1
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Dinesen A, Andersen VL, Elkhashab M, Pilati D, Bech P, Fuchs E, Samuelsen TR, Winther A, Cai Y, Märcher A, Wall A, Omer M, Nielsen JS, Chudasama V, Baker JR, Gothelf KV, Wengel J, Kjems J, Howard KA. An Albumin-Holliday Junction Biomolecular Modular Design for Programmable Multifunctionality and Prolonged Circulation. Bioconjug Chem 2024; 35:214-222. [PMID: 38231391 PMCID: PMC10886128 DOI: 10.1021/acs.bioconjchem.3c00491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/18/2024]
Abstract
Combinatorial properties such as long-circulation and site- and cell-specific engagement need to be built into the design of advanced drug delivery systems to maximize drug payload efficacy. This work introduces a four-stranded oligonucleotide Holliday Junction (HJ) motif bearing functional moieties covalently conjugated to recombinant human albumin (rHA) to give a "plug-and-play" rHA-HJ multifunctional biomolecular assembly with extended circulation. Electrophoretic gel-shift assays show successful functionalization and purity of the individual high-performance liquid chromatography-purified modules as well as efficient assembly of the rHA-HJ construct. Inclusion of an epidermal growth factor receptor (EGFR)-targeting nanobody module facilitates specific binding to EGFR-expressing cells resulting in approximately 150-fold increased fluorescence intensity determined by flow cytometric analysis compared to assemblies absent of nanobody inclusion. A cellular recycling assay demonstrated retained albumin-neonatal Fc receptor (FcRn) binding affinity and accompanying FcRn-driven cellular recycling. This translated to a 4-fold circulatory half-life extension (2.2 and 0.55 h, for the rHA-HJ and HJ, respectively) in a double transgenic humanized FcRn/albumin mouse. This work introduces a novel biomolecular albumin-nucleic acid construct with extended circulatory half-life and programmable multifunctionality due to its modular design.
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Affiliation(s)
- Anders Dinesen
- Interdisciplinary
Nanoscience Center (iNANO) and Department of Molecular Biology and
Genetics, Aarhus University, DK-8000 Aarhus
C, Denmark
| | - Veronica L. Andersen
- Interdisciplinary
Nanoscience Center (iNANO) and Department of Molecular Biology and
Genetics, Aarhus University, DK-8000 Aarhus
C, Denmark
| | - Marwa Elkhashab
- Interdisciplinary
Nanoscience Center (iNANO) and Department of Molecular Biology and
Genetics, Aarhus University, DK-8000 Aarhus
C, Denmark
| | - Diego Pilati
- Interdisciplinary
Nanoscience Center (iNANO) and Department of Molecular Biology and
Genetics, Aarhus University, DK-8000 Aarhus
C, Denmark
| | - Pernille Bech
- Interdisciplinary
Nanoscience Center (iNANO) and Department of Molecular Biology and
Genetics, Aarhus University, DK-8000 Aarhus
C, Denmark
| | - Elisabeth Fuchs
- Interdisciplinary
Nanoscience Center (iNANO) and Department of Molecular Biology and
Genetics, Aarhus University, DK-8000 Aarhus
C, Denmark
| | - Torbjørn R. Samuelsen
- Interdisciplinary
Nanoscience Center (iNANO) and Department of Molecular Biology and
Genetics, Aarhus University, DK-8000 Aarhus
C, Denmark
| | - Alexander Winther
- Interdisciplinary
Nanoscience Center (iNANO) and Department of Molecular Biology and
Genetics, Aarhus University, DK-8000 Aarhus
C, Denmark
| | - Yunpeng Cai
- Interdisciplinary
Nanoscience Center (iNANO) and Department of Molecular Biology and
Genetics, Aarhus University, DK-8000 Aarhus
C, Denmark
| | - Anders Märcher
- Interdisciplinary
Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Archie Wall
- Department
of Chemistry, University College London, London WC1H 0AJ, U.K.
| | - Marjan Omer
- Interdisciplinary
Nanoscience Center (iNANO) and Department of Molecular Biology and
Genetics, Aarhus University, DK-8000 Aarhus
C, Denmark
| | - Jesper S. Nielsen
- Interdisciplinary
Nanoscience Center (iNANO) and Department of Molecular Biology and
Genetics, Aarhus University, DK-8000 Aarhus
C, Denmark
| | - Vijay Chudasama
- Department
of Chemistry, University College London, London WC1H 0AJ, U.K.
| | - James R. Baker
- Department
of Chemistry, University College London, London WC1H 0AJ, U.K.
| | - Kurt V. Gothelf
- Interdisciplinary
Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Jesper Wengel
- Nucleic
Acid Center, Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Jørgen Kjems
- Interdisciplinary
Nanoscience Center (iNANO) and Department of Molecular Biology and
Genetics, Aarhus University, DK-8000 Aarhus
C, Denmark
| | - Kenneth A. Howard
- Interdisciplinary
Nanoscience Center (iNANO) and Department of Molecular Biology and
Genetics, Aarhus University, DK-8000 Aarhus
C, Denmark
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2
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Saher O, Zaghloul EM, Umek T, Hagey DW, Mozafari N, Danielsen MB, Gouda AS, Lundin KE, Jørgensen PT, Wengel J, Smith CIE, Zain R. Chemical Modifications and Design Influence the Potency of Huntingtin Anti-Gene Oligonucleotides. Nucleic Acid Ther 2023; 33:117-131. [PMID: 36735581 PMCID: PMC10066784 DOI: 10.1089/nat.2022.0046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Huntington's disease is a neurodegenerative, trinucleotide repeat (TNR) disorder affecting both males and females. It is caused by an abnormal increase in the length of CAG•CTG TNR in exon 1 of the Huntingtin gene (HTT). The resultant, mutant HTT mRNA and protein cause neuronal toxicity, suggesting that reduction of their levels would constitute a promising therapeutic approach. We previously reported a novel strategy in which chemically modified oligonucleotides (ONs) directly target chromosomal DNA. These anti-gene ONs were able to downregulate both HTT mRNA and protein. In this study, various locked nucleic acid (LNA)/DNA mixmer anti-gene ONs were tested to investigate the effects of varying ON length, LNA content, and fatty acid modification on HTT expression. Altering the length did not significantly influence the ON potency, while LNA content was critical for activity. Utilization of palmitoyl-modified LNA monomers enhanced the ON activity relatively to the corresponding nonmodified LNA under serum starvation conditions. Furthermore, the number of palmitoylated LNA monomers and their positioning greatly affected ON potency. In addition, we performed RNA sequencing analysis, which showed that the anti-gene ONs affect the "immune system process, mRNA processing, and neurogenesis." Furthermore, we observed that for repeat containing genes, there is a higher tendency for antisense off-targeting. Taken together, our findings provide an optimized design of anti-gene ONs that could potentially be developed as DNA-targeting therapeutics for this class of TNR-related diseases.
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Affiliation(s)
- Osama Saher
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden.,Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Eman M Zaghloul
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden.,Department of Pharmaceutics, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Tea Umek
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden
| | - Daniel W Hagey
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden
| | - Negin Mozafari
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden
| | - Mathias B Danielsen
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Odense, Denmark
| | - Alaa S Gouda
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Odense, Denmark.,Department of Chemistry, Faculty of Science, Benha University, Benha, Egypt
| | - Karin E Lundin
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden
| | - Per T Jørgensen
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Odense, Denmark
| | - Jesper Wengel
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Odense, Denmark
| | - C I Edvard Smith
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden
| | - Rula Zain
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-14186 Huddinge, Sweden.,Centre for Rare Diseases, Department of Clinical Genetics, Karolinska University Hospital, SE-17176 Stockholm, Sweden
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3
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Azevedo AS, Fernandes RM, Faria AR, Silvestre OF, Nieder JB, Lou C, Wengel J, Almeida C, Azevedo NF. Spectral imaging and nucleic acid mimics fluorescence in situ hybridization (SI-NAM-FISH) for multiplex detection of clinical pathogens. Front Microbiol 2022; 13:976639. [PMID: 36246234 PMCID: PMC9557775 DOI: 10.3389/fmicb.2022.976639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
The application of nucleic acid mimics (NAMs), such as locked nucleic acid (LNA) and 2′-O-methyl-RNA (2’OMe), has improved the performance of fluorescence in situ hybridization (FISH) methods for the detection/location of clinical pathogens since they provide design versatility and thermodynamic control. However, an important limitation of FISH techniques is the low number of distinguishable targets. The use of filters in fluorescence image acquisition limits the number of fluorochromes that can be simultaneously differentiated. Recent advances in fluorescence spectral image acquisition have allowed the unambiguous identification of several microorganisms in a single sample. In this work, we aimed to combine NAM-FISH and spectral image analysis to develop and validate a new FISH variant, the spectral imaging-NAM-FISH (SI-NAM-FISH), that allows a multiplexed, robust and rapid detection of clinical pathogens. In the first stage, to implement/validate the method, we have selected seven fluorochromes with distinct spectral properties and seven bacterial species (Pseudomonas aeruginosa, Citrobacter freundii, Staphylococcus aureus, Enterococcus faecalis, Klebsiella pneumoniae, Escherichia coli, and Acinetobacter calcoaceticus). As a strong variation in fluorescence intensities is found between species and between fluorochromes, seven versions of a EUB LNA/2’OMe probe, each conjugated to one of seven fluorochromes, were used to rank species/fluorochromes by FISH and then optimize species/fluorochrome pairing. Then, final validation tests were performed using mixed populations to evaluate the potential of the technique for separating/quantifying the different targets. Overall, validation tests with different proportions of bacteria labeled with the respective fluorochrome have shown the ability of the method to correctly distinguish the species.
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Affiliation(s)
- Andreia S. Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
- *Correspondence: Andreia S. Azevedo,
| | - Ricardo M. Fernandes
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- INIAV, IP-National Institute for Agrarian and Veterinary Research, Vila Do Conde, Portugal
| | - Ana R. Faria
- INL International Iberian Nanotechnology Laboratory, Av Mestre José Veiga s/n, Braga, Portugal
| | - Oscar F. Silvestre
- INL International Iberian Nanotechnology Laboratory, Av Mestre José Veiga s/n, Braga, Portugal
| | - Jana B. Nieder
- INL International Iberian Nanotechnology Laboratory, Av Mestre José Veiga s/n, Braga, Portugal
| | - Chenguang Lou
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense, Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense, Denmark
| | - Carina Almeida
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- INIAV, IP-National Institute for Agrarian and Veterinary Research, Vila Do Conde, Portugal
| | - Nuno F. Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
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4
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Duschmalé J, Schäublin A, Funder E, Schmidt S, Kiełpiński ŁJ, Nymark H, Jensen K, Koch T, Duschmalé M, Koller E, Møller MR, Schadt S, Husser C, Brink A, Sewing S, Minz T, Wengel J, Bleicher K, Li M. Investigating discovery strategies and pharmacological properties of stereodefined phosphorodithioate LNA gapmers. Molecular Therapy - Nucleic Acids 2022; 29:176-188. [PMID: 35860384 PMCID: PMC9271985 DOI: 10.1016/j.omtn.2022.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/15/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Jörg Duschmalé
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Adrian Schäublin
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Erik Funder
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, 2970 Hørsholm, Denmark
| | - Steffen Schmidt
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, 2970 Hørsholm, Denmark
| | - Łukasz J. Kiełpiński
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, 2970 Hørsholm, Denmark
| | - Helle Nymark
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, 2970 Hørsholm, Denmark
| | - Klaus Jensen
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, 2970 Hørsholm, Denmark
| | - Troels Koch
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, 2970 Hørsholm, Denmark
| | - Martina Duschmalé
- Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Erich Koller
- Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Marianne Ravn Møller
- Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Simone Schadt
- Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Christophe Husser
- Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Andreas Brink
- Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Sabine Sewing
- Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Tanja Minz
- Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | - Konrad Bleicher
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Meiling Li
- Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
- Corresponding author Meiling Li, Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland.
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5
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Lisowiec-Wąchnicka J, Danielsen MB, Nader EA, Jørgensen PT, Wengel J, Pasternak A. Evaluation of Gene Expression Knock-Down by Chemically and Structurally Modified Gapmer Antisense Oligonucleotides. Chembiochem 2022; 23:e202200168. [PMID: 35675170 DOI: 10.1002/cbic.202200168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 06/08/2022] [Indexed: 11/08/2022]
Abstract
We analyzed the effect of modified nucleotides within gapmer antisense oligonucleotides on RNase H mediated gene silencing. Additionally, short hairpins were introduced into antisense oligonucleotides as structural motifs, and their influence on biological and physicochemical properties of pre-structured gapmers was investigated for the first time. The results indicate that two LNA residues in specified positions of the gap flanking regions are sufficient and favorable for efficient knock-down of the β-actin gene. Furthermore, the introduction of other modified nucleotides, i. e. glycyl-amino-LNA-T, 2'-O-propagyluridine, polyamine functionalized uridine, and UNA, in specified positions, also increases the inhibition of β-actin expression. Importantly, the presence of hairpins within the gapmers improves their silencing properties.
