Historically, most drugs were discovered either by identifying the active ingredient from traditional medicines or by observing the pharmacological effect of compounds in living animals and it wasn’t until the 1960s that an understanding of the relationship between chemical structure and biological activity began to develop. Since then, attempts have been made to link discrete molecular targets (usually proteins) to particular diseases and to identify small molecules which will interfere with the function of these targets.
Contemporary drug discovery is dominated by this molecular target-based paradigm but, with the advent of high throughput cell-based assays, scientists are now also able to test compounds for a desirable activity in whole cells. A disadvantage of this approach is that the precise protein target is not always easy to identify but, writing in the journal PNAS, Ong et. al. have now described the use of quantitative proteomics (SILAC, stable isotope labelling with amino acids in cell culture) together with affinity enrichment to identify the protein targets.
SILAC is a technique based on mass-spectrometry which allows detection of differences in protein abundance between samples of cells. The growth medium of one cell population contains normal essential amino acids whilst that of the other cell population contains arginine or lysine labelled with stable heavy isotopes (13C or 15N). The growing cells incorporate these amino acids into their proteins, reaching full incorporation after 5 population doublings and producing a characteristic mass shift (6 Da with 13C6-Arg or 8 Da with 13C615N2-Lys). If the cells grown in the presence of the ‘heavy’ amino acids are also treated with a test compound, any difference in the ratio of peak intensities in the mass spectrum for protein pairs between treated and untreated cells indicates that the protein is, directly or indirectly, a target of the test compound. The authors describe the application of the method to the identification of targets for kinase inhibitors and immunophilin binders.