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Di Martino RMC, Maxwell BD, Pirali T. Deuterium in drug discovery: progress, opportunities and challenges. Nat Rev Drug Discov 2023; 22:562-584. [PMID: 37277503 PMCID: PMC10241557 DOI: 10.1038/s41573-023-00703-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2023] [Indexed: 06/07/2023]
Abstract
Substitution of a hydrogen atom with its heavy isotope deuterium entails the addition of one neutron to a molecule. Despite being a subtle change, this structural modification, known as deuteration, may improve the pharmacokinetic and/or toxicity profile of drugs, potentially translating into improvements in efficacy and safety compared with the non-deuterated counterparts. Initially, efforts to exploit this potential primarily led to the development of deuterated analogues of marketed drugs through a 'deuterium switch' approach, such as deutetrabenazine, which became the first deuterated drug to receive FDA approval in 2017. In the past few years, the focus has shifted to applying deuteration in novel drug discovery, and the FDA approved the pioneering de novo deuterated drug deucravacitinib in 2022. In this Review, we highlight key milestones in the field of deuteration in drug discovery and development, emphasizing recent and instructive medicinal chemistry programmes and discussing the opportunities and hurdles for drug developers, as well as the questions that remain to be addressed.
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Affiliation(s)
| | | | - Tracey Pirali
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale, Novara, Italy.
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2
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Hok L, Vianello R. Selective Deuteration Improves the Affinity of Adenosine A 2A Receptor Ligands: A Computational Case Study with Istradefylline and Caffeine. J Chem Inf Model 2023; 63:3138-3149. [PMID: 37155356 DOI: 10.1021/acs.jcim.3c00424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
We used a range of computational techniques to assess the effect of selective C-H deuteration on the antagonist istradefylline affinity for the adenosine A2A receptor, which was discussed relative to its structural analogue caffeine, a well-known and likely the most widely used stimulant. The obtained results revealed that smaller caffeine shows high receptor flexibility and exchanges between two distinct poses, which agrees with crystallographic data. In contrast, the additional C8-trans-styryl fragment in istradefylline locks the ligand within a uniform binding pose, while contributing to the affinity through the C-H···π and π···π contacts with surface residues, which, together with its much lower hydration prior to binding, enhances the affinity over caffeine. In addition, the aromatic C8-unit shows a higher deuteration sensitivity over the xanthine part, so when both of its methoxy groups are d6-deuterated, the affinity improvement is -0.4 kcal mol-1, which surpasses the overall affinity gain of -0.3 kcal mol-1 in the perdeuterated d9-caffeine. Yet, the latter predicts around 1.7-fold potency increase, being relevant for its pharmaceutical implementations, and also those within the coffee and energy drink production industries. Still, the full potential of our strategy is achieved in polydeuterated d19-istradefylline, whose A2A affinity improves by -0.6 kcal mol-1, signifying a 2.8-fold potency increase that strongly promotes it as a potential synthetic target. This knowledge supports deuterium application in drug design, and while the literature already reports about over 20 deuterated drugs currently in the clinical development, it is easily foreseen that more examples will hit the market in the years to come. With this in mind, we propose that the devised computational methodology, involving the ONIOM division of the QM region for the ligand and the MM region for its environment, with an implicit quantization of nuclear motions relevant for the H/D exchange, allows fast and efficient estimates of the binding isotope effects in any biological system.
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Affiliation(s)
- Lucija Hok
- Laboratory for the Computational Design and Synthesis of Functional Materials, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Robert Vianello
- Laboratory for the Computational Design and Synthesis of Functional Materials, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
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3
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Aprile S, Colombo G, Serafini M, Di Paola R, Pisati F, Bhela IP, Cuzzocrea S, Grosa G, Pirali T. An Unexpected Deuterium-Induced Metabolic Switch in Doxophylline. ACS Med Chem Lett 2022; 13:1278-1285. [PMID: 35978700 PMCID: PMC9377007 DOI: 10.1021/acsmedchemlett.2c00166] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/11/2022] [Indexed: 01/03/2023] Open
Abstract
Precision deuteration has become part of the medicinal chemist's toolbox, but its usefulness can be undermined by unpredictable metabolic switch effects. Herein we report the deuteration of doxophylline, a drug used in the treatment of asthma and COPD that undergoes extensive oxidative metabolism. Labeling of the main metabolic soft spots triggered an unexpected multidirectional metabolic switch that, while not improving the pharmacokinetic parameters, changed the metabolic scenario and, in turn, the pharmacodynamic features in two murine models of lung injury.
