1
|
Currie J, Dahlberg JR, Lundberg E, Thunberg L, Eriksson J, Schweikart F, Nilsson GA, Örnskov E. Stability indicating ion-pair reversed-phase liquid chromatography method for modified mRNA. J Pharm Biomed Anal 2024; 245:116144. [PMID: 38636193 DOI: 10.1016/j.jpba.2024.116144] [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: 11/24/2023] [Revised: 03/11/2024] [Accepted: 03/29/2024] [Indexed: 04/20/2024]
Abstract
Modified messenger RNA (mRNA) represents a rapidly emerging class of therapeutic drug product. Development of robust stability indicating methods for control of product quality are therefore critical to support successful pharmaceutical development. This paper presents an ion-pair reversed-phase liquid chromatography (IP-RPLC) method to characterise modified mRNA exposed to a wide set of stress-inducing conditions, relevant for pharmaceutical development of an mRNA drug product. The optimised method could be used for separation and analysis of large RNA, sized up to 1000 nucleotides. Column temperature, mobile phase flow rate and ion-pair selection were each studied and optimised. Baseline separations of the model RNA ladder sample were achieved using all examined ion-pairing agents. We established that the optimised method, using 100 mM Triethylamine, enabled the highest resolution separation for the largest fragments in the RNA ladder (750/1000 nucleotides), in addition to the highest overall resolution for the selected modified mRNA compound (eGFP mRNA, 996 nucleotides). The stability indicating power of the method was demonstrated by analysing the modified eGFP mRNA, upon direct exposure to heat, hydrolytic conditions and treatment with ribonucleases. Our results showed that the formed degradation products, which appeared as shorter RNA fragments in front of the main peak, could be well monitored, using the optimised method, and the relative stability of the mRNA under the various stressed conditions could be assessed.
Collapse
Affiliation(s)
- Jonathan Currie
- Innovation Strategies and External Liaison, Pharmaceutical Technology and Development, Operations & IT, AstraZeneca, Gothenburg, Sweden
| | - Jacob R Dahlberg
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Ester Lundberg
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Linda Thunberg
- Early Chemical Development, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Jonas Eriksson
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Fritz Schweikart
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Gunilla A Nilsson
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Eivor Örnskov
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
| |
Collapse
|
2
|
Ozaki M, Kuwayama T, Shimotsuma M, Hirose T. Separation and purification of short-, medium-, and long-stranded RNAs by RP-HPLC using different mobile phases and C 18 columns with various pore sizes. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:1948-1956. [PMID: 38445900 DOI: 10.1039/d4ay00114a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Nucleic acids, which have been employed in medicines for various diseases, are attracting attention as a new pharmaceutical model. Depending on the target substances, nucleic acid medicines with various nucleic acid chain lengths (several tens of nucleotides [nt] to several thousands of nt) exist. The purification of synthesized nucleic acids is crucial as various impurities remain in the crude product after synthesis. Presently, reversed-phase high-performance liquid chromatography (RP-HPLC) represents an effective purification method for nucleic acids. However, the information regarding the HPLC conditions for separating and purifying nucleic acids of various chain lengths is insufficient. Thus, this technical note describes the separation and purification of short-, medium-, and long-stranded nucleic acids (several tens of nt to thousands of nt) by RP-HPLC with various mobile phases and octadecyl-based columns with various pore sizes, such as normal (9-12 nm), wide (30 nm), and super wide (>30 nm) pores.
Collapse
Affiliation(s)
- Makoto Ozaki
- Research and Development Department, Nacalai Tesque, Inc., Ishibashi Kaide-cho, Muko-shi, Kyoto 617-0004, Japan.
| | - Tomomi Kuwayama
- Research and Development Department, Nacalai Tesque, Inc., Ishibashi Kaide-cho, Muko-shi, Kyoto 617-0004, Japan.
| | - Motoshi Shimotsuma
- Research and Development Department, Nacalai Tesque, Inc., Ishibashi Kaide-cho, Muko-shi, Kyoto 617-0004, Japan.
| | - Tsunehisa Hirose
- Research and Development Department, Nacalai Tesque, Inc., Ishibashi Kaide-cho, Muko-shi, Kyoto 617-0004, Japan.
| |
Collapse
|
3
|
Abdullah AM, Sommers C, Rodriguez JD, Zhang D, Kozak D, Hawes J, Sapru M, Yang K. Decoding Complexity in Synthetic Oligonucleotides: Unraveling Coeluting Isobaric Impurity Ions by High Resolution Mass Spectrometry. Anal Chem 2024; 96:904-909. [PMID: 38158374 PMCID: PMC10794994 DOI: 10.1021/acs.analchem.3c05016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
Analyzing coeluting impurities with similar masses in synthetic oligonucleotides by liquid chromatography-mass spectrometry (LC-MS) poses challenges due to inadequate separation in either dimension. Herein, we present a direct method employing fully resolved isotopic envelopes, enabled by high resolution mass spectrometry (HRMS), to identify and quantify isobaric impurity ions resulting from the deletion or addition of a uracil (U) or cytosine (C) nucleotide from or to the full-length sequence. These impurities may each encompass multiple sequence variants arising from various deletion or addition sites. The method utilizes a full or targeted MS analysis to measure accurate isotopic distributions that are chemical formula dependent but nucleotide sequence independent. This characteristic enables the quantification of isobaric impurity ions involving sequence variants, a capability typically unavailable in sequence-dependent MS/MS methods. Notably, this approach does not rely on standard curves to determine isobaric impurity compositions in test samples; instead, it utilizes the individual isotopic distributions measured for each impurity standard. Moreover, in cases where specific impurity standards are unavailable, the measured isotopic distributions can be adequately replaced with the theoretical distributions (calculated based on chemical formulas of standards) adjusted using experiment-specific correction factors. In summary, this streamlined approach overcomes the limitations of LC-MS analysis for coeluting isobaric impurity ions, offering a promising solution for the in-depth profiling of complex impurity mixtures in synthetic oligonucleotide therapeutics.
