LC-NMR-MS in drug discovery

The use of LC/MS, GC/MS, and LC/NMR hyphenated techniques to identify a drug degradation product in pharmaceutical development

Understanding drug degradation in the formulated product is critical in pharmaceutical development as it has significant impacts on drug efficacy, safety profile and storage conditions. As a result, identification of degradation compounds has taken an important role in the drug development process. In this study, various hyphenated analytical techniques, such as liquid chromatography mass spectrometry (LC/MS), gas chromatography mass spectrometry (GC/MS), and liquid chromatography nuclear magnetic resonance with a solid phase extraction interface (LC/SPE/NMR), have been applied to the identification of a drug degradation product which grew over time in the stability study of the drug product. The target unknown is less polar and more unsaturated than the drug substance based upon reverse phase HPLC relative retention time and UV spectra. It is not ionizable by electrospray ionization (ESI) or atmospheric pressure chemical ionization (APCI) in either a positive or a negative mode. The unknown was isolated by an HPLC fraction collector and enriched by solid phase extraction. GC/MS with chemical ionization (CI) was employed to determine the molecular weight of this compound. Its fragmentation pattern was determined by CI-MS/MS using an ion trap mass spectrometer. The isolated material was also analyzed by LC/SPE/NMR, from which the structure of this compound was further characterized. The study utilizes a combination of various hyphenated analytical techniques to obtain complimentary information for structure elucidation of the unknown. The combination approach is critical for unambiguous impurity structure elucidation in drug degradation studies of pharmaceutical drug products.

MetaSite: Understanding Metabolism in Human Cytochromes from the Perspective of the Chemist

Identification of metabolic biotransformations can significantly affect the drug discovery process. Since bioavailability, activity, toxicity, distribution, and final elimination all depend on metabolic biotransformations, it would be extremely advantageous if this information could be produced early in the discovery phase. Once obtained, this information can help chemists to judge whether a potential candidate should be eliminated from the pipeline or modified to improve chemical stability or safety of new compounds. The use of in silico methods to predict the site of metabolism in phase I cytochrome-mediated reactions is a starting point in any metabolic pathway prediction. This paper presents a new method, specifically designed for chemists, that provides the cytochrome involved and the site of metabolism for any human cytochrome P450 (CYP) mediated reaction acting on new substrates. The methodology can be applied automatically to all the cytochromes for which 3D structure is known and can be used by chemists to detect positions that should be protected in order to avoid metabolic degradation or to check the suitability of a new scaffold or prodrug. The fully automated procedure is also a valuable new tool in early ADME-Tox assays (absorption, distribution, metabolism, and excretion toxicity assays), where drug safety and metabolic profile patterns must be evaluated as soon, and as early, as possible.

The design of an on-line semi-preparative LC-SPE-NMR system for trace analysis

This paper reports the design of an on-line semi-preparative LC-SPE-NMR system and its use in the structural analysis of mixture components at the 0.02-1% level. The combination provides at least a five fold mass sensitivity increase over that obtained from typical analytical LC-SPE systems and a >30-fold total NMR sensitivity enhancement over analysis by LC-NMR. This is accomplished by using a novel on-line device to store, dilute (1-100-fold) and deliver (at an optimized flow-rate) the isolated component of interest to an SPE trap unit. The SPE unit consists of two cartridges connected in parallel to increase the overall SPE capacity and also to decrease the flow-rate through each trap for enhanced trapping efficiency. As the coupling of semi-preparative LC with NMR (through SPE) is well matched in terms of optimal mass loading for both techniques, only one LC-SPE cycle is required to enrich a 50 microg ml(-1) component (1% in a 5 mg ml(-1) mixture) for the acquisition of heteronuclear (1)H-(13)C NMR data using a conventional NMR flow probe. Furthermore, analytes at the 0.02% level (approximately 1 microg ml(-1)) can be studied using 2D (1)H NMR techniques if peak cuts from replicate sample injections (> or =3) are accumulated into the storage/dilution unit and the resulting solution processed by just one SPE trap and elute cycle.

