Application of conformational clustering in protein-ligand docking

Methods in Molecular Biology

Volumn 819, Issue , 2012, Pages 169-186

  Bottegoni, Giovanni ^a,b   Rocchia, Walter ^a,b   Cavalli, Andrea ^a,b  

^a ISTITUTO ITALIANO DI TECNOLOGIA   (Italy)

^b UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

AClAP; Cluster analysis; Conformational sampling; Hierarchical agglomerative clustering; Protein ligand docking

Indexed keywords

LIGAND; PROTEIN;

ARTICLE; BIOLOGY; CHEMISTRY; CLUSTER ANALYSIS; METABOLISM; METHODOLOGY; PROTEIN BINDING; PROTEIN CONFORMATION;

CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; LIGANDS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEINS;

EID: 84855959112     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-465-0_12     Document Type: Article

References (61)

1. Kuntz, I. D., Blaney, J. M., Oatley, S. J., Langridge, R., and Ferrin, T. E. (1982) A geometric approach to macromoleculeligand interactions, J Mol Biol 161, 269-288.
2. Halperin, I., Ma, B., Wolfson, H., and Nussinov, R. (2002) Principles of docking: An overview of search algorithms and a guide to scoring functions, Proteins 47, 409-443. (Pubitemid 34614722)
3. Kitchen, D. B., Decornez, H., Furr, J. R., and Bajorath, J. (2004) Docking and scoring in virtual screening for drug discovery: methods and applications, Nat Rev Drug Discov 3, 935-949. (Pubitemid 39529931)
4. Taylor, R. D., Jewsbury, P. J., and Essex, J. W. (2002) A review of protein-small molecule docking methods, J Comput Aided Mol Des 16, 151-166.
5. Kontoyianni, M., McClellan, L. M., and Sokol, G. S. (2004) Evaluation of docking performance: comparative data on docking algorithms, J Med Chem 47, 558-565. (Pubitemid 38129714)
6. Carlson, H. A., and McCammon, J. A. (2000) Accommodating protein flexibility in computational drug design, Mol Pharmacol 57, 213-218. (Pubitemid 30084497)
7. Welch, W., Ruppert, J., and Jain, A. N. (1996) Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites, Chemistry & Biology 3, 449-462. (Pubitemid 126663345)
8. Moitessier, N., Englebienne, P., Lee, D., Lawandi, J., and Corbeil, C. R. (2008) Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go, Br J Pharmacol 153 Suppl 1, S7-26.
9. Bursulaya, B. D., Totrov, M., Abagyan, R., and Brooks, C. L., 3rd. (2003) Comparative study of several algorithms for flexible ligand docking, J Comput Aided Mol Des 17, 755-763. (Pubitemid 38418287)
10. Cheng, T., Li, X., Li, Y., Liu, Z., andWang, R. (2009) Comparative assessment of scoring functions on a diverse test set, J Chem Inf Model 49, 1079-1093.
11. Brooijmans, N., and Kuntz, I. D. (2003) Molecular recognition and docking algorithms, Annu Rev Biophys Biomol Struct 32, 335-373. (Pubitemid 37056233)
12. Yongye, A. B., Bender, A., and MartÃnez-Mayorga, K. (2010) Dynamic clustering threshold reduces conformer ensemble size while maintaining a biologically relevant ensemble, Journal of Computer-Aided Molecular Design 24, 675-686.
13. Bottegoni, G., Cavalli, A., and Recanatini, M. (2006) A comparative study on the application of hierarchical-agglomerative clustering approaches to organize outputs of reiterated docking runs, Journal of Chemical Information and Modeling 46, 852-862.
14. Grazioso, G., Cavalli, A., De Amici, M., Recanatini, M., and De Micheli, C. (2008) Alpha7 nicotinic acetylcholine receptor agonists: Prediction of their binding affinity through a molecular mechanics poissonboltzmann surface area approach, Journal of Computational Chemistry 29, 2593-2602.
15. Masetti, M., Cavalli, A., Recanatini, M., and Gervasio, F. L. (2009) Exploring complex protein-ligand recognition mechanisms with coarse metadynamics, J Phys Chem B 113, 4807-4816.
