Chemical hijacking KRAS-driven proteolytic networks

One of the most important factors that determine the success of cancer treatment is the so- called therapeutic index (TI), which basically quantifies the window of opportunity in killing cancerous cells versus also killing healthy cells. The larger the TI, the better (and the more tolerable) is the treatment. There are two ways to maximize the TI of a drug. First, the drug can be designed to block a cellular pathway that is only active in cancer cells, for instance a pathway that is activated due to an oncogenic driver mutation. However, not all cancers are driven by mutations that can be targeted with drugs. For many cancers, there is hence an interest to target mechanisms that are required for all cells, including cancer cells, to survive. Here, the TI is optimized by designing the drug to block this pathway only in cancer cells. One approach to this goal is targeted delivery, for instance by antibody-drug conjugates. Here, we want to maximize the TI of drugs by restricting their mechanism of action to cancer cells. To this end, we focus on targeted protein degradation (TPD). TPD is a modality that depends on drugs (degraders) that recruit a target protein of interest (POI) to an E3 ubiquitin ligase. This causes the degradation of the POI and can thus cause complete POI elimination in cells that express the E3. Here, we want to develop approaches to identify and characterize degraders that leverage E3 ligases that are selectively expressed in cancer cells that are driven by mutations in the KRAS oncoprotein. To this end, we will first develop cellular tools that allow us to identify novel chemical ligands that degrade a well-characterized tool protein (FKBP12) only in cell lines and organoids where mutant KRAS is active. Next, by applying unbiased technologies, we will (i) identify which E3 is targeted by the identified degrader prototypes, and (ii) how E3 ligase activity is connected to hyperactive signaling through mutant KRAS. Based on these mechanistic insights, we will perform chemical optimization studies in which we will aim to improve the properties of the degrader, such as binding potency and selectivity. This will enable a faster and more pronounced degradation of the target. Once we have optimized properties of the E3 ligase binder, we will move from FKBP12 to a pan- essential target, the transcriptional kinase CDK9. CDK9 inhibitors have failed in the clinics due to a narrow TI which is not surprising since genetic knockdown of CDK9 has been shown to be broadly essential over hundreds of cancer cell lines. Here, we will address this issue by converting know CDK9 inhibitors (that block CDK9 activity in all cells) into a degrader that eliminates CDK9 exclusively in KRAS mutant cancer cells via the identified E3 ligand. Identified degraders are expected to only kill KRAS-driven cancer cells while sparing non- cancerous tissues that have normal, non-mutant KRAS activity and will be assessed in additional preclinical studies.