In cells, proteostasis is a constant and highly choreographed process that maintains a balance between the synthesis and degradation of proteins. The ubiquitin-proteasome system is a critical player in this orchestration through both ubiquitin-dependent and ubiquitin-independent pathways. The former pathway is mainly responsible for the degradation of folded proteins, or proteins with a stable 3D conformation, by using ubiquitin tags to flag proteins for degradation. Conversely, the ubiquitin-independent pathway targets proteins that lack stable 3D conformations, including intrinsically disordered proteins (IDPs). Proteostasis can become perturbed when the synthesis of proteins outpaces their degradation, leading to the accumulation of proteins within a cell. IDP accumulation is linked to various disorders, including neurodegenerative diseases. The small molecule enhancement of the ubiquitin-independent pathway represents a promising therapeutic target to modify protein degradation pathways for treating human diseases. The chemical space of small molecule proteasome enhancers is small, with only a few promising candidates. A significant reason for this lack of progress is the need for cellular systems that easily evaluate levels of IDPs and efficiently screen candidate compounds on a large scale. Two of the projects described in this dissertation directly address these problems. My first project focused on the development of a cell-based high throughput assay and its utilization to screen 30,000 compounds to identify novel small molecule proteasome enhancers. The second project focused on designing and synthesizing a library of 32 small molecules that enhance the ubiquitin-independent proteasomal pathway. Herein, the utilization of in silico molecular docking studies to refine structure-activity relationships is discussed. This approach led to the identification and synthesis of a new small molecule class that includes some of the most potent enhancers of the ubiquitin-independent pathway. In parallel, cellular disease models were developed that allowed for scoring the small molecules' therapeutic potential in treating waste protein accumulation in neurogenerative diseases.
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