Date of Award

Winter 3-22-2025

Document Type

Dissertation

Degree Name

Ph.D. in Chemistry and Biochemistry

Organizational Unit

College of Natural Science and Mathematics, Chemistry and Biochemistry

First Advisor

Sunil Kumar

Second Advisor

Brian Michel

Third Advisor

Brady Worrell

Fourth Advisor

Martin Margittai

Fifth Advisor

Daniel Linseman

Copyright Statement / License for Reuse

All Rights Reserved
All Rights Reserved.

Keywords

Alzheimer's disease, nano-foldamers, Oligopyridylamides, Parkinson's disease, Protein-protein interactions, Synthetic protein mimetics

Abstract

Protein-protein interactions (PPIs) are crucial for the regulation of a majority of, if not every fundamental cellular process. Despite their role in regular biological processes, dysregulated and/or aberrant protein-protein interactions (aPPIs) are often related to the onset of disease including cancer, viral infection, and amyloid diseases. aPPIs have historically been deemed ‘undruggable’ due to their large surface area and lack of a binding cavity; however, today, more than 40 disease-related aPPIs have been targeted with small molecules and several of those have reached clinical trials.

A class of synthetic protein mimetics called oligopyridylamides (OPs) has been shown to inhibit disease-related aPPIs by mimicking the α-helical secondary structure of proteins. These molecules, constrained by intramolecular hydrogen bonding, project their functional groups in the exact spacing to interact with the i, i + 3/4, and i + 7 residues on one-face of an α-helical protein. These molecules have been shown to disrupt aPPIs related to Alzheimer’s disease, HIV, cancer, and diabetes though libraries of OPs have been severely limited by their tedious synthetic pathway and lack systematic optimization.

To address this, we developed a 2-Dimensional Fragment-Assisted Structure-based Technique (2D-FAST) for the OP synthetic protein mimetic scaffold and applied it to the discovery of a potential therapeutic for Parkinson’s disease (PD). In this technique, we simplified the synthesis of OPs and optimized the activity of the mono-, di-, and tri-pyridyl against the aggregation of α-Synuclein (αS), the hallmark of PD. We anticipated that the carboxylic acid functional group of the most post potent tripyridyl antagonist (NS132) would limit its cell permeability. By synthetically modifying the carboxylic acid to its more lipophilic hydroxamic acid isostere, we optimized the permeability which enhanced its activity towards αS aggregation in human embryonic kidney (HEK) cells and the rescue of PD phenotypes in pre- and post-disease onset C. elegans models. We further showed that NS132 and SK-129 (a previously discovered oligoquinoline inhibitor of αS aggregation) inhibited the aggregation of αS that is phosphorylated at S-129, a common post-translational modification abundant in Lewy bodies and Lewy neurites present in synucleinopathies. This work successfully demonstrates the ability of the 2D-FAST to discover potent antagonists of pathological proteins related to a wide range of diseases.

Given that the treatment of diseases of the central nervous system is severely limited by the difficulty of discovering therapeutics which are able to penetrate the blood-brain barrier (BBB), we further developed an innovative, OP-based nanoparticle drug delivery system called nano-Foldamers. The advantage of our nano-Foldamers is the ability to synthetically modify and tune the size and specificity of the nanoparticle for the specific therapeutic cargo and drug target. There is accumulating evidence to support the therapeutic strategy of reducing Tau expression in the brains of Alzheimer’s disease patients to reduce the neuron loss and memory deficits associated with the disease. In this work, we used nano-Foldamers to deliver a functional antisense oligonucleotide (ASO) to reduce Tau expression in HEK cells as shown by confocal imaging and flow cytometry experiments. We further demonstrated the therapeutic potential of our nano-Foldamers by showing that delivery of the ASO significantly limited the puncta formation in the cells when transfected with pre-formed fibrils of the protein. We envision the nano-Foldamers drug delivery system being applicable to an array of diseases involving the central nervous system, from neurodegeneration to infectious diseases and cancer.

Copyright Date

3-2025

Publication Statement

Copyright is held by the author. User is responsible for all copyright compliance.

Rights Holder

Nicholas H. Stillman

Provenance

Received from ProQuest

File Format

application/pdf

Language

English (eng)

Extent

357 pgs

File Size

32 MB

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