Quantitative Structure-Activity Relationship Study of Radical Scavenging Peptides Based on Orac Method by Using Different Sets of Amino Acids Descriptor

Abstract:

Some radical scavenging peptides by ORAC method from different hydrolysates were used for the quantitative structure-activity relationships (QSAR) research. Partial least-squares regression analysis (PLSR) was treated as the method to build the model with 17 kinds of amino acid descriptors. In order to translate the sequence to the same length, two-terminal position numbering (TTPN) was applied. Two of amino acid descriptors VSHE and VSW were selected for their excellent performance (R², Q², and RMSE_c with VHSE and VSW descriptor are 0.995, 0.630, 0.318 and 0.966, 0.543, 0.181 respectively). VHSE has the definite physicochemical meanings and easy to understand while VSW has good predictive ability (Rand RMSE_p with VHSE and VSW are 0.404, 2.633 and 0.635, 2.298 respectively). It is believed that the position No.2 amino acid from N-terminal (N₂) have more importance than others in sequence, and most of electronic properties are negative to activity while all the steric properties are positive to activity as well as the hydrophobic properties. The suitable amino acids in sequence are as follow: G, R, K, W, Y, N, E, H, and Q are suitable for N₂ position which illustrated the importance of acidic amino acids in peptide sequence for radical scavenging activity.

• Periodical: Advanced Materials Research (Volume 365)
• Pages: 169-179
• DOI: https://doi.org/10.4028/www.scientific.net/AMR.365.169
• Online since: October 2011
• Authors: Yao Wang Li, Bo Li
• Keywords: Antioxidant Peptide, Descriptors, PLS, Quantitative Structure Activity Relationship, Radical Scavenging Activity

References

[1] B. Herna ndez-Ledesma, A. Quiro s, L. Amigo, and I. Recio, Identification of bioactive peptides after digestion of human milk and infant formula with pepsin and pancreatin, Int. Dairy J., vol. 17, pp.42-49, (2007).

DOI: 10.1016/j.idairyj.2005.12.012

[2] Y. Ma, Y. L. Xiong, J. Zhai, H. Zhu, and T. Dziubla, Fractionation and evaluation of radical scavenging peptides from in vitro digests of buckwheat protein, Food Chem., vol. 118, pp.582-588, (2010).

DOI: 10.1016/j.foodchem.2009.05.024

[3] S. V. Silva, A. Pihlanto and F. X. Malcata, Bioactive Peptides in Ovine and Caprine Cheeselike Systems Prepared with Proteases from Cynara cardunculus, J. Dairy Sci., vol. 89, pp.3336-3344, 2006-09-01 (2006).

DOI: 10.3168/jds.s0022-0302(06)72370-0

[4] K. Suetsuna, H. Ukeda and O. Hirotomo, Isolation and characterization of free radical scavenging activities peptides derived from casein, J. Nutr. Biochem., vol. 11, p.128 –131, (2000).

DOI: 10.1016/s0955-2863(99)00083-2

[5] R. R. Lu, P. Qian, Z. Sun, X. H. Zhou, T. P. Chen, J. F. He, H. Zhang, and J. Wu, Hempseed protein derived antioxidative peptides: Purification, identification and protection from hydrogen peroxide-induced apoptosis in PC12 cells, Food Chem., vol. 123, pp.1210-1218, (2010).

DOI: 10.1016/j.foodchem.2010.05.089

[6] I. C. Sheih, T. Wu and T. J. Fang, Antioxidant properties of a new antioxidative peptide from algae protein waste hydrolysate in different oxidation systems, Bioresour. Technol., vol. 100, pp.3419-3425, (2009).

DOI: 10.1016/j.biortech.2009.02.014

[7] E. MENDIS, N. RAJAPAKSE and S. KIM, Antioxidant Properties of a Radical-Scavenging Peptide Purified from Enzymatically Prepared Fish Skin Gelatin Hydrolysate, J. Agric. Food Chem., vol. 53, pp.581-587, (2005).

DOI: 10.1021/jf048877v

[8] S. Kim, J. Je and S. Kim, Purification and characterization of antioxidant peptide from hoki (Johnius belengerii) frame protein by gastrointestinal digestion, J. Nut. Biochem., vol. 18, pp.31-38, (2007).

