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Hunt KE, García-Sosa AT, Shalima T, Maran U, Vilu R, Kanger T. Synthesis of 6'-galactosyllactose, a deviant human milk oligosaccharide, with the aid of Candida antarctica lipase-B. Org Biomol Chem 2022; 20:4724-4735. [PMID: 35612321 DOI: 10.1039/d2ob00550f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Research on human milk oligosaccharides (HMOs) has increased over the past decade showing great interest in their beneficial effects. Here we describe a method for the selective deacetylation using immobilised Candida antarctica lipase-B, Novozyme N435 (N435), of pyranose saccharides in organic media with the aim of simplifying and improving the pathways for the synthesis of HMOs. By first studying in depth the deacetylation reaction of peracetylated D-glucose two reaction conditions were found, which were used on different HMO building blocks, peracetylated saccharides and thioglycosides. D-Glucose based saccharides showed selectivity towards the fourth and the sixth position deacetylation. While α-anomer of peracetylated D-galactose remained unreactive and β-anomer favoured the first position deacetylation. Peracetylated L-fucose, on the other hand, had no selectivity as the main product was fully unprotected L-fucose. Taking the peracetylated D-glucose deacetylation reaction product and selectively protecting the primary hydroxyl group in the sixth position left only the fourth position open for the glycosylation. Meanwhile, the deacetylation product of D-galactose thioglycoside, with the sixth position deacetylated, had both acceptor and donor capabilities. Using the two aforementioned products derived from the N435 deacetylation reactions a deviant HMO, 6'-galactosyllactose (6'-GL) was synthesised.
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Affiliation(s)
- Kaarel Erik Hunt
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia. .,Centre of Food and Fermentation Technologies, Akadeemia tee 15A, 12618 Tallinn, Estonia
| | - Alfonso T García-Sosa
- Department of Chemistry, University of Tartu, Ravila Street 14a, 50411 Tartu, Estonia
| | - Tatsiana Shalima
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia.
| | - Uko Maran
- Department of Chemistry, University of Tartu, Ravila Street 14a, 50411 Tartu, Estonia
| | - Raivo Vilu
- Centre of Food and Fermentation Technologies, Akadeemia tee 15A, 12618 Tallinn, Estonia
| | - Tõnis Kanger
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia.
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2
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Bakowski K, Vogel S. Evolution of complexity in non-viral oligonucleotide delivery systems: from gymnotic delivery through bioconjugates to biomimetic nanoparticles. RNA Biol 2022; 19:1256-1275. [PMID: 36411594 PMCID: PMC9683052 DOI: 10.1080/15476286.2022.2147278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
From the early days of research on RNA biology and biochemistry, there was an interest to utilize this knowledge and RNA itself for therapeutic applications. Today, we have a series of oligonucleotide therapeutics on the market and many more in clinical trials. These drugs - exploit different chemistries of oligonucleotides, such as modified DNAs and RNAs, peptide nucleic acids (PNAs) or phosphorodiamidate morpholino oligomers (PMOs), and different mechanisms of action, such as RNA interference (RNAi), targeted RNA degradation, splicing modulation, gene expression and modification. Despite major successes e.g. mRNA vaccines developed against SARS-CoV-2 to control COVID-19 pandemic, development of therapies for other diseases is still limited by inefficient delivery of oligonucleotides to specific tissues and organs and often prohibitive costs for the final drug. This is even more critical when targeting multifactorial disorders and patient-specific biological variations. In this review, we will present the evolution of complexity of oligonucleotide delivery methods with focus on increasing complexity of formulations from gymnotic delivery to bioconjugates and to lipid nanoparticles in respect to developments that will enable application of therapeutic oligonucleotides as drugs in personalized therapies.
