Discovery of novel types of inhibitors of S-adenosylmethionine synthesis by virtual screening

Journal of Medicinal Chemistry

Volumn 52, Issue 19, 2009, Pages 5967-5973

  Taylor, John C ^d   Bock, Charles W ^a,c   Takusagawa, Fusao ^b   Markham, George D ^a  

^a FOX CHASE CANCER CENTER   (United States)

^b UNIVERSITY OF KANSAS   (United States)

^c THOMAS JEFFERSON UNIVERSITY   (United States)

^d NONE

Author keywords

[No Author keywords available]

Indexed keywords

1 (4 CHLORO 2 NITROPHENYL) 3 (4-SULFAMOYLPHENYL) UREA; 1 [3 (2 ETHOXYPHENYL)UREIDOACETYL] 4 (2 METHYL 5 NITROPHENYL)SEMICARBAZIDE; ADENOSINE TRIPHOSPHATE; ANTIINFECTIVE AGENT; ANTINEOPLASTIC AGENT; ENZYME INHIBITOR; METHIONINE; METHIONINE ADENOSYLTRANSFERASE; S 867349; S 903566; S ADENOSYLMETHIONINE; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL CELL; BINDING AFFINITY; DRUG BINDING; DRUG STRUCTURE; DRUG SYNTHESIS; ENZYME INHIBITION; GROWTH INHIBITION; IC 50; NONHUMAN; NUCLEOTIDE BINDING SITE;

CATALYTIC DOMAIN; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; DRUG DISCOVERY; DRUG EVALUATION, PRECLINICAL; ESCHERICHIA COLI; INHIBITORY CONCENTRATION 50; METHIONINE ADENOSYLTRANSFERASE; PROTEIN BINDING; PROTEIN CONFORMATION; S-ADENOSYLMETHIONINE; SACCHAROMYCES CEREVISIAE;

EID: 70349643108     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm9006142     Document Type: Article

References (43)

