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

• development, immunity, and stress signaling [2][3]. In light of the burgeoning interest in the intersection of glycobiology and biomedicine, the characterization of new lectins has carved out a significant niche in scientific research. Specifically, lectins have emerged as invaluable tools for staining cells

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

• and conjugates are important for advancing glycobiology [12][13] and glyco-medicine [14][15]. However, the reliable installation of sialic acid residues in oligosaccharides is a rather difficult issue and poor predictability remains characteristic of the sialylation reaction [16][17][18][19][20][21

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

• were classified using current knowledge of glycobiology. Different classification methods meant to address different glycosylation pathways may result in different TF–glycopathway enrichments [44]. Third, while Cistrome Cancer DB systematically filters TF–gene relationships based on ChIP-Seq and RNA

• Information File 3 (Table S5). A systems glycobiology framework to link multi-OMICs data. a) Cell signaling proceeds to trigger TF activity. The binding of TFs to sites proximal to the TSS triggers glycogene expression. A complex set of reaction pathways then results in the synthesis of various carbohydrate

Fluorine effect in nucleophilic fluorination at C4 of 1,6-anhydro-2,3-dideoxy-2,3-difluoro-β-D-hexopyranose

• Danny Lainé,
• Vincent Denavit,
• Olivier Lessard,
• Laurie Carrier,
• Charles-Émile Fecteau,
• Paul A. Johnson and
• Denis Giguère

Beilstein J. Org. Chem. 2020, 16, 2880–2887, doi:10.3762/bjoc.16.237

• biochemical processes [1]. Therefore, the use of bioisosteres of carbohydrates functional groups is a popular approach in glycobiology [2]. As such, the synthesis of fluorosugars, including polyfluorinated analogues, is an interesting strategy to study biological systems [3][4][5][6][7]. The replacement of OH

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

• . Krambeck Kiyoko F. Aoki-Kinoshita Nathan E. Lewis See end of main text. 10.3762/bjoc.16.215 Abstract Systems glycobiology aims to provide models and analysis tools that account for the biosynthesis, regulation, and interactions with glycoconjugates. To facilitate these methods, there is a need for a

• compliance with FAIR standards. Here, we present Linear Code for Reaction Rules (LiCoRR), version 1.0, an unambiguous representation for describing glycosylation reactions in both literature and code. Keywords: glycoinformatics; linear code; systems glycobiology; Introduction Glycans are predominantly

• representations are not designed to be human-readable or included in the main text of a manuscript confining many design details to the supplement of a publication. As systems glycobiology develops, there is a need to develop a standard nomenclature for unambiguous and readable reaction rules to facilitate

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

• might not necessarily be experts in structural glycobiology. The fact that these glycans could not be matched to standard database entries should be enough to raise the question with depositors, and at the very least write a caveat on a deposited entry where glycans could not be correctly identified

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

• carried out in structural glycobiology, typically using various software. In this perspective article, we outline developments in the computational tools for the sketching, visualisation and modelling of glycans. The article also provides details on the standard representation of glycans, and

• glycobiologists or any researcher looking for a ready to use, simple program for the sketching or building of glycans. Keywords: bioinformatics; carbohydrate; glycan; glycobiology; nomenclature; oligosaccharide; polysaccharide; representation; structure; Introduction Glycoscience is a rapidly surfacing and

• the “Essentials of Glycobiology Symbol Nomenclature”, precursor of the SNFG symbol set [55]. The interface provides a wide choice of monosaccharides and substituents represented in SNFG symbols but lacks the standard colour scheme. The user can easily modify the structure with by click and drag, which

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

• glycobiology. Conclusion Glycan microarray technologies provide a wealth of information for functional glycomics, and in an efficient and decipherable manner. Once the microarrays are fabricated, the experiments can be performed within a few hours and the data analysis can be done in a day. Results from glycan

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

• large cohort glycomic studies, where the comparison of glyco-profiles is important to clinical studies, cellular biology, and glycobiology in general. Experimental Materials Sodium phosphate (Merck) and glycine·HCl (Merck) were purchased from Merck. Tris-HCl and EX-CELL Advanced CHO Fed-batch medium

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

• represents an essential resource to advance glycomics [11][12][13][14][15], while molecular simulations fit in very well as complementary and orthogonal techniques to support and advance structural glycobiology research. Indeed, current high performance computing (HPC) technology allows us to study realistic

• model systems [16][17] and to reach experimental timescales [18], so that computing can now contribute as one of the leading research methods in structural glycobiology. One of the most interesting and remarkably challenging areas in glycoscience research that HPC simulations can address is the study of

