Protein-ligand docking guided by ligand pharmacophore-mapping experiment by NMR

Journal of Molecular Graphics and Modelling

Volumn 31, Issue , 2011, Pages 20-27

  Fukunishi, Yoshifumi ^a   Mizukoshi, Yumiko ^a,b   Takeuchi, Koh ^a   Shimada, Ichio ^a,c   Takahashi, Hideo ^a,d   Nakamura, Haruki ^a,e  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b Koto ku   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

^d YOKOHAMA CITY UNIVERSITY   (Japan)

^e OSAKA UNIVERSITY   (Japan)

Author keywords

In silico docking; Ligand epitope mapping; NMR; Pharmacophore mapping; Protein compound complex structure; Protein ligand docking

Indexed keywords

COMPLEX STRUCTURE; EPITOPE MAPPING; LONGITUDINAL RELAXATION; NMR DATA; NOVEL LIGANDS; PHARMACOPHORE-MAPPING; PREDICTION ACCURACY; PROTEIN-LIGAND COMPLEXES; PROTEIN-LIGAND DOCKING; STRUCTURAL INFORMATION; TARGET PROTEINS;

ANTIGENS; COMPLEXATION; EXPERIMENTS; MAPPING; NUCLEAR MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PHARMACODYNAMICS; PROTEINS; PROTONS;

LIGANDS;

LIGAND;

ARTICLE; EPITOPE MAPPING; MOLECULAR DOCKING; NUCLEAR MAGNETIC RESONANCE; PHARMACOPHORE; PRIORITY JOURNAL; PROTEIN STRUCTURE;

BINDING SITES; EPITOPE MAPPING; LIGANDS; LONGITUDINAL STUDIES; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; PROTONS; SOFTWARE;

EID: 80053929156     PISSN: 10933263     EISSN: 18734243     Source Type: Journal    
DOI: 10.1016/j.jmgm.2011.08.002     Document Type: Article

References (53)

