Discovering the targets of drugs via computational systems biology

Journal of Biological Chemistry

Volumn 286, Issue 27, 2011, Pages 23653-23658

  Chua, Hon Nian ^a   Roth, Frederick P ^a,b  

^a HARVARD MEDICAL SCHOOL   (United States)

^b DANA FARBER CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL EFFECTS; COMPUTATIONAL APPROACH; COMPUTATIONAL SYSTEMS BIOLOGY; DRUG ACTION; DRUG DISCOVERY; EXPERIMENTAL DATA; UNDESIRABLE EFFECTS;

CHEMICAL COMPOUNDS; COMPUTATIONAL COMPLEXITY;

DRUG THERAPY;

ALPHA 2 ADRENERGIC RECEPTOR; CARBOPLATIN; CISPLATIN; CYCLOHEXIMIDE; CYCLOSPORIN A; DOPAMINE 3 RECEPTOR; DYCLONINE; EMETINE; FLUOXETINE; FULVESTRANT; HALOPERIDOL; HYDROXYUREA; ITRACONAZOLE; LOPERAMIDE; METHADONE; MEVINOLIN; MITOMYCIN C; MU OPIATE RECEPTOR; NEUROKININ 2 RECEPTOR; PACLITAXEL DERIVATIVE; PERGOLIDE; RABEPRAZOLE; RALOXIFENE; TACROLIMUS; TAMOXIFEN; TUNICAMYCIN;

BIOLOGY; COMPARATIVE STUDY; COMPUTATIONAL SYSTEMS BIOLOGY; COMPUTER ANALYSIS; DRUG DEVELOPMENT; DRUG MECHANISM; DRUG PROTEIN BINDING; DRUG TARGETING; DRUG THERAPY; FOOD AND DRUG ADMINISTRATION; GENE EXPRESSION PROFILING; GENE MAPPING; GENETIC VARIABILITY; HUMAN; NONHUMAN; PRIORITY JOURNAL; QUALITY CONTROL; SHORT SURVEY; UNSPECIFIED SIDE EFFECT;

ANIMALS; DRUG DISCOVERY; HUMANS; SYSTEMS BIOLOGY;

EID: 79959906421     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.R110.174797     Document Type: Short Survey

References (54)

