Identifying favorable regions of the conformational landscapes of peptides and peptidomimetics

PROJECT SUMMARY Therapeutic Potential of Macromolecules: The human interactome, potentially comprising over 650,000 protein-protein interactions (PPIs), remains an underexplored frontier for therapeutics discovery. As just one example, the interaction between the melanoma antigen, MAGE-A4, and an E3 ligase, RAD18, is hypothesized

to increase DNA damage tolerance, leading to increased resistance of cancer cells to chemotherapies. Disrupting this interaction could increase the efficacy of chemotherapies. Macromolecule therapeutics (e.g., peptides and peptidomimetics) are well-suited to disrupt disease-causing PPIs. However, their design is non-intuitive with challenges including entropic costs associated with protein

binding and limited cell permeability. While existing strategies to decrease the entropic cost, like peptide stapling and cyclization, have yielded potent therapeutics, they often result in molecules locked in a rigid conformation that struggle to access their targets within cells due to poor permeability. Interestingly, some bioactive peptides

and peptidomimetics have been identified benefit from some lack of rigidity for cell permeability. Identifying the role of macromolecule conformation, i.e., degree of disorder, in desirable properties including protein binding and cell permeability will facilitate the development of a new class of therapeutics.

We propose that compact, yet non-rigid, macromolecules offer valuable, yet under exploited scaffolds for bioactive macromolecules. This proposal aims to address key biological questions: How does macromolecule conformation impact binding to “undruggable” protein surfaces and other essential characteristics, such as cell

permeability? Accelerating Innovation in Macromolecule Therapeutic Design: Our vision is to accelerate the design of macromolecule-based therapeutics by developing rapid characterization strategies that guide predictive algorithms. These methods will provide unprecedented comparisons of macromolecule conformation, guiding

the design of macromolecular therapeutics. Three key challenges are addressed in this proposal: 1. Conformational Characterization: We will establish colorimetric and fluorimetric assays to assess average conformation and dynamics of disordered peptides and peptidomimetics. 2. Predictive Algorithm Development: Develop algorithms capable of identifying sequence spaces that

favor conformations with a desired degree of disorder. 3. Protein-Protein Interaction Disruption: By leveraging favorable sequences with desired conformations, we will identify effective, cell permeable, disruptors of protein-protein interactions using the MAGE-A4 and E3 ligase interaction as a model system.

Innovation and Impact: We aim to provide powerful predictive capabilities that leverage rapid conformational characterization to guide the design of potent macromolecule therapeutics, specifically for PPI disruption.