Protein Domain Mimics as Modulators of Biomolecular Interactions

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Abstract Interactions of proteins with other biomolecules regulate fundamental cellular events and misregulation of these interactions leads to disease states. Proteins often utilize small, folded domains for recognition of other biomolecules. The basic hypothesis guiding our research is that by mimicking these folded domains we can specifically inhibit chosen complex formation with rationally designed synthetic molecules. Based on this hypothesis, we have developed several classes of Protein Domain Mimics (PDMs) that faithfully reproduce structural epitopes on protein surfaces. This work has created a foundation for the development of a new class of structure– based therapeutics. Our efforts so far have focused on mimicry of a natural binding partner to inhibit complex formation. A challenge with this approach is that natural protein-protein interactions are often transient and characterized by weak binding affinities. Mimicry of one partner, therefore, often also leads to weak binders, which are undesirable as inhibitors of complex pathways in the cellular context. A new approach is, therefore, required for rational design of protein-based binders that does not begin with natural complexes. In this NIGMS MIRA proposal, we aim to develop new starting points for PDM design by utilizing secondary and tertiary structure-grafted protein displays for high affinity sequences. We will apply the new strategy to target therapeutically important protein-protein interactions for which there are no potent inhibitors, including intrinsically disordered proteins. Studies in each Aim will advance general approaches to inhibit protein-protein interactions and establish PDMs as distinct constructs spanning the molecular size space between small molecules and proteins.