Homology modeling and receptor-based 3D-QSAR study of carbonic anhydrase IX

Journal of Chemical Information and Modeling

Volumn 47, Issue 6, 2007, Pages 2253-2262

  Tuccinardi, Tiziano ^a   Ortore, Gabriella ^a   Rossello, Armando ^a   Supuran, Claudiu T ^b   Martinelli, Adriano ^a  

^a UNIVERSITY OF PISA   (Italy)

^b UNIVERSITY OF FLORENCE   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; COMPUTATIONAL METHODS; COMPUTER SOFTWARE; CRYSTAL STRUCTURE; MATHEMATICAL MODELS; TUMORS;

ALIGNMENT TOOL; CARBONIC ANHYDRASE; CATALYTIC DOMAIN; COMPUTATIONAL STRATEGY;

ENZYMES;

CARBONATE DEHYDRATASE; CARBONATE DEHYDRATASE INHIBITOR; ISOENZYME; LIGAND;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CLASSIFICATION; COMPUTER SIMULATION; HUMAN; METABOLISM; MOLECULAR GENETICS; MOUSE; NUCLEOTIDE SEQUENCE; QUANTITATIVE STRUCTURE ACTIVITY RELATION; SEQUENCE ALIGNMENT; STRUCTURAL HOMOLOGY; SURFACE PROPERTY; THREE DIMENSIONAL IMAGING; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; ANIMALS; CARBONIC ANHYDRASE INHIBITORS; CARBONIC ANHYDRASES; COMPUTER SIMULATION; CONSERVED SEQUENCE; CRYSTALLOGRAPHY, X-RAY; HUMANS; IMAGING, THREE-DIMENSIONAL; ISOENZYMES; LIGANDS; MICE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; SEQUENCE ALIGNMENT; STRUCTURAL HOMOLOGY, PROTEIN; SURFACE PROPERTIES;

EID: 37249040921     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci700214j     Document Type: Article

References (50)

