Directly coupled HPLC-NMR and HPLC-NMR-MS in pharmaceutical research and development

Mass spectrometry analysis of new chemical entities for pharmaceutical discovery

In this Section, we review the applications of mass spectrometry for the analysis and purification of new chemical entities (NCEs) for pharmaceutical discovery. Since the speed of synthesis of NCEs has dramatically increased over the last few years, new high throughput analytical techniques have been developed to keep pace with the synthetic developments. In this Section, we review both novel, as well as modifications of commonly used mass spectrometry techniques that have helped increase the speed of the analytical process. Part of the review is devoted to the purification of NCEs, which has undergone significant development in recent years, and the close integral association between characterization and purification to drive high throughput operations. At the end of the Section, we review potential future directions based on promising and exciting new developments.

High-precision frequency measurements: indispensable tools at the core of the molecular-level analysis of complex systems

This perspective article provides an assessment of the state-of-the-art in the molecular-resolution analysis of complex organic materials. These materials can be divided into biomolecules in complex mixtures (which are amenable to successful separation into unambiguously defined molecular fractions) and complex nonrepetitive materials (which cannot be purified in the conventional sense because they are even more intricate). Molecular-level analyses of these complex systems critically depend on the integrated use of high-performance separation, high-resolution organic structural spectroscopy and mathematical data treatment. At present, only high-precision frequency-derived data exhibit sufficient resolution to overcome the otherwise common and detrimental effects of intrinsic averaging, which deteriorate spectral resolution to the degree of bulk-level rather than molecular-resolution analysis. High-precision frequency measurements are integral to the two most influential organic structural spectroscopic methods for the investigation of complex materials-NMR spectroscopy (which provides unsurpassed detail on close-range molecular order) and FTICR mass spectrometry (which provides unrivalled resolution)-and they can be translated into isotope-specific molecular-resolution data of unprecedented significance and richness. The quality of this standalone de novo molecular-level resolution data is of unparalleled mechanistic relevance and is sufficient to fundamentally advance our understanding of the structures and functions of complex biomolecular mixtures and nonrepetitive complex materials, such as natural organic matter (NOM), aerosols, and soil, plant and microbial extracts, all of which are currently poorly amenable to meaningful target analysis. The discrete analytical volumetric pixel space that is presently available to describe complex systems (defined by NMR, FT mass spectrometry and separation technologies) is in the range of 10(8-14) voxels, and is therefore capable of providing the necessary detail for a meaningful molecular-level analysis of very complex mixtures. Nonrepetitive complex materials exhibit mass spectral signatures in which the signal intensity often follows the number of chemically feasible isomers. This suggests that even the most strongly resolved FTICR mass spectra of complex materials represent simplified (e.g. isomer-filtered) projections of structural space.

Functional group selective ion/molecule reactions: mass spectrometric identification of the amido functionality in protonated monofunctional compounds

A mass spectrometric method was developed for the screening of the amido functionality in monofunctional protonated analytes. This method is based on selective gas-phase derivatization of protonated analytes by (N,N-diethylamino)dimethylborane in a Fourier transform ion cyclotron resonance (FT-ICR) and triple quadrupole mass spectrometer. Examination of a series of protonated analytes demonstrated that only the compounds containing the amido functionality react with the aminoborane by the derivatization reaction. The mechanism involves proton transfer from the protonated analyte to the borane, followed by addition of the amide to the boron center, which leads to the elimination of neutral diethylamine. The derivatized analytes are readily identified on the basis of a shift of 40 m/z units relative to the m/z value of the protonated analyte and characteristic boron isotope patterns. Collision-activated dissociation was used to provide support for the structures assigned to the derivatized analytes. The structural information gained from this gas-phase derivatization method will aid in the functional group identification of unknown compounds and their mixtures.

Implementation of real-time two-dimensional nuclear magnetic resonance spectroscopy for on-flow high-performance liquid chromatography

Directly coupled HPLC-NMR has become a powerful tool for separation and structural elucidation of unknown compounds. However, there are only a few reports on application of on-flow two-dimensional (2D) NMR in HPLC-NMR. Here we present an alternative method for recording real-time 2D-NMR spectrum (total correlation spectroscopy, TOCSY) on a commercial HPLC-NMR system. The method is based on well-established Hadamard matrix for 2D-NMR frequency encoding. In addition, a modified/improved solvent suppression approach is incorporated. This makes it possible to carry out the experiment with both polar and gradient eluents, the widely used chromatographic conditions. The method is example using a synthesized mixture of three amino acids (His, Phe and Try) and a human urine sample. The method demonstrated here may be utilized for high-throughput structural or unknown component identification and fast dynamic study in a variety of applications.

