Potential 2006 Honours Project

Coupling immune regulating drugs to ferromagnetic beads for probing, isolating and identifying drug-binding proteins from cell homogenisates

Now that biological mass spectrometry has advanced to the point where proteins can be easily identified and possibly sequenced within a couple of hours, the idea of fishing for proteins within the contents of a cell is very realistic. Suppose a drug has a useful action but acts by an unknown mechanism. A general method for identifying important proteins in the action of the drug would be as follows: 1) couple the drug to a small ferromagnetic bead hopefully in such as way as to avoid reduced binding affinity; 2) expose the affinity bead to the homogenisate from human cells; 3) separate the beads using their magnetic properties and wash off unbound protein using buffer; 4) digest the proteins with trypsin and use a modern MALDI ToF-ToF mass spectrometer coupled to protein databases to identify the protein(s) bound to the ligand. The project will couple a new analogue of thalidomide, which is known to have immunomodulating properties, to ferromagnetic beads. The beads will be used in a fishing expedition aiming to find proteins involved in the biological action of the novel class of drug.

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Supervisors: Prof. Colin Pouton, Dr. Basil Danylec, Dr. Helen Irving