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

• sugar model [3], checks that structures match the nomenclature used for deposition in the PDB [14], compares glycan compositions to known structures as reported by glycomics (e.g., GlyConnect [19]) and glyco-informatics (e.g., GlyTouCan [20]) databases and repositories [15], and checks how close the

• nomenclature for glycan SVG, and an array of sugar entries. The validation data calculated by Privateer for each sugar entry is shown in Table 2, and that for each linkage is shown in Table 3. Visualising a validation report While the database is available on GitHub for programmatic access, viewing a

• available alongside the Privateer Web App [26], https://privateer.york.ac.uk/database. The first section of this visual report displays a global outlook on the validity of the model through two graphs. The first graph shows the conformational landscape for the pyranose sugars. For a sugar model to be deemed

Synthesis and properties of 6-alkynyl-5-aryluracils

• Ruben Manuel Figueira de Abreu,
• Till Brockmann,
• Alexander Villinger,
• Peter Ehlers and
• Peter Langer

Beilstein J. Org. Chem. 2024, 20, 898–911, doi:10.3762/bjoc.20.80

• proven medical potential of uracil, further investigation was carried out to fully utilize the synthetic possibilities uracil has to offer and to synthesize new drugs against existing or hitherto unknown targets. Moreover, studies have even shown that a sugar moiety is not always required to act against

Methodology for awakening the potential secondary metabolic capacity in actinomycetes

• Shun Saito and
• Midori A. Arai

Beilstein J. Org. Chem. 2024, 20, 753–766, doi:10.3762/bjoc.20.69

• higher yield of validamycin A (25) from Streptomyces hygroscopicus 5008 together with more rapid protein synthesis and sugar consumption by subjecting cultures to one or more NaOH shocks [66]. Ren et al. obtained enhanced ε-poly-ʟ-lysine (ε-PL, 26) production by acidic pH shock of Streptomyces sp. M-Z18

Chemoenzymatic synthesis of macrocyclic peptides and polyketides via thioesterase-catalyzed macrocyclization

• Senze Qiao,
• Zhongyu Cheng and
• Fuzhuo Li

Beilstein J. Org. Chem. 2024, 20, 721–733, doi:10.3762/bjoc.20.66

• , tylactone (39), and a dimethylamino sugar, which are synthetically challenging. Therefore, the synthesis and evaluation of tylosin-related macrolides are hot topics in medicinal chemistry [66][74]. With the experience in pikromycins synthesis, Sherman and co-workers investigated the capabilities of two

Isolation and structure determination of a new analog of polycavernosides from marine Okeania sp. cyanobacterium

• Kairi Umeda,
• Naoaki Kurisawa,
• Ghulam Jeelani,
• Tomoyoshi Nozaki,
• Kiyotake Suenaga and
• Arihiro Iwasaki

Beilstein J. Org. Chem. 2024, 20, 645–652, doi:10.3762/bjoc.20.57

• HMBC, δH 3.64 (H-3’)/δC 103.0 (C-1”), indicated that these two sugar structures were connected through a glycosidic bond. The geometries of the two olefins at C-16 and C-20 were determined to be trans based on the large coupling constants, 3JH-16/H-17 15.0 Hz and 3JH-20/H-21 15.0 Hz, respectively. The

Introduction of a human- and keyboard-friendly N-glycan nomenclature

• Friedrich Altmann,
• Johannes Helm,
• Martin Pabst and
• Johannes Stadlmann

Beilstein J. Org. Chem. 2024, 20, 607–620, doi:10.3762/bjoc.20.53

• ) (Figure 5). Another difficulty is posed by the blood group H α1,2-fucose, which is linked to galactose, which in turn can be linked β1,3- or β1,4 to GlcNAc. So just putting “F” as the terminal sugar would leave uncertainty. Therefore – using linear code [41] – we write F2-A4. We – again – can save one