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Affiliation(s)
- Kamil Bakowski
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Stefan Vogel
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark,CONTACT Stefan Vogel Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230Odense, Denmark
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3
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Seitz A, Wende RC, Roesner E, Niedek D, Topp C, Colgan AC, McGarrigle EM, Schreiner PR. Site-Selective Acylation of Pyranosides with Oligopeptide Catalysts. J Org Chem 2021; 86:3907-3922. [PMID: 33617252 DOI: 10.1021/acs.joc.0c02772] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Herein, we report the oligopeptide-catalyzed site-selective acylation of partially protected monosaccharides. We identified catalysts that invert site-selectivity compared to N-methylimidazole, which was used to determine the intrinsic reactivity, for 4,6-O-protected glucopyranosides (trans-diols) as well as 4,6-O-protected mannopyranosides (cis-diols). The reaction yields up to 81% of the inherently unfavored 2-O-acetylated products with selectivities up to 15:1 using mild reaction conditions. We also determined the influence of protecting groups on the reaction and demonstrate that our protocol is suitable for one-pot reactions with multiple consecutive protection steps.
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Affiliation(s)
- Alexander Seitz
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Raffael C Wende
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Emily Roesner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Dominik Niedek
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Christopher Topp
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Avene C Colgan
- Centre for Synthesis & Chemical Biology, UCD School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Eoghan M McGarrigle
- Centre for Synthesis & Chemical Biology, UCD School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
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4
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Niedek D, Erb FR, Topp C, Seitz A, Wende RC, Eckhardt AK, Kind J, Herold D, Thiele CM, Schreiner PR. In Situ Switching of Site-Selectivity with Light in the Acetylation of Sugars with Azopeptide Catalysts. J Org Chem 2020; 85:1835-1846. [PMID: 31763833 DOI: 10.1021/acs.joc.9b01913] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We present a novel concept for the in situ control of site-selectivity of catalytic acetylations of partially protected sugars using light as external stimulus and oligopeptide catalysts equipped with an azobenzene moiety. The isomerizable azobenzene-peptide backbone defines the size and shape of the catalytic pocket, while the π-methyl-l-histidine (Pmh) moiety transfers the electrophile. Photoisomerization of the E- to the Z-azobenzene catalyst (monitored via NMR) with an LED (λ = 365 nm) drastically changes the chemical environment around the catalytically active Pmh moiety, so that the light-induced change in the catalyst shape alters site-selectivity. As a proof of principle, we employed (4,6-O-benzylidene)methyl-α-d-pyranosides, which provide a change in regioselectivity from 2:1 (E) to 1:5 (Z) for the monoacetylated products at room temperature. The validity of this new catalyst-design concept is further demonstrated with the regioselective acetylation of the natural product quercetin. In situ irradiation NMR spectroscopy was used to quantify photostationary states under continuous irradiation with UV light.
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Affiliation(s)
- Dominik Niedek
- Institute of Organic Chemistry , Justus Liebig University , Heinrich-Buff-Ring 17 , 35392 Giessen , Germany
| | - Frederik R Erb
- Institute of Organic Chemistry , Justus Liebig University , Heinrich-Buff-Ring 17 , 35392 Giessen , Germany
| | - Christopher Topp
- Institute of Organic Chemistry , Justus Liebig University , Heinrich-Buff-Ring 17 , 35392 Giessen , Germany
| | - Alexander Seitz
- Institute of Organic Chemistry , Justus Liebig University , Heinrich-Buff-Ring 17 , 35392 Giessen , Germany
| | - Raffael C Wende
- Institute of Organic Chemistry , Justus Liebig University , Heinrich-Buff-Ring 17 , 35392 Giessen , Germany
| | - André K Eckhardt
- Institute of Organic Chemistry , Justus Liebig University , Heinrich-Buff-Ring 17 , 35392 Giessen , Germany
| | - Jonas Kind
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie , Technische Universität Darmstadt , Alarich-Weiss-Str. 16 , 64287 Darmstadt , Germany
| | - Dominik Herold
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie , Technische Universität Darmstadt , Alarich-Weiss-Str. 16 , 64287 Darmstadt , Germany
