Engineering protein fragments via evolutionary and protein–protein interaction algorithms: de novo design of peptide inhibitors for F_OF₁‐ATP synthase

Enzyme subunit interfaces have remarkable potential in drug design as both target and scaffold for their own inhibitors. We show an evolution‐driven strategy for the de novo design of peptide inhibitors targeting interfaces of the Escherichia coli FoF1‐ATP synthase as a case study. The evolutionary algorithm ROSE was applied to generate diversity‐oriented peptide libraries by engineering peptide fragments from ATP synthase interfaces. The resulting peptides were scored with PPI‐Detect, a sequence‐based predictor of protein–protein interactions. Two selected peptides were confirmed by in vitro inhibition and binding tests. The proposed methodology can be widely applied to design peptides targeting relevant interfaces of enzymatic complexes.