1. Sly, W. S.; Hu, P. Y. Human carbonic anhydrases and carbonic anhydrase deficiencies. Annu. Rev. Biochem. 1995, 64, 375-401.
2. Scozzafava, A.; Mastrolorenzo, A.; Supuran, C. T. Carbonic anhydrase inhibitors and activators and their use in therapy. Expert Opin. Ther. Pat. 2006, 16, 1627-1664.
3. Hilvo, M.; Tolvanen, M.; Clark, A.; Shen, B.; Shah, G. N.; Waheed, A.; Halmi, P.; Hanninen, M.; Hamalainen, J. M.; Vihinen, M.; Sly, W. S.; Parkkila, S. Characterization of CA XV, a new GPI-anchored form of carbonic anhydrase. Biochem. J. 2005, 392, 83-92.
4. Supuran, C. T.; Scozzafava, A.; Casini, A. Carbonic anhydrase inhibitors. Med. Res. Rev. 2003, 23, 146-189.
5. Supuran, C. T. Carbonic anhydrase inhibitors in the treatment and prophylaxis of obesity. Expert Opin. Ther. Pat. 2003, 13, 1545-1550.
6. Winum, J. Y.; Scozzafava, A.; Montero, J. L.; Supuran, C. T. Sulfamates and their therapeutic potential. Med. Res. Rev. 2005, 25, 186-228.
7. Cecchi, A.; Hulikova, A.; Pastorek, J.; Pastorekova, S.; Scozzafava, A.; Winum, J. Y.; Montero, J. L.; Supuran, C. T. Carbonic anhydrase inhibitors. Design of fluorescent sulfonamides as probes of tumorassociated carbonic anhydrase IX that inhibit isozyme IX-mediated acidification of hypoxic tumors. J. Med. Chem. 2005, 48, 4834-4841.
8. Tureci, O.; Sahin, U.; Vollmar, E.; Siemer, S.; Gotten, E.; Seitz, G.; Parkkila, A. K.; Shah, G. N.; Grubb, J. H.; Pfreundschuh, M.; Sly, W. S. Human carbonic anhydrase XII: cDNA cloning, expression, and chromosomal localization of a carbonic anhydrase gene that is overexpressed in some renal cell cancers. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 7608-7613.
9. Thiry, A.; Dogne, J. M.; Masereel, B.; Supuran, C. T. Targeting tumorassociated carbonic anhydrase IX in cancer therapy. Trends Pharmacol. Sci. 2006, 27, 566-573.
10. Pastorekova, S.; Parkkila, S.; Pastorek, J.; Supuran, C. T. Carbonic anhydrases: current state of the art, therapeutic applications and future prospects. J. Enzyme Inhib. Med. Chem. 2004, 19, 199-229.
11. Vicker, N.; Ho, Y.; Robinson, J.; Woo, L. L.; Purohit, A.; Reed, M. J.; Potter, B. V. Docking studies of sulphamate inhibitors of estrone sulphatase in human carbonic anhydrase II. Bioorg. Med. Chem. Lett. 2003, 13, 863-865.
12. Ho, Y. T.; Purohit, A.; Vicker, N.; Newman, S. P.; Robinson, J. J.; Leese, M. P.; Ganeshapillai, D.; Woo, L. W.; Potter, B. V.; Reed, M. J. Inhibition of carbonic anhydrase II by steroidal and non-steroidal sulphamates. Biochem. Biophys. Res. Commun. 2003, 305, 909-914.
13. Gruneberg, S.; Wendt, B.; Klebe, G. Subnanomolar Inhibitors from Computer Screening: A Model Study Using Human Carbonic Anhydrase II. Angew. Chem., Int. Ed. Engl. 2001, 40, 389-393.
14. Gruneberg, S.; Stubbs, M. T.; Klebe, G. Successful virtual screening for novel inhibitors of human carbonic anhydrase: strategy and experimental confirmation. J. Med. Chem. 2002, 45, 3588-3602.
15. Clare, B. W.; Supuran, C. T. QSAR studies of sulfonamide carbonic anhydrase inhibitors. In Carbonic Anhydrase, its Inhibitors and Activators; Supuran, C. T., Scozzafava, A., Conway, J., Eds.; CRC Press: 2004; pp 149-182.
16. Agrawal, V. K.; Singh, J.; Khadikar, P. V.; Supuran, C. T. QSAR study on topically acting sulfonamides incorporating GABA moieties: a molecular connectivity approach. Bioorg. Med. Chem. Lett. 2006, 16, 2044-2051.
17. Thakur, A.; Thakur, M.; Khadikar, P. V.; Supuran, C. T.; Sudele, P. QSAR study on benzenesulphonamide carbonic anhydrase inhibitors: topological approach using Balaban index. Bioorg. Med. Chem. 2004, 12, 789-793.
18. Hillebrecht, A.; Supuran, C. T.; Klebe, G. Integrated approach using protein and ligand information to analyze selectivity- and affinitydetermining features of carbonic anhydrase isozymes. Chem. Med. Chem. 2006, 1, 839-853.
19. Weber, A.; Bohm, M.; Supuran, C. T.; Scozzafava, A.; Sotriffer, C. A.; Klebe, G. 3D QSAR Selectivity Analyses of Carbonic Anhydrase Inhibitors: Insights for the Design of Isozyme Selective Inhibitors. J. Chem. Inf. Model. 2006, 46, 2737-2760.
20. Huang, H.; Pan, X.; Tan, N.; Zeng, G.; Ji, C. 3D-QSAR study of sulfonamide inhibitors of human carbonic anhydrase II. Eur. J. Med. Chem. 2007, 42, 365-372.
21. Tuccinardi, T.; Nuti, E.; Ortore, G.; Supuran, C. T.; Rossello, A.; Martinelli, A. Analysis of human carbonic anhydrase II: docking reliability and receptor-based 3D-QSAR study. J. Chem. Inf. Model. 2007, 47, 515-525.
22. Thiry, A.; Ledecq, M.; Cecchi, A.; Dogne, J. M.; Wouters, J.; Supuran, C. T.; Masereel, B. Indanesulfonamides as carbonic anhydrase inhibitors. Toward structure-based design of selective inhibitors of the tumor-associated isozyme CA IX. J. Med. Chem. 2006, 49, 2743-2749.
23. Alterio, V.; Vitale, R. M.; Monti, S. M.; Pedone, C.; Scozzafava, A.; Cecchi, A.; De Simone, G.; Supuran, C. T. Carbonic anhydrase inhibitors: X-ray and molecular modeling study for the interaction of a fluorescent antitumor sulfonamide with isozyme II and IX. J. Am. Chem. Soc. 2006, 128, 8329-8335.
24. Jaiswal, M.; Khadikar, P. V.; Scozzafava, A.; Supuran, C. T. Carbonic anhydrase inhibitors: the first QSAR study on inhibition of tumorassociated isoenzyme IX with aromatic and heterocyclic sulfonamides. Bioorg. Med. Chem. Lett. 2004, 14, 3283-3290.