Collapse
Affiliation(s)
- A. M. Abdullah
- Division
of Complex Drug Analysis, Office of Testing and Research, Office of
Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, Missouri 63110, United States
| | - Cynthia Sommers
- Division
of Complex Drug Analysis, Office of Testing and Research, Office of
Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, Missouri 63110, United States
| | - Jason D. Rodriguez
- Division
of Complex Drug Analysis, Office of Testing and Research, Office of
Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, Missouri 63110, United States
| | - Deyi Zhang
- Division
of Therapeutic Performance I, Office of Research and Standards, Office
of Generic Drugs, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20903, United States
| | - Darby Kozak
- Division
of Therapeutic Performance I, Office of Research and Standards, Office
of Generic Drugs, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20903, United States
| | - Jessica Hawes
- Division
of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas 72079, United States
| | - Mohan Sapru
- Division
of New Drug Product III, Office of New Drug Product, Office of Pharmaceutical
Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20903, United States
| | - Kui Yang
- Division
of Complex Drug Analysis, Office of Testing and Research, Office of
Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, Missouri 63110, United States
| |
Collapse
|
4
|
Gilar M, Doneanu C, Gaye MM. Liquid Chromatography Methods for Analysis of mRNA Poly(A) Tail Length and Heterogeneity. Anal Chem 2023; 95:14308-14316. [PMID: 37696042 PMCID: PMC10535021 DOI: 10.1021/acs.analchem.3c02552] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/28/2023] [Indexed: 09/13/2023]
Abstract
Messenger RNA (mRNA) is a new class of therapeutic compounds. The current advances in mRNA technology require the development of efficient analytical methods. In this work, we describe the development of several methods for measurement of mRNA poly(A) tail length and heterogeneity. Poly(A) tail was first cleaved from mRNA with the RNase T1 enzyme. The average length of a liberated poly(A) tail was analyzed with the size exclusion chromatography method. Size heterogeneity of the poly(A) tail was estimated with high-resolution ion-pair reversed phase liquid chromatography (IP RP LC). The IP RP LC method provides resolution of poly(A) tail oligonucleotide variants up to 150 nucleotide long. Both methods use a robust ultraviolet detection suitable for mRNA analysis in quality control laboratories. The results were confirmed by the LC-mass spectrometry (LC MS) analysis of the same mRNA sample. The poly(A) tail length and heterogeneity results were in good agreement.
Collapse
Affiliation(s)
- Martin Gilar
- Separations
R&D, Waters Corporation, Milford, Massachusetts 01757, United States
| | - Catalin Doneanu
- Discovery
and Development, Waters Corporation, Milford, Massachusetts 01757, United States
| | - Maissa M. Gaye
- Consumables
Research, Waters Corporation, Milford, Massachusetts 01757, United States
| |
Collapse
|
5
|
Sorensen MJ, Paulines MJ, Maloney TD. Evaluating orthogonality between ion-pair reversed phase, anion exchange, and hydrophilic interaction liquid chromatography for the separation of synthetic oligonucleotides. J Chromatogr A 2023; 1705:464184. [PMID: 37419013 DOI: 10.1016/j.chroma.2023.464184] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/09/2023]
Abstract
The orthogonality of separation between ion-pair reversed phase (IP-RP), anion exchange (AEX), and hydrophilic interaction liquid chromatography (HILIC) was evaluated for oligonucleotides. A polythymidine standard ladder was first used to evaluate the three methods and showed zero orthogonality, where retention and selectivity were based on oligonucleotide charge/size under all three conditions. Next, a model 23-mer synthetic oligonucleotide containing 4 phosphorothioate bonds with 2' fluoro and 2'-O-methyl ribose modifications typical of small interfering RNA was used for evaluating orthogonality. The resolution and orthogonality were evaluated between the three modes of chromatography in terms of selectivity differences for nine common impurities, including truncations (n-1, n-2), addition (n + 1), oxidation, and de-fluorination. We first evaluated different ion-pairing reagents that provided the best separation of the key impurities while suppressing diastereomer separation due to phosphorothioate linkages. Although different ion-pairing reagents affected resolution, very little orthogonality was observed. We then compared the retention times between IP-RP, HILIC, and AEX for each impurity of the model oligonucleotide and observed various selectivity changes. The results suggest that coupling HILIC with either AEX or IP-RP provide the highest degree of orthogonality due to the differences in retention for hydrophilic nucleobases and modifications under HILIC conditions. IP-RP provided the highest overall resolution for the impurity mixture, whereas more co-elution was observed with HILIC and AEX. The unique selectivity patterns offered by HILIC provides an interesting alternative to IP-RP or AEX, in addition to the potential for coupling with multidimensional separations. Future work should explore orthogonality for oligonucleotides with subtle sequence differences such as nucleobase modifications and base flip isomers, longer strands such as guide RNA and messenger RNA, and other biotherapeutic modalities such as peptides, antibodies, and antibody-drug-conjugates.
Collapse
Affiliation(s)
- Matthew J Sorensen
- Synthetic Molecule Design and Development, Lilly Research Labs, Eli Lilly and Company, Indianapolis, IN 46285, United States
| | - Mellie June Paulines
- Synthetic Molecule Design and Development, Lilly Research Labs, Eli Lilly and Company, Indianapolis, IN 46285, United States
| | - Todd D Maloney
- Synthetic Molecule Design and Development, Lilly Research Labs, Eli Lilly and Company, Indianapolis, IN 46285, United States.
| |
Collapse
|
6
|
Vanhinsbergh C, Hook EC, Oxby N, Dickman MJ. Optimization of orthogonal separations for the analysis of oligonucleotides using 2D-LC. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1227:123812. [PMID: 37454408 DOI: 10.1016/j.jchromb.2023.123812] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023]
Abstract
Oligonucleotides are commonly analysed using one dimensional chromatography (1D-LC) to resolve and characterise manufacturing impurities, structural isomers and (in respect to emerging oligonucleotide therapeutics) drug substance and drug product. Due to low selectivity and co-elution of closely related oligonucleotides using 1D-LC, analyte resolution is challenged. This leads to the requirement for improved analytical methods. Multidimensional chromatography has demonstrated utility in a range of applications as it increases peak capacity using orthogonal separations, however there are limited studies demonstrating the 2D-LC analysis of closely related oligonucleotides. In this study we optimised OGN size and sequence based separations using a variety of 1D-LC methods and coupled these orthogonal modes of chromatography within a 2D-LC workflow. Theoretical 2D-LC workflows were evaluated for optimal orthogonality using the minimum convex hull metric. The most orthogonal workflow identified in this study was ion-pair reversed phase using tributylammonium acetate (IP-RP-TBuAA) coupled with strong anion exchange in conjunction with sodium perchlorate (SAX-NaClO4) at high mobile phase pH. We developed a heart-cut (IP-RP-TBuAA)-(SAX-NaClO4) 2D-LC method for analysis of closely related size and sequence variant OGNs and OGN manufacturing impurities. The 2D-LC method resulted in an increased orthogonality and a reduction in co-elution (or close elution). Application of a UV based reference mapping strategy in conjunction with the 2D-LC method demonstrated a reduction in analytical complexity by reducing the reliance on mass based detection methods.
