The GNAT: A new tool for processing NMR data

Matrix-assisted DOSY

The analysis of mixtures by NMR spectroscopy is challenging. Diffusion-ordered NMR spectroscopy enables a pseudo-separation of species based on differences in their translational diffusion coefficients. Under the right circumstances, this is a powerful technique; however, when molecules diffuse at similar rates separation in the diffusion dimension can be poor. In addition, spectral overlap also limits resolution and can make interpretation challenging. Matrix-assisted diffusion NMR seeks to improve resolution in the diffusion dimension by utilising the differential interaction of components in the mixture with an additive to the solvent. Tuning these matrix-analyte interactions allows the diffusion resolution to be optimised. This review presents the background to matrix-assisted diffusion experiments, surveys the wide range of matrices employed, including chromatographic stationary phases, surfactants and polymers, and demonstrates the current state of the art.

The Ensemble of Conformations of Antifreeze Glycoproteins (AFGP8): A Study Using Nuclear Magnetic Resonance Spectroscopy

The primary sequence of antifreeze glycoproteins (AFGPs) is highly degenerate, consisting of multiple repeats of the same tripeptide, Ala–Ala–Thr*, in which Thr* is a glycosylated threonine with the disaccharide beta-d-galactosyl-(1,3)-alpha-N-acetyl-d-galactosamine. AFGPs seem to function as intrinsically disordered proteins, presenting challenges in determining their native structure. In this work, a different approach was used to elucidate the three-dimensional structure of AFGP8 from the Arctic cod Boreogadussaida and the Antarctic notothenioid Trematomusborchgrevinki. Dimethyl sulfoxide (DMSO), a non-native solvent, was used to make AFGP8 less dynamic in solution. Interestingly, DMSO induced a non-native structure, which could be determined via nuclear magnetic resonance (NMR) spectroscopy. The overall three-dimensional structures of the two AFGP8s from two different natural sources were different from a random coil ensemble, but their “compactness” was very similar, as deduced from NMR measurements. In addition to their similar compactness, the conserved motifs, Ala–Thr*–Pro–Ala and Ala–Thr*–Ala–Ala, present in both AFGP8s, seemed to have very similar three-dimensional structures, leading to a refined definition of local structural motifs. These local structural motifs allowed AFGPs to be considered functioning as effectors, making a transition from disordered to ordered upon binding to the ice surface. In addition, AFGPs could act as dynamic linkers, whereby a short segment folds into a structural motif, while the rest of the AFGPs could still be disordered, thus simultaneously interacting with bulk water molecules and the ice surface, preventing ice crystal growth.

3D-QSAR assisted identification of FABP4 inhibitors: An effective scaffold hopping analysis/QSAR evaluation

Following on the recent publication of pharmacologically relevant effects, small molecule inhibitors of adipocyte fatty-acid binding protein 4 (FABP4) have attracted high interest. FABP4 is mainly expressed in macrophages and adipose tissue, where it regulates fatty acid storage and lipolysis, being also an important mediator of inflammation. In this regard, FABP4 recently demonstrated an interesting molecular target for the treatment of type 2 diabetes, other metabolic diseases and some type of cancers. In the past years, hundreds of effective FABP4 inhibitors have been synthesized. In this paper, a quantitative structure-activity relationship (QSAR) model has been produced, in order to predict the bioactivity of FABP4 inhibitors. The methodology has been combined with a scaffold-hopping approach, allowing to identify three new molecules that act as effective inhibitors of this protein. These molecules, synthesized and tested for their FABP4 inhibitor activity, showed IC₅₀ values between 3.70 and 5.59 μM, with a high level of agreement with the predicted values.

Suppression of 13C satellites in 1H DOSY spectra

Diffusion-ordered spectroscopy (DOSY) is a valuable tool for the analysis of intact mixtures, since it can separate the signals of components according to their apparent diffusion coefficients. However, DOSY experiments are acutely sensitive to spectral quality, and especially to signal overlap, which can lead to misleading apparent diffusion coefficients. Here, we introduce a new NMR experiment to reduce signal overlap in mixtures with a wide range of concentrations, by removing one-bond ¹³C satellites. In such high dynamic range mixtures, ¹³C isotopomer signals from major components can overlap with signals from minor components, causing problematic distortions in the diffusion domain of a DOSY spectrum. The new method, Oneshot-iDISPEL, is a combination of the Oneshot and DISPEL experiments, and its performance has been demonstrated on a Greek alcoholic beverage, ouzo, which contains small amounts of anise flavour components and sucrose. Ethanol is a major component, and the suppression of its ¹³C satellites reduces signal overlap with minor components, offering significant improvement in DOSY spectra.

Improving the Interpretation of Small Molecule Diffusion Coefficients

Diffusion-ordered NMR spectroscopy (DOSY) is increasingly widely used for the analysis of mixtures by NMR spectroscopy, dispersing the signals of different species according to their diffusion coefficients. DOSY is used primarily to distinguish between the signals of different species, with the interpretation of the diffusion coefficients observed usually being purely qualitative, for example to deduce whether one species is bigger or smaller than another. In principle, the actual values of diffusion coefficient obtained carry important information about the sizes of different species and on interactions between species, but the relationship between diffusion coefficient and molecular mass is in general a very complex one. Here a recently proposed analytical relationship between diffusion coefficient and molecular mass for the restricted case of small organic molecules is tested against a wide range of data from the scientific literature and generalized to cover a range of solvents and temperatures.