Activity-based Chemical Proteomics Profiling of Natural Products and Drug-like Small Molecules

Abstract

Assigning the cellular target(s) of bioactive small molecules, whether the compounds are discovered by cell-based phenotypic or target-based screening of chemical libraries, remains an ongoing challenge. The ability of accurately and thoroughly determining of SM-target interaction profiles as well as mapping of metabolic and signaling pathways on the proteomic scale would therefore be more illuminating, as it could provide invaluable biological insights for a drug candidate either by understanding the primary mechanism-of-action, and at the same time, side effects due to unexpected ?off-target? interactions at a very early stage of drug development, which should help to reduce the attrition rate in development. In many cases such a capability could find new potential therapeutic value for an established drug as well as it could offer strong clues for compound optimization in order to maximize the therapeutic potential and minimize potential cellular toxicity of a drug. Recent advances in chemical proteomics (or activity-based proteomics), a multidisciplinary research area integrating biochemistry and cell biology with organic synthesis and mass spectrometry, have enabled a more direct and unbiased analysis of a drug?s mechanism of action in the context of the proteomes as expressed in the target cell or the tissue of interest. In this thesis, I describe the design and synthesis of orlistat-like natural product-based probes (Chapter 2, 3 and 4), K11777-like drug candidate-based probes (Chapter 5) and drug-like azadipeptide nitrile-based small molecules (Chapter 6), determination of structure-activity relationships of these compounds, target identification and validation in subsequent molecular biology as well as cell biological/genetic experiments in both mammalian cells and Trypanosoma brucei parasites.