O-nucleoside, S-nucleoside, and N-nucleoside probes of lumazine synthase and riboflavin synthase

Journal of Organic Chemistry

Volumn 77, Issue 14, 2012, Pages 6239-6261

  Talukdar, Arindam ^a   Zhao, Yujie ^a   Lv, Wei ^a   Bacher, Adelbert ^b   Illarionov, Boris ^b   Fischer, Markus ^b   Cushman, Mark ^a  

^a PURDUE UNIVERSITY   (United States)

^b UNIVERSITY OF HAMBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

C-NUCLEOSIDES; DEPROTECTION REACTION; ENZYME-CATALYZED REACTIONS; FREE-ENERGY CALCULATIONS; LIGAND BINDING; LUMAZINE SYNTHASE; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR FORCES; NITRO GROUP; POISSON-BOLTZMANN; POTENTIAL VALUES; PROTECTING GROUP; REACTIVE FUNCTIONALITY; SYNTHASE INHIBITOR; SYNTHASES; TARGET COMPOUND;

BIOCHEMISTRY; BIOSYNTHESIS; CATALYSIS; ENZYMES; LIGANDS; MOLECULAR DYNAMICS; OLEFINS; PROBES; REACTION INTERMEDIATES;

BIOMOLECULES;

2,4 BIS(BENZYLOXY) 5 NITRO 6 [( 2,2,2',2' TETRAMETHYL 4,4' BI(1,3 DIOXOLAN) 5 YL)METHOXY]PYRIMIDINE; 2,4 BIS(BENZYLOXY) 6 [( 2,2,2',2' TETRAMETHYL 4,4' BI(1,3 DIOXOLAN) 5 YL)METHOXY)PYRIMIDIN 5 AMINE; 2,4 DIMETHOXY 5 NITRO 6 [(2,2,2',2' TETRAMETHYL 4,4' BI(1,3 DIOXOLAN) 5 YL)METHOXY]PYRIMIDINE; 2,6 DIMETHOXY 5 NITRO N ( 2,3,4,5 TETRAKIS(TERT BUTYLDIMETHYLSILYLOXY) PENTYL)PYRIMIDINE 4 AMINE; 5 (2,6 BIS(BENZYLOXY) 5 NITROPYRIMIDIN 4 YLOXY)PENTANE 1,2,3,4 TETROL; 5 AMINO 6 ( 2,3,4,5 TETRAHYDROXYPENTYLOXY) PYRIMIDINE 2,4(1H,3H) DIONE; 5 NITRO 6 ( 2,3,4,5 TETRAHYDROXYPENTYLOXY)PYRIMIDINE 2,4(1H,3H) DIONE; ETHYL 2 (2,4 BIS(BENZYLOXY) 6 ( 2,3,4,5 TETRAHYDROXYPENTYLOXY)PYRIMIDIN 5 YLAMINO) 2 OXOACETATE; ETHYL 2 (2,4 BIS(BENZYLOXY) 6 [( 2,2,2?,2' TETRAMETHYL4,4' BI(1,3 DIOXOLAN) 5 YL)METHOXY)PYRIMIDIN 5 YLAMINO) 2 OXOACETATE; ETHYL 2 (2,4 DIOXO 6 ( 2,3,4,5 