1
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Smidt JM, Lykke L, Stidsen CE, Pristovšek N, Gothelf K. Synthesis of peptide-siRNA conjugates via internal sulfonylphosphoramidate modifications and evaluation of their in vitro activity. Nucleic Acids Res 2024; 52:49-58. [PMID: 37971296 PMCID: PMC10783514 DOI: 10.1093/nar/gkad1015] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/28/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023] Open
Abstract
Conjugates of therapeutic oligonucleotides (ONs) including peptide conjugates, provide a potential solution to the major challenge of specific tissue delivery faced by this class of drugs. Conjugations are often positioned terminal at the ONs, although internal placement of other chemical modifications are known to be of critical importance. The introduction of internal conjugation handles in chemically modified ONs require highly specialized and expensive nucleoside phosphoramidites. Here, we present a method for synthesizing a library of peptide-siRNA conjugates by conjugation at internal phosphorous positions via sulfonylphosphoramidate modifications incorporated into the sense strand. The sulfonylphosphoramidate modification offers benefits as it can be directly incorporated into chemically modified ONs by simply changing the oxidation step during synthesis, and furthermore holds the potential to create multifunctionalized therapeutic ONs. We have developed a workflow using a novel pH-controlled amine-to-amine linker that yields peptide-siRNA conjugates linked via amide bonds, and we have synthesized conjugates between GLP1 peptides and a HPRT1 siRNA as a model system. The in vitro activity of the conjugates was tested by GLP1R activity and knockdown of the HPRT1 gene. We found that conjugation near the 3'-end is more favorable than certain central internal positions and different internal conjugation strategies were compared.
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Affiliation(s)
- Jakob Melgaard Smidt
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, 8000 Aarhus, Denmark
| | - Lennart Lykke
- Research Chemistry, Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark
| | - Carsten Enggaard Stidsen
- Centre for Functional Assays and Screening, Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark
| | - Nuša Pristovšek
- Centre for Functional Assays and Screening, Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark
| | - Kurt V Gothelf
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, 8000 Aarhus, Denmark
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2
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Zhang H, Vandesompele J, Braeckmans K, De Smedt SC, Remaut K. Nucleic acid degradation as barrier to gene delivery: a guide to understand and overcome nuclease activity. Chem Soc Rev 2024; 53:317-360. [PMID: 38073448 DOI: 10.1039/d3cs00194f] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Gene therapy is on its way to revolutionize the treatment of both inherited and acquired diseases, by transferring nucleic acids to correct a disease-causing gene in the target cells of patients. In the fight against infectious diseases, mRNA-based therapeutics have proven to be a viable strategy in the recent Covid-19 pandemic. Although a growing number of gene therapies have been approved, the success rate is limited when compared to the large number of preclinical and clinical trials that have been/are being performed. In this review, we highlight some of the hurdles which gene therapies encounter after administration into the human body, with a focus on nucleic acid degradation by nucleases that are extremely abundant in mammalian organs, biological fluids as well as in subcellular compartments. We overview the available strategies to reduce the biodegradation of gene therapeutics after administration, including chemical modifications of the nucleic acids, encapsulation into vectors and co-administration with nuclease inhibitors and discuss which strategies are applied for clinically approved nucleic acid therapeutics. In the final part, we discuss the currently available methods and techniques to qualify and quantify the integrity of nucleic acids, with their own strengths and limitations.
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Affiliation(s)
- Heyang Zhang
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Kevin Braeckmans
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Stefaan C De Smedt
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Katrien Remaut
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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3
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2'-N-Alkylaminocarbonyl-2'-amino-LNA: Synthesis, duplex stability, nuclease resistance, and in vitro anti-microRNA activity. Bioorg Med Chem 2023; 78:117148. [PMID: 36580743 DOI: 10.1016/j.bmc.2022.117148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 12/25/2022]
Abstract
2'-Amino-LNA has the potential to acquire various functions through chemical modification at the 2'-nitrogen atom. This study focused on 2'-N-alkylaminocarbonyl 2'-amino-LNA, which is a derivative of 2'-amino-LNA. We evaluated its practical usefulness as a chemical modification of anti-miRNA oligonucleotide. The synthesis of phosphoramidites of 2'-N-alkylaminocarbonyl substituted 2'-amino-LNA bearing thymine and 5-methylcytosine proceeded in good yields. Incorporating the 2'-N-alkylaminocarbonyl-2'-amino-LNA monomers into oligonucleotides improved the duplex stability for complementary RNA strands and robust nuclease resistance. Moreover, 2'-N-alkylaminocarbonyl-2'-amino-LNA is a promising scaffold that significantly increases the potency of anti-miRNA oligonucleotides.
