VAMMPIRE: A matched molecular pairs database for structure-based drug design and optimization

Journal of Medicinal Chemistry

Volumn 56, Issue 12, 2013, Pages 5203-5207

  Weber, Julia ^a   Achenbach, Janosch ^a   Moser, Daniel ^a   Proschak, Ewgenij ^a  

^a GOETHE UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ATOM; BINDING AFFINITY; DATA BASE; DRUG DESIGN; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; STRUCTURE ACTIVITY RELATION;

DATABASES, PHARMACEUTICAL; DRUG DESIGN; LIGANDS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PROTEINS; USER-COMPUTER INTERFACE;

EID: 84879566401     PISSN: 00222623     EISSN: 15204804     Source Type: Journal    
DOI: 10.1021/jm400223y     Document Type: Article

References (23)

1. Bleicher, K. H.; Böhm, H.-J.; Müller, K.; Alanine, A. I. Hit and lead generation: beyond high-throughput screening Nature Rev. Drug Discovery 2003, 2, 369-378
2. Gohlke, H.; Klebe, G. Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors Angew. Chem., Int. Ed. Engl. 2002, 41, 2644-2676
3. Kitchen, D. B.; Decornez, H.; Furr, J. R.; Bajorath, J. Docking and scoring in virtual screening for drug discovery: methods and applications Nature Rev. Drug Discovery 2004, 3, 935-949
4. Leach, A. G.; Jones, H. D.; Cosgrove, D. A.; Kenny, P. W.; Ruston, L.; MacFaul, P.; Wood, J. M.; Colclough, N.; Law, B. Matched molecular pairs as a guide in the optimization of pharmaceutical properties: a study of aqueous solubility, plasma protein binding and oral exposure J. Med. Chem. 2006, 49, 6672-6682
5. Griffen, E.; Leach, A.; Robb, G.; Warner, D. Matched molecular pairs as a medicinal chemistry tool J. Med. Chem. 2011, 54, 7739-7750
6. Wirth, M.; Zoete, V.; Michielin, O.; Sauer, W. H. B. SwissBioisostere: a database of molecular replacements for ligand design Nucleic Acids Res. 2013, 41, 1137-1143
7. Wang, R.; Fang, X.; Lu, Y.; Wang, S. The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures J. Med. Chem. 2004, 47, 1675-1679
8. Wang, R.; Fang, X.; Lu, Y.; Yang, C.-Y.; Wang, S. The PDBbind database: methodologies and updates J. Med. Chem. 2005, 48, 4111-4119
9. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank Nucleic Acids Res. 2000, 28, 235-242
10. Gaulton, A.; Bellis, L. J.; Bento, A. P.; Chambers, J.; Davies, M.; Hersey, A.; Light, Y.; McGlinchey, S.; Michalovich, D.; Al-Lazikani, B. ChEMBL: a large-scale bioactivity database for drug discovery Nucleic Acids Res. 2011, 44, 1-8
11. Kim, K. H. Outliers in SAR and QSAR: Is unusual binding mode a possible source of outliers? J. Comput.-Aided Mol. Des. 2007, 21, 63-86
12. Penning, T. D.; Talley, J. J.; Bertenshaw, S. R.; Carter, J. S.; Collins, P. W.; Docter, S.; Graneto, M. J.; Lee, L. F.; Malecha, J. W.; Miyashiro, J. M.; Rogers, R. S.; Rogier, D. J.; Yu, S. S.; Anderson, G. D.; Burton, E. G.; Cogburn, J. N.; Gregory, S. A.; Koboldt, C. M.; Perkins, W. E.; Seibert, K.; Veenhuizen, A. W.; Zhang, Y. Y.; Isakson, P. C. Synthesis and Biological Evaluation of the 1,5-Diarylpyrazole Class of Cyclooxygenase-2 Inhibitors: Identification of 4-[5-(4-Methylphenyl)-3-(trifluoromethyl)-1 H -pyrazol-1-yl]benzenesulfonamide (SC-58635, Celecoxib) J. Med. Chem. 1997, 40, 1347-1365
13. Clark, T.; Hennemann, M.; Murray, J. S.; Politzer, P. Halogen bonding: the sigma-hole J. Mol. Model. 2007, 13, 291-296
14. Eskandari, K.; Zariny, H. Halogen bonding: A lump-hole interaction Chem. Phys. Lett. 2010, 492, 9-13
15. Zhang, Y.; Ma, N.; Wang, W. A new class of halogen bonds that avoids the s-hole Chem. Phys. Lett. 2012, 532, 27-30
16. Politzer, P.; Lane, P.; Concha, M. C.; Ma, Y.; Murray, J. S. An overview of halogen bonding J. Mol. Model. 2007, 13, 305-11
17. Wilcken, R.; Zimmermann, M. O.; Lange, A.; Joerger, A. C.; Boeckler, F. M. Principles and Applications of Halogen Bonding in Medicinal Chemistry and Chemical Biology J. Med. Chem. 2012, 56, 1363-1388
18. Labute, P. Protonate3D: Assignment of ionization states and hydrogen coordinates to macromolecular structures Proteins 2009, 75, 187-205
19. Wagener, M.; Lommerse, J. P. M. The quest for bioisosteric replacements J. Chem. Inf. Model. 2006, 46, 677-685
20. Hussain, J.; Rea, C. Computationally efficient algorithm to identify matched molecular pairs (MMPs) in large data sets J. Chem. Inf. Model. 2010, 50, 339-348
21. Papadatos, G.; Papadatos, G.; Alkarouri, M.; Gillet, V. J.; Willett, P.; Kadirkamanathan, V.; Luscombe, C. N.; Bravi, G.; Richmond, N. J.; Pickett, S. D.; Hussain, J.; Pritchard, J. M.; Cooper, A. W. J.; MacDonald, S. J. F. Lead optimization using matched molecular pairs: Inclusion of contextual information for enhanced prediction of hERG inhibition, solubility, and lipophilicity J. Chem. Inf. Model. 2010, 50, 1872-1886
22. Rahman, S. A.; Bashton, M.; Holliday, G. L.; Schrader, R.; Thornton, J. M. Small Molecule Subgraph Detector (SMSD) toolkit J. Cheminform. 2009, 1, 12
23. Steinbeck, C.; Han, Y.; Kuhn, S.; Horlacher, O.; Luttmann, E.; Willighagen, E. The Chemistry Development Kit (CDK): an open-source Java library for Chemo- and Bioinformatics J. Chem. Inf. Comput. Sci. 2003, 43, 493-500