Carbohydrate Research最新文献

{"title":"Unraveling the diversity of protein-carbohydrate interfaces: Insights from a multi-scale study","authors":"Aria Gheeraert ,&nbsp;Frédéric Guyon ,&nbsp;Serge Pérez ,&nbsp;Tatiana Galochkina","doi":"10.1016/j.carres.2025.109377","DOIUrl":"10.1016/j.carres.2025.109377","url":null,"abstract":"<div><div>Protein-carbohydrate interactions play a crucial role in numerous fundamental biological processes. Thus, description and comparison of the carbohydrate binding site (CBS) architecture is of great importance for understanding of the underlying biological mechanisms. However, traditional approaches for carbohydrate-binding protein analysis and annotation rely primarily on the sequence-based methods applied to specific protein classes. The recently released DIONYSUS database aims to fill this gap by providing tools for CBS comparison at different levels: both in terms of protein properties and classification, as well as in terms of atomistic CBS organization. In the current study, we explore DIONYSUS content using a combination of the suggested approaches in order to evaluate the diversity of the currently resolved non-covalent protein-carbohydrate interfaces at different scales. Notably, our analysis reveals evolutionary convergence of CBS in proteins with distinct folds and coming from organisms across different kingdoms of life. Furthermore, we demonstrate that a CBS structure based approach has the potential to facilitate functional annotation for the proteins with missing information in the existing databases. In particular, it provides reliable information for numerous carbohydrate-binding proteins from rapidly evolving organisms, whose analysis is particularly challenging for classical sequence-based methods.</div></div>","PeriodicalId":9415,"journal":{"name":"Carbohydrate Research","volume":"550 ","pages":"Article 109377"},"PeriodicalIF":2.4,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143000690","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A review of the latest advancements in using β-cyclodextrin-based as supramolecular catalysts for Heck reactions","authors":"Sara Payamifar ,&nbsp;Majid Abdouss ,&nbsp;Shahrzad Javanshir ,&nbsp;Ahmad Poursattar Marjani","doi":"10.1016/j.carres.2025.109381","DOIUrl":"10.1016/j.carres.2025.109381","url":null,"abstract":"<div><div>The Heck reaction is one of the most well-known C–C (carbon-carbon) coupling reactions and was identified with the Nobel Prize in Chemistry in 2010. These reactions have been broadly utilized to prepare a different spectrum of heterocycles with applications in agrochemical and pharmaceutical industries. These reactions are commonly catalyzed by palladium due to its tolerance and expansive variousness of functional groups, which bears a remarkable power in creating C–C bonds. Carbohydrate chemistry is a significant and crucial part of the organic chemistry field. Among existing carbohydrates, β-cyclodextrins (β-CDs) are natural cyclic oligosaccharides that contain glucose monomers and have played an active role in nearly every industrial and scientific field, attention and interest in them never aged. CDs can be utilized as a beneficial catalyst in numerous aqueous organic conversions. Their derivatives have demonstrated remarkable activity in water-mediated organic synthesis and are currently of continuing interest to multiple scientists in different fields. Being non-toxic, accessible, biodegradable, readily functionalized, low-cost, renewable, and producible in large-scale amounts are several of the benefits of CDs that make them a suitable nominee for catalyst applications. Different β-CDs catalysts have recently been widely employed for various C–C bond coupling reactions like the Heck coupling. Here, we review the latest advancements in using CD-based catalysts for Heck reactions.