1
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Yamashita T, Nakamoto K, Hitaoka S, Mizoguchi J, Watanabe T, Hasebe T. Influence of oligonucleotides structures for separation of diastereomers by capillary electrophoresis method using polyvinylpyrrolidone 1,300,000. J Chromatogr A 2024; 1725:464945. [PMID: 38688053 DOI: 10.1016/j.chroma.2024.464945] [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: 02/13/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
In the field of oligonucleotides drug discovery, phosphorothioate (PS) modification has been recognized as an effective tool to overcome the nuclease digestion, and generates 2n of possible diastereomers, where n equals the number of PS linkages. However, it is also well known that differences in drug efficacy and toxicity are caused by differences in stereochemistry of oligonucleotides. Therefore, the development of a high-resolution analytical method that enables stereo discrimination of oligonucleotides is desired. Under this circumstance, capillary electrophoresis (CE) using polyvinylpyrrolidone (PVP) is considered as one of the useful tools for the separation analysis of diastereomers. In this study, we evaluated the several oligonucleotides with the structural diversities in order to understand the separation mechanism of the diastereomers by CE. Especially, five kinds of 2'-moieties were deeply examined by CE with PVP 1,300,000 polymer solution. We found that different trend of the peak shapes and the peak resolution were observed among these oligonucleotides. For example, the better peak resolution was observed in 6 mer PS3-DNA compared to the rigid structure of 6 mer PS3-LNA. As for this reason, the computational simulation revealed that difference of accessible surface area caused by the steric structure of thiophosphate in each oligonucleotide is one of the key attributes to explain the separation of the diastereomers. In addition, we achieved the separation of sixteen peak tops of the diastereomers in 6 mer PS4-DNA, and the complete separation of fifteen diastereomers in 6 mer PS4-RNA. These knowledge for the separation of the diastereomers by CE will be expected to the quality control of the oligonucleotide drugs.
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Affiliation(s)
- Taro Yamashita
- Analytical Research, Pharmaceutical Science & Technology Unit, Pharmaceutical Profiling & Development Function, Deep Human Biology Learning, Eisai Co., Ltd., 5-1-3 Tokodai, Tsukuba, Ibaraki 300-2635, Japan.
| | - Kosuke Nakamoto
- Analytical Research, Pharmaceutical Science & Technology Unit, Pharmaceutical Profiling & Development Function, Deep Human Biology Learning, Eisai Co., Ltd., 5-1-3 Tokodai, Tsukuba, Ibaraki 300-2635, Japan
| | - Seiji Hitaoka
- Emerging Modality Generation Department, Discovery Evidence Generation Function, Deep Human Biology Learning, Eisai Co., Ltd., 5-1-3 Tokodai, Tsukuba, Ibaraki 300-2635, Japan
| | - Junichi Mizoguchi
- Analytical Research, Pharmaceutical Science & Technology Unit, Pharmaceutical Profiling & Development Function, Deep Human Biology Learning, Eisai Co., Ltd., 5-1-3 Tokodai, Tsukuba, Ibaraki 300-2635, Japan
| | - Tomohiro Watanabe
- Analytical Research, Pharmaceutical Science & Technology Unit, Pharmaceutical Profiling & Development Function, Deep Human Biology Learning, Eisai Co., Ltd., 5-1-3 Tokodai, Tsukuba, Ibaraki 300-2635, Japan
| | - Takashi Hasebe
- Analytical Research, Pharmaceutical Science & Technology Unit, Pharmaceutical Profiling & Development Function, Deep Human Biology Learning, Eisai Co., Ltd., 5-1-3 Tokodai, Tsukuba, Ibaraki 300-2635, Japan
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2
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Lardeux H, Stavenhagen K, Paris C, Dueholm R, Kurek C, De Maria L, Gnerlich F, Leek T, Czechtizky W, Guillarme D, Jora M. Unravelling the Link between Oligonucleotide Structure and Diastereomer Separation in Hydrophilic Interaction Chromatography. Anal Chem 2024. [PMID: 38855895 DOI: 10.1021/acs.analchem.4c01384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Therapeutic oligonucleotides (ONs) commonly incorporate phosphorothioate (PS) modifications. These introduce chiral centers and generate ON diastereomers. The increasing number of ONs undergoing clinical trials and reaching the market has led to a growing interest to better characterize the ON diastereomer composition, especially for small interfering ribonucleic acids (siRNAs). In this study, and for the first time, we identify higher-order structures as the major cause of ON diastereomer separation in hydrophilic interaction chromatography (HILIC). We have used conformational predictions and melting profiles of several representative full-length ONs to first analyze ON folding and then run mass spectrometry and HILIC to underpin the link between their folding and diastereomer separation. On top, we show how one can either enhance or suppress diastereomer separation depending on chromatographic settings, such as column temperature, pore size, stationary phase, mobile-phase ionic strength, and organic modifier. This work will significantly facilitate future HILIC-based characterization of PS-containing ONs; e.g., enabling monitoring of batch-to-batch diastereomer distributions in full-length siRNAs, a complex task that is now for the first time shown as possible on this delicate class of therapeutic double-stranded ONs.