| | - Christina M Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie , Technische Universität Darmstadt , Alarich-Weiss-Str. 16 , 64287 Darmstadt , Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry , Justus Liebig University , Heinrich-Buff-Ring 17 , 35392 Giessen , Germany
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5
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Nici F, Oliviero G, Falanga AP, D'Errico S, Marzano M, Musumeci D, Montesarchio D, Noppen S, Pannecouque C, Piccialli G, Borbone N. Anti-HIV activity of new higher order G-quadruplex aptamers obtained from tetra-end-linked oligonucleotides. Org Biomol Chem 2019. [PMID: 29543291 DOI: 10.1039/c7ob02346d] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
By combining the ability of short G-rich oligodeoxyribonucleotides (ODNs) containing the sequence 5'CGGA3' to form higher order G-quadruplex (G4) complexes with the tetra-end-linked (TEL) concept to produce aptamers targeting the HIV envelope glycoprotein 120 (gp120), three new TEL-ODNs (1-3) having the sequence 5'CGGAGG3' were synthesized with the aim of studying the effect of G4 dimerization on their anti-HIV activity. Furthermore, in order to investigate the effect of the groups at the 5' position, the 5' ends of 1-3 were left uncapped (1) or capped with either the lipophilic dimethoxytrityl (DMT) (2) or the hydrophilic glucosyl-4-phosphate (3) moieties. The here reported results demonstrate that only the DMT-substituted TEL-ODN 2 is effective in protecting human MT-4 cell cultures from HIV infection (76% max protection), notwithstanding all the three new aptamers proved to be capable of forming stable higher order dimeric G4s when annealed in K+-containing buffer, thus suggesting that the recognition of a hydrophobic pocket on the target glycoprotein by the aptamers represents a main structural feature for triggering their anti-HIV activity.
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Affiliation(s)
- F Nici
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
| | - G Oliviero
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Napoli, Italy
| | - A P Falanga
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
| | - S D'Errico
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
| | - M Marzano
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
| | - D Musumeci
- Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy
| | - D Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, Napoli, Italy
| | - S Noppen
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, B-3000 Leuven, Belgium
| | - C Pannecouque
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, B-3000 Leuven, Belgium
| | - G Piccialli
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
| | - N Borbone
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131, Napoli, Italy.
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6
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Hara RI, Kobayashi S, Noro M, Sato K, Wada T. Synthesis and properties of 2-deoxy-2-fluoromannosyl phosphate derivatives. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.06.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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7
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Musumeci D, Riccardi C, Montesarchio D. G-Quadruplex Forming Oligonucleotides as Anti-HIV Agents. Molecules 2015; 20:17511-32. [PMID: 26402662 PMCID: PMC6332060 DOI: 10.3390/molecules200917511] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/10/2015] [Accepted: 09/16/2015] [Indexed: 12/21/2022] Open
Abstract
Though a variety of different non-canonical nucleic acids conformations have been recognized, G-quadruplex structures are probably the structural motifs most commonly found within known oligonucleotide-based aptamers. This could be ascribed to several factors, as their large conformational diversity, marked responsiveness of their folding/unfolding processes to external stimuli, high structural compactness and chemo-enzymatic and thermodynamic stability. A number of G-quadruplex-forming oligonucleotides having relevant in vitro anti-HIV activity have been discovered in the last two decades through either SELEX or rational design approaches. Improved aptamers have been obtained by chemical modifications of natural oligonucleotides, as terminal conjugations with large hydrophobic groups, replacement of phosphodiester linkages with phosphorothioate bonds or other surrogates, insertion of base-modified monomers, etc. In turn, detailed structural studies have elucidated the peculiar architectures adopted by many G-quadruplex-based aptamers and provided insight into their mechanism of action. An overview of the state-of-the-art knowledge of the relevance of putative G-quadruplex forming sequences within the viral genome and of the most studied G-quadruplex-forming aptamers, selectively targeting HIV proteins, is here presented.
