Abstract
By applying a three-dimensional holographic vector of the atomic interaction field (3D-HoVAIF) to express the structure of three classical peptide drugs, quantitative structure activity relationship (QSAR) models are built by the multiple linear regression. The accuracy of the proposed model is illustrated using Q 2LOO (cross-validation) and r 2 (test set validation). Moreover, the r 2m metrics is used to further refine the predictive ability of the developed QSAR models. The results show that 3D-HoVAIF, due to the high predictive ability, offers a useful alternative to the costly and time-consuming experiments determining the bioactivity of peptide drugs.
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J. Jirácek, A. Yiotakis, B. Vincent, A. Lecoq, A. Nicolaou, F. Checler, and V. Dive, J. Biol. Chem., 270, 21701–21706 (1995).
M. Marraud and A. Aubry, J. Pept. Sci., 40, 45–83 (1996).
P. H. A. Sneath, J. Theor. Biol., 12, 157–195 (1966).
A. Kidera, Y. Konishi, M. Oka, T. Ooi, and H. A. Scheraga, J. Protein Chem., 4, 23–55 (1985).
P. Zhou, Y. Zhou, S. R. Wu, B. Li, F. F. Tian, and Z. L. Li, Chinese Sci. Bull., 51, 524–529 (2006).
S. Hellberg, L. Eriksson, J. Jonsson, F. Lindgren, M. Sjoström, B. Skagerberg, S. Wold, and P. Andrews, Int. J. Pept. Res. Ther., 37, 414–424 (1991).
S. Hellberg, M. Sjoestroem, B. Skagerberg, and S. Wold, J. Med. Chem., 30, 1126–1135 (1987).
S. Hellberg, M. Sjostrom, and S. Wold, Acta Chem. Scand. B: Org. Chem. Biochem., 40, 135–140 (1986).
S. Wold, L. Eriksson, S. Hellberg, J. Jonsson, M. Sjöström, B. Skagerberg, and C. Wikström, Can. J. Chem., 65, 1814–1820 (1987).
J. B. Tong, Y. Chen, S. L. Liu, T. Che, and X. M. Xu, J. Chemom., 26, 549–555 (2012).
B. Hemmateenejad, S. Yousefinejad, and A. R. Mehdipour, Amino Acids, 40, 1169–1183 (2011).
M. Sandberg, L. Eriksson, J. Jonsson, M. Sjöström, and S. Wold, J. Med. Chem., 41, 2481–2491 (1998).
X. Y. Wang, J. Wang, Y. Lin, Y. Ding, Y. Q. Wang, X. M. Cheng, and Z. H. Lin, J. Mol. Model., 17, 1599–1606 (2011).
J. B. Tong, Y. F. Li, S. L. Liu, and Y. L. Meng, Chin. J. Struct. Chem., 12, 1893–1899 (2010).
P. Zhou, F. F. Tian, and Z. L. Li, Chemom. Intell. Lab. Syst., 87, 88–94 (2007).
E. R. Collantes and W. J. Dunn, J. Med. Chem., 38, 2705–2713 (1995).
H. Mei, Y. Zhou, L. L. Sun, and Z. L. Li, Acta Phys. Chim. Sin., 20, 821–825 (2004).
M. Cocchi and E. Johansson, Quant. Struct.-Act. Rel., 12, 1–8 (1993).
A. Jain and D. Zongker, IEEE Trans. Pattern Anal., 19, 153–158 (1997).
I. Guttman, Linear Models: an Introduction, Wiley, New York (1982).
D. F. Morrison, Multivariate Statistical Methods, 3rd ed., McGraw-Hill, New York (1990).
K. Roy, I. Mitra, S. Kar, P. K. Ojha, R. N. Das, and H. Kabir, J. Chem. Inf. Model., 52, 396–408 (2012).
K. Roy, P. Chakraborty, I. Mitra, P. K. Ojha, S. Kar, and R. N. Das, J. Comput. Chem., 34, 1071–1082 (2013).
A. Golbraikh and A. Tropsha, Mol. Diversity, 5, 231–243 (2000).
A. Golbraikh, M. Shen, Z. Xiao, Y. D. Xiao, K. H. Lee, and A. Tropsha, J. Comput.-Aided Mol. Des., 17, 241–253 (2003).
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Original Russian Text © 2015 J. Tong, J. Chang, L. Li, M. Bai.
The text was submitted by the authors in English. Zhurnal Strukturnoi Khimii, Vol. 56, No. 7, pp. 1332-1338, November-December, 2015.
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Tong, J., Chang, J., Li, L. et al. QSAR study of peptide drugs by 3D-HoVAIF. J Struct Chem 56, 1268–1274 (2015). https://doi.org/10.1134/S0022476615070069
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DOI: https://doi.org/10.1134/S0022476615070069