Chemical Proteomics as a Tool in Target Discovery of BioactiveSmall Molecules

One of the main questions affecting the chemical biology is the comprehension of the mechanisms of action involved in the interaction between small bioactive molecules and their macromolecular partners. Although the therapeutic potential of most promising compounds is being evaluated in preclinical and clinical trials, often their intracellular targets and their interaction profile remain largely unknown.1 Nowadays, the progress in the field of chromatography and mass spectrometry has a significant impact on the biological target identification of small molecules. Chemical proteomics, a methodological approach that combines affinity purification (AP) and mass spectrometry (MS), has recently been applied for fishing macromolecular partners which specifically bind on immobilized small drugs1. The procedure usually requires the chemical modifications of the matrix beads with a spacer bound to the molecule of interest, followed by the AP of the potential target(s) from a complex matrix2, its identification by gel electrophoresis (SDS-PAGE), MS and bioinformatics3, and the pharmacological tests to assess the bioactivity of the compound. The application of this methodology to the case of petrosaspongiolide M, a marine natural product endowed with a peculiar anti-inflammatory profile, led us recently to identify the 26S proteasome as its specific target of inhibition4 and confirm the predicted bioactivity. In this communication we report the details of this study along with other recent findings on this topic. 1. Scholten A., van Veen T., Vos A.M., Heck A. J. Prot. Res. (2007), 6, 1705-17. 2. Yamamoto K., Yamazaki A., Tacheuchi M., Tanaka A. Anal. Biochem. (2006), 352, 15-23. 3. Shimizu N., Sugimoto K., Tang J., Nishi T., Sato I., Hiramoto M., Aizawa S., Hatakeyama M., Ohba R., Hatori H., Yoshikawa T., Suzuki F., Oomori A., Tanaka H., Kawaguchi H., Watanabe H., Handa H. Nature Biotech. (2000), 18, 877-81. 4. Margarucci L., Monti M.C., Riccio R., Casapullo A. Angew. Chem. Int. Ed., accepted for publication.