Quantifying effects of mutations in terms of allosteric free energy, we show that favorable mutations lead to stabilization of the catalytic sites and other function-relevant distal sites as well as increased dynamics of the IDE-N and IDE-C halves that allow efficient substrate entrance and cleavage. Mutation Lys898Ala results in increased catalytic activity of IDE on the other hand, Lys364Ala does not change the activity and Asp426Ala diminishes it. Our experiments show that three mutations (Ser137Ala, Phe807Ala, and Lys898Ala) decrease the K m of the Aβ substrate. Five candidates are selected for experimental follow-up and allosteric free energy calculations: Ser137Ala, Lys396Ala, Asp426Ala, Phe807Ala, and Lys898Ala. Recently developed theoretical concepts are used here to explore potential allosteric modulation of the IDE activity as a result of single-residue mutations.

There were previous indications that the allosteric mode of IDE activity regulation could potentially provide a highly specific path toward degradation of amyloid-like peptides, while not dramatically affecting activity against other substrates. The major challenge standing in the way of this goal is increasing the specific catalytic activity of IDE against the Aβ substrate. The physiological role of insulin-degrading enzyme (IDE) in the intracytosolic clearance of amyloid β (Aβ) and other amyloid-like peptides supports a hypothesis that human IDE hyperactivation could be therapeutically beneficial for the treatment of late-onset Alzheimer’s disease (AD).

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