Computational description of conformational and dynamic properties of anticoagulant heparin analogue pentasaccharides is of crucial importance in understanding their biological activities. We designed and synthesized idraparinux derivatives modified with sulfonatomethyl moieties at the D, F, and H glucose units that display varied potencies depending on the exact nature of the substitution. In this report we examined the capability of molecular dynamics (MD) simulations to describe the conformational behavior of these novel idraparinux derivatives. We used Gaussian accelerated MD (GAMD) simulations on the parent compound, idraparinux, to choose the most suitable carbohydrate force field for these type of compounds. GAMD provided significant acceleration of conformational transitions compared to classical MD. We compared descriptors obtained from GAMD with NMR spectroscopic parameters related to geometrical descriptors such as scalar couplings and nuclear Overhauser effects (NOE) measured on idraparinux. We found that the experimental data of idraparinux is best reproduced by the CHARMM carbohydrate force field. Furthermore, we propose a torsion angle parameter for the sulfonatomethyl group, which was developed for the chosen CHARMM force field using quantum chemical calculations and validated by comparison with NMR data. The work lays down the foundation of using MD simulations to gain insight into the conformational properties of sulfonato-methyl group modified idraparinux derivatives and to understand their structure−activity relationship thus enabling rational design of further modifications.

Novel CLIP‐COSY based homo‐ and heteronuclear correlation experiments are reported for the rapid, semi‐automated NMR assignment of small to medium‐sized molecules. The homonuclear CLIP‐COSY and corresponding relayed experiments employ the perfect‐echo based mixing sequence for in‐phase coherence transfer between directly and/or indirectly coupled proton spins. The combined analysis of the resulting CLIP‐COSY and relayed spectra made it possible to easily track down, layer by layer, the proton–proton connectivity network. In larger molecules the narrow chemical shift range of protons may, however, compromise the efficacy of the homonuclear correlation based assignment strategy. To overcome this limitation, an HSQC variant of the CLIP‐COSY experiment has now been devised. Combined treatment of HSQC‐CLIP‐COSY (relayed) and standard HSQC spectra facilitates simultaneous and semi‐automatic assignment of 1H and 13C resonances of medium‐sized molecules, such as pentasaccharides. The recently introduced PSYCHE broadband homonuclear decoupling scheme has been also implemented into the devised homo‐ and heteronuclear CLIP‐COSY based experiments, resulting in fully decoupled high‐resolution pure‐shift correlation spectra.

A novel two-dimensional method, SEA XLOC, for distinguishing between two- and three-bond correlations in heteronuclear NMR spectroscopy is introduced and demonstrated on ibuprofen and by a complete set of correlations with a simple and most complex quaternary 13C multiplet in strychnine.

Novel NMR experiments, BANGO SEA XLOC–H2OBC or BANGO HMBC–H2OBC, deliver complete heteronuclear correlations and assignments on a time scale of minutes on small molecules.

Elucidation and improvement of the blood coagulant properties of heparin are the focus of intense research. In this study, we performed conformational analysis using nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations on the heparin pentasaccharide analogue idraparinux, its disulfonatomethyl analogue, which features a slightly improved blood coagulation property, and a trisulfonatomethyl analogue, in which the activity has been totally abolished. As the ring conformation of the G subunit has been suggested as a major determinant of the biological properties, we analyzed the sugar ring conformations and dynamics of the interglycosidic linkages. We found that the conformation of the G ring is dominated by the 2SO skewed boat next to the 1C4 chair in all three derivatives. Both the thermodynamics and the kinetics of the conformational states were found to be highly similar in the three derivatives. Molecular kinetic analysis showed that the 2SO skewed boat state of the G ring is equally favorable in the three analogues, resulting in similar 2SO populations. Also, the transition kinetics from the 1C4 chair to the 2SO skewed boat was found to be comparable in the derivatives, which indicates a similar energy barrier between the two states of the G subunit. We also identified a slower conformational transition between the dominant 4C1 chair and the boat conformations on the E subunit. Both G and E ring flips are also accompanied by changes along the interglycosidic linkages, which take place highly synchronously with the ring flips. These findings indicate that conformational plasticity of the G ring and the dominance of the 2SO skewed boat populations do not necessarily warrant the biological activity of the derivatives and hence the impact of other factors also needs to be considered.