Sequence-dependent nanomolar binding of tripeptides containing N-terminal phenylalanine by Cucurbit[7]uril: A theoretical study

Molecular recognition towards peptides with high affinity and sequence selectivity by synthetic macrocyclic receptors is a great challenge in supramolecular chemistry. In this work, we investigate the molecular recognition of tripeptides containing N-terminal phenylalanine (Phe, F) by synthetic macrocyclic receptor Cucurbit[7]uril (CB[7]) in aqueous solution by molecular dynamics simulations. We found that among twenty amino acids (AAs), the binding of CB[7] to Phe is the strongest. Based on that a series of tripeptides containing N-terminal Phe (with the second residue Gly (G) fixed) are designed to explore the effects of adjacent AA residues on the binding to CB[7]. It is indicated that, in contrast to FGG, only when the 3rd-residue is Glu (E), Lys (K), or Arg (R), the binding affinity with CB[7] can reach the nanomolar level. For the most prominent FGE, the binding free energy with CB[7] is −12.8 kcal/mol, with association constant (K_a) of 2.1 × 10⁹ M⁻¹. It is surprising that once reversing the sequence order of the 2nd-residue and 3rd-residue from FGX to FXG (X = E, K, R), or inserting a second Gly in the middle of FGX, such as FGGX, the binding affinity is significantly changed, with K_a decreased more than 3 orders of magnitude. These results predicted the high binding affinity and sequence selectivity of CB[7] to containing N-terminal Phe peptides, which are beneficial to predict the recognition sites of specific proteins/peptides and to design host-guest complexes with high affinity.