Profiling of the known-unknown Passiflora variant complement by liquid chromatography - Ion mobility - Mass spectrometry.

Liquid Chromatography - Ion Mobility - Mass Spectrometry (LC-IM-MS) was utilized for non-targeted screening analysis to understand the variance in the composition of Passiflora species. Multivariate analysis was employed to explore a chemometric processing strategy for IM based Passiflora variant differentation. This approach was applied to the comparative analyses of extracts of the medicinal plants Passiflora alata, Passiflora edulis, Passiflora incarnata and Passiflora caerulea.

Metabolite identification using an ion mobility enhanced data-independent acquisition strategy and automated data processing.

Rationale: Liquid chromatography/mass spectrometry is an essential tool for efficient and reliable quantitative and qualitative analysis and underpins much of contemporary drug metabolism and pharmacokinetics. Data-independent acquisition methods such as MS have reduced the potential to miss metabolites, but do not formally generate quadrupole-resolved product ion spectra. The addition of ion mobility separation to these approaches, for example, in High-Definition MS (HDMS ) has the potential to reduce the time needed to set up an experiment and maximize the chance that all metabolites present can be resolved and characterized.

Profiling of hepatic clearance pathways of Pittsburgh compound B and human liver cytochrome p450 phenotyping.

Background: 11C-PiB has been developed as a positron-emission tomography (PET) ligand for evaluating fibrillar β-amyloid (Aβ) in the human brain. The ligand is rapidly metabolized, with approximately 10% of intact tracer remaining 30 min after injection. When 11C-PiB is used as a treatment endpoint in intervention studies for Alzheimer's disease (AD), a concern is whether the clearance of the tracer changes from one scan to the next, increasing within subject variability in the PET signal.

Identifying metabolite ions of peptide drugs in the presence of an in vivo matrix background.

Background: Peptides represent a growing class of potential drugs. Information on metabolic clearance can be valuable for peptide drug development but different challenges are encountered with the identification of peptide metabolites in comparison to the process used for small-molecule therapeutics.

Results: Enfuvirtide was selected as a test compound and dosed intravenously at 2 mg/kg to rats.

Product ion mobility as a promising tool for assignment of positional isomers of drug metabolites.

Travelling wave ion mobility spectrometry - mass spectrometry (TWIMS-MS) was evaluated as a tool for structural identification of metabolites of small molecule drugs in cases where the exact position of the biotransformation could not be identified by conventional tandem mass spectrometry. Test sets of compounds containing biotransformations at aromatic positions were analyzed. These present a problem for traditional MS methods since an atomic level localization of the biotransformation cannot normally be determined from MS(n) spectra.

A metabolomic comparison of mouse models of the Neuronal Ceroid Lipofuscinoses.

The Neuronal Ceroid Lipofuscinoses (NCL) are a group of fatal inherited neurodegenerative diseases in humans distinguished by a common clinical pathology, characterized by the accumulation of storage body material in cells and gross brain atrophy. In this study, metabolic changes in three NCL mouse models were examined looking for pathways correlated with neurodegeneration. Two mouse models; motor neuron degeneration (mnd) mouse and a variant model of late infantile NCL, termed the neuronal ceroid lipofuscinosis (nclf) mouse were investigated experimentally.

Deletion of btn1, an orthologue of CLN3, increases glycolysis and perturbs amino acid metabolism in the fission yeast model of Batten disease.

The neuronal ceroid lipofuscinoses (NCLs) constitute a group of autosomal recessive neurodegenerative diseases affecting children. To date, the disease pathogenesis remains unknown, although the role of lysosomal impairment is widely recognized across the different diseases. Recently, the creation of simple models of juvenile NCL (Batten disease) has provided additional insights into the disease mechanism at the molecular level.

Generic dealkylation: a tool for increasing the hit-rate of metabolite rationalization, and automatic customization of mass defect filters.

The use of exact mass liquid chromatography/mass spectrometry (LC/MS) for drug metabolism studies has increased significantly in recent years. Firstly, exact mass measurements facilitate identification of standard biotransformations through the use of narrow window extracted ion chromatograms, which are typically highly selective relative to signals from matrix or dosing components. Secondly, novel metabolites can be characterized via elemental formula calculations and high-resolution product ion spectra.

