Similarity between flavonoid biosynthetic enzymes and flavonoid protein targets captured by three-dimensional computing approach

Planta Medica

Volumn 81, Issue 6, 2015, Pages 467-473

  Sturm, Noé ^a,b   Quinn, Ronald J ^a   Kellenberger, Esther ^b  

^a GRIFFITH UNIVERSITY   (Australia)

^b UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

binding site similarity; biosynthetic enzyme; flavonoid; natural product

Indexed keywords

ENZYME; FLAVONOID; PROTEIN;

BINDING SITE; BIOSYNTHESIS; CHEMISTRY; METABOLISM; PROTEIN CONFORMATION; PROTEIN DATABASE;

BINDING SITES; DATABASES, PROTEIN; ENZYMES; FLAVONOIDS; PROTEIN CONFORMATION; PROTEINS;

EID: 84939979865     PISSN: 00320943     EISSN: 14390221     Source Type: Journal    
DOI: 10.1055/s-0035-1545697     Document Type: Article

References (27)

1. Demain A. L., Fang A. The natural functions of secondary metabolites. Adv Biochem Eng Biotechnol: 2000; 69 1 39
2. Newman D. J., Cragg G. M. Natural products as sources of new drugs over the 30 years from 1981 to 2010. J Nat Prod: 2012; 75 311 335
3. Lounkine E., Keiser M. J., Whitebread S., Mikhailov D., Hamon J., Jenkins J. L., Lavan P., Weber E., Doak A. K., Cote S., Shoichet B. K., Urban L. Large-scale prediction and testing of drug activity on side-effect targets. Nature: 2012; 486 361 367
4. Kellenberger E., Schalon C., Rognan D. How to measure the similiarty between protein ligand-binding sites. Curr Comput Aided Drug Des: 2008; 4 209 220
5. McArdle B. M., Campitelli M. R., Quinn R. J. A common protein fold topology shared by flavonoid biosynthetic enzymes and therapeutic targets. J Nat Prod: 2006; 69 14 17
6. Kellenberger E., Hofmann A., Quinn R. J. Similar interactions of natural products with biosynthetic enzymes and therapeutic targets could explain why nature produces such a large proportion of existing drugs. Nat Prod Rep: 2011; 28 1483 1492
7. Gutmanas A., Alhroub Y., Battle G. M., Berrisford J. M., Bochet E., Conroy M. J., Dana J. M., Fernandez Montecelo M. A., van Ginkel G., Gore S. P., Haslam P., Hatherley R., Hendrickx P. M., Hirshberg M., Lagerstedt I., Mir S., Mukhopadhyay A., Oldfield T. J., Patwardhan A., Rinaldi L., Sahni G., Sanz-Garcia E., Sen S., Slowley R. A., Velankar S., Wainwright M. E., Kleywegt G. J. PDBe: Protein Data Bank in Europe. Nucleic Acids Res: 2014; 42 D285 D291
8. Caspi R., Altman T., Dreher K., Fulcher C. A., Subhraveti P., Keseler I. M., Kothari A., Krummenacker M., Latendresse M., Mueller L. A., Ong Q., Paley S., Pujar A., Shearer A. G., Travers M., Weerasinghe D., Zhang P., Karp P. D. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res: 2012; 40 D742 D753
9. Desaphy J., Azdimousa K., Kellenberger E., Rognan D. Comparison and druggability prediction of protein-ligand binding sites from pharmacophore-annotated cavity shapes. J Chem Inf Model: 2012; 52 2287 2299
10. Consortium T. U. Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res: 2014; 42 D191 D198
11. Bairoch A., Apweiler R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res: 2000; 28 45 48
12. Bento A. P., Gaulton A., Hersey A., Bellis L. J., Chambers J., Davies M., Kruger F. A., Light Y., Mak L., McGlinchey S., Nowotka M., Papadatos G., Santos R., Overington J. P. The ChEMBL bioactivity database: an update. Nucleic Acids Res: 2014; 42 D1083 D1090
13. Sak K. Site-specific anticancer effects of dietary flavonoid quercetin. Nutr Cancer: 2014; 66 177 193
14. Peer W. A., Murphy A. S. The science of flavonoids. In: Grotewold E. editor Flavonoids as signal molecules: targets of flavonoid action. New York Springer: 2006; 239 268
15. Lu X., Jung J., Cho H. J., Lim D. Y., Lee H. S., Chun H. S., Kwon D. Y., Park J. H. Fisetin inhibits the activities of cyclin-dependent kinases leading to cell cycle arrest in HT-29 human colon cancer cells. J Nutr: 2005; 135 2884 2890
16. Havsteen B. H. The biochemistry and medical significance of the flavonoids. Pharmacol Ther: 2002; 96 67 202
17. Walker E. H., Pacold M. E., Perisic O., Stephens L., Hawkins P. T., Wymann M. P., Williams R. L. Structural determinants of phosphoinositide 3-kinase inhibition by wortmannin, LY294002, quercetin, myricetin, and staurosporine. Mol Cell: 2000; 6 909 919
18. Schalon C., Surgand J. S., Kellenberger E., Rognan D. A simple and fuzzy method to align and compare druggable ligand-binding sites. Proteins: 2008; 71 1755 1778
19. Swets J. A., Dawes R. M., Monahan J. Better decisions through science. Sci Am: 2000; 283 82 87
20. Hawkins P. C., Warren G. L., Skillman A. G., Nicholls A. How to do an evaluation: pitfalls and traps. J Comput Aided Mol Des: 2008; 22 179 190
21. Sturm N., Desaphy J., Quinn R. J., Rognan D., Kellenberger E. Structural insights into the molecular basis of the ligand promiscuity. J Chem Inf Model: 2012; 52 2410 2421
22. Puhl A. C., Bernardes A., Silveira R. L., Yuan J., Campos J. L., Saidemberg D. M., Palma M. S., Cvoro A., Ayers S. D., Webb P., Reinach P. S., Skaf M. S., Polikarpov I. Mode of peroxisome proliferator-activated receptor gamma activation by luteolin. Mol Pharmacol: 2012; 81 788 799
23. Ekinci D., Karagoz L., Ekinci D., Senturk M., Supuran C. T. Carbonic anhydrase inhibitors: in vitro inhibition of alpha isoforms (hCA I, hCA II, bCA III, hCA IV) by flavonoids. J Enzyme Inhib Med Chem: 2013; 28 283 288
24. El Amrani M., Lai D., Debbab A., Aly A. H., Siems K., Seidel C., Schnekenburger M., Gaigneaux A., Diederich M., Feger D., Lin W., Proksch P. Protein kinase and HDAC inhibitors from the endophytic fungus Epicoccum nigrum. J Nat Prod: 2014; 77 49 56
25. Tasdemir D., Mallon R., Greenstein M., Feldberg L. R., Kim S. C., Collins K., Wojciechowicz D., Mangalindan G. C., Concepcion G. P., Harper M. K., Ireland C. M. Aldisine alkaloids from the Philippine sponge Stylissa massa are potent inhibitors of mitogen-activated protein kinase kinase-1 (MEK-1). J Med Chem: 2002; 45 529 532
26. Desaphy J., Bret G., Rognan D., Kellenberger E. sc-PDB: a 3D-database of ligandable binding sites - 10 years on. Nucleic Acids Res: 2015; 43 D399 D404
27. Robin X., Turck N., Hainard A., Tiberti N., Lisacek F., Sanchez J. C., Müller M. pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinformatics: 2011; 12 77 84