Glycosaminoglycans: What Remains To Be Deciphered?

Glycosaminoglycans (GAGs) are complex polysaccharides exhibiting a vast structural diversity and fulfilling various functions mediated by thousands of interactions in the extracellular matrix, at the cell surface, and within the cells where they have been detected in the nucleus. It is known that the chemical groups attached to GAGs and GAG conformations comprise "glycocodes" that are not yet fully deciphered. The molecular context also matters for GAG structures and functions, and the influence of the structure and functions of the proteoglycan core proteins on sulfated GAGs and vice versa warrants further investigation.

Intramolecular crankshaft-type rearrangement in a photoisomerised glycoconjugate.

High-resolution NMR spectroscopy revealed that a novel glycoconjugate, consisting of two β-glucopyranoses attached to a quinazolinone-like structure, exhibited photoisomerization around the -N-N[double bond, length as m-dash] and [double bond, length as m-dash]CH-C- bonds of the -N-N[double bond, length as m-dash]CH-C- linkage in the same timeframe (the so-called "crankshaft rotation") upon exposure to UV light. Experimental NMR data combined with DFT calculations discovered that the attachment of carbohydrate residues to photoactive compounds significantly changed the isomerization process and intramolecular rearrangement compared to the unglycosylated system, while the overall molecular structure remained virtually unchanged.

Chemistry towards Biology.

Although it may not seem like it, chemical biology has existed for a long time from today's perspective [...

Chemistry towards Biology-Instruct: Snapshot.

The knowledge of interactions between different molecules is undoubtedly the driving force of all contemporary biomedical and biological sciences. Chemical biology/biological chemistry has become an important multidisciplinary bridge connecting the perspectives of chemistry and biology to the study of small molecules/peptidomimetics and their interactions in biological systems. Advances in structural biology research, in particular linking atomic structure to molecular properties and cellular context, are essential for the sophisticated design of new medicines that exhibit a high degree of druggability and very importantly, druglikeness.

A study of the photochemical behaviour and relaxation mechanisms of - isomerisation around quinazolinone -N-N[double bond, length as m-dash] bonds.

High-resolution NMR experiments revealed that differently substituted quinazolinone-based Schiff bases undergo to isomerisation on exposure to ultraviolet light in DMSO solution. The degree to conversion varied significantly upon substitution (between 5% and 100%) and also showed two noteworthy features: that relaxation back to the -form goes far faster (by at least 3 orders of magnitude) when the C rings B and C have -OH substituents, and that relaxation can also be significantly sped up by addition of acid. Two possible mechanisms explaining the differences in relaxation process have been proposed: (I) the interaction of the azomethine hydrogen with the carbonyl oxygen results in slower reversion to the -form and/or (II) suppression of conjugation of the N3 lone pair with the N[double bond, length as m-dash]CH double bond by protonation and/or internal H-bonding.

Evaluation of surface active and antimicrobial properties of alkyl D-lyxosides and alkyl L-rhamnosides as green surfactants.

The use of carbohydrates, as a part of surface-active compounds, has been studied due to their biodegradability and nontoxic profile. A series of alkyl glycosides containing d-lyxose and l-rhamnose with alkyl chains of 8-12 carbon atoms were investigated. The effects of structural variations on their physico-chemical and biological properties have been evaluated for a detailed understanding of their properties.

Photochemical - isomerization around the -N-N[double bond, length as m-dash] bond in heterocyclic imines.

EPR and NMR experiments on a quinazolinone-based Schiff's base in DMSO solution showed that irradiation with UV light (365 nm) leads to photochemically-induced isomerization from the - to the higher-energy -form around the -N-N[double bond, length as m-dash] linkage. The - to -isomerization was relatively fast, and the maximum amount of conversion detected (25%) was reached within 10 min; thermodynamic equilibrium re-established itself in about 15 min. DFT calculations were performed on the investigated compound and small model systems, and reproduced the experimental fact of the -conformer being lower in energy than the .

Solution Conformation of Heparin Tetrasaccharide. DFT Analysis of Structure and Spin⁻Spin Coupling Constants.

Density functional theory (DFT) has provided detailed information on the molecular structure and spin⁻spin coupling constants of heparin tetrasaccharide (GlcNS,6S-IdoA2S-GlcNS,6S-IdoA2S-OMe) representing the predominant heparin repeating-sequence. The fully optimised molecular structures of two tetrasaccharide conformations (differing from each other in the conformational form of the sulphated iduronic acid residue⁻one ¹₄ and the other ²₀) were obtained using the B3LYP/6-311+G(d,p) level of theory and applying explicit water molecules to simulate the presence of a solvent. The theoretical data provided insight into variations of the bond lengths, bond angles and torsion angles, formations of intra- and intermolecular hydrogen bonds and ionic interactions.

