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

• , usually proteins or lipids by the process of glycosylation producing glycoproteins or glycolipids, respectively. Nature executes these processes by enzymatic pathways [18] and is often flawless in its desired output. But the scarcity and the cumbersome purification of natural enzymes limit the use of

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

• constituting glycoproteins or glycolipids, respectively. Recently, glycan structures exposed on the cellular membrane have also been found to be associated with tRNA [2]. In other species, such as prokaryotes, plants or fungi, glycoconjugates comprise the cell wall, playing critical metabolic, structural and

• python framework that allows users to prepare carbohydrate structures for atomistic simulations of complex glycoproteins, glycolipids and carbohydrate polymers in the GROMACS force field format (see below). Polysaccharides can be prepared by using the prepreader.py tool, glycoproteins and glycolipids by

Synthesis of ether lipids: natural compounds and analogues

• Marco Antônio G. B. Gomes,
• Alicia Bauduin,
• Chloé Le Roux,
• Romain Fouinneteau,
• Wilfried Berthe,
• Mathieu Berchel,
• Hélène Couthon and
• Paul-Alain Jaffrès

Beilstein J. Org. Chem. 2023, 19, 1299–1369, doi:10.3762/bjoc.19.96

• compounds. Keywords: amphiphiles; edelfosine; GAEL; glycerol lipids; glycolipids; ohmline; plasmalogen; Introduction Ether lipids (ELs) are natural compounds that feature a glycerol unit linked with an ether function to an alkyl (alkyl acyl ether lipid) or alkenyl (plasmalogen) lipid chain. For the

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

• 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

• β3GlcNAc to this fucose. 15) Type 1 and 2 LacNAc: These enzymes help construct either Galβ1-3GlcNAc (type 1) or Galβ1-4GlcNAc (type 2) lactosamine chains on antennae of N-linked glycan, O-linked glycans, and glycolipids. Also included are GCNT1–3 that can facilitate formation of I-branches on N-glycans. 16

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

• those of the central nervous system, where they function in intercellular recognition and communication. We describe an in silico method for determining the metabolic pathways leading to the most common gangliosides, based on the known enzymes of their biosynthesis. A network of 41 glycolipids 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

• together either linearly or branched); (ii) polysaccharides (for glycan chains composed of more than ten monosaccharides); (iii) glycoconjugates (where the glycan chains are covalently linked to proteins (glycoproteins), lipids (glycolipids). The complexity of glycans is a consequence of their branched

• 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

• for preparing carbohydrate structures for atomistic simulations of glycoproteins, carbohydrate polymers and glycolipids using GROMACS [70][71] In the form of Python scripts; the tools are used to prepare the system, which generally includes the processing of a.pdb file using the pdb2gmx tool

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

• modifications of proteins (glycoproteins), but they are also linked to lipids (glycolipids) and occur as free molecules. Such glycomolecules have vital roles in a wide range of physiological functions and also participate in many pathologic conditions [2]. Some classic examples of important glycans include the

Synthesis of monophosphorylated lipid A precursors using 2-naphthylmethyl ether as a protecting group

• Jundi Xue,
• Ziyi Han,
• Gen Li,
• Khalisha A. Emmanuel,
• Cynthia L. McManus,
• Qiang Sui,
• Dongmian Ge,
• Qi Gao and
• Li Cai

Beilstein J. Org. Chem. 2020, 16, 1955–1962, doi:10.3762/bjoc.16.162

• ; lipid X; lipopolysaccharide; 2-naphthylmethyl ether; synthesis; Introduction Bacterial cell surfaces are decorated with various types of glycoconjugates (in the form of glycoproteins and glycolipids) that are known to participate in many biological processes, especially in the interactions between

Synthesis, docking study and biological evaluation of ᴅ-fructofuranosyl and ᴅ-tagatofuranosyl sulfones as potential inhibitors of the mycobacterial galactan synthesis targeting the galactofuranosyltransferase GlfT2

