GlycoBioinformatics

• Kiyoko F. Aoki-Kinoshita,
• Frédérique Lisacek,
• Niclas Karlsson,
• Daniel Kolarich and
• Nicolle H. Packer

Beilstein J. Org. Chem. 2021, 17, 2726–2728, doi:10.3762/bjoc.17.184

• , type and linkage of glycoconjugate (e.g., N-linked, O-linked glycoprotein, glycolipid, proteoglycan), association with, and regulation of, expression in particular tissues or cell types, and interaction with biological surroundings. With this definition, it is obvious that glycobioinformatics is

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

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

• glycoconjugate synthesis [8][9]. Furthermore, varied reactivity between differentially protected glycosyl fluorides as well as between glycosyl fluorides and other glycosyl donors makes these substrates relevant for more effective glycosylation via orthogonal activation [10][11]. According to the hard–soft acid

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

• then to subsequent ceramide-linked glycoconjugate acceptors, before transport and eventual incorporation into the plasma membrane via vesicular fusion. Gangliosides, which function as antigenic determinants [4], may play a role in membrane organization [5], cell signaling [6], apoptosis [7], and in

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

• rules (SRS), modification rules (MR), branch rules (BR), repetition rules (RR), glycoconjugate rules (GR), and uncertainty rules (UR). The saccharide unit (SU) refers to a structure with four elements: anomericity, position number, modifications, and monosaccharide (MS). Stereospecificity and ring

• connects to the reducing end, Ha3. But if Ab3 was connected to the second Ha3 from right instead, we can specify the point of the cycle using a “c,” nGa6Ga4(-Ab3-)Ub2Ha3Hca3Ha3. Glycoconjugate rules describe when a reducing end of a SU is connected to non-carbohydrate moieties, Glycoconjugate rules

• represent the number of times a certain MS appears, a common use of “ # ”. In LiCoRR, we deprecate the use of “ # ”, “ ; ”, and “ : ” to specify the glycoconjugate class. The number sigh “ # ” can be used to separate a glycan (on the left) from any conjugate (on the right). Colon and semicolon can therefore

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

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

• recently reported by Gao et al. [30] and McQuillan et al. [31]. Once the surface of choice is selected, the glycans need to be conjugated to an appropriate aglycone to form a glycoconjugate which can be used to link the glycan to the surface of the slide. If the glycans are already conjugated to an

• aglycone (for example, a glycolipid obtained directly by extraction from a natural origin), an appropriate surface needs to be selected which is compatible with the glycoconjugate. Printing methods Once the decision about the surface to which they are to be attached is made, the glycans are dissolved in

• to use depending on glycoconjugate and linker type, and scanning requirements. These linker types and surfaces are the most commonly used and there are more specialized surfaces and linker chemistries that are commercially available. Screenshot of microarray databases: (A) Screenshot of an example of

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

• acetate loss during isolation, purification, or protein conjugation leads to structurally altered CPS. Vaccines based on synthetic carbohydrate antigens [11][12][13][14][15] such as the first commercially available semisynthetic glycoconjugate vaccine Quimi Hib® against H. influenzae [16] and Shigella

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

• from E. coli O132 is accomplished in the form of its 2-aminoethyl glycoside. The 2-aminoethyl glycoside is particularly important as it allows further glycoconjugate formation utilizing the terminal amine without affecting the stereochemistry of the reducing end. The target was achieved through a [3

• manipulations on the commercially available monosaccharides and stereoselective chemical glycosylations. The 2-aminoethyl glycoside at the reducing end will facilitate further glycoconjugate formation without hampering the stereochemistry of the anomeric center. We have used similar glycosides in case of other

• Discussion It is important to select a suitable glycoside at the reducing end of the target oligosaccharide keeping in mind that the glycoside should allow further glycoconjugate formation without disturbing the stereochemistry of the anomeric center. Therefore, the 2-aminoethyl glycoside was selected at the

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

• Alexey G. Gerbst Vadim B. Krylov Dmitry A. Argunov Maksim I. Petruk Arsenii S. Solovev Andrey S. Dmitrenok Nikolay E. Nifantiev Laboratory of Glycoconjugate Chemistry, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospect 47, 119991 Moscow, Russia M.V

Design and synthesis of multivalent α-1,2-trimannose-linked bioerodible microparticles for applications in immune response studies of Leishmania major infection

• Chelsea L. Rintelmann,
• Tara Grinnage-Pulley,
• Kathleen Ross,
• Daniel E. K. Kabotso,
• Angela Toepp,
• Anne Cowell,
• Christine Petersen,
• Balaji Narasimhan and
• Nicola Pohl

Beilstein J. Org. Chem. 2019, 15, 623–632, doi:10.3762/bjoc.15.58

• glycoconjugate through recognition by phagocytic cells [43][44][45]. Here we discuss the design and synthesis of this new bioerodible microparticle 2 compared to our previously designed [11] trimannose-coated latex bead construct 1 (Figure 2) and evaluate the biocompatibility of the microparticle in spared dose

