Oxazolidinone antibiotics target the P site on Escherichia coli ribosomes

Detection of linezolid and vancomycin resistant Enterococcus isolates collected from healthy chicken caecum

AIM

The poultry industry represents an important economic sector in Tunisia. This study aims to determine the antimicrobial resistance phenotypes and genotypes and virulence factors of enterococci collected from chicken caecum in Tunisia.

METHODS AND RESULTS

Forty-nine composite chicken caecum samples were recovered in 49 different Tunisian farms (December 2019-March 2020). Each composite sample corresponds to six individual caecum from each farm. Composite samples were plated on Slanetz-Bartley agar both supplemented (SB-Van) and not supplemented (SB) with vancomycin and isolates were identified by matrix-assisted laser desorption/ionization time-of-flight. Antibiotic resistance and virulence genes were tested by Polymerase Chain Reaction (PCR) and sequencing and multilocus-sequence-typing of selected enterococci was performed. One hundred sixty seven enterococci of six different species were recovered. Acquired linezolid resistance was detected in 6 enterococci of 4/49 samples (8.1%): (A) four optrA-carrying Enterococcus faecalis isolates assigned to ST792, ST478, and ST968 lineages; (B) two poxtA-carrying Enterococcus faecium assigned to ST2315 and new ST2330. Plasmid typing highlighted the presence of the rep10, rep14, rep7, rep8, and pLG1 in these strains. One vancomycin-resistant E. faecium isolate (typed as ST1091) with vanA gene (included in Tn1546) was detected in SB-Van plates. The gelE, agg, esp, and hyl virulence genes were found in linezolid- and vancomycin-resistant enterococci. High resistance rates were identified in the enterococci recovered in SB plates: tetracycline [74.8%, tet(M) and tet(L) genes], erythromycin [65.9%, erm(B)], and gentamicin [37.1%, aac(6')-Ie-aph(2″)-Ia].

CONCLUSION

The detection of emerging mechanisms of resistance related to linezolid and vancomycin in the fecal enterococci of poultry farms has public health implications, and further surveillance should be carried out to control their dissemination by the food chain.

Recent advances in oxazolidinones as antituberculosis agents

Tuberculosis (TB) is an infectious and fatal disease caused by Mycobacterium tuberculosis (Mtb) and remains a serious public health threat; therefore, the development of new antitubercular agents is a priority for the World Health Organization's End TB strategy and the United Nations' Sustainable Development Goals to eradicate TB. Oxazolidinones are a class of synthetic antibacterial agents with a distinct mode of action developed for the treatment of Gram-positive bacterial infections. Many oxazolidinones exhibit good activity against Mtb, and some are currently in clinical trials for multidrug-resistant TB and extensively drug-resistant TB therapy. In this review, the mechanism of action, activity and toxicity of oxazolidinones and recent progress in the research and development of oxazolidinones as anti-TB agents are summarized.

Linezolid-Resistant Enterococcus spp. Isolates from Foods of Animal Origin-The Genetic Basis of Acquired Resistance

Enterococci are important opportunistic pathogens with the capacity to acquire and spread antibiotic resistance. At present, linezolid-resistant enterococci (LRE) pose a great challenge. Linezolid is considered as a last resort antibiotic in the treatment of enterococcal infections, so it is important to monitor the occurrence of LRE in various environments. The aim of this study was to define the genetic mechanisms of linezolid resistance in enterococci (E. faecalis, E. faecium, E. hirae, E. casseliflavus) isolated from foods of animal origin (n = 104). Linezolid resistance (LR) was shown by 26.9% of isolates. All of them displayed linezolid MICs of 8–32 µg/mL, and 96.4% of them were multidrug multidrug-resistant. The most common acquired linezolid resistance gene in LR isolates was poxtA (64%), followed by optrA (28%) and cfr (12%). According to the authors’ knowledge, this research is the first to indicate the presence of the cfr gene among isolates from food. In 28.6% of the isolates, the point mutation G2576T in the V domain of the 23S rRNA was responsible for linezolid resistance. All isolates harbored the wild-type rplC, rplD and rplV genes. The obtained results indicate that linezolid resistance among enterococci in animal-derived food may result from various genetic mechanisms. The most worrying is that this resistance is encoded on mobile genetic elements, so there is a risk of its rapid transmission, even despite the lack of selective pressure resulting from the use of antibiotics.