• Marek Baráth,
• Jana Jakubčinová,
• Zuzana Konyariková,
• Stanislav Kozmon,
• Katarína Mikušová and
• Maroš Bella

Beilstein J. Org. Chem. 2020, 16, 1853–1862, doi:10.3762/bjoc.16.152

• , control; GL3–5, glycolipids 3–5. GL3 and GL4 are products of GlfT1, GL5 is produced by GlfT2. TLC analysis of the dose effects of the compounds 1bα and 3a on production of lower lipid-linked galactan precursors. CON, control; GL3–GL5, glycolipids 3–5. GL3 and GL4 are the products of GlfT1, GL5 is produced

Towards the preparation of synthetic outer membrane vesicle models with micromolar affinity to wheat germ agglutinin using a dialkyl thioglycoside

• Dimitri Fayolle,
• Nathalie Berthet,
• Bastien Doumeche,
• Olivier Renaudet,
• Peter Strazewski and
• Michele Fiore

Beilstein J. Org. Chem. 2019, 15, 937–946, doi:10.3762/bjoc.15.90

• vesicles, alone or in mixture with phospholipids, mimicking bacterial outer membrane vesicles (OMV) with potential antiadhesive properties. Keywords: glycolipids; outer membrane vesicles; synthetic vaccines; Introduction Outer membrane vesicles (OMV) [1], lipid bilayer vesicles released from the outer

• -negative bacteria [7] are challenges for the current research in the field. Artificial OMV, composed of synthetic and non-toxic, non-immunogenic phospholipids and glycolipids are good candidates for drug or vaccine delivery. One of the most common reactions used to prepare monoalkyl glycosides is the

• glycosides cannot be carried out with unprotected thio-glycosides, implying orthogonal protection and deprotection steps in order to obtain unprotected glycolipids. We decided to investigate the formation of artificial OMV composed of long chain alkyl thioglycosides synthesized by the photoinduced radical

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

• the fast growing non-pathogenic species Mycobacterium smegmatis (M. smegmatis) contains inositol phosphate-capped LAM (PILAM) [54]. In addition to lipoglycans, various free, noncovalently associated glycolipids are present in the mycobacterial cell wall, such as the mycolic acid diester trehalose 6,6

• . It functions as an adhesin, where it recognizes and binds to sulfated glycolipids on epithelial host–cell surfaces. The ability of the bacteria to attach to and infect the epithelium of the upper respiratory tract is essential in the pathogenesis of the pertussis organism, underlining the crucial

• main carbohydrates of the Mtb cell envelope, a multi-layered structure composed of a mycolyl–arabinogalactan (AG)–peptidoglycan (PG) complex, the lipoglycans lipomannan (LM), and mannosylated lipoarabinomannan (ManLAM), as well as glycolipids, such as trehalose 6,6'-dimycolate (TDM) and trehalose 6

Aminosugar-based immunomodulator lipid A: synthetic approaches

• Alla Zamyatina

Beilstein J. Org. Chem. 2018, 14, 25–53, doi:10.3762/bjoc.14.3

• double glycosyl phosphodiesters. Keywords: glycoconjugate; glycolipids; glycosylation; immunomodulation; lipopolysaccharide; TLR4; Introduction The mammalian innate immune system possesses an efficient and incredibly complex evolutionary ancient machinery responsible for host defence against pathogens

Remarkable functions of sn-3 hydroxy and phosphocholine groups in 1,2-diacyl-sn-glycerolipids to induce clockwise (+)-helicity around the 1,2-diacyl moiety: Evidence from conformation analysis by ¹H NMR spectroscopy

• Yoshihiro Nishida,
• Mengfei Yuan,
• Kazuo Fukuda,
• Kaito Fujisawa,
• Hirofumi Dohi and
• Hirotaka Uzawa

