FINDSITEX: A structure-based, small molecule virtual screening approach with application to all identified human GPCRs

Molecular Pharmaceutics

Volumn 9, Issue 6, 2012, Pages 1775-1784

  Zhou, Hongyi ^a   Skolnick, Jeffrey ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

FINDSITE; GPCR modeling; TASSERVMT; template based modeling; virtual screening

Indexed keywords

G PROTEIN COUPLED RECEPTOR; LIGAND;

ALGORITHM; ARTICLE; BINDING SITE; CONTROLLED STUDY; DATA BASE; FINDSITE; HUMAN; MOLECULAR LIBRARY; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN STRUCTURE; SCREENING;

HUMANS; MODELS, THEORETICAL; PROTEIN STRUCTURE, SECONDARY; RECEPTORS, G-PROTEIN-COUPLED;

EID: 84862007546     PISSN: 15438384     EISSN: 15438392     Source Type: Journal    
DOI: 10.1021/mp3000716     Document Type: Article

References (71)

1. Skolnick, J.; Fetrow, J.; Kolinski, A. Structural genomics and its importance for gene function analysis. Nat. Biotechnol. 2000, 18, 283- 287.
2. Baker, D.; Sali, A. Protein structure prediction and structural genomics. Science 2001, 294, 93-96. (Pubitemid 32952955)
3. Pieper, U.; Eswar, N.; Braberg, H.; Madhusudhan, M. S.; Davis, F. P.; Stuart, A. C.; Mirkovic, N.; Rossi, A.; Marti-Renom, M. A.; Fiser, A.; Webb, B.; Greenblatt, D.; Huang, C. C.; Ferrin, T. E.; Sali, A. MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 2004, 32 (Database issue), D217-D222. (Pubitemid 38081642)
4. Structural Bioinformatics of Membrane Proteins; Springer: Wien, New York, 2010.
5. Altschul, S. F.; Madden, T. L.; Schäffer, A. A.; Zhang, J.; Zhang, Z.; Miller, W.; Lipman, D.-J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25, 3389-3402. (Pubitemid 27359211)
6. Sali, A.; Blundell, T. L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 1993, 234, 779-815. (Pubitemid 24007801)
7. Pandit, S. B.; Zhang, Y.; Skolnick, J. TASSER-Lite: An automated tool for protein comparative modeling. Biophys. J. 2006, 91, 4180- 4190.
8. Hildebrand, A.; Remmert, M.; Biegert, A.; Söding, J. Fast and accurate automatic structure prediction with HHpred. Proteins 2009, 77 (Suppl.9), 128-132.
9. Jaroszewski, L.; Rychlewski, L.; Li, W.; Godzik, A. Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci. 2000, 9, 232-241. (Pubitemid 30126996)
10. Fischer, D. Hybrid fold recognition: combining sequence derived properties with evolutionary information. Pac. Symp. Biocomput. 2000 2000, 5, 116-127.
11. Zhou, H.; Zhou, Y. SPARKS 2 and SP3 servers in CASP6. Proteins 2005, 61 (Suppl. 7), 152-156.
12. Zhang, Y. Progress and challenges in protein structure prediction. Curr. Opin. Struct. Biol. 2008, 18 (3), 342-348.
13. Brylinski, M.; Skolnick, J. FINDSITE: A threading-based method for ligand-binding site prediction and functional annotation. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 129-134.
14. Brylinski, M.; Skolnick, J. Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints. J. Comput. Chem. 2008, 29, 1574-1588.
15. Brylinski, M.; Skolnick, J. Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling. J. Comput. Chem. 2010,31, 1093-1105.
16. Wass, M. N.; Sternberg, M. J. Prediction of ligand binding sites using homologous structures and conservation at CASP8. Proteins 2009, 77 (S9), 147-151.
17. Wass, M. N.; Kelly, L. A.; Sternberg, M. J. 3DLigandSite: predicting ligand-binding sites using similar structures. Nucl. Acid. Res. 2010, 38 (Suppl. 2), W469-W473.
18. Brylinski, M.; Skolnick, J. Comprehensive Structural and Functional Characterization of the Human Kinome by Protein Structure Modeling and Ligand Virtual Screening. J. Chem. Inf. Model. 2010, 50 (10), 1839-1854.
19. Lee, H. S.; Zhang, Y. BSP-SLIM: A blind low-resolution ligandprotein docking approach using predicted protein structures. Proteins 2011, 80, 93-110.
20. Roy, A.; Xu, D.; Poisson, J.; Zhang, Y. A Protocol for Computer- Based Protein Structure and Function Prediction. J. Visualized Exp. 2011, 57, e3259.
21. Filmore, D. It's a GPCR world. Mod. Drug Discovery 2004, 2004, 24-28.
22. Zhang, Y.; Skolnick, J. Automated structure prediction of weakly homologous proteins on genomic scale. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 7594-7599. (Pubitemid 38658074)