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4
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Kupihár Z, Ferenc G, Petrovicz VL, Fáy VR, Kovács L, Martinek TA, Hegedüs Z. Improved Metal-Free Approach for the Synthesis of Protected Thiol Containing Thymidine Nucleoside Phosphoramidite and Its Application for the Synthesis of Ligatable Oligonucleotide Conjugates. Pharmaceutics 2023; 15:pharmaceutics15010248. [PMID: 36678876 PMCID: PMC9865093 DOI: 10.3390/pharmaceutics15010248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/04/2023] [Accepted: 01/07/2023] [Indexed: 01/13/2023] Open
Abstract
Oligonucleotide conjugates are versatile scaffolds that can be applied in DNA-based screening platforms and ligand display or as therapeutics. Several different chemical approaches are available for functionalizing oligonucleotides, which are often carried out on the 5' or 3' end. Modifying oligonucleotides in the middle of the sequence opens the possibility to ligate the conjugates and create DNA strands bearing multiple different ligands. Our goal was to establish a complete workflow that can be applied for such purposes from monomer synthesis to templated ligation. To achieve this, a monomer is required with an orthogonal functional group that can be incorporated internally into the oligonucleotide sequence. This is followed by conjugation with different molecules and ligation with the help of a complementary template. Here, we show the synthesis and the application of a thiol-modified thymidine nucleoside phosphoramidite to prepare ligatable oligonucleotide conjugates. The conjugations were performed both in solution and on solid phase, resulting in conjugates that can be assembled into multivalent oligonucleotides decorated with tissue-targeting peptides using templated ligation.
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Affiliation(s)
- Zoltán Kupihár
- Department of Medical Chemistry, University of Szeged, Dom ter 8., H-6720 Szeged, Hungary
| | - Györgyi Ferenc
- Institute of Plant Biology, Biological Research Centre, Eötvös Lóránd Research Network, H-6726 Szeged, Hungary
| | - Vencel L. Petrovicz
- Department of Medical Chemistry, University of Szeged, Dom ter 8., H-6720 Szeged, Hungary
| | - Viktória R. Fáy
- Department of Medical Chemistry, University of Szeged, Dom ter 8., H-6720 Szeged, Hungary
| | - Lajos Kovács
- Department of Medical Chemistry, University of Szeged, Dom ter 8., H-6720 Szeged, Hungary
| | - Tamás A. Martinek
- Department of Medical Chemistry, University of Szeged, Dom ter 8., H-6720 Szeged, Hungary
- ELKH-SZTE Biomimetic Systems Research Group, Eötvös Loránd Research Network, H-6720 Szeged, Hungary
- Correspondence: (T.A.M.); (Z.H.)
| | - Zsófia Hegedüs
- Department of Medical Chemistry, University of Szeged, Dom ter 8., H-6720 Szeged, Hungary
- Correspondence: (T.A.M.); (Z.H.)
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5
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Takegawa-Araki T, Yasukawa K, Iwazaki N, Maruyama H, Furukawa H, Sawamoto H, Obika S. Parallel synthesis of oligonucleotides containing N-acyl amino-LNA and their therapeutic effects as anti-microRNAs. Org Biomol Chem 2022; 20:9351-9361. [PMID: 36383101 DOI: 10.1039/d2ob01809h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
2'-Amino-locked nucleic acid (ALNA), maintains excellent duplex stability, and the nitrogen at the 2'-position is an attractive scaffold for functionalization. Herein, a facile and efficient method for the synthesis of various 2'-N-acyl amino-LNA derivatives by direct acylation of the 2'-amino moiety contained in the synthesized oligonucleotides and its fundamental properties are described. The introduction of the acylated amino-LNA enhances the potency of the molecules as therapeutic anti-microRNA oligonucleotides.