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Affiliation(s)
- Jolanta Lisowiec-Wąchnicka
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Mathias B Danielsen
- Biomolecular Nanonscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Eugenie Abi Nader
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Per T Jørgensen
- Biomolecular Nanonscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Jesper Wengel
- Biomolecular Nanonscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Anna Pasternak
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznań, Poland
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6
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Dinesen A, Winther A, Wall A, Märcher A, Palmfeldt J, Chudasama V, Wengel J, Gothelf KV, Baker JR, Howard KA. Albumin Biomolecular Drug Designs Stabilized through Improved Thiol Conjugation and a Modular Locked Nucleic Acid Functionalized Assembly. Bioconjug Chem 2022; 33:333-342. [PMID: 35129956 DOI: 10.1021/acs.bioconjchem.1c00561] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Albumin-nucleic acid biomolecular drug designs offer modular multifunctionalization and extended circulatory half-life. However, stability issues associated with conventional DNA nucleotides and maleimide bioconjugation chemistries limit the clinical potential. This work aims to improve the stability of this thiol conjugation and nucleic acid assembly by employing a fast-hydrolyzing monobromomaleimide (MBM) linker and nuclease-resistant nucleotide analogues, respectively. The biomolecular constructs were formed by site-selective conjugation of a 12-mer oligonucleotide to cysteine 34 (Cys34) of recombinant human albumin (rHA), followed by annealing of functionalized complementary strands bearing either a fluorophore or the cytotoxic drug monomethyl auristatin E (MMAE). Formation of conjugates and assemblies was confirmed by gel shift analysis and mass spectrometry, followed by investigation of serum stability, neonatal Fc receptor (FcRn)-mediated cellular recycling, and cancer cell killing. The MBM linker afforded rapid conjugation to rHA and remained stable during hydrolysis. The albumin-nucleic acid biomolecular assembly composed of stabilized oligonucleotides exhibited high serum stability and retained FcRn engagement mediating FcRn-mediated cellular recycling. The MMAE-containing assembly exhibited cytotoxicity in the human MIA PaCa-2 pancreatic cancer cell line with an IC50 of 342 nM, triggered by drug release from breakdown of an acid-labile linker. In summary, this work presents rHA-nucleic acid module-based assemblies with improved stability and retained module functionality that further promotes the drug delivery potential of this biomolecular platform.
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Affiliation(s)
- Anders Dinesen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Alexander Winther
- Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Archie Wall
- Department of Chemistry, University College London, London WC1H 0AJ, U.K
| | - Anders Märcher
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Johan Palmfeldt
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University, DK-8200 Aarhus N, Denmark
| | - Vijay Chudasama
- Department of Chemistry, University College London, London WC1H 0AJ, U.K
| | - Jesper Wengel
- Nucleic Acid Center, Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Kurt V Gothelf
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - James R Baker
- Department of Chemistry, University College London, London WC1H 0AJ, U.K
| | - Kenneth A Howard
- Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark
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7
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Pandey S, Mandal S, Danielsen MB, Brown A, Hu C, Christensen NJ, Kulakova AV, Song S, Brown T, Jensen KJ, Wengel J, Lou C, Mao H. Chirality transmission in macromolecular domains. Nat Commun 2022; 13:76. [PMID: 35013247 PMCID: PMC8748818 DOI: 10.1038/s41467-021-27708-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/07/2021] [Indexed: 11/17/2022] Open
Abstract
Chiral communications exist in secondary structures of foldamers and copolymers via a network of noncovalent interactions within effective intermolecular force (IMF) range. It is not known whether long-range chiral communication exists between macromolecular tertiary structures such as peptide coiled-coils beyond the IMF distance. Harnessing the high sensitivity of single-molecule force spectroscopy, we investigate the chiral interaction between covalently linked DNA duplexes and peptide coiled-coils by evaluating the binding of a diastereomeric pair of three DNA-peptide conjugates. We find that right-handed DNA triple helices well accommodate peptide triple coiled-coils of the same handedness, but not with the left-handed coiled-coil stereoisomers. This chiral communication is effective in a range (<4.5 nm) far beyond canonical IMF distance. Small-angle X-ray scattering and molecular dynamics simulation indicate that the interdomain linkers are tightly packed via hydrophobic interactions, which likely sustains the chirality transmission between DNA and peptide domains. Our findings establish that long-range chiral transmission occurs in tertiary macromolecular domains, explaining the presence of homochiral pairing of superhelices in proteins. Chiral communication can propagate in secondary structures within the effective intermolecular force (IMF) range but it is not known whether long-range chiral communication exists between tertiary peptide structures. Here, the authors use single-molecule force spectroscopy to investigate chiral interaction between DNA duplexes/triplexes and peptide coiled-coils and demonstrate chiral communication beyond the IMF distance.
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Affiliation(s)
- Shankar Pandey
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Shankar Mandal
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Mathias Bogetoft Danielsen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Asha Brown
- ATDBio Ltd., Magdalen Centre, Oxford Science Park, 1 Robert Robinson Avenue, Oxford, OX4 4GA, UK
| | - Changpeng Hu
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Niels Johan Christensen
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | | | - Shixi Song
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Tom Brown
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Knud J Jensen
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Chenguang Lou
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA.
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8
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Tomczyk MD, Zalewski M, Jørgensen PT, Wengel J, Walczak K. Polyamine-Oligonucleotide Conjugates: 2'- OMe-Triazole-Linked 1,4,7,10-Tetraazacyclododecane and Intercalating Dyes and Their Effect on the Thermal Stability of DNA Duplexes. Pharmaceutics 2021; 14:66. [PMID: 35056962 PMCID: PMC8778778 DOI: 10.3390/pharmaceutics14010066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/18/2021] [Accepted: 12/25/2021] [Indexed: 11/22/2022] Open
Abstract
Oligonucleotides with the sequences 5'-GTG AUPA TGC, 5'-GCA TAUP CAC and 5'-GUPG ATA UPGC, where UP is 2'-O-propargyl uridine, were subjected to post-synthetic Cu(I)-catalyzed azide-alkyne cycloaddition to attach 1,4,7,10-tetraazacyclododecane (cyclen) and two well-known DNA intercalating dyes: thioxanthone and 1,8-naphthalimide. We propose a convenient cyclen protection-deprotection strategy that allows efficient separation of the resulting polyamine-oligonucleotide conjugates from the starting materials by RP-HPLC to obtain high-purity products. In this paper, we present hitherto unknown macrocyclic polyamine-oligonucleotide conjugates and their hybridization properties reflected in the thermal stability of thirty-two DNA duplexes containing combinations of labeled strands, their unmodified complementary strands, and strands with single base pair mismatches. Circular dichroism measurements showed that the B-conformation is retained for all dsDNAs consisting of unmodified and modified oligonucleotides. An additive and destabilizing effect of cyclen moieties attached to dsDNAs was observed. Tm measurements indicate that placing the hydrophobic dye opposite to the cyclen moiety can reduce its destabilizing effect and increase the thermal stability of the duplex. Interestingly, the cyclen-modified U showed significant selectivity for TT mismatch, which resulted in stabilization of the duplex. We conclude the paper with a brief review and discussion in which we compare our results with several examples of oligonucleotides labeled with polyamines at internal strand positions known in the literature.
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Affiliation(s)
- Mateusz D. Tomczyk
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, Krzywoustego 4, 44-100 Gliwice, Poland;
| | - Mariusz Zalewski
- Department of Chemical Organic Technology and Petrochemistry, Silesian University of Technology, Krzywoustego 4, 44-100 Gliwice, Poland;
| | - Per T. Jørgensen
- BioNEC Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark; (P.T.J.); (J.W.)
| | - Jesper Wengel
- BioNEC Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark; (P.T.J.); (J.W.)
| | - Krzysztof Walczak
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, Krzywoustego 4, 44-100 Gliwice, Poland;
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9
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Araújo D, Mil-Homens D, Jørgensen PT, Fialho AM, Wengel J, Henriques M, Silva S. Exploration of anti EFG1 locked nucleic acid gapmers to control Candida albicans filamentation. Access Microbiol 2021. [DOI: 10.1099/acmi.cc2021.po0058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction:
Antisense oligonucleotides (ASOs) have been successfully utilized to silence gene expression for the treatment of many genetic human diseases, and particularly the locked nucleic acid (LNA) chemical modification is extensively used with this propose. However, LNA-modified ASOs have never been exploited for controlling virulence genes of Candida.
EFG1is an important determinant of virulence that is involved in the switch from yeast to filamentous forms in C. albicans. Thus, our main goal was to explore LNA antisense gapmers for controlling EFG1gene expression and to block C. albicans filamentation.
Methods:
A set of five LNA-modified gapmers were designed with different chemical modifications (phosphorothioate backbone (PS) and/or palmitoyl-2’-amino-LNA) and ASO length. The in vitro performance of the different ASOs was evaluatedon their ability to control EFG1 gene expression, by qRT-PCR, and to reduce C. albicans’ filamentation, through filaments’ enumeration by microscopy. The in vivo therapeutic potential of ASOs was assessed using a G. mellonella model of infection, through a survival assay.
Results:
In vitro results showed that all ASOs were able to reduce the levels of EFG1gene expression, consequently reducing the levels of C. albicans filamentation around 50%. Interestingly, in vivo tests showed that the LNA-modified gapmer with PS backbone and palmitoyl-2’-amino-LNA was more effective at preventing G. mellonella infections.
Conclusions:
Undeniably, this work promotes the development of a novel approach for the treatment of Candida infections based on the delivery of ASOs coupled with LNA chemical modification.
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Affiliation(s)
| | - Dalila Mil-Homens
- iBB-Institute of Bioengineering and Biosciences, Instituto Superior Técnico
| | | | - Arsénio M. Fialho
- iBB-Institute of Bioengineering and Biosciences, Instituto Superior Técnico
| | | | | | - Sónia Silva
- Centre of Biological Engineering, University of Minho
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10
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Araújo D, Mil-Homens D, Rodrigues ME, Henriques M, Jørgensen PT, Wengel J, Silva S. Antisense locked nucleic acid gapmers to control Candida albicans filamentation. Nanomedicine 2021; 39:102469. [PMID: 34606999 DOI: 10.1016/j.nano.2021.102469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 07/21/2021] [Accepted: 08/05/2021] [Indexed: 11/17/2022]
Abstract
Whereas locked nucleic acid (LNA) has been extensively used to control gene expression, it has never been exploited to control Candida virulence genes. Thus, the main goal of this work was to compare the efficacy of five different LNA-based antisense oligonucleotides (ASO) with respect to the ability to control EFG1 gene expression, to modulate filamentation and to reduce C. albicans virulence. In vitro, all LNA-ASOs were able to significantly reduce C. albicans filamentation and to control EFG1 gene expression. Using the in vivo Galleria mellonella model, important differences among the five LNA-ASOs were revealed in terms of C. albicans virulence reduction. The inclusion of PS-linkage and palmitoyl-2'-amino-LNA chemical modification in these five LNA gapmers proved to be the most promising combination, increasing the survival of G. mellonella by 40%. Our work confirms that LNA-ASOs are useful tools for research and therapeutic development in the candidiasis field.
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Affiliation(s)
- Daniela Araújo
- LIBRO-Laboratório de Investigação em Biofilmes Rosário Oliveira, CEB-Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Dalila Mil-Homens
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Lisbon University, Lisbon, Portugal
| | - Maria Elisa Rodrigues
- LIBRO-Laboratório de Investigação em Biofilmes Rosário Oliveira, CEB-Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Mariana Henriques
- LIBRO-Laboratório de Investigação em Biofilmes Rosário Oliveira, CEB-Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Per Trolle Jørgensen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Sónia Silva
- LIBRO-Laboratório de Investigação em Biofilmes Rosário Oliveira, CEB-Centre of Biological Engineering, University of Minho, Braga, Portugal; National Institute for Agrarian and Veterinary Research, Vairão, Vila do Conde, Portugal.
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11
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Umek T, Olsson T, Gissberg O, Saher O, Zaghloul EM, Lundin KE, Wengel J, Hanse E, Zetterberg H, Vizlin-Hodzic D, Smith CIE, Zain R. Oligonucleotides Targeting DNA Repeats Downregulate Huntingtin Gene Expression in Huntington's Patient-Derived Neural Model System. Nucleic Acid Ther 2021; 31:443-456. [PMID: 34520257 PMCID: PMC8713517 DOI: 10.1089/nat.2021.0021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Huntington's disease (HD) is one of the most common, dominantly inherited neurodegenerative disorders. It affects the striatum, cerebral cortex, and other subcortical structures leading to involuntary movement abnormalities, emotional disturbances, and cognitive impairments. HD is caused by a CAG•CTG trinucleotide-repeat expansion in exon 1 of the huntingtin (HTT) gene leading to the formation of mutant HTT (mtHTT) protein aggregates. Besides the toxicity of the mutated protein, there is also evidence that mtHTT transcripts contribute to the disease. Thus, the reduction of both mutated mRNA and protein would be most beneficial as a treatment. Previously, we designed a novel anti-gene oligonucleotide (AGO)-based strategy directly targeting the HTT trinucleotide-repeats in DNA and reported downregulation of mRNA and protein in HD patient fibroblasts. In this study, we differentiate HD patient-derived induced pluripotent stem cells to investigate the efficacy of the AGO, a DNA/Locked Nucleic Acid mixmer with phosphorothioate backbone, to modulate HTT transcription during neural in vitro development. For the first time, we demonstrate downregulation of HTT mRNA following both naked and magnetofected delivery into neural stem cells (NSCs) and show that neither emergence of neural rosette structures nor self-renewal of NSCs is compromised. Furthermore, the inhibition potency of both HTT mRNA and protein without off-target effects is confirmed in neurons. These results further validate an anti-gene approach for the treatment of HD.
