Chemical glycobiology

• Elisa Fadda,
• Rachel Hevey,
• Benjamin Schumann and
• Ulrika Westerlind

Beilstein J. Org. Chem. 2025, 21, 8–9, doi:10.3762/bjoc.21.2

• in the glycosciences. A key aspect is the modelling of protein–glycan interactions. Marcisz et al. study the power of umbrella sampling in distinguishing the interactions between different glycosaminoglycans and their receptors [14]. Nieto-Fabregat et al. provide a detailed overview on computational

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

• mannose (Man) directly binds a tryptophan residue [30]; iv) the covalent attachment to core protein of glycosaminoglycans (GAGs), anchored to a Ser, or at lesser extent to Thr or Asn, forms proteoglycans. GAGs are complex negatively charged polysaccharides composed by disaccharide repeats of GlcNAc or

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

• Experimental section)). In part, this is reminiscent to the LacdiNAc binding specificity of Clitocybe nebularis lectin (CNL; Figure 1a) [27]. An important finding from the ICL array was that CMA1 exhibited robust binding to glycosaminoglycans (GAGs; Figure 2e; Supporting Information File 1, table “imperial

• the keywords ‘terminal’ and ‘exhaustive’, to obtain significantly enriched motifs. *p < 0.05. (d) Common binding motif on the atomic level. Glycan 3D structures for the binding motifs were obtained from the GLYCAM web server [25][26]. (e) Binding of CMA1 to glycosaminoglycans. We grouped chondroitin

Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling

• Mateusz Marcisz,
• Sebastian Anila,
• Margrethe Gaardløs,
• Martin Zacharias and
• Sergey A. Samsonov

Beilstein J. Org. Chem. 2023, 19, 1933–1946, doi:10.3762/bjoc.19.144

• be a potential mechanism of GAG particular sequence recognition by proteins. Keywords: glycosaminoglycan; molecular docking; protein–glycosaminoglycan interaction specificity; RS-REMD; umbrella sampling; Introduction Glycosaminoglycans (GAGs) are long linear periodic anionic polydisperse

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

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

• , glycosaminoglycans, and glycolipids. Thus, multiple glycan changes may accompany oncological transformation. TF–glycogene communities in luminal and basal breast cancer Cytoscape plots were generated for luminal breast cancer (Figure 4a). Here, using the bipartite graph community detection methods [20], we

• core 3 and core 4 glycans can occur during disease, and thus this classification includes core 3-forming B3GNT6 and core 4-forming GCNT3. Other O-glycan core types are rare in nature. 8) Chondroitin sulfate and heparan sulfate initiation: Chondroitin and heparan sulfate glycosaminoglycans all have a

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

• program for sketching, building and 3D structure analysis of glycans and glycoconjugates. The scope of this work is relevant to N- and O-linked glycans, glycolipids, proteoglycans and glycosaminoglycans, lipopolysaccharides, plant, algal and bacterial polysaccharides. Review Methods To facilitate

• manually using the mouse or by importing text input files. The interface provides a list of templates: N- O- glycans, glycosphingolipids, glycosaminoglycans(GAGs). Rows of CFG notations for monosaccharides assist with glycan structure drawing on canvas. The application also supports the glycan symbol

• - and O-linked glycans, GAGs (glycosaminoglycans), glycosphingolipids and milk oligosaccharides. It also contains 68 entries from MonosaccharideDB (http://www.monosaccharidedb.org/) including monosaccharides, modifications (e.g. deoxy) and substituents. The tool provides options to modify a

Tools for generating and analyzing glycan microarray data

• Akul Y. Mehta,
• Jamie Heimburg-Molinaro and
• Richard D. Cummings

Beilstein J. Org. Chem. 2020, 16, 2260–2271, doi:10.3762/bjoc.16.187

• , and could possibly promote cancer [4], and the O-glycan of PSGL-1 which is recognized by P- and L-selectin, which is critical for leukocyte recruitment [5][6]. Other roles of glycans (including glycosaminoglycans/proteoglycans) and glycan binding proteins (GBPs) (including lectins and antibodies) in

Automated high-content imaging for cellular uptake, from the Schmuck cation to the latest cyclic oligochalcogenides

• Rémi Martinent,
• Javier López-Andarias,
• Dimitri Moreau,
• Yangyang Cheng,
• Naomi Sakai and
• Stefan Matile

Beilstein J. Org. Chem. 2020, 16, 2007–2016, doi:10.3762/bjoc.16.167

• attractive candidates for intracellular delivery. Already a small dipeptide 9 with two Schmuck amino acids shows a strong binding (KD = 100 nM) and clustering ability towards heparin due to the strong noncovalent interaction between GCP and sulfate anions, such as glycosaminoglycans (GAGs) in heparin [26

Natural and redesigned wasp venom peptides with selective antitumoral activity

• Marcelo D. T. Torres,
• Gislaine P. Andrade,
• Roseli H. Sato,
• Cibele N. Pedron,
• Tania M. Manieri,
• Giselle Cerchiaro,
• Anderson O. Ribeiro,
• Cesar de la Fuente-Nunez and
• Vani X. Oliveira Jr.

