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Österlund T, Aho A, Äärelä A, Tähtinen V, Korhonen H, Virta P. Immobilized Carbohydrates for Preparation of 3'-Glycoconjugated Oligonucleotides. ACTA ACUST UNITED AC 2021; 83:e122. [PMID: 33290641 DOI: 10.1002/cpnc.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A detailed protocol for preparation 3'-glycoconjugated oligonucleotides is described based on one-pot immobilization of 4,4'-dimethoxytrityl-protected carbohydrates to a solid support followed by on-support peracetylation and automated oligonucleotide assembly. Compared to an appropriate building block approach and post-synthetic manipulation of oligonucleotides, this protocol may simplify the synthesis scheme and increase overall yield of the conjugates. Furthermore, the immobilization to a solid support typically increases the stability of reactants, enabling prolonged storage, and makes subsequent processing convenient. Automated assembly on these carbohydrate-modified supports using conventional phosphoramidite chemistry produces 3'-glycoconjugated oligonucleotides in relatively high yield and purity. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of 1-O-tert-butyldimethylsilyl-6-O-(4,4'-dimethoxytrityl)-β-D-glucose Basic Protocol 2: Synthesis of 6-O-dimethoxytrityl-2,3,1',3',4',6'-hexa-O-benzoylsucrose Basic Protocol 3: Synthesis of 6″-O-dimethoxytrityl-N-trifluoroacetyl-protected aminoglycosides Basic Protocol 4: Synthesis of 3-O-dimethoxytrityl-propyl β-D-galactopyranoside Basic Protocol 5: Synthesis of trivalent N-acetyl galactosamine cluster Basic Protocol 6: Synthesis of carbohydrate monosuccinates and their immobilization to a solid support Basic Protocol 7: Oligonucleotide synthesis using immobilized carbohydrates.
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Affiliation(s)
- Tommi Österlund
- Department of Chemistry, University of Turku, Turku, Finland
| | - Aapo Aho
- Department of Chemistry, University of Turku, Turku, Finland
| | - Antti Äärelä
- Department of Chemistry, University of Turku, Turku, Finland
| | - Ville Tähtinen
- Department of Chemistry, University of Turku, Turku, Finland
| | - Heidi Korhonen
- Department of Chemistry, University of Turku, Turku, Finland
| | - Pasi Virta
- Department of Chemistry, University of Turku, Turku, Finland
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Aradi K, Di Giorgio A, Duca M. Aminoglycoside Conjugation for RNA Targeting: Antimicrobials and Beyond. Chemistry 2020; 26:12273-12309. [PMID: 32539167 DOI: 10.1002/chem.202002258] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/11/2020] [Indexed: 01/04/2023]
Abstract
Natural aminoglycosides are therapeutically useful antibiotics and very efficient RNA ligands. They are oligosaccharides that contain several ammonium groups able to interfere with the translation process in prokaryotes upon binding to bacterial ribosomal RNA (rRNA), and thus, impairing protein synthesis. Even if aminoglycosides are commonly used in therapy, these RNA binders lack selectivity and are able to bind to a wide number of RNA sequences/structures. This is one of the reasons for their toxicity and limited applications in therapy. At the same time, the ability of aminoglycosides to bind to various RNAs renders them a great source of inspiration for the synthesis of new binders with improved affinity and specificity toward several therapeutically relevant RNA targets. Thus, a number of studies have been performed on these complex and highly functionalized compounds, leading to the development of various synthetic methodologies toward the synthesis of conjugated aminoglycosides. The aim of this review is to highlight recent progress in the field of aminoglycoside conjugation, paying particular attention to modifications performed toward the improvement of affinity and especially to the selectivity of the resulting compounds. This will help readers to understand how to introduce a desired chemical modification for future developments of RNA ligands as antibiotics, antiviral, and anticancer compounds.
