WISDOM-II: Screening against multiple targets implicated in malaria using computational grid infrastructures

Malaria Journal

Volumn 8, Issue 1, 2009, Pages

  Kasam, Vinod ^a,c   Salzemann, Jean ^c   Botha, Marli ^d   Dacosta, Ana ^c   Degliesposti, Gianluca ^b   Isea, Raul ^f   Kim, Doman ^e   Maass, Astrid ^a   Kenyon, Colin ^d   Rastelli, Giulio ^b   Hofmann Apitius, Martin ^a   Breton, Vincent ^c  

^a FRAUNHOFER INSTITUTE FOR ALGORITHMS AND SCIENTIFIC COMPUTING SCAI   (Germany)

^b UNIVERSITY OF MODENA AND REGGIO EMILIA   (Italy)

^c UNIVERSITÉ BLAISE PASCAL   (France)

^d CSIR Biosciences   (South Africa)

^e Chonnam National University   (South Korea)

^f Fundacion IDEA   (Venezuela)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIMALARIAL AGENT; DIHYDROFOLATE REDUCTASE; GLUTATHIONE TRANSFERASE; DRUG; LIGAND; PROTOZOAL PROTEIN;

ARTICLE; CLINICAL CHEMISTRY; CLINICAL TRIAL; COMPUTER MODEL; COMPUTER PROGRAM; DATA BASE; DEVELOPING COUNTRY; DRUG DESIGN; DRUG PROTEIN BINDING; DRUG RESEARCH; DRUG SCREENING; DRUG TARGETING; HUMAN; IN VITRO STUDY; INFORMATION TECHNOLOGY; MALARIA; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR LIBRARY; MULTICENTER STUDY; PLASMODIUM FALCIPARUM; PLASMODIUM VIVAX; PROTEIN STRUCTURE; BIOLOGY; DRUG DELIVERY SYSTEM; MATRIX ATTACHMENT REGION; MEDICAL INFORMATICS; METHODOLOGY; ORGANIZATION AND MANAGEMENT; PROTEIN BINDING;

COMPUTATIONAL BIOLOGY; DRUG DELIVERY SYSTEMS; DRUG DESIGN; GLUTATHIONE TRANSFERASE; HUMANS; LIGANDS; MALARIA; MATRIX ATTACHMENT REGIONS; MEDICAL INFORMATICS; PHARMACEUTICAL PREPARATIONS; PROTEIN BINDING; PROTOZOAN PROTEINS; TETRAHYDROFOLATE DEHYDROGENASE;

EID: 67649191688     PISSN: None     EISSN: 14752875     Source Type: Journal    
DOI: 10.1186/1475-2875-8-88     Document Type: Article

References (63)

