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

Chemical and chemoenzymatic routes to bridged homoarabinofuranosylpyrimidines: Bicyclic AZT analogues

• Sandeep Kumar,
• Jyotirmoy Maity,
• Banty Kumar,
• Sumit Kumar and
• Ashok K. Prasad

Beilstein J. Org. Chem. 2022, 18, 95–101, doi:10.3762/bjoc.18.10

• -methyltetrahydrofuran following a chemoenzymatic pathway. Whereas, the protection of the primary hydroxy over the lone secondary hydroxy group in the key azido sugar precursor was achieved using bulky tert-butyldiphenylsilyl chloride (TBDPS-Cl) in pyridine in 92% yield following a chemical synthetic pathway. The

• chemotherapeutic agents used for the treatment of cancer were nucleoside analogues and nucleobases [10]. Azidothymidine (1, AZT) was the first approved drug for the treatment of human immunodeficiency virus (HIV) [11][12]. Subsequently, a large number of sugar modified nucleosides, such as ddC (zalcitabine) [13

• . [23] synthesized the tricyclic azido-isonucleoside analogue 5 and Imanishi et al. [24] synthesized the azido-nucleoside 6 with a conformationally restricted sugar moiety. Recently, we have developed a greener and efficient chemoenzymatic synthetic methodology for the synthesis of conformationally

Stepwise PEG synthesis featuring deprotection and coupling in one pot

• Logan Mikesell,
• Dhananjani N. A. M. Eriyagama,
• Yipeng Yin,
• Bao-Yuan Lu and
• Shiyue Fang

Beilstein J. Org. Chem. 2021, 17, 2976–2982, doi:10.3762/bjoc.17.207

• Logan Mikesell Dhananjani N. A. M. Eriyagama Yipeng Yin Bao-Yuan Lu Shiyue Fang Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA ChampionX, 11177 South Stadium Drive, Sugar Land, TX 77478, USA 10.3762/bjoc.17.207 Abstract The stepwise

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

• -methoxyphenyl glycoside form 1 was synthesized through a linear [1 + (1 + 1 = 2)] strategy. The target trisaccharide was synthesized as its p-methoxyphenyl glycoside that offered the unaltered stereochemistry of the sugar at the reducing end to mimic the glycosidic linkage of the natural polysaccharide. The

Synthetic strategies toward 1,3-oxathiolane nucleoside analogues

• Umesh P. Aher,
• Dhananjai Srivastava,
• Girij P. Singh and
• Jayashree B. S

Beilstein J. Org. Chem. 2021, 17, 2680–2715, doi:10.3762/bjoc.17.182

• Academy of Higher Education, Manipal-576104, Karnataka, India 10.3762/bjoc.17.182 Abstract Sugar-modified nucleosides have gained considerable attention in the scientific community, either for use as molecular probes or as therapeutic agents. When the methylene group of the ribose ring is replaced with a

• -oxathiolane nucleosides via resolution methods. The chemical as well as enzymatic procedures are reviewed and segregated in this review for effective synthesis of 1,3-oxathiolane nucleoside analogues. Keywords: chiral auxiliaries; enzymes; Lewis acids; N-glycosylation; 1,3-oxathiolane sugar and nucleosides

• -(−)-enantiomer 2, exhibits potential antiviral activity against HIV-1 (EC50 = 0.009 µM) in CEM cells. However, the corresponding ᴅ-(+)-enantiomer is less active against HIV-1 (EC50 = 0.84 µM) [15]. The fusion of an appropriate sugar element, carbacycle, or heterocyclic equivalent with an activated base results

Phenolic constituents from twigs of Aleurites fordii and their biological activities

• Kyoung Jin Park,
• Won Se Suh,
• Da Hye Yoon,
• Chung Sub Kim,
• Sun Yeou Kim and
• Kang Ro Lee

Beilstein J. Org. Chem. 2021, 17, 2329–2339, doi:10.3762/bjoc.17.151

• 5.51 (d, J = 6.1 Hz, H-7)], an anomeric proton of a sugar [δH 4.27 (d, J = 7.8 Hz, H-1′′)], and a methoxy group [δH 3.84 (s, 3-OCH3)]. The 13C NMR data (Table 1) showed 25 peaks including 12 aromatic carbons [δC 147.6 (C-3), 145.9 (C-4), 145.1 (C-4′), 140.4 (C-3′), 135.2 (C-1′), 133.7 (C-1), 128.3 (C-5

• (Figure 2). The locations of the glucose unit and the methoxy group were confirmed from the observed HMBC correlations of H-1′′/C-9′ and 3-OCH3/C-3, respectively (Figure 2). Acid hydrolysis of 1 was conducted to analyze the aglycone and sugar moiety. The structure of the aglycone (1a) was confirmed as

• absolute configuration. The planar structure of 3 was further confirmed by analysis of 2D NMR data, including COSY, HSQC, and HMBC (Figure 2). The determination of the stereochemistry for the sugar unit of 3 was conducted following the same method as for compound 2. The structure of the aglycone 3a

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

• polysaccharides longer than hexasaccharides. Shorter oligomers are discussed when they represent a key step towards the synthesis of the corresponding polysaccharide. Polymers based on a sugar backbone connected via glycosidic linkages are analyzed, excluding glycopolymers and other mimetics. Extraction

• ), β(1–3) or a combination of β(1–4)- and β(1–3)-linked β-ᴅ-xylopyranosyl units. Rarely, α(1–3) glycosidic linkages are present [194]. These backbones are often partially acetylated or appended with sugar side chains, mainly ʟ-arabinose, fucose, galactose and 4-O-methylglucuronic acid [195]. In general

Cationic oligonucleotide derivatives and conjugates: A favorable approach for enhanced DNA and RNA targeting oligonucleotides

• Mathias B. Danielsen and
• Jesper Wengel

Beilstein J. Org. Chem. 2021, 17, 1828–1848, doi:10.3762/bjoc.17.125

• strategy that has been employed to optimize the delivery profile of ASOs, is the functionalization of ASOs with cationic amine groups, either by direct conjugation onto the sugar, nucleobase or internucleotide linkage. The introduction of these positively charged groups has improved properties like

• been separated into three sections, nucleobase, sugar and backbone modifications, highlighting what impact the cationic amine groups have on the ONs/ASOs physiochemical and biological properties. Finally, a concluding section has been added, summarizing the important knowledge from the three chapters

• , and examining the future design for ASOs. Keywords: antisense oligonucleotides; backbone modifications; cations; nucleobase modifications; sugar modifications; Introduction Antisense oligonucleotides (ASOs) are single-stranded (ss) oligomers composed of typically 10–25 nucleotides linked by