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

• complement the growing glycan content of the PDB. Keywords: carbohydrates; database; N-glycans; N-glycosylation; polysaccharides; validation; website; Introduction Carbohydrate modelling is an important but often cumbersome stage in the macromolecular X-ray structure solution workflow. The accurate

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

• polysaccharides, with repeating disaccharide units comprised of a hexuronic acid (or galactose in keratan sulfate) and a hexosamine (N-acetylglycosamide, GlcNAc or N-acetylgalactososamide, GalNAc) throughout a regular alternation of 1→4 and 1→3-glycosidic linkages [1][2][3]. GAGs are mainly located on the cell

Linker, loading, and reaction scale influence automated glycan assembly

• Marlene C. S. Dal Colle,
• Manuel G. Ricardo,
• Nives Hribernik,
• José Danglad-Flores,
• Peter H. Seeberger and
• Martina Delbianco

Beilstein J. Org. Chem. 2023, 19, 1015–1020, doi:10.3762/bjoc.19.77

• purification steps. Keywords: automated glycan assembly; photocleavable linker; polysaccharides; solid-phase synthesis; Introduction Automated glycan assembly (AGA) is a solid-phase method that enables the rapid synthesis of complex oligo- and polysaccharides from protected monosaccharide building blocks

Insight into oral amphiphilic cyclodextrin nanoparticles for colorectal cancer: comprehensive mathematical model of drug release kinetic studies and antitumoral efficacy in 3D spheroid colon tumors

• Sedat Ünal,
• Gamze Varan,
• Juan M. Benito,
• Yeşim Aktaş and
• Erem Bilensoy

Beilstein J. Org. Chem. 2023, 19, 139–157, doi:10.3762/bjoc.19.14

• stable lactone form of encapsulated CPT due to their acidic chemical structure [8][9][11][13]. CDs are biocompatible cyclic polysaccharides formed by (1→4)-bound α-glucopyranose subunits obtained as a result of enzymatic degradation of starch by glucosyltransferase [21]. With their troncoconic structures

Preparation of β-cyclodextrin/polysaccharide foams using saponin

• Max Petitjean and
• José Ramón Isasi

Beilstein J. Org. Chem. 2023, 19, 78–88, doi:10.3762/bjoc.19.7

• polysaccharides. Xanthan gum, locust bean gum or chitosan can be crosslinked using citric acid in the presence of β-cyclodextrin to produce insoluble matrices. In this work, polymeric foams based on those polysaccharides and saponin have been prepared using a green synthesis method to increase the porosity of the

• of both lines gives us an approximate optimal foamability for a saponin concentration value of ca. 0.3%. These measurements correspond to solutions prepared using deionized water. Other factors such as the viscosity due to the polysaccharides or the ionic strength contributed by the catalyst can

• different polysaccharides (chitosan (CS), locust bean gum (LBG) and xanthan gum (XG)) were tested either by themselves or mixed in a 50:50 ratio with β-cyclodextrin. A fast emergence of the liquid fraction occurred with the solution containing cyclodextrin with no polysaccharides. These results show that

Polymer chemistry: fundamentals and applications

• Bernhard V. K. J. Schmidt

Beilstein J. Org. Chem. 2021, 17, 2922–2923, doi:10.3762/bjoc.17.200

• supramolecular chemistry for the assembly of polymer fibers and the synthesis of well-defined polysaccharides. In the direction of materials, cryogels and reinforced hydrogels are discussed, as well as 3D-printed poly(caprolactone) biomaterials. In addition, properties of thermoresponsive materials and self

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

• Tanmoy Halder Somnath Yadav Department of Chemistry, Indian Institute of Technology (ISM), Dhanbad, 826004, Jharkhand, India 10.3762/bjoc.17.199 Abstract Capsular polysaccharides of pathogenic bacteria have been reported to be effective vaccines against diseases caused by them. Providencia

• polysaccharides are one of the important constituents of the surface lipopolysaccharides (LPS) of the cell wall of Gram-negative bacteria. These antigens are responsible for several functions that include adhesion to the host cells and are also found to contribute to the evasion of the host immune responses

• may even lead to fatal bacteremia [22][25]. The structure of repeating oligosaccharide units of O-polysaccharides of several Providencia O-serogroups as well as P. stuartii O4 [26], O18 [27], O20 [28] O33 [29], O43 [30], O44 [31], O47 [32], and O57 [33] have been reported. With respect to the

Highly stereocontrolled total synthesis of racemic codonopsinol B through isoxazolidine-4,5-diol vinylation

• Lukáš Ďurina,
• Anna Ďurinová,
• František Trejtnar,
• Ľuboš Janotka,
• Lucia Messingerová,
• Jana Doháňošová,
• Ján Moncol and
• Róbert Fischer

Beilstein J. Org. Chem. 2021, 17, 2781–2786, doi:10.3762/bjoc.17.188

• , triterpenoids, polysaccharides, and alkaloids are responsible for the majority of the activities found in Codonopsis species. Although the polyhydroxylated pyrrolidine alkaloids from C. pilosula possess glycosidase inhibitory activities and they are considered to be anticancer species, their activity against