Metabonomics in pharmaceutical R&D

This minireview is based on a lecture given at the First Maga Circe Conference on metabolomics held at Sabaudia, Italy, in March 2006 in which the analytical and statistical techniques used in metabonomics, efforts at standardization and some of the major applications to pharmaceutical research and development are reviewed. Metabonomics involves the determination of multiple metabolites simultaneously in biofluids, tissues and tissue extracts. Applications to preclinical drug safety studies are illustrated by the Consortium for Metabonomic Toxicology, a collaboration involving several major pharmaceutical companies. This consortium was able, through the measurement of a dataset of NMR spectra of rodent urine and serum samples, to build a predictive expert system for liver and kidney toxicity. A secondary benefit was the elucidation of the endogenous biochemicals responsible for the classification. The use of metabonomics in disease diagnosis and therapy monitoring is discussed with an exemplification from coronary artery disease, and the concept of pharmaco-metabonomics as a way of predicting an individual's response to treatment is exemplified. Finally, some advantages and perceived difficulties of the metabonomics approach are summarized.

Detection of urinary drug metabolite (xenometabolome) signatures in molecular epidemiology studies via statistical total correlation (NMR) spectroscopy

Western populations use prescription and nonprescription drugs extensively, but large-scale population usage is rarely assessed objectively in epidemiological studies. Here we apply statistical methods to characterize structural pathway connectivities of metabolites of commonly used drugs detected routinely in 1H NMR spectra of urine in a human population study. 1H NMR spectra were measured for two groups of urine samples obtained from U.S. participants in a known population study. The novel application of a statistical total correlation spectroscopy (STOCSY) approach enabled rapid identification of the major and certain minor drug metabolites in common use in the population, in particular, from acetaminophen and ibuprofen metabolites. This work shows that statistical connectivities between drug metabolites can be established in routine "high-throughput" NMR screening of human samples from participants who have randomly self-administered drugs. This approach should be of value in considering interpopulation patterns of drug metabolism in epidemiological and pharmacogenetic studies.

Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry

BACKGROUND

Structure elucidation of unknown small molecules by mass spectrometry is a challenge despite advances in instrumentation. The first crucial step is to obtain correct elemental compositions. In order to automatically constrain the thousands of possible candidate structures, rules need to be developed to select the most likely and chemically correct molecular formulas.

RESULTS

An algorithm for filtering molecular formulas is derived from seven heuristic rules: (1) restrictions for the number of elements, (2) LEWIS and SENIOR chemical rules, (3) isotopic patterns, (4) hydrogen/carbon ratios, (5) element ratio of nitrogen, oxygen, phosphor, and sulphur versus carbon, (6) element ratio probabilities and (7) presence of trimethylsilylated compounds. Formulas are ranked according to their isotopic patterns and subsequently constrained by presence in public chemical databases. The seven rules were developed on 68,237 existing molecular formulas and were validated in four experiments. First, 432,968 formulas covering five million PubChem database entries were checked for consistency. Only 0.6% of these compounds did not pass all rules. Next, the rules were shown to effectively reducing the complement all eight billion theoretically possible C, H, N, S, O, P-formulas up to 2000 Da to only 623 million most probable elemental compositions. Thirdly 6,000 pharmaceutical, toxic and natural compounds were selected from DrugBank, TSCA and DNP databases. The correct formulas were retrieved as top hit at 80-99% probability when assuming data acquisition with complete resolution of unique compounds and 5% absolute isotope ratio deviation and 3 ppm mass accuracy. Last, some exemplary compounds were analyzed by Fourier transform ion cyclotron resonance mass spectrometry and by gas chromatography-time of flight mass spectrometry. In each case, the correct formula was ranked as top hit when combining the seven rules with database queries.

CONCLUSION

The seven rules enable an automatic exclusion of molecular formulas which are either wrong or which contain unlikely high or low number of elements. The correct molecular formula is assigned with a probability of 98% if the formula exists in a compound database. For truly novel compounds that are not present in databases, the correct formula is found in the first three hits with a probability of 65-81%. Corresponding software and supplemental data are available for downloads from the authors' website.

HPLC–NMR with severe column overloading: Fast-track metabolite identification in urine and bile samples from rat and dog treated with [14C]-ZD6126

