Computational toolbox for the analysis of protein–glycan interactions

• Ferran Nieto-Fabregat,
• Maria Pia Lenza,
• Angela Marseglia,
• Cristina Di Carluccio,
• Antonio Molinaro,
• Alba Silipo and
• Roberta Marchetti

Beilstein J. Org. Chem. 2024, 20, 2084–2107, doi:10.3762/bjoc.20.180

Polymer degrading marine Microbulbifer bacteria: an un(der)utilized source of chemical and biocatalytic novelty

• Weimao Zhong and
• Vinayak Agarwal

Beilstein J. Org. Chem. 2024, 20, 1635–1651, doi:10.3762/bjoc.20.146

• broad pH range between 5.0 and 9.0 and was highly expressed in Pichia pastoris [79]. Carrageenase Carrageenans are sulfated saccharide polymers with a wide range of commercial applications. The differential sulfation patterns allow for carrageenans to be differentiated into three basic forms – κ-, ι

Switchable molecular tweezers: design and applications

• Pablo Msellem,
• Maksym Dekthiarenko,
• Nihal Hadj Seyd and
• Guillaume Vives

Beilstein J. Org. Chem. 2024, 20, 504–539, doi:10.3762/bjoc.20.45

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

• ][24][25][26]. The structural analysis of GAGs improves the understanding of their biological functions and helps in the development of structure–activity relationships for these important biopolymers [27][28]. Although the composition of the individual saccharide components of GAGs is simple, the

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

• ) where the molecular structure is altered. However, the incorporation of a saccharide unit or an inositol moiety is included in subsequent sections. Modulation sn-1: In 1986, Morris-Natschke et al. [129][130] reported a racemic synthesis of thioether analogues of edelfosine using thioglycerol as

Discrimination of β-cyclodextrin/hazelnut (Corylus avellana L.) oil/flavonoid glycoside and flavonolignan ternary complexes by Fourier-transform infrared spectroscopy coupled with principal component analysis

• Nicoleta G. Hădărugă,
• Gabriela Popescu,
• Dina Gligor (Pane),
• Cristina L. Mitroi,
• Sorin M. Stanciu and
• Daniel Ioan Hădărugă

Beilstein J. Org. Chem. 2023, 19, 380–398, doi:10.3762/bjoc.19.30

• . On the contrary, the presence of highly hydrophilic groups such as saccharide moieties in flavonoid glycosides reduces the level of hydrophobic interactions with the CD cavity. However, less hydrophilic moieties of flavonoid glycosides or flavonolignans interact with CDs (i.e., 4-hydroxyphenyl, 3,4

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

•  5. Given multiple modifications, carbon numbers are written in ascending alphanumeric order. Therefore, dideoxy galactose, or abequose, is written “A[2,6D]” while N-aceytlfucosamine could be written “A[6D,2N]”. Branch rules specify which non-reducing saccharide unit (SU) should be in the branch and

• moieties (Table 3: GR1). For example, “GNb3Ab” connected to a “4-trifluoroacetamidophenol” is written as “GNb3Ab#4-Trifluoroacetamidophenol.” Ambiguous symbol 4 – “ * ”. Another ambiguous symbol is the asterisk “ * ”. In the original Linear Code context, “ * ” is used when an entire saccharide unit in 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

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

• citronellol derivative via a phosphodiester bridge. Moreover, a novel phosphoramidite chemistry-based method offers a straightforward approach for the non-enzymatic incorporation of the saccharide moiety in an anomerically pure form. Keywords: carbohydrates; citronellol; phosphoramidite; photoclickable

Synthesis and conformational preferences of short analogues of antifreeze glycopeptides (AFGP)

• Małgorzata Urbańczyk,
• Michał Jewgiński,
• Joanna Krzciuk-Gula,
• Jerzy Góra,
• Rafał Latajka and
• Norbert Sewald

Beilstein J. Org. Chem. 2019, 15, 1581–1591, doi:10.3762/bjoc.15.162

• the saccharide moiety is conformationally well-defined by the peptide backbone and the whole structure adopts a polyproline II (PP II) helix [17]. Antifreeze activity strongly relies on the stereochemistry of the amino acid residues. Earlier studies have shown that AFGP analogues containing either an

