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

• interface on the Privateer database homepage, carbohydrate-containing PDB entries can easily be found and filtered. Privateer database entries for specific glycosylation types, namely, N-glycosylation, O-glycosylation, S-glycosylation, or C-glycosylation can be filtered quickly and easily. Additional

Synthesis of ether lipids: natural compounds and analogues

• Marco Antônio G. B. Gomes,
• Alicia Bauduin,
• Chloé Le Roux,
• Romain Fouinneteau,
• Wilfried Berthe,
• Mathieu Berchel,
• Hélène Couthon and
• Paul-Alain Jaffrès

Beilstein J. Org. Chem. 2023, 19, 1299–1369, doi:10.3762/bjoc.19.96

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

• anchimeric assistance during glycosylation (Figure 4). However, the O-2 acyl group on the glycosyl acceptor hinders the 3-O-glycosylation sterically and electronically [126]. The decreased nucleophilicity of the C-3 hydroxy acceptor could lead to poor stereoselectivity [127]. This issue becomes even more

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

• configuration at C-6 was deduced as S (the stereochemical descriptor was flipped from R to S due to an O-glycosylation at C-2, see Figure 2C, right). The 9R configuration of 1 was determined by the modified Mosher’s method [23][24][25]. The hydrolysis product of 1 (1a) was esterified with the Mosher reagents

Semiautomated glycoproteomics data analysis workflow for maximized glycopeptide identification and reliable quantification

• Steffen Lippold,
• Arnoud H. de Ru,
• Jan Nouta,
• Peter A. van Veelen,
• Magnus Palmblad,
• Manfred Wuhrer and
• Noortje de Haan

Beilstein J. Org. Chem. 2020, 16, 3038–3051, doi:10.3762/bjoc.16.253

• quantification. Keywords: bioinformatics; cysteine oxidation; glycoproteomics; immunoglobulins; mass spectrometry; Introduction Protein glycosylation mainly occurs in the form of N- and O-glycosylation. N-Glycans are attached to Asn within an amino acid consensus sequence (Asn-Xxx-Ser/Thr, Xxx ≠ Pro) and O

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

• sequence of 20 amino acids (–His-Gly-Val-Thr-Ser-Ala-Pro-Asp-Thr-Arg-Pro-Ala-Pro-Gly-Ser-Thr-Ala-Pro-Pro-Ala–)n, and there are five sites where O-glycosylation may occur (indicated in bold). In cancerous cells, the glycans tend to be truncated or have additional sialylation [14]. For example, in mammary

• conformation of the peptide portion of the antigen and does not bind directly. Previous studies have shown that O-glycosylation may provide increased physical stability [20], rigid conformations for protein stability [21], induce the formation of stiff and extended peptide conformations [22], and may affect

• peptide conformations near the glycosylation site and at distant sites [23]. In glycopeptide enkephalin analogs, the only observed conformational effects due to O-glycosylation were on the residue of attachment and its neighboring residue [24]. While for prion peptides, the O-glycosylation (α-GalNAc) is

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

• hand, the Glycan Modeler allows in silico N-/O-glycosylation for glycan-protein complexes and generates a “most relevant” glycan structure through Glycan Fragment Database (GFDB) [68] search which gives proper orientations relative to the target protein. In the absence of target glycan sequence in GFDB

GlypNirO: An automated workflow for quantitative N- and O-linked glycoproteomic data analysis

• Toan K. Phung,
• Cassandra L. Pegg and
• Benjamin L. Schulz

Beilstein J. Org. Chem. 2020, 16, 2127–2135, doi:10.3762/bjoc.16.180

• statistical workflows. We used GlypNirO to analyse a published plasma glycoproteome dataset and identified changes in site-specific N- and O-glycosylation occupancy and structure associated with hepatocellular carcinoma as putative biomarkers of disease. Keywords: glycoproteomics; mass spectrometry; N

• -glycosylation; O-glycosylation; Python; Introduction Glycosylation is a key post-translational modification critical for protein folding and function in eukaryotes [1][2][3]. Diverse types of glycosylation are known, all involving modification of specific amino acid residues with complex carbohydrate