TETRAHYDROXYPENTYLOXY) 1,2,3,4 TETRAHYDROPYRIMIDIN 5 YLAMINO) 2 OXOACETATE; LUMAZINE SYNTHASE; METHYL 2 (2,4 BIS(BENZYLOXY) 6 ( 2,3,4,5 TETRAHYDROXYPENTYLOXY)PYRIMIDIN 5 YLAMINO) 2 OXOACETATE; METHYL 2 (2,4 DIOXO 6 ( 2,3,4,5 TETRAHYDROXYPENTYLOXY) 1,2,3,4 TETRAHYDROPYRIMIDIN 5 YLAMINO) 2 OXOACETATE; N (2,4 BIS(BENZYLOXY) 6 ( 2,3,4,5 TETRAHYDROXYPENTYLOXY)PYRIMIDIN 5 YLAMINO)METHACRYLAMIDE; N (2,4 BIS(BENZYLOXY) 6 ( 2,3,4,5 TETRAHYDROXYPENTYLOXY)PYRIMIDIN 5 YLAMINO)PROPIONAMIDE; N (2,4 BIS(BENZYLOXY) 6 (2,3,4,5 TETRAHYDROXYPENTYLOXY)PYRIMIDIN 5 YLAMINO)ISOBUTYRAMIDE; N (2,4 BIS(BENZYLOXY) 6 [( 2,2,2',2' TETRAMETHYL 4,4' BI(1,3 DIOXOLAN) 5 YL)METHOXY)PYRIMIDIN 5 YL) METHACRYLAMIDE; N (2,4 BIS(BENZYLOXY) 6 [( 2,2,2',2'TETRAMETHYL 4,4' BI(1,3 DIOXOLAN) 5 YL)METHOXY)PYRIMIDIN 5 YL) ISOBUTYRAMIDE; N (2,4 BIS(BENZYLOXY) 6 [(2,2,2',2' TETRAMETHYL 4,4' BI(1,3 DIOXOLAN) 5 YL)METHOXY)PYRIMIDIN 5 YL) PROPIONAMIDE; N (2,4 DIOXO 6 ( 2,3,4,5 TETRAHYDROXYPENTYLOXY) TETRAHYDROXYPENTYLOXY) 1,2,3,4 TETRAHYDROPYRIMIDIN 5 YL)PROPIONAMIDE; N (2,4 DIOXO 6 ( 2,3,4,5 TETRAHYDROXYPENTYLTHIO) 1,2,3,4 TETRAHYDROPYRIMIDIN 5 YL)METHACRYLAMIDE; N (2,4 DIOXO 6 ( 2,3,4,5 TETRAHYDROXYPENTYLTHIO) 1,2,3,4 TETRAHYDROPYRIMIDIN 5 YL)PROPIONAMIDE; N (2,4 DIOXO 6 [( 2,2,2',2' TETRAMETHYL 4,4' BI (1,3 DIOXOLAN) 5 YL)METHYLTHIO) 1,2,3,4 TETRAHYDROPYRIMIDIN 5 YL)METHACRYLAMIDE; N (2,4 DIOXO 6 [( 2,2,2',2' TETRAMETHYL 4,4' BI (1,3 DIOXOLAN) 5 YL)METHYLTHIO) 1,2,3,4 TETRAHYDROPYRIMIDIN 5 YL)PROPIONAMIDE; N (2,4 DIOXO) 6 ( 2,3,4,5 TETRAHYDROXYPENTYLOXY) 1,2,3,4 TETRAHYDROPYRIMIDIN 5 YL)ISOBUTYRAMIDE; N (2,4 DIOXO) 6 ( 2,3,4,5 TETRAHYDROXYPENTYLOXY) 1,2,3,4 TETRAHYDROPYRIMIDIN 5 YL)METHACRYLAMIDE; NUCLEOSIDE; RIBOFLAVIN SYNTHASE; S NUCLEOSIDE; SYNTHETASE; UNCLASSIFIED DRUG;

