Protein–Ligand Interactions as the Basis for Drug Action

What makes a ligand bind efficiently to a given protein is the subject of this chapter. Emil Fisher introduced the “lock-and-key” principle to describe the interaction of small molecules with macromolecular receptors. The strength of a protein-ligand interaction is measured by the binding constant. It quantifies the stability of a protein-ligand complex as a dissociation constant and is logarithmically related to the Gibbs free energy of binding. The latter consists of an enthalpic and an entropic part. The enthalpic part includes all terms related to the interaction energy of the binding partners. The entropic part considers the ordering of the system and how the energy content is distributed over the degrees of freedom of the system. Protein-ligand complexes are usually formed by noncovalent interactions, mainly hydrogen bonds. Their strength depends strongly on the charge distributions of the interacting functional groups. Whether a group is charged or not depends on its protonation state, which is defined by the pKa of the interacting functional groups. Depending on the local environment in a binding pocket, the pKa values of the involved groups can vary significantly, transforming a normal H-bond into a much stronger charge-assisted H-bond. Hydrophobic interactions are formed by the close proximity of nonpolar functional groups of the binding partners. By releasing water molecules from the binding pocket or the ligand surface in aqueous solution, they can make a significant contribution to binding. The strength of protein-ligand interactions is strongly influenced by the local water environment. Both, the protein binding pocket and the ligand are solvated prior to complex formation, and functional groups of the protein and ligand form hydrogen bonds with water molecules. The overall balance of the hydrogen bonding inventory before and after complex formation is important for binding affinity. A net increase in affinity will only occur if the newly formed hydrogen bonds in the complex are greater in number and stronger than those previously formed to water. The release of water molecules from hydrophobic surface patches can increase affinity by enthalpy and entropy. The release of fixed water molecules increases degrees of freedom and therefore the entropy contribution to binding. Replacement of highly disordered water molecules into the bulk water environment can contribute to an enthalpic gain. Entropic contributions to binding arise from an increase in the degrees of freedom of the protein-ligand-water system. As a first approximation, they correlate with the size of the hydrophobic surface buried in the formed complex. At the end of complex formation, the ligand forms a new surface with the protein, which is solvated. If optimal water networks can form around the exposed parts of the ligand participating in the shared surface, the bound ligand gains additional affinity. Proper rigidification (“pre-organization”) of a ligand into the conformation required at the binding site can lead to a significant increase in affinity for entropic reasons, provided that the pre-organized conformation is already populated in solution prior to protein binding. Variations in enthalpy and entropy are correlated due to extensive enthalpy/entropy compensation. The interdependence of both, together with dynamic versus interaction geometric phenomena, causes simple additive rules based on standard functional group contributions to fail and shows that pronounced cooperative effects are at work. A set of rules is proposed to be considered in the optimization of first hits to lead candidates. https://sn.pub/8ink1c