Experimentally Validated Novel Inhibitors of Helicobacter pylori Phosphopantetheine Adenylyltransferase Discovered by Virtual High-Throughput Screening

PLoS ONE

Volumn 8, Issue 9, 2013, Pages

  Cheng, Chao Sheng ^a   Jia, Kai Fan ^a   Chen, Ting ^a   Chang, Shun Ya ^a   Lin, Ming Shen ^b   Yin, Hsien Sheng ^a  

^a NATIONAL TSING HUA UNIVERSITY   (Taiwan)

^b TA INSTRUMENTS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AB 35543; ADENOSINE TRIPHOSPHATE; ANTIBIOTIC AGENT; BACTERIAL ENZYME; COENZYME A; CPD 6041; DEXTRO AMETHOPTERIN; ENALAPRILAT; LACTOLYLGLUTATHIONE LYASE; OMEPRAZOLE; PANTETHEINE PHOSPHATE; PANTETHEINE PHOSPHATE ADENYLYLTRANSFERASE; PANTETHEINE PHOSPHATE ADENYLYLTRANSFERASE INHIBITOR; T 5568745; T 5568746; UNCLASSIFIED DRUG; ZANAMIVIR;

ARTICLE; BACTERIAL VIABILITY; BINDING AFFINITY; BINDING SITE; BIOSYNTHESIS; CELL DEATH; CRYSTAL STRUCTURE; DRUG EFFICACY; DRUG MECHANISM; DRUG SCREENING; DRUG TARGETING; ENZYME INACTIVATION; ENZYME INHIBITION; HELICOBACTER PYLORI; HIGH THROUGHPUT SCREENING; NONHUMAN;

ADENOSINE TRIPHOSPHATE; ANTI-BACTERIAL AGENTS; BACTERIAL PROTEINS; BINDING SITES; COENZYME A; DATABASES, CHEMICAL; DRUG DISCOVERY; ENZYME INHIBITORS; HELICOBACTER PYLORI; HIGH-THROUGHPUT SCREENING ASSAYS; METHOTREXATE; MICROBIAL SENSITIVITY TESTS; MOLECULAR DOCKING SIMULATION; NUCLEOTIDYLTRANSFERASES; PANTETHEINE; PROTEIN BINDING;

EID: 84883525043     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0074271     Document Type: Article

References (49)

