Unraveling the impact of cyclic peptide primary structure on rotaxane formation through umbrella sampling molecular dynamics simulations

Peptide-based rotaxanes have attracted interest due to their expected unique physical and functional properties, which are not observed in conventional peptide-based materials. Cyclic peptides, when their primary structure is appropriately designed, are characterized by their ability to form stable host-guest complexes and have emerged as promising candidates as macrocycles that form rotaxanes. However, the effect of the primary structure of cyclic peptides on rotaxane formation remains unclear. Here, we investigated how variations in the primary structure of cyclic peptides affect their interactions with monocationic ammonium threads using umbrella sampling molecular dynamics simulations to elucidate the free energy landscapes of pseudorotaxane formation. Our results revealed that cyclic peptides adopting an all-<i>trans</i> configuration in pseudorotaxanes, such as cyclo(PG)₄, facilitated consistent hydrogen bond formation with the thread, leading to greater stability and higher rotaxane yields. In contrast, the presence of bulky side chains or conformational constraints induced by the <i>cis</i>-configuration, as observed in cyclo[GC(Ψ^Me,MePro)(GP)₃], reduced the stability of pseudorotaxanes. Demonstrating the critical role of cyclic peptide conformations and hydrogen bonding in stabilizing pseudorotaxanes provides strategic insights into the rational design of tailored cyclic peptides for rotaxane formation. Given the wide chemical diversity of natural and unnatural amino acids, this simulation method may facilitate the development of peptide-based rotaxanes with novel properties and functions.