The subject of this study was the determination of the major urinary and biliary metabolites of [(14)C]-ZD6126 following i.v. administration to female and male bile duct cannulated rats at 10 mg/kg and 20 mg/kg, respectively, and male bile duct cannulated dogs at 6 mg/kg by HPLC-NMR spectroscopy. ZD6126 is a phosphorylated pro-drug, which is rapidly hydrolysed to the active metabolite, ZD6126 phenol. The results presented here demonstrate that [(14)C]-ZD6126 phenol is subsequently metabolised extensively by male dogs and both, male and female rats. Recovery of the dose in bile and urine was determined utilising the radiolabel, revealing biliary excretion as the major route of excretion (93%) in dog, with the majority of the radioactivity recovered in both biofluids in the first 6 h. In the rat, greater than 92% recovery was obtained within the first 24 h. The major route of excretion was via the bile 51-93% within the first 12 h. The administered phosphorylated pro-drug was not observed in any of the excreta samples. Metabolite profiles of bile and urine samples were determined by high performance liquid chromatography with radiochemical detection (HPLC-RAD), which revealed a number of radiolabelled components in each of the biofluids. The individual metabolites were subsequently identified by HPLC-NMR spectroscopy and HPLC-MS. In the male dog, the major component in urine and bile was the [(14)C]-ZD6126 phenol glucuronide, which accounted for 3% and 77% of the dose, respectively. [(14)C]-ZD6126 phenol was observed in urine at 1% of dose, but was not observed in bile. A sulphate conjugate of demethylated [(14)C]-ZD6126 phenol was identified in bile by HPLC-NMR and confirmed by HPLC-MS. In the rat, the bile contained two major radiolabelled components. One was identified as the [(14)C]-ZD6126 phenol glucuronide, the other as a glucuronide conjugate of demethylated [(14)C]-ZD6126 phenol. However, a marked difference in the proportions of these two components was observed between male and female rats, either due to a sex difference in metabolism or a difference in dose level. The glucuronide conjugate of the demethylated [(14)C]-ZD6126 phenol was present at higher concentration in the bile of male rats (4-34%), while the phenol glucuronide was present at higher concentration in the bile of female rats (8-70%) over a 0-6 h collection period. A third component was only observed in the bile samples (0-6 h and 6-12 h) of male rats. This was identified as being the same sulphate conjugate of demethylated [(14)C]-ZD6126 phenol as the one observed in dog bile. The rat urines contained two main metabolites in greatly varying concentrations, namely the demethylated [(14)C]-ZD6126 phenol glucuronide and the glucuronide of [(14)C]-ZD6126 phenol. Again, the differences in relative amounts between male and female rats were observed, the major metabolite in the urines from male rats being the demethylated [(14)C]-ZD6126 phenol (0-17% in 0-24 h), whilst the phenol glucuronide, accounting for 0.5-50% of the dose over 0-24 h, was the major metabolite in females. Methanolic extracts of the pooled biofluid samples were submitted for HPLC-NMR for the quick identification of the major metabolites. Following a single injection of the equivalent of 6-28 ml of the biofluids directly onto the HPLC-column with minimal sample preparation, the metabolites could be largely successfully isolated. Despite severe column overloading, the major metabolites of [(14)C]-ZD6126 could be positively identified, and the results are presented in this paper.

High-performance liquid chromatography separations coupled with coulometric electrode array detectors: a unique approach to metabolomics

Metabolomics is the systematic and theoretically comprehensive study of the small molecules that comprise a biological sample, e.g., sera or plasma. The primary analytical tools used in metabolomics are nuclear magnetic resonance and mass spectroscopy. We here address a different tool, high-performance liquid chromatography (HPLC) separations coupled with coulometric electrode array detection. This system has unique advantages, notably sensitivity and high quantitative precision, but also has unique limitations, such as obtaining little structural information on the metabolites of interest and limited scale-up capacity. The system also only detects redox-active compounds, which can be either a benefit or a detriment, depending on the experimental goals and design. Here, we discuss the characteristics of this HPLC/coulometric electrode array system in the context of metabolomics, and then present the method as practiced in our groups.

Application of high-performance liquid chromatography–nuclear magnetic resonance coupling to the identification of limonoids from mahogany tree (Switenia macrophylla, Meliaceae) by stopped-flow 1D and 2D NMR spectroscopy

Separation and characterization of limonoids from Switenia macrophylla (Meliaceae) by HPLC-NMR technique has been described. Analyses were carried out using reversed-phase gradient HPLC elution coupled to NMR (600 MHz) spectrometer in stopped-flow mode. Separated peaks were collected into an interface unit prior to NMR measurements, which were performed with suppression of solvent signals by shaped pulses sequences. Structure elucidation of the limonoids was attained by data obtained from 1H NMR, TOCSY, gHSQC and gHMBC spectra without conventional isolation that is usually applied in natural products studies.

Metabonomics techniques and applications to pharmaceutical research & development

In this review, the background to the approach known as metabonomics is provided, giving a brief historical perspective and summarizing the analytical and statistical techniques used. Some of the major applications of metabonomics relevant to pharmaceutical Research & Development are then reviewed including the study of various influences on metabolism, such as diet, lifestyle, and other environmental factors. The applications of metabonomics in drug safety studies are explained with special reference to the aims and achievements of the Consortium for Metabonomic Toxicology. Next, the role that metabonomics might have in disease diagnosis and therapy monitoring is provided with some examples, and the concept of pharmacometabonomics as a way of predicting an individual's response to treatment is highlighted. Some discussion is given on the strengths and weaknesses, opportunities of, and threats to metabonomics.

Microdialysis as a tool in local pharmacodynamics

In many cases the clinical outcome of therapy needs to be determined by the drug concentration in the tissue compartment in which the pharmacological effect occurs rather than in the plasma. Microdialysis is an in vivo technique that allows direct measurement of unbound tissue concentrations and permits monitoring of the biochemical and physiological effects of drugs throughout the body. Microdialysis was first used in pharmacodynamic research to study neurotransmission, and this remains its most common application in the field. In this review, we give an overview of the principles, techniques, and applications of microdialysis in pharmacodynamic studies of local physiological events, including measurement of endogenous substances such as acetylcholine, catecholamines, serotonin, amino acids, peptides, glucose, lactate, glycerol, and hormones. Microdialysis coupled with systemic drug administration also permits the more intensive examination of the pharmacotherapeutic effect of drugs on extracellular levels of endogenous substances in peripheral compartments and blood. Selected examples of the physiological effects and mechanisms of action of drugs are also discussed, as are the advantages and limitations of this method. It is concluded that microdialysis is a reliable technique for the measurement of local events, which makes it an attractive tool for local pharmacodynamic research.

