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Malarvannan M, Ravichandiran V, Paul D. Advances in analytical technologies for emerging drug modalities and their separation challenges in LC-MS systems. J Chromatogr A 2024; 1732:465226. [PMID: 39111181 DOI: 10.1016/j.chroma.2024.465226] [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: 05/31/2024] [Revised: 07/30/2024] [Accepted: 08/01/2024] [Indexed: 08/23/2024]
Abstract
The last few years have seen a rise in the identification and development of bio-therapeutics through the use of cutting-edge delivery methods or bio-formulations, which has created bio-analytical difficulties. Every year, new bio-pharmaceutical product innovations come out, but the analytical development of these products is challenging. Quantifying the products and components of conjugated molecular structures is essential for preclinical and clinical research in order to guide therapeutic development, given their intrinsic complexity. Furthermore, a significant amount of information is needed for the measurement of these unique modalities by LC-MS techniques. Numerous LC-MS based methods have been developed, including AEX-HPLC-MS, RP-IP-LCMS, HILIC-MS, LCHRMS, Microflow-LC-MS, ASMS, Hybrid LBA/LC-MS, and more. However, these methods continue to face problems, prompting the development of alternative approaches. Therefore, developing bio-molecules that are this complicated and, low in concentration requires a skilled LC-MS based approach and knowledgeable personnel. This review covers general novel modalities classifications, sample preparation techniques, current status and bio-analytical strategies for analyzing various novel modalities, including gene bio-therapeutics, oligonucleotides, antibody-drug conjugates, monoclonal antibodies and PROTACs. It also covers how these strategies have been used in the past and how they are being used now to address challenges in the development of LC-MS based methods, as well as improvement strategies, current advancements and recent developed methods. We additionally covered on the benefits and drawbacks of different LC-MS based techniques for the examination of bio-pharmaceutical products and the future perspectives.
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Affiliation(s)
- M Malarvannan
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Maniktala, Kolkata, West Bengal 700054, India
| | - V Ravichandiran
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Maniktala, Kolkata, West Bengal 700054, India
| | - David Paul
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Maniktala, Kolkata, West Bengal 700054, India.
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2
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Zhan Y, Guo J, Hu P, Huang R, Ning J, Bao X, Chen H, Yan Z, Ding L, Shu C. A sensitive analytical strategy of oligonucleotide functionalized fluorescent probes for detection of nusinersen sodium in human serum. Talanta 2024; 275:126153. [PMID: 38692053 DOI: 10.1016/j.talanta.2024.126153] [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: 01/26/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
Abstract
Spinal muscular atrophy (SMA) is a rare autosomal recessive neuromuscular disease. Nusinersen sodium (NS) is the world's first antisense oligonucleotide (ASO) drug for SMA precise targeted therapy. However, the limited half-life of oligonucleotides and their tendency to accumulate in hepatic and renal tissues presented significant challenges for clinical investigation and therapeutic drug monitoring. In this study, we proposed an analytical strategy based on the specific capture of oligonucleotide functionalized fluorescent probes by single stranded binding proteins (SSB) for ultra-sensitive and high-throughput detection of nusinersen sodium in human serum. The magnetic nanoparticles modified with single-strand binding protein (MNPs-SSB) selectively bonded to the red fluorescent quantum dots functionalized with oligonucleotides (RQDs-ssDNA) that were complementary to nusinersen sodium. Upon interaction with nusinersen sodium, RQDs-ssDNA formed a double-stranded complex (RQDs-ssDNA-NS), resulting in enhanced red fluorescence after magnetic separation as it was no longer captured by MNPs-SSB but remained in the supernatant. A quantitative analysis of nusinersen sodium in biological samples was successfully achieved by establishing a relationship between fluorescence intensity and its concentration. The detection signal F/F0 exhibited a linear correlation (R2 = 0.9871) over a wide range from 0.1 nM to 200 nM, with a limit of detection (LOD) of 0.03 nM, demonstrating the high specificity and rapid analysis time (only 30 min). This method provided a novel approach for sensitive, high-throughput, and specific analysis of nusinersen sodium and similar ASO drugs.
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Affiliation(s)
- Yujuan Zhan
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, Nanjing, 210009, China; Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Jingru Guo
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, Nanjing, 210009, China; Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Penghui Hu
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, Nanjing, 210009, China; Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Ruiyan Huang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, Nanjing, 210009, China; Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Jiangyue Ning
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, Nanjing, 210009, China; Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Xingyan Bao
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, Nanjing, 210009, China; Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Haotian Chen
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, Nanjing, 210009, China; Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Zelong Yan
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, Nanjing, 210009, China; Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Li Ding
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, Nanjing, 210009, China; Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Chang Shu
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, Nanjing, 210009, China; Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
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3
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Zhang X, Sha C, Zhang W, Zhao F, Zhu M, Leng G, Liu W. Development, validation and application of an ion-pair reversed-phase liquid chromatography-tandem mass spectrometry method for the quantification of nusinersen. Bioanalysis 2024; 16:305-317. [PMID: 38334103 DOI: 10.4155/bio-2023-0218] [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] [Indexed: 02/10/2024] Open
Abstract
Background: The fully phosphorothioate-modified oligonucleotide (OGN) nusinersen has low ionization efficiency in the negative ion mode, resulting in a low mass spectrometry response. There have been no relevant reports on developing a LC-MS method for the determination of nusinersen by optimizing mobile phase composition. Materials & methods: Mobile phase additives comprised of 15 mM triethylamine/25 mM 1,1,1,3,3,3-hexafluoro-2-propanol with a pH of 9.6. Nusinersen was extracted from plasma using Oasis® HLB solid-phase extraction (Waters, MA, USA). Results & conclusion: By adjusting the pH of the mobile phase to 9.6 by optimizing the type and concentration of ion-pair reagents, a high mass spectrometry response was obtained. The developed method was applied to nusinersen and met the requirements for the pharmacokinetic study of nusinersen in rabbits.
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Affiliation(s)
- Xiao Zhang
- School of Pharmacy, Key Laboratory of Molecular Pharmacology & Drug Evaluation (Yantai University), Yantai University, Yantai, 264005, China
| | - Chunjie Sha
- Department of Traditional Chinese Medicine, Shandong College of Traditional Chinese Medicine, Yantai, China
| | - Wei Zhang
- National Key Laboratory of Advanced Drug Delivery & Release Systems, Luye Pharmaceutical Group, Yantai, China
| | - Fengjuan Zhao
- National Key Laboratory of Advanced Drug Delivery & Release Systems, Luye Pharmaceutical Group, Yantai, China
| | - Mingli Zhu
- National Key Laboratory of Advanced Drug Delivery & Release Systems, Luye Pharmaceutical Group, Yantai, China
| | - Guangyi Leng
- National Key Laboratory of Advanced Drug Delivery & Release Systems, Luye Pharmaceutical Group, Yantai, China
| | - Wanhui Liu
- School of Pharmacy, Key Laboratory of Molecular Pharmacology & Drug Evaluation (Yantai University), Yantai University, Yantai, 264005, China
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4
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Lippens JL, Timmons HC, Welch C, Kulkarni A, Flick TG. Rapid Intact Mass Analysis and Evaluation of the Separation Potential of Microfluidic Capillary Electrophoresis Mass Spectrometry for Oligonucleotides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2491-2497. [PMID: 37823612 DOI: 10.1021/jasms.3c00217] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Oligonucleotide characterization is a rapidly advancing field in the biopharmaceutical industry. Understanding critical quality attributes, such as intact mass and impurities, requires a toolbox of analytical techniques, which commonly includes liquid chromatography-mass spectrometry (LC-MS). Oligonucleotide LC-MS analysis frequently requires sample run times upward of 15 min to achieve separation of multiple oligonucleotide species. Additionally, LC methods frequently employ mobile phase additives such as triethylamine and 1,1,1,3,3,3-hexafluoro-2-propanol that are not always desired for use in MS instrumentation. Here, microfluidic capillary electrophoresis mass spectrometry (CE-MS) via ZipChip technology was employed to enable rapid intact mass analysis of oligonucleotide single strands. Baseline separation of equal length oligonucleotides was achieved in less than 4 min. Additionally, the potential of the ZipChip platform for separation of oligonucleotide full-length products (FLPs) and their impurities was evaluated.
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Affiliation(s)
- Jennifer L Lippens
- Pivotal Attribute Sciences, Amgen, Thousand Oaks, California 91320, United States
| | - Heath C Timmons
- Pivotal Attribute Sciences, Amgen, Thousand Oaks, California 91320, United States
| | - Crystal Welch
- 908 Devices, Boston, Massachusetts 94720-1460, United States
| | - Aditya Kulkarni
- 908 Devices, Boston, Massachusetts 94720-1460, United States
| | - Tawnya G Flick
- Pivotal Attribute Sciences, Amgen, Thousand Oaks, California 91320, United States
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5
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Gawlig C, Hanci G, Rühl M. Quantification of Oligonucleotides Using Tandem Mass Spectrometry with Isobaric Internal Standards. Int J Mol Sci 2023; 24:14691. [PMID: 37834137 PMCID: PMC10573027 DOI: 10.3390/ijms241914691] [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: 08/28/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
In recent years, oligonucleotides have become more important in research, drug approvals and medical therapies. Due to this growing interest in pharmaceutical applications, it is essential to develop reliable analytical methods for this substance class. In this work, we present a quantification method using liquid chromatography coupled with tandem mass spectrometry by applying an isobaric oligonucleotide standard. In addition to a proof of principle, we perform a method qualification to assess its readiness for validation according to ICH Q2 guidelines. In addition to good linearity, sensitivity, accuracy and recovery, the method showed no significant matrix effects. Furthermore, we demonstrated the application of the method by applying the quantification in a biological matrix, as well as an exemplary degradation of an oligonucleotide in bovine plasma.
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Affiliation(s)
| | | | - Michael Rühl
- BioSpring GmbH, Alt Fechenheim 34, 60386 Frankfurt am Main, Germany; (C.G.); (G.H.)
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6
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A Novel Hybridization LC-MS/MS Methodology for Quantification of siRNA in Plasma, CSF and Tissue Samples. Molecules 2023; 28:molecules28041618. [PMID: 36838605 PMCID: PMC9967190 DOI: 10.3390/molecules28041618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 02/10/2023] Open
Abstract
Therapeutic oligonucleotides, such as antisense oligonucleotide (ASO) and small interfering RNA (siRNA), are a new class of therapeutics rapidly growing in drug discovery and development. A sensitive and reliable method to quantify oligonucleotides in biological samples is critical to study their pharmacokinetic and pharmacodynamic properties. Hybridization LC-MS/MS was recently established as a highly sensitive and specific methodology for the quantification of single-stranded oligonucleotides, e.g., ASOs, in various biological matrices. However, there is no report of this methodology for the bioanalysis of double-stranded oligonucleotides (e.g., siRNA). In this work, we investigated hybridization LC-MS/MS methodology for the quantification of double-stranded oligonucleotides in biological samples using an siRNA compound, siRNA-01, as the test compound. The commonly used DNA capture probe and a new peptide nucleic acid (PNA) probe were compared for the hybridization extraction of siRNA-01 under different conditions. The PNA probe achieved better extraction recovery than the DNA probe, especially for high concentration samples, which may be due to its stronger hybridization affinity. The optimized hybridization method using the PNA probe was successfully qualified for the quantitation of siRNA-01 in monkey plasma, cerebrospinal fluid (CSF), and tissue homogenates over the range of 2.00-1000 ng/mL. This work is the first report of the hybridization LC-MS/MS methodology for the quantification of double-stranded oligonucleotides. The developed methodology will be applied to pharmacokinetic and toxicokinetic studies of siRNA-01. This novel methodology can also be used for the quantitative bioanalysis of other double-stranded oligonucleotides.