</div></div>","PeriodicalId":9415,"journal":{"name":"Carbohydrate Research","volume":"550 ","pages":"Article 109381"},"PeriodicalIF":2.4,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143000672","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Injectable vancomycin loaded hyaluronic acid-chitosan hydrogel for the treatment of Staphylococcus aureus septic arthritis","authors":"K. Kumaran ,&nbsp;Anil Kumar Vasudevan ,&nbsp;R. Jayakumar ,&nbsp;Raja Biswas","doi":"10.1016/j.carres.2025.109384","DOIUrl":"10.1016/j.carres.2025.109384","url":null,"abstract":"<div><div>Staphylococcus aureus (<em>S. aureus</em>) is a Gram positive opportunistic pathogen and a major cause for bacterial septic arthritis. Vancomycin is the preferred antibiotic for the treatment of methicillin resistance S. aureus septic arthritis. Patients undergoing vancomycin treatment need to be hospitalized and their serum vancomycin level should be monitored, as increase in vancomycin concentration in serum may lead to hepatotoxicity. To overcome vancomycin mediated cytotoxicity, we have prepared a local injectable delivery system by incorporating vancomycin into hyaluronic acid (HA)-chitosan (van-HA-chitosan) hydrogel. The prepared van-HA-chitosan hydrogel was characterized using Fourier Transform Infrared Spectroscopy (FTIR) and rheometer. The van-HA-chitosan hydrogel is injectable, has shear thinning behaviour; and is hemo- and cyto-compatible. <em>In vitro</em> drug release assay showed that 95 % of vancomycin was released from the hydrogel in 8 days. Under <em>in vitro</em> conditions the load of <em>S. aureus</em> decreased from 6.4 Log₁₀ CFU/ml to 3.5 Log₁₀ CFU/ml when treated with van-HA-chitosan hydrogel for 6 h. Significant decrease in bacterial counts was observed when <em>S. aureus</em> infected synovial fluid and bone samples were treated with van-HA-chitosan hydrogel. Our results suggest that the prepared van-HA-chitosan could be used for the treatment of septic arthritis caused by <em>S. aureus</em>.</div></div>","PeriodicalId":9415,"journal":{"name":"Carbohydrate Research","volume":"550 ","pages":"Article 109384"},"PeriodicalIF":2.4,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143000677","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Isolation, structural characterization of (1 → 4), (1 → 6)-α-D-glucan from Dioscorea Alata and synthesis and catalytic activity studies of (1 → 4), (1 → 6)-α-D-glucan derived carbon dots","authors":"Arnab Mallik ,&nbsp;Sukesh Patra ,&nbsp;Animesh Patra ,&nbsp;Akhil Pandey ,&nbsp;Madhumita Hazra ,&nbsp;Gobinda Prasad Sahoo","doi":"10.1016/j.carres.2025.109383","DOIUrl":"10.1016/j.carres.2025.109383","url":null,"abstract":"<div><div>Herein, a straightforward, productive protocol was adopted for the synthesis of carbon dots (CDs) by a simple microwave-assisted technique from (1 → 4), (1 → 6)-α-D-glucan polysaccharide (DAPS). The isolation and structural characterization of (1 → 4), (1 → 6)-α-D-glucan from the aqueous extracting of the <em>Diascorea Alata</em> was described here. The photo-physical and morphological studies of the prepared high quantum yield (27.70 %) CDs were systematically characterized using different analytical techniques: TEM, DLS, XPS, XRD, FT-IR, TCSPC, EDX, Fluorescence and UV–vis spectroscopy. In our study the carbon dots (CDs) obtained are non-toxic, highly water-soluble, spherical-shaped negatively charged particles with an average diameter of 3.28 nm. The photo-catalytic activity of carbon dots (CDs) was tested under the sunlight for photo-degradation of crystal violet (CV), a pollutant organic dye. Carbon dots (CDs) showed outstanding results regarding the photo degradation of CV (achieving 99.9 % degradation within 8 min) under sunlight.