Development of HPLC/ESI-MS and HPLC/1H NMR Methods for the Identification of Photocatalytic Degradation Products of Iodosulfuron

In the present study, HPLC/ESI-MS and stopped-flow HPLC/1H NMR methods were developed and applied to separate and characterize the byproducts arising from TiO2-catalyzed photodegradation of the herbicide iodosulfuron methyl ester (IOME) in aqueous solution under UV irradiation. Prior to identification, irradiated solutions of IOME (200 and 1000 mg.L(-1)) were concentrated by solid-phase extraction using two cartridges: Isolute C18 and Isolute ENV+. Analytical separation was achieved on a C18 reversed-phase column with ACN/H2O (HPLC/MS) or ACN/D2O (HPLC/NMR) as mobile phase and a linear gradient with a chromatographic run time of 35 min. The combination of UV and MS data allowed the structural elucidation of more than 20 degradation products, whereas 1H NMR data permitted an unequivocal confirmation of the identities of major products and the differentiation of several positional isomers, in particular, the hydroxylation isomers. The obtained results permitted us to propose a possible degradation scheme and to put in evidence the presence of privileged sites for the attack of OH radicals. This work shows, for the first time, the application of combined HPLC with UV, MS, and NMR detection for complete structural elucidation of photocatalytic degradation products, and it will be of particular value in studies on the elimination of pollutants in aqueous solutions by photocatalysis.

The design of a multi-dimensional LC-SPE-NMR system (LC(2)-SPE-NMR) for complex mixture analysis

In this communication, we describe the design of an online multi-chromatographic approach to the routine NMR analyses of low-level components ( approximately 0.1%) in complex mixtures. The technique, termed LC(2)-SPE-NMR, optimally combines multi-dimensional liquid chromatography with SPE technology for isolating, enriching and delivering trace analytes to the NMR probe. The fully automated LC(2)-SPE-NMR system allows for maximal loading capacity (in the first, preparative LC dimension), close to optimal peak resolution (in the second, analytical LC dimension) and enhanced sample concentration (through SPE). Using this system, it is feasible to conveniently conduct a wide range of NMR experiments on, for example, drug impurities at the low microgram per milliliter level, even for components poorly resolved in the first dimension. Such a sensitivity gain significantly elevates the analytical power of online NMR technology in terms of the level at which substances of pharmaceutical significance can be structurally characterized.

Online hyphenated liquid chromatography-nuclear magnetic resonance spectroscopy-mass spectrometry for drug metabolite and nature product analysis

Screening analysis that aims at rapidly distinguishing new molecules in the presence of a large number of known compounds becomes increasingly important in the fields of drug metabolite profiling and nature product investigation. In the past decade, online-coupled liquid chromatography-nuclear magnetic resonance spectroscopy-mass spectrometry (LC-NMR-MS) has emerged as a powerful tool for the detection and identification of known and, more important, emerging compounds in complex clinical, pharmaceutical samples and nature product extracts, due to the complementary information provided by the two detectors for unambiguous structure elucidation. This review discusses the practical conditions under which LC-NMR-MS is suitable as a routine tool for unknown analysis, as well as the fundamental concepts and their advantage aspects. Particular attention is paid to its major operating parameters that include the instrumental configurations, working modes, NMR probe improvement and LC mobile phase selection. Finally, the recent applications of LC-NMR-MS to clinical metabolite and nature product analysis are summarized which have shown the benefit of this promising hyphenated technique.

Metabonomics in preclinical drug development

Metabonomics has emerged as a key technology in preclinical drug discovery and development. The technology enables noninvasive systems assessment of untoward effects induced by candidate compounds characterising a broad spectrum of biological responses on an individual animal basis in a relatively rapid-throughput fashion, thus making it an ideal addition to early preclinical safety assessment. However, the implementation and interpretation of the technology and data it generates is not something that should be trivialised. Proper expertise in biological sciences, analytical sciences (nuclear magnetic resonance and/or mass spectrometry) and chemometrics should all be considered necessary prerequisites. If these factors are properly considered, the technology can add significant value as a tool for preclinical toxicologists.