1. Kusters JG, van Vliet AH, Kuipers EJ, (2006) Pathogenesis of Helicobacter pylori infection. Clin Microbiol Rev 19: 449-490. doi:10.1128/CMR.00054-05. PubMed: 16847081.
2. Smoot DT, (1997) How does Helicobacter pylori cause mucosal damage? Direct mechanisms. Gastroenterology 113: S31-S34; discussion S50 doi:10.1016/S0016-5085(97)70077-5. PubMed: 9394757.
3. Atherton JC, (2006) The pathogenesis of Helicobacter pylori-induced gastro-duodenal diseases. Annu Rev Pathol 1: 63-96. doi:10.1146/annurev.pathol.1.110304.100125. PubMed: 18039108.
4. Hirai Y, Hayashi S, Shimomura H, Oguma K, Yokota K, (1999) Association of Helicobacter pylori with gastroduodenal diseases. Jpn J Infect Dis 52: 183-197. PubMed: 10680084.
5. Proença-Modena JL, Acrani GO, Brocchi M, (2009) Helicobacter pylori: phenotypes, genotypes and virulence genes. Future Microbiol 4: 223-240. doi:10.2217/17460913.4.2.223. PubMed: 19257848.
6. Mirbagheri SA, Hasibi M, Abouzari M, Rashidi A, (2006) Triple, standard quadruple and ampicillin-sulbactam-based quadruple therapies for H pylori eradication: A comparative three-armed randomized clinical trial. World J Gastroenterol 12: 4888-4891. PubMed: 16937475.
7. Minakari M, Jazi AHD, Shavakhi A, Moghareabed N, Fatahi F, (2010) A Randomized Controlled Trial: Efficacy and Safety of Azithromycin, Ofloxacin, Bismuth, and Omeprazole Compared With Amoxicillin, Clarithromycin, Bismuth, and Omeprazole as Second-Line Therapy in Patients With Helicobacter pylori Infection. Helicobacter 15: 154-159. doi:10.1111/j.1523-5378.2009.00739.x. PubMed: 20402818.
8. Graham DY, Shiotani A, (2008) New concepts of resistance in the treatment of Helicobacter pylori infections. Nat Clin Practice Gastroenterol Hepatol 5: 321-331. doi:10.1038/ncpgasthep1138. PubMed: 18446147.
9. Begley TP, Kinsland C, Strauss E, (2001). iosynthesis Coenzyme In Bacteria Vitam Horm-Advances Res Applications, Vol 61 61: 157-171.
10. Geerlof A, Lewendon A, Shaw WV, (1999) Purification and characterization of phosphopantetheine adenylyltransferase from Escherichia coli. J Biol Chem 274: 27105-27111. doi:10.1074/jbc.274.38.27105. PubMed: 10480925.
11. Izard T, Geerlof A, (1999) The crystal structure of a novel bacterial adenylyltransferase reveals half of sites reactivity. EMBO J 18: 2021-2030. doi:10.1093/emboj/18.8.2021. PubMed: 10205156.
12. Izard T, (2002) The crystal structures of phosphopantetheine adenylyltransferase with bound substrates reveal the enzyme's catalytic mechanism. J Mol Biol 315: 487-495. doi:10.1006/jmbi.2001.5272. PubMed: 11812124.
13. Jackowski S, Rock CO, (1984) Metabolism of 4'-Phosphopantetheine in Escherichia-Coli. J Bacteriol 158: 115-120. PubMed: 6370952.
14. Zhyvoloup A, Nemazanyy I, Babich A, Panasyuk G, Pobigailo N, et al. (2002) Molecular cloning of CoA synthase- The missing link in CoA biosynthesis. J Biol Chem 277: 22107-22110. doi:10.1074/jbc.C200195200. PubMed: 11980892.
15. Aghajanian S, Worrall DM, (2002) Identification and characterization of the gene encoding the human phosphopantetheine adenylyltransferase and dephospho-CoA kinase bifunctional enzyme (CoA synthase). Biochem J 365: 13-18. PubMed: 11994049.
16. Gerdes SY, Scholle MD, D'Souza M, Bernal A, Baev MV, et al. (2002) From genetic footprinting to antimicrobial drug targets: examples in cofactor biosynthetic pathways. J Bacteriol 184: 4555-4572. doi:10.1128/JB.184.16.4555-4572.2002. PubMed: 12142426.
17. Morris VK, Izard T, (2004) Substrate-induced asymmetry and channel closure revealed by the apoenzyme structure of Mycobacterium tuberculosis phosphopantetheine adenylyltransferase. Protein Sci 13: 2547-2552. doi:10.1110/ps.04816904. PubMed: 15322293.
18. Jackowski S, Rock CO, (1981) Regulation of coenzyme A biosynthesis. J Bacteriol 148: 926-932. PubMed: 6796563.
19. Miller JR, Ohren J, Sarver RW, Mueller WT, de Dreu P, et al. (2007) Phosphopantetheine adenylyltransferase from Escherichia coli: investigation of the kinetic mechanism and role in regulation of coenzyme A biosynthesis. J Bacteriol 189: 8196-8205. doi:10.1128/JB.00732-07. PubMed: 17873050.
20. Rock CO, Park HW, Jackowski S, (2003) Role of feedback regulation of pantothenate kinase (CoaA) in control of coenzyme A levels in Escherichia coli. J Bacteriol 185: 3410-3415. doi:10.1128/JB.185.11.3410-3415.2003. PubMed: 12754240.
21. Cheng CS, Chen CH, Luo YC, Chen WT, Chang SY, et al. (2011) Crystal structure and biophysical characterisation of Helicobacter pylori phosphopantetheine adenylyltransferase. Biochem Biophys Res Commun 408: 356-361. doi:10.1016/j.bbrc.2011.04.058. PubMed: 21527250.
22. Zhao L, Allanson NM, Thomson SP, Maclean JK, Barker JJ, et al. (2003) Inhibitors of phosphopantetheine adenylyltransferase. Eur J Med Chem 38: 345-349. doi:10.1016/S0223-5234(03)00047-3. PubMed: 12750020.
23. Shaw WV, Lewendon A, (2000) Production and use of antimicrobial agents. In: Wo0017387, editor. European Patent Office.
