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http://dx.doi.org/10.5012/bkcs.2003.24.12.1742

Theoretical Study on Hydrophobicity of Amino Acids by the Solvation Free Energy Density Model  

Kim, Jun-Hyoung (Department of Chemistry and CAMD Research Center, Soongsil University)
Nam, Ky-Youb (Department of Chemistry and CAMD Research Center, Soongsil University)
Cho, Kwang-Hwi (Department of Bioinformatics and Life Science, Soongsil University)
Choi, Seung-Hoon (InSilico Tech Inc.)
Noh, Jae-Sung (Korea Research Institute of Chemical Technology)
No, Kyoung-Tai (Department of Biotechnology,Yonsei University, Member of Hyperstructured Organic Material Research Center)
Publication Information
Bulletin of the Korean Chemical Society / v.24, no.12, 2003 , pp. 1742-1750 More about this Journal
Abstract
In order to characterize the hydrophobic parameters of N-acetyl amino acid amides in 1-octanol/water, a theoretical calculation was carried out using a solvation free energy density model. The hydrophobicity parameters of the molecules are obtained with the consideration of the solvation free energy over the solvent volume surrounding the solute, using a grid model. Our method can account for the solvent accessible surface area of the molecules according to conformational variations. Through a comparison of the hydrophobicity of our calculation and that of other experimental/theoretical works, the solvation free energy density model is proven to be a useful tool for the evaluation of the hydrophobicity of amino acids and peptides. In order to evaluate the solvation free energy density model as a method of calculating the activity of drugs using the hydrophobicity of its building blocks, the contracture of Bradykinin potentiating pentapeptide was also predicted from the hydrophobicity of each residue. The solvation free energy density model can be used to employ descriptors for the prediction of peptide activities in drug discovery, as well as to calculate the hydrophobicity of amino acids.
Keywords
Hydrophobicity; Solvation free energy density model; Bradykinin potentiating pentapeptide; Quantitative structure-activity relationship;
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