1
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Gilar M, Schomann N, Schott S, Rühl M. Impact of nucleotide hydrophobicity on oligonucleotides separation in liquid chromatography. J Chromatogr A 2025; 1753:465968. [PMID: 40311268 DOI: 10.1016/j.chroma.2025.465968] [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: 03/10/2025] [Revised: 04/11/2025] [Accepted: 04/14/2025] [Indexed: 05/03/2025]
Abstract
We investigated the contribution of nucleotide (nt) type and modifications on the retention and resolution of 22-24 nt long oligonucleotides in ion-pairing reversed-phase (IP RP) liquid chromatography (LC) and hydrophilic interaction chromatography (HILIC) methods. The nucleotides relative hydrophobicity affects the oligonucleotide LC retention and separation selectivity. The ion-pairing reagents of higher hydrophobicity (dipropylamine < dibutylamine < dipentylamine) require a greater organic solvents concentration to elute the oligonucleotides in IP RP LC. We observed that higher concentration of organic solvent reduced the contribution of (oligo)nucleotide hydrophobicity to the retention and led to more uniform separation of full-length oligonucleotide from its truncated products. We also investigated the diastereomeric resolution of 24 nt oligonucleotides with a single phosphorothioate modification at 5'-end. The diastereomeric separation is nucleotide-motif dependent; G (and modified G) nucleotides adjacent to the phosphorothioate linkage yield higher resolution of isomers than other types of nucleotides in IP RP LC and HILIC.
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Affiliation(s)
- Martin Gilar
- Waters Corporation, 34 Maple Street, Milford, MA 01757, USA.
| | - Nils Schomann
- BioSpring GmbH, Alt-Fechenheim 34, Frankfurt am Main 60386, Germany
| | - Saskia Schott
- BioSpring GmbH, Alt-Fechenheim 34, Frankfurt am Main 60386, Germany
| | - Michael Rühl
- BioSpring GmbH, Alt-Fechenheim 34, Frankfurt am Main 60386, Germany
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2
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Vikram PRH, Kandula DR, Gunta U, Kumar G, Deka R, Chiriki DS, Chethan KS, Bannimath N, Yadav T, Beeraka NM, Gurupadayya BM. NDSRIs Crisis in Pharmaceuticals; Insights on Formation Pathways, Root Causes, Risk Management, and Novel Analytical Techniques. Curr Med Chem 2025; 32:1065-1081. [PMID: 39279119 DOI: 10.2174/0109298673322023240829081220] [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: 04/28/2024] [Revised: 07/10/2024] [Accepted: 07/29/2024] [Indexed: 09/18/2024]
Abstract
The discovery of a new class of nitrosamine impurities called nitrosamine drug substance related impurities (NDSRIs) in pharmaceuticals has emerged as a significant challenge for the pharmaceutical sector due to their significant genotoxic and mutagenic effects. Regulatory bodies globally in active collaboration with all the concerned stake holders, are taking effective measures to prevent and control NDSRIs. This comprehensive review on NDSRIs discusses formation pathways, root cause analysis, acceptable intake limits, case studies, control strategies and regulatory responses pertaining to recent NDSRI incidents. This review discusses the novel liquid chromatographic techniques (LC-MS/MS, GC-MS/MS) used to identify and quantify of NDSRIs. This review would aid pharmaceutical professionals, R&D analytical and formulation scientists, and regulatory bodies in gaining deeper insights into the NDSRIs crisis, controlling NDSRIs in drug products, and ensuring their sensitive detection with accurate risk evaluation.
