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

• -made analysis of over 1000 glycan array datasets from the CFG database (up to v5.1) via a web interface [48]. In this tool, rather than using predefined motifs, it utilizes Multiple Carbohydrate Alignment with Weights (MCAW) algorithm to align glycan structures as sequences based on their

• this software a user uploads a glycan binding protein complexed to a carbohydrate fragment in PDB format. This need not be a co-crystal structure, and can be a modeled structure as well. The application then finds glycans that contain this fragment which are present on the CFG microarray data and

GlypNirO: An automated workflow for quantitative N- and O-linked glycoproteomic data analysis

• Toan K. Phung,
• Cassandra L. Pegg and
• Benjamin L. Schulz

Beilstein J. Org. Chem. 2020, 16, 2127–2135, doi:10.3762/bjoc.16.180

• -glycosylation; O-glycosylation; Python; Introduction Glycosylation is a key post-translational modification critical for protein folding and function in eukaryotes [1][2][3]. Diverse types of glycosylation are known, all involving modification of specific amino acid residues with complex carbohydrate

Convenient access to pyrrolidin-3-ylphosphonic acids and tetrahydro-2H-pyran-3-ylphosphonates with multiple contiguous stereocenters from nonracemic adducts of a Ni(II)-catalyzed Michael reaction

• Alexander N. Reznikov,
• Dmitry S. Nikerov,
• Anastasiya E. Sibiryakova,
• Victor B. Rybakov,
• Evgeniy V. Golovin and
• Yuri N. Klimochkin

Beilstein J. Org. Chem. 2020, 16, 2073–2079, doi:10.3762/bjoc.16.174

• Micromonospora [5]. Dipeptide analogs with phosphonoproline 2 and piperidine-2-phosphonic acid 3 are potent inhibitors of dipeptidyl peptidase IV [6][7]. Oxygen-containing heterocycles containing a phosphoryl group are also of interest in the development of new drugs. It is known that phosphorylated carbohydrate

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

• implicated in the cell’s interactions with its environment, facilitating communication and infection [1][2]. These processes are often initiated by molecular recognition involving carbohydrate-binding proteins (lectins) or by glycan–glycan interactions [1][3][4][5], all events that hinge on specific

• also of how specific modifications affect molecular recognition. Computational Methods All starting structures were generated with the GLYCAM Carbohydrate Builder (http://www.glycam.org). For each sequence we selected the complete set of torsion angle values obtained by variation of the 1-6 dihedrals

• , namely the three gg, gt and tg conformations for each 1-6 torsion. The topology file for each structure was obtained using tleap [31], with parameters from the GLYCAM06-j1 [32] for the carbohydrate atoms and with TIP3P for water molecules [33]. All calculations were run with the AMBER18 software package

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

• . More importantly, we employed the 2-naphthylmethyl ether (Nap) group for protection of various hydroxy groups on the carbohydrate and acyl moieties, aiming to provide an advantage over previous methods that mainly used the benzyl group [4][14][15][16] in synthesizing lipid A derivatives. We also aim at

• reaction sequence of deprotection, acylation, phosphorylation, and global deprotection. The Nap protecting group has emerged as a particularly valuable addition to carbohydrate chemistry [24][25]. Not only does it not significantly alter carbohydrate reactivity, it also can be readily cleaved under

• hydrogenolytic conditions as well as a variety of oxidative [26] and acid-mediated conditions [25][27] that are orthogonal to benzyl ethers. Therefore, we employed the Nap ether as a “permanent” protecting group for the carbohydrate and the 3-hydroxy group of the acyl chain, aiming to provide an advantage over

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

• carbohydrate skeletons resembled the donor substrate: various RSO2 aglycons mimic an approaching acceptor substrate while the 1-O-phosphono moiety represents the leaving UDP [20]. The synthesis of target compounds 1–3 consisted of two different strategies. The first one was applied to a series of ᴅ