1. I.D. Kuntz, J.M. Blaney, S.J. Oatley, R. Langridge, and T.E. Ferrin A geometric approach to macromolecule-ligand interactions J. Mol. Biol. 161 1982 269 288
2. M. Rarey, B. Kramer, T. Lengauer, and G. Klebe A fast flexible docking method using an incremental construction algorithm J. Mol. Biol. 261 1996 470 489 (Pubitemid 26335901)
3. G. Jones, P. Willet, R.C. Glen, A.R. Leach, and R. Taylor Development and validation of a genetic algorithm for flexible docking J. Mol. Biol. 267 1997 727 748 (Pubitemid 27170693)
4. N. Paul, and D. Rognan ConsDock: a new program for the consensus analysis of protein-ligand interactions Proteins 47 2002 521 533 (Pubitemid 34614732)
5. C.A. Baxter, C.W. Murray, D.E. Clark, D.R. Westhead, and M.D. Eldridge Flexible docking using tabu search and an empirical estimate of binding affinity Proteins 33 1998 367 382 (Pubitemid 28516342)
6. D.S. Goodsell, and A.J. Olson Automated docking of substrates to proteins by simulated annealing Proteins 8 1990 195 202 (Pubitemid 20363304)
7. R. Abagyan, M. Totrov, and D. Kuznetsov ICM: a new method for structure modeling and design: application to docking and structure prediction from the disordered native conformation J. Comput. Chem. 15 1994 488 506
8. P.M. Colman Structure-based drug design Curr. Opin. Struct. Biol. 4 1994 868 874
9. A. Kramer, P.D. Kirchhoff, X. Jiang, C.M. Venkatachalam, and M. Waldman LigScore: a novel scoring function for predicting binding affinities J. Mol. Graph. Model. 23 2005 395 407 (Pubitemid 40386869)
10. Y. Fukunishi, Y. Mikami, and H. Nakamura Similarities among receptor pockets and among compounds: analysis and application to in silico ligand screening J. Mol. Graph. Model. 24 2005 34 45 (Pubitemid 41318116)
11. C. Zhang, S. Liu, Q. Zhu, and Y. Zhou A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes J. Med. Chem. 48 2005 2325 2335 (Pubitemid 40516427)
12. I. Muegge, and Y.C. Martin A general and fast scoring function for protein-ligand interactions: a simplified potential approach J. Med. Chem. 42 1999 791 804 (Pubitemid 29136170)
13. G.L. Warren, C. Webster Andrews, A.M. Capelli, B. Clarke, J. LaLonde, M.H. Lambert, M. Lindvall, N. Nevins, S.F. Semus, S. Senger, G. Tedesco, I.D. Wall, J.M. Woolven, C.E. Peishoff, and M.S. Head A critical assessment of docking programs and scoring functions J. Med. Chem. 49 2006 5912 5931 (Pubitemid 44484938)
14. J.B. Cross, D.C. Thompson, B.K. Rai, J.C. Baber, K.Y. Fan, Y. Hu, and C. Humblet Comparison of several molecular docking programs: pose prediction and virtual screening accuracy J. Chem. Inf. Model. 49 2009 1455 1474
15. S. Mukherjee, T.E. Balius, and R.C. Rizzo Docking validation resources: protein family and ligand flexibility experiments J. Chem. Inf. Model. 50 2010 1986 2000
16. M. Sandor, R. Kiss, and G.M. Keseru Virtual fragment docking by Glide: a validation study on 190 protein-fragment complexes J. Chem. Inf. Model. 50 2010 1165 1172
17. R. Thilagavathi, and R.L. Mancera Ligand-protein cross-docking with water molecules J. Chem. Inf. Model. 50 2010 415 421
18. J.A. Feng, and G.R. Marshall SKATE: a docking program that decouples systematic sampling from scoring J. Comput. Chem. 31 2010 2540 2554
19. A. Grosdidier, V. Zoete, and O. Michielin Fast docking using the CHARMM force field with EADock DSS J. Comput. Chem. 32 2011 2149 2159
20. P.S. Charifson, J.J. Corkery, M.A. Murcko, and W.P. Walters Consensus scoring: a method for obtaining improved hit rates from docking database of three-dimensional structures into proteins J. Med. Chem. 42 1999 5100 5109 (Pubitemid 30020261)
21. R. Wang, and S. Wang How does consensus scoring work for virtual library screening? An idealized computer experiment J. Chem. Inf. Comput. Sci. 41 2001 1422 1426
22. R.D. Clark, A. Strizhev, J.M. Leonard, J.F. Blake, and J.B. Matthew Consensus scoring for ligand/protein interactions J. Mol. Graph. Model. 20 2002 281 295 (Pubitemid 34017546)
23. R. Wang, Y. Lu, and S. Wang Comparative evaluation of 11 scoring functions for molecular docking J. Med. Chem. 46 2003 2287 2303 (Pubitemid 36637914)
24. J.M. Yang, Y.F. Chen, T.W. Shen, B.S. Kristal, and D.F. Hsu Consensus scoring criteria for improving enrichment in virtual screening J. Chem. Inf. Model. 45 2005 1134 1146 (Pubitemid 41156712)
25. R. Teramoto, and H. Fukunishi Supervised consensus scoring for docking and virtual screening J. Chem. Inf. Model. 47 2007 526 534 (Pubitemid 46615954)
26. J. Janin Assessing predictions of protein-protein interaction: the CAPRI experiment Protein. Sci. 14 2005 278 283 (Pubitemid 40194579)
27. I. Shimada NMR techniques for identifying the interface of a larger protein-protein complex: cross-saturation and transferred cross-saturation experiments Methods Enzymol. 394 2005 483 506 (Pubitemid 40460929)
28. H. Takahashi, T. Nakanishi, K. Kami, Y. Arata, and I. Shimada A novel NMR method for determining the interfaces of large protein-protein complexes Nat. Struct. Biol. 7 2000 220 223 (Pubitemid 30140768)
29. T. Matsuda, T. Ikegami, N. Nakajima, T. Yamazaki, and H. Nakamura Model building of a protein-protein complexed structure using saturation transfer and residual dipolar coupling without paired intermolecular NOE J. Biomol. NMR 29 2004 325 338 (Pubitemid 38864831)