• “HNK-1” (from human natural killer cells) with sulfated glucuronic acid [47]. Annotating a structure like this requires some form of linear code and the addition of abbreviations for non-sugar substituents, in this case sulfate. Note that the hyphen binds the “su” to “Ga”, which in turn is hyphenated

• -vertebrates contain numerous “unusual” and remarkable structural features such as methylation, sulfation, and zwitterionic non-sugar substituents, again glucuronic acid and often unusual architectures such as substituted core-fucose just as an example [44][52]. While the methylated moss glycans are accessible

A myo-inositol dehydrogenase involved in aminocyclitol biosynthesis of hygromycin A

• Michael O. Akintubosun and
• Melanie A. Higgins

Beilstein J. Org. Chem. 2024, 20, 589–596, doi:10.3762/bjoc.20.51

• PF01408, in which Hyg17 is a member (Figure 3). PF01408 is classified as an oxidoreductase with NAD-binding Rossmann fold family and contains over 340,000 sequences. Many of the family members act as sugar dehydrogenases with diverse sugar substrates (Supporting Information File 1, Table S1). These

• enzymes can have distinct biological functions, such as sugar metabolism and LPS biosynthesis [19][20][21][22][23]. By contrast, other members are involved in natural product biosynthetic pathways similar to Hyg17 [24][25][26]. Although many of the PF01408 enzymes have reported activities, the SSN shows

Elucidating the glycan-binding specificity and structure of Cucumis melo agglutinin, a new R-type lectin

• Jon Lundstrøm,
• Emilie Gillon,
• Valérie Chazalet,
• Nicole Kerekes,
• Antonio Di Maio,
• Ten Feizi,
• Yan Liu,
• Annabelle Varrot and
• Daniel Bojar

Beilstein J. Org. Chem. 2024, 20, 306–320, doi:10.3762/bjoc.20.31

• (Val6 to Asp132) could be modelled, and unambiguous electron density permitted us to locate and model four cation binding sites (three in each structure) and one sugar binding site (Figure 4a,b and Figure S4, Supporting Information File 2). The complexed structures allowed us to shed light on the

• 10 µL/min. Surfaces were regenerated with 30 s injections of 50 mM NaOH and 1 M NaCl. IC50 was measured using the response at equilibrium for each concentration of competitive sugar that were translated in percentage of inhibition, then plotted against the molar concentration of competitive sugar

• -up on the interactions between CMA1 and LacNAc (c) or GalNAc (d), with the 2mFo-DFc electron density map displayed around the sugar ligands at 1 sigma (LacNAc: 0.47 e·Å−3, GalNAc: 0.415 e·Å−3). Water molecules are indicated by red spheres and interactions by proximal residues are indicated by broken

Identification of the p-coumaric acid biosynthetic gene cluster in Kutzneria albida: insights into the diazotization-dependent deamination pathway

• Seiji Kawai,
• Akito Yamada,
• Yohei Katsuyama and
• Yasuo Ohnishi

Beilstein J. Org. Chem. 2024, 20, 1–11, doi:10.3762/bjoc.20.1

• had been difficult to achieve in our previous studies because of the low enzymatic activity of AvaA6. The kinetic values for AvaA7 are in a reasonable range for an enzyme of this family (e.g., some NADPH-dependent sugar epimerases reported to have kcat/Km values of 0.79 and 0.86 min−1 µM−1) and

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

• proteins. The structural and functional heterogeneities of GAGs as well as their ability to bind specific proteins are determined by the sugar composition of the GAG, the size of the GAG chains, and the degree and pattern of sulfation. A deep understanding of the interactions in protein–GAG complexes is

• . Additionally, since the ligands used in the study are longer, they expand over the binding site and interact with the other parts of the protein as well. Experimental structures cover only a small part of the actual GAG molecule that interacts with the protein (as GAGs are built of tens to thousands of sugar

Sulfur-containing spiroketals from Breynia disticha and evaluations of their anti-inflammatory effect

• Ken-ichi Nakashima,
• Naohito Abe,
• Masayoshi Oyama,
• Hiroko Murata and
• Makoto Inoue

