New descriptors of amino acids and their application to peptide QSAR study

Peptides

Volumn 29, Issue 10, 2008, Pages 1798-1805

  Lin, Zhi hua ^a   Long, Hai xia ^a   Bo, Zhu ^b   Wang, Yuan qiang ^a   Wu, Yu zhang ^b  

^a CHONGQING UNIVERSITY OF TECHNOLOGY   (China)

^b THIRD MILITARY MEDICAL UNIVERSITY   (China)

Author keywords

Multiple linear regression; Peptide; Quantitative structure activity relationship; Structure parameterization

Indexed keywords

AMINO ACID; DIPEPTIDYL CARBOXYPEPTIDASE INHIBITOR; PEPTIDE;

AMINO ACID SEQUENCE; ARTICLE; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; QUANTITATIVE STRUCTURE ACTIVITY RELATION; VALIDATION PROCESS;

AMINO ACIDS; DIPEPTIDES; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; TASTE;

EID: 52049120108     PISSN: 01969781     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.peptides.2008.06.004     Document Type: Article

References (33)

1. Agüero-Chapín G., Gonzalez-Díaz H., de la Riva G., Rodríguez E., Sanchez-Rodríguez A., Podda G., et al. RI.MMM-QSAR recognition of ribonucleases without alignment: comparison with an HMM model and isolation from Schizosaccharomyces pombe, prediction, and experimental assay of a new sequence. J Chem Inf Model 48 2 (2008) 434-448
2. Agüero-Chapin G., González-Díaz H., Molina R., Varona-Santos J., Uriarte E., and González-Díaz Y. Novel 2D maps and coupling numbers for protein sequences. The first QSAR study of polygalacturonases; isolation and prediction of a novel sequence from Psidium guajava L. FEBS Lett 580 3 (2006) 723-730
3. Chakraborty S., Sengupta C., and Roy K. Comparative QSAR modeling of COX-2 inhibitor 1,2-diarylimidazoles using E-state and physicochemical parameters. J Biochem Biophys 44 (2007) 169-175
4. Collantes E.R., and Dunn W.J. Amino acid side chain descriptors for quantitative structure-activity relationship studies of peptide analogues. J Med Chem 38 (1995) 2705-2713
5. Colosi L.M., Huang Q., and Weber W.J. Validation of a two-parameter quantitative structure-activity relationship as a legitimate tool for rational re-design of horseradish peroxidase. J Biotechnol Bioeng 98 (2007) 295-299
6. González-Díaz H., González-Díaz Y., Santana L., Ubeira F.M., and Uriarte E. Proteomics, networks and connectivity indices. Proteomics 8 4 (2008) 750-778
7. González-Díaz H., Molina R., and Uriarte E. Recognition of stable protein mutants with 3D stochastic average electrostatic potentials. FEBS Lett 579 20 (2005) 4297-4301
8. González-Díaz H., Pérez-Castillo Y., Podda G., and Uriarte E. Computational chemistry comparison of stable/nonstable protein mutants classification models based on 3D and topological indices. J Comput Chem 28 12 (2007) 1990-1995
9. González-Díaz H., Sánchez-González A., and González-Díaz Y. 3D-QSAR study for DNA cleavage proteins with a potential anti-tumor ATCUN-like motif. J Inorg Biochem 100 7 (2006) 1290-1297
10. González-Díaz H., Saíz-Urra L., Molina R., González-Díaz Y., and Sánchez-González A. Computational chemistry approach to protein kinase recognition using 3D stochastic van der Waals spectral moments. J Comput Chem 28 6 (2007) 1042-1048
11. Gonzalez-Díaz H., Saiz-Urra L., Molina R., Santana L., and Uriarte E. A model for the recognition of protein kinases based on the entropy of 3D van der Waals interactions. J Proteome Res 6 2 (2007) 904-908
12. González-Díaz H., and Uriarte E. Proteins QSAR with Markov average electrostatic potentials. Bioorg Med Chem Lett 15 22 (2005) 5088-5094
13. González-Díaz H., Vilar S., Santana L., and Uriarte E. Medicinal chemistry and bioinformatics-current trends in drugs discovery with networks topological indices. Curr Top Med Chem 7 10 (2007) 1015-1029
14. Gupta A.K., Jain A., Jain A., Agrawal K., Saraswat V., Revathi S., et al. QSAR analysis of indazole estrogens as selective beta-estrogen receptor ligands: rationalization of physicochemical properties. J Med Chem 3 (2007) 347-353