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Affiliation(s)
- Silvio Aprile
- Department
of Pharmaceutical Sciences, Università
del Piemonte Orientale, 28100 Novara, Italy
| | - Giorgia Colombo
- Department
of Pharmaceutical Sciences, Università
del Piemonte Orientale, 28100 Novara, Italy
| | - Marta Serafini
- Department
of Pharmaceutical Sciences, Università
del Piemonte Orientale, 28100 Novara, Italy
| | - Rosanna Di Paola
- Department
of Chemical, Biological, Pharmaceutical and Environmental Sciences, Università di Messina, 98166 Messina, Italy
| | - Federica Pisati
- Histopathology
Unit, Cogentech S.C.a.R.L., 20139 Milan, Italy
| | - Irene Preet Bhela
- Department
of Pharmaceutical Sciences, Università
del Piemonte Orientale, 28100 Novara, Italy
| | - Salvatore Cuzzocrea
- Department
of Chemical, Biological, Pharmaceutical and Environmental Sciences, Università di Messina, 98166 Messina, Italy
| | - Giorgio Grosa
- Department
of Pharmaceutical Sciences, Università
del Piemonte Orientale, 28100 Novara, Italy
| | - Tracey Pirali
- Department
of Pharmaceutical Sciences, Università
del Piemonte Orientale, 28100 Novara, Italy
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4
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Parente RM, Tarantino PM, Sippy BC, Burdock GA. Pharmacokinetic, pharmacological, and genotoxic evaluation of deuterated caffeine. Food Chem Toxicol 2021; 160:112774. [PMID: 34974129 DOI: 10.1016/j.fct.2021.112774] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/24/2021] [Accepted: 12/17/2021] [Indexed: 01/27/2023]
Abstract
Altering caffeine's negative physiological effects and extending its duration of activity is an active area of research; however, deuteration as a means of achieving these goals is unexplored. Deuteration substitutes one or more of the hydrogen atoms of a substance with deuterium, a stable isotope of hydrogen that contains an extra neutron. Deuteration can potentially alter the metabolic profile of a substance, while maintaining its pharmacodynamic properties. d9-Caffeine is a deuterated isotopologue of caffeine with the nine hydrogens contained in the 1, 3, and 7 methyl groups of caffeine substituted with deuterium. d9-Caffeine may prove to be an alternative to caffeine that may be consumed with less frequency, at lower doses, and with less exposure to downstream active metabolites of caffeine. Characterization of d9-caffeine's genotoxic potential, pharmacodynamic, and pharmacokinetic behavior is critical in establishing how it may differ from caffeine. d9-Caffeine was non-genotoxic with and without metabolic activation in both a bacterial reverse mutation assay and a human mammalian cell micronucleus assay at concentrations up to the ICH concentration limits. d9-Caffeine exhibited a prolonged systemic and brain exposure time in rats as compared to caffeine following oral administration. The adenosine receptor antagonist potency of d9-caffeine was similar to caffeine.
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Affiliation(s)
| | - Paul M Tarantino
- Lennham Pharmaceuticals, Inc., 53 Main Street Suite 206 Concord, MA, 01742, USA
| | - Bradford C Sippy
- Lennham Pharmaceuticals, Inc., 53 Main Street Suite 206 Concord, MA, 01742, USA
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5
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Hok L, Mavri J, Vianello R. The Effect of Deuteration on the H 2 Receptor Histamine Binding Profile: A Computational Insight into Modified Hydrogen Bonding Interactions. Molecules 2020; 25:molecules25246017. [PMID: 33353215 PMCID: PMC7766521 DOI: 10.3390/molecules25246017] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 01/04/2023] Open
Abstract
We used a range of computational techniques to reveal an increased histamine affinity for its H2 receptor upon deuteration, which was interpreted through altered hydrogen bonding interactions within the receptor and the aqueous environment preceding the binding. Molecular docking identified the area between third and fifth transmembrane α-helices as the likely binding pocket for several histamine poses, with the most favorable binding energy of −7.4 kcal mol−1 closely matching the experimental value of −5.9 kcal mol−1. The subsequent molecular dynamics simulation and MM-GBSA analysis recognized Asp98 as the most dominant residue, accounting for 40% of the total binding energy, established through a persistent hydrogen bonding with the histamine −NH3+ group, the latter further held in place through the N–H∙∙∙O hydrogen bonding with Tyr250. Unlike earlier literature proposals, the important role of Thr190 is not evident in hydrogen bonds through its −OH group, but rather in the C–H∙∙∙π contacts with the imidazole ring, while its former moiety is constantly engaged in the hydrogen bonding with Asp186. Lastly, quantum-chemical calculations within the receptor cluster model and utilizing the empirical quantization of the ionizable X–H bonds (X = N, O, S), supported the deuteration-induced affinity increase, with the calculated difference in the binding free energy of −0.85 kcal mol−1, being in excellent agreement with an experimental value of −0.75 kcal mol−1, thus confirming the relevance of hydrogen bonding for the H2 receptor activation.
