Target DNA Gyrase Research Articles

Design, Synthesis, Docking Study & Antibacterial Evaluation of 1,3- Diarylpyrazolyl Substituted Indolin-2-ones

In the present investigation, a series ofnovel 3-((1,3-diphenyl-1H-pyrazol-4-yl)methylene)indolin-2-one was synthesized by the Claisen-Schmidt condensation of indolin-2-one with substituted diaryl formylpyrazoles using alcoholic sodium hydroxide. The chemical structures of the newly synthesized compounds were characterized by IR, 1HNMR, and mass spectroscopy. The title compounds were evaluated for qualitative (zone of inhibition) and quantitative antibacterial activity (MIC) by agar diffusion and broth microdilution MIC (minimum inhibitory concentration) methods, respectively against Staphylococcus aureus, Bacillus subtilis, Escherichia coli, and Klebsiella pneumoniae. All the synthesized compounds were found active against Gram-positive bacteria, while showed very weak activity against Gram-negative bacteria. Docking study was performed to check interaction of synthesized compounds with the target DNA gyrase.

The role of bacterial membrane proteins in the internalization of microcin MccJ25 and MccB17

Microcins are gene-encoded antibacterial peptides of low molecular mass (<10 kDa), produced by Enterobactericeae. They are produced and secreted under conditions of limited essential nutrients and are active against related species. Bacterial strains under starvation conditions can produce and release microcins that can kill microcin-sensitive cells and therefore have more nutrients for survival. The outer-membrane protein OmpF and FhuA TonB-dependent pathways facilitate the internalization of the MccB17 and MccJ25 microcins into the target cell respectively. The inner-membrane protein SbmA transports the microcins through the inner membrane to the cytoplasmic face. Inside the cell, MccB17 targets DNA gyrase, whereas MccJ25 inhibits the bacterial RNA polymerase.

Novel DNA gyrase inhibitors: Microbiological characterisation of pyrrolamides

Pyrrolamides are a novel class of antibacterial agents that target DNA gyrase, resulting in inhibition of DNA synthesis and bacterial cell death. In these studies, advanced compounds were shown to have potent in vitro activity against selected Gram-positive and Gram-negative pathogens, including meticillin-resistant Staphylococcus aureus, meticillin- and quinolone-resistant S. aureus, vancomycin-resistant enterococci, penicillin-resistant Streptococcus pneumoniae and β-lactamase-producing Haemophilus influenzae and Moraxella catarrhalis. Representatives of the class were demonstrated to be bactericidal, with frequencies of spontaneous resistance ≤1×10−7 when plated at concentrations equivalent to their minimum inhibitory concentration. Mode of action studies suggested that the activity of these compounds is due to inhibition of the GyrB subunit of DNA gyrase in key pathogens. The antibacterial activity, spectrum and mode of action of these compounds underscore the promise of the pyrrolamide series as attractive candidates for the treatment of several clinical indications, including respiratory and soft tissue infections.

Pyrrolamide DNA Gyrase Inhibitors: Fragment-Based Nuclear Magnetic Resonance Screening To Identify Antibacterial Agents

DNA gyrase is an essential enzyme in bacteria, and its inhibition results in the disruption of DNA synthesis and, subsequently, cell death. The pyrrolamides are a novel class of antibacterial agents targeting DNA gyrase. These compounds were identified by a fragment-based lead generation (FBLG) approach using nuclear magnetic resonance (NMR) screening to identify low-molecular-weight compounds that bind to the ATP pocket of DNA gyrase. A pyrrole hit with a binding constant of 1 mM formed the basis of the design and synthesis of a focused library of compounds that resulted in the rapid identification of a lead compound that inhibited DNA gyrase with a 50% inhibitory concentration (IC(50)) of 3 μM. The potency of the lead compound was further optimized by utilizing iterative X-ray crystallography to yield DNA gyrase inhibitors that also displayed antibacterial activity. Spontaneous mutants were isolated in Staphylococcus aureus by plating on agar plates containing pyrrolamide 4 at the MIC. The resistant variants displayed 4- to 8-fold-increased MIC values relative to the parent strain. DNA sequencing revealed two independent point mutations in the pyrrolamide binding region of the gyrB genes from these variants, supporting the hypothesis that the mode of action of these compounds was inhibition of DNA gyrase. Efficacy of a representative pyrrolamide was demonstrated against Streptococcus pneumoniae in a mouse lung infection model. These data demonstrate that the pyrrolamides are a novel class of DNA gyrase inhibitors with the potential to deliver future antibacterial agents targeting multiple clinical indications.