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Affiliation(s)
- Honorine Lardeux
- School of Pharmaceutical Sciences, University of Geneva, CMU─Rue Michel Servet 1, Geneva 4 1211, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU─Rue Michel Servet 1, Geneva 4 1211, Switzerland
| | - Kathrin Stavenhagen
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal 431 83, Sweden
| | - Clément Paris
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal 431 83, Sweden
| | - Rikke Dueholm
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal 431 83, Sweden
| | - Camille Kurek
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal 431 83, Sweden
| | - Leonardo De Maria
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal 431 83, Sweden
| | - Felix Gnerlich
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal 431 83, Sweden
| | - Tomas Leek
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal 431 83, Sweden
| | - Werngard Czechtizky
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal 431 83, Sweden
| | - Davy Guillarme
- School of Pharmaceutical Sciences, University of Geneva, CMU─Rue Michel Servet 1, Geneva 4 1211, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU─Rue Michel Servet 1, Geneva 4 1211, Switzerland
| | - Manasses Jora
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal 431 83, Sweden
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3
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Shivakumar KM, Mahendran G, Brown JA. Locked Nucleic Acid Oligonucleotides Facilitate RNA•LNA-RNA Triple-Helix Formation and Reduce MALAT1 Levels. Int J Mol Sci 2024; 25:1630. [PMID: 38338910 PMCID: PMC10855403 DOI: 10.3390/ijms25031630] [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: 12/01/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and multiple endocrine neoplasia-β (MENβ) are two long noncoding RNAs upregulated in multiple cancers, marking these RNAs as therapeutic targets. While traditional small-molecule and antisense-based approaches are effective, we report a locked nucleic acid (LNA)-based approach that targets the MALAT1 and MENβ triple helices, structures comprised of a U-rich internal stem-loop and an A-rich tract. Two LNA oligonucleotides resembling the A-rich tract (i.e., A9GCA4) were examined: an LNA (L15) and a phosphorothioate LNA (PS-L15). L15 binds tighter than PS-L15 to the MALAT1 and MENβ stem loops, although both L15 and PS-L15 enable RNA•LNA-RNA triple-helix formation. Based on UV thermal denaturation assays, both LNAs selectively stabilize the Hoogsteen interface by 5-13 °C more than the Watson-Crick interface. Furthermore, we show that L15 and PS-L15 displace the A-rich tract from the MALAT1 and MENβ stem loop and methyltransferase-like protein 16 (METTL16) from the METTL16-MALAT1 triple-helix complex. Human colorectal carcinoma (HCT116) cells transfected with LNAs have 2-fold less MALAT1 and MENβ. This LNA-based approach represents a potential therapeutic strategy for the dual targeting of MALAT1 and MENβ.
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Affiliation(s)
| | | | - Jessica A. Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; (K.M.S.); (G.M.)
