Monitoring carbohydrate 3D structure quality with the Privateer database

• Jordan S. Dialpuri,
• Haroldas Bagdonas,
• Lucy C. Schofield,
• Phuong Thao Pham,
• Lou Holland and
• Jon Agirre

Beilstein J. Org. Chem. 2024, 20, 931–939, doi:10.3762/bjoc.20.83

• Jordan S. Dialpuri Haroldas Bagdonas Lucy C. Schofield Phuong Thao Pham Lou Holland Jon Agirre York Structural Biology Laboratory, Department of Chemistry, University of York, UK 10.3762/bjoc.20.83 Abstract The remediation of the carbohydrate data of the Protein Data Bank (PDB) has brought

• scientists. The Privateer software is a validation and analysis tool that provides access to a number of metrics and links to external experimental resources, allowing users to evaluate structures using carbohydrate-specific methods. Here, we present the Privateer database, a free resource that aims to

• complement the growing glycan content of the PDB. Keywords: carbohydrates; database; N-glycans; N-glycosylation; polysaccharides; validation; website; Introduction Carbohydrate modelling is an important but often cumbersome stage in the macromolecular X-ray structure solution workflow. The accurate

New variochelins from soil-isolated Variovorax sp. H002

• Jabal Rahmat Haedar,
• Aya Yoshimura and
• Toshiyuki Wakimoto

Beilstein J. Org. Chem. 2024, 20, 692–700, doi:10.3762/bjoc.20.63

• remove salt and carbohydrate residues. After the retained siderophores were extracted with methanol, the obtained crude extract was further fractionated through several rounds of column chromatography, guided by a colorimetric-based chrome azurol sulfonate siderophore assay (CAS assay) [13], to yield

Introduction of a human- and keyboard-friendly N-glycan nomenclature

• Friedrich Altmann,
• Johannes Helm,
• Martin Pabst and
• Johannes Stadlmann

Beilstein J. Org. Chem. 2024, 20, 607–620, doi:10.3762/bjoc.20.53

• contrasts with the strange awkwardness when structures of interest, e.g., a possible biomarker, shall be named. Uncompromising carbohydrate chemists will use chemical formulas drawn with ChemDraw, ChemSketch or alike. While this generates rather bulky pictures, chemists rely on the possibility to specify

Switchable molecular tweezers: design and applications

• Pablo Msellem,
• Maksym Dekthiarenko,
• Nihal Hadj Seyd and
• Guillaume Vives

Beilstein J. Org. Chem. 2024, 20, 504–539, doi:10.3762/bjoc.20.45

Elucidating the glycan-binding specificity and structure of Cucumis melo agglutinin, a new R-type lectin

• Jon Lundstrøm,
• Emilie Gillon,
• Valérie Chazalet,
• Nicole Kerekes,
• Antonio Di Maio,
• Ten Feizi,
• Yan Liu,
• Annabelle Varrot and
• Daniel Bojar

Beilstein J. Org. Chem. 2024, 20, 306–320, doi:10.3762/bjoc.20.31

• groundwork for further exploration of its biological and therapeutic potential. Keywords: carbohydrate; glycan array; melon; plant lectin; R-type; Introduction Lectins have long been the subject of intense scientific scrutiny, serving as molecular bridges that span the realms of biochemistry, cellular

• biology, and biomedicine. These carbohydrate-binding proteins boast a range of functions, acting as recognition modules in cell–molecule and cell–cell interactions, thereby playing vital roles in immune defense, regulation of growth, and apoptosis [1]. In plants, they serve as essential components in

• amino acids and is predicted to fold into two linked β-trefoil domains belonging to carbohydrate-binding module family 13 (CBM13) and placing it into the group of R-type lectins. Both CBM13 domains are likely to exhibit carbohydrate-binding activity due to the conservation of key amino acids in at least

Optimizations of lipid II synthesis: an essential glycolipid precursor in bacterial cell wall synthesis and a validated antibiotic target

• Milandip Karak,
• Cian R. Cloonan,
• Brad R. Baker,
• Rachel V. K. Cochrane and
• Stephen A. Cochrane

Beilstein J. Org. Chem. 2024, 20, 220–227, doi:10.3762/bjoc.20.22

• applications due to their improved solubility in aqueous systems. Assembly is achieved by integrating distinct carbohydrate, peptide, and polyprenyl phosphate building blocks. This modular synthetic method allows for the strategic substitution of constituent building blocks at different synthetic stages and

Comparison of glycosyl donors: a supramer approach

• Anna V. Orlova,
• Nelly N. Malysheva,
• Maria V. Panova,
• Nikita M. Podvalnyy,
• Michael G. Medvedev and
• Leonid O. Kononov

