AbstractBackgroundAll clinical BACE‐inhibitor trials for the treatment of Alzheimer´s Disease have failed due to insufficient efficacy or side effects like worsening of cognitive symptoms. The latter could have been the result of the inhibition of BACE at the synapse where it is expressed in high amounts. We have previously shown that prolonged inhibition of BACE interferes with structural and functional synaptic plasticity (Filser et al. Biol. Psych 2015, Blume et al. Front. Aging Neurosci. 2018), most likely due to the diminished processing of the physiological BACE substrate Seizure protein 6 (Sez6, Zhu et al. Biol. Psych. 2018), which is exclusively processed by BACE1 and it is required for dendritic spine plasticity. The aim of the current study was to elucidate the effects of selective BACE1 inhibitors on dendritic spine plasticity at a dose that affects Sez6 cleavage to various degrees but not completely.MethodBy using longitudinal in vivo two‐photon microscopy, we investigated the effect on dendritic spine dynamics of pyramidal layer V neurons in the somatosensory cortex in mice treated with 2 novel highly selective BACE1 inhibitors developed at Shionogi in comparison to Elenbecestat which reduce soluble Sez6 to 27% (Elenbecastat), 17% (Shionogi Compound 1) and 39% (Shionogi Compound2) of baseline levels in untreated animals. For the detection of the soluble Sez6 ectodomain, the BACE cleavage product from full‐length Sez6, Western blot analysis was performed using a highly specific Sez6 antibody generated in the lab of Stefan Lichtenthaler (Pigoni et al. Mol. Neurodeg. 2016).ResultWe observed that BACE1 selective inhibitors do not alter dendritic spine density and plasticity in cortical neurons if at least 27% of soluble Sez6 remains. In detail, the density of gained and lost spines does not change under the treatment with Shionogi Compound 2 or Elenbecastat. Also, no differences in the stability of dendritic spines were found during treatment with these two compounds. With Compound 1 however, a significant spine loss occurs after 21 days of treatment.ConclusionSelective BACE1 inhibitors do not alter dendritic spine plasticity in mice if dosing reduces synaptic BACE1 cleavage of Sez6 not below 27% of baseline soluble Sez6 levels. BACE1 selective inhibitors may be potential novel candidates for clinical trials treating AD if dosing is carefully adjusted to the amount of Sez6 cleavage, which can be easily monitored during the first weeks of treatment.