Complete 1H and 13C NMR chemical shift assignments of mono-to tetrasaccharides as basis for NMR chemical shift predictions of oligo- and polysaccharides using the computer program CASPER

A study on anticancer and antioxidant ability of selected brown algae biomass yielded polysaccharide and their chemical and structural properties analysis by FT-IR and NMR analyses

The study was conducted to determine the chemical and structural properties of polysaccharides extracted from the marine macroalgae Nemalion cari-cariense. Furthermore, evaluate the anticancer and free radical scavenging activity of purified N. cari-cariense polysaccharide. Approximately 41.6% (w/w) of crude polysaccharide was extracted from N. cari-cariense macroalgae biomass. After deproteinization, the purified polysaccharide's major chemical composition was found to be 92.6%, with all protein content removed. The purified polysaccharide had ash and moisture % of 23.01% and 4.03%, respectively. The C, H, and N of the test polysaccharide were analyzed using GC-MS, with results of 39.21%, 5.87%, and 4.29%, respectively. Furthermore, this analysis also revealed the monosaccharide composition such as glucose, galactose, mannose, xylose, and rhamnose glucose, galactose, mannose, xylose, and rhamnose 54.62%, 29.64%, 2.8%, 5.9%, and 6.8% respectively. The molecular weight of purified polysaccharide was found as 49kDa through PAGE analysis. The FT-IR analysis revealed that the presence of functional groups exactly attributed to polysaccharide and 1H and 13C-NMR analyses confirmed the structural properties of N. cari-cariense polysaccharide. The free radicals scavenging ability of purified N. cari-cariense polysaccharide was investigated by various assays such as total antioxidant assay (22.3%-72.5% at 50-250 μg mL-1), DPPH assay (23.6% to 76.9% at 10 to 160 μg mL-1), OH radical scavenging assay (13.6% to 70.2% at 50-250 μg mL-1 dosage, and SO radical scavenging assay (27.6-68.41% at 50-250 μg mL-1 concentration). The polysaccharide demonstrated 82.63% anticancer activity towards the A549 lung cancer cell line at 1000 μg mL-1 dosage. The findings suggest that this polysaccharide has biological applications.

Role of UDP-Glycosyltransferase (ugt) Genes in Detoxification and Glycosylation of 1-Hydroxyphenazine (1-HP) in Caenorhabditis elegans

Caenorhabditis elegans is a useful model organism to study the xenobiotic detoxification pathways of various natural and synthetic toxins, but the mechanisms of phase II detoxification are understudied. 1-Hydroxyphenazine (1-HP), a toxin produced by the bacterium Pseudomonas aeruginosa, kills C. elegans. We previously showed that C. elegans detoxifies 1-HP by adding one, two, or three glucose molecules in N2 worms. Our current study evaluates the roles that some UDP-glycosyltransferase (ugt) genes play in 1-HP detoxification. We show that ugt-23 and ugt-49 knockout mutants are more sensitive to 1-HP than reference strains N2 or PD1074. Our data also show that ugt-23 knockout mutants produce reduced amounts of the trisaccharide sugars, while the ugt-49 knockout mutants produce reduced amounts of all 1-HP derivatives except for the glucopyranosyl product compared to the reference strains. We characterized the structure of the trisaccharide sugar phenazines made by C. elegans and showed that one of the sugar modifications contains an N-acetylglucosamine (GlcNAc) in place of glucose. This implies broad specificity regarding UGT function and the role of genes other than ogt-1 in adding GlcNAc, at least in small-molecule detoxification.

Nuclear magnetic resonance-based structural elucidation of novel marine glycans and derived oligosaccharides

Marine glycans of defined structures are unique representatives among all kinds of structurally complex glycans endowed with important biological actions. Besides their unique biological properties, these marine sugars also enable advanced structure-activity relationship (SAR) studies given their distinct and defined structures. However, the natural high molecular weights (MWs) of these marine polysaccharides, sometimes even bigger than 100 kDa, pose a problem in many biophysical and analytical studies. Hence, the preparation of low MW oligosaccharides becomes a strategy to overcome the problem. Regardless of the polymeric or oligomeric lengths of these molecules, structural elucidation is mandatory for SAR studies. For this, nuclear magnetic resonance (NMR) spectroscopy plays a pivotal role. Here, we revisit the NMR-based structural elucidation of a series of marine sulfated poly/oligosaccharides discovered in our laboratory within the last 2 years. This set of structures includes the α-glucan extracted from the bivalve Marcia hiantina; the two sulfated galactans extracted from the red alga Botryocladia occidentalis; the fucosylated chondroitin sulfate isolated from the sea cucumber Pentacta pygmaea; the oligosaccharides produced from the fucosylated chondroitin sulfates from this sea cucumber species and from another species, Holothuria floridana; and the sulfated fucan from this later species. Specific 1H and 13C chemical shifts, generated by various 1D and 2D homonuclear and heteronuclear NMR spectra, are exploited as the primary source of information in the structural elucidation of these marine glycans.

