Mechanism of inhibition of beta-site amyloid precursor protein-cleaving enzyme (BACE) by a statine-based peptide

Inhibition of beta -site amyloid precursor protein-cleaving enzyme by a sta tine-based inhibitor has been studied using steady state and stopped-sow me thods. A slow onset rate of inhibition has been observed under steady state conditions, and a K-i of 22 nM has been derived using progress curves anal ysis. Simulation of stopped-flow protein fluorescence transients provided a n estimate of the K-d for initial inhibitor binding of 660 nM. A two-step i nhibition mechanism is proposed, wherein slower "tightening up" of the init ial encounter complex occurs, Two hypotheses have been proposed in the lite rature to address the nature of the slow step in the inhibition of aspartic proteases by peptidomimetic inhibitors: a conformational change related to the "flap" movement and displacement of a catalytic water. We compared sub strate and inhibitor binding rates under pre-steady-state conditions. Both ligands are likely to cause flap movement, whereas no catalytic mater repla cement occurs during substrate binding. Our results suggest that both ligan ds bind to the enzyme at a rate significantly lower than the diffusion limi t, but there are additional rate limitations involved in inhibitor binding, resulting in a k(on) of 3.5 x 10(4) M-1 s(-1) for the inhibitor compared w ith 3.5 x 10(5) M-1 s(-1) for the substrate. Even though specific intermedi ate formation steps might be different in the productive inhibitor and subs trate binding to p-site amyloid precursor protein-cleaving enzyme, a simila r final optimized conformation is achieved in both cases, as judged by the comparable free energy changes (Delta DeltaG of 2.01 versus 1.97 kcal/mol) going from the initial to the final enzyme-inhibitor or enzyme-substrate co mplexes.