Drug Design
A solvated ligand that binds the protein of interest is likely to exist as an equilibrium mixture of several conformers. Likewise the solvated protein also exists as several conformers in equilibrium. Formation of protein-ligand complex includes displacement of the solvent molecules that occupy the binding site of the ligand, to produce a solvated complex. Because this necessarily means that the interaction is entropically disfavored, highly favorable enthalpic contacts between the protein and the ligand must compensate for the entropic loss. The design of new ligands is usually based on the modification of known ligands for the target proteins. Proteases are enzymes that catalyze hydrolysis of a peptide bond. These proteins have evolved to recognize and bind the transition state of peptide hydrolysis reaction which is a tetrahedral intermediate. Therefore, the main protease inhibitors are tetrahedral intermediate mimics having an alcohol or a phosphate group. Examples are saquinavir, ritonavir, pepstatin, etc.
Read more about this topic: Tetrahedral Carbonyl Addition Compound, Applications in Biomedicine
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