Combining docking with pharmacophore filtering for improved virtual screening

Journal of Cheminformatics

Volumn 1, Issue 1, 2009, Pages

  Peach, Megan L ^a   Nicklaus, Marc C ^b  

^a SAIC FREDERICK INC   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 70349373859     PISSN: None     EISSN: 17582946     Source Type: Journal    
DOI: 10.1186/1758-2946-1-6     Document Type: Article

References (50)

1. ZINC - A free database of commercially available compounds for virtual screening. JJ Irwin BK Shoichet, J Chem Inf Model 2005 45 177 182 15667143 10.1021/ci049714+
2. ChemNavigator iResearch Library. http://www.chemnavigator.com/cnc/products/iRL.asp
3. National Cancer Institute Drug Information System 3D database. GWA Milne MC Nicklaus JS Driscoll S Wang D Zaharevitz, J Chem Inf Comput Sci 1994 34 1219 1224 7962217
4. The NCI/DTP Open Chemical Repository Collection. http://dtp.nci.nih.gov/branches/dscb/repo-open.html
5. A critical assessment of docking programs and scoring functions. GL Warren CW Andrews AM Capelli B Clarke J LaLonde MH Lambert M Lindvall N Nevins SF Semus S Senger G Tedesco ID Wall JM Woolven CE Peishoff MS Head, J Med Chem 2006 49 5912 5931 10.1021/jm050362n 17004707
6. Evaluation of library ranking efficacy in virtual screening. M Kontoyianni GS Sokol LM McClellan, J Comput Chem 2005 26 1 11 22 10.1002/jcc.20141 15526325
7. Minimizing false positives in kinase virtual screens. E Perola, Proteins 2006 64 422 435 10.1002/prot.21002 16708364
8. Target-biased scoring approaches and expert systems in structure-based virtual screening. JM Jansen EJ Martin, Curr Opin Chem Biol 2004 8 359 364 10.1016/j.cbpa.2004.06.002 15288244
9. Development and validation of a genetic algorithm for flexible docking. G Jones P Willett RC Glen AR Leach R Taylor, J Mol Biol 1997 267 727 748 10.1006/jmbi.1996.0897 9126849
10. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. RA Friesner JL Banks RB Murphy TA Halgren JJ Klicic DT Mainz MP Repasky EH Knoll M Shelley JK Perry DE Shaw P Francis PS Shenkin, J Med Chem 2004 47 1739 1749 10.1021/jm0306430 15027865
11. MOE: Molecular Operating Environment version 2005.06. Chemical Computing Group, Inc.: Montreal, Canada 2005
12. The computer program LUDI: A new method for the de novo design of enzyme inhibitors. HJ Böhm, J Comput Aided Mol Des 1992 6 61 78 10.1007/BF00124387 1583540
13. LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters. G Wolber T Langer, J Chem Inf Model 2005 45 160 169 10.1021/ci049885e 15667141
14. Influenza virus neuraminidase: structure, antibodies, and inhibitors. PM Colman, Protein Sci 1994 3 1687 1696 7849585 10.1002/pro.5560031007
15. Sensitivity of molecular docking to induced fit effects in influenza virus neuraminidase. L Birch CW Murray MJ Hartshorn IJ Tickle ML Verdonk, J Comput Aided Mol Des 2002 16 855 869 10.1023/A:1023844626572 12825619
16. Structural evidence for a second sialic acid binding site in avian influenza virus neuraminidases. JN Varghese PM Colman A van Donkelaar TJ Blick A Sahasrabudhe JL McKimm-Breschkin, Proc Natl Acad Sci USA 1997 94 11808 11812 9342319 10.1073/pnas.94.22.11808 (Pubitemid 27467799)
17. The Binding Database. http://www.bindingdb.org
18. BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. T Liu Y Lin X Wen RN Jorissen MK Gilson, Nucleic Acids Res 2007 35 198 201 17145705 10.1093/nar/gkl999 (Pubitemid 46056198)