Inhibition of type IA topoisomerase by a monoclonal antibody through perturbation of DNA cleavage–religation equilibrium

Type IA DNA topoisomerases, typically found in bacteria, are essential enzymes that catalyse the DNA relaxation of negative supercoils. DNA gyrase is the only type II topoisomerase that can carry out the opposite reaction (i.e. the introduction of the DNA supercoils). A number of diverse molecules target DNA gyrase. However, inhibitors that arrest the activity of bacterial topoisomerase I at low concentrations remain to be identified. Towards this end, as a proof of principle, monoclonal antibodies that inhibit Mycobacterium smegmatis topoisomerase I have been characterized and the specific inhibition of Mycobacterium smegmatis topoisomerase I by a monoclonal antibody, 2F3G4, at a nanomolar concentration is described. The enzyme-bound monoclonal antibody stimulated the first transesterification reaction leading to enhanced DNA cleavage, without significantly altering the religation activity of the enzyme. The stimulated DNA cleavage resulted in perturbation of the cleavage-religation equilibrium, increasing single-strand nicks and protein-DNA covalent adducts. Monoclonal antibodies with such a mechanism of inhibition can serve as invaluable tools for probing the structure and mechanism of the enzyme, as well as in the design of novel inhibitors that arrest enzyme activity.

Evaluation of gyrase B as a drug target in Mycobacterium tuberculosis.

New classes of drugs are needed to treat tuberculosis (TB) in order to combat the emergence of resistance to existing agents and shorten the duration of therapy. Targeting DNA gyrase is a clinically validated therapeutic approach using fluoroquinolone antibiotics to target the gyrase subunit A (GyrA) of the heterotetramer. Increasing resistance to fluoroquinolones has driven interest in targeting the gyrase subunit B (GyrB), which has not been targeted for TB. The biological activities of two potent small-molecule inhibitors of GyrB have been characterized to validate its targeting as a therapeutic strategy for treating TB. Novobiocin and aminobenzimidazole 1 (AB-1) were tested for their activity against Mycobacterium tuberculosis (Mtb) H37Rv and other mycobacteria. AB-1 and novobiocin were also evaluated for their interaction with rifampicin and isoniazid as well as their potential for cytotoxicity. Finally, AB-1 was tested for in vivo efficacy in a murine model of TB. Novobiocin and AB-1 have both been shown to be active against Mtb with MIC values of 4 and 1 mg/L, respectively. Only AB-1 exhibited time-dependent bactericidal activity against drug-susceptible and drug-resistant mycobacteria, including a fluoroquinolone-resistant strain. AB-1 had potent activity in the low oxygen recovery assay model for non-replicating persistent Mtb. Additionally, AB-1 has no interaction with isoniazid and rifampicin, and has no cross-resistance with fluoroquinolones. In a murine model of TB, AB-1 significantly reduced lung cfu counts in a dose-dependent manner. Aminobenzimidazole inhibitors of GyrB exhibit many of the characteristics required for their consideration as a potential front-line antimycobacterial therapeutic.

Pyrrolamide DNA gyrase inhibitors: Optimization of antibacterial activity and efficacy

The pyrrolamides are a new class of antibacterial agents targeting DNA gyrase, an essential enzyme across bacterial species and inhibition results in the disruption of DNA synthesis and subsequently, cell death. The optimization of biochemical activity and other drug-like properties through substitutions to the pyrrole, piperidine, and heterocycle portions of the molecule resulted in pyrrolamides with improved cellular activity and in vivo efficacy.

