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Leśko M, Kaczmarski K, Jora M, Stavenhagen K, Leek T, Czechtizky W, Fornstedt T, Samuelsson J. Strategies for predictive modeling of overloaded oligonucleotide elution profiles in ion-pair chromatography. J Chromatogr A 2023; 1711:464446. [PMID: 37865023 DOI: 10.1016/j.chroma.2023.464446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/20/2023] [Accepted: 10/10/2023] [Indexed: 10/23/2023]
Abstract
Due to their potential for gene regulation, oligonucleotides have moved into focus as one of the preferred modalities modulating currently undruggable disease-associated targets. In the course of synthesis and storage of oligonucleotides a significant number of compound-related impurities can be generated. Purification protocols and analytical methods have become crucial for the therapeutic application of any oligonucleotides, be they antisense oligonucleotides (ASOs), small interfering ribonucleic acids (siRNAs) or conjugates. Ion-pair chromatography is currently the standard method for separating and analyzing therapeutic oligonucleotides. Although mathematical modeling can improve the accuracy and efficiency of ion-pair chromatography, its application remains challenging. Simple models may not be suitable to treat advanced single molecules, while complex models are still inefficient for industrial oligonucleotide optimization processes. Therefore, fundamental research to improve the accuracy and simplicity of mathematical models in ion-pair chromatography is still a necessity. In this study, we predict overloaded concentration profiles of oligonucleotides in ion-pair chromatography and compare relatively simple and more advanced predictive models. The experimental system consists of a traditional C18 column using (dibutyl)amine as the ion-pair reagent and acetonitrile as organic modifier. The models were built and tested based on three crude 16-mer oligonucleotides with varying degrees of phosphorothioation, as well as their respective n - 1 and (P = O)1 impurities. In short, the proposed models were suitable to predict the overloaded concentration profiles for different slopes of the organic modifier gradient and column load.
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Affiliation(s)
- Marek Leśko
- Department of Engineering and Chemical Sciences, Karlstad University, SE-651 88 Karlstad, Sweden
| | - Krzysztof Kaczmarski
- Department of Chemical and Process Engineering, Rzeszów University of Technology, PL-35 959 Rzeszów, Poland
| | - Manasses Jora
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, SE-431 50 Mölndal, Sweden
| | - Kathrin Stavenhagen
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, SE-431 50 Mölndal, Sweden
| | - Tomas Leek
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, SE-431 50 Mölndal, Sweden
| | - Werngard Czechtizky
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, SE-431 50 Mölndal, Sweden
| | - Torgny Fornstedt
- Department of Engineering and Chemical Sciences, Karlstad University, SE-651 88 Karlstad, Sweden.
| | - Jörgen Samuelsson
- Department of Engineering and Chemical Sciences, Karlstad University, SE-651 88 Karlstad, Sweden
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Wesche F, De Maria L, Leek T, Narjes F, Bird J, Su W, Czechtizky W. Analyzing proteolytic stability and metabolic hotspots of therapeutic peptides in two rodent pulmonary fluids. J Pharm Biomed Anal 2023; 224:115156. [PMID: 36463768 DOI: 10.1016/j.jpba.2022.115156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/05/2022] [Accepted: 11/08/2022] [Indexed: 11/20/2022]
Abstract
Peptides and peptide drug conjugates are emerging modalities to treat pulmonary diseases. Peptides are susceptible to proteolytic cleavage. Expression levels of specific proteases in the lung can be significantly increased in disease state and may lead to exaggerated peptide proteolysis. To support optimization of peptides for inhaled administration, we have recently reported a streamlined high-throughput LC-HRMS protocol to determine enzymatic protease stability of peptides. This method has now been complemented with profiling of peptide metabolic stability in two respiratory fluids, a lung supernatant (lung S9) and a bronchioalveolar lavage fluid (BALF) taken from rats. We have tested a set of 28 peptides with high structural diversity, analyzed the whole data set for formed metabolites, and identified the differences of cleavage pattern in the two test fluids. Comparison of our experimental results and literature-derived cleavage site estimates based on e.g. MEROPS show significant differences for a number of peptides. This indicates the need for an experimental workflow using both protease panels and testing of metabolic stability in lung fluid (BALF) to guide peptide optimization and selection of peptides for inhaled in vivo PK/PD studies in our drug discovery projects.