• the saccharide subunits are located on the same side of the molecule, constructing a hydrophilic face, while Ala–CH3 groups are forming a hydrophobic face [17]. Conclusion Our research, although does not fully explain the mechanism of action of AFGPs, provides interesting structural and conformational

Anomeric sugar boronic acid analogues as potential agents for boron neutron capture therapy

• Daniela Imperio,
• Erika Del Grosso,
• Silvia Fallarini,
• Grazia Lombardi and
• Luigi Panza

Beilstein J. Org. Chem. 2019, 15, 1355–1359, doi:10.3762/bjoc.15.135

• . Galactose and fructose also allow tumor growth in the absence of glucose. Boronic acid derivatives have gained interest in the last years in different fields such as the development of enzyme inhibitors, drug delivery polymers, saccharide sensors and as boron carriers for BNCT, e.g., amino acid derivatives

Stereo- and regioselective hydroboration of 1-exo-methylene pyranoses: discovery of aryltriazolylmethyl C-galactopyranosides as selective galectin-1 inhibitors

• Alexander Dahlqvist,
• Axel Furevi,
• Niklas Warlin,
• Hakon Leffler and
• Ulf J. Nilsson

Beilstein J. Org. Chem. 2019, 15, 1046–1060, doi:10.3762/bjoc.15.102

• the anomeric position of the minimal D-galactose ligand allows for an additional affinity-enhancing hydrogen bond according to structural and affinity analyses [20][21]. A complementary strategy has been to, instead of a second saccharide unit, add non-natural structural elements to a monogalactoside

• scaffold, as such derivatives have been hypothesized to allow for tuning of galectin selectivities and to be designed to have improved pharmacokinetic properties over natural saccharide fragments. Early reports along this strategy involved C-galactosides that were shown to reach affinities approaching

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

• SO3− group at O5, due to its size, tends to have trans-orientation to C(3) (see Figure 2). In the case of galactose 3, however, the situation is more complex. This saccharide in its furanoside form has increased conformational flexibility around the C4–C5 bond, because for its lowest energy conformer

• constant in the mannofuranoside upon sulfation arises from the change of the conformational preference towards C1-exo (conformer D) in the sulfated saccharide. The changes in conformation of side chain from trans into gauche rotamers (H4–C4–C5–H5 dihedral angle) upon the sulfation were clearly seen from

Pathoblockers or antivirulence drugs as a new option for the treatment of bacterial infections

• Matthew B. Calvert,
• Varsha R. Jumde and
• Alexander Titz

Beilstein J. Org. Chem. 2018, 14, 2607–2617, doi:10.3762/bjoc.14.239

• . Therefore, multivalent display of lectin and ligand results in a higher avidity [22][23]. The Lindhorst group also synthesized and analyzed so-called glycoclusters, e.g., 7 (Figure 1), where the saccharide moiety is displayed in a multivalent fashion [17][24][25][26]. When this simple trimannosylated

Synthesis of 1,4-imino-L-lyxitols modified at C-5 and their evaluation as inhibitors of GH38 α-mannosidases

• Maroš Bella,
• Sergej Šesták,
• Ján Moncoľ,
• Miroslav Koóš and
• Monika Poláková

Beilstein J. Org. Chem. 2018, 14, 2156–2162, doi:10.3762/bjoc.14.189

• , target enzyme) and lysosomal α-mannosidase (LManII, enzyme not to be inhibited), and commercial enzyme jack bean α-mannosidase (JBMan) from Canavalia ensiformis. In a series of our previous papers, it has been found that a combination of a saccharide core (D-mannose, D-mannose with modification at C-6

• against GMIIb [28][29]. Therefore, the structural design was further developed and a modification of the saccharide core, i.e., a replacement of the D-mannose unit to five-membered imino-L-lyxitol core has been suggested. Indeed, such N-benzyl-substituted polyhydroxypyrrolidines 1 (Figure 1) were found to

• different carbohydrate based scaffolds and their evaluation against a given target is of importance with aim to reveal the role of the saccharide core and aromatic moiety for the interaction with the target enzyme. Conclusion A synthetic approach to imino-L-lyxitols with modification at C-5 is described