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Affiliation(s)
- Lucija Hok
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, HR-10000 Zagreb, Croatia;
| | - Janez Mavri
- Laboratory for Computational Biochemistry and Drug Design, National Institute of Chemistry, SI-1001 Ljubljana, Slovenia;
| | - Robert Vianello
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, HR-10000 Zagreb, Croatia;
- Correspondence:
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Levodopa inhibits the development of lens-induced myopia in chicks. Sci Rep 2020; 10:13242. [PMID: 32764736 PMCID: PMC7413395 DOI: 10.1038/s41598-020-70271-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 07/23/2020] [Indexed: 11/18/2022] Open
Abstract
Animal models have demonstrated a link between dysregulation of the retinal dopamine system and the development of myopia (short-sightedness). We have previously demonstrated that topical application of levodopa in chicks can inhibit the development of form-deprivation myopia (FDM) in a dose-dependent manner. Here, we examine whether this same protection is observed in lens-induced myopia (LIM), and whether levodopa’s protection against FDM and LIM occurs through a dopamine D1- or D2-like receptor mechanism. To do this, levodopa was first administered daily as an intravitreal injection or topical eye drop, at one of four ascending doses, to chicks developing LIM. Levodopa’s mechanism of action was then examined by co-administration of levodopa injections with D1-like (SCH-23390) or D2-like (spiperone) dopamine antagonists in chicks developing FDM or LIM. For both experiments, levodopa’s effectiveness was examined by measuring axial length and refraction after 4 days of treatment. Levodopa inhibited the development of LIM in a dose-dependent manner similar to its inhibition of FDM when administered via intravitreal injections or topical eye drops. In both FDM and LIM, levodopa injections remained protective against myopia when co-administered with SCH-23390, but not spiperone, indicating that levodopa elicits its protection through a dopamine D2-like receptor mechanism in both paradigms.
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7
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Hashemipour S, Yaftian MR, Kalhor H, Ghanbari M. Investigation of bovine serum albumin/tropicamide interaction using a quartz crystal microbalance sensor. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2018. [DOI: 10.1007/s13738-018-1317-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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8
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Barrie CD, Taylor KWR, Zumberge J. Measurement of compound-specific carbon isotope ratios (δ(13) C values) via direct injection of whole crude oil samples. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:843-853. [PMID: 26969925 DOI: 10.1002/rcm.7496] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 12/17/2015] [Accepted: 12/18/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE Stable isotope analysis is a powerful tool in understanding the generation, history and correlation of hydrocarbons. Compound-specific δ(13) C measurements of oils allow detailed comparison of individual compound groupings; however, most studies of these sample materials separate and isolate individual fractions based on the chemistries of particular compound groups, potentially losing considerable valuable isotopic data. Even if all fractions are analyzed, this represents a large increase in the data-processing burden, effectively multiplying data evaluation time and effort by the number of fractions produced. Gas chromatography/isotope ratio mass spectrometry (GC/IRMS) of untreated, whole crude oils allows the immediate collection of a larger suite of valuable isotopic data for these studies. METHODS Untreated ('neat', undiluted), whole crude oils were directly injected and measured on a GC/IRMS system, using split (40:1) injections and a 50 m HP-PONA column. The GC method, 97 min in duration, was designed to maximize baseline separation of target analyte peaks, while an additional oxygen flow was admitted into the combustion reactor to maximize the lifetime of the combustion chemicals. RESULTS The method and setup utilized allow the measurement of a much greater range of the n-alkanes (n-C4 to n-C25+ ) than traditional methods, while also retaining important cycloalkane, aromatic and isoprenoid peaks within the same analysis. Carbon isotope (δ(13) C) evaluation of these additional compound classes reveals trends in maturity and origins which are not identifiable when exclusively assessing the traditional n-alkane package (>n-C12 ). CONCLUSIONS The described setup and method open up new possibilities for assessing the origins and histories of crude oil samples. The data generated for the whole oil n-alkanes by this method is equivalent to that reported for isolated n-alkane studies, while also providing valuable additional data on many other important compounds. The end result of this method is a more complete assessment of the carbon isotopic composition of crude oils. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Craig D Barrie
- GeoMark Research, 9748 Whithorn Dr., Houston, TX, 77095, USA
| | | | - John Zumberge
- GeoMark Research, 9748 Whithorn Dr., Houston, TX, 77095, USA
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9
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Yu T, Campbell SC, Stockmann C, Tak C, Schoen K, Clark EAS, Varner MW, Spigarelli MG, Sherwin CMT. Pregnancy-induced changes in the pharmacokinetics of caffeine and its metabolites. J Clin Pharmacol 2015; 56:590-6. [PMID: 26358647 DOI: 10.1002/jcph.632] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 09/08/2015] [Indexed: 01/18/2023]
Abstract
This study sought to assess the pharmacokinetic (PK) changes of caffeine and its CYP1A2 metabolites across the 3 trimesters of pregnancy. A prospective, multicenter PK study was conducted among 59 pregnant women (93.2% white) who were studied once during a trimester. One beverage with 30-95 mg caffeine was consumed, and a blood/urine sample was collected within 1 hour postingestion. Concentrations of caffeine and its primary metabolites were quantified from serum and urine by LC-MS/MS. There was a significant increase in dose-normalized caffeine serum and urine concentrations between the first and third trimesters (P < .05 and P < .01, respectively). Normalized theophylline concentrations also increased significantly in the third trimester in serum (P < .001) and in urine (P < .05). The caffeine urine/serum concentration ratio also increased in the last trimester (P < .05). No significant difference was found in normalized paraxanthine or theobromine concentrations. This study identified decreased caffeine metabolism and an increase in the active metabolite theophylline concentrations during pregnancy, especially in the third trimester, revealing evidence of the large role that pregnancy plays in influencing caffeine metabolism.