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Affiliation(s)
- P R Hemanth Vikram
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research (JSSAHER), Mysuru, Karnataka, 570015, India
- Xenone Healthcare Pvt. Ltd, #318, Third Floor, US Complex, Jasola, New Delhi, 110076, India
| | - Dilipkumar Reddy Kandula
- Department of Pharmacy, Shri Jagdishprasad Jhabarmal Tibrewala University, Jhunjhunu, 333010, Rajasthan, India
| | - Upendra Gunta
- Department of Biotechnology, Dravidian University, Kuppam, 517426, Andhra Pradesh, India
| | - Gunjan Kumar
- Xenone Healthcare Pvt. Ltd, #318, Third Floor, US Complex, Jasola, New Delhi, 110076, India
| | - Rajashree Deka
- Department of Zoology, Bhattadev University, Pathsala, Bajali, Assam, India
| | - Devi Sri Chiriki
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research (JSSAHER), Mysuru, Karnataka, 570015, India
| | - K S Chethan
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education and Research (JSS AHER), Mysuru, Karnataka, India
| | - Namitha Bannimath
- Department of Pharmacology, University of Galway, University Road, Galway, H91TK33, Ireland
| | - Thirumalesh Yadav
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research (JSSAHER), Mysuru, Karnataka, 570015, India
| | - Narasimha Murthy Beeraka
- Department of Human Anatomy and Histology, I.M. Sechenov First Moscow State Medical University (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russian Federation
- Raghavendra Institute of Pharmaceutical Education and Research (RIPER), Anantapuramu, Chiyyedu, Andhra Pradesh, 515721, India
- Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - B M Gurupadayya
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research (JSSAHER), Mysuru, Karnataka, 570015, India
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3
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Zahn E, Xie Y, Liu X, Karki R, Searfoss RM, de Luna Vitorino FN, Lempiäinen JK, Gongora J, Lin Z, Zhao C, Yuan ZF, Garcia BA. Development of a High-Throughput Platform for Quantitation of Histone Modifications on a New QTOF Instrument. Mol Cell Proteomics 2025; 24:100897. [PMID: 39708910 PMCID: PMC11787651 DOI: 10.1016/j.mcpro.2024.100897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 12/12/2024] [Accepted: 12/13/2024] [Indexed: 12/23/2024] Open
Abstract
Histone post-translational modifications (PTMs) regulate gene expression patterns through epigenetic mechanisms. The five histone proteins (H1, H2A, H2B, H3, and H4) are extensively modified, with over 75 distinct modification types spanning more than 200 sites. Despite strong advances in mass spectrometry (MS)-based approaches, identification and quantification of modified histone peptides remains challenging because of factors, such as isobaric peptides, pseudo-isobaric PTMs, and low stoichiometry of certain marks. Here, we describe the development of a new high-throughput method to identify and quantify over 150 modified histone peptides by LC-MS. Fast gradient microflow liquid chromatography and variable window sequential windows acquisition of all theoretical spectra data-independent acquisition on a new quadrupole time-of-flight platform is compared to a previous method using nanoflow LC-MS on an Orbitrap hybrid. Histones extracted from cells treated with either a histone deacetylase inhibitor or transforming growth factor-beta 1 were analyzed by data-independent acquisition on two mass spectrometers: an Orbitrap Exploris 240 with a 55-min nanoflow LC gradient and the SCIEX ZenoTOF 7600 with a 10-min microflow gradient. To demonstrate the reproducibility and speed advantage of the method, 100 consecutive injections of one sample were performed in less than 2 days on the quadrupole time-of-flight platform. The result is the comprehensive characterization of histone PTMs achieved in less than 20 min of total run time using only 200 ng of sample. Results for drug-treated histone samples are comparable to those produced by the previous method and can be achieved using less than one-third of the instrument time.
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Affiliation(s)
- Emily Zahn
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, Missouri, United States
| | - Yixuan Xie
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, Missouri, United States; State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xingyu Liu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, Missouri, United States
| | - Rashmi Karki
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, Missouri, United States
| | - Richard M Searfoss
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, Missouri, United States
| | - Francisca N de Luna Vitorino
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, Missouri, United States
| | - Joanna K Lempiäinen
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, Missouri, United States
| | - Joanna Gongora
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, Missouri, United States
| | - Zongtao Lin
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, Missouri, United States
| | - Chenfeng Zhao
- Department of Computer Science and Engineering, Washington University in St Louis, St Louis, Missouri, United States
| | - Zuo-Fei Yuan
- Center for Proteomics and Metabolomics, St Jude Children's Research Hospital, Memphis, Tennessee, United States
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, Missouri, United States.
