Abstract
Due to their lack of a specific structure and dynamical nature, targeting of epitopes that are part of an intrinsically disordered region of a protein is a notoriously difficult task. Here, we describe a computational approach to overcome this problem, based on the use of a protein-folding algorithm and its confidence metrics within a Monte Carlo optimization pipeline to generate peptide-based binders. For different protein targets, we show by accurate free energy calculations that our approach is able to design peptides with binding free energies on the order of tens of kBT, i.e., with strengths comparable to covalent interactions. Direct observation of the bound complex through molecular simulations shows that the targeted epitope folds into structured domains with lowered thermal fluctuations upon binding, while remaining unstructured and dynamic in the unbound state, suggesting that the protein-folding algorithm must have learned the principles of induced (co-)folding. Given the ubiquitous presence of unstructured regions in proteins, our results suggest a potential pathway to design drugs targeting a large variety of previously untargetable epitopes, and open new possibilities for therapeutic intervention in diseases where disordered proteins play a key role.
