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

• much the same way as N-glycan antennae. It appears, however, that the particular core type has to be specified as shown in Figure 12. The very simple and frequently occurring O-glycans T-, Tn- and Sialyl-Tn-antigen may be exempted from such attempts. Likewise, will the rarer core types be left out for

• galactose”. Proglycan codes for HNK-1 structures, a brain glycan with substituted bisecting GlcNAc, a sulfated SDa antigen containing glycan from uromodulin and a hypothetical sulfated N-glycan. The colored codes are just for illustration. The bottom line reveals the hidden, invariable informations

Possible bi-stable structures of pyrenebutanoic acid-linked protein molecules adsorbed on graphene: theoretical study

• Yasuhiro Oishi,
• Motoharu Kitatani and
• Koichi Kusakabe

Beilstein J. Org. Chem. 2024, 20, 570–577, doi:10.3762/bjoc.20.49

• to carbon materials [2][3]. The properties and characteristics of these linker molecules are keys not only to the purpose of protein immobilization, but also to the behavior of the entire biosensor system. In oscillator-based biosensors, further adsorption on the sensor, such as viruses using antigen

• /antibody reactions, may be detected via elastic-wave measurements. For this purpose, the antibody protein must first be immobilized on graphene. The antibody that specifically reacts with the target antigen is immobilized onto a graphene surface via the PASE linker. After that, the antigen is injected on

• sensor chips and specifically binds to the antibody. The antigen is then detected by observing the change in the vibrational frequency before and after the injection of the antigen. The immobilization of a protein using a PASE linker on carbon nanotube [1], graphite [4], and graphene [5] has been

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

• actively and strongly prefers C2-substituted Gal, while RCA1 does not even tolerate these substitutions. Interestingly, we also find that fucosylation of the GlcNAc residue (as in Lewis antigen motifs) completely abrogates CMA1 binding (Figure S1, Supporting Information File 2), despite the presence of

• ]. Validating binding in solution and assessing binding affinity As CMA1 both exhibited multiple binding sites and robust binding to blood group epitopes (H-antigen), we hypothesized that it would be capable of agglutinating red blood cells, justifying its new name. When testing the protein recombinantly

• approximately 42 °C (Figure 3b). Then, we tested the binding of CMA1 to GlcNAc, GalNAc, and H type 2 blood group antigen (BGHT2; Fucα1-2Galβ1-4GlcNAcβ1-3Gal; Figure 3c). This resulted in clear melting points shifts for both GalNAc and BGHT2 to up to 50 °C, yet importantly not for GlcNAc, demonstrating both

Synthesis of the 3’-O-sulfated TF antigen with a TEG-N₃ linker for glycodendrimersomes preparation to study lectin binding

• Mark Reihill,
• Hanyue Ma,
• Dennis Bengtsson and
• Stefan Oscarson

Beilstein J. Org. Chem. 2024, 20, 173–180, doi:10.3762/bjoc.20.17

• Mark Reihill Hanyue Ma Dennis Bengtsson Stefan Oscarson Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland 10.3762/bjoc.20.17 Abstract The synthesis of gram quantities of the TF antigen (β-ᴅ-Gal-(1→3)-α-ᴅ-GalNAc) and its 3’-sulfated analogue with a

• TEG-N3 spacer attached is described. The synthesis of the TF antigen comprises seven steps, from a known N-Troc-protected galactosamine donor, with an overall yield of 31%. Both the spacer (85%) and the galactose moiety (79%) were introduced using thioglycoside donors in NIS/AgOTf-promoted

• glycosylation reactions. The 3’-sulfate was finally introduced through tin activation in benzene/DMF followed by treatment with a sulfur trioxide–trimethylamine complex in a 66% yield. Keywords: regioselective sulfation; thioglycoside donors; Thomsen–Friedenreich antigen; Introduction In a collaboration

Total synthesis of the O-antigen repeating unit of Providencia stuartii O49 serotype through linear and one-pot assemblies

