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

• spectra or vials. Therefore, scientists in the huge field of N-glycan research have soon begun to use acronyms. One early adopted system was developed for the antibody field, where basically the number of galactose residues was annotated. In the most fully developed format, the presence of fucose and

• allergy diagnosis community [25]. Our recent working with 40 isomeric N-glycans all composed of 5 hexoses, 4 HexNAcs and 1 fucose [26][27] reinforced our convictions that a simple and logical naming system is required and that the “proglycan” system could meet the demands. In the following chapters

• always the same core. Years later, colleagues from in- and outside my institution engaged in “humanization” of plant N-glycans, which at first entailed removal of the plant-typical residues α1,3-fucose and xylose [32][33]. Later, the glyco-engineering of plants with the introduction of human features

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

• xylopyranose branches, which can be further substituted at the C-2 position by a β-linked galactose or a α-ʟ-fucose unit (Figure 3). XGs are abundant components of the plant cell-wall, where they are believed to interact with cellulose promoting the integrity of the plant wall [95]. However, a recent study

• introduce the fucose residues [110]. Even though the complexity of plant polysaccharides hinders their synthesis, these compounds are highly desirable to dissect the different interactions taking place in the plant cell-wall. Recognition of the branched oligomers by glycosynthases proved to be limited and

• ), β(1–3) or a combination of β(1–4)- and β(1–3)-linked β-ᴅ-xylopyranosyl units. Rarely, α(1–3) glycosidic linkages are present [194]. These backbones are often partially acetylated or appended with sugar side chains, mainly ʟ-arabinose, fucose, galactose and 4-O-methylglucuronic acid [195]. In general

A systems-based framework to computationally describe putative transcription factors and signaling pathways regulating glycan biosynthesis

• Theodore Groth,
• Rudiyanto Gunawan and
• Sriram Neelamegham

Beilstein J. Org. Chem. 2021, 17, 1712–1724, doi:10.3762/bjoc.17.119

• attached. In particular, such extensions may be initiated by members of the B4GALT family or B3GALNT2. Specific variants are noted on α-dystroglycans. 14) O-linked fucose: This pathway includes POFUT1, the enzyme responsible for the addition of fucose to Ser/Thr residues. MFNG, LFNG, and RFNG can attach

• β3GlcNAc to this fucose. 15) Type 1 and 2 LacNAc: These enzymes help construct either Galβ1-3GlcNAc (type 1) or Galβ1-4GlcNAc (type 2) lactosamine chains on antennae of N-linked glycan, O-linked glycans, and glycolipids. Also included are GCNT1–3 that can facilitate formation of I-branches on N-glycans. 16

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

• mannose, Hex/H, 162.0528 Da), N-Acetylhexosamines (N-acetylglucosamine or N-acetylgalactosamine, HexNAc/N, 203.0794 Da), fucose (Fuc/F, 145.0579 Da), and sialic acid (N-acetylneuraminic acid, NeuAc/S, 291.0954 Da). The combinatorial possibilities of these building blocks and the variety of structural

• ]. Peptides with Cys oxidation had a similar elution behavior as the unoxidized isomeric counterparts (with an additional hexose instead of a fucose unit), leading to a high degree of ambiguous, albeit often illogical compositions (e.g.. for the LSL cluster, Figure S16, Supporting Information File 2 and Table

A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR)

• Benjamin P. Kellman,
• Yujie Zhang,
• Emma Logomasini,
• Eric Meinhardt,
• Karla P. Godinez-Macias,
• Austin W. T. Chiang,
• James T. Sorrentino,
• Chenguang Liang,
• Bokan Bao,
• Yusen Zhou,
• Sachiko Akase,
• Isami Sogabe,
• Thukaa Kouka,
• Elizabeth A. Winzeler,
• Iain B. H. Wilson,
• Matthew P. Campbell,
• Sriram Neelamegham,
• Frederick J. Krambeck,
• Kiyoko F. Aoki-Kinoshita and
• Nathan E. Lewis

Beilstein J. Org. Chem. 2020, 16, 2645–2662, doi:10.3762/bjoc.16.215

• facilitate the discovery of any monosaccharide–monosaccharide relation. For example, the fucose-galactose relation can be found in row 1479 of Table S6 (Supporting Information File 1). They differ by one hydroxy group therefore fucose could be represented as “A[6D]”. Similarly, abequose, a dideoxy galactose

