Binding of tryptophan and tryptophan-containing peptides in water by a glucose naphtho crown ether

• Gianpaolo Gallo and
• Bartosz Lewandowski

Beilstein J. Org. Chem. 2025, 21, 541–546, doi:10.3762/bjoc.21.42

• receptors; molecular recognition; monosaccharides; tryptophan; Introduction Tryptophan plays a crucial role in a variety of biological processes [1][2]. For example, it is critical for electron transfer in proteins [3] and is a key component of several membrane proteins as well as short antimicrobial

The effect of neighbouring group participation and possible long range remote group participation in O-glycosylation

• Rituparna Das and
• Balaram Mukhopadhyay

Beilstein J. Org. Chem. 2025, 21, 369–406, doi:10.3762/bjoc.21.27

• repeating units on the exposed cell surface of living organisms portray the combination of monosaccharides bound to each other by covalent glycosidic bonds created by a process known as glycosylation. These repeating units further remain covalently bound to the specific macromolecules in the cell surface

Computational toolbox for the analysis of protein–glycan interactions

• Ferran Nieto-Fabregat,
• Maria Pia Lenza,
• Angela Marseglia,
• Cristina Di Carluccio,
• Antonio Molinaro,
• Alba Silipo and
• Roberta Marchetti

Beilstein J. Org. Chem. 2024, 20, 2084–2107, doi:10.3762/bjoc.20.180

• (Figure 1): 1C4, 4C1 (chair forms) and an additional skew-boat shape (2S0) [9]. The glycosidic torsion angles Φ (H1–C1–Ox–Cx) and Ψ (C1–Ox–Cx–Hx) describe the relative orientation of two connected monosaccharide units; moreover, when dealing with monosaccharides containing an exocyclic hydroxymethyl group

• in bacteria, which are able to use most of the mammalian sugar units to construct their glycoconjugates but, in addition, can also use a wide variety of particular, and potentially endless, monosaccharides that are instead not present in eukaryotes (Figure 2). This huge diversity and complexity

• ], and sugars (GLYCAM_06j) [61]. Notably, as mentioned above, on the GLYCAM-web site, it is possible to easily construct glycans with GLYCAM force field nomenclature; however, it is worth to note that only a few bacterial monosaccharides are available in the GLYCAM-web carbohydrate builder. For most

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

• listing of the constituent monosaccharides (e.g., in the form of H5N4F2S1) might be considered as the most suitable annotation. Finally, and for the years to come, a platform for suggestions, updates and related information can be found at https://www.proglycan.info. Descriptions and depictions of a

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

• to whole monosaccharides), could make CMA1 an interesting candidate for probing synthetically produced glycans with novel substituents. It is of course interesting to speculate about the physiological role of CMA1 in melons, yet this is hard to probe. It is noteworthy, however, that the glycan types

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

• automatically identify and classify vibrational fingerprints of several monosaccharides. We report high performances of the obtained trained algorithm (GlAIcomics), that can be used to discriminate contamination and identify a molecule with a high degree of confidence. It opens the possibility to use artificial

• wavelength-dependent laser-induced fragmentation yield. When the frequency of the laser is resonant with a vibrational mode of the molecule, the molecule absorbs the radiation and accumulates internal energy until fragmentation [13]. In previous works we have demonstrated that the monosaccharides or

• ion trap mass analyzer. The following monosaccharides were analyzed: three stereoisomers of hexosamine of chemical formula C6H13NO5, namely glucosamine (GlcN), galactosamine (GalN), mannosamine (ManN); and N-acetyl glucosamine (GlcNAc, chemical formula C8H15NO6). One typical spectrum of each of the

Linker, loading, and reaction scale influence automated glycan assembly

• Marlene C. S. Dal Colle,
• Manuel G. Ricardo,
• Nives Hribernik,
• José Danglad-Flores,
• Peter H. Seeberger and
• Martina Delbianco

Beilstein J. Org. Chem. 2023, 19, 1015–1020, doi:10.3762/bjoc.19.77

• showed the presence of capped linker (*), capped dimer (†), and Lev-containing dimer (‡). The monosaccharides are represented following the symbol nomenclature for glycans (SNFG). Supporting Information Supporting Information File 120: Experimental procedures and characterization data. Funding We thank