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Affiliation(s)
- Tomo Takegawa-Araki
- Soyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Kai Yasukawa
- Soyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Norihiko Iwazaki
- Soyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Hideto Maruyama
- Soyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Hiroyuki Furukawa
- Soyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Hiroaki Sawamoto
- Soyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 2-26-1, Muraoka-Higashi, Fujisawa, Kanagawa, 251-8555, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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6
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Müggenburg F, Müller S. Azide-modified Nucleosides as Versatile Tools for Bioorthogonal Labeling and Functionalization. CHEM REC 2022; 22:e202100322. [PMID: 35189013 DOI: 10.1002/tcr.202100322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 02/06/2023]
Abstract
Azide-modified nucleosides are important building blocks for RNA and DNA functionalization by click chemistry based on azide-alkyne cycloaddition. This has put demand on synthetic chemistry to develop approaches for the preparation of azide-modified nucleoside derivatives. We review here the available methods for the synthesis of various nucleosides decorated with azido groups at the sugar residue or nucleobase, their incorporation into oligonucleotides and cellular RNAs, and their application in azide-alkyne cycloadditions for labelling and functionalization.
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Affiliation(s)
- Frederik Müggenburg
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Straße 4, 17487, Greifswald, Germany
| | - Sabine Müller
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Straße 4, 17487, Greifswald, Germany
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7
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Klabenkova K, Fokina A, Stetsenko D. Chemistry of Peptide-Oligonucleotide Conjugates: A Review. Molecules 2021; 26:5420. [PMID: 34500849 PMCID: PMC8434111 DOI: 10.3390/molecules26175420] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 12/25/2022] Open
Abstract
Peptide-oligonucleotide conjugates (POCs) represent one of the increasingly successful albeit costly approaches to increasing the cellular uptake, tissue delivery, bioavailability, and, thus, overall efficiency of therapeutic nucleic acids, such as, antisense oligonucleotides and small interfering RNAs. This review puts the subject of chemical synthesis of POCs into the wider context of therapeutic oligonucleotides and the problem of nucleic acid drug delivery, cell-penetrating peptide structural types, the mechanisms of their intracellular transport, and the ways of application, which include the formation of non-covalent complexes with oligonucleotides (peptide additives) or covalent conjugation. The main strategies for the synthesis of POCs are viewed in detail, which are conceptually divided into (a) the stepwise solid-phase synthesis approach and (b) post-synthetic conjugation either in solution or on the solid phase, especially by means of various click chemistries. The relative advantages and disadvantages of both strategies are discussed and compared.
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Affiliation(s)
- Kristina Klabenkova
- Faculty of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia; (K.K.); (D.S.)
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
| | - Alesya Fokina
- Faculty of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia; (K.K.); (D.S.)
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
| | - Dmitry Stetsenko
- Faculty of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia; (K.K.); (D.S.)
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
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8
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Tan DJY, Cheong VV, Lim KW, Phan AT. A modular approach to enzymatic ligation of peptides and proteins with oligonucleotides. Chem Commun (Camb) 2021; 57:5507-5510. [PMID: 34036975 DOI: 10.1039/d1cc01348c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Joining peptides and oligonucleotides offers potential benefits, but current methods remain laborious. Here we present a novel approach towards enzymatic ligation of the two modalities through the development of tag phosphoramidites as adaptors that can be readily incorporated onto oligonucleotides. This simple and highly efficient approach paves the way towards streamlined development and production of peptide/protein-oligonucleotide conjugates.
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Affiliation(s)
- Derrick Jing Yang Tan
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore.
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9
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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] [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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10
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Khatri S, Hansen J, Astakhova K. Antibodies to synthetic citrullinated peptide epitope correlate with disease activity and flares in rheumatoid arthritis. PLoS One 2020; 15:e0232010. [PMID: 32324839 PMCID: PMC7179858 DOI: 10.1371/journal.pone.0232010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 04/05/2020] [Indexed: 01/13/2023] Open
Abstract
Rheumatoid arthritis (RA), caused by the abnormal recognition of human joint cells by autoimmune antibodies, remains the world’s most prevalent autoimmune disease, with over five million people affected and as much as 4% of the population at risk of RA. To prevent rapid disease development, hormonal and anti-inflammatory therapies require fast and reliable RA diagnosis. However, difficulty in detecting early specific biomarkers for RA means that it is unclear when treatment needs to begin. Here, we combined synthesis of citrullinated peptide epitopes with molecular diagnostics to verify a new specific biomarker for early RA diagnosis and flare prediction. A fibrinogen-derived 21-amino-acid-long citrullinated peptide showed high reactivity toward autoantibodies in RA samples. Additionally, the level of antibodies to this epitope was elevated prior to flares. In contrast, other citrullinated protein variants had lower reactivity and poorer sensitivity to disease activity. In conclusion, fibrinogen-derived epitope E2 subjected to citrullination facilitated a reliable RA diagnosis with a strong correlation to disease activity. This is of a high value for the diagnosis and management of RA patients who respond poorly to treatment.
