Quantitative structure-activity relationships for a series of inhibitors of cruzain from Trypanosoma cruzi: Molecular modeling, CoMFA and CoMSIA studies

Journal of Molecular Graphics and Modelling

Volumn 28, Issue 1, 2009, Pages 3-11

  Trossini, Gustavo H G ^a   Guido, Rafael V C ^a   Oliva, Glaucius ^a   Ferreira, Elizabeth I ^a   Andricopulo, Adriano D ^a  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

Chagas' disease; CoMFA; CoMSIA; Cruzain; Drug design

Indexed keywords

CHAGAS' DISEASE; COMFA; COMSIA; CRUZAIN; DRUG DESIGN;

BINDING ENERGY; BINDING SITES; DYES; ENZYME INHIBITION; HEALTH RISKS; MOLECULAR BIOLOGY; MOLECULAR GRAPHICS; MOLECULAR MODELING; MOLECULAR RECOGNITION; ORGANIC CHEMICALS; SULFUR COMPOUNDS; THREE DIMENSIONAL; TOXIC MATERIALS;

STRUCTURAL DESIGN;

ANTITRYPANOSOMAL AGENT; CRUZIPAIN; CYSTEINE PROTEINASE INHIBITOR; SEMICARBAZONE DERIVATIVE; THIOSEMICARBAZONE DERIVATIVE;

ARTICLE; CHAGAS DISEASE; COMPARATIVE MOLECULAR FIELD ANALYSIS; COMPARATIVE MOLECULAR SIMILARITY INDICES ANALYSIS; DRUG DESIGN; DRUG POTENCY; DRUG STRUCTURE; DRUG TARGETING; MOLECULAR DOCKING; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; TRYPANOSOMA CRUZI; TRYPANOSOMIASIS; X RAY CRYSTALLOGRAPHY;

ANIMALS; CHAGAS DISEASE; COMPUTATIONAL BIOLOGY; CYSTEINE ENDOPEPTIDASES; CYSTEINE PROTEINASE INHIBITORS; HUMANS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROTOZOAN PROTEINS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; REGRESSION ANALYSIS; TRYPANOSOMA CRUZI;

TRYPANOSOMA CRUZI;

EID: 69249202661     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2009.03.001     Document Type: Article

References (48)