When metal-catalyzed C–H functionalization meets visible-light photocatalysis

• Lucas Guillemard and
• Joanna Wencel-Delord

Beilstein J. Org. Chem. 2020, 16, 1754–1804, doi:10.3762/bjoc.16.147

• , ortho-C–H activation delivering the photoactive intermediate. Under visible-light irradiation, the SET process from the excited ruthenacycle to the haloalkane coupling partner leads to the formation of a stabilized alkyl radical (Figure 39). Next, radical attack at the para-position of the carbohydrate

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

• individual building blocks (e.g., the phosphoramidites) will enable the creation of a series of molecular probes with different functional groups and varying linker lengths with relatively little effort. The crucial step in the synthetic pathway consists of the conversion of the carbohydrate intermediates

• configuration at the anomeric position and to prove the working principle of our synthetic strategy, we used 2D NMR experiments. Coupled HSQC measurements revealed the 1JCH coupling constants of our compounds and thereby the absolute configuration at the anomeric center of the carbohydrate [40][41][42]. For MPC

• achieved by following literature procedures [35][36], which provided the pure β-anomer as a crystalline solid. Secondly, suitable conditions had to be identified for the subsequent phosphitylation conditions under which no mutarotation of the carbohydrate occurs. Cooling of the reaction mixture and

One-pot synthesis of isosorbide from cellulose or lignocellulosic biomass: a challenge?

• Isaline Bonnin,
• Raphaël Mereau,
• Thierry Tassaing and
• Karine De Oliveira Vigier

Beilstein J. Org. Chem. 2020, 16, 1713–1721, doi:10.3762/bjoc.16.143

• hardwood and wheat straw led to the highest isosorbide yield of 7%. This can be due to a higher carbohydrate content and a lower amount of impurities than in the other raw materials. Based on this, the pretreatment of the delignified biomass will promote the synthesis of isosorbide. Hence, CIMV-delignified

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

• 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

A dynamic combinatorial library for biomimetic recognition of dipeptides in water

• Florian Klepel and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2020, 16, 1588–1595, doi:10.3762/bjoc.16.131

• developed a DCL composed of Cu2+, Ni2+ complexes. The addition of dipeptides caused characteristic spectral changes by ligand-exchange reactions [18]. We previously used a peptide derived DCL for the development of artificial carbohydrate receptors [19][20]. An intriguing example derived from that work is

• , which is in agreement with the apparently weaker interaction in D2O [25]. Conclusion In summary, we demonstrated that artificial peptide receptors can emerge from a peptide-based DCL under competitive conditions in water. In agreement with our previous works on carbohydrate recognition, this supports

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

• industrially infeasible [97]. Carbon spheres are also prepared by hydrothermal treatment of aqueous low cost biomass, such as lignocellulosic materials, or carbohydrate precursor solutions at defined temperatures in closed systems [100][101]. The proposed mechanism of the formation of carbon spheres seems

• conform to the LaMer model and starts with a polymerization step of the carbohydrate monomers and followed by a carbonization step when the nucleation is caused by the supersaturation of the solution. The resulting nuclei grow uniformly until the final size is obtained depending on the growth parameters

Synthesis of new asparagine-based glycopeptides for future scanning tunneling microscopy investigations

• Laura Sršan and
• Thomas Ziegler

Beilstein J. Org. Chem. 2020, 16, 888–894, doi:10.3762/bjoc.16.80

• containing glycopeptides were prepared in solution. The applicability of two common peptide coupling reagents, using an orthogonal Fmoc/t-Bu strategy along with acetyl protecting groups for the carbohydrate moiety, was studied. Thus, the prepared libraries of glycopeptides were designed as model systems of

Two antibacterial and PPARα/γ-agonistic unsaturated keto fatty acids from a coral-associated actinomycete of the genus Micrococcus

• Amit Raj Sharma,
• Enjuro Harunari,
• Naoya Oku,
• Nobuyasu Matsuura,
• Agus Trianto and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 297–304, doi:10.3762/bjoc.16.29