Strategies toward protecting group-free glycosylation through selective activation of the anomeric center

• A. Michael Downey and
• Michal Hocek

Beilstein J. Org. Chem. 2017, 13, 1239–1279, doi:10.3762/bjoc.13.123

• access glycosides is an ongoing area of research and one that could have implications that extend far beyond a synthetic chemist’s laboratory [2][3][4]. Glycosylation is a coupling reaction that takes place at the anomeric position (C1–OH) of a saccharide, termed donor, and another molecule, termed the

• attempting glycosylation, generally the other reactive (nucleophilic) groups on the saccharide must be protected to prevent reaction with itself. The accepting molecule is nucleophilic and very often complex as well, and, thus, must also be protected to squelch reactivity at undesired reactive groups. As a

• the synthesis of oligosaccharides, glycoproteins, and nucleosides, both, natural and synthetic. The advantages of utilizing this approach are obvious as the reactions take place using unprotected saccharide donors and acceptor molecules. However, these methods are not without substantial challenges. A

Glycoscience@Synchrotron: Synchrotron radiation applied to structural glycoscience

• Serge Pérez and
• Daniele de Sanctis

Beilstein J. Org. Chem. 2017, 13, 1145–1167, doi:10.3762/bjoc.13.114

• the anomeric configuration of the transferred saccharide, two possible stereo-chemical outcomes occur, either inversion or retention. Based on the CAZy classification, the number of GT families amounts to 90, in a context where sequence homology is low http://www.cazy.org) [36]. The increased number

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

• presentation of saccharide moieties and to exploit the peculiar optical properties of the metallic core. In this review, we present recent advances on glyco-gold nanoparticle applications in different biological fields, highlighting the key parameters which inspire the glyco nanoparticle design. Keywords

• ligand exchange protocol to introduce the thiolated saccharide molecules [20][21][22]. In this frame, the Turkevich method [23] is the most common protocol to produce citrate-capped spherical nanoparticles, with diameter size between 10 and 50 nm. Noteworthy, by employing surfactant or templating agents

• the nanomaterials. Moreover, when the metallic surface is decorated with an active target, the GAuNPs can act as a smart probe, even exploiting the multivalent effect. Several studies were focused on the investigation of synthetic techniques to improve saccharide density on the nanomaterial surface

Orthogonal protection of saccharide polyols through solvent-free one-pot sequences based on regioselective silylations

• Serena Traboni,
• Emiliano Bedini and
• Alfonso Iadonisi

Beilstein J. Org. Chem. 2016, 12, 2748–2756, doi:10.3762/bjoc.12.271

• literature, and can even be further accelerated with a catalytic amount of tetrabutylammonium bromide (TBAB). The strategy proved also useful for either the selective TBDMS protection of secondary alcohols or the fast per-O-trimethylsilylation of saccharide polyols. In the second part of the paper the scope

• of the silylation approach was significantly extended with the development of unprecedented “one-pot” and “solvent-free” sequences allowing the regioselective silylation/alkylation (or the reverse sequence) of saccharide polyols in short times. The developed methodologies represent a very useful and

• experimentally simple tool for the straightforward access to saccharide building-blocks useful in organic synthesis. Keywords: carbohydrates; one-pot synthesis; regioselective protection; silyl protecting group; solvent-free reaction; Introduction The application of an orthogonal set of protecting groups

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

• 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

• . It is obvious that the different saccharide moieties do not significantly influence the rotation barrier around the tertiary peptide bond. Furthermore, the calculated ΔG‡r values are in good accordance with those of other PNA derivates (17.9–19 kcal/mol) [27][28]. Conclusion We have described the

TMSBr-mediated solvent- and work-up-free synthesis of α-2-deoxyglycosides from glycals

• Mei-Yuan Hsu,
• Yi-Pei Liu,
• Sarah Lam,
• Su-Ching Lin and
• Cheng-Chung Wang

Beilstein J. Org. Chem. 2016, 12, 1758–1764, doi:10.3762/bjoc.12.164

• . Subsequently, 65 was coupled with the primary hydroxy saccharide acceptor 23 through a chloride-mediated preactivation glycosylation to afford 66 in 71% yield with moderate selectivity (α:β = 1:2) [16]. Two possible mechanisms are proposed for the α-selectivity observed here (Scheme 2). It is well-accepted

