Computational study on the encapsulation of glucosamine anomers by cucurbit[6]uril and cucurbit[8]uril in aqueous solution

Abstract

Recently, we have investigated the cucurbit[7]uril (CB7) recognition of the α- and β-anomers of neutral, protonated, and acetylated forms of glucosamine in water. In the present work, we employed molecular dynamics (MD) and thermodynamic integration methods (TI) to investigate the recognition of these molecules by cucurbit[6]uril (CB6) and cucurbit[8]uril (CB8). MD revealed the formation of stable 1:1 inclusion complexes by all studied molecules with cucurbit[n]urils (CBn), and 2:1 complex by the α-anomer of the acetylated form of glucosamine with the large homologue CB8. CB6 forms roughly twice as many hydrogen bonds with the guest molecules as CB8. MM-PBSA results indicated that the electrostatic contribution to the binding free energy of each guest:CB complex was larger for CB6 than for CB8, and that CB6 and CB8 have lower affinity toward the different forms of glucosamine compared to CB7. Furthermore, TI was used to estimate the relative affinities of CB6 and CB8 toward the α- and β-anomers for each form of the studied glucosamine and compare with CB7.

Keywords

• Cucurbiturils
• Glucosamine
• Molecular Dynamics
• Thermodynamic Integration
• MM-PBSA