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4
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Vaillant A. Oligonucleotide-Based Therapies for Chronic HBV Infection: A Primer on Biochemistry, Mechanisms and Antiviral Effects. Viruses 2022; 14:v14092052. [PMID: 36146858 PMCID: PMC9502277 DOI: 10.3390/v14092052] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/08/2022] [Accepted: 09/08/2022] [Indexed: 11/21/2022] Open
Abstract
Three types of oligonucleotide-based medicines are under clinical development for the treatment of chronic HBV infection. Antisense oligonucleotides (ASOs) and synthetic interfering RNA (siRNA) are designed to degrade HBV mRNA, and nucleic acid polymers (NAPs) stop the assembly and secretion of HBV subviral particles. Extensive clinical development of ASOs and siRNA for a variety of liver diseases has established a solid understanding of their pharmacodynamics, accumulation in different tissue types in the liver, pharmacological effects, off-target effects and how chemical modifications and delivery approaches affect these parameters. These effects are highly conserved for all ASO and siRNA used in human studies to date. The clinical assessment of several ASO and siRNA compounds in chronic HBV infection in recent years is complicated by the different delivery approaches used. Moreover, these assessments have not considered the large clinical database of ASO/siRNA function in other liver diseases and known off target effects in other viral infections. The goal of this review is to summarize the current understanding of ASO/siRNA/NAP pharmacology and integrate these concepts into current clinical results for these compounds in the treatment of chronic HBV infection.
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Affiliation(s)
- Andrew Vaillant
- Replicor Inc., 6100 Royalmount Avenue, Montreal, QC H4P 2R2, Canada
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5
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Roussis SG, Cedillo I, Rentel C. Characterizing the Diastereoisomeric Distribution of Phosphorothioate Oligonucleotides by Metal Ion Complexation Chromatography, In-Series Reversed Phase-Strong Anion Exchange Chromatography, and 31P NMR. Anal Chem 2021; 93:16035-16042. [PMID: 34813705 DOI: 10.1021/acs.analchem.1c03593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Replacement of a non-bridging oxygen atom of the phosphate diester linkage of an oligonucleotide by sulfur conveys pharmacokinetic benefits, such as increased nuclease resistance and enhanced protein binding. Substitution renders the internucleotide linkages chiral, and so phosphorothioate diester (PS) oligonucleotides comprise complex mixtures of diastereoisomers. Currently, chromatographic separation of individual diastereoisomers is limited to oligonucleotides that contain no more than about four or five PS linkages. The development of therapeutic PS oligonucleotides, which often contain >15 PS linkages, would be greatly aided by methods useful for assessing batch-to-batch stereo-reproducibility. To this effect, the relative sensitivities of metal ion complexation chromatography (MICC), in-series reversed phase-strong anion exchange chromatography (RP-SAX), and 31P NMR toward changes in the diastereoisomeric distributions of therapeutic PS oligonucleotides were compared. Model oligonucleotides synthesized under conditions known to impact PS stereochemistry were used to evaluate the method performance, and all three methods showed excellent sensitivity toward changes in the diastereoisomeric composition. Interactions via the solvent-accessible areas and a combination of hydrophobic and electrostatic forces may be responsible for the selectivity demonstrated by MICC and in-series RP-SAX, respectively.
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Affiliation(s)
- Stilianos G Roussis
- Ionis Pharmaceuticals, 2855 Gazelle Ct., Carlsbad, California 92010, United States
| | - Isaiah Cedillo
- Ionis Pharmaceuticals, 2855 Gazelle Ct., Carlsbad, California 92010, United States
| | - Claus Rentel
- Ionis Pharmaceuticals, 2855 Gazelle Ct., Carlsbad, California 92010, United States
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6
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Kiełpiński ŁJ, Funder ED, Schmidt S, Hagedorn PH. Characterization of Escherichia coli RNase H Discrimination of DNA Phosphorothioate Stereoisomers. Nucleic Acid Ther 2021; 31:383-391. [PMID: 34619060 PMCID: PMC8713576 DOI: 10.1089/nat.2021.0055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Phosphorothioate (PS) modification of antisense oligonucleotides (ASOs) is a
critical factor enabling their therapeutic use. Standard chemical synthesis
incorporates this group in a stereorandom manner; however, significant effort
was made over the years to establish and characterize the impact of chiral
control. In this work, we present our in-depth characterization of interactions
between Escherichia coli RNase H and RNA-DNA heteroduplexes
carrying chirally defined PS groups. First, using a massive parallel assay, we
showed that at least a single Rp-PS group is necessary for
efficient RNase H-mediated cleavage. We followed by demonstrating that this
group needs to be aligned to the phosphate-binding pocket of RNase H, and that
chiral status of other PS groups in close proximity to RNase H does not affect
cleavage efficiency. We have shown that RNase H's PS chiral preference
can be utilized to guide cleavage to a specific chemical bond. Finally, we
present a strategy for ASO optimization by mapping preferred RNase H cleavage
sites of a non-thioated compound, followed by introduction of
Rp-PS in a strategic position. This results in a cleaner
cleavage profile and higher knockdown activity compared with a compound carrying
an Sp-PS at the same location.
