Targeted and directed degradation of oncogenic MYC mRNA with non-enzymatic peptide nucleic acid degraders (degPNAs)

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The MYC oncogene is deregulated in more than 50% of human cancers. However, no clinical treatment is available to date due to the "undruggable" nature of the MYC protein towards small molecule inhibitors. A promising alternative represents the interference with its translation on the mRNA level through the use of antisense oligonucleotides (ASOs). ASOs are short nucleic acids with antisense to the targeted mRNA that induce enzymatic degradation or sterically block translation or splicing. Previous ASOs targeting MYC have shown initial promising clinical results but eventually failed. To overcome the shortcomings of past ASO-based strategies, this project proposes the development and application of peptide nucleic acids-based degraders (degPNAs) of the MYC mRNA utilising a chemical degradation mechanism. The degPNAs degrade the target mRNA upon hydridisation through attached degrader base handles on the peptide backbone, which induce base-mediated cleavage of the phosphodiester bond. This proposal describes the structure-based design and synthesis of MYC mRNA-targeting degPNAs and their optimisation towards efficiency RNA degradation. Further, the conjugation to cell-penetrating peptides (CPPs) is described followed by fluorophore labeling and microscopy to evaluate cell uptake. Finally, in vitro MYC targeting in several cancer cell lines is investigated through RNA and protein quantification as well as global transcriptomics. In conclusion, the proposed degPNAs combine the advantages of charge-neutral ASOs with the flexible design and catalytic mode of action of enzyme-recruiting ASOs, which offers a novel approach for targeted RNA degradation and could pave the way towards a general chemical gene silencer platform.