• key roles in lipid and carbohydrate metabolism [43][44]. PPARα upregulates lipid uptake and β-oxidation of fatty acids, whereas PPARγ promotes adipocyte differentiation and adipokine production in adipose tissues to improve insulin sensitivity in diabetic patients [45][46][47]. Owing to these

Combination of multicomponent KA² and Pauson–Khand reactions: short synthesis of spirocyclic pyrrolocyclopentenones

• Riccardo Innocenti,
• Elena Lenci,
• Gloria Menchi and
• Andrea Trabocchi

Beilstein J. Org. Chem. 2020, 16, 200–211, doi:10.3762/bjoc.16.23

• different compounds, such as (−)-kainic acid [51][52]. Previous similar approaches reported only planar pyrrolocyclopentenones starting from propargyl alcohol–cobalt complexes and allyl amides [50], or carbohydrate-derived allylpropargylamine [49] (Scheme 1a). Results and Discussion Cyclohexanone (1) and

Synthesis of C-glycosyl phosphonate derivatives of 4-amino-4-deoxy-α-ʟ-arabinose

• Lukáš Kerner and
• Paul Kosma

Beilstein J. Org. Chem. 2020, 16, 9–14, doi:10.3762/bjoc.16.2

• important, e.g., when connected to dolichol in mammalian systems or to undecaprenol in prokaryotic donor substrates for bacterial glycosyltransferases [2]. 4-Amino-4-deoxy-ʟ-arabinose (Ara4N) is an important microbial carbohydrate in bacterial lipopolysaccharides (LPS) and has been implicated in resistance

SnCl₄-catalyzed solvent-free acetolysis of 2,7-anhydrosialic acid derivatives

• Kesatebrhan Haile Asressu and
• Cheng-Chung Wang

Beilstein J. Org. Chem. 2019, 15, 2990–2999, doi:10.3762/bjoc.15.295

• . HMBC spectrum of carbohydrate 22. Concise synthesis of 2,7-anhydrosialic acid derivatives 2–6. Conditions for the preparation of 2 and 3, respectively, from 1 have been reported previously [6]. N- and C-1-functionalization of 2. Mechanism of the SnCl4-catalyzed acetolysis of 2,7-anhydro derivatives 15

Regioselectivity of glycosylation reactions of galactose acceptors: an experimental and theoretical study

• Enrique A. Del Vigo,
• Carlos A. Stortz and
• Carla Marino

Beilstein J. Org. Chem. 2019, 15, 2982–2989, doi:10.3762/bjoc.15.294

• amounts of carbohydrate-containing molecules. Due to the chemical nature of carbohydrates, with multiple possible linkage positions giving rise to different regioisomers, with two possible anomeric configurations, the chemical synthesis of complex oligosaccharides is difficult and a rather time-consuming

Indium-mediated C-allylation of melibiose

• Christian Denner,
• Manuel Gintner,
• Hanspeter Kählig and
• Walther Schmid

Beilstein J. Org. Chem. 2019, 15, 2458–2464, doi:10.3762/bjoc.15.238

• elongation methodology allows for a short, efficient and diastereoselective approach towards complex glycosylated carbohydrate structures. The stereochemical outcome of the key intermediates, allylated disaccharides, has been determined by X-ray analysis. Ozonolysis of the introduced double bond yielded the

• established as reliable and efficient approach in carbohydrate chemistry, shown by many examples reported in the literature [8][9][10][11][12]. Thus far, this method has been applied to monosaccharides [13][14]. In this context, the development of diastereoselective and efficient synthetic routes to elongated

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

• and Cβ carbons of the glycosylated Thr residue. The all-ᴅ-configured pentapeptide 4 turned out to adopt a much more rigid structure in comparison to the corresponding peptide 3 containing only ʟ-amino acids. Moreover, pentapeptide 4 showed the ability to “lock” the orientation of the carbohydrate ring

• anhydride (50 equiv), DIEA (12.5 equiv), 1-hydroxybenzotriazole (HOBt,1 equiv) in DMF at room temperature for 40 min. Subsequently, the carbohydrate moieties were deacetylated using 1.0 M hydrazine in dry THF at room temperature for 2 hours. The peptides were cleaved from the resin by treatment with 7–10

