Monitoring carbohydrate 3D structure quality with the Privateer database

• Jordan S. Dialpuri,
• Haroldas Bagdonas,
• Lucy C. Schofield,
• Phuong Thao Pham,
• Lou Holland and
• Jon Agirre

Beilstein J. Org. Chem. 2024, 20, 931–939, doi:10.3762/bjoc.20.83

• calculated by Privateer and, most importantly, the diagnostic provided by Privateer (Figure 4). A ‘yes’ diagnostic indicates the conformation is correct for the glycosylation type (e.g., 4C1 for GlcNAc in an N-glycan, 1C4 for mannose in a C-glycan), has the correct anomer, and has an acceptable fit to

Introduction of a human- and keyboard-friendly N-glycan nomenclature

• Friedrich Altmann,
• Johannes Helm,
• Martin Pabst and
• Johannes Stadlmann

Beilstein J. Org. Chem. 2024, 20, 607–620, doi:10.3762/bjoc.20.53

• pentasaccharide. No further definitions are required as the residues preceding the GlcNAcs are unambiguously determined by the biosynthetic pathway of N-glycans. Action of hexosaminidases would generate two isomers with just one GlcNAc and a terminal mannose residue. By defining the reading direction, we can

• occur on either arm of an N-glycan. The two antennae ascending from the same mannose are set in square brackets (Figure 7). The square exclusively and immediately tells us that this branch is further branched. By that the two basic types of triantennary glycans are readily told apart. The proglycan

• signifying additional branching. As no other branching point is given, the root residue is GlcNAc. LacNAc repeats The primary LacNAc disaccharide Galβ1-4GlcNAcβ1- that is linked to a mannose can be further elongated by the addition of GlcNAc (in β1-3 linkage to Gal), which usually is followed by the quick

Sulfur-containing spiroketals from Breynia disticha and evaluations of their anti-inflammatory effect

• Ken-ichi Nakashima,
• Naohito Abe,
• Masayoshi Oyama,
• Hiroko Murata and
• Makoto Inoue

Beilstein J. Org. Chem. 2023, 19, 1604–1614, doi:10.3762/bjoc.19.117

• nm was performed using a photodiode array detector. Compounds 2, 6, and 7 were derivatized and analyzed in a similar manner. Furthermore, derivatives of authentic sugars were analyzed, and peaks were observed at 8.34 (ᴅ-mannose), 12.17 (ᴅ-galactose), 12.74 (ʟ-glucose), 13.96 (ᴅ-glucose), 15.18 (ʟ

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

CuAAC-inspired synthesis of 1,2,3-triazole-bridged porphyrin conjugates: an overview

• Dileep Kumar Singh

Beilstein J. Org. Chem. 2023, 19, 349–379, doi:10.3762/bjoc.19.29

• protected α-propargylglucose 42a or mannose 42b in the presence of CuCl in a toluene/H2O (4:1) (Scheme 7). Further a fully deprotected mannosyl residue 42c was also introduced via "click reaction”, yielding the glycoporphyrin 43c. Moreover, this methodology can also be utilized to introduce various

Synthesis, α-mannosidase inhibition studies and molecular modeling of 1,4-imino-ᴅ-lyxitols and their C-5-altered N-arylalkyl derivatives

• Martin Kalník,
• Sergej Šesták,
• Juraj Kóňa,
• Maroš Bella and
• Monika Poláková

Beilstein J. Org. Chem. 2023, 19, 282–293, doi:10.3762/bjoc.19.24

• configurations of all its stereogenic centers match those of swainsonine. Furthermore, DIM is a micromolar GMII inhibitor, which is easily accessible on a large scale from ᴅ-mannose by well-established methods [15][29]. In general, improvements of physicochemical and inhibitory properties of monocyclic

Synthesis of C6-modified mannose 1-phosphates and evaluation of derived sugar nucleotides against GDP-mannose dehydrogenase

• Sanaz Ahmadipour,
• Alice J. C. Wahart,
• Jonathan P. Dolan,
• Laura Beswick,
• Chris S. Hawes,
• Robert A. Field and
• Gavin J. Miller