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Affiliation(s)
- Łukasz J Kiełpiński
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Erik Daa Funder
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Steffen Schmidt
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, Hørsholm, Denmark
| | - Peter H Hagedorn
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, Hørsholm, Denmark
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7
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Angelini A, Saha PK, Jain A, Jung SY, Mynatt RL, Pi X, Xie L. PHDs/CPT1B/VDAC1 axis regulates long-chain fatty acid oxidation in cardiomyocytes. Cell Rep 2021; 37:109767. [PMID: 34610308 PMCID: PMC8658754 DOI: 10.1016/j.celrep.2021.109767] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 05/19/2021] [Accepted: 09/02/2021] [Indexed: 12/23/2022] Open
Abstract
Cardiac metabolism is a high-oxygen-consuming process, showing a preference for long-chain fatty acid (LCFA) as the fuel source under physiological conditions. However, a metabolic switch (favoring glucose instead of LCFA) is commonly reported in ischemic or late-stage failing hearts. The mechanism regulating this metabolic switch remains poorly understood. Here, we report that loss of PHD2/3, the cellular oxygen sensors, blocks LCFA mitochondria uptake and β-oxidation in cardiomyocytes. In high-fat-fed mice, PHD2/3 deficiency improves glucose metabolism but exacerbates the cardiac defects. Mechanistically, we find that PHD2/3 bind to CPT1B, a key enzyme of mitochondrial LCFA uptake, promoting CPT1B-P295 hydroxylation. Further, we show that CPT1B-P295 hydroxylation is indispensable for its interaction with VDAC1 and LCFA β-oxidation. Finally, we demonstrate that a CPT1B-P295A mutant constitutively binds to VDAC1 and rescues LCFA metabolism in PHD2/3-deficient cardiomyocytes. Together, our data identify an oxygen-sensitive regulatory axis involved in cardiac metabolism.
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Affiliation(s)
- Aude Angelini
- Department of Medicine, Section of Athero & Lipo, Baylor College of Medicine, Houston, TX 77030, USA; Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Pradip K Saha
- Department of Medicine, Division of Diabetes, Endocrinology & Metabolism, Diabetes Research Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Antrix Jain
- Department of Biochemistry and Molecular Biology, Mass Spectrometry Proteomics Core, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sung Yun Jung
- Department of Biochemistry and Molecular Biology, Mass Spectrometry Proteomics Core, Baylor College of Medicine, Houston, TX 77030, USA
| | - Randall L Mynatt
- Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA
| | - Xinchun Pi
- Department of Medicine, Section of Athero & Lipo, Baylor College of Medicine, Houston, TX 77030, USA; Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Liang Xie
- Department of Medicine, Section of Athero & Lipo, Baylor College of Medicine, Houston, TX 77030, USA; Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX 77030, USA.
