Molecular modeling on pyruvate phosphate dikinase of Entamoeba histolytica and in silico virtual screening for novel inhibitors

Journal of Computer-Aided Molecular Design

Volumn 22, Issue 9, 2008, Pages 647-660

  Stephen, Preyesh ^a   Vijayan, Ramachandran ^a   Bhat, Audesh ^a   Subbarao, N ^a   Bamezai, R N K ^a  

^a JAWAHARLAL NEHRU UNIVERSITY   (India)

Author keywords

Amoebiasis; Drug designing; Entamoeba histolytica; Homology modeling; Interaction study; Pyruvate phosphate dikinase (PPDK); Small molecule library; Virtual screening

Indexed keywords

BIOLOGY; DIGITAL LIBRARIES; ENZYME ACTIVITY; MOLECULES;

AMEBIASIS; DRUG DESIGNING; ENTAMOEBA HISTOLYTICA; HOMOLOGY MODELING; IN-SILICO; INTERACTION STUDIES; PYRUVATE PHOSPHATE DIKINASE; SMALL-MOLECULE LIBRARY; VIRTUAL SCREENING;

LIGANDS;

(1 BENZENESULFONYLPYRROLIDIN 2 YL)(3,5 DIMETHYL 4 TOLYLSULFANYLPYRAZOL 1 YL)METHANONE; (7 BENZYL 3 METHYL 2,6 DIOXO 2,3,6,7 TETRAHYDRO 1H PURIN 8 YLSULFANYL)ACETIC ACID BENZYL ESTER; 2 (1 BENZYL 1H BENZOIMIDAZOL 2 YLMETHYLSULFANYL) 3H QUINAZOLIN 4 ONE; 2 (1H BENZOIMIDAZOL 2 YLSULFANYL) N (5 PHENYL[1,3,4]THIADIAZOL 2 YL)ACETAMIDE; 2 (1H BENZOIMIDAZOL 2 YLSULFANYL) N [4 (PYRIDIN 2 YLSULFAMOYL)PHENYL]ACETAMIDE; 2 (9 ALLYL 9H 1,3,4,9 TETRAAZAFLUOREN 2 YLSULFANYL) N (5 METHYLISOXAZOL 3 YL)BUTYRAMIDE; 2 (9 BENZYL 9H 1,3,4,9 TETRAAZAFLUOREN 2 YLSULFANYL) N FURAN 2 YLMETHYLACETAMIDE; 2 BENZYLSUFLANYL N [5 (3,4 DICHLOROBENZYL)[1,3,4]THIADIAZOL 2 YL]ACETAMIDE; 2 [2 (1 BENZYL 1H BENZOIMIDAZOL 2 YLSULFANYLMETHYL)BENZOIMIDAZOL 1 YL]ACETAMIDE; 3 (2,6 DICHLOROPHENYL) 5 METHYLISOXAZOLE 4 CARBOXYLIC ACID 4 (6 AMINO 5 CYANO 3 METHYL 1,4 DIHYDROPYRANO[2,3 C]PYRAZOL 4 YL)PHENYL ESTER; 4 CHLORO N [2 (1 PHENYL 1H TETRAZOL 5 YLSULFANYL)ACENAPHTHEN 1 YL]BENZENESULFONAMIDE; 4 [4 HYDROXY 5 OXO 2 (3 PHENOXYPHENYL) 1 PYRIDIN 3 YLMETHYL 2,5 DIHYDRO 1H PYRROLE 3 CARBONYL] N,N DIMETHYLBENZENESULFONAMIDE; 5 BENZYL 2 (4 CHLOROPHENYL) 3 (4 FLUOROPHENYL)TETRAHYDROPYRROLO[3,4 D]ISOXAZOLE 4,6 DIONE; 5 PHENYL 2 [2 ([1,2,4]TRIAZOLO[4,3 A]PYRIDIN 3 YLSULFANYL)ACETYLAMINO]THIOPHENE 3 CARBOXYLIC ACID ETHYL ESTER; 6 (4 BENZYL 5 PHENYL 4H[1,2,4]TRIAZOL 3 YLSULFANYLMETHYL) N PHENYL[1,3,5]TRIAZINE 2,4 DIAMINE; 6 [5 (2 CHLOROPHENYL) 4 PHENYL 4H[1,2,4]TRIAZOL 3 YLSULFANYLMETHYL] N PHENYL[1,3,5]TRIAZINE 2,4 DIAMINE; ARGININE; ASPARTIC ACID; GLUTAMIC ACID; GLUTAMINE; LYSINE; N (3 CYANO 4,5 DIPHENYLDURAN 2 YL) 2 (1,3 DIOXO 1,3 DIHYDROISOINDOL 2 YL)ACETAMIDE; N (3 CYANO 4,5 DIPHENYLFURAN 2 YL) 4 (1,3 DIOXO 1,3 DIHYDROISOINDOL 2 YL)BUTYRAMIDE; N [5 (3 CHLOROBENZYL)THIAZOL 2 YL] 3 [5 (2 METHYLCYCLOPROPYL)FURAN 2YL]PROPIONAMIDE; PHOSPHOTRANSFERASE INHIBITOR; PYRUVATE PHOSPHATE DIKINASE; PYRUVATE PHOSPHATE DIKINASE INHIBITOR; TRANSFERASE INHIBITOR; UNINDEXED DRUG; [3 METHYL 7 (3 METHYLBENZYL) 2,6 DIOXO 2,3,6,7 TETRAHYDRO 1H PURIN 8 YLSULFANYL]ACETIC ACID BENZYL ESTER;

AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; COMPUTER MODEL; COMPUTER PREDICTION; COMPUTER PROGRAM; CONTROLLED STUDY; DATA BASE; DRUG DESIGN; DRUG RESEARCH; DRUG SCREENING; DRUG STRUCTURE; DRUG TARGETING; ENTAMOEBA HISTOLYTICA; ENZYME ACTIVE SITE; ENZYME INHIBITION; ENZYME STRUCTURE; GENETIC ALGORITHM; MOLECULAR DOCKING; MOLECULAR MODEL; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SCORING SYSTEM; SEQUENCE HOMOLOGY; STEREOCHEMISTRY; VIRTUAL REALITY;

EID: 50249121995     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-007-9130-2     Document Type: Article

References (48)

1. Walsh JA (1986) Rev Infect Dis 8:228
2. Spinella S, Levavasseur E, Petek F, Rigothier MC (1999) Eur J Biochem 266:170
3. http://www.who.int/entity/vaccine_research/documents/ Parasitic_Diseases.pdf
4. Petri WA Jr (2003) Trends Parasitol 19:523
5. Samarawickrema NA, Brown DM, Upcroft JA, Thammapalerd N, Upcroft P (1997) J Antimicrob Chemother 40:833
6. Que X, Brinen LS, Perkins P, Herdman S, Hirata K, Torian BE, Rubin H, McKerrow JH, Reed SL (2002) Mol Biochem Parasitol 119:23
7. de Meester F, Shaw E, Scholze H, Stolarsky T, Mirelman D (1990) Infect Immun 58:1396
8. Byington CL, Dunbrack RL Jr, Whitby FG, Cohen FE, Agabian N (1997) Exp Parasitol 87:194
9. Reeves RE (1984) Adv Parasitol 23:105
10. McLaughlin J, Aley S (1985) J Protozool 32:221
11. Saavedra E, Encalada R, Pineda E, Jasso-Chavez R, Moreno-Sanchez R (2005) FEBS J 272:1767
12. Saavedra-Lira E, Perez-Montfort R (1996) Arch Med Res 27:257
13. Cosenza LW, Bringaud F, Baltz T, Vellieux FM (2000) Acta Crystallogr D Biol Crystallogr 56:1688
14. Wood HG, O'Brien EW, Micheales G (1977) Adv Enzymol Relat Areas Mol Biol 45:85
15. Herzberg O, Chen CC, Kapadia G, McGuire M, Carroll LJ, Noh SJ, Dunaway-Mariano D (1996) Proc Natl Acad Sci USA 93:2652
16. Ye D, Wei M, McGuire M, Huang K, Kapadia G, Herzberg O, Martin BM, Dunaway-Mariano D (2001) J Biol Chem 276:37630
17. Thrall SH, Dunaway-Mariano D (1994) Biochemistry 33:1103
18. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) J Mol Biol 215:403
19. Hubbard T, Andrews D, Caccamo M, Cameron G, Chen Y, Clamp M, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez XM, Gilbert J, Hammond M, Herrero J, Hotz H, Howe K, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Keenan S, Kokocinsci F, London D, Longden I, McVicker G, Melsopp C, Meidl P, Potter S, Proctor G, Rae M, Rios D, Schuster M, Searle S, Severin J, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Trevanion S, Ureta-Vidal A, Vogel J, White S, Woodwark C, Birney E (2005) Nucleic Acids Res 33:D447
20. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD (2003) Nucleic Acids Res 31:3497
21. Shindyalov IN, Bourne PE (1998) Protein Eng 11:739
22. Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, Feng Z, Gilliland GL, Iype L, Jain S, Fagan P, Marvin J, Padilla D, Ravichandran V, Schneider B, Thanki N, Weissig H, Westbrook JD, Zardecki C (2002) Acta Crystallogr D Biol Crystallogr 58:899
23. Sali A, Blundell TL (1993) J Mol Biol 234:779
24. Eswar N, John B, Mirkovic N, Fiser A, Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, Madhusudhan MS, Yerkovich B, Sali A (2003) Nucleic Acids Res 31:3375
25. Wu CH, Yeh L-SL, Huang H, Arminski L, Castro-Alvear J, Chen Y, Hu Z, Kourtesis P, Ledley RS, Suzek BE, Vinayaka CR, Zhang J, Barker WC (2003) Nucleic Acids Res 31:345
26. Karplus M, Petsko GA (1990) Nature 347:631
27. Hagler AT, Huler E, Lifson S (1974) J Am Chem Soc 96:5319
28. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) J Appl Crystallogr 26:283
29. Ramachandran GN, Ramakrishnan C, Sasisekharan V (1963) J Mol Biol 7:95
30. Eisenberg D, Luthy R, Bowie JU (1997) Methods Enzymol 277:396
31. Huang B, Schroeder M (2006) BMC Struct Biol 6:19
32. Lipinski CA, Lombardo F, Dominy B, Wand Feeney PJ (1997) Adv Drug Delivery Rev 23:3
33. Veber DF, Johnson SR, Cheng HY, Smith BR, Ward KW, Kopple KD (2002) J Med Chem 45:2615
34. CORINA Version 3.0, Molecular Networks GmbH, Erlangen, Germany (2004)
35. Tetko I.V, Gasteiger J, Todeschini R, Mauri A, Livingstone D, Ertl P, Palyulin VA, Radchenko EV, Zefirov NS, Makarenko AS, Tanchuk VY, Prokopenko VV (2005) J Comput Aided Mol Des 19:453
36. Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) J Mol Biol 267:727
37. Wang R, Lai L, Wang S (2002) J Comput Aided Mol Des 16:11
38. Csizmadia F (2000) J Chem Inf Comput Sci 40:323
39. Buntrock RE (2002) J Chem Inf Comput Sci 42:1505
40. Wallace AC, Laskowski RA, Thornton JM (1995) Protein Eng 8:127
41. Ewing TJ, Makino S, Skillman AG, Kuntz ID (2001) J Comput Aided Mol Des 15:411
42. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) Nucleic Acids Res 25:4876
43. Kolaczkowski B, Thornton JW (2004) Nature 431:980
44. Felsenstein J (1995) In: PHYLIP (Phylogeny Inference Package) Version 3.57c. Department of Genetics, University of Washington, Seattle, WA
45. Ferrara P, Gohlke H, Price DJ, Klebe G, Brooks CL 3rd (2004) J Med Chem 47:3032
46. Mohan V, Gibbs AC, Cummings MD, Jaeger EP, DesJarlais RL (2005) Curr Pharm Des 11:323
47. Wang R, Lu Y, Wang S (2003) J Med Chem 46:2287
48. Charifson PS, Corkery JJ, Murcko MA, Walters WP (1999) J Med Chem 42:5100