HPLC-SPE-NMR hyphenation in natural products research: optimization of analysis of Croton membranaceus extract

The HPLC-SPE-NMR technique was used for the analysis of a root-bark extract of Croton membranaceus. The components of the extract were separated on an analytical-size reversed-phase HPLC column, the chromatographic peaks were trapped on SPE (solid-phase extraction) cartridges after post-column dilution of the eluate with water and the compounds were eluted from the cartridges with acetonitrile-d(3) into a 30 microl 600 MHz NMR probe in a fully automated procedure. The trapping efficiency of scopoletin (1), the major extract constituent, was much higher on a GP (general phase, a polystyrene-type polymer) SPE phase than on a C18 phase. Thus, under the conditions used, up to 100 microg of scopoletin per cartridge could be accumulated linearly after repeated trappings. The maximum achievable NMR signal-to-noise ratio using the GP cartridges was at least four times higher than that achievable with the C18 cartridges. It was shown that excessively long T(1) relaxation times may compromise experiments in which acetonitrile-d(3) is used as the cartridge eluent. Nevertheless, the sensitivity gain provided by the HPLC-SPE-NMR technique through repeated peak trappings allowed the acquisition of good-quality proton-detected 2D NMR spectra without the need for solvent suppression.

Identification of secondary metabolites from Streptomyces violaceoruber TU22 by means of on-flow LC-NMR and LC-DAD-MS

For rapid screening of natural products from Actinomycetes, a combination of on-line couplings LC-NMR, LC-DAD-MS and HPLC-PDA, as well as MALDI-TOF-MS is particularly suitable. Simultaneous use of these coupling techniques provides considerable advantages for the rapid identification of natural compounds in mixtures. The results of our present investigation on secondary metabolite products of Streptomyces violaceoruber TU 22 showed that more than 50% of the identified metabolites are new compounds. The structures of four new polyketides (granaticin C, metenaticin A, B and C) as well as four known ones (granaticin A, granatomycin E, daidzein and genistein) have been elucidated using LC-NMR, LC-MS/MS and -MS(n) techniques in combination with two-dimensional NMR spectroscopy.

Screening for new metabolites from marine microorganisms

This article gives an overview of current analysis techniques for the screening and the activity analysis of metabolites from marine (micro)organisms. The sequencing of marine genomes and the techniques of functional genomics (including transcriptome, proteome, and metabolome analyses) open up new possibilities for the screening of new metabolites of biotechnological interest. Although the sequencing of microbial marine genomes has been somewhat limited to date, selected genome sequences of marine bacteria and algae have already been published. This report summarizes the application of the techniques of functional genomics, such as transcriptome analysis in combination with high-resolution two-dimensional polyacrylamide gelelectrophoresis and mass spectrometry, for the screening for bioactive compounds of marine microorganisms. Furthermore, the target analysis of antimicrobial compounds by proteome or transcriptome analysis of bacterial model systems is described. Recent high-throughput screening techniques are explained. Finally, new approaches for the screening of metabolites from marine microorganisms are discussed.

Hyphenation of capillary high-performance liquid chromatography to microcoil magnetic resonance spectroscopy—determination of various carotenoids in a small-sized spinach sample

The development of miniaturized hyphenated systems such as capillary high-performance liquid chromatography--and nuclear magnetic resonance spectroscopy (HPLC-NMR) remains challenging in the field of structure elucidation. In combination with a highly specific sample preparation technique, matrix solid-phase dispersion (MSPD), and a highly selective C30 reverse phase HPLC-NMR enables the identification of small amounts of natural compounds. Here, the investigation of five carotenoids in a standard solution and two carotenoids from a spinach sample demonstrate the potential of this new development. The separation of the carotenoids is performed with self-packed fused-silica capillaries with a binary solvent gradient consisting of acetone and water. The miniaturized system allows the use of fully deuterated solvents for on-line HPLC-NMR coupling. The 1H NMR spectra of the various carotenoids obtained in stopped-flow mode gave a high signal-to-noise ratio with a sample amount in the low nanogram range. All necessary parameters for structure elucidation such as multiplet structure, coupling constants and integration values can be detected unambiguously.

NMR-based metabonomic approaches for evaluating physiological influences on biofluid composition

Strategies such as genomics, proteomics and metabonomics are being applied with increasing frequency in the pharmaceutical industry. For each of these approaches, toxicological response can be measured by terms of deviation from control or baseline status. However, in order to accurately define drug-induced response, it is necessary to characterize the normal degree of physiological variation in the absence of stimuli. Here, 1H NMR spectroscopic-based analyses of the metabolic composition of urine in experimental animals under various normal physiological conditions are reviewed. In particular, the effects of inter-animal and diurnal variation, gender, age, diet, species, strain, hormonal status and stress on the biochemical composition of urine are explored. Pattern recognition methods facilitate the comparison of urine NMR spectra over a given time-course, enabling the establishment of changes in profile and highlighting the dynamic metabolic status of an organism. Thus metabonomic approaches based on information-rich spectroscopic data sets can be used to evaluate normal physiological variation and for investigation of drug safety issues.

