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Analysis of biological fluids using 600 MHz proton NMR spectroscopy: application of homonuclear two-dimensional J-resolved spectroscopy to urine and blood plasma for spectral simplification and assignment.

The application of 600 MHz two-dimensional J-resolved 1H NMR spectroscopy (JRES) to the analysis of human urine and blood plasma is demonstrated. This method when applied at very high field gives a rapid means of simplifying and aiding the assignment of highly overlapped resonances of minor metabolites in biofluids. Using this approach, mixtures of drug and endogenous metabolites were identified in untreated urine samples, the signals of which were extensively overlapped in single pulse 600 MHz spectra. For untreated blood plasma samples the JRES experiment was also effective for the selective attenuation of signals from the plasma proteins thus revealing strong well-resolved signals from the low molecular weight components. For the first time it was shown to be possible to assign in detail the spectra region from 3 to 4 ppm in blood plasma, including the complete assignment of the signals from alpha- and beta-glucose. JRES spectra of plasma were much easier to interpret and had a much higher information content than equivalent one-dimensional Hahn spin-echo spectra, thus aiding the identification of non protein-bound low molecular weight metabolites in plasma.

Adult↗

Automatic reduction of NMR spectroscopic data for statistical and pattern recognition classification of samples.

A general method of automatically reducing NMR spectra to provide numerical descriptors of samples has been developed and investigated. These descriptors can be used as input to pattern recognition or multivariate algorithms for sample classification. The methods have been tested using 600 MHz one-dimensional 1H NMR spectra of biofluids which are complex mixtures. The approach is, in principle, applicable to multidimensional and heteronuclear NMR spectra and to other types of liquid samples such as oils and foodstuffs as well as to situations such as 1H or 31P NMR in vivo and solid state NMR in drug formulation analysis. The method relies upon apportioning the information in the spectra to individual contiguous segments and allowing specified regions of the spectra to be omitted. Three approaches, based on the number of peaks, the summed peak heights and the summed peak areas respectively in each segment, have been tested. The effect of segment width and overlap and the effects of manipulation of the NMR spectra have been evaluated in terms of the classification of the samples using principal components analysis. A simple method of generating NMR based spectral descriptors for object classification is thus proposed.

Algorithms↗

Application of radioreceptor assays for systematic toxicological analysis--2. Theoretical considerations and evaluation.

In this paper the applicability of radioreceptor assays for systematic toxicological analysis will be evaluated on a theoretical basis as well as on the basis of the outcomes of the analysis of a large number of urine samples collected after administration of a selected number of drugs to healthy volunteers and patients. Many drugs and other substances of toxicological relevance exert their action through an interaction with one or more receptor (sub)types. Whether the number of persons are using particular drugs intentionally or unintentionally, radioreceptor assays can be a useful tool for systematic toxicological analysis in that they can be applied to the identification of entire pharmacological classes of substances as well as pharmacologically active metabolites. In part 1 of this paper detailed procedures for radioreceptor assays for benzodiazepines, anticholinergics and antihistaminics have been described in detail in order to illustrate not only the potentials but also the limitations of assay conditions. Fifteen drugs were administered to patients and volunteers and urine samples were collected and determined with the three radioreceptor assays. The results of this study underline the theoretical applicability of receptor assays in systematic toxicological analysis though sample pretreatment procedures may contribute to an improvement in sensitivity and applicability to other biofluids.

Benzodiazepines↗

Immobilized metal ion affinity chromatography.

The introduction of immobilized metal ion affinity chromatography, directed toward specific protein side chains, has opened a new dimension in protein purification. This review covers the principles and practice of IMAC that can be performed under very mild, nondenaturing conditions. IMAC is particularly suitable for preparative group fractionation of complex extracts and biofluids, but can also be used in high-performance mode: "HP-IMAC." Single-step purifications of 1000-fold or more may allow isolation of a particular protein from crude extracts on a milligram or gram scale. With respect to separation efficiency, IMAC compares well with biospecific affinity chromatography, and the immobilized metal ion ligand complexes are more likely to withstand wear and tear than are antibodies or enzymes. The enormous potential of IMAC and related metal affinity techniques is only in the initial stages of being explored and exploited. Synthesis of IMA adsorbents, and various modes of performing IMAC are discussed and exemplified with selected applications. Advantages and disadvantages are listed. Effective means of counteracting the few undesirable effects that can occur are suggested.