Comparison of Anti-Microbic and Anti-Biofilm Activity Among Tedizolid and Radezolid Against Linezolid-Resistant Enterococcus faecalis Isolates

Background

The emergence and spread of linezolid-resistant Enterococcus faecalis (E. faecalis) have emerged as a serious threat to human health globally. Therefore, this study aims to compare the anti-microbic as well as the anti-biofilm activity of linezolid, tedizolid, and radezolid against linezolid-resistant E. faecalis.

Methods

A total of 2128 E. faecalis isolates were assessed from the First Affiliated Hospital of Wenzhou Medical University from 2011 to 2019. Antibiotic sensitivity was evaluated using the micro broth dilution method. Oxazolidinone-resistant chromosomal and plasmid-borne genes such as cfr, cfr(A), cfr(B), cfr(C), cfr(D), optrA, and poxtA were detected by PCR and then sequenced to detect the presence of mutations in the domain V of the 23S rRNA and the ribosomal proteins L3, L4, and L22. Conjugation experiments were conducted using the broth method. The inhibition and eradication of biofilm were evaluated through crystal violet staining, whereas the efflux pump activities were detected by agar dilution.

Results

Out of 2128 isolated E. faecalis, 71 (3.34%) were linezolid-resistant isolates in which the MICs of tedizolid and radezolid ranged from 1 to 4 μg/mL and 0.5–1 μg/mL, respectively. The MIC₅₀/MIC₉₀ of tedizolid and radezolid were 4 and 8-fold lower than the linezolid, respectively. Out of 71 resistant isolates, 57 (80.28%) carried optrA, 1 (1.41%) carried cfr, 4 (5.63%) carried optrA and cfr, and 6 (8.45%) carried optrA and cfr(D), with no mutations of 23S rRNA gene and ribosomal proteins L3, L4, and L22. Besides, the transfer rate of the optrA, cfr, and cfr(D) was 17.91%, 0% and 0%, respectively. Radezolid showed more effectiveness in eradicating biofilm (8 × MIC). However, tedizolid was more effective than radezolid and linezolid in inhibiting the biofilm formation (1/4 MIC, 1/8MIC, and 1/16MIC). Additionally, in combination with CCCP, the MICs of radezolid in all linezolid-resistant isolates decreased ≥4-fold.

Conclusion

Radezolid showed greater antimicrobial activity than tedizolid and linezolid against linezolid-resistant E. faecalis. However, both tedizolid and radezolid showed differential activity on biofilm inhibition, eradication, and efflux pump compared to linezolid. Thus, our study might bring important clinical value in the application of these drugs for resistant pathogenic strains.

Synthesis of oxazolidinones through ring-opening and annulation of vinylene carbonate with 2-pyrrolyl/indolylanilines under Rh(III) catalysis

Herein, we have developed a rhodium-catalyzed C-H functionalization and subsequent intramolecular ring-opening/cyclization of vinylene carbonate with 2-pyrrolyl/indolylanilines, which leads to oxazolidinones in moderate to good yields. In this transformation, vinylene carbonate only eliminates one oxygen atom rather than -CO₃ or CO₂. Furthermore, some control experiments are conducted to elucidate the reaction mechanism.

Presence and Characterization of a Novel cfr-Carrying Tn558 Transposon Derivative in Staphylococcus delphini Isolated From Retail Food

Antimicrobial resistance has become a major public health threat. Food-related Staphylococcus species have received much attention due to their multidrug resistance. The cfr gene associated with multidrug resistance has been consistently detected in food-derived Staphylococcus species. In this retrospective study, we examined the prevalence of cfr-positive Staphylococcus strains isolated from poultry meat in different geographical areas of China from 2011 to 2016. Two cfr-positive Staphylococcus delphini strains were identified from poultry meat in China. Comparative and whole-genome analyses were performed to characterize the genetic features and overall antimicrobial resistance genes in the two S. delphini isolates 245-1 and 2794-1. Whole-genome sequencing showed that they both harbored a novel 20,258-bp cfr-carrying Tn558 transposon derivative on their chromosomes. The Tn558 derivative harbors multiple antimicrobial resistance genes, including the transferable multiresistance gene cfr, chloramphenicol resistance gene fexA, aminoglycoside resistance genes aacA-aphD and aadD, and bleomycin resistance gene ble. Surprisingly, within the Tn558 derivative, an active unconventional circularizable structure containing various resistance genes and a copy of a direct repeat sequence was identified by two-step PCR. Furthermore, core genome phylogenetic analysis revealed that the cfr-positive S. delphini strains were most closely related to S. delphini 14S03313-1 isolated from Japan in 2017 and 14S03319-1 isolated from Switzerland in 2017. This study is the first report of S. delphini harboring a novel cfr-carrying Tn558 derivative isolated from retail food. This finding raises further concerns regarding the potential threat to food safety and public health safety. The occurrence and dissemination of similar cfr-carrying transposons from diverse Staphylococcus species need further surveillance.