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7
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Goto A, Yamamoto S, Iwasaki S. Biodistribution and delivery of oligonucleotide therapeutics to the central nervous system: Advances, challenges, and future perspectives. Biopharm Drug Dispos 2023; 44:26-47. [PMID: 36336817 DOI: 10.1002/bdd.2338] [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: 08/31/2022] [Revised: 10/27/2022] [Accepted: 10/29/2022] [Indexed: 11/09/2022]
Abstract
Considerable advances have been made in the research and development of oligonucleotide therapeutics (OTs) for treating central nervous system (CNS) diseases, such as psychiatric and neurodegenerative disorders, because of their promising mode of action. However, due to the tight barrier function and complex physiological structure of the CNS, the efficient delivery of OTs to target the brain has been a major challenge, and intensive efforts have been made to overcome this limitation. In this review, we summarize the representative methodologies and current knowledge of biodistribution, along with the pharmacokinetic/pharmacodynamic (PK/PD) relationship of OTs in the CNS, which are critical elements for the successful development of OTs for CNS diseases. First, quantitative bioanalysis methods and imaging-based approaches for the evaluation of OT biodistribution are summarized. Next, information available on the biodistribution profile, distribution pathways, quantitative PK/PD modeling, and simulation of OTs following intrathecal or intracerebroventricular administration are reviewed. Finally, the latest knowledge on the drug delivery systems to the brain via intranasal or systemic administration as noninvasive routes for improved patient quality of life is reviewed. The aim of this review is to enrich research on the successful development of OTs by clarifying OT distribution profiles and pathways to the target brain regions or cells, and by identifying points that need further investigation for a mechanistic approach to generate efficient OTs.
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Affiliation(s)
- Akihiko Goto
- Drug Metabolism and Pharmacokinetics Research Laboratories, Preclinical and Translational Sciences, Research, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Syunsuke Yamamoto
- Drug Metabolism and Pharmacokinetics Research Laboratories, Preclinical and Translational Sciences, Research, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Shinji Iwasaki
- Drug Metabolism and Pharmacokinetics Research Laboratories, Preclinical and Translational Sciences, Research, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
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8
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Investigation of the Influence of Charge State and Collision Energy on Oligonucleotide Fragmentation by Tandem Mass Spectrometry. Molecules 2023; 28:molecules28031169. [PMID: 36770836 PMCID: PMC9921629 DOI: 10.3390/molecules28031169] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/20/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023] Open
Abstract
Due to the increasing pharmaceutical interest of oligonucleotides, for example in antisense therapy and vaccines, their analytical characterization is of fundamental importance due to their complex structure. For this purpose, mass spectrometry is a viable tool for structural studies of nucleic acids. Structural information regarding the primary sequence of a nucleic acid can reliably be gained via tandem mass spectrometry (MSMS) fragmentation. In this work, we present the characteristic fragmentation behavior of short-chain oligonucleotides (15-35 nucleotides) with respect to the collision-induced dissociation (CID) voltage used. The relationship and influence of the length of the oligonucleotide and its charge state is also discussed. The results presented here can be helpful for estimating the required fragmentation energies of short-chain oligonucleotides and their sequencing.
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9
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Bioanalysis of Oligonucleotide by LC-MS: Effects of Ion Pairing Regents and Recent Advances in Ion-Pairing-Free Analytical Strategies. Int J Mol Sci 2022; 23:ijms232415474. [PMID: 36555119 PMCID: PMC9779676 DOI: 10.3390/ijms232415474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 12/12/2022] Open
Abstract
Oligonucleotides (OGNs) are relatively new modalities that offer unique opportunities to expand the therapeutic targets. Reliable and high-throughput bioanalytical methods are pivotal for preclinical and clinical investigations of therapeutic OGNs. Liquid chromatography-mass spectrometry (LC-MS) is now evolving into being the method of choice for the bioanalysis of OGNs. Ion paring reversed-phase liquid chromatography (IP-RPLC) has been widely used in sample preparation and LC-MS analysis of OGNs; however, there are technical issues associated with these methods. IP-free methods, such as hydrophilic interaction liquid chromatography (HILIC) and anion-exchange techniques, have emerged as promising approaches for the bioanalysis of OGNs. In this review, the state-of-the-art IP-RPLC-MS bioanalytical methods of OGNs and their metabolites published in the past 10 years (2012-2022) are critically reviewed. Recent advances in IP-reagent-free LC-MS bioanalysis methods are discussed. Finally, we describe future opportunities for developing new methods that can be used for the comprehensive bioanalysis of OGNs.
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10
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Thevis M, Piper T, Thomas A. Recent advances in identifying and utilizing metabolites of selected doping agents in human sports drug testing. J Pharm Biomed Anal 2021; 205:114312. [PMID: 34391136 DOI: 10.1016/j.jpba.2021.114312] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 12/29/2022]
Abstract
Probing for evidence of the administration of prohibited therapeutics, drugs and/or drug candidates as well as the use of methods of doping in doping control samples is a central assignment of anti-doping laboratories. In order to accomplish the desired analytical sensitivity, retrospectivity, and comprehensiveness, a considerable portion of anti-doping research has been invested into studying metabolic biotransformation and elimination profiles of doping agents. As these doping agents include lower molecular mass drugs such as e.g. stimulants and anabolic androgenic steroids, some of which further necessitate the differentiation of their natural/endogenous or xenobiotic origin, but also higher molecular mass substances such as e.g. insulins, growth hormone, or siRNA/anti-sense oligonucleotides, a variety of different strategies towards the identification of employable and informative metabolites have been developed. In this review, approaches supporting the identification, characterization, and implementation of metabolites exemplified by means of selected doping agents into routine doping controls are presented, and challenges as well as solutions reported and published between 2010 and 2020 are discussed.
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Affiliation(s)
- Mario Thevis
- Center for Preventive Doping Research - Institute of Biochemistry, German Sport University Cologne, Am Sportpark Müngersdorf 6, 50933, Cologne, Germany; European Monitoring Center for Emerging Doping Agents (EuMoCEDA), Cologne, Bonn, Germany.
| | - Thomas Piper
- Center for Preventive Doping Research - Institute of Biochemistry, German Sport University Cologne, Am Sportpark Müngersdorf 6, 50933, Cologne, Germany
| | - Andreas Thomas
- Center for Preventive Doping Research - Institute of Biochemistry, German Sport University Cologne, Am Sportpark Müngersdorf 6, 50933, Cologne, Germany
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11
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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.
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Affiliation(s)
- Inês C Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas, USA
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12
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Mukai H, Watanabe Y. Review: PET imaging with macro- and middle-sized molecular probes. Nucl Med Biol 2021; 92:156-170. [PMID: 32660789 DOI: 10.1016/j.nucmedbio.2020.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/22/2020] [Accepted: 06/22/2020] [Indexed: 12/16/2022]
Abstract
Recent progress in radiolabeling of macro- and middle-sized molecular probes has been extending possibilities to use PET molecular imaging for dynamic application to drug development and therapeutic evaluation. Theranostics concept also accelerated the use of macro- and middle-sized molecular probes for sharpening the contrast of proper target recognition even the cellular types/subtypes and proper selection of the patients who should be treated by the same molecules recognition. Here, brief summary of the present status of immuno-PET, and then further development of advanced technologies related to immuno-PET, peptidic PET probes, and nucleic acids PET probes are described.
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Affiliation(s)
- Hidefumi Mukai
- Laboratory for Molecular Delivery and Imaging Technology, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
| | - Yasuyoshi Watanabe
- Laboratory for Pathophysiological and Health Science, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
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13
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Kilanowska A, Studzińska S. In vivo and in vitro studies of antisense oligonucleotides - a review. RSC Adv 2020; 10:34501-34516. [PMID: 35514414 PMCID: PMC9056844 DOI: 10.1039/d0ra04978f] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/06/2020] [Indexed: 01/22/2023] Open
Abstract
The potential of antisense oligonucleotides in gene silencing was discovered over 40 years ago, which resulted in the growing interest in their chemistry, mechanism of action, and metabolic pathways. This review summarizes the selected mechanisms of antisense drug action, as well as therapeutics which are to date approved by the Food and Drug Administration and European Medicines Agency. Moreover, bioanalytical methods used for ASO pharmacokinetics and metabolism studies are briefly summarized. Special attention is paid to the primary pharmacokinetic properties of the different chemistry classes of antisense oligonucleotides. Moreover, in vivo and in vitro metabolic pathways of these compounds are widely described with the emphasis on the different animal models as well as in vitro models, including tissues homogenates, enzyme solutions, and human liver microsomes.
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Affiliation(s)
- Anna Kilanowska
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń 7 Gagarin Str. PL-87-100 Toruń Poland +48 56 6114837 +48 56 6114308
| | - Sylwia Studzińska
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń 7 Gagarin Str. PL-87-100 Toruń Poland +48 56 6114837 +48 56 6114308
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14
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Kilanowska A, Nuckowski Ł, Studzińska S. Studying in vitro metabolism of the first and second generation of antisense oligonucleotides with the use of ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. Anal Bioanal Chem 2020; 412:7453-7467. [PMID: 32856108 PMCID: PMC7533254 DOI: 10.1007/s00216-020-02878-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/17/2020] [Accepted: 08/11/2020] [Indexed: 12/25/2022]
Abstract
The aim of the present investigation was the analysis and identification of antisense oligonucleotide metabolism products after incubation with human liver microsomes regarding four different oligonucleotide modifications. Separation and detection methods based on the use of liquid chromatography coupled with quadrupole time-of-flight mass spectrometry were developed for this purpose. Firstly, the optimization of mass spectrometer parameters was done to select those which ensure the highest possible sensitivity of oligonucleotide analysis. This step was conducted for two chromatographic modes-ion pair chromatography and hydrophilic interaction liquid chromatography-due to their common application in oligonucleotide analysis. Based on sensitivity results, ion pair chromatography coupled with mass spectrometry was selected for the separation of model oligonucleotide mixtures in order to verify its selectivity for N-deleted metabolite separation. Next, the developed method was applied in the examination of oligonucleotides in vitro metabolism. First, wide optimization of incubation parameters was conducted including the concentration of the reaction buffer components. Obtained results indicated that both 3'-exonucleases and 5'-exonucleases contributed to the biotransformation of oligonucleotides. Moreover, it may be concluded that the number of metabolites depends on oligonucleotide modification and consequently its resistance to enzymatic attack. Thus, the number of the oligonucleotide metabolites decreased with the decrease of the resultant polarity of oligonucleotide caused by chemical modification. Graphical abstract.
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Affiliation(s)
- Anna Kilanowska
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin Str., PL-87-100, Toruń, Poland
| | - Łukasz Nuckowski
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin Str., PL-87-100, Toruń, Poland
| | - Sylwia Studzińska
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin Str., PL-87-100, Toruń, Poland.
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15
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Liu R, Luo Q, Liu Z, Gong L. Optimizing sample preparation workflow for bioanalysis of oligonucleotides through liquid chromatography tandem mass spectrometry. J Chromatogr A 2020; 1629:461473. [PMID: 32841769 DOI: 10.1016/j.chroma.2020.461473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/08/2020] [Accepted: 08/10/2020] [Indexed: 10/23/2022]
Abstract
Liquid chromatography tandem mass spectrometry has been a widely used technique for quantifying oligonucleotides in biological samples. However, lack of simple and efficient sample cleanup approach remains a challenge. Our study aimed to evaluate the major factors during the sample pretreatment process for developing optimal sample preparation workflow for oligonucleotides. In this study, we have employed a model formed with rat plasma containing a 16 mer oligonucleotide standard in order to comprehensively optimize the sample preparation procedures. These included liquid-liquid extraction (LLE), solid-phase extraction (SPE), protein precipitation (PPT) and LLE combined with SPE. LLE with phenol: dichloromethane (2:1, v:v) was found to be the most efficient sample cleanup procedure with low cost and less toxicity. Followed by the extraction, ethanol precipitation (-80 °C, 5 min) was determined to be the optimal drying conditions. Also, mass spectrometric parameters were tuned to optimal conditions. It was found that the central composite design suite was proved to be highly practical for optimizing MS parameters. Finally, the thoroughly optimized sample preparation workflow was fully validated. The developed assay provided a quantitative range of 0.25-1000 nM, with accuracy and precision were < 7.45% and < 12.20%, respectively. Matrix effect and carryover were also evaluated and no significant effect was observed.
