Design of new plasmepsin inhibitors: A virtual high throughput screening approach on the EGEE grid

Journal of Chemical Information and Modeling

Volumn 47, Issue 5, 2007, Pages 1818-1828

  Kasam, Vinod ^a,b   Zimmermann, Marc ^a   Maaß, Astrid ^a   Schwichtenberg, Horst ^a   Wolf, Antje ^a   Jacq, Nicolas ^b   Breton, Vincent ^b   Hofmann Apitius, Martin ^a  

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

^b UNIVERSITÉ BLAISE PASCAL   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DEGRADATION; DISEASES; GRID COMPUTING; HEMOGLOBIN; METABOLISM;

ASPARTIC PROTEASES; GUANIDINO SCAFFOLDS; MOLECULAR DOCKING; PLASMODIUM;

GENE ENCODING;

ANTIMALARIAL AGENT; ASPARTIC PROTEINASE; CARBANILIDE DERIVATIVE; GUANIDINE DERIVATIVE; HEMOGLOBIN; ISOENZYME; LIGAND; PLASMEPSIN; PROTEINASE INHIBITOR; THIOUREA;

ANIMAL; ARTICLE; CHEMISTRY; CLUSTER ANALYSIS; COMPUTER PROGRAM; COMPUTER SIMULATION; CRYSTALLIZATION; DATA BASE; DRUG ANTAGONISM; DRUG DESIGN; DRUG EFFECT; DRUG SCREENING; GENETICS; METABOLISM; METHODOLOGY; PLASMODIUM FALCIPARUM; REPRODUCIBILITY; SYNTHESIS;

ANIMALS; ANTIMALARIALS; ASPARTIC ACID ENDOPEPTIDASES; CARBANILIDES; CLUSTER ANALYSIS; COMPUTER SIMULATION; CRYSTALLIZATION; DATABASES AS TOPIC; DRUG DESIGN; DRUG EVALUATION, PRECLINICAL; GUANIDINES; HEMOGLOBINS; ISOENZYMES; LIGANDS; PLASMODIUM FALCIPARUM; PROTEASE INHIBITORS; REPRODUCIBILITY OF RESULTS; SOFTWARE; THIOUREA;

EID: 35248866302     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci600451t     Document Type: Article

References (50)

