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

• are able to recognise carboxylic acid and sulphate groups along glycosaminoglycan chains using clusters of positively charged amino acids [33], also mediate a wide variety of cell–cell and cell–pathogen communication, controlling immune cell functions, and overseeing cellular trafficking [34]. Another

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

• ), which we contrasted with the established R-type lectin Ricinus communis agglutinin 1 (RCA1). We also report binding of specific glycosaminoglycan subtypes and a general enhancement of binding by sulfation. Further validation using agglutination, thermal shift assays, and surface plasmon resonance

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

• of Munich, Garching, Germany 10.3762/bjoc.19.144 Abstract In the past few decades, glycosaminoglycan (GAG) research has been crucial for gaining insights into various physiological, pathological, and therapeutic aspects mediated by the direct interactions between the GAG molecules and diverse

• 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

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

• cancer metastasis [27]. CREB3L4 was found to regulate B4GALT3 glycogene (ρ = 0.56, RP = 0.94), which adds galactose in a β1-4 linkage. PRDM1 was found to regulate B3GNT5, which is critical for lacto/neolacto series of glycolipids (ρ = 0.60, RP = 0.84). MEF2C disproportionately regulates glycosaminoglycan

• directly impacted by TGF-β signaling, and thus increasing the metastatic potential of cancer [28]. MEF2C was found to be inhibited by MECP2 based on Reactome pathway enrichment. Since the glycosaminoglycan elongation pathways positively correlate to MEFC2 expression and MEFC2 is amplified in cancer, it is

• MECP2 regulation were all found to disproportionately regulate sialic acid and GAG synthesis pathways. Several of the TFs enriched to glycosylation pathways were either regulated by or involved in TGF-β signaling and Wnt β-catenin signaling. These TFs primarily affected glycosaminoglycan synthesis

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

• biomedical applications due to their ability to inhibit the glycan and glycosaminoglycan biosynthesis [34][35][36][37]. The fluorine substituent has typically been introduced into these GlcNAc and GalNAc analogues using nucleophilic fluorination. The primary position (C6 hydroxy group) was fluorinated by

Selected peptide-based fluorescent probes for biological applications

• Debabrata Maity

Beilstein J. Org. Chem. 2020, 16, 2971–2982, doi:10.3762/bjoc.16.247

• highly sulfated glycosaminoglycan with the highest negative charge density among known biomacromolecules. It is widely used as both a prophylactic and a therapeutic agent, especially as an anticoagulant in surgery [52][53]. But its overdose causes different adverse effects such as hemorrhages

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

• (MSHA), C-type lectins, and R-type lectins. Furthermore, the filamentous hemagglutinin (FHA) and the heparin-binding hemagglutinin (HBHA) as glycosaminoglycan-binding protein families are also discussed (Table 3, Figure 4). Agglutinin-like sequences Based on bioinformatic analysis, the two Mtb gene

• glycosaminoglycan-binding proteins to date. However, agglutination-inhibition and adhesion assays, genome analyses, and immunological studies have provided the first indications that glycan-binding proteins might be important mediators of TB infections and Mtb pathogenesis. Detection of appendages on the

• modified version of an image originally published by V. Chandrasekaran et al. [76]. Computer-based genome analysis supports the existence of mycobacterial glycan-binding proteins, which can be associated with known lectin and glycosaminoglycan-binding protein families, including agglutinin-like sequences

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

• their strategy to the synthesis of heparin (HP) and heparan sulfate (HS), which are more complex members of the glycosaminoglycan family [40]. A pentasaccharide 48 was chosen as the synthetic target (Figure 2). A major challenge of HP and HS synthesis lies in the coupling of an azido glucoside with a

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

• modifications. Transporters and proteins purely involved in recognition (lectin, antibodies, carbohydrate binding modules, glycosaminoglycan binding proteins) are the other important classes of carbohydrate-binding proteins. Figure 7 shows the evolution of the number of carbohydrate interacting proteins that

• . 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

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

• glycan and glycosaminoglycan biosynthesis [2][3], to inhibit amino sugars processing enzymes [4][5], to probe interactions of amino sugars with their target enzymes and lectins [6][7], or to increase the hydrolytic stability of the glycosidic bond in amino sugar glycosides [8][9]. For example, acetylated

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