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

• functions results principally from their unique physicochemical and structural features, including high negative charge, high viscosity and lubrication propensities, unbranched polysaccharide structures, low compressibility as well as the ability to attract and imbibe large amounts of water [17]. Unlike

Radical chemistry in polymer science: an overview and recent advances

• Zixiao Wang,
• Feichen Cui,
• Yang Sui and
• Jiajun Yan

Beilstein J. Org. Chem. 2023, 19, 1580–1603, doi:10.3762/bjoc.19.116

• lacquerwares several thousand years ago [5]. The surface coating of lacquerwares was made up of a sap from a lacquer tree growing in Asia. The lacquer sap obtained from Rhus vernicifera lacquer tree mainly consists of urushiol (60–65%), water (20–30%), lacquer polysaccharide (3–7%), water-insoluble

pH-Responsive fluorescent supramolecular nanoparticles based on tetraphenylethylene-labelled chitosan and a six-fold carboxylated tribenzotriquinacene

• Nan Yang,
• Yi-Yan Zhu,
• Wei-Xiu Lin,
• Yi-Long Lu and
• Wen-Rong Xu

Beilstein J. Org. Chem. 2023, 19, 635–645, doi:10.3762/bjoc.19.45

• -induced emission (AIE) character [20][21]. Chitosan (CS) is a natural cationic polysaccharide, which is considered an ideal material for the construction of drug delivery systems due to its nontoxic, biocompatible, biodegradable, and easily functionalized properties [22]. Herein, we designed and

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

• polysaccharide networks using cyclodextrin to prepare green adsorbents [37]. The use of saponins added into the reactive mixture in order to produce a foam allows us to prepare porous materials, in order to enhance their sorption capabilities when a low amount of the sorbate is present in the solution. The

• a maximum of foam volume will be produced. This value will correspond to the minimum amount of this ingredient required to produce the cyclodextrin/polysaccharide foams. As can be seen in Figure 1 (left), two linear fittings were applied in the foam volume vs concentration plot, where the junction

• affect this value. Nevertheless, a concentration of 0.5% of saponin was selected as an initial value to prepare the polysaccharide foams. In order to study their stability, the foams were introduced into a graduated cylinder after stirring each mixture solution (Figure 1, right). Samples with three

Synthesis of protected precursors of chitin oligosaccharides by electrochemical polyglycosylation of thioglycosides

• Md Azadur Rahman,
• Kana Kuroda,
• Hirofumi Endo,
• Norihiko Sasaki,
• Tomoaki Hamada,
• Hiraku Sakai and
• Toshiki Nokami

Beilstein J. Org. Chem. 2022, 18, 1133–1139, doi:10.3762/bjoc.18.117

• is an abundant β-1,4-linked polysaccharide composed of N-acetylglucosamine as repeating unit (Figure 1) [1]. Biological activities of longer oligosaccharides, such as octasaccharide, have been paid much attention for many years. However, it is difficult to obtain pure oligosaccharides by isolation

Recent developments and trends in the iron- and cobalt-catalyzed Sonogashira reactions

• Surendran Amrutha,
• Sankaran Radhika and
• Gopinathan Anilkumar

Beilstein J. Org. Chem. 2022, 18, 262–285, doi:10.3762/bjoc.18.31

• reaction (Scheme 31). Non-nanoparticle-based protocols Nanoparticles are materials with sizes around nanometer scales. The used nanoparticles are environmentally friendly magnetic cross-linked chitosan fibers which is a natural polysaccharide polymer. In this regard the use of such polymers is promising

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

• . Structurally, the O-antigens consist of polysaccharide repeating units bearing several different monosaccharides. Due to their importance in regulating the host’s immune system, the bacterial cell surface LPS in general and the O-antigens in particular have been proposed and reported as candidates for vaccine

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

• current literature, despite the importance of it for applications such as scaffold materials [29]. A recent review article by Savina et al. highlights biodegradable cryogels and their applications, including a variety of biocompatible polysaccharide-based cryogels [8]. 3. Stimuli-responsive cryogels

• groups (i.e., -NH2), and (iii) polyamphoterics with both weakly acidic and weakly basic groups. The scientific community is especially interested in using these properties in specific drug-delivery systems; the potential of using polysaccharide-based specific drug-delivery systems in the colon has been

• lasting T cells. Similar positive results were attained by Tam et al., who synthesized biomimetic cryogels whilst also analysing the mechanism of their formation [7][94]. They examined the effects of mono/disaccharide additives on the size of pores and how they interact with polysaccharide polymers to

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

• ]. Nevertheless, the complexity and diversity of polysaccharides makes synthetic processes extremely laborious and time consuming. Several aspects are crucial to plan a successful polysaccharide synthesis. Properly designed starting materials and/or catalysts are required to ensure regio- and stereocontrol during