DOI: 10.1016/j.jnutbio.2006.02.006

[9] N. Rajapaksea, E. Mendisa, H. Byunb, and S. Kim, Purification and in vitro antioxidative effects of giant squid muscle peptides on free radical-mediated oxidative systems, J. Nutr. Biochem., vol. 16, pp.562-569, (2005).

DOI: 10.1016/j.jnutbio.2005.02.005

[10] E. Kim, S. Lee, B. Jeon, S. Moon, B. Kim, T. Park, J. Han, and P. Park, Purification and characterisation of antioxidative peptides from enzymatic hydrolysates of venison protein, Food Chem., vol. 114, pp.1365-1370, (2009).

DOI: 10.1016/j.foodchem.2008.11.035

[11] Jae-Young Je, Zhong-Ji Qian, Sang-Hoon Lee, Hee-Guk Byun, and A. S. Kim, Purification and Antioxidant Properties of Bigeye Tuna (Thunnus obesus) Dark Muscle Peptide on Free Radical-Mediated Oxidative Systems, J. Med. Food., vol. 11, p.629–637, (2008).

DOI: 10.1089/jmf.2007.0114

[12] R. Marcuse, Antioxidative effect of amino-acids, Nature, vol. 186, pp.886-887, (1960).

DOI: 10.1038/186886a0

[13] H. Chen, K. Muramoto, F. Yamauchi, and K. Nokihara, Antioxidant Activity of Designed Peptides Based on the Antioxidative Peptide Isolated from Digests of a Soybean Protein, J. Agric. Food Chem., vol. 44, pp.2619-2623, (1996).

DOI: 10.1021/jf950833m

[14] H. Chen, K. Muramoto and F. Yamauchi, Structural Analysis of Antioxidative Peptides from Soybean . beta. -Conglycinin, J. Agric. Food Chem., vol. 43, pp.574-578, (1995).

DOI: 10.1021/jf00051a004

[15] A. Saiga, S. Tanabe and T. Nishimura, Antioxidant Activity of Peptides Obtained from Porcine Myofibrillar Proteins by Protease Treatment, J. Agric. Food Chem., vol. 51, p.3661−3667, (2003).

DOI: 10.1021/jf021156g

[16] C. Hansch and A. Leo, Exploring QSAR: fundamentals and application in chemistry and biology. Washington DC: American Chemical Society, (1995).

[17] A. H. Pripp, T. Isaksson, L. Stepaniak, and T. Sørhaug, Quantitative structure-activity relationship modelling of ACE-inhibitory peptides derived from milk proteins, Eur. Food Res. Technol., vol. 219, pp.579-583, (2004).

DOI: 10.1007/s00217-004-1004-4

[18] A. H. Pripp and Y. Ardo, Modelling relationship between angiotensin-(I)-converting enzyme inhibition and the bitter taste of peptides, Food Chem., vol. 102, pp.880-888, (2007).

DOI: 10.1016/j.foodchem.2006.06.026

[19] R. D. Brown, Descriptors for diversity analysis, Perspect. Drug Discov. Design, vol. 7-8, pp.31-49, (1997).

[20] P. H. A. Sneath, Relations between chemical structure and biological activity in peptides, J. Theor. Biol., vol. 12, pp.157-195, (1966).

[21] A. Kidera, Y. Konishi, M. Oka, T. Ooi, and H. A. Scheraga, Statistical analysis of the physical properties of the 20 naturally occurring amino acids, J. Protein Chem., vol. 4, pp.23-55, (1985).

DOI: 10.1007/bf01025492

[22] S. Hellberg, M. Sjoestroem, B. Skagerberg, and S. Wold, Peptide quantitative structure-activity relationships, a multivariate approach, J. Med. Chem., vol. 30, pp.1126-1135, 2002-05-01 (1987).

DOI: 10.1021/jm00390a003

[23] J. Wu and R. E. Aluko, Quantitative structure-activity relationship study of bitter di- and tri-peptides including relationship with angiotensin I-converting enzyme inhibitory activity, J. Pept. Sci., vol. 13, pp.63-69, (2007).

DOI: 10.1002/psc.800

[24] H. Kim and E. C. Y. Li-Chan, Quantitative Structure−Activity Relationship Study of Bitter Peptides, J. Agric. Food Chem., vol. 54, pp.10102-10111, 2006-11-22 (2006).

