Small molecule metabolites are conventionally viewed as the elementary constituents of life, functioning as cellular building blocks, energy currency, and waste products. Beyond anabolic and catabolic metabolism, it is increasingly evident that metabolites serve as signaling molecules, directly regulating protein function to provide a rapid and adaptive mechanism for metabolism to coordinate diverse cellular processes that are energetically or biosynthetically demanding. Furthermore, in healthy tissues, metabolism is internally balanced through evolved metabolic surveillance, more specifically, metabolite-mediated regulation of enzyme activity. Aberrant dysregulation of these regulatory protein-metabolite interactions likely contributes to the mechanisms driving many metabolically-dependent diseases including cancer, diabetes, heart disease, and inborn errors of metabolism. A deeper understanding of endogenous metabolite interactions with disease-relevant proteins will also benefit allosteric drug discovery. The true scale and function of the protein-metabolite interactome is almost completely unknown and represents a major void in our understanding of cellular biology and metabolism.

To begin to reveal the protein-metabolite interactome, we developed the MIDAS platform to systematically identify interactions between proteins and metabolites (DOI: 10.1126/science.abm3452). The MIDAS platform is uniquely situated to identify low millimolar and stronger binding between soluble proteins and metabolites from a multiplexed metabolite library representative of the human metabolome. As such, the MIDAS platform is a powerful tool to discover and investigate the form and function of the interactions spanning the proteome and metabolome.

The Hicks lab is focused on two broad areas of research and development:

1. Understanding how metabolism regulates metabolism. There are many well established examples of metabolites regulating specific metabolic enzymes via allosteric and orthosteric interactions. These intra- and inter-pathway protein-metabolite interactions serve as feedforward and feedback mechanisms to govern metabolic pathway function, flux, and directionality. The extent of these regulatory protein-metabolite interactions across metabolism is unknown. The Hicks lab uses innovative and systematic mass spectrometry approaches to identify enzyme-metabolite interactions and a compliment of molecular, biochemical, genetic, and cellular tools to reveal their biological function. Systematically revealing the mechanisms of metabolic regulation of human metabolic pathways is critical for a complete understanding of metabolism and how diverse cellular processes are regulated or dysregulated in healthy and disease states.
   
   
2. Development of interactome discovery technologies. The strengths of the MIDAS platform can be harnessed to reveal interactions between molecules beyond soluble proteins and metabolites, opening new avenues of biological investigation. We are adapting the MIDAS platform to identify membrane protein-metabolite, protein-metabolome, protein-peptide, protein-chemical fragment, and RNA-metabolite interactions using targeted and non-targeted liquid chromatography mass spectrometry. These interactomics platforms will broaden our understanding of the scope, depth, and functions of interacting biological networks, provide inclusive discovery platforms for the scientific community, and catalyze therapeutic discovery.