Generation of the first structure-based pharmacophore model containing a selective "zinc binding group" feature to identify potential glyoxalase-1 inhibitors

Molecules

Volumn 17, Issue 12, 2012, Pages 13740-13758

  Al Balas, Qosay ^a   Hassan, Mohammad ^a   Al Oudat, Buthina ^a   Alzoubi, Hassan ^a   Mhaidat, Nizar ^a   Almaaytah, Ammar ^a  

^a JORDAN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Jordan)

Author keywords

2D similarity search; CDOCKER; Glyoxlase 1 enzyme; GOLD; Molecular docking; Zinc binding group

Indexed keywords

CARRIER PROTEIN; LACTOYLGLUTATHIONE LYASE; ZINC; ZINC BINDING PROTEIN; ZINC-BINDING PROTEIN;

ALGORITHM; ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; DRUG ANTAGONISM; ENZYME ACTIVE SITE; FACTUAL DATABASE; HUMAN; MOLECULAR DOCKING; PROTEIN BINDING; STRUCTURE ACTIVITY RELATION; SYNTHESIS;

ALGORITHMS; BINDING SITES; CARRIER PROTEINS; CATALYTIC DOMAIN; DATABASES, FACTUAL; HUMANS; LACTOYLGLUTATHIONE LYASE; MOLECULAR DOCKING SIMULATION; MOLECULAR STRUCTURE; PROTEIN BINDING; STRUCTURE-ACTIVITY RELATIONSHIP; ZINC;

EID: 84871583907     PISSN: None     EISSN: 14203049     Source Type: Journal    
DOI: 10.3390/molecules171213740     Document Type: Article

References (49)