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Affiliation(s)
- Rong Liu
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, PR China
| | - Qing Luo
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, PR China
| | - Zhongqiu Liu
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, PR China
| | - Lingzhi Gong
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, PR China.
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16
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Li P, Gong Y, Kim J, Liu X, Gilbert J, Kerns HM, Groth R, Rooney M. Hybridization Liquid Chromatography-Tandem Mass Spectrometry: An Alternative Bioanalytical Method for Antisense Oligonucleotide Quantitation in Plasma and Tissue Samples. Anal Chem 2020; 92:10548-10559. [PMID: 32628461 DOI: 10.1021/acs.analchem.0c01382] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Quantitative bioanalysis in plasma and tissues samples is required to study the pharmacokinetic and pharmacodynamic properties of antisense oligonucleotides (ASOs). To overcome intrinsic drawbacks in specificity, sensitivity, and throughput of traditional ligand-binding assay (LBA) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) methods, an alternative bioanalytical method was developed by combining oligonucleotide hybridization and LC-MS/MS technologies. Target ASOs were extracted from biological samples by hybridization with biotinylated sense-strand oligonucleotides coupled to streptavidin magnetic beads. Using ion-pairing chromatography and tandem mass spectrometry, this method demonstrated high sensitivity (0.5 ng/mL using 100 μL of plasma), high specificity, wide linear range, complete automation, and generic applications in tests with multiple ASOs. The typical challenge of sensitivity drop in traditional ion-pairing LC-MS/MS was for the first time overcome by the introduction of a ternary pump system. Due to the high specificity, quantitation in various biological matrixes was achieved using calibration standards in plasma, largely improving efficiency and consistency. Another major advantage was the capability of simultaneous quantitation of ASO metabolites. The hybridization LC-MS/MS was considered an improved alternative for quantitation of ASOs and metabolites in plasma and tissue samples, showing a great potential to replace traditional LBA and LC-MS/MS methods.
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Affiliation(s)
- Pei Li
- Drug Metabolism and Pharmacokinetics, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Yuqing Gong
- Drug Metabolism and Pharmacokinetics, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Jaeah Kim
- Atrium Staffing, 361 Newbury Street, Fifth Floor, Boston, Massachusetts 02116, United States
| | - Xingrong Liu
- Drug Metabolism and Pharmacokinetics, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - James Gilbert
- External Innovations and New Indications, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Hannah M Kerns
- External Innovations and New Indications, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Rachel Groth
- External Innovations and New Indications, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Michael Rooney
- Drug Metabolism and Pharmacokinetics, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
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17
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Application of hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry for the retention and sensitivity studies of antisense oligonucleotides. J Chromatogr A 2020; 1622:461100. [PMID: 32359780 DOI: 10.1016/j.chroma.2020.461100] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/30/2020] [Accepted: 03/31/2020] [Indexed: 11/20/2022]
Abstract
The aim of the present investigation was application of hydrophilic interaction liquid chromatography as an alternative chromatographic approach for the study of antisense oligonucleotides. The influence of several mobile phases, differing with the salt type, their concentration and pH value on the retention and the separation of antisense oligonucleotides has been examined for this purpose. Four different stationary phases were also applied including unmodified silica, silica modified with the use of sulfobetaine groups, polyhydroxy and aminopropyl groups. Such wide range of tested conditions has been useful in better understanding of the retention mechanism of tested compounds. The results obtained during this investigation indicated that greater retention, greater peaks symmetry, as well as more effective separation of oligonucleotides, were obtained for the zwitterionic stationary phase. Moreover, the optimization of tandem mass spectrometry parameters with the use of Central Composite Design was performed and different mobile phases were tested to choose that one, which provided the greatest antisense oligonucleotides peak areas in Multiple Reaction Monitoring mode and consequently, the greatest possible sensitivity. Hydrophilic interaction liquid chromatography was compared with the ion pair chromatography, commonly used in the analysis of oligonucleotides. Both techniques were compared in terms of selectivity of separation as well as the sensitivity of their determination. Obtained results proved that ion pair chromatography provided better results in terms of separation efficiency and peak areas in Multiple Reaction Monitoring for tested conditions. However, these results do not preclude application of hydrophilic interaction liquid chromatography as an alternative chromatographic approach for the oligonucleotides analysis especially when a mobile phase without ion pair reagents is required.
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18
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Discovery of a novel deaminated metabolite of a single-stranded oligonucleotide in vivo by mass spectrometry. Bioanalysis 2020; 11:1955-1965. [PMID: 31829055 DOI: 10.4155/bio-2019-0118] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Aim: A novel single-stranded deaminated oligonucleotide metabolite resulting from a REVERSIR™ oligonucleotide was discovered and identified in monkey liver after subcutaneous administration. Results & methodology: REVERSIR-A and its metabolites were extracted from biological matrices by solid phase extraction and analyzed using LC coupled with high-resolution MS under negative ionization mode. A novel 9-mer metabolite of REVERSIR-A, resulting from deamination of the 3' terminal 2'-O-methyl-adenosine nucleotide to 2'-O-methyl-inosine, was discovered at significant levels in monkey liver. The metabolite's identity was confirmed by LC-MS/MS. Conclusion: This report describes the first observation of a long-chain deaminated metabolite of a single-stranded REVERSIR oligonucleotide in vivo in monkey liver.
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19
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Oligonucleotide quantification and metabolite profiling by high-resolution and accurate mass spectrometry. Bioanalysis 2020; 11:1967-1980. [PMID: 31829056 DOI: 10.4155/bio-2019-0137] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Aim: Advancements in RNA interference therapeutics have triggered development of improved bioanalytical methods for oligonucleotide metabolite profiling and high-throughput quantification in biological matrices. Results & methodology: HPLC coupled with high-resolution mass spectrometry (LC-HRMS) methods were developed to investigate the metabolism of a REVERSIR™ molecule in vivo. Plasma and tissue samples were extracted using solid-phase extraction followed by LC-HRMS analysis for metabolite profiling and quantification. The method was qualified from 10 to 5000 ng/ml (plasma) and 100 to 50000 ng/g (liver and kidney). In rat liver, intra and interday accuracy ranged from 80.9 to 118.5% and 88.4 to 111.9%, respectively, with acceptable precision (<20% CV). Conclusion: The LC-HRMS method can be applied for metabolite profiling and quantification of oligonucleotides in biological matrices.
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20
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Castellanos-Rizaldos E, Brown CR, Dennin S, Kim J, Gupta S, Najarian D, Gu Y, Aluri K, Enders J, Brown K, Xu Y. RT-qPCR Methods to Support Pharmacokinetics and Drug Mechanism of Action to Advance Development of RNAi Therapeutics. Nucleic Acid Ther 2020; 30:133-142. [PMID: 32202961 DOI: 10.1089/nat.2019.0840] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The goal of this study was to develop a reverse transcription quantitative polymerase chain reaction (RT-qPCR) method for the accurate quantification of chemically modified small interfering RNA (siRNA) including but not restricted to thermally destabilizing modifications such as glycol nucleic acid (GNA). RT-qPCR was found to be superior to mass spectrometry-based siRNA detection in terms of sensitivity and throughput. However, mass spectrometry is still the preferred method when specific metabolite detection is required and is also insensitive to siRNA chemical modifications such as GNA. The RT-qPCR approach can be optimized to take chemical modifications into account and works robustly in different matrices without optimization, unlike mass spectrometry. RT-qPCR and mass spectrometry both have their strengths and weaknesses for the detection of siRNA and must be used appropriately depending on the questions at hand. Considerations such as desired throughput, assay sensitivity, and metabolite identification must be weighed when choosing which methodology to apply.
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Affiliation(s)
| | | | - Sean Dennin
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts, USA
| | - Joohwan Kim
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts, USA
| | - Swati Gupta
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts, USA
| | - Diana Najarian
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts, USA
| | - Yongli Gu
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts, USA
| | - Krishna Aluri
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts, USA
| | - Jennifer Enders
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts, USA
| | - Kirk Brown
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts, USA
| | - Yuanxin Xu
- Alnylam Pharmaceuticals, Inc., Cambridge, Massachusetts, USA
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21
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Pendergraff H, Schmidt S, Vikeså J, Weile C, Øverup C, W. Lindholm M, Koch T. Nuclear and Cytoplasmatic Quantification of Unconjugated, Label-Free Locked Nucleic Acid Oligonucleotides. Nucleic Acid Ther 2020; 30:4-13. [PMID: 31618108 PMCID: PMC6987631 DOI: 10.1089/nat.2019.0810] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 08/28/2019] [Indexed: 12/23/2022] Open
Abstract
Methods for the quantification of antisense oligonucleotides (AONs) provide insightful information on biodistribution and intracellular trafficking. However, the established methods have not provided information on the absolute number of molecules in subcellular compartments or about how many AONs are needed for target gene reduction for unconjugated AONs. We have developed a new method for nuclear AON quantification that enables us to determine the absolute number of AONs per nucleus without relying on AON conjugates such as fluorophores that may alter AON distribution. This study describes an alternative and label-free method using subcellular fractionation, nucleus counting, and locked nucleic acid (LNA) sandwich enzyme-linked immunosorbent assay to quantify absolute numbers of oligonucleotides in nuclei. Our findings show compound variability (diversity) by which 247,000-693,000 LNAs/nuclei results in similar target reduction for different compounds. This method can be applied to any antisense drug discovery platform providing information on specific and clinically relevant AONs. Finally, this method can directly compare nuclear entry of AON with target gene knockdown for any compound design and nucleobase sequence, gene target, and phosphorothioate stereochemistry.
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Affiliation(s)
- Hannah Pendergraff
- Roche Pharma Research and Early Development, RNA Therapeutics Research, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Steffen Schmidt
- Roche Pharma Research and Early Development, RNA Therapeutics Research, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Jonas Vikeså
- Roche Pharma Research and Early Development, RNA Therapeutics Research, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Christian Weile
- Roche Pharma Research and Early Development, RNA Therapeutics Research, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Charlotte Øverup
- Roche Pharma Research and Early Development, RNA Therapeutics Research, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Marie W. Lindholm
- Roche Pharma Research and Early Development, RNA Therapeutics Research, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Troels Koch
- Roche Pharma Research and Early Development, RNA Therapeutics Research, Roche Innovation Center Copenhagen, Hørsholm, Denmark
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22
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Kim J, Basiri B, Hassan C, Punt C, van der Hage E, den Besten C, Bartlett MG. Metabolite Profiling of the Antisense Oligonucleotide Eluforsen Using Liquid Chromatography-Mass Spectrometry. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 17:714-725. [PMID: 31422288 PMCID: PMC6704339 DOI: 10.1016/j.omtn.2019.07.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 11/26/2022]
Abstract
Eluforsen (previously known as QR-010) is a 33-mer 2′-O-methyl modified phosphorothioate antisense oligonucleotide targeting the F508del mutation in the gene encoding CFTR protein of cystic fibrosis patients. In this study, eluforsen was incubated with endo- and exonucleases and mouse liver homogenates to elucidate its in vitro metabolism. Mice and monkeys were used to determine in vivo liver and lung metabolism of eluforsen following inhalation. We developed a liquid chromatography-mass spectrometry method for the identification and semi-quantitation of the metabolites of eluforsen and then applied the method for in vitro and in vivo metabolism studies. Solid-phase extraction was used following proteinase K digestion for sample preparation. Chain-shortened metabolites of eluforsen by 3′ exonuclease were observed in mouse liver in an in vitro incubation system and by either 3′ exonuclease or 5′ exonuclease in liver and lung samples from an in vivo mouse and monkey study. This study provides approaches for further metabolite characterization of 2′-ribose-modified phosphorothioate oligonucleotides in in vitro and in vivo studies to support the development of oligonucleotide therapeutics.