• glycosidic bond formation. Control over the polysaccharide length (degree of polymerization, DP) and regioselective insertion of modifications or branches are additional challenges. Three main approaches are available (Figure 1): A) enzymatic polymerization [10][11][12][13][14][15][16][17], B) chemical

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

• Eleni Dimitriou Gavin J. Miller Lennard-Jones Laboratory, School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire, ST5 5BG, U. K. 10.3762/bjoc.17.110 Abstract Alginate is a biocompatible and industrially relevant polysaccharide that derives many of its important

• properties from the charged carboxylate groups within its polyuronic acid backbone. The design and inclusion of isosteric replacements for these carboxylates would underpin provision of new oligo-/polysaccharide materials with alternate physicochemical properties. Presented herein is our synthesis of

• ; Introduction Alginate is an important, industrially relevant polysaccharide chemically composed of β-1,4-linked ᴅ-mannuronic acid (M) and α-ʟ-guluronic acid (G) monosaccharide building blocks (Figure 1a). Because of its biocompatibility, alginate has several commercial industrial applications; for example, it

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

Selected peptide-based fluorescent probes for biological applications

• Debabrata Maity

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

• bacteria [57]. It is a glycolipid consisting of a variable polysaccharide domain connected to a conserved glucosamine-based phospholipid called lipid A. It is highly negatively charged due to two phosphorylated groups in the lipid A part and carboxylated groups in the polysaccharide part. It is amphiphilic

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

• . The “Ma6 or Ma3” constraint promotes the reaction if either Ma6 or Ma3 exists. “~Ma6” means the reaction will not happen if Ma6 is present in the glycan. The structure denotations are indicators of certain parts of the glycan. The entry “ ... ” can be replaced with either nothing or any polysaccharide

• with matched parenthesis. The entry “ _ ”, in Krambeck et al., can be replaced with either nothing or any polysaccharide where each left parenthesis is matched to a right parenthesis but where right parentheses are not necessarily matched. Entry “ | ” represents a possible branch. We expand on the

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

• glycobiologists or any researcher looking for a ready to use, simple program for the sketching or building of glycans. Keywords: bioinformatics; carbohydrate; glycan; glycobiology; nomenclature; oligosaccharide; polysaccharide; representation; structure; Introduction Glycoscience is a rapidly surfacing and

• when depicting carbohydrates, but such features are simply absent in most of the existing glycan sketching tools. Another feature that may become essential when the carbohydrate at hand is a polysaccharide is the possibility of building repeating units. Without this option, it would be simply

• -builder.cermav.cnrs.fr/) with an interactive and more usable interface (Figure 10). The software translates a glycan sequence or polysaccharide repeat unit into the coordinate set of the corresponding tertiary structure, in one or several of its low energy conformations. The construction follows an intuitive scheme

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

• , Poland 10.3762/bjoc.16.188 Abstract Mechanochemistry is an emerging and reliable alternative to conventional solution (batch) synthesis of complex molecules under green and solvent-free conditions. In this regard, we report here on the conjugation of a dextran polysaccharide with a fluorescent probe, a

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

• differs by the addition or removal of some glycans from the list. The mammalian glycan arrays contain between 200–611 different glycan compounds printed per microarray. The pathogen array consists of glycans/polysaccharide isolated from bacterial sources and currently has over 300 compounds printed, with

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

• ]. The mycobacterial cell wall core is formed by the mycolyl–arabinogalactan–peptidoglycan (mAGP) complex, which provides a highly hydrophobic and resistant barrier surrounding the bacterium [3]. The galactan component of the cell wall consists of polysaccharide chains composed of approximately 22

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

• the O-specific polysaccharide of Azospirillum doebereinerae type strain GSF71T in a very good yield adopting sequential glycosylation followed by removal of the p-methoxybenzyl (PMB) group in the same pot. Further, the synthetic strategy was modified by carrying out three stereoselective iterative

• glycosyl activator. Keywords: Azospirillum doebereinerae; glycosylation; HClO4-SiO2; O-polysaccharide; tetrasaccharide; Introduction The development of plant-growth-promoting agents has become an attractive area of research in the agricultural sciences to reduce the need for chemical fertilizers, which

• ]. Recently, Sigida and co-workers reported the structure of the tetrasaccharide repeating unit of the O-specific polysaccharide of Azospirillum doebereinerae type strain GSF71T, which is composed of three α-ʟ-rhamnose units and one β-ᴅ-glucosamine moiety [21]. It also contains two O-acetyl groups which might

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

• Chemistry and Biochemistry, Arnimallee 22, 14195 Berlin, Germany 10.3762/bjoc.16.140 Abstract Streptococcus pneumoniae (SP) bacteria cause serious invasive diseases. SP bacteria are covered by a capsular polysaccharide (CPS) that is a virulence factor and the basis for SP polysaccharide and glycoconjugate