• across the plasma glycoproteome in HCC. O-Glycoproteome analysis The plasma O-glycoproteome is perhaps somewhat neglected [25], despite the importance of O-glycosylation to diverse aspects of fundamental biology, health, and disease. We therefore investigated all O-glycosylation sites that we were able

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

• effect of the ester groups. In a recently reported gold(III)-mediated reaction Vankar and co-workers disclosed that a AuCl3–phenylacetylene complex promotes the O-glycosylation of armed 1-O-acetyl pyranosides and furanosides [17][27]. The authors also observed that 5 mol % AuCl3 alone promoted the O

• benzoylated glycosyl donors which is usually considered low, could be achieved using a catalytic amount of the mildly Lewis acidic AuBr3 and an excellent azide source, trimethylsilyl azide. Further, we checked the possibility of O-glycosylation and C-glycosylation of peracetylated sugars with 10 mol % AuBr3

• -glycosylation albeit in low yields, thus indicating the possible utility of the oxophilic character of Au(III) towards the acetylated sugars. Among the N-glycosides, anomeric azido glycosides are important intermediates due to various applications in the synthesis of various glycosyl amides [28][29

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

• , the optimized method is also utilized for the regioselective O-glycosylation by using a partially protected acceptor. Keywords: cooperative catalysis; electron-deficient pyridinium salts; O-glycoside; regioselectivity; thiourea; Introduction The glycosidic linkage is the principal bond present in a

• the formation of the glycoside, which indirectly supports that the pyridinium salt is a decisive catalyst for the activation of the glycosyl trichloroacetimidate donor (Table 1, entry 14). Therefore, the optimal reaction conditions for O-glycosylation are the following: the use of 3,5-di

• ) aryl thiourea and (d) a mixture of 2a, 3a (10 mol %) and 4 (10 mol %) in CD2Cl2 at room temperature. Plausible reaction mechanism. Mechanistic hypothesis for work. Synergistic electron-deficient pyridinium salt/aryl thiourea-catalyzed regioselective O-glycosylation. Optimization of reaction conditionsa

Intramolecular glycosylation

• Xiao G. Jia and
• Alexei V. Demchenko

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

• technique to glycosidic bond formation has been hampered by the difficulty in the formation of the palladium π-allyl intermediates and their poor reactivity in the electron-rich glycal systems [120]. To overcome this challenge the Liu group explored the application of palladium π-allyl intermediates to O

• -glycosylation through the use of a picoloyl group to direct palladium binding at the C-3 position [121]. Glycosylation results are indicative of two reaction pathways with differing in the selectivity outcome based on the hard/soft properties of the nucleophiles. In both pathways, the first step involves

Enzymatic synthesis of glycosides: from natural O- and N-glycosides to rare C- and S-glycosides

• Jihen Ati,
• Pierre Lafite and
• Richard Daniellou

Beilstein J. Org. Chem. 2017, 13, 1857–1865, doi:10.3762/bjoc.13.180

• in the enzymatic reaction, several regioselectivities were observed. A mechanistic study in 2013 by Gutmann and Nidetzky demonstrated that C-glycosylation occurred through a direct nucleophilic attack of an acidic carbon, and showed evidence against an O-glycosylation followed by an O-to-C

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

Silyl-protective groups influencing the reactivity and selectivity in glycosylations

• Mikael Bols and
• Christian Marcus Pedersen

Beilstein J. Org. Chem. 2017, 13, 93–105, doi:10.3762/bjoc.13.12

• C-glycosides it has been possible to obtain conformationally derived stereocontrol so that persilylated donors adopting a 1C4 conformation give the β-products. However, for O-glycosylation, this type of selectivity has been difficult to achieve. Some very useful stereoselectivities are obtained with

A selective and mild glycosylation method of natural phenolic alcohols

• Mária Mastihubová and
• Monika Poláková

Beilstein J. Org. Chem. 2016, 12, 524–530, doi:10.3762/bjoc.12.51

• by the reduction of the corresponding acetylated aldehydes or acids. Various stereoselective 1,2-trans-O-glycosylation methods were studied, including the DDQ–iodine or ZnO–ZnCl2 catalyst combination. Among them, ZnO–iodine has been identified as a new glycosylation promoter and successfully applied