Leveraging glycomics data in glycoprotein 3D structure validation with Privateer

• Haroldas Bagdonas,
• Daniel Ungar and
• Jon Agirre

Beilstein J. Org. Chem. 2020, 16, 2523–2533, doi:10.3762/bjoc.16.204

• model by renaming one of the fucose residues from FUL to FUC due to an anomer mismatch between the three letter code and the actual coordinates of the monomer. The new model thus generated the GlyTouCan ID G21290RB, which in turn could be matched to the GlyConnect ID 54. Under further manual review of

• mFo-DFc difference density map, a (1→3)-linked fucose was added, along with additional corrections to the coordinates of the molecule [41]. The newly generated WURCS notation for the model returned a GlyTouCan ID of G63564LA, with a GlyConnect ID of 145. The iterative steps taken to rebuild the

Clustering and curation of electropherograms: an efficient method for analyzing large cohorts of capillary electrophoresis glycomic profiles for bioprocessing operations

• Ian Walsh,
• Matthew S. F. Choo,
• Sim Lyn Chiin,
• Amelia Mak,
• Shi Jie Tay,
• Pauline M. Rudd,
• Yang Yuansheng,
• Andre Choo,
• Ho Ying Swan and
• Terry Nguyen-Khuong

Beilstein J. Org. Chem. 2020, 16, 2087–2099, doi:10.3762/bjoc.16.176

• interesting observations can be concluded from the quantitation including: a) core fucose sialic acid based glycans had increased abundances in bioreactor condition b7, b8, and b9, b) mannosylation was increased in b7 and b9, c) neutral fucosylation decreased for b7 and b9. However, FA1 did not follow this

• trend perhaps because it was co-eluting with A2 and FA2G2S1, d) neutral galactosylation decreased for b7 and b9, e) fucosylated and galactosylated glycans FA2G2, FA2[6]G1, and FA2[3]G1 decreased for b7, b9 and b2. Conversely, the fucose agalactosylation glycan FA2 was increased for the b2 condition

• . Database matched glycans are shown in Oxford linear notation [19]. The CE APTS database hits are marked with a circle and a corresponding error bar showing the GU tolerance. All glycans with core fucose were α-1→6 linkage, galactose were β-1→4 linkage and all sialic acid linkages were α-2→3 linkage. All

How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates

• Carl A. Fogarty,
• Aoife M. Harbison,
• Amy R. Dugdale and
• Elisa Fadda

Beilstein J. Org. Chem. 2020, 16, 2046–2056, doi:10.3762/bjoc.16.171

• relationships in complex carbohydrates, with important implications in glycoengineering design. Keywords: complex carbohydrates; fucose; glycoblocks; molecular dynamics; molecular recognition; N-glycans; xylose; Introduction Complex carbohydrates (or glycans) are an essential class of biomolecules, directly

• ][21][22][23]. More specifically, we investigate how core α(1-3)-linked fucose (Fuc) and β(1-2)-linked xylose (Xyl) affect the structure and dynamics of plants N-glycoforms [23] and of hybrid constructs with mammalian N-glycoforms [24]. At first glance plants protein N-glycosylation [23] is quite

• -3)-Fuc, instead of the α(1-6)-Fuc commonly found in mammalian complex N-glycans. Additionally, the arms can be further functionalised with terminal galactose (Gal) in β(1-3) instead of β(1-4) [23], commonly found in vertebrates, which forces the addition of fucose in the α(1-4) position of the

Convenient synthesis of the pentasaccharide repeating unit corresponding to the cell wall O-antigen of Escherichia albertii O4

• Tapasi Manna,
• Arin Gucchait and
• Anup Kumar Misra

Beilstein J. Org. Chem. 2020, 16, 106–110, doi:10.3762/bjoc.16.12

• . albertii O4 strain [11], which is a pentasaccharide comprising of α-linked ᴅ-galactosamine, β-linked ᴅ-glucosamine, β-linked ᴅ-galactose, α-linked ʟ-fucose and α-linked ʟ-rhamnose moieties. In the recent past, several vaccine candidates have been developed to control bacterial infections by conjugating

