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Bulletin of the Korean Chemical Society (BKCS)

ISSN 0253-2964(Print)
ISSN 1229-5949(Online)
Volume 24, Number 12
BKCSDE 24(12)
December 20, 2003 

Theoretical Study on Hydrophobicity of Amino Acids by the Solvation Free Energy Density Model
Junhyoung Kim, Ky-Youb Nam, Kwang-Hwi Cho Seung-Hoon Choi, Jae Sung Noh, Kyoung Tai No*
Hydrophobicity, Solvation free energy density model, Bradykinin potentiating pentapeptide, Quantitative structure-activity relationship
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.
1742 - 1750
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