DOI: 10.1021/jf062422j

[25] M. Sandberg, L. Eriksson, J. Jonsson, M. Sjöström, and S. Wold, New chemical descriptors relevant for the design of biologically active peptides. A multivariate characterization of 87 amino acids, J. Med. Chem., vol. 41, pp.2481-2491, (1998).

DOI: 10.1021/jm9700575

[26] H. Mei, Z. H. Liao, Y. Zhou, and S. Z. Li, A New Set of Amino Acid Descriptors and Its Application in Peptide QSARs, Pept. Sci., vol. 80, p.775–786, (2005).

DOI: 10.1002/bip.20296

[27] F. Tian, L. Yang, F. Lv, Q. Yang, and P. Zhou, In silico quantitative prediction of peptides binding affinity to human MHC molecule: an intuitive quantitative structure–activity relationship approach, Amino Acids, vol. 36, pp.535-554, (2009).

DOI: 10.1007/s00726-008-0116-8

[28] F. Tian, P. Zhou and Z. Li, T-scale as a novel vector of topological descriptors for amino acids and its application in QSARs of peptides, J. Mol. Struct., vol. 830, pp.106-115, (2007).

DOI: 10.1016/j.molstruc.2006.07.004

[29] M. Shu, H. Mei, S. Yang, L. Liao, and Z. Li, Structural Parameter Characterization and Bioactivity Simulation Based on Peptide Sequence, QSAR & Comb. Sci., vol. 28, pp.27-35, (2009).

DOI: 10.1002/qsar.200710169

[30] S. Z. Li, B. Fu, Yuanqiang, and S. Liu, On Structural Parameterization and Molecular Modeling of Peptide Analogues by Molecular Electronegativity Edge Vector (VMEE): Estimation and Prediction for Biological Activity of Dipeptides, J. Chin. Chem. Soc., vol. 48, pp.937-944, (2001).

DOI: 10.1002/jccs.200100137

[31] H. Mei, Y. Zhou, L. L. Sun, and Z. L. Li, A new descriptor of amino acids and its application in peptide QSAR, Acta Phys. Chim. Sin., vol. 20, pp.821-825, (2004).

[32] G. Z. Liang, P. Zhou, Y. Zhou, Q. X. Zhang, and Z. L. Li, New descriptors of aminoacids and their applications to peptide quantitative structure-activity relationship, Acta Chim. Sinica, vol. 64, pp.393-396, (2006).

[33] G. Liang and Z. Li, Factor Analysis Scale of Generalized Amino Acid Information as the Source of a New Set of Descriptors for Elucidating the Structure and Activity Relationships of Cationic Antimicrobial Peptides, QSAR & Comb. Sci., vol. 26, pp.754-763, (2007).

DOI: 10.1002/qsar.200630145

[34] L. Yang, M. Shu, K. Ma, H. Mei, Y. Jiang, and Z. Li, ST-scale as a novel amino acid descriptor and its application in QSAM of peptides and analogues, Amino Acids, vol. 38, pp.805-816, (2010).

DOI: 10.1007/s00726-009-0287-y

[35] Z. Li, G. Li, M. Shu, J. Sun, S. Yang, H. Mei, M. Zhang, P. Zhou, S. Wu, G. Chen, F. Lu, and T. Lu, A novel vector of topological and structural information for amino acids and its QSAR applications for peptides and analogues, Sci. China Ser. B, vol. 51, pp.946-957, (2008).

DOI: 10.1007/s11426-008-0040-5

[36] Z. Lin, H. Long, Z. Bo, Y. Wang, and Y. Wu, New descriptors of amino acids and their application to peptide QSAR study, Peptides, vol. 29, pp.1798-1805, (2008).

DOI: 10.1016/j.peptides.2008.06.004

[37] J. B. TONG, S. L. Liu, Y. T. Liu, Y. M. Ma, and X. M. Tong, A New SVG descriptor of amino acids and its application to peptide QSAR, Fines chem., vol. 25, (2008).

[38] J. Tong, S. Liu, P. Zhou, B. Wu, and Z. Li, A novel descriptor of amino acids and its application in peptide QSAR, J. Theor. Biol., vol. 253, pp.90-97, (2008).

