Spectroelectrochemical studies on the effect of cations in the alkaline glycerol oxidation reaction over carbon nanotube-supported Pd nanoparticles

• Dennis Hiltrop,
• Steffen Cychy,
• Karina Elumeeva,
• Wolfgang Schuhmann and
• Martin Muhler

Beilstein J. Org. Chem. 2018, 14, 1428–1435, doi:10.3762/bjoc.14.120

• from starch, sugar or oils and fats [2][3]. The transesterification of oils and fats produces glycerol as a byproduct, which requires further processing to reduce the costs of biofuels [4]. The comparably high energy density of glycerol of 5965 Wh L−1 assuming its total oxidation to CO2 suggests its

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

• charged moieties attached to nucleobases or the ribose sugar. Some selected examples 1–6 of resulting nucleic acid structures are provided in Figure 2 [30][31][32][33][34][35][36][37]. Oligonucleotides of this type are at least partially zwitterionic, but overall densely charged. With respect to the

• ' (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

An overview of recent advances in duplex DNA recognition by small molecules

• Sayantan Bhaduri,
• Nihar Ranjan and
• Dev P. Arya

Beilstein J. Org. Chem. 2018, 14, 1051–1086, doi:10.3762/bjoc.14.93

• several ways such as helical sense, pitch, groove width, base orientation and sugar pucker (Table 1). The major differences in the two generally encountered A- and B-forms of DNA is in the sugar pucker and their groove widths. In A-form DNA, the major groove is narrower but has a wide/shallow minor groove

• -form DNA, Z-DNA is a left handed structure formed by alternating G and C base pairs and contains some features of both A- and B-DNA such as the sugar pucker and a slightly bigger number of base pairs per turn [7]. The discovery of multistranded DNA structures such as G-quadruplexes [9], which uses

• eight Hoogsteen-paired hydrogen bonds to form a tetrad (Figure 1) has further enhanced our understanding of the diversity of DNA shapes and structures. In a parallel tetramolecular quadruplex d(TG4T), the features of nucleotides at each base resemble that of the B-DNA (C2’-endo sugar pucker, anti

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

• Reactions of nucleoside sugar and nucleobase moieties An early example of the application of mechanochemistry for nucleoside derivatisation was reported by Khalafi-Nezhad and Mokhtari who effected regioselective 5′-protection of ribonucleosides and thymidine using a mortar and pestle with trityl

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

• sugar moiety. The difference between Dau and Dox is a hydroxy group substituted at the C-14 carbon atom on Dox providing an extra conjugation site for ester linkage (Figure 6). The mechanism of action of anthracyclines is based on their intercalation to DNA inhibiting the macromolecular biosynthesis

A stereoselective and flexible synthesis to access both enantiomers of N-acetylgalactosamine and peracetylated N-acetylidosamine

• Bettina Riedl and
• Walther Schmid

Beilstein J. Org. Chem. 2018, 14, 856–860, doi:10.3762/bjoc.14.71

• relationship studies. Several strategies for the synthesis of 2-amino sugars have been published so far. In one exemplary straightforward approach, GalNAc was prepared by inverting the stereogenic center at the C-4 position of N-acetylglucosamine (GlcNAc) [10]. However, the necessity of using a 2-amino sugar

• of the four desired stereogenic centers. By extending compound 5 via a Horner–Wadsworth–Emmons (HWE) reaction [15] and subsequent stereoselective introduction of the corresponding nitrogen functionality, a route to four different 2-amino sugar stereoisomers has been elaborated. Results and Discussion

• cleaved by the use of acidic ion exchange (DOWEX H+). Subsequent ozonolysis caused the formation of the aldehyde by the oxidation of the methylene functionality. Consequently, intramolecular hemiacetal formation resulted immediately in the cyclization of the unprotected azido sugar, which was

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

• conditions. The hydrogen sulfide ion is 105 times less basic than the hydroxide ion and, hence, able to compete with the sugar oxyanions as a leaving group upon breakdown of the thiophosphorane intermediate (the bond energies of P–O and P–S bonds are 86 kcal mol−1 and 55 kcal mol−1, respectively [103

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

• maneuver stereochemistry as well as to incorporate structural modifications. In this review, we describe recent reports on the modular synthesis of C-nucleosides with a focus on D-ribonolactone and sugar modifications that have resulted in potent lead molecules. Keywords: C-nucleosides; convergent

