Molecular dynamics studies of a hexameric purine nucleoside phosphorylase

Journal of Molecular Modeling

Volumn 16, Issue 3, 2010, Pages 543-550

  Zanchi, Fernando Berton ^a,b   Caceres, Rafael Andrade ^c,d   Stabeli, Rodrigo Guerino ^a,b   De Azevedo Jr , Walter Filgueira ^d  

^a UNIVERSIDADE FEDERAL DE RONDÔNIA   (Brazil)

^b INSTITUTO OSWALDO CRUZ   (Brazil)

^c PONTIFICAL CATHOLIC UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

^d Instituto Nacional de Ciência e Tecnologia em Tuberculose INCT TB   (Brazil)

Author keywords

Antimalarial drugs; Immucillin; Molecular dynamics; Plasmodium falciparum; Purine nucleoside phosphorylase

Indexed keywords

ANTIMALARIAL AGENT; FORODESINE; PHOSPHATE; PURINE NUCLEOSIDE PHOSPHORYLASE; SULFATE; PURINE NUCLEOSIDE; PYRIMIDINONE DERIVATIVE;

ARTICLE; BINDING SITE; CATALYSIS; CONFORMATIONAL TRANSITION; DRUG PROTEIN BINDING; MOLECULAR DYNAMICS; NONHUMAN; PLASMODIUM FALCIPARUM; PRIORITY JOURNAL; PROTEIN CLEAVAGE; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; PROTEIN STRUCTURE; X RAY CRYSTALLOGRAPHY; BIOCATALYSIS; CHEMISTRY; ENZYME STABILITY; ENZYMOLOGY; METABOLISM; PLIABILITY; PROTEIN MULTIMERIZATION; PROTEIN TERTIARY STRUCTURE; TIME;

PLASMODIUM FALCIPARUM;

BINDING SITES; BIOCATALYSIS; ENZYME STABILITY; MOLECULAR DYNAMICS SIMULATION; PHOSPHATES; PLASMODIUM FALCIPARUM; PLIABILITY; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, TERTIARY; PURINE NUCLEOSIDES; PURINE-NUCLEOSIDE PHOSPHORYLASE; PYRIMIDINONES; SULFATES; TIME FACTORS;

EID: 77951212820     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-009-0557-3     Document Type: Article

References (53)

