Structural basis for the transformation of the traditional medicine berberine by bacterial nitroreductase.

The bacterial nitroreductases (NRs) NfsB and NfsA are conserved homodimeric FMN-dependent flavoproteins that are responsible for the reduction of nitroaromatic substrates. Berberine (BBR) is a plant-derived isoquinoline alkaloid with a large conjugated ring system that is widely used in the treatment of various diseases. It was recently found that the gut microbiota convert BBR into dihydroberberine (dhBBR, the absorbable form) mediated by bacterial NRs. The molecular basis for the transformation of BBR by the gut microbiota remains unclear. Here, kinetic studies showed that NfsB from Escherichia coli (EcNfsB), rather than EcNfsA, is responsible for the conversion of BBR to dhBBR in spite of a low reaction rate. The crystal structure of the EcNfsB-BBR complex showed that BBR binds into the active pocket at the dimer interface, and its large conjugated plane stacks above the plane of the FMN cofactor in a nearly parallel orientation. BBR is mainly stabilized by π-stacking interactions with both neighboring aromatic residues and FMN. Structure-based mutagenesis studies further revealed that the highly conserved Phe70 and Phe199 are important residues for the conversion of BBR. The structure revealed that the C6 atom of BBR (which receives the hydride) is ∼7.5 Šfrom the N5 atom of FMN (which donates the hydride), which is too distant for hydride transfer. Notably, several well ordered water molecules make hydrogen-bond/van der Waals contacts with the N1 atom of BBR in the active site, which probably donate protons in conjunction with electron transfer from FMN. The structure-function studies revealed the mechanism for the recognition and binding of BBR by bacterial NRs and may help to understand the conversion of BBR by the gut microbiota.

Development of immobilized beta1-adrenoceptor chromatography for rapid discovery of ligands specifically binding to the receptor from herbal extract.

The discovery of beta1-adrenoceptor (ß1-AR) ligands is viewed as an enormous demand for fighting ailments mediated by the receptor including cardiovascular diseases. Such pursuit is gravely challenged due to the lack of lead screening methods with high efficiency. This work developed a chromatographic method for pursuing ß1-AR ligand from the herbal extract by fusing epidermal growth factor receptor (EGFR) as a tag at its C-terminus to stably express the fusion receptor in E. coli, immobilizing the expressed EGFR-tagged ß1-AR onto ibrutinib-derivatized amino microspheres, and applying the immobilized receptor in the analysis of ligand-receptor interaction and herbal extract. Comprehensive characterizations like X-ray photoelectron spectroscopy and retention behaviors of canonical drugs demonstrated high specificity and good stability of the immobilized ß1-AR prepared through the covalent reaction between the EGFR and ibrutinib decorated on the microsphere surface. Frontal analysis of atenolol, metoprolol, and esmolol confirmed their bindings to ß1-AR with association constants of 1.07 × 104, 6.54 × 103, and 1.45 × 104 M-1. The thermodynamic analysis provided proof of electrostatic interaction, hydrogen bonds, and van der Waals force driving those interactions. Pulegone was recognized as a bioactive compound that specifically binding to ß1-AR from the extract of Ziziphora clinopodioides Lam by analyzing the retention peak through reverse-phase high performance liquid chromatography coupled with tandem mass spectrometry. These results, taken together, indicated that the current method is possible to provide an alternative for discovering ß1-AR ligands with high efficiency from complex matrices like herbal extract.

Blood fatty acid analysis reveals similar n-3 fatty acid composition in non-pregnant and pregnant women and their neonates in an Israeli pilot study.

Maternal docosahexaenoic acid (DHA) is required during pregnancy to supply for normal fetal growth and development. This pilot study aimed to assess the unknown fatty acid (FA) composition in a cohort of non-pregnant and pregnant Israeli women at term and their offspring on a normal diet without n-3 FA supplementation. The fatty acid profile, analyzed using gas chromatography, showed significantly higher plasma monounsaturated (MUFA) and lower n-6 FA percent distribution with similar n-3 index, in pregnant compared to non-pregnant women. RBC exhibited significantly higher MUFA with similar n-3 index, in pregnant compared to non-pregnant women. N-3 FA significantly correlated between neonates' plasma, with higher n-3 index, and pregnant women's DHA. Conclusion: DHA levels in non-pregnant and pregnant Israeli women at term were comparable and the DHA in pregnant women's plasma positively correlated with their neonate's level, suggesting an efficient mother-fetus FA transfer and/or fetal fatty acid metabolism to longer FA products.

Isolation of Fully Vancomycin-Resistant Streptococcus thoraltensis from the Nasal Cavity of a Healthy Young Adult.

