Abstract:Alzheimer’s disease (AD) is hypothesized to result from elevated brain levels of β‐amyloid peptide (Aβ) which is the main component of plaques found in AD brains and which cause memory impairment in mice. Therefore, there has been a major focus on the development of inhibitors of the Aβ producing enzymes γ‐secretase and β‐site amyloid precursor protein‐cleaving enzyme 1 (BACE1). In this study, we investigated the Aβ‐lowering effects of the BACE1 inhibitor LY2434074 in vitro and in vivo, comparing it to the well characterized γ‐secretase inhibitor LY450139. We sampled interstitial fluid Aβ from awake APPswe/PS1dE9 AD mice by in vivo Aβ microdialysis. In addition, we measured levels of endogenous brain Aβ extracted from wildtype C57BL/6 mice. In our in vitro assays both compounds showed similar Aβ‐lowering effects. However, while systemic administration of LY450139 resulted in transient reduction of Aβ in both in vivo models, we were unable to show any Aβ‐lowering effect by systemic administration of the BACE1 inhibitor LY2434074 despite brain exposure exceeding the in vitro IC50 value several fold. In contrast, significant reduction of 40–50% of interstitial fluid Aβ and wildtype cortical Aβ was observed when infusing LY2434074 directly into the brain by means of reverse microdialysis or by dosing the BACE1 inhibitor to p‐glycoprotein (p‐gp) mutant mice. The effects seen in p‐gp mutant mice and subsequent data from our cell‐based p‐gp transport assay suggested that LY2434074 is a p‐gp substrate. This may partly explain why BACE1 inhibition by LY2434074 has lower in vivo efficacy, with respect to decreased Aβ40 levels, compared with γ‐secretase inhibition by LY450139.