• %, Scheme 3). It was decided to follow a sequential glycosylation strategy to achieve a significant quantity of compound 11. Accordingly, a stereoselective glycosylation was carried out using compound 9 with ʟ-fucose thioglycoside derivative 6 in the presence of a combination [26][27] of NIS and HClO4/SiO2

SnCl₄-catalyzed solvent-free acetolysis of 2,7-anhydrosialic acid derivatives

• Kesatebrhan Haile Asressu and
• Cheng-Chung Wang

Beilstein J. Org. Chem. 2019, 15, 2990–2999, doi:10.3762/bjoc.15.295

• (Scheme 5). However, the desired acetolysis products 30, 34, and 38 were not obtained. Replacing the more reactive fucose moiety and the benzylidene acetal ring of 29, i.e., using the less reactive complement 33, was also unsuccessful. The branched fucose, benzylidene, and isopropylidene rings of the

• disaccharides were cleaved and acetylated, as shown in Scheme 5. The difficulty of these reactions might have been attributed to the more liable nature of the tertiary acetal center C-1 of fucose as compared to the sterically hindered quaternary ketal functionality C-2 of the 2,7-anhydro skeleton. To our

• disappointment, an attempted acetolysis upon changing the fucose-containing disaccharides 29 and 33 with substrate 37 did not provide the desired ring-opening product 38 albeit it bore a robust N-5/O-4-oxazolidinone-based sialyl group (Scheme 5). Furthermore, 8,9-di-O-acetylated disaccharide 39 was subjected to

Lectins of Mycobacterium tuberculosis – rarely studied proteins

• Katharina Kolbe,
• Sri Kumar Veleti,
• Norbert Reiling and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2019, 15, 1–15, doi:10.3762/bjoc.15.1

• products of Rv1753 and Rv2082 were reported to have 27% and 25% amino acid sequence similarity to the ALS1 gene from Candida albicans, which encodes the candida adhesin [78]. This lectin is cell surface-localized and mediates adherence of the fungus to endothelial and epithelial cells [86][87]. Fucose

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

• conjugates in the minor groove by marinating a stable hairpin structure [96]. The authors tethered various monosaccharides such as β-xylose, α-xylose, β-galactose, β-glucose and β-L-fucose to a minor groove binding residue, Py-γ-Py-Ind, structurally analogous to distamycin and netropsin. A new set of novel

What contributes to an effective mannose recognition domain?

• Christoph P. Sager,
• Deniz Eriş,
• Martin Smieško,
• Rachel Hevey and
• Beat Ernst

Beilstein J. Org. Chem. 2017, 13, 2584–2595, doi:10.3762/bjoc.13.255

• -mannopyranoside (2) [40][41][42][43][44]. In contrast, the receptors G and H of bacterial origin show affinities in the micromolar range (71 and 2.8 µM, respectively) for methyl α-D-mannose (2) [31][45]. Despite the 71 µM affinity, LecB (G) preferably binds L-fucose (3 µM) and methyl α-L-fucoside (0.4 µM) [45

Glycoscience@Synchrotron: Synchrotron radiation applied to structural glycoscience

• Serge Pérez and
• Daniele de Sanctis

Beilstein J. Org. Chem. 2017, 13, 1145–1167, doi:10.3762/bjoc.13.114

• is a fucose-binding lectin having similarity with tumour necrosis factor. The structure of the other domain (C-terminal part) which belongs to the superfamily of calcium-dependent lectins displays specificity for mannose and L-glycero-D-manno-heptose monosaccharides. The two domains are linked by a

• electron microscopy). Figure 15 displays the reconstruction of the full macromolecular complex as a flexible arrangement of three mannose/heptose-specific dimers flanked by two fucose-specific TNF-α-like trimers [48]. This study (along with many other examples) highlights the potential of SAXS to decipher

Glyco-gold nanoparticles: synthesis and applications

• Federica Compostella,
• Olimpia Pitirollo,
• Alessandro Silvestri and
• Laura Polito