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8
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Hansen HF, Albaek N, Hansen BR, Shim I, Bohr H, Koch T. In vivo uptake of antisense oligonucleotide drugs predicted by ab initio quantum mechanical calculations. Sci Rep 2021; 11:6321. [PMID: 33737567 PMCID: PMC7973520 DOI: 10.1038/s41598-021-85453-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 02/17/2021] [Indexed: 11/10/2022] Open
Abstract
Liver and kidney uptake and antisense activity is studied for a series of Locked Nucleic Acid (LNA) oligonucleotides with fully stereo-defined, internucleoside linkages. These stereo-specific phosphorothioates are made with a newly developed synthesis method and are being analyzed both theoretically and experimentally. Their structures are obtained theoretically by using many-body Schrödinger equations applied to a group of 11 stereo-defined LNA antisense oligonucleotides selected for biological experiments. The fully converged electronic structures were obtained from ab initio quantum calculations providing the specific electronic structures. One important result was the observation that the calculated electronic structure, represented by the iso-surface area of the electron density in Å2, correlated linearly with LNA oligonucleotide uptake in the liver and kidney. This study also shows that more complex biological phenomena, such as drug activity, will require more molecular and cellular identifiers than used here before a correlation can be found. Establishing biological correlations between quantum mechanical (QM) calculated structures and antisense oligonucleotides is novel, and this method may constitute new tools in drug discovery.
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Affiliation(s)
| | - Nanna Albaek
- Roche Innovation Center Copenhagen, Fremtidsvej 3, 2970, Hoersholm, Denmark
| | - Bo Rode Hansen
- Roche Innovation Center Copenhagen, Fremtidsvej 3, 2970, Hoersholm, Denmark
| | - Irene Shim
- Department of Chemistry, B-206-DTU, The Technical University of Denmark, 2800, Lyngby, Denmark
| | - Henrik Bohr
- Department of Chemical Engineering, B-229-DTU, The Technical University of Denmark, Lyngby, Denmark.
| | - Troels Koch
- Roche Innovation Center Copenhagen, Fremtidsvej 3, 2970, Hoersholm, Denmark
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9
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Yarahmadi A, Shahrokhi SZ, Mostafavi-Pour Z, Azarpira N. MicroRNAs in diabetic nephropathy: From molecular mechanisms to new therapeutic targets of treatment. Biochem Pharmacol 2020; 189:114301. [PMID: 33203517 DOI: 10.1016/j.bcp.2020.114301] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 12/16/2022]
Abstract
Despite considerable investigation in diabetic nephropathy (DN) pathogenesis and possible treatments, current therapies still do not provide competent prevention from disease progression to end-stage renal disease (ESRD) in most patients. Therefore, investigating exact molecular mechanisms and important mediators underlying DN may help design better therapeutic approaches for proper treatment. MicroRNAs (MiRNAs) are a class of small non-coding RNAs that play a crucial role in post-transcriptional regulation of many gene expression within the cells and present an excellent opportunity for new therapeutic approaches because their profile is often changed during many diseases, including DN. This review discusses the most important signaling pathways involved in DN and changes in miRNAs profile in each signaling pathway. We also suggest possible approaches for miRNA derived interventions for designing better treatment of DN.
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Affiliation(s)
- Amir Yarahmadi
- Department of Clinical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyedeh Zahra Shahrokhi
- Department of Laboratory Medicine, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zohreh Mostafavi-Pour
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Negar Azarpira
- Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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10
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Funder ED, Albæk N, Moisan A, Sewing S, Koch T. Refining LNA safety profile by controlling phosphorothioate stereochemistry. PLoS One 2020; 15:e0232603. [PMID: 32530964 PMCID: PMC7292364 DOI: 10.1371/journal.pone.0232603] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 04/17/2020] [Indexed: 01/01/2023] Open
Abstract
Drug discovery with phosphorothioate oligonucleotides is an area of intensive research. In this study we have controlled the stereochemistry of the phosphorothioate backbone of LNA oligonucleotides to investigate the differences in safety profile, target mRNA knock down, and cellular uptake in vitro. The study reveals that controlling only four stereocenters in an isomeric phosphorothioate mixture can improve the therapeutic index significantly by improving safety without compromising activity.