23. Zhang, Y.; DeVries, M. E.; Skolnick, J. Structure modeling of all identified G protein-coupled receptors in the human genome. PLoS Comput. Biol. 2006, 2 (2), e13.
24. Yarnitzky, T.; Levit, A.; Niv, M. Y. Homology modeling of Gprotein- coupled-receptors with X-ray structures on the rise. Curr. Opin. Drug Discovery Dev. 2010, 13, 317-325.
25. Peng, J.; Xu, J. A multiple-template approach to protein threading. Proteins 2011, 79 (6), 1930-1939.
26. Cheng, J. A multi-template combination algorithm for protein comparative modeling. BMC Struct. Biol. 2008, 8, 18.
27. Zhou, H.; Skolnick, J. Template-based protein structure modeling using TASSERVMT. Proteins 2011, 80 (2), 352-361.
28. Zhang, J.; Zhang, Y. GPCRRD: G protein-coupled receptor spatial restraint database for 3D structure modeling and function annotation. Bioinformatics 2010, 26, 3004-3005.
29. Zhang, Y. Template-based modeling and free modeling by ITASSER in CASP7. Proteins 2007, 69 (Suppl.8), 108-117. (Pubitemid 350210118)
30. Barth, P.; Wallner, B.; Baker, D. Prediction of membrane protein structures with complex topologies using limited constraints. Proc. Natl. Acad. Sci. U.S.A. 2009, 106 (5), 1409-1414.
31. Nikiforovich, G.; Taylor, C.; Marshall, G.; Baranski, T. Modeling the possible conformations of the extracellular loops in G-proteincoupled receptors. Proteins 2010, 78 (2), 271-285.
32. Mehler, E.; Hassen, S.; Kortagere, S.; Weinstein, H. Ab initio computational modeling of loops in G-protein-coupled recepotrs: Lessons from the crystal structures of rhodopsin. Proteins 2006, 64 (3), 673-690. (Pubitemid 44100733)
33. Niv, M.; Skrabanek, L.; Filizola, M.; Weinstein, H. Modeling activated states of GPCRs: The rhodopsin template. J. Comput.-Aided Mol. Des. 2006, 20, 437-448. (Pubitemid 44823882)
34. Foquet, N.; M'Kadmi, C.; Perahia, D.; Gagne, D.; Berge, G.; Marie, J.; Baneres, J.; Galleyrand, J.; Hehrentz, J.; Martinez, J. Activation of the ghrelin receptor is described by a privileged collective motion: A model for constitutive and agonist-induced activation of sub-class A G-protein-coupled receptor (GPCR). J. Mol. Biol. 2010, 395 (4), 769-784.
35. Abrol, R.; Bray, J.; Goddard, W., III. Bihelix: Towards de novo structure prediction of an ensemble of G-protein coupled receptor conformations. Proteins 2012, 80 (2), 505-518.
36. Kimura, S.; Tebben, A.; Langley, D. Expanding GPCR homology model binding sites via a balloon potential: A molecular dynamics refinement approach. Proteins 2008, 71 (4), 1919-1929. (Pubitemid 351732945)
37. Capra, J.; Laskowski, R.; Thornton, J.; Singh, M.; Funkhouser, T. Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure. PLoS Comput. Biol. 2009, 5, 12.
38. Radestock, S.; Weil, T.; Renner, S. Homology Model-Based Virtual Screening for GPCR Ligands Using Docking and Target- Biased Scoring. J. Chem. Inf. Model. 2008, 48 (5), 1104-1117.
39. Bernstein, F. C.; Koetzle, T. F.; Williams, G. J. B.; Meyer, E. F., Jr.; M., D. B.; Rodgers, J. R.; Kennard, O.; Shimanouchi, T.; Tasumi, M. The Protein Data Bank: A Computer-based Archival File for Macromolecular Structures. J. Mol. Biol. 1977, 112, 535-542.
40. Evers, A.; Klabunde, T. Structure-based drug discovery using GPCR homology modeling: successful virtual screening for antagonists of the Alpha1A adrenergic receptor. J. Med. Chem. 2005, 48, 1088-1097. (Pubitemid 40270452)
41. Pandit, S.; Skolnick, J. Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score. BMC Bioinf. 2008, 9, 531.
42. Henikoff, S.; Henikoff, J. G. Amino Acid Substitution Matrices from Protein Blocks. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 10915-10919.
43. Altschul, S. F.; Gish, W.; Miller, W.; Myers, E.; Lipman, D. Basic local alignment tool. J. Mol. Biol. 1990, 215, 403-410.
44. Zhang, Y.; Skolnick, J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res. 2005, 33, 2302-2309. (Pubitemid 41439897)
45. Zhang, Y.; Hubner, I.; Arakaki, A.; Shakhnovich, E.; Skolnick, J. On the origin and highly likely completeness of single-domain protein structures. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 2605-2610.
46. Brylinski, M.; Skolnick, J. Comparison of structure-based and threading-based approaches to protein functional annotation. Proteins 2010, 78 (1), 118-134.