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4
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Guo Y. Separation of nucleobases, nucleosides, nucleotides and oligonucleotides by hydrophilic interaction liquid chromatography (HILIC): A state-of-the-art review. J Chromatogr A 2024; 1738:465467. [PMID: 39486254 DOI: 10.1016/j.chroma.2024.465467] [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: 07/31/2024] [Revised: 10/16/2024] [Accepted: 10/21/2024] [Indexed: 11/04/2024]
Abstract
The polar nature of nucleobases, nucleosides and nucleotides makes hydrophilic interaction chromatography (HILIC) a good choice of technology for separation. Both naturally occurring and modified nucleosides and nucleotides have been successfully separated in HILIC. A wide range of stationary phases with different retention and selectivity are suitable for the separation of nucleobases, nucleosides and nucleotides; and a sufficient knowledge base is also available to guide method development. Although oligonucleotides are significantly different from nucleotides in terms of polarity and charges, HILIC has been shown to be a viable alternative to ion-pairing reversed-phase liquid chromatography (IP-RPLC). Only a few polar stationary phases have been shown to provide satisfactory performance; however, the requirements for the mobile phase composition including organic solvent, mobile phase pH and salt concentration are sufficiently understood. This review provides a comprehensive evaluation of the chromatographic conditions with a historical perspective on adopting and developing HILIC for the separation of nucleobases, nucleosides, nucleotides and oligonucleotides. The areas for more research and potential directions for future development activities are identified and discussed.
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Affiliation(s)
- Yong Guo
- School of Pharmacy and Health Sciences, Fairleigh Dickinson University, 230 Park Ave. Florham Park, New Jersey 07932, USA.
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Vikram P.R. H, Kumar G, Deka R, Beeraka NM, Kandula DR, Gorti SKK, Bannimath N, Kumar P, Kumar TP, Nikolenko VN, Gurupadayya B. Simultaneous multianalyte trace-level quantification of eight genotoxic nitrosamine impurities in valsartan Active Pharmaceutical Ingredient and tablet formulation using UFLC-MS/MS and greenness assessment. Microchem J 2024; 207:111678. [DOI: 10.1016/j.microc.2024.111678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2025]
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Yuan J, Yang L, Zhang H, Beeraka NM, Zhang D, Wang Q, Wang M, Pr HV, Sethi G, Wang G. Decoding tumor microenvironment: EMT modulation in breast cancer metastasis and therapeutic resistance, and implications of novel immune checkpoint blockers. Biomed Pharmacother 2024; 181:117714. [PMID: 39615165 DOI: 10.1016/j.biopha.2024.117714] [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: 08/14/2024] [Revised: 11/15/2024] [Accepted: 11/25/2024] [Indexed: 12/21/2024] Open
Abstract
Tumor microenvironment (TME) and epithelial-mesenchymal transition (EMT) play crucial roles in the initiation and progression of tumors. TME is composed of various cell types, such as immune cells, fibroblasts, and endothelial cells, as well as non-cellular components like extracellular matrix (ECM) proteins and soluble factors. These elements interact with tumor cells through a complex network of signaling pathways involving cytokines, growth factors, metabolites, and non-coding RNA-carrying exosomes. Hypoxic conditions within the TME further modulate these interactions, collectively influencing tumor growth, metastatic potential, and response to therapy. EMT represents a dynamic and reversible process where epithelial cells undergo phenotypic changes to adopt mesenchymal characteristics in several cancers, including breast cancers. This transformation enhances cell motility and imparts stem cell-like properties, which are closely associated with increased metastatic capability and resistance to conventional cancer treatments. Thus, understanding the crosstalk between the TME and EMT is essential for unraveling the underlying mechanisms of breast cancer metastasis and therapeutic resistance. This review uniquely examines the intricate interplay between the tumor TME and epithelial-mesenchymal transition EMT in driving breast cancer metastasis and treatment resistance. It explores the therapeutic potential of targeting the TME-EMT axis, specifically through CD73-TGF-β dual-blockade, to improve outcomes in triple-negative breast cancer. Additionally, it underscores new strategies to enhance immune checkpoint blockade (ICB) responses by modulating EMT, thereby offering innovative insights for more effective cancer treatment.
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Affiliation(s)
- Jie Yuan
- Department of Breast, Thyroid and Vascular Surgery, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, China.
| | - Li Yang
- Department of Clinical Laboratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, China.
| | - Hua Zhang
- Department of Breast, Thyroid and Vascular Surgery, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, China.
| | - Narasimha M Beeraka
- Department of Human Anatomy and Histology, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Str., Moscow 119991, Russia; Raghavendra Institute of Pharmaceutical Education and Research (RIPER), Chiyyedu, Anantapuramu, Andhra Pradesh 515721, India; Department of Studies in Molecular Biology, Faculty of Science and Technology, University of Mysore, Mysore, Karnataka, 570006, India.
| | - Danfeng Zhang
- Department of Breast, Thyroid and Vascular Surgery, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, China.
| | - Qun Wang
- Department of Breast, Thyroid and Vascular Surgery, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, China.
| | - Minghua Wang
- Department of Breast, Thyroid and Vascular Surgery, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, China.
| | - Hemanth Vikram Pr
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research (JSS AHER), Mysuru, Karnataka, India.