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Affiliation(s)
- Jaeah Kim
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602-2352, USA
| | - Babak Basiri
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602-2352, USA
| | | | - Carine Punt
- ProQR Therapeutics N.V., Leiden, the Netherlands
| | | | | | - Michael G Bartlett
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602-2352, USA.
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23
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Kaczmarkiewicz A, Nuckowski Ł, Studzińska S. Analysis of the first and second generation of antisense oligonucleotides in serum samples with the use of ultra high performance liquid chromatography coupled with tandem mass spectrometry. Talanta 2019; 196:54-63. [DOI: 10.1016/j.talanta.2018.12.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 12/05/2018] [Accepted: 12/10/2018] [Indexed: 12/22/2022]
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24
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Palazzolo A, Feuillastre S, Pfeifer V, Garcia‐Argote S, Bouzouita D, Tricard S, Chollet C, Marcon E, Buisson D, Cholet S, Fenaille F, Lippens G, Chaudret B, Pieters G. Efficient Access to Deuterated and Tritiated Nucleobase Pharmaceuticals and Oligonucleotides using Hydrogen-Isotope Exchange. Angew Chem Int Ed Engl 2019; 58:4891-4895. [PMID: 30768844 PMCID: PMC6593778 DOI: 10.1002/anie.201813946] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/13/2019] [Indexed: 01/01/2023]
Abstract
A general approach for the efficient hydrogen-isotope exchange of nucleobase derivatives is described. Catalyzed by ruthenium nanoparticles, using mild reaction conditions, and involving either D2 or T2 as isotopic sources, this reaction possesses a wide substrate scope and a high solvent tolerability. This novel method facilitates the access to essential diagnostic tools in drug discovery and development: tritiated pharmaceuticals with high specific activities and deuterated oligonucleotides suitable for use as internal standards during LC-MS quantification.
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Affiliation(s)
| | | | - Viktor Pfeifer
- SCBM, CEAUniversité Paris Saclay91191Gif-sur-YvetteFrance
| | | | - Donia Bouzouita
- LPCNO; Laboratoire de Physique et Chimie de Nano-Objets, UMR 5215 INSA-CNRS-UPSInstitut National des Sciences Appliquées135, Avenue de Rangueil31077ToulouseFrance
| | - Simon Tricard
- LPCNO; Laboratoire de Physique et Chimie de Nano-Objets, UMR 5215 INSA-CNRS-UPSInstitut National des Sciences Appliquées135, Avenue de Rangueil31077ToulouseFrance
| | - Céline Chollet
- SCBM, CEAUniversité Paris Saclay91191Gif-sur-YvetteFrance
| | - Elodie Marcon
- SCBM, CEAUniversité Paris Saclay91191Gif-sur-YvetteFrance
| | | | - Sophie Cholet
- Service de Pharmacologie et d'Immunoanalyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRAUniversité Paris Saclay, MetaboHUB91191Gif-sur-YvetteFrance
| | - François Fenaille
- Service de Pharmacologie et d'Immunoanalyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRAUniversité Paris Saclay, MetaboHUB91191Gif-sur-YvetteFrance
| | - Guy Lippens
- LISBPUniversité de Toulouse, CNRS, INRA, INSA, UPS135 avenue de Rangueil31077ToulouseFrance
| | - Bruno Chaudret
- LPCNO; Laboratoire de Physique et Chimie de Nano-Objets, UMR 5215 INSA-CNRS-UPSInstitut National des Sciences Appliquées135, Avenue de Rangueil31077ToulouseFrance
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25
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Palazzolo A, Feuillastre S, Pfeifer V, Garcia‐Argote S, Bouzouita D, Tricard S, Chollet C, Marcon E, Buisson D, Cholet S, Fenaille F, Lippens G, Chaudret B, Pieters G. Efficient Access to Deuterated and Tritiated Nucleobase Pharmaceuticals and Oligonucleotides using Hydrogen‐Isotope Exchange. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201813946] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | | | - Viktor Pfeifer
- SCBM, CEAUniversité Paris Saclay 91191 Gif-sur-Yvette France
| | | | - Donia Bouzouita
- LPCNO; Laboratoire de Physique et Chimie de Nano-Objets, UMR 5215 INSA-CNRS-UPSInstitut National des Sciences Appliquées 135, Avenue de Rangueil 31077 Toulouse France
| | - Simon Tricard
- LPCNO; Laboratoire de Physique et Chimie de Nano-Objets, UMR 5215 INSA-CNRS-UPSInstitut National des Sciences Appliquées 135, Avenue de Rangueil 31077 Toulouse France
| | - Céline Chollet
- SCBM, CEAUniversité Paris Saclay 91191 Gif-sur-Yvette France
| | - Elodie Marcon
- SCBM, CEAUniversité Paris Saclay 91191 Gif-sur-Yvette France
| | | | - Sophie Cholet
- Service de Pharmacologie et d'Immunoanalyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRAUniversité Paris Saclay, MetaboHUB 91191 Gif-sur-Yvette France
| | - François Fenaille
- Service de Pharmacologie et d'Immunoanalyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRAUniversité Paris Saclay, MetaboHUB 91191 Gif-sur-Yvette France
| | - Guy Lippens
- LISBPUniversité de Toulouse, CNRS, INRA, INSA, UPS 135 avenue de Rangueil 31077 Toulouse France
| | - Bruno Chaudret
- LPCNO; Laboratoire de Physique et Chimie de Nano-Objets, UMR 5215 INSA-CNRS-UPSInstitut National des Sciences Appliquées 135, Avenue de Rangueil 31077 Toulouse France
| | - Grégory Pieters
- SCBM, CEAUniversité Paris Saclay 91191 Gif-sur-Yvette France
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Application of Locked Nucleic Acid Oligonucleotides for siRNA Preclinical Bioanalytics. Sci Rep 2019; 9:3566. [PMID: 30837588 PMCID: PMC6401054 DOI: 10.1038/s41598-019-40187-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 02/06/2019] [Indexed: 12/21/2022] Open
Abstract
Despite the exquisite potential of siRNA as a therapeutic, the mechanism(s) responsible for the robust indirect exposure-response relationships have not been fully elucidated. To understand the siRNA properties linked to potent activity, requires the disposition of siRNA to be characterized. A technical challenge in the characterization is the detection and quantitation of siRNA from biological samples. Described herein, a Locked Nucleic Acid (LNA) Hybridization-Ligation ECL ELISA was designed for ultra-sensitive quantification of both sense and antisense strands of siRNA independent of structural modifica-tions. This assay was applied to measure siRNA in serum and tissue homogenate in preclinical species. We observed rapid clearance of siRNA from the systemic circulation which contrasted the prolonged accumulation within the tissue. The assay was also able to distinguish and quantify free siRNA from RNA-induced silencing complex (RISC) and Argonaute 2 (Ago2) associated with therapeutic siRNA. We utilized an orthogonal method, LC-MS, to investigate 3′ exonuclease activity toward the antisense strand metabolism. Taken together, we have demonstrated that the LNA Hybridization-Ligation ECL ELISA is arobust analytical method with direct application to measuring the exposure of siRNA therapeutics seamlessly across biological matrices.
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27
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Montevecchi G, Setti L, Olmi L, Buti M, Laviano L, Antonelli A, Sgarbi E. Determination of Free Soluble Phenolic Compounds in Grains of Ancient Wheat Varieties ( Triticum sp. pl.) by Liquid Chromatography-Tandem Mass Spectrometry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:201-212. [PMID: 30525569 DOI: 10.1021/acs.jafc.8b05629] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A method of liquid chromatography coupled with tandem mass spectrometry was developed and validated for the determination of free soluble phenolic compounds in eight ancient varieties of wheat ( Triticum sp. pl.): Autonomia, Gentil rosso, Inallettabile, Leone aristato, Mentana, Poulard di Ciano, Risciola, and Terminillo. Trace compounds such as two conjugated flavones, vitexin (17.13-34.32 μg/kg) and isovitexin (9.76-30.01 μg/kg), were also determined. Poulard di Ciano, presumably an autochthonous wheat of the Reggio Emilia province (northern Italy), showed a peculiar quali/quantitative phenolic profile (7097.03 μg/kg sum of total phenolic compounds and 1.97 sum of hydroxycinnamic acids to sum of hydroxybenzoic acids ratio) along with a tetraploid genome. Terminillo, Risciola, Gentil rosso, Mentana, and Leone aristato showed hexaploid genomes and high concentrations of phenolic compounds (ranging from 6796.12 to 7605.78 μg/kg), also in comparison with two modern varieties of bread wheat, Bolero and Blasco. The targeted metabolomic approach proved to be effective to determine some secondary metabolites of wheat. The richness in phenolic compounds combined with high rusticity and adaptability to marginal soils showed by ancient wheat varieties make them suitable for sustainable agricultural and organic cultivation.
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Affiliation(s)
- Giuseppe Montevecchi
- BIOGEST - SITEIA Interdepartmental Centre , University of Modena and Reggio Emilia , Piazzale Europa 1 , 42124 Reggio Emilia , Italy
| | - Leonardo Setti
- Agro-Food Science Area, Department of Life Sciences , University of Modena and Reggio Emilia , Via G. Amendola 2 (Padiglione Besta) , 42122 Reggio Emilia , Italy
| | - Linda Olmi
- BIOGEST - SITEIA Interdepartmental Centre , University of Modena and Reggio Emilia , Piazzale Europa 1 , 42124 Reggio Emilia , Italy
| | - Matteo Buti
- Agro-Food Science Area, Department of Life Sciences , University of Modena and Reggio Emilia , Via G. Amendola 2 (Padiglione Besta) , 42122 Reggio Emilia , Italy
| | - Luca Laviano
- Agro-Food Science Area, Department of Life Sciences , University of Modena and Reggio Emilia , Via G. Amendola 2 (Padiglione Besta) , 42122 Reggio Emilia , Italy
| | - Andrea Antonelli
- BIOGEST - SITEIA Interdepartmental Centre , University of Modena and Reggio Emilia , Piazzale Europa 1 , 42124 Reggio Emilia , Italy
- Agro-Food Science Area, Department of Life Sciences , University of Modena and Reggio Emilia , Via G. Amendola 2 (Padiglione Besta) , 42122 Reggio Emilia , Italy
| | - Elisabetta Sgarbi
- BIOGEST - SITEIA Interdepartmental Centre , University of Modena and Reggio Emilia , Piazzale Europa 1 , 42124 Reggio Emilia , Italy
- Agro-Food Science Area, Department of Life Sciences , University of Modena and Reggio Emilia , Via G. Amendola 2 (Padiglione Besta) , 42122 Reggio Emilia , Italy
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28
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Kaczmarkiewicz A, Nuckowski Ł, Studzińska S, Buszewski B. Analysis of Antisense Oligonucleotides and Their Metabolites with the Use of Ion Pair Reversed-Phase Liquid Chromatography Coupled with Mass Spectrometry. Crit Rev Anal Chem 2019; 49:256-270. [PMID: 30612436 DOI: 10.1080/10408347.2018.1517034] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Antisense oligonucleotides (ASOs) have been widely investigated as a potential drugs because of their ability to bind with the target DNA or RNA strands, which may lead to inhibition of translational processes. This review presents currently approved oligonucleotide (OGN) drugs and summarizes their modification types, mechanisms of action, and application of ion pair reversed phase liquid chromatography for the analysis. Special attention was paid to the stationary phases selection for the separation of OGNs and the impact of different compositions of mobile phases on retention and signal intensity in mass spectrometry (MS). Moreover, the application of ion pair liquid chromatography coupled with MS for the separation and determination of metabolites of ASOs was described. The type of matrix, time of analysis, lower limits of quantification and detection, as well as precision, accuracy, and linearity of developed methods have been included as part of this contribution.
