Orthogonal photoswitching of heterobivalent azobenzene glycoclusters: the effect of glycoligand orientation in bacterial adhesion

• Leon M. Friedrich and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2025, 21, 736–748, doi:10.3762/bjoc.21.57

• diverse interactions with primary and secondary carbohydrate binding sites of the protein [13]. For example, when an α-ᴅ-mannopyranosyl (Man) and a β-ᴅ-glucopyranosyl (Glc) unit were conjugated such that the relative orientation of the two sugar portions is varied – be it on enantiomeric or regioisomeric

• proton of the terminal sugar units in the 1H NMR spectrum (Table 1 and Supporting Information File 1, Figures S8, S10, and S12). Irradiation with 365 nm light excites the π–π* band of the ortho-fluorinated S-azobenzene units (ABF4) of both 3 and 4 and the π–π* band of the O-azobenzene (AB) unit of 5

• to the O-azobenzene (AB) photoswitch. (Orthogonal) photoswitching alters the relative spatial orientation of the two sugar units. Glucose (Glc) moieties are colored in blue and mannose (Man) in green according to the symbol nomenclature for carbohydrates (SNFG) [29][30]. A: Wavelength-selective

Origami with small molecules: exploiting the C–F bond as a conformational tool

• Patrick Ryan,
• Ramsha Iftikhar and
• Luke Hunter

Beilstein J. Org. Chem. 2025, 21, 680–716, doi:10.3762/bjoc.21.54

• recognition processes. Therefore, methods for controlling the conformations of sugars are likely to have diverse and valuable applications in biotechnology and medicine. The structure of a sugar molecule offers several potential locations where fluorine can be introduced. Typical patterns include the

• envelope conformation in which the fluorinated carbon is projected above the ring plane, stabilised by dual σC–H → σ*C–F hyperconjugation [138]. Let us now consider ways in which fluorine can influence bond rotations outside the sugar ring (Figure 10). We will focus initially on the C-5–C-6 bond. In

• in which fluorine can control the rotation of the C-5–C-6 bond is seen when a C-6-fluorinated sugar is converted into an oxocarbenium ion (e.g., 73, Figure 10). The C-6–F bond of 73 preferentially orients over the sugar ring, due to a combination of electrostatic attraction between the partially

The effect of neighbouring group participation and possible long range remote group participation in O-glycosylation

• Rituparna Das and
• Balaram Mukhopadhyay

Beilstein J. Org. Chem. 2025, 21, 369–406, doi:10.3762/bjoc.21.27

• C-2 position also renders neighbouring group assistance (Scheme 9) with the anomeric carbon thereby forming the acetoxonium intermediate complex 53. It significantly blocks the α-face of the sugar ring causing the acceptor to attack from the exposed β-face. Moreover, this protecting group is also

• in the subsequent nucleophilic attack by the acceptor [137]. This α-glycosyl triflate was readily converted to its skew-boat conformation 62 which led to the attack of the glycosyl acceptor 64 from the β-face of the sugar pyranoside ring exclusively to form the 1,2-trans glycoside 65. Thus, the N

• protecting groups in the C-2 position in glycosyl donors, on the elimination of the activated leaving group from the anomeric position, the flattened oxocarbenium ion formed causes the incoming nucleophilic acceptor to attack from either the β or the α-face of the sugar ring, thereby leading to the formation

Advances in the use of metal-free tetrapyrrolic macrocycles as catalysts

• Mandeep K. Chahal

Beilstein J. Org. Chem. 2024, 20, 3085–3112, doi:10.3762/bjoc.20.257

• other binding sites required for substrate binding and/or promotion of the catalytic activity. Past studies have shown that modifying the porphyrin core with urea functionalities and amino acid substituents leads to the formation of ureaporphyrins, which significantly enhance sugar binding in non-polar

Cyclodextrin-based rotaxanes for polymer materials: challenge on simultaneous realization of inexpensive production and defined structures

• Yosuke Akae

Beilstein J. Org. Chem. 2024, 20, 3026–3049, doi:10.3762/bjoc.20.252

• Synthesis and structure of cyclodextrin-based (poly)rotaxanes CDs are cyclic sugar molecules in which multiple glucose units that are connected by α-1,4 bonds, e.g., α-CD, β-CD, and γ-CD (glucose-unit numbers 6, 7, and 8, respectively), are used for scientific studies and industrial productions (Figure 2

N-Glycosides of indigo, indirubin, and isoindigo: blue, red, and yellow sugars and their cancerostatic activity

• Peter Langer

Beilstein J. Org. Chem. 2024, 20, 2840–2869, doi:10.3762/bjoc.20.240

• containing the sugar moiety attached to the amine-type nitrogen are less stable than the corresponding compounds containing the sugar moiety attached to the amide-type nitrogen atom. Unfortunately, the synthesis of β-31a was not a general method for the synthesis of indirubin-N-glycosides. Analogues of

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

• , proteins, and nucleic acids. In humans and animals, they form the so-called glycocalyx, a protecting sugar coat decorating the cell surface and modulating a myriad of cell–cell interactions [1]. It is composed of branched or elongated glycan chains covalently linked to proteins or lipids, hereby

• in bacteria, which are able to use most of the mammalian sugar units to construct their glycoconjugates but, in addition, can also use a wide variety of particular, and potentially endless, monosaccharides that are instead not present in eukaryotes (Figure 2). This huge diversity and complexity

• able to add branching points and some sugar derivatisation, including methylation and acetylation. The user has also the possibility to choose the ring type and the anomeric configuration of each monosaccharide. Once the structure is complete, it is possible to download not only the generated .pdb

Multicomponent syntheses of pyrazoles via (3 + 2)-cyclocondensation and (3 + 2)-cycloaddition key steps

• Ignaz Betcke,
• Alissa C. Götzinger,
• Maryna M. Kornet and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2024, 20, 2024–2077, doi:10.3762/bjoc.20.178

• solution and in the solid state [127]. Furthermore, even sugar-functionalized pyrazoles have been accessed by this approach [128], and it was readily implemented in a continuous flow reactor [129]. Besides traditional Sonogashira catalyst systems, highly reactive and reusable immobilized Pd-complexes, such

The Groebke–Blackburn–Bienaymé reaction in its maturity: innovation and improvements since its 21st birthday (2019–2023)

• Cristina Martini,
• Muhammad Idham Darussalam Mardjan and
• Andrea Basso

Beilstein J. Org. Chem. 2024, 20, 1839–1879, doi:10.3762/bjoc.20.162

• the tolerability of a wide range of aldehydes, starting from one of the most used, benzaldehyde, passing through heteroaromatic and aliphatic structures with different substituents. In this context, some examples where the aldehyde functionality is incorporated into sugar derivatives, natural

• yields up to 87%. The use of sugar-derived building blocks has been reported by various authors. Prasad et al. studied the synthesis of 2-(β-ᴅ-glucopyranosyl)-3-N-alkylamino-1-azaindolizines 28 to get novel bioconjugates [38] and of 5-(3”-alkyl/arylamino-1”-azaindolizin-2”-yl)-2’-deoxyuridines 31 to

• potassium carbonate was almost quantitative (97–99% yield). It is worth mentioning that the GBB reaction starting from the deacetylated substrate also leads to good results (83–91% of yield), but the overall yield is lowered due to a sluggish deacetylation reaction of 29. Sugar-based aldehydes were employed

Chemo-enzymatic total synthesis: current approaches toward the integration of chemical and enzymatic transformations

• Ryo Tanifuji and
• Hiroki Oguri

Beilstein J. Org. Chem. 2024, 20, 1693–1712, doi:10.3762/bjoc.20.151

• considered a remarkable example of utilizing the complementarity between chemical and enzymatic transformations (Scheme 1 and Scheme 2). The cotylenin and fusicoccin families comprise structurally related diterpene glucosides with a 5/8/5 fused tricyclic aglycon and a sugar moiety linked through the C9

Photoswitchable glycoligands targeting Pseudomonas aeruginosa LecA

• Yu Fan,
• Ahmed El Rhaz,
• Stéphane Maisonneuve,
• Emilie Gillon,
• Maha Fatthalla,
• Franck Le Bideau,
• Guillaume Laurent,
• Samir Messaoudi,
• Anne Imberty and
• Juan Xie

Beilstein J. Org. Chem. 2024, 20, 1486–1496, doi:10.3762/bjoc.20.132

• formation of the 1,2-anhydro sugar through intramolecular attack of the 2-hydroxy group of the DMC-activated β-intermediate, followed by dihydroxyazobenzene attacking the anomeric center in an SN2 manner, or by direct nucleophilic SN2 attack on the DMC-activated α-intermediate, to produce the corresponding

Synthesis of 1,4-azaphosphinine nucleosides and evaluation as inhibitors of human cytidine deaminase and APOBEC3A

• Maksim V. Kvach,
• Stefan Harjes,
• Harikrishnan M. Kurup,
• Geoffrey B. Jameson,
• Elena Harjes and
• Vyacheslav V. Filichev

Beilstein J. Org. Chem. 2024, 20, 1088–1098, doi:10.3762/bjoc.20.96

• ssDNA. Results and Discussion Synthesis of nucleosides It is more straightforward to start the synthesis of a modified nucleoside from the assembly of a nucleobase that can be coupled to the sugar afterwards using the Hilbert–Johnson reaction or a silyl variation of it as described in the literature [65

• C5 and C6 atoms (Figure 1). Towards this end, we developed a synthetic strategy for these nucleosides and identified that assembly of the nucleobase on the sugar was more viable than coupling of the final nucleobase to Hoffer’s chlorosugar (13). It is interesting that only the charge-neutral

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