• developing countries [3]. With increasing antimicrobial resistance to antibiotics, vaccines are becoming even more important to control these pathogens. Despite the availability of multivalent polysaccharide and glycoconjugate vaccines such as Pneumovax, Prevnar® 13, and Synflorix, pneumonococcal diseases

• degree of acetylation of the same pentasaccharide RU. The positions and degree of RU acetylation has been revised several times since the initial structure 1 was proposed in 1981 (2 and 3 in Figure 1) [20][21][22]. Antibodies raised against the natural 9V polysaccharide recognize the natural and the de-O

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

• 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

• fragments with adequate purity. In this direction, the total synthesis of the pentasaccharide repeating unit corresponding to the cell wall O-antigenic polysaccharide of the E. albertii O4 strain using a sequential glycosylation strategy is presented herein (Figure 1). Results and Discussion The synthesis

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

• Debasish Pal Balaram Mukhopadhyay Sweet Lab, Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, Nadia 741246, India 10.3762/bjoc.15.249 Abstract The total chemical synthesis of the pentasaccharide repeating unit of the O-polysaccharide

• glycoside; diarrhea; galactofuranose; O-specific polysaccharide; total synthesis; Introduction O-Polysaccharides are the most complex molecular systems present in the bacterial cell wall owing to the presence of various sugar residues connected through diverse glycosidic linkages. These complex structures

• the causative agent for septicemia in chicken [3], diarrhea in children under three years of age [4], diarrhea in calves and rabbits [5][6]. Recently, Knirel et al. [7] reported the structure of the O-polysaccharide of E. coli O132 as a pentasaccharide repeating unit consisting of GlcNAcp, Glcp, Rhap

An overview of the cycloaddition chemistry of fulvenes and emerging applications

• Ellen Swan,
• Kirsten Platts and
• Anton Blencowe

Beilstein J. Org. Chem. 2019, 15, 2113–2132, doi:10.3762/bjoc.15.209

• room temperature and the resulting polymers were processed as thin films. As a result of the dynamic nature of the Diels–Alder adducts, the films were shown to possess self-healing capabilities [190]. Similarly, Wei et al. employed DAC to create a self-healing hydrogel using a polysaccharide

Mechanochemical amorphization of chitin: impact of apparatus material on performance and contamination

• Thomas Di Nardo and
• Audrey Moores

Beilstein J. Org. Chem. 2019, 15, 1217–1225, doi:10.3762/bjoc.15.119

• expedite polysaccharide hydrolytic cleavage [20][21][22][23]. Milling can also facilitate chitin depolymerization [24] and when used with base simultaneously deacetylate and depolymerize chitin [42]. One of the key processes in the context of biomass upgrading is amorphization. Indeed, both chitin and

• of polysaccharides In a typical experiment, 200 mg of polysaccharide, chitin was placed in a jar equipped with one ball and milled in a MM 400 mixer mill for 30 min at 29.5 Hz. The resulting powder was used as is for analysis. Powder X-ray diffraction (PXRD) Sample diffractogram was recorded from 5

Convergent synthesis of the pentasaccharide repeating unit of the biofilms produced by Klebsiella pneumoniae

• Arin Gucchait,
• Angana Ghosh and
• Anup Kumar Misra

Beilstein J. Org. Chem. 2019, 15, 431–436, doi:10.3762/bjoc.15.37

• pentasaccharide derivative using phase-transfer reaction conditions furnished the target compound in satisfactory yield. Keywords: beta-D-mannoside; biofilms; D-glucuronic acid; glycosylation; Klebsiella pneumoniae; pentasaccharide; polysaccharide; Introduction Klebsiella pneumoniae (K. pneumoniae) is a Gram

• nucleic acids and (c) loss of homogeneity of the polysaccharide fragments to name a few. It has already been established that in many cases the oligosaccharide repeating units resemble similar antigenic potential to those of the native polysaccharides [8][9][10]. Therefore, the best alternative way to get

• acid corresponding to the repeating unit of the biofilm producing polysaccharide secreted by K. pneumoniae. The unique feature of this pentasaccharide is that it contains a β-D-mannosidic moiety and a α-D-glucuronic acid moiety, which are known to be challenging from the synthetic point of view. In

Unexpected loss of stereoselectivity in glycosylation reactions during the synthesis of chondroitin sulfate oligosaccharides

• Teresa Mena-Barragán,
• José L. de Paz and
• Pedro M. Nieto

Beilstein J. Org. Chem. 2019, 15, 137–144, doi:10.3762/bjoc.15.14

• substitution pattern of GlcA units for the efficient synthesis of CS oligomers. Keywords: carbohydrate chemistry; chondroitin sulfate; glycosylation; oligosaccharide synthesis; stereoselectivity; Introduction Chondroitin sulfate (CS) is a highly heterogeneous polysaccharide, constituted by the repetition of