UC San Diego

Neurodegenerative diseases are pathologically characterized by the presence and aggregation of misfolded proteins known as amyloids. These amyloids lead to neurotoxicity and are present in both Alzheimer’s Disease (AD) and Parkinson’s Disease (PD). They precede clinical symptoms by as many as 20 years, and are a current target for earlier diagnostic in the clinic.This thesis documents the development of analogues of Aryl Cyano Amide (ARCAM) to improve discrimination properties between different amyloids. Chapter 2 describes how introducing small aliphatic substituents affects the rotatability of molecular rotor probes and their fluorescence enhancement upon binding to Amyloid-β (Aβ) aggregates. It was observed that introducing substituents near the electron donor lowered the enhancement upon binding, but did not affect the overall brightness of the probes. On the other hand, introducing the substituents near the electron acceptor increased the enhancement upon binding, but drastically decreased the quantum yield of the probes. Chapter 3 investigates how aliphatic substituents on both ARCAM and a benzyl analogue affects the ability of these probes to act as viscosity sensors. Interestingly, the vinyl substituents led to an enhanced viscosity sensitivity for the ARCAM scaffold, but a decreased sensitivity in the case of the benzyl probes. Computational analysis in conjunction with the Paesani lab was performed to explain these results. Chapter 4 describes how aliphatic substituents in the 2-pipdierinyl position led to an enhanced fluorescence response to aggregated α-Synuclein (αS) compared to Aβ both in solution and in tissue. Molecular docking analysis revealed that this may be due to the available space for these probes to rotate when in the protein binding pockets. In Chapter 5, improving binding affinity and selectivity between amyloids through introducing multivalent ligands was investigated. It was determined that having a dimeric ARCAM probe led to an enhanced binding affinity to aggregated αS, while there was no significant change in binding to Aβ, potentially due to the probe length and binding site densities of the amyloids.