Binding mode analyses and pharmacophore model development for stilbene derivatives as a novel and competitive class of α-glucosidase inhibitors

PLoS ONE

Volumn 9, Issue 1, 2014, Pages

  Lee, Yuno ^a   Kim, Songmi ^a   Kim, Jun Young ^a   Arooj, Mahreen ^a   Kim, Siu ^a   Hwang, Swan ^a   Kim, Byeong Woo ^a   Park, Ki Hun ^a   Lee, Keun Woo ^a  

^a Gyeongsang National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA GLUCOSIDASE INHIBITOR; STILBENE DERIVATIVE;

AMINO TERMINAL SEQUENCE; ARTICLE; BINDING AFFINITY; BINDING SITE; CHEMICAL INTERACTION; CONTROLLED STUDY; CRYSTAL STRUCTURE; HYDROGEN BOND; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR MODEL; NONHUMAN; PHARMACOPHORE; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION; SACCHAROMYCES CEREVISIAE; STATIC ELECTRICITY; VALIDATION PROCESS;

ALPHA-GLUCOSIDASES; AMINO ACID SEQUENCE; BACILLUS CEREUS; ENZYME INHIBITORS; GLUTAMIC ACID; HYDROGEN BONDING; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; INHIBITORY CONCENTRATION 50; KINETICS; LIGANDS; MODELS, MOLECULAR; MOLECULAR DOCKING SIMULATION; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; REPRODUCIBILITY OF RESULTS; SACCHAROMYCES CEREVISIAE; SEQUENCE ALIGNMENT; STILBENES; STRUCTURAL HOMOLOGY, PROTEIN; THERMODYNAMICS;

EID: 84908191388     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0085827     Document Type: Article

References (38)

