Revealing cancer dependencies through inhibition of SLiM interactions using competitor peptides

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Short Linear Motifs (SLiMs) are an elegant and spatially efficient solution for encoding interaction interfaces. Consequently, SLiMs mediate many cellular functions such as directing ligand binding in dynamic complexes, providing docking sites for modifying enzymes, controlling protein stability by recruiting ubiquitin ligases and acting as subcellular localization signals. This project will evaluate the therapeutic potential of inhibiting SLiM-mediated protein-protein interactions by expressing genetically encoded competitor peptides and characterising the cancer subtype dependencies of specific SLiM competitors. First, a peptide expression chassis will be optimized to potentiate competition of expressed peptides with endogenous SLiMs. Next, a lentiviral library expressing all validated SLiM peptides (5,621 motifs) will be constructed and transduced to cancer cell lines. The effect of each peptide will be studied in a pooled competitive growth assay. The peptide phenotype data will be integrated with data from prior cancer gene dependency studies to prioritise peptides for in-depth validation. In contrast to the protein level information of CRISPR- and RNAi-based dependency studies, this study will directly pinpoint a binding pocket for therapeutic intervention. Consequently, the SLiM dependency screen will provide proof of principle for the inhibition of SLiM-binding pockets and allow inexpensive, high-throughput and information-rich triage and prioritisation of targets for small molecule drug development. During the project, the researcher will switch from the basic research field of the yeast cell cycle to a translational field focusing on cancer biology. He will expand his skillset by working with high-throughput methods across multiple cell lines, and improve his transferable skills by managing the project, networking, communicating with the public and disseminating the results. Together, these skills will allow him to transition to an independent researcher.