vitro inhibitory activity against E-coli DNA gyrase. These compounds displayed significant inhibitory activity against the DNA gyrase enzyme with an IC50 value of 0.08 – 0.5 µM.

Structure based design and synthesis of 3-(7-nitro-3-oxo-3,4-dihydroquinoxalin-2-yl)propanehydrazide derivatives as novel bacterial DNA-gyrase inhibitors: In-vitro, In-vivo, In-silico and SAR studies

Antimicrobial resistance (AMR) is one of the critical challenges that have been encountered over the past years. On the other hand, bacterial DNA gyrase is regarded as one of the most outstanding biological targets that quinolones can extensively inhibit, improving AMR. Hence, a novel series of 3-(7-nitro-3-oxo-3,4-dihydroquinoxalin-2-yl)propanehydrazide derivatives (3-6j) were designed and synthesized employing the quinoxaline-2-one scaffold and relying on the pharmacophoric features experienced by the quinolone antibiotic; ciprofloxacin. The antibacterial activity of the synthesized compounds was assessed via in-vitro approaches using eight different Gram-positive and Gram-negative bacterial species. Most of the synthesized compounds revealed eligible antibacterial activities. In particular, compounds 6d and 6e displayed promising antibacterial activity among the investigated compounds. For example, compounds 6d and 6e displayed MIC values of 9.40 and 9.00 µM, respectively, regarding S. aureus, and 4.70 and 4.50 µM, respectively, regarding S. pneumonia in comparison to ciprofloxacin (12.07 µM). The cytotoxicity of compounds 6d and 6e were performed on normal human WI-38 cell lines with IC50 values of 288.69 and 227.64 μM, respectively assuring their safety and selectivity. Besides, DNA gyrase inhibition assay of compounds 6d and 6e was carried out in comparison to ciprofloxacin, and interestingly, compounds 6d and 6e disclosed promising IC50 values of 0.242 and 0.177 μM, respectively, whereas ciprofloxacin displayed an IC50 value of 0.768 μM, assuring the proposed mechanism of action for the afforded compounds. Consequently, compounds 6d and 6e were further assessed via in-vivo approaches by evaluating blood counts, liver and kidney functions, and histopathological examination. Both compounds were found to be safer on the liver and kidney than the reference ciprofloxacin. Moreover, in-silico molecular docking studies were established and revealed reasonable binding affinities for all afforded compounds, particularly compound 6d which exhibited a binding score of −7.51 kcal/mol, surpassing the reference ciprofloxacin (−7.29 kcal/mol) with better anticipated stability at the DNA gyrase binding pocket. Moreover, ADME studies were conducted, disclosing an eligible bioavailability score of >0.55 for all afforded compounds, and reasonable GIT absorption without passing the blood brain barrier was attained for most investigated compounds, ensuring their efficacy and safety. Lastly, a structure activity relationship study for the synthesized compounds was established and unveiled that not only the main pharmacophores required for DNA gyrase inhibition are enough for exerting promising antimicrobial activities, but also derivatization with diverse aryl/hetero aryl aldehydes is essential for their enhanced antimicrobial potential.

Synthesis, molecular docking, ADME study, and antimicrobial potency of piperazine based cinnamic acid bearing coumarin moieties as a DNA gyrase inhibitor.

A series of novel piperazine based cinnamic acid bearing coumarin derivatives were designed and synthesized by piperazine based cinnamic acids esterification with 4-hydroxycoumarin and characterized by various spectral techniques like infrared, 1 H nuclear magnetic resonance (NMR), 13 C NMR, and mass. The novel bioactive compounds (7a-7m) screen their potential against different bacterial and fungal strains. Compound 7g (minimum inhibitory concentration [MIC] = 12.5 µg/ml) exhibited potent antibacterial activity against Escherichia colistrain. Compounds 7d, 7f, 7g, 7k, 7l, and 7m showed potent antibacterial activity against all bacterial strains. Compounds 7a, 7g, 7h, 7k, 7l, and 7m exhibited potent antifungal activity against all fungal strains. Furthermore, a molecular docking study revealed that compounds 7d, 7f, 7g, and 7k could bind to the active site of E. coli DNA gyrase subunit B protein and form hydrogen bonding with crucial amino acid residues Arg136 in the active sites. Comprehensively, our study recommends that 7d, 7f, 7g, and 7k could be a promising lead for developing more efficient antimicrobial drug candidates and DNA gyrase inhibitors.