Beilstein J. Org. Chem. 2022, 18, 1379–1384, doi:10.3762/bjoc.18.142

• pathogen in these cases is mucoid Pseudomonas aeruginosa. Such infections are characterised by overproduction of the exopolysaccharide alginate. We present herein the design and chemoenzymatic synthesis of sugar nucleotide tools to probe a critical enzyme within alginate biosynthesis, GDP-mannose

• dehydrogenase (GMD). We first synthesise C6-modified glycosyl 1-phosphates, incorporating 6-amino, 6-chloro and 6-sulfhydryl groups, followed by their evaluation as substrates for enzymatic pyrophosphorylative coupling. The development of this methodology enables access to GDP 6-chloro-6-deoxy-ᴅ-mannose and its

• evaluation against GMD. Keywords: alginate; chemical probe; enzymatic synthesis; GDP-mannose dehydrogenase; sugar nucleotide; Introduction The opportunistic Gram-negative pathogen, Pseudomonas aeruginosa (PA), becomes the dominant pathogen in patients suffering from cystic fibrosis (CF) and causes a

Synthetic strategies toward 1,3-oxathiolane nucleoside analogues

• Umesh P. Aher,
• Dhananjai Srivastava,
• Girij P. Singh and
• Jayashree B. S

Beilstein J. Org. Chem. 2021, 17, 2680–2715, doi:10.3762/bjoc.17.182

• , which was subsequently acetylated with acetic anhydride to afford 8 as a 2:1 mixture of anomers. Chu and co-workers [40] applied a novel strategy for the synthesis of enantiomerically pure (+)-BCH-189 (1a) using ᴅ-mannose (3c) as a starting material (Scheme 3). 1,2,3,4-Tetraacetyl-ᴅ-mannose derivative 9

• was prepared from ᴅ-mannose (3c) by protecting the primary alcohol with a tosyl group, followed by protection of the four hydroxy groups by acetylation. Further, bromo-substituted sugar compound 10 was obtained by a bromination reaction of the anomeric acetyl group. 1,6-Thioanhydro-β-mannose

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

• differences in the conformational behavior of the two analogues (β(1–3) vs β(1–4) oligomers), it was observed that the β(1–3)-mimetic was still recognized by wheat germ agglutinin and a chitinase enzyme, and could act as a moderate inhibitor of chitin hydrolysis [268]. Mannose- and rhamnose-based

• polysaccharides Due to the structural analogies between Rha (both ᴅ and ʟ) and Man, we describe the polysaccharides based on these two units in the same section. From a chemical point of view mannose and rhamnose are ‘double-faced’ monosaccharides, as chemically constructing α-linkage is relatively easy, whereas

• not allow for access to mannans with defined length. Total syntheses of mannose polysaccharides including a 30mer [276], 50mer [277] and 100mer [278] were achieved by AGA. Key optimizations including tuning of the PGs [277], adjustment of coupling time and temperature [278], and introduction of a

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

• community. In the third community, O-linked mannose and LacdiNAc synthesis were disproportionately regulated. Overall, the pathway maps suggest that chromatin remodeling enzymes could potentially play roles in regulating glycan synthesis in luminal breast cancer. Like luminal, basal breast cancer TF

• extension: This pathway includes glycogenes responsible for the synthesis of GPI-anchored proteins in the ER. This involves the synthesis of a glycan–lipid precursor that is en bloc transferred to proteins. 13) O-Mannose: This is initiated by the addition of mannose to Ser/Thr using POMT1 or POMT2. β1-2 or

• β1-4 GlcNAc linkages can then be made using POMGNT1 or POMGNT2 to yield M1 or M3 O-linked mannose structures, respectively. MGAT5B can facilitate β1-4 GlcNAc linkage onto the M1 structure to yield the M2 core. Additional carbohydrates typically found on complex N-linked glycan antennae can then be