Beilstein J. Org. Chem. 2023, 19, 1604–1614, doi:10.3762/bjoc.19.117

• electrospray ionization HRESIMS analysis, and quantum chemical electronic CD calculations. Furthermore, the absolute configurations of sugar residues were determined by derivatization of the hydrolysates with ʟ-cysteine methyl ester and o-tolyl isothiocyanate followed by HPLC analysis. The anti-inflammatory

• ′′′′. The linkages in the sugar moiety were determined based on the HMBC correlations of H-1′/C-3, H-1′′/C-2′, H-1′′′/C-3′′′, and H-1′′′′/C-2′′ and the SSCCs of the anomeric protons. The sugars contained in 1 and their absolute configurations were confirmed by analyzing the monosaccharide mixture obtained

• HRESIMS. The 1H NMR spectrum (Table 1) showed no sugar moiety signals, but the characteristic signals of a methyl group [δH 0.88 (d, J = 6.9 Hz, 3H, H3-18)] and a p-hydroxybenzoate moiety [δH 7.99 (d, J = 8.7 Hz, 2H, H-21, 25), 6.90 (d, J = 8.7 Hz, 2H, H-22, 24)] were detected. The 13C NMR spectrum (Table

Two new lanostanoid glycosides isolated from a Kenyan polypore Fomitopsis carnea

• Winnie Chemutai Sum,
• Sherif S. Ebada,
• Didsanutda Gonkhom,
• Cony Decock,
• Rémy Bertrand Teponno,
• Josphat Clement Matasyoh and
• Marc Stadler

Beilstein J. Org. Chem. 2023, 19, 1161–1169, doi:10.3762/bjoc.19.84

• (C-21), 175.0 (C-5'), and 172.4 (C-1') as well as four olefinic carbon signals at δC 156.7 (C-24), 136.3 (C-9), 135.2 (C-8), and 107.4 (C-31). The 1H and 13C NMR spectral data of compound 1 (Table 1) also revealed the presence of a sugar moiety through the presence of the characteristic anomeric

• and 13C NMR data (Table 1) of the sugar moiety with that reported for a related fungal lanostanoside, ganosinoside A [26] and other glycosidic moieties [27], it was confirmed to be a β-ᴅ-glucopyranosyl residue. The HMBC spectrum of compound 1 (Figure 2) also revealed key correlations from two

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

• light (λ = 360 nm), L1 releases the glycan equipped with an aminoalkyl spacer at the reducing end, whereas L2 affords the free reducing sugar (α/β mixture). Previous data suggested that UV cleavage of L1 and L2 was equally efficient, permitting the isolation of a tetramannoside in around 60% yield [3

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

• ; green synthesis; locust bean gum; saponin; sorption; xanthan gum; Introduction Saponins are a family of natural molecules consisting of a hydrophobic aglycone backbone grafted with hydrophilic sugar molecules, allowing the plant to be protected from illnesses [1] and from herbivores endangerment [2

• , their aglycone forms but also the number of sugar molecules involved [11]. They can be found in beverage emulsions [12], and as food surfactants [13], because they are useful also to prevent the development of virus or bacteria in food or beverages [14][15]. As for medical purposes, it has been reported

A study of the DIBAL-promoted selective debenzylation of α-cyclodextrin protected with two different benzyl groups

• Naser-Abdul Yousefi,
• Morten L. Zimmermann and
• Mikael Bols

Beilstein J. Org. Chem. 2022, 18, 1553–1559, doi:10.3762/bjoc.18.165

• and 13C NMR (800/201 MHz), COSY, HSQC, TOCSY, and ROESY (Supporting Information File 1) which gave the NMR assignments shown in Table 2 and identification of 8 as the 6A,D diol. The most significant observations in this assignment were 1) the compound is symmetric with only 3 different sugar residues

Synthesis of C6-modified mannose 1-phosphates and evaluation of derived sugar nucleotides against GDP-mannose dehydrogenase

• Sanaz Ahmadipour,
• Alice J. C. Wahart,
• Jonathan P. Dolan,
• Laura Beswick,
• Chris S. Hawes,
• Robert A. Field and
• Gavin J. Miller

Beilstein J. Org. Chem. 2022, 18, 1379–1384, doi:10.3762/bjoc.18.142

• pathogen in these cases is mucoid Pseudomonas aeruginosa. Such infections are characterised by overproduction of the exopolysaccharide alginate. We present herein the design and chemoenzymatic synthesis of sugar nucleotide tools to probe a critical enzyme within alginate biosynthesis, GDP-mannose

• evaluation against GMD. Keywords: alginate; chemical probe; enzymatic synthesis; GDP-mannose dehydrogenase; sugar nucleotide; Introduction The opportunistic Gram-negative pathogen, Pseudomonas aeruginosa (PA), becomes the dominant pathogen in patients suffering from cystic fibrosis (CF) and causes a

• interventions that could halt its production would be of significant value. Within the biosynthetic assembly of alginate there is a critical dependence upon the provision of one sugar nucleotide building block, GDP-mannuronic acid (GDP-ManA, 5). This material is sourced from the cytosolic metabolic pool

Ferrocenoyl-adenines: substituent effects on regioselective acylation

• Mateja Toma,
• Gabrijel Zubčić,
• Jasmina Lapić,
• Senka Djaković,
• Davor Šakić and
• Valerije Vrček

Beilstein J. Org. Chem. 2022, 18, 1270–1277, doi:10.3762/bjoc.18.133

• the acylation of purines from a regioselective to a regiospecific mode. Keywords: DFT; ferrocene; nucleophilicity; purine; steric effect; Introduction Nucleosides in which the sugar part is replaced with an organometallic moiety have attracted remarkable interest [1][2][3]. One important class are

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

• , including hydroxy-substituted sugar 9 and trehalose product 10, are shown in Figure 6. These byproducts were obtained as inseparable mixture because of the same molecular weight and similar polarity. Moreover, the trehalose product of longer oligosaccharides has more than two possible structures. For

Enzymes in biosynthesis

• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2022, 18, 1131–1132, doi:10.3762/bjoc.18.116

• products, nature has evolved a large number of enzyme classes for more specific transformations, including cytochromes P450 or α-ketoglutarate-dependent dioxygenases for late-stage oxidations and transferases for the attachment of sugar units, acyl, or methyl groups. Moreover, some enzymes can catalyze

Shift of the reaction equilibrium at high pressure in the continuous synthesis of neuraminic acid

• Jannis A. Reich,
• Miriam Aßmann,
• Kristin Hölting,
• Paul Bubenheim,
• Jürgen Kuballa and
• Andreas Liese

Beilstein J. Org. Chem. 2022, 18, 567–579, doi:10.3762/bjoc.18.59

• initial activity was analyzed using a standard activity assay. High-performance liquid chromatography (HPLC) For quantification of the product N-acetylneuraminic acid, an Agilent HPLC system connected with a variable wavelength detector at 210 nm was used. Separation was realized with a Nucleogel Sugar

Terpenoids from Glechoma hederacea var. longituba and their biological activities

• Dong Hyun Kim,
• Song Lim Ham,
• Zahra Khan,
• Sun Yeou Kim,
• Sang Un Choi,
• Chung Sub Kim and
• Kang Ro Lee

Beilstein J. Org. Chem. 2022, 18, 555–566, doi:10.3762/bjoc.18.58

• spectrum of 1S,4S,5R,8S,10R-(1a). Finally, the ᴅ-glucopyranosyl moiety was identified by GC–MS analysis of a chiral derivatization product of the sugar obtained by enzyme hydrolysis of 1 [9][10]. The retention time of glucopyranose (11.3 min) corresponded to that of the standard ᴅ-glucopyranose (11.3 min

