A screening pattern recognition method finds new and divergent targets for drugs and natural products

ACS Chemical Biology

Volumn 9, Issue 7, 2014, Pages 1622-1631

  Wassermann, Anne Mai ^a   Lounkine, Eugen ^a   Urban, Laszlo ^a   Whitebread, Steven ^a   Chen, Shanni ^a   Hughes, Kevin ^a   Guo, Hongqiu ^a   Kutlina, Elena ^a   Fekete, Alexander ^a   Klumpp, Martin ^b   Glick, Meir ^a  

^a NOVARTIS INSTITUTES FOR BIOMEDICAL RESEARCH   (United States)

^b NOVARTIS PHARMA AG   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLOOXYGENASE 1; CYCLOOXYGENASE 2; ETRETIN; FISETIN; MELITRACEN; MEMBRANE RECEPTOR; PERHEXILINE; TIPRANAVIR; BIOLOGICAL PRODUCT; DRUG; MOLECULAR LIBRARY;

ARTICLE; CONTROLLED STUDY; DRUG SCREENING; DRUG STRUCTURE; HEART MUSCLE METABOLISM; HUMAN; IN VITRO STUDY; MOLECULAR WEIGHT; PATTERN RECOGNITION; PHYLOGENY; PLASMA PROTEIN BINDING; PRIORITY JOURNAL; STRUCTURE ACTIVITY RELATION; CHEMICAL STRUCTURE; CHEMISTRY; DRUG DATABASE; DRUG DEVELOPMENT; MOLECULAR LIBRARY; MOLECULARLY TARGETED THERAPY; PHARMACOLOGY; PROCEDURES;

BIOLOGICAL PRODUCTS; DATABASES, PHARMACEUTICAL; DRUG DISCOVERY; HUMANS; MODELS, MOLECULAR; MOLECULAR TARGETED THERAPY; PHARMACEUTICAL PREPARATIONS; PHARMACOLOGY; SMALL MOLECULE LIBRARIES;

EID: 84904556443     PISSN: 15548929     EISSN: 15548937     Source Type: Journal    
DOI: 10.1021/cb5001839     Document Type: Article

References (45)

