A practical and accessible computational workflow for constrained peptide-enzyme interaction analysis

Cyclic peptides offer stable, well-defined scaffolds for probing enzyme recognition and inhibition, yet capturing how a macrocycle engages a catalytic environment remains challenging. This chapter presents an integrated workflow that links de novo macrocycle modeling, data-guided docking, and explicit-solvent molecular dynamics to examine peptide-enzyme complexes in a coherent, end-to-end manner. Starting from plausible conformers, we generate enzyme-bound poses and follow their relaxation in solvent to obtain an equilibrated ensemble from which representative conformations and interaction patterns can be interpreted. Designed to balance methodological rigor with ease of use, the workflow enables the generation of accurate cyclic peptide models, prediction of binding modes with target enzyme, and evaluation of complex stability and interactions. Implemented with widely available tools and standard hardware, the workflow lowers the barrier for non-specialists while remaining rigorous enough for reproducible studies of macrocycle-enzyme mechanisms.