Survey of Oxolinic Acid-Resistant Erwinia amylovora in Korean Apple and Pear Orchards, and the Fitness Impact of Constructed Mutants.

Fire blight caused by Erwinia amylovora (Ea) is a devastating disease in apple and pear trees. Oxolinic acid (OA), a quinolone family antibiotic that inhibits DNA gyrase, has been employed to control fire blight in South Korea since 2015. The continuous use of this bactericide has resulted in the emergence of OA-resistant strains in bacterial pathogens in other countries. To investigate the occurrence of OA-resistant Ea strains in South Korea, we collected a total of 516 Ea isolates from diseased apple and pear trees in 2020–2021 and assessed their sensitivities to OA. We found that all isolates were susceptible to OA. To explore the possibility of emerging OA-resistant Ea by continuous application of OA, we exposed Ea stains to a range of OA concentrations and constructed OA-resistant mutant strains. Resistance was associated with mutations in the GyrA at codons 81 and 83, which result in glycine to cysteine and serine to arginine amino acid substitutions, respectively. The in vitro growth of the mutants in nutrient media and their virulence in immature apple fruits were lower than those of wild-type. Our results suggest that OA-resistance decreases the fitness of Ea. Future work should clarify the mechanisms by which OA-resistance decreases virulence of this plant pathogen. Continuous monitoring of OA-resistance in Ea is required to maintain the efficacy of this potent bactericide.

Synthesis and molecular docking of new N4-piperazinyl ciprofloxacin hybrids as antimicrobial DNA gyrase inhibitors.

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 0.06-42.23µg/mL compared to ciprofloxacin with an MIC range of 0.15-3.25µg/mL. Among the tested compounds, hybrids 2b, 2c, 5a, 5b, 5h, and 5i exhibited remarkable antibacterial activity with MIC range of 0.06-1.53µg/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 2.03-3.89µg/mL and 2.6µg/mL, respectively. Further investigations showed that some ciprofloxacin hybrids have inhibitory activity against DNA gyrase as potential molecular target compared to ciprofloxacin with IC50 range of 0.231 ± 0.01-7.592 ± 0.40µM and 0.323 ± 0.02µM, 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.

Integrated Genotoxicity Testing of three anti-infective drugs using the TGx-DDI transcriptomic biomarker and high-throughput CometChip® assay in TK6 cells.

Genotoxicity testing relies on the detection of gene mutations and chromosome damage and has been used in the genetic safety assessment of drugs and chemicals for decades. However, the results of standard genotoxicity tests are often difficult to interpret due to lack of mode of action information. The TGx-DDI transcriptomic biomarker provides mechanistic information on the DNA damage-inducing (DDI) capability of chemicals to aid in the interpretation of positive in vitro genotoxicity data. The CometChip® assay was developed to assess DNA strand breaks in a higher-throughput format. We paired the TGx-DDI biomarker with the CometChip® assay in TK6 cells to evaluate three model agents: nitrofurantoin (NIT), metronidazole (MTZ), and novobiocin (NOV). TGx-DDI was analyzed by two independent labs and technologies (nCounter® and TempO-Seq®). Although these anti-infective drugs are, or have been, used in human and/or veterinary medicine, the standard genotoxicity testing battery showed significant genetic safety findings. Specifically, NIT is a mutagen and causes chromosome damage, and MTZ and NOV cause chromosome damage in conventional in vitro tests. Herein, the TGx-DDI biomarker classified NIT and MTZ as non-DDI at all concentrations tested, suggesting that NIT’s mutagenic activity is bacterial specific and that the observed chromosome damage by MTZ might be a consequence of in vitro test conditions. In contrast, NOV was classified as DDI at the second highest concentration tested, which is in line with the fact that NOV is a bacterial DNA-gyrase inhibitor that also affects topoisomerase II at high concentrations. The lack of DNA damage for NIT and MTZ was confirmed by the CometChip® results, which were negative for all three drugs except at overtly cytotoxic concentrations. This case study demonstrates the utility of combining the TGx-DDI biomarker and CometChip® to resolve conflicting genotoxicity data and provides further validation to support the reproducibility of the biomarker.

