Glycosylation reactions mediated by hypervalent iodine: application to the synthesis of nucleosides and carbohydrates

• Yuichi Yoshimura,
• Hideaki Wakamatsu,
• Yoshihiro Natori,
• Yukako Saito and
• Noriaki Minakawa

Beilstein J. Org. Chem. 2018, 14, 1595–1618, doi:10.3762/bjoc.14.137

• , Tokushima, 770-8505, Japan 10.3762/bjoc.14.137 Abstract To synthesize nucleoside and oligosaccharide derivatives, we often use a glycosylation reaction to form a glycoside bond. Coupling reactions between a nucleobase and a sugar donor in the former case, and the reaction between an acceptor and a sugar

• ; nucleoside; oligosaccharide; Introduction Nucleic acids and oligosaccharides are both mandatory polymers for the maintenance of life and cell growth. The former exists in nuclei and codes genetic information, which is transformed into proteins through a transcription process known as the “central dogma

• studies by supplying biological tools for the analyses of these polymers, as well as by synthesizing effective drug candidates for the diseases mentioned above [4][8][9][10][11][12][13][14]. To synthesize nucleoside and oligosaccharide derivatives, glycosylation reactions are often used to form a

Oligonucleotide analogues with cationic backbone linkages

• Melissa Meng and
• Christian Ducho

Beilstein J. Org. Chem. 2018, 14, 1293–1308, doi:10.3762/bjoc.14.111

• ' (Figure 5) [72][73][74]. In principle, the NAA-modification is inspired by 'high-carbon' nucleoside structures (i.e., nucleosides having more than five carbon atoms in the sugar unit) found in naturally occurring nucleoside antibiotics [75][76][77]. In muraymycin- and caprazamycin-type nucleoside

• antibiotics, among others, such 'high-carbon' nucleosides are uridine-derived amino acid structures ('glycyluridine', GlyU) [78][79][80], which are aminoribosylated at the 5'-hydroxy group. As part of our ongoing research program on muraymycin nucleoside antibiotics (e.g., muraymycin A1 (44)) and their

Mechanochemistry of nucleosides, nucleotides and related materials

• Olga Eguaogie,
• Joseph S. Vyle,
• Patrick F. Conlon,
• Manuela A. Gîlea and
• Yipei Liang

Beilstein J. Org. Chem. 2018, 14, 955–970, doi:10.3762/bjoc.14.81

• exploited grinding to facilitate disaggregation of DNA from tightly bound proteins through selective denaturation of the latter. Despite the wide application of ball milling to amino acid chemistry, there have been limited reports of mechanochemical transformations involving nucleoside or nucleotide

• : specifically, solid solutions, cocrystals, polymorph transitions, carbon nanotube dissolution and inclusion complex formation. Keywords: DNA; green chemistry; mechanochemistry; nucleoside; nucleotide; Introduction Several definitions of mechanochemistry have been attempted since Ostwald included it as one of

• vessel (and its shape); the mass of the ball(s); and the hardness of the colliding materials. In order of descending hardness, zirconia, stainless steel, copper and PTFE have all been used to effect mechanochemical transformation of nucleoside or nucleotide substrates. During a study of amide coupling

On the design principles of peptide–drug conjugates for targeted drug delivery to the malignant tumor site

• Eirinaios I. Vrettos,
• Gábor Mező and
• Andreas G. Tzakos

Beilstein J. Org. Chem. 2018, 14, 930–954, doi:10.3762/bjoc.14.80

• diminishing expressed nucleoside receptors responsible for the cell uptake of gemcitabine [6]. Additionally, chemotherapy with anticancer agents is often hampered by their poor aqueous solubility, low oral bioavailability and metabolic instability. These drawbacks are linked to the unfavorable ADME

• loading that is usually preferred, mostly due to poor physicochemical properties. Below we analyze a set of drugs that have been tailored and incorporated in PDCs. Gemcitabine (Gem): Gemcitabine (dFdC) is a nucleoside analog of deoxycytidine in which the hydrogen atoms on the 2' carbon are replaced by

• deactivation through deamination in its inactive metabolite dFdU, the acquired multidrug resistance (MDR) and its high hydrophilicity deterring its prolonged drug release from various vehicles [88], which therefore reduces the effective concentration of gemcitabine. It enters cells through nucleoside

