Inhibitor-based validation of a homology model of the active-site of tripeptidyl peptidase II

Journal of Molecular Graphics and Modelling

Volumn 23, Issue 5, 2005, Pages 409-418

  De Winter, Hans ^a   Breslin, Henry ^a   Miskowski, Tamara ^a   Kavash, Robert ^a   Somers, Marijke ^a  

^a JANSSEN RESEARCH AND DEVELOPMENT   (Belgium)

Author keywords

Active site; Butabindide; Homology modeling; Inhibitors; Obesity; Structure based drug design; TPP II

Indexed keywords

CRYSTAL STRUCTURE; DRUG DOSAGE; POLYPEPTIDES; PRODUCT DESIGN;

HOMOLOGY MODELS; PHARMACOPHORE; STRUCTURE-BASED DRUG DESIGN;

ENZYME INHIBITION;

BUTABINDIDE; ENZYME INHIBITOR; PEPTIDASE; SUBTILISIN; TRIPEPTIDYL PEPTIDASE 2 INHIBITOR; TRIPEPTIDYL PEPTIDASE II; UNCLASSIFIED DRUG;

ARTICLE; CORRELATION ANALYSIS; CRYSTAL STRUCTURE; DRUG DESIGN; ENZYME ACTIVE SITE; PHARMACOPHORE; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; STRUCTURE ACTIVITY RELATION; VALIDATION PROCESS;

AMINO ACID SEQUENCE; CATALYTIC DOMAIN; COMPUTER GRAPHICS; COMPUTER SIMULATION; DRUG DESIGN; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; SEQUENCE HOMOLOGY, AMINO ACID; SERINE ENDOPEPTIDASES; SERINE PROTEINASE INHIBITORS; SINCALIDE; STRUCTURE-ACTIVITY RELATIONSHIP; THERMODYNAMICS;

EID: 15244345068     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2004.11.009     Document Type: Article

References (29)