Phenyl substituted 3-chloro 2-azetidinones: Design, green synthesis, antimicrobial activity, and molecular docking studies

In the present study, by applying an effective microwave-assisted synthesis method for some new phenyl substituted 3-chloro 2-azetidinone derivatives, starting with methyl 2-(4-amino-3-iodophenyl)acetate were synthesized with excellent yield and in-vitro screening for antimicrobial activity. The microwave synthesis offers a shorter reaction time (20-45 min), moderate reaction conditions, high returns (81%-96%), and easier operation than conventional heating. Spectroscopic techniques like 1H NMR, LCMS, IR, and 13C NMR analysis have been used to examine the structure of the newly synthesized compounds. All newly synthesized β-lactam derivatives (8a-h) were tested for antimicrobial activity against diverse bacterial and fungus strains using the broth dilution technique. Most of the investigated substances showed promising effectiveness against bacterial and fungal strains, with values ranging from 0.78 to 50 µg/mL. In contrast to the standard Ciprofloxacin for antibacterial activity and Ketoconazole for antifungal activity, compound 8c demonstrated good robust antibacterial activity against Escherichia coli and antifungal activity against Aspergillus niger with a value of 0.78 µg/mL of concentration. The final targets were performed to the inhibition of DNA gyrase by molecular docking experiments to acquire insight into relevant proteins. The results of silico molecular docks coincide with the in vitro antimicrobial investigations and may be regarded as a good DNA gyrase inhibitor.

Activity of Secondary Metabolites of Momordica Charantia as a DNA Gyrase Inhibitor of Helicobacter Pylori: Homology Modelling and Molecular Docking

Helicobacter pylori can induce gastritis, ulcers, and gastric cancer. H. pylori is also responsible for causing oropharynx, endocrine, respiratory, central nervous system, eye, and reproductive system diseases. Treatment of H. pylori includes relieving gastritis or pain but this is not specific for H. pylori. Therefore, it is necessary to develop drugs of new therapeutic molecules to treat H. pylori. The purpose of this study was to determine which metabolite compounds from the Momordica charantia plant could provide activity as a DNA gyrase inhibitor. The target protein used in this study was prepared using the homology modeling method with the SWISS-MODEL web tools. Secondary metabolite compounds of M. charantia were processed using SwissADME web tools to find predictions for their pharmacokinetic profiles. The secondary metabolite compounds used for molecular docking using autodock 4.2 were compounds in the BOILED-Egg method range. From the homology modeling results, the quaternary structure quality estimate was 0.57 and the global mean quality estimate was 0.52. From the BOILED-Egg, six compounds were predicted to have good bioavailability. The molecular docking found that diosgenin had the lowest binding free energy (-5.35 kcal/mol) and inhibition constant (119.52 uM), so it was predicted that diosgenin could be used as an inhibitor of DNA gyrase in H. pylori.
 Keywords: Helicobacter pylori, DNA gyrase, Momordica charantia, homology modelling, molecular docking

Studies in instant water disinfection using natural oils

The present research reveals an instant and simple process for drinking water treatment by employing specific natural oils having antimicrobial properties to ensure complete elimination of harmful bacteria. The disinfection was studied for two different model bacteria, Gram-negative E. coli and Gram-positive, S. aureus. Seven natural oils, ajwain, thyme, oregano, peppermint, harsingar, cinnamon leaf and black pepper oil were evaluated and were found to yield 100% water disinfection within 1 min except for harsingar and black pepper oil. The process was also effective for the instant and 100% disinfection of real well water. The methodology for altering zeta potential, to an extent of 130%, for instant disinfection in drinking water treatment helps in selecting natural oils. Molecular docking studies indicated natural oils action as potential inhibitors of bacterial DNA gyrase. The studies indicate one of the lowest operating costs comparable to conventional chlorination. The simple methodology not requiring complex equipment has the potential to provide many options for implementations- from portability, household application to large scale water treatment plants.