15. Hellberg S., Eriksson L., Jonsson J., Lindgren F., Sjostrom M., Skagerberg B., et al. Minimum analogue peptide sets (MAPS) for quantitative structure-activity relationships. J Int Pept Protein Res 37 (1991) 414-418
16. Hellberg S., Sjostrom M., Skagerberg B., and Wold S. Peptide quantitative structure-activity relationships, a multivariate approach. J Med Chem 30 (1987) 1126-1135
17. Hellberg S., Sjostrom M., and Wold S. The prediction of bradykinin potentiating potency of pentapeptides. An example of a peptide quantitative structure-activity relationship. J Acta Chem Scand 40 (1986) 135-139
18. Jonsson J., Eriksson L., Hellberg S., Sjoestroem M., and Wold S. A multivariate approach to saccharide quantitative structure-activity relationships exemplified by two series of 9-hydroxyellipticine glycosides. J Acta Chem Scand 43 (1989) 286-293
19. Kidera A., konishi Y., Oka M., Ooi T., and Scheraga H. Statistical analysis of the physical properties of the 20 naturally occurring amino acids. J Protein Chem 4 (1985) 23-55
20. Kuz'min V.E., Artemenko A.G., Muratov E.N., Volineckaya I.L., Makarov V.A., Riabova O.B., et al. Quantitative structure-activity relationship studies of [(biphenyloxy) propyl] isoxazole derivatives Inhibitors of human rhinovirus replication. J Med Chem 50 (2007) 4205-4213
21. Li Y., Pan D., Liu J., Kern P.S., Gerberick G.F., Hopfinger A.J., et al. Categorical QSAR models for skin sensitization based upon local lymph node assay classification measures. Part 2. 4D-fingerprint three-state and two-2-state logistic regression models. J Toxicol Sci 99 (2007) 532-544
22. Liu S.S., Yin C.S., Li Z.L., and Cai S.X. QSAR study of steroid benchmark and dipeptides based on MEDV-13. J Chem Inf Comput Sci 41 2 (2001) 321-329
23. Nakai K., Kidera A., and Kanehisa M. Cluster analysis of amino acid indices for prediction of protein structure and function. J Protein Eng 2 (1988) 93-100
24. Raevsky O.A. Conformation of 18-Crown-5 and its influence on complexation with alkali and ammonium cations: why 18-Crown-5 binds more than 1000 times weaker than 18C6. J Phys Org Chem 10 (1997) 405-412
25. Ramos de Armas R., González-Díaz H., Molina R., Pérez-González M., and Uriarte E. Stochastic-based descriptors studying peptides biological properties: modeling the bitter tasting threshold of dipeptides. Bioorg Med Chem 12 (2004) 4815-4822
26. Raychaudhury C., Banerjee A., Bag P., and Roy S. Topological shape and size of peptides: identification of potential allele specific helper T cell antigenic sites. J Chem Inf Comput Sci 39 (1999) 248-254
27. Rose G.D., Geslowitz A.R., Lesser G.J., Lee R.H., and Zahfus. Hydrophobicity of amino acid residues in globular proteins. Science 229 (1985) 834-838
28. Sachan N., Kadam S.S., and Kulkarni V.M. Human protein tyrosine phosphatase 1B inhibitors: QSAR by genetic function approximation. J Enzyme Inhib Med Chem 22 (2007) 267-76, 371-3
29. Sciabola S., Carosati E., Cucurull-Sanchez L., Baroni M., and Mannhold R. Novel TOPP descriptors in 3D-QSAR analysis of apoptosis inducing 4-aryl-4H-chromenes: comparison versus other 2D- and 3D-descriptors. J Bioorg Med Chem 15 (2007) 6450-6462
30. Toropov A.A., and Benfenati E. SMILES in QSPR/QSAR modeling: results and perspectives. J Curr Drug Discov Technol 4 (2007) 77-116
31. Wold S., Eriksson L., Hellberg S., Jonsson J., Sjoestroem M., Skagerberg B., et al. Can peptide quantitative structure-activity relationships, a multivariate approach. J Med Chem 30 (1987) 1126-1130
32. Wu J., Aluko R.E., and Nakai S. Structural requirements of angiotensin I-converting enzyme inhibitory peptides: quantitative structure-and-activity relationship study of di- and tri-peptides. J Agric Food Chem 54 (2006) 732-738
33. Zaliani A., Gromo G., Pinori M., and Mascagni P. Rational design of a new C-myristylamido peptide exerting potent and selective PKC inhibitory activity. J Drug Des Disco 13 (1996) 63-74