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Affiliation(s)
- Tian Yu
- Division of Clinical Pharmacology, School of Medicine, University of Utah, Salt Lake City, UT, USA
| | - Sarah C Campbell
- Division of Clinical Pharmacology, School of Medicine, University of Utah, Salt Lake City, UT, USA
| | - Chris Stockmann
- Division of Clinical Pharmacology, School of Medicine, University of Utah, Salt Lake City, UT, USA
| | - Casey Tak
- Clinical Trials Office, Department of Pediatrics, School of Medicine, University of Utah, Salt Lake City, UT, USA
| | - Katherine Schoen
- Division of Clinical Pharmacology, School of Medicine, University of Utah, Salt Lake City, UT, USA
| | - Erin A S Clark
- Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, School of Medicine, University of Utah, Salt Lake City, UT, USA
| | - Michael W Varner
- Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, School of Medicine, University of Utah, Salt Lake City, UT, USA.,Intermountain Healthcare, Women and Newborns Clinical Programs, Salt Lake City, Utah, USA
| | - Michael G Spigarelli
- Division of Clinical Pharmacology, School of Medicine, University of Utah, Salt Lake City, UT, USA.,Clinical Trials Office, Department of Pediatrics, School of Medicine, University of Utah, Salt Lake City, UT, USA
| | - Catherine M T Sherwin
- Division of Clinical Pharmacology, School of Medicine, University of Utah, Salt Lake City, UT, USA.,Clinical Trials Office, Department of Pediatrics, School of Medicine, University of Utah, Salt Lake City, UT, USA
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10
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Abstract
INTRODUCTION Deuterated versions of existing drugs can exhibit improved pharmacokinetic or toxicological properties due the stronger deuterium- carbon bond modifying their metabolism. There is great interest in the current state of development of this approach. AREAS COVERED This review covers recent US patent applications and prosecutions in this area that are based on beneficial modifications in metabolism of deuterated versions of existing drugs. The current state of 35 U.S.C. §103 'obviousness' rejections are emphasized, as is the development of strategies to overcome such rejections. Current trials and market considerations are also discussed. EXPERT OPINION Deuterated drugs collectively are worth at least US$1 billion. It would seem that the likelihood of obviousness rejections is increasing in this area. However, careful elucidation of metabolic outcomes from deuteration that would not be anticipated from the prior art, and are instead unexpected and unobvious, has enabled allowance. Showing that drug deuteration alters pharmacokinetics by mechanisms not currently part of the prior art surrounding deuterated drugs has also been successful. Development of these and other strategies, combined with developing the extensive base of issued patents will enable the field to remain commercially attractive for some time.
