A new set of amino acid descriptors and its application in peptide QSARs

In this work, a new set of amino acid descriptors, i.e., VHSE (principal components score Vectors of Hydrophobic, Steric, and Electronic properties), is derived from principal components analysis (PCA) on independent families of 18 hydrophobic properties, 17 steric properties, and 15 electronic properties, respectively, which are included in total 50 physicochemical variables of 20 coded amino acids. Using the stepwise multiple regression (SMR) method combined with partial least squares (PLS), the VHSE scales are then applied to QSAR studies of bitter-tasting dipeptides (BTD), angiotensin-converting enzyme (ACE) inhibitors, and bradykinin-potentiating pentapeptides (BPP). To validate the predictive power of resulting models, external validation are also performed. A comparison of the results to those obtained with z scores and other two-dimensional (2D) or three-dimensional(3D) descriptors shows that the VHSE scales are comparable for parameterizing the structural variability of the peptide series.