</div></div>","PeriodicalId":9415,"journal":{"name":"Carbohydrate Research","volume":"549 ","pages":"Article 109383"},"PeriodicalIF":2.4,"publicationDate":"2025-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143000669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Design and synthesis of a carbohydrate-derived chemosensor for selective Ni(II) ion detection: A turn-off approach","authors":"Aditi Arora ,&nbsp;Sumit Kumar ,&nbsp;Shivani Sapra ,&nbsp;Gautam Deo ,&nbsp;Mrityunjay K. Tiwari ,&nbsp;Brajendra K. Singh ,&nbsp;Sandeep Kumar","doi":"10.1016/j.carres.2025.109380","DOIUrl":"10.1016/j.carres.2025.109380","url":null,"abstract":"<div><div>Nickel, an essential transition metal, plays a vital role in biological systems and industries. However, exposure to nickel can cause severe health issues, such as asthma, dermatitis, pneumonitis, neurological disorders, and cancers of the nasal cavity and lungs. Due to nickel's toxicity and extensive industrial use, efficient sensors for detecting Ni²⁺ ions in environmental and biological contexts are essential. Carbohydrates, with their inherent water solubility and biocompatibility, are ideal for constructing chemosensors. Incorporating a pyridyl group enhances the selectivity and sensitivity of these sensors. We present a carbohydrate-derived colorimetric chemosensor 5-(2′-Pyridoylethene-1′-yl)-4-(2''-phenylethene-1''-yl)-2,3-<em>O</em>-isopropylidene-2,3-dihydrofuran-2,3-diol (<strong>7a</strong>) that exhibits a distinct colour change and significant fluorescence quenching upon binding with Ni²⁺ ions. The synthesis of receptor (<strong>7a</strong>) was validated by using ¹H, ¹³C NMR, HRMS, and single crystal X-ray analysis. Detection limit of receptor (<strong>7a</strong>) for Ni²⁺ was calculated to be 0.97 μM, which is below the standard (1.2 μM) set by the United States Environmental Protection Agency (EPA). The binding ratio of receptor (<strong>7a</strong>) to Ni²⁺ was determined to be 1:1 by using Job's plot. The binding constant of receptor (<strong>7a</strong>) and Ni²⁺ was calculated as 4.38 × 10⁴ M⁻¹ by using the Benesi-Hildebrand equation. This sensor demonstrates exceptional selectivity for Ni²⁺ ions over other metal cations. Receptor (<strong>7a</strong>) is stable and can be used to detect Ni²⁺ in the range of pH from 6 to 10. The sensor responded to Ni²⁺ ions selectively and a large number of coexisting ions showed almost no obvious interference with the detection. Our findings shed light on the potential of carbohydrate-derived chemosensors for nickel detection, paving the way for further exploration in this field. The binding mechanism of receptor (<strong>7a</strong>) to Ni²⁺ ions was proposed by Job's plot, UV–vis spectra and DFT (Density Functional Theory) calculations.</div></div>","PeriodicalId":9415,"journal":{"name":"Carbohydrate Research","volume":"549 ","pages":"Article 109380"},"PeriodicalIF":2.4,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142982240","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"O-GlcNAc glycans in the mammalian extracellular environment","authors":"Yohei Tsukamoto ,&nbsp;Tetsuya Okajima","doi":"10.1016/j.carres.2025.109378","DOIUrl":"10.1016/j.carres.2025.109378","url":null,"abstract":"<div><div>Extracellular O-GlcNAc is a unique post-translational modification that occurs in the epidermal growth factor-like (EGF) domain of the endoplasmic reticulum (ER) lumen. The EGF domain-specific O-GlcNAc transferase (EOGT), catalyzes the transfer of O-GlcNAc to serine/threonine residues of the C-terminal EGF domain. Thus, EOGT-dependent O-GlcNAc modifications are mainly found in selective proteins that are localized in the extracellular spaces or extracellular regions of membrane proteins. In mammals, O-GlcNAc glycans can be extended to oligosaccharide structures similar to other types of EGF domain-specific O-glycans. The <em>in vivo</em> importance of O-GlcNAc glycans in mammals has been demonstrated in a human congenital disease caused by <em>EOGT</em> mutations and is extensively supported by genetic deletion in mice. This article reviews the findings on the structure and biochemical mechanism of EOGT-catalyzed O-GlcNAc biosynthesis, modified proteins, and <em>in vivo</em> functions elucidated by recent research in mammals.