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Affiliation(s)
- Tea Umek
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Thomas Olsson
- Department of Physiology, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Pathology and Cytology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Olof Gissberg
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Osama Saher
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, Sweden.,Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Eman M Zaghloul
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, Sweden.,Department of Pharmaceutics, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Karin E Lundin
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Jesper Wengel
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Odense M, Denmark
| | - Eric Hanse
- Department of Physiology, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden.,Department of Neurodegenerative Disease, Institute of Neurology, University College London, London, United Kingdom.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,UK Dementia Research Institute at UCL, London, United Kingdom
| | - Dzeneta Vizlin-Hodzic
- Department of Physiology, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden.,Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - C I Edvard Smith
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, Sweden
| | - Rula Zain
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, Sweden.,Department of Clinical Genetics, Center for Rare Diseases, Karolinska University Hospital, Stockholm, Sweden
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12
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Danielsen MB, Wengel J. Cationic oligonucleotide derivatives and conjugates: A favorable approach for enhanced DNA and RNA targeting oligonucleotides. Beilstein J Org Chem 2021; 17:1828-1848. [PMID: 34386102 PMCID: PMC8329367 DOI: 10.3762/bjoc.17.125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/14/2021] [Indexed: 12/20/2022] Open
Abstract
Antisense oligonucleotides (ASOs) have the ability of binding to endogenous nucleic acid targets, thereby inhibiting the gene expression. Although ASOs have great potential in the treatment of many diseases, the search for favorable toxicity profiles and distribution has been challenging and consequently impeded the widespread use of ASOs as conventional medicine. One strategy that has been employed to optimize the delivery profile of ASOs, is the functionalization of ASOs with cationic amine groups, either by direct conjugation onto the sugar, nucleobase or internucleotide linkage. The introduction of these positively charged groups has improved properties like nuclease resistance, increased binding to the nucleic acid target and improved cell uptake for oligonucleotides (ONs) and ASOs. The modifications highlighted in this review are some of the most prevalent cationic amine groups which have been attached as single modifications onto ONs/ASOs. The review has been separated into three sections, nucleobase, sugar and backbone modifications, highlighting what impact the cationic amine groups have on the ONs/ASOs physiochemical and biological properties. Finally, a concluding section has been added, summarizing the important knowledge from the three chapters, and examining the future design for ASOs.
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Affiliation(s)
- Mathias B Danielsen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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13
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Laanesoo A, Urgard E, Periyasamy K, Laan M, Bochkov YA, Aab A, Magilnick N, Pooga M, Gern JE, Johnston SL, Coquet JM, Boldin MP, Wengel J, Altraja A, Bochenek G, Jakiela B, Rebane A. Dual role of the miR-146 family in rhinovirus-induced airway inflammation and allergic asthma exacerbation. Clin Transl Med 2021; 11:e427. [PMID: 34185416 PMCID: PMC8161513 DOI: 10.1002/ctm2.427] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 04/29/2021] [Accepted: 05/04/2021] [Indexed: 12/30/2022] Open
Abstract
Rhinovirus (RV) infections are associated with asthma exacerbations. MicroRNA-146a and microRNA-146b (miR-146a/b) are anti-inflammatory miRNAs that suppress signaling through the nuclear factor kappa B (NF-κB) pathway and inhibit pro-inflammatory chemokine production in primary human bronchial epithelial cells (HBECs). In the current study, we aimed to explore whether miR-146a/b could regulate cellular responses to RVs in HBECs and airways during RV-induced asthma exacerbation. We demonstrated that expression of miR-146a/b and pro-inflammatory chemokines was increased in HBECs and mouse airways during RV infection. However, transfection with cell-penetrating peptide (CPP)-miR-146a nanocomplexes before infection with RV significantly reduced the expression of the pro-inflammatory chemokines CCL5, IL-8 and CXCL1, increased interferon-λ production, and attenuated infection with the green fluorescent protein (GFP)-expressing RV-A16 in HBECs. Concordantly, compared to wild-type (wt) mice, Mir146a/b-/- mice exhibited more severe airway neutrophilia and increased T helper (Th)1 and Th17 cell infiltration in response to RV-A1b infection and a stronger Th17 response with a less prominent Th2 response in house dust mite extract (HDM)-induced allergic airway inflammation and RV-induced exacerbation models. Interestingly, intranasal administration of CPP-miR-146a nanocomplexes reduced HDM-induced allergic airway inflammation without a significant effect on the Th2/Th1/Th17 balance in wild-type mice. In conclusion, the overexpression of miR-146a has a strong anti-inflammatory effect on RV infection in HBECs and a mouse model of allergic airway inflammation, while a lack of miR-146a/b leads to attenuated type 2 cell responses in mouse models of allergic airway inflammation and RV-induced exacerbation of allergic airway inflammation. Furthermore, our data indicate that the application of CPP-miR-146a nanocomplexes has therapeutic potential for targeting airway inflammation.
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Affiliation(s)
- Anet Laanesoo
- Institute of Biomedicine and Translational MedicineUniversity of TartuTartuEstonia
| | - Egon Urgard
- Institute of Biomedicine and Translational MedicineUniversity of TartuTartuEstonia
| | - Kapilraj Periyasamy
- Institute of Biomedicine and Translational MedicineUniversity of TartuTartuEstonia
| | - Martti Laan
- Institute of Biomedicine and Translational MedicineUniversity of TartuTartuEstonia
| | - Yury A. Bochkov
- School of Medicine and Public Health University of Wisconsin‐MadisonMadisonWisconsinUSA
| | - Alar Aab
- Institute of Biomedicine and Translational MedicineUniversity of TartuTartuEstonia
| | - Nathaniel Magilnick
- Department of Molecular and Cellular BiologyBeckman Research Institute of City of Hope National Medical CenterDuarteCaliforniaUSA
| | - Margus Pooga
- Institute of TechnologyUniversity of TartuTartuEstonia
| | - James E. Gern
- School of Medicine and Public Health University of Wisconsin‐MadisonMadisonWisconsinUSA
| | - Sebastian L. Johnston
- National Heart and Lung InstituteImperial College LondonLondonUK
- Imperial College Healthcare NHS TrustLondonUK
| | - Jonathan M. Coquet
- Department of MicrobiologyTumor and Cell Biology (MTC)Karolinska InstitutetStockholmSweden
| | - Mark P. Boldin
- Department of Molecular and Cellular BiologyBeckman Research Institute of City of Hope National Medical CenterDuarteCaliforniaUSA
| | - Jesper Wengel
- Nucleic Acid CenterDepartment of PhysicsChemistry and PharmacyUniversity of Southern DenmarkOdenseDenmark
| | - Alan Altraja
- Department of Pulmonary MedicineUniversity of TartuTartuEstonia
- Lung Clinic of the Tartu University HospitalTartuEstonia
| | - Grazyna Bochenek
- Department of MedicineJagiellonian University Medical CollegeKrakowPoland
| | - Bogdan Jakiela
- Department of MedicineJagiellonian University Medical CollegeKrakowPoland
| | - Ana Rebane
- Institute of Biomedicine and Translational MedicineUniversity of TartuTartuEstonia
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14
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Pereira S, Yao R, Gomes M, Jørgensen PT, Wengel J, Azevedo NF, Sobral Santos R. Can Vitamin B12 Assist the Internalization of Antisense LNA Oligonucleotides into Bacteria? Antibiotics (Basel) 2021; 10:antibiotics10040379. [PMID: 33916701 PMCID: PMC8065541 DOI: 10.3390/antibiotics10040379] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/18/2021] [Accepted: 04/01/2021] [Indexed: 11/17/2022] Open
Abstract
The emergence of bacterial resistance to traditional small-molecule antibiotics is fueling the search for innovative strategies to treat infections. Inhibiting the expression of essential bacterial genes using antisense oligonucleotides (ASOs), particularly composed of nucleic acid mimics (NAMs), has emerged as a promising strategy. However, their efficiency depends on their association with vectors that can translocate the bacterial envelope. Vitamin B12 is among the largest molecules known to be taken up by bacteria and has very recently started to gain interest as a trojan-horse vector. Gapmers and steric blockers were evaluated as ASOs against Escherichia coli (E. coli). Both ASOs were successfully conjugated to B12 by copper-free azide-alkyne click-chemistry. The biological effect of the two conjugates was evaluated together with their intracellular localization in E. coli. Although not only B12 but also both B12-ASO conjugates interacted strongly with E. coli, they were mostly colocalized with the outer membrane. Only 6–9% were detected in the cytosol, which showed to be insufficient for bacterial growth inhibition. These results suggest that the internalization of B12-ASO conjugates is strongly affected by the low uptake rate of the B12 in E. coli and that further studies are needed before considering this strategy against biofilms in vivo.
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Affiliation(s)
- Sara Pereira
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, R. Dr. Roberto Frias, 4200-465 Porto, Portugal; (S.P.); (M.G.); (N.F.A.)
| | - Ruwei Yao
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark; (R.Y.); (P.T.J.); (J.W.)
| | - Mariana Gomes
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, R. Dr. Roberto Frias, 4200-465 Porto, Portugal; (S.P.); (M.G.); (N.F.A.)
| | - Per Trolle Jørgensen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark; (R.Y.); (P.T.J.); (J.W.)
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark; (R.Y.); (P.T.J.); (J.W.)
| | - Nuno Filipe Azevedo
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, R. Dr. Roberto Frias, 4200-465 Porto, Portugal; (S.P.); (M.G.); (N.F.A.)
| | - Rita Sobral Santos
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, R. Dr. Roberto Frias, 4200-465 Porto, Portugal; (S.P.); (M.G.); (N.F.A.)
- Correspondence:
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15
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Danielsen MB, Christensen NJ, Jørgensen PT, Jensen KJ, Wengel J, Lou C. Polyamine-Functionalized 2'-Amino-LNA in Oligonucleotides: Facile Synthesis of New Monomers and High-Affinity Binding towards ssDNA and dsDNA. Chemistry 2020; 27:1416-1422. [PMID: 33073896 DOI: 10.1002/chem.202004495] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/16/2020] [Indexed: 12/15/2022]
Abstract
Attachment of cationic moieties to oligonucleotides (ONs) promises not only to increase the binding affinity of antisense ONs by reducing charge repulsion between the two negatively charged strands of a duplex, but also to augment their in vivo stability against nucleases. In this study, polyamine functionality was introduced into ONs by means of 2'-amino-LNA scaffolds. The resulting ONs exhibited efficient binding towards ssDNA, ssRNA and dsDNA targets, and the 2'-amino-LNA analogue carrying a triaminated linker showed the most pronounced duplex- and triplex-stabilizing effect. Molecular modelling revealed that favourable conformational and electrostatic effects led to salt-bridge formation between positively charged polyamine moieties and the Watson-Hoogsteen groove of the dsDNA targets, resulting in the observed triplex stabilization. All the investigated monomers showed increased resistance against 3'-nucleolytic digestion relative to the non-functionalized controls.
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Affiliation(s)
- Mathias B Danielsen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Niels Johan Christensen
- Department of Chemistry, Biomolecular Nanoscale Engineering Center, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, 1871, Denmark
| | - Per T Jørgensen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Knud J Jensen
- Department of Chemistry, Biomolecular Nanoscale Engineering Center, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, 1871, Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Chenguang Lou
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
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16
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Gouda AS, Przypis Ł, Walczak K, Jørgensen PT, Wengel J. Carbazole modified oligonucleotides: synthesis, hybridization studies and fluorescence properties. Org Biomol Chem 2020; 18:6935-6948. [PMID: 32936176 DOI: 10.1039/d0ob01553a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Synthesis of the novel thiophenyl carbazole phosphoramidite DNA building block 5 was accomplished in four steps using a Suzuki-Miyaura cross-coupling reaction from the core carbazole and it was seamlessly accommodated into a 9-mer DNA-based oligonucleotide by incorporation at the flanking 5'-end in combination with a central insertion of an LNA-T nucleotide. The carbazole-containing oligonucleotide was combined in different duplex hybrids, which were characterized by thermal denaturation, circular dichroism and fluorescence studies. The carbazole monomer modulates the duplex stability in various ways. Thus, monomer Z increased the thermal stability of the 9-mer towards the complementary 9-mer/15-mer DNA duplex by 4.2 °C. Furthermore, indications of its intercalation into the duplex were obtained by modeling studies and robust decreases in fluorescence emission intensities upon duplex formation. In contrast, no clear intercalating tendency was corroborated for monomer Z within the DNA/RNA hybrid duplex as indicated by moderate quenching of the fluorescence and similar duplex thermal stabilities relative to the corresponding control duplex. The recognition efficiencies of the carbazole modified oligonucleotide toward single nucleotide mismatches were studied with two 15-mer model targets (DNA and RNA). For both systems, mismatches positioned at the juxtaposition of the carbazole monomer showed pronounced deceases in thermal denaturation temperature. Steady-state fluorescence emission studies of all mismatched duplexes with incorporation of Z monomer typically displayed efficient fluorescence quenching.