DOI: 10.1016/j.jtbi.2008.02.030

[39] E. R. Collantes and W. J. Dunn III, Amino acid side chain descriptors for quantitative structure-activity relationship studies of peptide analogues, J. Med. Chem., vol. 38, pp.2705-2713, (1995).

DOI: 10.1021/jm00014a022

[40] G. Bravi, E. Gancia, P. Mascagni, M. Pegna, R. Todeschini, and A. Zaliani, MS-WHIM, new 3D theoretical descriptors derived from molecular surface properties: A comparative 3D QSAR study in a series of steroids, J. Comput. Aid. Molec. Design, vol. 11, pp.79-92, (1997).

DOI: 10.1023/a:1008079512289

[41] J. B. Z. S. Tong, A new 3D-descriptor of amino acids and its application in quantitative structure activity relationship of peptide drugs, Wuli Huaxue Xuebao/ Acta Phys. Chim. Sinica, vol. 23, pp.37-43, (2007).

[42] J. J. D. X. Ding, New 3D amino acid structure descriptors and its application to the polypeptide QSAR, Yaoxue Xuebao, vol. 40, pp.340-346, (2005).

[43] B. Hernández-Ledesma, A. Dávalos, B. Bartolomé, and L. Amigo, Preparation of Antioxidant Enzymatic Hydrolysates from a-Lactalbumin and b-Lactoglobulin. Identification of Active Peptides by HPLC-MSMS, J. Agric. Food Chem., vol. 53, p.588−593, (2005).

DOI: 10.1021/jf048626m

[44] B. Hernandez-Ledesma, L. Amigo, I. Recio, and B. Bartolome, ACE-Inhibitory and Radical-Scavenging Activity of Peptides Derived from β-Lactoglobulin f(19−25). Interactions with Ascorbic Acid, J. Agric. Food Chem. vol. 55, pp.3392-3397, 2007-04-06 (2007).

DOI: 10.1021/jf063427j

[45] G. Shen, B. Chahal, K. Majumder, S. J. You, and J. Wu, Identification of novel antioxidative peptides derived from a thermolytic Hydrolysate of ovotransferrin by LC-MS/MS, J. Agric. Food Chem., vol. 58, pp.7664-7672, (2010).

DOI: 10.1021/jf101323y

[46] E. R. Collantes and W. J. Dunn, Amino Acid Side Chain Descriptors for Quantitative Structure-Activity Relationship Studies of Peptide Analogs, J. Med. Chem., vol. 38, pp.2705-2713, 1995-07-01 (1995).

DOI: 10.1021/jm00014a022

[47] S. Wold, M. Sjöström and L. Eriksson, PLS-regression: A basic tool of chemometrics, Chemometr. Intell. Lab. Syst, vol. 58, pp.109-130, (2001).

DOI: 10.1016/s0169-7439(01)00155-1

[48] S. Wold, J. Trygg, A. Berglund, and H. Antti, Some recent developments in PLS modeling, Chemometr. Intell. Lab. Syst., vol. 58, pp.131-150, (2001).

DOI: 10.1016/s0169-7439(01)00156-3

[49] N. D. Tracy, J. C. Young and R. L. Mason, Multivariate Control Charts for Individual Observations, J. Qual. Technol., vol. 24, pp.88-95, (1992).

[50] R. Topp and G. Gómez, Residual analysis in linear regression models with an interval-censored covariate, Stat. Med., vol. 23, pp.3377-3391, (2004).

DOI: 10.1002/sim.1731

[51] R. D. M. Y. Brown, The information content of 2D and 3D structural descriptors relevant to ligand-receptor binding, Journal of Chemical Information and Computer Sciences, vol. 37, pp.1-9, (1997).

DOI: 10.1021/ci960373c

[52] D. J. B. C. Wild, Comparison of 2D Fingerprint Types and Hierarchy Level Selection Methods for Structural Grouping Using Ward's Clustering, J. Chem. Inform. Comput. Sci., vol. 40, pp.155-162, (2000).

DOI: 10.1021/ci990086j

[53] W. Jung, N. Rajapakse and S. Kim, Antioxidative activity of a low molecular weight peptide derived from the sauce of fermented blue mussel, Mytilus edulis, Eur. Food Res. Technol., vol. 220, pp.535-539, (2005).

DOI: 10.1007/s00217-004-1074-3