Chemical synthesis of C6-tetrazole ᴅ-mannose building blocks and access to a bioisostere of mannuronic acid 1-phosphate

• Eleni Dimitriou and
• Gavin J. Miller

Beilstein J. Org. Chem. 2021, 17, 1527–1532, doi:10.3762/bjoc.17.110

Double-headed nucleosides: Synthesis and applications

• Vineet Verma,
• Jyotirmoy Maity,
• Vipin K. Maikhuri,
• Ritika Sharma,
• Himal K. Ganguly and
• Ashok K. Prasad

Beilstein J. Org. Chem. 2021, 17, 1392–1439, doi:10.3762/bjoc.17.98

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

• synthesis of unprotected multiply-deoxyfluorinated monosaccharides, including a complete series of mono-, di-, and trifluorinated ᴅ-glucose [15], difluorinated [20] and tetrafluorinated [13] ᴅ-galactose, and 2,3,4-trifluoro analogs of ᴅ-mannose, ᴅ-galactose, ᴅ-allose, ᴅ-talose, and ᴅ-altrose [13][21

Metal-free glycosylation with glycosyl fluorides in liquid SO₂

• Krista Gulbe,
• Jevgeņija Lugiņina,
• Edijs Jansons,
• Artis Kinens and
• Māris Turks

Beilstein J. Org. Chem. 2021, 17, 964–976, doi:10.3762/bjoc.17.78

• armed and disarmed glucose and mannose-derived glycosyl fluorides in moderate to excellent yields. A series of pivaloyl-protected O- and S-mannosides, as well as one example of a C-mannoside, are synthesized to demonstrate the scope of the glycosyl acceptors. The formation of the fluorosulfite species

• through the neighboring ester type protecting group assistance. At lower temperatures the glycosylation yield was lower, although full conversion of glucosyl fluoride β-9 was still observed. Compared to the analogue mannose derivative α-1a, glucose β-9 turned out to be less stable and more prone to

• mannose α-11. Glucosides 14 were isolated in a moderate yield, but without any α,β-selectivity due to the mismatched interaction between the anomeric effect and neighboring protecting group assistance. The diminished selectivity compared to the series of pivaloyl-protected glucosides 10 leads to the

Supramolecular polymerization of sulfated dendritic peptide amphiphiles into multivalent L-selectin binders

• David Straßburger,
• Svenja Herziger,
• Katharina Huth,
• Moritz Urschbach,
• Rainer Haag and
• Pol Besenius

Beilstein J. Org. Chem. 2021, 17, 97–104, doi:10.3762/bjoc.17.10

• recently reported the successful application of functional supramolecular polymers in a biological context [30]. By decoration of the discotic peptide amphiphile monomers with dendritic mannose moieties, a specific cell targeting of macrophages and internalization in those antigen presenting cells has been

Semiautomated glycoproteomics data analysis workflow for maximized glycopeptide identification and reliable quantification

• Steffen Lippold,
• Arnoud H. de Ru,
• Jan Nouta,
• Peter A. van Veelen,
• Magnus Palmblad,
• Manfred Wuhrer and
• Noortje de Haan

Beilstein J. Org. Chem. 2020, 16, 3038–3051, doi:10.3762/bjoc.16.253

• mannose, Hex/H, 162.0528 Da), N-Acetylhexosamines (N-acetylglucosamine or N-acetylgalactosamine, HexNAc/N, 203.0794 Da), fucose (Fuc/F, 145.0579 Da), and sialic acid (N-acetylneuraminic acid, NeuAc/S, 291.0954 Da). The combinatorial possibilities of these building blocks and the variety of structural

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

• 3 is the stereochemistry of the fluorine atom at C2. Finally, only decomposition originated from the use of mannose analogue 5 as substrate. The difference in terms of reactivity between 5 and 2 was unexpected since they only differ from the stereochemistry of the fluorine atom at C2 (distal to the

• arising from an inversion of configuration could generate the desired trifluorinated mannose analogue 14, inaccessible from the DAST-mediated fluorodeoxygenation (Table 2) [33]. We first used 15 equivalents of Et3N·3HF at 80 °C for 24 h with the addition of 50 equivalents of Et3N as solvent (Table 2