1. Gilles HM (2002) In: Warrell DA, Gilles HM (eds) Essential Malariology. Arnold, New York, pp 1-7
2. World Health Organization (2007) Malaria, Fact Sheet No. 94. Geneva, Switzerland
3. Suh KN, Kain KC, Keystone JS (2004) Malaria. Can Med Assoc J 170:1693-1702
4. Sachs JD (2002) A new global effort to control malaria. Science 298:122-124
5. Wellems TE (2002) Plasmodium chloroquine resistance and the search for a replacement antimalarial drug. Science 298:124-125
6. Hassan HF, Coombs GH (1988) Purine and pyrimidine metabolism in parasitic protozoa. FEMS Microbiol Rev 4:47-83
7. Asahi H, Kanazawa T, Kajihara Y, Takahashi K, Takahashi T (1996) Hypoxanthine: a low molecular weight factor essential for growth of erythrocytic Plasmodium falciparum in a serum-free medium. Parasitology 113:19-23
8. Kicska GA, Tyler PC, Evans GB, Furneaux RH, Kim K, Schramm VL (2002) Transition state analogue inhibitors of purine nucleoside phosphorylase from Plasmodium falciparum. J Biol Chem 277:3219-3225
9. Kicska GA, Tyler PC, Evans GB, Furneaux RH, Schramm VL, Kim K (2002) Purine-less death in Plasmodium falciparum induced by immucillin-H, a transition state analogue of purine nucleoside phosphorylase. J Biol Chem 277:3226-3231 (Pubitemid 34953185)
10. Ting LM, Shi W, Lewandowicz A, Singh V, Mwakingwe A, Birck MR, Ringia EA, Bench G, Madrid DC, Tyler PC, Evans GB, Furneaux RH, Schramm VL, Kim K (2005) Targeting a novel Plasmodium falciparum purine recycling pathway with specific immucillins. J Bio Chem 280:9547-9554
11. Schnick C, Robien MA, Brzozowski AM, Dodson EJ, Murshudov GB, Anderson L, Luft, Mehlin C, Hol WGJ, Brannigan JA, Wilkinson AJ (2005) Structures of Plasmodium falciparum purine nucleoside phosphorylase complexed with sulfate and its natural substrate inosine. Acta Crystallogr D Biol Crystallogr 61:1245-1254
12. Shi W, Ting LM, Kicska GA, Lewandowicz A, Tyler PC, Evans GB, Furneaux RH, Kim K, Almo SC, Schramm VL (2004) Plasmodium falciparum purine nucleoside phosphorylase. J Biol Chem 279:18103-18106
13. 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) The Protein Data Bank. Acta Crystallogr D Biol Crystallogr 58:899-907
14. van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJC (2005) GROMACS: fast, flexible, and free. J Comp Chem 26:1701-1718 http://www.gromacs.org
15. Ooestenbrink C, Soares TA, van der Vegt NF, van Gunsteren WF (2005) Validation of the 53A6 GROMOS force field. Eur Biophys J 34:273-284
16. van Aalten DM, Bywater B, Findlay JB, Hendlich M, Hooft RW, Vriend G (1996) PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. Comput Aided Mol Des 10:255-262 http://davapc1.bioch.dundee.ac.uk/programs/prodrg/prodrg.html
17. Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JH, Koseki S, Matsunaga N, Nguyen KA, Su S, Windus TL, Dupuis M, Montgomery JA (1993) General atomic and molecular electronic structure system. J Comput Chem 14:1347-1363
18. Guex N, Peitsch MC (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18:2714-2723
19. Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J (1981) Interaction models for water in relation to protein hydration. In: Pullman B (ed) Intermolecular forces. Reidel D Publishing Company Dordrecht, The Netherlands, pp 331-342
20. Hess B, Bekker H, Berendsen HJC, Fraaije JGEM (1997) LINCS: a linear constraint solver for molecular simulations. J Comput Chem 18:1463-1472
21. Miyamoto S, Kollman PA (1992) Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches. J Comput Chem 16:226-245
22. Chowdhuri S, Tan ML, Ichiye T (2006) Dynamical properties of the soft sticky dipole-quadrupole-octupole water model: a molecular dynamics study. J Chem Phys 125:144513
23. Darden T, York D, Pedersen L (1993) Particle Mesh Ewald - an n. log(n) method for ewald sums in large systems. J Chem Phys 98:10089-10092
24. Timmers LFSM, Caceres RA, Vivan AL, Gava LM, Dias R, Ducati RG, Basso LA, Santos DS, de Azevedo WF (2008) Structural studies of human purine nucleoside phosphorylase: towards a new specific empirical scoring function. Arch Biochem Biophys 479:28-38
25. Silva RG, Nunes JE, Canduri F, Borges JC, Gava LM, Moreno FB, Basso LA, Santos DS (2007) Purine nucleoside phosphorylase: a potential target for the development of drugs to treat T-cell- and apicomplexan parasite-mediated diseases. Curr Drugs Target 8:413-422
26. de Azevedo WF Jr, Canduri F, dos Santos DM, Silva RG, de Oliveira JS, de Carvalho LPS, Basso LA, Mendes MA, Palma MS, Santos DS (2003) Crystal structure of human purine nucleoside phosphorylase at 2.3 Å resolution. Biochem Biophys Res Commun 308:545-552 (Pubitemid 36945527)
