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Synthesis of Nucleosides, Nucleotides and Their Derivatives

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A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Molecular Diversity".

Deadline for manuscript submissions: closed (31 August 2013) | Viewed by 92077

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Prof. Dr. Carlo Siciliano

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Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, I-87036 Arcavacata di Rende, Italy
Interests: high-resolution instrumental analysis of complex vegetable and animal matrices; synthesis of biomolecules and their analogues; amino acid and peptide chemistry; modification of natural amino acids; chiral templates; design and synthesis of protease inhibitors
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Special Issue Information

Dear Colleagues,

Nucleosides, nucleotides and their synthetic analogues have been proposed for the diagnostic control and the therapeutic treatment of different kinds of grave pathologies which are related to viral infections and to many types of cancer. The history of these classes of compounds is certainly characterized by their wide biological and pharmaceutical potentialities, while a critical and key role has been played by the plethora of synthetic methodologies developed, time by time, for the preparation on non-natural analogues. A good number of compounds featuring modified heterocycles as nucleobases and/or sugar moieties, and phosphorylated frames showing high similarities with respect to those found in natural congeners, are now available. The scope of this Special Issue is to collect the most recent acquisitions and state of the art concerning chemical procedures used in the design and structural characterization of nucleosides, nucleotides and their modified analogues, corroborated by the results obtained from biological tests. This Special Issue will focus on all aspects regarding the description of new synthetic approaches and methodologies which can usefully be applied to modification of nucleobases, sugar moieties and phosphodiester linkages. Research papers and reviews dealing with the presented fields are welcome for the preparation of this Special Issue of Molecules.

Prof. Dr. Carlo Siciliano
Guest Editor

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Keywords

nuleosides
nucleotides
modified analogues
nucleobases modification
sugar moiety modification
phosphorylation methods
nucleic acid building blocks
biological activity
anticancer action
antiviral action
enzyme Inhibition
diagnostic potentialities

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Published Papers (12 papers)

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251 KiB

Open AccessArticle

A Tractable and Efficient One-Pot Synthesis of 5'-Azido-5'-deoxyribonucleosides

by Theodore V. Peterson, Tobin U. B. Streamland and Ahmed M. Awad

Molecules 2014, 19(2), 2434-2444; https://doi.org/10.3390/molecules19022434 - 21 Feb 2014

Cited by 7 | Viewed by 8404

Abstract

Synthetic routes to 5'-azidoribonucleosides are reported for adenosine, cytidine, guanosine, and uridine, resulting in a widely applicable one-pot methodology for the synthesis of these and related compounds. The target compounds are appropriate as precursors in a variety of purposive syntheses, as the synthetic and therapeutic relevance of azido- and amino-modified nucleosides is expansive. Furthermore, in the conversion of alcohols to azides, these methods offer a tractable alternative to the Mitsunobu and other more difficult reactions. Full article

(This article belongs to the Special Issue Synthesis of Nucleosides, Nucleotides and Their Derivatives)

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345 KiB

Open AccessArticle

Novel Method of Synthesis of 5''-Phosphate 2'-O-ribosyl-ribonucleosides and Their 3'-Phosphoramidites

by Marcin K. Chmielewski and Wojciech T. Markiewicz

Molecules 2013, 18(12), 14780-14796; https://doi.org/10.3390/molecules181214780 - 29 Nov 2013

Cited by 1 | Viewed by 7300

Abstract

Synthesis of 5''-phosphate 2'-O-ribosylribonucleosides [Nr(p)] of four common ribonucleosides, and 3'-phosphoramidites of 5''-phosphate 2'-O-ribosyladenosine and 2'-O-ribosylguanosine using the H-phosphonate chemistry is described. An additional ring protected by benzoyl groups was incorporated into the main ribosyl ring in the reaction with 1-O-acetyl-2,3,5-tri-O-benzoyl-β-d-ribofuranose in the presence of SnCl₄. The obtained 2'-O-ribosylribonucleosides (Nr) were applied in the subsequent transformations with selective deprotection. Ethanolamine was applied as a very convenient reagent for selective removal of benzoyl groups. Additionally, the tetraisopropyldisiloxane-1,3-diyl (TIPDSi) group was found to be stable under these deprotection conditions. Thus, the selectively deprotected 5''-hydroxyl group of Nr was transformed into an H-phosphonate monoester which was found to be stable under the following conditions: the removal of the TIPDSi group with triethylammonium fluoride and the dimethoxytritylation of the 5''-hydroxyl function. The 5''-H-phosphonate of Nr precursors was easily transformed to the corresponding dicyanoethyl 5''-O-phosphotriesters before phosphitylation, which gave 3'-phosphoramidite units of Nr(p) in high yield. The derived phosphoramidite units were used in an automated oligonucleotide synthesizer to produce dimer Ar(p)T via the phosphoramidite approach. The obtained products were fully deprotected under standard deprotection conditions giving dimers with a 5''-phosphate monoester function. Application of an alkaline phosphatase to prove the presence of an additional phosphate group was described. Full article