Copper(II) Thiosemicarbazone Complexes and Their Proligands upon UVA Irradiation: An EPR and Spectrophotometric Steady-State Study.

X- and Q-band electron paramagnetic resonance (EPR) spectroscopy was used to characterize polycrystalline Cu(II) complexes that contained sodium 5-sulfonate salicylaldehyde thiosemicarbazones possessing a hydrogen, methyl, ethyl, or phenyl substituent at the terminal nitrogen. The ability of thiosemicarbazone proligands to generate superoxide radical anions and hydroxyl radicals upon their exposure to UVA irradiation in aerated aqueous solutions was evidenced by the EPR spin trapping technique. The UVA irradiation of proligands in neutral or alkaline solutions and dimethylsulfoxide (DMSO) caused a significant decrease in the absorption bands of aldimine and phenolic chromophores.

Solution Structure of Heparin Pentasaccharide: NMR and DFT Analysis.

High-resolution NMR and density functional theory (DFT) calculations have been applied to analysis of heparin pentasaccharide 3D structure in aqueous solution. The fully optimized molecular geometry of two pentasaccharide conformations (differing from each other in the form, one (1)C4 and the other (2)S0, of the sulfated iduronic acid residue) were obtained using the B3LYP/6-311+G(d,p) level of theory in the presence of solvent, the latter included as explicit water molecules. The presented approach enabled insight into variations of the bond lengths, bond angles, and torsion angles, formations of intra- and intermolecular hydrogen bonds, and ionic interactions in the two pentasaccharide conformations.

Cationization of heparin for film applications.

Trimethylammonium-2-hydroxypropyl-(TMAHP) spacer was introduced into heparin (H) and the prepared films were characterized by elemental analysis, NMR, SEC-MALS, TG/DTG/DTA, AFM and mechanical tester. When quaternized at the ratio of H/NaOH/alkylating agent/H2O=0.1-1/0-2/0.

NMR and DFT analysis of trisaccharide from heparin repeating sequence.

NMR and density functional theory (DFT) have afforded detailed information on the molecular geometry and spin-spin coupling constants of a trisaccharide from the heparin repeating-sequence. The fully optimized molecular structures of two trisaccharide conformations (differing from each other in the form of the central iduronic acid residue) were obtained using the B3LYP/6-311+G(d,p) level of theory in the presence of solvent, the latter included as either explicit water molecules or via a continuum solvent model. NMR spin-spin coupling constants were also computed using various basis sets and functionals and then compared with measured experimental values.

A new type of rearrangement in branched-chain carbohydrates: isomerization of 3-C-branched aldoses.

A new type of rearrangement is described for 3-C-branched chain aldoses. The studied transformation is based on the Mo(VI)-catalyzed isomerization of carbohydrate carbon skeleton and allows preparation of C-3 isomers of 3-C-branched aldoses in a simple way without formation of side products. This rearrangement at C-3 carbon differs from the previously described epimerization at C-2 of aldoses catalyzed by Mo(VI) ions, known as Bílik reaction.

Effect of solvent and counterions upon structure and NMR spin-spin coupling constants in heparin disaccharide.

Density functional theory (DFT) has been used to analyze structure and NMR spin-spin coupling constants in heparin disaccharide. Both B3LYP/6-311++G** and M05-2X/6-311++G** methods have been used for optimization of disaccharide geometry. Solvent effect was treated by use of explicit water molecules.

The conformation and structure of GAGs: recent progress and perspectives.

The glycosaminoglycan (GAG) family of linear sulphated polysaccharides are involved in most regulatory processes in the extracellular matrix of higher organisms. The relationship between GAG substitution pattern and activity, however, remains unclear and experimental evidence suggests that subtle conformational factors play an important role. The difficulty of modelling these complex charged molecules shifts the burden of investigation towards experimental techniques.

Spectroscopic and theoretical approaches for the determination of heparin saccharide structure and the study of protein-glycosaminoglycan complexes in solution.

Glycosaminoglycans (GAGs), such as heparin and heparan sulphate, are a class of linear, anionic polysaccharides that constitute the carbohydrate component of proteoglycans. The structure of GAG complexes with proteins can reveal details of their mechanisms of action in living systems and help to design new pharmaceuticals. Molecular modelling together with nuclear magnetic resonance (NMR) and other spectroscopic techniques such as circular dichroism (CD) provide indispensable information on structure and dynamics of GAGs and their complexes.

Residual dipolar coupling investigation of a heparin tetrasaccharide confirms the limited effect of flexibility of the iduronic acid on the molecular shape of heparin.