DNA gyrase inhibitor targets M. tuberculosis.

DNA gyrase inhibitor targets M. tuberculosis.

Novel and Structurally Diversified Bacterial DNA Gyrase Inhibitors Discovered through a Fluorescence-Based High-Throughput Screening Assay.

Bacterial DNA gyrase, a type IIA DNA topoisomerase that plays an essential role in bacterial DNA replication and transcription, is a clinically validated target for discovering and developing new antibiotics. In this article, based on a supercoiling-dependent fluorescence quenching (SDFQ) method, we developed a high-throughput screening (HTS) assay to identify inhibitors targeting bacterial DNA gyrase and screened the National Institutes of Health's Molecular Libraries Small Molecule Repository library containing 370,620 compounds in which 2891 potential gyrase inhibitors have been identified. According to these screening results, we acquired 235 compounds to analyze their inhibition activities against bacterial DNA gyrase using gel- and SDFQ-based DNA gyrase inhibition assays and discovered 155 new bacterial DNA gyrase inhibitors with a wide structural diversity. Several of them have potent antibacterial activities. These newly discovered gyrase inhibitors include several DNA gyrase poisons that stabilize the gyrase-DNA cleavage complexes and provide new chemical scaffolds for the design and synthesis of bacterial DNA gyrase inhibitors that may be used to combat multidrug-resistant bacterial pathogens. Additionally, this HTS assay can be applied to screen inhibitors against other DNA topoisomerases.

Novel fluoroquinolone hybrids as dual DNA gyrase and urease inhibitors with potential antibacterial activity: Design, synthesis, and biological evaluation

Fluoroquinolones (FQs) are well known antibacterial chemotherapeutics with DNA gyrase inhibitory activity and a potential urease inhibitory activity. New FQ hybrids (4a−h and 5a−h) have been synthesized by combining ciprofloxacin or norfloxacin with different thiouracil and thioxopyrimidine derivatives. The purity of the newly developed compounds was assessed through thin-layer chromatography, and the elucidation of their structures was confirmed through proton nuclear magnetic resonance, infrared spectroscopy, high resolution mass spectrometry, and microanalyses. The new hybrids were evaluated for their antibacterial, DNA gyrase, and urease inhibitory activities. The potential co- and cross-resistance in Escherichia coli (E. coli) as well as the frequencies of the resistance were evaluated for the new hybrids. The new hybrid compounds displayed a significant antibacterial activity against a panel of Gram-positive and Gram-negative bacterial strains. The majority of the tested ciprofloxacin and norfloxacin hybrids displayed a superior activity against E. coli. The 4 g and 4 h hybrids were the most active E. coli DNA gyrase inhibitors (IC50: 0.62 and 0.58 µM, respectively), and displayed an inhibitory activity that was comparable to that of ciprofloxacin (IC50: 0.40 µM). The 5 g and 5e hybrids exhibited an improved inhibitory activity (IC50: 0.76 and 0.80 µM, respectively) when compared to norfloxacin (IC50: 0.93 µM). Most of the tested hybrids were shown to be able to additionally inhibit the urease activity (IC50 range: 9.71–80.64 μM). Hybrids 4e and 5c were the most potent urease inhibitors (IC50: 11.68 and 9.71 μM, respectively), capable of displaying a 3 − 4-fold increase in their activity when compared to ciprofloxacin, norfloxacin, and thiourea (IC50: 42.74, 36.07, and 32.25 μM, respectively).

Anti-microbial efficacy, mechanisms and druggability evaluation of the natural flavonoids.

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. Glabridin, a natural isoflavonoid isolated from Glycyrrhiza glabra L., was identified to be highly active with a MIC of 8-16 μg ml-1 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: IC50 = 0.8516 μmol L-1 , ciprofloxacin: IC50 = 0.04697 μmol L-1 ), DHFR inhibition assays (glabridin: inhibition ratio=29%, methotrexate: inhibition ratio=45% under 100 μmol L-1 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. These findings suggest that glabridin represents the prototypical member of an exciting structural class of natural antimicrobial agents. This study reports a novel mechanism of bactericidal activity of glabridin against Staph. aureus.

