pK_a‐Determination and Conformational Studies by NMR Spectroscopy of D‐Altrose‐Containing and other Pseudodisaccharides as Glycosidase Inhibitor Candidates

Abstract

The pKa values of six amine‐linked pseudodisaccharides have been determined by using an NMR‐based titration method. The pKa varies significantly depending on the linkage position and is inversely correlated with the number of electronegative groups in the β‐position to the amino group. Four of the pseudodisaccharides contain α‐altroside moieties, the conformations of which were determined in the protonated and neutral states, again by using NMR techniques. In the neutral state, 2‐amino‐2‐deoxyaltrosides and 3‐amino‐3‐deoxyaltrosides were both found to occupy 4C1 and OS2 conformations. On protonation, little change in the population distribution was seen for the 3‐amino‐3‐deoxyaltrosides, but for the 2‐amino‐2‐deoxyaltrosides, a shift in equilibrium position towards the skew conformer (more than 80 % populated) takes place, and also a small amount of the other chair conformer (i.e., 1C4, approximately 10 % populated) was observed. 3‐Amino‐3‐deoxyaltrosides have been shown to act as glycosidase inhibitors and insights into conformational equilibria as a function of protonation state should facilitate the design of better glycosidase inhibitors based on flexible monosaccharide amines.

Revision of the GROMOS 56A6CARBO force field: Improving the description of ring‐conformational equilibria in hexopyranose‐based carbohydrates chains

“…This has the advantage of enforcing “textbook” chair conformations, certainly dominant in most “standard” situations. However, there are also many “nonstandard” situations where ring flexibility plays a key role, including in particular functionalized sugar derivatives, protein–carbohydrate recognition and processing, and AFM pulling experiments . In fact, it is even unclear whether the “textbook” picture strictly applies to “standard” situations.…”

“…Further validation and refinement of the 56A6 CARBO_R force field will be pursued, among other things, by the simulation of the handful of functionalized monomers and dimers for which experimental NMR data on the ring‐conformational equilibrium is available, by the systematic comparison of the simulation results with corresponding ΔF i values calculated by QM and QM/MM methods, and by the calculation of AFM stretching curves and comparison with experiment …”

“…Second, there is lack of direct experimental data against which to perform the parametrization, at least beyond the monosaccharide level . Although it is known that the 4 C 1 chair conformation is the most stable one for nearly all unfunctionalized hexopyranoses of the d ‐series in water, d ‐idose being an exception, the conformational equilibrium of the six‐membered ring may be affected by many environmental factors, e.g., functionalization of the exocyclic groups, neighbouring residues within an oligosaccharide chain, surrounding aminoacids in an enzyme active site, consideration of a nonaqueous solvent or of a crystal/fiber environment, or pulling forces in an atomic force microscopy (AFM) experiment . Because these effects are experimentally and biologically relevant, and because the timescale of plain MD simulations is reaching the microsecond regime, artificially locking the hexopyranose ring in a 4 C 1 chair conformation for the d ‐series ( 1 C 4 for the l ‐series) is no longer a viable procedure nowadays.…”

Chair interconversion and reactivity of mannuronic acid esters

“…The application of empirical J coupling data for conformational analysis of coalesced spectra is a good complement to the methodology based on Karplus-type relationships, employed in other studies. 9,10 Discussion Tables 1 and 2 summarize all data we obtained for the dynamic conformational equilibria of compounds 1-7. It is clear from Table 1 that the anomeric triflates and methyl mannosides have a different conformational preference.…”

Recent Advances in NMR Studies of Carbohydrates

“…NMR spectroscopy can be used to determine the protonation state of the molecule which has functional groups that may be readily protonated or deprotonated. R€ onnols et al [114] studied the conformational behavior of D-altrose-containing pseudodisaccharides as glycosyl inhibitor candidates. Authors defined the relationship between protonation of the nitrogen atom and conformation distribution (Fig.…”