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Affiliation(s)
- Sangita Khatri
- Department of Chemistry, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Jonas Hansen
- Department of Chemistry, Technical University of Denmark, Kgs Lyngby, Denmark
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Kira Astakhova
- Department of Chemistry, Technical University of Denmark, Kgs Lyngby, Denmark
- * E-mail:
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11
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Jandl B, Sedghiniya S, Carstens A, Astakhova K. Peptide-Fluorophore Hydrogel as a Signal Boosting Approach in Rapid Detection of Cancer DNA. ACS OMEGA 2019; 4:13889-13895. [PMID: 31497706 PMCID: PMC6714519 DOI: 10.1021/acsomega.9b01586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/02/2019] [Indexed: 05/30/2023]
Abstract
Cancer is a major health risk in the modern society that requires rapid, reliable, and inexpensive diagnostics. Because of the low abundance of cancer DNA in biofluids, current detection methods require DNA amplification. The amplification can be challenging; it provides only relative quantification and extends time and cost of an assay. Herein, we report a new oligonucleotide hybridization platform for amplification-free detection of human cancer DNA. Using a large PEG-capture probe allows rapid separation of the bound (mutant) versus unbound (wild type) DNA. Next, a supramolecular hydrogel forming peptide attached to a detection oligonucleotide probe serves as a signal amplification tool. Having screened multiple short peptides and fluorophores, we identified the system P1 + cyanine 3.5 that allows for sensitive quantitative detection of mutation L858R in EGFR oncogene. The peptide-fluorophore-based assay provides absolute target DNA quantification at the detection limit of 20 ng cancer DNA versus >500 ng for Cy3.5-labeled oligonucleotide in only 1 hour.
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Affiliation(s)
- Bernhard Jandl
- Department
of Chemistry, Technical University of Denmark, 206-207 Kemitorvet, 2800 Kgs Lyngby, Denmark
- Institute
of Applied Synthetic Chemistry, TU Wien
(Vienna University of Technology), Getreidemarkt 9, 1060 Wien, Austria
| | - Sima Sedghiniya
- Department
of Chemistry, Technical University of Denmark, 206-207 Kemitorvet, 2800 Kgs Lyngby, Denmark
- School
of Chemistry, College of Science, University
of Tehran, Tehran 14155-6455, Iran
| | - Annika Carstens
- Department
of Chemistry, Technical University of Denmark, 206-207 Kemitorvet, 2800 Kgs Lyngby, Denmark
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Kira Astakhova
- Department
of Chemistry, Technical University of Denmark, 206-207 Kemitorvet, 2800 Kgs Lyngby, Denmark
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12
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Gandioso A, Massaguer A, Villegas N, Salvans C, Sánchez D, Brun-Heath I, Marchán V, Orozco M, Terrazas M. Efficient siRNA-peptide conjugation for specific targeted delivery into tumor cells. Chem Commun (Camb) 2018; 53:2870-2873. [PMID: 28218319 DOI: 10.1039/c6cc10287e] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Despite the broad applicability of the Huisgen cycloaddition reaction, the click functionalization of RNAs with peptides still remains a challenge. Here we describe a straightforward method for the click functionalization of siRNAs with peptides of different sizes and complexities. Among them, a promising peptide carrier for the selective siRNA delivery into HER2+ breast cancer cell lines has been reported.
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Affiliation(s)
- Albert Gandioso
- Department of Inorganic and Organic Chemistry, Section of Organic Chemistry, IBUB, University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Anna Massaguer
- Department of Biology, University of Girona, Campus Montilivi, 17071 Girona, Spain
| | - Núria Villegas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Joint IRB-BSC Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain. and The Join IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Spain
| | - Cándida Salvans
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Joint IRB-BSC Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain.
| | - Dani Sánchez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Joint IRB-BSC Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain.
| | - Isabelle Brun-Heath
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Joint IRB-BSC Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain.
| | - Vicente Marchán
- Department of Inorganic and Organic Chemistry, Section of Organic Chemistry, IBUB, University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Joint IRB-BSC Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain. and The Join IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Spain and Department of Biochemistry and Biomedicine, University of Barcelona, 08028 Barcelona, Spain
| | - Montserrat Terrazas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Joint IRB-BSC Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain.