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Affiliation(s)
- Klara Aradi
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice (ICN), 06100, Nice, France
| | - Audrey Di Giorgio
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice (ICN), 06100, Nice, France
| | - Maria Duca
- Université Côte d'Azur, CNRS, Institute of Chemistry of Nice (ICN), 06100, Nice, France
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Granqvist L, Tähtinen V, Virta P. Synthesis of Glycosidic (β-1''→6, 3' and 4') Site Isomers of Neomycin B and their Effect on RNA and DNA Triplex Stability. Molecules 2019; 24:molecules24030580. [PMID: 30736311 PMCID: PMC6385478 DOI: 10.3390/molecules24030580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 02/03/2019] [Accepted: 02/04/2019] [Indexed: 01/02/2023] Open
Abstract
Glycosidic (β-1''→6, 3' and 4') site isomers of neomycin B (i.e., neobiosamine (β-1''→6, 3' and 4') neamines) have been synthesized in a straightforward manner. Peracetylated neomycin azide was used as a common starting material to obtain neobiosamine glycosyl donor and 6, 3',4'-tri-O-acetyl neamine azide that after simple protecting group manipulation was converted to three different glycosyl acceptors (i.e., 5,6,4'-, 5,3',4'- and 5,6,3'-tri-O-acetyl neamine azide). Glycosylation between the neobiosamine glycosyl donor and the neamine-derived acceptors gave the protected pseudo-tetrasaccharides, which were converted, via global deprotection (deacetylation and reduction of the azide groups), to the desired site isomers of neomycin. The effect of these aminoglycosides on the RNA and DNA triplex stability was studied by UV-melting profile analysis.
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Affiliation(s)
- Lotta Granqvist
- Department of Chemistry, University of Turku, 20014 Turku, Finland.
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Ukale DU, Lönnberg T. Triplex Formation by Oligonucleotides Containing Organomercurated Base Moieties. Chembiochem 2018; 19:1096-1101. [PMID: 29575511 DOI: 10.1002/cbic.201800112] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Indexed: 12/26/2022]
Abstract
Homothymine oligonucleotides with a single 5-mercuricytosine or 5-mercuriuracil residue at their termini have been synthesized and their capacity to form triplexes has been examined with an extensive array of double-helical targets. UV and circular dichroism (CD) melting experiments revealed the formation and thermal denaturation of pyrimidine⋅purine*pyrimidine-type triple helices with all oligonucleotide combinations studied. Nearly all triplexes were destabilized upon mercuration of the 3'-terminal residue of the triplex-forming oligonucleotide, in all likelihood due to competing intramolecular HgII -mediated base pairing. Two exceptions from this general pattern were, however, observed: 5-mercuricytosine was stabilizing when placed opposite to a T⋅A or A⋅T base pair. The stabilization was further amplified in the presence of 2-mercaptoethanol (but not hexanethiol, thiophenol or cysteine), suggesting a stabilizing interaction other than HgII -mediated base pairing.
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Affiliation(s)
| | - Tuomas Lönnberg
- University of Turku, Department of Chemistry, Vatselankatu 2, 20014, Turku, Finland
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Thamban Chandrika N, Garneau-Tsodikova S. Comprehensive review of chemical strategies for the preparation of new aminoglycosides and their biological activities. Chem Soc Rev 2018; 47:1189-1249. [PMID: 29296992 PMCID: PMC5818290 DOI: 10.1039/c7cs00407a] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A systematic analysis of all synthetic and chemoenzymatic methodologies for the preparation of aminoglycosides for a variety of applications (therapeutic and agricultural) reported in the scientific literature up to 2017 is presented. This comprehensive analysis of derivatization/generation of novel aminoglycosides and their conjugates is divided based on the types of modifications used to make the new derivatives. Both the chemical strategies utilized and the biological results observed are covered. Structure-activity relationships based on different synthetic modifications along with their implications for activity and ability to avoid resistance against different microorganisms are also presented.
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Affiliation(s)
- Nishad Thamban Chandrika
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596, USA.
