Development of proteolysis-targeting chimeras for Alzheimer disease
Abstract
We propose to explore a novel therapeutic concept for Alzheimer disease (AD) based on the promotion of clearance for pathologic proteins. Proteolysis-targeting chimeras (PROTACs) are hetero-bifunctional molecules that can bring the ubiquitin ligase (E3) into the vicinity of the protein of interest (POI), which results in the protein ubiquitination, followed by proteasomal degradation. PROTACs can be developed to target aberrant tau, α-synuclein, TDP43, intracellular amyloid β (Aβ), GSK-3β and other proteins involved in AD pathology. We hypothesis that well-developed PROTACs can be applied to the treatment of AD and other neurodegenerative diseases, to promote the clearance of pathologic proteins accumulated in the brain.
Here we will focus on tau. To develop more specific and potent PROTACs, we will develop novel ligands binding to tau or E3 ligases. Then we will use different linkers to combine ligands and design new PROTACs. The designed PROTACs will be screened for the expected ternary complex by molecular modelling. Ternary complexes will be subjected to molecular dynamics simulations to understand their stability, which is an important criterion for us to select PROTACs for synthesis. The last 100 frames of the simulation trajectory will be used for MM-PBSA-based binding free energy calculations to assess cooperativity within the ternary complex. PROTAC with stable conformation and stability will be further evaluated for their ability to cross the cell membrane using a system consisting of neuronal membrane model and PROTAC placed on the upper leaflet of the membrane. This provides insights into the molecule’s ability to pass the neuronal membrane. Besides, the PROTAC delivery efficiency will also be tested using liposome models. In a BBB model membrane, the liposomes placed on upper leaflet and simulation for 500 ns at minimum. With this MD simulation, we investigate the feasibility of the delivery of the PROTAC using liposomes. Protein-binding affinities and tau-reducing effects in vitro will be evaluated with follow-up structure-based optimization. The most potent PROTACs with the least off-target effects will move on to in vivo study.
Specific aims:
Aim 1: Explore tau-targeting E3 ligases in human AD brains by interaction proteomics and classical verification
Aim 2: Development of novel PROTACs: screen and develop ligands binding to tau or E3 ligase, and design and synthesis PROTACs
Aim 3: In vitro evaluation in cell models and structure-based hit-to-lead compound optimization
Aim 4: In vivo evaluation of hit PROTACs: pharmacokinetic study and treatment effects in tau transgenic rT2/T2 mice model
Overall, this project will increase our understanding of tau-targeting E3 ligases in AD brains, generate pre-clinical data for novel, disease-modifying PROTACs to combat pathologic proteins in AD and bring a novel class of small molecules into clinical translation. If successful, it will bring cost-effective new drugs for AD and other neurodegenerative diseases.
