Homology modeling and docking studies of phosphoenolpyruvate carboxykinase in Schistosoma mansoni

Medicinal Chemistry Research

Volumn 22, Issue 6, 2013, Pages 2870-2878

  Swargiary, Ananta ^a   Verma, Akalesh Kumar ^a   Sarma, Kishore ^b  

^a NORTH EASTERN HILL UNIVERSITY   (India)

^b MAULANA ABUL KALAM AZAD UNIVERSITY OF TECHNOLOGY   (India)

Author keywords

Docking; Homology modeling; Phosphoenolpyruvate carboxykinase; Schistosoma mansoni

Indexed keywords

AMINO ACID; GUANOSINE DIPHOSPHATE; PHOSPHOENOLPYRUVATE CARBOXYKINASE (GTP);

ARTICLE; ATOM; BIOCHEMICAL COMPOSITION; COMPUTER PROGRAM; CONSTRUCT VALIDITY; CRYSTAL STRUCTURE; CYTOSOL; ENZYME ACTIVE SITE; HOMOLOGY MODELING; MODEL; MOLECULAR DOCKING; NONHUMAN; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN STRUCTURE; RELIABILITY; SCHISTOSOMA MANSONI; SEQUENCE ANALYSIS; THREE DIMENSIONAL IMAGING;

EID: 84879686737     PISSN: 10542523     EISSN: 15548120     Source Type: Journal    
DOI: 10.1007/s00044-012-0289-2     Document Type: Article

References (50)

