Synthesis of multiply fluorinated N-acetyl-D-glucosamine and D-galactosamine analogs via the corresponding deoxyfluorinated glucosazide and galactosazide phenyl thioglycosides

• Vojtěch Hamala,
• Lucie Červenková Šťastná,
• Martin Kurfiřt,
• Petra Cuřínová,
• Martin Dračínský and
• Jindřich Karban

Beilstein J. Org. Chem. 2021, 17, 1086–1095, doi:10.3762/bjoc.17.85

• . These observations are consistent with the recently reported instability of O-acylated GlcNAc under basic conditions due to elimination reactions of transient hemiacetal intermediates [38]. This instability of amino sugar hemiacetals underscores the requirement to both protect the anomeric position with

• resulting from the low stability of amino sugar hemiacetals. The prepared polyfluorinated thiodonors and hemiacetals are valuable intermediates in oligosaccharide synthesis and their utility in glycosylation is currently being studied in our group. Retrosynthetic analysis of the target fluoro analogs

Synthetic accesses to biguanide compounds

• Oleksandr Grytsai,
• Cyril Ronco and
• Rachid Benhida

Beilstein J. Org. Chem. 2021, 17, 1001–1040, doi:10.3762/bjoc.17.82

• demonstrated by Schenker and Hasspacher for the synthesis of potential blood sugar-lowering biguanides, derived from cyclic secondary amines (Scheme 32) [66]. Besides, Bernatowicz et al. showed in a methodological study that primary amines are more reactive toward N-amidinopyrazole than N-amidino

Beyond ribose and phosphate: Selected nucleic acid modifications for structure–function investigations and therapeutic applications

• Christopher Liczner,
• Kieran Duke,
• Gabrielle Juneau,
• Martin Egli and
• Christopher J. Wilds

Beilstein J. Org. Chem. 2021, 17, 908–931, doi:10.3762/bjoc.17.76

• oligonucleotides that have been explored for gene silencing. Keywords: antisense; chemically modified oligonucleotides; crystallography; siRNA; structure; Introduction The natural nucleic acids sugar-phosphate backbone comes in two flavors, 2'-deoxyribose in DNA and ribose in RNA. However, this relative

• modifications reported by chemists along with the synthesis of 2'-deoxy-2'-fluoro-nucleosides (FRNA) [24]. The negatively charged phosphodiester linkages in the backbones of DNA and RNA are of fundamental importance for reactivity, stability, conformation and hydration [25][26]. The sugar moieties in DNA and

• group between the sugars in DNA and RNA is at the origin of the vastly expanded fold [29][30][31][32] and functional spaces of RNA [33][34][35][36][37][38][39]. Perhaps less known is the fact that the sugar moiety in the backbone of a nucleic acid determines the base pairing priorities. For example, in

Synthesis of bis(aryloxy)fluoromethanes using a heterodihalocarbene strategy

• Carl Recsei and
• Yaniv Barda

Beilstein J. Org. Chem. 2021, 17, 813–818, doi:10.3762/bjoc.17.70

• led us to attempt to displace a single fluoride ion from 5 with the anion of 6 (Scheme 3), with fluorophilic calcium hydroxide as a base, in analogy to a report where phenoxide moieties are introduced to the anomeric position of a fluorinated sugar [9]. This gave only traces of 4, while adjustments in

DNA with zwitterionic and negatively charged phosphate modifications: Formation of DNA triplexes, duplexes and cell uptake studies

• Yongdong Su,
• Maitsetseg Bayarjargal,
• Tracy K. Hale and
• Vyacheslav V. Filichev

Beilstein J. Org. Chem. 2021, 17, 749–761, doi:10.3762/bjoc.17.65

• [47][48], a sugar [49][50], or the DNA backbone [51][52][53] leading to the formation of more stable duplexes and triplexes [54]. The introduction of sulfonamide RNA (SaRNA monomers) to replace the phosphodiester backbone led to charge-neutral sulfonamide antisense oligonucleotides (SaASOs), which