1. WHO-World Health Organization, Technical Report Series, 2002.
2. A.M. Strosberg, K. Barrio, V.H. Stinger, J. Tashker, J.C. Wilbur, L. Wilson, K. Woo, Chagas disease: A Latin American Nemesis, Institute for OneWorld Health-IOWH, Technical Report, 2007, 1-110.
3. Sanders J.W., Fuhrer G.S., Johnson M.D., and Riddle M.S. The epidemiological transition: the current status of infectious diseases in the developed world versus the developing world. Sci. Prog. 91 (2008) 1-37
4. Molyneux D.H. Control of human parasitic diseases: context and overview. Adv. Parasitol. 61 (2006) 1-45
5. Pink R., Hudson A., Mouriès M.A., and Bendig M. Opportunities and challenges in antiparasitic drug discovery. Nat. Rev. Drug Discov. 9 (2005) 727-740
6. Nwaka S., and Ridley R.G. Virtual drug discovery and development for neglected diseases through public-private partnerships. Nat. Rev. Drug Discov. 11 (2003) 919-928
7. Nwaka S., and Hudson A. Innovative lead discovery strategies for tropical diseases. Nat. Rev. Drug Discov. 11 (2006) 941-955
8. Hotez P.J., Molyneux D.H., Fenwick A., Kumaresan J., Sachs S.E., Sachs J.D., and Savioli L. Control of neglected tropical diseases. N. Engl. J. Med. 357 (2007) 1018-1027
9. Turk B. Targeting proteases: successes, failures and future prospects. Nat. Rev. Drug Discov. 5 (2006) 785-799
10. Rosenthal P.J. Cysteine proteases of malaria parasites. Int. J. Parasitol. 34 (2004) 1489-1499
11. O'Brien T.C., Mackey Z.B., Fetter R.D., Choe Y., O'Donoghue A.J., Zhou M., Craik C.S., Caffrey C.R., and McKerrow J.H. A parasite cysteine protease is key to host protein degradation and iron acquisition. J. Biol. Chem. 283 (2008) 28934-28943
12. Mackey Z.B., O'Brien T.C., Greenbaum D.C., Blank R.B., and McKerrow J.H. A cathepsin B-like protease is required for host protein degradation in Trypanosoma brucei. J. Biol. Chem. 279 (2004) 48426-48433
13. Cazzulo J.J., Stoka V., and Turk V. Cruzipain, the major cysteine proteinase from the protozoan parasite Trypanosoma cruzi. Biol. Chem. 378 (1997) 1-10
14. Sajid M., and McKerrow J.H. Cysteine proteases of parasitic organisms. Mol. Biochem. Parasitol. 120 (2002) 1-21
15. Jia Z., Hasnain S., Hirama T., Lee X., Mort J.S., To R., and Huber C.P. Crystal structures of recombinant rat cathepsin B and a cathepsin B-inhibitor complex. Implications for structure-based inhibitor design. J. Biol. Chem. 270 (1995) 5527-5533
16. McKerrow J.H., Caffrey C., Kelly B., Loke P., and Sajid M. Proteases in parasitic diseases. Annu. Rev. Pathol. 1 (2006) 497-536
17. Brak K., Doyle P.S., McKerrow J.H., and Ellman J.A. Identification of a new class of nonpeptidic inhibitors of cruzain. J. Am. Chem. Soc. 130 (2008) 6404-6410
18. Guido R.V.C., Oliva G., and Andricopulo A.D. Virtual screening and its integration with modern drug design technologies. Curr. Med. Chem. 15 (2008) 37-46
19. Andricopulo A.D., Akoachere M.B., Krogh R., Nickel C., McLeish M.J., Kenyon G.L., Arscott L.D., Williams C.H., Davioud-Charvet E., and Becker K. Specific inhibitors of Plasmodium falciparum thioredoxin reductase as potential antimalarial agents. Bioorg. Med. Chem. Lett. 16 (2006) 2283-2292
20. Eckert H., and Bajorath J. Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches. Drug Discov. Today 12 (2007) 225-233
21. Salum L.B., Polikarpov I., and Andricopulo A.D. Structural and chemical basis for enhanced affinity and potency for a large series of estrogen receptor ligands: 2D and 3D QSAR studies. J. Mol. Graph. Modell. 26 (2007) 434-442
22. Guido R.V.C., Trossini G.H.G., Castilho M.S., Oliva G., Ferreira E.I., and Andricopulo A.D. Structure-activity relationships for a class of selective inhibitors of the major cysteine protease from Trypanosoma cruzi. J. Enz. Inhib. Med. Chem. 23 (2008) 964-973
23. Castilho M.S., Guido R.V.C., and Andricopulo A.D. 2D quantitative structure-activity relationship studies on a series of cholesteryl ester transfer protein inhibitors. Bioorg. Med. Chem. 15 (2007) 6242-6252
24. Castilho M.S., Guido R.V.C., and Andricopulo A.D. Classical and hologram QSAR studies on a series of tacrine derivatives as butyryleholinesterase inhibitors. Lett. Drug Des. Discov. 4 (2007) 106-113