47. Camerino, D.; Tricarico, D.; Desaphy, J. Ion channel pharmacology. Neurotherapeutics 2007, 4 (2), 184-198. (Pubitemid 46467548)
48. Manning, G.; Whyte, D.; Martinez, R.; Hunter, T.; Sudarssanam, S. The protein kinase complement of the human genome. Science 2002, 298, 5600.
49. Barrett, A. J.; Rawlings, N.; Woessner, J. The Handbook of Proteolytic Enzymes, 2nd ed.; Academic Press: 2003; ISBN 0-12- 079610-4.
50. Barford, D. Molecular mechanisms of the protein serine/ threonine phosphatases. Trends Biochem. Sci. 1996, 21 (11), 407-412. (Pubitemid 26393726)
51. Zhang, Z. Protein tyrosine phosphatases: structure and function, substrate specificity, and inhibitor development. Annu. Rev. Pharmacol. Toxicol. 2002, 42 (1), 209-34. (Pubitemid 34160526)
52. Tanimoto, T. T., An elementary mathematical theory of classification and prediction. IBM Internal Report 1958, (Nov 1958).
53. Zhang, Y.; Skolnick, J. A scoring function for the automated assessment of protein structure template quality. Proteins 2004, 57, 702-710. (Pubitemid 39626992)
54. Willett, P. Chemical similarity searching. J. Chem. Inf. Comput. Sci. 1998, 38, 983-996. (Pubitemid 128591261)
55. Okuno, Y.; Tamon, A.; Yabuuchi, H.; Niijima, S.; Minowa, Y.; Tonomura, K.; Kunimoto, R.; Feng, C. GLIDA: GPCR - ligand database for chemical genomics drug discovery - database and tools update. Nucleic Acids Res. 2007, 36, D907-D912. (Pubitemid 351149843)
56. Zhou, H.; Skolnick, J. Ab initio protein structure prediction using chunk-TASSER. Biophys. J. 2007, 93, 1510-1518. (Pubitemid 47403296)
57. Jones, T. D. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 1999, 292, 195-202.
58. Irwin, J. J.; Shoichet, B. K. ZINC - A Free Database of Commercially Available Compounds for Virtual Screening. J. Chem. Inf. Model. 2005, 45, 177-182. (Pubitemid 40736970)
59. Needleman, S.; Wunsch, C. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 1970, 48, 443-453.
60. Nordström, K. J.; Sällmen Almén, M.; Edstam, M. M.; Fredriksson, R.; Schiöth, H. B. Independent HHsearch, Needleman-Wunsch- Based, and Motif Analyses Reveal the Overall Hierarchy for Most of the G Protein-Coupled Receptor Families. Mol. Biol. Evol. 2011, 28 (9), 2471-2480.
61. Kendall, M. G. A new measure of rank correlation. Biometrika 1938, 30 (Parts 1-2), 81-89.
62. Brylinski, M.; Skolnick, J. Cross-Reactivity Virtual Profiling of the Human Kinome by X-ReactKIN: A Chemical Systems Biology Approach. Mol. Pharmaceutics 2010, 7 (6), 2324-2333.
63. Wishart, D.; Knox, C.; Guo, A.; Shrivastava, S.; Hassanali, M.; Stothard, P.; Chang, Z.; Woolsey, J. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res. 2006, 34 (Database), D668-D672.
64. Wang, Y.; Xiao, J.; Suzek, T.; Zhang, J.; Wang, J.; Zhou, Z.; Han, L.; Karapetyan, K.; Dracheva, S.; Shoemaker, B.; Bolton, E.; Gindulyte, A.; Bryant, S. PubChem's BioAssay Database. Nucleic Acids Res. 2012, 40 (1), D400-D412.
65. Gaulton, A.; Bellis, L.; Bento, A.; Chambers, J.; Davies, M.; Hersey, A.; Light, Y.; McGlinchey, S.; Michalovich, D.; Al-Lazikani, B.; Overington, J. ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res. 2012, 40 (D1), D1100-D1107.
66. Kanehisa, M.; Goto, S.; Kawashima, S.; Okuno, Y.; Hattori, M. The KEGG resource for deciphering the genome. Nucleic Acids Res. 2004, 32, D277-D280. (Pubitemid 38081656)
67. Kosloff, M.; Kolodny, R. Sequence-similar, structure-dissimilar protein pairs in the PDB. Proteins 2008, 71 (2), 891-902. (Pubitemid 351430023)
68. Huang, B.; Schroeder, M. LIGSITEcsc: predicting protein binding sites using the Connolly surface and degree of conservation. BMC Struct. Biol. 2006, 6, 19.
69. Tan, K.; Varadarajan, R.; Madhusudhan, M. DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins. Nucl. Acid. Res. 2011, 39 (Web Server), W242-W248.
70. Zhang, Z.; Li, Y.; Lin, B.; Schroeder, M.; Huang, B. Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction. Bioinformatics 2011, 27 (15), 2083-2088.
71. Ngan, C.; Hall, D.; Zerbe, B.; Grove, L.; Kozakov, D.; Vajda, S. FTSite: High accuracy detection of ligand binding sites on unbound protein structures. Bioinformatics 2012, 28 (2), 286-287.