Phosphodiester models for cleavage of nucleic acids

• Satu Mikkola,
• Tuomas Lönnberg and
• Harri Lönnberg

Beilstein J. Org. Chem. 2018, 14, 803–837, doi:10.3762/bjoc.14.68

• studies with small molecular phosphodiesters. Keywords: Cleavage; DNA; kinetics; mechanism; RNA; Introduction Nucleic acids are polymeric diesters of phosphoric acid that store and transfer biological information. In biological systems, the diester linkages bridging 3´-O of one nucleoside to the 5´-O of

• transphosphorylation by departure of the 5´-linked nucleoside [3]. The half-life at pH 6–7 and 25 °C is around 10 years [4][5], the enzymatic cleavage by RNase A being 3∙1011 times faster [6]. Interestingly, the RNA phosphodiester bonds are additionally subject to cleavage by RNA itself, viz. by RNA sequences known as

• leaving groups that are less basic than EtO−, such as 5´-O− of nucleoside, the lifetime expectedly is shorter. If the leaving group is very good, such as an aryl group, a synchronous concerted mechanism (ANDN) may take over the stepwise mechanism (AN + DN). Model compounds and experimental tools Studies

Recent advances in synthetic approaches for medicinal chemistry of C-nucleosides

• Kartik Temburnikar and
• Katherine L. Seley-Radtke

Beilstein J. Org. Chem. 2018, 14, 772–785, doi:10.3762/bjoc.14.65

• and supramolecular complexes [10][11][12][13][14][15][16][17][18][19][20][21][22]. Nucleic acids are composed of a monomeric nucleoside unit that features an aromatic nitrogenous moiety (a nucleobase) connected to a pentose sugar, which in turn is attached to a phosphate group (Figure 1) [7]. The

• pentose sugar and the nucleobase are connected by a carbon–nitrogen bond that is adjacent to the sugar oxygen resulting in an hemiaminal ether bond, also known as the glycosidic bond. Because of their key role in many biological processes, modifications to the nucleoside structure have been widely

• employed in the design of drugs, most notably in the fields of virology and cancer research [13][14][15]. Variations in the nucleoside scaffold are typically accomplished by the insertion, deletion or transposition of functional groups or atoms [23][24][25][26][27][28][29]. The varied properties of such

AuBr₃-catalyzed azidation of per-O-acetylated and per-O-benzoylated sugars

• Jayashree Rajput,
• Srinivas Hotha and
• Madhuri Vangala

Beilstein J. Org. Chem. 2018, 14, 682–687, doi:10.3762/bjoc.14.56

• purine and pyrimidine nucleoside synthesis using per-O-acyl/per-O-benzoyl furanosyl and pyranosyl o-hexynylbenzoates [23]. Subsequently, Hotha and co-workers utilized propargyl 1,2-orthoesters and alkynyl glycosyl carbonate donors for the synthesis of pyrimidine nucleosides [24][25]. In addition, N

Enzyme-free genetic copying of DNA and RNA sequences

• Marilyne Sosson and
• Clemens Richert

Beilstein J. Org. Chem. 2018, 14, 603–617, doi:10.3762/bjoc.14.47

• oligonucleotide is present, stacking with the base of its 5'-terminal nucleoside further adds to the attractive forces experienced by incoming monomers. This is shown schematically in Figure 5. Because downstream-binding strands favorably affect the rate and selectivity of primer extension, we have dubbed them

Stimuli-responsive oligonucleotides in prodrug-based approaches for gene silencing

• Françoise Debart,
• Christelle Dupouy and
• Jean-Jacques Vasseur

Beilstein J. Org. Chem. 2018, 14, 436–469, doi:10.3762/bjoc.14.32

Preparation of trinucleotide phosphoramidites as synthons for the synthesis of gene libraries

• Ruth Suchsland,
• Bettina Appel and
• Sabine Müller

Beilstein J. Org. Chem. 2018, 14, 397–406, doi:10.3762/bjoc.14.28

• of two suitably protected monomers to generate a dinucleotide, which then can be extended in either 5'- or 3'-direction (Figure 3). Surprisingly, only one report has made use of this "economy", first coupling a 5'-O-DMTr-protected nucleoside-3'-ortho-chlorophenylphosphotriester to a 3'-O-levulinoyl