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Affiliation(s)
- Domenica Musumeci
- Department of Chemical Sciences, University of Napoli Federico II, via Cintia 21, Napoli I-80126, Italy.
| | - Claudia Riccardi
- Department of Chemical Sciences, University of Napoli Federico II, via Cintia 21, Napoli I-80126, Italy.
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Napoli Federico II, via Cintia 21, Napoli I-80126, Italy.
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8
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Guzaev AP. Solid-phase supports for oligonucleotide synthesis. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2013; Chapter 3:3.1.1-3.1.60. [PMID: 23775808 DOI: 10.1002/0471142700.nc0301s53] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This unit attempts to provide a reasonably complete inventory of over 280 solid supports available to oligonucleotide chemists for preparation of natural and 3'-modified oligonucleotides. Emphasis is placed on non-nucleosidic solid supports. The relationship between the structural features of linkers and their behavior in oligonucleotide synthesis and deprotection is discussed wherever the relevant observations are available.
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9
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Santra A, Ghosh T, Misra AK. Removal of benzylidene acetal and benzyl ether in carbohydrate derivatives using triethylsilane and Pd/C. Beilstein J Org Chem 2013; 9:74-8. [PMID: 23400301 PMCID: PMC3566760 DOI: 10.3762/bjoc.9.9] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 12/17/2012] [Indexed: 11/23/2022] Open
Abstract
Clean deprotection of carbohydrate derivatives containing benzylidene acetals and benzyl ethers was achieved under catalytic transfer hydrogenation conditions by using a combination of triethylsilane and 10% Pd/C in CH3OH at room temperature. A variety of carbohydrate diol derivatives were prepared from their benzylidene derivatives in excellent yield.
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Affiliation(s)
- Abhishek Santra
- Bose Institute, Division of Molecular Medicine, P-1/12, C.I.T. Scheme VII-M, Kolkata-700054, India; FAX: 91-33-2355 3886
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10
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Zhang YJ, Dayoub W, Chen GR, Lemaire M. TMDS as a Dual-Purpose Reductant in the Regioselective Ring Cleavage of Hexopyranosyl Acetals to Ethers. European J Org Chem 2012. [DOI: 10.1002/ejoc.201101682] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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11
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Morvan F, Vidal S, Souteyrand E, Chevolot Y, Vasseur JJ. DNA glycoclusters and DNA-based carbohydrate microarrays: From design to applications. RSC Adv 2012. [DOI: 10.1039/c2ra21550k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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12
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Kedracki D, Safir I, Gour N, Ngo KX, Vebert-Nardin C. DNA–Polymer Conjugates: From Synthesis, Through Complex Formation and Self-assembly to Applications. BIO-SYNTHETIC POLYMER CONJUGATES 2012. [DOI: 10.1007/12_2012_181] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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13
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Pastore A, Valerio S, Adinolfi M, Iadonisi A. An Easy and Versatile Approach for the Regioselective De-O-benzylation of Protected Sugars Based on the I2/Et3SiH Combined System. Chemistry 2011; 17:5881-9. [DOI: 10.1002/chem.201003332] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Indexed: 11/12/2022]
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14
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Ikeda Y, Kubota D, Nagasaki Y. Simple solid-phase synthesis and biological properties of carbohydrate-oligonucleotide conjugates modified at the 3'-terminus. Bioconjug Chem 2010; 21:1685-90. [PMID: 20704260 DOI: 10.1021/bc100205v] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A novel synthesis method for oligonucleotides possessing a functional moiety at the 3'-terminus was established based on solid-phase synthesis. In order to install the functional group at the 3'-terminus of the oligonucleotide, a solid support possessing the functional group was prepared. A carbohydrate was employed in this study for the functionalization of the oligonucleotide. To prepare a glycosylated solid support, a novel glycosyl acceptor (2) was synthesized using 4,4-dihydroxymethyl-cyclopenta-1-ene as the starting compound. The glycosylation reaction proceeded smoothly (yield = 95%) to yield the suitable glycosylated compound (3). After 8 was immobilized on the solid support, it was subjected to solid-phase oligonucleotide synthesis by the standard phosphoramidite coupling method. An oligonucleotide possessing a sugar moiety at the 3'-terminus was obtained after the products were deprotected and cleaved from the solid support. The stability of the carbohydrate-modified oligonucleotide was greatly increased even in the serum buffer, indicating that the sugar moiety at the 3'-position improved the resistance against enzymatic degradation. This technique was also applied to RNA synthesis. Galactose-ended siRNA was prepared and was confirmed to possess enough ability, at a concentration of 10 nM, to regulate the expression of the target gene.