30. E. Kanamori, S. Igarashi, M. Osawa, Y. Fukunishi, I. Shimada, and H. Nakamura Structure determination of a protein assembly by amino acid selective cross-saturation Proteins 79 2011 179 190
31. M. Matsumoto, T. Ueda, and I. Shimada Theoretical analyses of the transferred cross-saturation method J. Magn. Reson. 205 2010 114 124
32. I. Shimada, T. Ueda, M. Matsumoto, M. Sakakura, M. Osawa, K. Takeuchi, N. Nishida, and H. Takahashi Cross-saturation and transferred cross-saturation experiments Prog. Nucl. Magn. Reson. Spectrosc. 54 2009 123 140
33. M. Mayer, and B. Meyer Characterization of ligand binding by saturation transfer difference NMR spectroscopy Angew. Chem. Int. Ed. 38 1999 1784 1788 (Pubitemid 29290947)
34. M. Mayer, and B. Meyer Group epitope mapping by saturation transfer difference NMR to identify segments of a ligand in direct contract with a protein receptor J. Am. Chem. Soc. 123 2001 6108 6117 (Pubitemid 32888480)
35. J. Yan, A.D. Kline, H. Mo, M.J. Shapiro, and E.R. Zart ler The effect of relaxation on the epitope mapping by saturation transfer difference NMR J. Magn. Reson. 163 2003 270 276
36. Y. Mizukoshi, A. Abe, T. Takizawa, H. Hanzawa, Y. Fukunishi, I. Shimada, H. Takahashi, An accurate pharmacophore mapping method by NMR, submitted for publication.
37. I. Bertini, M. Fragai, A. Giachetti, C. Luchinat, M. Maletta, G. Parigi, and K.J. Yen Combining in silico tools and NMR data to validate protein-ligand structural models: application to matrix metalloproteinases J. Med. Chem. 48 2005 7544 7559 (Pubitemid 41698797)
38. K. Ono, H. Ueda, Y. Yoshizawa, D. Akazawa, R. Tanimura, I. Shimada, and H. Takahashi Structural basis for platelet anti-aggregation by angiotensin II type 1-receptor antagonist losartan (DuP-753) via glycoprotein VI J. Med. Chem. 53 2010 2087 2093
39. J.W.M. Nissink, C. Murray, M. Hartshorn, M.L. Verdonk, J.C. Cole, and R. Taylor A new test set for validating predictions of protein-ligand interaction Proteins 49 2002 457 471 (Pubitemid 35388132)
40. Y. Fukunishi, Y. Mikami, S. Kubota, and H. Nakamura Multiple target screening method for robust and accurate in silico ligand screening J. Mol. Graph. Model. 25 2005 61 70 (Pubitemid 44376445)
41. Y. Fukunishi, S. Kubota, and H. Nakamura Noise reduction method for molecular interaction energy: application to in silico drug screening and in silico target protein screening J. Chem. Inf. Model. 46 2006 2071 2084 (Pubitemid 44625978)
42. Y. Fukunishi, Y. Mikami, K. Takedomi, M. Yamanouchi, H. Shima, and H. Nakamura Classification of chemical compounds by protein-compound docking for use in designing a focused library J. Med. Chem. 49 2006 523 533 (Pubitemid 43157486)
43. Y. Fukunishi, S. Hojo, and H. Nakamura An efficient in silico screening method based on the protein-compound affinity matrix and its application to the design of a focused library for cytochrome P450 (CYP) ligands J. Chem. Inf. Model. 46 2006 2610 2622 (Pubitemid 46008132)
44. D.A. Case, T.A. Darden, T.E. Cheatham III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, K.M. Merz, B. Wang, D.A. Pearlman, M. Crowley, S. Brozell, V. Tsui, H. Gohlke, J. Mongan, V. Hornak, G. Cui, P. Beroza, C. Schafmeister, J.W. Caldwell, W.S. Ross, and P.A. Kollman AMBER 8 2004 UCSF
45. Y. Fukunishi, Y. Mikami, and H. Nakamura The filling potential method: a method for estimating the free energy surface for protein-ligand docking J. Phys. Chem. B 107 2003 13201 13210
46. J. Wang, R.M. Wolf, J.W. Caldwell, P.A. Kollman, and D.A. Case Development and testing of a general amber force field J. Comput. Chem. 25 2004 1157 1174
47. J. Wang, P. Cieplak, and P.A. Kollman How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 21 2000 1049 1074
48. M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, V.G. Zakrzewski, J.A. Montgomery, R.E. Stratmann Jr., J.C. Burant, S. Dapprich, J.M. Millam, A.D. Daniels, K.N. Kudin, M.C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G.A. Petersson, P.Y. Ayala, Q. Cui, K. Morokuma, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B. Foresman, J. Cioslowski, J.V. Ortiz, A.G. Baboul, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R.L. Martin, D.J. Fox, T. Keith, M.A. Al-Laham, C.Y. Peng, A. Nanayakkara, C. Gonzalez, M. Challacombe, P.M.W. Gill, B. Johnson, W. Chen, M.W. Wong, J.L. Andres, C. Gonzalez, M. Head-Gordon, E.S. Replogle, and J.A. Pople Gaussian 98, Revision A.9 1998 Gaussian, Inc. Pittsburgh, PA
49. J. Gasteiger, and M. Marsili Iterative partial equalization of orbital electronegativity - a rapid access to atomic charges Tetrahedron 36 1980 3219 3228
50. J. Gasteiger, and M. Marsili A new model for calculating atomic charges in molecules Tetrahedron Lett. 1978 3181 3184
51. V. Jayalakshmi, and N.R. Krishna Complete relaxation and conformational exchange matrix (CORCEMA) analysis of intermolecular saturation transfer effects in reversibly forming ligand-receptor complexes J. Magn. Reson. 155 2002 106 118
52. A. Kalk, and H.J.C. Berendsen Proton magnetic relaxation and spin diffusion in proteins J. Magn. Reson. 24 1976 343 366
53. M. Orita, K. Ohno, M. Warizaya, Y. Amano, and T. Niimi Lead generation and examples: opinion regarding how to follow up hits Methods Enzymol. 493 2011 383 419