1. Breton, V.; Jacq, N.; Kasam, V; Hofmann-Apitius, M. Grid added value to address malaria. IEEE Trans. Inf. Technol. Biomed. 2007, in press.
2. Malaria Vaccine Initiative. Bethesda, MD, U.S.A. http://www. malariavaccine.org (accessed Apr 7, 2005).
3. Curing Malaria Together. Medicines for Malaria Venture. http://www.mmv.org (accessed Apr 7, 2005).
4. Roll back Malaria Partnership, http://www.rbm.who.int (accessed Apr 7, 2005).
5. Saffron Media Pvt Ltd. Mumbai, India. http://www.pharmabiz.com (accessed Apr 11, 2005).
6. Gagliardi, F.; Jones, B.; Grey, F.; Bégin, M. E.; Heikkurinen, F. Building an infrastructure for scientific Grid computing: status and goals of the EGEE project. Philos. Trans. R. Soc. London, Ser. A 2005, 363, 1729-1742.
7. Breman, J. G.; Alilio, M. S.; Mills, A. Conquering the intolerable burden of malaria: what's new, what's needed: a summary. Am. J. Trop. Med. Hyg. 2004, 71S, 1-15.
8. Malaria Site. All about malaria. http://www.malariasite.com (accessed Apr 15, 2005)
9. Centers for Disease Control and Measures. http://www.cdc.gov (accessed Apr 22, 2005)
10. Weisner, J.; Ortmann, R.; Jomaa, H.; Schlitzer, M. New Antimalarial Drugs. Angew. Chem. Int. Ed. 2003, 42, 5274-5293.
11. White, N. J. Antimalarial drug resistance. J. Clin. Invest. 2004, 113, 1084-1092.
12. Robert, A.; Benoit-Vical, F.; Dechy-Cabaret, O.; Meunier, B. From Classical Antimalarial Drugs to New Compounds Based on the Mechanism of Action. Pure Appl. Chem. 2001, 73, 1173-1188.
13. Coombs, G. H.; Goldberg, D. E.; Klemba, M.; Berry, C.; Kay, J.; Mottram, J. C. Aspartic Proteases of Plasmodium falciparum and other parasitic protozoa as drug targets. Trends Parasitol. 2001, 17, 532-537.
14. Francis, S. E.; Sullivan, D. J., Jr.; Goldberg, D. E. Hemoglobin Metabolism in the Malaria Parasite Plasmodium falciparum. Annu. Rev. Microbiol. 1997, 51, 97-123.
15. Banerjee, R.; Liu, J.; Beatty, W.; Pelosof, L.; Klemba, M.; Goldberg, D. E. Four Plasmepsins are Active in the Plasmodium falciparum Food Vacuole, Including a Protease with an Active-site Histidine. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 990-995.
16. Silva, A. M.; Lee, A. Y.; Gulnik, S. V.; Majer, P.; Collins, J.; Bhat, T. N.; Collins, P. J.; Cachau, R. E.; Luker, K. E.; Gluzman, I. Y.; Francis, S. E.; Oksman, A.; Goldberg, D. E.; Erickson, J. W. Structure and Inhibition of Plasmepsin II, a Hemoglobin-Degrading Enzyme from Plasmodium falciparum. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 10034-10039.
17. Jiang, S.; Prigge, S. T.; Wei, L.; Gao, Y. E.; Hudson, T. H; Gerena, L.; Dame, J. B.; Kyle, D. E. New Class of Small Nonpeptidyl Compounds Blocks Plasmodium falciparum Development In Vitro by Inhibiting Plasmepsins. Antimicrob. Agents Chemother. 2001, 45, 2577-2584.
18. Ersmark, K.; Feierberg, I.; Bjelic, S.; Hamelink, E.; Hackett, F.; Blackman, M. J.; Hulten, J.; Samuelsson, B.; Aqvist, J.; Hallberg, A. Potent Inhibitors of the Plasmodium falciparum Enzymes Plasmepsin I and II Devoid of Cathepsin D Inhibitory Activity. J. Med. Chem. 2004, 47, 110-122.
19. Spencer, R. W. High Throughput Virtual Screening of Historic Collections on the File size, Biological targets and File diversity. Biotechnol. Bioeng. 1998, 61, 61-67.
20. Gruneberg, S.; Wendt, B.; Klebe, K. Subnanomolar Inhibitors From Computer Screening: A Model Study Using Human Carbonic anhydrase II. Angew. Chem., Int. Ed. Engl. 2001, 40, 389-393.
21. Doman, T.; N.; McGovern, S. L.; Witherbee, B. J.; Kasten, T. P.; Kurumbail, R.; Stallings, W. C.; Connolly. D. T.; Shoichet, B. K. Molecular Docking and High Throughput Screening for Novel Inhibitors of Protein Tyrosine Phosphatase 1B. J. Med. Chem. 2002, 45, 2213-2221.
22. Baxter, C. A.; Murray, C. W.; Waszkowycz, B.; Li, J.; Sykes, R. A.; Bone, R. G. A.; Perkins, T. D. J.; Wylie, W. New Approach to Molecular Docking and its Application to Virtual Screening of Chemical Databases. J. Chem. Inf. Comput. Sci. 2000, 40, 254-262.
23. Waszkowycz, B.; Perkins, T. D. J.; Sykes, R. A.; Li, J. Large Scale Virtual Screening for Discovering Leads in the Postgenomic era. IBM Syst. J. 2001, 40, 360-376.
24. Buyya, R.; Branson, K.; Giddy, J.; Abramson, D. The Virtual Laboratory. A Toolset to Enable Distributed Molecular Modeling for Drug Design on the Worldwide Grid. Concurrency Computat. Pract. Exper. 2003, 15, 1-25.
25. Jacq, N.; Salzemann, J.; Legré, Y.; Reichstadt, M.; Jacq, F.; Zimmermann, M.; Maass, M.; Sridhar, M.; Kasam, V. K.; Schwichtenberg, H.; Hofmann, M.; Breton, V. Demonstration of In Silico Docking at a Large Scale on Grid Infrastructure. Stud. Health Technol. Informatics 2006, 120, 155-157.