Simulating the enzymes of ganglioside biosynthesis with Glycologue

• Andrew G. McDonald and
• Gavin P. Davey

Beilstein J. Org. Chem. 2021, 17, 739–748, doi:10.3762/bjoc.17.64

• negative charge. Figure 1 shows the structure of the monosialylated ganglioside GM1a. The biosynthesis of gangliosides occurs in the endoplasmic reticulum and Golgi, where specific glycosyltransferases act, in stepwise fashion, by adding monosaccharides from sugar nucleotide donors, first to ceramide, and

• . The method involves a set of regular-expression-based rules acting on strings of characters that representing the monosaccharide units, x, model the actions of transferases in the general form, Ax + B = A + xB, where Ax is a nucleotide sugar and B is the carbohydrate moiety of the acceptor, be it a

• , sugars, and are read from right to left starting with the base (reducing-end) sugar. The letters a and b are reserved for α and β-anomers, respectively, while brackets are used to delimit branches, and the letter T is used to denote the connection point to ceramide, or to another conjugate depending on

Synthesis and properties of oligonucleotides modified with an N-methylguanidine-bridged nucleic acid (GuNA[Me]) bearing adenine, guanine, or 5-methylcytosine nucleobases

• Naohiro Horie,
• Takao Yamaguchi,
• Shinji Kumagai and
• Satoshi Obika

Beilstein J. Org. Chem. 2021, 17, 622–629, doi:10.3762/bjoc.17.54

• synthesis of 2'-amino-LNA (Figure 1) functionalized with a peptide or sugar at the N2'-position, with the aim of modulating the physicochemical properties and specific organ distributions of the therapeutic oligonucleotides [13][14]. A more favorable example is the covalent attachment of a guanidine moiety

¹⁹F NMR as a tool in chemical biology

• Diana Gimenez,
• Aoife Phelan,
• Cormac D. Murphy and
• Steven L. Cobb

Beilstein J. Org. Chem. 2021, 17, 293–318, doi:10.3762/bjoc.17.28

Direct synthesis of anomeric tetrazolyl iminosugars from sugar-derived lactams

• Michał M. Więcław and
• Bartłomiej Furman

Beilstein J. Org. Chem. 2021, 17, 115–123, doi:10.3762/bjoc.17.12

• , we have performed a number of different functionalizations of such cyclic systems with various complexity, and with a particular focus on the modification of sugar-derived lactams. As summarized in Scheme 1, this includes simple nucleophile addition to in situ-generated imines [23], the consecutive

• molecule incorporating both an iminosugar and a tetrazole fragment is of particular interest, due to the interesting properties of both moieties (Figure 1). It is probably hard to overestimate the importance of sugar scaffolds in nature, and we believe that it speaks for itself, however, a significance of

• have, however, only reported one example of lactam functionalization which only proceeded with moderate efficiency (1-tert-butylazepan-2-one, 41% yield of the desired product). Unfortunately, this approach cannot be utilized for the functionalization of secondary amides, like sugar-derived lactams, due

Chemical constituents of Chaenomeles sinensis twigs and their biological activity

• Joon Min Cha,
• Dong Hyun Kim,
• Lalita Subedi,
• Zahra Khan,
• Sang Un Choi,
• Sun Yeou Kim and
• Chung Sub Kim

Beilstein J. Org. Chem. 2020, 16, 3078–3085, doi:10.3762/bjoc.16.257

• at 23.3 min for ᴅ-glucopyranose by the LC–MS analysis, which corresponded with that of the ᴅ-form of the authentic sugar (23.3 min for ᴅ-glucopyranose and 21.4 min for ʟ-glucopyranose). Aglycone (1a). Colorless gum; 1H (700 MHz) and 13C NMR (175 MHz) data, see Table 1. Cytotoxicity assessment. The

Changed reactivity of secondary hydroxy groups in C8-modified adenosine – lessons learned from silylation

• Jennifer Frommer and
• Sabine Müller

Beilstein J. Org. Chem. 2020, 16, 2854–2861, doi:10.3762/bjoc.16.234

• conjugation of the desired moiety. A C8-alkynyl-modified adenosine derivative was synthesized, reviving an old synthetic pathway for iodination of purine nucleobases. Silylation of the C8-alkynyl-modified adenosine revealed unexpected selectivity of the two secondary sugar hydroxy groups, with the 3'-O-isomer

