Structure-Based Dissection of the Natural Product Cyclopentapeptide Chitinase Inhibitor Argifin

Chemistry and Biology

Volumn 15, Issue 3, 2008, Pages 295-301

  Andersen, Ole A ^a   Nathubhai, Amit ^a   Dixon, Mark J ^a   Eggleston, Ian M ^a   van Aalten, Daan M F ^a  

^a UNIVERSITY OF DUNDEE   (United Kingdom)

Author keywords

CHEMBIO; PROTEINS

Indexed keywords

ARGIFIN; ARGININE; BIOLOGICAL PRODUCT; CHITINASE; CYCLOPEPTIDE; DRUG DERIVATIVE; OLIGOPEPTIDE; PEPTIDE FRAGMENT; UNCLASSIFIED DRUG; UREA;

ARTICLE; ASPERGILLUS FUMIGATUS; CHEMISTRY; DRUG ANTAGONISM; DRUG DESIGN; ENZYMOLOGY; METABOLISM; STRUCTURE ACTIVITY RELATION; SYNTHESIS; X RAY CRYSTALLOGRAPHY;

ARGININE; ASPERGILLUS FUMIGATUS; BIOLOGICAL PRODUCTS; CHITINASE; CRYSTALLOGRAPHY, X-RAY; DRUG DESIGN; OLIGOPEPTIDES; PEPTIDE FRAGMENTS; PEPTIDES, CYCLIC; STRUCTURE-ACTIVITY RELATIONSHIP; UREA;

ASPERGILLUS FUMIGATUS; MURINAE;

EID: 40749152751     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2008.02.015     Document Type: Article

References (42)