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

• inhibitor:enzyme complexes were analyzed by molecular modeling. Keywords: glycosidase inhibitor; Golgi mannosidase II; iminosugar; inhibition; molecular modeling; Introduction Iminosugars are analogs of monosaccharides in which the endocyclic oxygen atom is replaced with a nitrogen atom [1][2][3][4][5]. These

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

• (Figure 2, dotted line). The C···π (mean plane) distance of 3.60 Å corresponded to an H···π distance of ca. 2.6 Å, consistent with the expected values for similar interactions among aryl-substituted monosaccharides [13][14]. The remaining weak interactions in the extended structure largely consist of

Synthesis of protected precursors of chitin oligosaccharides by electrochemical polyglycosylation of thioglycosides

• Md Azadur Rahman,
• Kana Kuroda,
• Hirofumi Endo,
• Norihiko Sasaki,
• Tomoaki Hamada,
• Hiraku Sakai and
• Toshiki Nokami

Beilstein J. Org. Chem. 2022, 18, 1133–1139, doi:10.3762/bjoc.18.117

• from natural sources or by synthesis via chemical glycosylation [2]. Total syntheses of chitin and chitosan oligosaccharides based on conventional chemical glycosylation of protected monosaccharides as building blocks have already been reported. Convergent synthesis using oligosaccharide building

• process, which involved anodic oxidation at −80 °C and glycosylation at −50 °C. The crude product of the reaction was purified by gel permeation chromatography (GPC), and the monosaccharides 1a–d and oligosaccharides 2a–d (n = 2)–7a–d (n = 7) were isolated. Only thioglycoside 1a (Ar = 4-FC6H4, Eox = 1.70

Terpenoids from Glechoma hederacea var. longituba and their biological activities

• Dong Hyun Kim,
• Song Lim Ham,
• Zahra Khan,
• Sun Yeou Kim,
• Sang Un Choi,
• Chung Sub Kim and
• Kang Ro Lee

Beilstein J. Org. Chem. 2022, 18, 555–566, doi:10.3762/bjoc.18.58

• using GC–MS. Monosaccharides (1, 0.4 mg; 2, 0.3 mg; 3, 0.4 mg; 4, 0.4 mg), obtained by hydrolysis, were dissolved in pyridine (0.5 mL), then ʟ-cysteine methyl ester hydrochloride (2 mg) was added. The reaction mixtures were then stirred at 60 °C for 2 h. After adding 1-trimethylsilylimidazole (0.1 mL

• ), the reaction mixture was allowed to react again at 60 °C for 2 h. The reactant was suspended in distilled H2O (1 mL) and then partitioned with n-hexane (1 mL). The n-hexane soluble layer was analyzed using GC–MS analysis. All monosaccharides were detected at 11.3 min, the same detection time (11.3 min

• : HRESIMS and 1D and 2D NMR data of compounds 1–5, experimental ECD data of 1–3, comparison with standard samples and monosaccharides of 1–5, coordinates of the conformers, cytotoxic activity, NO production, NGF secretion, and cell viability assays. Acknowledgements We are thankful to the Korea Basic

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

• involving the [1 + (1 + 1 = 2)] assembly, followed by a one-pot synthesis involving [1 + 1 + 1] strategy from the corresponding monosaccharides. The one-pot method provided a higher yield of the protected trisaccharide intermediate (73%) compared to the two step synthesis (66%). The protected trisaccharide

• . Structurally, the O-antigens consist of polysaccharide repeating units bearing several different monosaccharides. Due to their importance in regulating the host’s immune system, the bacterial cell surface LPS in general and the O-antigens in particular have been proposed and reported as candidates for vaccine

• acceptor. We also demonstrated a follow-up one-pot synthesis involving a [1 + 1 + 1] strategy using the corresponding appropriately protected monosaccharides, providing the opportunity for rapid access to the desired target molecule. Results and Discussion The retrosynthesis of the target trisaccharide 1

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

• were removed with hydrazine under reflux and the free amino groups were acetylated to obtain the fully N-acetylated COS [255]. Control over the pattern of N-acetylation was for the first time achieved using two monosaccharides bearing an azido (N3) and a N-Phth moieties as precursors of the free and N

