Predicting protein druggability

Drug Discovery Today

Volumn 10, Issue 23-24, 2005, Pages 1675-1682

  Hajduk, Philip J ^a   Huth, Jeffrey R ^a   Tse, Christin ^a  

^a ABBOTT LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SMALL INTERFERING RNA;

BINDING AFFINITY; BINDING SITE; BIOINFORMATICS; CORRELATION ANALYSIS; DATA ANALYSIS; DATA BASE; DRUG TARGETING; GENETIC ANALYSIS; GENOMICS; HUMAN; NUCLEAR MAGNETIC RESONANCE; PREDICTION; PROTEIN BINDING; PROTEIN INTERACTION; PROTEIN STRUCTURE; REVIEW; SURFACE PROPERTY;

BINDING SITES; COMPUTATIONAL BIOLOGY; DRUG DESIGN; GENOMICS; LIGANDS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEINS;

EID: 29144483936     PISSN: 13596446     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1359-6446(05)03624-X     Document Type: Review

References (40)

1. A.L. Hopkins, C.R. Groom The druggable genome Nat. Rev. Drug Discov. 1 2002 727 730
2. T.C. Terwilliger Structural genomics in North America Nat. Struct. Biol. 7 Suppl 2000 935 939
3. U. Heinemann Structural genomics in Europe: slow start, strong finish? Nat. Struct. Biol. 7 Suppl 2000 940 942
4. S. Yokoyama Structural genomics projects in Japan Nat. Struct. Biol. 7 Suppl 2000 943 945
5. E. Michalsky SuperLigands - a database of ligand structures derived from the Protein Data Bank BMC Bioinformatics 6 2005 122
6. M. Schneider A rational approach to maximize success rate in target discovery Arch. Pharm. (Weinheim) 337 2004 625 633
7. U.A. Betz How many genomics targets can a portfolio afford? Drug Discov Today 10 2005 1057 1063
8. L.W. Hardy, N.P. Peet The multiple orthogonal tools approach to define molecular causation in the validation of druggable targets Drug Discov. Today 9 2004 117 126
9. U.A. Betz Genomics: success or failure to deliver drug targets? Curr Opin. Chem. Biol. 9 2005 387 391
10. B.P. Zambrowicz, A.T. Sands Knockouts model the 100 best-selling drugs-will they model the next 100? Nat Rev. Drug Discov. 2 2003 38 51
11. H. Xin High-throughput siRNA-based functional target validation J. Biomol. Screen. 9 2004 286 293
12. D. Wan Large-scale cDNA transfection screening for genes related to cancer development and progression Proc. Natl. Acad. Sci. U. S. A. 101 2004 15724 15729
13. D.G. Albertson Chromosome aberrations in solid tumors Nat. Genet. 34 2003 369 376
14. N.J. Mulder InterPro, progress and status in 2005 Nucleic Acids Res. 33 2005 D201 D205 (Database issue)
15. L.T. Vassilev In vivo activation of the p53 pathway by small-molecule antagonists of MDM2 Science 303 2004 844 848
16. T. Oltersdorf An inhibitor of Bcl-2 family proteins induces regression of solid tumours Nature 435 2005 677 681
17. R.A. Laskowski SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions J. Mol. Graph. 13 1995 323 330 307-308
18. M. Hendlich LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins J. Mol. Graph. Model. 15 1997 359 363 389
19. K.P. Peters The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria J. Mol. Biol. 256 1996 201 213
20. J. Liang Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design Protein Sci. 7 1998 1884 1897
21. G.P. Brady, P.F.W. Stouten Fast prediction and visualization of protein binding pockets with PASS J. Comput. Aided Mol. Des. 14 2000 383 401
22. F.K. Pettit, J.U. Bowie Protein surface roughness and small molecular binding sites J. Mol. Biol. 285 1999 1377 1382
23. R.A. Laskowski Protein clefts in molecular recognition and function Protein Sci. 5 1996 2438 2452
24. P.J. Goodford A computational procedure for determining energetically favorable binding sites on biologically important macromolecules J. Med. Chem. 28 1985 849 857
25. A.A. Bliznyuk, J.E. Gready Simple method for locating possible ligand binding sites on protein surfaces J. Comp. Chem. 20 1999 983 988
26. J. An Comprehensive identification of 'druggable' protein ligand binding sites Genome Inform. Ser. Workshop Genome Inform. 15 2004 31 41
27. S. Dennis Computational mapping identifies the binding sites of organic solvents on proteins Proc. Natl. Acad. Sci. U. S. A. 99 2002 4290 4295
28. T. Kortvelyesi Improved mapping of protein binding sites J. Comput. Aided Mol. Des. 17 2003 173 186
29. P.J. Hajduk Druggability indices for protein targets derived from NMR-based screening data J. Med. Chem. 48 2005 2518 2525
30. R.S. Bohacek The art and practice of structure-based drug design: a molecular modeling perspective Med. Res. Rev. 16 1996 3 50
31. D.J. Diller, D.W. Hobbs Deriving knowledge through data mining high-throughput screening data J. Med. Chem. 47 2004 6373 6383
32. P.J. Hajduk, D.J. Burns Integration of NMR and High-Throughput Screening Comb. Chem. High Throughput Screen 5 2002 613 622
33. P.J. Hajduk Discovering high-affinity ligands for proteins Science 278 1997 497 499
34. T. Fink Virtual exploration of the small-molecule chemical universe below 160 Daltons Angew. Chem. Int. Ed. Engl. 44 2005 1504 1508
35. G.R. Smith Incorporation of flexibility into rigid-body docking: applications in rounds 3-5 of CAPRI Proteins 60 2005 263 268
36. R. Norel Electrostatic contributions to protein-protein interactions: fast energetic filters for docking and their physical basis Protein Sci. 10 2001 2147 2161
37. S.B. Shuker Discovering high-affinity ligands for proteins: SAR by NMR Science 274 1996 1531 1534
38. P.J. Hajduk NMR-based screening in drug discovery Q. Rev. Biophys. 32 1999 211 240
39. B.J. Stockman, C. Dalvit NMR screening techniques in drug discovery and drug design Prog. NMR Spect. 41 2002 187 231
40. B. Meyer, T. Peters NMR spectroscopy techniques for screening and identifying ligand binding to receptors Angew. Chem. Int. Ed. Engl. 42 2003 864 890