Chromatography, Affinity↗

Improved methods for the acquisition and interpretation of NMR metabolomic data.

The high spectral congestion typically observed in one-dimensional (1D) 1H nuclear magnetic resonance (NMR) spectra of tissue extracts and biofluids limits the metabolic information that can be extracted. This study evaluates the application of two-dimensional J-resolved (JRES) spectroscopy for metabolomics, which can provide proton-decoupled projected 1D spectra (p-JRES). This approach is illustrated by an investigation of embryogenesis in Japanese medaka (Oryzias latipes), an established fish model for developmental toxicology. When combined with optimized spectral pre-processing,(2) including a 0.005-ppm bin width for data segmentation and a logarithmic transformation, the reduced congestion in the p-JRES spectra increases the likelihood that a specific metabolite can be accurately integrated and thus increases the extractable information content of the spectra. Principal components analysis of the p-JRES spectra reveals the concept of a developmental trajectory that summarizes the changes in the NMR-visible metabolome throughout medaka embryogenesis. Advantages and potential disadvantages of the p-JRES approach are discussed.

Animals↗

1H NMR analysis as a diagnostic probe for human saliva.

The applications of high resolution (1)H NMR analysis as a diagnostic probe for human saliva are reviewed with special reference to diabetes mellitus, and a recently published report regarding the ability of this technique to detect advanced glycation endproducts (AGEs) in this biofluid [Biochem. Biophys. Res. Commun. 323 (2004) 377-381]. We also demonstrate that hypochlorous acid/hypochlorite (HOCl/OCl(-))-induced modifications to the (1)H NMR profiles of human salivary supernatants arise from the chlorination and, where appropriate, oxidation of amino acids and malodorous amines, together with the oxidation of carbohydrates and alpha-keto acid anions. The attack of HOCl/OCl(-) on carbohydrates yields formate (singlet, delta = 8.46 ppm), the (1)H NMR signal of which was erroneously assigned to AGE species by the authors of [Biochem. Biophys. Res. Commun. 323 (2004) 377-381].

Amines↗

A branched-chain organic acid linked to multiple sclerosis: first identification by NMR spectroscopy of CSF.

(1)H NMR spectroscopy of cerebrospinal fluid (CSF) is currently being used to study metabolic profiles characteristic of distinct multiple sclerosis (MS) manifestations. For select MS patient groups, we have previously detected significantly increased concentrations of several identified metabolites and one unidentified compound. We now present, for the first time, the identification of the latter molecule, beta-hydroxyisobutyrate (BHIB). A combination of dedicated 1D and 2D (1)H NMR experiments was employed for signal assignment. To our knowledge, BHIB has not previously been identified in (1)H NMR spectra of biofluids or biological tissues. Our assignment suggests new biochemical pathways involved in specific MS pathologies.

Acids↗

Hydrophilic molecular rotor derivatives-synthesis and characterization.

Recent research shows high potential for some p-N,N-dialkylaminobenzylidenecyanoacetates, part of a group known as fluorescent molecular rotors, to serve as fluorescent, non-mechanical viscosity sensors. Of particular interest are molecules compatible with aqueous environments. In this study, we present the synthesis and physical characterization of derivatives from 9-(2-carboxy-2-cyanovinyl)-julolidine and related molecules. All compounds show a power-law relationship of fluorescence emission with the viscosity of the solvent, different mixtures of ethylene glycol and glycerol to modulate viscosity. Compounds with high water solubility exhibit the same behavior in aqueous solutions of dextran, where the dextran concentration was varied to modulate viscosity. In addition, some compounds have been found to have low sensitivity towards changes in the pH in the physiological range. The compounds presented show promise to be used in biofluids, such as blood plasma or lymphatic fluid, to rapidly and non-mechanically determine viscosity.

Acetates↗

The "pro-apoptotic genies" get out of mitochondria: oxidative lipidomics and redox activity of cytochrome c/cardiolipin complexes.