Glycan Shape, Motions, and Interactions Explored by NMR Spectroscopy

Glycans in the form of oligosaccharides, polysaccharides, and glycoconjugates are ubiquitous in nature, and their structures range from linear assemblies to highly branched and decorated constructs. Solution state NMR spectroscopy facilitates elucidation of preferred conformations and shapes of the saccharides, motions, and dynamic aspects related to processes over time as well as the study of transient interactions with proteins. Identification of intermolecular networks at the atomic level of detail in recognition events by carbohydrate-binding proteins known as lectins, unraveling interactions with antibodies, and revealing substrate scope and action of glycosyl transferases employed for synthesis of oligo- and polysaccharides may efficiently be analyzed by NMR spectroscopy. By utilizing NMR active nuclei present in glycans and derivatives thereof, including isotopically enriched compounds, highly detailed information can be obtained by the experiments. Subsequent analysis may be aided by quantum chemical calculations of NMR parameters, machine learning-based methodologies and artificial intelligence. Interpretation of the results from NMR experiments can be complemented by extensive molecular dynamics simulations to obtain three-dimensional dynamic models, thereby clarifying molecular recognition processes involving the glycans.

NMR chemical shift prediction and structural elucidation of linker-containing oligo- and polysaccharides using the computer program CASPER

Carbohydrate structures containing alkyl groups as aglycones are useful for investigating enzyme activity and glycan-protein interactions. Moreover, linker-containing oligosaccharides with a spacer group are commonly used to print glycan microarrays or to prepare protein-conjugates as vaccine candidates. The structural accuracy of these synthesized glycans are essential for interpretation of results from biological experiments in which the compounds have been used and NMR spectroscopy can unravel and confirm their structures. An approach for efficient 1H and 13C NMR chemical shift assignments employed a parallel NOAH-10 measurement followed by NMR spin-simulation to refine the 1H NMR chemical shifts, as exemplified for a disaccharide with an azidoethyl group as an aglycone, the NMR chemical shifts of which have been used to enhance the quality of CASPER (http://www.casper.organ.su.se/casper/). The CASPER program has been further developed to aid characterization of linker-containing oligo- and polysaccharides, either by chemical shift prediction for comparison to experimental NMR data or as structural investigation of synthesized glycans based on acquired unassigned NMR data. The ability of CASPER to elucidate structures of linker-containing oligosaccharides is demonstrated and comparisons to assigned or unassigned NMR data show the utility of CASPER in supporting a proposed oligosaccharide structure. Prediction of NMR chemical shifts of an oligosaccharide, corresponding to the repeating unit of an O-antigen polysaccharide, having a linker as an aglycone and a non-natural substituent derivative thereof are presented to exemplify the diversity of structures handled. Furthermore, NMR chemical shift predictions of synthesized polysaccharides, corresponding to bacterial polysaccharides, containing a linker are described showing that in addition to oligosaccharide structures also polysaccharide structures having an aglycone spacer group can be analyzed by CASPER.

Resolving the complexity in human milk oligosaccharides using pure shift NMR methods and CASPER

Human milk oligosaccharides belong to an important class of bioactive molecules with diverse effects on the development of infants. NMR is capable of providing vital structural information about oligosaccharides which can aid in determining structure-function relationships. However, this information is often concealed by signal overlap in ¹H spectra, due to the narrow chemical shift range and signal multiplicity. Signal overlap in oligosaccharide spectra can be greatly reduced, and resolution improved, by utilising pure shift methods. Here the benefits of combining pure shift methods with the CASPER computational approach to resonance assignment in oligosaccharides are demonstrated.

Structural characteristics and antioxidant and hypoglycemic activities of a heteropolysaccharide from Anemarrhena asphodeloides Bunge

In this study, an acid polysaccharide (AABP-1B) was extracted from the rhizome of Anemarrhena asphodeloides Bunge and purified using 60 % alcohol precipitation and DEAE-52 cellulose. The molecular weight of AABP-1B was 105 kDa, and it consisted of mannose (Man), rhamnose (Rha), galacturonic acid (GalA), glucose (Glc), galactose (Gal), and arabinose (Ara) in a ratio of 6.3:1.3:1.1:0.2:0.4:0.7. Methylation and NMR analyses revealed that the backbone of AABP-1 consists of 4)-β-D-Manp-(1 and 4)-2-O-acetyl-β-D-Manp-(1. In addition, the biological activity assays showed that AABP-1B not only displays potential antioxidant activity but also exhibits the α-glucosidase and α-amylase inhibitory effect. Moreover, AABP-1B enhanced glucose consumption and glycogen synthesis in insulin-resistant (IR) HepG2 cells. These results suggest that AABP-1B has potential hypoglycemic activity.