Design, synthesis and antibacterial evaluation of novel oxazolidinone derivatives nitrogen-containing fused heterocyclic moiety

A series of novel oxazolidinone derivatives with nitrogen-containing fused heterocyclic moiety were designed and synthesized in this article. Their antibacterial activities were measured against S. aureus, MRSA and MSSA by MIC assay. Most of them exhibited potent activity against Gram-positive pathogens comparable to Linezolid and Radezolid. Compound 3b, which exhibited significant antibacterial activity with MIC values ranging 0.5-1.0 μg/mL, might be a promising drug candidate for further investigation.

Characteristics of linezolid-resistant Enterococcus faecalis isolates from broiler breeder farms

Linezolid is an oxazolidinone class antibiotic used for treatment infections caused by various multidrug-resistant gram-positive pathogens including enterococci. However, recently, linezolid-resistant isolates in animals are considered as a human health hazard. In a broiler operation system, antimicrobial resistance can be transferred to the environment and commercial broiler via the fecal-oral route. Therefore, this study was conducted to investigate the prevalence and characteristics of linezolid-resistant Enterococcus faecalis (E. faecalis) from broiler parent stock in a broiler operation system. Among 297 E. faecalis isolates from 85 flocks in 8 broiler breeder farms, the prevalence of chloramphenicol- and linezolid-resistant isolates was 0 to 12.1% and 0 to 8.0%, respectively; however, there were no significant differences between farms. Therefore, a total of 14 (4.7%) chloramphenicol- and/or linezolid-resistant E. faecalis showed resistance to 7 or more antimicrobial classes. The drug-resistance gene optrA, which can confer resistance to linezolid, tedizolid, and phenicols, was found in 8 (2.69%) isolates, and 7 (2.36%) of the 8 optrA-positive isolates co-carried the phenicol exporter gene fexA. However, E. faecalis isolates from 3 of 8 broiler breeder farms only carried the optrA and/or fexA genes. As linezolid is one of the last antimicrobial treatments of choice for multidrug-resistant gram-positive pathogens including E. faecalis, the presence of antibiotic-resistant E. faecalis in broiler breeder farms should be monitored to prevent the introduction of linezolid-resistant strains to the food chain.

Emerging Treatment Options for Infections by Multidrug-Resistant Gram-Positive Microorganisms

Antimicrobial agents are currently the mainstay of treatment for bacterial infections worldwide. However, due to the increased use of antimicrobials in both human and animal medicine, pathogens have now evolved to possess high levels of multi-drug resistance, leading to the persistence and spread of difficult-to-treat infections. Several current antibacterial agents active against Gram-positive bacteria will be rendered useless in the face of increasing resistance rates. There are several emerging antibiotics under development, some of which have been shown to be more effective with an improved safety profile than current treatment regimens against Gram-positive bacteria. We will extensively discuss these antibiotics under clinical development (phase I-III clinical trials) to combat Gram-positive bacteria, such as Staphylococcus aureus, Enterococcus faecium and Streptococcus pneumoniae. We will delve into the mechanism of actions, microbiological spectrum, and, where available, the pharmacokinetics, safety profile, and efficacy of these drugs, aiming to provide a comprehensive review to the involved stakeholders.