• participation is usually exploited in the trans-O-glycosylation of appropriate aglycones. In the course of our synthetic studies, 1,2-trans-glycosylation reactions utilizing per-O-acetyl-D-glucopyranose as a donor were initially investigated. However, the reaction of 6b with per-O-acetylated-D-glucopyranose

Synthesis of D-fructose-derived spirocyclic 2-substituted-2-oxazoline ribosides

• Madhuri Vangala and
• Ganesh P. Shinde

Beilstein J. Org. Chem. 2015, 11, 2289–2296, doi:10.3762/bjoc.11.249

• oxacarbenium-ion intermediate by a nitrile and subsequent intramolecular nucleophilic attack of the vicinal C2 ether or a free hydroxy group [32][33][34]. Such glycooxazolines are exploited for the generation of N-glycan structures [35]. In O-glycosylation reactions, an oxacarbenium-ion intermediate interacts

Carbohydrate PEGylation, an approach to improve pharmacological potency

• M. Eugenia Giorgi,
• Rosalía Agusti and
• Rosa M. de Lederkremer

Beilstein J. Org. Chem. 2014, 10, 1433–1444, doi:10.3762/bjoc.10.147

• is transferred to the glycan by a sialyltransferase. The serine or threonine residues in the O-glycosylation sites serve as acceptors for GalNAc using a convenient GalNAc transferase. This unit can be galactosylated by a galactosyltransferase and both, the monosaccharide and the disaccharide, may be

• chitosan derivative, adapted from [61]. Chitosan/PEG functionalized with a mannose at the distal end, adapted from [62]. Chemoenzymatic method for the preparation of PEG-CMP-SA, adapted from [32][33]. GlycoPEGylation by sequential in vitro, enzyme mediated, O-glycosylation followed by transfer of PEGylated

Synthesis of mucin-type O-glycan probes as aminopropyl glycosides

• David Benito-Alifonso,
• Rachel A. Jones,
• Anh-Tuan Tran,
• Hannah Woodward,
• Nichola Smith and
• M. Carmen Galan

Beilstein J. Org. Chem. 2013, 9, 1867–1872, doi:10.3762/bjoc.9.218

• help us understand the biological and disease implications of these glycosylation patterns at both molecular and functional levels. However, despite the need for functional studies of O-glycosylation patterns, there are comparatively few reported syntheses leading to the basic mucin-type cores [9][10

Short synthesis of the common trisaccharide core of kankanose and kankanoside isolated from Cistanche tubulosa

• Goutam Guchhait and
• Anup Kumar Misra

Beilstein J. Org. Chem. 2013, 9, 705–709, doi:10.3762/bjoc.9.80

• presence of molecular iodine [13] furnished compound 5 in 86% yield. Regioselective 3-O-glycosylation of compound 5 with L-rhamnose derived trichloroacetimidate derivative 3 [11] in the presence of NOBF4 [14] followed by acetylation in the same pot furnished disaccharide derivative 6 in 76% yield. In this

• stereoselective 6-O-glycosylation of compound 7 with D-glucose-derived trichloroacetimidate derivative 4 [12] furnished trisaccharide derivative 8 in 71% yield, which was confirmed by the spectral analysis [signals at δ 4.75 (br s, H-1B), 4.54 (d, J = 8.0 Hz, H-1C), 4.22 (d, J = 8.0 Hz, H-1A) in the 1H NMR and at

Synthetic glycopeptides and glycoproteins with applications in biological research

• Ulrika Westerlind

Beilstein J. Org. Chem. 2012, 8, 804–818, doi:10.3762/bjoc.8.90

• ]. EPO consists of 166 amino-acid residues with four glycosylation sites, one O-glycosylation site positioned at serine 126 and three N-glycosylation sites positioned at aspargines 24, 38 and 83. EPO has been found to contain multiple glycoforms and the efficacy of EPO is heavily dependent on the type