X-ray crystal structure and binding mode analysis of human S-adenosylhomocysteine hydrolase complexed with novel mechanism-based inhibitors, haloneplanocin A analogues

Journal of Medicinal Chemistry

Volumn 54, Issue 4, 2011, Pages 930-938

  Lee, Kang Man ^a   Choi, Won Jun ^a,b   Lee, Yoonji ^a   Lee, Hyun Joo ^a   Zhao, Long Xuan ^a,c   Lee, Hyuk Woo ^a   Park, Jae Gyu ^a   Kim, Hea Ok ^a   Hwang, Kwang Yeon ^d   Heo, Yong Seok ^e   Choi, Sun ^a   Jeong, Lak Shin ^a  

^a Ewha Womans University   (South Korea)

^b Dongguk University   (South Korea)

^c LIAONING NORMAL UNIVERSITY   (China)

^d Korea University   (South Korea)

^e Konkuk University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSYLHOMOCYSTEINASE; HALOGEN; NEPLANOCIN A;

ARTICLE; BIOLOGICAL ACTIVITY; CRYSTAL STRUCTURE; ENZYME BINDING; ENZYME INHIBITION; HUMAN; MOLECULAR MODEL; NONHUMAN; PHARMACOPHORE; X RAY CRYSTALLOGRAPHY;

ADENOSINE; ADENOSYLHOMOCYSTEINASE; CRYSTALLOGRAPHY, X-RAY; ENZYME INHIBITORS; HUMANS; INHIBITORY CONCENTRATION 50; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; OPTICAL ROTATION; SPECTROMETRY, MASS, FAST ATOM BOMBARDMENT;

EID: 79951844831     PISSN: 00222623     EISSN: 15204804     Source Type: Journal    
DOI: 10.1021/jm1010836     Document Type: Article

References (26)