• 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

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

• . In a similar fashion using 10 mol % AuBr3, 2,3,4,6-tetra-O-acetyl-β-D-galactopyranosyl azide (2) and 2,3,4,6-tetra-O-acetyl-β-D-mannopyranosyl azide (3) were obtained from their corresponding per-O-acetylated sugar precursors (Table 1, entries 1 and 2) in 3 h at 25 °C in 87% and 90% yield

Carbohydrate inhibitors of cholera toxin

• Vajinder Kumar and
• W. Bruce Turnbull

Beilstein J. Org. Chem. 2018, 14, 484–498, doi:10.3762/bjoc.14.34

• pocket. Both of these terminal sugar residues show hydrogen bonding interactions with the protein and associated water molecules. The GM1 oligosaccharide (GM1os) binds very tightly to CTB with a dissociation constant (Kd) of around 40 nM (measured by isothermal titration calorimetry, ITC), while simple

• linker emerging through the central channel. c) Close-up view of the two sugar binding sites. Figure prepared using the PyMOL programme from Protein Data Bank files 1XTC.pdb, 3CHB.pdb and 3EFX.pdb. Bernardi and co-workers’ designed oligosaccharide mimetics of GM1. Structure of monomeric ligands. X

• -bifunctional inhibitor designed by Bundle and co-workers. Glycopolymers with exchangeable sugar ligands and variable length linkers. Acknowledgements This review is part of a project that has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska

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

• the modification in the nucleotide: the internucleosidic phosphate, the nucleobase, the sugar or the extremities of ONs. Moreover, the review provides a current and detailed account of stimuli-responsive ONs with the main goal of gene silencing. However, for some stimuli-responsive ONs reported in

• ) backbone in the replacement of the phosphate ester internucleotide linkages. This modification provides nuclease stability and favorable pharmacokinetic properties but can lead to some toxicity. In addition, the most extensively used sugar modifications are represented by the 2’-modifications: 2’-O-methyl

• , their gene silencing effects were weaker than those of PS AONs when tested using the same model assay. It seems that the conversion of the modified ONs into native ONs might occur too slowly inside cells to improve gene silencing. Modifications at the sugar 2’-OH Several permanent 2’-O-modifications (2

Synthetic and semi-synthetic approaches to unprotected N-glycan oxazolines

• Antony J. Fairbanks

Beilstein J. Org. Chem. 2018, 14, 416–429, doi:10.3762/bjoc.14.30

• chloride (DMC), and related reagents, which can direct convert an oligosaccharide with a 2-acetamido sugar at the reducing terminus directly into the corresponding oxazoline in water. Therefore, oxazoline formation can now be achieved in water as the final step of any synthetic sequence, obviating the need

• protected (typically peracetylated) GlcNAc or other 2-acetamido sugar [37][38][39][40]. Oxazoline formation is achieved by activation of the leaving group at the anomeric centre and neighbouring group participation by the 2-acetamide. Unfortunately application of these reaction conditions to oligosaccharide

• substrates leads to significant cleavage of interglycosidic linkages, and correspondingly low yields of products. However, two methods that are useful for the production of oligosaccharide oxazolines are treatment of the peracetylated sugar with either TMSOTf in dichloroethane [39], or with TMSBr, BF3·Et2O

Fluorogenic PNA probes

• Tirayut Vilaivan

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

• oligonucleotide mimics that consist of a peptide-like backbone. Although the idea of replacing the whole sugar-phosphate backbone of DNA with a completely unrelated scaffold such as peptide had been around since the 1970s [20], it was not until the 1990s that the first PNA system with an N-2-aminoethylglycine

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

• analogues The development of synthesis methods of nucleobase analogues remains a challenge. This is mainly due to the presence of multiple reactive functional groups both on the nucleobase as well as the sugar moiety and requires the introduction of orthogonal protection groups. A careful consideration of

• synthesis of tCnitro followed the procedure of Roth et al. [39] to furnish the aromatic core 13 (Scheme 3). Compound 13 was then glycosylated by making the sodium salt and reacting it with Hoffer´s α-chloro sugar yielding 14 in 11% yield after isolation [46]. The p-toluoyl protection groups were cleaved by

• sodium-salt method [42]. The deoxyribosylation was then achieved using the same Hoffer’s α-chloro sugar, but in presence of a Lewis acid yielding the protected nucleosides 19a–c [48]. The cleavage of the protection groups was achieved with sodium methoxide to furnish compounds 20a–c. The improved

