Rescue of ApoE4-related lysosomal autophagic failure in Alzheimer’s disease by targeted small molecules

Homozygosity for the ε4 allele of APOE increases the odds of developing Alzheimer’s by 12 to 15 times relative to the most common ε3;ε3 genotype, and its association with higher plaque loads comports with evidence that APOE ε4 compromises autophagy. The ApoE4 protein specifically binds a cis element (“CLEAR”) in the promoters of several autophagy genes to block their transcription. We used a multifaceted approach to identify a druggable site in ApoE4, and virtual screening of lead-like compounds identified small molecules that specifically bind to this site to impede ApoE4::DNA binding. We validated these molecules both in vitro and in vivo with models expressing ApoE4, including ApoE4 targeted-replacement mice. One compound was able to significantly restore transcription of several autophagy genes and protected against amyloid-like aggregation in a C. elegans AD model. Together, these findings provide proof-of-principle evidence for pharmacological remediation of lysosomal autophagy by ApoE4 via ApoE4-targeted lead molecules that represent a novel tack on neurodegenerative disorders. In-silico based in vitro and in vivo validations identified a lead molecule that specifically targets: ApoE4 protein; inhibits ApoE4::CLEAR DNA binding; rescues thwarted lysosomal autophagy; and protects against Aβ aggregation.