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Affiliation(s)
- Frank Wesche
- Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Birkendorfer Strasse 65, 88400 Biberach an der Riss, Germany; Medicinal Chemistry, Research and Early Development, Respiratory & Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
| | - Leonardo De Maria
- Medicinal Chemistry, Research and Early Development, Respiratory & Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Tomas Leek
- Medicinal Chemistry, Research and Early Development, Respiratory & Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Frank Narjes
- Medicinal Chemistry, Research and Early Development, Respiratory & Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - James Bird
- Drug Metabolism and Pharmacokinetics, Research and Early Development, Respiratory & Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Wu Su
- Medicinal Chemistry, Research and Early Development, Respiratory & Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Werngard Czechtizky
- Medicinal Chemistry, Research and Early Development, Respiratory & Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
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Reid LM, Guzzetti I, Svensson T, Carlsson AC, Su W, Leek T, von Sydow L, Czechtizky W, Miljak M, Verma C, De Maria L, Essex JW. How well does molecular simulation reproduce environment-specific conformations of the intrinsically disordered peptides PLP, TP2 and ONEG? Chem Sci 2022; 13:1957-1971. [PMID: 35308859 PMCID: PMC8848758 DOI: 10.1039/d1sc03496k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 01/03/2022] [Indexed: 12/31/2022] Open
Abstract
Understanding the conformational ensembles of intrinsically disordered proteins and peptides (IDPs) in their various biological environments is essential for understanding their mechanisms and functional roles in the proteome, leading to a greater knowledge of, and potential treatments for, a broad range of diseases. To determine whether molecular simulation is able to generate accurate conformational ensembles of IDPs, we explore the structural landscape of the PLP peptide (an intrinsically disordered region of the proteolipid membrane protein) in aqueous and membrane-mimicking solvents, using replica exchange with solute scaling (REST2), and examine the ability of four force fields (ff14SB, ff14IDPSFF, CHARMM36 and CHARMM36m) to reproduce literature circular dichroism (CD) data. Results from variable temperature (VT) 1H and Rotating frame Overhauser Effect SpectroscopY (ROESY) nuclear magnetic resonance (NMR) experiments are also presented and are consistent with the structural observations obtained from the simulations and CD. We also apply the optimum simulation protocol to TP2 and ONEG (a cell-penetrating peptide (CPP) and a negative control peptide, respectively) to gain insight into the structural differences that may account for the observed difference in their membrane-penetrating abilities. Of the tested force fields, we find that CHARMM36 and CHARMM36m are best suited to the study of IDPs, and accurately predict a disordered to helical conformational transition of the PLP peptide accompanying the change from aqueous to membrane-mimicking solvents. We also identify an α-helical structure of TP2 in the membrane-mimicking solvents and provide a discussion of the mechanistic implications of this observation with reference to the previous literature on the peptide. From these results, we recommend the use of CHARMM36m with the REST2 protocol for the study of environment-specific IDP conformations. We believe that the simulation protocol will allow the study of a broad range of IDPs that undergo conformational transitions in different biological environments.
