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

• . [12] in the context of photoswitchable ligands to the lectin LecA. Staying in the theme of lectin characterization, Lundstrøm et al. study the glycan binding profile of CMA1 originating from melon [13]. A time that sees great opportunities in computational biology also breeds innovative applications

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

• a wide array of glycan-binding proteins (GBP) [17], which have a unique capability to specifically interact with endogenous and/or exogenous glycans [18][19]. Thus, disclosing the molecular basis of protein–glycan interactions has a unique potential to help modulate a myriad of complex biological

• events affecting the health and well-being of living organisms and the natural environment. Being key participants in the molecular dialogue, glycan binding proteins emerge as fascinating and critical components of molecular events that regulate life at its core. Their functions span from the catalysis

• networks (NN), that allows the user to predict protein-glycan binding. Taking a glycan structure as input, this model is able to predict the strength of the interaction based on the relative fluorescence units (RFUs) measured in the Consortium for Functional Glycomics glycan arrays and extrapolating these

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

• garnered attention for their roles as laboratory probes and potential therapeutics. Here, we report the discovery and characterization of Cucumis melo agglutinin (CMA1), a new R-type lectin from melon. Our findings reveal CMA1’s unique glycan-binding profile, mechanistically explained by its 3D structure

• experiments, thermal shift assays, and high-resolution X-ray crystallography not only confirms its classification as a functional R-type lectin but also provides a deep dive into its unique glycan-binding profile and high-resolution 3D structure. Overall, we present a deeply characterized new lectin with a

• around W63 for the N-terminal domain and F273 for the C-terminal domain of CMA1. As binding specificities of melon lectins in general (beyond chitooligosaccharides), and CMA1 in particular, are still unknown, we set out to measure, quantify, and understand the glycan-binding properties of CMA1 in depth

GlycoBioinformatics

• Kiyoko F. Aoki-Kinoshita,
• Frédérique Lisacek,
• Niclas Karlsson,
• Daniel Kolarich and
• Nicolle H. Packer

Beilstein J. Org. Chem. 2021, 17, 2726–2728, doi:10.3762/bjoc.17.184

• tightly connected to mainstream bioinformatics. For example, databases and tools from genomics can be used for gaining information about genes encoding for glycosyltransferases, glycosidases, and glycan-binding proteins (lectins), and search engines initially designed for the detection of

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

• the mammalian body. They play a vital role in a number of physiologic and pathologic conditions. Glycan microarrays allow a plethora of information to be obtained on protein–glycan binding interactions. In this review, we describe the intricacies of the generation of glycan microarray data and the

• structural informatics tools. Keywords: data analysis; glycan binding; glycan microarray; glycomics; informatics; Introduction Glycans represent a major type of biomolecule in all living things, along with DNA, RNA, lipids and proteins [1]. In mammals, glycans commonly occur as post-translational

• , 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

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

• interactions strongly contribute to bacterial adhesion and uptake, and are also associated with the capability of Mtb to survive, replicate, and persist within macrophages [21][22][23][24][25]. Ubiquitous in both eukaryotes and prokaryotes, lectins comprise a subclass of glycan-binding proteins most commonly

• species [12]. The presence of mycobacterial lectins was further supported by Abhinav et al. using in silico genome analysis. A bioinformatics homology-based search of lectin-encoding gene regions in 30 fully or partially sequenced mycobacterial genomes identified 94 potential glycan-binding proteins. The

• observed between different mycobacterial species, as described above [12][74]. While three potential glycan-binding proteins were identified in the Mtb (H37Rv) genome in this study (Table 3) [77], Singh et al., using a different suite of bioinformatic tools, identified eleven, of which nine were annotated

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

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

• single high-affinity interaction with a target macromolecule, glycans’ interactions with glycan-binding proteins (GPB) or lectins are typically low affinity. However high avidity and specificity is achieved through the concerted interactions of multiple ligands with well-defined spatial geometry [5]. The

• 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

The use of glycoinformatics in glycochemistry

• Thomas Lütteke

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

• with glycans from the GlycoMinds Ltd. seed database. Primary data of MS experiments and glycan array screens are also available via the CFG website. If a glycan structure has been detected to be bound by a glycan-binding protein in a CFG glycan array experiment, links to the corresponding protein pages

• major chemical databases would not only make it easier to find specific carbohydrates, but also provide a linkage between biological and chemical information. Databases on glycosyltransferases and glycan binding proteins As an alternative or complement to chemical synthesis it is possible to make use of

• the enzymes that build or degrade the glycan chains in vivo, the glycosyltransferases or glycoside hydrolases, respectively [46][47][48][49]. To plan such experiments, however, detailed knowledge of the substrate-specificity of these enzymes is required. The same applies to glycan-binding proteins

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

• summary, these novel neo-glycoconjugates are interesting tools for extensive binding studies of a variety of glycan binding proteins (lectins, antibodies) and for possible therapeutic applications. Conclusion Novel poly-LacNAc derivatives have been produced on a micro-gram scale, which can be used for

• binding studies with different glycan-binding proteins, for the evaluation of binding mechanisms and biological functions. Our present study gives further insight into the reaction of galactose oxidase with poly-LacNAc substrates and has led to optimised reaction conditions, proving also the chemical

• regulation [62][63]. Binding analysis of different galectins to these novel poly-LacNAc derivatives is currently under investigation. The production of poly-LacNAc chains with one or more modified galactose residues will allow further insight in detailed protein-glycan binding mechanisms. In the past mainly