One of the prominent consequences of the symbiogenic origin of eukaryotic cells is the unique presence of one particular class of phospholipids, cardiolipin (CL), in mitochondria. As the product originated from the evolution of symbiotic bacteria, CL is predominantly confined to the inner mitochondrial membrane in normally functioning cells. Recent findings identified CL and its oxidation products as important participants and signaling molecules in the apoptotic cell death program. Early in apoptosis, massive membrane translocations of CL take place resulting in its appearance in the outer mitochondrial membrane. Consequently, significant amounts of CL become available for the interactions with cyt c, one of the major proteins of the intermembrane space. Binding of CL with cytochrome c (cyt c) yields the cyt c/CL complex that acts as a potent CL-specific peroxidase and generates CL hydroperoxides. In this review, we discuss the catalytic mechanisms of CL oxidation by the peroxidase activity of cyt c as well as the role of oxidized CL (CLox) in the release of pro-apoptotic factors from mitochondria into the cytosol. Potential implications of cyt c/CL peroxidase intracellular complexes in disease conditions (cancer, neurodegeneration) are also considered. The discovery of the new role of cyt c/CL complexes in early mitochondrial apoptosis offers interesting opportunities for new targets in drug discovery programs. Finally, exit of cyt c from damaged and/or dying (apoptotic) cells into extracellular compartments and its accumulation in biofluids is discussed in lieu of the formation of its peroxidase complexes with negatively charged lipids and their significance in the development of systemic oxidative stress in circulation.

Animals↗

Biomolecular NMR: a chaperone to drug discovery.

Biomolecular NMR now contributes routinely to every step in the development of new chemical entities ahead of clinical trials. The versatility of NMR--from detection of ligand binding over a wide range of affinities and a wide range of drug targets with its wealth of molecular information, to metabolomic profiling, both ex vivo and in vivo--has paved the way for broadly distributed applications in academia and the pharmaceutical industry. Proteomics and initial target selection both benefit from NMR: screenings by NMR identify lead compounds capable of inhibiting protein-protein interactions, still one of the most difficult development tasks in drug discovery. NMR hardware improvements have given access to the microgram domain of phytochemistry, which should lead to the discovery of novel bioactive natural compounds. Steering medicinal chemists through the lead optimisation process by providing detailed information about protein-ligand interactions has led to impressive success in the development of novel drugs. The study of biofluid composition--metabonomics--provides information about pharmacokinetics and helps toxicological safety assessment in animal model systems. In vivo, magnetic resonance spectroscopy interrogates metabolite distributions in living cells and tissues with increasing precision, which significantly impacts the development of anticancer or neurological disorder therapeutics. An overview of different steps in recent drug discovery is presented to illuminate the links with the most recent advances in NMR methodology.

Drug Design↗

A comprehensive analysis of supermere, exomere, and extracellular vesicle isolation and cargo in colorectal cancer.

Biofluids contain a heterogeneous mixture of extracellular vesicles and non-vesicular nanoparticles (including exomeres and supermeres) that transport a diverse array of proteins, RNA, and lipids. Our previous efforts to characterize the contents of these carriers in colorectal cancer relied on 2D culture systems requiring large-scale setups and time-consuming ultracentrifugation-based isolation. To streamline this process, we have combined 3D hollow-fiber bioreactor production and fast-protein liquid chromatography-based size-exclusion chromatography. Here, we compare the impact of culture methods and purification strategies on small extracellular vesicle, exomere, and supermere cargo. Proteomic analyses show consistently distinct profiles for extracellular vesicles, exomeres, and supermeres regardless of culture conditions or isolation method. In contrast, these two variables influence small RNAs, their base modifications, and lipidomic profiles. We present an online tool to query these and future secretome datasets (https://superomics.shinyapps.io/browse).

Humans↗

Micellar electrokinetic capillary chromatography and data alignment analysis: a new tool in urine profiling.