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Affiliation(s)
- Alaa S Gouda
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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17
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Zeng D, Salvatore P, Karlsen KK, Zhang J, Wengel J, Ulstrup J. Reprint of "Electrochemical intercalator binding to single- and double-strand DNA- and LNA-based molecules on Au(111)-electrode surfaces". J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2020.114527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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18
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Zeng D, Salvatore P, Karlsen KK, Zhang J, Wengel J, Ulstrup J. Electrochemical intercalator binding to single- and double-strand DNA- and LNA-based molecules on Au(111)-electrode surfaces. J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2020.114138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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19
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Lou C, Boesen JT, Christensen NJ, Sørensen KK, Thulstrup PW, Pedersen MN, Giralt E, Jensen KJ, Wengel J. Self‐Assembly of DNA–Peptide Supermolecules: Coiled‐Coil Peptide Structures Templated by
d
‐DNA and
l
‐DNA Triplexes Exhibit Chirality‐Independent but Orientation‐Dependent Stabilizing Cooperativity. Chemistry 2020; 26:5676-5684. [DOI: 10.1002/chem.201905636] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/31/2020] [Indexed: 01/08/2023]
Affiliation(s)
- Chenguang Lou
- Biomolecular Nanoscale Engineering CenterDepartment of Physics, Chemistry and PharmacyUniversity of Southern Denmark Campusvej 55 5230 Odense M Denmark
| | - Josephine Tuborg Boesen
- Biomolecular Nanoscale Engineering CenterDepartment of ChemistryUniversity of Copenhagen Thorvaldsensvej 40 1871 Frederiksberg Denmark
| | - Niels Johan Christensen
- Biomolecular Nanoscale Engineering CenterDepartment of ChemistryUniversity of Copenhagen Thorvaldsensvej 40 1871 Frederiksberg Denmark
| | - Kasper K. Sørensen
- Biomolecular Nanoscale Engineering CenterDepartment of ChemistryUniversity of Copenhagen Thorvaldsensvej 40 1871 Frederiksberg Denmark
| | - Peter W. Thulstrup
- Department of ChemistryUniversity of Copenhagen Universitetsparken 5 2100 Copenhagen Ø Denmark
| | - Martin Nors Pedersen
- X-ray and Neutron ScienceNiels Bohr InstituteUniversity of Copenhagen Universitetsparken 5 2100 Copenhagen Ø Denmark
| | - Ernest Giralt
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10 Barcelona 08028 Spain
- Department of Inorganic and Organic ChemistryUniversity of Barcelona Martí i Franquès 1–11 Barcelona 08028 Spain
| | - Knud J. Jensen
- Biomolecular Nanoscale Engineering CenterDepartment of ChemistryUniversity of Copenhagen Thorvaldsensvej 40 1871 Frederiksberg Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering CenterDepartment of Physics, Chemistry and PharmacyUniversity of Southern Denmark Campusvej 55 5230 Odense M Denmark
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20
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Raguraman P, Wang T, Ma L, Jørgensen PT, Wengel J, Veedu RN. Alpha-l-Locked Nucleic Acid-Modified Antisense Oligonucleotides Induce Efficient Splice Modulation In Vitro. Int J Mol Sci 2020; 21:ijms21072434. [PMID: 32244535 PMCID: PMC7177859 DOI: 10.3390/ijms21072434] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/27/2020] [Accepted: 03/29/2020] [Indexed: 01/04/2023] Open
Abstract
Alpha-l-Locked nucleic acid (α-l-LNA) is a stereoisomeric analogue of locked nucleic acid (LNA), which possesses excellent biophysical properties and also exhibits high target binding affinity to complementary oligonucleotide sequences and resistance to nuclease degradations. Therefore, α-l-LNA nucleotides could be utilised to develop stable antisense oligonucleotides (AO), which can be truncated without compromising the integrity and efficacy of the AO. In this study, we explored the potential of α-l-LNA nucleotides-modified antisense oligonucleotides to modulate splicing by inducing Dmd exon-23 skipping in mdx mouse myoblasts in vitro. For this purpose, we have synthesised and systematically evaluated the efficacy of α-l-LNA-modified 2'-O-methyl phosphorothioate (2'-OMePS) AOs of three different sizes including 20mer, 18mer and 16mer AOs in parallel to fully-modified 2'-OMePS control AOs. Our results demonstrated that the 18mer and 16mer truncated AO variants showed slightly better exon-skipping efficacy when compared with the fully-23 modified 2'-OMePS control AOs, in addition to showing low cytotoxicity. As there was no previous report on using α-l-LNA-modified AOs in splice modulation, we firmly believe that this initial study could be beneficial to further explore and expand the scope of α-l-LNA-modified AO therapeutic molecules.
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Affiliation(s)
- Prithi Raguraman
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth 6150 Australia; (P.R.); (T.W.)
- Perron Institute for Neurological and translational Science, Perth 6005, Australia
| | - Tao Wang
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth 6150 Australia; (P.R.); (T.W.)
- Perron Institute for Neurological and translational Science, Perth 6005, Australia
| | - Lixia Ma
- School of Statistics, Henan University of Economics and Law, Zhengzhou 450001, China;
| | - Per Trolle Jørgensen
- Nucleic Acid Center, Department of Physics and Chemistry and Pharmacy, University of Southern Denmark, M 5230 Odense, Denmark; (P.T.J.); (J.W.)
| | - Jesper Wengel
- Nucleic Acid Center, Department of Physics and Chemistry and Pharmacy, University of Southern Denmark, M 5230 Odense, Denmark; (P.T.J.); (J.W.)
| | - Rakesh N. Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth 6150 Australia; (P.R.); (T.W.)
- Perron Institute for Neurological and translational Science, Perth 6005, Australia
- Nucleic Acid Center, Department of Physics and Chemistry and Pharmacy, University of Southern Denmark, M 5230 Odense, Denmark; (P.T.J.); (J.W.)
- Correspondence:
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21
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Duschmalé J, Hansen HF, Duschmalé M, Koller E, Albaek N, Møller MR, Jensen K, Koch T, Wengel J, Bleicher K. In vitro and in vivo properties of therapeutic oligonucleotides containing non-chiral 3' and 5' thiophosphate linkages. Nucleic Acids Res 2020; 48:63-74. [PMID: 31754711 PMCID: PMC6943131 DOI: 10.1093/nar/gkz1099] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 10/28/2019] [Accepted: 11/07/2019] [Indexed: 11/12/2022] Open
Abstract
The introduction of non-bridging phosphorothioate (PS) linkages in oligonucleotides has been instrumental for the development of RNA therapeutics and antisense oligonucleotides. This modification offers significantly increased metabolic stability as well as improved pharmacokinetic properties. However, due to the chiral nature of the phosphorothioate, every PS group doubles the amount of possible stereoisomers. Thus PS oligonucleotides are generally obtained as an inseparable mixture of a multitude of diastereoisomeric compounds. Herein, we describe the introduction of non-chiral 3′ thiophosphate linkages into antisense oligonucleotides and report their in vitro as well as in vivo activity. The obtained results are carefully investigated for the individual parameters contributing to antisense activity of 3′ and 5′ thiophosphate modified oligonucleotides (target binding, RNase H recruitment, nuclease stability). We conclude that nuclease stability is the major challenge for this approach. These results highlight the importance of selecting meaningful in vitro experiments particularly when examining hitherto unexplored chemical modifications.
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Affiliation(s)
- Jörg Duschmalé
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
- To whom correspondence should be addressed. Tel: +41 61 68 86081; Fax: +41 61 68 88714;
| | - Henrik Frydenlund Hansen
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Martina Duschmalé
- Pharmaceutical Sciences, Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - Erich Koller
- Pharmaceutical Sciences, Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - Nanna Albaek
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Marianne Ravn Møller
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Klaus Jensen
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Troels Koch
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Copenhagen A/S, Femtidsvej 3, DK-2970 Hørsholm, Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Konrad Bleicher
- RNA Therapeutics, Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
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22
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Danielsen MB, Lou C, Lisowiec-Wachnicka J, Pasternak A, Jørgensen PT, Wengel J. Gapmer Antisense Oligonucleotides Containing 2',3'-Dideoxy-2'-fluoro-3'-C-hydroxymethyl-β-d-lyxofuranosyl Nucleotides Display Site-Specific RNase H Cleavage and Induce Gene Silencing. Chemistry 2020; 26:1368-1379. [PMID: 31682037 DOI: 10.1002/chem.201904540] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Indexed: 01/14/2023]
Abstract
Off-target effects remain a significant challenge in the therapeutic use of gapmer antisense oligonucleotides (AONs). Over the years various modifications have been synthesized and incorporated into AONs, however, precise control of RNase H-induced cleavage and target sequence selectivity has yet to be realized. Herein, the synthesis of the uracil and cytosine derivatives of a novel class of 2'-deoxy-2'-fluoro-3'-C-hydroxymethyl-β-d-lyxo-configured nucleotides has been accomplished and the target molecules have been incorporated into AONs. Experiments on exonuclease degradation showed improved nucleolytic stability relative to the unmodified control. Upon the introduction of one or two of the novel 2'-fluoro-3'-C-hydroxymethyl nucleotides as modifications in the gap region of a gapmer AON was associated with efficient RNase H-mediated cleavage of the RNA strand of the corresponding AON:RNA duplex. Notably, a tailored single cleavage event could be engineered depending on the positioning of a single modification. The effect of single mismatched base pairs was scanned along the full gap region demonstrating that the modification enables a remarkable specificity of RNase H cleavage. A cell-based model system was used to demonstrate the potential of gapmer AONs containing the novel modification to mediate gene silencing.
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Affiliation(s)
- Mathias B Danielsen
- Biomolecular Nanonscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Chenguang Lou
- Biomolecular Nanonscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Jolanta Lisowiec-Wachnicka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Anna Pasternak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Per T Jørgensen
- Biomolecular Nanonscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Jesper Wengel
- Biomolecular Nanonscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
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23
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Matta A, Sharma AK, Tomar S, Cao P, Kumar S, Balwani S, Ghosh B, Prasad AK, Van der Eycken EV, DePass AL, Wengel J, Parmar VS, Len C, Singh BK. Synthesis and anti-inflammatory activity evaluation of novel chroman derivatives. NEW J CHEM 2020. [DOI: 10.1039/d0nj02125c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In an effort to develop potent anti-inflammatory agents, a series of novel chroman derivatives including acyclic amidochromans, chromanyl esters and chromanyl acrylates have been designed, synthesized and fully characterized.
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24
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Christou M, Wengel J, Sokratous K, Kyriacou K, Nikolaou G, Phylactou LA, Mastroyiannopoulos NP. Systemic Evaluation of Chimeric LNA/2'-O-Methyl Steric Blockers for Myotonic Dystrophy Type 1 Therapy. Nucleic Acid Ther 2019; 30:80-93. [PMID: 31873063 PMCID: PMC7133450 DOI: 10.1089/nat.2019.0811] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a dominantly inherited, multisystemic disorder characterized clinically by delayed muscle relaxation and weakness. The disease is caused by a CTG repeat expansion in the 3′ untranslated region (3′ UTR) of the DMPK gene, which leads to the expression of a toxic gain-of-function mRNA. The expanded CUG repeat mRNA sequesters the MBNL1 splicing regulator in nuclear-retained foci structures, resulting in loss of protein function and disruption of alternative splicing homeostasis. In this study, we used CAG repeat antisense oligonucleotides (ASOs), composed of locked nucleic acid (LNA)- and 2′-O-methyl (2′OMe)-modified bases in a chimeric design, to alleviate CUGexpanded-mediated toxicity. Chimeric 14–18mer LNA/2′OMe oligonucleotides, exhibiting an LNA incorporation of ∼33%, significantly ameliorated the misregulated alternative splicing of Mbnl1-dependent exons in primary DM1 mouse myoblasts and tibialis anterior muscles of DM1 mice. Subcutaneous delivery of 14mer and 18mer LNA/2′OMe chimeras in DM1 mice resulted in high levels of accumulation in all tested skeletal muscles, as well as in the diaphragm and heart tissue. Despite the efficient delivery, chimeric LNA/2′OMe oligonucleotides were not able, even at a high-dosage regimen (400 mg/kg/week), to correct the misregulated splicing of Serca1 exon 22 in skeletal muscles. Nevertheless, oligonucleotide doses were well-tolerated as determined by histological and plasma biochemistry analyses. Our results provide proof of concept that inhibition of MBNL1 sequestration by systemic delivery of a steric-blocking ASO is extremely challenging, considering the large number of target sites that need to be occupied per RNA molecule. Although not suitable for DM1 therapy, chimeric LNA/2′OMe oligonucleotides could prove to be highly beneficial for other diseases, such as Duchenne muscular dystrophy, that require inhibition of a single target site per RNA molecule.
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Affiliation(s)
- Melina Christou
- Department of Molecular Genetics, Function & Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Jesper Wengel
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Odense M, Denmark
| | - Kleitos Sokratous
- Department of Electron Microscopy and Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Bioinformatics Group, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Kyriacos Kyriacou
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Department of Electron Microscopy and Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Georgios Nikolaou
- Veterinary Diagnostic Laboratory, Vet Ex Machina Ltd, Nicosia, Cyprus
| | - Leonidas A Phylactou
- Department of Molecular Genetics, Function & Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Nikolaos P Mastroyiannopoulos
- Department of Molecular Genetics, Function & Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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25
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Abdelrahman A, Gouda AS, Jørgensen PT, Wengel J. Novel assemblies based on oligonucleotides containing intercalating nucleic acid monomers. Nucleosides Nucleotides Nucleic Acids 2019; 39:82-96. [PMID: 31674270 DOI: 10.1080/15257770.2019.1683188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
This is the first report exploring the capability of twisted intercalating nucleic acid (TINA) and naphthalene-functionalized non-nucleosidic linkers to stabilize and engage in double-helical structures. Four designs were studied with respect to the formation of duplexes and/or other types of self-assemblies. One of the constructs involving TINA provides a thermostable duplex. The biophysical properties of the individual constructs were investigated by UV thermal melting experiments, circular dichroism, and fluorescence emission spectroscopy. Molecular modeling studies were performed in attempts of explaining the biophysical measurements for the duplex based on the TINA-containing oligonucleotide strands.