Synthesis and antibacterial evaluation of novel oxazolidinone derivatives containing a piperidinyl moiety

In this article, a series of novel oxazolidinone derivatives containing a piperidinyl moiety was designed and synthesized. Their antibacterial activities were measured against S. aureus, MRSA, MSSA, LREF and VRE by MIC assay. Most of them exhibited potent activity against Gram-positive pathogens comparable to linezolid. Among them, compound 9h exhibited comparable activity with linezolid against human MAO-A for safety evaluation and showed moderate metabolism in human liver microsome. The most promising compound 9h, which showed remarkable antibacterial activity against S. aureus, MRSA, MSSA, LREF and VRE pathogens with MIC value of 0.25-1 μg/mL, was an interesting candidate for further investigation.

[Linezolid-induced Apoptosis through Mitochondrial Damage and Role of Superoxide Dismutase-1 in Human Monocytic Cell Line U937]

 Cytopenia is a major adverse event associated with linezolid therapy. The objective of this study was to examine whether the cytotoxicity of linezolid to eukaryotic cells was associated with mitochondrial dysfunction and apoptosis-like cell death in human leukemic monocyte lymphoma cell line U937. Apoptosis-like cell death was clearly observed when cells were incubated with linezolid, depending on the duration and linezolid concentration. Mitochondrial membrane potential of cells treated with linezolid collapsed in a short period of time, but the number of mitochondria did not decrease. Cytotoxicity of linezolid was relieved by the knockdown of superoxide dismutase-1 in U937 cells. On the other hand, no autophagy was observed in cells treated with linezolid. These results suggest that mitochondrial damages would be linked to the induction of apoptosis in U937 cells treated with linezolid and that its mechanism does not involve autophagy.

Synthesis and antibacterial activity evaluation of C-5 side chain modified analogues of FYL-66, a potential agent against methicillin-resistant Staphylococcus aureus

Monofluoro- (39), difluoro- (40) and trifluoro- (41) substituted analogues showed different biological activities, and 40 is a potent antibacterial agent in animal models.

tRNAs as antibiotic targets

Transfer RNAs (tRNAs) are central players in the protein translation machinery and as such are prominent targets for a large number of natural and synthetic antibiotics. This review focuses on the role of tRNAs in bacterial antibiosis. We will discuss examples of antibiotics that target multiple stages in tRNA biology from tRNA biogenesis and modification, mature tRNAs, aminoacylation of tRNA as well as prevention of proper tRNA function by small molecules binding to the ribosome. Finally, the role of deacylated tRNAs in the bacterial “stringent response” mechanism that can lead to bacteria displaying antibiotic persistence phenotypes will be discussed.

Linezolid-dependent function and structure adaptation of ribosomes in a Staphylococcus epidermidis strain exhibiting linezolid dependence

Linezolid-dependent growth was recently reported in Staphylococcus epidermidis clinical strains carrying mutations associated with linezolid resistance. To investigate this unexpected behavior at the molecular level, we isolated active ribosomes from one of the linezolid-dependent strains and we compared them with ribosomes isolated from a wild-type strain. Both strains were grown in the absence and presence of linezolid. Detailed biochemical and structural analyses revealed essential differences in the function and structure of isolated ribosomes which were assembled in the presence of linezolid. The catalytic activity of peptidyltransferase was found to be significantly higher in the ribosomes derived from the linezolid-dependent strain. Interestingly, the same ribosomes exhibited an abnormal ribosomal subunit dissociation profile on a sucrose gradient in the absence of linezolid, but the profile was restored after treatment of the ribosomes with an excess of the antibiotic. Our study suggests that linezolid most likely modified the ribosomal assembly procedure, leading to a new functional ribosomal population active only in the presence of linezolid. Therefore, the higher growth rate of the partially linezolid-dependent strains could be attributed to the functional and structural adaptations of ribosomes to linezolid.

Linezolid dampens neutrophil-mediated inflammation in methicillin-resistant Staphylococcus aureus-induced pneumonia and protects the lung of associated damages

BACKGROUND

Linezolid is considered as a therapeutic alternative to the use of glycopeptides for the treatment of pneumonia caused by methicillin-resistant Staphylococcus aureus (MRSA). Clinical studies reported a potent survival advantage conferred by the oxazolidinone and called into question the use of glycopeptides as first-line therapy.

METHODS

In a mouse model of MRSA-induced pneumonia, quantitative bacteriology, proinflammatory cytokine concentrations in lung, myeloperoxidase activity, Ly6G immunohistochemistry, and endothelial permeability were assessed to compare therapeutic efficacy and immunomodulative properties of linezolid and vancomycin administered subcutaneously every 12 hours.