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Affiliation(s)
- Graham S Timmins
- University of New Mexico Health Sciences Center, College of Pharmacy, Department of Pharmaceutical Sciences , Albuquerque, NM 87131 , USA +1 505 272 4103 ; +1 505 272 6749 ;
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11
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Deuterium Tracer Studies and Gas Chromatography–Mass Spectrometry Analysis of Deuterated Products during Fischer–Tropsch Synthesis. Top Catal 2013. [DOI: 10.1007/s11244-013-0202-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Affiliation(s)
- Katarzyna Swiderek
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology , Zeromskiego 116, 90-924 Lodz, Poland
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13
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McCullagh JSO. Mixed-mode chromatography/isotope ratio mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:483-494. [PMID: 20162548 DOI: 10.1002/rcm.4322] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Liquid chromatography coupled to molecular mass spectrometry (LC/MS) has been a standard technique since the early 1970s but liquid chromatography coupled to high-precision isotope ratio mass spectrometry (LC/IRMS) has only been available commercially since 2004. This development has, for the first time, enabled natural abundance and low enrichment delta(13)C measurements to be applied to individual analytes in aqueous mixtures creating new opportunities for IRMS applications, particularly for the isotopic study of biological molecules. A growing number of applications have been published in a range of areas including amino acid metabolism, carbohydrates studies, quantification of cellular and plasma metabolites, dietary tracer and nucleic acid studies. There is strong potential to extend these to new compounds and complex matrices but several challenges face the development of LC/IRMS methods. To achieve accurate isotopic measurements, HPLC separations must provide baseline-resolution between analyte peaks; however, the design of current liquid interfaces places severe restrictions on compatible flow rates and in particular mobile phase compositions. These create a significant challenge on which reports associated with LC/IRMS have not previously focused. Accordingly, this paper will address aspects of chromatography in the context of LC/IRMS, in particular focusing on mixed-mode separations and their benefits in light of these restrictions. It aims to provide an overview of mixed-mode stationary phases and of ways to improve high aqueous separations through manipulation of parameters such as column length, temperature and mobile phase pH. The results of several practical experiments are given using proteogenic amino acids and nucleosides both of which are of noted importance in the LC/IRMS literature. This communication aims to demonstrate that mixed-mode stationary phases provide a flexible approach given the constraints of LC/IRMS interface design and acts as a practical guide for the development of new chromatographic methods compatible with LC/IRMS applications.
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Affiliation(s)
- James S O McCullagh
- Chemistry Research Laboratory, University of Oxford, Mansfield Rd, Oxford OX1 3TA, UK.
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Balssa F, Bonnaire Y. Easy preparative scale syntheses of labelled xanthines: caffeine, theophylline and theobromine. J Labelled Comp Radiopharm 2007. [DOI: 10.1002/jlcr.1154] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Kenani A, Bernier JL, Henichart JP. Synthesis and E.I.M.S. fragmentation analysis of [1,3-15N2] xanthine and [1,3-15N2] caffeine. J Labelled Comp Radiopharm 2006. [DOI: 10.1002/jlcr.2580360211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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16
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Rechavi D, Scarso A, Rebek J. Isotopomer Encapsulation in a Cylindrical Molecular Capsule: A Probe for Understanding Noncovalent Isotope Effects on a Molecular Level. J Am Chem Soc 2004; 126:7738-9. [PMID: 15212496 DOI: 10.1021/ja048366p] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Isotope effects for the encapsulation of deuterated versus nondeuterated guests are determined. This system involves the use of social isomers, and the origin of the isotope effect is localized to methyl groups interacting with aromatic rings.
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Affiliation(s)
- Dalit Rechavi
- The Skaggs Institute for Chemical Biology and the Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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17
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Lucas LH, Yan J, Larive CK, Zartler ER, Shapiro MJ. Transferred nuclear overhauser effect in nuclear magnetic resonance diffusion measurements of ligand-protein binding. Anal Chem 2003; 75:627-34. [PMID: 12585494 DOI: 10.1021/ac020563o] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The drug discovery process relies on characterizing structure-activity relationships, since specific ligand-target interactions often result in important biological functions. Measuring diffusion coefficients by nuclear magnetic resonance spectroscopy is a useful way to study binding, because changes can be detected when a small ligand interacts with a macromolecular target. Diffusion coefficients can be miscalculated, however, due to magnetization transfer between the receptor and ligand. This transferred nuclear Overhauser effect (trNOE) disrupts the observed signal decay due to diffusion as a function of the experimental diffusion time. Since longer diffusion times also selectively edit free ligand signal, the measured diffusion coefficients become biased toward the fraction of bound ligand. Despite this discrepancy, under these experimental conditions, the trNOE selectively influences the measured signals of binding ligands and can be used to gain insight into ligand-protein interactions. These phenomena have been studied for caffeine and L-tryptophan, which bind to human serum albumin, and the antimalarial agent trimethoprim, which interacts with dihydrofolate reductase. The results provide insight into the nature of ligand-protein binding and are thus useful for elucidating the molecular features of the ligand that interact with the protein.