• , entry 1). To our delight, mannose analogue 14 was formed as the major product (44% yield), along with 21% of the talose analogue 12 and the elimination product 15 in 20% yield, as determined after analysis of the 19F NMR spectra of the crude reaction mixture. Figure 2 shows a representative 19F NMR

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

• )Mb4. Here the “|” uncertainty operator is used to allow for the possible presence of a bisecting GlcNAc on the root mannose: Ma3(GNb4)(…Ma6)Mb4. The “*” indicates the site of the enzyme action. Possible branch “|” – As discussed, parsing a linear glycan from left to right, we can encounter matched

• ” means the reaction will not happen if a β-galactose is present. Ambiguous symbol 2 – “ | ”. For reaction rules, “ | ” is widely used to represent a potential branched structure in a substrate [7][10][13][32]. For example, “(GNb2|Ma3” represents a glycan structure with a potential branch on the mannose

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

• similar to the one of higher species [25], carrying the distinctive trimannose core (Man3), which can be further functionalised with β(1-2)-linked GlcNAc residues on the arms. As a trademark feature, shown in Figure 1, plants N-glycans can also have a β(1-2)-Xyl linked to the central mannose and core α(1

• GlcNAc-β(1-4)-GlcNAc linkage, see Tables S1 and S2 in Supporting Information File 1, relative to the α(1-6) core fucosylated or non-fucosylated chitobiose [24], where the average psi value is −127.8° (14.8) [24], but doesn’t affect the structure of the linkage to the central mannose. As shown by the low

Nonenzymatic synthesis of anomerically pure, mannosyl-based molecular probes for scramblase identification studies

• Giovanni Picca,
• Markus Probst,
• Simon M. Langenegger,
• Oleg Khorev,
• Peter Bütikofer,
• Anant K. Menon and
• Robert Häner

Beilstein J. Org. Chem. 2020, 16, 1732–1739, doi:10.3762/bjoc.16.145

• glycosylation is described. Two short-chain glycolipid analogs that mimic the naturally occurring substrate mannosyl phosphoryl dolichol exhibit either photoreactive and clickable properties or allow the use of a fluorescence readout. Both probes consist of a hydrophilic mannose headgroup that is linked to a

• glycolipid analogs; scramblase; Introduction Mannosyl phosphoryl dolichol (MPD), an important, multifunctional glycolipid, is used as a mannose donor for protein N-glycosylation, O- and C-mannosylation, and glycosylphosphatidylinositol (GPI) anchoring in the luminal leaflet of the endoplasmic reticulum (ER

• -mannose (the α-anomer also shows biological activity, but to a lesser extent) [13][14][15], a short-chain (citronellol) mimic of dolichol [1][2][13], and a functional tag. The latter may either be a chemically reactive group (in MPC-1) or a fluorescent reporter group (in MPC-2). MPC-1 bears a benzophenone

Synthesis of Streptococcus pneumoniae serotype 9V oligosaccharide antigens

• Sharavathi G. Parameswarappa,
• Claney L. Pereira and
• Peter H. Seeberger

Beilstein J. Org. Chem. 2020, 16, 1693–1699, doi:10.3762/bjoc.16.140

• pentasaccharide RU with glucuronic acid at the non-reducing end. Results and Discussion The SP 9V linear pentasaccharide RU 1 contains ᴅ-glucuronic acid (ᴅ-GlcpA), ᴅ-galactose (ᴅ-Galp), 2-acetamido-2-deoxy-ᴅ-mannose (ᴅ-ManpNAc), and ᴅ-glucose (ᴅ-Glcp) units. Several cis glycosidic linkages, including a β

Synthesis of new asparagine-based glycopeptides for future scanning tunneling microscopy investigations