RESULTS

Significant antibacterial activity was achieved after 48 hours of treatment for linezolid and vancomycin. Levels of interleukin 1β, a major proinflammatory cytokine, and macrophage inflammatory protein 2, a chemokine involved in the recruitment of neutrophils, were decreased by both antimicrobials. Only linezolid was able to dramatically reduce the production of tumor necrosis factor α. Analysis of myeloperoxidase activity and Ly6G immunostaining showed a dramatic decrease of neutrophil infiltration in infected lung tissues for linezolid-treated animals. A time-dependent increase of endothelial permeability was observed for the control and vancomycin regimens. Of interest, in the linezolid group, decreased endothelial permeability was detected 48 hours after infection.

CONCLUSIONS

Our results indicate that linezolid could be superior to vancomycin for the management of MRSA pneumonia by attenuating an excessive inflammatory reaction and protecting the lung from pathogen-associated damages.

Hepatitis C virus translation inhibitors targeting the internal ribosomal entry site

The internal ribosome entry site (IRES) in the 5' untranslated region (UTR) of the hepatitis C virus (HCV) genome initiates translation of the viral polyprotein precursor. The unique structure and high sequence conservation of the 5' UTR render the IRES RNA a potential target for the development of selective viral translation inhibitors. Here, we provide an overview of approaches to block HCV IRES function by nucleic acid, peptide, and small molecule ligands. Emphasis will be given to the IRES subdomain IIa, which currently is the most advanced target for small molecule inhibitors of HCV translation. The subdomain IIa behaves as an RNA conformational switch. Selective ligands act as translation inhibitors by locking the conformation of the RNA switch. We review synthetic procedures for inhibitors as well as structural and functional studies of the subdomain IIa target and its ligand complexes.

Rapid emergence of resistance to linezolid and mutator phenotypes in Staphylococcus aureus isolates from an adult cystic fibrosis patient

Linezolid has emerged as an important therapeutic option for the treatment of Staphylococcus aureus in patients with cystic fibrosis. We report the rapid emergence, upon treatment with linezolid, of linezolid-resistant S. aureus clinical isolates through the accumulation of resistance-associated 23S rRNA mutations, together with acquisition of an altered mutator phenotype.

A new approach for antibiotic drugs determination in human plasma by liquid chromatography-mass spectrometry

Sensitive and selective analytical procedures based on high performance liquid chromatography with mass spectrometric detection were developed for the determination of linezolid (LIN) and amoxicillin (AMOX) in human plasma samples. Samples were prepared by applying protein precipitation (PP), solid phase extraction (SPE), and microextraction in packed syringe (MEPS). The analytical separation was carried out using reversed phase liquid chromatography in isocratic mode. All analytes were monitored by mass spectrometry (MS) detection in the product ion mode and the method was validated covering the corresponding therapeutic range of 1-30 μg/mL and 1-50 μg/mL for LIN and AMOX respectively. The assay was linear over AMOX and LIN concentration ranges. The method provided good validation data: accuracy (102.9% (LIN), 100.9% (AMOX)), limit of detection (0.1407 ng/mL (LIN); 0.1341 ng/mL (AMOX); quantification (0.3814 ng/mL (LIN), 0.4249 ng/mL (AMOX)) and acceptable stability within 24h in the auto-sampler. Three different methods were compared as regards precision, accuracy, recovery and matrix effects. The proposed methods offer a fast and simple way to determine selected antibiotic drugs in human plasma that could be applied in pharmacokinetic studies.

Development of novel molecularly imprinted solid-phase microextraction fibers and their application for the determination of antibiotic drugs in biological samples by SPME-LC/MS(n)

Novel molecularly imprinted polymer (MIP)-coated fibers for solid-phase microextraction (SPME) fibers were prepared by using linezolid as the template molecule. The characteristics and application of these fibers were investigated. The polypyrrole, polythiophene, and poly(3-methylthiophene) coatings were prepared in the electrochemical polymerization way. The molecularly imprinted SPME coatings display a high selectivity toward linezolid. Molecularly imprinted coatings showed a stable and reproducible response without any influence of interferents commonly existing in biological samples. High-performance liquid chromatography with spectroscopic UV and mass spectrometry (MS) detectors were used for the determination of selected antibiotic drugs (linezolid, daptomycin, amoxicillin). The isolation and preconcentration of selected antibiotic drugs from new types of biological samples (acellular and protein-free simulated body fluid) and human plasma samples were performed. The SPME MIP-coated fibers are suitable for the selective extraction of antibiotic drugs in biological samples.