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13
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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] [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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14
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Meghani NM, Amin HH, Lee BJ. Mechanistic applications of click chemistry for pharmaceutical drug discovery and drug delivery. Drug Discov Today 2017; 22:1604-1619. [PMID: 28754291 DOI: 10.1016/j.drudis.2017.07.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 06/18/2017] [Accepted: 07/17/2017] [Indexed: 01/30/2023]
Abstract
The concept of click chemistry (CC), first introduced by K.B. Sharpless, has been widely adopted for use in drug discovery, novel drug delivery systems (DDS), polymer chemistry, and material sciences. In this review, we outline novel aspects of CC related to drug discovery and drug delivery, with a brief overview of molecular mechanisms underlying each click reaction commonly used by researchers, and the main patents that paved the way for further diverse medicinal applications. We also describe recent progress in drug discovery and polymeric and carbon material-based drug delivery for potential pharmaceutical applications and advancements based on the CC approach, and discuss some intrinsic limitations of this popular conjugation reaction. The use of CC is likely to significantly advance drug discovery and bioconjugation development.
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Affiliation(s)
- Nilesh M Meghani
- College of Pharmacy, Ajou University, Suwon 16499, Republic of Korea
| | - Hardik H Amin
- College of Pharmacy, Ajou University, Suwon 16499, Republic of Korea
| | - Beom-Jin Lee
- College of Pharmacy, Ajou University, Suwon 16499, Republic of Korea; Institute of Pharmaceutical Science and Technology, Ajou University, Suwon 16499, Republic of Korea.
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15
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Taskova M, Mantsiou A, Astakhova K. Synthetic Nucleic Acid Analogues in Gene Therapy: An Update for Peptide-Oligonucleotide Conjugates. Chembiochem 2017; 18:1671-1682. [PMID: 28614621 DOI: 10.1002/cbic.201700229] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Indexed: 12/29/2022]
Abstract
The main objective of this work is to provide an update on synthetic nucleic acid analogues and nanoassemblies as tools in gene therapy. In particular, the synthesis and properties of peptide-oligonucleotide conjugates (POCs), which have high potential in research and as therapeutics, are described in detail. The exploration of POCs has already led to fruitful results in the treatment of neurological diseases, lung disorders, cancer, leukemia, viral, and bacterial infections. However, delivery and in vivo stability are the major barriers to the clinical application of POCs and other analogues that still have to be overcome. This review summarizes recent achievements in the delivery and in vivo administration of synthetic nucleic acid analogues, focusing on POCs, and compares their efficiency.
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Affiliation(s)
- Maria Taskova
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Anna Mantsiou
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Kira Astakhova
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.,Technical University of Denmark, Department of Chemistry, Kemitorvet, 2800, Kongens Lyngby, Denmark
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16
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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] [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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17
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Lou C, Samuelsen SV, Christensen NJ, Vester B, Wengel J. Oligonucleotides Containing Aminated 2'-Amino-LNA Nucleotides: Synthesis and Strong Binding to Complementary DNA and RNA. Bioconjug Chem 2017; 28:1214-1220. [PMID: 28332825 DOI: 10.1021/acs.bioconjchem.7b00061] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mono- and diaminated 2'-amino-LNA monomers were synthesized and introduced into oligonucleotides. Each modification imparts significant stabilization of nucleic acid duplexes and triplexes, excellent sequence selectivity, and significant nuclease resistance. Molecular modeling suggested that structural stabilization occurs via intrastrand electrostatic attraction between the protonated amino groups of the aminated 2'-amino-LNA monomers and the host oligonucleotide backbone.