Exploration of the Activity of 7-Pyrrolidino-8-methoxyisothiazoloquinolones against Methicillin-Resistant Staphylococcus aureus (MRSA)

A series of 7-(3'-substituted)pyrrolidino-8-methoxyisothiazoloquinolone (ITQ) analogues were prepared, and their antibacterial potency against methicillin-sensitive Staphylococcus aureus (MSSA), methicillin-resistant Staphylococcus aureus (MRSA), and Escherichia coli were compared. Many of these analogues had MIC ≤ 0.25 μg/mL against quinolone-resistant MRSA strains. The stereochemical preference was explored for a series of 1''-methyl-3'-aminomethylpyrrolidine analogues. Antibacterial activity was generally more favorable with 3'-R, 1''-S configuration. Substitution on the 3'-aminomethyl nitrogen tended to decrease activity, while potency was maintained with disubstitution or aryl substitution at the 1''-carbon. The 7-[(R)-3-((S)-1-aminoethyl)pyrrolidin-1-yl] analogue (6a(R,S)) and the (R)-7-[3-(2-aminopropan-2-yl)pyrrolidin-1-yl] analogue (7a(R)) were found to be the ITQs with the most promising antibacterial profiles. The MICs of these select ITQs versus a panel of clinical MRSA strains were determined, and the ITQs were found to have 8- to 16-fold greater potency than linezolid. These analogues were also evaluated for inhibition of the target enzymes, topoisomerase IV and DNA gyrase, from both wild-type and multidrug resistant strains. The ITQs were up to >30 times more inhibitory against these targets than the fluoroquinolone moxifloxacin.

Anti-tubercular drug designing by structure based screening of combinatorial libraries

In the current study, the applicability and scope of descriptor based QSAR models to complement virtual screening using molecular docking approach have been applied to identify potential virtual screening hits targeting DNA gyrase A from Mycobacterium tuberculosis, an effective and validated anti-mycobacterial target. Initially QSAR models were developed against M. fortuitum and M. smegmatis using a series of structurally related fluoroquinolone derivatives as DNA gyrase inhibitors. Both the QSAR models yielded significant cross validated Q² values of 0.6715 and 0.6944 and R² values of 0.7250 and 0.7420, respectively. The statistically significant models were validated by a test set of 22 compounds with predictive R² value of 0.7562 and 0.7087 for M. fortuitum and M. smegmatis respectively. To aid the creation of novel antituberculosis compounds, combinatorial library was developed on fluoroquinolone template to derive a data set of 5280 compounds whose activity values have been measured by the above models. Highly active compounds predicted from the models were subjected to molecular docking study to investigate the mechanism of drug binding with the DNA gyrase A protein of M. tuberculosis and the compounds showing similar type of binding patterns with that of the existing drug molecules, like sparfloxacin, were finally reported. It is seen that hydrophobic characteristics of molecular structure together with few hydrogen bond interactions are playing an essential role in antimicrobial activity for the fluoroquinolone derivatives. A representative set of seven compounds with high predicted MIC values were sorted out in the present study.

Structural Insights into the Quinolone Resistance Mechanism of Mycobacterium tuberculosis DNA Gyrase

Mycobacterium tuberculosis DNA gyrase, an indispensable nanomachine involved in the regulation of DNA topology, is the only type II topoisomerase present in this organism and is hence the sole target for quinolone action, a crucial drug active against multidrug-resistant tuberculosis. To understand at an atomic level the quinolone resistance mechanism, which emerges in extensively drug resistant tuberculosis, we performed combined functional, biophysical and structural studies of the two individual domains constituting the catalytic DNA gyrase reaction core, namely the Toprim and the breakage-reunion domains. This allowed us to produce a model of the catalytic reaction core in complex with DNA and a quinolone molecule, identifying original mechanistic properties of quinolone binding and clarifying the relationships between amino acid mutations and resistance phenotype of M. tuberculosis DNA gyrase. These results are compatible with our previous studies on quinolone resistance. Interestingly, the structure of the entire breakage-reunion domain revealed a new interaction, in which the Quinolone-Binding Pocket (QBP) is blocked by the N-terminal helix of a symmetry-related molecule. This interaction provides useful starting points for designing peptide based inhibitors that target DNA gyrase to prevent its binding to DNA.

Novel Variants of the qnrB Gene, qnrB22 and qnrB23 , in Citrobacter werkmanii and Citrobacter freundii

