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Bioorg Med Chem Lett. 2010 Mar 15;20(6):1885-9. doi: 10.1016/j.bmcl.2010.01.137. Epub 2010 Feb 4.

SAR of tertiary carbinamine derived BACE1 inhibitors: role of aspartate ligand amine pKa in enzyme inhibition.

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  • 1Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA.


The optimization of tertiary carbinamine derived inhibitors of BACE1 from its discovery as an unstable lead to low nanomolar cell active compounds is described. Five-membered heterocycles are reported as stable and potency enhancing linkers. In the course of this work, we have discovered a clear trend where the activity of inhibitors at a given assay pH is dependent on pK(a) of the amino group that interacts directly with the catalytic aspartates. The potency of compounds as inhibitors of Alphabeta production in a cell culture assay correlated much better with BACE1 enzyme potency measured at pH 7.5 than at pH 4.5.

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