Insulin-degrading Enzyme - Working Mechanism

Working Mechanism

Despite the enormous attention dedicated to IDE the catalytic mechanism of this enzyme remain poorly understood. Studies present in literature explored many aspects concerning IDE, but none of them deals with the mechanistic details of the proteolysis performed by this enzyme. It is understood that IDE cleaves insulin B chain as well as amyloid β at several sites. Recently, Orazio and colleagues unveil how the cleavage of two peptides occurs by using the density functional theory at the active site of IDE (Scheme 1) to explore the catalytic mechanism of IDE; hence, they provide novel fundamental insights into the behavior of this enzyme.

Scheme 1

The steps involved in the whole process are collected in Scheme 2.

Scheme 2

The first step of the mechanism includes a zinc-bound hydroxide group performing a nucleophilic attack on a carbon substrate that materializes into the intermediate INT1. In this species, we can note that the zinc-bound hydroxide is completely transferred on the carbonyl carbon of substrate as a consequence of the Zn2+−OH bond breaking. In TS2, the Glu111 residue rotates to assume the right disposition to form two hydrogen bonds with the amide nitrogen and the −OH group linked to the carbon atom of substrate, thus behaving as hydrogen donor and acceptor, simultaneously. The formation of the second cited bond favors the re-establishment of the Zn2+−OH bond broken previously at the INT1 level. The nucleophilic addition and the protonation of peptide amide nitrogen is a very fast process that is believed to occur as a single step in the catalytic process. The final species on the path is the product PROD. As a consequence of transfer of the proton of Glu111 onto the amide nitrogen of substrate that occurred in TS3, the peptide N—C bond is broken.

A look at the whole reaction path indicates that the rate-determining step in this process is the nucleophilic addition that implies an expense of 17.2 kcal/mol. After this point, the catalytic event should proceed without particular obstacles.