Collapse
Affiliation(s)
- Christina Vanhinsbergh
- Department of Chemical and Biological Engineering, Mappin Street, University of Sheffield, S1 3JD, UK
| | - Elliot C Hook
- GlaxoSmithKline, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Herts SG1 2NY, UK
| | - Nicola Oxby
- GlaxoSmithKline, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Herts SG1 2NY, UK
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, Mappin Street, University of Sheffield, S1 3JD, UK.
| |
Collapse
|
7
|
Roussis SG, Rentel C. Exploring the use of the desirability function to optimize the separation of oligonucleotide impurities by ion pair-RP LCMS. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1220:123666. [PMID: 36921438 DOI: 10.1016/j.jchromb.2023.123666] [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: 01/17/2023] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023]
Abstract
The use of small alkyl amines as ion pair reagents permits enhanced separation of impurities of phosphate diester oligonucleotides, which can be beneficial to quality control applications, and aid elucidation of the mechanisms of impurity formation. In general, however, separation of the individual components that comprise the majority of oligonucleotide impurities requires development of several independent chromatographic methods. Ideally, a single method capable of separating the individual components of all impurity classes would be developed. The mathematical concept of the desirability function has been explored here for its ability to determine the combination of experimental factors that result in a single, globally optimized chromatographic method. The optimized mobile phase, consisting of 1 mM propylamine (PA), 30 mM ammonium bicarbonate (ABC), and 1 mM octanoic acid (C8A), produced excellent agreement between measured and predicted peak resolution values for a set of n - 1 impurities. The relative importance of the mobile phase constituents on the mechanism of separation has been discussed. The approach holds great promise for the improved separation of components in complex chromatographic systems.
Collapse
Affiliation(s)
| | - Claus Rentel
- Ionis Pharmaceuticals, Carlsbad, CA 92010, United States
| |
Collapse
|
8
|
Enmark M, Samuelsson J, Fornstedt T. Development of a unified gradient theory for ion-pair chromatography using oligonucleotide separations as a model case. J Chromatogr A 2023; 1691:463823. [PMID: 36716595 DOI: 10.1016/j.chroma.2023.463823] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/20/2023] [Accepted: 01/21/2023] [Indexed: 01/23/2023]
Abstract
Ion-pair chromatography is the de facto standard for separating oligonucleotides and related impurities, particularly for analysis but also often for small-scale purification. Currently, there is limited understanding of the quantitative modeling of both analytical and overloaded elution profiles obtained during gradient elution in ion-pair chromatography. Here we will investigate a recently introduced gradient mode, the so-called ion-pairing reagent gradient mode, for both analytical and overloaded separations of oligonucleotides. The first part of the study demonstrates how the electrostatic theory of ion-pair chromatography can be applied for modeling gradient elution of oligonucleotides. When the ion-pair gradient mode is used in a region where the electrostatic surface potential can be linearized, a closed-form expression of retention time can be derived. A unified retention model was then derived, applicable for both ion-pair reagent gradient mode as well as co-solvent gradient mode. The model was verified for two different experimental systems and homo- and heteromeric oligonucleotides of different lengths. Quantitative modeling of overloaded chromatography using the ion-pairing reagent gradient mode was also investigated. Firstly, a unified adsorption isotherm model was developed for both gradient modes. Then, adsorption isotherms parameter of a model oligonucleotide and two major synthetic impurities were estimated using the inverse method. Secondly, the parameters of the adsorption isotherm were then used to investigate how the productivity of oligonucleotide varies with injection volume, gradient slope, and initial retention factor. Here, the productivity increased when using a shallow gradient slope combined with a low initial retention factor. Finally, experiments were conducted to confirming some of the model predictions. Comparison with the conventional co-solvent gradient mode showed that the ion-pairing reagent gradient leads to both higher yield and productivity while consuming less co-solvent.
Collapse
Affiliation(s)
- Martin Enmark
- 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.
| | - Torgny Fornstedt
- Department of Engineering and Chemical Sciences, Karlstad University, SE-651 88 Karlstad, Sweden.
| |
Collapse
|
9
|
Studzińska S, Li F, Szumski M, Buszewski B, Lämmerhofer M. Cholesterol Stationary Phase in the Separation and Identification of siRNA Impurities by Two-Dimensional Liquid Chromatography-Mass Spectrometry. Int J Mol Sci 2022; 23:ijms232314960. [PMID: 36499291 PMCID: PMC9738757 DOI: 10.3390/ijms232314960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/19/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
The aim of this research was to develop a simple and efficient ion-pair reagent-free chromatographic method for the separation and qualitative determination of oligonucleotide impurities, exemplified by synthesis of raw products of the two single strands of patisiran siRNA. The stationary phases with mixed hydrophobic/hydrophilic properties (cholesterol and alkylamide) were firstly used for this purpose with reversed-phased high-performance liquid chromatography. Several different chromatographic parameters were tested for their impact on impurities separation: type, concentration, pH of salt, as well as organic solvent type in the mobile phase. The pH was the most influential factor on the separation and signal intensities in mass spectrometry detection. Finally, the optimized method included the application of cholesterol stationary phase, with mobile phase containing 20 mM ammonium formate (pH 6.5) and methanol. It allowed good separation and the identification of most impurities within 25 min. Since not all closely related impurities could be fully resolved from the main peak in this oligonucleotide impurity profiling, two-dimensional liquid chromatography was used for peak purity determination of the target oligonucleotides. The Ethylene Bridged Hybrid (BEH) Amide column in hydrophilic interaction liquid chromatography was applied in the second dimension, allowing additional separation of three closely related impurities.
