Vinylogous amide analogues of diaminopimelic acid (DAP) as inhibitors of enzymes involved in bacterial lysine biosynthesis

[reaction: see text] Vinylogous amides 5 and 6 have been synthesized from L-propargyl glycine and tested against diaminopimelate (DAP) enzymes involved in bacterial lysine biosynthesis. Both are reversible inhibitors of DAP D-dehydrogenase and DAP epimerase with IC(50) values in the 500 microM range. Compound 5 shows competitive inhibition against the L-dihydrodipicolinate (DHDP) reductase with a K(i) value of 32 microM, which is comparable to the planar dipicolinate 16 (K(i) = 26 microM), the best known inhibitor of the enzyme.     

Elution behavior of diaminopimelic acid and related diamino acids using the advanced Marfey's method

The advanced Marfey's method consists of a chromatography technique for the separation of amino acids into each enantiomer by derivatization with 1-fluoro-2,4-dinitrophenyl-5-L-leucinamide (L-FDLA), and a detection method using liquid chromatography/mass spectrometry (LC/MS) which can determine the non-empirically the absolute configuration of various amino acids including the non-protein ones. However, this method has not been applied to the determination of the absolute configuration of an amino acid with a "meso" configuration such as diaminopimelic acid (A2pm). In the present study, this method was successfully applied to determine the absolute configurations of diaminosuccinic acid (DAS), A2pm, cystine (Cys), selenocystine (SeCys) and homocystine (HomoCys) using a racemization procedure and the DL-FDLA method, and the resulting elution behavior was summarized as follows: (1) the LL- and meso-isomers were eluted prior to the DD-isomer except for one case; (2) the LL- and meso-isomers are closely eluted and the elution was occasionally reversed; (3) the retention time for both the L- and D-derivatives of the meso-isomer was not changed; (4) the complementary use of the two solvent systems using CH3CN and MeOH was effective to obtain a chromatogram with a high resolution; (5) the abnormality, such as the elution order and peak shape, was observed in the elution behavior of DAS.     

Ion-pair high-performance liquid chromatography of diaminopimelic acid in hydrolysates of physiological samples.

A method is reported for the determination of diaminopimelic acid (DAPA) in physiological samples. DAPA is derivatized with an o-phthaldialdehyde reagent solution, subjected to reversed-phase high-performance liquid chromatography and detected spectrofluorometrically. The method is a significant advance over previous methods because it uses the ion-pairing agent hexadecyltrimethylammonium bromide (HTMA) to facilitate DAPA measurement. Ion-pairing with HTMA avoids interference with co-eluting derivatives to provide simultaneous, sensitive, reproducible measurement of both DAPA peaks (DD,LL-DAPA and DL-DAPA).     

GC-MS analysis of diaminopimelic acid stereoisomers and amino acid enantiomers in rumen bacteria

The amounts and the configuration of the stereoisomers of 2,6-diaminopimelic acid (Dap) and the enantiomeric content of other amino acids were determined in five individual species (Fibrobacter succinogenes, Streptococcus bovis, Selenomonas ruminantium, Prevotella ruminicola and Anaerovibrio lipolytica) of rumen bacteria, and in samples of mixed rumen bacteria isolated from sheep. The separation and quantification of the Dap stereoisomers was achieved by gas chromatography (GC) of trifluoroacetyl 2-propyl esters on a Chirasil-L-Val fused silica column, and detection was achieved by selected ion monitoring mass spectrometry (SIM-MS). No isomers of Dap were detected in S. bovis and P. ruminicola, two of the bacterial isolates. LL- and DD-Dap were not detected in any of the bacterial samples. As only the meso-isomer of Dap was detected in these microorganisms, it was quantified by adding LL-Dap as an internal standard before the bacteria were acid-hydrolyzed. Amounts of between 4.8 and 12.0 mg meso-Dap per gram of bacterial dry matter (DM) were determined. The presence in the rumen bacteria of free amino acid enantiomers, extractable with 70% aqueous ethanol, were determined by GC-SIM-MS; the D-amino acids were predominantly Ala, Asp and Glu, but there was considerable variation between the species.     