Worldwide Glycoscience Informatics Infrastructure: The GlySpace Alliance

The GlySpace Alliance was formed in 2018 among the principal investigators of three major glycoscience portals: Glyco@Expasy, GlyCosmos, and GlyGen, representing Europe, Asia, and the United States, respectively. While each of these portals has its unique user interface, the aim is to provide the same basic data set of glycan-related omics data. These portals will be introduced with the aim to enable users to find their target information in the most efficient manner, in particular, in terms of the chemical structures of glycans and their functions.

Primary Structure of Glycans by NMR Spectroscopy

Glycans, carbohydrate molecules in the realm of biology, are present as biomedically important glycoconjugates and a characteristic aspect is that their structures in many instances are branched. In determining the primary structure of a glycan, the sugar components including the absolute configuration and ring form, anomeric configuration, linkage(s), sequence, and substituents should be elucidated. Solution state NMR spectroscopy offers a unique opportunity to resolve all these aspects at atomic resolution. During the last two decades, advancement of both NMR experiments and spectrometer hardware have made it possible to unravel carbohydrate structure more efficiently. These developments applicable to glycans include, inter alia, NMR experiments that reduce spectral overlap, use selective excitations, record tilted projections of multidimensional spectra, acquire spectra by multiple receivers, utilize polarization by fast-pulsing techniques, concatenate pulse-sequence modules to acquire several spectra in a single measurement, acquire pure shift correlated spectra devoid of scalar couplings, employ stable isotope labeling to efficiently obtain homo- and/or heteronuclear correlations, as well as those that rely on dipolar cross-correlated interactions for sequential information. Refined computer programs for NMR spin simulation and chemical shift prediction aid the structural elucidation of glycans, which are notorious for their limited spectral dispersion. Hardware developments include cryogenically cold probes and dynamic nuclear polarization techniques, both resulting in enhanced sensitivity as well as ultrahigh field NMR spectrometers with a ¹H NMR resonance frequency higher than 1 GHz, thus improving resolution of resonances. Taken together, the developments have made and will in the future make it possible to elucidate carbohydrate structure in great detail, thereby forming the basis for understanding of how glycans interact with other molecules.

Purification, Characterization and Bioactivities of Polysaccharides Extracted from Safflower (Carthamus tinctorius L.)

Polysaccharides are the main bioactive components in safflower. In this study, safflower polysaccharides (SPs) were extracted by ultrasonic assisted extraction, and four purified safflower polysaccharide fractions (named SSP1, SSP2, SSP3, and SSP4, respectively) were obtained. The physicochemical properties and in vitro physiological activities of the four fractions were investigated. The molecular weights (M_W) of the SSPs were 38.03 kDa, 43.17 kDa, 54.49 kDa, and 76.92 kDa, respectively. Glucuronic acid, galactose acid, glucose, galactose, and arabinose were the main monosaccharides. The Fourier transform infrared spectroscopy (FT-IR) indicated that the polysaccharides had α- and β-glycosidic bonds. Nuclear magnetic resonance (NMR) analysis showed that SSP1 had 6 different types of glycosidic bonds, while SSP3 had 8 different types. SSP3 exhibited relatively higher ABTS⁺ scavenging activity, Fe⁺³-reduction activity, and antiproliferative activity. The results will offer a theoretical framework for the use of SPs in the industry of functional foods and medications.

The Polysaccharidic Nature of the Skeleton of Marennine as Determined by NMR Spectroscopy

The water-soluble blue-green pigment marennine, produced and partly excreted by the diatom Haslea ostrearia, and known for a long time for its role in the greening of oysters, was isolated from the culture medium, purified, and analyzed by Nuclear Magnetic Resonance (NMR) in order to gain insight into its chemical structure. The spectra show mainly carbohydrates of a complex composition, apparently highly branched, and with a mass in the order of 10 kDa. There are, in addition, some signals of aliphatic and, much weaker, aromatic groups that present aglycons. The latter might be responsible for the color. These carbohydrates are always associated with the blue-green color and cannot be separated from it by most treatments; they are interpreted as constituting the frame of the pigment. NMR after hydrolysis identifies the most abundant monosaccharides in marennine as galactose, xylose, mannose, rhamnose, and fucose.