Stereo- and regioselective hydroboration of 1-exo-methylene pyranoses: discovery of aryltriazolylmethyl C-galactopyranosides as selective galectin-1 inhibitors

• Alexander Dahlqvist,
• Axel Furevi,
• Niklas Warlin,
• Hakon Leffler and
• Ulf J. Nilsson

Beilstein J. Org. Chem. 2019, 15, 1046–1060, doi:10.3762/bjoc.15.102

• Alexander Dahlqvist Axel Furevi Niklas Warlin Hakon Leffler Ulf J. Nilsson Centre for Analysis and Synthesis, Department of Chemistry, Lund University, Box 124, SE-221 00 LUND, Sweden Division of Microbiology, Immunology and Glycobiology, Lund University, BMC C12, SE-221 84 LUND, Sweden 10.3762

Synthesis of α-D-GalpN₃-(1-3)-D-GalpN₃: α- and 3-O-selectivity using 3,4-diol acceptors

• Emil Glibstrup and
• Christian Marcus Pedersen

Beilstein J. Org. Chem. 2018, 14, 2805–2811, doi:10.3762/bjoc.14.258

• acceptors and donors are made from common building blocks, limiting protective manipulations, and in this context, unavoidable side reactions. Keywords: diastereoselectivity; glycosylation; regioselectivity; Introduction The disaccharide α-D-GalpNAc-(1-3)-β-D-GalpNAc is a widespread motif in glycobiology

• pentasaccharide chain [5][6]. The pioneering work by Paulsen was later followed up by a total synthesis by the Ogawa group [7] and an oligosaccharide synthesis by the Magnusson group [8]. With the increasing understanding of glycobiology, the Forssman antigen has remained an interesting target for vaccine

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

• subject of much debate (Scheme 4B) [21]. The utility of these enzymes is very clear and even extends beyond glycobiology. They are applicable to natural product synthesis as the aglycone of a natural product glycoside can be forged to the saccharide component using either a natural or engineered GT [22

Aqueous semisynthesis of C-glycoside glycamines from agarose

• Juliana C. Cunico Dallagnol,
• Alexandre Orsato,
• Diogo R. B. Ducatti,
• Miguel D. Noseda,
• Maria Eugênia R. Duarte and
• Alan G. Gonçalves

Beilstein J. Org. Chem. 2017, 13, 1222–1229, doi:10.3762/bjoc.13.121

• obtained in the absence of its epimer, epi-8. Moreover, the chemical entities described herein offer opportunities for studies in glycobiology, biomedicinal chemistry and drug design. The use of these compounds as starting material to access new small ligands as GPCR modulators is ongoing in our

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

• molecules and macromolecules that form the collection of substrates investigated by glycoscience. The present review illustrates how synchrotron-based experiments have contributed to our understanding in the field of structural glycobiology. Structural characterization of protein–carbohydrate interactions

• sources. Figure 1 summarizes the differences and the complementarity of the information that can be gathered from analyses performed with the respective sources. The synergistic use of both sources becomes particularly relevant when accurate hydrogen details are necessary. Structural glycobiology gained

• recognition with the elucidation of glycosyl hydrolases mechanism by X-ray crystallography, but the scope of applications in glycobiology is much broader: it encompasses the range of glycan containing (macro)-molecules and their conjugates. The present article reviews the application of synchrotron radiation

DNA display of glycoconjugates to emulate oligomeric interactions of glycans

• Alexandre Novoa and
• Nicolas Winssinger

Beilstein J. Org. Chem. 2015, 11, 707–719, doi:10.3762/bjoc.11.81

• standard technology and customized arrays with 104–106 discrete sequences are readily available. Screening for glycan binding in a microarray format has also proven extremely valuable in glycobiology [46][47]. Based on earlier reports that small molecules [48][49] and protein microarrays [50] can be

Synthesis of carbohydrate-scaffolded thymine glycoconjugates to organize multivalency

• Anna K. Ciuk and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2015, 11, 668–674, doi:10.3762/bjoc.11.75

• on the cell surface that are essential for cell–cell communication [1][2][3][4]. During the last two decades it has become clear that there is not one mechanism underlying multivalency effects in glycobiology, but that there are a multitude of biological processes involving multivalency in one or the

Molecular recognition of surface-immobilized carbohydrates by a synthetic lectin

• Melanie Rauschenberg,
• Eva-Corrina Fritz,
• Christian Schulz,
• Tobias Kaufmann and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2014, 10, 1354–1364, doi:10.3762/bjoc.10.138