• polysaccharides Due to the structural analogies between Rha (both ᴅ and ʟ) and Man, we describe the polysaccharides based on these two units in the same section. From a chemical point of view mannose and rhamnose are ‘double-faced’ monosaccharides, as chemically constructing α-linkage is relatively easy, whereas

• polysaccharide to date (i.e., 151mer). To speed up and simplify the solution phase synthesis of long and well-defined polymannosides, iterative coupling strategies are generally adopted [271][272]. Two monosaccharides are coupled yielding a disaccharide, which is parted and converted to the new donor and

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

• synthesis of unprotected multiply-deoxyfluorinated monosaccharides, including a complete series of mono-, di-, and trifluorinated ᴅ-glucose [15], difluorinated [20] and tetrafluorinated [13] ᴅ-galactose, and 2,3,4-trifluoro analogs of ᴅ-mannose, ᴅ-galactose, ᴅ-allose, ᴅ-talose, and ᴅ-altrose [13][21

Metal-free glycosylation with glycosyl fluorides in liquid SO₂

• Krista Gulbe,
• Jevgeņija Lugiņina,
• Edijs Jansons,
• Artis Kinens and
• Māris Turks

Beilstein J. Org. Chem. 2021, 17, 964–976, doi:10.3762/bjoc.17.78

• - and glucopyranoses in liquid SO2 (Table S7, Supporting Information File 1). Most of these glycosyl donors were not fully consumed at 100 °C and formed a complex mixture of monosaccharides. Finally, in order to make our glycosylation procedure more attractive and more accessible to the synthetic

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 context. In this work, we consider only four monosaccharides and their corresponding letters: Glc (G), Gal (L), Neu5Ac (S) and GalNAc (V). In IUPAC form (see Table 1), we can write the carbohydrate portion of the ganglioside GM1a (Figure 1) as any of the following: Galb1-3GalNAcb1-4[Neu5Aca2-3

• monosaccharides, Ax is the nucleotide-sugar donor, and yB the acceptor substrate. The formation of a single branch along a linear chain is described as decoration, where the pattern is (Equation 2). Here we have assumed that [x]y is a substring of the parent acceptor and is a shorthand for *[x]y*B, the asterisks

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

• -glycans are attached to Ser or Thr. Glycan compositions can range from monosaccharides (e.g., Tn antigen for O-glycans [1]) to large polysaccharides (e.g., N-glycans of recombinant human erythropoietin [2]). The most common building blocks of human protein glycans are hexoses (glucose, galactose, and

• high complexity of glycosylation itself, data analysis is further complicated by interfering background signals from biological matrices and isomeric and near-isobaric ambiguities resulting from combinations of monosaccharides, adducts, amino acids, and amino acid modifications [10][11]. Efforts have

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

• synthesized through the serial addition of monosaccharides to form large polysaccharides. To build computational models of glycan synthesis, the biochemical reactions involved must be defined and described mathematically in a form that can be interpreted by computers [1][2][3]. Several groups have created

• monosaccharides and abbreviates the glycan symbols, thereby simplifying the representation without limiting flexibility. Given its readability and parsability, Linear Code has become a popular choice for representing reaction rules in computational models of glycan synthesis (Table 1). However, with the rise of

• Linear Code adaptations to represent reaction rules, we have seen increasing diversity in the syntax, including branch constraints, duplicate monosaccharides omission, logical operators, etc. Here we critically review reaction rule nomenclature. In doing so, we seek to promote the development of a

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

• that are linked to protein backbones in the input glycoprotein model. For every glycan chain in the model, the algorithm computes a list of all detected monosaccharides that are unique and stores that information internally in memory. Then, the algorithm calculates the unit counts in a glycan chain

• – how many unique monosaccharides are modelled in the glycan chain, the total length of the glycan chain and computes the total number linkages between monosaccharides. After the composition calculations are carried out, the algorithm begins the generation of the notation by printing out the unit counts

• monosaccharides. Finally, the linkage information between monosaccharide pairs are generated by assigning individual monosaccharides a unique letter ID according to their position in the glycan chain. Alongside a unique letter ID, a numerical term is added that describes a carbon position from which the bond 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