Collapse
Affiliation(s)
- Sylwia Studzińska
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7 Gagarin Str., 87-100 Toruń, Poland
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Correspondence: ; Tel.: +48-56-6114753
| | - Feiyang Li
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Michał Szumski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, 4 Wilenska St., 87-100 Toruń, Poland
| | - Bogusław Buszewski
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7 Gagarin Str., 87-100 Toruń, Poland
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| |
Collapse
|
10
|
Lardeux H, Goyon A, Zhang K, Nguyen JM, Lauber MA, Guillarme D, D'Atri V. The impact of low adsorption surfaces for the analysis of DNA and RNA oligonucleotides. J Chromatogr A 2022; 1677:463324. [PMID: 35858489 DOI: 10.1016/j.chroma.2022.463324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 12/20/2022]
Abstract
As interest in oligonucleotide (ON) therapeutics is increasing, there is a need to develop suitable analytical methods able to properly analyze those molecules. However, an issue exists in the adsorption of ONs on different parts of the instrumentation during their analysis. The goal of the present paper was to comprehensively evaluate various types of bioinert materials used in ion-pairing reversed-phase (IP-RPLC) and hydrophilic interaction chromatography (HILIC) to mitigate this issue for 15- to 100-mer DNA and RNA oligonucleotides. The whole sample flow path was considered under both conditions, including chromatographic columns, ultra-high-performance liquid chromatography (UHPLC) system, and ultraviolet (UV) flow cell. It was found that a negligible amount of non-specific adsorption might be attributable to the chromatographic instrumentation. However, the flow cell of a detector should be carefully subjected to sample-based conditioning, as the material used in the UV flow cell was found to significantly impact the peak shapes of the largest ONs (60- to 100-mer). Most importantly, we found that the choice of column hardware had the most significant impact on the extent of non-specific adsorption. Depending on the material used for the column walls and frits, adsorption can be more or less pronounced. It was proved that any type of bioinert RPLC/HILIC column hardware offered some clear benefits in terms of adsorption in comparison to their stainless-steel counterparts. Finally, the evaluation of a large set of ONs was performed, including a DNA duplex and DNA or RNA ONs having different base composition, furanose sugar, and modifications occurring at the phosphate linkage or at the sugar moiety. This work represents an important advance in understanding the overall ON adsorption, and it helps to define the best combination of materials when analyzing a wide range of unmodified and modified 20-mer DNA and RNA ONs.
Collapse
Affiliation(s)
- Honorine Lardeux
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, CMU-Rue Michel Servet 1, Geneva 4 1211, Switzerland; School of Pharmaceutical Sciences, University of Geneva, CMU-Rue Michel Servet 1, Geneva 4 1211, Switzerland
| | - Alexandre Goyon
- Small Molecule Pharmaceutical Sciences, Genentech Inc., DNA Way, South San Francisco, CA 94080, USA
| | - Kelly Zhang
- Small Molecule Pharmaceutical Sciences, Genentech Inc., DNA Way, South San Francisco, CA 94080, USA
| | | | | | - Davy Guillarme
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, CMU-Rue Michel Servet 1, Geneva 4 1211, Switzerland; School of Pharmaceutical Sciences, University of Geneva, CMU-Rue Michel Servet 1, Geneva 4 1211, Switzerland
| | - Valentina D'Atri
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, CMU-Rue Michel Servet 1, Geneva 4 1211, Switzerland; School of Pharmaceutical Sciences, University of Geneva, CMU-Rue Michel Servet 1, Geneva 4 1211, Switzerland.
| |
Collapse
|
11
|
Chen T, Tang S, Fu Y, Napolitano JG, Zhang K. Analytical techniques for characterizing diastereomers of phosphorothioated oligonucleotides. J Chromatogr A 2022; 1678:463349. [PMID: 35908512 DOI: 10.1016/j.chroma.2022.463349] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 07/07/2022] [Accepted: 07/15/2022] [Indexed: 12/18/2022]
Abstract
Oligonucleotides have emerged as powerful therapeutics for treating diverse diseases. To fully unlock the therapeutic potential of oligonucleotides, there is still a great need to further improve their drug-like properties. Numerous chemical modifications have been explored to achieve this goal, with phosphorothioation being one of the most widely used strategies. However, phosphorothioate modification produces diastereomers that are reported to have different properties and performances, demanding detailed characterization of these diastereomers. Here we provide an overview of phosphorothioated oligonucleotide diastereomers, covering their origin and configurations, physicochemical and pharmacological properties, and stereo-selective chemical synthesis, followed by a summary of currently available analytical techniques for characterizing these diastereomers, with a focus on liquid chromatography-based approaches, including ion-pair reversed-phase liquid chromatography, anion exchange chromatography, mixed-mode chromatography, and hybrid approaches. Non-chromatographic techniques, such as capillary electrophoresis, spectroscopy and other methods, are also being reviewed.
Collapse
Affiliation(s)
- Tao Chen
- Small Molecule Analytical Chemistry, Small Molecule Pharmaceutical Sciences, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Shijia Tang
- Small Molecule Analytical Chemistry, Small Molecule Pharmaceutical Sciences, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Yige Fu
- Small Molecule Analytical Chemistry, Small Molecule Pharmaceutical Sciences, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - José G Napolitano
- Small Molecule Analytical Chemistry, Small Molecule Pharmaceutical Sciences, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Kelly Zhang
- Small Molecule Analytical Chemistry, Small Molecule Pharmaceutical Sciences, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States.
| |
Collapse
|
12
|
Kadlecová Z, Kalíková K, Tesařová E, Gilar M. Phosphorothioate oligonucleotides separation in ion-pairing reversed-phase liquid chromatography: effect of ion-pairing system. J Chromatogr A 2022; 1676:463201. [DOI: 10.1016/j.chroma.2022.463201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/03/2022] [Accepted: 06/05/2022] [Indexed: 02/04/2023]
|
13
|
Rentel C, Gaus H, Bradley K, Luu N, Kolkey K, Mai B, Madsen M, Pearce M, Bock B, Capaldi D. Assay, Purity, and Impurity Profile of Phosphorothioate Oligonucleotide Therapeutics by Ion Pair-High-Performance Liquid Chromatography-Mass Spectrometry. Nucleic Acid Ther 2022; 32:206-220. [PMID: 35238617 DOI: 10.1089/nat.2021.0056] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The relatively large molecular size, diastereoisomeric nature, and complex impurity profiles of therapeutic phosphorothioate oligonucleotides create significant analytical challenges for the quality control laboratory. To overcome the lack of selectivity inherent to traditional chromatographic approaches, an ion pair liquid chromatography-mass spectrometry (LCMS) method combining ultraviolet and mass spectrometry quantification was developed and validated for >35 different oligonucleotide drug substances and products, including several commercialized drugs. The selection of chromatographic and spectrometric conditions, data acquisition and processing, critical aspects of sample and buffer preparation and instrument maintenance, and results from method validation experiments are discussed.
