A Modeling Study for Structure Features of β-N-acetyl-D-hexosaminidase from Ostrinia furnacalis and its Novel Inhibitor Allosamidin: Species Selectivity and Multi-Target Characteristics

Chemical Biology and Drug Design

Volumn 79, Issue 4, 2012, Pages 572-582

  Wang, Yanli ^a   Liu, Tian ^b   Yang, Qing ^b,c   Li, Zhong ^a   Qian, Xuhong ^a  

^a EAST CHINA UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^b DALIAN UNIVERSITY OF TECHNOLOGY   (China)

^c EAST CHINA UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

Allosamidin; Hexosaminidase; Molecular modeling; Multi target; Species selectivity

Indexed keywords

ALLOSAMIDIN; BETA N ACETYLHEXOSAMINIDASE; CHITINASE; OFHEX1 ENZYME; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; BINDING SITE; CHEMICAL STRUCTURE; LEPIDOPTERA; MOLECULAR DOCKING; MOLECULAR MODEL; NONHUMAN; NUCLEOTIDE SEQUENCE; OSTRINIA FURNACALIS; PRIORITY JOURNAL;

ACETYLGLUCOSAMINE; AMINO ACID SEQUENCE; ANIMALS; BETA-N-ACETYLHEXOSAMINIDASES; BINDING SITES; CHITINASE; HUMANS; INSECTICIDES; LEPIDOPTERA; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; SEQUENCE ALIGNMENT; TRISACCHARIDES;

AVES; HEXAPODA; OSTRINIA; OSTRINIA FURNACALIS;

EID: 84862792216     PISSN: 17470277     EISSN: 17470285     Source Type: Journal    
DOI: 10.1111/j.1747-0285.2011.01301.x     Document Type: Article

References (38)