•  3C). The experimental ECD spectrum of 2 showed a negative Cotton effect at 233 nm and positive Cotton effects at 217 and 257 nm, which showed a similarity with those of calculated ECD spectrum of 1R,4R,5S,6S,8S,10S-(ent-2a). Enzyme hydrolysis and following sugar identification were performed using

• configuration of 3 was confirmed by comparing the calculated ECD spectrum of 3a (aglycone of 3) with the experimental ECD spectrum of 3. The experimental ECD of 3 displayed positive Cotton effects at 217 and 243 nm, which was similar to those of 1R,4R,5S,6S,10S-(3a) (Figure 4B). Enzyme hydrolysis and sugar

Menadione: a platform and a target to valuable compounds synthesis

• Acácio S. de Souza,
• Ruan Carlos B. Ribeiro,
• Dora C. S. Costa,
• Fernanda P. Pauli,
• David R. Pinho,
• Matheus G. de Moraes,
• Fernando de C. da Silva,
• Luana da S. M. Forezi and
• Vitor F. Ferreira

Beilstein J. Org. Chem. 2022, 18, 381–419, doi:10.3762/bjoc.18.43

• epoxides are formed through oxidation reactions in vivo, that occur in protein processes dependent on vitamin K [96][97]. Dwyer and co-workers described a procedure using sugar-derived hydroperoxides for the synthesis of epoxides in the presence of 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) as base [98][99

Site-selective reactions mediated by molecular containers

• Rui Wang and
• Yang Yu

Beilstein J. Org. Chem. 2022, 18, 309–324, doi:10.3762/bjoc.18.35

• reported the cyclodextrin-mediated site-selective ring-opening reductive reaction of epoxide 16 by sodium borohydride in aqueous solution (Figure 4b) [58]. The sugar-based hosts show good water solubility and can be used for driving organic reactions in water. In this case, the cyclodextrin host and the

Glycosylated coumarins, flavonoids, lignans and phenylpropanoids from Wikstroemia nutans and their biological activities

• Meifang Wu,
• Xiangdong Su,
• Yichuang Wu,
• Yuanjing Luo,
• Ying Guo and
• Yongbo Xue

Beilstein J. Org. Chem. 2022, 18, 200–207, doi:10.3762/bjoc.18.23

• distinctive peaks for two anomeric protons at δH 5.71 (d, J = 7.7 Hz, H-1'') and 4.94 (d, J = 7.1 Hz, H-1'''), implied the co-existences of two sugar moieties. Analyses of the 13C NMR (Table 1) coupled with DEPT and HSQC spectra of 1 displayed 29 carbon signals assignable to two ester carbonyls (δC 161.3 and

• -d6) established the C(6)–O–C(7') ether linkage. Therefore, a bis-coumarin-based aglycone was determined as shown (Figure 1), which is identical with that of daphnogitin [10]. In addition, two sugar units in substructure C (Figure 2 and Figure 3), including a β-glucopyranosyl and a β-xylopyranosyl

• by a ROESY correlation between H-6'' and H-1'''. Subsequently, an acid hydrolysis of 1 afforded the products including daphnogitin, a ᴅ-glucose, and a ᴅ-xylose. The absolute configurations of glucopyranosyl and xylopyranosyl was further determined by HPLC analysis of the sugar derivatives (Supporting

Tenacibactins K–M, cytotoxic siderophores from a coral-associated gliding bacterium of the genus Tenacibaculum

• Yasuhiro Igarashi,
• Yiwei Ge,
• Tao Zhou,
• Amit Raj Sharma,
• Enjuro Harunari,
• Naoya Oku and
• Agus Trianto

Beilstein J. Org. Chem. 2022, 18, 110–119, doi:10.3762/bjoc.18.12

• [30], terminal blocking by acylation [29][31][32], formation of sugar ester [33], imine oxide [34], oxime [35], or functional group transformation into a hydroxy [33] or nitro group [35]. To the best of our knowledge, compounds 1–3 are the first to have a hydroxamic acid terminus. Similar to the