The complex nature of biofluids demands efficient, sensitive and high-resolution analytical methodologies to examine how the 'metabolic fingerprint' changes during disease. This paper describes how sulphated beta-cyclodextrin-modified micellar electrokinetic capillary chromatography (SbetaCD-MECC) has been combined with data alignment analysis and may prove a useful new tool in urine profiling, allowing for separation of over 80 urinary analytes in under 25 min. The optimised and validated SbetaCD-MECC methodology combined with data alignment analysis provides rapid identification of 'mismatches' between urine profiles which are not easily detected with the naked eye as well as a 'similarity score' which indicates the total sum of differences between one profile and another. The combination of SbetaCD-MECC with data alignment software should prove a useful alternative tool in metabonomic studies for rapid comparison of urine profiles.

Acetaminophen↗

Sequential injection extraction based on restricted access material for determination of furosemide in serum.

Restricted access material (RAM) column containing 25 microm C18 alkyl-diol support was integrated into the sequential injection analysis (SIA) manifold and the SIA-RAM system was tested for direct determination of furosemide in serum. LiChrospher ADS column based on restricted access material is proposed to direct injection of biofluids. The integration of RAM material into SIA enabled creation of a comprehensive on-line sample clean-up technique combined with fluorescence quantitation of analyte. Centrifuged and diluted serum sample was aspirated into the system and loaded onto the column using acetonitrile-water (2:98), pH 2.7. The analyte was retained on the column while proteins contained in the sample were removed to the waste without precipitation and clogging the column. Interfering substances complicating the detection were washed out by acetonitrile-water (15:85), pH 2.7 in the next step. The extracted analyte was eluted by means of acetonitrile-water (25:75), pH 2.3 to the fluorescence detector (emission filter 385 nm). The whole procedure comprising sample pre-treatment, analyte detection and column reconditioning took 20 min. The recoveries of furosemide from serum lay between 101.4 and 103.4% for three concentrations of analyte.

Adsorption↗

Sulphonic acid strong cation-exchange restricted access columns in sample cleanup for profiling of endogenous peptides in multidimensional liquid chromatography. Structure and function of strong cation-exchange restricted access materials.

In this work, the pore structural parameters and size exclusion properties of LiChrospher strong cation-exchange and reverse phase restricted access materials (RAM) are analysed. The molecular weight size exclusion limit for polystyrenes was found to be about 17.7 kDa, while for standard proteins, the molecular weight size exclusion limit was higher, at approximately 25 kDa. The average pore diameter on a volume basis calculated from the pore network model changes from 8.5 nm (native LiChrospher) to 8.6 nm (diol derivative) to 8.2 nm (sulphonic acid derivative) to 6.9 nm (n-octadecyl derivative). Additional characterisations were performed on restricted access materials with nitrogen sorption at 77 K, water adsorption at 25 degrees C, intrusion-extrusion of water (in order to evaluate the hydrophobic properties of the pores of the hydrophobic RAM), and zeta potential measurements by microelectrophoresis. For peptide analysis out of the biofluids, the strong cation-exchange functionality seems to be particularly suitable mainly because of the high loadability of the strong cation-exchange restricted access material (SCX-RAM) and the fact that one can work under non-denaturing conditions to perform effective chromatographic separations. For bacitracin, the dynamic capacity of the SCX-RAM columns does not reach its maximum value in the analysed range. For lysozyme, the dynamic capacity reaches a value of 0.08 mg/ml of column volume before column is overloaded. Additionally, the proper column operating conditions that lead to the total effective working time of the RAM column to be equal to approximately 500 injections (depending on the type of sample), is comprehensively described. The SCX-RAM column was used in the same system analysing urine samples for the period of 1 month (approximately 150 injections) with run-to-run reproducibility below 5% RSD and below 10% RSD for the relative fractions.

Cation Exchange Resins↗

PANAMA-enabled high-sensitivity dual nanoflow LC-MS metabolomics and proteomics analysis.

High-sensitivity nanoflow liquid chromatography (nLC) is seldom employed in untargeted metabolomics because current sample preparation techniques are inefficient at preventing nanocapillary column performance degradation. Here, we describe an nLC-based tandem mass spectrometry workflow that enables seamless joint analysis and integration of metabolomics (including lipidomics) and proteomics from the same samples without instrument duplication. This workflow is based on a robust solid-phase micro-extraction step for routine sample cleanup and bioactive molecule enrichment. Our method, termed proteomic and nanoflow metabolomic analysis (PANAMA), improves compound resolution and detection sensitivity without compromising the depth of coverage as compared with existing widely used analytical procedures. Notably, PANAMA can be applied to a broad array of specimens, including biofluids, cell lines, and tissue samples. It generates high-quality, information-rich metabolite-protein datasets while bypassing the need for specialized instrumentation.

