General Principles

Ligand-receptor interactions in vivo are determined by a number of diverse factors. The first issue to consider is whether the ligand and receptor can approach close enough to recognize and bind to each other. Does a ligand have to cross a membrane to reach the same cellular compartment as a receptor? How will an orally administered drug reach the bloodstream and then its target receptor? To answer these questions, the physicochemical properties of the ligand need to be considered as well as its mechanism of transportation to its receptor. This may involve diffusion and active transport, including interaction with transport or membrane pore proteins. These aspects are discussed in detail in Chapter 5.28.

Once the ligand and receptor are sufficiently close, the ligand can diffuse up to and dock into its binding site on the receptor. This requires recognition between the ligand and receptor. This may first be mediated by the long-range electrostatic interactions between the ligand and the receptor and then strengthened by short-range hydrogen bonds and van der Waals' interactions. The relative importance of these terms varies widely from case to case. Water molecules will be displaced upon binding though some may be retained at the interface and mediate binding and influence specificity. Binding is accompanied by conformational changes ranging from modest shifts of a few atoms to movements of whole protein domains.

The binding process described in the preceding paragraph corresponds to the process determining the bimolecular association rate constant, the on-rate, kon. The unbinding process determines the bimolecular dissociation rate constant, the off-rate, koff. For ligand, L, and receptor, R:

koff

The binding affinity is quantified by the equilibrium dissociation constant, Kd = koff/kon = [L][R]/[LR]. The selectivity of a receptor for one ligand compared to another is due to different binding affinities and may arise due to differences in on- or off-rates (or both).

The dissociation constant is related to the binding free energy, AG by:

where R is the universal gas constant and T the temperature in K. Kd is given in units of M (moles per liter) and the free energy is given at the standard state concentration, Co, of 1 M (ImolL- 1 or 1 solute molecule per 1661 A3 aqueous solvent).

Thermodynamically, AG is given by the balance between binding enthalpy, AH, and binding entropy, AS:

Ligand-receptor interactions are often characterized by enthalpy-entropy compensation in which one term favors and the other disfavors binding. While enthalpic contributions include electrostatic, hydrogen bond, and van der Waals' interactions, entropic contributions arise from several sources. Binding is accompanied by an entropic cost due to loss of translational and rotational entropy upon binding. In addition, loss of flexibility upon binding will entropically disfavor binding. On the other hand, the displacement of ordered water molecules upon binding can entropically favor binding. Entropic contributions are discussed in more detail in Section 4.09.3.5.

In the first model of ligand-receptor binding, Emil Fischer proposed that receptor and ligand (specifically, enzyme and substrate) fit together like a lock and key.1 In this analogy, specificity can be conveniently viewed in terms of distinguishing between locks and keys. However, in the lock and key picture, the receptor and ligand are rigid entities. In reality, binding is accompanied by some degree of conformational change. This can be considered in 'zipper'2 or 'hand-into-glove' analogies to describe receptor-ligand interactions. The conformational change can be considered to be an induced fit due to binding3 or the selection of different dominant conformations from the conformational ensemble of the molecule in the bound and unbound states4 or a combination of both. Some of the binding models are shown in Figure 1. Of particular interest for drug design is the observation that drug molecules can bind to parts of the protein that are not revealed at the surface in structures determined for either the unbound form or for a form with a natural ligand bound.5-7 Conformational changes upon ligand-receptor binding are discussed in more detail in Section 4.09.4.

The solvent surroundings of the ligand and the receptor have a very important influence on their binding. Binding affinities will be very different in a polar solvent like water compared with a more nonpolar environment like methanol or the hydrophobic interior of a lipid membrane. This is because binding always involves the competition between ligand-receptor interactions and ligand-solvent and receptor-solvent interactions. The ionic strength and pH of the surroundings will influence the strength of electrostatic interactions between ligand and receptor. Viscogens and crowding agents can also affect ligand-receptor binding. They may affect the binding kinetics through their viscosity or the binding affinity through alteration of dielectric properties or through local concentration effects.

In the next section, the physical factors affecting ligand-receptor interactions are discussed in more detail, drawing attention to how these can be modeled and how they can be exploited in ligand design.

Receptor Ligand

Figure 1 Models of receptor-ligand binding. (a) In the lock-and-key model, the ligand (green) exactly fits into the receptor binding site (violet). (b) The ligand associates weakly with the receptor and induces conformational changes resulting in binding. (c) The ligand binds preferentially to certain conformations in the conformational ensemble of the receptor.

Figure 1 Models of receptor-ligand binding. (a) In the lock-and-key model, the ligand (green) exactly fits into the receptor binding site (violet). (b) The ligand associates weakly with the receptor and induces conformational changes resulting in binding. (c) The ligand binds preferentially to certain conformations in the conformational ensemble of the receptor.

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