• -azidomethylbenzoyl)-protected nucelosides, followed by removal of the 5'-O-DMTr group and extension of the dimer to the trimer by coupling of another N-acyl-3'-O-(o-chlorophenylphosphate)nucleoside. The final removal of the 2-azidomethylbenzoyl group occurred by reduction of the azide with triphenylphosphine in

• , although using phosphite triester chemistry [27]. In this case, the synthesis started with the coupling of an N-acyl-5'-O-DMTr-protected nucleoside-3'-O-phosphoramidite to an N-acyl-3'-O-TBDMS-protected nucleoside, followed by oxidation of the internucleotide phosphorous. Upon cleavage of the 5'-O-DMTr

Fluorogenic PNA probes

• Tirayut Vilaivan

Beilstein J. Org. Chem. 2018, 14, 253–281, doi:10.3762/bjoc.14.17

• derivative. 5-Benzothiophene- and 5-benzofuran-modified uracil in aegPNA exhibited a fluorescence that was marginally sensitive to the environment [195]. When incorporated into PNA, benzothiophene-uracil exhibited an increased fluorescence compared to the free nucleoside. The opposite effect was observed

Fluorescent nucleobase analogues for base–base FRET in nucleic acids: synthesis, photophysics and applications

• Mattias Bood,
• Sangamesh Sarangamath,
• Moa S. Wranne,
• Morten Grøtli and
• L. Marcus Wilhelmsson

Beilstein J. Org. Chem. 2018, 14, 114–129, doi:10.3762/bjoc.14.7

• sodium methoxide in MeOH, which yielded the free nucleoside 15 in 71%. Standard DMTr protection furnished compound 16 which was then activated for oligonucleotide solid-phase synthesis (SPS) by phosphitylation using CEP-Cl. The total yield of tCnitro deoxyribose phosphoramidite was 0.8% over 6 steps

• nucleoside in 65% yield. Subsequent phosphitylation followed by salt-formation finally furnished compound 35 in 52% over two steps. Since the quadracyclic adenine presented an overall structural similarity with adenine and keeping a very rigid heterocyclic system suggesting few options for the molecule to

Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

• Tamara Šmidlehner,
• Ivo Piantanida and
• Gennaro Pescitelli

Beilstein J. Org. Chem. 2018, 14, 84–105, doi:10.3762/bjoc.14.5

• adequately prepared and characterized. For that reason, a short description of the most important issues in sample preparation is summarized in chapters 2.2 and 2.3. 2.1. Relation between DNA or RNA secondary structure and polarization spectroscopy Nucleobases are achiral but nucleoside and nucleotide

Acid-catalyzed ring-opening reactions of a cyclopropanated 3-aza-2-oxabicyclo[2.2.1]hept-5-ene with alcohols

• Katrina Tait,
• Alysia Horvath,
• Nicolas Blanchard and
• William Tam

Beilstein J. Org. Chem. 2017, 13, 2888–2894, doi:10.3762/bjoc.13.281

• the structure against cleavage by nucleoside phosphorylases or hydrolases [18][19]. The addition of a cyclopropane unit could provide further rigidity that could better stabilize the compound, thereby enhancing its biological activity. Both of these reported ring-openings of cyclopropanated 3-aza-2

Synthetic mRNA capping

• Fabian Muttach,
• Nils Muthmann and
• Andrea Rentmeister

Beilstein J. Org. Chem. 2017, 13, 2819–2832, doi:10.3762/bjoc.13.274

• nucleophiles such as nucleoside mono-, -di- or -triphosphates and are typically reacted in anhydrous DMF in the presence of zinc chloride. The GMP imidazolide (18) is reacted with m7GDP (17) in the presence of ZnCl2 as catalyst to yield m7GpppG (12) [49]. In the past years, variations of this general synthetic

CF₃SO₂X (X = Na, Cl) as reagents for trifluoromethylation, trifluoromethylsulfenyl-, -sulfinyl- and -sulfonylation and chlorination. Part 2: Use of CF₃SO₂Cl

• Hélène Chachignon,
• Hélène Guyon and
• Dominique Cahard

Beilstein J. Org. Chem. 2017, 13, 2800–2818, doi:10.3762/bjoc.13.273

• surprising formation of a 5’-chloro nucleoside, when used in an attempt to prepare the corresponding 5’-OTf nucleoside [54]. Moreover, considering the excellent selectivity of the combination CF3SO2Cl/Et3N towards the chlorination of substrates displaying a hydroxy group, the reaction could be further