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Affiliation(s)
| | | | - Niels Johan Christensen
- Department of Chemistry, Biomolecular Nanoscale Engineering Center, University of Copenhagen , Thorvaldsensvej 40, Frederiksberg 1871, Denmark
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18
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Taskova M, Madsen CS, Jensen KJ, Hansen LH, Vester B, Astakhova K. Antisense Oligonucleotides Internally Labeled with Peptides Show Improved Target Recognition and Stability to Enzymatic Degradation. Bioconjug Chem 2016; 28:768-774. [PMID: 28292178 DOI: 10.1021/acs.bioconjchem.6b00567] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Specific target binding and stability in diverse biological media is of crucial importance for applications of synthetic oligonucleotides as diagnostic and therapeutic tools. So far, these issues have been addressed by chemical modification of oligonucleotides and by conjugation with a peptide, most often at the terminal position of the oligonucleotide. Herein, we for the first time systematically investigate the influence of internally attached short peptides on the properties of antisense oligonucleotides. We report the synthesis and internal double labeling of 21-mer oligonucleotides that target the BRAF V600E oncogene, with a library of rationally designed peptides employing CuAAC "click" chemistry. The peptide sequence has an influence on the specificity and affinity of target DNA/RNA binding. We also investigated the impact of locked nucleic acids (LNAs) on the latter. Lysine residues improve binding of POCs to target DNA and RNA, whereas the distance to lysine correlates exclusively with a decrease in binding of mismatched RNA targets. Glycine and tyrosine residues affect target binding as well. Importantly, the resistance of POCs to enzymatic degradation is dramatically improved by the internal attachment of peptides but not by LNA alone. Independently of the peptide sequence, the conjugates are stable for up to 24 h in 90% human serum and duplexes of POCs with complementary DNA for up to 160 h in 90% human serum. Such excellent stability has not been previously reported for DNA and makes internally labeled POCs an exciting object of study, i.e., showing high target specificity and simultaneous stability in biological media.
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Affiliation(s)
| | - Charlotte S Madsen
- Department of Chemistry, University of Copenhagen , Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Knud J Jensen
- Department of Chemistry, University of Copenhagen , Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
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19
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Peptide-substituted oligonucleotide synthesis and non-toxic, passive cell delivery. Signal Transduct Target Ther 2016; 1:16019. [PMID: 29263901 PMCID: PMC5661639 DOI: 10.1038/sigtrans.2016.19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 09/01/2016] [Accepted: 09/04/2016] [Indexed: 12/18/2022] Open
Abstract
Chemically modified oligodeoxynucleotides (ODNs) are known to modulate gene expression by interacting with RNA. An efficient approach for synthesizing amino acid- or peptide-substituted triazolylphosphonate analogs (TP ODNs) has been developed to provide improved stability and cell uptake. The chemistry is quite general, as peptides can be introduced throughout the TP ODN at any preselected internucleotide linkage. These synthetic TP ODNs enter cells through endocytosis in the absence of transfection reagents and localize into perinuclear organelles. The entrapped ODNs are released into the cytoplasm by treatment with endosomal-releasing agents and several are then active as microRNA inhibitors.
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20
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Flett FJ, Walton JGA, Mackay CL, Interthal H. Click chemistry generated model DNA-peptide heteroconjugates as tools for mass spectrometry. Anal Chem 2016; 87:9595-9. [PMID: 26335278 DOI: 10.1021/acs.analchem.5b02047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
UV cross-linking of nucleic acids to proteins in combination with mass spectrometry is a powerful technique to identify proteins, peptides, and the amino acids involved in intermolecular interactions within nucleic acid-protein complexes. However, the mass spectrometric identification of cross-linked nucleic acid-protein heteroconjugates in complex mixtures and MS/MS characterization of the specific sites of cross-linking is extremely challenging. As a tool for the optimization of sample preparation, ionization, fragmentation, and detection by mass spectrometry, novel synthetic DNA-peptide heteroconjugates were generated to act as mimics of UV cross-linked heteroconjugates. Click chemistry was employed to cross-link peptides to DNA oligonucleotides. These heteroconjugates were fully characterized by high resolution FTICR mass spectrometry and by collision-induced dissociation (CID) following nuclease P1 digestion of the DNA moiety to a single nucleotide monophosphate. This allowed the exact site of the cross-linking within the peptide to be unambiguously assigned. These synthetic DNA-peptide heteroconjugates have the potential to be of use for a variety of applications that involve DNA-peptide heteroconjugates.