• halide to iodine, taking into account that direct iodination of purines has been claimed being troublesome [26], although not impossible [27]. For C8-iodination of adenosine, first the hydroxy groups at the sugar moiety were protected with tert-butyldimethylsilyl (TBDMS) groups. The silylated nucleoside

• not protected, side reactions were not observed and good yields (79%) of the C8-iodo derivative 3 were achieved. Prior to Sonogashira coupling of the linker moiety, the exocyclic amine of the nucleoside derivative was protected with an isobutyryl group, and the silyl groups at the sugar hydroxy

Dirhamnolipid ester – formation of reverse wormlike micelles in a binary (primerless) system

• David Liese,
• Hans Henning Wenk,
• Xin Lu,
• Jochen Kleinen and
• Gebhard Haberhauer

Beilstein J. Org. Chem. 2020, 16, 2820–2830, doi:10.3762/bjoc.16.232

• Pseudomonas aeruginosa, a Gram-negative rod-shaped bacterium [5][6][7][8]. RL are built up by one or two rhamnose sugar units as well as one to three β-hydroxy fatty acids, which can also be unsaturated. These highly functional biomolecules exhibit interesting biological and antibacterial properties, as

• micelles are entangled at ambient temperature, so that a network-like structure is formed. An illustration of the formation of RWLM by the dirhamnolipid esters is shown in Figure 9. The hydrophilic sugar parts are oriented towards the interior of the micelle and the lipophilic alkyl chains are pointed

Anion exchange resins in phosphate form as versatile carriers for the reactions catalyzed by nucleoside phosphorylases

• Julia N. Artsemyeva,
• Ekaterina A. Remeeva,
• Tatiana N. Buravskaya,
• Irina D. Konstantinova,
• Roman S. Esipov,
• Anatoly I. Miroshnikov,
• Natalia M. Litvinko and
• Igor A. Mikhailopulo

Beilstein J. Org. Chem. 2020, 16, 2607–2622, doi:10.3762/bjoc.16.212

• problems associated with the reversibility of enzymatic phosphorolysis/synthesis reactions, along with the solubility of heterocyclic bases and accessibility of PF-1Pis. Despite all this, in a number of cases these problems have been successfully solved and, as a result, the desired base and/or sugar

Water-soluble host–guest complexes between fullerenes and a sugar-functionalized tribenzotriquinacene assembling to microspheres

• Si-Yuan Liu,
• Xin-Rui Wang,
• Man-Ping Li,
• Wen-Rong Xu and
• Dietmar Kuck

Beilstein J. Org. Chem. 2020, 16, 2551–2561, doi:10.3762/bjoc.16.207

• Department of Chemistry, Center for Molecular Materials (CM2), Bielefeld University, 33615 Bielefeld, Germany 10.3762/bjoc.16.207 Abstract A sugar-functionalized water-soluble tribenzotriquinacene derivative bearing six glucose residues, TBTQ-(OG)6, was synthesized and its interaction with C60 and C70

• motif. In the work presented here, we have introduced sugar motifs that possess good water solubility and biocompatibility [36][37][38] at the six outer peripheral positions of the TBTQ framework to provide, for the first time, a water-soluble TBTQ-based host bearing an extended cavity. The complexation

• Discussion Synthesis of the host TBTQ-(OG)6. The sugar-functionalized host TBTQ-(OG)6 was synthesized starting from the known compound TBTQ-(OH)6 (Scheme 1) [31][32][33]. The reaction of TBTQ-(OH)6 with propargyl bromide in the presence of potassium carbonate gave the hexakis-propargyl ether, TBTQ-(OP)6, in

Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding

• Christopher B. Barnett,
• Tharindu Senapathi and
• Kevin J. Naidoo

Beilstein J. Org. Chem. 2020, 16, 2540–2550, doi:10.3762/bjoc.16.206

• approach, we aim to use the tools and workflows available as part of the Galaxy project to analyze MD simulations to find out if the sugar moiety of the Tn-antigen binds directly to the antibody. Further, if the sugar does not bind directly (as found previously), then we will use these analyses to observe

• how the sugar modulates binding. Methods The inputs, simulation scripts, Galaxy workflows (a series of tools and dataset actions that run in sequence), and data for these simulations are available at https://github.com/chrisbarnettster/bjoc-paper-2020-sm. Simulation There is an increasing number of

• pre-organized for antibody binding. A Ramachandran plot can be used to understand the role of the sugar moiety, by comparison of the dihedral angle distribution of the glycosidic linkage between the glycan and peptide portion of the Tn-antigen (Figure S3 in Supporting Information File 1). In solution

NMR Spectroscopy of supramolecular chemistry on protein surfaces

• Peter Bayer,
• Anja Matena and
• Christine Beuck

Beilstein J. Org. Chem. 2020, 16, 2505–2522, doi:10.3762/bjoc.16.203

• ligand consisting of a fusicoccane diterpene core combined with different sugar moieties was designed to improve its properties as molecular glue for the 14-3-3/p53 complex [105]. Upon peptide binding in the absence of ligand, the 14-3-3 resonances of the binding site show reduced signal intensities. The

Computational tools for drawing, building and displaying carbohydrates: a visual guide

• Kanhaya Lal,
• Rafael Bermeo and
• Serge Perez

Beilstein J. Org. Chem. 2020, 16, 2448–2468, doi:10.3762/bjoc.16.199

• structure is output in the specified notation: either ASCII IUPAC sugar nomenclature or a graph which can be rendered in different themes which include Heidelberg, Oxford, Tokyo, CFG and extended CFG (Figure 4, middle). The output images for the glycan structure and the legends can be saved and downloaded

• , it only uses the sugar units that are defined in GLYCAM. The topologies generated for glycosylated proteins and glycolipids are compatible with the OPLS [72] and AMBER [73] force fields. The topology for carbohydrate polymers is based on the GLYCAM force field. The user needs to provide the ceramide

• representation that twists and changes its orientation according to the relative position of following sugar residues, hence provides an important conformational detail in polysaccharides. Combination

A proposed sustainability index for synthesis plans based on input provenance and output fate: application to academic and industrial synthesis plans for vanillin as a case study

• John Andraos

Beilstein J. Org. Chem. 2020, 16, 2346–2362, doi:10.3762/bjoc.16.196

• scales that are several orders of magnitude longer than organism time scales. (4) Lignosulfonic acid liquor and sawdust were considered renewable inputs since they ultimately originate from trees. Ferulic acid and ᴅ-glucose were considered renewable inputs since they originate from sugar beet biomass [47

Host–guest interaction of cucurbit[8]uril with oroxin A and its effect on the properties of oroxin A

• Zhishu Zeng,
• Jun Xie,
• Guangyan Luo,
• Zhu Tao and
• Qianjun Zhang

Beilstein J. Org. Chem. 2020, 16, 2332–2337, doi:10.3762/bjoc.16.194

• that the molecular size of the flavonoids and the length of the sugar chains have a greater impact on the assembly mode of supramolecular systems. Results and Discussion Host–guest interactions The host–guest interaction can be effectively observed using 1H NMR spectroscopy, and the mode of action of

Syntheses of spliceostatins and thailanstatins: a review

• William A. Donaldson

Beilstein J. Org. Chem. 2020, 16, 1991–2006, doi:10.3762/bjoc.16.166

• -1–C-5 segment of thailanstatin methyl esters Both syntheses of the C-1–C-5 tetrahydropyran segment of thailanstatin A (7) utilize sugar precursors. In the Ghosh synthesis [31], the triacetyl ᴅ-glucal 60 is converted into the trans C-1-allylated tetrahydropyran 98 according to literature procedures

• C-1–C-6 tetrahydropyran fragments of FR901464 (1). The preparation of the C-1–C-5 tetrahydropyran fragment of the thailanstatins has, so far, utilized sugar-derived precursors. A variety of reactions have been utilized for union of these fragments via a diene segment. While a Ru-catalyzed cross

