Development of Self-Assembling Pyrrole-Imidazole Polyamides for the Treatment of Friedreich’s Ataxia and Prostate Cancer Using Proximity-Induced Bioorthogonal Chemistry - PROJECT SUMMARY Developing a new drug typically takes over a decade and costs over $500 millions dollars. Despite this, 90% of drug candidates fail in clinical trials, often due to undesired off-target effects or poor pharmacokinetic (PK) properties. One promising strategy that could overcome these issues and provide a new level of control over therapeutic activity would be the in-situ assembly of a drug at the site of interest. Rather than administering a single compound, two smaller, inactive fragments can be delivered that selectively combine at the target site to furnish the active drug. Lower molecular weight compounds display enhanced PK properties, such as high membrane permeability, due to their smaller size and could avoid off-target effects by only combining at the site of disease. This approach could address PK issues that are inherently associated with the growing demand for large bifunctional molecules that break Lipinski’s rule of five, such as proteolysis-targeting chimeras. This strategy has seldom been explored as identifying a bioorthogonal reaction that will selectively unite the fragments—present only in low concentrations in a cell—remains challenging. The studies described in this proposal seek to develop strategies for the design of self-assembling pyrrole- imidazole polyamides (Py-Im PA), small molecules that can bind DNA and control gene expression, potentially stopping disease at its root. Numerous Py-Im PAs have been developed to treat different diseases yet there are no FDA-approved Py-Im PA pharmaceuticals, in part due to their poor PK properties. By leveraging the natural binding of these compounds to DNA to generate a high local concentration and template a proximity-induced bioorthogonal reaction, one could achieve their selective in situ self-assembly. In Aim 1, a self-assembling linear Py-Im PA that targets the DNA triplet repeats that cause the incurable neurodegenerative disease Friedreich’s ataxia will be designed and evaluated. This PA previously showed promise in cellulo yet suffered from poor membrane permeability due to its high molecular weight. In Aim 2, a proximity-induced azide-alkyne cycloaddition for the in situ synthesis of hairpin polyamides from their linear fragments will be developed. A hairpin Py-Im PA that binds the prostate-specific antigen promoter androgen response element for the treatment of prostate cancer will be prepared. Performing this research in Prof. Bertozzi’s group at Stanford aligns well with their success with developing bioorthogonal chemistry (2022 Nobel prize) and will augment my prior training in organic synthesis to prepare me for a future academic career as a professor. Overall, the proposed research is significant because it could unlock the therapeutic potential of Py-Im PAs for the treatment of Friedreich’s ataxia and prostate cancer by improving their PK properties. This proposal is unique as it represents the first in-situ self-assembly of PAs in cellulo from more bioavailable components. More broadly, this proposal represents a novel approach to addressing PK issues in drug design and could be expanded to solve long-standing challenges encountered by other drug candidates.