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Affiliation(s)
| | - Nanna Albæk
- Roche Innovation Center Copenhagen A/S, Hørsholm, Denmark
| | - Annie Moisan
- Roche Innovation Center Basel, Basel, Switzerland
| | | | - Troels Koch
- Roche Innovation Center Copenhagen A/S, Hørsholm, Denmark
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11
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Crooke ST, Vickers TA, Liang XH. Phosphorothioate modified oligonucleotide-protein interactions. Nucleic Acids Res 2020; 48:5235-5253. [PMID: 32356888 PMCID: PMC7261153 DOI: 10.1093/nar/gkaa299] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/08/2020] [Accepted: 04/17/2020] [Indexed: 12/18/2022] Open
Abstract
Antisense oligonucleotides (ASOs) interact with target RNAs via hybridization to modulate gene expression through different mechanisms. ASO therapeutics are chemically modified and include phosphorothioate (PS) backbone modifications and different ribose and base modifications to improve pharmacological properties. Modified PS ASOs display better binding affinity to the target RNAs and increased binding to proteins. Moreover, PS ASO protein interactions can affect many aspects of their performance, including distribution and tissue delivery, cellular uptake, intracellular trafficking, potency and toxicity. In this review, we summarize recent progress in understanding PS ASO protein interactions, highlighting the proteins with which PS ASOs interact, the influence of PS ASO protein interactions on ASO performance, and the structure activity relationships of PS ASO modification and protein interactions. A detailed understanding of these interactions can aid in the design of safer and more potent ASO drugs, as illustrated by recent findings that altering ASO chemical modifications dramatically improves therapeutic index.
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12
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Xu D, Rivas-Bascón N, Padial NM, Knouse KW, Zheng B, Vantourout JC, Schmidt MA, Eastgate MD, Baran PS. Enantiodivergent Formation of C-P Bonds: Synthesis of P-Chiral Phosphines and Methylphosphonate Oligonucleotides. J Am Chem Soc 2020; 142:5785-5792. [PMID: 32109356 DOI: 10.1021/jacs.9b13898] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Phosphorus Incorporation (PI, abbreviated Π) reagents for the modular, scalable, and stereospecific synthesis of chiral phosphines and methylphosphonate nucleotides are reported. Synthesized from trans-limonene oxide, this reagent class displays an unexpected reactivity profile and enables access to chemical space distinct from that of the Phosphorus-Sulfur Incorporation reagents previously disclosed. Here, the adaptable phosphorus(V) scaffold enables sequential addition of carbon nucleophiles to produce a variety of enantiopure C-P building blocks. Addition of three carbon nucleophiles to Π, followed by stereospecific reduction, affords useful P-chiral phosphines; introduction instead of a single methyl group reveals the first stereospecific synthesis of methylphosphonate oligonucleotide precursors. While both Π enantiomers are available, only one isomer is required-the order of nucleophile addition controls the absolute stereochemistry of the final product through a unique enantiodivergent design.
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Affiliation(s)
- Dongmin Xu
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Nazaret Rivas-Bascón
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Natalia M Padial
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Kyle W Knouse
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Bin Zheng
- Chemistry Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Julien C Vantourout
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Michael A Schmidt
- Chemistry Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Martin D Eastgate
- Chemistry Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Phil S Baran
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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13
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Demelenne A, Gou MJ, Nys G, Parulski C, Crommen J, Servais AC, Fillet M. Evaluation of hydrophilic interaction liquid chromatography, capillary zone electrophoresis and drift tube ion-mobility quadrupole time of flight mass spectrometry for the characterization of phosphodiester and phosphorothioate oligonucleotides. J Chromatogr A 2019; 1614:460716. [PMID: 31761437 DOI: 10.1016/j.chroma.2019.460716] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 11/09/2019] [Accepted: 11/14/2019] [Indexed: 01/23/2023]
Abstract
Oligonucleotide-based medicines that can modulate gene expression have numerous potential applications in targeted therapies. Most of the commercialized therapeutic oligonucleotides are chemically modified to increase their in vivo lifetime. In this work, we studied poly-deoxy(thymidylic) acids (dT) and modified phosphorothioate oligonucleotides (PS). Several analytical techniques, including ion-pair reverse phase liquid chromatography, are described in the literature to assess their quality but most of them present significant drawbacks. In the present study, dT and PS mixtures were analyzed by hydrophilic interaction liquid chromatography (HILIC) and capillary zone electrophoresis (CZE) coupled to ultraviolet detection. In HILIC, the selectivities of three types of stationary phases (dihydroxypropane, phosphorylcholine and amide) were compared. Optimal conditions were determined and consisted of an amide stationary phase with a mobile phase made up of water, acetonitrile and 15 mM ammonium acetate (pH 5.5). In those conditions, high resolving power and good repeatability were achieved. In CZE, the effect of the background electrolyte (BGE), its pH and concentration were evaluated. A BGE made up of 300 mM ammonium acetate adjusted to pH 6.0 was selected. Finally, the two techniques were compared in terms of selectivity, repeatability and peak efficiency. In the second part of the study, HILIC and CZE were both coupled to a drift-tube ion-mobility quadrupole time-of-flight MS detector (DTIMS-QTOF) to assess the added value of this coupling for oligonucleotide characterization. Indeed, by using the measured collision cross section (CCS), the evaluation of the number of nucleotides was performed. Looking across the results, HILIC and CZE coupled to DTIMS-QTOF can be considered as promising tools for the quality control of oligonucleotides.