Hyphenation of Solid-Phase Extraction with Liquid Chromatography and Nuclear Magnetic Resonance: Application of HPLC-DAD-SPE-NMR to Identification of Constituents of Kanahia laniflora

The introduction of on-line solid-phase extraction (SPE) in HPLC-NMR has dramatically enhanced the sensitivity of this technique by concentration of the analytes in a small-volume NMR flow cell and by increasing the amount of the analyte by multiple peak trapping. In this study, the potential of HPLC-DAD-SPE-NMR hyphenation was demonstrated by structure determination of complex constituents of flower, leaf, root, and stem extracts of an African medicinal plant Kanahia laniflora. The technique was shown to allow acquisition of high-quality homo- and heteronuclear 2D NMR data following analytical-scale HPLC separation of extract constituents. Four flavonol glycosides [kaempferol 3-O-(6-O-alpha-l-rhamnopyranosyl)-beta-d-glucopyranoside; kaempferol 3-O-(2,6-di-O-alpha-l-rhamnopyranosyl)-beta-d-glucopyranoside; quercetin 3-O-(2,6-di-O-alpha-l-rhamnopyranosyl)-beta-d-glucopyranoside (rutin); and isorhamnetin, 3-O-(6-O-alpha-l-rhamnopyranosyl)-beta-d-glucopyranoside] and three 5alpha-cardenolides [coroglaucigenin 3-O-6-deoxy-beta-d-allopyranoside; coroglaucigenin 3-O-(4-O-beta-d-glucopyranosyl)-6-deoxy-beta-d-glucopyranoside; 3'-O-acetyl-3'-epiafroside] were identified, with complete assignments of 1H and 13C resonances based on HSQC and HMBC spectra whenever required. Confirmation of the structures was provided by HPLC-MS data. The HPLC-DAD-SPE-NMR technique therefore speeds up the dereplication of complex mixtures of natural origin significantly, by characterization of individual extract components prior to preparative isolation work.

Measuring the metabolome: current analytical technologies

The post-genomics era has brought with it ever increasing demands to observe and characterise variation within biological systems. This variation has been studied at the genomic (gene function), proteomic (protein regulation) and the metabolomic (small molecular weight metabolite) levels. Whilst genomics and proteomics are generally studied using microarrays (genomics) and 2D-gels or mass spectrometry (proteomics), the technique of choice is less obvious in the area of metabolomics. Much work has been published employing mass spectrometry, NMR spectroscopy and vibrational spectroscopic techniques, amongst others, for the study of variations within the metabolome in many animal, plant and microbial systems. This review discusses the advantages and disadvantages of each technique, putting the current status of the field of metabolomics in context, and providing examples of applications for each technique employed.

Rapid analysis of nucleotide-activated sugars by high-performance liquid chromatography coupled with diode-array detection, electrospray ionization mass spectrometry and nuclear magnetic resonance

A generally applicable method for HPLC analysis of sugar nucleotides was established. Separation was achieved using ion-pair chromatography on a reversed-phase column. Ion-pair reagents were selected and various parameters optimized with respect to separation of 11 of the most important sugar nucleotides and compatibility with on-line detection by electrospray ionization MS and NMR. The method was applied to the on-line analysis of the GDP-D-mannose-4,6-dehydratase (Gmd) and GDP-4-keto-6-deoxy-D-mannose reductase (Rmd) catalyzed conversion of GDP-D-mannose to GDP-D-rhamnose. By LC-NMR, the intermediate product of the reaction was shown to be a mixture of GDP-4-keto-6-deoxy-D-mannose and GDP-3-keto-6-deoxy-D-mannose. Nucleotide co-factors of enzymatic reactions such as ATP and NADH did not interfere with the analysis of nucleotide-activated sugars.

Metabonomics technologies and their applications in physiological monitoring, drug safety assessment and disease diagnosis

In this review, metabonomics, a combination of data-rich analytical chemical measurements and chemometrics for profiling metabolism in complex systems, is described and its applications are reviewed. Metabonomics is typically carried out using biofluids or tissue samples. The relevance of the technique is reviewed in relation to other '-omics', and it is shown how the methods can be applied to physiological evaluation, drug safety assessment, characterization of genetically modified animal models of disease, diagnosis of human disease, and drug therapy monitoring. The different types of analytical data, mainly from nuclear magnetic resonance spectroscopy and mass spectrometry, are summarized. The outputs from a metabonomics study allow sample classification, for example according to phenotype, drug safety or disease diagnosis, and interpretation of the reasons for classification yields information on combination biomarkers of effect. Transcriptomic and metabonomic data is currently being further integrated into a holistic understanding of systems biology. An assessment of the possible future role and impact of metabonomics is presented.

Screening and identification of acidic carbohydrates in bovine colostrum by using ion/molecule reactions and Fourier transform ion cyclotron resonance mass spectrometry: specificity toward phosphorylated complexes

A screening method was developed for the identification of acidic saccharides from biological mixtures utilizing gas-phase derivatization and mass spectrometry. Phosphorylated compounds were differentiated from other acidic species by exploiting the selective reactivity of chlorotrimethylsilane with the phosphate ions (phosphorylated compounds shift by 72 Da, allowing rapid compound detection). A 13-component mock mixture was used to demonstrate the viability of the method, and a detection limit of 600 nM (30 fmol) was determined. This method was applied to the identification of acidic compounds from bovine colostrum. To further verify the selectivity of the ion/molecule reaction, exact mass measurements were used to determine the elemental composition of 14 compounds. Eight novel acidic carbohydrate species were observed in bovine colostrum, six of which have never been reported previously in milks. Tandem mass spectrometric experiments allowed compound characterization for two of these components.