1. National Cancer Institute. Available online: http://www.cancer.gov/ (accessed 2 June 2012).
2. Jemal, A.; Bray, F.; Center, M.; Ferlay, J.; Ward, E.; Forman, D. Global cancer statistics. CA Cancer J. Clin. 2011, 61, 69-90.
3. World Health Organization (WHO). The Global Burden of Disease: 2004 Update. WHO: Geneva, Switzerland. Available online: http://www.who.int/topics/ global-burden-of-disease/en/ (accessed 2 June 2012).
4. Aziz, N.M.; Rowland, J.H. Trends and advances in cancer survivorship research: Challenge and opportunity. Semin. Radiat. Oncol. 2003, 13, 248-266.
5. Petrelli, N.J.; Winer, E.P.; Brahmer, J.; Dubey, S.; Smith, S.; Thomas, T.; Vahdat, L.T.; Obel, J.; Vogelzang, N.; Markman, M.; et al. Clinical Cancer Advances 2009: Major Research Advances in Cancer Treatment, Prevention, and Screening: A Report from the American Society of Clinical Oncology. J. Clin. Oncol. 2009, 27, 6052-6069.
6. Davidson, S.; Milanesa, D.; Mallouh, C.; Choudhury, M.; Tazaki, H.; Konno, S. A possible regulatory role of glyoxalase I in cell viability of human prostate cancer. Urol. Res. 2002, 30, 116-121.
7. Rabbani, N.; Thornalley, P. Glyoxalase in diabetes, Obesity and related disorders. Semin. Cell. Dev. Biol. 2011, 22, 309-317.
8. Thornalley, P.; Rabbani, N. Glyoxalase in tumourigenesis and multidrug resistance. Semin. Cell. Dev. Biol. 2011, 22, 318-325.
9. Xue, M.; Rabbani, N.; Thornalley, P. Glyoxalase in ageing. Semin. Cell. Dev. Biol. 2011, 22, 293-301.
10. Sakamoto, H.; Mashima, T.; Kizaki, A.; Dan, S.; Hashimoto, Y.; Naito, M.; Tsuruo, T. Glyoxalase I is involved in resistance of human leukemia cells to antitumor agent-induced apoptosis. Blood 2000, 95, 3214-3218.
11. National Toxicology Program. Final Report on Carcinogens Background Document for Formaldehyde. Rep. Carcinog. Backgr. Doc. 2010, 10-5981, i-512.
12. Chaplen, F. Incidence and potential implications of the toxic metabolite methylglyoxal in cell culture: A review. Cytotechnology 1998, 26, 173-183.
13. Suttisansanee, U.; Honek, J.F. Bacterial glyoxalase enzymes. Semin. Cell. Dev. Biol. 2011, 22, 285-292.
14. Feierberg, I.; Luzhkov, V.; Aqvist, J. Computer Simulation of Primary Kinetic Isotope Effects in the Proposed Rate-limiting Step of the Glyoxalase I Catalyzed Reaction. J. Biol. Chem. 2000, 275, 22657-22662.
15. Thornalley, P. Protecting the genome: Defence against nucleotide glycation and emerging role of glyoxalase I overexpression in multidrug resistance in cancer chemotherapy. Biochem. Soc. Trans. 2003, 31, 1372-1377.
16. Thornalley, P. Glyoxalase I- Structure, Function and a critical role in the enzymatic defence against glycation. Biochem. Soc. Trans. 2003, 31, 1343-1348.
17. Cameron, A.; Olin, B.; Ridderström, M.; Mannervik, B.; Jones, T. Crystal structure of human glyoxalase I-evidence for gene duplication and 3D domain swapping. EMBO J. 1997, 16, 3386-3395.
18. Cameron, A.; Ridderström, M.; Olin, B.; Kavarana, M.; Creighton, D.; Mannervik, B. Reaction Mechanism of Glyoxalase I Explored by an X-ray Crystallographic Analysis of the Human Enzyme in Complex with a Transition State Analogue. Biochemistry 1999, 38, 13480-13490.
19. Vince, R.; Daluge, S.; Wadd, W. Inhibition of glyoxalase I by S-substituted glutathiones. J. Med. Chem. 1971, 14, 402-404.
20. More, S.; Vince, R. A metabolically stable tight-binding transition-state inhibitor of glyoxalase-I. Bioorg. Med. Chem. Lett. 2006, 16, 6039-6042.
21. More, S.; Vince, R. Design, synthesis, and binding studies of bidentate Zn-chelating peptidic inhibitors of glyoxalase-I. Bioorg. Med. Chem. Lett. 2007, 17, 3793-3797.
22. More, S.; Vince, R. Inhibition of Glyoxalase I: The First Low-Nanomolar Tight-Binding Inhibitors. J. Med. Chem. 2009, 52, 4650-4656.
23. Takayoshi, N. Rational Design of Non-Hydroxamate Histone Deacetylase Inhibitors. Mini Rev. Med. Chem. 2006, 6, 515-526.
24. Maingot, L.; Leroux, F.; Landry, V.; Dumont, J.; Nagase, H.; Villoutreix, B.; Sperandio, O.; Deprez-Poulain, R.; Deprez, B. New non-hydroxamic ADAMTS-5 inhibitors based on the 1,2,4-triazole-3-thiol scaffold. Bioorg. Med. Chem. Lett. 2010, 20, 6213-6216.
25. Takasawa, R.; Saeki, K.; Tao, A.; Yoshimori, A.; Uchiro, H.; Fujiwara, M.; Tanuma, S. Delphinidin, a dietary anthocyanidin in berry fruits, inhibits human glyoxalase I. Bioorg. Med. Chem. 2010, 18, 7029-7033.