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Affiliation(s)
- Anna Kaczmarkiewicz
- a Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry , Nicolaus Copernicus University , Toruń , Poland
| | - Łukasz Nuckowski
- a Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry , Nicolaus Copernicus University , Toruń , Poland
| | - Sylwia Studzińska
- a Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry , Nicolaus Copernicus University , Toruń , Poland
| | - Bogusław Buszewski
- a Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry , Nicolaus Copernicus University , Toruń , Poland
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Yokoi H, Kasahara Y, Obika S, Doi T, Kamada H. Development of a detection method for antisense oligonucleotides in mouse kidneys by matrix-assisted laser desorption/ionization imaging mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:1984-1990. [PMID: 30152908 DOI: 10.1002/rcm.8274] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 08/20/2018] [Accepted: 08/21/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE Oligonucleotide therapeutics have recently gained much attention, but its pharmacokinetic evaluation methods are still not sufficient, and, in particular, more tools are needed to evaluate their tissue distribution and metabolites. We developed a matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS)-based method to evaluate the tissue distribution of oligonucleotide therapeutics. METHODS We used an antisense oligonucleotide containing locked nucleic acids (LNA-A). Various washing protocols were examined using mouse kidney homogenate sections. Next, we applied a two-step matrix preparation strategy. As a first step, 3-hydroxypicolinic acid (3-HPA) matrix containing citrate and amines was sprayed using an airbrush and subsequently 3-HPA matrix containing citrate only was sprayed using the ImagePrep. Finally, kidney sections prepared from LNA-A-dosed mice were treated with our optimized method and analyzed with MALDI-IMS. RESULTS The selected washing method made it possible to detect LNA-A with MALDI-IMS and, furthermore, our developed matrix pretreatment method enhanced signal intensity approximately two-fold. MALDI-IMS revealed that LNA-A localized in a portion presumed to be the renal cortex. We also obtained information on LNA-A metabolites, which showed the same distribution profile as LNA-A in kidneys. CONCLUSIONS This study shows that MALDI-IMS can be applied to evaluate the tissue distribution of oligonucleotide therapeutics. Our method can evaluate the tissue distribution along with metabolites and has the potential to help the development of novel oligonucleotide therapeutics.
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Affiliation(s)
- Hiroyuki Yokoi
- Otsuka Pharmaceutical Co., Ltd, Tokushima Research Institute, Tokushima, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Yuya Kasahara
- National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
- National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Takefumi Doi
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - Haruhiko Kamada
- National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
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Mukai H, Hatanaka K, Yagi N, Warashina S, Zouda M, Takahashi M, Narushima K, Yabuuchi H, Iwano J, Kuboyama T, Enokizono J, Wada Y, Watanabe Y. Pharmacokinetic evaluation of liposomal nanoparticle-encapsulated nucleic acid drug: A combined study of dynamic PET imaging and LC/MS/MS analysis. J Control Release 2018; 294:185-194. [PMID: 30529725 DOI: 10.1016/j.jconrel.2018.12.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 12/04/2018] [Accepted: 12/06/2018] [Indexed: 12/13/2022]
Abstract
In vivo biodistribution analyses, especially in tumors, of nucleic acids delivered with nanoparticles are important to develop drug delivery technologies for medical use. We previously developed wrapsome® (WS), an ~100 nm liposomal nanoparticle that can encapsulate siRNA, and reported that WS accumulates in tumors in vivo and inhibits their growth by an enhanced permeability and retention effect. In the present study, we evaluated the pharmacokinetics of nucleic acid-containing nanoparticles by combining dynamic positron emission tomography (PET) imaging and liquid chromatography-tandem mass spectrometry (LC/MS/MS) analysis. An 18-mer phosphorothioate oligodeoxynucleotide (ODN), trabedersen, was used as a model drug and was encapsulated in WS. Dynamic PET imaging and time-activity curve analysis of WS-encapsulated 64Cu-labeled ODNs administered to mice with MIA PaCa-2 subcutaneous xenograft tumors showed tumor accumulation (~3% injected dose per gram (%ID/g)) and liver accumulation (~30 %ID/g) at 24 h. Under these conditions, LC/MS/MS analysis showed that the level of intact ODNs was 1.62 %ID/g in the tumor and 1.70 %ID/g in the liver. From these pharmacokinetic data, the intact/accumulated ODN ratios were calculated using the following equation: intact/accumulated ODN ratio (%) = %ID/g LC/MS/MS, tissue, mean/%ID/g PET, tissue, mean × 100. Interestingly, the ratios for the tumor and kidney were maintained at 20-50% over 48 h after administration of the WS-encapsulated form. In contrast, the ratio for the liver rapidly decreased at 24 h, showing the same pattern as that for naked ODN. These different patterns indicate that WS effectively protected the ODN in the tumor and kidney, but protected it less efficiently in the liver. A combined approach of dynamic PET imaging and LC/MS/MS analysis will assist the development of nanoparticle-encapsulated nucleic acid drugs, such as those using WSs, to determine their detailed pharmacokinetics.
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Affiliation(s)
- Hidefumi Mukai
- Molecular Network Control Imaging Unit, Molecular Network Control Research Project, Center Director's Strategic Program, RIKEN Center for Life Science Technologies, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Laboratory for Molecular Delivery and Imaging Technology, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
| | - Kentaro Hatanaka
- Research Core Function Laboratories, Research Function Unit, R&D Division, Kyowa Hakko Kirin Co., Ltd., 3-6-6, Asahi-machi, Machida-shi, Tokyo 194-8533, Japan
| | - Nobuhiro Yagi
- Research Core Function Laboratories, Research Function Unit, R&D Division, Kyowa Hakko Kirin Co., Ltd., 3-6-6, Asahi-machi, Machida-shi, Tokyo 194-8533, Japan
| | - Shota Warashina
- Molecular Network Control Imaging Unit, Molecular Network Control Research Project, Center Director's Strategic Program, RIKEN Center for Life Science Technologies, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Laboratory for Molecular Delivery and Imaging Technology, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Maki Zouda
- Molecular Network Control Imaging Unit, Molecular Network Control Research Project, Center Director's Strategic Program, RIKEN Center for Life Science Technologies, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Laboratory for Molecular Delivery and Imaging Technology, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Maiko Takahashi
- Molecular Network Control Imaging Unit, Molecular Network Control Research Project, Center Director's Strategic Program, RIKEN Center for Life Science Technologies, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Laboratory for Molecular Delivery and Imaging Technology, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Kazuya Narushima
- Research Core Function Laboratories, Research Function Unit, R&D Division, Kyowa Hakko Kirin Co., Ltd., 3-6-6, Asahi-machi, Machida-shi, Tokyo 194-8533, Japan
| | - Hayato Yabuuchi
- Research Core Function Laboratories, Research Function Unit, R&D Division, Kyowa Hakko Kirin Co., Ltd., 3-6-6, Asahi-machi, Machida-shi, Tokyo 194-8533, Japan
| | - Junko Iwano
- Research Core Function Laboratories, Research Function Unit, R&D Division, Kyowa Hakko Kirin Co., Ltd., 3-6-6, Asahi-machi, Machida-shi, Tokyo 194-8533, Japan
| | - Takeshi Kuboyama
- Research Core Function Laboratories, Research Function Unit, R&D Division, Kyowa Hakko Kirin Co., Ltd., 3-6-6, Asahi-machi, Machida-shi, Tokyo 194-8533, Japan.
| | - Junichi Enokizono
- Research Core Function Laboratories, Research Function Unit, R&D Division, Kyowa Hakko Kirin Co., Ltd., 3-6-6, Asahi-machi, Machida-shi, Tokyo 194-8533, Japan
| | - Yasuhiro Wada
- Pathophysiological and Health Science Team, Imaging Platform and Innovation Group, Division of Bio-Function Dynamics Imaging, RIKEN Center for Life Science Technologies, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Laboratory for Pathophysiological and Health Science, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yasuyoshi Watanabe
- Pathophysiological and Health Science Team, Imaging Platform and Innovation Group, Division of Bio-Function Dynamics Imaging, RIKEN Center for Life Science Technologies, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Laboratory for Pathophysiological and Health Science, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
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31
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Development of SPE method for the extraction of phosphorothioate oligonucleotides from serum samples. Bioanalysis 2018; 10:1667-1677. [PMID: 30354278 DOI: 10.4155/bio-2018-0166] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
AIM Comprehensive development of a method for SPE extraction of antisense phosphorothioate oligonucleotide and its metabolites and their determination with the use of UHPLC. RESULTS Polymer-based adsorbent and high percentage of methanol in elution solvent provided high recoveries compared with silica-based octadecyl cartridge. As to the type and concentration of ion pair reagent and organic solvent, the mixture of 5 mM of N,N-dimethylbutylamine/150 mM of 1,1,1,3,3,3-hexafluoroisopropanol and methanol was selected. Relatively high recoveries in the range of 79.2-81.2% with the SDs of 3.4-6.2% were obtained for the oligonucleotide and its metabolites extracted from human serum. CONCLUSION The developed method may be successfully applied for routine analysis of antisense oligonucleotides in serum since it is relatively easy, quick and reliable.
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Nuckowski Ł, Kaczmarkiewicz A, Studzińska S. Review on sample preparation methods for oligonucleotides analysis by liquid chromatography. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1090:90-100. [PMID: 29803869 DOI: 10.1016/j.jchromb.2018.05.025] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 05/10/2018] [Accepted: 05/17/2018] [Indexed: 02/01/2023]
Abstract
Antisense oligonucleotides have been successfully investigated for the treatment of different types of diseases. Detection and determination of antisense oligonucleotides and their metabolites are necessary for drug development and evaluation. This review focuses mainly on the first step of the analysis of oligonucleotides i.e. the sample preparation stage, and in particular on the techniques used for liquid chromatography and liquid chromatography coupled with mass spectrometry. Exceptional sample preparation techniques are required as antisense oligonucleotides need to be determined in complex biological matrices. The text discusses general issues in oligonucleotide sample preparation and approaches to their solution. The most popular techniques i.e. protein precipitation, protein enzyme digestion and liquid-liquid extraction are reviewed. Solid phase extraction methods are discussed and the issues connected with the application of each method are highlighted. Other newly reported promising techniques are also described. Finally, there is a summary of actually used techniques and the indication of the direction of future research.
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Affiliation(s)
- Łukasz Nuckowski
- Chair of the Environmental Chemistry & Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7 Gagarin St., PL-87 100 Toruń, Poland
| | - Anna Kaczmarkiewicz
- Chair of the Environmental Chemistry & Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7 Gagarin St., PL-87 100 Toruń, Poland
| | - Sylwia Studzińska
- Chair of the Environmental Chemistry & Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7 Gagarin St., PL-87 100 Toruń, Poland.