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Affiliation(s)
- Lauren M Reid
- School of Chemistry, University of Southampton Highfield Southampton SO17 1BJ UK
- Bioinformatics Institute (ASTAR) 30 Biolpolis Street Matrix 138671 Singapore
- MedChemica Ltd Alderley Park Macclesfield Cheshire SK10 4TG UK
| | - Ileana Guzzetti
- Medical Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D AstraZeneca Gothenburg Sweden
| | - Tor Svensson
- Medical Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D AstraZeneca Gothenburg Sweden
| | - Anna-Carin Carlsson
- Early Chemical Development, Pharmaceutical Sciences, BioPharmaceuticals R&D AstraZeneca Gothenburg Sweden
| | - Wu Su
- Medical Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D AstraZeneca Gothenburg Sweden
| | - Tomas Leek
- Medical Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D AstraZeneca Gothenburg Sweden
| | - Lena von Sydow
- Medical Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D AstraZeneca Gothenburg Sweden
| | - Werngard Czechtizky
- Medical Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D AstraZeneca Gothenburg Sweden
| | - Marija Miljak
- School of Chemistry, University of Southampton Highfield Southampton SO17 1BJ UK
| | - Chandra Verma
- Bioinformatics Institute (ASTAR) 30 Biolpolis Street Matrix 138671 Singapore
- Department of Biological Sciences, National University of Singapore 16 Science Drive 4 117558 Singapore
- School of Biological Sciences, Nanyang Technological University 60 Nanyang Dr 637551 Singapore
| | - Leonardo De Maria
- Medical Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D AstraZeneca Gothenburg Sweden
| | - Jonathan W Essex
- School of Chemistry, University of Southampton Highfield Southampton SO17 1BJ UK
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4
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Wesche F, De Maria L, Leek T, Narjes F, Bird J, Su W, Czechtizky W. Automated high-throughput in vitro assays to identify metabolic hotspots and protease stability of structurally diverse, pharmacologically active peptides for inhalation. J Pharm Biomed Anal 2021; 211:114518. [DOI: 10.1016/j.jpba.2021.114518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 11/27/2022]
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5
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Dispas A, Marini R, Desfontaine V, Veuthey JL, Kotoni D, Losacco LG, Clarke A, Muscat Galea C, Mangelings D, Jocher BM, Regalado EL, Plachká K, Nováková L, Wuyts B, François I, Gray M, Aubin AJ, Tarafder A, Cazes M, Desvignes C, Villemet L, Sarrut M, Raimbault A, Lemasson E, Lesellier E, West C, Leek T, Wong M, Dai L, Zhang K, Grand-Guillaume Perrenoud A, Brunelli C, Hennig P, Bertin S, Mauge F, Da Costa N, Farrell WP, Hill M, Desphande N, Grangrade M, Sadaphule S, Yadav R, Rane S, Shringare S, Iguiniz M, Heinisch S, Lefevre J, Corbel E, Roques N, Heyden YV, Guillarme D, Hubert P. First inter-laboratory study of a Supercritical Fluid Chromatography method for the determination of pharmaceutical impurities. J Pharm Biomed Anal 2018; 161:414-424. [DOI: 10.1016/j.jpba.2018.08.042] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 08/20/2018] [Accepted: 08/21/2018] [Indexed: 12/01/2022]
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6
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Åsberg D, Leśko M, Leek T, Samuelsson J, Kaczmarski K, Fornstedt T. Estimation of Nonlinear Adsorption Isotherms in Gradient Elution RP-LC of Peptides in the Presence of an Adsorbing Additive. Chromatographia 2017; 80:961-966. [PMID: 28725083 PMCID: PMC5486455 DOI: 10.1007/s10337-017-3298-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/13/2017] [Accepted: 03/17/2017] [Indexed: 11/25/2022]
Abstract
ABSTRACT In electrostatic repulsive interaction chromatography, using a charged surface hybrid sorbent carrying positive charges can improve the peak shape of peptides in reversed-phase liquid chromatography (RP-LC), especially in overloaded conditions, compared with standard C18 sorbents. However, the positive surface charges can interact with anionic additives commonly used in peptide separations, e.g., trifluoroacetic acid (TFA), complicating adsorption isotherm estimation. We investigated how the competition for available adsorption sites between TFA and two peptides influenced the adsorption isotherm in gradient elution. A model accounting for the competition with TFA was compared with a model neglecting TFA adsorption. We found that the two models predicted elution profiles with the same accuracy. We also found that the adsorption isotherms were extremely similar in shape, leading to the conclusion that neglecting the competition with TFA is a valid approximation enabling faster and more robust adsorption isotherm estimation for the studied type of sorbent. GRAPHICAL ABSTRACT
