Metal-ligand interactions: An analysis of zinc binding groups using the Protein Data Bank

European Journal of Medicinal Chemistry

Volumn 51, Issue , 2012, Pages 271-276

  Kawai, Kentaro ^a   Nagata, Naoya ^a  

^a KAKEN PHARMACEUTICAL CO LTD   (Japan)

Author keywords

Metal ligand interaction; Protein Data Bank; Zinc binding group; Zinc metalloproteins

Indexed keywords

CARBOXYLIC ACID; HYDROXAMIC ACID; LIGAND; METALLOPROTEIN; NITROGEN; OXYGEN; PHOSPHATE; PHOSPHONIC ACID DERIVATIVE; SULFONAMIDE; SULFUR; ZINC; ZINC BINDING PROTEIN;

ARTICLE; CRYSTAL STRUCTURE; LIGAND BINDING; PHYSICAL CHEMISTRY; PROTEIN ANALYSIS; PROTEIN DATA BANK;

COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; DRUG DESIGN; LIGANDS; METALLOPROTEINS; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; ZINC;

EID: 84860269884     PISSN: 02235234     EISSN: 17683254     Source Type: Journal    
DOI: 10.1016/j.ejmech.2012.02.028     Document Type: Article

References (17)

1. Z. Wang, S. Zhang, H. Jin, W. Wang, J. Huo, L. Zhou, Y. Wang, F. Feng, and L. Zhang Angiotensin-I-converting enzyme inhibitory peptides: chemical feature based pharmacophore generation Eur. J. Med. Chem. 46 2011 3428 3433
2. Z. Brzozowski, J. Sławiński, M. Gdaniec, A. Innocenti, and C.T. Supuran Carbonic anhydrase inhibitors. Synthesis, molecular structures, and inhibition of the human cytosolic isozymes I and II and transmembrane isozymes IX, XII (cancer-associated) and XIV with novel 3-pyridinesulfonamide derivatives Eur. J. Med. Chem. 46 2011 4403 4410
3. E. Attolino, V. Calderone, E. Dragoni, M. Fragai, B. Richichi, C. Luchinat, and C. Nativi Structure-based approach to nanomolar, water soluble matrix metalloproteinases inhibitors (MMPIs) Eur. J. Med. Chem. 45 2010 5919 5925
4. J.E. Sheppeck II, J.L. Gilmore, A. Yang, X.T. Chen, C.B. Xue, J. Roderick, R.Q. Liu, M.B. Covington, C.P. Decicco, and J.J. Duan Discovery of novel hydantoins as selective non-hydroxamate inhibitors of tumor necrosis factor-alpha converting enzyme (TACE) Bioorg. Med. Chem. Lett. 17 2007 1413 1417 (Pubitemid 46240831)
5. N. Kamei, T. Tanaka, K. Kawai, K. Miyawaki, A. Okuyama, Y. Murakami, Y. Arakawa, M. Haino, T. Harada, and M. Shimano Reverse hydroxamate-based selective TACE inhibitors Bioorg. Med. Chem. Lett. 14 2004 2897 2900 (Pubitemid 38569759)
6. P. Conti, L. Tamborini, A. Pinto, L. Sola, R. Ettari, C. Mercurio, and C. De Micheli Design and synthesis of novel isoxazole-based HDAC inhibitors Eur. J. Med. Chem. 45 2010 4331 4338
7. S. Duez, L. Coudray, E. Mouray, P. Grellier, and J. Dubois Towards the synthesis of bisubstrate inhibitors of protein farnesyltransferase: synthesis and biological evaluation of new farnesylpyrophosphate analogues Bioorg. Med. Chem. 18 2010 543 556
8. M.G. Natchus, R.G. Bookland, B. De, N.G. Almstead, and S. Pikul Development of new hydroxamate matrix metalloproteinase inhibitors derived from functionalized 4-aminoprolines J. Med. Chem. 43 2000 4948 4963 (Pubitemid 32039016)
9. P. Dunten, U. Kammlott, R. Crowther, W. Levin, L.H. Foley, P. Wang, and R. Palermo X-ray structure of a novel matrix metalloproteinase inhibitor complexed to stromelysin Protein Sci. 10 2001 923 926 (Pubitemid 32367482)
10. A.K. Ghose, T. Herbertz, D.A. Pippin, J.M. Salvino, and J.P. Mallamo Knowledge based prediction of ligand binding modes and rational inhibitor design for kinase drug discovery J. Med. Chem. 51 2008 5149 5171
11. A.C. Pierce, G. Rao, and G.W. Bemis BREED: generating novel inhibitors through hybridization of known ligands. Application to CDK2, p38, and HIV protease J. Med. Chem. 47 2004 2768 2775 (Pubitemid 38656730)
12. A. Bondi van der Waals Volumes Radii J. Phys. Chem. 68 1964 441 451
13. RCSB PDB advanced search, http://www.rcsb.org/pdb/search/advSearch.do (accessed 09.06.11).
14. J. Kirchmair, P. Markt, S. Distinto, D. Schuster, G.M. Spitzer, K.R. Liedl, T. Langer, and G. Wolber The Protein Data Bank (PDB), its related services and software tools as key components for in silico guided drug discovery J. Med. Chem. 51 2008 7021 7040
15. RCSB PDB, http://www.rcsb.org/pdb/home/home.do (accessed 17.01.12).
16. M.M. Harding Geometry of metal-ligand interactions in proteins Acta Crystallogr. Sect. D 57 2001 401 411 (Pubitemid 32203174)
17. C. Campestre, M. Agamennone, P. Tortorella, S. Preziuso, A. Biasone, E. Gavuzzo, G. Pochetti, F. Mazza, O. Hiller, H. Tschesche, V. Consalvi, and C. Gallina N-Hydroxyurea as zinc binding group in matrix metalloproteinase inhibition: mode of binding in a complex with MMP-8 Bioorg. Med. Chem. Lett. 16 2006 20 24 (Pubitemid 41625633)