• a continuous development and evolution of the description of monosaccharides [2]. Glycans are puzzles to many chemists, and biologists as well as bioinformaticians. This complexity occurs at different levels (which makes it incremental). Amongst the most recognisable “sugars”, glucose is merely one

• of 60+ monosaccharides, all of which are, in truth, pairs of mirror-image enantiomers (ʟ and ᴅ). Moreover, monosaccharides occur as two forms: 5-atom ring (furanose) and 6-atom ring (pyranose). With the occurrence of a statistically rarer “open form,” we obtain at least 6 “correct” representations of

• glucose. And yet, monosaccharides are only the chemical units and the individual building blocks of much more complex molecules; the carbohydrates, also referred to as glycans. The glycan family can be grouped in the following categories: (i) oligosaccharides (comprising two to ten monosaccharides linked

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

• monosaccharides. We define these “glycoblocks” as self-contained 3D units, uniquely identified by the nature of the residues they comprise, their linkages and structural/dynamic features. This alternative description of glycans’ 3D architecture can potentially lead to an easier prediction of sequence-to-structure

• invoked when discussing other biopolymers or complex carbohydrates. In the specific case of glycans, the structural complexity, in terms of the diversity of monosaccharides, the linkages’ stereochemistry and the branched scaffolds, makes the already difficult case even more intricate. Nevertheless, the

• different N-glycoforms can be represented as a combination of spatial self-contained units, named “glycoblocks”, rather than in terms of monosaccharides and linkages. We find that this approach helps our understanding of N-glycans architecture in terms of equilibrium structures and relative populations and

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

• thiosialoside and halide donors. Keywords: acetolysis; acetolysis products; 2,7-anhydrosialic acid; SnCl4; Introduction Sialic acids are the most prevalent monosaccharides that are found at the nonreducing ends of glycans, and they are involved in many biologically important ligand–receptor interactions [1

Chemical synthesis of the pentasaccharide repeating unit of the O-specific polysaccharide from Escherichia coli O132 in the form of its 2-aminoethyl glycoside

• Debasish Pal and
• Balaram Mukhopadhyay

Beilstein J. Org. Chem. 2019, 15, 2563–2568, doi:10.3762/bjoc.15.249

• manipulations on the commercially available monosaccharides and stereoselective chemical glycosylations. The 2-aminoethyl glycoside at the reducing end will facilitate further glycoconjugate formation without hampering the stereochemistry of the anomeric center. We have used similar glycosides in case of other

Indium-mediated C-allylation of melibiose

• Christian Denner,
• Manuel Gintner,
• Hanspeter Kählig and
• Walther Schmid

Beilstein J. Org. Chem. 2019, 15, 2458–2464, doi:10.3762/bjoc.15.238

• established as reliable and efficient approach in carbohydrate chemistry, shown by many examples reported in the literature [8][9][10][11][12]. Thus far, this method has been applied to monosaccharides [13][14]. In this context, the development of diastereoselective and efficient synthetic routes to elongated

• showing that these have only minor effects on the conversion. However, the best results were obtained with a ratio of 4:1 (v/v) ethanol/water (Table 1, entries 2–4). Although activation via sonication proved to be beneficial in our previous studies in the C-allylation of monosaccharides [16], in this case

• monosaccharides. Temperatures up to 65 °C led to elevated reaction rates (Table 1, entries 3, 5 and 6). However, higher temperatures caused concentration phenomena, which derived from the reflux of ethanol leading to precipitation of the starting material, which resulted in a significant decrease of the reaction

Anomeric sugar boronic acid analogues as potential agents for boron neutron capture therapy

• Daniela Imperio,
• Erika Del Grosso,
• Silvia Fallarini,
• Grazia Lombardi and
• Luigi Panza

Beilstein J. Org. Chem. 2019, 15, 1355–1359, doi:10.3762/bjoc.15.135

• or DNA ligands [4][5]. In the frame of a more general research program, we have recently published the synthesis of boronic acids derivatives of monosaccharides in which one of the sugar hydroxy groups is substituted by a boronic acid moiety [6]. A related approach has been described [7] recently