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Affiliation(s)
- Yutaka Ikeda
- Grauate School of Pure and Applied Science, Tsukuba Research Center for Interdisciplinary Materials Science, University of Tsukuba, CREST, Japan Science and Technology Agency
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15
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Coppola C, Virno A, De Napoli L, Randazzo A, Montesarchio D. Synthesis and conformational analysis of a novel carbohydrate-fused bis-crown ether: crown-CyPLOS. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.09.100] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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16
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Lönnberg H. Solid-phase synthesis of oligonucleotide conjugates useful for delivery and targeting of potential nucleic acid therapeutics. Bioconjug Chem 2009; 20:1065-94. [PMID: 19175328 DOI: 10.1021/bc800406a] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Olignucleotide-based drugs show promise as a novel form of chemotherapy. Among the hurdles that have to be overcome on the way of applicable nucleic acid therapeutics, inefficient cellular uptake and subsequent release from endosomes to cytoplasm appear to be the most severe ones. Covalent conjugation of oligonucleotides to molecules that expectedly facilitate the internalization, targets the conjugate to a specific cell-type or improves the parmacokinetics offers a possible way to combat against these shortcomings. Since workable chemistry is a prerequisite for biological studies, development of efficient and reproducible methods for preparation of various types of oligonucleotide conjugates has become a subject of considerable importance. The present review summarizes the advances made in the solid-supported synthesis of oligonucleotide conjugates aimed at facilitating the delivery and targeting of nucleic acid drugs.
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Affiliation(s)
- Harri Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland.
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17
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Morales JC, Reina JJ, Díaz I, Aviñó A, Nieto PM, Eritja R. Experimental measurement of carbohydrate-aromatic stacking in water by using a dangling-ended DNA model system. Chemistry 2008; 14:7828-35. [PMID: 18637649 DOI: 10.1002/chem.200800335] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Protein-carbohydrate recognition is of fundamental importance for a large number of biological processes; carbohydrate-aromatic stacking is a widespread, but poorly understood, structural motif in this recognition. We describe, for the first time, the measurement of carbohydrate-aromatic interactions from their contribution to the stability of a dangling-ended DNA model system. We observe clear differences in the energetics of the interactions of several monosaccharides with a benzene moiety depending on the number of hydroxy groups, the stereochemistry, and the presence of a methyl group in the pyranose ring. A fucose-benzene pair is the most stabilizing of the studied series (-0.4 Kcal mol(-1)) and this interaction can be placed in the same range as other more studied interactions with aromatic residues of proteins, such as Phe-Phe, Phe-Met, or Phe-His. The noncovalent forces involved seem to be dispersion forces and nonconventional hydrogen bonds, whereas hydrophobic effects do not seem to drive the interaction.
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Affiliation(s)
- Juan C Morales
- Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas, CSIC-Universidad de Sevilla, Sevilla, Spain.