(This article belongs to the Special Issue Synthesis of Nucleosides, Nucleotides and Their Derivatives)

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289 KiB

Open AccessArticle

Pd⁰-Catalyzed Methyl Transfer on Nucleosides and Oligonucleotides, Envisaged as a PET Tracer

by Damien James, Jean-Marc Escudier, Magali Szlosek-Pinaud and Eric Fouquet

Molecules 2013, 18(11), 13654-13665; https://doi.org/10.3390/molecules181113654 - 5 Nov 2013

Cited by 6 | Viewed by 4796

Abstract

The methyl transfer reaction from activated monomethyltin, via a modified Stille coupling reaction, was studied under “ligandless” conditions on fully deprotected 5'-modified nucleosides and one dinucleotide. The reaction was optimized to proceed in a few minutes and quantitative yield, even under dilute conditions, [...] Read more.

(This article belongs to the Special Issue Synthesis of Nucleosides, Nucleotides and Their Derivatives)

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558 KiB

Open AccessCommunication

Oligonucleotide Labelling Using a Fluorogenic “Click” Reaction with a Hemicarboxonium Salt

by Marie-Pierre Maether, Kristie Lapin, Andreea Muntean, Corinne Payrastre and Jean-Marc Escudier

Molecules 2013, 18(10), 12966-12976; https://doi.org/10.3390/molecules181012966 - 17 Oct 2013

Viewed by 6427

Abstract

Two fluorescent streptocyanine labelled oligonucleotides have been synthesized by a simple “click” reaction between a non-fluorescent hemicarboxonium salt and aminoalkyl functionalized thymidines within the oligonucleotide and their spectrophotometric properties have been studied. Full article

(This article belongs to the Special Issue Synthesis of Nucleosides, Nucleotides and Their Derivatives)

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199 KiB

Open AccessArticle

An Efficient and Facile Methodology for Bromination of Pyrimidine and Purine Nucleosides with Sodium Monobromoisocyanurate (SMBI)

by Jyotirmoy Maity and Roger Stromberg

Molecules 2013, 18(10), 12740-12750; https://doi.org/10.3390/molecules181012740 - 15 Oct 2013

Cited by 8 | Viewed by 7476

Abstract

An efficient and facile strategy has been developed for bromination of nucleosides using sodium monobromoisocyanurate (SMBI). Our methodology demonstrates bromination at the C-5 position of pyrimidine nucleosides and the C-8 position of purine nucleosides. Unprotected and also several protected nucleosides were brominated in [...] Read more.

(This article belongs to the Special Issue Synthesis of Nucleosides, Nucleotides and Their Derivatives)

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414 KiB

Open AccessArticle

Enzymatic Synthesis of Highly Fluorescent 8-Azapurine Ribosides Using a Purine Nucleoside Phosphorylase Reverse Reaction: Variable Ribosylation Sites

by Alicja Stachelska-Wierzchowska, Jacek Wierzchowski, Beata Wielgus-Kutrowska and Goran Mikleušević

Molecules 2013, 18(10), 12587-12598; https://doi.org/10.3390/molecules181012587 - 11 Oct 2013

Cited by 19 | Viewed by 6450

Abstract

Various forms of purine-nucleoside phosphorylase (PNP) were used as catalysts of enzymatic ribosylation of selected fluorescent 8-azapurines. It was found that the recombinant calf PNP catalyzes ribosylation of 2,6-diamino-8-azapurine in a phosphate-free medium, with ribose-1-phosphate as ribose donor, but the ribosylation site is predominantly N7 and N8, with the proportion of N8/N7 ribosylated products markedly dependent on the reaction conditions. Both products are fluorescent. Application of the E. coli PNP gave a mixture of N8 and N9-substituted ribosides. Fluorescence of the ribosylated 2,6-diamino-8-azapurine has been briefly characterized. The highest quantum yield, ~0.9, was obtained for N9-β-d-riboside (λ_max 365 nm), while for N8-β-d-riboside, emitting at ~430 nm, the fluorescence quantum yield was found to be close to 0.4. Ribosylation of 8-azaguanine with calf PNP as a catalyst goes exclusively to N9. By contrast, the E. coli PNP ribosylates 8-azaGua predominantly at N9, with minor, but highly fluorescent products ribosylated at N8/N7. Full article