Collapse
Affiliation(s)
- Claus Rentel
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Hans Gaus
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Kym Bradley
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Nhuy Luu
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Kimmy Kolkey
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Bao Mai
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Mark Madsen
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Megan Pearce
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Brandon Bock
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
| | - Daniel Capaldi
- Analytical Development Quality Control, Ionis Pharmaceuticals, Carlsbad, California, USA
| |
Collapse
|
14
|
Enmark M, Häggström J, Samuelsson J, Fornstedt T. Building machine-learning-based model for retention time and resolution predictions in ion pair chromatography of oligonucleotides. J Chromatogr A 2022; 1671:462999. [DOI: 10.1016/j.chroma.2022.462999] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/22/2022] [Accepted: 03/25/2022] [Indexed: 01/29/2023]
|
15
|
Donegan M, Nguyen JM, Gilar M. Effect of ion-pairing reagent hydrophobicity on liquid chromatography and mass spectrometry analysis of oligonucleotides. J Chromatogr A 2022; 1666:462860. [PMID: 35123169 DOI: 10.1016/j.chroma.2022.462860] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/19/2022] [Accepted: 01/25/2022] [Indexed: 10/19/2022]
Abstract
We performed a systematic study of thirteen alkylamines used as ion-pairing reagents for ion-pair reversed-phase liquid chromatography (IP RP LC) separations of oligonucleotides on a C18 column. We proposed a method to classify the hydrophobicity of alkylamines by their retention in RP LC. The IP reagent hydrophobicity correlated with the retention and resolution of oligonucleotides in the corresponding IP mobile phases. The baseline resolution was achieved up to 30 mer for hydrophilic, or up to 50 mer for hydrophobic IP reagents. Hydrophobic alkylamines permitted useful oligonucleotide separations at relatively low buffer concentrations, such as 5-10 mM alkylamine-acetate IP systems. These buffers were compatible with mass spectrometry detection, however, replacement of acetic acid with hexafluoroisopropanol in the mobile phase improved the MS signal by 2-3 orders of magnitude. Experiments with native and chemically modified oligonucleotides highlighted the mixed-mode nature of IP RP LC. When using hydrophobic IP reagents, the ionic retention mechanism of oligonucleotides is enhanced while hydrophobic retention is diminished.
Collapse
Affiliation(s)
| | | | - Martin Gilar
- Waters Corporation, 34 Maple Street, Milford, MA 01757, USA.
| |
Collapse
|
16
|
Roussis SG, Cedillo I, Rentel C. Characterizing the Diastereoisomeric Distribution of Phosphorothioate Oligonucleotides by Metal Ion Complexation Chromatography, In-Series Reversed Phase-Strong Anion Exchange Chromatography, and 31P NMR. Anal Chem 2021; 93:16035-16042. [PMID: 34813705 DOI: 10.1021/acs.analchem.1c03593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Replacement of a non-bridging oxygen atom of the phosphate diester linkage of an oligonucleotide by sulfur conveys pharmacokinetic benefits, such as increased nuclease resistance and enhanced protein binding. Substitution renders the internucleotide linkages chiral, and so phosphorothioate diester (PS) oligonucleotides comprise complex mixtures of diastereoisomers. Currently, chromatographic separation of individual diastereoisomers is limited to oligonucleotides that contain no more than about four or five PS linkages. The development of therapeutic PS oligonucleotides, which often contain >15 PS linkages, would be greatly aided by methods useful for assessing batch-to-batch stereo-reproducibility. To this effect, the relative sensitivities of metal ion complexation chromatography (MICC), in-series reversed phase-strong anion exchange chromatography (RP-SAX), and 31P NMR toward changes in the diastereoisomeric distributions of therapeutic PS oligonucleotides were compared. Model oligonucleotides synthesized under conditions known to impact PS stereochemistry were used to evaluate the method performance, and all three methods showed excellent sensitivity toward changes in the diastereoisomeric composition. Interactions via the solvent-accessible areas and a combination of hydrophobic and electrostatic forces may be responsible for the selectivity demonstrated by MICC and in-series RP-SAX, respectively.
Collapse
Affiliation(s)
- Stilianos G Roussis
- Ionis Pharmaceuticals, 2855 Gazelle Ct., Carlsbad, California 92010, United States
| | - Isaiah Cedillo
- Ionis Pharmaceuticals, 2855 Gazelle Ct., Carlsbad, California 92010, United States
| | - Claus Rentel
- Ionis Pharmaceuticals, 2855 Gazelle Ct., Carlsbad, California 92010, United States
| |
Collapse
|
17
|
Talap J, Zhao J, Shen M, Song Z, Zhou H, Kang Y, Sun L, Yu L, Zeng S, Cai S. Recent advances in therapeutic nucleic acids and their analytical methods. J Pharm Biomed Anal 2021; 206:114368. [PMID: 34571322 DOI: 10.1016/j.jpba.2021.114368] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 12/11/2022]
Abstract
Therapeutic nucleic acids are various chemically modified RNA or DNA with different functions, which mainly play roles at the gene level. Owing to its accurately targeting at pathogenic genes, nucleic acid based therapeutics have a wide range of application prospects. Recently, the improvement on chemical synthesis and delivery materials accelerated the development of therapeutic nucleic acids rapidly. Up to now, 17 nucleic acid based therapeutics approved by Food and Drug Administration (FDA) or European Medicines Agency (EMA). The development of therapeutics raised higher requirements for analytical methods, both in quality control and in clinical research. The first part of this review introduces different classes of therapeutic nucleic acids, including antisense oligonucleotide (ASO), RNA interference (RNAi) therapy, mRNA, aptamer and other classes which are under research. The second part reviews the therapeutic nucleic acids commercialized from 2019 to now. The third part discusses the analytical methods for nucleic acid based therapeutics, including liquid chromatography-based methods, capillary gel electrophoresis (CGE), hybridization enzyme-linked immunosorbent assay (ELISA) and other infrequently used methods. Finally, the advantages and shortcomings of these methods are summarized, and the future development of analysis methods are prospected.