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18
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D'Onofrio J, Petraccone L, Martino L, Di Fabio G, Iadonisi A, Balzarini J, Giancola C, Montesarchio D. Synthesis, biophysical characterization, and anti-HIV activity of glyco-conjugated G-quadruplex-forming oligonucleotides. Bioconjug Chem 2008; 19:607-16. [PMID: 18254584 DOI: 10.1021/bc7003395] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Novel hybrid oligonucleotides carrying the G-quadruplex-forming d(5'TGGGAG3') sequence, conjugated with mono- or disaccharides at the 3' or 5'-end through phosphodiester bonds, have been synthesized as potential anti-HIV agents, via a fully automated, online phosphoramidite-based solid-phase strategy. CD-monitored thermal denaturation studies on the resulting quadruplexes indicated the insertion of a single monosaccharide at the 3'-end as the optimal modification, conferring improved stability to the quadruplex complex. In addition, the 3'-conjugation with glucose or mannose converted the anti-HIV inactive unmodified oligomer into active compounds. On the contrary, the 5'-tethering with these monosaccharides, as well as the conjugation, either at the 5' or 3'-end, with sucrose, were in all cases detrimental to quadruplex stability and did not improve the biological activity. On the basis of the assumption that the kinetically and thermodynamically favored formation of the quadruplex complex is a prerequisite for efficient antiviral activity, a novel bis-conjugated oligonucleotide was designed. This combined a mannose residue at the 3'-phosphate end with bulky aromatic tert-butyldiphenylsilyl (TBDPS) group at the 5'-end, previously shown to markedly favor the formation of quadruplex complexes. The 5',3'-bis-conjugated 6-mer, for which a detailed biophysical characterization has been carried out, resulted in 3-fold greater antiviral activity against HIV-1 than the sole 3'-glyco-conjugated oligonucleotide.
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Affiliation(s)
- Jennifer D'Onofrio
- Dipartimento di Chimica Organica e Biochimica and Dipartimento di Chimica Paolo Corradini, Università degli Studi di Napoli Federico II, Via Cintia 4, I-80126 Napoli, Italy
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19
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Bouillon C, Meyer A, Vidal S, Jochum A, Chevolot Y, Cloarec JP, Praly JP, Vasseur JJ, Morvan F. Microwave assisted "click" chemistry for the synthesis of multiple labeled-carbohydrate oligonucleotides on solid support. J Org Chem 2007; 71:4700-2. [PMID: 16749812 DOI: 10.1021/jo060572n] [Citation(s) in RCA: 159] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A versatile approach has been developed for the multiple labeling of oligonucleotides. First, three linkers as a H-phosphonate monoester derivative were condensed on a solid-supported T12 to introduce H-phosphonate diester linkages which were oxidized in the presence of propargylamine. Second, three galactosyl azide derivatives were conjugated to the solid-supported three-alkyne-modified T12 by a 1,3-cycloaddition so-called "click chemistry" in the presence of Cu(I) assisted by microwaves.
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Affiliation(s)
- Camille Bouillon
- Laboratoire de Chimie Organique Biomoléculaire de Synthèse, UMR 5625 CNRS-Université Montpellier II, Place E. Bataillon, 34095 Montpellier Cedex 5, France
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20
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Zatsepin TS, Oretskaya TS. Synthesis and applications of oligonucleotide-carbohydrate conjugates. Chem Biodivers 2007; 1:1401-17. [PMID: 17191787 DOI: 10.1002/cbdv.200490104] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Nowadays, oligonucleotide-carbohydrate conjugates are used in antisense biotechnology and in the study of glycosylated DNA functioning in vitro. The application of mono- and disaccharide phosphoramidites, solid-phase supports with immobilized carbohydrates, glycosylated nucleoside phosphoramidites, and postsynthetic conjugation of reactive sugar derivatives with oligonucleotides for preparation of oligonucleotide-carbohydrate conjugates have been systematically studied. The advantages and disadvantages of these approaches are considered. Possible strategies for synthesis of glycoclusters with different topologies conjugated to DNA are discussed. Applications of oligonucleotide-carbohydrate conjugates are highlighted. Studies of interactions of glycosylated oligonucleotides with proteins and effective cell-specific delivery of oligonucleotide-carbohydrate conjugates are discussed.