The A-Z of bacterial translation inhibitors

Protein synthesis is one of the major targets in the cell for antibiotics. This review endeavors to provide a comprehensive "post-ribosome structure" A-Z of the huge diversity of antibiotics that target the bacterial translation apparatus, with an emphasis on correlating the vast wealth of biochemical data with more recently available ribosome structures, in order to understand function. The binding site, mechanism of action, and modes of resistance for 26 different classes of protein synthesis inhibitors are presented, ranging from ABT-773 to Zyvox. In addition to improving our understanding of the process of translation, insight into the mechanism of action of antibiotics is essential to the development of novel and more effective antimicrobial agents to combat emerging bacterial resistance to many clinically-relevant drugs.

An efficient and practical synthesis of antibacterial linezolid

A convergent and efficient synthesis of linezolid was developed using the cycloaddition of commercially available ( R)-epichlorohydrin with morpholine substituted phenylisocyanate catalysed by MgI2 or MgBr2 etherate as the key step in the 50% overall yield.

Characterization of YafO, an Escherichia coli toxin

YafO is a toxin encoded by the yafN-yafO antitoxin-toxin operon in the Escherichia coli genome. Our results show that YafO inhibits protein synthesis but not DNA or RNA synthesis. The in vivo [35S]methionine incorporation was inhibited within 5 min after YafO induction. In in vivo primer extension experiments with two different mRNAs, the specific cleavage bands appeared 11-13 bases downstream of the initiation codon, AUG, 2.5 min after the induction of YafO. An identical band was also detected in in vitro toeprinting experiments when YafO was added to the reaction mixture containing 70 S ribosomes and the same mRNAs even in the absence of tRNA(f)(Met). Notably, this band was not detected in the presence of YafO alone, indicating that YafO by itself does not have endoribonuclease activity under the conditions used. The full-length mRNAs almost completely disappeared 30 min after YafO induction in in vivo primer extension experiments, consistent with Northern blotting analysis. Over 84% of [35S]methionine-tRNA(f)(Met) was released from the translation initiation complex at 5.43 microM YafO in vitro. We demonstrated that the 70 S ribosome peak significantly increased upon YafO induction, and when the 70 S ribosomes dissociated into 50 and 30 S subunits, YafO was found to be associated with 50 S subunits. These results demonstrate that YafO is a ribosome-dependent mRNA interferase inhibiting protein synthesis.

Influence of recombination on development of mutational resistance to linezolid in Enterococcus faecalis JH2-2

We compared the propensities of Enterococcus faecalis JH2-2 and of the recombination-deficient JH2-2 recA strain to develop mutational resistance to linezolid. In both organisms, a mutation in a single rrl copy conferred resistance to linezolid. Delay in acquisition of the mutation by other rrl copies in JH2-2 recA showed that gene conversion contributed to the acquisition of resistance.

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 inhibitory mechanism of protein synthesis by YoeB, an Escherichia coli toxin

YoeB is a toxin encoded by the yefM-yoeB antitoxin-toxin operon in the Escherichia coli genome. Here we show that YoeB, a highly potent protein synthesis inhibitor, specifically blocks translation initiation. In in vivo primer extension experiments using two different mRNAs, a major band was detected after YoeB induction at three bases downstream of the initiation codon at 2.5 min. An identical band was also detected in in vitro toeprinting experiments after the addition of YoeB to the reaction mixtures containing 70 S ribosomes and the same mRNAs, even in the absence of tRNA(f)(Met). Notably, this band was not detected in the presence of YoeB alone, indicating that YoeB by itself does not have endoribonuclease activity under the conditions used. The 70 S ribosomes increased upon YoeB induction, and YoeB was found to be specifically associated with 50 S subunits. Using tetracycline and hygromycin B, we demonstrated that YoeB binds to the 50 S ribosomal subunit in 70 S ribosomes and interacts with the A site leading to mRNA cleavage at this site. As a result, the 3'-end portion of the mRNA was released from ribosomes, and translation initiation was effectively inhibited. These results demonstrate that YoeB primarily inhibits translation initiation.