Extracting metabolite ions out of a matrix background by combined mass defect, neutral loss and isotope filtration.

Mass defect, neutral loss and isotope filtration techniques were applied to electrospray ionization mass spectrometry (ESI-MS) data obtained for in vivo and in vitro samples of drug metabolism studies. A combination of these post-acquisition processing techniques was shown to be more powerful than the use of one of these tools alone for the detection in complex matrices of metabolites of candidate drugs with a characteristic isotope pattern (e.g.

IsoScore: automated localization of biotransformations by mass spectrometry using product ion scoring of virtual regioisomers.

We describe a novel approach for the automated localization of biotransformations, which we term IsoScore. Accurate mass measurement spectra of a parent drug and its metabolites are acquired. All virtual regioisomers of a given biotransformation are generated in silico by iterating over all plausible sites of oxidation around the parent drug.

Metabolomic investigation of CLN6 neuronal ceroid lipofuscinosis in affected South Hampshire sheep.

The neuronal ceroid lipofuscinoses (NCLs; Batten disease) are a group of fatal inherited neurodegenerative diseases in humans and animals distinguished by a common clinical pathology, characteristic storage body accumulation in cells, and gross brain atrophy. An (1)H NMR spectroscopy- and GC-MS-based metabolomic investigation of changes in the cerebellum, frontal and occipital lobes, and cerebrospinal fluid (CSF) of CLN6 NCL affected South Hampshire sheep charted changes from the preclinical state to advanced disease. Glutamine and succinate concentrations increased in all brain regions in affected sheep relative to controls, whereas concentrations of aspartate, acetate, glutamate, N-acetyl aspartate (NAA), and gamma-aminobutyric acid (GABA) decreased.

High resolution 1H NMR-based metabolomics indicates a neurotransmitter cycling deficit in cerebral tissue from a mouse model of Batten disease.

The neuronal ceroid lipofuscinoses (NCLs) constitute a range of progressive neurological disorders primarily affecting children. Although six of the causative genes have been characterized, the underlying disease pathogenesis for this family of disorders is unknown. Using a metabolomics approach based on high resolution 1H NMR spectroscopy of the cortex, cerebellum, and remaining regions of the brain in conjunction with statistical pattern recognition, we report metabolic deficits associated with juvenile NCL in a Cln3 knock-out mouse model.

Accelerated throughput metabolic route screening in early drug discovery using high-resolution liquid chromatography/quadrupole time-of-flight mass spectrometry and automated data analysis.

The resource investment required to characterise the metabolic fate of a compound is relatively large, meaning that within a drug discovery environment relatively few compounds are characterised in depth. Rate-limiting steps include the setting up of a complex array of mass spectrometry experiments and the subsequent analysis of the large data sets produced. We describe here a strategy for the evaluation of metabolic routes using full-scan high-resolution liquid chromatography/quadrupole time-of-flight mass spectrometry (LC/QToFMS) with automated data analysis using Metabolynx, a commercially available software package.

'All-in-one' analysis for metabolite identification using liquid chromatography/hybrid quadrupole time-of-flight mass spectrometry with collision energy switching.

The removal of bottlenecks in discovery stage metabolite identification studies is an ongoing challenge for the pharmaceutical industry. We describe the use of an 'All-in-One' approach to metabolite characterization that leverages the fast scanning and high mass accuracy of hybrid quadrupole time-of-flight mass spectrometry (QqToFMS) instruments. Full-scan MS and MS/MS data is acquired using collision energy switching without the preselection, either manually or in a data-dependent manner, of precursor ions.

1H NMR study of the conformation and absolute stereochemistry of two spirocyclic NK-1 antagonists.

The binding affinities at the human NK-1 receptor of two spirocyclic compounds were found to be similar despite being epimeric at a key stereocentre. This unexpected result prompted a thorough investigation of the solution conformations of the two compounds. This revealed that a conformational switch in the tetrahydrofuran ring enabled the C-3-aryl group to be equatorial in both cases, leading to a similar juxtaposition of the aryl rings.