Collapse
Affiliation(s)
- Jadera Talap
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jing Zhao
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao
| | - Minzhe Shen
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zihan Song
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hui Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yu Kang
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lianli Sun
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lushan Yu
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Cancer Center of Zhejiang University, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Hangzhou, China.
| | - Sheng Cai
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Cancer Center of Zhejiang University, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Hangzhou, China.
| |
Collapse
|
18
|
Enmark M, Harun S, Samuelsson J, Örnskov E, Thunberg L, Dahlén A, Fornstedt T. Selectivity limits of and opportunities for ion pair chromatographic separation of oligonucleotides. J Chromatogr A 2021; 1651:462269. [PMID: 34102400 DOI: 10.1016/j.chroma.2021.462269] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 05/12/2021] [Accepted: 05/15/2021] [Indexed: 12/12/2022]
Abstract
Here it was investigated how oligonucleotide retention and selectivity factors are affected by electrostatic and non-electrostatic interactions in ion pair chromatography. A framework was derived describing how selectivity depends on the electrostatic potential generated by the ion-pair reagent concentration, co-solvent volume fraction, charge difference between the analytes, and temperature. Isocratic experiments verified that, in separation problems concerning oligonucleotides of different charges, selectivity increases with increasing surface potential and analyte charge difference and with decreasing co-solvent volume fraction and temperature. For analytes of the same charge, for example, diastereomers of phosphorothioated oligonucleotides, selectivity can be increased by decreasing the co-solvent volume fraction or the temperature and has only a minor dependency on the ion-pairing reagent concentration. An important observation is that oligonucleotide retention is driven predominantly by electrostatic interaction generated by the adsorption of the ion-pairing reagent. We therefore compared classical gradient elution in which the co-solvent volume fraction increases over time versus gradient elution with a constant co-solvent volume fraction but with decreasing ion-pair reagent concentration over time. Both modes decrease the electrostatic potential. Oligonucleotide selectivity was found to increase with decreasing ion-pairing reagent concentration. The two elution modes were finally applied to two different model antisense oligonucleotide separation problems, and it was shown that the ion-pair reagent gradient increases the selectivity of non-charge-based separation problems while maintaining charge-difference-based selectivity.
Collapse
Affiliation(s)
- Martin Enmark
- Department of Engineering and Chemical Sciences, Karlstad University, SE-651 88 Karlstad, Sweden
| | - Said Harun
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca,Gothenburg, 431 83, Mölndal, Sweden
| | - Jörgen Samuelsson
- Department of Engineering and Chemical Sciences, Karlstad University, SE-651 88 Karlstad, Sweden.
| | - Eivor Örnskov
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca,Gothenburg, 431 83, Mölndal, Sweden
| | - Linda Thunberg
- Early Chemical Development, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 431 83, Mölndal, Sweden
| | - Anders Dahlén
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 431 83, Mölndal, Sweden
| | - Torgny Fornstedt
- Department of Engineering and Chemical Sciences, Karlstad University, SE-651 88 Karlstad, Sweden.
| |
Collapse
|
19
|
Pourshahian S. THERAPEUTIC OLIGONUCLEOTIDES, IMPURITIES, DEGRADANTS, AND THEIR CHARACTERIZATION BY MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2021; 40:75-109. [PMID: 31840864 DOI: 10.1002/mas.21615] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Oligonucleotides are an emerging class of drugs that are manufactured by solid-phase synthesis. As a chemical class, they have unique product-related impurities and degradants, characterization of which is an essential step in drug development. The synthesis cycle, impurities produced during the synthesis and degradation products are presented and discussed. The use of liquid chromatography combined with mass spectrometry for characterization and quantification of product-related impurities and degradants is reviewed. In addition, sequence determination of oligonucleotides by gas-phase fragmentation and indirect mass spectrometric methods is discussed. © 2019 John Wiley & Sons Ltd. Mass Spec Rev.
Collapse
Affiliation(s)
- Soheil Pourshahian
- Janssen Pharmaceutical Companies of Johnson & Johnson, South San Francisco, CA, 94080
| |
Collapse
|
20
|
Roussis SG, Rodriguez AA, Rentel C. Determination of individual oligonucleotide impurities by small amine ion pair-RP HPLC MS and MS/MS: n - 1 impurities. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1169:122611. [PMID: 33706187 DOI: 10.1016/j.jchromb.2021.122611] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/09/2021] [Accepted: 02/18/2021] [Indexed: 12/01/2022]
Abstract
Ion pair-reversed phase (IP-RP) HPLC is one of the most widely used methods for the analysis of oligonucleotide impurities. The method is compatible with mass spectrometry and has been used to guide the development of improved synthesis and purification approaches. The ability to detect and characterize impurities depends on the reagents and the IP buffer system employed, as each can directly affect the degree of chromatographic separation and the sensitivity of detection by MS. Previous work in our laboratory has shown that small alkyl amines are suitable IP reagents for the analysis of impurities in phosphate diester oligonucleotides and can be used to differentiate among individual members of composite impurity families. The addition of an alkyl acid often further enhances peak separation, but at the detriment of ion signal. An improved method with increased chromatographic performance and sensitivity of detection is presented here. Improvements were mainly realized through the use of lower concentrations of small alkyl amine (i.e., 5 mM) and acid (0.5 mM) IP reagents, and ammonium bicarbonate (20 mM) as a buffer. The improved capabilities of the new method are demonstrated by separation of the individual components of the composite n - 1 impurity in a set of four production-scale batches of a single oligonucleotide. Addition of the alkyl acid resulted in resolution of most individual n - 1 impurities. The observed enhanced sensitivity of detection allowed multiple reaction monitoring (MRM) experiments, which were used to differentiate among unresolved impurities.
Collapse
Affiliation(s)
| | | | - Claus Rentel
- Ionis Pharmaceuticals, Carlsbad, CA 92010, United States
| |
Collapse
|
21
|
Santos IC, Brodbelt JS. Recent developments in the characterization of nucleic acids by liquid chromatography, capillary electrophoresis, ion mobility, and mass spectrometry (2010-2020). J Sep Sci 2021; 44:340-372. [PMID: 32974962 PMCID: PMC8378248 DOI: 10.1002/jssc.202000833] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 12/25/2022]
Abstract
The development of new strategies for the analysis of nucleic acids has gained momentum due to the increased interest in using these biomolecules as drugs or drug targets. The application of new mass spectrometry ion activation techniques and the optimization of separation methods including liquid chromatography, capillary electrophoresis, and ion mobility have allowed more detailed characterization of nucleic acids and oligonucleotide therapeutics including confirmation of sequence, localization of modifications and interaction sites, and structural analysis as well as identification of failed sequences and degradation products. This review will cover tandem mass spectrometry methods as well as the recent developments in liquid chromatography, capillary electrophoresis, and ion mobility coupled to mass spectrometry for the analysis of nucleic acids and oligonucleotides.
