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Vosáhlová Z, Gilar M, Kalíková K. Impact of ion-pairing systems choice on diastereomeric selectivity of phosphorothioated oligonucleotides in reversed-phase liquid chromatography. J Chromatogr A 2024; 1730:465074. [PMID: 38870581 DOI: 10.1016/j.chroma.2024.465074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/28/2024] [Accepted: 06/10/2024] [Indexed: 06/15/2024]
Abstract
Ion-pairing reversed-phase liquid chromatography was utilized for the analysis of native and phosphorothioated oligonucleotides differing in the length (2-6mers and 21mer) and the number and position of phosphorothioate modifications. We investigated the influence of counterion (acetate vs. hexafluoroisopropanol) on the adsorption of eleven alkylamines on the stationary phases. A stronger adsorption of charged alkylamines on octadecyl- and phenyl-based stationary phases led to greater retention of oligonucleotides, and the adsorption of alkylamines was promoted with greater concentration of hexafluoroisopropanol in the mobile phase. Selected amines (triethylamine, dipropylamine, hexylamine) were used to study the resolution of n and n-x mers (main peak and its impurities shortened at 5´end), and diastereomeric separation of phosphorothioated oligonucleotides. The results confirmed a crucial role of alkylamine and counterion choice on the diastereomeric separation. The increasing hydrophobicity of alkylamine led to diminished diastereomeric selectivity which produced narrower phosphorothioated oligonucleotides peaks and led to improved n/n-x separation. Using hexafluoroisopropanol instead of acetate as counterion further enhances this effect (except for 100 mM concentration of hexafluoroisopropanol in combination with highly hydrophobic hexylamine). The elevated column temperature led to suppression of the diastereomeric resolution and improved resolution of n and n-x mers oligonucleotides. Baseline separation of oligonucleotides with different number of phosphorothioate linkages was achieved; this may be useful for therapeutic oligonucleotide analysis.
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Affiliation(s)
- Zuzana Vosáhlová
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, Prague 12800, Czech Republic
| | - Martin Gilar
- Waters Corporation, 34 Maple Street, Milford, MA 01757, USA
| | - Květa Kalíková
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, Prague 12800, Czech Republic.
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Studzińska S, Szymarek J, Mazurkiewicz-Bełdzińska M. Improvement of serum sample preparation and chromatographic analysis of nusinersen used for the treatment of spinal muscular atrophy. Talanta 2024; 267:125173. [PMID: 37690419 DOI: 10.1016/j.talanta.2023.125173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 08/29/2023] [Accepted: 09/05/2023] [Indexed: 09/12/2023]
Abstract
The present investigation showed that each of the three different liquid chromatography modes may be successfully used for the qualitative analysis of nusinersen metabolites in a patient's serum sample extract. However, the smallest number was detected by the hydrophilic interaction liquid chromatography. Furthermore, the response of the mass spectrometry is several times greater for ion pair chromatography compared to reversed-phase one. Various extraction methods were applied for the extraction of nusinersen metabolites from serum. Silica with bonded capture strand for hybridization was applied, as well as silica modified with amino and carboxyl groups for dispersive solid phase extraction. The hybridization allows selective extraction of nusinersen analogs, however, it fails in extraction of short metabolites. On the contrary, the efficiency of weak ion exchange-based extraction was high, even in the case of the direct extraction of nusinersen metabolites from diluted serum samples without a protein removal step. The new material is a great alternative to liquid-liquid extraction and hybridization for the isolation of nusinersen metabolites from the serum of patients with spinal muscular atrophy (SMA). It is a very simple method that uses a low concentration of organic salt and desorption occurs after changing its pH. Such complex studies were performed for the first time for nusinersen metabolites extracted from the serum of SMA patients treated with Spinraza.
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Affiliation(s)
- Sylwia Studzińska
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7 Gagarin Str., PL-87-100 Toruń, Poland; Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, 4 Wilenska St., 87-100, Toruń, Poland.
| | - Jakub Szymarek
- Department of Developmental Neurology, Medical University of Gdansk, 7 Dębinki Str., PL-80-952, Gdańsk, Poland
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Stoll D, Sylvester M, Meston D, Sorensen M, Maloney TD. Development of multiple heartcutting two-dimensional liquid chromatography with ion-pairing reversed-phase separations in both dimensions for analysis of impurities in therapeutic oligonucleotides. J Chromatogr A 2024; 1714:464574. [PMID: 38103311 DOI: 10.1016/j.chroma.2023.464574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/02/2023] [Accepted: 12/09/2023] [Indexed: 12/19/2023]
Abstract
Oligonucleotides constitute an emerging and highly complex bioanalytical challenge and it is becoming increasingly clear that 1D methodologies are unable to fully resolve all possible impurities present in these samples. 2D-LC therefore constitutes a perfect solution wherein critical pairs can be sampled from a steep gradient 1D and separated in a shallower 2D gradient. Herein, we provide a facile 2D-LC method development approach to quickly generate high selectivity gradients utilizing ion pairing reverse phase (IPRP-IPRP). In particular we demonstrate how to iteratively generate a 12 % gradient from two training runs and then to utilize that data to predict retentions of analytes with a 2 % gradient with retention prediction errors as low as 3 and 11 %, respectively. This iterative method development workflow was applied to impurity profiling down to 1:1000 for the full-length product and phosphorothioate modified impurities. Additionally, we demonstrated the elucidation of critical pairs in complex crude pharmaceutical oligonucleotide samples by applying tailored high selectivity gradients in the second dimension. It was found that the iterative retention modeling approach allows fast and facile 2D-LC method development for complex oligonucleotide separations.
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Affiliation(s)
- Dwight Stoll
- Department of Chemistry, Gustavus Adolphus College, Saint Peter, MN 56082, USA.
| | - Maria Sylvester
- Department of Chemistry, Gustavus Adolphus College, Saint Peter, MN 56082, USA
| | - Daniel Meston
- Department of Chemistry, Gustavus Adolphus College, Saint Peter, MN 56082, USA
| | - Matt Sorensen
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Todd D Maloney
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
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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: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [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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