Beilstein J. Org. Chem. 2017, 13, 1999–2009, doi:10.3762/bjoc.13.196

• –4). The helical conformational properties of these α-glycolipids are determined by Equation 2 applying the 1H NMR data reported in a preceding paper [16]. The results of the 1H NMR analyses are compared with those calculated by Equation 4. Entries 1–4 (Table 4) indicate that Equation 4 can reproduce

• also the helical conformational properties of these α-glycolipids. Conclusion In this study, a 1H NMR spectroscopy analysis of 1,2-dipalmitoyl-sn-glycerols 1–4 in the solution state was carried out to elucidate their helical conformational properties around the 1,2-diacyl moiety. In addition, the

2-Methyl-2,4-pentanediol (MPD) boosts as detergent-substitute the performance of ß-barrel hybrid catalyst for phenylacetylene polymerization

• Julia Kinzel,
• Daniel F. Sauer,
• Marco Bocola,
• Marcus Arlt,
• Tayebeh Mirzaei Garakani,
• Andreas Thiel,
• Klaus Beckerle,
• Tino Polen,
• Jun Okuda and
• Ulrich Schwaneberg

Beilstein J. Org. Chem. 2017, 13, 1498–1506, doi:10.3762/bjoc.13.148

• molecules start to cluster around the hydrophobic transmembrane region. Membrane proteins are normally stabilized by incorporation in a protecting membrane layer formed by ionic detergent molecules such as lipids, SDS or nonionic glycolipids. In contrast, in MD simulations with the two highest

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 the families of most glycan-interacting proteins (including glycosyl transferases and hydrolases, lectins, antibodies and GAG-binding proteins) are presented. Examples concerned with glycolipids and colloids are also covered as well as some dealing with the structures and multiscale architectures

• 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

• to some key areas of glycoscience potentially of interest to the growing number of non-specialist users. Structural characterization of protein–carbohydrate interactions are covered as well as some involving glycolipids and colloids and the structure and architecture of polysaccharides. Insights into

An eco-compatible strategy for the diversity-oriented synthesis of macrocycles exploiting carbohydrate-derived building blocks

• Sushil K. Maurya and
• Rohit Rana

Beilstein J. Org. Chem. 2017, 13, 1106–1118, doi:10.3762/bjoc.13.110

• , macrocyclic glycolipids have shown phosphatase inhibition, cytotoxicity and antiviral activities [12][14]. Generally, the synthesis of these molecules involves a multi-step construction of linear precursors incorporating synthetically compatible functional groups followed by a cyclization in the late stage of

• ] glycosides and macrocyclic glycolipids [11]. Similarly, the copper-catalyzed azide–alkyne cycloaddition (CuAAC) reaction has found wide application in medicinal chemistry [33], biology [34][35], polymer chemistry [36], carbohydrates [37][38][39][40], peptides [41][42][43][44] and in materials science [45][46

Lipids: fatty acids and derivatives, polyketides and isoprenoids

• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2017, 13, 793–794, doi:10.3762/bjoc.13.78

• , sphingolipids and glycolipids. Lipids also constitute important post-translational protein modifications in lipoproteins. The amphiphilic nature of compounds such as phospholipids with a polar headgroup and a long apolar chain results in the spontaneous formation of lipid bilayers in aqueous environments. This

Silyl-protective groups influencing the reactivity and selectivity in glycosylations

• Mikael Bols and
• Christian Marcus Pedersen

Beilstein J. Org. Chem. 2017, 13, 93–105, doi:10.3762/bjoc.13.12

• 2-phthalimido, N-Troc or N-Ac group. It was suggested that the bulky DTBS group is shielding the β-face and thereby preventing attack from that face of the oxocarbenium ion. This methodology has been applied to the synthesis of glycolipids and was shown to also work with 2-O-benzyl [56] or 2-O-TBS

O-Alkylated heavy atom carbohydrate probes for protein X-ray crystallography: Studies towards the synthesis of methyl 2-O-methyl-L-selenofucopyranoside