1. Knowles, J. and Gromo, G. (2003) A guide to drug discovery: Target selection in drug discovery Nat. Rev. Drug Discovery 2, 63-69 (Pubitemid 37361625)
2. Sams-Dodd, F. (2005) Target-based drug discovery: is something wrong? Drug Discovery Today 10, 139-147 (Pubitemid 40247812)
3. Swinney, D. C. and Anthony, J. (2011) How were new medicines discovered? Nat. Rev. Drug Discovery 10, 507-519
4. Zheng, W., Thorne, N., and McKew, J. C. (2013) Phenotypic screens as a renewed approach for drug discovery Drug Discovery Today 18, 1067-1073
5. Feng, Y., Mitchison, T. J., Bender, A., Young, D. W., and Tallarico, J. A. (2009) Multi-parameter phenotypic profiling: using cellular effects to characterize small-molecule compounds Nat. Rev. Drug Discovery 8, 567-578
6. Lee, J. and Bogyo, M. (2013) Target deconvolution techniques in modern phenotypic profiling Curr. Opin. Chem. Biol. 17, 118-126
7. Lombardino, J. G. and Lowe, J. A. (2004) The role of the medicinal chemist in drug discovery-then and now Nat. Rev. Drug Discovery 3, 853-862 (Pubitemid 39405946)
8. Rask-Andersen, M., Almén, M. S., and Schiöth, H. B. (2011) Trends in the exploitation of novel drug targets Nat. Rev. Drug Discovery 10, 579-590
9. Fliri, A. F., Loging, W. T., Thadeio, P. F., and Volkmann, R. A. (2005) Analysis of drug-induced effect patterns to link structure and side effects of medicines Nat. Chem. Biol. 1, 389-397
10. 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) The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease Science 313, 1929-1935 (Pubitemid 44497995)
11. Dunkel, M., Günther, S., Ahmed, J., Wittig, B., and Preissner, R. (2008) SuperPred: drug classification and target prediction Nucleic Acids Res. 36, W55-59
12. 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. H., Edwards, D. D., Shoichet, B. K., and Roth, B. L. (2009) Predicting new molecular targets for known drugs Nature 462, 175-181
13. Cheng, T., Li, Q., Wang, Y., and Bryant, S. H. (2011) Identifying compound-target associations by combining bioactivity profile similarity search and public databases mining J. Chem. Inf. Model. 51, 2440-2448
14. Dakshanamurthy, S., Issa, N. T., Assefnia, S., Seshasayee, A., Peters, O. J., Madhavan, S., Uren, A., Brown, M. L., and Byers, S. W. (2012) Predicting new indications for approved drugs using a proteochemometric method J. Med. Chem. 55, 6832-6848
15. Lounkine, E., Keiser, M. J., Whitebread, S., Mikhailov, D., Hamon, J., Jenkins, J. L., Lavan, P., Weber, E., Doak, A. K., Côté, S., Shoichet, B. K., and Urban, L. (2012) Large-scale prediction and testing of drug activity on side-effect targets Nature 486, 361-367
16. Gregori-Puigjané, E., Setola, V., Hert, J., Crews, B. a, Irwin, J. J., Lounkine, E., Marnett, L., Roth, B. L., and Shoichet, B. K. (2012) Identifying mechanism-of-action targets for drugs and probes Proc. Natl. Acad. Sci. U.S.A. 109, 11178-11183
17. Mohd Fauzi, F., Koutsoukas, A., Lowe, R., Joshi, K., Fan, T.-P., Glen, R. C., and Bender, A. (2013) Chemogenomics approaches to rationalizing the mode-of-action of traditional Chinese and ayurvedic medicines J. Chem. Inf. Model. 53, 661-673
18. Petrone, P. M., Simms, B., Nigsch, F., Lounkine, E., Kutchukian, P., Cornett, A., Deng, Z., Davies, J. W., Jenkins, J. L., and Glick, M. (2012) Rethinking molecular similarity: comparing compounds on the basis of biological activity ACS Chem. Biol. 7, 1399-1409
19. Hopkins, A. L. and Groom, C. R. (2002) The druggable genome Nat. Rev. Drug Discovery 1, 727-730 (Pubitemid 37361545)
20. Gaulton, A., Bellis, L. J., Bento, A. P., Chambers, J., Davies, M., Hersey, A., Light, Y., McGlinchey, S., Michalovich, D., Al-Lazikani, B., and Overington, J. P. (2012) ChEMBL: a large-scale bioactivity database for drug discovery Nucleic Acids Res. 40, D1100-1107
21. Knox, C., Law, V., Jewison, T., Liu, P., Ly, S., Frolkis, A., Pon, A., Banco, K., Mak, C., Neveu, V., Djoumbou, Y., Eisner, R., Guo, A. C., and Wishart, D. S. (2011) DrugBank 3.0: a comprehensive resource for "omics" research on drugs Nucleic Acids Res. 39, D1035-1041
