ActivX: pulling out proteins by their activity.

“Suppose you could develop a chemical tool so powerful that you could go into a cell and identify all the members of one family — all the protein kinases, or all the hydrolases or the phosphatases,” proposes John Kozarich, president and chief scientific officer at the drug discovery and development company ActivX in La Jolla, California. The activity-based proteomics technology to do just that was originally developed by Ben Cravatt's group at the Scripps Institute and has been commercialized by ActivX.

The approach is based on a simple idea: proteins in the same family tend to have conserved active sites which a well-designed chemical reagent can pick up. In the chemistry literature are thousands of publications probing the structure and functions of proteins, defining inhibitors and ligand interactions. “We harvest that information. We are interested in tools that allow us to look at families related by a common trait,” explains Kozarich.

For serine hydrolases, for example, ActivX has designed chemical tools that recognize the underlying catalytic motif — three amino acids in a particular spatial configuration. The system adds a highly fluorescent covalent tag to one of the unique amino-acid residues, and this allows all the serine hydrolases to be pulled out of a sample by capillary electrophoresis, and analysed and identified by mass spectrometry. Early in drug development, a domain scan can compare different animal models to help resolve toxicity issues. Another use is to characterize off-target interactions of drug leads, as the probes are designed to recognize just those protein motifs that are the same as the active sites that are the real drug target.

L.M.