Structure-Based Approaches to Improving Selectivity through Utilizing Explicit Water Molecules: Discovery of Selective β‑Secretase (BACE1) Inhibitors over BACE2

BACE1
is an attractive target for disease-modifying treatment of
Alzheimer’s disease. BACE2, having high homology around the
catalytic site, poses a critical challenge to identifying selective
BACE1 inhibitors. Recent evidence indicated that BACE2 has various
roles in peripheral tissues and the brain, and therefore, the chronic
use of nonselective inhibitors may cause side effects derived from
BACE2 inhibition. Crystallographic analysis of the nonselective inhibitor
verubecestat identified explicit water molecules with different levels
of free energy in the S2′ pocket. Structure-based design targeting
them enabled the identification of propynyl oxazine 3 with improved selectivity. Further optimization efforts led to the
discovery of compound 6 with high selectivity. The cocrystal
structures of 7, a close analogue of 6,
bound to BACE1 and BACE2 confirmed that one of the explicit water
molecules is displaced by the propynyl group, suggesting that the
difference in the relative water displacement cost may contribute
to the improved selectivity.