1. Abad-Zapatero C., and Metz J.T. Ligand efficiency indices as guideposts for drug discovery. Drug Discov. Today 10 (2005) 464-469
2. Andersen O.A., Dixon M.J., Eggleston I.M., and van Aalten D.M.F. Natural product family 18 chitinase inhibitors. Nat. Prod. Rep. 22 (2005) 563-579
3. Arai N., Shiomi K., Yamaguchi Y., Masuma R., Iwai Y., Turberg A., Koelbl H., and Omura S. Argadin, a new chitinase inhibitor, produced by clonostachys sp. fo-7314. Chem. Pharm. Bull. (Tokyo) 48 (2000) 1442-1446
4. Berecibar A., Grandjean C., and Siriwardena A. Synthesis and biological activity of natural aminocyclopentitol glycosidase inhibitors: mannostatins, trehazolin, allosamidins and their analogues. Chem. Rev. 99 (1999) 779-844
5. Boot R.G., Renkema G.H., Verhoek M., Strijland A., Bliek J., de Meulemeester T.M.A.M.O., Mannens M.M.A.M., and Aerts J.M.F.G. The human chitotriosidase gene - nature of inherited enzyme deficiency. J. Biol. Chem. 273 (1998) 25680-25685
6. Brunger A.T., Adams P.D., Clore G.M., Gros P., Grosse-Kunstleve R.W., Jiang J.-S., Kuszewski J., Nilges M., Pannu N.S., Read R.J., et al. Crystallography and NMR system: A new software system for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54 (1998) 905-921
7. Davies G.J., Wilson K.S., and Henrissat B. Nomenclature for sugar-binding subsites in glycosyl hydrolases. Biochem. J. 321 (1997) 557-559
8. Dharmasena M.N., Jewell D.A., and Taylor R.K. Development of peptide mimics of a protective epitope of vibrio cholerae ogawa O-antigen and investigation of the structural basis of peptide mimicry. J. Biol. Chem. 282 (2007) 33805-33816
9. Dixon M.J., Andersen O.A., van Aalten D.M.F., and Eggleston I.M. An efficient synthesis of argifin: a natural product chitinase inhibitor with chemotherapeutic potential. Bioorg. Med. Chem. Lett. 15 (2005) 4717-4721
10. Dixon M.J., Andersen O.A., van Aalten D.M.F., and Eggleston I.M. First synthesis of Argadin: A nanomolar inhibitor of family-18 chitinases. Eur. J. Org. Chem. 2006 (2006) 5002-5006
11. Hajduk P.J. Fragment-based drug design: how big is too big?. J. Med. Chem. 49 (2006) 6972-6976
12. Harris M.T., Lai K., Arnold K., Martinez H.F., Specht C.A., and Fuhrman J.A. Chitin synthase in the filarial parasite, brugia malayi. Mol. Biochem. Parasitol. 111 (2000) 351-362
13. Hopkins A.L., Groom C.R., and Alex A. Ligand efficiency: a useful metric for lead selection. Drug Discov. Today 9 (2004) 430-431
14. Houston D.R., Eggleston I., Synstad B., Eijsink V.G.H., and van Aalten D.M.F. The cyclic dipeptide ci-4 inhibits family 18 chitinases by structural mimicry of a reaction intermediate. Biochem. J. 368 (2002) 23-27
15. Houston D.R., Shiomi K., Arai N., Omura S., Peter M.G., Turberg A., Synstad B., Eijsink V.G.H., and van Aalten D.M.F. High-resolution structures of a chitinase complexed with natural product cyclopentapeptide inhibitors: Mimicry of carbohydrate substrate. Proc. Natl. Acad. Sci. USA 99 (2002) 9127-9132
16. Houston D.R., Synstad B., Eijsink V.G.H., Stark M.J.R., Eggleston I.M., and van Aalten D.M.F. Structure-based exploration of cyclic dipeptide chitinase inhibitors. J. Med. Chem. 47 (2004) 5713-5720
17. Izumida H., Imamura N., and Sano H. A novel chitinase inhibitor from a marine bacterium Pseudomonas sp. J. Antibiot. (Tokyo) 49 (1996) 76-80
18. Izumida H., Nishijima M., Takadera T., Nomoto A.M., and Sano H. The effect of chitinase inhibitors, cyclo(arg-pro) against cell separation of Saccharomyces cerevisiae and the morphological change of Candida albicans. J. Antibiot. (Tokyo) 49 (1996) 829-831
19. Johnson M.A., and Pinto B.M. Molecular mimicry of carbohydrates by peptides. Aust. J. Chem. 55 (2002) 13-25
20. Jones T.A., Zou J.Y., Cowan S.W., and Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47 (1991) 110-119
21. Kuntz I.D., Chen K., Sharp K.A., and Kollman P.A. The maximal affinity of ligands. Proc. Natl. Acad. Sci. USA 96 (1999) 9997-10002
22. Kuranda M.J., and Robbins P.W. Chitinase is required for cell-separation during growth of Saccharomyces cerevisiae. J. Biol. Chem. 266 (1991) 19758-19767
23. Leatherbarrow R.J. GraFit Version 5 (2001), Erithacus Software Ltd., Horley, UK
24. Lipinski C.A. Drug-like properties and the causes of poor solubility and poor permeability. J. Pharmacol. Toxicol. Methods 44 (2000) 235-249
25. McMillan S.J., and Lloyd C.M. Prolonged allergen challenge in mice leads to persistent airway remodelling. Clin. Exp. Allergy 34 (2004) 497-507
26. Merzendorfer H. Insect chitin synthases: a review. J. Comp. Physiol. [B] 176 (2006) 1-15
27. Munro C.A., and Gow N.A.R. Chitin synthesis in human pathogenic fungi. Med. Mycol. 39 (2001) 41-53
28. Newman D.J., and Cragg G.M. Natural products as sources of new drugs over the last 25 years. J. Nat. Prod. 70 (2007) 461-477
29. Omura S., Arai N., Yamaguchi Y., Masuma R., Iwai Y., Namikoshi M., Turberg A., Kölbl H., and Shiomi K. Argifin, a new chitinase inhibitor, produced by gliocladium sp. FTD-0668. i. taxonomy, fermentation, and biological activities. J. Antibiot. (Tokyo) 53 (2000) 603-608
30. Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276 (1997) 307-326
31. Rao F.V., Andersen O.A., Vora K.A., DeMartino J.A., and van Aalten D.M.F. Methylxanthine drugs are chitinase inhibitors: Investigation of inhibition and binding modes. Chem. Biol. 12 (2005) 973-980
32. Rao F.V., Houston D.R., Boot R.G., Aerts J.M.F.G., Hodkinson M., Adams D.J., Shiomi K., Omura S., and van Aalten D.M.F. Specificity and affinity of natural product cyclopentapeptide inhibitors against Aspergillus fumigatus, human and bacterial chitinases. Chem. Biol. 12 (2005) 65-76
33. Rao F.V., Houston D.R., Boot R.G., Aerts J.M.F.G., Hodkinson M., Adams D.J., Shiomi K., Omura S., and van Aalten D.M.F. Specificity and affinity of natural product cyclopentapeptide inhibitors against a. fumigatus, human, and bacterial chitinases. Chem. Biol. 12 (2005) 65-76
34. Sakuda S. Studies on the chitinase inhibitors, allosamidins. In: Muzzarelli R.A.A. (Ed). Chitin Enzymology Volume 2 (1996), Atec Edizione, Grottammare, Italy 203-212
35. Sakuda S., Nishimoto Y., Ohi M., Watanabe M., Takayama S., Isogai A., and Yamada Y. Effects of demethylallosamidin, a potent yeast chitinase inhibitor, on the cell-division of yeast. Agric. Biol Chem 54 (1990) 1333-1335
36. Schüttelkopf A.W., Andersen O.A., Rao F.V., Allwood M., Lloyd C., Eggleston I.M., and van Aalten D.M.F. J. Biol. Chem. 281 (2006) 27278-27285
37. Schüttelkopf A.W., and van Aalten D.M.F. Prodrg: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr. D Biol. Crystallogr. 60 (2004) 1355-1363
38. Terwisscha van Scheltinga A.C., Kalk K.H., Beintema J.J., and Dijkstra B.W. Crystal-structures of hevamine, a plant defense protein with chitinase and lysozyme activity, and its complex with an inhibitor. Structure 2 (1994) 1181-1189
39. Tsai Y.-L., Hayward R.E., Langer R.C., Fidock D.A., and Vinetz J.M. Disruption of Plasmodium falciparum chitinase markedly impairs parasite invasion of mosuito midgut. Infect. Immun. 69 (2001) 4048-4054
40. van Aalten D.M.F., Komander D., Synstad B., Gåseidnes S., Peter M.G., and Eijsink V.G.H. Structural insights into the catalytic mechanism of a family 18 exo-chitinase. Proc. Natl. Acad. Sci. USA 98 (2001) 8979-8984
41. Vyas N.K., Vyas M.N., Chervenak M.C., Bundle D.R., Pinto B.M., and Quiocho F.A. Structural basis of peptide-carbohydrate mimicry in an antibody-combining site. Proc. Natl. Acad. Sci. USA 100 (2003) 15023-15028
42. Zhu Z., Zheng T., Homer R.J., Kim Y.K., Chen N.Y., Cohn L., Hamid Q., and Elias J.A. Acidic mammalian chitinase in asthmatic th2 inflammation and il-13 pathway activation. Science 304 (2004) 1678-1682