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A protein contains a large amount of water molecules, and the nature of the interactions of the water molecules with a protein play an important role in the thermodynamics of the ligand binding process. In this paper, thermodynamic aspects of drug-receptor interactions, enthalpy-entropy compensation or reinforcement, hydrophobicity, and biological 2D- and 3D-QSAR are discussed. Comparisons of the thermodynamic QSAR of phenyl esters of N-benzoyl L-alanine in phosphate buffer and pentanol provide useful insight for the ligand-enzyme interactions.