Mass spectrometry and affinity capillary electrophoresis for characterization of host-guest interactions.

Affinity capillary electrophoresis (ACE) in a free solution must be used to confirm the molecular interaction observed in electrospray ionization mass spectrometry (ESI-MS) for affinity binding analysis in the drug discovery process. In this article, the affinity of ibuprofen with three cyclodextrin species of different cavity sizes is investigated by both ESI-MS and ACE methods. Because the binding interactions are measured in different environments using ESI-MS (gas phase) and ACE (liquid phase), the experimental results show significant differences. To better illustrate the major factors influencing the binding constants in different environments, two types of simulations (molecular docking and molecular force field evaluation) are employed in the theoretical discussion. The molecular docking results were consistent with the ESI-MS experimental phenomena. Due to lack of the water molecules in the gas phase, a substantial difference in molecular interaction can contribute to a different binding affinity. By using the molecular modeling based on the force field evaluation with considering solvent molecules, β-CD is expected to form the most stable complex with ibuprofen in the liquid phase and the binding affinity of ibuprofen to γ-CD is much less significant than it is in gas phase. This prediction is in good agreement with the ACE results. Therefore, this work demonstrates that, by using ESI-MS in the first-step screening and ACE in the follow-up determination, a more accurate understanding can be achieved.