Beilstein J. Org. Chem. 2024, 20, 181–192, doi:10.3762/bjoc.20.18

• structure and the reaction mechanism are the keys to understanding chemical reactivity and selectivity [65][66][67]. In the area of carbohydrate chemistry, a lot of efforts are devoted to finding relationships between the fine details of molecular structures of both glycosylation partners (glycosyl donor

Synthesis of the 3’-O-sulfated TF antigen with a TEG-N₃ linker for glycodendrimersomes preparation to study lectin binding

• Mark Reihill,
• Hanyue Ma,
• Dennis Bengtsson and
• Stefan Oscarson

Beilstein J. Org. Chem. 2024, 20, 173–180, doi:10.3762/bjoc.20.17

• project with groups from Universities in Munich and Pennsylvania we are investigating carbohydrate–lectin interactions using programmable glycodendrimersomes based on synthetic glycans. We have earlier synthesized 2-[2-(2-azidoethoxy)ethoxy]ethyl (TEG-N3) glycosides of lactose, 3’-Su-lactose and LacdiNAc

GlAIcomics: a deep neural network classifier for spectroscopy-augmented mass spectrometric glycans data

• Thomas Barillot,
• Baptiste Schindler,
• Baptiste Moge,
• Elisa Fadda,
• Franck Lépine and
• Isabelle Compagnon

Beilstein J. Org. Chem. 2023, 19, 1825–1831, doi:10.3762/bjoc.19.134

• .19.134 Abstract Carbohydrate sequencing is a formidable task identified as a strategic goal in modern biochemistry. It relies on identifying a large number of isomers and their connectivity with high accuracy. Recently, gas phase vibrational laser spectroscopy combined with mass spectrometry tools have

• impact for the society in regard to the United Nations sustainable development goal [1]. The major roadblock to carbohydrate sequencing is intrinsically due to their unique molecular properties, among biopolymers. In contrast with proteins and DNA, which are linear polymers made of a limited number of

• anomericity). In this context, designing generic carbohydrate sequencing methods is both a major scientific challenge and a strategic priority [2][3]. Few years ago we proposed an original solution by bringing together the best of both sides of the analytical chemistry world: Spectroscopy and mass

Synthesis and biological evaluation of Argemone mexicana-inspired antimicrobials

• Jessica Villegas,
• Bryce C. Ball,
• Katelyn M. Shouse,
• Caleb W. VanArragon,
• Ashley N. Wasserman,
• Hannah E. Bhakta,
• Allen G. Oliver,
• Danielle A. Orozco-Nunnelly and
• Jeffrey M. Pruet

Beilstein J. Org. Chem. 2023, 19, 1511–1524, doi:10.3762/bjoc.19.108

• ) protein [16][17], as well as perturbing carbohydrate metabolism to generate reactive oxygen species that damage the DNA [18], as modes of action for berberine’s antibacterial effects. The antitumor properties of berberine have been attributed to DNA binding, and in particular regulating the activity of

One-pot nucleophilic substitution–double click reactions of biazides leading to functionalized bis(1,2,3-triazole) derivatives

• Hans-Ulrich Reissig and
• Fei Yu

Beilstein J. Org. Chem. 2023, 19, 1399–1407, doi:10.3762/bjoc.19.101

• carbohydrate mimetics, but the reductive cleavage of the 1,2-oxazine rings to aminopyran moieties did not proceed cleanly with these compounds. Keywords: alkynes; azides; copper catalysis; nucleophilic substitution; 1,2-oxazines; Introduction The concept of click reactions [1][2], in particular, the

• these results [37][38]. For several years, our group was interested in preparing multivalent carbohydrate mimetics [39][40][41][42][43] on the basis of efficient coupling reactions of aminopyran and aminooxepane derivatives with suitable linker elements. Hence, the aminopyran derivatives A could be

• good yields and furnished another set of multivalent carbohydrate mimetics [48][49][50]. In the current report, we want to disclose our experience with an “inverted” approach to multivalent systems [51]: bicyclic 1,2-oxazine derivatives of type G [52][53], which can be regarded as internally protected

CuAAC-inspired synthesis of 1,2,3-triazole-bridged porphyrin conjugates: an overview

• Dileep Kumar Singh

Beilstein J. Org. Chem. 2023, 19, 349–379, doi:10.3762/bjoc.19.29

• -base analogues 41a,b were also obtained by the treatment with HCl in dioxane. The conjugation of carbohydrate with porphyrin improves the solubility of porphyrin in aqueous medium and also improves the optical and medicinal properties of porphyrins [30]. Considering these properties of glycoporphyrins

