A small molecule-guided structure-function exploration of mitochondrial aldehyde dehydrogenase

Abstract

Plants have been used as medicines in cultures across the globe for millennia. The pharmacological activity of plants is often derived from specialized metabolites, also called natural products. Despite this wealth of medical tradition, modern medicine was unable to precisely characterize the wealth of chemistry and individual bioactivities locked in whole plant tissues until recently. In the last four decades, almost 50% of all new FDA-approved small molecule drugs in the United States have been natural products or natural product derivatives, thanks to the advent of modern tools and techniques that confer the dual abilities to isolate and characterize individual molecules from whole plants, as well as precisely describe their effects on human physiology. The goal of this thesis is to describe the mechanism of action of one plant-based pharmacotherapy: the observed enhancement of human small aldehyde metabolism by kudzu flowers. First, we selected mitochondrial aldehyde dehydrogenase 2 (ALDH2) as a representative enzyme for small aldehyde metabolism. We subsequently identify one kudzu flower-derived isoflavone, kakkalide, that is able to enhance the activity of ALDH2, and we characterize the binding and kinetics of this interaction. Finally, while we were trying to visualize the kakkalide:ALDH2 complex using X-ray crystallography, we serendipitously discovered a novel ALDH2 complexed with NAD+ and polyethylene glycol (PEG) that provides insights into the dynamic mechanism of ALDH2 catalysis, informing both basic biology and downstream development efforts. Overall, this thesis aims to describe the biochemical and structural basis for ALDH2 activity enhancement by kakkalide, and provides new insight into the mechanism of action of ALDH2.