Projects in the Woo group bridge chemistry and biology to control regulatory allosteric hotspots in the proteome.
The human proteome consists of 20,000 proteins, yet less than 3% of these are “druggable” by a small molecule agent. A central challenge in the expansion of the druggable proteome is the need to better define global small molecule–protein interactions. By contrast, small molecules are essential mediators of native cellular processes [e.g., post-translational modifications (PTMs)], in addition to vehicles of human intervention (e.g., small molecule therapeutics). Nature regulates the entire proteome through PTMs to protein regulatory hotspots that alter protein–protein interactions. We are working to reveal natural allosteric regulatory hotspots for endogenous PTMs that are likewise modulated by exogenous small molecules.
Chemical control of the glycoproteome
Modification of proteins with sugars produces glycoproteins, one of the essential chemical codes that cells use for regulatory signaling. However, functions for the thousands of glycoproteins, how glycan-modifying enzymes dynamically select from these substrates, and why we need glycan PTMs for life remain unanswered. We developed a proximity-directed glycosyltransferase system for protein-specific introduction of an endogenous PTM, O-linked N-acetyl glucosamine (O-GlcNAc), in live cells. We are applying our proximity-directed glycosyltransferase system to a series of proteins that carry high levels of O-GlcNAc during cellular transformation in models of inflammation, pain, and neurodegeneration. We are further expanding the technology to additional sugar-modifying enzymes to ultimately discover chemically controllable regulatory hotspots throughout the proteome.
Discovery of small molecule binding site hotspots
In parallel, we are developing a complete understanding of proteomic recognition of small molecules with their biological targets. We use chemical biology approaches to map and manipulate small molecule interaction sites in the global proteome of live cells. We developed a chemical proteomics platform to study the binding sites of exogenous small molecules to the global proteome, termed small molecule interactome mapping by photo-affinity labeling (SIM-PAL). SIM-PAL uses a small molecule embedded with a diazirine and alkyne to capture and enrich binding sites to the whole cell proteome, which are structurally elucidated by mass-independent mass spectrometry. We applied SIM-PAL to several non-steroidal anti-inflammatory drugs and revealed new stabilizing interactions within the global proteome. Close investigation of the underlying photo-chemistry and development of new chemistries to label the proteome will enable high-resolution structural insight to small molecule–protein interactions in a cellular context.
Peering into the Cellular Black Box: We are combining chemical biology and mass spectrometry to reveal how small molecules interact with the proteome.
From Form to Function: We are engineering glycan stoichiometry on specific proteins in cells to understand cellular signaling pathways in models of inflammation, pain, and neurodegeneration.
Gain of Function Natural Products: We are accessing unique chemical scaffolds to evaluate the regulation of protein interactions by novel mechanisms.
Thank you to the following organizations for supporting our research:
Milton Fund, Merk Fellowship Fund, Dean’s Competitive Fund, Broad Institute.