• carbohydrate sequences suitable for tumor-binding-associated lectins on the porphyrin periphery. Continuing our work on the functionalization of porphyrin at the meso-position [32][33], we used the CuAAC click protocol to synthesize meso-phenyltriazole-linked porphyrin-coumarin dyads 44–48 in good to excellent

Synthesis, α-mannosidase inhibition studies and molecular modeling of 1,4-imino-ᴅ-lyxitols and their C-5-altered N-arylalkyl derivatives

• Martin Kalník,
• Sergej Šesták,
• Juraj Kóňa,
• Maroš Bella and
• Monika Poláková

Beilstein J. Org. Chem. 2023, 19, 282–293, doi:10.3762/bjoc.19.24

• compounds have been attracting attention due to their broad spectrum of biological activities [6]. A number of synthetic and naturally occurring iminosugars are able to inhibit various enzymes of medicinal interest including glycosidases, glycosyltransferases and many other carbohydrate processing enzymes

Strategies to access the [5-8] bicyclic core encountered in the sesquiterpene, diterpene and sesterterpene series

• Cécile Alleman,
• Charlène Gadais,
• Laurent Legentil and
• François-Hugues Porée

Beilstein J. Org. Chem. 2023, 19, 245–281, doi:10.3762/bjoc.19.23

1,4-Dithianes: attractive C2-building blocks for the synthesis of complex molecular architectures

• Bram Ryckaert,
• Ellen Demeyere,
• Frederick Degroote,
• Hilde Janssens and
• Johan M. Winne

Beilstein J. Org. Chem. 2023, 19, 115–132, doi:10.3762/bjoc.19.12

• -fused dihydrodithiin ring is first hydrodesulfurized and then dehydroxylated in a stereospecific and stereoselective manner [62]. The dihydrodithiin building block 66 thus acts as a synthetic equivalent of an allyl alcohol anion and serves as a versatile synthon for de novo carbohydrate synthesis [63

Preparation of β-cyclodextrin/polysaccharide foams using saponin

• Max Petitjean and
• José Ramón Isasi

Beilstein J. Org. Chem. 2023, 19, 78–88, doi:10.3762/bjoc.19.7

• -cyclodextrin/polysaccharide (CS: chitosan, LBG: locust bean gum) mixtures (right). SEM images of crushed β-c-LBG as a function of the synthesis pathways (see below, Experimental section). Part “45Pow” of Figure 2 was reprinted from [39], Carbohydrate Polymers, vol. 288, by M. Petitjean; N. Lamberto; A. Zornoza

A study of the DIBAL-promoted selective debenzylation of α-cyclodextrin protected with two different benzyl groups

• Naser-Abdul Yousefi,
• Morten L. Zimmermann and
• Mikael Bols

Beilstein J. Org. Chem. 2022, 18, 1553–1559, doi:10.3762/bjoc.18.165

• ; cyclodextrin; debenzylation; 2,4-dichlorobenzyl; selective; Introduction α-Cyclodextrin (1) is a cyclic carbohydrate consisting of six α-1,4-linked ᴅ-glucose molecules (Figure 1). It has a donut-like structure with the glucose residues all aligned with the α-side towards the center of the ring and the polar

Synthesis of C6-modified mannose 1-phosphates and evaluation of derived sugar nucleotides against GDP-mannose dehydrogenase

• Sanaz Ahmadipour,
• Alice J. C. Wahart,
• Jonathan P. Dolan,
• Laura Beswick,
• Chris S. Hawes,
• Robert A. Field and
• Gavin J. Miller

Beilstein J. Org. Chem. 2022, 18, 1379–1384, doi:10.3762/bjoc.18.142

• chronic respiratory infection that infects more than 80% of those affected [1]. PA strains colonising the respiratory tract in CF undergo a phenomenon known as mucoid conversion, a phenotype characterised by the secretion of copious amounts of the carbohydrate exopolysaccharide alginate. The manifestation

New advances in asymmetric organocatalysis

• Radovan Šebesta

Beilstein J. Org. Chem. 2022, 18, 240–242, doi:10.3762/bjoc.18.28

• early to stimulate greater developments. Things started to change in the late 1990s when short-chain peptides [3], carbohydrate-based ketones [4][5], and thioureas [6] were shown to catalyze enantioselective transformations. The real breakthrough came in the year 2000 when two teams independently

Anomeric 1,2,3-triazole-linked sialic acid derivatives show selective inhibition towards a bacterial neuraminidase over a trypanosome trans-sialidase

• Peterson de Andrade,
• Sanaz Ahmadipour and
• Robert A. Field

Beilstein J. Org. Chem. 2022, 18, 208–216, doi:10.3762/bjoc.18.24

• developed to date. The most potent TcTS inhibitors described are non-carbohydrate-based molecules (anthraquinones [14], chalcones and quinolones [15]) with low micromolar activity, whereas sialic acid-based analogues typically show high millimolar inhibitory activity [16], with few exceptions such as a