Beilstein J. Org. Chem. 2017, 13, 1008–1021, doi:10.3762/bjoc.13.100

• -SIGN targeting through GAuNPs has also been exploited differently in a study on GAuNPs functionalized with α-fucosylamide, an efficacious synthetic DC-SIGN ligand, analogue of the natural fucose-containing Lewisx trisaccharide [98]. This paper shows that GAuNPs bearing 50% of fucosylamide are able to

Total synthesis of a Streptococcus pneumoniae serotype 12F CPS repeating unit hexasaccharide

• Peter H. Seeberger,
• Claney L. Pereira and
• Subramanian Govindan

Beilstein J. Org. Chem. 2017, 13, 164–173, doi:10.3762/bjoc.13.19

• the C3 O-acetate to yield building block 26 (Scheme 5). Fucosazide building block 8 was derived from diacetyl fucal 27 that in turn was prepared in two steps from L-fucose [30]. Azido-selenation of 27 and hydrolysis of the seleno fucosazide with NIS in aqueos THF [31] provided hemiacetal 28, which was

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

• protective groups on the donor a TES-protected trichloroacetimidate of fucose, 4, was employed by Myers et al. [7] in order to have protective groups compatible with their synthesis of neocarzinostatin. It was found that optimal glycosylation was performed with TMSOTf as a catalyst at low temperature and

• excess donor in diethyl ether since this gave the best α-selectivity (Scheme 2). Using other protective groups on the fucose part, such as 2,3-TIPDS and 4-O-TES led to glycosylation with only poor stereoselectivity [8]. The TES groups were also used successfully on the 2-methylamino analogue of 4. A

O-Alkylated heavy atom carbohydrate probes for protein X-ray crystallography: Studies towards the synthesis of methyl 2-O-methyl-L-selenofucopyranoside

• Roman Sommer,
• Dirk Hauck,
• Annabelle Varrot,
• Anne Imberty,
• Markus Künzler and
• Alexander Titz

Beilstein J. Org. Chem. 2016, 12, 2828–2833, doi:10.3762/bjoc.12.282

• revision and further optimization due to the intrinsic lability of alkyl selenoglycosides, in particular for the labile fucose. Here, we describe a successful synthetic access to methyl 2-O-methyl-L-selenofucopyranoside in 9 linear steps and 26% overall yield starting from allyl L-fucopyranoside. Keywords

• : carbohydrate chemistry; fucose; lectin; selenoglycoside; Introduction Since the discovery of seleno mercaptan by Siemens in 1847 [1], organoselenium compounds have attracted high attention. Besides their biological and pharmaceutical relevance, e.g., selenocysteine or ebselen [2][3][4][5], selenium-containing

• glycans in pathogens or parasites, numerous other lectins recognize such O-alkylated ligands, e.g., the pilus adhesin from Pseudomonas aeruginosa PAK [31] or PapG from Escherichia coli [32]. In contrast, methylation of lectin ligands can also prevent binding, as observed with O-methylated fucose and

Interactions between cyclodextrins and cellular components: Towards greener medical applications?

• Loïc Leclercq

Beilstein J. Org. Chem. 2016, 12, 2644–2662, doi:10.3762/bjoc.12.261

• -mannose, D- and L-fucose, and methyl α-D-fucopyranoside) were not complexed (binding constants ≈ “0” M−1). These binding constants can be directly correlated to the hydrophobicity of the sugar. Nevertheless, the H-bonds between the hydroxy groups of bound sugar and the OH groups of β-CD are also extremely

Elucidation of a masked repeating structure of the O-specific polysaccharide of the halotolerant soil bacteria Azospirillum halopraeferens Au4

• Elena N. Sigida,
• Yuliya P. Fedonenko,
• Alexander S. Shashkov,
• Nikolay P. Arbatsky,
• Evelina L. Zdorovenko,
• Svetlana A. Konnova,
• Vladimir V. Ignatov and
• Yuriy A. Knirel

Beilstein J. Org. Chem. 2016, 12, 636–642, doi:10.3762/bjoc.12.62

• carbohydrate and glycolipid parts [15] followed by fractionation of the released water-soluble carbohydrate portion by Sephadex G-50 Superfine size-exclusion chromatography. It was demonstrated that the OPS contained 2-O-methyl-6-deoxyhexose, L-rhamnose (Rha), D-fucose (Fuc), D-xylose (Xyl), and D-glucose (Glc

