Abstract:

Human serum albumin (HSA) has two main drug binding sites termed Site I and Site II. Most small molecules like ibuprofen (a well-known anti-inflammatory drug) bind to Site II preferentially. In this study, molecular simulation methods were used to investigate the dynamic binding process of ibuprofen to Site II. A system of 50 ibuprofen molecules distributed randomly around HSA was constructed. After a 50-ns molecular dynamics simulation, one ibuprofen molecule bound stably to Site II. Based on trajectory analysis of this ibuprofen molecule, the binding process of ibuprofen onto Site II can be divided into four phases:(i) long-range attraction; (ii) adjustment on the surface; (iii) entering to Site II pocket; and (iv) stable binding at Site II. After evaluating van der Waals' and electrostatic interaction energies during the binding process, it was found that the initial major driving force involves electrostatic attractions. Subsequently, ibuprofen locks between two polar regions on the surface near Site II and then moves to Site II. Ibuprofen then enters the pocket of Site II by combinatorial effects of polar and hydrophobic residues nearby the entrance of Site II. Electrostatic and hydrophobic interactions form the stable binding of ibuprofen in Site II. The molecular surface near Site II was observed to change significantly during binding, which indicates an induced fit mechanism. The binding mode obtained with molecular simulations is consistent with the crystal structure of the ibuprofen-HSA complex. The results show that molecular simulations would help to evaluate the dynamic binding processes of small molecules to proteins and improve our understanding of the binding mechanisms at the molecular level.

Key words: Human serum albumin, Site II, Ibuprofen, Dynamic binding, Molecular simulation