ARTICLE; BACILLUS SUBTILIS; ENZYME STRUCTURE; HYDROGENOLYSIS; LIGAND BINDING; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MYCOBACTERIUM TUBERCULOSIS; PROTEIN SYNTHESIS; SCHIZOSACCHAROMYCES POMBE;

ENZYME INHIBITORS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR DYNAMICS SIMULATION; MULTIENZYME COMPLEXES; NUCLEOSIDES; RIBOFLAVIN SYNTHASE; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84864056402     PISSN: 00223263     EISSN: 15206904     Source Type: Journal    
DOI: 10.1021/jo3010364     Document Type: Article

References (60)

1. Wang, A. I Chuan Hsueh Pao 1992, 19, 362
2. Oltmanns, O.; Lingens, F. Z. Naturforsch. 1967, 22b, 751
3. Logvinenko, E. M.; Shavlovsky, G. M. Mikrobiologiya 1967, 41, 978
4. Neuberger, G.; Bacher, A. Biochem. Biophys. Res. Commun. 1985, 127, 175
5. Rollenhagen, C.; Bumann, D. Infect. Immun. 2006, 74, 1649
6. Becker, D.; Selbach, M.; Rollenhagen, C.; Ballmaier, M.; Meyer, T. F.; Mann, M.; Bumann, D. Nature 2006, 440, 303
7. Fischer, M.; Bacher, A. Nat. Prod. Rep. 2005, 22, 324
8. Fischer, M.; Bacher, A. Physiol. Plant. 2006, 126, 304
9. Foor, F.; Brown, G. M. J. Biol. Chem. 1975, 250, 3545
10. Foor, F.; Brown, G. M. Methods Enzymol. 1980, 66, 303
11. Burrows, R. B.; Brown, G. M. J. Bacteriol. 1978, 136, 657
12. Hollander, I.; Brown, G. M. Biochem. Biophys. Res. Commun. 1979, 89, 759
13. Nielsen, P.; Bacher, A. Biochem. Biophys. Acta 1981, 662, 312
14. Richter, G.; Krieger, C.; Volk, R.; Kis, K.; Ritz, H.; Gotze, E.; Bacher, A. Methods Enzymol. 1997, 280, 374
15. Fischer, M.; Romisch, W.; Saller, S.; Illarionov, B.; Richter, G.; Rohdich, F.; Eisenreich, W.; Bacher, A. J. Biol. Chem. 2004, 279, 36299
16. Fischer, M.; Romisch, W.; Schiffmann, S.; Kelly, M.; Oschkinat, H.; Steinbacher, S.; Huber, R.; Eisenreich, W.; Richter, G.; Bacher, A. J. Biol. Chem. 2002, 277, 41410
17. Volk, R.; Bacher, A. J. Am. Chem. Soc. 1988, 110, 3651
18. Volk, R.; Bacher, A. J. Biol. Chem. 1990, 265, 19479
19. Neuberger, G.; Bacher, A. Biochem. Biophys. Res. Commun. 1986, 139, 1111
20. Kis, K.; Volk, R.; Bacher, A. Biochemistry 1995, 34, 2883
21. Fischer, M.; Haase, I.; Feicht, R.; Schramek, N.; Kohler, P.; Schieberle, P.; Bacher, A. Biol. Chem. 2005, 386, 417
22. Gerhardt, S.; Schott, A.-K.; Kairies, N.; Cushman, M.; Illarionov, B.; Eisenreich, W.; Bacher, A.; Huber, R.; Steinbacher, S.; Fischer, M. Structure 2002, 10, 1371
23. Illarionov, B.; Eisenreich, W.; Bacher, A. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 7224
24. Illarionov, B.; Eisenreich, W.; Schramek, N.; Bacher, A.; Fischer, M. J. Biol. Chem. 2005, 280, 28541
25. Illarionov, B.; Kemter, K.; Eberhardt, S.; Richter, G.; Cushman, M.; Bacher, A. J. Biol. Chem. 2001, 276, 11524
26. Maley, G. F.; Plaut, G. W. E. J. Biol. Chem. 1959, 234, 641
27. Plaut, G. W. E. J. Biol. Chem. 1963, 238, 2225
28. Plaut, G. W. E.; Harvey, R. A. Methods Enzymol. 1971, 18B, 515
29. Wacker, H.; Harvey, R. A.; Winestock, C. H.; Plaut, G. W. E. J. Biol. Chem. 1964, 239, 3493
30. Kim, R.-R.; Illarionov, B.; Joshi, M.; Cushman, M.; Lee, C. Y.; Eisenreich, W.; Fischer, B.; Bacher, A. J. Am. Chem. Soc. 2010, 132, 2983
31. Meining, W.; Mörtl, S.; Fischer, M.; Cushman, M.; Bacher, A.; Ladenstein, R. J. Mol. Biol. 2000, 299, 181