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Affiliation(s)
- Asmaa Abdelrahman
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark.,Department of Photochemistry, National Research Centre, Giza, Egypt
| | - Alaa S Gouda
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark.,Department of Chemistry, Faculty of Science, Benha University, Benha, Egypt
| | - Per T Jørgensen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
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26
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Yadav Y, Sharma D, Kaushik K, Kumar V, Jha A, Prasad AK, Len C, Malhotra SV, Wengel J, Parmar VS. Synthetic, Structural, and Anticancer Activity Evaluation Studies on Novel Pyrazolylnucleosides. Molecules 2019; 24:molecules24213922. [PMID: 31671703 PMCID: PMC6864788 DOI: 10.3390/molecules24213922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/22/2019] [Accepted: 10/28/2019] [Indexed: 11/16/2022] Open
Abstract
The synthesis of novel pyrazolylnucleosides 3a–e, 4a–e, 5a–e, and 6a–e are described. The structures of the regioisomers were elucidated by using extensive NMR studies. The pyrazolylnucleosides 5a–e and 6a–e were screened for anticancer activities on sixty human tumor cell lines. The compound 6e showed good activity against 39 cancer cell lines. In particular, it showed significant inhibition against the lung cancer cell line Hop-92 (GI50 9.3 µM) and breast cancer cell line HS 578T (GI50 3.0 µM).
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Affiliation(s)
- Yogesh Yadav
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi 110 007, India.
- Medicinal Chemistry Laboratory, Department of Chemistry, Acadia University, Wolfville, NS B4P 2R6, Canada.
- SUN Pharmaceuticals R&D, Gurgaon, Sarhaul, Sector-18, Haryana-122 015, India.
| | - Deepti Sharma
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi 110 007, India.
- Sri Venkateswara College, Benito Juarez Road, Dhaula Kuan, University of Delhi, Delhi 110 021, India.
| | - Kumar Kaushik
- Department of Chemistry and Environmental Science, Medgar Evers College, The City University of New York, 1638 Bedford Avenue, Brooklyn, NY 11225, USA.
| | - Vineet Kumar
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi 110 007, India.
- Laboratory of Synthetic Chemistry, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 2170, USA.
- Department of Radiation Oncology, Stanford University, 1050A Arastradero Road, A252, Palo Alto, CA 94304, USA.
| | - Amitabh Jha
- Medicinal Chemistry Laboratory, Department of Chemistry, Acadia University, Wolfville, NS B4P 2R6, Canada.
| | - Ashok K Prasad
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi 110 007, India.
| | - Christophe Len
- Chimie ParisTech, PSL University, CNRS Institute of Chemistry for Life and Health Sciences-i-CLeHS, 11 rue Pierre et Marie Curie, F-75005 Paris, France.
| | - Sanjay V Malhotra
- Laboratory of Synthetic Chemistry, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 2170, USA.
- Department of Radiation Oncology, Stanford University, 1050A Arastradero Road, A252, Palo Alto, CA 94304, USA.
| | - Jesper Wengel
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark.
| | - Virinder S Parmar
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi 110 007, India.
- Department of Chemistry and Environmental Science, Medgar Evers College, The City University of New York, 1638 Bedford Avenue, Brooklyn, NY 11225, USA.
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark.
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Gasparri F, Wengel J, Grutter T, Pless SA. Molecular determinants for agonist recognition and discrimination in P2X2 receptors. J Gen Physiol 2019; 151:898-911. [PMID: 31126967 PMCID: PMC6605687 DOI: 10.1085/jgp.201912347] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/06/2019] [Indexed: 12/26/2022] Open
Abstract
P2X receptors (P2XRs) are ligand-gated cation channels involved in pain and inflammation. Gasparri et al. show that the backbone carbonyl atoms of amino acid residue Thr184 are involved in ligand discrimination, while those of Lys69 contribute mostly to ligand recognition by rat P2X2Rs. P2X receptors (P2XRs) are trimeric ligand-gated ion channels that open a cation-selective pore in response to ATP binding. P2XRs contribute to synaptic transmission and are involved in pain and inflammation, thus representing valuable drug targets. Recent crystal structures have confirmed the findings of previous studies with regards to the amino acid chains involved in ligand recognition, but they have also suggested that backbone carbonyl atoms contribute to ATP recognition and discrimination. Here we use a combination of site-directed mutagenesis, amide-to-ester substitutions, and a range of ATP analogues with subtle alterations to either base or sugar component to investigate the contributions of backbone carbonyl atoms toward ligand recognition and discrimination in rat P2X2Rs. Our findings demonstrate that while the Lys69 backbone carbonyl makes an important contribution to ligand recognition, the discrimination between different ligands is mediated by both the side chain and the backbone carbonyl oxygen of Thr184. Together, our data demonstrate how conserved elements in P2X2Rs recognize and discriminate agonists.
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Affiliation(s)
- Federica Gasparri
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Thomas Grutter
- University of Strasbourg, Centre National de la Recherche Scientifique, Conception et Application de Molécules Bioactives Unité Mixte de Recherche 7199, Strasbourg, France
| | - Stephan A Pless
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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28
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Andersen VL, Vinther M, Kumar R, Ries A, Wengel J, Nielsen JS, Kjems J. A self-assembled, modular nucleic acid-based nanoscaffold for multivalent theranostic medicine. Am J Cancer Res 2019; 9:2662-2677. [PMID: 31131060 PMCID: PMC6525989 DOI: 10.7150/thno.32060] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/21/2019] [Indexed: 12/20/2022] Open
Abstract
Rationale: Within the field of personalized medicine there is an increasing focus on designing flexible, multifunctional drug delivery systems that combine high efficacy with minimal side effects, by tailoring treatment to the individual. Methods: We synthesized a chemically stabilized ~4 nm nucleic acid nanoscaffold, and characterized its assembly, stability and functional properties in vitro and in vivo. We tested its flexibility towards multifunctionalization by conjugating various biomolecules to the four modules of the system. The pharmacokinetics, targeting capability and bioimaging properties of the structure were investigated in mice. The role of avidity in targeted liver cell internalization was investigated by flow cytometry, confocal microscopy and in vivo by fluorescent scanning of the blood and organs of the animals. Results: We have developed a nanoscaffold that rapidly and with high efficiency can self-assemble four chemically conjugated functionalities into a stable, in vivo-applicable system with complete control of stoichiometry and site specificity. The circulation time of the nanoscaffold could be tuned by functionalization with various numbers of polyethylene glycol polymers or with albumin-binding fatty acids. Highly effective hepatocyte-specific internalization was achieved with increasing valencies of tri-antennary galactosamine (triGalNAc) in vitro and in vivo. Conclusion: With its facile functionalization, stoichiometric control, small size and high serum- and thermostability, the nanoscaffold presented here constitutes a novel and flexible platform technology for theranostics.
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29
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Moura J, Sørensen A, Leal EC, Svendsen R, Carvalho L, Willemoes RJ, Jørgensen PT, Jenssen H, Wengel J, Dalgaard LT, Carvalho E. microRNA-155 inhibition restores Fibroblast Growth Factor 7 expression in diabetic skin and decreases wound inflammation. Sci Rep 2019; 9:5836. [PMID: 30967591 PMCID: PMC6456606 DOI: 10.1038/s41598-019-42309-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 03/28/2019] [Indexed: 12/13/2022] Open
Abstract
Treatment for chronic diabetic foot ulcers is limited by the inability to simultaneously address the excessive inflammation and impaired re-epithelization and remodeling. Impaired re-epithelization leads to significantly delayed wound closure and excessive inflammation causes tissue destruction, both enhancing wound pathogen colonization. Among many differentially expressed microRNAs, miR-155 is significantly upregulated and fibroblast growth factor 7 (FGF7) mRNA (target of miR-155) and protein are suppressed in diabetic skin, when compared to controls, leading us to hypothesize that topical miR-155 inhibition would improve diabetic wound healing by restoring FGF7 expression. In vitro inhibition of miR-155 increased human keratinocyte scratch closure and topical inhibition of miR-155 in vivo in wounds increased murine FGF7 protein expression and significantly enhanced diabetic wound healing. Moreover, we show that miR-155 inhibition leads to a reduction in wound inflammation, in accordance with known pro-inflammatory actions of miR-155. Our results demonstrate, for the first time, that topical miR-155 inhibition increases diabetic wound fibroblast growth factor 7 expression in diabetic wounds, which, in turn, increases re-epithelization and, consequently, accelerates wound closure. Topical miR-155 inhibition targets both excessive inflammation and impaired re-epithelization and remodeling, being a potentially new and effective treatment for chronic diabetic foot ulcers.
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Affiliation(s)
- João Moura
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Anja Sørensen
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Ermelindo C Leal
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Rikke Svendsen
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Lina Carvalho
- Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Rie Juul Willemoes
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Per Trolle Jørgensen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Håvard Jenssen
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Jesper Wengel
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | | | - Eugénia Carvalho
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal. .,Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States. .,Arkansas Children's Research Institute, Little Rock, Arkansas, United States.
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Vejlegaard K, Wegeberg C, McKee V, Wengel J. Novel conformationally constrained 2'-C-methylribonucleosides: synthesis and incorporation into oligonucleotides. Org Biomol Chem 2019; 16:1312-1321. [PMID: 29392247 DOI: 10.1039/c7ob02663c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Synthesis of two novel conformationally constrained bicyclic ribonucleoside phosphoramidites bearing a 2'-C-methyl substituent has been accomplished. These phosphoramidites were used to incorporate the corresponding 2'-C-methyl nucleotides into oligonucleotides and to study their effects on duplex thermal stability. Whereas the C2'-O4'-linked LNA-type derivative induced severe destabilization of duplexes formed with complementary DNA and RNA, the C3'-O4'-linked derivative induced RNA-selective hybridization with increased affinity relative to that of the unmodified DNA-based probe.
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Affiliation(s)
- Kim Vejlegaard
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark. jwe@sdu
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Umek T, Sollander K, Bergquist H, Wengel J, Lundin KE, Smith CIE, Zain R. Oligonucleotide Binding to Non-B-DNA in MYC. Molecules 2019; 24:E1000. [PMID: 30871121 PMCID: PMC6429085 DOI: 10.3390/molecules24051000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 02/25/2019] [Accepted: 03/06/2019] [Indexed: 11/16/2022] Open
Abstract
MYC, originally named c-myc, is an oncogene deregulated in many different forms of cancer. Translocation of the MYC gene to an immunoglobulin gene leads to an overexpression and the development of Burkitt's lymphoma (BL). Sporadic BL constitutes one subgroup where one of the translocation sites is located at the 5'-vicinity of the two major MYC promoters P₁ and P₂. A non-B-DNA forming sequence within this region has been reported with the ability to form an intramolecular triplex (H-DNA) or a G-quadruplex. We have examined triplex formation at this site first by using a 17 bp triplex-forming oligonucleotide (TFO) and a double strand DNA (dsDNA) target corresponding to the MYC sequence. An antiparallel purine-motif triplex was detected using electrophoretic mobility shift assay. Furthermore, we probed for H-DNA formation using the BQQ-OP based triplex-specific cleavage assay, which indicated the formation of the structure in the supercoiled plasmid containing the corresponding region of the MYC promoter. Targeting non-B-DNA structures has therapeutic potential; therefore, we investigated their influence on strand-invasion of anti-gene oligonucleotides (ON)s. We show that in vitro, non-B-DNA formation at the vicinity of the ON target site facilitates dsDNA strand-invasion of the anti-gene ONs.
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Affiliation(s)
- Tea Umek
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, 141 86 Huddinge, Sweden.
| | - Karin Sollander
- Department of Molecular Biology and Functional Genomics, Stockholm University, 171 65 Stockholm, Sweden.
| | - Helen Bergquist
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, 141 86 Huddinge, Sweden.
| | - Jesper Wengel
- Biomolecular Nanoscale Engineerng Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, M5230 Odense, Denmark.
| | - Karin E Lundin
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, 141 86 Huddinge, Sweden.
| | - C I Edvard Smith
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, 141 86 Huddinge, Sweden.
| | - Rula Zain
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, 141 86 Huddinge, Sweden.
- Department of Clinical Genetics, Centre for Rare Diseases, Karolinska University Hospital, SE-171 76 Stockholm, Sweden.