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Affiliation(s)
- Laura H Lucas
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
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18
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Alexandrino M, Knief C, Lipski A. Stable-isotope-based labeling of styrene-degrading microorganisms in biofilters. Appl Environ Microbiol 2001; 67:4796-804. [PMID: 11571187 PMCID: PMC93234 DOI: 10.1128/aem.67.10.4796-4804.2001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2001] [Accepted: 07/16/2001] [Indexed: 11/20/2022] Open
Abstract
Deuterated styrene ([(2)H(8)]styrene) was used as a tracer in combination with phospholipid fatty acid (PLFA) analysis for characterization of styrene-degrading microbial populations of biofilters used for treatment of waste gases. Deuterated fatty acids were detected and quantified by gas chromatography-mass spectrometry. The method was evaluated with pure cultures of styrene-degrading bacteria and defined mixed cultures of styrene degraders and non-styrene-degrading organisms. Incubation of styrene degraders for 3 days with [(2)H(8)]styrene led to fatty acids consisting of up to 90% deuterated molecules. Mixed-culture experiments showed that specific labeling of styrene-degrading strains and only weak labeling of fatty acids of non-styrene-degrading organisms occurred after incubation with [(2)H(8)]styrene for up to 7 days. Analysis of actively degrading filter material from an experimental biofilter and a full-scale biofilter by this method showed that there were differences in the patterns of labeled fatty acids. For the experimental biofilter the fatty acids with largest amounts of labeled molecules were palmitic acid (16:0), 9,10-methylenehexadecanoic acid (17:0 cyclo9-10), and vaccenic acid (18:1 cis11). These lipid markers indicated that styrene was degraded by organisms with a Pseudomonas-like fatty acid profile. In contrast, the most intensively labeled fatty acids of the full-scale biofilter sample were palmitic acid and cis-11-hexadecenoic acid (16:1 cis11), indicating that an unknown styrene-degrading taxon was present. Iso-, anteiso-, and 10-methyl-branched fatty acids showed no or weak labeling. Therefore, we found no indication that styrene was degraded by organisms with methyl-branched fatty fatty acids, such as Xanthomonas, Bacillus, Streptomyces, or Gordonia spp.
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Affiliation(s)
- M Alexandrino
- Abteilung Mikrobiologie, Fachbereich Biologie/Chemie, Universität Osnabrück, 49069 Osnabrück, Germany
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19
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Abstract
Compound-specific isotope analysis (CSIA) by isotope ratio mass spectrometry (IRMS) following on-line combustion (C) of compounds separated by gas chromatography (GC) is a relatively young analytical method. Due to its ability to measure isotope distribution at natural abundance level with great accuracy and high precision, GC-C-IRMS has increasingly become the method of choice in authenticity control of foodstuffs and determination of origin in archaeology, geochemistry, and environmental chemistry. In combination with stable isotope labelled compounds, GC-C-IRMS is also used more and more in biochemical and biomedical application as it offers a reliable and risk-free alternative to the use of radioactive tracers. The literature on these topics is reviewed from the advent of commercial GC-C-IRMS systems in 1990 up to the beginning of 1998. Demands on sample preparation and quality of GC separation for GC-C-IRMS are discussed also.
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Affiliation(s)
- W Meier-Augenstein
- Department of Anatomy and Physiology, University of Dundee, Scotland, UK.
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Abstract
The topic of deuterium isotope effects is usually concerned with the effects on chemical reactions that are caused by the substitution of deuterium atoms for protium, or hydrogen, atoms in a molecule. These effects include changes in the rate of cleavage of covalent bonds to deuterium, or to an atom located adjacent to deuterium, in a reactant molecule. Deuterium isotope effects on other, noncovalent, interactions between molecules are known to occur, but they are generally considered to be insignificant, especially in biological experiments where deuterium substituted molecules are used as tracers. Noncovalent interactions between molecules include hydrogen bonding, and ionic and van der Waals interactions. This article reviews evidence for deuterium isotope effects on noncovalent interactions, with an emphasis on binding interactions between molecules of biological interest, but also including examples of nonbiological molecules in order to demonstrate the generality of these effects. The reality of this effect relies on the assumption that the only difference between the isotopomers considered is the presence of deuterium or hydrogen; there are no impurities present. The physical basis of the effect may be due to differences in the polarities and/or sizes of deuterated versus nondeuterated isomers, and the extent of a deuterium isotope effect on a noncovalent interaction depends on the site of deuteration within a biomolecule. The presence of this effect requires careful interpretation of results obtained in experiments with deuterium labeled compounds.
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Affiliation(s)
- D Wade
- Faculty of Medicine, Department of Biochemistry, Kuwait University, Safat.
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21
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Affiliation(s)
- A L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-0446, USA
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Benchekroun Y, Dautraix S, Desage M, Brazier JL. Deuterium isotope effects on caffeine metabolism. Eur J Drug Metab Pharmacokinet 1997; 22:127-33. [PMID: 9248780 DOI: 10.1007/bf03189795] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The aim of this work was to study the influence of labelling on caffeine metabolism according to the incubation mode. It has been observed that labelling induces an isotopic effect on metabolisation speed: apparent half-lives are systematically increased. Moreover, isotopic effects are in agreement with those previously observed for retention times. Qualitatively, caffeine labelling systematically induces metabolic variations to the detriment of the metabolic pathway that induces the loss of the trideuteromethyl group. Caffeine accumulation and the release of the main metabolites have been studied with respect to isotopic effects on crossing the cell membrane. It has been demonstrated that, in most of the cases, accumulation decreased and that either metabolite release was increased or no isotopic effect was observed.