Hydroxyapatite nanoparticle based fluorometric turn-on determination of dipicolinic acid,a biomarker of bacterial spores

Hydroxyapatite nanoparticles (HAP-NPs) were rendered fluorescence by doping with Eu(III) ion. The resulting fluorescent NPs are shown to be viable probes for sensitive and selective determination of dipicolinic acid (DPA), a major constituent of bacterial spores as used in bioterrorism. It is found that the addition of DPA to solutions of such HAP-NPs result in an enhancement of fluorescence due to the coordination of DPA with the Eu(III) dopant. The assay allows DPA to be detected in the 0.1 to 40 μM concentration range and with a 77 nM detection limit. The assay was applied to the detection of spores of Bacillus subtilis. The attractive properties of the probe make it a promising candidate for used in rapid detection of pathogenic bacterial spores.

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Graphical abstract Fluorescent hydroxyapatite nanoparticles (HAP-NPs) are shown to be a viable probe for detection of dipicolinic acid, a major constituent of bacterial spores. The red asterisks represent the fluorescence intensity of the HAP-NPs.

     

Bead affinity chromatography in a temperature-controllable microsystem for biomarker detection

This paper describes a temperature-controllable bead affinity chromatography (BAC) in a microsystem for biomarker detection, and preparing samples for matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) analysis. Cancer marker proteins were captured in the microsystem by BAC with RNA aptamer-immobilized microbeads. The captured proteins were then denatured and released from the microbeads by controlling temperature. The microsystem consists of a microreactor for trapping microbeads and a temperature control unit for thermal treatment of the trapped beads. We used polymethylsilxoane or single crystalline silicon in fabricating two different types of reaction chamber to compare the differences in performance originated from the materials. Carcinoembryonic antigen was concentrated and purified from human serum using the microsystem and detected by MALDI-TOF MS to demonstrate the usefulness of the microsystem. The microsystem simplifies a sample preparation process required for protein analysis and cancer biomarker detection, which will accelerate the process of cancer research.     

Fast gradient elution reversed-phase high-performance liquid chromatography with diode-array detection as a high-throughput screening method for drugs of abuse. I. Chromatographic conditions

A new approach for the high-throughput screening of biological samples to detect the presence of regulated intoxicants has been developed by modifying a conventional gradient elution high-performance liquid chromatograph (HPLC). The goal of this work was to improve the speed of gradient elution screening methods over current approaches by optimizing the operational parameters of both the column and the instrument without compromising the reproducibility of the retention times, which is the basis for the identification of intoxicant compounds. Most importantly, the novel instrument configuration substantially reduces the time needed to re-equilibrate the column between consecutive gradient runs, thereby reducing the total time for each analysis. The total analysis time for each gradient elution run is only 2.80 min, including 0.30 min for column re-equilibration between analyses. Retention times of standard calibration solutes are reproducible to better than 0.002 min in consecutive runs. A corrected retention index was adopted to account for day-to-day and column-to-column variations in retention time. For a set of forty-seven target compounds, the discriminating power and mean list length were found to be 0.95 and 3.26, respectively. In comparison to previous work with similar numbers of target compounds, the current approach provides an order of magnitude improvement in analysis time, and a four-fold decrease in mean list length.     

Chromatographic separation for domoic acid using a fragment imprinted polymer

A method for real-time visualisation of reactions performed in-capillary by the technique of electrophoretically mediated microanalysis (EMMA) is described, using a two dimensional imaging detection system. The UV absorbance detector is based on a complementary metal oxide semiconductor (CMOS) active pixel sensor. Imaging of analyte peaks absorbing at 200 nm and migrating over length of 14 mm in the capillary dimension allowed measurement of velocities and lengths of reactant and product zones. By contrast with use of single point detection, velocities of species generated by reaction anywhere within the capillary are readily measured with CMOS imaging: this is of particular benefit for EMMA experiments where reaction occurs during zone overlap. For the oxidation of glutathione by hydrogen peroxide, reaction times were varied over the range 0.5-20 s by changing voltages for electrokinetic injection and zone migration, and reactant and product peak areas were obtained for kinetic analysis of the reaction. The use of EMMA conditions with CMOS imaging allows the whole process of reaction, separation and quantification to be carried out in nanolitre volumes on-capillary in a single run on a time scale of less than 5 min.     

Conjugate addition of radicals generated from diacyloxyiodobenzenes to dehydroamino acid derivatives; a synthesis of diaminopimelic acid analogues

Radical decomposition of bis((2S)-N-benzyloxycarbonyl-2-aminopentan-5-carboxy-1-methyl ester)iodobenzene followed by decarboxylation and subsequent conjugate addition with a series of selectively protected dehydroamino acids leads to new analogues of diaminopimelic acid.     