24. Sassetti CM, Boyd DH, Rubin EJ, (2003) Genes required for mycobacterial growth defined by high density mutagenesis. Mol Microbiol 48: 77-84. doi:10.1046/j.1365-2958.2003.03425.x. PubMed: 12657046.
25. Shoichet BK, (2004) Virtual screening of chemical libraries. Nature 432: 862-865. doi:10.1038/nature03197. PubMed: 15602552.
26. Rester U, (2008) From virtuality to reality- Virtual screening in lead discovery and lead optimization: a medicinal chemistry perspective. Curr Opin Drug Discov Dev 11: 559-568. PubMed: 18600572.
27. Rollinger JM, Stuppner H, Langer T, (2008) Virtual screening for the discovery of bioactive natural products. Prog Drug Res 65211: 213-249. PubMed: 18084917.
28. Wu GS, Robertson DH, Brooks CL, Vieth M, (2003) Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm. J Comput Chem 24: 1549-1562. doi:10.1002/jcc.10306. PubMed: 12925999.
29. Venkatachalam CM, Jiang X, Oldfield T, Waldman M, (2003) LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. J Mol Graph Modell 21: 289-307. doi:10.1016/S1093-3263(02)00164-X. PubMed: 12479928.
30. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, et al. (1983) Charmm- a Program for Macromolecular Energy, Minimization, and Dynamics Calculations. J Comput Chem 4: 187-217. doi:10.1002/jcc.540040211.
31. Discovery Studio vASISD (2007).
32. Maple JR, Hwang MJ, Jalkanen KJ, Stockfisch TP, Hagler AT, (1998) Derivation of class II force fields: V. Quantum force field for amides, peptides, and related compounds. J Comput Chem 19: 430-458. doi:10.1002/(SICI)1096-987X(199803)19:4.
33. Krammer A, Kirchhoff PD, Jiang X, Venkatachalam CM, Waldman M, (2005) LigScore: a novel scoring function for predicting binding affinities. J Mol Graph Modell 23: 395-407. doi:10.1016/j.jmgm.2004.11.007. PubMed: 15781182.
34. Willett P, Barnard JM, Downs GM, (1998) Chemical similarity searching. J Chem Inf Comput Sci 38: 983-996. doi:10.1021/ci9800211.
35. Muegge I, Martin YC, (1999) A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J Med Chem 42: 791-804. doi:10.1021/jm980536j. PubMed: 10072678.
36. Gehlhaar DK, Verkhivker GM, Rejto PA, Sherman CJ, Fogel DB, et al. (1995) Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming. Chem Biol 2: 317-324. doi:10.1016/1074-5521(95)90050-0. PubMed: 9383433.
37. DeLano WL, (2002) The PyMOL Molecular Graphics System Delano: Scientific Publishing House, San Carlos, CA, USA.
38. Wallace AC, Laskowski RA, Thornton JM, (1995) LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng 8: 127-134. doi:10.1093/protein/8.2.127. PubMed: 7630882.
39. Webb MR, (1992) A continuous spectrophotometric assay for inorganic phosphate and for measuring phosphate release kinetics in biological systems. Proc Natl Acad Sci U S A 89: 4884-4887. doi:10.1073/pnas.89.11.4884. PubMed: 1534409.
40. Wang X, Hirmo S, Willén R, Wadström T, (2001) Inhibition of Helicobacter pylori infection by bovine milk glycoconjugates in a BAlb/cA mouse model. J Med Microbiol 50: 430-435. PubMed: 11339250.
41. Miller JR, Thanabal V, Melnick MM, Lall M, Donovan C, et al. (2010) The use of biochemical and biophysical tools for triage of high-throughput screening hits- A case study with Escherichia coli phosphopantetheine adenylyltransferase. Chem Biol Drugs Des 75: 444-454. doi:10.1111/j.1747-0285.2010.00957.x. PubMed: 20486930.
42. Bartlett MS, Shaw M, Navaran P, Smith JW, Queener SF, (1995) Evaluation of potent inhibitors of dihydrofolate reductase in a culture model for growth of Pneumocystis carinii. Antimicrob Agents Chemother 39: 2436-2441. doi:10.1128/AAC.39.11.2436. PubMed: 8585722.
43. Wubben TJ, Mesecar AD, (2010) Kinetic, thermodynamic, and structural insight into the mechanism of phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis. J Mol Biol 404: 202-219. doi:10.1016/j.jmb.2010.09.002. PubMed: 20851704.
44. Berg JMT, Tymoczko JL, Stryer L, (2007) Biochemistry. New York: Freeman.
45. Kusters JG, Gerrits MM, VanStrijp JAG, VandenbrouckeGrauls CMJE, (1997) Coccoid forms of Helicobacter pylori are the morphologic manifestation of cell death. Infect Immun 65: 3672-3679. PubMed: 9284136.
46. Lin JT, Bertino JR, (1991) Update on trimetrexate, a folate antagonist with antineoplastic and antiprotozoal properties. Cancer Invest 9: 159-172. doi:10.3109/07357909109044227. PubMed: 1830825.
47. Harris RE, McCallister JA, Provisor DS, Weetman RM, Baehner RL, (1980) Methotrexate/L-asparaginase combination chemotherapy for patients with acute leukemia in relapse: a study of 36 children. Cancer 46: 2004-2008. doi:10.1002/1097-0142(19801101)46:9. PubMed: 6968621.
48. Sawaya MR, Kraut J, (1997) Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: Crystallographic evidence. Biochemistry 36: 586-603. doi:10.1021/bi962337c. PubMed: 9012674.
49. Thillet J, Absil J, Stone SR, Pictet R, (1988) Site-Directed Mutagenesis of Mouse Dihydrofolate-Reductase- Mutants with Increased Resistance to Methotrexate and Trimethoprim. J Biol Chem 263: 12500-12508. PubMed: 3045118.