Synthesis, docking study and biological evaluation of ᴅ-fructofuranosyl and ᴅ-tagatofuranosyl sulfones as potential inhibitors of the mycobacterial galactan synthesis targeting the galactofuranosyltransferase GlfT2

• Marek Baráth,
• Jana Jakubčinová,
• Zuzana Konyariková,
• Stanislav Kozmon,
• Katarína Mikušová and
• Maroš Bella

Beilstein J. Org. Chem. 2020, 16, 1853–1862, doi:10.3762/bjoc.16.152

• enzymes require an activated sugar donor uridine diphosphate (UDP)-Galf, which is synthesized from UDP-galactopyranose (UDP-Galp) by the enzyme UDP-Galp mutase [9] (Supporting Information File 1, Figure S1). The recently published GlfT2 X-ray structure with a UDP donor part [10] was used in the reaction

• -up of lipid-linked galactan precursors. The crude enzymes used in the assay allow for in situ synthesis of the acceptor for galactan polymerization, decaprenyl-P-P-GlcNAc-Rha (GL2), from endogenous decaprenyl phosphate and sugar nucleotides UDP-GlcNAc and TDP-Rha supplied in the reaction mixture

When metal-catalyzed C–H functionalization meets visible-light photocatalysis

• Lucas Guillemard and
• Joanna Wencel-Delord

Beilstein J. Org. Chem. 2020, 16, 1754–1804, doi:10.3762/bjoc.16.147

• N-heterocyclic compounds such as phenanthridine, carbazole, and dibenzo[b,d]azepine. Simultaneously, Guo’s group published the arylation of nucleosides bearing a purine moiety. The transformation was regioselective and tolerated various substituents at the N9 position of the purine, including sugar

• synthetically meaningful σ-bromo esters. The mildness of the reaction conditions warranted tolerance of sensitive and/or biologically relevant sugar, menthol, and steroid motifs (Figure 37). The mechanistic studies conducted by Ackermann et al. clearly showed that the metallacyclic intermediates resulting from

Nonenzymatic synthesis of anomerically pure, mannosyl-based molecular probes for scramblase identification studies

• Giovanni Picca,
• Markus Probst,
• Simon M. Langenegger,
• Oleg Khorev,
• Peter Bütikofer,
• Anant K. Menon and
• Robert Häner

Beilstein J. Org. Chem. 2020, 16, 1732–1739, doi:10.3762/bjoc.16.145

• -Dod-NBD was obtained in 10 steps, starting from citronellol and tert-butyldimethylsilyl (TBDMS)-protected dodecanediol [39]. The reaction of either of the alcohols with the sugar phosphoramidite using ETT led to phosphite intermediates 1a and 1b, respectively. The intermediates were then oxidized with

One-pot synthesis of isosorbide from cellulose or lignocellulosic biomass: a challenge?

• Isaline Bonnin,
• Raphaël Mereau,
• Thierry Tassaing and
• Karine De Oliveira Vigier

Beilstein J. Org. Chem. 2020, 16, 1713–1721, doi:10.3762/bjoc.16.143

• conversion of cellulose and even spruce in a one-step hydrogenolysis reactions to form C4 to C6 sugar alcohols [20]. For the C6 sugar alcohols including the isosorbide formation, the yield was below 6% whatever catalyst was used at 160 °C, under 50 bar of H2 in a 36 mL stainless steel autoclave equipped with

Recent synthesis of thietanes

• Jiaxi Xu

Beilstein J. Org. Chem. 2020, 16, 1357–1410, doi:10.3762/bjoc.16.116

• -thioanhydro-α-D-gulopyranoside (84), the thietane-containing gulopyranoside [48] (Scheme 18). For the preparation of thioanhydro sugar derivatives, Cubero and co-workers treated methyl 6-S-acetyl-2,4-di-O-benzoyl-3-O-methanesulfonyl-6-thio-α-D-galactopyranoside (85) with methanolic sodium methoxide to