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. The lack of dedicated bioinformatic tools for mining GAG data sets contributes to a partial characterization of the structural and functional landscape and interactions of GAGs. These pending issues will benefit from the development of new approaches reviewed here, namely (i) the synthesis of GAG oligosaccharides to build large and diverse GAG libraries, (ii) GAG analysis and sequencing by mass spectrometry (e.g., ion mobility-mass spectrometry), gas-phase infrared spectroscopy, recognition tunnelling nanopores, and molecular modeling to identify bioactive GAG sequences, biophysical methods to investigate binding interfaces, and to expand our knowledge and understanding of glycocodes governing GAG molecular recognition, and (iii) artificial intelligence for in-depth investigation of GAGomic data sets and their integration with proteomics.

Intramolecular crankshaft-type rearrangement in a photoisomerised glycoconjugate.

High-resolution NMR spectroscopy revealed that a novel glycoconjugate, consisting of two ß-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.

A study of the photochemical behaviour and relaxation mechanisms of anti-syn 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 anti to syn isomerisation on exposure to ultraviolet light in DMSO solution. The degree anti to syn conversion varied significantly upon substitution (between 5% and 100%) and also showed two noteworthy features: that relaxation back to the anti-form goes far faster (by at least 3 orders of magnitude) when the C6 rings B and C have ortho-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 anti-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. Both of these mechanisms have been analysed theoretically.

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. Alkyl glycosides were tested on their toxicity against bacterial cells of the genus Pseudomonas (MTT assay), microbiological adhesion to hydrocarbons (MATH assay), cell surface hydrophobicity (Congo red assay), cell membrane permeability (crystal violet assay), and bacterial biofilm formation. Furthermore, their antifungal activity against two pathogenic microorganisms Candida albicans and Aspergillus niger was investigated using the disc diffusion method. Toxicological studies revealed that compounds could reduce the metabolic activity of bacterial cells only moderately but they increased the hydrophobicity of cell surface in Pseudomonas strains. In addition, alkyl glycosides changed the permeability of the cell membranes to the level of 30-40% for this strain. The compounds with an even number of carbon atoms in their alkyl chain promoted stronger bacterial biofilm formation on the glass surface. All studied derivatives demonstrated very strong antifungal activity against fungus A. niger but very small effect against C. albicans. Overall, the results showed that long-chain alkyl glycosides could be considered as inexpensive, biocompatible, nontoxic agents, and serve for the surface design to avoid bacterial adhesion as an alternative solution to antibiotic treatment.

Photochemical anti-syn 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 anti- to the higher-energy syn-form around the -N-N[double bond, length as m-dash] linkage. The anti- to syn-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 anti-conformer being lower in energy than the syn. Theoretical analysis of excited states, including visualisation of natural transition orbitals, identified possible pathways for syn-anti isomerisation, although the details vary with π-system size, making the use of small models of limited utility. The investigated compound probably isomerises through the third singlet excited state (S3), a π-π* excitation, relaxing through S2, also a π-π* state.

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 ¹C4 and the other ²S0) 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. Optimised molecular structures indicated the formation of a complex hydrogen bond network, including interresidue and intraresidue bonds. The ionic interactions strongly influence the first hydration shell and, together with hydrogen bonds, play an important role in shaping the 3D tetrasaccharide structure. DFT-derived indirect three⁻bond proton⁻proton coupling constants (³JH-C-C-H) showed that the best agreement with experiment was obtained with a weighted average of 67:33 (¹C4:²S0) of the IdoA2S forms. Detailed analysis of Fermi-contact contributions to ³JH-C-C-H showed that important contributions arise from the oxygen lone pairs of neighbouring oxygen atoms. The analysis also showed that the magnitude of diamagnetic spin⁻orbit contributions are sufficiently large to determine the magnitude of some proton⁻proton coupling constants. The data highlight the need to use appropriate quantum-chemical calculations for a detailed understanding of the solution properties of heparin oligosaccharides.

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. Mixing of proligand solutions with the equimolar amount of copper(II) ions resulted in the formation of 1:1 Cu(II)-to-ligand complex, with the EPR and UV-Vis spectra fully compatible with those obtained for the dissolved Cu(II) thiosemicarbazone complexes. The formation of the complexes fully inhibited the photoinduced generation of reactive oxygen species, and only subtle changes were found in the electronic absorption spectra of the complexes in aqueous and DMSO solutions upon UVA steady-state irradiation. The dark redox activity of copper(II) complexes and proligand/Cu(II) aqueous solutions towards hydrogen peroxide which resulted in the generation of hydroxyl radicals, was confirmed by spin trapping experiments.