16. Colizzi, F., Perozzo, R., Scapozza, L., Recanatini, M., and Cavalli, A. (2010) Single-molecule pulling simulations can discern active from inactive enzyme inhibitors, Journal of the American Chemical Society 132, 7361-7371.
17. Piazzi, L., Cavalli, A., Belluti, F., Bisi, A., Gobbi, S., Rizzo, S., Bartolini, M., Andrisano, V., Recanatini, M., and Rampa, A. (2007) Extensive SAR and computational studies of 3-{4-[(benzylmethylamino)methyl] phenyl}-6, 7-dimethoxy-2H-2-chromenone (AP2238) derivatives, Journal of Medicinal Chemistry 50, 4250-4254. (Pubitemid 47301756)
18. Tumiatti, V., Milelli, A., Minarini, A., Rosini, M., Bolognesi, M. L., Micco, M., Andrisano, V., Bartolini, M., Mancini, F., Recanatini, M., Cavalli, A., and Melchiorre, C. (2008) Structure-activity relationships of acetylcholinesterase noncovalent inhibitors based on a polyamine backbone. 4. Further investigation on the inner spacer, Journal of Medicinal Chemistry 51, 7308-7312.
19. Belluti, F., Piazzi, L., Bisi, A., Gobbi, S., Bartolini, M., Cavalli, A., Valenti, P., and Rampa, A. (2009) Design, synthesis, and evaluation of benzophenone derivatives as novel acetylcholinesterase inhibitors, European Journal of Medicinal Chemistry 44, 1341-1348.
20. Rivera-Becerril, E., Joseph-Nathan, P., Perez-Ãlvarez, V. M., and Morales-Rios, M. S. (2008) Synthesis and biological evaluation of (-)-and (+)-debromoflustramine B and its analogues as selective butyrylcholinesterase inhibitors, Journal of Medicinal Chemistry 51, 5271-5284.
21. Bolognesi, M. L., Banzi, R., Bartolini, M., Cavalli, A., Tarozzi, A., Andrisano, V., Minarini, A., Rosini, M., Tumiatti, V., Bergamini, C., Fato, R., Lenaz, G., Hrelia, P., Cattaneo, A., Recanatini, M., and Melchiorre, C. (2007) Novel class of quinone-bearing polyamines as multi-target-directed ligands to combat Alzheimer's disease, Journal of Medicinal Chemistry 50, 4882-4897. (Pubitemid 47525472)
22. Bolognesi, M. L., Cavalli, A., Valgimigli, L., Bartolini, M., Rosini, M., Andrisano, V., Recanatini, M., and Melchiorre, C. (2007) Multi-target-directed drug design strategy: From a dual binding site acetylcholinesterase inhibitor to a trifunctional compound against Alzheimer's disease, Journal of Medicinal Chemistry 50, 6446-6449. (Pubitemid 350309081)
23. Piazzi, L., Cavalli, A., Colizzi, F., Belluti, F., Bartolini, M., Mancini, F., Recanatini, M., Andrisano, V., and Rampa, A. (2008) Multitarget-directed coumarin derivatives: hAChE and BACE1 inhibitors as potential anti-Alzheimer compounds, Bioorganic and Medicinal Chemistry Letters 18, 423-426.
24. Rosini, M., Simoni, E., Bartolini, M., Cavalli, A., Ceccarini, L., Pascu, N., McClymont, D. W., Tarozzi, A., Bolognesi, M. L., Minarini, A., Tumiatti, V., Andrisano, V., Mellor, I. R., and Melchiorre, C. (2008) Inhibition of acetylcholinesterase, I 2-amyloid aggregation, and NMDA receptors in Alzheimer's disease: A promising direction for the multi-targetdirected ligands gold rush, Journal of Medicinal Chemistry 51, 4381-4384.
25. Rizzo, S., Bartolini, M., Ceccarini, L., Piazzi, L., Gobbi, S., Cavalli, A., Recanatini, M., Andrisano, V., and Rampa, A. (2010) Targeting Alzheimer's disease: Novel indanone hybrids bearing a pharmacophoric fragment of AP2238, Bioorganic and Medicinal Chemistry 18, 1749-1760.
26. Hu, Q., Negri, M., Jahn-Hoffmann, K., Zhuang, Y., Olgen, S., Bartels, M., Muller-Vieira, U., Lauterbach, T., and Hartmann, R. W. (2008) Synthesis, biological evaluation, and molecular modeling studies of methylene imidazole substituted biaryls as inhibitors of human 17alpha-hydroxylase-17, 20-lyase (CYP17)-Part II: Core rigidification and influence of substituents at the methylene bridge, Bioorganic and Medicinal Chemistry 16, 7715-7727.