• Roman Sommer,
• Dirk Hauck,
• Annabelle Varrot,
• Anne Imberty,
• Markus Künzler and
• Alexander Titz

Beilstein J. Org. Chem. 2016, 12, 2828–2833, doi:10.3762/bjoc.12.282

• fucosides are generally α-linked across all kingdoms of life, in glycoproteins, glycolipids, bacterial lipopolysaccharides, or low-molecular weight glycoconjugates such as glycosylated natural products. β-Linked fucosides are rarely observed, for example in the bacterial polysaccharide colanic acid [39][40

Benzothiadiazole oligoene fatty acids: fluorescent dyes with large Stokes shifts

• Lukas J. Patalag and
• Daniel B. Werz

Beilstein J. Org. Chem. 2016, 12, 2739–2747, doi:10.3762/bjoc.12.270

• sufficient to understand membrane dynamics and function. Often membrane domains are formed in which certain lipids, glycolipids or proteins are enriched [2][3][4]. Such domains – also called lipid rafts – do not only differ in their chemical composition, but also show different physical properties (e.g

• as the carbohydrate part of glycolipids [7][8]. A further alternative is to render the lipid and especially the fatty acid part fluorescently active by the introduction of fluorescent moieties (Figure 1). Prominent examples in this area are NBD- (nitrobenzoxadiazole) [9][10], BODIPY- (boron

Interactions between cyclodextrins and cellular components: Towards greener medical applications?

• Loïc Leclercq

Beilstein J. Org. Chem. 2016, 12, 2644–2662, doi:10.3762/bjoc.12.261

• view, they can be divided into eight categories: fatty acids (and their derivatives: mono-, di- and triglycerides and phospholipids), acylglycerols, phosphoglycerides, sphingolipids, glycolipids and polyketides, which result from the condensation of ketoacyl groups, sterols (e.g., cholesterol) and

• stomatocytes, while DM-β-CD leads to echinocytes. This difference is ascribed to the cavity size of the CDs and their ability to extract either sphingomyelin and/or cholesterol of lipid rafts. Lipid rafts are constituted of cholesterol, glycolipids, and sphingomyelin. Nevertheless, their structures have

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

• glycoproteins, glycolipids and proteoglycans. As such, they participate in functions performed by cell-surface glycans including cell adhesion and signaling [1]. Unnatural analogs of these amino sugars prepared by a selective replacement of a hydroxy group by fluorine have proved valuable tools to perturb

Mycothiol synthesis by an anomerization reaction through endocyclic cleavage

• Shino Manabe and
• Yukishige Ito

Beilstein J. Org. Chem. 2016, 12, 328–333, doi:10.3762/bjoc.12.35

• glycolipids [35][36][37]. Sulfated sugars are isomerized from pyranosides to furanosides [38]. The anomerization reaction would be a useful methodology to prepare 1,2-cis-glycosides such as heparin and glycosylphosphatidylinositol (GPI) anchors. Structure of mycothiol 1. Detoxification pathway mediated by MSH

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

• Alexandre Novoa Nicolas Winssinger Department of Organic Chemistry, NCCR Chemical Biology, University of Geneva 30, quai Ernest Ansermet, 1211 Geneva, Switzerland 10.3762/bjoc.11.81 Abstract Glycans (carbohydrate portion of glycoproteins and glycolipids) frequently exert their function through

Effects of RAMEA-complexed polyunsaturated fatty acids on the response of human dendritic cells to inflammatory signals

• Éva Rajnavölgyi,
• Renáta Laczik,
• Viktor Kun,
• Lajos Szente and
• Éva Fenyvesi

Beilstein J. Org. Chem. 2014, 10, 3152–3160, doi:10.3762/bjoc.10.332

• cell surface directly from the cytosol and also can acquire polar lipids from exogenous sources [44]. Considering that the most important biological function of the CD1a protein is the recognition, binding and presentation of glycolipids for innate immune cells [32], we hypothesized that upon