Self and directed assembly: people and molecules

• Tony D. James

Beilstein J. Org. Chem. 2016, 12, 391–405, doi:10.3762/bjoc.12.42

• mechanism to report saccharide binding (Figure 4). Sensei (Seiji Shinkai) then gave me my next and most important academic lesson – if you discover “gold” in one area of research you should keep on digging in that area – the hope is that you will discover a “seam of gold” leading to even more research

• . Independent research – Bath One of the first things I did at Bath was to expand and develop the modular saccharide selective fluorescent sensors which was part of the project with Beckmann-coulter started as a Royal Society University Research Fellow at the University of Birmingham [54][55]. My family also

• pore formers. Reproduced with permission from [6]. Copyright 1990 Elsevier. (b) Unimolecular ion channel. Reproduced with permission from [9]. Copyright 1993 The American Chemical Society. An intelligent liquid crystal to read out saccharide structure as a color-change. Picture provided by Seiji

Supramolecular chemistry: from aromatic foldamers to solution-phase supramolecular organic frameworks

• Zhan-Ting Li

Beilstein J. Org. Chem. 2015, 11, 2057–2071, doi:10.3762/bjoc.11.222

• diameter of approximately 0.8 nm. Thus, 21 complexed alkylated saccharide derivatives and a guest with three hydroxyl groups in chloroform. The binding also induced the backbone of 21 to produce helicity bias [38]. The methoxy groups of 22a–c are all located inwards. These oxygen atoms are potential

Towards inhibitors of glycosyltransferases: A novel approach to the synthesis of 3-acetamido-3-deoxy-D-psicofuranose derivatives

• Maroš Bella,
• Miroslav Koóš and
• Chun-Hung Lin

Beilstein J. Org. Chem. 2015, 11, 1547–1552, doi:10.3762/bjoc.11.170

• charge distribution as it was calculated for the TS [9][10]. In this contribution, attention is focused on the synthesis of the saccharide moiety of potential GnTs inhibitors (framed structure in Figure 1). In this respect, a novel approach to 3-acetamido-3-deoxy-D-psicofuranose derivatives, based on the

• transformation of D-mannose, is described. In addition, the thioglycosylation of fully protected 3-acetamido-3-deoxy-D-psicofuranose 11 with ethanethiol was examined under various conditions. Results and Discussion The synthesis of the saccharide moiety of potential GnTs inhibitors started from commercially

• 1H NMR signals of the acetamide group in derivatives 8, a 3:2 ratio of the anomers was determined, albeit without the exact assignment of anomeric configurations to particular anomers. In the context of the synthesis of the saccharide part of GnTs inhibitors, psicose derivative 7 was subjected to a

Synthesis and evaluation of the biostability and cell compatibility of novel conjugates of nucleobase, peptidic epitope, and saccharide

• Dan Yuan,
• Xuewen Du,
• Junfeng Shi,
• Ning Zhou,
• Abdulgader Ahmed Baoum,
• Khalid Omar Al Footy,
• Khadija Omar Badahdah and
• Bing Xu

Beilstein J. Org. Chem. 2015, 11, 1352–1359, doi:10.3762/bjoc.11.145

• .11.145 Abstract This article reports the synthesis of a new class of conjugates containing a nucleobase, a peptidic epitope, and a saccharide and the evalution of their gelation, biostability, and cell compatibility. We demonstrate a facile synthetic process, based on solid-phase peptide synthesis of

• nucleopeptides, to connect a saccharide with the nucleopeptides for producing the target conjugates. All the conjugates themselves (1–8) display excellent solubility in water without forming hydrogels. However, a mixture of 5 and 8 self-assembles to form nanofibers and results in a supramolecular hydrogel. The

• ; peptidic epitope; saccharide; Introduction This article describes the synthesis and evaluation of a new class of molecular conjugates that consist of a nucleobase, a peptidic epitope, and a saccharide. Nucleobases, amino acids, and saccharides are part of the unified building blocks of life [1] because