Physiological role of insulin degrading enzyme (IDE) in the intracytosolic clearance of amyloid beta (Aβ) and other amyloid-like peptides supports a hypothesis that human IDE hyperactivation could be therapeutically beneficial in the treatment of the late onset Alzhimer’s disease (AD). The major challenge towards this goal is to increase specific catalytic activity of IDE against the Aβ-substrate. There were previous indications that allosteric mode of IDE activity regulation could potentially provide a highly specific path towards degradation of amyloid-like peptides, while not dramatically affecting activity against other substrates. Recently developed theoretical concepts are used here for exploring potential allosteric modulation of the IDE activity as a result of single-residue mutations. Five candidates are selected for experimental follow up and allosteric free energy calculations: Ser137Ala, Lys396Ala, Asp426Ala, Phe807Ala, and Lys898Ala. Our experiments show that three mutations (Ser137Ala, Phe807Ala, and Lys898Ala) decrease Km of the Aβ-substrate, mutation Lys898Ala results in increased catalytic activity of IDE, whereas Lys364Ala does not change the activity and Asp426Ala diminishes it. Quantifying effects of mutations in terms of allosteric free energy, we show that favorable mutations lead to stabilization of the catalytic and other function-relevant distal sites, as well as increased dynamic of the IDE-N and IDE-C halves that allow an efficient substrate entrance and cleavage. A possibility for intramolecularly up-regulation of IDE activity against amyloid peptides via allosteric mutations calls for further investigations in this direction. Ultimately, it will, hopefully, lead to development of the IDE-based drugs for the treatment of late-onset form of AD characterized by an overall impairment in the Aβ clearance.
Biochemistry 2016, doi: 10.1021/acs.biochem.6b00783