Resistance to quinolones in Gram-negative bacteria is usually mediated by the following: (i) chromosomal mutations that alter the target enzymes, DNA gyrase and topoisomerase IV, in their quinolone resistance-determining regions (QRDR), (ii) changes in drug entry (loss of porin channels), and (iii) the presence of plasmid-mediated quinolone resistance (PMQR) determinants [qnrA, qnrB, qnrS, qnrC, and qnrD, coding for Qnr proteins that protect DNA gyrase from quinolone attack; aac(6′)-Ib-cr, coding for a protein that acetylates quinolones; and qepA, coding for a quinolone efflux pump] (2, 12). The recent worldwide emergence of PMQR due to the qnr and aac(6′)-Ib-cr genes is a concerning fact among human and animal Gram-negative pathogens (8). The aim of this study was to determine the prevalence of qnr genes among 93 consecutive nonrepetitive Enterobacteriaceae of animal origin and to characterize positive isolates. These isolates were collected from chickens (n = 37) and pigs (n = 56) at five farms near the city of Seoul (South Korea) in 2007. The presence of PMQR determinants and QRDR mutations was investigated by PCR-based detection and sequencing (2, 5, 6). The qnrA, qnrS, qnrC, qnrD, aac(6′)-Ib-cr, and qepA genes were not found. Two isolates (2.2%) were found to carry qnr-like genes (Citrobacter werkmanii PS012 and Citrobacter freundii S008). Sequence analysis identified two novel qnrB variants, qnrB22 and qnrB23, in C. werkmanii PS012 (isolated from a pig at the Daeyoung Farm) and C. freundii S008 (isolated from a chicken at the Hanmi Farm), respectively. These new variants were assigned according to the qnr numbering scheme shown in the Lahey website (http://www.lahey.org/qnrStudies). The qnrB22 gene had 99.7% nucleotide identity with qnrB4. The qnrB23 gene had 99.9% nucleotide identity with qnrB9. The deduced QnrB22 product had two amino acid substitutions (Ser36Cys and Gly188Val) compared with the amino acid sequence of QnrB4. Compared with the amino acid sequence of QnrB9, QnrB23 showed one amino acid substitution (Asn27Tyr). C. werkmanii PS012 showed a reduced susceptibility (MIC > 0.125 μg/ml) to fluoroquinolones (ofloxacin, norfloxacin, levofloxacin, and ciprofloxacin) (Table ​(Table1).1). C. freundii S008 was nonsusceptible (resistant or intermediate) to the fluoroquinolones (Table ​(Table1).1). The MICs were determined by E-test (AB Biodisk, Solna, Sweden) and interpreted according to Clinical and Laboratory Standards Institute guidelines (4). The QRDR mutations associated with fluoroquinolone resistance were not detected in the two isolates (Table ​(Table11). TABLE 1. Characteristics of the two Citrobacter isolates, their transconjugants, Escherichia coli DH5α transformants, and reference (recipient or host) strains The transfer of qnrB22- and qnrB23-harboring plasmids to Escherichia coli J53 AzideR was accomplished through mating experiments described previously (9). Transconjugants were selected on Mueller-Hinton agar plates containing sodium azide (150 μg/ml) and ciprofloxacin (0.125 μg/ml). Fluoroquinolone (or nalidixic acid) MICs of the two transconjugants (TrcPS012 and TrcS008) were similar to those of the donor strains (Table ​(Table1).1). Strain TrcS008, carrying qnrB23, had MIC values for nalidixic acid and fluoroquinolones that were higher than those of TrcPS012, harboring qnrB22 (Table ​(Table11). The PCR amplicons of the qnrB22 and qnrB23 genes were cloned into the vector pCR-BluntII-TOPO and transformed into the E. coli DH5α host strain (Invitrogen, Karlsruhe, Germany). Primers used were as follows: for cloning of qnrB22, 5′-ATGACTCTGGCGTTAGTTGG-3′ and 5′-TTAACCCATGACAGCGATACCAA-3′; and for cloning of qnrB23, 5′-ATGACGCCATTACTGTATAAAAAAACA-3′ and 5′-CTAGCCAATAATCGCGATGCC-3′. A decrease in quinolone susceptibility was observed with both transformants, even though the qnrB23-carrying transformant showed higher MICs than that carrying qnrB22 (Table ​(Table1).1). Fluoroquinolone (or nalidixic acid) MICs of two transformants (TrfPS012 and TrfS008) were lower than those of two transconjugants (TrcPS012 and TrcS008), which was compatible with a recent finding (11). The differences observed between transconjugants and transformants might be related to recipient susceptibility (E. coli DH5α was more susceptible than E. coli J53 AzideR), plasmid copy number, and/or the presence of additional PMQR determinants in the two plasmids. The conjugative plasmids of C. werkmanii PS012 and C. freundii S008 showed identical patterns (showing 13 distinct bands) and similar molecular sizes (about 23 kb) in restriction fragment length polymorphism analysis after digestion with BglII, as described previously (1). qnrB22- and qnrB23-harboring plasmids belonged to an incompatibility group, IncL/M, according to a PCR-based replicon-typing scheme (3). These results suggest that conjugative IncL/M plasmids might play a role in the dissemination and evolution of qnrB genes. The association of various antibiotic resistance genes, including PMQR determinants with conjugative IncL/M plasmids from human isolates of the Enterobacteriaceae, has been described in several reports (7, 10, 13, 14). Despite the currently low prevalence (2.2%) of qnrB22 and qnrB23, surveillance for bacterial isolates carrying these resistance determinants in animals is warranted.