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Kotkowiak W, Wengel J, Scotton CJ, Pasternak A. Improved RE31 Analogues Containing Modified Nucleic Acid Monomers: Thermodynamic, Structural, and Biological Effects. J Med Chem 2019; 62:2499-2507. [PMID: 30735377 DOI: 10.1021/acs.jmedchem.8b01806] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
RE31 is a 31-nt DNA aptamer, consisting of the G-quadruplex and a duplex domain, which is able to effectively prolong thrombin time. This article reports on the influence of certain modified nucleotide residues on thermodynamic and biological properties as well as the folding topology of RE31. Particularly, the effect of the presence of nucleosides in unlocked nucleic acid (UNA), locked nucleic acid (LNA), or β-l-RNA series was evaluated. The studies presented herein show that all modified residues can influence thermal and biological stabilities of G-quadruplex in a position-dependent manner. The aptamers modified simultaneously with UNA at the T15 position and LNAs in the duplex part possess the highest value of melting temperature and a 2-fold higher anticoagulant effect. Importantly, RE31 variants modified with nucleosides in UNA, LNA, or β-l-RNA series exhibit unchanged G-quadruplex folding topology. Crucially, introduction of any of the modified residues into RE31 causes prolongation of aptamer stability in human serum.
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Affiliation(s)
- Weronika Kotkowiak
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry , Polish Academy of Sciences , Noskowskiego 12/14 , 61-704 Poznan , Poland
| | - Jesper Wengel
- Department of Physics, Chemistry, and Pharmacy, Biomolecular Nanoscale Engineering Center , University of Southern Denmark , Campusvej 55 , Odense M 5230 , Denmark
| | - Chris J Scotton
- Institute of Biomedical and Clinical Science, College of Medicine & Health , University of Exeter, St Luke's Campus , Exeter EX1 2LU , U.K
| | - Anna Pasternak
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry , Polish Academy of Sciences , Noskowskiego 12/14 , 61-704 Poznan , Poland
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Garcia JP, Stein J, Cai Y, Riemers F, Wexselblatt E, Wengel J, Tryfonidou M, Yayon A, Howard KA, Creemers LB. Fibrin-hyaluronic acid hydrogel-based delivery of antisense oligonucleotides for ADAMTS5 inhibition in co-delivered and resident joint cells in osteoarthritis. J Control Release 2018; 294:247-258. [PMID: 30572032 DOI: 10.1016/j.jconrel.2018.12.030] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 12/16/2018] [Indexed: 02/06/2023]
Abstract
To date no disease-modifying drugs for osteoarthritis (OA) are available, with treatment limited to the use of pain killers and prosthetic replacement. The ADAMTS (A Disintegrin and Metallo Proteinase with Thrombospondin Motifs) enzyme family is thought to be instrumental in the loss of proteoglycans during cartilage degeneration in OA, and their inhibition was shown to reverse osteoarthritic cartilage degeneration. Locked Nucleic Acid (LNA)-modified antisense oligonucleotides (gapmers) released from biomaterial scaffolds for specific and prolonged ADAMTS inhibition in co-delivered and resident chondrocytes, is an attractive therapeutic strategy. Here, a gapmer sequence identified from a gapmer screen showed 90% ADAMTS5 silencing in a monolayer culture of human OA chondrocytes. Incorporation of the gapmer in a fibrin-hyaluronic acid hydrogel exhibited a sustained release profile up to 14 days. Gapmers loaded in hydrogels were able to transfect both co-embedded chondrocytes and chondrocytes in a neighboring gapmer-free hydrogel, as demonstrated by flow cytometry and confocal microscopy. Efficient knockdown of ADAMTS5 was shown up to 14 days in both cell populations, i.e. the gapmer-loaded and gapmer-free hydrogel. This work demonstrates the use applicability of a hydrogel as a platform for combined local delivery of chondrocytes and an ADAMTS-targeting gapmer for catabolic gene modulation in OA.
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Affiliation(s)
- João Pedro Garcia
- Department of Orthopedics, University Medical Center Utrecht, the Netherlands
| | - Jeroen Stein
- Department of Orthopedics, University Medical Center Utrecht, the Netherlands
| | - Yunpeng Cai
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Frank Riemers
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, the Netherlands
| | | | - Jesper Wengel
- Nucleic Acid Center, University of Southern Denmark, Denmark
| | - Marianna Tryfonidou
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, the Netherlands
| | | | - Kenneth A Howard
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Laura B Creemers
- Department of Orthopedics, University Medical Center Utrecht, the Netherlands.
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Ferino A, Miglietta G, Picco R, Vogel S, Wengel J, Xodo LE. MicroRNA therapeutics: design of single-stranded miR-216b mimics to target KRAS in pancreatic cancer cells. RNA Biol 2018; 15:1273-1285. [PMID: 30306823 PMCID: PMC6284578 DOI: 10.1080/15476286.2018.1526536] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Datasets reporting microRNA expression profiles in normal and cancer cells show that miR-216b is aberrantly downregulated in pancreatic ductal adenocarcinoma (PDAC). We found that KRAS, whose mutant G12D allele drives the pathogenesis of PDAC, is a target of miR-216b. To suppress oncogenic KRAS in PDAC cells, we designed single-stranded (ss) miR-216b mimics with unlocked nucleic acid (UNA) modifications to enhance their nuclease resistance. We prepared variants of ss-miR-216b mimics with and without a 5ʹ phosphate group. Both variants strongly suppressed oncogenic KRAS in PDAC cells and inhibited colony formation in pancreatic cancer cells. We observed that the designed ss-miR-216b mimics engaged AGO2 to promote the silencing of KRAS. We also tested a new delivery strategy based on the use of palmityl-oleyl-phosphatidylcholine (POPC) liposomes functionalized with ss-miR-216b conjugated with two palmityl chains and a lipid-modified cell penetrating peptide (TAT). These versatile nanoparticles suppressed oncogenic KRAS in PDAC cells.
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Affiliation(s)
- Annalisa Ferino
- a Department of Medicine, Laboratory of Biochemistry , University of Udine , Italy
| | - Giulia Miglietta
- a Department of Medicine, Laboratory of Biochemistry , University of Udine , Italy
| | - Raffaella Picco
- a Department of Medicine, Laboratory of Biochemistry , University of Udine , Italy
| | - Stefan Vogel
- b Nucleic Acids Centre , University of Southern Denmark , Odense , Denmark
| | - Jesper Wengel
- b Nucleic Acids Centre , University of Southern Denmark , Odense , Denmark
| | - Luigi E Xodo
- a Department of Medicine, Laboratory of Biochemistry , University of Udine , Italy
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Le BT, Hughes Q, Rakesh S, Baker R, Jørgensen PT, Wengel J, Veedu RN. Unlocked nucleic acid modified primer-based enzymatic polymerization assay: towards allele-specific genotype detection of human platelet antigens. RSC Adv 2018; 8:32770-32774. [PMID: 35547719 PMCID: PMC9086379 DOI: 10.1039/c8ra06050a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 08/24/2018] [Indexed: 12/12/2022] Open
Abstract
Accurate detection of single nucleotide polymorphisms (SNPs) is paramount for the appropriate therapeutic intervention of debilitating diseases associated with SNPs. However, in some cases current nucleic acid probes fail to detect allele-specific mutations, for example, human platelet antigens, HPA-15a (TCC) and HPA-15b (TAC) alleles associated with neonatal alloimmune thrombocytopenia. Towards this, it is necessary to develop a novel assay for detection of allele-specific mutations. In this study, we investigated the potential of unlocked nucleic acid (UNA)-modified primers in SNP detection utilising an enzymatic polymerisation-based approach. Our results of primer extension and asymmetric polymerase chain reaction by KOD XL DNA polymerase revealed that UNA-modified primers achieved excellent allele-specificity in discriminating the human platelet antigen DNA template, whereas the DNA control primers were not able to differentiate between the normal and mutant alleles, demonstrating the scope of this novel UNA-based enzymatic approach as a robust methodology for efficient detection of allele-specific mismatches. Although further evaluation is required for other disease conditions, we firmly believe that our findings offer a great promise for the diagnosis of neonatal alloimmune thrombocytopenia and other SNP-related diseases.
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Affiliation(s)
- Bao T Le
- Centre for Comparative Genomics, Murdoch University Perth Australia-6150
- Perron Institute for Neurological and Translational Science Perth Australia-6009
| | | | | | - Ross Baker
- Perth Blood Institute Nedlands Perth WA Australia
| | - Per T Jørgensen
- BioNEC, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark Odense M 5231 Denmark
| | - Jesper Wengel
- BioNEC, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark Odense M 5231 Denmark
| | - Rakesh N Veedu
- Centre for Comparative Genomics, Murdoch University Perth Australia-6150
- Perron Institute for Neurological and Translational Science Perth Australia-6009
- BioNEC, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark Odense M 5231 Denmark
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Ejlersen M, Lou C, Sanghvi YS, Tor Y, Wengel J. Modification of oligodeoxynucleotides by on-column Suzuki cross-coupling reactions. Chem Commun (Camb) 2018; 54:8003-8006. [PMID: 29967912 DOI: 10.1039/c8cc01360h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The on-column functionalization of oligodeoxynucleotides via base-free Suzuki cross-coupling reactions is reported herein. These cross-coupling reactions were carried out with various boronic acids and either full-length modified oligonucleotides containing one or more 2'-deoxy-5-iodouridine (5IdU) monomer(s) or on oligonucleotide fragments immediately after incorporation of 5IdU. Five different functionalities were coupled to oligonucleotides containing one or three attachment points.
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Affiliation(s)
- Maria Ejlersen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark.
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Cai Y, Makarova AM, Wengel J, Howard KA. Palmitoylated phosphodiester gapmer designs with albumin binding capacity and maintained in vitro gene silencing activity. J Gene Med 2018; 20:e3025. [PMID: 29800498 DOI: 10.1002/jgm.3025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 05/09/2018] [Accepted: 05/16/2018] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Antisense gapmer oligonucleotide drugs require delivery and biodistribution enabling technologies to increase in vivo efficacy. An attractive approach is their binding and consequent transport by the endogenous human serum albumin pool as mediated by fatty acid incorporation into the gapmer design. METHODS The present study investigated the effect of palmitoyl modification and position on albumin-binding, cellular uptake and in vitro gene silencing of gapmers with either a phosphorothioate (PS) or phosphodiester (PO) backbone. RESULTS Two palmitoyls positioned exclusively at the 5' end, or a single palmitoyl at both the 3' and 5' positions, showed similar binding to human serum albumin as demonstrated by a gel-shift assay. Decreased cellular uptake determined by flow cytometry (27% compared to nonpalmitoyl gapmers) was observed for palmitoylated Cy5.5 labelled gapmers. However, HER3 (human epidermal growth factor receptor 3) gene silencing was exhibited by the palmitoylated gapmers with transfection agent in PC-3 and Caco-2 cells (68% and 62%, respectively), which was comparable to nonpalmitoyl gapmers (68% and 82%, respectively). Importantly, PO gapmers with a single palmitoyl positioned at both the 3' and 5' positions showed high silencing efficiencies (68% and 66% in PC-3 and Caco-2 cells, respectively) similar to those of PS nonpalmitoylated gapmers (67% and 66% in PC-3 and Caco-2 cells, respectively) in the absence of a transfection agent. CONCLUSIONS The present study defines phosphodiester gapmer design criteria exhibiting high gene silencing activity and albumin binding that may be utilized with potentially less in vivo toxicity that can be associated with phosphorothioate gapmer designs.
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Affiliation(s)
- Yunpeng Cai
- The Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | | | - Jesper Wengel
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Kenneth A Howard
- The Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
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Lima JF, Carvalho J, Pinto-Ribeiro I, Almeida C, Wengel J, Cerqueira L, Figueiredo C, Oliveira C, Azevedo NF. Targeting miR-9 in gastric cancer cells using locked nucleic acid oligonucleotides. BMC Mol Biol 2018; 19:6. [PMID: 29879907 PMCID: PMC5992815 DOI: 10.1186/s12867-018-0107-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 05/28/2018] [Indexed: 12/21/2022] Open
Abstract
Background Gastric cancer is the third leading cause of cancer-related mortality worldwide. Recently, it has been demonstrated that gastric cancer cells display a specific miRNA expression profile, with increasing evidence of the role of miRNA-9 in this disease. miRNA-9 upregulation has been shown to influence the expression of E-cadherin-encoding gene, triggering cell motility and invasiveness. Results In this study, we designed LNA anti-miRNA oligonucleotides with a complementary sequence to miRNA-9 and tested their properties to both detect and silence the target miRNA. We could identify and visualize the in vitro uptake of low-dosing LNA-based anti-miRNA oligonucleotides without any carrier or transfection agent, as early as 2 h after the addition of the oligonucleotide sequence to the culture medium. Furthermore, we were able to assess the silencing potential of miRNA-9, using different LNA anti-miRNA oligonucleotide designs, and to observe its subsequent effect on E-cadherin expression. Conclusions The administration of anti-miRNA sequences even at low-doses, rapidly repressed the target miRNA, and influenced the expression of E-cadherin by significantly increasing its levels.