• inhibition with hydrophobic substituents as observed for the high affinity reported for C-sialoside. Additionally, we limited the substituent flexibility by placing the 1,2,3-triazole ring directly at C-2 as a means to mimic the rigidity of the low micromolar non-carbohydrate-based inhibitors. A similar

Asymmetric organocatalytic Michael addition of cyclopentane-1,2-dione to alkylidene oxindole

• Estelle Silm,
• Ivar Järving and
• Tõnis Kanger

Beilstein J. Org. Chem. 2022, 18, 167–173, doi:10.3762/bjoc.18.18

• in carbohydrate chemistry [15]. Cyclic six-membered 1,2-diketones have been shown to react with benzylidene malononitriles [7][16], β-nitrostyrenes [17] and substituted propionaldehydes [18]. For a while, there were no examples related to cyclopentane-1,2-dione (CPD). In 2004, the first instance of

Total synthesis of the O-antigen repeating unit of Providencia stuartii O49 serotype through linear and one-pot assemblies

• Tanmoy Halder and
• Somnath Yadav

Beilstein J. Org. Chem. 2021, 17, 2915–2921, doi:10.3762/bjoc.17.199

• was then deprotected and N-acetylated to finally afford the desired trisaccharide repeating unit as its α-p-methoxyphenyl glycoside. Keywords: capsular polysaccharide; carbohydrate vaccines; O-antigen; oligosaccharide synthesis; one-pot synthesis; Introduction O-antigens or O-specific

Synthetic strategies toward 1,3-oxathiolane nucleoside analogues

• Umesh P. Aher,
• Dhananjai Srivastava,
• Girij P. Singh and
• Jayashree B. S

Beilstein J. Org. Chem. 2021, 17, 2680–2715, doi:10.3762/bjoc.17.182

• accompanied by coupling nucleobases via N-glycosylation. However, over the last three decades, efforts were made for the synthesis of 1,3-oxathiolane nucleosides by selective N-glycosylation of carbohydrate precursors at C-1, and this approach has emerged as a strong alternative that allows simple

• natural nucleosides with β-ᴅ-configuration in the carbohydrate part. These molecules are known to have a common HIV transcriptase inhibition mechanism, in which cytoplasmic enzymes progressively phosphorylate the analogues to 5'-triphosphates. This then competes with the naturally occurring nucleoside

Advances in mercury(II)-salt-mediated cyclization reactions of unsaturated bonds

• Sumana Mandal,
• Raju D. Chaudhari and
• Goutam Biswas

Beilstein J. Org. Chem. 2021, 17, 2348–2376, doi:10.3762/bjoc.17.153

• was achieved by increasing the reaction time and acidity of the reaction medium, while elevated temperature showed no effect (Scheme 3) [40]. The mercuricyclization was also employed in the field of carbohydrate chemistry for the synthesis of α-ᴅ-C-glycopyranosyl derivatives. The reaction between

• carbohydrate alkene precursor 7 and Hg(OAc)2 proceeds with high stereoselectivity to give the α-ᴅ-C-glycopyranosyl derivative (1,5-trans-isomer) 8 as a single isomer [41]. Treatment of compound 8 with sodium borohydride (NaBH4) under phase transfer conditions (PTC) yields compound 9 as the only product. The

• allyl alcohol. Stepwise synthesis of 2,6-distubstituted dioxane derivatives. Cyclization of carbohydrate alkene precursor. Hg(II)-mediated synthesis of C-glucopyranosyl derivatives. Synthesis of C-glycosyl amino acid derivative using Hg(TFA)2. Hg(OAc)2-mediated synthesis of α-ᴅ-ribose derivative

Progress and challenges in the synthesis of sequence controlled polysaccharides

• Giulio Fittolani,
• Theodore Tyrikos-Ergas,
• Denisa Vargová,
• Manishkumar A. Chaube and
• Martina Delbianco

Beilstein J. Org. Chem. 2021, 17, 1981–2025, doi:10.3762/bjoc.17.129

• geometries were observed with a block wise arrangement of methyl groups. As chemical synthesis offers high flexibility in terms of manipulation, non-carbohydrate moieties can be exploited to guide the geometry of the resulting compounds. β(1–4)-Linked glucose chains were connected parallel via an

• β-linkages are still considered a major challenge in carbohydrate chemistry (Figure 5). While long α-mannosides could be accessed either by chemical synthesis or by polymerization approaches, only relatively short β-mannan analogues could be synthesized to date. In addition, limited enzymatic