1. Turner, M. A.; Yang, X.; Yin, D.; Kuczera, K.; Borchardt, R. T.; Howell, P. L. Structure and function of S -adenosylhomocysteine hydrolase Cell Biochem. Biophys. 2000, 33, 101-125
2. Cantoni, G. L. The Centrality of S -Adenosylhomocysteinase in the Regulation of the Biological Utilization of S -Adenosylmethionine. In Biological Methylation and Drug Design; Borchardt, R. T.; Creveling, C. R.; Ueland, P. M., Eds.; Humana Press: Clifton, NJ, 1986; pp 227 - 238.
3. Snoeck, R.; Andrei, G.; Neyts, J.; Schols, D.; Cools, M.; Balzarini, J.; De Clercq, E. Inhibitory activity of S -adenosylhomocysteine hydrolase inhibitors against human cytomegalovirus replication Antiviral Res. 1993, 21, 197-216 (Pubitemid 23188003)
4. Liu, S.; Wolfe, M. S.; Borchardt, R. T. Rational approaches to the design of antiviral agents based on S -adenosyl- l -homocysteine hydrolase as a molecular target Antiviral Res. 1992, 19, 247-265
5. Wolfe, M. S.; Borchardt, R. T. S -Adenosyl- l -homocysteine hydrolase as a target for antiviral chemotherapy J. Med. Chem. 1991, 34, 1521-1530
6. Keller, B. T.; Borchardt, R. T. Metabolism and Mechanism of Action of Neplanocin A: A Potent Inhibitor of S -Adenosylhomocysteine Hydrolase. In Biological Methylation and Drug Design; Borchardt, R. T.; Creveling, C. R.; Ueland, P. M., Eds.; Humana Press: Clifton, NJ, 1986; pp 385 - 396.
7. Jeong, L. S.; Yoo, S. J.; Lee, K. M.; Koo, M. J.; Choi, W. J.; Kim, H. O.; Moon, H. R.; Lee, M. Y.; Park, J. G.; Lee, S. K.; Chun, M. W. Design, synthesis, and biological evaluation of fluoroneplanocin A as the novel mechanism-based inhibitor of S -adenosylhomocysteine hydrolase J. Med. Chem. 2003, 46, 201-203 (Pubitemid 36078138)
8. The preliminary accounts were published in the Proceedings of XV International Roundtable, Leuven, Belgium, September 10-14, 2002. Jeong, L. S.; Moon, H. R.; Park, J. G.; Shin, D. H.; Choi, W. J.; Lee, K. M.; Kim, H. O.; Chun, M. W.; Kim, H. D.; Kim, J. H. Synthesis and biological evaluation of halo-neplanocin A as novel mechanism-based inhibitors of S -adenosylhomocysteine hydrolase Nucleosides, Nucleotides Nucleic Acids 2003, 22, 589-592 (Pubitemid 37139213)
9. Jeong, L. S.; Park, J. G.; Choi, W. J.; Moon, H. R.; Lee, K. M.; Kim, H. O.; Kim, H. D.; Chun, M. W.; Park, H. Y.; Kim, K.; Sheen, Y. Y. Synthesis of halogenated 9-(dihydroxycyclopent-4′-enyl) adenines and their inhibitory activities against S -adenosylhomocysteine hydrolase Nucleosides, Nucleotides Nucleic Acids 2003, 22, 919-921 (Pubitemid 37139290)
10. Moon, H. R.; Choi, W. J.; Kim, H. O.; Jeong, L. S. Preparative synthesis of the key intermediate, (4 R,5 R)-3-benzyloxymethyl-4,5- isopropylidenedioxycyclopent-2-enone for carbocyclic nucleosides Chem. Lett. 2004, 33, 506-507
11. Moon, H. R.; Choi, W. J.; Kim, H. O.; Jeong, L. S. Improved and alternative synthesis of d-and l -cyclopentenone derivatives, the versatile intermediates for the synthesis of carbocyclic nucleosides Tetrahedron: Asymmetry 2002, 13, 1189-1193 (Pubitemid 34786576)
12. Kim, H. O.; Yoo, S. J.; Ahn, H. S.; Choi, W. J.; Moon, H. R.; Lee, K. M.; Chun, M. W.; Jeong, L. S. Synthesis of fluorinated cyclopentenyladenine as potent inhibitor of S -adenosylhomocysteine hydrolase Bioorg. Med. Chem. Lett. 2004, 14, 2091-2093 (Pubitemid 38481367)
13. Yang, X. D.; Hu, Y. B.; Yin, D. H.; Turner, M. A.; Wang, M.; Borchardt, R. T.; Howell, P. L.; Kuczera, K.; Schowen, R. L. Catalytic strategy of S -adenosyl- l -homocysteine hydrolase: transition-state stabilization and the avoidance of abortive reactions Biochemistry 2003, 42, 1900-1909 (Pubitemid 36258662)
14. Turner, M. A.; Yuan, C. S.; Borchardt, R. T.; Hershfield, M. S.; Smith, G. D.; Howell, P. L. Structure determination of selenomethionyl S -adenosylhomocysteine hydrolase using data at a single wavelength Nat. Struct. Biol. 1998, 5, 369-376 (Pubitemid 28211175)
15. Hu, Y. B.; Komoto, J.; Huang, Y.; Gomi, T.; Ogawa, H.; Takata, Y.; Fujioka, M.; Takusagawa, F. Crystal structure of S -adenosylhomocysteine hydrolase from rat liver Biochemistry 1999, 38, 8323-8333
16. Stepkowski, T.; Brzezinski, K.; Legocki, A. B.; Jaskolski, M.; Bena, G. Bayesian phylogenetic analysis reveals two-domain topology of S -adenosylhomocysteine hydrolase protein sequences Mol. Phylogenet. Evol. 2005, 34, 15-28 (Pubitemid 39584193)
17. Reddy, M. C. M.; Kuppan, G.; Shetty, N. D.; Owen, J. L.; Ioerger, T. R.; Sacchettini, J. C. Crystal structures of Mycobacterium tuberculosis S -adenosyl- l -homocysteine hydrolase in ternary complex with substrate and inhibitors Protein Sci. 2008, 17, 2134-2144
18. Tanaka, N.; Nakanishi, M.; Kusakabe, Y.; Shiraiwa, K.; Yabe, S.; Ito, Y.; Kitade, Y.; Nakamura, K. T. Crystal structure of S -adenosyl- l -homocysteine hydrolase from the human malaria parasite Plasmodium falciparum J. Mol. Biol. 2004, 343, 1007-1017 (Pubitemid 39345960)
19. Yamada, T.; Takata, Y.; Komoto, J.; Gomi, T.; Ogawa, H.; Fujioka, M.; Takusagawa, F. Catalytic mechanism of S -adenosylhomocysteine hydrolase: roles of His 54, Asp130, Glu155, Lys185, and Asp189 Int. J. Biochem. Cell Biol. 2005, 37, 2417-2435
20. Rowland, R. S.; Taylor, R. Intermolecular nonbonded contact distances in organic crystal structures: comparison with distances expected from van der Waals radii J. Phys. Chem. 1996, 100, 7384-7391 (Pubitemid 126789411)
21. Park, A.-Y.; Kim, K. R.; Lee, H.-R.; Kang, J.-A.; Kim, W. H.; Chun, P.; Ahmad, P.; Jeong, L. S.; Moon, H. R. Design and synthesis of 5″-iodoneplanocin A and its analogues as potential S -adenosylhomocysteine hydrolase inhibitor Bull. Korean Chem. Soc. 2008, 29, 2487-2490
22. Yuan, C. S.; Yeh, J.; Liu, S.; Borchardt, R. T. Mechanism of inactivation of S -adenosylhomocysteine hydrolase by (Z)-4′,5′-didehydro- 5′-deoxy-5′-fluoroadenosine J. Biol. Chem. 1993, 268, 17030-17037 (Pubitemid 23236929)
23. Bradford, M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding Anal. Biochem. 1976, 72, 248-254
24. Otwinowski, Z.; Minor, W. Processing of X-ray Diffraction Data Collected in Oscillation Mode. In Macromolecular Crystallography. Part A; Carter, C. W.; Sweet, R. M., Eds.; Methods in Enzymology, Vol. 276; Academic Press: San Diego, CA, 1997; pp 307 - 326. (Pubitemid 27085611)
25. Brunger, A. T.; Adams, P. D.; Clore, G. M.; DeLano, W. L.; Gros, P.; Grosse-Kunstleve, R. W.; Jiang, J. S.; Kuszewski, J.; Nilges, M.; Pannu, N. S.; Read, R. J.; Rice, L. M.; Simonson, T.; Warren, G. L. Crystallography & NMR system: a new software suite for macromolecular structure determination Acta Crystallogr., Sect. D: Biol. Crystallogr. 1998, 54, 905-921
26. Emsley, P.; Cowtan, K. Coot: model-building tools for molecular graphics Acta Crystallogr., Sect. D: Biol. Crystallogr. 2004, 60, 2126-2132 (Pubitemid 41742764)