Ensemble Molecular Dynamics of a Protein-Ligand Complex: Residual Inhibitor Entropy Enhances Drug Potency in Butyrylcholinesterase

Abstract

Butyrylcholinesterase is a key enzyme that catalyzes the hydrolysis of the neurotransmitter acetylcholine and shows an increased activity in patients suffering from Alzheimer's disease (AD), making this enzyme a primary target in treating AD. Central to this problem, and to similar scenarios involving biomolecular recognition, is our understanding of the nature of the protein-ligand complex. The butyrylcholinesterase enzyme was studied via all-atom, explicit solvent, ensemble molecular dynamics simulations sans inhibitor and in the presence of three dialkyl phenyl phosphate inhibitors of known potency to a cumulative sampling of over 40 μs. Following the relaxation of these ensembles to conformational equilibria, binding modes for each inhibitor were identified. While classical models, which assume significant reduction in protein and ligand conformational entropies, continue to be favored in contemporary studies, our observations contradict those assumptions: bound ligands occupy many conformational states, thereby stabilizing the complex, while also promoting protein flexibility.

Keywords: BChE; Distributed computing; Docking; Molecular simulation; Phenyl phosphate.

Figure 1

X-ray structure of BChE (1P0I.pdb) with the binding pocket magnified and a schematic of the DAPP inhibitors studied. Active site residues are color coded for easy identification including the catalytic triad (yellow), the oxyanion hole (orange), the choline binding site (green), the acyl binding site (blue), and the peripheral anionic site (red).

Figure 2

Populations of observed DAPP5 binding modes versus time, with binding mode populations split into three panels for visual clarity.

Figure 3

Top: The root-mean-squared fluctuation (RMSF) for each residue is shown for the enzyme sans inhibitor (black), and for the enzyme in the presence of the DAPP1 (blue), DAPP3 (green), and DAPP5 (red) inhibitors. Bottom: The percentage change in RMSF per residue compared to BChE sans inhibitor, is shown for each BChE-DAPP complex, following the same color scheme used in the top panel. Dashed vertical lines in the background identify residues in the BChE binding pocket.

Figure 4

Average binding conformations for the DAPP5 inhibitor, which is shown in stick mode with phenyl and alkyl carbons shown in cyan and phosphorus, oxygen, and hydrogen atoms shown in yellow, red, and white, respectively. Water molecules have been removed from these images for visual clarity, and residues in the binding pocket are colored as noted in the key. Binding modes are labeled from the bottom up, with mode 0 being the most populated (lowest binding free energy) and mode 23 being the least populated (highest binding free energy), and the binding mode free energy (relative to the lowest energy mode) specified in the bottom right corner of each frame. All images are viewed down the ~20 Å deep BChE active site gorge from the same reference point and at approximately the same relative magnification.