Self and directed assembly: people and molecules

• Tony D. James

Beilstein J. Org. Chem. 2016, 12, 391–405, doi:10.3762/bjoc.12.42

• the same colour changes for D- and L-fucose). On observing these amazing colour changes of the “green” liquid crystal system [13], we realised that the obvious place to publish the work was “Chem. Commun.” [14] (given that the green was a similar colour of the cover [15] of the Journal at that time

Expeditive synthesis of trithiotriazine-cored glycoclusters and inhibition of Pseudomonas aeruginosa biofilm formation

• Meriem Smadhi,
• Sophie de Bentzmann,
• Anne Imberty,
• Marc Gingras,
• Raoudha Abderrahim and
• Peter G. Goekjian

Beilstein J. Org. Chem. 2014, 10, 1981–1990, doi:10.3762/bjoc.10.206

• glycoclusters based on a triazine core bearing D-galactose and L-fucose epitopes are able to inhibit biofilm formation by Pseudomonas aeruginosa. These multivalent ligands are simple to synthesize, are highly soluble, and can be either homofunctional or heterofunctional. The galactose-decorated cluster shows

• promoting its dissolution is thus particularly appealing. Because the formation of PA biofilm is a complex process partly mediated by the D-galactose-specific lectin lecA (PA-IL) [7][8][9][10] and the L-fucose-specific lectin lecB (PA-IIL) [11][12][13], lectin-carbohydrate interactions can provide a new

• unprotected azidosugars were obtained by straightforward deprotection of the corresponding acetyl-protected azides [38]. The trivalent glycoclusters decorated with D-galactose, 1, D-glucose, 13, and L-fucose, 14, epitopes were thus obtained directly in 53%, 50%, and 44% yields, respectively, after reversed

Bifunctional dendrons for multiple carbohydrate presentation via carbonyl chemistry

• Davide Bini,
• Francesco Nicotra and
• Laura Cipolla

Beilstein J. Org. Chem. 2014, 10, 1686–1691, doi:10.3762/bjoc.10.177

• carbonyl groups can be exploited for carbohydrate functionalization [15][16] by reductive amination, oxime or hydrazone formation to yield suitably functionalized saccharides (Figure 1). Given the relevance of L-fucose in mammal oligosaccharides, α-L-(2-aminoethyl) fucoside [17] and α-O-L

• reactions with levulinic acid (15). Building blocks 13 and 14 were synthesized starting from bis-(hydroxymethyl)propionic acid (bis-MPA) and bromo-1-pentene [11] in one and four steps, respectively. L-Fucose derivatives synthesis α-L-(2-Aminoethyl) fucopyranoside (4) and α-O-L-fucopyranosyloxyamine (5) were

• synthesized from commercial L-fucopyranose in 4 and 5 steps, respectively, as already reported by Flitsch and co-workers [17] and Dumy and co-workers [18]. Dendron conjugation to L-fucose by reductive amination α-L-(2-Aminoethyl) fucopyranoside (4) was conjugated first to G0 dendron 1 by reductive amination

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

• units of mannose, fucose or lactose, have been incorporated into the surface of PEGylated dendritic polymers by means of click chemistry. The larger dendrimer generations have demonstrated an increased capacity to aggregate lectins [47]. Analogs of lactose have been reported as inhibitors of the enzyme

Human dendritic cell activation induced by a permannosylated dendron containing an antigenic GM₃-lactone mimetic

• Renato Ribeiro-Viana,
• Elena Bonechi,
• Javier Rojo,
• Clara Ballerini,
• Giuseppina Comito,
• Barbara Richichi and
• Cristina Nativi

Beilstein J. Org. Chem. 2014, 10, 1317–1324, doi:10.3762/bjoc.10.133

• , dendritic cell-specific ICAM-3 grabbing non-integrin (DC-SIGN), which belongs to the class of CLRs, is expressed mainly on the surface of immature DCs and plays a crucial role in the uptake of specific pathogens. DC-SIGN is able to bind in a Ca2+-dependent manner mannose and fucose residues on highly