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33
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Franzoni S, Vezzelli A, Turtoro A, Solazzo L, Greco A, Tassone P, Di Martino M, Breda M. Development and validation of a bioanalytical method for quantification of LNA-i-miR-221, a 13-mer oligonucleotide, in rat plasma using LC–MS/MS. J Pharm Biomed Anal 2018; 150:300-307. [DOI: 10.1016/j.jpba.2017.12.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 12/11/2017] [Accepted: 12/12/2017] [Indexed: 10/18/2022]
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Tang Q, Cai A, Bian K, Chen F, Delaney JC, Adusumalli S, Bach AC, Akhlaghi F, Cho BP, Li D. Characterization of Byproducts from Chemical Syntheses of Oligonucleotides Containing 1-Methyladenine and 3-Methylcytosine. ACS OMEGA 2017; 2:8205-8212. [PMID: 29214236 PMCID: PMC5709782 DOI: 10.1021/acsomega.7b01482] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 11/01/2017] [Indexed: 06/07/2023]
Abstract
Oligonucleotides serve as important tools for biological, chemical, and medical research. The preparation of oligonucleotides through automated solid-phase synthesis is well-established. However, identification of byproducts generated from DNA synthesis, especially from oligonucleotides containing site-specific modifications, is sometimes challenging. Typical high-performance liquid chromatography (HPLC), mass spectrometry (MS), and gel electrophoresis methods alone are not sufficient for characterizing unexpected byproducts, especially for those having identical or very similar molecular weight (MW) to the products. We used a rigorous quality control procedure to characterize byproducts generated during oligonucleotide syntheses: (1) purify oligonucleotides by different HPLC systems; (2) determine exact MW by high-resolution MS; (3) locate modification position by MS/MS or exonuclease digestion with matrix-assisted laser desorption ionization-time of flight analysis; and (4) conduct, where applicable, enzymatic assays. We applied these steps to characterize byproducts in the syntheses of oligonucleotides containing biologically important methyl DNA adducts 1-methyladenine (m1A) and 3-methylcytosine (m3C). In m1A synthesis, we differentiated a regioisomeric byproduct 6-methyladenine, which possesses a MW identical to uncharged m1A. As for m3C, we identified a deamination byproduct 3-methyluracil, which is only 1 Da greater than uncharged m3C in the ∼4900 Da context. The detection of these byproducts would be very challenging if the abovementioned procedure was not adopted.
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Affiliation(s)
- Qi Tang
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, Rhode Island 02881, United States
| | - Ang Cai
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, Rhode Island 02881, United States
| | - Ke Bian
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, Rhode Island 02881, United States
| | - Fangyi Chen
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, Rhode Island 02881, United States
| | - James C. Delaney
- Visterra
Inc., One Kendall Square, Cambridge, Massachusetts 02139, United States
| | - Sravani Adusumalli
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, Rhode Island 02881, United States
| | - Alvin C. Bach
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, Rhode Island 02881, United States
| | - Fatemeh Akhlaghi
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, Rhode Island 02881, United States
| | - Bongsup P. Cho
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, Rhode Island 02881, United States
| | - Deyu Li
- Department
of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 7 Greenhouse Road, Kingston, Rhode Island 02881, United States
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35
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Studzińska S. Review on investigations of antisense oligonucleotides with the use of mass spectrometry. Talanta 2017; 176:329-343. [PMID: 28917758 DOI: 10.1016/j.talanta.2017.08.025] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/03/2017] [Accepted: 08/07/2017] [Indexed: 11/17/2022]
Abstract
Antisense oligonucleotides have been investigated as potential drugs for years. They inhibit target gene or protein expression. The present review summarizes their modifications, modes of action, and applications of liquid chromatography coupled with mass spectrometry for qualitative and quantitative analysis of these compounds. The most recent reports on a given topic were given prominence, while some early studies were reviewed in order to provide a theoretical background. The present review covers the issues of using ion-exchange chromatography, ion-pair reversed-phase high performance liquid chromatography and hydrophilic interaction chromatography for the separation of antisense oligonucleotides. The application of mass spectrometry was described with regard to the ionization type used for the determination of these potential therapeutics. Moreover, the current approaches and applications of mass spectrometry for quantitative analysis of antisense oligonucleotides and their metabolites as well as their impurities during in vitro and in vivo studies were discussed. Finally, certain conclusions and perspectives on the determination of therapeutic oligonucleotides in various samples were briefly described.
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Affiliation(s)
- Sylwia Studzińska
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin Str., PL-87-100 Toruń, Poland.
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36
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Quantitative determination of a siRNA (AD00370) in rat plasma using peptide nucleic acid probe and HPLC with fluorescence detection. Bioanalysis 2017; 9:861-872. [PMID: 28617037 DOI: 10.4155/bio-2017-0017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
AIM Toxicokinetic and pharmacokinetic studies of therapeutic oligonucleotides require validated bioanalytical methods for sensitive and specific quantification of oligonucleotide drug candidates in biological samples. RESULTS A peptide nucleic acid (PNA) hybridization-based HPLC-fluorescence assay was developed and validated for quantification of Arrowhead Pharmaceuticals' proprietary siRNA in rat plasma samples via hybridization and anion-exchange-HPLC (AEX-HPLC) with fluorescence detection. CONCLUSION The validated method provided a sensitive and selective approach for quantification of siRNA in biological samples at a linear quantitation range of 1-1000 ng/ml. The assay requires only 25 μl of plasma sample and shows excellent accuracy and precision even without using an internal standard, providing a useful quantification method for siRNA determination in biological matrix with limited sample volume.
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37
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Studzińska S, Bocian S, Siecińska L, Buszewski B. Application of phenyl-based stationary phases for the study of retention and separation of oligonucleotides. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1060:36-43. [PMID: 28595118 DOI: 10.1016/j.jchromb.2017.05.033] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 05/15/2017] [Accepted: 05/27/2017] [Indexed: 12/11/2022]
Abstract
The main goal of our work was to apply three different phenyl-bonded stationary phases in ion pair chromatography for the analysis of synthetic oligonucleotides of various sequences. The influence of the stationary phase structure and the impact of ion-pairing reagent concentration on the retention of oligonucleotides were tested. Moreover the influence of oligonucleotide sequence on their interactions with phenyl-based stationary phases was also investigated. Such complex studies for analysis of oligonucleotides with these adsorbents were done for the first time. Investigations were implemented in the Quantitative Structure Retention Relationships analysis in order to improve the discussion on the retention mechanism of analyzed compounds. The retention of oligonucleotides was the lowest for polar embedded phenyl stationary phase, however its selectivity was high and allowed for complete separation of studied compounds in the shortest time. It was shown that the low retention factor value was observed for oligonucleotides forming secondary structures, such as hairpin loops. Moreover obtained data showed that except for electrostatic and hydrophobic interactions, π-π also influences on the retention mechanism. These interactions cause higher retention factor values for phenyl-based stationary phases compared to octadecyl ones.
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Affiliation(s)
- Sylwia Studzińska
- Chair of the Environmental Chemistry & Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin St., PL-87 100 Toruń, Poland.
| | - Szymon Bocian
- Chair of the Environmental Chemistry & Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin St., PL-87 100 Toruń, Poland
| | - Lena Siecińska
- Chair of the Environmental Chemistry & Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin St., PL-87 100 Toruń, Poland
| | - Bogusław Buszewski
- Chair of the Environmental Chemistry & Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin St., PL-87 100 Toruń, Poland
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38
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Husser C, Brink A, Zell M, Müller MB, Koller E, Schadt S. Identification of GalNAc-Conjugated Antisense Oligonucleotide Metabolites Using an Untargeted and Generic Approach Based on High Resolution Mass Spectrometry. Anal Chem 2017; 89:6821-6826. [PMID: 28520401 DOI: 10.1021/acs.analchem.7b01244] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Antisense oligonucleotides linked by phosphorothioates are an important class of therapeutics under investigation in various pharmaceutical companies. Antisense oligonucleotides may be coupled to high-affinity ligands (triantennary N-acetyl galactosamine = GalNAc) for hepatocyte-specific asialoglycoprotein receptors (ASGPR) to enhance uptake to hepatocytes and to increase potency. Since disposition and biotransformation of GalNAc-conjugated oligonucleotides is different from unconjugated oligonucleotides, appropriate analytical methods are required to identify main cleavage sites and degradation products of GalNAc conjugated and unconjugated oligonucleotides in target cells. A highly sensitive method was developed to identify metabolites of oligonucleotides using capillary flow liquid chromatography with column switching coupled to a high resolution Orbitrap Fusion mass spectrometer. Detection of GalNAc-conjugated oligonucleotides and their metabolites was achieved by combining full scan MS with two parallel MS2 experiments, one data-dependent scan and an untargeted MS2 experiment (all ion fragmentation) applying high collision energy. In the all ion fragmentation scan, a diagnostic fragment originating from the phosphorothioate backbone (O2PS-: m/z 94.936) was formed efficiently upon collisional activation. Based on this fragment an accurate determination of metabolites of oligonucleotides was achieved, independent of their sequence or conjugation in an untargeted but highly selective manner. The method was effectively applied to investigate uptake and metabolism of GalNAc-conjugated oligonucleotides in incubations of primary rat hepatocytes; the elucidation of expected and unexpected degradation products was achieved in subnanomolar range.
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Affiliation(s)
- Christophe Husser
- Roche Pharma Research and Early Development, Roche Innovation Center Basel , Grenzacherstr. 124, CH-4070 Basel, Switzerland
| | - Andreas Brink
- Roche Pharma Research and Early Development, Roche Innovation Center Basel , Grenzacherstr. 124, CH-4070 Basel, Switzerland
| | - Manfred Zell
- Roche Pharma Research and Early Development, Roche Innovation Center Basel , Grenzacherstr. 124, CH-4070 Basel, Switzerland
| | - Martina B Müller
- Roche Pharma Research and Early Development, Roche Innovation Center Basel , Grenzacherstr. 124, CH-4070 Basel, Switzerland
| | - Erich Koller
- Roche Pharma Research and Early Development, Roche Innovation Center Basel , Grenzacherstr. 124, CH-4070 Basel, Switzerland
| | - Simone Schadt
- Roche Pharma Research and Early Development, Roche Innovation Center Basel , Grenzacherstr. 124, CH-4070 Basel, Switzerland
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Friese OV, Sperry JB, He Y, Joseph L, Carroll JA, Rouse JC. Characterization of Apolipoprotein C3 (Apo C3) LNA/DNA Impurities and Degradation Products by LC-MS/MS. AAPS JOURNAL 2017; 19:1735-1744. [PMID: 28488174 DOI: 10.1208/s12248-017-0088-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 04/07/2017] [Indexed: 01/22/2023]
Abstract
Apolipoprotein C3 (Apo C3) LNA/DNA gapmer was evaluated under various stress and formulation conditions for the purpose of its development as a potential biotherapeutic for low density lipoprotein (LDL) lowering. Using ion-pairing (IP) reversed-phase (RP) liquid chromatography ultra-high resolution (UHR) tandem mass spectrometry (IP-RPLC-MS/MS), a combination of accurate mass measurements and collision-induced dissociation enabled in-depth characterization of Apo C3 LNA/DNA oligonucleotide, in particular the inherent impurities following synthesis and degradation products after exposure to stress conditions. In this study, oligonucleotide samples were stressed under different pH and UV exposure conditions. The primary impurities in Apo C3 LNA/DNA were losses of nucleotide moieties from both the 5'- and 3'-terminus leading to n-1, n-2, etc. species. Desulfurization and depurination were observed in Apo C3 LNA/DNA after a week under UV light stress conditions at low pH. Guanine oxidation and dimerization were the primary degradation products detected under UV light exposure for 1 week at high pH. The effect of antioxidants on the levels of these degradation products was evaluated under neutral pH conditions. In the presence of all antioxidants, levels of guanine oxidation and desulfurization under tested conditions were the same as those in the unstressed sample, except for sodium ascorbate. The thorough understanding of the Apo C3 LNA/DNA oligonucleotide structure, its impurities, and degradation products laid the foundation for the successful formulation development of this novel biotherapeutic modality.