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Affiliation(s)
- Y Benchekroun
- Laboratoire d'Etudes Analytiques et Cinétiques du Médicament, Institut des Sciences Pharmaceutiques et Biologiques de Lyon, France
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23
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Benchekroun Y, Dautraix S, Désage M, Brazier JL. Isotopic effects on retention times of caffeine and its metabolites 1,3,7-trimethyluric acid, theophylline, theobromine and paraxanthine. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 1997; 688:245-54. [PMID: 9061462 DOI: 10.1016/s0378-4347(96)00323-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Physicochemical parameters that influence gas chromatographic separation are numerous. Consequently, isotope labelling, because it modifies physicochemical properties, can induce isotopic effects on retention time. Caffeine has been chosen to study this influence because as itself and its metabolites, it allows the preparation of different methylxanthine isotopomers and thus is one of the best models to study isotopic effects induced by stable isotope labelling. Using a caffeine molecule labelled with deuterium at different positions and rat hepatocytes to obtain metabolites, it was possible to study the influence of labelling on retention time [(14% cyanopropylphenyl)methylpolysiloxane] and to point out the role of each labelled site. It appears that isotopic effects induced by the labelling depend not only on the number of labelling atoms but also on whether this labelling is at position 1, 3 or 7 and, consequently, on the role of the labelled site on the function of the molecule.
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Affiliation(s)
- Y Benchekroun
- Laboratoire d'Etudes Analytiques et Cinétiques du Médicament, Institut des Sciences Pharmaceutiques et Biologiques de Lyon, France
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24
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Influence of gas chromatographic parameters on measurement of 13C/12C isotope ratios by gas-liquid chromatography-combustion isotope ratio mass spectrometry. I. J Chromatogr A 1996. [DOI: 10.1016/s0021-9673(96)00498-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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26
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Szabo GK, Pylilo RJ, Perchalski RJ, Browne TR. Simultaneous separation and determination (in serum) of phenytoin and carbamazepine and their deuterated analogues by high-performance liquid chromatography--ultraviolet detection for tracer studies. J Chromatogr A 1990; 535:271-7. [PMID: 2089056 DOI: 10.1016/s0021-9673(01)88952-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The use of stable isotope-labeled tracer compounds is the safest and most effective method to perform many steady state pharmacokinetic and drug interaction studies. We describe a method by which the heavily deuterated 2H10 analogues of carbamazepine (2H10 CBZ) and phenytoin (2H10 PHT) can be chromatographically separated by high-performance liquid chromatography from unlabeled CBZ and PHT. All compounds are quantitated against an internal standard (IS) (10,11-dihydrocarbamazepine) and measured using conventional UV detection rather than mass spectrometry. Baseline resolution of extracted serum containing 2H10 CBZ, CBZ, 2H10 PHT, PHT and IS is achieved on a heated (55 degrees C) 25 cm x 4.6 mm BioAnalytical Systems Phase II 5 microns ODS column with an isocratic mobile phase consisting of water-acetonitrile-tetrahydrofuran (80:16:4, v/v/v) at 1.2 ml/min. Eluting compounds were monitored at a UV wavelength of 214 nm. Calculated resolution of 2H10 CBZ from CBZ and of 2H10 PHT from PHT were 1.3. Serum standard curves were linear (R greater than or equal to 0.999) over a range of 0.5-14 micrograms/ml for 2H10 CBZ, 0.5-20 micrograms/ml for CBZ, 0.5-20 micrograms/ml for 2H10 PHT, and 0.5-30 micrograms/ml for PHT. Within-day percent relative standard deviations (precision) were less than 6% in all cases.
