Contributions to Protein-Ligand Interactions

The experimentally determined binding constants Kj are typically in the range of 10 to 10 mol/L, corresponding to a Gibbs free energy of binding AG between -10 and -70kJ/mol in aqueous solution. 

There exists a growing body of experimental data on 3D structures of protein-ligand complexes and binding affinities.These data indicate that several features can be found in almost all complexes of tightly bound ligands. These features include 

A high steric complementarity between the protein and the ligand. This observation is consistent with the long established lock-and-key paradigm. 

A high complementarity of the surface properties. Lipophilic parts of the ligands are most frequently found to be in contact with lipophilic parts of the protein. Polar groups are usually paired with suitable polar protein groups to form hydrogen bonds or ionic interactions. 

The ligand usually adopts an energetically favorable conformation. 

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Finally, so-called hydrophobic or lipophilic interactions are often mentioned as additional contribution to protein-ligand interactions. These term s are used to describe the preferential association of nonpolar groups in aqueous solution. It should be emphasized, however, that in contrast to what the name suggests, there is no special hydrophobic force. Instead, one should speak of a hydrophobic effect. As further mentioned below, according to the generally accepted view, it arises primarily from the entropically favorable replacement and release of water molecules (42, 43). The association between the nonpolar surfaces itself is simply based on weak London forces... 

Br. . . It interactions as an important contribution to protein-ligand binding affinity. Angewandte Chemie, 121, 2955-2960. 

Also, very slow dissociation kinetics can contribute to slow clearing of a drug, which can be problematic in the event of adverse reactions such as an undesired allergic response. Therefore, methods to accurately determine the dissociation kinetics for protein-ligand interactions are of great value to the drug discovery process. 

Fig. 3. Traditional" binding site model compared to the Spider model of PPI. In traditional binding sites, the scaffold is part of the cavity and gives major contribution to the ligand binding affinity whereas at the protein-protein interface, the scaffold is more open to bulk solvent and plays the role of a connector ( C ) of highly interacting chemical groups anchoring to hot spots of the cavity of one of the protein partner.

What are the major contributions to the enthalpy and entropy of binding Direct interactions between the protein and the ligand are obviously very important for the enthalpy of binding. Besides that, an essential factor is that protein-ligand interactions occur in... 

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