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Affiliation(s)
- Fiona J Flett
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh , Edinburgh EH9 3FF, Scotland, United Kingdom
| | - Jeffrey G A Walton
- School of Chemistry, University of Edinburgh , Edinburgh EH9 3FJ, Scotland, United Kingdom
| | - C Logan Mackay
- School of Chemistry, University of Edinburgh , Edinburgh EH9 3FJ, Scotland, United Kingdom
| | - Heidrun Interthal
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh , Edinburgh EH9 3FF, Scotland, United Kingdom
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21
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Zacco E, Anish C, Martin CE, v. Berlepsch H, Brandenburg E, Seeberger PH, Koksch B. A Self-Assembling Peptide Scaffold for the Multivalent Presentation of Antigens. Biomacromolecules 2015; 16:2188-97. [DOI: 10.1021/acs.biomac.5b00572] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Elsa Zacco
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Chakkumkal Anish
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
- Department
of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany
- Bacterial Vaccines Discovery and Early Development, Janssen Pharmaceuticals (Johnson & Johnson), Leiden, The Netherlands
| | - Christopher E. Martin
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
- Department
of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany
| | - Hans v. Berlepsch
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
- Research
Center of Electron Microscopy and Core Facility BioSupraMol, Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Fabeckstraße
36a, 14195 Berlin, Germany
| | - Enrico Brandenburg
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Peter H. Seeberger
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
- Department
of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany
| | - Beate Koksch
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
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22
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Nåbo LJ, Madsen CS, Jensen KJ, Kongsted J, Astakhova K. Ultramild protein-mediated click chemistry creates efficient oligonucleotide probes for targeting and detecting nucleic acids. Chembiochem 2015; 16:1163-7. [PMID: 25940911 DOI: 10.1002/cbic.201500145] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Indexed: 12/16/2022]
Abstract
Functionalized synthetic oligonucleotides are finding growing applications in research, clinical studies, and therapy. However, it is not easy to prepare them in a biocompatible and highly efficient manner. We report a new strategy to synthesize oligonucleotides with promising nucleic acid targeting and detection properties. We focus in particular on the pH sensitivity of these new probes and their high target specificity. For the first time, human copper(I)-binding chaperon Cox17 was applied to effectively catalyze click labeling of oligonucleotides. This was performed under ultramild conditions with fluorophore, peptide, and carbohydrate azide derivatives. In thermal denaturation studies, the modified probes showed specific binding to complementary DNA and RNA targets. Finally, we demonstrated the pH sensitivity of the new rhodamine-based fluorescent probes in vitro and rationalize our results by electronic structure calculations.
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Affiliation(s)
- Lina J Nåbo
- Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, 5230 Odense M (Denmark)
| | - Charlotte S Madsen
- Department of Chemistry, University of Copenhagen (Denmark), Thorvaldsensvej 40, 1871 Copenhagen (Denmark)
| | - Knud J Jensen
- Department of Chemistry, University of Copenhagen (Denmark), Thorvaldsensvej 40, 1871 Copenhagen (Denmark)
| | - Jacob Kongsted
- Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, 5230 Odense M (Denmark)
| | - Kira Astakhova
- Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, 5230 Odense M (Denmark).
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23
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Astakhova IK, Wengel J. Scaffolding along nucleic acid duplexes using 2'-amino-locked nucleic acids. Acc Chem Res 2014; 47:1768-77. [PMID: 24749544 DOI: 10.1021/ar500014g] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
CONSPECTUS: Incorporation of chemically modified nucleotide scaffolds into nucleic acids to form assemblies rich in function is an innovative area with great promise for nanotechnology and biomedical and material science applications. The intrinsic biorecognition potential of nucleic acids combined with advanced properties of the locked nucleic acids (LNAs) provide opportunities to develop new nanomaterials and devices like sensors, aptamers, and machines. In this Account, we describe recent research on preparation and investigation of the properties of LNA/DNA hybrids containing functionalized 2'-amino-LNA nucleotides. By application of different chemical reactions, modification of 2'-amino-LNA scaffolds can be efficiently performed in high yields and with various tags, postsynthetically or during the automated oligonucleotide synthesis. The choice of a synthetic method for scaffolding along 2'-amino-LNA mainly depends on the chemical nature of the modification, its price, its availability, and applications of the product. One of the most useful applications of the product LNA/DNA scaffolds containing 2'-amino-LNA is to detect complementary DNA and RNA targets. Examples of these applications include sensing of