DTU Chemistry - PhD 2014

Structural Studies of Small Molecules using NMR Spectroscopy

NMR spectroscopy is an important analytical technique that, among other things, is used for exploring the three-dimensional world of molecules.

Many natural products, whether proteins, carbohydrates, or secondary metabolites, require specific configurations to be recognized in the body. If a protein, peptide or oligosaccharide is folded incorrectly, the biological function disappears. Similarly, a small change in the stereochemistry of a bioactive molecule can lead to a change in the biological activity from therapeutic to toxic. It is thus very important to know the absolute structure of new molecules, either created as drug candidates or for other scientific purposes. Absolute structure means knowing the configuration of all stereo-centers in the molecule. Nuclear Magnetic Resonance (NMR) is a well-established method to aid in such studies. The thesis work is centered around the use of NMR spectroscopy in three main projects ranging from the design of new NMR experiments, over discovery of bacterial and fungal natural products, to NMR structural studies of human milk oligosaccharides.

The NMR structural studies of human milk oligosaccharides (HMO) was key in a larger project with the goal of producing HMOs by synthetic and enzymatic approaches. Oligosaccharides in human milk play a role in the development and protection of newborns and are commercially interesting as potential additives in infant formula. They have rather well-defined structures consisting of a backbone with disaccharides lactose, N-acetyllactosamine and/or lacto-N-biose whereupon the monosaccharides fucose and/or sialic acid are attached. NMR spectroscopy was used, among other techniques to identify the chemically and enzymatically produced HMO molecules, and to screen a range of enzymes for their trans-fycosylation abilities.

In a separate part of the project, a range of new natural products were discovered, isolated and described. These included the solonamides and the ngercheumicins; two families of cyclic depsipeptides isolated from a marine bacterium with the ability to prevent virulence in the pathogenic S. aureus. A. fijiensis, a relatively unknown fungal species, was also investigated to explore its chemistry in the search for new biological active compounds. This resulted in the discovery of one novel metabolite.

Finding the three-dimensional structure of molecules involves obtaining knowledge of several structural parameters, such as angular and distance information between the nuclei in the molecule. In the project, a new NMR experiment was developed for measurement of J coupling constants that so far have been difficult to obtain. The new NMR experiment was applied to several known smaller molecules and has yielded new structural information that allows for the computation of more reliable three-dimensional structures. The experiment has also been tested on new molecules and given excellent results both in studies of oligosaccharides and other natural products. With both the experiment and the subsequent processing running smoothly, the hope is that a range of NMR users, both experienced and less experienced, will make use of this experiment for easier structural analysis of complex molecules.

DTU Chemistry - PhD 2014

Charlotte H. Gotfredsen

Funded by:
The project was funded by the Danish Council for Strategic Research (DSF).

Link to the thesis!