1. Al Lazikani B, Jung J, Xiang Z, Honig B (2001) Protein structure prediction. Curr Opin Chem Biol 5:51-56
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403-410
3. Asahi H, Osman A, Cook RM, LoVerde PT, Stadecker MJ (2000) Schistosoma mansoni phosphoenolpyruvate carboxykinase, a novel egg antigen: immunological properties of the recombinant protein and identification of a T-cell epitope. Infect Immun 68(6):3385-3393
4. Banerjee AK, Arora N, Murty USN (2009) Structural model of the Plasmodium falciparum thioredoxin reductase: a novel target for antimalarial drugs. J Vector Borne Dis 46:171-183
5. Barrett J (2009) Forty years of helminth biochemistry. Parasitology 136:633-1642
6. Berriman M, Haas BJ, LoVerde PT, Wilson RA, Dillon GP, Cerqueira GC, Mashiyama ST, Al-Lazikani B, Andrade LF, Ashton PD, Aslett MA, Bartholomeu DC, Blandin G, Caffrey CR, Coghlan A, Coulson R, Day TA, Delcher A, DeMarco R, Djikeng A, Eyre T, Gamble JA, Ghedin E, Gu Y, Hertz-Fowler C, Hirai H, Hirai Y, Houston R, Ivens A, Johnston DA, Lacerda D, Macedo CD, McVeigh P, Ning Z, Oliveira G, Overington JP, Parkhill J, Pertea M, Pierce RJ, Protasio AV, Quail MA, Rajandream MA, Rogers J, Sajid M, Salzberg SL, Stanke M, Tivey AR, White O, Williams DL, Wortman J, Wu W, Zamanian M, Zerlotini A, Fraser-Liggett CM, Barrell BG, El-Sayed NM (2009) The genome of the blood fluke Schistosoma mansoni. Nature 460(7253):352-358
7. Binkowski TA, Naghibzadeh S, Liang J (2003) CASTp: computed atlas of surface topography of proteins. Nucl Acids Res 31(13):3352-3355
8. Bueding E (1950) Effect of drugs on metabolism and enzyme systems of parasites. J Parasitol 36(3):201-210
9. Bundy DA (1994) Immuno-epidemiology of intestinal helminthic infection. The global burden of intestinal nematode disease. Trans R Soc Trop Med Hyg 88(3):259-261
10. Cavasotto CN, Phatak SS (2009) Homology modeling in drug discovery: current trends and applications. Drug Discov Today 14(13/14):676-683
11. Chirac P, Torreele E (2006) Global framework on essential health R&D. Lancet 367(9522):1560-1561
12. Dundas J, Ouyang Z, Tseng J, Binkowski A, Turpaz Y, Liang J (2006) CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucl Acid Res 34:W116-W118
13. Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wooley J, Wuthrich K, Wilson IA (2010) The JCSG high-throughput structural biology pipeline. Acta Crystallogr F66:1137-1142
14. Eswar N, Eramian D, Webb B, Shen M, Sali A (2008) Protein structure modeling with Modeller. Methods Mol Biol 426(1):145-159
15. Fiser A, Do RK, Sali A (2000) Modeling of loops in protein structures. Prot Sci 9:1753-1773
16. Fiser A, Feig M, Brooks CL, Sali A (2002) Evolution and physics in comparative protein structure modeling. Acc Chem Res 35:413-421
17. Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A (2003) ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucl Acids Res 31(13):3784-3788
18. Geary TG, Winterrowd CA, Alexander-Bowman SJ, Favreau MA, Nulf SC, Klein RD (1993) Ascaris suum: cloning of a cDNA encoding phosphoenolpyruvate carboxykinase. Exp Parasitol 77:155-161
19. Guruprasad K, Reddy BV, Pandit MW (1990) Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Eng 4(2):155-161
20. Hotez PJ (2008) Forgotten people and forgotten diseases: the neglected tropical diseases and their impact on global health and development. ASM Press, Washington, DC
21. Khan HN, Rashid H, Kulsoom S (2011) Homology modeling of γ-aminobutyrate-aminotransferase, a pyridoxal phosphate-dependent enzyme of Homo sapiens: molecular modeling approach to rational drug design against epilepsy. Afr J Biotechnol 10(31):5916-5926
22. Kherraz K, Kherraz K, Kameli A (2011) Homology modeling of ferredoxin-nitrite reductase from Arabidopsis thaliana. Bioinformation 6(3):115-119
23. Knudsen GM, Medzihradszky KF, Lim KC, Hansell E, McKerrow JH (2005) Proteomic analysis of Schistosoma mansoni cercarial secretions. Mol Cell Proteomics 4:1862-1875
24. Laskowski RA (2009) PDBsum new things. Nucl Acid Res 37:D355-D359
25. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26(2):283-291
26. Laskowski RA, Rullmann JAC, MacArthur MW, Kaptein R, Thornton JM (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8(4):477-486
27. Mansour TE (2002) Chemotherapeutic targets in parasites contemporary strategies. Cambridge University Press, Cambridge, pp 156-187
28. McKellar QA, Jackson F (2004) Veterinary anthelmintics: old and new. Trends Parasitol 20:456-461
29. Melo F, Feytmans E (1998) Assessing protein structures with a non-local atomic interaction energy. J Mol Biol 277:1141-1152
30. Melo F, Devos D, Depiereux E, Feytmans E (1997) ANOLEA: a www server to assess protein structures. In: Proceedings of the international conference on intelligent systems for molecular biology, vol 5, pp 187-190
31. Morris AL, MacArthur MW, Hutchinson EG, Thornton JM (1992) Stereochemical quality of protein structure coordinates. Proteins 2(4):345-364
32. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ (1998) Automated docking using a Lamarckian genetic algorithm and empirical binding free energy function. J Comput Chem 19:1639-1662
33. Omura S, Miyadera H, Ui H, Shiomi Z, Yamaguchi Y, Masuma R, Nagamitsu T, Takano D, Sunazuka T, Harder A, Kolbl H, Namikoshii M, Miyoshi H, Sakamoto K, Kita K (2001) An anthelmintic compound, nafuredin, shows selective inhibition of complex I in helminth mitochondria. Proc Natl Acad Sci USA 98:60-62
34. Rohrer SP, Saz HJ, Nowak T (1986) Purification and characterization of phosphoenolpyruvate carboxykinase from the parasitic helminth Ascaris suum. J Biol Chem 261(28):13049-13055
35. Roy B, Swargiary A (2009) Anthelmintic efficacy of ethanolic shoot extract of Alpinia nigra on tegumental enzymes of Fasciolopsis buski, a giant intestinal parasite. J Parasit Dis 33:48-53
36. Roy B, Swargiary A, Syiem D, Tandon V (2010) Potentilla fulgens (Family Rosaceae), a medicinal plant of Northeast India: a natural anthelmintic? J Parasit Dis 34:83-88
37. Russell RB, Barton GJ (1992) Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels. Proteins 14:309-323
38. Sali A, Blundell TL (1993) Comparative protein modeling by satisfaction of spatial restraints. J Mol Biol 234:779-815
39. Sharma P, Bhattacharya A (2012) 3-D structure prediction of aquaporin-2, virtual screening and in silico docking studies of gold and silver derivatives, used as potent inhibitors. Int J Pharma Pharm Sci 4(1):574-579
40. Sippl MJ (1993) Recognition of errors in three-dimensional structures of proteins. Proteins 17:355-362
41. Somvanshi P, Singh V (2008) Homology modeling and prediction of catalytic amino acid in the neurotoxin from Indian cobra (Naja naja). Open Bioinfor J 2:97-102
42. Sullivan SM, Holyoak T (2007) Structures of rat cytosolic PEPCK: insight into the mechanism of phosphorylation and decarboxylation of oxaloacetic acid. Biochemistry 46(35):10078-10088
43. Sumathi K, Ananthalakshmi P, Roshan MNA, Sekar K (2006) 3dSS: 3D structural superposition. Nucl Acids Res 34:w128-w132
44. Swargiary A, Roy B (2011) Kinetics of Acetylcholinesterase inhibition in Fasciolopsis buski and Raillietina echinobothrida by shoot extract of Alpinia nigra, an indigenous medicinal plant. Med Plants 3(2):145-150
45. Verma AK, Swargiary A, Prasad SB, Arjun J (2012) Homology modeling of phosphoenolpyruvate carboxykinase of Ascaris suum. J Pharm Res 5(2):1248-1255
46. Vokral I, Krizova V, Lamka J, Kubicek V, Szotakova B, Varady B, Nobilis M, Skalova L (2010) Effect of flubendazole on biotransformation enzymes activities in Haemonchus contortus. Open Parasitol J 4:24-28
47. Wallace AC, Laskowski RA, Thornton JM (1996) LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng 8:127-134
48. WHO (2002) WHO traditional medicine strategy 2002-2005. WHO/EDM/TRM/2002.1. 61 pp
49. WHO (2010) Report on neglected tropical diseases: working to overcome the global impact of neglected tropical diseases? ISBN 978 92 4 1564090 (NLM Classification: WC 680)
50. Wiederstein M, Sippl MJ (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucl Acids Res 35:w407-w410