Beilstein J. Org. Chem. 2018, 14, 1693–1703, doi:10.3762/bjoc.14.144

• cancer cells is typically negatively charged due to a higher expression of anionic molecules such as phosphatidylserines, and negatively charged glycoproteins and glycosaminoglycans [22][23]. Here, we devised a strategy to exploit the negatively charged environment of cancer cells by targeting it with

A stereoselective and flexible synthesis to access both enantiomers of N-acetylgalactosamine and peracetylated N-acetylidosamine

• Bettina Riedl and
• Walther Schmid

Beilstein J. Org. Chem. 2018, 14, 856–860, doi:10.3762/bjoc.14.71

• : asymmetric synthesis; carbohydrates; N-acetylgalactosamine; N-acetylidosamine; Introduction N-Acetylgalactosamine (GalNAc, Figure 1) and N-acetylidosamine (IdoNAc) belong to the group of 2-amino-2-deoxysugars, which can be found in a wide range of organisms as building blocks of, e.g., glycosaminoglycans

Preactivation-based chemoselective glycosylations: A powerful strategy for oligosaccharide assembly

• Weizhun Yang,
• Bo Yang,
• Sherif Ramadan and
• Xuefei Huang

Beilstein J. Org. Chem. 2017, 13, 2094–2114, doi:10.3762/bjoc.13.207

• oligosaccharides 123 from fungal cells [68][69], oligomannan containing multiple challenging β-mannosyl linkages 124 [54] (Figure 6), chitotetraose [70], mammalian glycans including complex type bisected N-glycan dodecasaccharide 125 [71], glycosaminoglycans including hyaluronic acid oligosaccharides 126 [72][73

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

• of polysaccharides. Insights into the kinetics of catalytic events observed in the crystalline state are also presented as well as some aspects of structure determination of protein in solution. Keywords: antibodies; carbohydrate binding domains; cellulose; glycosaminoglycans; glycolipids; glycosyl

• . Glycosaminoglycan–protein complexes: As members of the proteoglycan family, glycosaminoglycans (GAGs) are linear polysaccharides, constituted by 40 to 100 repeating disaccharide units, which are usually found to be linked to core proteins. These polysaccharides are components of the peri- and extracellular matrix

• and are present on surfaces or close to surfaces of animal cells. Based on their core repeat disaccharide units, glycosaminoglycans are classified in four groups: the heparin/heparin group; the chondroitin/dermatan sulfate group, the keratin sulfate group, and the hyaluronic group. With the exception

Synthesis and in vitro cytotoxicity of acetylated 3-fluoro, 4-fluoro and 3,4-difluoro analogs of D-glucosamine and D-galactosamine

• Štěpán Horník,
• Lucie Červenková Šťastná,
• Petra Cuřínová,
• Jan Sýkora,
• Kateřina Káňová,
• Roman Hrstka,
• Ivana Císařová,
• Martin Dračínský and
• Jindřich Karban

Beilstein J. Org. Chem. 2016, 12, 750–759, doi:10.3762/bjoc.12.75

• 4-fluoro analogs of D-glucosamines 1–3, D-galactosamine 4, and 6-fluoro-D-galactosamine 9 (Figure 1) acted as metabolic inhibitors of the biosynthesis of cell-surface O- and N-linked glycans (including their lactosamine and sialyl LewisX terminal epitopes) [2][3][10][11], and glycosaminoglycans [3

Automated solid-phase synthesis of oligosaccharides containing sialic acids

• Chian-Hui Lai,
• Heung Sik Hahm,
• Chien-Fu Liang and
• Peter H. Seeberger

Beilstein J. Org. Chem. 2015, 11, 617–621, doi:10.3762/bjoc.11.69

• glycopeptides [6], glycosaminoglycans [7][8][9], and chains as long as 30-mers [10]. Key to automated assembly is the identification of reliable monosaccharide building blocks to construct particular linkages. To date, α-(2,3)- and α-(2,6)-sialylated glycans have been accessible by automation only via