27. Caceres RA, Saraiva Timmers LF, Dias R, Basso LA, Santos DS, de Azevedo WF (2008) Molecular modeling and dynamics simulations of PNP from Streptococcus agalactiae. Bioorg Med Chem 16:4984-4993
28. Timmers LFSM, Caceres RA, Basso LA, Santos DS, de Azevedo Jr. WF (2008) Structural Bioinformatics Study of PNP from Listeria monocytogenes. Protein Pep Lett 15:843-849
29. de Azevedo WF Jr, Canduri F, dos Santos DM, Pereira JH, Dias MVB, Silva RG, Mendes MA, Basso LA, Palma MS, Santos DS (2003) Structural basis for inhibition of human PNP by immucillin-H. Biochem Biophys Res Commun 309:917
30. Canduri F, Fadel V, Basso LA, Palma MS, Santos DS, de Azevedo WF (2005) New catalytic mechanism for human purine nucleoside phosphorylase. Biochem Biophys Res Commun 327:646-649
31. Santos DM, Canduri F, Pereira JH, Dias MVB, Silva RG, Mendes MA, Palma MS, Basso LA, de Azevedo WF, Santos DS (2003) Crystal structure of human purine nucleoside phosphorylase complexed with acyclovir. Biochem Biophys Res Commun 308:553-559 (Pubitemid 36945528)
32. de Azevedo WF, Canduri F, dos Santos DM, Pereira JH, Dias MVB, Silva RG, Mendes MA, Basso LA, Palma MS, Santos DS (2003) Crystal structure of human PNP complexed with guanine. Biochem Biophys Res Commun 312:767-772
33. Silva RG, Pereira JH, Canduri F, de Azevedo WF, Basso LA, Santos DS (2005) Kinetics and crystal structure of human purine nucleoside phosphorylase in complex with 7-methyl-6-thioguanosine. Arch Biochem Biophys 442:49-58
34. Canduri F, dos Santos DM, Silva RG, Mendes MA, Basso LA, Palma MS, de Azevedo WF, Santos DS (2004) Structures of human purine nucleoside phosphorylase complexed with inosine and ddI. Biochem Biophys Res Comum 313:907-914
35. Canduri F, Silva RG, dos Santos DM, Palma MS, Basso LA, Santos DS, de Azevedo WF (2005) Structure of human PNP complexed with ligands. Acta Crystallogr D Biol Crystallogr 61:856-862
36. Nolasco DO, Canduri F, Pereira JH, Cortinóz, Palma MS, Oliveira JS, Basso LA, de Azevedo WF, Santos DS (2004) Crystallographic structure of PNP from Mycobacterium tuberculosis at 1.9 Å resolution. Biochem Biophys Res Comum 324:789-794
37. de Azevedo WF, Dias R (2008) Computational methods for calculation of ligand-binding affinity. Curr Drug Targets 9:1031-1039
38. de Azevedo WF (2008) Protein-drug interactions. Curr Drug Targets 9:1030-1030
39. Dias R, de Azevedo WF (2008) Molecular docking algorithms. Curr Drug Targets 9:1040-1047
40. Canduri F, de Azevedo WF (2008) Protein crystallography in drug discovery. Curr Drug Targets 9:1048-1053
41. Pauli I, Timmers LFSM, Caceres RA, Soares MBP, de Azevedo WF (2008) In silico and in vitro. Identifying new drugs. Curr Drug Targets 9:1054-1061
42. Dias R, Timmers LFSM, Caceres RA, de Azevedo WF (2008) Evaluation of molecular docking using polynomial empirical scoring functions. Curr Drug Targets 9:1062-1070
43. de Azevedo WF, Dias R (2008) Experimental approaches to evaluate the thermodynamics of protein-drug interactions. Curr Drug Targets 9:1071-1076
44. Caceres RA, Pauli I, Timmers LFSM, de Azevedo WF (2008) Molecular recognition models: a challenge to overcome. Curr Drug Targets 9:1077-1083
45. Barcellos GB, Pauli I, Caceres RA, Timmers LFSM, Dias R, de Azevedo WF (2008) Molecular modeling as tool for drug discovery. Curr Drug Targets 9:1084-1091
46. Timmers LFSM, Pauli I, Caceres RA, de Azevedo WF (2008) Drug-binding databases. Curr Drug Targets 9:1092-1099
47. de Azevedo WF, Canduri F, Fadel V, Teodoro LG, Hial V, Gomes RA (2001) Biochem Biophys Res Commun 287:277-281
48. de Azevedo WF (2007) Editorial. Current Drug Targets 8:387-387
49. Canduri F, Perez PC, Caceres RA, de Azevedo WF (2007) Protein kinases as targets for antiparasitic chemotherapy drugs. Curr Drug Targets 8:389-398
50. Marques MR, Pereira JH, Oliveira JS, Basso LA, Santos DS, de Azevedo WF, Palma MS (2007) The inhibition of 5-enolpyruvylshikimate-3-phosphate synthase as a model for development of novel antimicrobials. Curr Drug Targets 8:445-457
51. Dias MVB, Ely F, Palma MS, de Azevedo WF, Basso LA, Santos DS (2007) Chorismate synthase: an attractive target for drug development against orphan diseases. Curr Drug Targets 8:437-444
52. Pereira JH, Vasconcelos IB, Oliveira JS, Caceres RA, de Azevedo WF, Basso LA, Santos DS (2007) Shikimate kinase: a potential target for development of novel antitubercular. Curr Drug Targets 8:459-468
53. de Amorim HLN, Caceres RA, Netz PA (2008) Linear Interaction Energy (LIE) method in lead discovery and optimization. Curr Drug Targets 9:1100-1105