• . From the general design elements in Figure 3, we proposed the following synthetic motifs. For PRR binding, a dendrimeric scaffold provides a multivalent display of the α-1,2-trimannose glycoconjugate, similar to Leishmania LPG and additionally may promote glycodendrimer antigen presentation when

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

• based on the glycoconjugate derivatives of these polysaccharides. Isolation of polysaccharides by fermentation of bacterial strains suffer from a number of limitations, which include (a) handling of live strains of bacteria; (b) difficulties in separating biological impurities such as proteins or

• addition, two α-linked D-mannose moieties and one β-linked D-glucose unit are present in the molecule. In view of the importance of oligosaccharides in the development of glycoconjugate-based therapeutics, it was decided to undertake the synthesis of a pentasaccharide corresponding to the repeating unit of

Synthesis of α-D-GalpN₃-(1-3)-D-GalpN₃: α- and 3-O-selectivity using 3,4-diol acceptors

• Emil Glibstrup and
• Christian Marcus Pedersen

Beilstein J. Org. Chem. 2018, 14, 2805–2811, doi:10.3762/bjoc.14.258

• and present in several distinct entities. One of the most studied glycoconjugates, containing this sequence, is the Forssman antigen, in which this disaccharide is the terminal unit. The many biological roles attributed to this particular glycoconjugate and its appearance in some human tumors [1][2

Anomeric modification of carbohydrates using the Mitsunobu reaction

• Julia Hain,
• Patrick Rollin,
• Werner Klaffke and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2018, 14, 1619–1636, doi:10.3762/bjoc.14.138

• important method in the synthetic toolbox for anomeric modification of sugars and glycoconjugate preparation. Left: The Mitsunobu reaction is essentially a nucleophilic substitution of alcohols occurring with inversion of configuration at the alcohol stereocenter. The auxiliary reagents are involved in a

Glycosylation reactions mediated by hypervalent iodine: application to the synthesis of nucleosides and carbohydrates

• Yuichi Yoshimura,
• Hideaki Wakamatsu,
• Yoshihiro Natori,
• Yukako Saito and
• Noriaki Minakawa

Beilstein J. Org. Chem. 2018, 14, 1595–1618, doi:10.3762/bjoc.14.137

• greatly improved the efficiency of the synthesis of nucleosides and oligosaccharides. The results of these syntheses demonstrate the power of glycoside bond-forming reactions, and should assist in the future identification or synthesis of biologically active nucleoside and glycoconjugate derivatives

A stereoselective and flexible synthesis to access both enantiomers of N-acetylgalactosamine and peracetylated N-acetylidosamine

• Bettina Riedl and
• Walther Schmid

Beilstein J. Org. Chem. 2018, 14, 856–860, doi:10.3762/bjoc.14.71

• , glycoproteins serve as ligands for specific extracellular recognition processes toward, e.g., enzymes, lectins or antibodies [2]. In O-linked glycoproteins, also known as mucins, GalNAc becomes covalently α-linked to serine or threonine during post-translational modifications [3][4][5]. This glycoconjugate

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

• were successfully utilized as build-in-adjuvants in fully synthetic self-adjuvanting glycoconjugate cancer vaccines [108][109][110]. 2.3. Synthesis of lipid A from Rhizobium sin-1 The Rhizobiaceae family refers collectively to the group of Gram-negative nitrogen-fixing plant endosymbiont bacteria

Intramolecular glycosylation

• Xiao G. Jia and
• Alexei V. Demchenko

Beilstein J. Org. Chem. 2017, 13, 2028–2048, doi:10.3762/bjoc.13.201

• proteins in the human body are glycosylated [3], and cells display a multitude of glycostructures [4]. Since glycan and glycoconjugate biomarkers are present in all body fluids, they offer a fantastic opportunity for diagnostics. Changes in the level of glycans, as well as changes in glycosylation and

Glyco-gold nanoparticles: synthesis and applications

• Federica Compostella,
• Olimpia Pitirollo,
• Alessandro Silvestri and
• Laura Polito

Beilstein J. Org. Chem. 2017, 13, 1008–1021, doi:10.3762/bjoc.13.100

• on the identification of sugar epitopes of the surface envelope glycoprotein of HIV-1, capable of eliciting a protective response. GAuNPs coated with high-mannose type oligosaccharide of HIV-1 gp120, were prepared as glycoconjugate systems able to mimic the natural presentation of gp-120 high-mannose

Total synthesis of a Streptococcus pneumoniae serotype 12F CPS repeating unit hexasaccharide

• Peter H. Seeberger,
• Claney L. Pereira and
• Subramanian Govindan

Beilstein J. Org. Chem. 2017, 13, 164–173, doi:10.3762/bjoc.13.19

• better immunological understanding of the epitopes that protect from bacterial infection requires defined oligosaccharides obtained by total synthesis. The key to the synthesis of the S. pneumoniae serotype 12F CPS hexasaccharide repeating unit that is not contained in currently used glycoconjugate