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

• derivatives are optically active. The π→π* transitions of the bases (Scheme 1) contribute to the electronic circular dichroism mostly as a result of the chiral perturbation exerted by the sugar moiety. The ECD signals of single nucleosides/nucleotides are, accordingly, quite small. Coupling into

• vibrational modes of the sugar moieties. The VCD appearing in this region is less dependent on the base composition [42]. 5.2. Practical information Choice of solvent and sample cell: Although the analysis of biomolecule interactions is best performed

Aminosugar-based immunomodulator lipid A: synthetic approaches

• Alla Zamyatina

Beilstein J. Org. Chem. 2018, 14, 25–53, doi:10.3762/bjoc.14.3

Recent applications of click chemistry for the functionalization of gold nanoparticles and their conversion to glyco-gold nanoparticles

• Vivek Poonthiyil,
• Thisbe K. Lindhorst,
• Vladimir B. Golovko and
• Antony J. Fairbanks

Beilstein J. Org. Chem. 2018, 14, 11–24, doi:10.3762/bjoc.14.2

• attach these sugar-containing thiol ligands to AuNPs [70][71][72][73], there has so far only been one study that reported the use of the CuAAC to click sugars directly onto the surface of AuNPs. In 2008, Chikae et al. reported the use of CuAAC to react alkyne-terminated thiol-functionalized AuNPs that

• with carbohydrates using the azide–alkyne Huisgen cycloaddition. The three major methods for the synthesis of GAuNPs. (a) Direct reduction of an Au3+ salt in the presence of thiol-linked sugar derivatives to obtain GAuNPs of sizes smaller than 10 nm. (b) Exchange of citrate molecules (cit) on citrate

• -stabilized AuNPs with thiol-linked sugar derivatives to obtain GAuNPs of various sizes. (c) Reactions of AuNPs (obtained after ligand exchange) with suitably functionalized sugar derivatives. The non-catalysed azide–alkyne Huisgen cycloaddition (NCAAC) between an organic azide (1,3-dipole) and an alkyne

Electron-deficient pyridinium salts/thiourea cooperative catalyzed O-glycosylation via activation of O-glycosyl trichloroacetimidate donors

• Mukta Shaw,
• Yogesh Kumar,
• Rima Thakur and
• Amit Kumar

Beilstein J. Org. Chem. 2017, 13, 2385–2395, doi:10.3762/bjoc.13.236

• crucial class of biomolecules such as oligosaccharides and glycoconjugates, where one sugar unit is linked with another sugar unit or any other molecules (aglycons) [1][2][3][4]. Owing to their high importance, several efficient protocols have been developed for the stereoselective glycosylation in the

• catalyst loading and produced the desired glucosides 5j–m, respectively, in moderate to good yields (43–67%) and with good α-selectivity (Table 2, entries 9–12). As expected, on treatment with a sugar-based acceptor such as 1,2:3,4-di-O-isopropylidene-D-galactose (2n), the corresponding glycoside 5n was

Diosgenyl 2-amino-2-deoxy-β-D-galactopyranoside: synthesis, derivatives and antimicrobial activity

• Henryk Myszka,
• Patrycja Sokołowska,
• Agnieszka Cieślińska,
• Andrzej Nowacki,
• Maciej Jaśkiewicz,
• Wojciech Kamysz and
• Beata Liberek

Beilstein J. Org. Chem. 2017, 13, 2310–2315, doi:10.3762/bjoc.13.227

• , particularly antifungal [3][4][5][6] and antitumor [7][8][9]. The aglycone part of a saponin is termed sapogenin. Diosgenin, yamogenin, tigogenin, smilagenin and sarsapogenin are the most abundant sapogenins in nature [10]. They are linked via a glycosidic bond to a sugar unit, mainly D-glucose. Diosgenyl

• the condensation of saccharides with ureas or the reaction of glycosylamines, amino sugar, or aminoglycosides with isocyanates, or their equivalents such as carbamates [32][33]. Ureido saponins presented here were obtained in the reaction of ethyl isocyanate (8), chloroethyl isocyanate (9) and phenyl

Synthesis and application of trifluoroethoxy-substituted phthalocyanines and subphthalocyanines

• Satoru Mori and
• Norio Shibata

Beilstein J. Org. Chem. 2017, 13, 2273–2296, doi:10.3762/bjoc.13.224

• suppressing its aggregation property. It is also necessary to improve the water solubility of the lipophilic phthalocyanine in order to increase its biocompatibility [88][89]. One frequent method to increase the water solubility of phthalocyanine involves the combination of a biomolecule such as a sugar [90