1. Research and Training in Tropical Diseases. http://www.who.int/tdr/ diseases/malaria/default.htm
2. Drugs for Neglected Diseases Initiative. http://www.dndi.org/
3. Hit and lead generation: beyond high-throughput screening. KH Bleicher HJ Boehm K Mueller AI Alanine, Nat Rev Drug Discov 2003 2 369 378 12750740 (Pubitemid 37361707)
4. HJ Boehm G Schneider, Virtual screening for bioactive molecules New York: John Wiley & Sons, Inc 2000
5. High throughput virtual screening of historic collections on the file size, biological targets and file diversity. RW Spencer, Biotechnol Bioeng 1998 61 61 67 10099497 (Pubitemid 28561945)
6. The protein data bank. HM Berman J Westbrook Z Feng G Gilliland TN Bhat H Weissig IN Shindyalov PE Bourne, Nucleic Acids Res 2000 28 235 242 10592235 (Pubitemid 30047768)
7. HD Hoeltje W Sippl D Rognan G Folkers, Molecular Modeling, Basics Principles And Applications New York: John Wiley & Sons, Inc 2003
8. Integration of virtual and high-throughput screening. J Bajorath, Nat Rev Drug Discov 2002 1 882 894 12415248 (Pubitemid 37361583)
9. The virtual laboratory. A toolset to enable distributed molecular modeling for drug design on the worldwide grid. R Buyya K Branson J Giddy D Abramson, Concurrency Computat Pract Exper 2003 15 1 25
10. Demonstration of in silico docking at a large scale on grid infrastructure. N Jacq J Salzemann Y Legre M Reichstadt F Jacq M Zimmermann A Maass M Sridhar V Kasam H Schwichtenberg M Hofmann V Breton, Stud Health Technol Inform 2006 120 155 157 16823133
11. Computational Grids. I Foster C Kesselman, The Grid: Blueprint for a New Computing Infrastructure San Fransisco: Morgan Kaufmann Publishers 1999
12. Enabling Grids for E-Science. http://www.eu-egee.org
13. Auvergrid. http://www.auvergrid.fr
14. E-Science grid facility for Europe and Latin America. http://www.eu-eela.org
15. EUChinagrid. http://www.euchinagrid.org
16. EUmedgrid. http://www.eumedgrid.org
17. The Smallpox Research Grid. http://www.chem.ox.ac.uk/smallpox/news.html
18. The Anthrax Research Project. http://www.chem.ox.ac.uk/anthrax/
19. United Devices Cancer Research Project. http://www.computerworld.com/ action/article.do?command=viewArticleBasic&articleId=9045698
20. Virtual screening grid computing: The screensaver project. WG Richards, Nat Rev Drug Discov 2002 1 551 555 12120261 (Pubitemid 37361507)
21. Grid enabled virtual screening against malaria. N Jacq J Salzemann Y Legré M Reichstadt F Jacq E Medernach M Zimmermann A Maa M Sridhar K Vinod-Kusam J Montagnat H Schwichtenberg M Hofmann V Breton, J Grid Comput 2008 1 29 43 (Pubitemid 351210944)
22. Design of plasmepsin inhibitors: A virtual high throughput screening approach on the EGEE grid. V Kasam M Zimmermann A Maa H Schwichtenberg A Wolf N Jacq V Breton M Hofmann, J Chem Inf Model 2007 47 1818 1828 17727268 (Pubitemid 47561129)
23. Design and discovery of novel plasmepsin inhibitors using an automated workflow on large scale grids. G Degliesposti V Kasam A Da Costa HK Kang DW Kim V Breton D Doman Kim G Rastelli, Chem Med Chem
24. Large scale deployment of molecular docking application on computational grid infrastructures for combating malaria. V Kasam J Salzemann N Jacq A Mass V Breton, Proceedings of the Seventh IEEE International Symposium on Cluster Computing and the Grid: May 14-17 2007; Rio de Janeiro IEEE Computer Society 2007 691 700
25. Spread of malaria by P. Vivax. http://usachppm.apgea.army.mil/Documents/ FACT/18-041-0107-Vivax-Malaria.pdf
26. Redox and antioxidant systems of the malaria parasite Plasmodium falciparum. S Muller, Mol Microbiol 2004 53 5 1291 1305 15387810 (Pubitemid 39209105)
27. Oxidative stress in malaria parasite-infected erythrocytes, host-parasite interactions. K Becker L Tilley JL Vennerstrom D Roberts, Int J Parasitol 2004 34 163 189 15037104 (Pubitemid 38229822)
28. Characterization of the electrophile binding site and substrate binding mode of 26 kDa glutathione S-transferase form Schistosoma japonicum. RFM Cardoso DS Daniels CM Bruns JA Tainer, Proteins 2003 5 137 146 (Pubitemid 36293039)
29. Structure function and evolution of glutathione transferases, implication for classification of non-mammalian members of an ancient super family. D Sheenan G Meade VM Foley CA Dowd, Biochem J 2001 360 1 16 11695986 (Pubitemid 33081943)
30. Glutathione S-transferase activity in malaria parasites. P Srivastva SK Puri KK Kamboj VC Pandey, Trop Med Int Health 1999 4 251 254 10320651 (Pubitemid 29217428)
31. Plasmodium berghei, implication of intracellular glutathione and its related enzyme in chloroquine resistance in vivo. VL Dubois DF Platel G Pauly J Tribouley-Duret, Exp Parasitol. 1995 81 1 117 124 7628559
32. The pathogenic basis of malaria. LH Miller LD Baruch K Marsh OK Doumbo, Nature 2002 415 673 679 11832955 (Pubitemid 34136400)
33. X-ray structure of glutathione S-transferase from the malarial parasite Plasmodium falciparum. K Fritz-Wolf A Becker S Rahlfs P Harwalt RH Schirmer W Kansch K Becker, Proc Natl Acad Sci U S A 2003 100 13821 13826 14623980 (Pubitemid 37499150)