(This article belongs to the Special Issue Synthesis of Nucleosides, Nucleotides and Their Derivatives)

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417 KiB

Open AccessArticle

Glycosyl-Nucleolipids as New Bioinspired Amphiphiles

by Laurent Latxague, Amit Patwa, Eric Amigues and Philippe Barthélémy

Molecules 2013, 18(10), 12241-12263; https://doi.org/10.3390/molecules181012241 - 30 Sep 2013

Cited by 11 | Viewed by 7893

Abstract

Four new Glycosyl-NucleoLipid (GNL) analogs featuring either a single fluorocarbon or double hydrocarbon chains were synthesized in good yields from azido thymidine as starting material. Physicochemical studies (surface tension measurements, differential scanning calorimetry) indicate that hydroxybutanamide-based GNLs feature endothermic phase transition temperatures like the previously reported double chain glycerol-based GNLs. The second generation of GNFs featuring a free nucleobase reported here presents a better surface activity (lower g_lim) compared to the first generation of GNFs. Full article

(This article belongs to the Special Issue Synthesis of Nucleosides, Nucleotides and Their Derivatives)

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248 KiB

Open AccessArticle

Synthesis of a Novel Carbocyclic Analog of Bredinin

by Vasu Nair and Fan Zhang

Molecules 2013, 18(9), 11576-11585; https://doi.org/10.3390/molecules180911576 - 17 Sep 2013

Cited by 4 | Viewed by 6668

Abstract

The natural nucleoside antibiotic, bredinin, exhibits antiviral and other biological activities. While various nucleosides related to bredinin have been synthesized, its carbocyclic analog has remained unknown. Synthesis of this heretofore unknown analog of bredinin is described. The key precursor, (3aS,4R,6R,6aR)-6-((methoxy-methoxy)methyl)-2,2-dimethyltetrahydro-3aH-cyclopenta[d][1,3]dioxol-4-amine (5), was prepared from the commercially available compound, (1R,4S)-2-azabicyclo[2.2.1] hept-5-en-3-one (4). Our initial approach used intermediate 6, derived in three transformations from 5, for the key photolytic step to produce the desired ring-opened precursor to the target compound. This photochemical transformation was unsuccessful. However, an appropriately protected and related precursor was synthesized from 5 through the following side-chain functional group transformations: elaboration of the amino group through malonyl ester formation, oximation at the central carbon, conversion of ester to amide and catalytic reduction of the oxime group. This precursor, on treatment with triethylorthoformate and catalytic acetic acid in ethanol, underwent cyclization to produce the desired 4-carbamoyl-imidazolium-5-olate ring. Deprotection of the latter product proceeded smoothly to give the carbocyclic analog of bredinin. This target molecule exhibits antiviral activity, albeit low, against a number of RNA viruses. Further biological evaluations are in progress. Full article

(This article belongs to the Special Issue Synthesis of Nucleosides, Nucleotides and Their Derivatives)

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494 KiB

Open AccessArticle

Synthesis and Biological Evaluation of a New Acyclic Pyrimidine Derivative as a Probe for Imaging Herpes Simplex Virus Type 1 Thymidine Kinase Gene Expression

by Andrijana Meščić, Thomas Betzel, Adrienne Müller, Roger Slavik, Stjepko Čermak, Silvana Raić-Malić and Simon M. Ametamey

Molecules 2013, 18(7), 8535-8549; https://doi.org/10.3390/molecules18078535 - 19 Jul 2013

Cited by 1 | Viewed by 6280

Abstract

With the idea of finding a more selective radiotracer for imaging herpes simplex virus type 1 thymidine kinase (HSV1-tk) gene expression by means of positron emission tomography (PET), a novel [¹⁸F]fluorine radiolabeled pyrimidine with 4-hydroxy-3-(hydroxymethyl)butyl side chain at N-1 (HHB-5-[¹⁸F]FEP) was prepared and evaluated as a potential PET probe. Unlabeled reference compound, HHB-5-FEP, was synthesized via a five-step reaction sequence starting from 5-(2-acetoxyethyl)-4-methoxypyrimidin-2-one. The radiosynthesis of HHB-[¹⁸F]-FEP was accomplished by nucleophilic radiofluorination of a tosylate precursor using [¹⁸F]fluoride-cryptate complex in 45% ± 4 (n = 4) radiochemical yields and high purity (>99%). The biological evaluation indicated the feasibility of using HHB-5-[¹⁸F]FEP as a PET radiotracer for monitoring HSV1-tk expression in vivo. Full article