• Tanmoy Halder and
• Somnath Yadav

Beilstein J. Org. Chem. 2021, 17, 2915–2921, doi:10.3762/bjoc.17.199

• , we herein report the total synthesis of a trisaccharide repeating unit of the O-antigen polysaccharide of the P. stuartii O49 serotype containing the →6)-β-ᴅ-Galp-(1→3)-β-ᴅ-GalpNAc(1→4)-α-ᴅ-Galp(1→ linkage. The synthesis of the trisaccharide repeating unit was carried out first by a linear strategy

• was then deprotected and N-acetylated to finally afford the desired trisaccharide repeating unit as its α-p-methoxyphenyl glycoside. Keywords: capsular polysaccharide; carbohydrate vaccines; O-antigen; oligosaccharide synthesis; one-pot synthesis; Introduction O-antigens or O-specific

• development [1][2][3][4][5][6][7][8]. This objective has been proposed to be achieved by the synthesis of chemically homogeneous glycoconjugates bearing the O-antigen oligosaccharide conjugated to peptides for eliciting the desired immune response through vaccines [9][10][11][12][13][14][15][16][17][18][19

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

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

• residues to being core 1 and 2 O-linked glycan synthesis. Thus, SMAD2 may play a key role in regulating Tn antigen expression in proteins such as MUC-1 that are associated with breast cancer progression. Refinement of TF–glycopathway enrichments after false discovery correction The number of enrichments

• -Gal:ceramide galactosyltransferase (UGT8). These structures can be further sulfated by GAL3ST1 or sialylated by ST3GAL5. 2) P1-Pk blood group: The Pk, P1, and P antigens are synthesized on lactosylceramide glycolipid core. The activity of α1-4GalT (A4GALT) on this core results in the Pk antigen, followed by β1

• -3GalNAcT (B3GALNT1) to form the P antigen. The P1 antigen, on the other hand, is formed by the sequential action of β1-3GlcNAcT (B3GNT5), β1-4GalT (B4GALT1-6), and α1-4GalT (A4GALT) on the glycolipid core. 3) Gangliosides: This pathway encompasses all glycogenes responsible for synthesizing a/b/c

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

• Nikita Brodyagin,
• Martins Katkevics,
• Venubabu Kotikam,
• Christopher A. Ryan and
• Eriks Rozners

Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116

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

• structures including the TN and T antigen and their sialylated forms [24]. A complete series of O-protected monofluorinated [22][25][26][27][28][29][30][31][32] and several difluorinated [22][26][33][34] GlcNAc/GalNAc analogs have been prepared. Some acylated mono- and difluorinated analogs have potential in

Enhanced target cell specificity and uptake of lipid nanoparticles using RNA aptamers and peptides

• Roslyn M. Ray,
• Anders Højgaard Hansen,
• Maria Taskova,
• Bernhard Jandl,
• Jonas Hansen,
• Citra Soemardy,
• Kevin V. Morris and
• Kira Astakhova

Beilstein J. Org. Chem. 2021, 17, 891–907, doi:10.3762/bjoc.17.75

• no need for additional reactions after cleavage [27][28][29]. One approach to generate LNP formulations with higher specificity for antigen-expressing cells is to use RNA aptamers. RNA aptamers are short oligonucleotides that are evolved using a process called systematic evolution of ligands by

• % increase in cellular uptake through the BBB and into target cells and that these cells had higher LNP uptake (measured by a higher MFI) than the non-antigen-expressing counterparts, while the gp160 aptamer (A-1) had no apparent effect on target cell uptake. One could speculate that this may be the result

• , effective transport systems for brain drug delivery are highly warranted. Herein, we find that the LNP platform can be applied as a vehicle to circumvent the BBB and effectively deliver oligonucleotide probes to antigen-expressing cell lines. For HIV-1 there is currently a need for more effective delivery

