Developing a new medical drug often requires a detailed understanding of how and where the drug compound binds to the target protein. However, for large protein-ligand complexes, it is often difficult to find the ‘binding mode’ of the ligand on the protein.

As part of a new Australian Research Council (ARC) Grant, Professor Gottfried Otting and his team will use Nuclear Magnetic Resonance (NMR) spectroscopy to enhance our understanding of such complexes, with a view on the creation of high-value drugs for diseases such as Dengue fever and the Zika virus.

Gottfried’s grant builds on years of work in which Gottfried has created ‘labelling’ procedures to help identify ligand binding modes in protein-ligand complexes by NMR.

“NMR spectroscopy is the most powerful spectroscopic technique that a chemist has,” Gottfried explains. “You put your sample into a tube that has half a millilitre of solution. The magnetic field is very strong and each nucleus with a ‘spin’, in particular hydrogen, has a magnetic moment that generates a signal in the NMR spectrum at a frequency that is specific for the chemical environment of the individual nuclei.”

This can be used to identify the ligand binding sites within protein-ligand complexes. As Gottfried explains:

“In the NMR spectrum we can attribute each signal to particular hydrogens in the molecule. And not only hydrogens but also carbons and nitrogens.” “What we gain there is signals for all those sites in the protein that act like local spies for what’s happening. The moment that a drug molecule binds to a protein it will change the chemical environment for the nearby nuclear spins. When we see that in the NMR spectrum, we say ‘ah that’s where it must bind’.”

“This is something the pharmaceutical industry uses already, and has been for a long time,” Gottfried explains. “They would not let a drug go to clinical trials if they haven’t confirmed by NMR that it binds specifically to a defined site on the target protein.”

To improve a ligand, however, also its orientation and structure must be known.

“This problem is much harder,” Gottfried says, “because the NMR signals of the ligand can be difficult to identify against the background of protein signals. Labelling the ligand molecule chemically with a ’t-butyl’ group, however, gives us a very intense ligand signal.”

Gottfried and his team have taken this approach further by furnishing the protein with paramagnetic chemical tags that change the frequency of the NMR signal from the t-butyl group.

“This gives us the coordinates of the t-butyl group on the protein just like the GPS signal from satellites gives us our coordinates on the planet,” explains Gottfried.

At present, his team applies these new methods to develop a drug against the Zika virus.

“The problem with Zika is that the available vaccines can’t be deployed because they seem to aggravate subsequent Dengue infections. Therefore, it would help to have a drug available for pregnant woman with acute Zika infection. This is what we are working on.”