Molecular recognition of tripeptides containing tryptophan by cucurbit[8]uril: A computational study

Abstract

In this work, molecular dynamics (MD) simulations and time-dependent density functional theory (TD-DFT) calculations were applied to study the formation of binary and ternary complexes between cucurbit[8]uril (CB8) and three tryptophan-containing tripeptides (WGG, GWG, and GGW), as well as heteroternary complexes of the tripeptides in the presence of methyl viologen (MV) as an auxiliary ligand. All complexes were stable in water, and exhibited encapsulation of the indole moiety of W. Analysis of the MD trajectories of the homoternary complexes revealed π-π stacking within the CB8 cavity between the indole rings. MM-PBSA analysis indicated higher binding energy for tripeptides containing W residue at the N-terminus. The heteroternary complexes showed two binding modes, one with MV fully included (and π-π stacked with the indole ring) and the other with MV mostly excluded. The computed UV–Visible spectra of the free guests and their heteroternary complexes exhibited new bands emerged in the spectra of the complexes, which resulted from the transitions from HOMO and HOMO–1 to LUMO related to W–MV charge transfer (CT) complexes.

Keywords

• Cucurbit[8]uril
• Tripeptides
• Molecular recognition
• Molecular dynamics
• MM-PBSA
• TD-DFT