</div></div>","PeriodicalId":9415,"journal":{"name":"Carbohydrate Research","volume":"549 ","pages":"Article 109378"},"PeriodicalIF":2.4,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143000670","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural elucidation of the O-antigen polysaccharide from shigatoxin-producing E. coli O179 using genetic information, NMR spectroscopy and the CASPER program","authors":"Carolina Fontana ,&nbsp;Andrej Weintraub ,&nbsp;Göran Widmalm","doi":"10.1016/j.carres.2025.109382","DOIUrl":"10.1016/j.carres.2025.109382","url":null,"abstract":"<div><div>The serological properties of the O-antigen polysaccharide region of the lipopolysaccharides are used to differentiate <em>E. coli</em> strains into serogroups. In this study, we report the structure elucidation of the O-specific chain of <em>E. coli</em> O179 using NMR data, the program CASPER and analysis of biosynthetic information available in the <em>E. coli</em> O-antigen Database (ECODAB). The presence of genes that encode enzymes involved in the biosynthesis of the GDP-Man and UDP-GlcA within the O-antigen gene cluster of the bacteria indicates that the corresponding residues could be present in the polysaccharide. Furthermore, the occurrence of four genes that encode for glycosyltransferases indicates that the polysaccharide is composed of pentasaccharide repeating units; a bioinformatics approach based on predictive glycosyltransferase functions present in ECODAB revealed that the β-<span>d</span>-Man<em>p</em>-(1→4)-β-<span>d</span>-Man<em>p</em>-(1→3)-<span>d</span>-Glc<em>p</em>NAc structural element could be present in the O-specific chain. NMR spectroscopy data obtained from homonuclear and heteronuclear 2D NMR spectra (¹H,¹H-TOCSY, ¹H,¹³C-HSQC, ¹H,¹³C-H2BC and ¹H,¹³C-HMBC) were analyzed using the CASPER program, revealing the following arrangement of monosaccharide residues as the most probable structure: →4)-α-<span>d</span>-Glc<em>p</em>A-(1→3)-[β-<span>d</span>-Glc<em>p</em>-(1→2)]β-<span>d</span>-Man<em>p</em>-(1→4)-β-<span>d</span>-Man<em>p</em>-(1→3)-β-<span>d</span>-Glc<em>p</em>NAc-(1→, which was further confirmed using 2D homonuclear ¹H,¹H-COSY and ¹H,¹H-NOESY spectra. The functions of the α-gluconosyltransferase and the β-glucosyltransferase were predicted using structural alignment of AlphaFold-predicted 3D structures. This O-antigen polysaccharide shares structural similarities with those of <em>E. coli</em> O6 and O188, <em>S. boydii</em> type 16, and the capsular polysaccharide of <em>E. coli</em> K43, explaining the serological cross-reactivities observed with strains belonging these O- and K-antigen groups.</div></div>","PeriodicalId":9415,"journal":{"name":"Carbohydrate Research","volume":"550 ","pages":"Article 109382"},"PeriodicalIF":2.4,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143027850","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synthesis of a di-O-acylated deoxynojirimycin (DNJ) derivative and evaluation of its antibacterial and antibiofilm activity against Staphylococcus aureus and Stenotrophomonas maltophilia","authors":"Anna Esposito ,&nbsp;Daniele D'Alonzo ,&nbsp;Maria Stabile ,&nbsp;Vincenzo Firpo ,&nbsp;Antonella Migliaccio ,&nbsp;Rosaria Artiano ,&nbsp;Stefano D'Errico ,&nbsp;Eliana De Gregorio ,&nbsp;Annalisa Guaragna","doi":"10.1016/j.carres.2025.109379","DOIUrl":"10.1016/j.carres.2025.109379","url":null,"abstract":"<div><div>Herein we report the synthesis of a novel di-<em>O</em>-acylated DNJ derivative, conceived to study whether iminosugar derivatization with a lipophilic acyl moiety could positively affect its antibacterial properties. The well-known PS-TPP/I₂/ImH activating system was used to readily install the acyl chains on the iminosugar, leading to the desired compound in high yield. Biological assays revealed that a di<em>-O</em>-lauroyl DNJ derivative enhanced the antibacterial effect of gentamicin and amikacin against <em>S. aureus</em> and <em>S. maltophilia</em> strains, respectively, suggesting a potential role as antibiotic adjuvant. Furthermore, even though this compound displayed only a weak concentration-dependent inhibitory effect on biofilm formation in <em>S. aureus</em>, it was able to significantly reduce the viability of <em>S. aureus</em> and <em>S. maltophilia</em> preformed biofilms. The results confirm the antibacterial potential of piperidine iminosugars and open the way to further studies involving novel lipophilic derivatives to optimize the antibacterial adjuvant effect herein observed for iminosugar <strong>12</strong>.