Collapse
Affiliation(s)
- Inês C Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas, USA
| | | |
Collapse
|
22
|
Sutton JM, Guimaraes GJ, Annavarapu V, van Dongen WD, Bartlett MG. Current State of Oligonucleotide Characterization Using Liquid Chromatography-Mass Spectrometry: Insight into Critical Issues. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1775-1782. [PMID: 32812756 DOI: 10.1021/jasms.0c00179] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
As interests increase in oligonucleotide therapeutics, there has been a greater need for analytical techniques to properly analyze and quantitate these biomolecules. This article looks into some of the existing chromatographic approaches for oligonucleotide analysis, including anion exchange, hydrophilic interaction liquid chromatography, and ion pair chromatography. Some of the key advantages and challenges of these chromatographic techniques are discussed. Colloid formation in mobile phases of alkylamines and fluorinated alcohols, a recently discovered analytical challenge, is discussed. Mass spectrometry is the method of choice to directly obtain structural information about oligonucleotide therapeutics. Mass spectrometry sensitivity challenges are reviewed, including comparison to other oligonucleotide techniques, salt adduction, and the multiple charge state envelope. Ionization of oligonucleotides through the charge residue model, ion evaporation model, and chain ejection model are analyzed. Therapeutic oligonucleotides have to undergo approval from major regulatory agencies, and the impurities and degradation products must be well-characterized to be approved. Current accepted thresholds for oligonucleotide impurities are reported. Aspects of the impurities and degradation products from these types of molecules are discussed as well as optimal analytical strategies to determine oligonucleotide related substances. Finally, ideas are proposed on how the field of oligonucleotide therapeutics may improve to aid in future analysis.
Collapse
Affiliation(s)
- J Michael Sutton
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, Georgia 30602-2352, United States
| | - Guilherme J Guimaraes
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, Georgia 30602-2352, United States
| | - Vidya Annavarapu
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, Georgia 30602-2352, United States
| | | | - Michael G Bartlett
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, Georgia 30602-2352, United States
| |
Collapse
|
23
|
Andraws G, Trefi S. Ionisable substances chromatography: A new approach for the determination of Ketoprofen, Etoricoxib, and Diclofenac sodium in pharmaceuticals using ion - pair HPLC. Heliyon 2020; 6:e04613. [PMID: 32793832 PMCID: PMC7408326 DOI: 10.1016/j.heliyon.2020.e04613] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 07/17/2020] [Accepted: 07/29/2020] [Indexed: 11/17/2022] Open
Abstract
An ion-pair HPLC method was developed and validated to analyze three of non-steroidal anti-inflammatory drugs (Ketoprofen, Etoricoxib, and Diclofenac sodium) in their pure and pharmaceuticals based on their ionisable characteristics. Cetyltrimethylammonium bromide (Cetrimide) was used as an ion pair reagent since it had not been used before for this purpose. Chromatographic analysis was accomplished using the C18 (250 × 4.6 mm, 5μm) column. Mobile phase consisted of a mixture of 50% Cetrimide 10 - 3 M and 50% acetonitrile to analyze Ketoprofen and Etoricoxib, whereas for Diclofenac sodium, mobile phase was a mixture of 30% Cetrimide 10 - 3 M and 70% acetonitrile. pH value was adjusted if necessary to 10 with ammonium hydroxide. The flow rate was 1mL/min and detection wavelengths were at 254 nm, 234 nm, and 254 nm for Ketoprofen, Etoricoxib, and Diclofenac sodium; respectively under ambient temperature. Retention times ( R t ) were 9.41, 7.34, and 6.66 for Ketoprofen, Etoricoxib, and Diclofenac sodium; respectively. The proposed method was evaluated for linearity, accuracy, precision, and specificity according to ICH guidelines. Ketoprofen, Etoricoxib, and Diclofenac sodium were detected in the following linear ranges: (0.031-0.500mg/mL), (0.007-0.110g/mL), and (0.016-0.250mg/mL); respectively with excellent mean recovery values (98.0-102.0%). RSD% was in an acceptable range (less than 2), proving the precision of the developed method. Specificity was proved in the presence of degradation products. Furthermore, a comparison between the results of this study and the reported HPLC methods indicated that this developed method was better in terms of simplicity, analysis time, and no use of buffers in the mobile phase. In conclusion, the developed method can successfully detect Ketoprofen, Etoricoxib, and Diclofenac sodium quantitatively and qualitatively in their dosage forms without any interference with excipients, making this method valuable, reliable, and practical to be applied in quality control laboratories.
Collapse
Affiliation(s)
- Georgeos Andraws
- Pharmaceutical Quality and Pharmaceutical Chemistry Department, Faculty of Pharmacy, University of Aleppo, Syria
| | - Saleh Trefi
- Pharmaceutical Quality and Pharmaceutical Chemistry Department, Faculty of Pharmacy, University of Aleppo, Syria
| |
Collapse
|
24
|
Li F, Su X, Bäurer S, Lämmerhofer M. Multiple heart-cutting mixed-mode chromatography-reversed-phase 2D-liquid chromatography method for separation and mass spectrometric characterization of synthetic oligonucleotides. J Chromatogr A 2020; 1625:461338. [PMID: 32709362 DOI: 10.1016/j.chroma.2020.461338] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 01/20/2023]
Abstract
Until today, ion-pair reversed-phase chromatography is still the dominating method for analytical characterization of synthetic oligonucleotides. Its hyphenation with mass spectrometry, however, has some drawbacks such as ion-suppression in electrospray ionization. To overcome this problem, we present in this work a multiple heart-cutting (MHC) two-dimensional liquid chromatography (2D-LC) method with ultra-violet (UV) and electrospray ionization (ESI) mass spectrometry (MS) detection. A reversed-phase/weak anion-exchange (RP/WAX) stationary phase in the first dimension (1D) provides the selectivity for separation of structurally closely related oligonucleotide sequences and deletions (shortmers), respectively, using a mixed pH/triethylammonium phosphate buffer gradient at constant organic modifier content. Heart cuts of the oligonucleotide peaks are transferred to the second dimension (2D) via a multiple heart-cutting valve which is equipped with two loop decks. The 2D RP column is used for desalting via a diverter valve. Active solvent modulation enables to refocus the oligonucleotide peak into a sharp zone by 2D RP entirely free of non-volatile buffer components and ion-pair agents. Oligonucleotides can thus be sensitively detected by ESI-QTOF-MS under MS-compatible conditions.