1. Kola, I., and Landis, J. (2004) Nat. Rev. Drug. Discov. 3, 711-715
2. Sams-Dodd, F. (2005) Drug Discov. Today 10, 139-147
3. Brown, D. (2007) Drug Discov. Today 12, 1007-1012
4. Tatonetti, N. P., Liu, T., and Altman, R. B. (2009) Genome Biol. 10, 238
5. Hughes, T. R., Marton, M. J., Jones, A. R., Roberts, C. J., Stoughton, R., Armour, C. D., Bennett, H. A., Coffey, E., Dai, H., He, Y. D., Kidd, M. J., King, A. M., Meyer, M. R., Slade, D., Lum, P. Y., Stepaniants, S. B., Shoemaker, D. D., Gachotte, D., Chakraburtty, K., Simon, J., Bard, M., and Friend, S. H. (2000) Cell. 102, 109-126
6. Lum, P. Y., Armour, C. D., Stepaniants, S. B., Cavet, G., Wolf, M. K., Butler, J. S., Hinshaw, J. C., Garnier, P., Prestwich, G. D., Leonardson, A., Garrett- Engele, P., Rush, C. M., Bard, M., Schimmack, G., Phillips, J. W., Roberts, C. J., and Shoemaker, D. D. (2004) Cell. 116, 121-137
7. Parsons, A. B., Brost, R. L., Ding, H., Li, Z., Zhang, C., Sheikh, B., Brown, G. W., Kane, P. M., Hughes, T. R., and Boone, C. (2004) Nat. Biotechnol. 22, 62-69
8. Parsons, A. B., Lopez, A., Givoni, I. E., Williams, D. E., Gray, C. A., Porter, J., Chua, G., Sopko, R., Brost, R. L., Ho, C. H., Wang, J., Ketela, T., Brenner, C., Brill, J. A., Fernandez, G. E., Lorenz, T. C., Payne, G. S., Ishihara, S., Ohya, Y., Andrews, B., Hughes, T. R., Frey, B. J., Graham, T. R., Andersen, R. J., and Boone, C. (2006) Cell. 126, 611-625
9. Hillenmeyer, M. E., Fung, E., Wildenhain, J., Pierce, S. E., Hoon, S., Lee, W., Proctor, M., St Onge, R. P., Tyers, M., Koller, D., Altman, R. B., Davis, R. W., Nislow, C., and Giaever, G. (2008) Science 320, 362-365
10. Perlstein, E. O., Ruderfer, D. M., Roberts, D. C., Schreiber, S. L., and Kruglyak, L. (2007) Nat. Genet. 39, 496-502
11. Giaever, G., Shoemaker, D. D., Jones, T. W., Liang, H., Winzeler, E. A., Astromoff, A., and Davis, R. W. (1999) Nat. Genet. 21, 278-283
12. Hoon, S., Smith, A. M., Wallace, I. M., Suresh, S., Miranda, M., Fung, E., Proctor, M., Shokat, K. M., Zhang, C., Davis, R. W., Giaever, G., St Onge, R. P., and Nislow, C. (2008) Nat. Chem. Biol. 4, 498-506
13. Kuhn, M., von Mering, C., Campillos, M., Jensen, L. J., and Bork, P. (2008) Nucleic Acids Res. 36, D684-D688
14. Wishart, D. S., Knox, C., Guo, A. C., Shrivastava, S., Hassanali, M., Stothard, P., Chang, Z., and Woolsey, J. (2006) Nucleic Acids Res. 34, D668-D672
15. Lenoir, T., and Giannella, E. (2006) J. Biomed. Discov. Collab. 1, 11
16. Marton, M. J., DeRisi, J. L., Bennett, H. A., Iyer, V. R., Meyer, M. R., Roberts, C. J., Stoughton, R., Burchard, J., Slade, D., Dai, H., Bassett, D. E., Jr., Hartwell, L. H., Brown, P. O., and Friend, S. H. (1998) Nat. Med. 4, 1293-1301
17. Lamb, J., Crawford, E. D., Peck, D., Modell, J. W., Blat, I. C., Wrobel, M. J., Lerner, J., Brunet, J. P., Subramanian, A., Ross, K. N., Reich, M., Hieronymus, H., Wei, G., Armstrong, S. A., Haggarty, S. J., Clemons, P. A., Wei, R., Carr, S. A., Lander, E. S., and Golub, T. R. (2006) Science 313, 1929-1935
18. Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., and Mesirov, J. P. (2005) Proc. Natl. Acad. Sci. U.S.A. 102, 15545-15550
19. Gardner, T. S., di Bernardo, D., Lorenz, D., and Collins, J. J. (2003) Science 301, 102-105
20. di Bernardo, D., Thompson, M. J., Gardner, T. S., Chobot, S. E., Eastwood, E. L., Wojtovich, A. P., Elliott, S. J., Schaus, S. E., and Collins, J. J. (2005) Nat. Biotechnol. 23, 377-383
21. Shoemaker, R. H. (2006) Nat. Rev. Cancer. 6, 813-823
22. Weinstein, J. N., Myers, T. G., O'Connor, P. M., Friend, S. H., Fornace, A. J., Jr., Kohn, K. W., Fojo, T., Bates, S. E., Rubinstein, L. V., Anderson, N. L., Buolamwini, J. K., van Osdol, W. W., Monks, A. P., Scudiero, D. A., Sausville, E. A., Zaharevitz, D. W., Bunow, B., Viswanadhan, V. N., Johnson, G. S., Wittes, R. E., and Paull, K. D. (1997) Science 275, 343-349
23. Brem, R. B., and Kruglyak, L. (2005) Proc. Natl. Acad. Sci. U.S.A. 102, 1572-1577
24. Stöcklein, W., and Piepersberg, W. (1980) Antimicrob. Agents Chemother. 18, 863-867
25. Lindsley, D. L., Sandler, L., Baker, B. S., Carpenter, A. T., Denell, R. E., Hall, J. C., Jacobs, P. A., Miklos, G. L., Davis, B. K., Gethmann, R. C., Hardy, R. W., Steven, A. H., Miller, M., Nozawa, H., Parry, D. M., and Gould- Somero, M. (1972) Genetics 71, 157-184