25. Guido R.V.C., Castilho M.S., Mota S.G.R., Oliva G., and Andricopulo A.D. Classical and hologram QSAR studies on a series of inhibitors of trypanosomatid glyceraldehyde-3-phosphate dehydrogenase. QSAR Comb. Sci. 27 (2008) 768-781
26. Du X., Guo C., Hansell E., Doyle P.S., Caffrey C.R., Holler T.P., McKerrow J.H., and Cohen F.E. Synthesis and structure-activity relationship study of potent trypanocidal thio semicarbazone inhibitors of the trypanosomal cysteine protease cruzain. J. Med. Chem. 45 (2002) 2695-2707
27. Clark M., Cramer R.D., and Van Opdenbosch N. Validation of the general purpose Tripos 5.2 force field. J. Comput. Chem. 10 (1989) 982-1012
28. Powell M.J.D. Restart procedures for the conjugate gradient method. Math. Program. 12 (1977) 241-254
29. Gasteiger J., and Marsili M. Iterative partial equalization of orbital electronegativity-a rapid access to atomic charges. Tetrahedron 36 (1980) 3219-3228
30. Huang L., Brinen L.S., and Ellman J.A. Crystal structures of reversible ketone-based inhibitors of the cysteine protease cruzain. Bioorg. Med. Chem. 11 (2003) 21-29
31. Rarey M., Kramer B., Lengauer T., and Klebe G. A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol. 261 (1996) 470-489
32. Gohlke H., Hendlich M., and Klebe G. Knowledge-based scoring-function to predict protein-ligand interactions. J. Mol. Biol. 295 (2000) 337-356
33. ONLINE, version 0.9, 2008, available at: http://www.agklebe.de/.
34. Cramer R.D., Patterson D.E., and Bunce J.D. Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. J. Am. Chem. Soc. 110 (1988) 5959-5967
35. Cramer R.D., Patterson D.E., and Bunce J.D. Recent advances in comparative molecular field analysis (CoMFA). Prog. Clin. Biol. Res. 291 (1989) 161-165
36. Klebe G., Abraham U., and Mietzner T. Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity. J. Med. Chem. 37 (1994) 4130-4146
37. Klebe G., and Abraham U. Comparative molecular similarity index analysis (CoMSIA) to study hydrogen-bonding properties and to score combinatorial libraries. J. Comput. -Aided Mol. Des. 13 (1999) 1-10
38. Bush B.L., and Nachbar Jr. R.B. Sample-distance partial least squares: PLS optimized for many variables, with application to CoMFA. J. Comput. -Aided. Mol. Des. 7 (1993) 587-619
39. Guido R.V.C., Oliva G., Montanari C.A., and Andricopulo A.D. Structural basis for selective Inhibition of trypanosomatid glyceraldehyde-3-phosphate dehydrogenase: molecular docking and 3D QSAR studies. J. Chem. Inf. Model. 48 (2008) 918-929
40. Honório K.M., Garratt R.C., Polikarpov I., and Andricopulo A.D. 3D QSAR comparative molecular field analysis on nonsteroidal farnesoid X receptor activators. J. Mol. Graph. Modell. 25 (2007) 921-927
41. Moda T.L., Torres L.G., Carrara A.E., and Andricopulo A.D. PK/DB: database for pharmacokinetic properties and predictive in silico ADME models. Bioinformatics 24 (2008) 2270-2271
42. Davis A.M., Teague S.J., and Kleywegt G.J. Application and limitations of X-ray crystallographic data in structure-based ligand and drug design. Angew. Chem. Int. Ed. Engl. 42 (2003) 2718-2736
43. Salum L.B., Polikarpov I., and Andricopulo A.D. Structure-based approach for the study of estrogen receptor binding affinity and subtype selectivity. J. Chem. Inf. Model. 48 (2008) 2243-2253
44. Golbraikh A., and Tropsha A. Beware of q2!. J. Mol. Graphics Modell. 20 (2002) 269-276
45. Golbraikh A., Shen M., Xiao Z., Xiao Y.D., Lee K.H., and Tropsha A. Rational selection of training and test sets for the development of validated QSAR models. J. Comput. -Aided Mol. Des. 17 (2003) 241-253
46. Doweyko A.M. 3D-QSAR illusions. J. Comput. -Aided Mol. Des. 18 (2004) 587-596
47. AbdulHameed M.D., Hamza A., Liu J., and Zhan C.G. Combined 3D-QSAR modeling and molecular docking study on indolinone derivatives as inhibitors of 3-phosphoinositide-dependent protein kinase-1. J. Chem. Inf. Model. 48 (2008) 1760-1772
48. Andricopulo A.D., and Montanari C.A. Structure-activity relationships for the design of small-molecule inhibitors. Mini Rev. Med. Chem. 5 (2005) 585-593