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Affiliation(s)
- Timofei S Zatsepin
- Department of Chemistry, M. V. Lomonosov Moscow State University, Leninskie Gory, Moscow, Russia, 119992
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Yan H, Tram K. Glycotargeting to improve cellular delivery efficiency of nucleic acids. Glycoconj J 2007; 24:107-23. [PMID: 17268860 DOI: 10.1007/s10719-006-9023-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2006] [Revised: 11/07/2006] [Accepted: 11/14/2006] [Indexed: 10/23/2022]
Abstract
Nucleic acids bearing glycans of various structures have been under vigorous investigation in the past decade. The carbohydrate moieties of such complexes can serve as recognition sites for carbohydrate-binding proteins-lectins-and initiate receptor-mediated endocytosis. Therefore, carbohydrates can enhance cell targeting and internalization of nucleic acids that are associated with them and thus improve the bioavailability of nucleic acids as therapeutic agents. This review summarizes nucleic acid glycosylation in nature and approaches for the preparation of both non-covalently associated and covalently-linked carbohydrate-nucleic acid complexes.
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Affiliation(s)
- Hongbin Yan
- Department of Chemistry, Brock University, 500 Glenridge Ave., St. Catharines, ON, Canada.
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Di Fabio G, Randazzo A, D'Onofrio J, Ausín C, Pedroso E, Grandas A, De Napoli L, Montesarchio D. Cyclic Phosphate-Linked Oligosaccharides: Synthesis and Conformational Behavior of Novel Cyclic Oligosaccharide Analogues. J Org Chem 2006; 71:3395-408. [PMID: 16626119 DOI: 10.1021/jo0600757] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
CyPLOS (cyclic phosphate-linked oligosaccharides), that is, novel cyclic oligosaccharide surrogates, consisting of two, three, and four phenyl-beta-D-glucopyranoside units, 4,6-linked through stable phosphodiester bonds, were prepared by a straightforward and efficient solid-phase protocol. The assembly of the linear precursors was achieved by standard phosphoramidite chemistry on an automated DNA synthesizer, using a suitably protected 4-phosphoramidite derivative of D-glucose as the building block. For the crucial cyclization step a phosphotriester methodology was exploited, followed by a mild basic treatment releasing the desired cyclic molecules in solution in a highly pure form. The cyclic dimer and trimer were also independently prepared by classical solution synthesis, basically following the same approach. The solution structural preferences of the cyclic dimer and trimer, obtained by detailed NMR analysis, are also reported.
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Affiliation(s)
- Giovanni Di Fabio
- Dipartimento di Chimica Organica e Biochimica, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte S. Angelo, via Cynthia, 4, I-80126 Napoli, Italy
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Niu H, Yao J, Wang Y, Wang G. Cp2TiCl2 used as a catalyst for the transesterification between dimethyl carbonate and phenol to diphenyl carbonate. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.molcata.2005.03.023] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Procopio A, Dalpozzo R, De Nino A, Maiuolo L, Nardi M, Romeo G. Mild and efficient method for the cleavage of benzylidene acetals by using erbium (iii) triflate. Org Biomol Chem 2005; 3:4129-33. [PMID: 16267593 DOI: 10.1039/b511314h] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Er(OTf)3 is proposed as new efficient Lewis acid catalyst in a mild deprotection protocol of benzylidene derivatives. In a modified procedure, where acetic anhydride is used as the reaction solvent, the simultaneous cleavage of the benzylidene acetal and the peracetylation of the substrates is obtained in quantitative yields and very short reaction times.
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Affiliation(s)
- Antonio Procopio
- Dipartimento di Scienze Farmaco-Biologiche, Università della Magna Graecia, Complesso Ninì Barbieri, 88021 Roccelletta di Borgia (Cz), Italy.
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Virta P, Katajisto J, Niittymäki T, Lönnberg H. Solid-supported synthesis of oligomeric bioconjugates. Tetrahedron 2003. [DOI: 10.1016/s0040-4020(03)00704-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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