BACKGROUND: Streptococcus thoraltensis was first isolated from pigs and rabbits. Later, isolation from human oral and nasal cavities and from throat and oropharynx was documented. S. thoraltensis was isolated from patients with periodontitis, tonsillopharyngitis, and chorioamnionitis suggesting a possible pathological role in human infections. All S. thoraltensis isolates of animal and human origins were sensitive to vancomycin. METHODS: Standard microbiological identification methods, biochemical analysis, and antibiotic susceptibility testing using disk diffusion and E methods were used. Automatic species identification and antibiotic susceptibility testing were carried out using the Vitek 2 compact system. Molecular analysis of vancomycin resistance gene was carried out using a PCR with specific primers for vanA. RESULTS: We report a healthy young female adult, aged 19 years, with history of exposure to pet rabbit who had nasal colonization with S. thoraltensis. Identification of S. thoraltensis was based on traditional microbiological methods (culture, Gram stain, and biochemical tests), and the Vitek 2 compact system with 97% confidence rate. Antibiotic susceptibility testing of the isolate indicated resistance to most antibiotics, including penicillins, cephalosporins, methicillin, and glycopeptides. The minimal inhibitory concentration for vancomycin and teicoplanin was exceptionally high (>256 µg/mL). Molecular analysis indicated the absence of vanA gene in S. thoraltensis. CONCLUSION: We report for the first time the isolation of a fully vancomycin-resistant S. thoraltensis independent of vanA from a healthy human anterior nasal cavity. The pathological role of this newly identified organism with an exceptionally rare resistance pattern in human infections is yet to be identified.

Identification of subclinical transmission of vancomycin-resistant enterococcus within an intensive care unit in Taiwan.

BACKGROUND/PURPOSE: Colonization, infection, and clonal dissemination of vancomycin-resistant enterococcus (VRE) have been reported in the literature. We aimed to investigate the incidence rate of VRE acquisition and route of transmission of VRE within the medical intensive care unit (ICU) to prove whether subclinical transmission occurs in medical ICUs. METHODS: Between March 1, 2012 and September 30, 2013, rectal cultures were obtained from all inpatients on admission and after admission to medical ICU. Strain types of VRE were determined by both multilocus sequence typing and pulsed-field gel electrophoresis. RESULTS: A total of 66 of the 405 rectal swab surveillance cultures obtained from 46 inpatients were positive for VRE, among which 27 inpatients were culture-positive for VRE on admission to medical ICU, and 19 inpatients were initially culture-negative but converted to culture-positive after admission. All isolates carried vanA gene consisting of 51 Enterococcus gallinarum, 13 Enterococcus faecium, and two Eenterococcus casseliflavus. Of the 51 E. gallinarum isolates, 40 were type ST 341, seven were ST 252, two were ST 78, and two were ST 64. The Enterococcus spp., MLST and PFGE subtypes were almost similar among these two groups of inpatients. Linezolid and tigecycline were most active against VRE in vitro. CONCLUSION: Subclinical VRE cross transmission may occur in ICU. Active surveillance and maximal barrier precautions of VRE are required at ICU with high colonization rate of VRE and shall be beneficial.

Molecular docking to flexible targets.

It is widely accepted that protein receptors exist as an ensemble of conformations in solution. How best to incorporate receptor flexibility into virtual screening protocols used for drug discovery remains a significant challenge. Here, stepwise methodologies are described to generate and select relevant protein conformations for virtual screening in the context of the relaxed complex scheme (RCS), to design small molecule libraries for docking, and to perform statistical analyses on the virtual screening results. Methods include equidistant spacing, RMSD-based clustering, and QR factorization protocols for ensemble generation and ROC analysis for ensemble selection.

Selection of fecal enterococci exhibiting tcrB-mediated copper resistance in pigs fed diets supplemented with copper.