clinically important single-nucleotide polymorphisms (SNPs) and imaging of nucleic acids in vitro, in cell culture, and in vivo. According to our studies, 2'-amino-LNA scaffolds are efficient within diagnostic probes for DNA and RNA targets and as therapeutics, whereas both 2'-amino- and isomeric 2'-α-l-amino-LNA scaffolds have promising properties for stabilization and detection of DNA nanostructures. Attachment of fluorescent groups to the 2'-amino group results in very high fluorescent quantum yields of the duplexes and remarkable sensitivity of the fluorescence signal to target binding. Notably, fluorescent LNA/DNA probes bind nucleic acid targets with advantages of high affinity and specificity. Thus, molecular motion of nanodevices and programmable self-assembly of chemically modified LNA/DNA nanomaterials can be followed by bright fluorescence signaling from the functionalized LNA units. Another appealing aspect of the amino-LNA scaffolds is specific targeting of nucleic acids and proteins for therapeutic applications. 2'-Amino-LNA/DNA conjugates containing peptide and polyaromatic hydrocarbon (PAH) groups are promising in this context as well as for advanced imaging and diagnostic purposes in vivo. For imaging applications, photostability of fluorescence dyes is of crucial importance. Chemically stable and photostable fluorescent PAH molecules attached to 2'-amino functionality of the 2'-amino-LNA are potent for in vitro and in vivo imaging of DNA and RNA targets. We believe that rational evolution of the biopolymers of Nature may solve the major challenges of the future material science and biomedicine. However, this requires strong scientific progress and efficient interdisciplinary research. Examples of this Account demonstrate that among other synthetic biopolymers, synthetic nucleic acids containing functionalized 2'-amino-LNA scaffolds offer great opportunities for material science, diagnostics, and medicine of the future.
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Affiliation(s)
- I. Kira Astakhova
- Nucleic Acid Center,
Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Jesper Wengel
- Nucleic Acid Center,
Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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24
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Lee MK, Lim YB. Facile synthesis, optical and conformational characteristics, and efficient intracellular delivery of a peptide-DNA conjugate. Bioorg Med Chem 2014; 22:4204-9. [PMID: 24924424 DOI: 10.1016/j.bmc.2014.05.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 05/17/2014] [Accepted: 05/19/2014] [Indexed: 12/01/2022]
Abstract
Covalent conjugation of disparate peptide and oligonucleotide biomacromolecular species produces peptide-oligonucleotide conjugates (POCs), which are interesting molecules with great potential for use in diverse bioapplications. However, peptide-oligonucleotide conjugation methods are not well established, and the intracellular delivery efficacy of POCs is debatable. Here, we describe a simple method for the synthesis and purification of POCs. When peptides are carefully designed to have a near-neutral charge state, a relatively hydrophobic polarity, and receptor-targeting ligands, synthesis and purification become highly efficient and straightforward. UV-vis, fluorescence, and circular dichroism studies show that both types of molecules mutually influence each other, changing their optical and conformational characteristics in the context of POCs. The combined effect of peptide design strategy, targeting ligands, and relatively hydrophobic property, enables the efficient cellular delivery of POCs.
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Affiliation(s)
- Mun-kyung Lee
- Translational Research Center for Protein Function Control and Department of Materials Science & Engineering, Yonsei University, Seoul 120-749, Republic of Korea
| | - Yong-beom Lim
- Translational Research Center for Protein Function Control and Department of Materials Science & Engineering, Yonsei University, Seoul 120-749, Republic of Korea.
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25
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Peptide conjugation via CuAAC 'click' chemistry. Molecules 2013; 18:13148-74. [PMID: 24284482 PMCID: PMC6270195 DOI: 10.3390/molecules181113148] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 10/09/2013] [Accepted: 10/10/2013] [Indexed: 01/14/2023] Open
Abstract
The copper (I)-catalyzed alkyne azide 1,3-dipolar cycloaddition (CuAAC) or ‘click’ reaction, is a highly versatile reaction that can be performed under a variety of reaction conditions including various solvents, a wide pH and temperature range, and using different copper sources, with or without additional ligands or reducing agents. This reaction is highly selective and can be performed in the presence of other functional moieties. The flexibility and selectivity has resulted in growing interest in the application of CuAAC in various fields. In this review, we briefly describe the importance of the structural folding of peptides and proteins and how the 1,4-disubstituted triazole product of the CuAAC reaction is a suitable isoster for an amide bond. However the major focus of the review is the application of this reaction to produce peptide conjugates for tagging and targeting purpose, linkers for multifunctional biomacromolecules, and reporter ions for peptide and protein analysis.
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