Semiconductor sensor embedded microfluidic chip for protein biomarker detection using a bead-based immunoassay combined with deoxyribonucleic acid strand labeling

Two major issues need to be addressed in applying semiconductor biosensors to detecting proteins in immunoassays. First, the length of the antibody on the sensor surface surpasses the Debye lengths (approximately 1 nm, in normal ionic strength solution), preventing certain specifically bound proteins from being tightly attached to the sensor surface. Therefore, these proteins do not contribute to the sensor’s surface potential change. Second, these proteins carry a small charge and can be easily affected by the pH of the surrounding solution. This study proposes a magnetic bead-based immunoassay using a secondary antibody to label negatively charged DNA fragments for signal amplification. An externally imposed magnetic force attaches the analyte tightly to the sensor surface, thereby effectively solving the problem of the analyte protein’s distance to the sensor surface surpassing the Debye lengths. In addition, a normal ion intensity buffer can be used without dilution for the proposed method. Experiments revealed that the sensitivity can be improved by using a longer DNA fragment for labeling and smaller magnetic beads as solid support for the antibody. By using a 90 base pair DNA label, the signal was 15 times greater than that without labeling. In addition, by using a 120 nm magnetic bead, a minimum detection limit of 12.5 ng mL⁻¹ apolipoprotein A1 can be measured. Furthermore, this study integrates a semiconductor sensor with a microfluidic chip. With the help of microvalves and micromixers in the chip, the length of the mixing step for each immunoassay has been reduced from 1 h to 20 min, and the sample volume has been reduced from 80 μL to 10 μL. In practice, a protein biomarker in a urinary bladder cancer patient’s urine was successfully measured using this technique. This study provides a convenient and effective method to measure protein using a semiconductor sensor.     

Validated Stability-Indicating Chromatographic Methods for the Determination of Veralipride in Presence of Its Degradation Products

Two sensitive and selective chromatographic methods were developed and validated for determination of veralipride in presence of its degradation products. Forced degradation studies were performed, using HCl, NaOH and 3% H₂O₂. The first method is based on thin-layer chromatographic separation of the intact drug spot from its degradation, followed by densitometric measurements. The second method is based on isocratic liquid chromatographic separation of the studied drug from its degradation on a reversed phase C₁₈ column. The proposed LC method was utilized to investigate the kinetics of alkaline degradation process of the selected drug at different temperatures.     

Development of a temperature gradient focusing method for in situ extraterrestrial biomarker analysis

Scanning temperature gradient focusing (TGF) is a recently described technique for the simultaneous concentration and separation of charged analytes. It allows for high analyte peak capacities and low LODs in microcolumn electrophoretic separations. In this paper, we present the application of scanning TGF for chiral separations of amino acids. Using a mixture of seven carboxyfluorescein succinimidyl ester-labeled amino acids (including five chiral amino acids) which constitute the Mars7 standard, we show that scanning TGF is a very simple and efficient method for chiral separations. The modulation of TGF separation parameters (temperature window, pressure scan rate, temperature range, and chiral selector concentration) allows optimization of peak efficiencies and analyte resolutions. The use of hydroxypropyl-beta-CD at low concentration (1-5 mmol/L) as a chiral selector, with an appropriate pressure scan rate ( -0.25 Pa/s) and with a low temperature range (3-25 degrees C over 1 cm) provided high resolution between enantiomers (Rs >1.5 for each pair of enantiomers) using a short, 4 cm long capillary. With these new results, the scanning TGF method appears to be a viable method for in situ trace biomarker analysis for future missions to Mars or other solar system bodies.     