27. Jagusch, C., Negri, M., Hille, U. E., Hu, Q., Bartels, M., Jahn-Hoffmann, K., Mendieta, M. A. E. P. B., Rodenwaldt, B., Mãller-Vieira, U., Schmidt, D., Lauterbach, T., Recanatini, M., Cavalli, A., and Hartmann, R. W. (2008) Synthesis, biological evaluation and molecular modelling studies of methyleneimidazole substituted biaryls as inhibitors of human 17alphahydroxylase-17, 20-lyase (CYP17). Part I: Heterocyclic modifications of the core structure, Bioorganic and Medicinal Chemistry 16, 1992-2010. (Pubitemid 351226569)
28. Hille, U. E., Hu, Q., Vock, C., Negri, M., Bartels, M., Muller-Vieira, U., Lauterbach, T., and Hartmann, R. W. (2009) Novel CYP17 inhibitors: Synthesis, biological evaluation, structure-activity relationships and modelling of methoxy-and hydroxy-substituted methyleneimidazolyl biphenyls, European Journal of Medicinal Chemistry 44, 2765-2775.
29. Hu, Q., Negri, M., Olgen, S., and Hartmann, R. W. (2010) The role of fluorine substitution in biphenyl methylene imidazole-type CYP17 inhibitors for the treatment of prostate carcinoma, ChemMedChem 5, 899-910.
30. Gobbi, S., Cavalli, A., Negri, M., Schewe, K. E., Belluti, F., Piazzi, L., Hartmann, R. W., Recanatini, M., and Bisi, A. (2007) Imidazolylmethylbenzophenones as highly potent aromatase inhibitors, Journal of Medicinal Chemistry 50, 3420-3422. (Pubitemid 47195449)
31. Di Fenza, A., Rocchia, W., and Tozzini, V. (2009) Complexes of HIV-1 integrase with HAT proteins: Multiscale models, dynamics, and hypotheses on allosteric sites of inhibition, Proteins: Structure, Function and Bioformatics 76, 946-958.
32. Tomlinson, S. M., Malmstrom, R. D., and Watowich, S. J. (2009) New approaches to structure-based discovery of Dengue protease inhibitors, Infectious Disorders -Drug Targets 9, 327-343.
33. Totrov, M., and Abagyan, R. (2008) Flexible ligand docking to multiple receptor conformations: a practical alternative, Curr Opin Struct Biol 18, 178-184.
34. Damm, K. L., and Carlson, H. A. (2007) Exploring experimental sources of multiple protein conformations in structure-based drug design, J Am Chem Soc 129, 8225-8235. (Pubitemid 47039084)
35. Barril, X., and Morley, S. D. (2005) Unveiling the Full Potential of Flexible Receptor Docking Using Multiple Crystallographic Structures, J. Med. Chem. 48, 4432-4443. (Pubitemid 40884945)
36. Bottegoni, G., Kufareva, I., Totrov, M., and Abagyan, R. (2009) Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking, J Med Chem 52, 397-406.
37. Rueda, M., Bottegoni, G., and Abagyan, R. (2010) Recipes for the selection of experimental protein conformations for virtual screening, J Chem Inf Model 50, 186-193.
38. Kiviranta, P. H., Salo, H. S., Leppanen, J., Rinne, V. M., Kyrylenko, S., Kuusisto, E., Suuronen, T., Salminen, A., Poso, A., Lahtela-Kakkonen, M., and Wallen, E. A. A. (2008) Characterization of the binding properties of SIRT2 inhibitors with a N-(3-phenylpropenoyl)-glycine tryptamide backbone, Bioorganic and Medicinal Chemistry 16, 8054-8062.
39. Kranjc, A., Bongarzone, S., Rossetti, G., Biarnes, X., Cavalli, A., Bolognesi, M. L., Roberti, M., Legname, G., and Carloni, P. (2009) Docking ligands on protein surfaces: The case study of prion protein, Journal of Chemical Theory and Computation 5, 2565-2573.
40. Xiang, Z., Soto, C. S., and Honig, B. (2002) Evaluating conformational free energies: The colony energy and its application to the problem of loop prediction, Proceedings of the National Academy of Sciences of the United States of America 99, 7432-7437. (Pubitemid 34568708)
41. Chang, M. W., Belew, R. K., Carroll, K. S., Olson, A. J., and Goodsell, D. S. (2008) Empirical entropic contributions in computational docking: Evaluation in APS reductase complexes, Journal of Computational Chemistry 29, 1753-1761.
42. Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., and Olson, A. J. (2009) AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility, J Comput Chem 30, 2785-2791.
43. Jones, G., Willett, P., Glen, R. C., Leach, A. R., and Taylor, R. (1997) Development and validation of a genetic algorithm for flexible docking, Journal of Molecular Biology 267, 727-748. (Pubitemid 27170693)
44. Abagyan, R., Totrov, M., and Kuznetsov, D. (1994) Icm -a New Method for Protein Modeling and Design -Applications to Docking and Structure Prediction from the Distorted Native Conformation, Journal of Computational Chemistry 15, 488-506.
45. Bottegoni, G., Rocchia, W., Recanatini, M., and Cavalli, A. (2006) AClAP, Autonomous hierarchical agglomerative Cluster Analysis based protocol to partition conformational datasets, Bioinformatics 22.
46. Lin, J. H., Perryman, A. L., Schames, J. R., and McCammon, J. A. (2002) Computational drug design accommodating receptor flexibility: the relaxed complex scheme, J Am Chem Soc 124, 5632-5633. (Pubitemid 34533490)
47. Landon, M. R., Amaro, R. E., Baron, R., Ngan, C. H., Ozonoff, D., McCammon, J. A., and Vajda, S. (2008) Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble, Chem Biol Drug Des 71, 106-116. (Pubitemid 351160979)
48. Schames, J. R., Henchman, R. H., Siegel, J. S., Sotriffer, C. A., Ni, H., and McCammon, J. A. (2004) Discovery of a novel binding trench in HIV integrase, J Med Chem 47, 1879-1881. (Pubitemid 38453905)
49. Amaro, R. E., Baron, R., and McCammon, J. A. (2008) An improved relaxed complex scheme for receptor flexibility in computeraided drug design, J Comput Aided Mol Des 22, 693-705.
50. Daura, X., Gademann, K., Jaun, B., Seebach, D., Van Gunsteren, W. F., and Mark, A. E. (1999) Peptide folding: When simulation meets experiment, Angewandte Chemie -International Edition 38, 236-240. (Pubitemid 29051239)
51. Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., and Berendsen, H. J. C. (2005) GROMACS: Fast, flexible, and free, pp 1701-1718, Wiley Subscription Services, Inc., A Wiley Company.
52. de Hoon, M. J. L., Imoto, S., Nolan, J., and Miyano, S. (2004) Open source clustering software, Bioinformatics 20, 1453-1454. (Pubitemid 38931415)
53. Kaufman, L., and Rousseeuw, P. J. (1990) Finding Groups in Data: an Introduction to Cluster Analysis., Wiley, New York.
54. Hopkins, B. (1954) A new method for determining the type of distribution of plant individuals., Ann. Bot. 18, 213-227.
55. Kelley, L. A., Gardner, S. P., and Sutcliffe, M. J. (1997) An automated approach for defining core atoms and domains in an ensemble of NMR-derived protein structures, Protein Engineering 10, 737-741. (Pubitemid 27332083)
56. Cole, J. C., Murray, C. W., Nissink, J. W., Taylor, R. D., and Taylor, R. (2005) Comparing protein-ligand docking programs is difficult, Proteins 60, 325-332. (Pubitemid 41061629)
57. Hawkins, P. C., Warren, G. L., Skillman, A. G., and Nicholls, A. (2008) How to do an evaluation: pitfalls and traps, J Comput Aided Mol Des 22, 179-190.
58. Marcou, G., and Rognan, D. (2007) Optimizing fragment and scaffold docking by use of molecular interaction fingerprints, J Chem Inf Model 47, 195-207. (Pubitemid 46237537)
59. Abagyan, R., and Kufareva, I. (2009) The flexible pocketome engine for structural chemogenomics, Methods Mol Biol 575, 249-279.
60. Everitt, B. S., Landau, S., and Leese, M. (2001) Cluster analysis, Arnold, a member of the Hodder Headline Group, London.
61. Ward, J. H. J., and Hook, M. E. (1963) Application of a hierarchical grouping procedure to problem of grouping profiles, Educ. Psychol. Meas. 23, 69-92.