Structural elucidation of the O-antigen polysaccharide from Escherichia coli O125ac and biosynthetic aspects thereof

Enteropathogenic Escherichia coli O125, the cause of infectious diarrheal disease, is comprised of two serogroups, viz., O125ab and O125ac, which display the aggregative adherence pattern with epithelial cells. Herein, the structure of the O-antigen polysaccharide from E. coli O125ac:H6 has been elucidated. Sugar analysis revealed the presence of fucose, mannose, galactose and N-acetyl-galactosamine as major components. Unassigned 1H and 13C NMR data from one- and two-dimensional NMR experiments of the O125ac O-antigen in conjunction with sugar components were used as input to the CASPER program, which can determine polysaccharide structure in a fully automated way, and resulted in the following branched pentasaccharide structure of the repeating unit: →4)[β-d-Galp-(1 → 3)]-β-d-GalpNAc-(1 → 2)-α-d-Manp-(1 → 3)-α-l-Fucp-(1 → 3)-α-d-GalpNAc-(1→, where the side chain is denoted by square brackets. The proposed O-antigen structure was confirmed by 1H and 13C NMR chemical shift assignments and determination of interresidue connectivities. Based on this structure, that of the O125ab O-antigen, which consists of hexasaccharide repeating units with an additional glucosyl group, was possible to establish in a semi-automated fashion by CASPER. The putative existence of gnu and gne in the gene clusters of the O125 serogroups is manifested by N-acetyl-d-galactosamine residues as the initial sugar residue of the biological repeating unit as well as within the repeating unit. The close similarity between O-antigen structures is consistent with the presence of two subgroups in the E. coli O125 serogroup.

An N-linked tetrasaccharide from Halobacterium salinarum presents a novel modification, sulfation of iduronic acid at the O-3 position

Halobacterium salinarum, a halophilic archaeon that grows at near-saturating salt concentrations, provided the first example of N-glycosylation outside Eukarya. Yet, almost 50 years later, numerous aspects of such post-translational protein processing in this microorganism remain to be determined, including the architecture of glycoprotein-bound glycans. In the present report, nuclear magnetic resonance spectroscopy was used to define a tetrasaccharide N-linked to both archaellins, building blocks of the archaeal swimming device (the archaellum), and the S-layer glycoprotein that comprises the protein shell surrounding the Hbt. salinarum cell as β-GlcA(2S)-(1 → 4)-α-IdoA(3S)-(1 → 4)-β-GlcA-(1 → 4)-β-Glc-Asn. The structure of this tetrasaccharide fills gaps remaining from previous studies, including confirmation of the first known inclusion of iduronic acid in an archaeal N-linked glycan. At the same time, the sulfation of this iduronic acid at the O-3 position has not, to the best of our knowledge, been previously seen. As such, this may represent yet another unique facet of N-glycosylation in Archaea.

ROESY and 13C NMR to distinguish between D- and L-rhamnose in the α-D-Manp-(1 → 4)-β-Rhap-(1 → 3) repeating motif

Many children suffering from autism spectrum disorder (ASD) experience gastrointestinal (GI) conditions. Enterocloster bolteae has been regularly detected in the stool of individuals suffering from GI symptoms and autism. Literature has suggested that E. bolteae strains WAL 16351 and WAL 14578 produce an immunogenic capsular polysaccharide (CPS) comprised of disaccharide repeating units: α-D-Man-(1 → 4)-β-Rha-(1 → 3) that could be used for the development of an immunotherapeutic vaccine. Ambiguity in the configuration of rhamnose led to the synthesis of tri- and disaccharide analogues containing D-rhamnose and L-rhamnose, respectively. ROESY-NMR spectra showed that CH₃-6 of rhamnose and H-2 of mannose in the L-Rha containing disaccharide gave correlation. No such correlation was seen between the CH₃-6 of rhamnose and the H-2 of mannose in the D-Rha containing trisaccharide. Molecular dynamics studies on hexasaccharide containing L-Rha or D-Rha confirmed that these structures adopt conformations resulting in different distances between the C6-rhamnose and the H-2 mannose of the preceding residue. We also demonstrate that assignment of the absolute configuration of the rhamnosyl residue in the β-Rhap-(1 → 3)-D-Man linkage can be determined using the ¹³C chemical shift of C-2 in of D-Mannose. While β-D-Rha will lead to an upfield shift of C-2 due to γ-gauche interaction between H-1 Rha and H-2 Man, β-L-Rha will not. Our results provide insights to distinguish between D- and L-rhamnose in the α-D-Manp-(1 → 4)-β-Rhap-(1 → 3) repeating motif.