HPLC-SPE-NMR in pharmaceutical development: capabilities and applications

High-performance liquid chromatography-solid phase extraction-NMR spectroscopy (HPLC-SPE-NMR) has recently become commercially available and has been evaluated with regard to its applicability in a pharmaceutical environment. The addition of an automated SPE unit to an HPLC-NMR system for peak trapping results in an improved NMR signal-to-noise ratio (S/N) and also has other practical advantages. The trapping efficiency is shown to depend on compound polarity and is highest for compounds eluting late on reversed-phase HPLC systems. Multiple peak trapping further increases the S/N, again with the best results for less polar compounds. For polar compounds, multiple peak trapping resulted in no S/N gain as the amount of material retained on the SPE cartridge was equivalent to that from a single injection. When compared with conventional HPLC-NMR, a S/N gain of up to five-fold could be achieved for some compounds in a single trapping step. A major advantage of the technique is the independence of the chromatographic step from the NMR step, resulting in greater versatility than conventional HPLC-NMR in the HPLC solvents and NMR solvents that can be used. Practical applications from both drug metabolite and drug impurity identification are presented.

A comparison of capillary-scale LC-NMR with alternative techniques: spectroscopic and practical considerations

Experimental and practical details for the use of capillary LC (CapLC)-NMR are reported. The capillary NMR probe has high sensitivity and excellent flow characteristics and we found CapLC-NMR to be best suited to samples that are truly mass limited. CapLC-NMR relies on good capillary-scale chromatography where highly concentrated peaks with a volume closely matched to the NMR flow cell are achievable. Provided that the loading capacity of the capillary column is not limiting, the combination of high sensitivity and high solvent suppression quality makes CapLC-NMR an excellent choice. For many real samples, however, the loading is limiting and we found the combination of LC-SPE-MS-NMR with a cryoprobe enables more material to be purified for NMR analysis, while retaining sensitivity.

Identification of impurities in acarbose by using an integrated liquid chromatography-nuclear magnetic resonance and liquid chromatography-mass spectrometry approach

The usefulness of applying an integrated LC-NMR and LC-MS approach to acarbose bulk drug impurity profiling is demonstrated. LC-MS and LC-NMR methodologies were employed for the online separation and structural elucidation of a final drug product. Combining data provided by the stop-flow LC-NMR and LC-MS experiments made it possible to identify the main components present in the acarbose sample. Spectral analysis revealed that A and B were known impurities while C was an unknown compound. LC-MS and LC-NMR analyses revealed that C was a pentasaccharide differing from the acarbose in number and nature of sugar subunits in the molecule. It was subsequently isolated and its structure was confirmed by the offline 1- and 2-D NMR experiments, and atom assignment was made.

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.

Application of capillary-scale NMR for the structure determination of phytochemicals

Employing a capillary-scale NMR probe enables the miniaturisation of structure determination and de-replication of purified natural products from plants using only 5-100 microg of material. Approximately 5 microg are required to perform one-dimensional proton and two-dimensional homonuclear (COSY and NOESY) NMR experiments; some 30 microg are needed to acquire HMQC- or HSQC-NMR spectra; ca. 75-100 microg are necessary to measure HMBC-NMR spectra; and around 200 microg of a compound are needed to perform 13C- and DEPT-NMR experiments. In order to illustrate the integration of the outputs from high-throughput natural product chemistry methods with the capabilities of the state-of-the-art CapNMR technology, the preparation of a natural product library from the extract of Penstemon centranthifolius, and the subsequent isolation, purification and structure determination of six known iridoid glycosides with 25-300 microg of material are presented.

Use of quadrupole time-of-flight mass spectrometry in the elucidation of unknown compounds present in environmental water

Target compound monitoring is often not sufficient to assess the quality of water, as many of the unknown micro-contaminants present might be a threat to the environment and human health. In this work, the potential of hybrid quadrupole time-of-flight mass spectrometry (QTOF-MS) coupled to liquid chromatography (LC) in the elucidation of unknown compounds in environmental water samples has been explored. Based on accurate mass measurement, possible elemental compositions for the precursor ions were calculated. Using model compounds, a useful strategy was developed, enabling determination and evaluation of potential molecular formulae for the detected unknowns. The possibility of performing tandem mass spectrometric (MS/MS) acquisitions to obtain product ion spectra in accurate mass mode also helped to elucidate the structures of these unknowns or to detect some functional groups, to further evaluate potential formulae. The remaining formulae were searched against available databases such as the Merck Index and the NIST library. Where standards were commercially available, retention time and MS/MS data were both also used as confirmatory tools. The approach developed was applied for the identification of unknown compounds in different types of water. To improve sensitivity, environmental water samples were preconcentrated on-line in a polymeric cartridge by direct injection of 2 mL water into the SPE-LC/MS/MS system. For three unknowns, structures were proposed and confirmed with standards. Although other compounds could not be unequivocally identified based on the data available within this study, details about the possible structures of some are given.

