Developing Chemical Proteomic Tools Connecting Proteins and Small Molecules

Abstract

The completion of the human genome sequencing project has provided a wealth of new information about the genomic blueprint of the cell. The promise of this information is likely to re-define the way researchers approach the study of complex biological systems and drug development. But genes do not tell the entire story of life and living processes until proteins are translationally produced and post-translationally modified. Proteins are not only integral part of life but also are required for its regulation and diversification. Diseases can be caused by minor changes in protein dysfunction. Although there are roughly 20,000 genes in the human genome, only a few proteins have known functions. Little is understood about the physiological roles, substrate specificity, and downstream targets of the vast majority of these important proteins. The major challenge for fighting human disease lies in translating genomic information into understanding of the cellular functions of these proteins in both normal and pathological process. A key step toward the biological characterization of proteins, as well as their adoption as drug targets, is the development of global solutions that bridge the gap in understanding these proteins and their interactions. Recently developed chemical proteomics approaches are alternative and complementary approaches for gene expression analysis and thus are ideal utensils in decoding this flood of genomic information. This approach makes use of synthetic small molecules that can be used to covalently modify a set of related proteins and subsequently allow their purification and/or identification as valid drug targets. Furthermore, such methods enable rapid biochemical analysis and small molecule screening of targets there by accelerating the often difficult process of target validation and drug discovery. This thesis examines and addresses these challenges by introducing a series of chemical proteomics tools that span various analytical modes, effectively expanding the chemical proteomics labelling?s application on both specificity and scope. These include chemical (small molecules inhibitor) labelling (Chapter 2, 3 and 4) and metabolites (endogenous small molecules) analogue labelling (Chapters 5) platforms, for which I demonstrate with examples, novel strategies to garner implicit understanding of protein functions, enzyme-substrate interactions, protein-drug interactions, protein localizations and protein?s post-translational modifications. Cohesively, these methodologies are applied (but not limited) to different phases of drug development--- protein targets identification, lead discovery and drug efficacy assessment.