Metabonomics and its role in drug development and disease diagnosis

This article describes the new approach known as metabonomics, a combination of data-rich analytical chemistry and chemometrics for profiling metabolism in complex systems. Two main analytical approaches have been used, namely nuclear magnetic resonance spectroscopy and mass spectrometry, however, most literature on mammalian systems pertains to nuclear magnetic resonance spectroscopy. The technologies are reviewed in relation to other -omics, and how these methods can be applied to drug safety assessment, characterization of genetically modified animal models of disease, diagnosis of human disease and drug therapy monitoring is demonstrated.

Pharmaceutical impurity identification: A case study using a multidisciplinary approach

A multidisciplinary team approach to identify pharmaceutical impurities is presented in this article. It includes a representative example of the methodology. The first step is to analyze the sample by LC-MS. If the structure of the unknown impurity cannot be conclusively determined by LC-MS, LC-NMR is employed. If the sample is unsuitable for LC-NMR, the impurity needs to be isolated for conventional NMR characterization. Although the technique of choice for isolation is preparative HPLC, enrichment is often necessary to improve preparative efficiency. One such technique is solid-phase extraction. For complete verification, synthesis may be necessary to compare spectroscopic characteristics to those observed in the original sample. Although not widely practiced, an effective means of getting valuable structural information is to conduct a degradation study on the purified impurity itself. This systematic strategy was successfully applied to the identification of an impurity in the active pharmaceutical ingredient 1-(1,2,3,5,6,7-hexahydro-s-indacen-4-yl)-3-[4-(1-hydroxy-1-methyl-ethyl)-furan-2-sulphonylurea. Identification required the use of all of the previously mentioned techniques. The instability of the impurity under acidic chromatographic conditions presented an additional challenge to purification and identification. However, we turned this acidic instability to an advantage, conducting a degradation study of the impurity, which provided extensive and useful information about its structure. The following discussion describes how the information gained from each analytical technique was brought together in a complementary fashion to elucidate a final structure.

Separation and detection methods for covalent drug–protein adducts

Covalent binding of reactive metabolites of drugs to proteins has been a predominant hypothesis for the mechanism of toxicity caused by numerous drugs. The development of efficient and sensitive analytical methods for the separation, identification, quantification of drug-protein adducts have important clinical and toxicological implications. In the last few decades, continuous progress in analytical methodology has been achieved with substantial increase in the number of new, more specific and more sensitive methods for drug-protein adducts. The methods used for drug-protein adduct studies include those for separation and for subsequent detection and identification. Various chromatographic (e.g., affinity chromatography, ion-exchange chromatography, and high-performance liquid chromatography) and electrophoretic techniques [e.g., sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), two-dimensional SDS-PAGE, and capillary electrophoresis], used alone or in combination, offer an opportunity to purify proteins adducted by reactive drug metabolites. Conventionally, mass spectrometric (MS), nuclear magnetic resonance, and immunological and radioisotope methods are used to detect and identify protein targets for reactive drug metabolites. However, these methods are labor-intensive, and have provided very limited sequence information on the target proteins adducted, and thus the identities of the protein targets are usually unknown. Moreover, the antibody-based methods are limited by the availability, quality, and specificity of antibodies to protein adducts, which greatly hindered the identification of specific protein targets of drugs and their clinical applications. Recently, the use of powerful MS technologies (e.g., matrix-assisted laser desorption/ionization time-of-flight) together with analytical proteomics have enabled one to separate, identify unknown protein adducts, and establish the sequence context of specific adducts by offering the opportunity to search for adducts in proteomes containing a large number of proteins with protein adducts and unmodified proteins. The present review highlights the separation and detection technologies for drug-protein adducts, with an emphasis on methodology, advantages and limitations to these techniques. Furthermore, a brief discussion of the application of these techniques to individual drugs and their target proteins will be outlined.

Accelerated metabolite identification by “Extraction-NMR”

Examples of the use of extraction-NMR, an efficient and rapid method to obtain structural information on metabolites without prior separation, are described. Crude ethyl acetate extracts of in vitro microsomal incubations were analysed by NMR spectroscopy. The region downfield of 5.5 ppm in the proton spectra of these crude extracts was found to be essentially clear of endogenous resonances. As a consequence, sites of aromatic hydroxylation can often be determined without prior separation of the crude extracts. Sites of metabolism close to the aromatic region may also be accessible via two-dimensional (2D) homonuclear experiments (e.g. COSY, NOESY, TOCSY). One-dimensional (1D) and 2D fluorine experiments also can provide additional information on the structure of metabolites. Depending on the complexity of the aromatic region of the parent compound, signal overlap and the relative abundance of the individual components, extraction-NMR has the potential to provide information for unambiguous structure elucidation of two or three major metabolites. Should extraction-NMR produce inconclusive results, i.e. too many metabolites are present or metabolism occurred exclusively on aliphatic regions, it is possible to re-use the extraction-NMR sample and proceed with traditional methods of analysis.