Synthetic strategies of phosphonodepsipeptides

• Jiaxi Xu

Beilstein J. Org. Chem. 2021, 17, 461–484, doi:10.3762/bjoc.17.41

• acids and hydroxy esters through phosphonochloridates as in situ-generated intermediates. To prepare an antigen to induce monoclonal catalytic antibodies capable of catalyzing peptide-bond formation reactions, the phosphonodepsidipeptide 39 was synthesized via the coupling of the hydroxy analog of

¹⁹F NMR as a tool in chemical biology

• Diana Gimenez,
• Aoife Phelan,
• Cormac D. Murphy and
• Steven L. Cobb

Beilstein J. Org. Chem. 2021, 17, 293–318, doi:10.3762/bjoc.17.28

• presence of DNA, and another intrinsically disordered binding partner, breast cancer antigen 1 (BRCA1) (Figure 12). In this work the strategy employed involved the introduction of a perfluorinated [19F]3,5‐bis(trifluoromethyl)benzyl-based tag into the single cysteine residue of Myc. This modification

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

Molecular basis for protein–protein interactions

• Brandon Charles Seychell and
• Tobias Beck

Beilstein J. Org. Chem. 2021, 17, 1–10, doi:10.3762/bjoc.17.1

• functionality and the corresponding pathways. Important roles of PPIs include hormone reception [2], protease inhibition [3], antibody–antigen complexes [4], gene regulation [5], and large biomolecular assemblies [6]. PPI identification and prediction are important for targeting anticancer strategies [7

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

• -glycans are attached to Ser or Thr. Glycan compositions can range from monosaccharides (e.g., Tn antigen for O-glycans [1]) to large polysaccharides (e.g., N-glycans of recombinant human erythropoietin [2]). The most common building blocks of human protein glycans are hexoses (glucose, galactose, and

Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding

• Christopher B. Barnett,
• Tharindu Senapathi and
• Kevin J. Naidoo

Beilstein J. Org. Chem. 2020, 16, 2540–2550, doi:10.3762/bjoc.16.206

• are commonly associated with cancerous cells [14]. Movahedin et al. confirmed that the glycosylation of MUC1 influences its binding to the AR20.5 murine antibody [16], specifically the Tn-antigen binds more strongly than the nonglycosylated antigen. AR20.5 is known to bind a specific epitope within

• the MUC1 VNTR domain. Thus, a synthetic 8-amino acid peptide (APDTRPAP) and the corresponding Tn glycopeptide were synthesized. It was found from the co-crystallization of the AR20.5 antigen-binding fragment (Fab) with the MUC1 peptide and glycopeptide that the glycan moiety of the glycopeptide did

• conformation of the peptide portion of the antigen and does not bind directly. Previous studies have shown that O-glycosylation may provide increased physical stability [20], rigid conformations for protein stability [21], induce the formation of stiff and extended peptide conformations [22], and may affect

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

• blood group antigens (A, B, O), which are glycan structures found on blood cells and tissues that play a critical role in determining transfusion compatibility during blood and organ donation [3], sialyl-LewisA antigen, known more commonly as CA19-9, which is a known tumor marker for pancreatic cancer

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

• the absence of β(1-3) Gal. LeA stands for Lewis A antigen. The N-glycans structures are shown with the (1-3) and (1-6) arms on the left and on the right, respectively. The monosaccharides colouring follows the SFNG nomenclature. The plants N-glycan characteristic linkages are indicated in the legend

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

• -antigen [2]. While O-antigen and the core oligosaccharide are exposed to the external environment, lipid A, the hydrophobic domain of LPS, is embedded in the cell wall. The lipid A substructure is relatively conserved that consists of a β-1,6-linked diglucosamine with 1,4′-di-O-phosphorylation and 2,2′-N

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

• . Here, we demonstrate a convergent [2 + 3] synthetic strategy to prepare the pentasaccharide repeating unit of 9V with and without an acetate group at the C-6 position of mannosamine. Keywords: antigen; carbohydrate chemistry; oligosaccharide; Streptococcus pneumoniae; vaccines; Introduction

