A Computational Workflow for Structure-Guided Design of Potent and Selective Kinase Peptide Substrates.

ABSTRACT: Kinases are pivotal cell signaling regulators and prominent drug targets. Short peptide substrates are widely used in kinase activity assays essential for investigating kinase biology and drug discovery. However, designing substrates with high activity and specificity remains challenging. Here, we present Subtimizer (substrate optimizer), a streamlined computational pipeline for structure-guided kinase peptide substrate design using AlphaFold-Multimer for structure modeling, ProteinMPNN for sequence design, and AlphaFold2-based interface evaluation. Applied to five kinases, four showed substantially improved activity (up to 350%) with designed peptides. Kinetic analyses revealed >2-fold reductions in Michaelis constant (K_m), indicating improved enzyme-substrate affinity. Two des

SUBMITTER: Yekeen AA 

PROVIDER: S-EPMC12236476 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature