How Effectively Can Adaptive Sampling Methods Capture Spontaneous Ligand Binding?

Molecular dynamics (MD) simulations that capture the spontaneous binding of drugs and other ligands to their target proteins can reveal a great deal of useful information, but most drug-like ligands bind on time scales longer than those accessible to individual MD simulations. Adaptive sampling methods-in which one performs multiple rounds of simulation, with the initial conditions of each round based on the results of previous rounds-offer a promising potential solution to this problem. No comprehensive analysis of the performance gains from adaptive sampling is available for ligand binding, however, particularly for protein-ligand systems typical of those encountered in drug discovery. Moreover, most previous work presupposes knowledge of the ligand's bound pose. Here we outline existing methods for adaptive sampling of the ligand-binding process and introduce several improvements, with a focus on methods that do not require prior knowledge of the binding site or bound pose. We then evaluate these methods by comparing them to traditional, long MD simulations for realistic protein-ligand systems. We find that adaptive sampling simulations typically fail to reach the bound pose more efficiently than traditional MD. However, adaptive sampling identifies multiple potential binding sites more efficiently than traditional MD and also provides better characterization of binding pathways. We explain these results by showing that protein-ligand binding is an example of an exploration-exploitation dilemma. Existing adaptive sampling methods for ligand binding in the absence of a known bound pose vastly favor the broad exploration of protein-ligand space, sometimes failing to sufficiently exploit intermediate states as they are discovered. We suggest potential avenues for future research to address this shortcoming.

N-terminal T4 lysozyme fusion facilitates crystallization of a G protein coupled receptor.

A highly crystallizable T4 lysozyme (T4L) was fused to the N-terminus of the ß(2) adrenergic receptor (ß(2)AR), a G-protein coupled receptor (GPCR) for catecholamines. We demonstrate that the N-terminal fused T4L is sufficiently rigid relative to the receptor to facilitate crystallogenesis without thermostabilizing mutations or the use of a stabilizing antibody, G protein, or protein fused to the 3rd intracellular loop. This approach adds to the protein engineering strategies that enable crystallographic studies of GPCRs alone or in complex with a signaling partner.

Inhibition of ligand binding to G protein-coupled receptors by arachidonic acid.

Arachidonic acid (AA), released in response to muscarinic acetylcholine receptor (mAChR) stimulation, previously has been reported to function as a reversible feedback inhibitor of the mAChR. To determine if the effects of AA on binding to the mAChR are subtype specific and whether AA inhibits ligand binding to other G protein-coupled receptors (GPCRs), the effects of AA on ligand binding to the mAChR subtypes (M1, M2, M3, M4, and M5) and to the micro-opioid receptor, beta2-adrenergic receptor (beta2-AR), 5-hydroxytryptamine receptor (5-HTR), and nicotinic receptors were examined. AA was found to inhibit ligand binding to all mAChR subtypes, to the beta2-AR, the 5-HTR, and to the micro-opioid receptor. However, AA does not inhibit ligand binding to the nicotinic receptor, even at high concentrations of AA. Thus, AA inhibits several types of GPCRs, with 50% inhibition occurring at 3-25 MuM, whereas the nicotinic receptor, a non-GPCR, remains unaffected. Further research is needed to determine the mechanism by which AA inhibits GPCR function.

Ligand binding to the porcine adipose tissue beta-adrenergic receptor.

We measured ligand binding to the beta-adrenergic receptor from porcine adipocytes using tritiated radioligands, dihydroalprenolol (DHA) and CGP-12177 (CGP), and an iodinated radioligand, cyanopindolol (ICP). Binding was measured in a crude plasma membrane preparation. Equilibrium saturation binding was regular for all three ligands; the Kd were approximately 4,000 pM for DHA, 600 pM for CGP, and 100 pM for ICP. Binding was stereospecific with each radioligand. Association of each radioligand was relatively rapid; dissociation was rapid and complete for DHA, initially rapid but ultimately incomplete for CGP, and minimal for ICP. The Kd estimated from kinetic data were approximately 1,000 pM for DHA and 100 pM for CGP. The receptor did not bind phentolamine, an alpha-adrenergic antagonist, except at concentrations greater than 10(-5) M. Propranolol was bound to the receptor with a Ki of approximately 8 nM regardless of the radioligand used. Metoprolol, a purported beta 1-adrenergic specific antagonist, was bound to the receptor with a Ki of approximately 300 nM when the radioligands were CGP or ICP but with a Ki of approximately 1,000 nM when the radioligand was DHA. The Ki for ICI 118,551, a purported beta 2-adrenergic specific antagonist, were approximately 500 nM when the radioligands were DHA or CGP but 125 nM when the radioligand was ICP. Thus, the choice of radioligand can influence the characterization of the beta-adrenergic receptor being studied.