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
| | - Geng Wang
- Department of Breast, Thyroid and Vascular Surgery, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, China.
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7
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Bartlett MG. Current state of hydrophilic interaction liquid chromatography of oligonucleotides. J Chromatogr A 2024; 1736:465378. [PMID: 39293276 DOI: 10.1016/j.chroma.2024.465378] [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: 07/26/2024] [Revised: 09/11/2024] [Accepted: 09/13/2024] [Indexed: 09/20/2024]
Abstract
There has been a significant increase in the use of hydrophilic interaction liquid chromatography (HILIC) to separate oligonucleotides. This rise in the use of HILIC has correlated to the increasing success of oligonucleotides as therapeutic treatments and reagents in biomedical research. As more scientists need to routinely analyze oligonucleotides in addition to small molecules, peptides, and proteins using the same analytical instruments, it becomes difficult to use traditional types of analyses such as ion-pair reversed-phase chromatography. This increased use has led to new approaches that have improved the utility of HILIC to the point where it has become a legitimate alternative approach to ion-pair reversed-phase chromatography. This review highlights recent advances in HILIC separations of oligonucleotides with a focus on the underlying mechanisms of action. While HILIC has made significant gains in performance, there still remain challenges, which if properly addressed will continue to propel this approach forward.
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Affiliation(s)
- Michael G Bartlett
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA.
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8
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Kundu S, Selvaraj R, Reddy K, Vikram Pr H, Gurupadayya B. Determination of ursolic acid in ethanolic extract of Rotheca serrata (L.) Steane & Mabb. by HPLC method. Nat Prod Res 2024:1-7. [PMID: 39290190 DOI: 10.1080/14786419.2024.2405007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 08/07/2024] [Accepted: 09/09/2024] [Indexed: 09/19/2024]
Abstract
Rotheca serrata (L.) Steane & Mabb. a plant having significant medicinal value is used in treating a fever, rheumatism, inflammation, pain, and malarial fever. Ursolic acid has a five-ringed pentacyclic structure belongs to the family of triterpenoids. It has antioxidant, antitumor, and hepato-protective properties. The method in HPLC was developed on a SHIMADZU, Shimpack ODS (25 cm × 4.6 mm, 5 µm) column. The mobile phase consisted of a 70:25:5 (v/v/v) mixture of methanol, acetonitrile, and 0.02 M ammonium acetate buffer (pH 3.5). A flow rate of 1.2 mL/min and λmax of 215 nm. Ursolic acid from the extract and standard was eluted at the same retention time of 4.1 min. 20-120 µg/mL was the linearity range chosen and was found to be linear (R2=0.996). The value of LOD was 0.85 µg/mL and LOQ was 1.96 µg/mL. The method for analysis of ursolic was found to be accurate with good repeatability.
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Affiliation(s)
- Sumedha Kundu
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research (JSSAHER), Mysuru, Karnataka, India
| | - Rajeshwari Selvaraj
- Department of Pharmacognosy, JSS College of Pharmacy, JSS Academy of Higher Education and Research (JSSAHER), Mysuru, Karnataka, India
| | - Kalyani Reddy
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research (JSSAHER), Mysuru, Karnataka, India
| | - Hemanth Vikram Pr
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research (JSSAHER), Mysuru, Karnataka, India
- Department of Quality Control, Xenone Healthcare Pvt. Ltd, Jasola, New Delhi, India
| | - Bannimath Gurupadayya
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research (JSSAHER), Mysuru, Karnataka, India
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Ewles M, Ledvina AR, Powers B, Thomas CE. Observations from a decade of oligonucleotide bioanalysis by LC-MS. Bioanalysis 2024; 16:615-629. [PMID: 38634379 PMCID: PMC11352704 DOI: 10.4155/bio-2024-0007] [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: 01/10/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024] Open
Abstract
There is a growing need for efficient bioanalysis of oligonucleotide therapeutics. This broad class of molecules presents numerous challenges relative to traditional small molecule therapeutics. Methodologies including ligand-binding assays or polymerase chain reaction may be fit-for-purpose in many instances, but liquid chromatography coupled to mass spectrometry (LC-MS) often delivers the best balance of sensitivity and selectivity. Over the last decade, we have engaged with many such molecules and derived insights into challenges and solutions. Herein, we provide four case studies illustrating challenges we have encountered. These issues include low or variable analyte recovery, poor resolution from related species, chromatographic abnormalities or challenging sensitivity. We present a summary of considerations, based on these experiences, to assist others working in the area.