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Affiliation(s)
- G K Szabo
- Department of Neurology, Boston University School of Medicine, MA 02118
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27
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Bechalany A, El Tayar N, Carrupt PA, Testa B, Falconnet JB, Cherrah Y, Benchekroun Y, Brazier JL. Isotope Effects on the Lipophilicity of Deuterated Caffeines. Helv Chim Acta 1989. [DOI: 10.1002/hlca.19890720308] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Cherrah Y, Falconnet JB, Desage M, Brazier JL, Zini R, Tillement JP. Study of isotope effects on protein binding by gas chromatography/mass spectrometry of theophylline-phenobarbitone and 2H, 13C, 15N isotopomers. BIOMEDICAL & ENVIRONMENTAL MASS SPECTROMETRY 1988; 17:245-50. [PMID: 3191256 DOI: 10.1002/bms.1200170403] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We describe a comparative study of human serum albumin (HSA) binding by equilibrium dialysis (pH 7.4, 37 degrees C, 3 h) for two groups of isotopic analogues: theophylline and 1-C(2H3)theophylline; unlabelled, 5(ethyl(2H5],-5(phenyl(2H5] and 1,3-15N;2-13C-phenobarbitone. Bound and free drug fractions are quantified by combined gas chromatography/mass spectrometry. In three instances, protein binding parameters are greatly affected by isotopic substitution, namely for: theophylline and 1-C(2H3)theophylline with isotope effects on total binding site concentration (N), affinity constant (Ka) and extent of HSA binding (%) respectively, equal to: NL/NH = 0.51; KaL/KaH = 1.78; %L/%H = 0.96 (L (light) and H (heavy) represent the unlabelled and labelled analogue respectively); phenobarbitone/-5-(phenyl(2H5]phenobarbitone, NL/NH = 1.72; KaL/KaH = 0.56; %L/%H = 1.26; phenobarbitone/1,3-15N;2-13C phenobarbitone, NL/NH = 2.95; KaL/KaH = 0.44; %L/%H = 1.32, together with a change from one (saturable) to two (saturable + non-saturable) families of albumin binding sites in the latter case. Contrasting with these data, no HSA binding isotope effect was observed on phenobarbitone C5 ethyl deuteration.
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Affiliation(s)
- Y Cherrah
- LEACM Faculty of Pharmacy, Lyon, France
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Cherrah Y, Zini R, Falconnet JB, Desage M, Tillement JP, Brazier JL. Study of deutero-isotopomer-induced inhibition of caffeine and phenobarbitone binding to human serum albumin. Biochem Pharmacol 1988; 37:1311-5. [PMID: 3355603 DOI: 10.1016/0006-2952(88)90788-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The present study of inhibition provides confirmation to previously observed deuterium isotope effects on in vitro caffeine and phenobarbitone binding to human serum albumin (HSA). Addition of either 3,7(C(2H)3)2 or 1,3,7(C(2H)3)3 caffeine induces a 50% loss in both the extent of binding and binding parameters of the unlabelled analog, understandably so in view of the stronger individual HSA binding of the two labelled isotopomers. As concerns caffeine displacement from its HSA sites, we show phenobarbitone and its 5-pentadeuterophenyl analog are equally potent inhibitors of caffeine binding, though their individual HSA binding profiles differ. As for HSA binding interactions between phenobarbitone isotopomers, a 50% decrease in unlabelled phenobarbitone extent of binding is observed in the presence of its 5-pentadeuterophenyl analog. Our results favor the hypothesis of differing binding sites for each isotopomer.
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Affiliation(s)
- Y Cherrah
- L.E.A.C.M. Faculty of Pharmacy, Lyon, France
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30
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Dillen L, Duchateau A, De Potter WP, Claeys M. Selected ion monitoring analysis of monoamine metabolites in cerebrospinal fluid. Application to the study of in vivo effects of alpha 2-antagonists. BIOMEDICAL & ENVIRONMENTAL MASS SPECTROMETRY 1987; 14:675-82. [PMID: 2892549 DOI: 10.1002/bms.1200141119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The technique of isotope dilution mass spectrometry has been used for the measurement of biogenic amine metabolites in cerebrospinal fluid (CSF). CSF samples were collected from rabbits treated with alpha 2-antagonists. The aim of our study was to determine the specificity of these drugs on the central nervous noradrenergic, dopaminergic and serotonergic activity as measured by the release of corresponding monoamine metabolites. 3-Methoxy-4-hydroxyphenylethylene glycol (MHPG) and vanilmandelic acid (VMA) were used as parameters for the noradrenergic activity, whereas homovanillic acid (HVA) and 5-hydroxyindole-3-acetic acid (5-HIAA) were employed to follow the dopaminergic and serotonergic activity, respectively. For the measurement of the biogenic amine metabolites a published GCMS method has been adapted. Samples of 200 microliters CSF were processed. Following addition of deuterated internal standards and acidification, extraction was carried out with ethyl acetate. Preliminary experiments with the analysis of MHPG using diethyl ether for extraction gave rise to emulsion formation and resulted in poor recoveries for MHPG and in irreproducibility problems due to a preferential extraction of non-labelled MHPG, effects which were not observed with ethyl acetate extraction. Derivatization was done with a mixture of pentafluoropropionic anhydride/pentafluoropropanol (or hexafluoroisopropanol) in order to derivatize both hydroxyl and carboxylic acid groups. The derivatization procedure was optimized for the analysis of 5-HIAA by carrying out a second reaction step with pentafluoropropionic anhydride alone in order to complete the derivatization for the indolic NH moiety. The molecular ions of the derivatized products were selected for detection.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- L Dillen
- Department of Medicine, University of Antwerp, Wilrijk, Belgium
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