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

Homozygosity for the epsilon 4 allele of APOE increases the odds of developing Alzheimer's by 12 to 15 times relative to the most common epsilon 3;epsilon 3 genotype, and its association with higher plaque loads comports with evidence that APOE epsilon 4 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 A beta aggregation.