Collapse
Affiliation(s)
- Feiyang Li
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Xiaoli Su
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Stefanie Bäurer
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
| |
Collapse
|
25
|
Catani M, De Luca C, Medeiros Garcia Alcântara J, Manfredini N, Perrone D, Marchesi E, Weldon R, Müller-Späth T, Cavazzini A, Morbidelli M, Sponchioni M. Oligonucleotides: Current Trends and Innovative Applications in the Synthesis, Characterization, and Purification. Biotechnol J 2020; 15:e1900226. [PMID: 32298041 DOI: 10.1002/biot.201900226] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/17/2020] [Indexed: 12/12/2022]
Abstract
Oligonucleotides (ONs) are gaining increasing importance as a promising novel class of biopharmaceuticals. Thanks to their fundamental role in gene regulation, they can be used to develop custom-made drugs (also called N-to-1) able to act on the gene expression at pre-translational level. With recent approvals of ON-based therapeutics by the Food and Drug Administration (FDA), a growing demand for high-quality chemically modified ONs is emerging and their market is expected to impressively prosper in the near future. To satisfy this growing market demand, a scalable and economically sustainable ON production is needed. In this paper, the state of the art of the whole ON production process is illustrated with the aim of highlighting the most promising routes toward the auspicated market-size production. In particular, the most recent advancements in both the upstream stage, mainly based on solid-phase synthesis and recombinant technology, and the downstream one, focusing on chromatographic techniques, are reviewed. Since ON production is projected to expand to the large scale, automatized multicolumn countercurrent technologies will reasonably be required soon to replace the current ones based on batch single-column operations. This consideration is supported by a recent cutting-edge application of continuous chromatography for the ON purification.
Collapse
Affiliation(s)
- Martina Catani
- Department of Chemistry and Pharmaceutical Sciences, University of Ferrara, via L. Borsari 46, Ferrara, 44121, Italy
| | - Chiara De Luca
- Department of Chemistry and Pharmaceutical Sciences, University of Ferrara, via L. Borsari 46, Ferrara, 44121, Italy
| | - João Medeiros Garcia Alcântara
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta,", Politecnico di Milano, via Mancinelli 7, Milano, 20131, Italy
| | - Nicolò Manfredini
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta,", Politecnico di Milano, via Mancinelli 7, Milano, 20131, Italy
| | - Daniela Perrone
- Department of Chemistry and Pharmaceutical Sciences, University of Ferrara, via L. Borsari 46, Ferrara, 44121, Italy
| | - Elena Marchesi
- Department of Chemistry and Pharmaceutical Sciences, University of Ferrara, via L. Borsari 46, Ferrara, 44121, Italy
| | - Richard Weldon
- ChromaCon AG, Technoparkstrasse 1, Zürich, 8005, Switzerland
| | | | - Alberto Cavazzini
- Department of Chemistry and Pharmaceutical Sciences, University of Ferrara, via L. Borsari 46, Ferrara, 44121, Italy
| | - Massimo Morbidelli
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta,", Politecnico di Milano, via Mancinelli 7, Milano, 20131, Italy
| | - Mattia Sponchioni
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta,", Politecnico di Milano, via Mancinelli 7, Milano, 20131, Italy
| |
Collapse
|
26
|
Goyon A, Yehl P, Zhang K. Characterization of therapeutic oligonucleotides by liquid chromatography. J Pharm Biomed Anal 2020; 182:113105. [PMID: 32004766 DOI: 10.1016/j.jpba.2020.113105] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/21/2019] [Accepted: 01/08/2020] [Indexed: 12/27/2022]
Abstract
Marketed therapies in the pharmaceutical landscape are rapidly evolving and getting more diverse. Small molecule medicines have dominated in the past while antibodies have grown dramatically in recent years. However, the failure of traditional small and large molecules in accessing certain targets has led to increased R&D efforts to develop alternative modalities. Therapeutic oligonucleotides (ONs) can accurately be directed against their ribonucleic acid (RNA) target and represent a promising approach in previously untreated diseases. Established automated synthesis of ONs coupled with chemical improvements and the advance of new drug delivery technologies has recently brought ONs to a heightened level of interest. The first part of the present review describes the different classes of oligonucleotides, namely antisense oligonucleotide (ASO), small interfering RNA (siRNA), microRNA (miRNA), aptamer and immunostimulatory ON, with a focus on their delivery systems relevant for future analytical characterization. The second part reviews the typical impurities in therapeutic ON products. The third part discusses the use of historical methods anion exchange chromatography (AEX), ion-pair reversed phase liquid chromatography (IP-RP), mixed-mode chromatography (MMC) and recent analytical methodologies of hydrophilic interaction liquid chromatography (HILIC), two-dimensional liquid chromatography (2D-LC) mass spectrometry for the characterization of ASO and siRNA modalities. The effects of physicochemical properties of RPLC columns and ion-pair agents on ON separation are specifically addressed with possible future directions for method development provided. Finally, some innovative analytical developments for the analysis of siRNAs and their delivery materials to pave the way toward the use of multi-attribute methods in the near future are discussed.
Collapse
Affiliation(s)
- Alexandre Goyon
- Small Molecules Pharmaceutical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Peter Yehl
- Small Molecules Pharmaceutical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Kelly Zhang
- Small Molecules Pharmaceutical Sciences, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
| |
Collapse
|
27
|
Goyon A, Zhang K. Characterization of Antisense Oligonucleotide Impurities by Ion-Pairing Reversed-Phase and Anion Exchange Chromatography Coupled to Hydrophilic Interaction Liquid Chromatography/Mass Spectrometry Using a Versatile Two-Dimensional Liquid Chromatography Setup. Anal Chem 2020; 92:5944-5951. [DOI: 10.1021/acs.analchem.0c00114] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alexandre Goyon
- Research and Early Development, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Kelly Zhang
- Research and Early Development, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| |
Collapse
|