26. Fisher, E., and Scambler, P. (1994) Nat. Genet. 7, 5-7
27. Tong, A. H., Evangelista, M., Parsons, A. B., Xu, H., Bader, G. D., Pagé, N., Robinson, M., Raghibizadeh, S., Hogue, C. W., Bussey, H., Andrews, B., Tyers, M., and Boone, C. (2001) Science 294, 2364-2368
28. Dueck, D., Morris, Q. D., and Frey, B. J. (2005) Bioinformatics 21, i144-i151
29. Yan, Z., Costanzo, M., Heisler, L. E., Paw, J., Kaper, F., Andrews, B. J., Boone, C., Giaever, G., and Nislow, C. (2008) Nat. Methods 5, 719-725
30. Schuldiner, M., Collins, S. R., Thompson, N. J., Denic, V., Bhamidipati, A., Punna, T., Ihmels, J., Andrews, B., Boone, C., Greenblatt, J. F., Weissman, J. S., and Krogan, N. J. (2005) Cell 123, 507-519
31. Luesch, H., Wu, T. Y., Ren, P., Gray, N. S., Schultz, P. G., and Supek, F. (2005) Chem. Biol. 12, 55-63
32. Butcher, R. A., Bhullar, B. S., Perlstein, E. O., Marsischky, G., LaBaer, J., and Schreiber, S. L. (2006) Nat. Chem. Biol. 2, 103-109
33. Meijer, D., van Agthoven, T., Bosma, P. T., Nooter, K., and Dorssers, L. C. (2006) Mol. Cancer Res. 4, 379-386
34. Ho, C. H., Magtanong, L., Barker, S. L., Gresham, D., Nishimura, S., Natarajan, P., Koh, J. L., Porter, J., Gray, C. A., Andersen, R. J., Giaever, G., Nislow, C., Andrews, B., Botstein, D., Graham, T. R., Yoshida, M., and Boone, C. (2009) Nat. Biotechnol. 27, 369-377
35. Ohya, Y., Sese, J., Yukawa, M., Sano, F., Nakatani, Y., Saito, T. L., Saka, A., Fukuda, T., Ishihara, S., Oka, S., Suzuki, G., Watanabe, M., Hirata, A., Ohtani, M., Sawai, H., Fraysse, N., Latgé, J. P., François, J. M., Aebi, M., Tanaka, S., Muramatsu, S., Araki, H., Sonoike, K., Nogami, S., and Morishita, S. (2005) Proc. Natl. Acad. Sci. U.S.A. 102, 19015-19020
36. Neumann, B., Held, M., Liebel, U., Erfle, H., Rogers, P., Pepperkok, R., and Ellenberg, J. (2006) Nat. Methods 3, 385-390
37. Loo, L. H., Wu, L. F., and Altschuler, S. J. (2007) Nat. Methods 4, 445-453
38. Neumann, B., Walter, T., Hériché, J. K., Bulkescher, J., Erfle, H., Conrad, C., Rogers, P., Poser, I., Held, M., Liebel, U., Cetin, C., Sieckmann, F., Pau, G., Kabbe, R., Wünsche, A., Satagopam, V., Schmitz, M. H., Chapuis, C., Gerlich, D. W., Schneider, R., Eils, R., Huber, W., Peters, J. M., Hyman, A. A., Durbin, R., Pepperkok, R., and Ellenberg, J. (2010) Nature 464, 721-727
39. Lieschke, G. J., and Currie, P. D. (2007) Nat. Rev. Genet. 8, 353-367
40. Peterson, R. T., Shaw, S. Y., Peterson, T. A., Milan, D. J., Zhong, T. P., Schreiber, S. L., MacRae, C. A., and Fishman, M. C. (2004) Nat. Biotechnol. 22, 595-599
41. Kaletta, T., and Hengartner, M. O. (2006) Nat. Rev. Drug. Discov. 5, 387-398
42. Burns, A. R., Wallace, I. M., Wildenhain, J., Tyers, M., Giaever, G., Bader, G. D., Nislow, C., Cutler, S. R., and Roy, P. J. (2010) Nat. Chem. Biol. 6, 549-557
43. Paolini, G. V., Shapland, R. H., van Hoorn, W. P., Mason, J. S., and Hopkins, A. L. (2006) Nat. Biotechnol. 24, 805-815
44. Yamanishi, Y., Araki, M., Gutteridge, A., Honda, W., and Kanehisa, M. (2008) Bioinformatics 24, i232-i240
45. Smith, T. F., and Waterman, M. S. (1981) J. Mol. Biol. 147, 195-197
46. Hattori, M., Okuno, Y., Goto, S., and Kanehisa, M. (2003) J. Am. Chem. Soc. 125, 11853-11865
47. He, Z., Zhang, J., Shi, X. H., Hu, L. L., Kong, X., Cai, Y. D., and Chou, K. C. (2010) PLoS ONE 5, e9603
48. Chou, K. C., and Cai, Y. D. (2002) J. Biol. Chem. 277, 45765-45769
49. Chou, K. C. (2001) Proteins Struct. Funct. Genet. 43, 246-255
50. Keiser, M. J., Roth, B. L., Armbruster, B. N., Ernsberger, P., Irwin, J. J., and Shoichet, B. K. (2007) Nat. Biotechnol. 25, 197-206
51. Keiser, M. J., Setola, V., Irwin, J. J., Laggner, C., Abbas, A. I., Hufeisen, S. J., Jensen, N. H., Kuijer, M. B., Matos, R. C., Tran, T. B., Whaley, R., Glennon, R. A., Hert, J., Thomas, K. L., Edwards, D. D., Shoichet, B. K., and Roth, B. L. (2009) Nature 462, 175-181
52. Campillos, M., Kuhn, M., Gavin, A. C., Jensen, L. J., and Bork, P. (2008) Science 321, 263-266
53. Günther, S., Kuhn, M., Dunkel, M., Campillos, M., Senger, C., Petsalaki, E., Ahmed, J., Urdiales, E. G., Gewiess, A., Jensen, L. J., Schneider, R., Skoblo, R., Russell, R. B., Bourne, P. E., Bork, P., and Preissner, R. (2008) Nucleic Acids Res. 36, D919-D922
54. Roth, B. L., Lopez, E., Patel, S., and Kroeze, W. K. (2000) Neuroscientist 6, 252-262