Discovery of Novel Inhibitors of Bacterial DNA Gyrase Using a QSAR-Based Approach.

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 in-house-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 in vitro 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 in-house-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 Escherichia coli 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.

The Inactivation of LPS Biosynthesis Genes in E. coli Cells Leads to Oxidative Stress.

Impaired lipopolysaccharide biosynthesis in Gram-negative bacteria results in the “deep rough” phenotype, which is characterized by increased sensitivity of cells to various hydrophobic compounds, including antibiotics novobiocin, actinomycin D, erythromycin, etc. The present study showed that E. coli mutants carrying deletions of the ADP-heptose biosynthesis genes became hypersensitive to a wide range of antibacterial drugs: DNA gyrase inhibitors, protein biosynthesis inhibitors (aminoglycosides, tetracycline), RNA polymerase inhibitors (rifampicin), and β-lactams (carbenicillin). In addition, it was found that inactivation of the gmhA, hldE, rfaD, and waaC genes led to dramatic changes in the redox status of cells: a decrease in the pool of reducing NADPH and ATP equivalents, the concentration of intracellular cysteine, a change in thiol homeostasis, and a deficiency in the formation of hydrogen sulfide. In “deep rough” mutants, intensive formation of reactive oxygen species was observed, which, along with a lack of reducing agents, such as reactive sulfur species or NADPH, leads to oxidative stress and an increase in the number of dead cells in the population. Within the framework of modern ideas about the role of oxidative stress as a universal mechanism of the bactericidal action of antibiotics, inhibition of the enzymes of ADP-heptose biosynthesis is a promising direction for increasing the effectiveness of existing antibiotics and solving the problem of multidrug resistance.

Evybactin is a DNA gyrase inhibitor that selectively kills Mycobacterium tuberculosis.

The antimicrobial resistance crisis requires the introduction of novel antibiotics. The use of conventional broad-spectrum compounds selects for resistance in off-target pathogens and harms the microbiome. This is especially true for Mycobacterium tuberculosis, where treatment requires a 6-month course of antibiotics. Here we show that a novel antimicrobial from Photorhabdus noenieputensis, which we named evybactin, is a potent and selective antibiotic acting against M. tuberculosis. Evybactin targets DNA gyrase and binds to a site overlapping with synthetic thiophene poisons. Given the conserved nature of DNA gyrase, the observed selectivity against M. tuberculosis is puzzling. We found that evybactin is smuggled into the cell by a promiscuous transporter of hydrophilic compounds, BacA. Evybactin is the first, but likely not the only, antimicrobial compound found to employ this unusual mechanism of selectivity.

What is a supercoiling-sensitive gene? Insights from topoisomerase I inhibition in the Gram-negative bacterium Dickeya dadantii.

DNA supercoiling is an essential mechanism of bacterial chromosome compaction, whose level is mainly regulated by topoisomerase I and DNA gyrase. Inhibiting either of these enzymes with antibiotics leads to global supercoiling modifications and subsequent changes in global gene expression. In previous studies, genes responding to DNA relaxation induced by DNA gyrase inhibition were categorised as ‘supercoiling-sensitive’. Here, we studied the opposite variation of DNA supercoiling in the phytopathogen Dickeya dadantii using the non-marketed antibiotic seconeolitsine. We showed that the drug is active against topoisomerase I from this species, and analysed the first transcriptomic response of a Gram-negative bacterium to topoisomerase I inhibition. We find that the responding genes essentially differ from those observed after DNA relaxation, and further depend on the growth phase. We characterised these genes at the functional level, and also detected distinct patterns in terms of expression level, spatial and orientational organisation along the chromosome. Altogether, these results highlight that the supercoiling-sensitivity is a complex feature, which depends on the action of specific topoisomerases, on the physiological conditions, and on their genomic context. Based on previous in vitro expression data of several promoters, we propose a qualitative model of SC-dependent regulation that accounts for many of the contrasting transcriptomic features observed after DNA gyrase or topoisomerase I inhibition.