Substrate specificity analysis and inhibitor design of homoisocitrate dehydrogenase

Homoisocitrate dehydrogenase is involved in the α-aminoadipate pathway of biosynthesis of l-lysine in fungi, yeast, some prokaryotic bacteria, and archaea. This enzyme catalyzes the oxidative decarboxylation of (2R, 3S)-homoisocitrate into 2-oxoadipate using NAD+ as a coenzyme. Substrate specificity of two homoisocitrate dehydrogenases derived from Deinococcus radiodurans and Saccharomyces cerevisiae was analyzed using a series of synthetic substrate analogs, which indicated a relatively broad substrate specificity of these enzymes. Based on the substrate specificity, 3-hydroxyalkylidene- and 3-carboxyalkylidenemalate derivatives were designed as a specific inhibitor for homoisocitrate dehydrogenase. The synthetic inhibitors showed a moderate competitive inhibitory activity and (R, Z)-3-carboxypropylidenemalate was the most inhibitory among the synthesized inhibitors. Therefore, homoisocitrate dehydrogenase appeared to recognize preferentially an extended conformation of homoisocitrate.

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