(This article belongs to the Special Issue Synthesis of Nucleosides, Nucleotides and Their Derivatives)

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237 KiB

Open AccessArticle

A Straightforward Diphenylmethyl Protection Method and Deprotection of Some Pyrimidine Nucleosides

by Milind Saudi and Arthur Van Aerschot

Molecules 2013, 18(7), 8524-8534; https://doi.org/10.3390/molecules18078524 - 18 Jul 2013

Cited by 11 | Viewed by 7404

Abstract

Benzhydryl protection of primary and secondary alcohols has been reported previously via reaction with metal alcoholates. Our aim was to find generally useful and very mild conditions for the alcoholic protection and deprotection of nucleosides with the diphenylmethyl group. This was accomplished for some pyrimidine nucleosides using PdCl₂ as the transition metal catalyst, and with optimization yields of 70–90% have been achieved. A lack of solubility of other nucleosides hampers its more general use. Full article

(This article belongs to the Special Issue Synthesis of Nucleosides, Nucleotides and Their Derivatives)

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Review

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1305 KiB

Open AccessReview

Fluorescent Probes for Nucleic Acid Visualization in Fixed and Live Cells

by Alexandre S. Boutorine, Darya S. Novopashina, Olga A. Krasheninina, Karine Nozeret and Alya G. Venyaminova

Molecules 2013, 18(12), 15357-15397; https://doi.org/10.3390/molecules181215357 - 11 Dec 2013

Cited by 92 | Viewed by 13920

Abstract

This review analyses the literature concerning non-fluorescent and fluorescent probes for nucleic acid imaging in fixed and living cells from the point of view of their suitability for imaging intracellular native RNA and DNA. Attention is mainly paid to fluorescent probes for fluorescence microscopy imaging. Requirements for the target-binding part and the fluorophore making up the probe are formulated. In the case of native double-stranded DNA, structure-specific and sequence-specific probes are discussed. Among the latest, three classes of dsDNA-targeting molecules are described: (i) sequence-specific peptides and proteins; (ii) triplex-forming oligonucleotides and (iii) polyamide oligo(N-methylpyrrole/N-methylimidazole) minor groove binders. Polyamides seem to be the most promising targeting agents for fluorescent probe design, however, some technical problems remain to be solved, such as the relatively low sequence specificity and the high background fluorescence inside the cells. Several examples of fluorescent probe applications for DNA imaging in fixed and living cells are cited. In the case of intracellular RNA, only modified oligonucleotides can provide such sequence-specific imaging. Several approaches for designing fluorescent probes are considered: linear fluorescent probes based on modified oligonucleotide analogs, molecular beacons, binary fluorescent probes and template-directed reactions with fluorescence probe formation, FRET donor-acceptor pairs, pyrene excimers, aptamers and others. The suitability of all these methods for living cell applications is discussed. Full article

(This article belongs to the Special Issue Synthesis of Nucleosides, Nucleotides and Their Derivatives)

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1331 KiB

Open AccessReview

General Approach for Introduction of Various Chemical Labels in Specific RNA Locations Based on Insertion of Amino Linkers

by Dmitri Graifer and Galina Karpova

Molecules 2013, 18(12), 14455-14469; https://doi.org/10.3390/molecules181214455 - 25 Nov 2013

Cited by 6 | Viewed by 6707

Abstract

Introduction of reporter groups at designed RNA sites is a widely accepted approach to gain information about the molecular environment of RNAs in their complexes with other biopolymers formed during various cellular processes. A general approach to obtain RNAs bearing diverse reporter groups at designed locations is based on site-specific insertion of groups containing primary aliphatic amine functions (amino linkers) with their subsequent selective derivatization by appropriate chemicals. This article is a brief review on methods for site-specific introduction of amino linkers in different RNAs. These methods comprise: (i) incorporation of a nucleoside carrying an amino-linker or a function that can be substituted with it into oligoribonucleotides in the course of their chemical synthesis; (ii) assembly of amino linker-containing RNAs from short synthetic fragments via their ligation; (iii) synthesis of amino linker-modified RNAs using T7 RNA polymerase; (iv) insertion of amino linkers into unmodified RNAs at functional groups of a certain type such as the 5'-phosphates and N7 of guanosine residues and (v) introduction of an amino linker into long highly structured RNAs exploiting an approach based on sequence-specific modification of nucleic acids. Particular reporter groups used for derivatization of amino linker-containing RNAs together with types of RNA derivatives obtained and fields of their application are presented. Full article

(This article belongs to the Special Issue Synthesis of Nucleosides, Nucleotides and Their Derivatives)

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