Targeting DNA Gyrase

Targeting DNA Gyrase

Inhibitory Mechanism of Escherichia coli RelE-RelB Toxin-Antitoxin Module Involves a Helix Displacement Near an mRNA Interferase Active Site

In Escherichia coli, RelE toxin participates in growth arrest and cell death by inducing mRNA degradation at the ribosomal A-site under stress conditions. The NMR structures of a mutant of E. coli RelE toxin, RelE(R81A/R83A), with reduced toxicity and its complex with an inhibitory peptide from RelB antitoxin, RelB(C) (Lys(47)-Leu(79)), have been determined. In the free RelE(R81A/R83A) structure, helix alpha4 at the C terminus adopts a closed conformation contacting with the beta-sheet core and adjacent loops. In the RelE(R81A/R83A)-RelB(C) complex, helix alpha3(*) of RelB(C) displaces alpha4 of RelE(R81A/R83A) from the binding site on the beta-sheet core. This helix replacement results in neutralization of a conserved positively charged cluster of RelE by acidic residues from alpha3(*) of RelB. The released helix alpha4 becomes unfolded, adopting an open conformation with increased mobility. The displacement of alpha4 disrupts the geometry of critical residues, including Arg(81) and Tyr(87), in a putative active site of RelE toxin. Our structures indicate that RelB counteracts the toxic activity of RelE by displacing alpha4 helix from the catalytically competent position found in the free RelE structure.

The Use of Structure-Guided Design to Discover New Anti-Microbial Agents: Focus on Antibacterial Resistance

Serious attempts to address antibiotic resistance, a worldwide public health concern, have recently become more intensive. In hospital settings, resistance to antibacterial agents has been recognized by clinicians for several decades. Resistant strains are now isolated on a daily basis from patients with community-acquired infections further elevating the level of concern among public health officials. The pharmaceutical industry has generally focused its attentions on chronic therapeutic indications in recent years (e.g. cardiovascular and metabolic diseases), but will likely be forced to reengage in antibacterial discovery efforts as therapeutic options diminish for the treatment of infections caused by multidrug resistant pathogens. The ability to squeeze additional utility out of known classes of antibacterial agents has become limited and antibacterial discovery scientists will need to focus on new approaches and targets. These new approaches will need to include strategies that explicitly address resistance up front and simultaneously attempt to facilitate the slower development of resistance as new compound classes enter clinical use. One approach that can be a useful component of antibacterial discovery efforts and prospectively address resistance is structure-guided design (SGD). This review will describe several recent examples in which SGD was applied as part of a multidisciplinary effort to address antibacterial resistance. These include dihydrofolate reductase inhibitors, broad-spectrum β-lactamase inhibitors, novel oxazolidinones, aminoglycoside mimetics, peptide deformylase inhibitors, and inhibitors that simultaneously target DNA gyrase and topoisomerase IV. Keywords: Antibiotic resistance, antibiotic drug discovery, resistance mechanisms, structure-guided design, dual targeting

Molecular Characterization and Typing of Enrofloxacin-Resistant Clinical Isolates of Mycoplasma gallisepticum

Emergence of resistance to fluoroquinolones is mainly due to chromosomal mutations in genes encoding the subunits of the drug's target enzymes, DNA gyrase and topoisomerase IV, which are essential for DNA replication. The quinolone resistance-determining regions (QRDRs) of these genes were characterized in 25 Mycoplasma gallisepticum strains isolated from commercial poultry flocks during 1997-2007, which exhibited different levels of susceptibility to fluoroquinolones. All enrofloxacin-resistant isolates harbored amino acid substitutions in the QRDRs of each of three proteins (GyrA, GyrB, and ParC). Molecular typing of those strains by random amplification of polymorphic DNA and gene-targeted sequencing supports ongoing, stepwise selection of resistant strains from the existing reservoir of susceptible M. gallisepticum strains.