32. Zhang, X.; Meining, W.; Cushman, M.; Haase, I.; Fischer, M.; Bacher, A.; Ladenstein, R. J. Mol. Biol. 2003, 328, 167
33. Zheng, Y. J.; Viitanen, P. V.; Jordan, D. B. Bioorg. Chem. 2000, 28, 89
34. Haase, I.; Fischer, M.; Bacher, A.; Schramek, N. J. Biol. Chem. 2003, 278, 37909
35. Schramek, N.; Haase, I.; Fischer, M.; Bacher, A. J. Am. Chem. Soc. 2003, 125, 4460
36. Ritsert, K.; Huber, R.; Turk, D.; Ladenstein, R.; Schmidt-Bäse, K.; Bacher, A. J. Mol. Biol. 1995, 253, 151
37. Cushman, M.; Jin, G.; Illarionov, B.; Fischer, M.; Ladenstein, R.; Bacher, A. J. Org. Chem. 2005, 70, 8162
38. Zhang, Y. L.; Jin, G. Y.; Illarionov, B.; Bacher, A.; Fischer, M.; Cushman, M. J. Org. Chem. 2007, 72, 7176
39. Cushman, M.; Mihalic, J. T.; Kis, K.; Bacher, A. J. Org. Chem. 1999, 64, 3838
40. Morgunova, K.; Meining, W.; Illarionov, B.; Haase, I.; Jin, G.; Bacher, A.; Cushman, M.; Fischer, M.; Ladenstein, R. Biochemistry 2005, 44, 2746
41. Morgunova, E.; Illarionov, B.; Sambaiah, T.; Haase, I.; Bacher, A.; Cushman, M.; Fischer, M.; Ladenstein, R. FEBS J 2006, 273, 4790
42. Morgunova, E.; Saller, S.; Haase, I.; Cushman, M.; Bacher, A.; Fischer, M.; Ladenstein, R. J. Biol. Chem. 2007, 282, 17231
43. Yu, T. Y.; O'Connor, R. D.; Sivertsen, A. C.; Chiauzzi, C.; Poliks, B.; Fischer, M.; Bacher, A.; Haase, I.; Cushman, M.; Schaefer, J. Biochemistry 2008, 47, 13942
44. Ramsperger, A.; Augustin, M.; Schott, A. K.; Gerhardt, S.; Krojer, T.; Eisenreich, W.; Illarionov, B.; Cushman, M.; Bacher, A.; Huber, R.; Fischer, M. J. Biol. Chem. 2006, 281, 1224
45. Amoo, V. E.; Debernardo, S.; Weigele, M. Tetrahedron Lett. 1988, 29, 2401
46. Nutiu, R.; Boulton, A. J. J. Chem. Soc., Perkin Trans. 1 1976, 1327
47. Sakamoto, T.; Uchiyama, D.; Kondo, Y.; Yamanaka, H. Chem. Pharm. Bull. 1993, 41, 478
48. Zhang, Y. L.; Illarionov, B.; Morgunova, E.; Jin, G. Y.; Bacher, A.; Fischer, M.; Ladenstein, R.; Cushman, M. J. Org. Chem. 2008, 73, 2715
49. Talukdar, A.; Illarionov, B.; Bacher, A.; Fischer, M.; Cushman, M. J. Org. Chem. 2007, 72, 7167
50. Cushman, M.; Sambaiah, T.; Jin, G.; Illarionov, B.; Fischer, M.; Bacher, A. J. Org. Chem. 2004, 69, 601
51. Chen, J.; Sambaiah, T.; Illarionov, B.; Fischer, M.; Bacher, A.; Cushman, M. J. Org. Chem. 2004, 69, 6996
52. Talukdar, A.; Morgunova, E.; Duan, J. X.; Meining, W.; Foloppe, N.; Nilsson, L.; Bacher, A.; Illarionov, B.; Fischer, M.; Ladenstein, R.; Cushman, M. Bioorg. Med. Chem. 2010, 18, 3518
53. Al-Hassan, S. S.; Kulick, R. J.; Livingston, D. B.; Suckling, C. J.; Wood, H. C. S.; Wrigglesworth, R.; Ferone, R. J. Chem. Soc., Perkin Trans. 1 1980, 2645
54. Winestock, C. H.; Aogaichi, T.; Plaut, G. W. E. J. Biol. Chem. 1963, 238, 2866
55. Cushman, M.; Yang, D.; Kis, K.; Bacher, A. J. Org. Chem. 2001, 66, 8320
56. Kim, R.-R.; Illarionov, B.; Joshi, M.; Cushman, M.; Lee, C. Y.; Eisenreich, W.; Fischer, M.; Bacher, A. J. Am. Chem. Soc. 2010, 132, 2983
57. Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S. H.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E. Acc. Chem. Res. 2000, 33, 889
58. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, revision C.02 ed.; Gaussian, Inc.: Wallingford, CT, 2004.
59. Talukdar, A.; Breen, M.; Bacher, A.; Illarionov, B.; Fischer, M.; Georg, G.; Ye, Q.-Z.; Cushman, M. J. Org. Chem. 2009, 74, 5123
60. Kuzmic, P. Anal. Biochem. 1960, 237, 260