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Synthesis and Applicability of Base-Discriminating DNA-Triplex-Forming19F NMR Probes. European J Org Chem 2017. [DOI: 10.1002/ejoc.201701110] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Granqvist L, Kraszewski A, Tähtinen V, Virta P. Synthesis of Aminoglycoside-2'-O-Methyl Oligoribonucleotide Fusions. Molecules 2017; 22:molecules22050760. [PMID: 28481305 PMCID: PMC6154110 DOI: 10.3390/molecules22050760] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 05/04/2017] [Accepted: 05/06/2017] [Indexed: 11/24/2022] Open
Abstract
Phosphoramidite building blocks of ribostamycin (3 and 4), that may be incorporated at any position of the oligonucleotide sequence, were synthesized. The building blocks, together with a previously described neomycin-modified solid support, were applied for the preparation of aminoglycoside-2′-O-methyl oligoribonucleotide fusions. The fusions were used to clamp a single strand DNA sequence (a purine-rich strand of c-Myc promoter 1) to form triple helical 2′-O-methyl RNA/DNA-hybrid constructs. The potential of the aminoglycoside moieties to stabilize the triple helical constructs were studied by UV-melting profile analysis.
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Affiliation(s)
- Lotta Granqvist
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014 Turku, Finland.
| | - Andrzej Kraszewski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02 097 Warsaw, Poland.
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2c, 02 097 Warsaw, Poland.
| | - Ville Tähtinen
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014 Turku, Finland.
| | - Pasi Virta
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014 Turku, Finland.
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Granqvist L, Virta P. Characterization of G-Quadruplex/Hairpin Transitions of RNAs by 19 F NMR Spectroscopy. Chemistry 2016; 22:15360-15372. [PMID: 27603896 DOI: 10.1002/chem.201602898] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Indexed: 12/21/2022]
Abstract
2'-O-[(4-Trifluoromethyl-triazol-1-yl)methyl] reporter groups have been incorporated into guanosine-rich RNA models (including a known bistable Qd/Hp RNA and two G-rich regions of mRNA of human prion protein, PrP) and applied for the 19 F NMR spectroscopic characterization of plausible G-quadruplex/hairpin (Qd/Hp) transitions in these RNA structures. For the synthesis of the CF3 -labeled RNAs, phosphoramidite building blocks of 2'-O-[(4-CF3 -triazol-1-yl)methyl] nucleosides (cytidine, adenosine, and guanosine) were prepared and used as an integral part of the standard solid-phase RNA synthesis. The obtained 19 F NMR spectra supported the usual characterization data (obtained by UV- and CD-melting profiles and by 1 H NMR spectra of the imino regions) and additionally gave more detailed information on the Qd/Hp transitions. The molar fractions of the secondary structural species (Qd, Hp) upon thermal denaturation and under varying ionic conditions could be determined from the intensities and shifts of the 19 F NMR signals. For a well-behaved Qd/Hp transition, thermodynamic parameters could be extracted.
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Affiliation(s)
- Lotta Granqvist
- Department of Chemistry, University of Turku, Turku, 20014, Finland.
| | - Pasi Virta
- Department of Chemistry, University of Turku, Turku, 20014, Finland.
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Castro V, Rodríguez H, Albericio F. CuAAC: An Efficient Click Chemistry Reaction on Solid Phase. ACS COMBINATORIAL SCIENCE 2016; 18:1-14. [PMID: 26652044 DOI: 10.1021/acscombsci.5b00087] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Click chemistry is an approach that uses efficient and reliable reactions, such as Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC), to bind two molecular building blocks. CuAAC has broad applications in medicinal chemistry and other fields of chemistry. This review describes the general features and applications of CuAAC in solid-phase synthesis (CuAAC-SP), highlighting the suitability of this kind of reaction for peptides, nucleotides, small molecules, supramolecular structures, and polymers, among others. This versatile reaction is expected to become pivotal for meeting future challenges in solid-phase chemistry.
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Affiliation(s)
- Vida Castro
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology 08028-Barcelona, Spain
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, 08028-Barcelona, Spain
| | - Hortensia Rodríguez
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology 08028-Barcelona, Spain
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, 08028-Barcelona, Spain
- School
of Chemistry, Yachay Tech, Yachay City of Knowledge, Urcuqui, Ecuador
| | - Fernando Albericio
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology 08028-Barcelona, Spain
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, 08028-Barcelona, Spain
- Department
of Organic Chemistry, University of Barcelona, 08028-Barcelona, Spain
- School of Chemistry & Physics, University of KwaZulu-Natal, 4001-Durban, South Africa
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