1. Borges de Melo E, da Silveira Gomes A, Carvalho I (2006) α-and β-Glucosidase inhibitors: chemical structure and biological activity. Tetrahedron 62: 10277-10302.
2. Aschenbrenner D, Venable S (2008) Drug therapy in nursing: Lippincott Williams & Wilkins.
3. Kordik C, Reitz A (1999) Pharmacological treatment of obesity: therapeutic strategies. J Med Chem 42: 181-201. (Pubitemid 29069852)
4. Scott L, Spencer C (2000) Miglitol: a review of its therapeutic potential in type 2 diabetes mellitus. Drugs 59: 521-549. (Pubitemid 30213863)
5. Cheng A, Josse R (2004) Intestinal absorption inhibitors for type 2 diabetes mellitus: prevention and treatment. Drug Discovery Today: Therapeutic Strategies 1: 201-206. (Pubitemid 40197628)
6. Zheng W, Padia J, Urban DJ, Jadhav A, Goker-Alpan O, et al. (2007) Three classes of glucocerebrosidase inhibitors identified by quantitative high-throughput screening are chaperone leads for Gaucher disease. Proceedings of the National Academy of Sciences 104: 13192-13197. (Pubitemid 351737615)
7. Houston TA, Blanchfield JT (2003) Back to (non)-basics: Recent developments in neutral and charge-balanced glycosidase inhibitors. Mini Reviews in Medicinal Chemistry 3: 669-678.
8. Tomich C, da Silva P, Carvalho I, Taft C (2005) Homology modeling and molecular interaction field studies of α-glucosidases as a guide to structure-based design of novel proposed anti-HIV inhibitors. Journal of computer-aided molecular design 19: 83-92. (Pubitemid 40974009)
9. Asano N, Nishida M, Kato A, Kizu H, Matsui K, et al. (1998) Homonojirimycin isomers and N-alkylated homonojirimycins: structural and conformational basis of inhibition of glycosidases. J Med Chem 41: 2565-2571. (Pubitemid 28321905)
10. Liang P, Cheng W, Lee Y, Yu H, Wu Y, et al. (2006) Novel Five Membered Iminocyclitol Derivatives as Selective and Potent Glycosidase Inhibitors: New Structures for Antivirals and Osteoarthritis. ChemBioChem 7: 165-173. (Pubitemid 43076300)
11. Kim J, Lee J, Kim Y, Lee Y, Ryu Y, et al. (2010) A Novel Competitive Class of α-Glucosidase Inhibitors:(E)-1-Phenyl-3-(4-Styrylphenyl) Urea Derivatives. ChemBioChem 11: 2125-2131.
12. Bharatham K, Bharatham N, Park K, Lee K (2008) Binding mode analyses and pharmacophore model development for sulfonamide chalcone derivatives, a new class of [alpha]-glucosidase inhibitors. Journal of Molecular Graphics and Modelling 26: 1202-1212.
13. Park H, Hwang KY, Oh KH, Kim YH, Lee JY, et al. (2008) Discovery of novel alpha-glucosidase inhibitors based on the virtual screening with the homology-modeled protein structure. Bioorg Med Chem 16: 284-292.
14. Ferreira SB, Sodero AC, Cardoso MF, Lima ES, Kaiser CR, et al. (2010) Synthesis, biological activity, and molecular modeling studies of 1H-1,2,3-triazole derivatives of carbohydrates as alpha-glucosidases inhibitors. J Med Chem 53: 2364-2375.
15. Watanabe K, Hata Y, Kizaki H, Katsube Y, Suzuki Y (1997) The refined crystal structure of Bacillus cereus oligo-1, 6-glucosidase at 2.0 a resolution: structural characterization of proline-substitution sites for protein thermostabilization 1. Journal of molecular biology 269: 142-153. (Pubitemid 27243627)
16. Larkin M, Blackshields G, Brown N, Chenna R, McGettigan P, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947.
17. Accelrys Software Inc DISCOVERY STUDIO. Accelrys, San Diego, CA.
18. Seo W, Kim J, Kang J, Ryu H, Curtis-Long M, et al. (2005) Sulfonamide chalcone as a new class of [alpha]-glucosidase inhibitors. Bioorganic & medicinal chemistry letters 15: 5514-5516. (Pubitemid 41562981)
19. Laskowski R, MacArthur M, Moss D, Thornton J (1993) PROCHECK: a program to check the stereochemical quality of protein structures. Journal of Applied Crystallography 26: 283-291.
20. Wiederstein M, Sippl MJ (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35: W407-410.
21. Wu G, Robertson DH, Brooks III CL, Vieth M (2003) Detailed analysis of grid-based molecular docking: A case study of CDOCKER - A CHARMm-based MD docking algorithm. Journal of computational chemistry 24: 1549-1562.
22. Rapp C, Kalyanaraman C, Schiffmiller A, Schoenbrun EL, Jacobson MP (2011) A Molecular Mechanics Approach to Modeling Protein-Ligand Interactions: Relative Binding Affinities in Congeneric Series. Journal of Chemical Information and Modeling.
23. Naïm M, Bhat S, Rankin KN, Dennis S, Chowdhury SF, et al. (2007) Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 1. Exploring the parameter space. Journal of Chemical Information and Modeling 47: 122-133. (Pubitemid 46225568)
24. McGaughey GB, Gagné M, Rappé AK (1998) π-Stacking interactions alive and well in proteins. Journal of Biological Chemistry 273: 15458-15463. (Pubitemid 28298153)
25. Muraki M, Harata K, Sugita N, Sato K-i (2000) Protein-carbohydrate interactions in human lysozyme probed by combining site-directed mutagenesis and affinity labeling. Biochemistry 39: 292-299. (Pubitemid 30056462)
26. Umezawa Y, Nishio M (1998) CH/π interactions in the crystal structure of class I MHC antigens and their complexes with peptides. Bioorganic & medicinal chemistry 6: 2507-2515. (Pubitemid 29002937)
27. Matsui I, Matsui E, Sakai Y, Kikuchi H, Kawarabayasi Y, et al. (2000) The molecular structure of hyperthermostable aromatic aminotransferase with novel substrate specificity from Pyrococcus horikoshii. Journal of Biological Chemistry 275: 4871-4879. (Pubitemid 30108880)
28. Berendsen H, Van der Spoel D, Van Drunen R (1995) GROMACS: a message-passing parallel molecular dynamics implementation. Computer Physics Communications 91: 43-56.
29. Van der Spoel D, Lindahl E, Hess B, van Buuren A, Apol E, et al. (2006) GROMACS user manual version 3.3. Department of Biophysical Chemistry, University of Groningen Nijenborgh 4: 9747.
30. Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, et al. (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Journal of computational chemistry 24: 1999-2012.
31. Darden T, York D, Pedersen L (1993) Particle mesh Ewald: An N log (N) method for Ewald sums in large systems. The Journal of chemical physics 98: 10089.
32. Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of a general amber force field. Journal of computational chemistry 25: 1157-1174.
33. Walker RC, Crowley MF, Case DA (2008) The implementation of a fast and accurate QM/MM potential method in Amber. Journal of computational chemistry 29: 1019-1031. (Pubitemid 351535401)
34. Wang J, Wang W, Kollman PA, Case DA (2006) Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics and Modelling 25: 247-260. (Pubitemid 44363172)
35. Hess B, Bekker H, Berendsen HJC, Fraaije JGEM (1997) LINCS: a linear constraint solver for molecular simulations. Journal of computational chemistry 18: 1463-1472. (Pubitemid 127637344)
36. Bussi G, Donadio D, Parrinello M (2007) Canonical sampling through velocity rescaling. The Journal of chemical physics 126: 014101.
37. Parrinello M, Rahman A (1981) Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics 52: 7182-7190. (Pubitemid 12456820)
38. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. Journal of molecular graphics 14: 33-38. (Pubitemid 26152973)