Evaluation of the hydrophobic parameters of the amino acid side chains of peptides and their application in QSAR and conformational studies

We statistically analyzed the experimentally determined 1-octanol/water partition coefficient, log P, of a wide variety of N-acetyl-di- and tripeptide amides and unblocked di- and tripeptides to evaluate the hydrophobic parameters of the amino acid side chains of peptides. For blocked peptides, hydrophobic parameters were defined for amino acids having un-ionizable and ionizable side chains. For unblocked peptides, hydrophobic parameters were evaluated for 12 amino acids with un-ionizable side chains. In older to estimate the hydrophobic parameters for unnatural and ionizable amino acids, a procedure was developed based on the relationship between our hydrophobic parameters and the log P values of model amino acids calculated by the fragment constant method. Use of the hydrophobic parameters in quantitative Structure-activity relationship (QSAR)studies of bioactive peptides and conformational studies of proteins have also been presented. (C) 1997 Elsevier Science B.V.