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Affiliation(s)
- Alice Demelenne
- Laboratory for the Analysis of Medicines, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege, Quartier Hospital, Avenue Hippocrate 15, Liege 4000, Belgium
| | - Marie-Jia Gou
- Laboratory for the Analysis of Medicines, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege, Quartier Hospital, Avenue Hippocrate 15, Liege 4000, Belgium
| | - Gwenaël Nys
- Laboratory for the Analysis of Medicines, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege, Quartier Hospital, Avenue Hippocrate 15, Liege 4000, Belgium
| | - Chloé Parulski
- Laboratory for the Analysis of Medicines, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege, Quartier Hospital, Avenue Hippocrate 15, Liege 4000, Belgium
| | - Jacques Crommen
- Laboratory for the Analysis of Medicines, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege, Quartier Hospital, Avenue Hippocrate 15, Liege 4000, Belgium
| | - Anne-Catherine Servais
- Laboratory for the Analysis of Medicines, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege, Quartier Hospital, Avenue Hippocrate 15, Liege 4000, Belgium
| | - Marianne Fillet
- Laboratory for the Analysis of Medicines, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege, Quartier Hospital, Avenue Hippocrate 15, Liege 4000, Belgium.
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14
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Shen W, De Hoyos CL, Migawa MT, Vickers TA, Sun H, Low A, Bell TA, Rahdar M, Mukhopadhyay S, Hart CE, Bell M, Riney S, Murray SF, Greenlee S, Crooke RM, Liang XH, Seth PP, Crooke ST. Chemical modification of PS-ASO therapeutics reduces cellular protein-binding and improves the therapeutic index. Nat Biotechnol 2019; 37:640-650. [PMID: 31036929 DOI: 10.1038/s41587-019-0106-2] [Citation(s) in RCA: 180] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 03/15/2019] [Indexed: 12/13/2022]
Abstract
The molecular mechanisms of toxicity of chemically modified phosphorothioate antisense oligonucleotides (PS-ASOs) are not fully understood. Here, we report that toxic gapmer PS-ASOs containing modifications such as constrained ethyl (cEt), locked nucleic acid (LNA) and 2'-O-methoxyethyl (2'-MOE) bind many cellular proteins with high avidity, altering their function, localization and stability. We show that RNase H1-dependent delocalization of paraspeckle proteins to nucleoli is an early event in PS-ASO toxicity, followed by nucleolar stress, p53 activation and apoptotic cell death. Introduction of a single 2'-O-methyl (2'-OMe) modification at gap position 2 reduced protein-binding, substantially decreasing hepatotoxicity and improving the therapeutic index with minimal impairment of antisense activity. We validated the ability of this modification to generally mitigate PS-ASO toxicity with more than 300 sequences. Our findings will guide the design of PS-ASOs with optimal therapeutic profiles.