Anthelmintic drug discovery: target identification, screening methods and the role of open science

• Frederick A. Partridge,
• Ruth Forman,
• Carole J. R. Bataille,
• Graham M. Wynne,
• Marina Nick,
• Angela J. Russell,
• Kathryn J. Else and
• David B. Sattelle

Beilstein J. Org. Chem. 2020, 16, 1203–1224, doi:10.3762/bjoc.16.105

• circulating filarial antigen levels. A second trial also found that a single dose of the three drug (IVE + DEC + ALB) therapy had a greater ability to reduce W. bancrofti microfilariae for 24 months after treatment, compared to annual dosing of two drug (IVE + ALB) therapy [51], although microfilarial

Convenient synthesis of the pentasaccharide repeating unit corresponding to the cell wall O-antigen of Escherichia albertii O4

• Tapasi Manna,
• Arin Gucchait and
• Anup Kumar Misra

Beilstein J. Org. Chem. 2020, 16, 106–110, doi:10.3762/bjoc.16.12

• corresponding to the cell wall O-antigen of the Escherichia albertii O4 strain in very good yield with the desired configuration at the glycosidic linkages using thioglycosides and trichloroacetimidate derivatives as glycosyl donors and perchloric acid supported over silica (HClO4/SiO2) as a solid supported

• protic acid glycosyl activator. The expected configuration at the glycosidic linkages was achieved using a reasonable selection of protecting groups in the manosaccharide intermediates. Keywords: Escherichia albertii O4; glycosylation; HClO4/SiO2; O-antigen; pentasaccharide; Introduction Diarrheal

• pentasaccharide repeating unit of the cell wall O-antigen of Escherichia albertii O4 in very good yield. Although the target compound can be achieved by block synthetic approach but a better yield of the product was obtained by a sequential approach. HClO4/SiO2 was used as a solid acid activator in the

Chemical synthesis of the pentasaccharide repeating unit of the O-specific polysaccharide from Escherichia coli O132 in the form of its 2-aminoethyl glycoside

• Debasish Pal and
• Balaram Mukhopadhyay

Beilstein J. Org. Chem. 2019, 15, 2563–2568, doi:10.3762/bjoc.15.249

• chemically synthesized oligosaccharides before [8][9][10]. The corresponding aminopropyl linker has also been used by others [11]. The chemically synthesized oligosaccharide structure will help to elucidate further biological implications of the O-antigen concerned and possible vaccine potential. Results and

Current understanding and biotechnological application of the bacterial diterpene synthase CotB2

• Ronja Driller,
• Daniel Garbe,
• Norbert Mehlmer,
• Monika Fuchs,
• Keren Raz,
• Dan Thomas Major,
• Thomas Brück and
• Bernhard Loll

Beilstein J. Org. Chem. 2019, 15, 2355–2368, doi:10.3762/bjoc.15.228

• isolated in 1985 from cigarette smoke condensate and identified as anticancer agents [76]. With quite similar potency (α-CBT: 25.2 µM and β-CBT: 21.9 µM [77]), they showed inhibition of the induction of Epstein–Barr virus early antigen by lymphoblastoid cancer cells. In the tobacco plant itself, both

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

• investigated in the mouse model using ovalbumin as an antigen. Their activities were compared to the previously described mannosylated adamantane-containing desmuramyl peptide and peptidoglycan monomer. Tested compounds exhibited adjuvant activity and the strongest enhancement of IgG production was stimulated

• innate immunity through macrophage response as well as to more distally affect adaptive immunity through the production of antigen-specific T cells [5]. MDP binding to NOD2 has been confirmed [6] as well as the crystal structure of NOD2 in the inactive ADP-bound state [7]. MDP is the structural fragment

• with derivatives lacking the adamantane moiety. Immunostimulating properties of synthesized derivatives were assessed in vivo using ovalbumin as an antigen. Results and Discussion Design Desmuramyl peptides enter into the cell by passive absorption and this process depends on lipophilicity [25