19. Symyx Databases: Current bioactivity findings for newly launched and developmental drugs. http://www.symyx.com/products/databases/bioactivity/mddr/index.jsp
20. Pipeline Pilot version 5.0. SciTegic, Inc.: San Diego, CA 2005
21. GOLD Support: Scientific FAQs. http://www.ccdc.cam.ac.uk/products/life-sciences/gold/faqs/scientific-faq.php#bindingaffinity
22. The PyMOL Molecular Graphics System version 0.99. WL Delano, DeLano Scientific: Palo Alto, CA 2002
23. Mammalian cyclin-dependent kinases. M Malumbres M Barbacid, Trends Biochem Sci 2005 30 630 641 10.1016/j.tibs.2005.09.005 16236519
24. Protein structures in virtual screening: a case study with CDK2. MP Thomas C McInnes PM Fischer, J Med Chem 2006 49 92 104 10.1021/jm050554i 16392795
25. Imidazo[1,2-a]pyridines: a potent and selective class of cyclin-dependent kinase inhibitors identified through structure-based hybridisation. M Anderson JF Beattie GA Breault J Breed KF Byth JD Culshaw RP Ellston S Green CA Minshull RA Norman RA Pauptit J Stanway AP Thomas PJ Jewsbury, Bioorg Med Chem Lett 2003 13 3021 3026 10.1016/S0960-894X(03)00638-3 12941325
26. Oxindole-based inhibitors of cyclin-dependent kinase 2 (CDK2): design, synthesis, enzymatic activities, and X-ray crystallographic analysis. HN Bramson J Corona ST Davis SH Dickerson M Edelstein SV Frye RT Gampe PA Harris A Hassell WD Holmes RN Hunter KE Lackey B Lovejoy MJ Luzzio V Montana WJ Rocque D Rusnak L Shewchuk JM Veal DH Walker LF Kuyper, J Med Chem 2001 44 4339 4358 10.1021/jm010117d 11728181
27. Imidazo[1,2-b]pyridazines: a potent and selective class of cyclin-dependent kinase inhibitors. KF Byth N Cooper JD Culshaw DW Heaton SE Oakes CA Minshull RA Norman RA Pauptit JA Tucker J Breed A Pannifer S Rowsell JJ Stanway AL Valentine AP Thomas, Bioorg Med Chem Lett 2004 14 2249 2252 10.1016/j.bmcl.2004.02.008 15081018 (Pubitemid 38481399)
28. Protein kinase C: Structural and spatial recognition by phosphorylation, cofactors, and macromolecular interactions. AC Newton, Chem Rev 2001 101 2353 2364 10.1021/cr0002801 11749377
29. Structural basis of protein kinase C activation by tumor promoters. Y Kishi RR Rando, Acc Chem Res 1998 31 163 172 10.1021/ar9600751
30. Synthetic diacylglycerols (DAG) and DAG-lactones as activators of protein kinase C (PK-C). VE Marquez PM Blumberg, Acc Chem Res 2003 36 434 443 10.1021/ar020124b 12809530
31. Conformationally constrained analogues of diacylglycerol (DAG). 25. Exploration of the sn-1 and sn-2 carbonyl functionality reveals the essential role of the sn-1 carbonyl at the lipid interface in the binding of DAG-lactones to protein kinase C. JH Kang ML Peach Y Pu NE Lewin MC Nicklaus PM Blumberg VE Marquez, J Med Chem 2005 48 5738 5748 16134942 10.1021/jm050352m (Pubitemid 41298347)
32. Crystal structure of the cys2 activator-binding domain of protein kinase C in complex with phorbol ester. G Zhang MG Kazanietz P Blumberg JH Hurley, Cell 1995 81 917 924 10.1016/0092-8674(95)90011-X 7781068
33. Iridals are a novel class of ligands for phorbol ester receptors with modest selectivity for the RasGRP receptor subfamily. L Shao NE Lewin PS Lorenzo Z Hu IJ Enyedy SH Garfield JC Stone FJ Marner PM Blumberg S Wang, J Med Chem 2001 44 3872 3880 10.1021/jm010258f 11689073