• with 85% [17]. In order to improve current glycoconjugate vaccines additional serotypes such as 12F should be included in next-generation preparations [18]. Synthetic oligosaccharides are important tools for the identification of vaccine epitopes and have been the key to the creation of monoclonal

• immunological analysis of S. pneumoniae serotype 12F can be undertaken, and future work will address the expanded inclusion of this antigen in next-generation glycoconjugate vaccines. Abbreviations Ac: acetate ester; BAIB: bis(acetoxy)iodobenzene; Bz: benzoyl; CPS: capsular polysaccharide; DMF: N,N

Synthesis and NMR studies of malonyl-linked glycoconjugates of N-(2-aminoethyl)glycine. Building blocks for the construction of combinatorial glycopeptide libraries

• Markus Nörrlinger,
• Sven Hafner and
• Thomas Ziegler

Beilstein J. Org. Chem. 2016, 12, 1939–1948, doi:10.3762/bjoc.12.183

• Markus Norrlinger Sven Hafner Thomas Ziegler Institute of Organic Chemistry, University of Tuebingen, Auf der Morgenstelle 18, 72076 Tuebingen, Germany 10.3762/bjoc.12.183 Abstract Four glycoconjugate building blocks for the construction of combinatorial PNA like glycopeptide libraries were

• removed and the intermediate amine 9 was condensed with 2a to afford the corresponding glycosylated AEG dipeptide 4 in 58% yield. All glycoconjugate building blocks showed the presence of cis and trans rotamers. Compounds 1a, 1b and 4 were subjected to temperature dependent 1H NMR spectroscopy in order to

• saccharide synthesis makes it sometimes impossible to prepare a certain saccharide or glycoconjugate [9]. Therefore, gaining access to new glycoconjugates which are easily accessible by chemical synthesis and which are able to mimic the interaction between a specific protein and its natural oligosaccharide

Are D-manno-configured Amadori products ligands of the bacterial lectin FimH?

• Tobias-Elias Gloe,
• Insa Stamer,
• Cornelia Hojnik,
• Tanja M. Wrodnigg and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2015, 11, 1096–1104, doi:10.3762/bjoc.11.123

• respective 1-amino-1-deoxyketoheptoses (C-glycosyl-type hexose analogues) can be obtained in exclusively one anomeric form as well as in excellent yields (Scheme 1) [2][3]. Thus, the Amadori rearrangement can be utilised to convert a respectively configured aldoheptose into a C-glycosyl-type glycoconjugate

Orthogonal dual-modification of proteins for the engineering of multivalent protein scaffolds

• Michaela Mühlberg,
• Michael G. Hoesl,
• Christian Kuehne,
• Jens Dernedde,
• Nediljko Budisa and
• Christian P. R. Hackenberger

Beilstein J. Org. Chem. 2015, 11, 784–791, doi:10.3762/bjoc.11.88

• improvements over the alternative active ester immobilization. Although not directly demonstrated in the current paper, our approach required considerably lower amounts of the inhibiting glycoconjugate in comparison to the reverse approach, which involves immobilization of lectin and titration of the binder

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

• programmability of the assemblies lends itself to a combinatorial display of multiple ligands. Recent efforts in the synthesis and applications of such conjugates are discussed. Keywords: glycan; glycoconjugate; DNA display; multivalency; nucleic acid conjugates; oligomeric interaction; Introduction Cell

• spacers and capped by 3 different aryl groups (Figure 9). The fact that the library can be prepared by mix and split synthesis and reformatted in a spatially addressable microarray by simple hybridization [48] greatly facilitates access to diverse glycoconjugate arrays. Screening the library against a

• designed to emulate HIV's gp120 epitope. Combinatorial assembly and selection of two PNA glycoconjugate libraries on DNA templates. DNA display of ligand bridging opposing binding sites in a lectin (ECL). A glycan array prepared by hybridization of glycan–DNA conjugates and screening of RCA120. Multivalent

Synthesis of carbohydrate-scaffolded thymine glycoconjugates to organize multivalency

• Anna K. Ciuk and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2015, 11, 668–674, doi:10.3762/bjoc.11.75

• appropriate carbohydrate conjugation the same molecular architecture could be applied for organization of a divalent glycoconjugate (Figure 1B). We selected thymine as a photocontrollable element as it can undergo [2 + 2] photocycloaddition upon irradiation with light of hν ≥ 290 nm [5][9][10]. Furthermore

• used as scaffold molecule, and α-D-mannosides as specific carbohydrate ligands for the fabrication of the envisaged divalent glycoconjugate (Figure 1C). In the following, we report the synthesis of the divalent glycoconjugates outlined in Figure 1 and their [2 + 2] photocycloaddition. Results and

• of the targeted divalent thymine glycoconjugate started with the known 2-azidoethyl α-D-mannoside (1, Scheme 1) [11][12][13]. The kinetically controlled reaction of mannoside 1 with 2-methoxypropene delivers the 4,6-isopropylidene-protected derivative 2 in good yield, leaving the 2- and 3-hydroxy