• Laura Sršan and
• Thomas Ziegler

Beilstein J. Org. Chem. 2020, 16, 888–894, doi:10.3762/bjoc.16.80

• -linked structures are N-acetylglycosylamines, glucose, galactose, mannose, cellobiose, lactose, and maltose [19]. Therefore, we intended to prepare glycopeptide structures containing these sugars in a stepwise way, up to tripeptides. An orthogonal Fmoc/t-Bu protecting group strategy was chosen along with

• synthesis of a series of new glycopeptides containing asparagine, tryptophane, alanine, and phenylalanine linked to various saccharides, such as glucose, galactose, mannose, cellobiose, lactose, and maltose. We further compared two common peptide coupling procedures that use HBTU and HATU, respectively. We

Automated glycan assembly of arabinomannan oligosaccharides from Mycobacterium tuberculosis

• Alonso Pardo-Vargas,
• Priya Bharate,
• Martina Delbianco and
• Peter H. Seeberger

Beilstein J. Org. Chem. 2019, 15, 2936–2940, doi:10.3762/bjoc.15.288

• -step purification and global deprotection [25]. Linear α-(1,6)-hexamannoside 4 was synthesized using six coupling cycles and 6.5 equiv of mannose building block (BB) 1. No deletion sequences were observed and the crude product was purified using normal-phase HPLC to obtain hexamannoside 4 in 55% yield

• 8 were addressed using building block 1 and arabinose BB 3 for the α-(1,5)-Ara linkage. Procedure A efficiently provided the linear mannose backbone, but resulted only in partial glycosylation of arabinose BB 3, thus giving the hexamannoside as main product as well as multiple side products missing

Design, synthesis and biological evaluation of immunostimulating mannosylated desmuramyl peptides

• Rosana Ribić,
• Ranko Stojković,
• Lidija Milković,
• Mariastefania Antica,
• Marko Cigler and
• Srđanka Tomić

Beilstein J. Org. Chem. 2019, 15, 1805–1814, doi:10.3762/bjoc.15.174

• and increase of lipophilicity are important approaches in the preparation of muramyl dipeptide analogues with improved pharmacological properties. Mannose receptors present on immunocompetent cells are pattern-recognition receptors and by mannose ligands binding they affect the immune system. Here we

• present the design, synthesis and biological evaluation of novel mannosylated desmuramyl peptide derivatives. Mannose was coupled to dipeptides containing a lipophilic adamantane on N- or C-terminus through a glycolyl or hydroxyisobutyryl linker. Adjuvant activities of synthesized compounds were

• by compound 21 (Man-OCH2-ᴅ-(1-Ad)Gly-ʟ-Ala-ᴅ-isoGln). Keywords: adamantane; adjuvant activity; desmuramyl peptide; mannose; Introduction Dendritic cells capture and internalize invading pathogens. Pathogen-associated molecular patterns have been known for a long time to affect the immune system of

Influence of per-O-sulfation upon the conformational behaviour of common furanosides

• Alexey G. Gerbst,
• Vadim B. Krylov,
• Dmitry A. Argunov,
• Maksim I. Petruk,
• Arsenii S. Solovev,
• Andrey S. Dmitrenok and
• Nikolay E. Nifantiev

Beilstein J. Org. Chem. 2019, 15, 685–694, doi:10.3762/bjoc.15.63

• drastic changes of the ring conformation occurred while sometimes only the conformation of the exocyclic C4–C5 linkage changed. Herein we describe a combined quantum chemical and NMR conformational investigation of three common monosaccharide furanosides as their propyl glycosides: α-mannose, β-glucose

• -sulfated furanosides is reported. Results and Discussion Synthesis of per-O-sulfated furanosides Propyl α-D-mannofuranoside (1) was prepared from D-mannose and n-propanol via Fischer reaction using ion-exchange resin IR-120(H+) as acidic catalyst. The reaction was performed under kinetic control and was

• stopped at low conversion of the starting mannose to avoid formation of the pyranoside product [23]. The desired furanoside 1 was isolated from the reaction mixture by column chromatography with a yield of 12%. Parent propyl β-D-glucofuranoside (2) and propyl β-D-galactofuranoside (3) were prepared using