HomoSAR: Bridging comparative protein modeling with quantitative structural activity relationship to design new peptides

Peptides play significant roles in the biological world. To optimize activity for a specific therapeutic target, peptide library synthesis is inevitable; which is a time consuming and expensive. Computational approaches provide a promising way to simply elucidate the structural basis in the design of new peptides. Earlier, we proposed a novel methodology termed HomoSAR to gain insight into the structure activity relationships underlying peptides. Based on an integrated approach, HomoSAR uses the principles of homology modeling in conjunction with the quantitative structural activity relationship formalism to predict and design new peptide sequences with the optimum activity. In the present study, we establish that the HomoSAR methodology can be universally applied to all classes of peptides irrespective of sequence length by studying HomoSAR on three peptide datasets viz., angiotensin‐converting enzyme inhibitory peptides, CAMEL‐s antibiotic peptides, and hAmphiphysin‐1 SH3 domain binding peptides, using a set of descriptors related to the hydrophobic, steric, and electronic properties of the 20 natural amino acids. Models generated for all three datasets have statistically significant correlation coefficients (r2) and predictive r2 (rpred 2) and cross validated coefficient ( qLOO 2). The daintiness of this technique lies in its simplicity and ability to extract all the information contained in the peptides to elucidate the underlying structure activity relationships. The difficulties of correlating both sequence diversity and variation in length of the peptides with their biological activity can be addressed. The study has been able to identify the preferred or detrimental nature of amino acids at specific positions in the peptide sequences. © 2013 Wiley Periodicals, Inc. HomoSAR is an integrated approach using the principles of homology modeling and the quantitative structural activity relationship (QSAR) formalism to predict and design new peptide sequences. Although homology modeling establishes a relationship between peptide sequences, structures, and function, it does not quantify the relationship with activity, which is the domain of QSAR. A union of the two approaches provides a novel means to understand quantitative variations in peptide sequences with biological activity.