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Affiliation(s)
- Joana Filipa Lima
- Department of Chemical Engineering, LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering of the University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal. .,Biomode, 2 S.A., Braga, Portugal. .,i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal. .,IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.
| | - Joana Carvalho
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Inês Pinto-Ribeiro
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.,FMUP, Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Carina Almeida
- National Institute for Agricultural and Veterinary Research (INIAV), Vairão, Vila do Conde, Portugal
| | - Jesper Wengel
- Department of Physics, Chemistry and Pharmacy, Nucleic Acid Center, University of Southern Denmark, Odense, Denmark
| | - Laura Cerqueira
- Department of Chemical Engineering, LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering of the University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal.,Biomode, 2 S.A., Braga, Portugal
| | - Céu Figueiredo
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.,FMUP, Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Carla Oliveira
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.,FMUP, Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Nuno Filipe Azevedo
- Department of Chemical Engineering, LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering of the University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
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Moreno PMD, Ferreira AR, Salvador D, Rodrigues MT, Torrado M, Carvalho ED, Tedebark U, Sousa MM, Amaral IF, Wengel J, Pêgo AP. Hydrogel-Assisted Antisense LNA Gapmer Delivery for In Situ Gene Silencing in Spinal Cord Injury. Mol Ther Nucleic Acids 2018; 11:393-406. [PMID: 29858074 PMCID: PMC5992461 DOI: 10.1016/j.omtn.2018.03.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 03/04/2018] [Accepted: 03/15/2018] [Indexed: 12/16/2022]
Abstract
After spinal cord injury (SCI), nerve regeneration is severely hampered due to the establishment of a highly inhibitory microenvironment at the injury site, through the contribution of multiple factors. The potential of antisense oligonucleotides (AONs) to modify gene expression at different levels, allowing the regulation of cell survival and cell function, together with the availability of chemically modified nucleic acids with favorable biopharmaceutical properties, make AONs an attractive tool for novel SCI therapy developments. In this work, we explored the potential of locked nucleic acid (LNA)-modified AON gapmers in combination with a fibrin hydrogel bridging material to induce gene silencing in situ at a SCI lesion site. LNA gapmers were effectively developed against two promising gene targets aiming at enhancing axonal regeneration-RhoA and GSK3β. The fibrin-matrix-assisted AON delivery system mediated potent RNA knockdown in vitro in a dorsal root ganglion explant culture system and in vivo at a SCI lesion site, achieving around 75% downregulation 5 days after hydrogel injection. Our results show that local implantation of a AON-gapmer-loaded hydrogel matrix mediated efficient gene silencing in the lesioned spinal cord and is an innovative platform that can potentially combine gene regulation with regenerative permissive substrates aiming at SCI therapeutics and nerve regeneration.
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Affiliation(s)
- Pedro M D Moreno
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
| | - Ana R Ferreira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
| | - Daniela Salvador
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
| | - Maria T Rodrigues
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
| | - Marília Torrado
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
| | - Eva D Carvalho
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
| | - Ulf Tedebark
- GE Healthcare Bio-Sciences AB, 75184 Uppsala, Sweden; SynMer AB, 17568 Järfälla, Sweden
| | - Mónica M Sousa
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; IBMC - Instituto de Biologia Molecular e Celular, Nerve Regeneration Group, Universidade do Porto, 4200-135 Porto, Portugal
| | - Isabel F Amaral
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
| | - Jesper Wengel
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense, Denmark
| | - Ana P Pêgo
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal; Faculdade de Engenharia da Universidade do Porto, 4200-465 Porto, Portugal; Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313 Porto, Portugal.
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Ejlersen M, Christensen NJ, Sørensen KK, Jensen KJ, Wengel J, Lou C. Synergy of Two Highly Specific Biomolecular Recognition Events: Aligning an AT-Hook Peptide in DNA Minor Grooves via Covalent Conjugation to 2'-Amino-LNA. Bioconjug Chem 2018; 29:1025-1029. [PMID: 29505242 DOI: 10.1021/acs.bioconjchem.8b00101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two highly specific biomolecular recognition events, nucleic acid duplex hybridization and DNA-peptide recognition in the minor groove, were coalesced in a miniature ensemble for the first time by covalently attaching a natural AT-hook peptide motif to nucleic acid duplexes via a 2'-amino-LNA scaffold. A combination of molecular dynamics simulations and ultraviolet thermal denaturation studies revealed high sequence-specific affinity of the peptide-oligonucleotide conjugates (POCs) when binding to complementary DNA strands, leveraging the bioinformation encrypted in the minor groove of DNA duplexes. The significant cooperative DNA duplex stabilization may pave the way toward further development of POCs with enhanced affinity and selectivity toward target sequences carrying peptide-binding genetic islands.
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Affiliation(s)
- Maria Ejlersen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , Campusvej 55 , 5230 Odense M , Denmark
| | - Niels Johan Christensen
- Biomolecular Nanoscale Engineering Center, Department of Chemistry , University of Copenhagen , Thorvaldsensvej 40 , 1871 Frederiksberg , Denmark
| | - Kasper K Sørensen
- Biomolecular Nanoscale Engineering Center, Department of Chemistry , University of Copenhagen , Thorvaldsensvej 40 , 1871 Frederiksberg , Denmark
| | - Knud J Jensen
- Biomolecular Nanoscale Engineering Center, Department of Chemistry , University of Copenhagen , Thorvaldsensvej 40 , 1871 Frederiksberg , Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , Campusvej 55 , 5230 Odense M , Denmark
| | - Chenguang Lou
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , Campusvej 55 , 5230 Odense M , Denmark
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Kotkowiak W, Lisowiec-Wachnicka J, Grynda J, Kierzek R, Wengel J, Pasternak A. Thermodynamic, Anticoagulant, and Antiproliferative Properties of Thrombin Binding Aptamer Containing Novel UNA Derivative. Mol Ther Nucleic Acids 2018; 10:304-316. [PMID: 29499943 PMCID: PMC5862132 DOI: 10.1016/j.omtn.2017.12.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/21/2017] [Accepted: 12/21/2017] [Indexed: 12/25/2022]
Abstract
Thrombin is a serine protease that plays a crucial role in hemostasis, fibrinolysis, cell proliferation, and migration. Thrombin binding aptamer (TBA) is able to inhibit the activity of thrombin molecule via binding to its exosite I. This 15-nt DNA oligonucleotide forms an intramolecular, antiparallel G-quadruplex structure with a chair-like conformation. In this paper, we report on our investigations on the influence of certain modified nucleotide residues on thermodynamic stability, folding topology, and biological properties of TBA variants. In particular, the effect of single incorporation of a novel 4-thiouracil derivative of unlocked nucleic acid (UNA), as well as single incorporation of 4-thiouridine and all four canonical UNAs, was evaluated. The studies presented herein have shown that 4-thiouridine in RNA and UNA series, as well as all four canonical UNAs, can efficiently modulate G-quadruplex thermodynamic and biological stability, and that the effect is strongly position dependent. Interestingly, TBA variants containing the modified nucleotide residues are characterized by unchanged folding topology. Thrombin time assay revealed that incorporation of certain UNA residues may improve G-quadruplex anticoagulant properties. Noteworthy, some TBA variants, characterized by decreased ability to inhibit thrombin activity, possess significant antiproliferative properties reducing the viability of the HeLa cell line even by 95% at 10 μM concentration.
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Affiliation(s)
- Weronika Kotkowiak
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Jolanta Lisowiec-Wachnicka
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Jakub Grynda
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Gabriela Narutowicza 11/12, 80-233 Gdansk, Poland
| | - Ryszard Kierzek
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Jesper Wengel
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
| | - Anna Pasternak
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
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42
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Kuhlmann M, Hamming JBR, Voldum A, Tsakiridou G, Larsen MT, Schmøkel JS, Sohn E, Bienk K, Schaffert D, Sørensen ES, Wengel J, Dupont DM, Howard KA. An Albumin-Oligonucleotide Assembly for Potential Combinatorial Drug Delivery and Half-Life Extension Applications. Mol Ther Nucleic Acids 2017; 9:284-293. [PMID: 29246307 PMCID: PMC5676087 DOI: 10.1016/j.omtn.2017.10.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 10/04/2017] [Accepted: 10/04/2017] [Indexed: 01/31/2023]
Abstract
The long blood circulatory property of human serum albumin, due to engagement with the cellular recycling neonatal Fc receptor (FcRn), is an attractive drug half-life extension enabling technology. This work describes a novel site-specific albumin double-stranded (ds) DNA assembly approach, in which the 3′ or 5′ end maleimide-derivatized oligodeoxynucleotides are conjugated to albumin cysteine at position 34 (cys34) and annealed with complementary strands to allow single site-specific protein modification with functionalized ds oligodeoxynucleotides. Electrophoretic gel shift assays demonstrated successful annealing of complementary strands bearing Atto488, 6-carboxyfluorescein (6-FAM), or a factor IXa aptamer to the albumin-oligodeoxynucleotide conjugate. A fluorometric factor IXa activity assay showed retained aptamer inhibitory activity upon assembly with the albumin and completely blocked factor IXa at a concentration of 100 nM for 2 hr. The assembled construct exhibited stability in serum-containing buffer and FcRn engagement that could be increased using an albumin variant engineered for higher FcRn affinity. This work presents a novel albumin-oligodeoxynucleotide assembly technology platform that offers potential combinatorial drug delivery and half-life extension applications.
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Affiliation(s)
- Matthias Kuhlmann
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Jonas B R Hamming
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Anders Voldum
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Georgia Tsakiridou
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Maja T Larsen
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Julie S Schmøkel
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Emil Sohn
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Konrad Bienk
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - David Schaffert
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Esben S Sørensen
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Jesper Wengel
- Nucleic Acid Center, Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Daniel M Dupont
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Kenneth A Howard
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark.
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43
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Zaghloul EM, Gissberg O, Moreno PMD, Siggens L, Hällbrink M, Jørgensen AS, Ekwall K, Zain R, Wengel J, Lundin KE, Smith CIE. CTG repeat-targeting oligonucleotides for down-regulating Huntingtin expression. Nucleic Acids Res 2017; 45:5153-5169. [PMID: 28334749 PMCID: PMC5435994 DOI: 10.1093/nar/gkx111] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 02/06/2017] [Indexed: 12/12/2022] Open
Abstract
Huntington's disease (HD) is a fatal, neurodegenerative disorder in which patients suffer from mobility, psychological and cognitive impairments. Existing therapeutics are only symptomatic and do not significantly alter the disease progression or increase life expectancy. HD is caused by expansion of the CAG trinucleotide repeat region in exon 1 of the Huntingtin gene (HTT), leading to the formation of mutant HTT transcripts (muHTT). The toxic gain-of-function of muHTT protein is a major cause of the disease. In addition, it has been suggested that the muHTT transcript contributes to the toxicity. Thus, reduction of both muHTT mRNA and protein levels would ideally be the most useful therapeutic option. We herein present a novel strategy for HD treatment using oligonucleotides (ONs) directly targeting the HTT trinucleotide repeat DNA. A partial, but significant and potentially long-term, HTT knock-down of both mRNA and protein was successfully achieved. Diminished phosphorylation of HTT gene-associated RNA-polymerase II is demonstrated, suggestive of reduced transcription downstream the ON-targeted repeat. Different backbone chemistries were found to have a strong impact on the ON efficiency. We also successfully use different delivery vehicles as well as naked uptake of the ONs, demonstrating versatility and possibly providing insights for in vivo applications.
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Affiliation(s)
- Eman M Zaghloul
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Stockholm, Sweden.,Department of Pharmaceutics, Faculty of Pharmacy, Alexandria University, El-Khartoum square, Azareeta, 21 521 Alexandria, Egypt
| | - Olof Gissberg
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Stockholm, Sweden
| | - Pedro M D Moreno
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Stockholm, Sweden.,Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
| | - Lee Siggens
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden, SE-141 86, Huddinge, Stockholm, Sweden
| | - Mattias Hällbrink
- Department of Neurochemistry, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Anna S Jørgensen
- Department of Physics and Chemistry, Nucleic Acid Centre University of Southern Denmark, DK-5230 Odense, Denmark
| | - Karl Ekwall
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden, SE-141 86, Huddinge, Stockholm, Sweden
| | - Rula Zain
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Stockholm, Sweden.,Department of Clinical Genetics, Centre for Rare Diseases, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Jesper Wengel
- Department of Physics and Chemistry, Nucleic Acid Centre University of Southern Denmark, DK-5230 Odense, Denmark
| | - Karin E Lundin
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Stockholm, Sweden
| | - C I Edvard Smith
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Stockholm, Sweden
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44
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Pabon-Martinez YV, Xu Y, Villa A, Lundin KE, Geny S, Nguyen CH, Pedersen EB, Jørgensen PT, Wengel J, Nilsson L, Smith CIE, Zain R. LNA effects on DNA binding and conformation: from single strand to duplex and triplex structures. Sci Rep 2017; 7:11043. [PMID: 28887512 PMCID: PMC5591256 DOI: 10.1038/s41598-017-09147-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 07/20/2017] [Indexed: 12/19/2022] Open
Abstract
The anti-gene strategy is based on sequence-specific recognition of double-strand DNA by triplex forming (TFOs) or DNA strand invading oligonucleotides to modulate gene expression. To be efficient, the oligonucleotides (ONs) should target DNA selectively, with high affinity. Here we combined hybridization analysis and electrophoretic mobility shift assay with molecular dynamics (MD) simulations to better understand the underlying structural features of modified ONs in stabilizing duplex- and triplex structures. Particularly, we investigated the role played by the position and number of locked nucleic acid (LNA) substitutions in the ON when targeting a c-MYC or FXN (Frataxin) sequence. We found that LNA-containing single strand TFOs are conformationally pre-organized for major groove binding. Reduced content of LNA at consecutive positions at the 3'-end of a TFO destabilizes the triplex structure, whereas the presence of Twisted Intercalating Nucleic Acid (TINA) at the 3'-end of the TFO increases the rate and extent of triplex formation. A triplex-specific intercalating benzoquinoquinoxaline (BQQ) compound highly stabilizes LNA-containing triplex structures. Moreover, LNA-substitution in the duplex pyrimidine strand alters the double helix structure, affecting x-displacement, slide and twist favoring triplex formation through enhanced TFO major groove accommodation. Collectively, these findings should facilitate the design of potent anti-gene ONs.