34. Native and inhibited structure of a Mu class related glutathione S- transferase from Plasmodium falciparum. M Perbandt C Burmeister RD Walter C Betzel E Liebau, J Biol Chem. 2004 279 2 1336 1342 12972411 (Pubitemid 38082659)
35. Ligand based protein alignment and isozyme specificity of glutathione S-transferase inhibitors. RT Koehler HO Villar KE Bauer DL Higgins, Proteins 1997 28 202 216 9188738 (Pubitemid 27276307)
36. The glutathione S-transferase from Plasmodium falciparum. E Liebau B Bergmann AM Campbell P Teesdale-Spittle PM Brophy K Luersen RD Walter, Mol Biochem Parasitol 2002 124 85 90 12387854 (Pubitemid 35223306)
37. Chloroquine resistance in Plasmodium vivax. JK Baird, Antimicrob Agents Chemother 2004 48 4075 4083 15504824 (Pubitemid 39434858)
38. Chloroquine-resistant Plasmodium vivax in Borneo. C Ahlm J Wistrom H Carlsson, J Travel Med 1996 3 124 9815438
39. Pyrimethamine resistance in Plasmodium vivax malaria. MD Young RW Burgess, Bull World Health Organ. 1959 20 1 27 36 13638787
40. Association of genetic mutations in Plasmodium vivax DHFR with resistance to sulfadoxine-pyrimethamine: geographical and clinical correlatos. M Imwong S Pukrittakayamee S Looareesuwan G Pasvol J Poirreiz NJ White G Sno, Antimicrob Agents Chemother 2001 45 3122 3127 11600366 (Pubitemid 32988838)
41. Crystal structure of dihydrofolate reductase from Plasmodium vivax: pyrimethamine displacement linked with mutation-induced resistance. P Kongsaeree P Khongsuk U Leartsakulpanich P Chitnumsub B Tarnchompoo MD Walkinshaw Y Yuthavong, Proc Natl Acad Sci USA 2005 102 13046 13051 16135570 (Pubitemid 41324976)
42. Drug resistance in malaria. N White, Br Med Bull 1998 54 703 715 10326295 (Pubitemid 28477205)
43. Antifolate-resistant mutants of Plasmodium falciparum dihydrofolate reductase. W Sirawaraporn T Sathitkul R Sirawaraporn Y Yuthavong DV Santi, Proc Natl Acad Sci USA 1997 94 1124 1129 9037017 (Pubitemid 27087815)
44. Basis for antifolate action and resistance in malaria. Y Yuthavong, Microbes Infect. 2002 4 2 175 182 11880049 (Pubitemid 34183491)
45. Interaction of pyrimethamine, cycloguanil, WR99210 and their analogues with Plasmodium falciparum dihydrofolate reductase: structural basis of antifolate resistance. G Rastelli W Sirawaraporn P Sompornpisut T Vilaivan S Kamchonwongpaisan R Quarrel G Lowe Y Thebtaranonth Y Yuthavong, Bioorg Med Chem 2000 8 1117 1128 10882022 (Pubitemid 30336406)
46. Structure of Plasmodium vivax dihydrofolate reductase determined by homology modeling and molecular dynamics refinement. G Rastelli S Pacchioni W Sirawaraporn R Sirawaraporn MD Parenti AM Ferrari, Bioorg Med Chem Lett 2003 13 3257 3260 12951104 (Pubitemid 37093839)
47. Insights into antifolate resistance from malarial DHFR-TS structures. J Yuvaniyama P Chitnumsub S Kamchonwongpaisan J Vanichtanankul W Sirawaraporn P Taylor MD Walkinshaw Y Yuthavong, Nat Struct Biol 2003 10 357 365 12704428 (Pubitemid 36523270)
48. Modeller. http://salilab.org/modeller/
49. The amber biomolecular simulation programs. DA Case TE Cheatham III T Darden H Gohlke R Luo KM Merz A Onufriev Jr C Simmerling B Wang R Woods, J Comput Chem 2005 26 1668 1688 16200636 (Pubitemid 43076180)
50. Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method. A Jakalian BL Bush DB Jack CI Bayly, J Comput Chem 2000 21 132 146
51. Development and testing of a general amber force field. J Wang RM Wolf JW Caldwell PA Kollamn DA Case, J Comput Chem 2004 25 1157 1174 15116359
52. ZINC: A free database for virtual screening. http://blaster.docking.org/ zinc/
53. ZINC A free database of commercially available compounds for virtual screening. JJ Irwin BK Shoichet, J Chem Inf Model 2005 45 177 182 15667143
54. A fast flexible docking method using an incremental construction algorithm. M Rarey B Kramer T Lengauer G Klebe, J Mol Biol 1996 261 470 489 8780787 (Pubitemid 26335901)
55. FlexX Version 2.0; BioSolveIT Gmbh. http://www.biosolveit.de/
56. The particle concept: placing discrete water molecules during protein-ligand docking predictions. M Rarey B Kramer T Lengauer, Proteins. 1999 34 1 17 28 10336380 (Pubitemid 29019529)
57. Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors. AM Ferrari G Degliesposti M Sgobba G Rastelli, Bioorg Med Chem 2007 15 7865 7877 17870536 (Pubitemid 47575902)
58. Binding estimation after refinement, a new automated procedure for the refinement and rescoring of docked ligands in virtual screening. G Rastelli G Degliesposti A Del Rio M Sgobba, Chem Biol Drug Des 2009 73 283 286 19207463
59. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices. J Srinivasan E Thomas I Cheatham P Cieplak PA Kollman DA Case, J Am Chem Soc 1998 120 9401 9409 (Pubitemid 28452628)
60. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. PA Kollman Massova C Reyes B Kuhn S Huo L Chong M Lee T Lee Y Duan W Wang O Donini P Cieplak J Srinivasan DA Case TE Cheatham III, Acc Chem Res 2000 33 889 97 11123888
61. UCSF Chimera. http://www.cgl.ucsf.edu/chimera/
62. Molecular Operating Environment. http://www.chemcomp.com/
63. Chemical similarity searching. JM Barnard GM Downs PJ Willett, Chem Inf Comput Sci 1998 38 983 996 (Pubitemid 128591261)