1. Cohen E. (2001) Chitin synthesis and inhibition: a revisit. Pest Manag Sci;57:946-950.
2. Patil R.S., Ghormade V., Deshpande M.V. (2000) Chitinolytic enzymes: an exploration. Enzyme Microb Technol;26:473-483.
3. Mahuran D.J. (1999) Biochemical consequences of mutations causing the GM2 gangliosidoses. Biochim Biophys Acta;1455:105-138.
4. Cheng Q., Li H., Merdek K., Park J.T. (2000) Molecular characterization of the beta-N-acetylglucosaminidase of Escherichia coli and its role in cell wall recycling. J Bacteriol;182:4836-4840.
5. Chet I., Barak Z., Oppenheim A. (1993) Genetic engineering of micro-organisms for improved biocontrol activity. In: Chet I., editor. Biotechnology in plant disease control, Wiley-Liss, Inc New York, USA, p. 211-235.
6. Zobell C.E., Rittenberg S.C. (1938) The Occurrence and characteristics of chitinoclastic bacteria in the sea. J Bacteriol;35:275-287.
7. Spindler K.D., Spindler-Barth M., Londershausen M. (1990) Chitin metabolism: a target for drugs against parasites. Parasitol Res;76:283-288.
8. Fukamizo T. (2000) Chitinolytic enzymes: catalysis, substrate binding, and their application. Curr Protein Pept Sci;1:105-124.
9. Qing Y., Tian L., Fengyi L., Mingbo Q., Xuhong Q. (2008) A novel b-N-acetyl-d-hexosaminidase from the insect Ostrinia furnacalis (Guene′e). FEBS J;275:5690-5702.
10. Liu T., Liu F., Yang Q., Yang J. (2009) Expression, purification and characterization of the chitinolytic beta-N-acetyl-d-hexosaminidase from the insect Ostrinia furnacalis. Protein Expr Purif;68:99-103.
11. Liu T. (2009) Molecular cloning, purification and characterization of OfHexl, the 13-N-acetyl-d-hexosaminidase from the insect Ostrinia furnacalis. PhD Thesis, Dalian, China PR: Dalian University of Technology.
12. Saua S.F., Karlsen V., Sakuda S., Eijsink V.G.H., Sorlie M. (2007) Thermodynamic analysis of allosamidin binding to a family 18 chitinase. Biochemistry;46:12347-12354.
13. Balcewich M.D., Stubbs K.A., He Y., James T.W., Davies G.J., Vocadlo D.J., Mark B.L. (2009) Insight into a strategy for attenuating AmpC-mediated beta-lactam resistance: structural basis for selective inhibition of the glycoside hydrolase NagZ. Protein Sci;18:1541-1551.
14. Williams S.J., Mark B.L., Vocadlo D.J., James M.N., Withers S.G. (2002) Aspartate 313 in the Streptomyces plicatus hexosaminidase plays a critical role in substrate-assisted catalysis by orienting the 2-acetamido group and stabilizing the transition state. J Biol Chem;277:40055-40065.
15. Mark B.L., Vocadlo D.J., Zhao D., Knapp S., Withers S.G., James M.N. (2001) Biochemical and structural assessment of the 1-N-azasugar GalNAc-isofagomine as a potent family 20 beta-N-acetylhexosaminidase inhibitor. J Biol Chem;276:42131-42137.
16. Mark B.L., Vocadlo D.J., Knapp S., Triggs-Raine B.L., Withers S.G., James M.N. (2001) Crystallographic evidence for substrate-assisted catalysis in a bacterial beta-hexosaminidase. J Biol Chem;276:10330-10337.
17. Tews I., Perrakis A., Oppenheim A., Dauter Z., Wilson K.S., Vorgias C.E. (1996) Bacterial chitobiase structure provides insight into catalytic mechanism and the basis of Tay-Sachs disease. Nat Struct Biol;3:638-648.
18. Prag G., Papanikolau Y., Tavlas G., Vorgias C.E., Petratos K., Oppenheim A.B. (2000) Structures of chitobiase mutants complexed with the substrate Di-N-acetyl-d-glucosamine: the catalytic role of the conserved acidic pair, aspartate 539 and glutamate 540. J Mol Biol;300:611-617.
19. Langley D.B., Harty D.W., Jacques N.A., Hunter N., Guss J.M., Collyer C.A. (2008) Structure of N-acetyl-beta-d-glucosaminidase (GcnA) from the endocarditis pathogen Streptococcus gordonii and its complex with the mechanism-based inhibitor NAG-thiazoline. J Mol Biol;377:104-116.
20. Sumida T., Ishii R., Yanagisawa T., Yokoyama S., Ito M. (2009) Molecular cloning and crystal structural analysis of a novel beta-N-Acetylhexosaminidase from Paenibacillus sp. TS12 capable of degrading glycosphingolipids. J Mol Biol;392(1):87-99.
21. Lemieux M.J., Mark B.L., Cherney M.M., Withers S.G., Mahuran D.J., James M.N. (2006) Crystallographic structure of human beta-hexosaminidase A: interpretation of Tay-Sachs mutations and loss of GM2 ganglioside hydrolysis. J Mol Biol;359:913-929.
22. Maier T., Strater N., Schuette C.G., Klingenstein R., Sandhoff K., Saenger W. (2003) The X-ray crystal structure of human beta-hexosaminidase B provides new insights into Sandhoff disease. J Mol Biol;328:669-681.
23. Mark B.L., Mahuran D.J., Cherney M.M., Zhao D., Knapp S., James M.N. (2003) Crystal structure of human beta-hexosaminidase B: understanding the molecular basis of Sandhoff and Tay-Sachs disease. J Mol Biol;327:1093-1109.
24. Cavasotto C.N., Orry A.J.W., Murgolo N.J., Czarniecki M.F., Kocsi S.A., Hawes B.E., O'Neill K.A., Hine H., Burton M.S., Voigt J.H., Abagyan R.A., Bayne M.L., Monsma F.J. (2008) Discovery of novel chemotypes to a G-protein-coupled receptor through ligand-steered homology modeling and structure-based virtual screening. J Med Chem;51:581-588.
25. Evers A., Klebe G. (2004) Successful virtual screening for a submicromolar antagonist of the neurokinin-1 receptor based on a ligand-supported homology model. J Med Chem;47:5381-5392.
26. Evers A., Klebe G. (2004) Ligand-supported homology modeling of G-protein-coupled receptor sites: models sufficient for successful virtual screening. Angew Chem Int Ed Engl;43:248-251.
27. Sali A., Blundell T. (1994) Comparative protein modelling by satisfaction of spatial restraints. In: H. Bohr, S. Brunak, editors. Protein Structure by Distance Analysis, Washington, DC, USA, p. 64-86.
28. Pearlman D.A., Case D.A., Caldwell J.W., Ross W.S., Cheatham T.E. (1995) AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comp Phys Commun;91:1-41.
29. Evers A., Gohlke H., Klebe G. (2003) Ligand-supported homology modelling of protein binding-sites using knowledge-based potentials. J Mol Biol;334:327-345.
30. Laskowski R., MacArthur M., Moss D., Thornton J. (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr;26:283-291.
31. Gohlke H., Hendlich M., Klebe G. (2000) Knowledge-based scoring function to predict protein-ligand interactions1. J Mol Biol;295:337-356.
32. Marcel L.V., Jason C.C., Michael J.H., Christopher W.M., Richard D.T. (2003) Improved protein-ligand docking using GOLD. Proteins;52:609-623.
33. Ettrich R., Kopecky V. Jr, Hofbauerova K., Baumruk V., Novak P., Pompach P., Man P., Plihal O., Kuty M., Kulik N., Sklenar J., Ryslava H., Kren V., Bezouska K. (2007) Structure of the dimeric N-glycosylated form of fungal beta-N-acetylhexosaminidase revealed by computer modeling, vibrational spectroscopy, and biochemical studies. BMC Struct Biol;7:32.
34. Tews I., Terwisscha van Scheltinga A.C., Perrakis A., Wilson K.S., Dijkstra B.W. (1997) Substrate-assisted catalysis unifies two families of chitinolytic enzymes. J Am Chem Soc;119:7954-7959.
35. Papanikolau Y., Tavlas G., Vorgias C., Petratos K. (2003) De novo purification scheme and crystallization conditions yield high-resolution structures of chitinase A and its complex with the inhibitor allosamidin. Acta Crystallogr D Biol Crystallogr;59:400-403.
36. Aronson N. Jr, Halloran B., Alexyev M., Amable L., Madura J., Pasupulati L., Worth C., Van Roey P. (2003) Family 18 chitinase-oligosaccharide substrate interaction: subsite preference and anomer selectivity of Serratia marcescens chitinase A. Biochem J;376:87.
37. Liu T., Zhang H., Liu F., Wu Q., Shen X., Yang Q. (2011) Structural determinants of an insect beta-N-Acetyl-d-hexosaminidase specialized as a chitinolytic enzyme. J Biol Chem;286:4049.
38. Wouters M.A., Fan S.W., Haworth N.L. (2010) Disulfides as redox switches: from molecular mechanisms to functional significance. Antioxid Redox Signal;12:53-91.