Development of a novel immunobiosensor method for the rapid detection of okadaic acid contamination in shellfish extracts

The mouse bioassay is the methodology that is most widely used to detect okadaic acid (OA) in shellfish samples. This is one of the best-known toxins, and it belongs to the family of marine biotoxins referred to as the diarrhetic shellfish poisons (DSP). Due to animal welfare concerns, alternative methods of toxin detection are being sought. A rapid and specific biosensor immunoassay method was developed and validated for the detection of OA. An optical sensor instrument based on the surface plasmon resonance (SPR) phenomenon was utilised. A polyclonal antibody to OA was raised against OA–bovine thyroglobulin conjugate and OA–N-hydroxy succinimide ester was immobilised onto an amine sensor chip surface. The assay parameters selected for the analysis of the samples were: antibody dilution, 1/750; ratio of antibody to standard, 1:1; volume of sample injected, 25 μl min⁻¹; flow rate, 25 μl min⁻¹. An assay action limit of 126 ng g⁻¹ was established by analysing of 20 shellfish samples spiked with OA at the critical concentration of 160 ng g⁻¹, which is the action limit established by the European Union (EU). At this concentration of OA, the assay delivered coefficient of variations (CVs) of <10%. The chip surface developed was shown to be highly stable, allowing more than 50 analyses per channel. When the concentrations of OA determined with the biosensor method were compared with the values obtained by LC–MS in contaminated shellfish samples, the correlation between the two analytical methods was found to be highly satisfactory (r ² = 0.991). Figure Biacore     

Chromatographic analysis of some alkylphosphonic acids using a conductimetric detection. Application to fosfomycin determination

Summary This paper describes an ion chromatographic technique with conductimetric detection for the rapid quantitative analysis of alkylphosphonic acids. The choice of the mixture of acetonitrile/borategluconate buffer (1288 v/v) as the mobile phase is discussed: acetonitrile was added to decrease the retention time of phenylphosphonic acid and fosfomycin. Simultaneously the background conductivity was smaller. Borate/gluconate buffer showed the good buffer capacity at pH=8.5 required for the injection of strong acids. The pH was set at 8.5 to obtain the fully dissociated species since their monoionic forms are poorly retained. No eluent suppression process was necessary since the mobile phase led to a low background conductivity. The validation of the method has been studied. Linearity was determined over a concentration range of from 10 to 80 g·ml^–1. Intra- and inter-day reproducibilities were satisfactory with relative standard deviations respectively less than 1.0 and 4.8%. The lowest detectable limits were from 0.2 to 1.0 g depending on the analysed compound. The method has been successfully applied to the determination of fosfomycin in biological samples.     

Single-step,paper-based concentration and detection of a malaria biomarker

The lateral-flow immunoassay (LFA) is an inexpensive and rapid paper-based assay that can potentially detect infectious disease biomarkers in resource-poor settings. Despite its many advantages that make it suitable for point-of-care diagnosis, LFA is limited by its inferior sensitivity relative to sophisticated laboratory-based assays. Our group previously introduced the use of a micellar aqueous two-phase system (ATPS), comprised of the nonionic Triton X-114 surfactant, to concentrate biomarkers in a sample and enhance their detection with LFA. However, achieving complete phase separation and target concentration using the Triton X-114 system required many hours, and the concentrated sample needed to be manually extracted and applied to LFA. Here, we successfully integrated the concentration and detection steps into a single step that occurs entirely within a portable paper-based diagnostic strip. In a novel approach, we applied the micellar ATPS to a 3-D paper design and effectively reduced the macroscopic phase separation time from 8 h to approximately 3 min. The 3-D design was integrated with LFA to simultaneously concentrate and detect Plasmodium lactate dehydrogenase (pLDH), a malaria biomarker, in both phosphate-buffered saline and fetal bovine serum within 20 min at room temperature. Compared to a conventional LFA setup with a pLDH detection limit of 10 ng μL⁻¹, our single-step diagnostic successfully detected pLDH at 1.0 ng μL⁻¹, demonstrating a 10-fold detection limit improvement and resulting in a sensitive and user-friendly assay that can be used at the point-of-care. The integration of a micellar ATPS and LFA represents a new platform that can improve and promote the use of paper-based diagnostic assays for malaria and other diseases within resource-poor settings.     

A rapid sample pretreatment protocol: improved sensitivity in the detection of a low-abundant serum biomarker for prostate cancer.

We have developed a rapid immunoglobulin G (IgG) and a human serum albumin (HSA) depletion protocol. We depleted both HSA and IgG (> 97%) separately, and in a single procedure. The method is specific and reproducible (RSD < 1.0%), and substantially lowered the detection limit of prostate-specific antigen, a prostate cancer biomarker. The method can be applied to other biomarkers and proteomic studies. Interestingly, the depletion of HSA might not be blankly as beneficial as widely portrayed. Our study suggests the depletion of IgG to be more beneficial than albumin depletion.