Cryogels: recent applications in 3D-bioprinting, injectable cryogels, drug delivery, and wound healing

• Luke O. Jones,
• Leah Williams,
• Tasmin Boam,
• Martin Kalmet,
• Chidubem Oguike and
• Fiona L. Hatton

Beilstein J. Org. Chem. 2021, 17, 2553–2569, doi:10.3762/bjoc.17.171

• explored [43], as within the colon are many polysaccharides and a large number of bacteria which secrete enzymes [41]. Within this work, varying the concentration of various pH-sensitive polymers was considered in terms of swelling, and it was shown that abrupt changes in swelling could be obtained at a

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

• 22, 14195 Berlin, Germany 10.3762/bjoc.17.129 Abstract The sequence, length and substitution of a polysaccharide influence its physical and biological properties. Thus, sequence controlled polysaccharides are important targets to establish structure–properties correlations. Polymerization techniques

• and enzymatic methods have been optimized to obtain samples with well-defined substitution patterns and narrow molecular weight distribution. Chemical synthesis has granted access to polysaccharides with full control over the length. Here, we review the progress towards the synthesis of well-defined

• polysaccharides. For each class of polysaccharides, we discuss the available synthetic approaches and their current limitations. Keywords: enzymes; glycans; polysaccharides; synthesis; well-defined polymers; Introduction Polysaccharides are an abundant class of natural polymers that play important roles in the

Volatile emission and biosynthesis in endophytic fungi colonizing black poplar leaves

• Christin Walther,
• Pamela Baumann,
• Katrin Luck,
• Beate Rothe,
• Peter H. W. Biedermann,
• Jonathan Gershenzon,
• Tobias G. Köllner and
• Sybille B. Unsicker

Beilstein J. Org. Chem. 2021, 17, 1698–1711, doi:10.3762/bjoc.17.118

• mixture was incubated for 1 h at 60 °C. For separation of polysaccharides, 180 µL 5 M NaCl and 80 µL 10% CTAB were added and the mixture incubated further for 10 min at 65 °C. To extract nucleic acids by phase separation, 860 µL chloroform/isoamyl alcohol (24:1) was added and incubated on ice for 30 min

Valorisation of plastic waste via metal-catalysed depolymerisation

• Francesca Liguori,
• Carmen Moreno-Marrodán and
• Pierluigi Barbaro

Beilstein J. Org. Chem. 2021, 17, 589–621, doi:10.3762/bjoc.17.53

• acids, polysaccharides), which are "susceptible to degradation by biological activity by lowering of the molar masses of macromolecules". Therefore, in this situation, “chain cleavage” and “degradation” are used interchangeably. To avoid confusion, instead of “(bio)degradation”, in the present review

Regioselective chemoenzymatic syntheses of ferulate conjugates as chromogenic substrates for feruloyl esterases

• Olga Gherbovet,
• Fernando Ferreira,
• Apolline Clément,
• Mélanie Ragon,
• Julien Durand,
• Sophie Bozonnet,
• Michael J. O'Donohue and
• Régis Fauré

Beilstein J. Org. Chem. 2021, 17, 325–333, doi:10.3762/bjoc.17.30

• -based polysaccharides, such as arabinoxylans and arabinans. In this respect, Faes are important components of plant-cell-wall-degrading enzymatic arsenals since the hydrolysis of trans-ferulate–polysaccharide linkages contributes to the breakdown of intermolecular bonds that structure the

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

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

• synthesized through the serial addition of monosaccharides to form large polysaccharides. To build computational models of glycan synthesis, the biochemical reactions involved must be defined and described mathematically in a form that can be interpreted by computers [1][2][3]. Several groups have created

Leveraging glycomics data in glycoprotein 3D structure validation with Privateer

• Haroldas Bagdonas,
• Daniel Ungar and
• Jon Agirre

Beilstein J. Org. Chem. 2020, 16, 2523–2533, doi:10.3762/bjoc.16.204

• developers of those databases. Support for lipopolysaccharides and polysaccharides may be added in future, too, owing to the general purpose of the integrated databases – i.e., they are not limited to protein glycosylation. Currently, the generated WURCS strings are matched against an identical sequence in

Palladium nanoparticles supported on chitin-based nanomaterials as heterogeneous catalysts for the Heck coupling reaction

• Tony Jin,
• Malickah Hicks,
• Davis Kurdyla,
• Sabahudin Hrapovic,
• Edmond Lam and
• Audrey Moores

Beilstein J. Org. Chem. 2020, 16, 2477–2483, doi:10.3762/bjoc.16.201

• transformations [7][8][9]. Furthermore, the chiral nature of polysaccharides has also been used as a tool for enantioselective catalysis such as carbonyl hydrogenations and amino acid hydrolysis, proving the unique ability of these biomass-based supports [10][11]. Chitin is another type of biomass feedstock that

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

• structure and the range of building blocks available. Other levels of complexity include the nature of the glycosidic linkage (anomeric configuration, position and angles), the number of repeating units (polysaccharides) as well as the substitutions of the monosaccharides. Regardless of the different