Structural diversity in the host–guest complexes of the antifolate pemetrexed with native cyclodextrins: gas phase, solution and solid state studies

• Magdalena Ceborska,
• Magdalena Zimnicka,
• Aneta Aniela Kowalska,
• Kajetan Dąbrowa and
• Barbara Repeć

Beilstein J. Org. Chem. 2017, 13, 2252–2263, doi:10.3762/bjoc.13.222

• α-glucopyranoside (Δδ = 0.04–0.07 ppm, Supporting Information File 1, Figure S4, Table S2). This strongly supports the assumption that the PTX dianion interacts with hydroxy groups of the sugar moieties, and this phenomenon was already highlighted in the literature [23][24]. Keeping in mind that

• from NMR experiments performed for PTX mixtures with CDs simplest analogue – methyl α-D-glucopyranoside showed that PTX dianion interacts with hydroxy groups of sugar moieties. This additionally proved that unusually large changes of chemical shifts for PTX upon addition of α-CD were caused by carboxyl

An efficient synthesis of a C₁₂-higher sugar aminoalditol

• Łukasz Szyszka,
• Anna Osuch-Kwiatkowska,
• Mykhaylo A. Potopnyk and
• Sławomir Jarosz

Beilstein J. Org. Chem. 2017, 13, 2146–2152, doi:10.3762/bjoc.13.213

• the coupling of two simple monosaccharides and subsequent transformation of the resulting enone into the protected C12-sugar 1. The conversion of the latter into alditol 2 allowed us to prepare derivative 3 having a 18-membered ring (Figure 1) [8]. Higher sugar 1 has a substantial synthetic potential

• in diol 2 is not possible. Thus we decided to differentiate the terminal positions in the stage of higher sugar 1. The replacement of the hydroxy group at the C12-position with an azide, accomplished successfully under Mistunobu conditions, afforded azide 4 in 95% yield (Scheme 1). The crucial step

• was the liberation of the anomeric position (C1), which, as we noticed, can cause problems. We subjected azide 4 to acetolysis and, although this reaction is very capricious in higher sugar chemistry [7][8], succeeded in the preparation of the desired hemiacetal acetate 5 in very good yield (86%) 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

• ribo-trihydroxy sugar derivative starting from diacetone-D-glucose led to the formation of an inseparable 1:1 mixture of the required compound and its C-3 epimer, i.e., 4-C-hydroxymethyl-1,2-O-isopropylidene-α-D-xylofuranose [10]. Lipases have been used extensively for the selective manipulation of

• hydroxy groups present in different sugars and sugar moieties of synthetic or naturally occurring glycosides, nucleosides, etc. Gotor et al. [11] have reported a lipase-mediated acylation of an equimolecular mixture of D/L-thymidine with acetonoxime levulinate as acylating agent and Pseudomonas cepacia

Intramolecular glycosylation

• Xiao G. Jia and
• Alexei V. Demchenko

Beilstein J. Org. Chem. 2017, 13, 2028–2048, doi:10.3762/bjoc.13.201

• (1→4) glycoside.” Indeed, after sequential glycosylation in the presence of TsOH at 50 oC, methanolysis, and per-acetylation, disaccharide 4 was isolated in 20% yield. The authors then very reasonably concluded that “Consequently, the presence of the ester linkage which kept the two sugar moieties in

• disaccharide 9 in 74% as a pure 1,2-trans isomer [52]. Expansion of this approach to other positions and sugar series showed that the stereoselectivity could be relaxed, and seemed to be dependent of the donor–acceptor match–mismatch. Thus, when succinoyl was attached to the 6-OH of the galactosyl acceptor

• category was extensively studied and applied to a variety of sugar series and targets [58][73][74]. Phthaloyl and related tethers Phthaloyl tethering was also introduced by Ziegler [53] and practically concomitantly by Valverde et al. [54] as “template-directed cyclo-glycosylation.” In the latter

1,3-Dibromo-5,5-dimethylhydantoin as promoter for glycosylations using thioglycosides

• Fei-Fei Xu,
• Claney L. Pereira and
• Peter H. Seeberger

Beilstein J. Org. Chem. 2017, 13, 1994–1998, doi:10.3762/bjoc.13.195

• group at C-6 and C-4 position, respectively. The DBDMH/TfOH system activates glycosyl donors including neutral monosaccharides of different configurations (D-gluco 5 and 6, D-galacto 1 and 4, D-manno 8, L-rhamno 9), amino sugar 7 and uronic acid 10. All thioglycosides reacted equally well, irrespective