Clerocidin selectively modifies the gyrase-DNA gate to induce irreversible and reversible DNA damage

Clerocidin (CL), a microbial diterpenoid, reacts with DNA via its epoxide group and stimulates DNA cleavage by type II DNA topoisomerases. The molecular basis of CL action is poorly understood. We establish by genetic means that CL targets DNA gyrase in the Gram-positive bacterium Streptococcus pneumoniae, and promotes gyrase-dependent single- and double-stranded DNA cleavage in vitro. CL-stimulated DNA breakage exhibited a strong preference for guanine preceding the scission site (−1 position). Mutagenesis of −1 guanines to A, C or T abrogated CL cleavage at a strong pBR322 site. Surprisingly, for double-strand breaks, scission on one strand consistently involved a modified (piperidine-labile) guanine and was not reversed by heat, salt or EDTA, whereas complementary strand scission occurred at a piperidine-stable −1 nt and was reversed by EDTA. CL did not induce cleavage by a mutant gyrase (GyrA G79A) identified here in CL-resistant pneumococci. Indeed, mutations at G79 and at the neighbouring S81 residue in the GyrA breakage-reunion domain discriminated poisoning by CL from that of antibacterial quinolones. The results suggest a novel mechanism of enzyme inhibition in which the −1 nt at the gyrase-DNA gate exhibit different CL reactivities to produce both irreversible and reversible DNA damage.

The ε Subunit of DNA Polymerase III Is Involved in the Nalidixic Acid-Induced SOS Response in Escherichia coli

Quinolone antibacterial drugs such as nalidixic acid target DNA gyrase in Escherichia coli. These inhibitors bind to and stabilize a normally transient covalent protein-DNA intermediate in the gyrase reaction cycle, referred to as the cleavage complex. Stabilization of the cleavage complex is necessary but not sufficient for cell killing--cytotoxicity apparently results from the conversion of cleavage complexes into overt DNA breaks by an as-yet-unknown mechanism(s). Quinolone treatment induces the bacterial SOS response in a RecBC-dependent manner, arguing that cleavage complexes are somehow converted into double-stranded breaks. However, the only proteins known to be required for SOS induction by nalidixic acid are RecA and RecBC. In hopes of identifying additional proteins involved in the cytotoxic response to nalidixic acid, we screened for E. coli mutants specifically deficient in SOS induction upon nalidixic acid treatment by using a dinD::lacZ reporter construct. From a collection of SOS partially constitutive mutants with disruptions of 47 different genes, we found that dnaQ insertion mutants are specifically deficient in the SOS response to nalidixic acid. dnaQ encodes DNA polymerase III epsilon subunit, the proofreading subunit of the replicative polymerase. The deficient response to nalidixic acid was rescued by the presence of the wild-type dnaQ gene, confirming involvement of the epsilon subunit. To further characterize the SOS deficiency of dnaQ mutants, we analyzed the expression of several additional SOS genes in response to nalidixic acid using real-time PCR. A subset of SOS genes lost their response to nalidixic acid in the dnaQ mutant strain, while two tested SOS genes (recA and recN) continued to exhibit induction. These results argue that the replication complex plays a role in modulating the SOS response to nalidixic acid and that the response is more complex than a simple on/off switch.

Dual Targeting of DNA Gyrase and Topoisomerase IV: Target Interactions of Heteroaryl Isothiazolones in Staphylococcus aureus