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Affiliation(s)
- Y Vladimir Pabon-Martinez
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86, Huddinge, Stockholm, Sweden
| | - You Xu
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 83, Huddinge, Sweden
| | - Alessandra Villa
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 83, Huddinge, Sweden
| | - Karin E Lundin
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86, Huddinge, Stockholm, Sweden
| | - Sylvain Geny
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86, Huddinge, Stockholm, Sweden
| | - Chi-Hung Nguyen
- Institut Curie, PSL Research University, UMR 9187-U 1196, CNRS-Institut Curie, INSERM, Centre Universitaire, Orsay, France
| | - Erik B Pedersen
- Department of Physics, Chemistry and Pharmacy, Nucleic Acid Center, University of Southern Denmark, DK-5230, Odense M, Denmark
| | - Per T Jørgensen
- Department of Physics, Chemistry and Pharmacy, Nucleic Acid Center, University of Southern Denmark, DK-5230, Odense M, Denmark
| | - Jesper Wengel
- Department of Physics, Chemistry and Pharmacy, Nucleic Acid Center, University of Southern Denmark, DK-5230, Odense M, Denmark
| | - Lennart Nilsson
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 83, Huddinge, Sweden
| | - C I Edvard Smith
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86, Huddinge, Stockholm, Sweden
| | - Rula Zain
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86, Huddinge, Stockholm, Sweden.
- Department of Clinical Genetics, Centre for Rare Diseases, Karolinska University Hospital, SE-171 76, Stockholm, Sweden.
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45
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Lou C, Christensen NJ, Martos-Maldonado MC, Midtgaard SR, Ejlersen M, Thulstrup PW, Sørensen KK, Jensen KJ, Wengel J. Inside Back Cover: Folding Topology of a Short Coiled-Coil Peptide Structure Templated by an Oligonucleotide Triplex (Chem. Eur. J. 39/2017). Chemistry 2017. [DOI: 10.1002/chem.201701745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Chenguang Lou
- Biomolecular Nanoscale Engineering Center; Department of Physics, Chemistry and Pharmacy; University of Southern Denmark; Campusvej 55 5230 Odense M Denmark
| | - Niels Johan Christensen
- Biomolecular Nanoscale Engineering Center; Department of Chemistry; University of Copenhagen; Thorvaldsensvej 40 1871 Frederiksberg Denmark
| | - Manuel C. Martos-Maldonado
- Biomolecular Nanoscale Engineering Center; Department of Chemistry; University of Copenhagen; Thorvaldsensvej 40 1871 Frederiksberg Denmark
| | - Søren Roi Midtgaard
- Niels Bohr Institute; University of Copenhagen; Universitetsparken 5 2100 Copenhagen Ø Denmark
| | - Maria Ejlersen
- Biomolecular Nanoscale Engineering Center; Department of Physics, Chemistry and Pharmacy; University of Southern Denmark; Campusvej 55 5230 Odense M Denmark
| | - Peter W. Thulstrup
- Department of Chemistry; University of Copenhagen; Universitetsparken 5 2100 Copenhagen Ø Denmark
| | - Kasper K. Sørensen
- Biomolecular Nanoscale Engineering Center; Department of Chemistry; University of Copenhagen; Thorvaldsensvej 40 1871 Frederiksberg Denmark
| | - Knud J. Jensen
- Biomolecular Nanoscale Engineering Center; Department of Chemistry; University of Copenhagen; Thorvaldsensvej 40 1871 Frederiksberg Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center; Department of Physics, Chemistry and Pharmacy; University of Southern Denmark; Campusvej 55 5230 Odense M Denmark
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46
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Hvam ML, Cai Y, Dagnæs-Hansen F, Nielsen JS, Wengel J, Kjems J, Howard KA. Fatty Acid-Modified Gapmer Antisense Oligonucleotide and Serum Albumin Constructs for Pharmacokinetic Modulation. Mol Ther 2017. [PMID: 28641935 DOI: 10.1016/j.ymthe.2017.05.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Delivery technologies are required for realizing the clinical potential of molecular medicines. This work presents an alternative technology to preformulated delivery systems by harnessing the natural transport properties of serum albumin using endogenous binding of gapmer antisense oligonucleotides (ASOs)/albumin constructs. We show by an electrophoretic mobility assay that fatty acid-modified gapmer and human serum albumin (HSA) can self-assemble into constructs that offer favorable pharmacokinetics. The interaction was dependent on fatty acid type (either palmitic or myristic acid), number, and position within the gapmer ASO sequence, as well as phosphorothioate (PS) backbone modifications. Binding correlated with increased blood circulation in mice (t1/2 increased from 23 to 49 min for phosphodiester [PO] gapmer ASOs and from 28 to 66 min for PS gapmer ASOs with 2× palmitic acid modification). Furthermore, a shift toward a broader biodistribution was detected for PS compared with PO gapmer ASOs. Inclusion of 2× palmitoyl to the ASOs shifted the biodistribution to resemble that of natural albumin. This work, therefore, presents a novel strategy based on the proposed endogenous assembly of gapmer ASOs/albumin constructs for increased circulatory half-life and modulation of the biodistribution of gapmer ASOs that offers tunable pharmacokinetics based on the gapmer modification design.
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Affiliation(s)
- Michael Lykke Hvam
- The Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Yunpeng Cai
- The Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | | | - Jesper Sejrup Nielsen
- The Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Jesper Wengel
- Nucleic Acid Center, Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, 5230 Odense, Denmark
| | - Jørgen Kjems
- The Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Kenneth A Howard
- The Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark.
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47
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Hartono Y, Pabon-Martinez YV, Uyar A, Wengel J, Lundin KE, Zain R, Smith CIE, Nilsson L, Villa A. Role of Pseudoisocytidine Tautomerization in Triplex-Forming Oligonucleotides: In Silico and in Vitro Studies. ACS Omega 2017; 2:2165-2177. [PMID: 30023656 PMCID: PMC6044803 DOI: 10.1021/acsomega.7b00347] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 05/02/2017] [Indexed: 06/08/2023]
Abstract
Pseudoisocytidine (ΨC) is a synthetic cytidine analogue that can target DNA duplex to form parallel triplex at neutral pH. Pseudoisocytidine has mainly two tautomers, of which only one is favorable for triplex formation. In this study, we investigated the effect of sequence on ΨC tautomerization using λ-dynamics simulation, which takes into account transitions between states. We also performed in vitro binding experiments with sequences containing ΨC and furthermore characterized the structure of the formed triplex using molecular dynamics simulation. We found that the neighboring methylated or protonated cytidine promotes the formation of the favorable tautomer, whereas the neighboring thymine or locked nucleic acid has a poor effect, and consecutive ΨC has a negative influence. The deleterious effect of consecutive ΨC in a triplex formation was confirmed using in vitro binding experiments. Our findings contribute to improving the design of ΨC-containing triplex-forming oligonucleotides directed to target G-rich DNA sequences.
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Affiliation(s)
- Yossa
Dwi Hartono
- Department
of Biosciences and Nutrition, Karolinska
Institutet, SE-141 83 Huddinge, Sweden
- Division
of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Y. Vladimir Pabon-Martinez
- Department
of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Sweden
| | - Arzu Uyar
- Department
of Biosciences and Nutrition, Karolinska
Institutet, SE-141 83 Huddinge, Sweden
| | - Jesper Wengel
- Department
of Physics, Chemistry and Pharmacy, Nucleic Acid Center, University of Southern Denmark, 5230 Odense M, Denmark
| | - Karin E. Lundin
- Department
of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Sweden
| | - Rula Zain
- Department
of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Sweden
- Department
of Clinical Genetics, Centre for Rare Diseases, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - C. I. Edvard Smith
- Department
of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Sweden
| | - Lennart Nilsson
- Department
of Biosciences and Nutrition, Karolinska
Institutet, SE-141 83 Huddinge, Sweden
| | - Alessandra Villa
- Department
of Biosciences and Nutrition, Karolinska
Institutet, SE-141 83 Huddinge, Sweden
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48
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Kumar R, Ries A, Wengel J. Synthesis and Excellent Duplex Stability of Oligonucleotides Containing 2'-Amino-LNA Functionalized with Galactose Units. Molecules 2017; 22:molecules22050852. [PMID: 28531137 PMCID: PMC6153924 DOI: 10.3390/molecules22050852] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 05/17/2017] [Accepted: 05/17/2017] [Indexed: 02/07/2023] Open
Abstract
A convenient method for the preparation of oligonucleotides containing internally-attached galactose and triantennary galactose units has been developed based on click chemistry between 2′-N-alkyne 2′-amino-LNA nucleosides and azido-functionalized galactosyl building blocks. The synthesized oligonucleotides show excellent binding affinity and selectivity towards complementary DNA/RNA strands with an increase in the melting temperature of up to +23.5 °C for triply-modified variants.
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Affiliation(s)
- Rajesh Kumar
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
- Department of Chemistry, University of Delhi, Delhi 110007, India.
| | - Annika Ries
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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49
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Schmøkel J, Voldum A, Tsakiridou G, Kuhlmann M, Cameron J, Sørensen ES, Wengel J, Howard KA. Site-selective conjugation of an anticoagulant aptamer to recombinant albumins and maintenance of neonatal Fc receptor binding. Nanotechnology 2017; 28:204004. [PMID: 28362634 DOI: 10.1088/1361-6528/aa6a9b] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Aptamers are an attractive molecular medicine that offers high target specificity. Nucleic acid-based aptamers, however, are prone to nuclease degradation and rapid renal excretion that require blood circulatory half-life extension enabling technologies. The long circulatory half-life, predominately facilitated by engagement with the cellular recycling neonatal Fc receptor (FcRn), and ligand transport properties of albumin promote it as an attractive candidate to improve the pharmacokinetic profile of aptamers. This study investigates the effect of Cys34 site-selective covalent attachment of a factor IXa anticoagulant aptamer on aptamer functionality and human FcRn (hFcRn) engagement using recombinant human albumin (rHA) of either a wild type (WT) or an engineered human FcRn high binding variant (HB). Albumin-aptamer conjugates, connected covalently through a heterobifunctional succinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate linker, were successfully prepared and purified by high performance liquid chromatography as confirmed by gel electrophoresis band-shift analysis and matrix-assisted laser desorption/ionization time of flight. Minimal reduction (∼25%) in activity of WT-linked aptamer to that of aptamer alone was found using an anticoagulant activity assay measuring temporal levels of activated partial thrombin. Covalent albumin-aptamer conjugation, however, substantially compromized binding to hFcRn, to 10% affinity of that of non-conjugated WT, determined by biolayer interferometry. Binding could be rescued by aptamer conjugation to recombinant albumin engineered for higher FcRn affinity (HB) that exhibited an 8-fold affinity compared to WT alone. This work describes a novel albumin-based aptamer delivery system whose hFcRn binding can be increased using a HB engineered albumin.
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Affiliation(s)
- Julie Schmøkel
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
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50
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Lou C, Christensen NJ, Martos-Maldonado MC, Midtgaard SR, Ejlersen M, Thulstrup PW, Sørensen KK, Jensen KJ, Wengel J. Folding Topology of a Short Coiled-Coil Peptide Structure Templated by an Oligonucleotide Triplex. Chemistry 2017; 23:9297-9305. [PMID: 28383784 DOI: 10.1002/chem.201700971] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Indexed: 12/29/2022]
Abstract
The rational design of a well-defined protein-like tertiary structure formed by small peptide building blocks is still a formidable challenge. By using peptide-oligonucleotide conjugates (POC) as building blocks, we present the self-assembly of miniature coiled-coil α-helical peptides guided by oligonucleotide duplex and triplex formation. POC synthesis was achieved by copper-free alkyne-azide cycloaddition between three oligonucleotides and a 23-mer peptide, which by itself exhibited multiple oligomeric states in solution. The oligonucleotide domain was designed to furnish a stable parallel triplex under physiological pH, and to be capable of templating the three peptide sequences to constitute a small coiled-coil motif displaying remarkable α-helicity. The formed trimeric complex was characterized by ultraviolet thermal denaturation, gel electrophoresis, circular dichroism (CD) spectroscopy, small-angle X-ray scattering (SAXS), and molecular modeling. Stabilizing cooperativity was observed between the trimeric peptide and the oligonucleotide triplex domains, and the overall molecular size (ca. 12 nm) in solution was revealed to be independent of concentration. The topological folding of the peptide moiety differed strongly from those of the individual POC strands and the unconjugated peptide, exclusively adopting the designed triple helical structure.
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Affiliation(s)
- Chenguang Lou
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Niels Johan Christensen
- Biomolecular Nanoscale Engineering Center, Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Manuel C Martos-Maldonado
- Biomolecular Nanoscale Engineering Center, Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Søren Roi Midtgaard
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Maria Ejlersen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Peter W Thulstrup
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Kasper K Sørensen
- Biomolecular Nanoscale Engineering Center, Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Knud J Jensen
- Biomolecular Nanoscale Engineering Center, Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
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