Proteomics↗

Analysis of enterolignan glucuronides in serum and urine by HPLC-ESI-MS.

A method involving the coupling of high-performance liquid chromatography with electrospray ionisation mass spectrometry (HPLC-ESI-MS) for the quantitative determination of the mammalian lignans enterolactone and enterodiol in human blood and urine has been developed. In contrast to techniques previously published, the method allows direct measurement of free enterolignans as well as their monoglucuronide conjugates in human biofluids with minimal sample preparation. Thereby the method is suitable for large-scale intervention, case-control and epidemiologic studies. Comprehensive, high-precision (1)H and (13)C nuclear magnetic resonance data (CD3OD as solvent) obtained at 11.7 T in combination with polarimetric data show that the major form of lignan precursor in the linseeds used is (-)-secoisolariciresinol diglucoside ((2R,3R)-2,3-bis(4'-hydroxy-3'-methoxy-benzyl)-1,4-butanediyl-bis-beta-d-glucopyranoside) which is transformed by human intestinal bacteria into (+)-enterodiol and (+)-enterolactone. However, these metabolites are mono-glucuronidated after absorption and are detected as (-)-enterodiol 3'-beta-d-glucuronide=(2R,3R)-2-(3'-O-(beta-d-glucopyranosyluronic acid)benzyl)-3-(3''-hydroxybenzyl)-butane-1,4,diol and (-)-enterolactone 3'-beta-d-glucuronide=(2R,3R)-2-(3'-O-(beta-d-glucopyranosyluronic acid)benzyl)-3-(3''-hydroxybenzyl)-beta-butyrolactone in blood and urine.

Chromatography, High Pressure Liquid↗

Stability and pharmacokinetic studies of O-palmitoyl amylopectin anchored dipyridamole liposomes.

Modified polysaccharides have been used widely to increase physico-chemical stability of liposomes. However, the stability and pharmacokinetic studies on the polysaccharides modified anchored liposomes containing hydrophobic drugs which exist in lipid bilayer membranes were insufficient as compared with the liposomes carrying hydrophilic or ionic drugs in inner aqueous phase. In the present study, a hydrophobic drug, dipyridamole (DIP), was entrapped into liposomes through film hydration. Amylopectin was palmitoylated and anchored on the surface of plain DIP liposomes. Subsequently, the stabilities of DIP ethanol solution, plain DIP liposomes (PDL) and anchored DIP liposomes (ODL) against irradiation, disperse medium, biofluid, long-term storage were determined and compared. The concentrations of DIP in plasma of rats and its pharmacokinetic behaviors after intravenous administration of DIP injection, PDL and ODL were studied by RP-HPLC. The pharmacokinetic parameters were computed by software 3p97 programme. The results showed that ODL could increase stabilities more of DIP in vitro as compared with PDL. The plasma concentration-time curves of DIP after intravenous administration of DIP injection, PDL and ODL were all in accordance with open two-compartment model. Pharmacokinetic parameters of DIP injection, PDL and ODL in rats were significantly different. The present findings suggest that anchored liposomes could increase stabilities of DIP in vitro as compared with plain liposomes. Furthermore, the difference of pharmacokinetic profiles was due to the targetability of anchored liposomes.

Amylopectin↗

HPLC-MS-based methods for the study of metabonomics.

The development and use of HPLC-MS for the study of metabonomics is reviewed. To date the technique has been applied to the analysis of urine samples obtained from studies in rodents in investigations of physiological variation (e.g., factors such as strain, gender, diurnal variation, etc.) and toxicity. Examples are provided of the use of conventional HPLC, capillary methods and the recently introduced high-resolution systems based on a combination of high pressure and small particle size ("UPLC"). Comparison is also made of the use of 1H NMR spectroscopy and HPLC-MS for the analysis of biofluid samples and the advantages and limitations of the two approaches are assessed. Likely future developments are considered.

Animals↗