1. Cantoni, G. L. Biological methylation: selected aspects. Annu. Rev. Biochem. 1975, 44, 435-451.
2. Tabor, C. W.; Tabor, H. Polyamines. Annu. Rev. Biochem. 1984, 53, 749-790.
3. Markham, G. D. S-Adenosylmethionine. In Encyclopedia of Life Sciences; John Wiley & Sons: London, Chichester, 2003; http://www.els.net/ DOI: 10.1038/npg.els.0000662.
4. Fontecave, M.; Atta, M.; Mulliez, E. S-Adenosylmethionine: nothing goes to waste. Trends Biochem. Sci. 2004, 29, 243-249.
5. Lu, S. C.; Mato, J. M. S-Adenosylmethionine in cell growth, apoptosis and liver cancer. J. Gastroenterol. Hepatol. 2008, 23 (Suppl. 1), S73-S77.
6. Mato, J. M.; Martinez-Chantar, M. L.; Lu, S. C. Methionine metabolism and liver disease. Annu. Rev. Nutr. 2008, 28, 273-293.
7. Markham, G. D.; Pajares, M. A. Structure-function relationships in methionine adenosyltransferases. Cell. Mol. Life Sci. 2009, 66, 636-648.
8. Coulter, A. W.; Lombardini, J. B.; Sufrin, J. R.; Talalay, P. Structural and conformational analogues of L-methionine as inhibitors of the enzymatic synthesis of S-adenosyl-l-methionine. 3. Carbocyclic and heterocyclic amino acids. Mol. Pharmacol. 1974, 10, 319-334.
9. Goldberg, B.; Rattendi, D.; Lloyd, D.; Sufrin, J. R.; Bacchi, C. J. Effects of intermediates of methionine metabolism and nucleoside analogs on S-adenosylmethionine transport by Trypanosoma brucei brucei and a drug-resistant Trypanosoma brucei rhodesiense. Biochem. Pharmacol. 1998, 56, 95-103.
10. Sufrin, J. R.; Lombardini, J. B.; Keith, D. D. L-2-Amino-4-methoxy-cis- but-3-enoic acid, a potent inhibitor of the enzymatic synthesis of S-adenosylmethionine. Biochem. Biophys. Res. Commun. 1982, 106, 251-255.
11. Sufrin, J. R.; Lombardini, J. B.; Alks, V. Differential kinetic properties of L-2-amino-4-methylthio-cis-but-3-enoic acid, a methionine analog inhibitor of S-adenosylmethionine synthetase. Biochim. Biophys. Acta 1993, 1202, 87-91.
12. Lavrador, K.; Guillerm, D.; Guillerm, G. A new series of cyclic amino acids as inhibitors of S-adenosyl-L-methionine synthetase. Bioorg. Med. Chem. Lett. 1998, 8, 1629-1634.
13. Lavrador, K.; Allart, B.; Guillerm, D.; Guillerm, G. A new series of S-adenosyl-L-methionine synthetase inhibitors. J. Enzyme Inhib. 1998, 13, 361-367. (Pubitemid 28441954)
14. Vrudhula, V. M.; Kappler, F.; Hampton, A. Isozyme-specific enzyme inhibitors. 13. S-[5′(R)-[(N- triphosphoamino)methyl]-adenosyl]-L- homocysteine, a potent inhibitor of rat methionine adenosyltransferases. J. Med. Chem. 1987, 30, 888-894.
15. Reczkowski, R. S.; Markham, G. D. Slow binding inhibition of S-adenosylmethionine synthetase by imidophosphate analogues of an intermediate and product. Biochemistry 1999, 38, 9063-9068. (Pubitemid 129515240)
16. Krasky, A.; Rohwer, A.; Schroeder, J.; Selzer, P. M. A combined bioinformatics and chemoinformatics approach for the development of new antiparasitic drugs. Genomics 2007, 89, 36-43. (Pubitemid 44873185)
17. Sanchez-Perez, G. F.; Bautista, J. M.; Pajares, M. A. Methionine adenosyltransferase as a useful molecular systematics tool revealed by phylogenetic and structural analyses. J. Mol. Biol. 2004, 335, 693-706.
18. Porter, C. W.; Sufrin, J. R.; Keith, D. D. Growth inhibition by methionine analog inhibitors of S-adenosylmethionine biosynthesis in the absence of polyamine depletion. Biochem. Biophys. Res. Commun. 1984, 122, 350-357.
19. Kramer, D. L.; Sufrin, J. R.; Porter, C. W. Relative effects of S-adenosylmethionine depletion on nucleic acid methylation and polyamine biosynthesis. Biochem. J. 1987, 247, 259-265.
20. Kramer, D. L.; Sufrin, J. R.; Porter, C. W. Modulation of polyamine-biosynthetic activity by S-adenosylmethionine depletion. Biochem. J. 1988, 249, 581-586.
21. Lim, H.; Kappler, F.; Hai, T. T.; Hampton, A. Isozyme-specific enzyme inhibitors. 12. C- and N-methylmethionines as substrates and inhibitors of methionine adenosyltransferases of normal and hepatoma rat tissues. J. Med. Chem. 1986, 29, 1743-1748.
22. Kappler, F.; Vrudhula, V. M.; Hampton, A. Isozyme-specific enzyme inhibitors. 14. 5′(R)-C-[(L-homocystein-S-yl)methyl]-adenosine 50-(beta,gamma-imidotriphosphate), a potent inhibitor of rat methionine adenosyltransferases. J. Med. Chem. 1987, 30, 1599-1603.