Copper, as copper sulfate, is increasingly used as an alternative to in-feed antibiotics for growth promotion in weaned piglets. Acquired copper resistance, conferred by a plasmid-borne, transferable copper resistance (tcrB) gene, has been reported in Enterococcus faecium and E. faecalis. A longitudinal field study was undertaken to determine the relationship between copper supplementation and the prevalence of tcrB-positive enterococci in piglets. The study was done with weaned piglets, housed in 10 pens with 6 piglets per pen, fed diets supplemented with a normal (16.5 ppm; control) or an elevated (125 ppm) level of copper. Fecal samples were randomly collected from three piglets per pen on days 0, 14, 28, and 42 and plated on M-Enterococcus agar, and three enterococcal isolates were obtained from each sample. The overall prevalence of tcrB-positive enterococci was 21.1% (38/180) in piglets fed elevated copper and 2.8% (5/180) in the control. Among the 43 tcrB-positive isolates, 35 were E. faecium and 8 were E. faecalis. The mean MICs of copper for tcrB-negative and tcrB-positive enterococci were 6.2 and 22.2 mM, respectively. The restriction digestion of the genomic DNA of E. faecium or E. faecalis with S1 nuclease yielded a band of ∼194-kbp size to which both tcrB and the erm(B) gene probes hybridized. A conjugation assay demonstrated cotransfer of tcrB and erm(B) genes between E. faecium and E. faecalis strains. The higher prevalence of tcrB-positive enterococci in piglets fed elevated copper compared to that in piglets fed normal copper suggests that supplementation of copper in swine diets selected for resistance.

Novel naphthalene-based inhibitors of Trypanosoma brucei RNA editing ligase 1.

BACKGROUND: Neglected tropical diseases, including diseases caused by trypanosomatid parasites such as Trypanosoma brucei, cost tens of millions of disability-adjusted life-years annually. As the current treatments for African trypanosomiasis and other similar infections are limited, new therapeutics are urgently needed. RNA Editing Ligase 1 (REL1), a protein unique to trypanosomes and other kinetoplastids, was identified recently as a potential drug target. METHODOLOGY/PRINCIPAL FINDINGS: Motivated by the urgent need for novel trypanocidal therapeutics, we use an ensemble-based virtual-screening approach to discover new naphthalene-based TbREL1 inhibitors. The predicted binding modes of the active compounds are evaluated within the context of the flexible receptor model and combined with computational fragment mapping to determine the most likely binding mechanisms. Ultimately, four new low-micromolar inhibitors are presented. Three of the four compounds may bind to a newly revealed cleft that represents a putative druggable site not evident in any crystal structure. CONCLUSIONS/SIGNIFICANCE: Pending additional optimization, the compounds presented here may serve as precursors for future novel therapies useful in the fight against several trypanosomatid pathogens, including human African trypanosomiasis, a devastating disease that afflicts the vulnerable patient populations of sub-Saharan Africa.

Clinical implications of vancomycin-resistant Enterococcus faecium (VRE) with VanD phenotype and vanA genotype.

OBJECTIVES: To investigate the clinical implications of vancomycin-resistant Enterococcus faecium (VRE) with VanD phenotype and vanA genotype (VanD-vanA VRE). METHODS: We tested in vitro and in vivo efficacies of teicoplanin against VanD-vanA VRE strains. Change in teicoplanin MICs was monitored during incubation with teicoplanin. In vitro and in vivo time-kill assay and survival analysis using a mouse peritonitis model were performed. RESULTS: Teicoplanin MICs of VanD-vanA VRE strains increased to 128 mg/L within 48 h when they were cultured with 120 mg/L teicoplanin. In vitro and in vivo time-kill assay showed that VanD-vanA VRE strains were not eliminated by 120 mg/L teicoplanin in contrast to vancomycin-susceptible E. faecium and VanD-vanB strains. The survival rate of mice infected with VanD-vanA VRE strains treated with teicoplanin was comparable with that of untreated mice. CONCLUSION: Data suggest that teicoplanin would fail in the treatment of VanD type VRE infections if the strains contained the vanA gene, which cannot be detected in the clinical microbiology laboratory.

Failure of daptomycin monotherapy for endocarditis caused by an Enterococcus faecium strain with vancomycin-resistant and vancomycin-susceptible subpopulations and evidence of in vivo loss of the vanA gene cluster.

A patient with native valve endocarditis caused by a vancomycin "heteroresistant" strain of Enterococcus faecium experienced failure of daptomycin monotherapy without evidence of daptomycin resistance. The infecting organism exhibited in vivo emergence of a vancomycin-susceptible subpopulation lacking vanA. Treatment with a combination of high-dose daptomycin, gentamicin, and high-dose ampicillin cleared the infection.

In vitro activity of daptomycin against vancomycin-resistant enterococci of various Van types and comparison of susceptibility testing methods.