25. Gasteiger, E.; Gattiker, A.; Hoogland, C.; Ivanyi, I.; Appel, R. D.; Bairoch, A. ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 2003, 57, 3784-3788.
26. Altschul, S. F.; Madden, T. L.; Schäffer, A. A.; Zhang, J.; Zhang, Z.; Miller, W.; Lipman, D. J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25, 3389-3402.
27. Whittington, D. A.; Grubb, J. H.; Waheed, A.; Shah, G. N.; Sly, W. S.; Christianson, D. W. Expression, assay, and structure of the extracellular domain of murine carbonic anhydrase XIV: implications for selective inhibition of membrane-associated isozymes. J. Biol. Chem. 2004, 279, 7223-7228.
28. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank. Nucl. Acids Res. 2000, 28, 235-242.
29. Thompson, J. D.; Higgins, D. G.; Gibson, T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22, 4673-4680.
30. Fiser, A.; Do, R. K.; Sali, A. Modeling of loops in protein structures. Protein Sci. 2000, 9, 1753-1773.
31. Laskowski, R. A.; MacArthur, M. W.; Moss, D. S.; Thorton, J. M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 1993, 26, 283-291.
32. Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Merz, K. M.; Pearlman, D. A.; Crowley, M.; Walker, R. C.; Zhang, W.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Wong, K. F.; Paesani, F.; Wu, X.; Brozell, S.; Tsui, V.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Beroza, P.; Mathews, D. H.; Schafmeister, C.; Ross, W. S.; Kollman, P. A. AMBER 9; University of California: San Francisco, CA, 2006.
33. Merz, K. M., Jr; Murcko, M. A.; Kollman, P. A. Inhibition of Carbonic Anhydrase. J. Am. Chem. Soc. 1991, 113, 4484-4490.
34. Essman, U.; Perela, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. A smooth particle mesh Ewald method. J. Chem. Phys. 1995, 103, 8577-8592.
35. Maestro, version 7.5; Schrödinger Inc.: Portland, OR, 1999.
36. Macromodel, version 8.5; Schrödinger Inc.: Portland, OR, 1999.
37. QuACPAC 1.1; OpenEye Scientific Software Inc.: 9 Bisbee Ct, Suite D, Santa Fe, NM 87508, 2007.
38. Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 1997, 267, 727-748.
39. Nair, S. K.; Krebs, J. F.; Christianson, D. W.; Fierke, C. A. Structural basis of inhibitor affinity to variants of human carbonic anhydrase II. Biochemistry 1995, 34, 3981-3989.
40. GOLPE 4.5; Multivariate Infometric Analysis Srl.: Viale dei Castagni 16, Perugia, Italy, 1999.
41. GRID version 22a; Molecular Discovery Ltd.: West Way House, Elms Parade, Oxford, U.K., 2004.
42. Puccetti, L.; Fasolis, G.; Vullo, D.; Chohan, Z. H.; Scozzafava, A.; Supuran, C. T. Carbonic anhydrase inhibitors. Inhibition of cytosolic/ tumor-associated carbonic anhydrase isozymes I, II, IX, and XII with Schiffs bases incorporating chromone and aromatic sulfonamide moieties, and their zinc complexes. Bioorg. Med. Chem. Lett. 2005, 15, 3096-3101.
43. Wilkinson, B. L.; Bornaghi, L. F.; Houston, T. A.; Innocenti, A.; Vullo, D.; Supuran, C. T.; Poulsen, S. A. Carbonic anhydrase inhibitors: inhibition of isozymes I, II, and IX with triazole-linked O-glycosides of benzene sulfonamides. J. Med. Chem. 2007, 50, 1651-1657.
44. Pastor, M.; Cruciani, G.; Clementi, S. Smart region definition: a new way to improve the predictive ability and interpretability of three-dimensional quantitative structure-activity relationships. J. Med. Chem. 1997, 40, 1455-1464.
45. Rush, T. S.; Grant, J. A.; Mosyak, L.; Nicholls, A. A Shape-Based 3-D Scaffold Hopping Method and its Application to a Bacterial Protein-Protein Interaction. J. Med. Chem. 2005, 48, 1489-1495.
46. Boström, J.; Greenwood, J. R.; Gottfries, J. Assessing the performance of OMEGA with respect to retrieving bioactive conformations. J. Mol. Graphics Modell. 2003, 21, 449-462.
47. Garaj, V.; Puccetti, L.; Fasolis, G.; Winum, J. Y.; Montero, J. L.; Scozzafava, A.; Vullo, D.; Innocenti, A.; Supuran, C. T. Carbonic anhydrase inhibitors: novel sulfonamides incorporating 1,3,5-triazine moieties as inhibitors of the cytosolic and tumour-associated carbonic anhydrase isozymes I, II and IX. Bioorg. Med. Chem. Lett. 2005, 15, 3102-3108.
48. Winum, J. Y.; Dogne, J. M.; Casini, A.; de Levai, X.; Montero, J. L.; Scozzafava, A.; Vullo, D.; Innocenti, A.; Supuran, C. T. Carbonic anhydrase inhibitors: synthesis and inhibition of cytosolic/membrane-associated carbonic anhydrase isozymes I, II, and DC with sulfonamides incorporating hydrazino moieties. J. Med. Chem. 2005, 48, 2121-2125.
49. Wilkinson, B. L.; Bornaghi, L. F.; Houston, T. A.; Innocenti, A.; Supuran, C. T.; Poulsen, S. A. A novel class of carbonic anhydrase inhibitors: glycoconjugate benzene sulfonamides prepared by "clicktailing". J. Med. Chem. 2006, 49, 6539-6548.
50. Saczewski, F.; Slawinski, J.; Kornicka, A.; Brzozowski, Z.; Pomarnacka, E.; Innocenti, A.; Scozzafava, A.; Supuran, C. T. Carbonic anhydrase inhibitors. Inhibition of the cytosolic human isozymes I and II, and the transmembrane, tumor-associated isozymes IX and XII with substituted aromatic sulfonamides activatable in hypoxic tumors. Bioorg. Med. Chem. Lett. 2006, 16, 4846-4851.