</div></div>","PeriodicalId":9415,"journal":{"name":"Carbohydrate Research","volume":"550 ","pages":"Article 109379"},"PeriodicalIF":2.4,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037024","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hydrophobic modification of starch via enzymatic grafting polymerization of fluorinated vinyl monomer","authors":"Wenda Wang,&nbsp;Qiang Wang,&nbsp;Ping Wang","doi":"10.1016/j.carres.2025.109376","DOIUrl":"10.1016/j.carres.2025.109376","url":null,"abstract":"<div><div>The synthesis of starch grafted with poly (hexafluorobutyl methacrylate) (PHFBMA) was achieved using the horseradish peroxidase (HRP)/acetophenone (ACAC) green initiating system. The modified starch was characterized through FT-IR, ¹⁹F NMR, XPS and EDS to confirm the successful grafting of PHFBMA onto starch backbone. The SEM analysis revealed that the introduction of PHFBMA led to a partial disruption of the crystalline structure of starch, suggesting that PHFBMA did not undergo physical adsorption onto starch. Compared to natural starch film, the modified starch film displays a significantly enhanced hydrophobicity, which can lead to substantial improvements in both the hydrophobicity and tensile properties when applied to hydrophilic paper substrates.</div></div>","PeriodicalId":9415,"journal":{"name":"Carbohydrate Research","volume":"549 ","pages":"Article 109376"},"PeriodicalIF":2.4,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142969739","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and structural characterization of glucosylceramides in Holothuria (Halodeima) grisea: Insights from TLC and NMR techniques","authors":"Matheus Pires Miranda","doi":"10.1016/j.carres.2024.109374","DOIUrl":"10.1016/j.carres.2024.109374","url":null,"abstract":"<div><div>Sea cucumbers are widely used in oriental cuisine due to their medicinal properties. Antioxidant, antifungal, antiviral, anticancer and neuroprotective activities have already been identified in several species and in different tissues. Among the class of compounds with biological activity are cerebrosides, which have important functions for the proper functioning of cells, especially neuronal cells. The identification of this class of compounds can be carried out using simple techniques such as thin layer chromatography (TLC) or more sophisticated techniques such as nuclear magnetic resonance (NMR), providing different information depending on the technique used. Therefore, this work aimed to identify the presence of cerebrosides in different tissues of <em>Holothuria (Halodeima) grisea</em>. TLC analysis and separation on a silica column made it possible to accurately identify the positive fractions for cerebrosides. This selectivity is crucial to ensure that the compounds identified are genuine cerebrosides, eliminating interference from other non-pertinent bands. NMR spectroscopy analyses confirmed the presence of glucosylceramide in the tissues studied. The identification of a β-glucose linked to the ceramide, with specific structural characteristics such as hydroxyl on the 3′ carbon of the sphingosine and a double bond between the 4′ and 5′ carbons, highlights the accuracy of the structural determination obtained with the techniques used.</div></div>","PeriodicalId":9415,"journal":{"name":"Carbohydrate Research","volume":"549 ","pages":"Article 109374"},"PeriodicalIF":2.4,"publicationDate":"2025-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143000668","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}