34. DTP - Natural Products Set Information. http://dtp.nci.nih.gov/branches/dscb/natprod-explanation.html
35. CHMIS-C: A comprehensive herbal medicine information system for cancer. X Fang L Shao H Zhang S Wang, J Med Chem 2005 48 1481 1488 10.1021/jm049838d 15743190
36. A marine natural product database. J Lei J Zhou, J Chem Inf Comput Sci 2002 42 742 748 12086536
37. Automatic generation of 3D-atomic coordinates for organic molecules. J Gasteiger C Rudolph J Sadowski, Tetrahedron Comput Methodol 1990 3 547 547 10.1016/0898-5529(90)90156-3
38. Structural basis of binding of high-affinity ligands to protein kinase C: Prediction of the binding modes through a new molecular dynamics method and evaluation by site-directed mutagenesis. Y Pak IJ Enyedy J Varady JW Kung PS Lorenzo PM Blumberg S Wang, J Med Chem 2001 44 1690 1701 10.1021/jm000488e 11356104
39. Identification of compounds with nanomolar binding affinity for checkpoint kinase-1 using knowledge-based virtual screening. PD Lyne PW Kenny DA Cosgrove C Deng S Zabludoff JJ Wendoloski S Ashwell, J Med Chem 2004 47 1962 1968 10.1021/jm030504i 15055996
40. Virtual screening for submicromolar leads of tRNA-guanine transglycosylase based on a new unexpected binding mode detected by crystal structure analysis. R Brenk L Naerum U Grädler HD Gerber GA Garcia K Reuter MT Stubbs G Klebe, J Med Chem 2003 46 1133 1143 10.1021/jm0209937 12646024
41. Pharmacophore-based molecular docking to account for ligand flexibility. D Joseph-McCarthy BE Thomas IV M Belmarsh D Moustakas JC Alvarez, Proteins 2003 51 2 172 188 12660987 10.1002/prot.10266 (Pubitemid 36397751)
42. Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions. Z Deng C Chuaqui J Singh, J Med Chem 2004 47 337 344 10.1021/jm030331x 14711306
43. Optimizing fragment and scaffold docking by use of molecular interaction fingerprints. G Marcou D Rognan, J Chem Inf Model 2007 47 195 207 10.1021/ci600342e 17238265
44. Assessment of docking poses: interactions-based accuracy classification (IBAC) versus crystal structure deviations. RT Kroemer A Vulpetti JJ McDonald DC Rohrer JY Trosset F Giordanetto S Cotesta C McMartin M Kihlén PFW Stouten, J Chem Inf Comput Sci 2004 44 871 881 15154752
45. 50training data. EJ Martin DC Sullivan, J Chem Inf Model 2008 48 861 872 10.1021/ci7004548 18380449
46. Virtual screening using protein-ligand docking: avoiding artificial enrichment. ML Verdonk V Berdini MJ Hartshorn WTM Mooij CW Murray RD Taylor P Watson, J Chem Inf Comput Sci 2004 44 793 806 15154744
47. Flexible docking under pharmacophore type constraints. SA Hindle M Rarey C Buning T Lengauer, J Comput Aided Mol Des 2002 16 129 149 10.1023/A:1016399411208 12188022
48. Evaluation of docking performance: comparative data on docking algorithms. M Kontoyianni LM McClellan GS Sokol, J Med Chem 2004 47 558 565 10.1021/jm0302997 14736237
49. Comparative evaluation of eight docking tools for docking and virtual screening accuracy. E Kellenberger J Rodrigo D Rognan, Proteins 2004 57 225 242 10.1002/prot.20149 15340911
50. Directed discovery of agents targeting the Met tyrosine kinase domain by virtual screening. ML Peach N Tan SJ Choyke A Giubellino G Athauda TR Burke Jr MC Nicklaus DP Bottaro, J Med Chem 2009 52 943 951 19199650 10.1021/jm800791f