Metal-mediated base pairs in parallel-stranded DNA

• Jens Müller

Beilstein J. Org. Chem. 2017, 13, 2671–2681, doi:10.3762/bjoc.13.265

• Nucleic acids are increasingly being applied in areas beyond their original biological context, e.g., as a scaffold for the defined spatial arrangement of functional entities [1][2][3]. This often goes along with the formal substitution of a canonical nucleoside (or any other nucleic acid component) by an

• -mediated pyrrolocytosine:pyrrolocytosine base pairs [62]. These investigations not only included the 2PyrPC and 3PyrPC residues reported above, but also a PhPC nucleoside bearing a phenyl substituent. Accordingly, a possible additional stabilization due to the presence of the (potentially coordinating

Pyrene–nucleobase conjugates: synthesis, oligonucleotide binding and confocal bioimaging studies

• Artur Jabłoński,
• Yannic Fritz,
• Hans-Achim Wagenknecht,
• Rafał Czerwieniec,
• Tytus Bernaś,
• Damian Trzybiński,
• Krzysztof Woźniak and
• Konrad Kowalski

Beilstein J. Org. Chem. 2017, 13, 2521–2534, doi:10.3762/bjoc.13.249

• –nucleoside conjugates that are bound and assembled along the (dA)10 or T10 template are kept soluble in aqueous media. A higher concentrated stock solution of each chromophore–nucleobase conjugate was prepared in DMSO and added as aliquots to an aqueous solution (2.5 μM) of the (dA)10 or T10 template. The

• was prehybridized, so that canonical base pairing of the chromophore–nucleoside conjugates with the template could be excluded. After centrifugation, compound 3 shows no effective self-assembly to single or double-stranded templates in buffer; only in water an assembly occurring to both single

Phosphonic acid: preparation and applications

• Charlotte M. Sevrain,
• Mathieu Berchel,
• Hélène Couthon and
• Paul-Alain Jaffrès

Beilstein J. Org. Chem. 2017, 13, 2186–2213, doi:10.3762/bjoc.13.219

• commonly used as precursors of phosphonic acids especially for the synthesis of aminophosphonic acids (α [209][210], β [211] or γ [212]) and also for the synthesis of nucleoside analogues [213]. The use of these intermediates is likely explained by the possibility to use chiral diamine that can act as a

Enzymatic separation of epimeric 4-C-hydroxymethylated furanosugars: Synthesis of bicyclic nucleosides

• Neha Rana,
• Manish Kumar,
• Vinod Khatri,
• Jyotirmoy Maity and
• Ashok K. Prasad

Beilstein J. Org. Chem. 2017, 13, 2078–2086, doi:10.3762/bjoc.13.205

• : bicyclonucleosides; biocatalysis; lipase; Novozyme®-435; separation of epimers; Introduction Sugar-modified bicyclic nucleosides have drawn the attention of synthetic chemists because of their effect on the conformational restriction of the furanose moiety of the nucleoside [1][2][3][4][5][6][7][8][9]. The

• conformational restriction has led to the enhancement in target selectivity and in vivo stability of the nucleoside-based drug candidates. One of the important precursors for the synthesis of different types of bicyclonucleosides is 4-C-hydroxymethyl-1,2-O-isopropylidene-α-D-ribofuranose. The synthesis of the

• sulfonate (TMS-triflate) in acetonitrile yielded the triacetylated nucleoside 8 in 94% yield. Subsequently, deacetylation of acetoxy groups in nucleoside 8 with 2 M NaOH solution in water/dioxane (1:1) also led to the concomitant cylization between suitably placed C-3′-OH and C-1′′-tosyl groups to afford 3

Effect of uridine protecting groups on the diastereoselectivity of uridine-derived aldehyde 5’-alkynylation

• Raja Ben Othman,
• Mickaël J. Fer,
• Laurent Le Corre,
• Sandrine Calvet-Vitale and
• Christine Gravier-Pelletier

Beilstein J. Org. Chem. 2017, 13, 1533–1541, doi:10.3762/bjoc.13.153

• ; nucleoside; protecting groups; uridine; Introduction Nucleoside and nucleotide derivatives or analogues are biologically active compounds of major interest [1][2]. Their widespread applications span from therapeutic agents, such as antibacterial [3][4][5], antiviral [6] or antitumor [7][8] drugs, to