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Affiliation(s)
- Dennis Åsberg
- Department of Engineering and Chemical Sciences, Karlstad University, 651 88 Karlstad, Sweden
| | - Marek Leśko
- Department of Chemical and Process Engineering, Rzeszów University of Technology, 359 59 Rzeszów, Poland
| | - Tomas Leek
- Respiratory, Inflammation and Autoimmunity, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, 431 83 Mölndal, Sweden
| | - Jörgen Samuelsson
- Department of Engineering and Chemical Sciences, Karlstad University, 651 88 Karlstad, Sweden
| | - Krzysztof Kaczmarski
- Department of Chemical and Process Engineering, Rzeszów University of Technology, 359 59 Rzeszów, Poland
| | - Torgny Fornstedt
- Department of Engineering and Chemical Sciences, Karlstad University, 651 88 Karlstad, Sweden
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7
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Åsberg D, Langborg Weinmann A, Leek T, Lewis RJ, Klarqvist M, Leśko M, Kaczmarski K, Samuelsson J, Fornstedt T. The importance of ion-pairing in peptide purification by reversed-phase liquid chromatography. J Chromatogr A 2017; 1496:80-91. [PMID: 28363419 DOI: 10.1016/j.chroma.2017.03.041] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/07/2017] [Accepted: 03/18/2017] [Indexed: 10/19/2022]
Abstract
The adsorption mechanism for three peptides was studied under overloaded conditions through adsorption isotherm measurements in the presence of an ion-pairing reagent, trifluoroacetic acid (TFA), on an end-capped C18-bonded stationary phase. The overall aim of the study was to obtain a better understanding of how the acetonitrile and the TFA fractions in the eluent affected the overloaded elution profiles and the selectivity between peptides using mechanistic modelling and multivariate design of experiments. When studying the effect of TFA, direct evidence for ion pair formation between a peptide and TFA in acetonitrile-water solutions was provided by fluorine-proton nuclear Overhauser NMR enhancement experiments and the adsorption of TFA on the stationary phase was measured by frontal analysis. The adsorption isotherms for each peptide were then determined by the inverse method at eight TFA concentrations ranging from 2.6mM to 37.3mM (0.02-0.29vol-%) in isocratic elution. The equilibrium between the peptide ion and the peptide-TFA complex was modelled by coupling the mass-balance to reaction kinetics and determining separate adsorption isotherms for the two species. We found that a Langmuir isotherm described the elution profile of peptide-TFA complex well while the peptide ion was described by a bi-Langmuir adsorption isotherm since it exhibited strong secondary interactions. The elution profiles had an unfavorable shape at low TFA concentrations consisting of a spike in their front and a long tailing rear due to the secondary interactions for the peptide ion having very low saturation capacity. The acetonitrile dependence on the adsorption isotherms was studied by determination of adsorption isotherms directly from elution profiles obtained in gradient elution which enabled a broad acetonitrile interval to be studied. Here, it was found that the column saturation capacity was quickly reached at very low acetonitrile fractions and that there were significant variations in adsorption with the molecular weight. Finally, practical implications for method development are discussed based on an experimental design where gradient slope and TFA concentrations are used as factors.
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Affiliation(s)
- Dennis Åsberg
- Department of Engineering and Chemical Sciences, Karlstad University, SE-651 88 Karlstad, Sweden
| | - Annika Langborg Weinmann
- Respiratory, Inflammation and Autoimmunity, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, SE 431 83 Mölndal, Sweden
| | - Tomas Leek
- Respiratory, Inflammation and Autoimmunity, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, SE 431 83 Mölndal, Sweden
| | - Richard J Lewis
- Respiratory, Inflammation and Autoimmunity, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, SE 431 83 Mölndal, Sweden
| | - Magnus Klarqvist
- Respiratory, Inflammation and Autoimmunity, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, SE 431 83 Mölndal, Sweden
| | - Marek Leśko
- Department of Chemical and Process Engineering, Rzeszów University of Technology, PL-359 59 Rzeszów, Poland
| | - Krzysztof Kaczmarski
- Department of Chemical and Process Engineering, Rzeszów University of Technology, PL-359 59 Rzeszów, Poland
| | - Jörgen Samuelsson
- Department of Engineering and Chemical Sciences, Karlstad University, SE-651 88 Karlstad, Sweden
| | - Torgny Fornstedt
- Department of Engineering and Chemical Sciences, Karlstad University, SE-651 88 Karlstad, Sweden.