1. I. Wickelgren Obesity, how big a problem? Science 280 1998 1364 1367
2. J.-A. Fernandez-Lopez, X. Remesar, M. Foz, and M. Alemany Pharmacological approaches for the treatment of obesity Drugs 62 2002 915 944
3. H. Hauner Current pharmacological approaches to the treatment of obesity Int. J. Obesity 25 2001 102 106
4. I.L. Mertens, and L.F. Van Gaal Promising new approaches to the management of obesity Drugs 60 2000 1 9
5. C.P. Kordik, and A.B. Reitz Pharmacological treatment of obesity: therapeutic strategies J. Med. Chem. 42 1999 181 201
6. C. Rose, F. Vargas, P. Facchinetti, P. Bourgeat, R.B. Bambal, P.B. Bishop, S.M.T. Chan, A.N.J. Moore, C.R. Ganellin, and J.-C. Schwartz Characterization and inhibition of a cholecystokinin-inactivating serine protease Nature 380 1996 403 409
7. R.-M. Bålöw, U. Ragnarsson, and Ö. Zetterqvist Tripeptidyl aminopeptidase in the extralysosomal fraction of rat liver J. Biol. Chem. 258 1983 11622 11628
8. B. Tomkinson Nucleotide sequence of cDNA covering the N-terminus of human tripeptidyl peptidase II Biomed. Biochim. Acta 50 1991 4 6
9. R.-M. Bålöw, and I. Eriksson Tripeptidyl peptidase II in haemolysates and liver homogenates of various species Biochem. J. 241 1987 75 80
10. B. Tomkinson Tripeptidyl peptidases: enzymes that count TIBS 24 1999 355 359
11. C.R. Ganellin, P.B. Bishop, R.B. Bambal, S.M.T. Chan, J.K. Law, B. Marabout, P.M. Luthra, A.N.J. Moore, O. Peschard, P. Bourgeat, C. Rose, F. Vargas, and J.-C. Schwartz Inhibitors of tripeptidyl peptidase II. 2. Generation of the first novel lead inhibitor of cholecystokinin-8-inactivating peptidase: a strategy for the design of peptidase inhibitors J. Med. Chem. 43 2000 664 674
12. H.J. Breslin, T.A. Miskowski, M.J. Kukla, W.H. Leister, H.L. De Winter, D.A. Gauthier, M.V.F. Somers, D.C.G. Peeters, and P.W.M. Roevens Design, synthesis, and tripeptidyl peptidase II inhibitory activity of a novel series of (S)-2,3-dihydro-2-(4-alkyl-1H-imidazol-2-yl)-1H-indoles J. Med. Chem. 45 2002 5303 5310
13. H.J. Breslin, T.A. Miskowski, M.J. Kukla, H.L. De Winter, M.V.F. Somers, P.W.M. Roevens, and R.W. Kavash Tripeptidyl-peptidase II (TPP II) inhibitory activity of (S)-2,3-dihydro-2-(1H-imidazol-2-yl)-1H-indoles, a systematic SAR evaluation. Part 2 Bioorg. Med. Chem. Lett. 13 2003 4467 4471
14. B. Tomkinson, and A.-K. Jonsson Characterization of cDNA for human tripeptidyl peptidase II: the N-terminal part of the enzyme is similar to subtilisin Biochemistry 30 1991 168 174
15. B. Tomkinson, C. Wernstedt, U. Hellman, and Ö. Zetterqvist Active site of tripeptidyl peptidase II from human erythrocytes is of the subtilisin type Proc. Natl. Acad. Sci. U.S.A. 84 1987 7508 7512
16. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weiss, I.N. Shindylov, and P.E. Bourne The protein data bank Nucleic Acids Res. 28 2000 235 242
17. P.A. Fitzpatrick, A.C. Steinmetz, D. Ringe, and A.M. Klibanov Enzyme crystal structure in a neat organic solvent Proc. Natl. Acad. Sci. U.S.A. 90 1993 8653 8657
18. R. Bott, M. Ultsch, A. Kossiakoff, T. Graycar, B. Katz, and S. Power The three-dimensional structure of Bacillus amyloliquefaciens subtilisin at 1.8 å and an analysis of the structural consequences of peroxide inactivation J. Biol. Chem. 263 1988 7895 7906
19. P. Gros, K.H. Kalk, and W.G.J. Hol Calcium binding to thermitase. Crystallographic studies of thermitase at 0, 5, and 100 mM calcium J. Biol. Chem. 266 1991 2953 2961
20. A. Mueller, W. Hinrichs, W.M. Wolf, and W. Saenger Crystal structure of calcium-free proteinase K at 1.5 å resolution J. Biol. Chem. 269 1994 23108 23111
21. J. Wojcik, J.P. Mornon, and J. Chomilier New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification J. Mol. Biol. 289 1999 1469 1490
22. B. Das, and H. Meirovitch Solvation parameters for predicting the structure of surface loops in proteins: transferability and entropic effects Proteins 51 2003 470 483
23. H.W.T. van Vlijmen, and M. Karplus PDB-based protein loop prediction: parameters for selection and methods for optimization J. Mol. Biol. 267 1997 975 1001
24. M.J. Dudek, and H.A. Scheraga Protein structure prediction using a combination of sequence homology and global energy minimization. I. Global energy minimization of surface loops J. Comput. Chem. 11 1990 121 151
25. T. Blundell, D. Carney, S. Gardner, F. Hayes, B. Howlin, T. Hubbard, J. Overington, D.A. Singh, B.L. Sibamda, and M. Sutcliffe Knowledge-based protein modeling and design Eur. J. Biochem. 172 1988 513 520
26. M. Das Bedamati Solvation parameters for predicting the structure of surface loops in proteins: transferability and entropic effects Proteins 51 2003 470 483
27. A. Salî, and T.L. Blundell Comparative protein modeling by satisfaction od spatial restraints J. Mol. Biol. 234 1993 779 815
28. G. Jones, P. Willett, R.C. Glen, A.R. Leach, and R. Taylor Development and validation of a genetic algorithm for flexible docking J. Mol. Biol. 267 1997 727 748
29. P.J. Goodford A computational procedure for determining energetically favorable binding sites on biologically important macromolecules J. Med. Chem. 28 1985 849 857