The solution conformation of a fully sulfated heparin-derived tetrasaccharide, I, was studied in the presence of a 4-fold excess of Ca(2+). Proton-proton and proton-carbon residual dipolar couplings (RDCs) were measured in a neutral aligning medium. The order parameters of two rigid hexosamine rings of I were determined separately using singular value decomposition and ab initio structures of disaccharide fragments of I.

Minimum FGF2 binding structural requirements of heparin and heparan sulfate oligosaccharides as determined by NMR spectroscopy.

Heparin and heparan sulfate (HS) glycosaminoglycans (HSGAGs) are sulfated polysaccharidesthat play important roles in fundamental biological processes by binding to proteins. The prototypic exampleof HSGAG-protein interactions is that with the fibroblast growth factors (FGFs), specifically FGF1 andFGF2. Structural and biochemical studies have shown that the chain length, sulfation pattern, andconformation of HSGAGs play a critical role in FGF binding and activity.

Interaction of heparins with fibroblast growth factors: conformational aspects.

Heparin and heparin-like oligo- and polysaccharides bind to fibroblast growth factors (FGFs) and modulate their ability to form active ternary complexes with FGF receptors (FGFRs). Considerable efforts have been made in recent years to identify the minimal heparin and heparan sulfate (HS) sequences that bind and activate individual FGFs. Heparin sequences involved in interaction with FGFs invariably contain at least one residue of 2-O-sulfated iduronic acid (IdoA2S), which adopts either the (1)(4) chair conformation or the equi-energetic skew-boat (2)S(0).

B3LYP/6-311++G* * study of structure and spin-spin coupling constant in heparin disaccharide.

Structures of heparin disaccharide have been analyzed by DFT using the B3LYP/6-311++G( * *) method. The optimized geometries of two forms of this disaccharide, differing in the conformation ((1)C(4) and (2)S(0)) of the IdoA2S residue, confirmed considerable influences of the sulfate and the carboxylate groups upon the pyranose ring geometries. The computed energies showed that disaccharide having the (1)C(4) form of the IdoA2S residue is more stable than that with the (2)S(0) form.

Relationship between structure and three-bond proton-proton coupling constants in glycosaminoglycans.

Theoretical calculations using the DFT theory at the B3LYP/6-311++G(**) level were used to determine the molecular geometry of various glycosaminoglycan (GAG) molecules. Three-bond proton-proton spin-spin coupling constants ((3)J(H-C-C-H)) were then computed and compared with the published experimental data of selected mono- and disaccharides. The computed (3)J(H-C-C-H) values showed a strong dependence on the molecular geometry and varied up to 12 Hz.

A simple NMR analysis of the protonation equilibrium that accompanies aminoglycoside recognition: dramatic alterations in the neomycin-B protonation state upon binding to a 23-mer RNA aptamer.

A complete characterisation of the protonation equilibrium that accompanies the molecular recognition of neomycin-B by a specific RNA receptor has been achieved by employing simple NMR measurements.

B3LYP/6-311++G** study of structure and spin-spin coupling constant in methyl 2-O-sulfo-alpha-L-iduronate.

Structures of three most stable conformers ((1)C4, (4)C1, (2)S0) of methyl 2-O-sulfo-alpha-L-iduronate monosodium salt have been analyzed by DFT using the B3LYP/6-311++G** method. The optimized geometries confirmed the influence of both 2-O-sulfate and carboxylate groups upon the pyranose ring geometry. The computed energies showed that the chair (1)C4 form is the most stable one.

Dynamic properties of biologically active synthetic heparin-like hexasaccharides.

A complete study of the dynamics of two synthetic heparin-like hexasaccharides, D-GlcNHSO3-6-SO4-alpha-(1-->4)-L-IdoA-2-SO4-alpha-(1-->4)-D-GlcNHSO3-6-SO4-alpha-(1-->4)-L-IdoA-2-SO4-alpha-(1-->4)-D-GlcNHSO3-6-SO4-alpha-(1-->4)-L-IdoA-2-SO4-alpha-1-->iPr (1) and -->4)-L-IdoA-2-SO4-alpha-(1-->4)-D-GlcNHAc-6-SO4-alpha-(1-->4)-L-IdoA-alpha-(1-->4)-D-GlcNHSO3-alpha-(1-->4)-L-IdoA-2-SO4-alpha-1-->iPr (2), has been performed using 13C-nuclear magnetic resonance (NMR) relaxation parameters, T1, T2, and heteronuclear nuclear Overhauser effect (NOEs). Compound 1 is constituted from sequences corresponding to the major polysaccharide heparin region, while compound 2 contains a sequence never found in natural heparin. They differ from each other only in sulphation patterns, and are capable of stimulating fibroblast growth factors (FGFs)-1 induced mitogenesis.