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8
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Gargano AF, Lämmerhofer M, Lönn H, Schoenmakers PJ, Leek T. Mucin-based stationary phases as tool for the characterization of drug–mucus interaction. J Chromatogr A 2014; 1351:70-81. [DOI: 10.1016/j.chroma.2014.05.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 04/25/2014] [Accepted: 05/13/2014] [Indexed: 10/25/2022]
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9
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Gargano AF, Leek T, Lindner W, Lämmerhofer M. Mixed-mode chromatography with zwitterionic phosphopeptidomimetic selectors from Ugi multicomponent reaction. J Chromatogr A 2013; 1317:12-21. [DOI: 10.1016/j.chroma.2013.07.095] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 07/24/2013] [Accepted: 07/26/2013] [Indexed: 10/26/2022]
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Bergqvist Y, Funding L, Kaneko A, Krysén B, Leek T. Improved method for the simultaneous determination of proguanil and its metabolites by high-performance liquid chromatography and solid-phase extraction of 100-microl capillary blood samples dried on sampling paper. J Chromatogr B Biomed Sci Appl 1998; 719:141-9. [PMID: 9869374 DOI: 10.1016/s0378-4347(98)00382-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An improved method is presented for the determination of proguanil, cycloguanil and 4-chlorophenylbiguanide in 100-microl capillary blood samples applied to sampling paper. This method also utilises a solid-phase extraction technique and high-performance liquid chromatography. Different kinds of sampling paper, such as ion-exchange and cellulose sampling paper were tested. The best elution recovery (70-80%) was obtained after treatment of cellulose sampling paper with a quaternary ammonium compound. The limit of determination was 50 nmol/l for cycloguanil and 4-chlorophenylbiguanide and 125 nmol/l for proguanil using 100 microl capillary blood. The stability of the analytes and elution performance from sampling paper was validated at different temperature and storage time. Venous blood and capillary blood concentrations of proguanil and metabolites were found to be similar.
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Affiliation(s)
- Y Bergqvist
- Dalarna University College, Borlänge, Sweden
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11
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Bergqvist Y, Funding L, Krysèn B, Leek T, Yvell K. Improved validated assay for the determination of proguanil and its metabolites in plasma, whole blood, and urine using solid-phase extraction and high-performance liquid chromatography. Ther Drug Monit 1998; 20:325-30. [PMID: 9631931 DOI: 10.1097/00007691-199806000-00014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
An improved and validated method is presented for the determination of proguanil, cycloguanil, and 4-chlorophenylbiguanide in plasma, whole blood, and urine using solid-phase extraction (SPE) technique and reversed-phase high-performance liquid chromatography (HPLC). The HPLC method uses isocratic elution with acetonitrile:phosphate buffer 0.1 mol/l, pH 2.6 (21.5:78.5 vol/vol) at a flow rate of 1.0 ml/min for the separation. The recovery of proguanil and metabolites ranged from 82% to 104%. The limit of determination was 20 nmol/l for proguanil and its metabolites in plasma and approximately 50 nmol/l for proguanil and metabolites in whole blood. Different stationary phases for HPLC and SPE were tested and the best chromatographic separation from endogenous constituents and other antimalarial drugs was achieved with cyanopropyl stationary phases.
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Affiliation(s)
- Y Bergqvist
- Dalarna University College, Borlänge, Sweden
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