26. Takasawa, R.; Takahashi, S.; Saeki, K.; Sunaga, S.; Yoshimori, A.; Tanuma, S. Structure activity relationship of human GLO I inhibitory natural flavonoids and their growth inhibitory effects. Bioorg. Med. Chem. 2008, 16, 3969-3975.
27. Takasawa, R.; Tao, A.; Saeki, K.; Shionozaki, N.; Tanaka, R.; Uchiro, H.; Takahashi, S.; Yoshimori, A.; Tanuma, S. Discovery of a new type inhibitor of human glyoxalase I by myricetinbased 4-point pharmacophore. Bioorg. Med. Chem. Lett. 2011, 21, 4337-4342.
28. Liu, M.; Yuan, M.; Luo, M.; Bu, X.; Luo, H.B.; Hu, X. Binding of curcumin with glyoxalase I: Molecular docking, Molecular dynamics simulations, and kinetics analysis. Biophys. Chem. 2010, 147, 28-34.
29. Yuan, M.; Luo, M.; Song, Y.; Xu, Q.; Wang, X.; Cao, Y.; Bu, X.; Ren, Y.; Hu, X. Identification of curcumin derivatives as human glyoxalase I inhibitors: A combination of biological evaluation, Molecular docking, 3D-QSAR and molecular dynamics simulation studies. Bioorg. Med. Chem. 2011, 19, 1189-1196.
30. Bender, A.; Glen, R. Molecular similarity: A key technique in molecular informatics. Org. Biomol. Chem. 2004, 2, 3204-3218.
31. Mark, A.; Johnson, G. Concepts and Applications of Molecular Similarity, 1st ed.; Wiley-Interscience: New York, NY, USA, 1990.
32. Eckert, H.; Bajorath, J. Molecular similarity analysis in virtual screening: Foundations, Limitations and novel approaches. Drug Discov. Today 2007, 12, 225-233.
33. Willett, P. Similarity-based virtual screening using 2D fingerprints. Drug Discov. Today 2006, 11, 1046-1053.
34. Irwin, J.; Raushel, F.; Shoichet, B. Virtual Screening against Metalloenzymes for Inhibitors and Substrates. Biochemistry 2005, 44, 12316-12328.
35. Milletti, F.; Vulpetti, A. Tautomer Preference in PDB Complexes and its Impact on Structure-Based Drug Discovery. J. Chem. Inf. Model. 2010, 50, 1062-1074.
36. Martin, Y. Let's not forget tautomers. J. Comput.-Aided. Mol. Des. 2009, 23, 693-704.
37. Böhm, H. The computer program LUDI: A new method for the de novo design of enzyme inhibitors. J. Comput. Aided Mol. Des. 1992, 6, 61-78.
38. Mulder, G.; Meerman, J. Sulfation and glucuronidation as competing pathways in the metabolism of hydroxamic acids: the role of N,O-sulfonation in chemical carcinogenesis of aromatic amines. Environ. Health Perspect. 1983, 49, 27-32.
39. Vassiliou, S.; Mucha, A.; Cuniasse, P.; Georgiadis, D.; Lucet-Levannier, K.; Beau, F.; Kannan, R.; Murphy, G.; Knäuper, V.; Rio, M.C.; et al. Phosphinic Pseudo-Tripeptides as Potent Inhibitors of Matrix Metalloproteinases: A Structure-Activity Study. J. Med. Chem. 1999, 42, 2610-2620.
40. Whittaker, M.; Floyd, C.D.; Brown, P.; Gearing, A.J. Design and Therapeutic Application of Matrix Metalloproteinase Inhibitors. Chem. Rev. 1999, 99, 2735-2776.
41. Douglass, R.; Heckman, G. Drug-related taste disturbance. Can. Fam. Physician 2010, 56, 1142-1147.
42. Irwin, J.; Shoichet, B.; ZINC: A Free Database of Commercially Available Compounds for Virtual Screening. J. Chem. Inf. Model. 2004, 45, 177-182.
43. Irwin, J.J.; Sterling, T.; Mysinger, M.M.; Bolstad, E.S.; Coleman, R.G. ZINC: A Free Tool to Discover Chemistry for Biology. J. Chem. Inf. Model. 2012, in press.
44. Jones, G.; Willett, P.; Glen, R.C..; Leach, A.R.; Taylor, R. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 1997, 267, 727-748.
45. Verdonk, M.L.; Cole, J.C.; Hartshorn, M.J.; Murray, C.W.; Taylor, R.D. Improved protein-ligand docking using GOLD. Proteins: Struct. Funct. Bioinf. 2003, 52, 609-623.
46. Wu, G.; Robertson, D.H.; Brooks, C.L.; Vieth, M. Detailed analysis of grid-based molecular docking: A case study of CDOCKER- A CHARMm-based MD docking algorithm. J. Comput. Chem. 2003, 24, 1549-1562.
47. Diller, D.; Merz, K. High throughput docking for library design and library prioritization. Proteins: Struct. Funct. Bioinf. 2001, 43, 113-124.
48. Diller, D.; Li, R. Kinases, Homology Models, and High Throughput Docking. J. Med. Chem. 2003, 46, 4638-4647.
49. Rao, S.N.; Head, M.S.; Kulkarni, A.; LaLonde, J.M. Validation Studies of the Site-Directed Docking Program LibDock. J. Chem. Inf. Model. 2007, 47, 2159-2171.