• sequencing, automated synthesis and high-throughput microarray screening are lacking in glycobiology [5]. However, during the last decade, these methods have also been adapted to carbohydrates [6][7][8]. Carbohydrate microarrays on chips proved to be a particularly useful tool in glycomics [9][10][11] since

Synthesis of enantiopure sugar-decorated six-armed triptycene derivatives

• Paola Bonaccorsi,
• Maria Luisa Di Gioia,
• Antonella Leggio,
• Lucio Minuti,
• Teresa Papalia,
• Carlo Siciliano,
• Andrea Temperini and
• Anna Barattucci

Beilstein J. Org. Chem. 2013, 9, 2410–2416, doi:10.3762/bjoc.9.278

• higher binding affinities owing to the sum of the individual interactions [5]. The synthesis of sugar-decorated molecular systems represents a significant tool in glycobiology and glycomic research fields [6]. The general prototype of a glycoconjugate comprises a core molecule that serves as an

Synthesis of homo- and heteromultivalent carbohydrate-functionalized oligo(amidoamines) using novel glyco-building blocks

• Felix Wojcik,
• Sinaida Lel,
• Alexander G. O’Brien,
• Peter H. Seeberger and
• Laura Hartmann

Beilstein J. Org. Chem. 2013, 9, 2395–2403, doi:10.3762/bjoc.9.276

• –protein receptor interactions play a key role for many events in glycobiology such as cell–cell or pathogen recognition [1]. Therefore, carbohydrate functionalization of non-natural materials such as polymers or dendrimers allows for bioactive materials that are used to modulate cellular behavior [1][2][3

Glycosylation efficiencies on different solid supports using a hydrogenolysis-labile linker

• Mayeul Collot,
• Steffen Eller,
• Markus Weishaupt and
• Peter H. Seeberger

Beilstein J. Org. Chem. 2013, 9, 97–105, doi:10.3762/bjoc.9.13

• reagents to drive reactions to completion, as any leftovers are easily removed by washing of the resin between reaction steps. Given the repetitive character of solid-supported synthesis, the process was successfully automated for all types of biopolymers [5][6][7]. As glycobiology is rapidly expanding [8

The Amadori rearrangement as glycoconjugation method: Synthesis of non-natural C-glycosyl type glycoconjugates

• Katharina Gallas,
• Gerit Pototschnig,
• Florian Adanitsch,
• Arnold E. Stütz and
• Tanja M. Wrodnigg

Beilstein J. Org. Chem. 2012, 8, 1619–1629, doi:10.3762/bjoc.8.185

• the repertoire of ligation methods, with the advantage that no protecting-group manipulations are necessary in the carbohydrate moiety and the reaction can be carried out in aqueous environment offering obvious advantages in glycobiology. In preliminary studies, several disaccharidic structures, such

Automated synthesis of sialylated oligosaccharides

• Davide Esposito,
• Mattan Hurevich,
• Bastien Castagner,
• Cheng-Chung Wang and
• Peter H. Seeberger

Beilstein J. Org. Chem. 2012, 8, 1601–1609, doi:10.3762/bjoc.8.183

• ; sialosides; Introduction Sialic acid (Sia) belongs to a family of nonulosonic acids, i.e., monosaccharides equipped with a carboxylic moiety and a nine-carbon backbone, which play a unique role in glycobiology. Sia-containing glycans mediate pathogen invasion [1] and are involved in signalling cascades

• antigens in antibody selection by phage-display methods [31]. Thus, trisaccharide 16 (Scheme 7) was reacted with biotin derivative 31 in PBS buffer to afford compound 32 in 80% yield after gel filtration. Conclusion The synthesis of sialosides is important to create tools for glycobiology. The work

The use of glycoinformatics in glycochemistry

• Thomas Lütteke

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

• that it provides information on proteins to which specific glycans were found to be attached, including details on glycosylation sites. The Japan Consortium for Glycobiology and Glycotechnology DataBase (JCGGDB) [34] provides a collection of individual databases that are cross-linked with each other

2-Allylphenyl glycosides as complementary building blocks for oligosaccharide and glycoconjugate synthesis

• Hemali D. Premathilake and
• Alexei V. Demchenko

Beilstein J. Org. Chem. 2012, 8, 597–605, doi:10.3762/bjoc.8.66

• efficient oligosaccharide assembly. Keywords: carbohydrates; glycosylation; leaving group; oligosaccharides; orthogonal strategy; selective activation; Introduction Current knowledge about the key roles of carbohydrates is still limited. However, thanks to the explosive growth of the field of glycobiology