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Affiliation(s)
- Olga V Friese
- Biotherapeutics Pharmaceutical Sciences, Pfizer WRD, St. Louis, Missouri, USA.
| | - Justin B Sperry
- Biotherapeutics Pharmaceutical Sciences, Pfizer WRD, St. Louis, Missouri, USA
| | - Yan He
- Biotherapeutics Pharmaceutical Sciences, Pfizer WRD, St. Louis, Missouri, USA
| | - Liji Joseph
- Biotherapeutics Pharmaceutical Sciences, Pfizer WRD, St. Louis, Missouri, USA
| | - James A Carroll
- Biotherapeutics Pharmaceutical Sciences, Pfizer WRD, St. Louis, Missouri, USA
| | - Jason C Rouse
- Biotherapeutics Pharmaceutical Sciences, Pfizer WRD, Andover, Massachusetts, USA
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40
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Studzińska S, Rola R, Buszewski B. The impact of ion-pairing reagents on the selectivity and sensitivity in the analysis of modified oligonucleotides in serum samples by liquid chromatography coupled with tandem mass spectrometry. J Pharm Biomed Anal 2017; 138:146-152. [PMID: 28208106 DOI: 10.1016/j.jpba.2017.02.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 02/04/2017] [Accepted: 02/06/2017] [Indexed: 11/28/2022]
Abstract
Present study highlights the usage of various ion-pairing agents and their impact on the process of separation and ionization of oligonucleotides in the fortified human serum samples. What is more, retention studies involved different stationary phases, including: octadecyl, phenyl, pentafluorophenyl groups and ligands with embedded polar groups. It was proved that retention of oligonucleotides strongly depends on the alkyl chain branching in the structure of ion pairing reagent. Furthermore ion-pairing agents build of straight alkyl chain are more easily adsorbed on the stationary phase modified with octadecyl groups, while branching of alkyl chain caused more effective adsorption of studied compounds at phenyl groups compared to octadecyl ones. The lowest limit of quantification values were obtained for 5mMN,N-dimethylbutylamine, while the highest values are characteristic for hexylamine. Moreover it was shown that a 2-fold increase of ion-pairing agent concentration results in higher LOQ. The greatest sensitivity was obtained for 2.5mMN,N-dimethylbutylamine/150mM hexafluoroisopropanol. On the other hand Hypersil GOLD aQ column was the most appropriate in terms of time and separation effectiveness. The developed method was successfully used for the determination of studied oligonucleotides and their metabolites in human serum samples. The compounds were separated in just 3.5min with high sensitivity (0.09-0.16ng).
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Affiliation(s)
- Sylwia Studzińska
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin Str., PL-87-100 Toruń, Poland.
| | - Rafał Rola
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin Str., PL-87-100 Toruń, Poland
| | - Bogusław Buszewski
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin Str., PL-87-100 Toruń, Poland
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Birdsall RE, Gilar M, Shion H, Yu YQ, Chen W. Reduction of metal adducts in oligonucleotide mass spectra in ion-pair reversed-phase chromatography/mass spectrometry analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:1667-1679. [PMID: 28328039 PMCID: PMC5094505 DOI: 10.1002/rcm.7596] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 04/28/2016] [Accepted: 05/01/2016] [Indexed: 05/09/2023]
Abstract
RATIONALE Electrospray ionization mass spectrometry (ESI-MS)-based techniques commonly used in oligonucleotide analyses are known to be sensitive to alkali metal adduct formation. Adducts directly impact the sensitivity of MS-based analyses as the available charge is distributed across the parent peak and adduct(s). The current study systematically evaluated common liquid chromatography (LC) components in LC/ESI-MS configurations used in oligonucleotide analysis to identify metal adduct contributions from LC instrumentation. METHODS A UPLC liquid chromatography system was configured with a single quadrupole MS detector (ACQUITY QDa, Waters Corp.) to monitor adduct formation in oligonucleotide separations. An ion-pairing mobile phase comprised of 15 mM triethylamine and 400 mM hexafluoro-2-propanol was used in conjunction with an oligonucleotide separation column (Waters OST BEH C18, 2.1 mm × 50 mm) for all separations. A 10-min method was used to provide statistical figures of merit and evaluate adduct formation over time. RESULTS Trace alkali metal salts in the mobile phase and reagents were determined to be the main source of metal salt adducts in LC/ESI-MS-based configurations. Non-specific adsorption sites located throughout the fluidic path contribute to adduct formation in oligonucleotide analyses. Ion-pairing mobile phases prepared at neutral or slightly basic pH result in up to a 57% loss of spectral abundance to adduct formation in the current study. CONCLUSIONS Implementation of a short low pH reconditioning step was observed to effectively displace trace metal salts non-specifically adsorbed to surfaces in the fluidic path and was able to maintain an average MS spectral abundance ≥94% with a high degree of repeatability (relative standard deviation (R.S.D.) 0.8%) over an extended time study. The proposed method offers the ability to rapidly regenerate adsorption sites with minimal impact on productivity while retaining assay sensitivity afforded by MS detection with reduced adduct formation. © 2016 The Authors. Rapid Communications in Mass Spectrometry Published by John Wiley & Sons Ltd.
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Affiliation(s)
| | - Martin Gilar
- Waters Corp., 34 Maple St, Milford, MA, 01757-3604, USA
| | - Henry Shion
- Waters Corp., 34 Maple St, Milford, MA, 01757-3604, USA
| | - Ying Qing Yu
- Waters Corp., 34 Maple St, Milford, MA, 01757-3604, USA
| | - Weibin Chen
- Waters Corp., 34 Maple St, Milford, MA, 01757-3604, USA
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42
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Mateos-Vivas M, Rodríguez-Gonzalo E, Domínguez-Álvarez J, García-Gómez D, Carabias-Martínez R. Determination of nucleosides and nucleotides in baby foods by hydrophilic interaction chromatography coupled to tandem mass spectrometry in the presence of hydrophilic ion-pairing reagents. Food Chem 2016; 211:827-35. [PMID: 27283702 DOI: 10.1016/j.foodchem.2016.05.091] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 04/21/2016] [Accepted: 05/13/2016] [Indexed: 10/21/2022]
Abstract
In this work we propose a rapid and efficient method for the joint determination of nucleosides and nucleotides in dairy and non-dairy baby foods based on hydrophilic interaction chromatography coupled to tandem mass spectrometry in the presence of diethylammonium (DEA) as a hydrophilic ion-pairing reagent (IP-HILIC-MS/MS). Sample treatment of the baby food included dilution with water and centrifugal ultrafiltration (CUF) with an additional washing step that notably improved the global performance of the process. Later dilution of the extract with acetonitrile allowed adequate separation in the HILIC system. With the proposed treatment, we obtained extraction recoveries higher than 80% and, additionally, no matrix effects were observed. The CUF-IP-HILIC-MS/MS method was validated according to the 2002/657/EC decision and was used for the quantification of nucleotides and nucleosides in sixteen samples of commercial baby foods.
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Affiliation(s)
- María Mateos-Vivas
- Department of Analytical Chemistry, Nutrition and Food Science, University of Salamanca, 37008 Salamanca, Spain.
| | | | - Javier Domínguez-Álvarez
- Department of Analytical Chemistry, Nutrition and Food Science, University of Salamanca, 37008 Salamanca, Spain.
| | - Diego García-Gómez
- Department of Analytical Chemistry, Nutrition and Food Science, University of Salamanca, 37008 Salamanca, Spain.
| | - Rita Carabias-Martínez
- Department of Analytical Chemistry, Nutrition and Food Science, University of Salamanca, 37008 Salamanca, Spain.
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Application of a cholesterol stationary phase in the analysis of phosphorothioate oligonucleotides by means of ion pair chromatography coupled with tandem mass spectrometry. Talanta 2016; 154:270-7. [PMID: 27154674 DOI: 10.1016/j.talanta.2016.03.082] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/22/2016] [Accepted: 03/25/2016] [Indexed: 12/14/2022]
Abstract
The main aim of this study was the investigation of the influence of several ion pair reagents towards both the retention and the mass spectrometry sensitivity of phosphorothioate oligonucleotides. A cholesterol stationary phase was applied for the first time in the analysis of this group of compounds. The mobile phase composition was modified by changing the concentration and the type of amines and acetates or 1,1,1,3,3,3-hexafluoroisopropanol. It has been shown that the increase of amines concentration results in the retention factor increase for each oligonucleotide, on each adsorbent. The only exception was the mobile phase composed of triethylamine and 1,1,1,3,3,3-hexafluoroisopropanol. This is a consequence of interactions taking place between a cholesterol molecule and an alcohol. This effect was convenient when the mass spectrometry detection was applied, since it allowed an increase in the sensitivity. Moreover, optimization of the mobile phase composition and its impact on the efficiency of ionization process and on the sensitivity in mass spectrometry were also presented. The optimization of this new method, based on cholesterol stationary phase coupled with mass spectrometry detection, was finally applied for the determination of phosphorothioate oligonucleotides impurity in a real sample.
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Studzińska S, Rola R, Buszewski B. Development of a method based on ultra high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry for studying the in vitro metabolism of phosphorothioate oligonucleotides. Anal Bioanal Chem 2016; 408:1585-95. [PMID: 26758600 PMCID: PMC4737794 DOI: 10.1007/s00216-015-9266-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 11/15/2015] [Accepted: 12/10/2015] [Indexed: 11/29/2022]
Abstract
Ultra high performance liquid chromatography hyphenated with quadrupole time-of-flight mass spectrometry was used to determine the products of the in vitro metabolism of phosphorothioate oligonucleotides. These compounds may be used during antisense therapy as synthetic fragments of genes. For this reason, both a sample preparation method and a qualification method were developed during this study. Liquid–liquid extraction, protein or oligonucleotide precipitation, and solid-phase extraction were tested and compared in order to select the method that yielded the highest recoveries. Ion pair chromatography was used for separation while mass spectrometry was applied for metabolite identification. The influence of the type of ion pair reagent used on the resolution and sensitivity was investigated. Results indicated that a mixture of 1,1,1,3,3,3-hexafluoro-2-propanol, N,N-dimethylbutylamine, and methanol was the best mobile phase for maximizing both of these parameters. The developed method was applied to investigate the compounds that form during the incubation of phosphorothioate oligonucleotides with human liver microsomes. Metabolites with short sequences were created after 8 hours, while oligonucleotides constructed from a large number of nucleotide units were obtained after 12 hours of incubation. Moreover, regardless of the length of the polynucleotide chain, metabolites were produced by the same mechanism: enzymatic cleavage at the 3′ end of the sequence.
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Affiliation(s)
- Sylwia Studzińska
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin St., PL-87 100, Torun, Poland.
| | - Rafał Rola
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin St., PL-87 100, Torun, Poland
| | - Bogusław Buszewski
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin St., PL-87 100, Torun, Poland
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45
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Smith M, Beck T. Quantitation of a low level coeluting impurity present in a modified oligonucleotide by both LC-MS and NMR. J Pharm Biomed Anal 2015; 118:34-40. [PMID: 26512997 DOI: 10.1016/j.jpba.2015.10.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 10/07/2015] [Accepted: 10/13/2015] [Indexed: 01/13/2023]
Abstract
This paper describes the use of two complementary techniques, LC-MS and NMR, to quantify a low level mono phosphate substituted impurity in an oligonucleotide drug substance. This impurity is the result of a sulphurisation failure, leading to the production of a sequence where a phosphorothioate linkage is replaced by a phosphate. Few quantitative methods are possible to analyse these challenging molecules especially if reversed phase ion pair chromatography, one of the most commonly used techniques for the separation of oligonucleotides, is unable to resolve the impurity in question. With the use of a standard addition method it could be demonstrated that both analytical techniques show equivalency and furthermore, the LC-MS method alone with additional validation has the potential to perform this quantitative assay with a high degree of accuracy.