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Affiliation(s)
- Wen Shen
- Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | | | | | | | - Hong Sun
- Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Audrey Low
- Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | | | | | | | | | | | - Stan Riney
- Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
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15
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Knouse KW, deGruyter JN, Schmidt MA, Zheng B, Vantourout JC, Kingston C, Mercer SE, Mcdonald IM, Olson RE, Zhu Y, Hang C, Zhu J, Yuan C, Wang Q, Park P, Eastgate MD, Baran PS. Unlocking P(V): Reagents for chiral phosphorothioate synthesis. Science 2018; 361:1234-1238. [PMID: 30072577 DOI: 10.1126/science.aau3369] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 07/12/2018] [Indexed: 12/21/2022]
Abstract
Phosphorothioate nucleotides have emerged as powerful pharmacological substitutes of their native phosphodiester analogs with important translational applications in antisense oligonucleotide (ASO) therapeutics and cyclic dinucleotide (CDN) synthesis. Stereocontrolled installation of this chiral motif has long been hampered by the systemic use of phosphorus(III) [P(III)]-based reagent systems as the sole practical means of oligonucleotide assembly. A fundamentally different approach is described herein: the invention of a P(V)-based reagent platform for programmable, traceless, diastereoselective phosphorus-sulfur incorporation. The power of this reagent system is demonstrated through the robust and stereocontrolled synthesis of various nucleotidic architectures, including ASOs and CDNs, via an efficient, inexpensive, and operationally simple protocol.
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Affiliation(s)
- Kyle W Knouse
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Justine N deGruyter
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Michael A Schmidt
- Chemical and Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, NJ 08903, USA.
| | - Bin Zheng
- Chemical and Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, NJ 08903, USA
| | - Julien C Vantourout
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Cian Kingston
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Stephen E Mercer
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Ivar M Mcdonald
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Richard E Olson
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Ye Zhu
- Chemical and Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, NJ 08903, USA
| | - Chao Hang
- Chemical and Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, NJ 08903, USA
| | - Jason Zhu
- Chemical and Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, NJ 08903, USA
| | - Changxia Yuan
- Chemical and Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, NJ 08903, USA
| | - Qinggang Wang
- Chemical and Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, NJ 08903, USA
| | - Peter Park
- Department of Discovery Chemistry, Bristol-Myers Squibb, P.O. Box 5400, Princeton, NJ 08543, USA
| | - Martin D Eastgate
- Chemical and Synthetic Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, NJ 08903, USA.
| | - Phil S Baran
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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16
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Hagedorn PH, Persson R, Funder ED, Albæk N, Diemer SL, Hansen DJ, Møller MR, Papargyri N, Christiansen H, Hansen BR, Hansen HF, Jensen MA, Koch T. Locked nucleic acid: modality, diversity, and drug discovery. Drug Discov Today 2017; 23:101-114. [PMID: 28988994 DOI: 10.1016/j.drudis.2017.09.018] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 09/01/2017] [Accepted: 09/27/2017] [Indexed: 01/05/2023]
Abstract
Over the past 20 years, the field of RNA-targeted therapeutics has advanced based on discoveries of modified oligonucleotide chemistries, and an ever-increasing understanding of how to apply cellular assays to identify oligonucleotides with improved pharmacological properties in vivo. Locked nucleic acid (LNA), which exhibits high binding affinity and potency, is widely used for this purpose. Our understanding of RNA biology has also expanded tremendously, resulting in new approaches to engage RNA as a therapeutic target. Recent observations indicate that each oligonucleotide is a unique entity, and small structural differences between oligonucleotides can often lead to substantial differences in their pharmacological properties. Here, we outline new principles for drug discovery exploiting oligonucleotide diversity to identify rare molecules with unique pharmacological properties.
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Affiliation(s)
- Peter H Hagedorn
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Robert Persson
- Pharmaceutical Sciences, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Erik D Funder
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Nanna Albæk
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Sanna L Diemer
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Dennis J Hansen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Marianne R Møller
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Natalia Papargyri
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Helle Christiansen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Bo R Hansen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Henrik F Hansen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Mads A Jensen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Troels Koch
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark.
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