Heteroaryl isothiazolones (HITZs) are antibacterial agents that display excellent in vitro activity against Staphylococcus aureus. We recently identified a series of these compounds that show potent bactericidal activities against methicillin-resistant Staphylococcus aureus (MRSA). We report here the results of in vitro resistance studies that reveal potential underlying mechanisms of action. HITZs selected gyrA mutations exclusively in first-step mutants of wild-type S. aureus, indicating that in contrast to the case with most quinolones, DNA gyrase is the primary target. The compounds displayed low mutation frequencies (10(-9) to 10(-10)) at concentrations close to the MICs and maintained low MICs (< or =0.016 microg/ml) against mutants with single mutations in either gyrA or grlA (parC). These data suggested that HITZs possess significant inhibitory activities against target enzymes, DNA gyrase and topoisomerase IV. This dual-target inhibition was supported by low 50% inhibitory concentrations against topoisomerase IV as measured in a decatenation activity assay and against DNA gyrase as measured in a supercoiling activity assay. Good antibacterial activities (< or =1 microg/ml) against staphylococcal gyrA grlA double mutants, as well as low frequencies (10(-9) to 10(-10)) of selection of still higher-level mutants, also suggested that HITZs remained active against mutant enzymes. We further demonstrated that HITZs exhibit good inhibition of both S. aureus mutant enzymes and thus continue to possess a novel dual-targeting mode of action against these mutant strains. In stepwise acquisition of mutations, HITZs selected quinolone resistance determining region mutations gyrA(Ser84Leu), grlA(Ser80Phe), grlA(Ala116Val), and gyrA(Glu88Lys) sequentially, suggesting that the corresponding amino acids are key amino acids involved in the binding of HITZs to topoisomerases. The overall profile of these compounds suggests the potential utility of HITZs in combating infections caused by S. aureus, including multidrug-resistant MRSA.

The action of the bacterial toxin, microcin B17, on DNA gyrase

Microcin B17 (MccB17) is a peptide-based bacterial toxin that targets DNA gyrase, the bacterial enzyme that introduces supercoils into DNA. The site and mode of action of MccB17 on gyrase are unclear. We review what is currently known about MccB17-gyrase interactions and summarise approaches to understanding its mode of action that involve modification of the toxin. We describe experiments in which treatment of the toxin at high pH leads to the deamidation of two asparagine residues to aspartates. The modified toxin was found to be inactive in vivo and in vitro, suggesting that the Asn residues are essential for activity. Following on from these studies we have used molecular modelling to suggest a 3D structure for microcin B17. We discuss the implications of this model for MccB17 action and investigate the possibility that it binds metal ions.

Comment on: Quinolone resistance determinant qnrA3 in clinical isolates of Salmonella in 2000-2005 in Hong Kong

Sir, In their recent correspondence, Chu et al. noted the first observation of qnrA3 in salmonellae in Hong Kong, underlining the spread and diversity of plasmidic quinoloneresistance determinants worldwide. Such determinants now include qnrA1–5, qnrB and qnrS, some of which, at least, protect DNA gyrase, as well as the fluoroquinolone-acetylating variant of the aminoglycoside-modifying enzyme AAC(60)Ib, named AAC(60)Ib-cr. These proteins may influence the development of high-level resistance to at least some fluoroquinolones. In our recent article, we sought to explore the unexplained significant association between chromosomal fluoroquinolone resistance and plasmidic resistances to other antibiotic classes (such as ESBLs), which is seen in several bacterial genera. We were pleased to note that Chu et al. cited our article, but would like to clarify a misinterpretation of our hypothesis. Multiresistance plasmids can encode toxin–antitoxin systems to prevent their own loss from the cell, and some toxins target DNA gyrase. We asked whether the development of quinolone resistance by plasmid-bearing strains might be associated with such DNA gyrase-targeting toxins. We speculated on whether a cell might escape addiction to toxin–antitoxin systems by developing resistance to the toxin. Mutational events in DNA gyrase could play a role in cells escaping addiction to plasmids with gyrase-targeting toxins, and we suggested that these mutations might fortuitously confer a degree of cross-resistance to quinolones. Notably, whilst at least three qnrA variants likely originated from the chromosome of Shewanella algae, and although Qnr-type proteins inhibit/protect DNA gyrase, their precise cellular role(s) remains unknown. We would like to emphasize that we did not state, or wish to imply, that Qnr proteins could be part of a toxin–antitoxin pair as was attributed to our article by Chu et al. Rather, we postulated that gyrase ‘inhibitors/protectors’ such as Qnr might give some crossresistance to gyrase-targeting toxins in addition to the more obvious resistance to quinolones. By so doing these proteins might open a ‘window’ and influence the frequency at which cells could eject the toxin–antitoxin encoding replicons without suffering apoptosis, thereby providing the host organism with a toxin–antitoxin evasion mechanism. This might provide a competitive advantage in demanding psychrophilic aquatic environments, the natural environment of S. algae, by allowing enhanced ejection of ‘accessory’ replicons.