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Affiliation(s)
- Marco Smith
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, UK.
| | - Tony Beck
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, UK
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46
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Hydrophilic interaction chromatography coupled to tandem mass spectrometry in the presence of hydrophilic ion-pairing reagents for the separation of nucleosides and nucleotide mono-, di- and triphosphates. J Chromatogr A 2015; 1414:129-37. [PMID: 26341591 DOI: 10.1016/j.chroma.2015.08.040] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 08/14/2015] [Accepted: 08/20/2015] [Indexed: 11/23/2022]
Abstract
A fast and efficient method for the simultaneous separation of highly polar compounds, in this case nucleosides and nucleotide mono-, di- and triphosphates, using hydrophilic interaction chromatography coupled with tandem mass spectrometry (HILIC-MS/MS) is proposed. This new separation method revealed the possibilities of the formation of hydrophilic ion-pairing compounds. Three stationary phases (HILIC XBridge-Amide, HILIC-CoreShell and ZIC-HILIC) were assayed for the separation of 20 target analytes, and a detailed study of the composition of the mobile phase was made using different salts at different concentrations in a organic-rich mobile phase. We report that in order to prevent the adsorption of nucleotides on the LC-MS setup and to enhance their retention on the HILIC stationary phase, a mobile phase containing hexafluoro-2-propanol and different cations should be used. Four cations were evaluated: ammonium, diethylammonium, triethylammonium and tetrabutylammonium. The results revealed the formation of an ionic-association compound between the phosphorylated analytes and the cationic ion-pairing reagents, whose retention increased with the polarity of the cationic ion-pairing reagent. HILIC XBridge-Amide was found to be the most suitable column for the separation of these analytes, and the optimized mobile phase consisted of an ACN/UHQ water mixture (3min of isocratic elution using 82:18%, v/v and then a fast gradient from 18% to 22% of water) with 100mM hexafluoro-2-propanol and 50mM diethylamine (w(w)pH 9-w(s)pH 10). In a total analysis time of 8min, good results were achieved in terms of resolution. Under these optimum conditions, a further comprehensive study of the retention mechanism was carried out.
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Cen Y, Li X, Yin Z, Yan Z, Liu D, Peng W, Pan F, Zhou H. Pharmacokinetic Profile and Acute Toxicological Properties of a Novel Radiosensitizer Cytosine-Phosphate-Guanosine Oligodeoxynucleotide 107 in Mice Following Intravenous and Orthotopic Administration. Nucleic Acid Ther 2015. [PMID: 26213852 DOI: 10.1089/nat.2015.0538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The synthetic cytosine-phosphate-guanosine oligodeoxynucleotide 107 (CpG ODN107) is a novel radiosensitizer for glioma treatment. However, the information related to its pharmacokinetics and toxicity remains unclear. Therefore, the plasma pharmacokinetics, distribution, elimination, and acute toxicity of CpG ODN107 in mice were investigated in the present experiments. The results from the liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay showed that the plasma elimination half-life (t1/2β) of CpG ODN107 in BALB/c mice varied slightly with the dose, and it was 0.65, 0.49, and 0.50 h at the intravenous doses of 2.5, 5, and 10 mg/kg, respectively. CpG ODN107 rapidly and widely distributed in organs/tissues, except the brain and testes. The highest concentrations were found in the liver (28.6% of the administered dose after 0.5 h) and the kidneys (5.7% of the administered dose after 1 h). CpG ODN107 (0.3, 3, and 30 μg/mL) could highly bind to human and mouse plasma proteins in vitro. CpG ODN107 in the forms of prototype was excreted in urine (1.79%) and feces (0.91%), and its shortened metabolites were excreted in urine (2.1%) and feces (2.2%) within the first 24 h. The mice in vivo optical image showed CpG ODN107 labeled with Alexa Fluor 680 fluorochrome (AF680) accumulated in the brain after orthotopic injection, eliminated very slowly, and excreted in urine compared with poly T labeled with AF680. The median lethal dose (LD50) of CpG ODN107 was 75.7 mg/kg for mice; this dose only could produce apparent spleen and liver damage, in line with the distribution features of CpG ODN. In conclusion, our present pharmacokinetic and toxicity investigation will provide helpful information to further pharmacodynamic and pharmacokinetic research of CpG ODN107 and other oligodeoxynucleotide drugs in the future.
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Affiliation(s)
- Yanyan Cen
- 1 Department of Pharmacology, College of Pharmacy, The Third Military Medical University , Chongqing, People's Republic of China
| | - Xiaoli Li
- 1 Department of Pharmacology, College of Pharmacy, The Third Military Medical University , Chongqing, People's Republic of China
| | - Zhiwei Yin
- 2 No. 546 Hospital of China People's Liberation Army , Urumqi, People's Republic of China
| | - Zifei Yan
- 1 Department of Pharmacology, College of Pharmacy, The Third Military Medical University , Chongqing, People's Republic of China
| | - Dan Liu
- 1 Department of Pharmacology, College of Pharmacy, The Third Military Medical University , Chongqing, People's Republic of China
| | - Wei Peng
- 1 Department of Pharmacology, College of Pharmacy, The Third Military Medical University , Chongqing, People's Republic of China
| | - Feng Pan
- 3 Biomedical Analysis Center, The Third Military Medical University , Chongqing, People's Republic of China
| | - Hong Zhou
- 1 Department of Pharmacology, College of Pharmacy, The Third Military Medical University , Chongqing, People's Republic of China
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Abstract
Recent findings have elucidated numerous novel biological functions for oligonucleotides. Current standard methods for the study of oligonucleotides (i.e., hybridization and PCR) are not fully equipped to deal with the experimental needs arising from these new discoveries. More importantly, as the intracellular capacity of oligonucleotides is being harnessed for biomedical applications, alternative bioanalytical techniques become indispensable in order to comply with ever-increasing regulatory requirements. Owing to its ability to detect oligonucleotides independent of their sequence, LC-MS is emerging as the analytical method of choice for oligonucleotides. In this article, the current applications of LC-MS in the analysis of oligonucleotides, with an emphasis on RNA therapeutics and biomarkers, will be examined. In addition, the theoretical framework of oligonucleotide ESI is carefully inspected with the purpose of identifying the contributing factors to MS signal intensity.
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49
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Studzińska S, Mounicou S, Szpunar J, Łobiński R, Buszewski B. New approach to the determination phosphorothioate oligonucleotides by ultra high performance liquid chromatography coupled with inductively coupled plasma mass spectrometry. Anal Chim Acta 2014; 855:13-20. [PMID: 25542085 DOI: 10.1016/j.aca.2014.12.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 12/03/2014] [Accepted: 12/04/2014] [Indexed: 01/27/2023]
Abstract
This text presents a novel method for the separation and detection of phosphorothioate oligonucleotides with the use of ion pair ultra high performance liquid chromatography coupled with inductively coupled plasma mass spectrometry The research showed that hexafluoroisopropanol/triethylamine based mobile phases may be successfully used when liquid chromatography is coupled with such elemental detection. However, the concentration of both HFIP and TEA influences the final result. The lower concentration of HFIP, the lower the background in ICP-MS and the greater the sensitivity. The method applied for the analysis of serum samples was based on high resolution inductively coupled plasma mass spectrometry. Utilization of this method allows determination of fifty times lower quantity of phosphorothioate oligonucleotides than in the case of quadrupole mass analyzer. Monitoring of (31)P may be used to quantify these compounds at the level of 80 μg L(-1), while simultaneous determination of sulfur is very useful for qualitative analysis. Moreover, the results presented in this paper demonstrate the practical applicability of coupling LC with ICP-MS in determining phosphorothioate oligonucleotides and their metabolites in serum within 7 min with a very good sensitivity. The method was linear in the concentration range between 0.2 and 3 mg L(-1). The limit of detection was in the range of 0.07 and 0.13 mg L(-1). Accuracy varied with concentration, but was in the range of 3%.
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Affiliation(s)
- Sylwia Studzińska
- Chair of the Environmental Chemistry & Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin St., PL-87 100 Torun, Poland.
| | - Sandra Mounicou
- CNRS/UPPA, Laboratoire de Chimie Analytique Bio-inorganique et Environnement, UMR 5254, Hélioparc, 2 av. Pr. Angot, F-64053 Pau, France
| | - Joanna Szpunar
- CNRS/UPPA, Laboratoire de Chimie Analytique Bio-inorganique et Environnement, UMR 5254, Hélioparc, 2 av. Pr. Angot, F-64053 Pau, France
| | - Ryszard Łobiński
- CNRS/UPPA, Laboratoire de Chimie Analytique Bio-inorganique et Environnement, UMR 5254, Hélioparc, 2 av. Pr. Angot, F-64053 Pau, France
| | - Bogusław Buszewski
- Chair of the Environmental Chemistry & Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarin St., PL-87 100 Torun, Poland
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50
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Mateos-Vivas M, Rodríguez-Gonzalo E, Domínguez-Álvarez J, García-Gómez D, Ramírez-Bernabé R, Carabias-Martínez R. Analysis of free nucleotide monophosphates in human milk and effect of pasteurisation or high-pressure processing on their contents by capillary electrophoresis coupled to mass spectrometry. Food Chem 2014; 174:348-55. [PMID: 25529691 DOI: 10.1016/j.foodchem.2014.11.051] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 11/03/2014] [Accepted: 11/08/2014] [Indexed: 10/24/2022]
Abstract
A simple, efficient and green analytical method for the determination of free nucleotide monophosphates in human milk is proposed. It involves centrifugal ultrafiltration (CUF) as sample treatment and capillary electrophoresis-electrospray mass spectrometry (CE-ESI-MS) for separation and simultaneous quantification. The optimised method, applied to the analysis of human milk samples, included their dilution (1:5) with water followed by CUF treatment. No matrix effects were found. The method provided limits of detection between 0.08 and 0.13 μg mL(-1) and limits of quantification between 0.26 and 0.43 μg mL(-1). The intralaboratory repeatability and reproducibility afforded relative standard deviation values lower than 10%. The method was applied to the study of the effects of Holder pasteurisation and high-pressure processing on the nucleotide contents in samples from a human milk bank. The results showed concentration values between 0.5 and 10 μg mL(-1), with higher concentrations for the samples treated by pasteurisation. The effect of freezing time on the content of nucleotides was also assessed.
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Affiliation(s)
- María Mateos-Vivas
- Analytical Chemistry, Nutrition and Food Science Department, University of Salamanca, Plaza de los Caídos s/n, 37008 Salamanca, Spain
| | - Encarnación Rodríguez-Gonzalo
- Analytical Chemistry, Nutrition and Food Science Department, University of Salamanca, Plaza de los Caídos s/n, 37008 Salamanca, Spain.
| | - Javier Domínguez-Álvarez
- Analytical Chemistry, Nutrition and Food Science Department, University of Salamanca, Plaza de los Caídos s/n, 37008 Salamanca, Spain
| | - Diego García-Gómez
- Analytical Chemistry, Nutrition and Food Science Department, University of Salamanca, Plaza de los Caídos s/n, 37008 Salamanca, Spain
| | | | - Rita Carabias-Martínez
- Analytical Chemistry, Nutrition and Food Science Department, University of Salamanca, Plaza de los Caídos s/n, 37008 Salamanca, Spain
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