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

• boron-containing carbohydrate derivatives for BNCT has received special attention because of the sugar-preferential uptake by tumor cells [3]. Tumor cells perform glycolysis at a faster rate than their noncancerous tissue counterparts, so increasing the glucose consumption with respect to healthy cells

Steroid diversification by multicomponent reactions

• Leslie Reguera,
• Cecilia I. Attorresi,
• Javier A. Ramírez and
• Daniel G. Rivera

Beilstein J. Org. Chem. 2019, 15, 1236–1256, doi:10.3762/bjoc.15.121

• and complexity-generating processes [2][3] have proven success in peptide ligation [4] and macrocyclization [5][6], protein glycoconjugation [7], lipidation of peptides [8] and glycosides [9], and carbohydrate modification [10]. A special class of lipidic biomolecules are the steroids, which can be

• , thus producing unique types of steroidal conjugates. Scheme 17 depicts the strategy toward steroidal conjugates using the Ugi-4CR, which allows accessing a high level of diversity by varying the combinations of the carbohydrate, peptide and steroidal functional groups reacting on the multicomponent

• of skeletal diversity attached to the steroid ring system, while many other modern methods have also shown success using steroidal as one of their components. In addition, we showed that the synthesis of steroid–peptide and steroid–carbohydrate conjugates is feasible by means of both solution and

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

• /bjoc.15.102 Abstract Galectins are carbohydrate recognition proteins that bind carbohydrates containing galactose and are involved in cell signaling and cellular interactions, involving them in several diseases. We present the synthesis of (aryltriazolyl)methyl galactopyranoside galectin inhibitors

• ; galectin-1; hydroboration; inhibition; selective; triazole; Introduction Galectins are defined by a typically about 130 amino acid carbohydrate recognition domain (CRD) that binds to carbohydrates with at least one β-galactose subunit within a binding pocket large enough to accommodate a tetrasaccharide

Towards the preparation of synthetic outer membrane vesicle models with micromolar affinity to wheat germ agglutinin using a dialkyl thioglycoside

• Dimitri Fayolle,
• Nathalie Berthet,
• Bastien Doumeche,
• Olivier Renaudet,
• Peter Strazewski and
• Michele Fiore

Beilstein J. Org. Chem. 2019, 15, 937–946, doi:10.3762/bjoc.15.90

• ]. Some of them have been obtained by coupling protected glycosyl thiolates and n-alkyl halides [14][15][16]. Moreover, mechanochemical thioglycosylation of glycosyl acetates was used for the synthesis of n-alkyl 1-thio-α--glycosides as carbohydrate mesogens [17]. Unfortunately, the preparation of alkyl

• thiyl-radical-mediated reactions have been extensively investigated for the preparation of carbohydrate derivatives [20] and some dithioether phospholipid and glycolipid analogues [21][22], no examples were reported for the synthesis of n-alkyl thioglycosides by using thiol–ene coupling [18][19]. In

• affinities to GlcNAc [31]. The proximity of adjacent binding sites (≈14 Å) [32] makes this lectin an excellent candidate to investigate multivalent carbohydrate–protein interactions [33]. Although the scientific literature is rich of remarkable examples of biologically active carbohydrate-based compounds

The LANCA three-component reaction to highly substituted β-ketoenamides – versatile intermediates for the synthesis of functionalized pyridine, pyrimidine, oxazole and quinoxaline derivatives

• Tilman Lechel,
• Roopender Kumar,
• Mrinal K. Bera,
• Reinhold Zimmer and
• Hans-Ulrich Reissig

Beilstein J. Org. Chem. 2019, 15, 655–678, doi:10.3762/bjoc.15.61

• carboxylic acids with tertiary centers are possible candidates for the route to β-ketoenamides. The last example shown in Scheme 5 demonstrates that allenes with chiral alkoxy substituents are also suitable starting materials in the three-component reaction. We did not study lithiated carbohydrate-derived