• numerous approaches, this 5′ stereogenic center comes from the chiral pool and the nucleobase is introduced under Vorbrüggen conditions [20][21][22][23][24][25][26]. It can also be created directly on the nucleoside, either by functionalization of an alkene at C-5’ [27][28][29][30][31][32] or by the

• organometallic reagents onto nucleoside aldehyde (Table 1), we decided to investigate the influence of the protecting groups of the uridine aldehyde on the stereochemical outcome of the nucleophilic addition of a Grignard reagent and we wish to report herein the results of our study. Results and Discussion We

Synthesis of oligonucleotides on a soluble support

• Harri Lönnberg

Beilstein J. Org. Chem. 2017, 13, 1368–1387, doi:10.3762/bjoc.13.134

• order by esterification of phosphoric acid with the 3´-OH of one and the 5´-OH of the other nucleoside. Usually, the 3´-OH is first esterified with an appropriate derivative of phosphoric acid and the resulting building block is then reacted with the 5´-OH (Figure 1). Either a linear or a convergent

• protected nucleoside 3´-(2-cyanoethyl-N,N-dialkylphosphoramidite)s (1 in Scheme 1) or 3´-(H-phosphonate)s are usually preferred as building blocks [3] (2 in Scheme 1). The attacking 5´-OH apart, all other nucleophilic functionalities must be kept protected during the coupling. The primary amino groups of

• derivatives 2-ethyl- and 2-benzylthiotetrazole [8] or 4,5-dicyanoimidazole [9]. The activator has a dual role donating a proton to the departing dialkylamino group and attacking as an anionic species on phosphorus [10]. Nucleoside H-phosphonates are, in turn, converted in situ to reactive mixed anhydrides

Strategies toward protecting group-free glycosylation through selective activation of the anomeric center

• A. Michael Downey and
• Michal Hocek

Beilstein J. Org. Chem. 2017, 13, 1239–1279, doi:10.3762/bjoc.13.123

• nucleosides [23][24]. The enzymes typically employed for these purposes are nucleoside phosphorylases (NPs) or nucleoside deoxyribosyltransferases (NDTs) in the presence of inorganic phosphate in a tandem enzymatic process [25]. In Scheme 5 we highlight a very recent example of this methodology for the

First total synthesis of kipukasin A

• Chuang Li,
• Haixin Ding,
• Zhizhong Ruan,
• Yirong Zhou and
• Qiang Xiao

Beilstein J. Org. Chem. 2017, 13, 855–862, doi:10.3762/bjoc.13.86

• subsequent Vorbrüggen glycosylation, the protecting group could be removed smoothly in the presence of 5 mol % Ph3PAuOTf in dichloromethane to provide kipukasin A in high yield and regioselectivity. Keywords: gold catalysis; kipukasin A; marine nucleoside; total synthesis; Vorbrüggen glycosylation

• , ester protection is preferred for Vorbrüggen glycosylations in nucleoside syntheses. Very recently, ortho-alkynylbenzoate was successfully developed by our group as neighboring participation group to synthesize 2’-modified nucleosides [24], which could be removed smoothly in the presence of gold(I

• ) [36]. With glycosylation donor 16 in hand, we proceeded to investigate the crucial Vorbrüggen glycosylation with uracil (4). To our delight, in a similar manner as our described in [17], it proved to be efficient to give nucleoside 17 with exclusive β-configuration in 89% yield. At last, using our

Synthesis of ribavirin 2’-Me-C-nucleoside analogues

• Fanny Cosson,
• Aline Faroux,
• Jean-Pierre Baltaze,
• Jonathan Farjon,
• Régis Guillot,
• Jacques Uziel and
• Nadège Lubin-Germain

Beilstein J. Org. Chem. 2017, 13, 755–761, doi:10.3762/bjoc.13.74

• carbon atom in the 2’-position are an indium-mediated alkynylation and a 1,3-dipolar cyclization. Keywords: alkynylation; antiviral; cancer; C-nucleosides; ribavirin; Introduction The triazole nucleoside ribavirin (RBV, Figure 1) is used for the treatment of a number of viral infections and may be

• the combination, due to its particular role. Recently, we developed an alkynyl glycosylation protocol allowing us to obtain C-nucleoside derivatives and we turned our attention to ribavirin C-nucleoside analogues. Moreover, recently De Clerq [13] outlined the potential of C-nucleosides in the arsenal