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Affiliation(s)
- Matthew Ewles
- Labcorp Early Development Laboratories Limited; Otley Road, Harrogate; North Yorkshire, HG3 1PY, UK
| | - Aaron R Ledvina
- Labcorp Early Development Laboratories, Inc.; 3301 Kinsman Blvd., Madison, WI 53704, USA
| | - Brendan Powers
- Labcorp Early Development Laboratories, Inc.; 3301 Kinsman Blvd., Madison, WI 53704, USA
| | - C Eric Thomas
- Labcorp Central Laboratory Services Limited Partnership; 8211 SciCor Drive, Indianapolis, IN 46214, USA
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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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Guimaraes GJ, Leach FE, Bartlett MG. Microflow Liquid Chromatography – Multi-Emitter Nanoelectrospray Mass Spectrometry of Oligonucleotides. J Chromatogr A 2023; 1696:463976. [PMID: 37054634 DOI: 10.1016/j.chroma.2023.463976] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/08/2023]
Abstract
While the most sensitive LC-MS methods for oligonucleotide analysis contain ion-pairs in the mobile phase, these modifiers have been associated with instrument contamination and ion suppression. Typically, entire LC-MS systems are reserved for oligonucleotide LC-MS when using ion-pairing buffers. To overcome these limitations, numerous HILIC methods, liberated from ion-pairs, have been recently developed. Since ion-pairs play a role in analyte desorption from ESI droplets, their removal from mobile phases tend to impact method sensitivity. An effective way to recover MS sensitivity is to reduce the LC flow rate and therefore reduce ESI droplet size. With a focus on MS sensitivity, this study investigates the applicability of a microflow LC- nanoelectrospray MS platform in oligonucleotide ion-pair RP and HILIC LC-MS methods. The platform is effective and substantially increased the MS sensitivity of HILIC methods. Furthermore, LC method development for both types of separations provide insight into microflow chromatography of oligonucleotides, an under investigated chromatographic scale.
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12
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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: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [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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MacNeill R. Pursuing the Polar Routes with Penguins and Polar Bears: Balancing the Choice of Chromatographic Mode. LCGC NORTH AMERICA 2022. [DOI: 10.56530/lcgc.na.cl3487f8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Reversed-phase liquid chromatography (RPLC) may have historical popularity, but it is not the only LC technique available to chromatographers. To help balance the choice of chromatographic technique, a discussion of the merits of being flexible when making the choice of LC technique for a given application is presented. Because having a flexible perspective is particularly important for biotherapeutics, it is important that choosing which technique to use is determined based on good science and begins with a physicochemical property assessment of the analytes, followed by subsequent alignment with the most appropriate retentive mode. An Earth-based figurative analogy is used to help highlight several popular LC techniques.
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MacNeill R. Hydrophilic-Phase Extraction: A New Avenue of Solid-Phase Extraction for Oligonucleotide Bioanalysis. LCGC EUROPE 2022. [DOI: 10.56530/lcgc.eu.kt3381t8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A novel mode of bioanalytical solid-phase extraction (SPE) has been developed and used for a quantitative application involving an RNA oligonucleotide therapeutic candidate. Previously established protocols and media showed very little recovery, and so this new approach, based on hydrophilic interaction liquid chromatography (HILIC) with an aminopropyl-bonded phase on a silica support and providing an essentially uncharted avenue of selectivity, was explored. The procedure featured only one step prior to sample load, high-organic sorbent conditioning, two washes following the load that switched between low and high pH, followed by elution in an a highly eluotropic HILIC composition. The moniker of “hydrophilic-phase extraction” (HPE) was given to the procedure. The HPE was proven to be a critical part of a fully quantitative HILIC–high-resolution mass spectrometry (HRMS) method for the RNA oligonucleotide and has potential for general application.
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