The increasing prevalence of vancomycin-resistant enterococcal (VRE) infections and the limited number of antimicrobial agents for their treatment emphasize a need for new, more effective agents. In this study, the in vitro activity of daptomycin was determined against a collection of 156 VRE from seven different institutions. Van types were characterized by PCR, and pulsed-field gel electrophoresis was performed to exclude isolates with >85% relatedness by dendrogram. Included were 126 Enterococcus faecium (109 vanA, 17 vanB) isolates, 5 Enterococcus faecalis (3 vanA, 2 vanB) isolates, 2 Enterococcus avium (vanA) isolates, 1 Enterococcus durans (vanA) isolate, 10 Enterococcus gallinarum (vanC1) isolates, and 12 Enterococcus casseliflavus (vanC2) isolates. MICs of daptomycin and five additional agents were determined by the NCCLS broth microdilution method with Mueller-Hinton (MH) broth containing supplemental calcium. MICs were also determined using two investigational E-test strip formulations, and disk diffusion testing was performed by the standard NCCLS method. The MIC of daptomycin at which 50% of the isolates tested were inhibited for this isolate collection was 4 microg/ml, and the MIC at which 90% of the isolates tested were inhibited was 8 microg/ml. Two isolates of vanA E. faecium were resistant to linezolid, and one isolate was resistant to quinupristin-dalfopristin. MICs of daptomycin determined by the E test with and without added calcium varied by 8- to 16-fold, and disk diffusion zones varied by 3 to 6 mm according to the calcium content of the commercial MH agar lots used in the study. This study has shown daptomycin to have good activity against a diverse collection of contemporary VRE isolates. However, improved standardization of the calcium content of MH agar will be important for reliable testing of daptomycin by clinical laboratories using either the E test or disk diffusion methods.

Glycopeptide derivatives.

Resistance to glycopeptides in enterococci, which first emerged in the late 1980's and is now widespread mainly in the United States, is posing a serious clinical problem due to the lack of alternative and efficacious therapeutic options, particularly against infections caused by VanA strains that are highly resistant to glycopeptides and almost all other antibiotics. In addition, isolates of Staphylococcus aureus, known as GISA, that are poorly susceptible to vancomycin and teicoplanin have been identified. Thus, there is an urgent need to develop new and more potent glycopeptides that are active against these problematic organisms. The following review will focus on the development of second-generation glycopeptides, namely LY333328 (Eli Lilly) and BI 397 (Biosearch Italia, in license to Versicor for North America), which are currently undergoing clinical trials in humans for their promising activity against VanA enterococci (LY333328), staphylococci (BI 397), and penicillin-resistant pneumococci. Both compounds were identified as the result of chemical programs that were aimed at pursuing activity of vancomycin-like or teicoplanin-like natural glycopeptides against VanA enterococci and multidrug-resistant staphylococci. More recent approaches toward glycopeptides modified in their heptapeptide core are also described. These include compounds in which amino acids 1 and 3 are replaced with other amino acid moieties such as in the modification of the asparagine side chain on residue 3 as well as attempts to change the structure of the heptapeptide backbone in positions that are critical for the molecular interaction with susceptible D-Ala-D-Ala and resistant D-Ala-D-Lactate targets. Covalently linked glycopeptide dimers and vancomycin derivatives in which vancosamine is suitably replaced with other sugar moieties will also be covered.

From vanA Enterococcus hirae to vanA Enterococcus faecium: a study of feed supplementation with avoparcin and tylosin in young chickens.

Fifteen newborn chickens were isolated in separate cages after 1 month of living together, divided into three groups, and challenged for 5 weeks with seed food which either was supplemented with avoparcin (10 mg/kg of animal food) or tylosin (40 mg/kg) or was nonsupplemented. At 9 weeks of age and after the 5-week challenge, all chickens received nonsupplemented feed for 4 additional weeks. At 4, 9, and 13 weeks of life, feces were collected and inoculated on M-Enterococcus agar plates with and without vancomycin (4 micrograms/ml). vanA-containing Enterococcus hirae was isolated from 11 of 15 chickens before antibiotic challenge, without detection of vancomycin-resistant Enterococcus faecium. At 9 weeks of age and after the 5-week avoparcin challenge, vanA E. hirae strains were no longer detected, but five of five chickens now had vanA E. faecium. At a lower frequency, vanA E. faecium had also displaced vanA E. hirae in both the tylosin group (one of four chickens) and the control group (two of five chickens). One month after avoparcin discontinuation, the number of chickens colonized with vanA E. faecium decreased from five to one. All vanA-containing E. hirae strains detected in the first month of life and most of the vanA-containing E. faecium strains detected in the second month of life showed identical ApaI and SmaI restriction patterns, respectively, when analyzed by pulsed-field gel electrophoresis. All vanA E. hirae isolates transferred glycopeptide and macrolide resistance to Enterococcus faecalis JH2-2 in vitro; the level of glycopeptide resistance was higher in the transconjugants than in the donor E. hirae strains. These data suggest that E. hirae may be a significant source of vanA determinants with the potential of transfer to other enterococcal species from humans or animals.