A functional analysis of mouse models of cardiac disease through metabolic profiling.

Since the completion of the human and mouse genomes, the focus in mammalian biology has been on assessing gene function. Tools are needed for assessing the phenotypes of the many mouse models that are now being generated, where genes have been "knocked out," "knocked in," or mutated, so that gene expression can be understood in its biological context. Metabolic profiling of cardiac tissue through high resolution NMR spectroscopy in conjunction with multivariate statistics has been used to classify mouse models of cardiac disease.

Length preferences and periodicity in beta-strands. Antiparallel edge beta-sheets are more likely to finish in non-hydrogen bonded rings.

We analysed the length distributions of different types of beta-strand in a high resolution, non-homologous set of 500 protein structures, finding differences in their mean lengths. Antiparallel edge strands in strand-turn-strand motifs show a preference for an even number of residues. This propensity is enhanced if the length is corrected for beta-bulges, which insert an extra residue into the strand.

Use of metabonomics to identify impaired fatty acid metabolism as the mechanism of a drug-induced toxicity.

An increased diversity of therapeutic targets in the pharmaceutical industry in recent years has led to a greater diversity of toxicological effects. This, and the increased pace of drug discovery, leads to a need for new technologies for the rapid elucidation of toxicological mechanisms. As part of an evaluation of the utility of metabonomics in drug safety assessment, 1H NMR spectra were acquired on urine and liver tissue samples obtained from rats administered vehicle or a development compound (MrkA) previously shown to induce hepatotoxicity in several animal species.

NMR spectroscopic-based metabonomic studies of urinary metabolite variation in acclimatizing germ-free rats.

Understanding metabolic variation in "normal" animals is critical to the evaluation of drug-induced metabolic perturbation related to toxicity or pharmacology. NMR spectroscopic-based metabonomic methods were used to evaluate the acclimatization pathways of germ-free (axenic) rats to standard laboratory conditions concomitant with the associated development of gut microfloral communities. Urine samples from male Fischer 344 germ-free rats were collected over 21 days following introduction to a standard laboratory environment and analyzed using NMR spectroscopy.

Metabolite identification in drug discovery.

Recent developments in the technologies and approaches to identify metabolites in a drug discovery environment are reviewed. Samples may be generated using either in vitro systems--typically, but not exclusively, liver subcellular fractions, such as microsomes, or whole cells, such as hepatocytes. Alternatively, metabolites are generated in vivo using excreta obtained following dosing in preclinical species.

Enantiomeric separation of substituted 2-arylindoles on derivatised polysaccharide chiral stationary phases.

The enantiomeric separation of a series of 2-arylindoles, developed as 5HT(2A) receptor antagonists for the treatment of schizophrenia, was investigated. Evaluation of a number of chiral stationary phases (CSPs) suggested that Chiralcel OD-H and Chiralpak AD were the most versatile for these compounds, and were employed for more detailed studies. A degree of complementarity between the CSPs was observed, such that Chiralcel OD-H was more effective for piperidine-containing molecules and Chiralpak AD for piperazine- and morpholine-containing molecules.

Synthesis and conformational dynamics of tricyclic pyridones containing a fused seven-membered ring.

A new synthetic approach to tricyclic pyridones bearing a fused seven-membered ring is described. These compounds exhibit atropisomerism and exist in enantiomeric forms. Chiral HPLC separation of the enantiomers has allowed the rates of racemization to be measured and hence the free energy barrier for flipping the seven-membered ring to be deduced.

Metabolic profiling of rodent biological fluids via 1H NMR spectroscopy using a 1 mm microlitre probe.

The application of a 1 mm TXI (1H/13C/15N) microlitre NMR probe with z-gradient for metabolic profiling of biofluids is described. The probe was used to provide spectral profiles for rat blood plasma using only approximately 2 microl of fluid with a range of solvent suppression techniques. Using a similar amount of fluid, spectra were obtained from rat and mouse cerebrospinal fluid, demonstrating that the probe could be used to profile rodents metabolically via biofluids previously inaccessible to NMR analysis without the need for termination.