Synthesis of a hexasaccharide partial sequence of hyaluronan for click chemistry and more

• Marina Bantzi,
• Stephan Rigol and
• Athanassios Giannis

Beilstein J. Org. Chem. 2015, 11, 604–607, doi:10.3762/bjoc.11.67

• , monosaccharides, fibrous proteins (collagens), glycosaminoglycans (GAGs), and proteoglycans (PGs). The latter are complex proteins containing at least one covalently bound glycosaminoglycan part [3]. GAGs are long, unbranched polysaccharides comprising repeating disaccharide units, which are constituted of a

Acylsulfonamide safety-catch linker: promise and limitations for solid–phase oligosaccharide synthesis

• Jian Yin,
• Steffen Eller,
• Mayeul Collot and
• Peter H. Seeberger

Beilstein J. Org. Chem. 2012, 8, 2067–2071, doi:10.3762/bjoc.8.232

• cleavage products revealed shortcomings for oligosaccharide synthesis. Keywords: glycosaminoglycans (GAGs); glycosylation; resins; safety-catch linker; solid-phase synthesis; Findings Solid-phase oligosaccharide synthesis [1][2] has been automated [3][4][5] to rapidly assemble complex oligosaccharides

• employed in the successful synthesis of a sialyl LewisX tetrasaccharide [15] and a sialyl Tn antigen [16]. In the search for a linker suitable for the solid-phase synthesis of complex glycosaminoglycans (GAGs) [17][18], we designed a new acylsulfonamide safety-catch linker that combined the advantageous

• linker (Scheme 4). In conclusion, we described a new acylsulfonamide safety-catch linker with an additional Zemplén cleavage site, designed for automated solid-phase synthesis of glycosaminoglycans. With this novel linker, inherent but previously unknown limitations of the safety-catch concept for solid

Dimerization of a cell-penetrating peptide leads to enhanced cellular uptake and drug delivery

• Jan Hoyer,
• Ulrich Schatzschneider,
• Michaela Schulz-Siegmund and
• Ines Neundorf

Beilstein J. Org. Chem. 2012, 8, 1788–1797, doi:10.3762/bjoc.8.204

• the peptides, which is considered to be crucial for initial membrane interaction through binding to negatively charged phospholipids and glycosaminoglycans [6]. Endocytic and non-endocytic processes have been proposed to be involved in cellular uptake; however, the exact mechanism triggering

The use of glycoinformatics in glycochemistry

• Thomas Lütteke

Beilstein J. Org. Chem. 2012, 8, 915–929, doi:10.3762/bjoc.8.104

• input files for AMBER simulations. The list of residues that are available, however, is more limited than in Sweet-2. Sulfated residues, which frequently occur in glycosaminoglycans [101], for example, are only supported by Sweet-2 at the moment. GlycanReader [96] as part of the CHARMM-GUI [102] creates

An easily accessible sulfated saccharide mimetic inhibits in vitro human tumor cell adhesion and angiogenesis of vascular endothelial cells

• Grazia Marano,
• Claas Gronewold,
• Martin Frank,
• Anette Merling,
• Christian Kliem,
• Sandra Sauer,
• Manfred Wiessler,
• Eva Frei and
• Reinhard Schwartz-Albiez

Beilstein J. Org. Chem. 2012, 8, 787–803, doi:10.3762/bjoc.8.89

• saccharides. Glycosaminoglycans (GAG) are long polysaccharide chains containing sulfated saccharides of uronic acids (either iduronic or glucuronic acid) and glucosamine or galactosamine as repetitive disaccharide units. GAGs exist at the cell-surface as well as in the ECM and are attached to proteins [16

Chemo-enzymatic modification of poly-N-acetyllactosamine (LacNAc) oligomers and N,N-diacetyllactosamine (LacDiNAc) based on galactose oxidase treatment

• Christiane E. Kupper,
• Ruben R. Rosencrantz,
• Birgit Henßen,
• Helena Pelantová,
• Stephan Thönes,
• Anna Drozdová,
• Vladimir Křen and
• Lothar Elling

Beilstein J. Org. Chem. 2012, 8, 712–725, doi:10.3762/bjoc.8.80

• of glycoconjugates with hydrazide or hydroxylamine reagents [30][31][32][33][34], coupling with amino-modified glycan moieties [35], chemical oxidation of the carbonyl to a carboxyl group in the synthesis of immunoreactive neo-glycosaminoglycans [12], and the synthesis of deoxysugars [36], have been