• represented in eleven shapes and ten colours. There is the hope that it will cope better with the rapidly growing information on the structure and functions of glycans and polysaccharides from microbes, plants and algae. The rendering of glycan drawing and symbol representations motivated the development of

The B & B approach: Ball-milling conjugation of dextran with phenylboronic acid (PBA)-functionalized BODIPY

• Patrizia Andreozzi,
• Lorenza Tamberi,
• Elisamaria Tasca,
• Gina Elena Giacomazzo,
• Marta Martinez,
• Mirko Severi,
• Marco Marradi,
• Stefano Cicchi,
• Sergio Moya,
• Giacomo Biagiotti and
• Barbara Richichi

Beilstein J. Org. Chem. 2020, 16, 2272–2281, doi:10.3762/bjoc.16.188

• characteristics generally associated to dextran polysaccharides: they are highly soluble in water, biodegradable, biocompatible, commercially available, and cheap. Furthermore, the presence of hydroxy groups allows for an easy chemical functionalization with complementary functional groups. Indeed, dextrans and

Synthesis of the tetrasaccharide repeating unit of the O-specific polysaccharide of Azospirillum doebereinerae type strain GSF71^T using linear and one-pot iterative glycosylations

• Arin Gucchait,
• Pradip Shit and
• Anup Kumar Misra

Beilstein J. Org. Chem. 2020, 16, 1700–1705, doi:10.3762/bjoc.16.141

• Azospirillum rely on capsular and O-specific polysaccharides present in the bacteria cell wall [12]. Due to their structural orientation, cell-wall polysaccharides play a pivotal role in the initial stage of the host–microbes interactions and colonization of rhizobacteria in the plant roots [13]. Therefore, it

• is quite pertinent to study the effect of the cell-wall polysaccharides of rhizobacteria on the growth of leguminous plants. As a consequence, the structural elucidation of a variety of cell-wall polysaccharides of several strains of Azospirillum have been reported in the past [14][15][16][17][18][19

• ]. However, detailed biological studies to understand the biochemical role of cell-wall polysaccharides require significant quantities of the polysaccharides with adequate purity, which are difficult to achieve through isolation from the natural sources. Therefore, the development of chemical synthetic

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

• escape the host immune response [1][7]. These polysaccharides of SP consist of repeating units (RU) that range from di- to heptasaccharides that may be branched and/or charged [8]. Modifications such as O-acetylation, phosphorylation, and sulfation further increase CPS complexity. Many bacterial

• polysaccharides are O-acetylated [9][10]. Especially SP serotypes, such as 9 (A, V) and 18C differ in O-acetylation. Two O-acetylated serotypes (9V and 18C) are part of the commercial vaccine Prevnar® 13. The traditional CPS isolation approach produces varying length CPS with different degrees of acetylation. An

Mechanochemical green synthesis of hyper-crosslinked cyclodextrin polymers

• Alberto Rubin Pedrazzo,
• Fabrizio Caldera,
• Marco Zanetti,
• Silvia Lucia Appleton,
• Nilesh Kumar Dhakar and
• Francesco Trotta

Beilstein J. Org. Chem. 2020, 16, 1554–1563, doi:10.3762/bjoc.16.127

• . Polysaccharides and, among them, starch derivatives such as cyclodextrins (CD), have recently emerged as they are safe, of low cost and biodegradable. Cyclodextrin nanosponges (CD-NS) are crosslinked cyclodextrin polymers characterized by a nanosized three-dimensional network. The reactive hydroxy groups of CDs

Heterogeneous photocatalysis in flow chemical reactors

• Christopher G. Thomson,
• Ai-Lan Lee and
• Filipe Vilela

Beilstein J. Org. Chem. 2020, 16, 1495–1549, doi:10.3762/bjoc.16.125

Activated carbon as catalyst support: precursors, preparation, modification and characterization

• Melanie Iwanow,
• Tobias Gärtner,
• Volker Sieber and
• Burkhard König

Beilstein J. Org. Chem. 2020, 16, 1188–1202, doi:10.3762/bjoc.16.104

• with a production of 1011–1012 tons per year, followed by lignin as second most abundant raw material [16]. Lignin is a three-dimensional phenolic polymer and is responsible for the cementation of cellulose fibres in plants [17]. Hemicelluloses, predominantly xylan, are non-cellulosic polysaccharides

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

• of devastating diarrheal infections in different countries [9]. The role of cell wall O-polysaccharides in regulating the virulence properties of bacteria is well established [10]. Recently, Naumenko et al. [11] reported the structure of the repeating unit of the cell wall O-polysaccharide of the E

• cell wall polysaccharides with suitable proteins, which include vaccines against Haemophilia influenza type b (Hib) [12][13], meningitis [14], pneumococcal infections [15][16] and enteric diseases such as cholera [17], diarrhea [18] and urinary tract infections [19]. Despite the possibility of

• isolating the polysaccharides by fermentation techniques, it is difficult to get a significant quantity of polysaccharide fragments from natural sources with adequate purity. Therefore, the development of chemical synthetic strategies is quite pertinent to obtain a requisite quantity of oligosaccharide