Peptide reagent design based on physical and chemical properties of amino acid residues

Du, Qi‐Shi; Huang, Ri‐Bo; Wei, Yu‐Tuo; Wang, Cheng‐Hua; Chou, Kuo‐Chen

It has tremendous values for both drug discovery and basic research to develop a solid bioinformatical tool for guiding peptide reagent design. Based on the physical and chemical properties of amino acids, a new strategy for peptide reagent design, the so‐called AABPD (amino acid based‐peptide design), is proposed. The peptide samples in a training dataset are described by a series of HMLP (heuristic molecular lipophilicity potential) parameters and other physicochemical properties of amino acid residues that form a three‐dimensional data matrix where each component is defined by three indexes: the first index refers to the peptide samples, the second to the amino acid positions, and the third to the amino acid parameters. The binding free energy between a peptide ligand and its protein receptor is calculated by a linear free energy equation through the physicochemical parameters, resulting in a set of simultaneous linear equations between the bioactivity of the peptides and the physicochemical properties of amino acids. An iterative double least square technique is developed for the solution of the three‐dimensional simultaneous linear equation set to determine the amino acid position coefficients of peptide sequence and the physicochemical parameter coefficients of amino acid residues alternately. The two sets of coefficients thus obtained are used for predicting the bioactivity of other query peptide reagents. Two calculation examples, the peptide substrate specificity of the SARS coronavirus 3C‐like proteinase and the affinity prediction for epitope‐peptides with Class I MHC molecules are studied by using the peptide reagent design strategy. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007