LC-DAD-MS/SPE-NMR Hyphenation. A Tool for the Analysis of Pharmaceutically Used Plant Extracts: Identification of Isobaric Iridoid Glycoside Regioisomers from Harpagophytum procumbens

LC-DAD-MS monitored fractionation of a Harpagophytum procumbens DC. (Pedaliaceae) root extract was combined with a hyphenated LC-DAD-MS/SPE-NMR technique, thus providing the spectral data needed for structure elucidation. This approach allowed the characterization of isobaric iridoid glycoside regioisomers present only as minor constituents. The analytes were identified as the (E/Z) pairs of 6'-O-(p-coumaroyl)harpagide (6'-PCHG) and 8-O-(p-coumaroyl)-harpagide (8-PCHG). The fact that 8-(Z)-PCHG constitutes a new natural product underlines the analytical power of this combined approach. Furthermore, derivatives 6'-(Z)- and 6'-(E)-PCHG are new constituents for H. procumbens.

The role of natural product chemistry in drug discovery

Although traditionally natural products have played an important role in drug discovery, in the past few years most Big Pharma companies have either terminated or considerably scaled down their natural product operations. This is despite a significant number of natural product-derived drugs being ranked in the top 35 worldwide selling ethical drugs in 2000, 2001, and 2002. There were 15 new natural product-derived drugs launched from 2000 to 2003, as well as 15 natural product-derived compounds in Phase III clinical trials or registration at the end of 2003. Recently, there has been a renewed interest in natural product research due to the failure of alternative drug discovery methods to deliver many lead compounds in key therapeutic areas such as immunosuppression, anti-infectives, and metabolic diseases. To continue to be competitive with other drug discovery methods, natural product research needs to continually improve the speed of the screening, isolation, and structure elucidation processes, as well addressing the suitability of screens for natural product extracts and dealing with issues involved with large-scale compound supply.

Using NMR for ligand discovery and optimization

Several recent technology-driven advances in the area of NMR have rekindled an interest in the application of the technology to problems in drug discovery and development. A unique aspect of NMR is that it has applicability in broadly different areas of the drug discovery and optimization processes. NMR techniques for screening aimed at the discovery of novel ligands or low molecular weight structures for fragment-based build up procedures are being applied commonly in the industry. Application of NMR in structure-guided drug design and metabonomics are also becoming routine. We present an overview of some of the most recent NMR developments in these areas.

Strategies for dealing with metabolite elucidation in drug discovery and development

Structural information on metabolites can be a considerable asset for enhancing and streamlining the process of developing new drug candidates. Modern approaches that generate and use metabolite structural information can accelerate the drug discovery and development process by eliminating potentially harmful candidates earlier in the process and improving the safety of new drugs. This review examines the relative merits of current and potential strategies for dealing with metabolite characterization.

Multidimensional separations in the pharmaceutical arena

The introduction of novel, powerful and rapid multidimensional separation and characterization methods has produced revolutionary global changes at the genome, proteome and metabolome level, bringing about a radical transition in our views of living systems, at the molecular level. The age of proteomics and metabolomics demands high-resolution multidimensional separation techniques. Multidimensional gas and liquid chromatography techniques, in addition to capillary and microchip electrophoresis methods, offer increased resolution and sensitivity, while also affording adequate throughput and reproducibility to meet the demands of the modern pharmaceutical industry. Coupled with MS, these techniques provide not only separation but also reliable identification of the sample components. The resolving power of these methods has proved to be superior over individual one-dimensional approaches, enabling the comprehensive separation of complex biological mixtures, with excellent resolution and reproducibility. High capacity computer systems that are capable of rigorous qualitative and quantitative analysis of the separation profiles allow the establishment and mining of large databases. Examples of various modern multidimensional separation techniques, and their integration with MS, are reviewed, here, with respect to pharmaceutical analysis.