Method development in high-performance liquid chromatography for high-throughput profiling and metabonomic studies of biofluid samples

"Metabonomics" has in the past decade demonstrated enormous potential in furthering the understanding of, for example, disease processes, toxicological mechanisms, and biomarker discovery. The same principles can also provide a systematic and comprehensive approach to the study of food ingredient impact on consumer health. However, "metabonomic" methodology requires the development of rapid, advanced analytical tools to comprehensively profile biofluid metabolites within consumers. Until now, NMR spectroscopy has been used for this purpose almost exclusively. Chromatographic techniques and in particular HPLC, have not been exploited accordingly. The main drawbacks of chromatography are the long analysis time, instabilities in the sample fingerprint and the rigorous sample preparation required. This contribution addresses these problems in the quest to develop generic methods for high-throughput profiling using HPLC. After a careful optimization process, stable fingerprints of biofluid samples can be obtained using standard HPLC equipment. A method using a short monolithic column and a rapid gradient with a high flow-rate has been developed that allowed rapid and detailed profiling of larger numbers of urine samples. The method can be easily translated into a slow, shallow-gradient high-resolution method for identification of interesting peaks by LC-MS/NMR. A similar approach has been applied for cell culture media samples. Due to the much higher protein content of such samples non-porous polymer-based small particle columns yielded the best results. The study clearly shows that HPLC can be used in metabonomic fingerprinting studies.

Mass spectrometric analysis of combinatorial peptide libraries derived from the tandem repeat unit of MUC2 mucin

Four 19-member synthetic peptide libraries, based on the TX1TX2T epitope motif of the mucin-2 gastrointestinal glycoprotein (MUC2) and ranging in peptide length from dipeptides to 15-mers (XT, TXT, TQTXT and KVTPTPTPTGTQTXT), were synthesized by combinatorial solid phase peptide synthesis using the portioning-mixing combinatorial approach, and analysed by electrospray ionization mass spectrometry at different (1000-10000) resolutions. Most of the components of the individual libraries could be easily identified in a single-stage molecular mass screening experiment. The resolving power of the instrument becomes an important factor above 800-1000 Da molecular mass, when predominantly multiply charged molecular ions are formed. Approaches to the identification of isobars (glutamine/lysine), isomers leucine/isoleucine) and sequence variations by tandem mass spectrometry, and/or by high-performance liquid chromatography-mass spectrometry are outlined.

Flow NMR applications in combinatorial chemistry

Flow NMR techniques are now well accepted and widely used in many areas of drug discovery. Although natural-product-, rational-drug-design-, and NMR-screening-programs have begun to use flow NMR more routinely, flow NMR has not yet gained widespread acceptance in combinatorial chemistry, even though it has been shown to be a potentially useful tool. Recent developments in DI-NMR, FIA-NMR, and LC-NMR will help flow NMR eventually gain a wider acceptance within combinatorial chemistry. These developments include LC-NMR-MS instrumentation, flow probe improvements, new pulse sequences, improved automation of NMR data analysis, and the application of flow NMR to related fields in drug discovery.

Liquid chromatography/atmospheric pressure ionization-mass spectrometry in drug metabolism studies

The study of the metabolic fate of drugs is an essential and important part of the drug development process. The analysis of metabolites is a challenging task and several different analytical methods have been used in these studies. However, after the introduction of the atmospheric pressure ionization (API) technique, electrospray and atmospheric pressure chemical ionization, liquid chromatography/mass spectrometry (LC/MS) has become an important and widely used method in the analysis of metabolites owing to its superior specificity, sensitivity and efficiency. In this paper the feasibility of LC/API-MS techniques in the identification, structure characterization and quantitation of drug metabolites is reviewed. Sample preparation, LC techniques, isotope labeling, suitability of different MS techniques, such as tandem mass spectrometry, and high-resolution MS in drug metabolite analysis, are summarized and discussed. Automation of data acquisition and interpretation, special techniques and possible future trends are also the topics of the review.

The metabolism of 2-trifluormethylaniline and its acetanilide in the rat by 19F NMR monitored enzyme hydrolysis and 1H/19F HPLC-NMR spectroscopy

The urinary excretion profile and identity of the metabolites of 2-trifluoromethyl aniline (2-TFMA) and 2-trifluoromethyl acetanilide (2-TFMAc), following i.p. administration to the rat at 50 mg kg(-1), were determined using a combination of 19F NMR monitored enzyme hydrolysis, SPEC-MS and 19F/1H HPLC-NMR. A total recovery of approximately 96.4% of the dose was excreted into the urine as seven metabolites. The major routes of metabolism were N-conjugation (glucuronidation), and ring-hydroxylation followed by sulphation (and to a lesser extent glucuronidation). The major metabolites excreted into the urine for both compounds were a labile N-conjugated metabolite (a postulated N-glucuronide) and a sulphated ring-hydroxylated metabolite (a postulated 4-amino-5-trifluoromethylphenyl sulphate) following dosing of 2-TFMA. These accounted for approximately 53.0 and 31.5% of the dose, respectively. This study identifies problems on sample component instability in the preparation and analysis procedures.