Chemical Biology of the Control of Neddylation by DCN1

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Abstract The long-term goal is to generate and use complimentary chemical and biological probes to study the cullin RING ubiquitin ligases (CRL’s) and understand their activation controlled by the interaction of by the Defective in Cullin Neddylation 1 (DCN1) and UBE2M proteins. Because the CRL’s ultimately control ubiquitination of many diverse proteins, thus regulating their stability, intracellular localization, and function, having spatiotemporal control over DCN-mediated CRL activity has the potential to unravel the mechanism regulating key cellular signaling networks and driving disease progression. The health relatedness of this project lies in two facts: 1) DCN1 is an oncoprotein, amplified in squamous cell carcinomas, that drives a highly malignant phenotype, and 2) CRL driven ubiquitination is a validated target in multiple diseases, particularly cancer and immune dysfunction. Therefore, inhibitors of the DCN1-UB2M interaction that are potent, selective, and bioavailable have the potential to be developed as antitumor drugs and possibly for other diseases. Ubiquitination is regulated by a highly complex, dynamic, and redundant network. Inhibitors of DCN1-UB2M will allow direct interrogation of the function of sub-portions of the network and are likely to unveil fundamental principles of the regulation ubiquitination. The generation of complementary cellular and mouse genetic models will enable independent verification of hypotheses. Finally, the DCN1-UBE2M interaction requires N-terminal acetylation of UBE2M, a common posttranslational modification controlling protein interactions. Therefore, a strategy for targeting N- terminal acetylation dependent protein interactions could be widely applicable. The research design and methods for achieving these goals involves the integrated and recursive use of structure-driven, hypothesis- based medicinal chemistry; in vitro biochemical measures of affinity and inhibitory potency; in vivo measures of compound efficacy and pharmacodynamic responses; and in vitro and in vivo measures of compound bioavailability, distribution, metabolism, excretion, and toxicity. The overall goal is to develop new complimentary chemical and biological tools to understand the regulation of the ubiquitin-like protein NEDD8, and uncover the specific role of DCN-mediated neddylation in Cullin-RING ligase substrate receptor exchange, growth factor signaling, and driving tumor progression. Our aims are: Aim 1: Improve the potency and oral exposure of our current DCN1/2 inhibitors and generate new chemical probes with sufficient potency and selectivity to enable ourselves and others to study the consequences of inhibiting this E2-E3 interaction in cells and animals. Aim 2. Investigate how the composition of cellular CUL1 and CUL3 ligases dynamically responds to environmental perturbations and the importance of DCN1/2 in this process. Aim 3: Use genetic and pharmacological approaches to study the effects of inhibiting DCN1 activity in animal tumor models.