26. Foster, I.; Kesselman, C. Computational Grids. In The Grid: Blueprint for a New Computing Infrastructure, 1st ed.; Penrose, D. E. M., Eds.; Morgan Kaufmann Publishers: San Fransisco, CA, U.S.A., 1999; pp 15-25.
27. The Smallpox Reasearch Grid. http://grid.org/projects/smallpox/index.htm (accessed May 25, 2005).
28. The Anthrax Research Project. http://grid.org/projects/anthrax/index.htm (accessed May 25, 2005).
29. United Devices Cancer Research Project. http://grid.org/projects/cancer/ index.htm (accessed May 25, 2005).
30. Richards, W. G. Virtual Screening Grid Computing: The Screensaver Project. Nat. Rev. Drug. Discovery 2002, 1, 551-555.
31. Mehlin, C. Structure based drug discovery for Plasmodium falciparum. Comb. Chem. High Throughput Screening 2005, 8, 5-14.
32. Drug Targets for P. falciparum. Compiled by Yeh, I. http://plasmocyc. stanford.edu/target.html (accessed Mar 25, 2005).
33. National Institute of Allergy and Infectious Diseases. National Institutes of Health. http://www.niaid.nih.gov (accessed Apr 28, 2005).
34. Pattanaik, P.; Raman, J.; Balaram, H. Perspectives in drug design against malaria. Curr. Top. Med. Chem. 2002, 2, 483-505.
35. The Brookhoven Protein Database, www.pdb.org (accessed Mar 25, 2005).
36. Asojo, O. A.; Afonina, E.; Gulnik, S. V.; Yu, B.; Erickson, J. W.; Randad, R.; Medjahed, D.; Silva, A. M. Structures of Ser205 Mutant Plasmepsin II from Plasmodium falciparum at 1.8 Åin Complex with the Inhibitors rs367 and rs370. Acta Crystallogr. 2002, D58, 2001-2008.
37. Silva, A. M.; Lee, A. Y.; Gulnik, S. V.; Majer, P.; Collins, J.; Bhat, T. N.; Collins, P. J.; Cachau, R. E.; Luker, K. E.; Gluzman, I. Y.; Francis, S. E.; Oksman, A.; Goldberg, D. E.; Erickson, J. W. Structure and Inhibition of Plasmepsin II, a Hemoglobin-Degrading Enzyme from Plasmodium falciparum. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 10034-10039.
38. A free database for virtual screening. ZINC is not commercial. UCSF, University of California: San Francisco, CA. http://blaster.docking.org/zinc/ (accessed Jun 25, 2005).
39. Irwin, J. J.; Shoichet, B. K. ZINC - A Free Database of Commercially Available Compounds for Virtual Screening. J. Chem. Inf. Model. 2005, 45, 177-182.
40. ADT Tools, Version 2.0; Molecular Graphics Lab, The Scripps Research Institute: La Jolla, CA, 2005.
41. Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol. 1996, 261, 470-489.
42. FlexX, Version 2.0; BioSolvelT Gmbh: Sankt Augustin, Germany, 2005.
43. Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. Automated Docking Using a Lamarckian Genetic Algorithm and an Empirical Binding Free Energy Function. J. Comput. Chem. 1998, 19, 1639-1662.
44. AutoDock, Version 3.0.5; Molecular Graphics Laboratory, The Scripps Research Institute: LA Jolla, CA, 2005.
45. Rarey, M.; Kramer, B.; Lengauer, T. The Particle Concept: Placing discrete Water Molecules During Protein-Ligand Docking Predictions. Proteins: Struct., Funct., Genet. 1999, 34, 17-28.
46. Herrera, F.; Lozano, M.; Molina, D. Continuous Scatter Search: An Analysis of the Integration of Some Combination Methods and Improvement Strategies. Eur. J. Oper. Res. 2006, 169, 450-476.
47. Kramer, B.; Rarey, M.; Lengauer, T. Evaluation of the FlexX Incremental Construction Algorithm for Protein Ligand Docking. Proteins: Struct., Funct., Genet. 1999, 37, 228-241.
48. Jacq, N.; Breton, V.; Chen, H.-Y.; Ho, L.-Y.; Hofmann, M.; Lee, H.-C.; Legre, Y.; Lin, S. C.; Maaβ, A.; Medernach, E.; Merelli, I.; Milanesi, L.; Rastelli, G.; Reichstadt, M.; Salzemann, J.; Schwichtenberg, H.; Sridhar, M.; Kasam, V.; Wu, Y.-T.; Zimmermann, M. Virtual Screening on Large Scale Grids. Parallel Comput. 2007, 33, 289-301.
49. Jacq, N.; Salzemann, J.; Jacq, F.; Legré, Y.; Medernach, E.; Montagnat, J.; Maaβ, A.; Reichstadt, M.; Schwichtenberg, H.; Sridhar, M.; Kasam, V.; Zimmermann, M.; Hofmann, M.; Breton, V. Gridenabled Virtual Screening against malaria. J. Grid Comput. 2007, in press.
50. Kasam, V.; Salzemann, J.; Jacq, N.; Mass, A.; Breton, V. Large Scale Deployment of Molecular Docking Application on Computational Grid infrastructures for Combating Malaria. In Cluster Computing and the Grid, 2007. CCGRID 2007. Proceedings of the Seventh IEEE International Symposium, Rio de Janeiro, Brazil, May 14-17; IEEE Computer Society: Washington, DC, U.S.A., 2007; pp 691-700, 10.1109/CCGRID.2007.66.