23. Kappler, F.; Vrudhula, V. M.; Hampton, A. Toward the synthesis of isozyme-specific enzyme inhibitors. Potent inhibitors of rat methionine adenosyltransferases. Effect of one-atom elongation of the ribose-P alpha bridge in two covalent adducts of L-methionine and beta,gamma-imido-ATP. J. Med. Chem. 1988, 31, 384-389.
24. Kappler, F.; Hampton, A. Approaches to isozyme-specific inhibitors. 17. Attachment of a selectivity-inducing substituent to a multisubstrate adduct. Implications for facilitated design of potent, isozyme-selective inhibitors. J. Med. Chem. 1990, 33, 2545-2551.
25. Kappler, F.; Hai, T. T.; Cotter, R. J.; Hyver, K. J.; Hampton, A. Isozyme-specific enzyme inhibitors. 11. L-Homocysteine-ATP S-C5′ covalent adducts as inhibitors of rat methionine adenosyltransferases. J. Med. Chem. 1986, 29, 1030-1038.
26. Fu, Z.; Hu, Y.; Markham, G. D.; Takusagawa, F. Flexible loop in the structure of S-adenosylmethionine synthetase crystallized in the tetragonal modification. J. Biomol. Struct. Dyn. 1996, 13, 727-739.
27. Takusagawa, F.; Kamitori, S.; Markham, G. D. Structure and function of S-adenosylmethionine synthetase: crystal structures of S-adenosylmethionine synthetase with ADP, BrADP, and PPi at 2.8 angstroms resolution. Biochemistry 1996, 35, 2586-2596.
28. A preliminary description of this work was present at the 2006 Federation of American Societies for Experimental Biology Meeting.
29. Komoto, J.; Yamada, T.; Takata, Y.; Markham, G. D.; Takusagawa, F. Crystal structure of the S-adenosylmethionine synthetase ternary complex: a novel catalytic mechanism of S-adenosylmethionine synthesis from ATP and Met. Biochemistry 2004, 43, 1821-1831. (Pubitemid 38233245)
30. Lu, Z. J.; Markham, G. D. Enzymatic properties of S-adenosylmethionine synthetase from the archaeon Methanococcus jannaschii. J. Biol. Chem. 2002, 277, 16624-16631.
31. Gazdar, A. F.; Minna, J. D. NCI series of cell lines: an historical perspective. J. Cell. Biochem. Suppl. 1996, 24, 1-11.
32. Marx, K. A.; O'Neil, P.; Hoffman, P.; Ujwal, M. L. Data mining the NCI cancer cell line compound GI(50) values: identifying quinone subtypes effective against melanoma and leukemia cell classes. J. Chem. Inf. Comput. Sci. 2003, 43, 1652-1667.
33. Lawrence, S. H.; Ramirez, U. D.; Tang, L.; Fazliyez, F.; Kundrat, L.; Markham, G. D.; Jaffe, E. K. Shape shifting leads to small-molecule allosteric drug discovery. Chem. Biol. 2008, 15, 586-596.
34. 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.
35. Halgren, T. A. Merck molecular force field 0.1. Basis, form, scope, parameterization, and performance of MMFF94. J. Comput. Chem. 1996, 17, 490-519.
36. Cheng, A.; Best, S. A.; Merz, K. M., Jr.; Reynolds, C. H. GB/SA water model for the Merck molecular force field (MMFF). J. Mol. Graph. Model. 2000, 18, 273-282.
37. Taylor, J. C.; Takusagawa, F.; Markham, G. D. The active site loop of S-adenosylmethionine synthetase modulates catalytic efficiency. Biochemistry 2002, 41, 9358-9369.
38. Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shelley, M.; Perry, J. K.; Shaw, D. E.; Francis, P.; Shenkin, P. S. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J. Med. Chem. 2004, 47, 1739-1749.
39. Kaminski, G. A.; Friesner, R. A.; Tirado-Rives, J.; Jorgensen, W. L. Evaluation and reparametrization of th OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J. Phys. Chem. B 2001, 105, 6474-6487.
40. Halgren, T. A.; Murphy, R. B.; Friesner, R. A.; Beard, H. S.; Frye, L. L.; Pollard, W. T.; Banks, J. L. Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J. Med. Chem. 2004, 47, 1750-1759.
41. Eldridge, M.; Murray, C. W.; Auton, T. A.; Paolini, G. V.; Lee, R. P. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J. Comput.-Aided Mol. Des. 1997, 11, 425-445.
42. Markham, G. D.; Hafner, E. W.; Tabor, C. W.; Tabor, H. S-Adenosylmethionine synthetase from Escherichia coli. J. Biol. Chem. 1980, 255, 9082-9092.
43. Li, J. M.; Umanoff, H.; Proenca, R.; Russell, C. S.; Cosloy, S. D. Cloning of the Escherichia coli K-12 hemB gene. J. Bacteriol. 1988, 170, 1021-1025.