Crystal structure of the oxazolidinone antibiotic linezolid bound to the 50S ribosomal subunit

The oxazolidinone antibacterials target the 50S subunit of prokaryotic ribosomes. To gain insight into their mechanism of action, the crystal structure of the canonical oxazolidinone, linezolid, has been determined bound to the Haloarcula marismortui 50S subunit. Linezolid binds the 50S A-site, near the catalytic center, which suggests that inhibition involves competition with incoming A-site substrates. These results provide a structural basis for the discovery of improved oxazolidinones active against emerging drug-resistant clinical strains.

The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning

The oxazolidinones represent the first new class of antibiotics to enter into clinical usage within the past 30 years, but their binding site and mechanism of action has not been fully characterized. We have determined the crystal structure of the oxazolidinone linezolid bound to the Deinococcus radiodurans 50S ribosomal subunit. Linezolid binds in the A site pocket at the peptidyltransferase center of the ribosome overlapping the aminoacyl moiety of an A-site bound tRNA as well as many clinically important antibiotics. Binding of linezolid stabilizes a distinct conformation of the universally conserved 23S rRNA nucleotide U2585 that would be nonproductive for peptide bond formation. In conjunction with available biochemical data, we present a model whereby oxazolidinones impart their inhibitory effect by perturbing the correct positioning of tRNAs on the ribosome.

Initiation of protein synthesis: a target for antimicrobials

BACKGROUND

Translation initiation is a basic and universal biological process that employs significantly different components and displays substantially different mechanisms in bacterial, archaeal and eukaryotic cells. A large amount of detailed mechanistic and structural information on the bacterial translation initiation apparatus has been uncovered in recent years.

OBJECTIVE

to understand which translation initiation steps could represent a novel or underexploited target for the discovery of new and specific antibacterial drugs.

METHODS

Brief descriptions of the properties and mechanism of action of the major antibiotics that have a documented direct inhibitory effect on bacterial translation initiation are presented.

RESULTS/CONCLUSIONS

Considerations and predictions concerning a future scenario for research and identification of bacterial translation initiation inhibitors are presented.

Interactions of elongation factor EF-P with the Escherichia coli ribosome

EF-P (eubacterial elongation factor P) is a highly conserved protein essential for protein synthesis. We report that EF-P protects 16S rRNA near the G526 streptomycin and the S12 and mRNA binding sites (30S T-site). EF-P also protects domain V of the 23S rRNA proximal to the A-site (50S T-site) and more strongly the A-site of 70S ribosomes. We suggest that EF-P: (a) may play a role in translational fidelity and (b) prevents entry of fMet-tRNA into the A-site enabling it to bind to the 50S P-site. We also report that EF-P promotes a ribosome-dependent accommodation of fMet-tRNA into the 70S P-site.

Synthesis and antibacterial activity of potent heterocyclic oxazolidinones and the identification of RBx 8700

Several potent oxazolidinone antibacterial agents were obtained by systematic modification of the linker between the five-membered heterocycle and the piperazinyl ring of RBx 7644 (Ranbezolid, 1) and its thienyl analogue 2, leading to the identification of an expanded spectrum compound RBx 8700 (6b).

Novel Substituted (Pyridin-3-yl)phenyloxazolidinones: Antibacterial Agents with Reduced Activity against Monoamine Oxidase A and Increased Solubility

Oxazolidinones represent a new and promising class of antibacterial agents. Current research in this area is mainly concentrated on improving the safety profile and the antibacterial spectrum. Oxazolidinones bearing a (pyridin-3-yl)phenyl moiety (e.g., 3) generally show improved antibacterial activity compared to linezolid but suffer from potent monoamine oxidase A (MAO-A) inhibition and low solubility. We now disclose the finding that new analogues of 3 with acyclic substituents on the pyridyl moiety exhibit excellent activity against Gram-positive pathogens, including linezolid-resistant Streptococcus pneumoniae. Generally, more bulky substituents yielded significantly reduced MAO-A inhibition relative to the unsubstituted compound 3. The MAO-A SAR can be rationalized on the basis of docking studies using a MAO-A/MAO-B homology model. Solubility was enhanced with incorporation of polar groups. One optimized analogue, compound 13, showed low clearance in the rat and efficacy against S. pneumoniae in a mouse pneumonia model.