22. Rogers, D. and Hahn, M. (2010) Extended-connectivity fingerprints J. Chem. Inf. Model. 50, 742-754
23. Griffith, M., Griffith, O. L., Coffman, A. C., Weible, J. V., McMichael, J. F., Spies, N. C., Koval, J., Das, I., Callaway, M. B., Eldred, J. M., Miller, C. A., Subramanian, J., Govindan, R., Kumar, R. D., Bose, R., Ding, L., Walker, J. R., Larson, D. E., Dooling, D. J., Smith, S. M., Ley, T. J., Mardis, E. R., and Wilson, R. K. (2013) DGIdb: mining the druggable genome Nat. Methods 10, 1209-1210
24. Lipinski, C. A., Lombardo, F., Dominy, B. W., and Feeney, P. J. (2001) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings Adv. Drug Delivery Rev. 46, 3-26 (Pubitemid 33653411)
25. Graff, J., von Hentig, N., Kuczka, K., Angioni, C., Gute, P., Klauke, S., Babacan, E., and Harder, S. (2008) Significant effects of tipranavir on platelet aggregation and thromboxane B2 formation in vitro and in vivo J. Antimicrob. Chemother. 61, 394-399
26. Mestre, J. R., Subbaramaiah, K., Sacks, P. G., and Dannenberg, A. J. (1997) Retinoids suppress phorbol ester-mediated induction of cyclooxygenase-2 Cancer Res. 57, 1081-1085 (Pubitemid 27138605)
27. Geiger, J. M. and Brindley, C. J. (1988) Cis-trans interconversion of acitretin in man Skin Pharmacol. 1, 230-236 (Pubitemid 19179265)
28. Gillman, P. K. (2007) Tricyclic antidepressant pharmacology and therapeutic drug interactions updated Br. J. Pharmacol. 151, 737-748 (Pubitemid 47075311)
29. Michelotti, G. A., Price, D. T., and Schwinn, D. A. (2000) α1-Adrenergic receptor regulation: basic science and clinical implications Pharmacol. Ther. 88, 281-309 (Pubitemid 32406055)
30. Izumi, N., Mizuguchi, H., Umehara, H., Ogino, S., and Fukui, H. (2008) Evaluation of efficacy and sedative profiles of H(1) antihistamines by large-scale surveillance using the visual analogue scale (VAS) Allergol. Int. 57, 257-263
31. Kennedy, J. A., Unger, S. A., and Horowitz, J. D. (1996) Inhibition of carnitine palmitoyltransferase-1 in rat heart and liver by perhexiline and amiodarone Biochem. Pharmacol. 52, 273-280 (Pubitemid 26233756)
32. Ashrafian, H., Horowitz, J. D., and Frenneaux, M. P. (2007) Perhexiline Cardiovasc. Drug Rev. 25, 76-97 (Pubitemid 46625291)
33. Gleeson, M. P., Hersey, A., Montanari, D., and Overington, J. (2011) Probing the links between in vitro potency, ADMET and physicochemical parameters Nat. Rev. Drug Discovery 10, 197-208
34. Azzaoui, K., Hamon, J., Faller, B., Whitebread, S., Jacoby, E., Bender, A., Jenkins, J. L., and Urban, L. (2007) Modeling promiscuity based on in vitro safety pharmacology profiling data ChemMedChem. 2, 874-880
35. Drury, N. E., Licari, G., Chong, C.-R., Howell, N. J., Frenneaux, M. P., Horowitz, J. D., Pagano, D., and Sallustio, B. C. (2014) Relationship between plasma, atrial and ventricular perhexiline concentrations in humans: insights into factors affecting myocardial uptake Br. J. Clin. Pharmacol. 77, 789-795
36. Stahl, S. M. (1998) Mechanism of action of serotonin selective reuptake inhibitors. Serotonin receptors and pathways mediate therapeutic effects and side effects J. Affective Disord. 51, 215-235 (Pubitemid 29202172)
37. Syed, D. N., Afaq, F., Maddodi, N., Johnson, J. J., Sarfaraz, S., Ahmad, A., Setaluri, V., and Mukhtar, H. (2011) Inhibition of human melanoma cell growth by the dietary flavonoid fisetin is associated with disruption of Wnt/β-catenin signaling and decreased Mitf levels J. Invest. Dermatol. 131, 1291-1299
38. Bhat, T. A., Nambiar, D., Pal, A., Agarwal, R., and Singh, R. P. (2012) Fisetin inhibits various attributes of angiogenesis in vitro and in vivo-implications for angioprevention Carcinogenesis 33, 385-393
39. Mukhopadhyay, T., Sasaki, J., Ramesh, R., and Roth, J. A. (2002) Mebendazole elicits a potent antitumor effect on human cancer cell lines both in vitro and in vivo Clin. Cancer Res. 8, 2963-2969 (Pubitemid 35025745)
40. D'Alise, A. M., Amabile, G., Iovino, M., Di Giorgio, F. P., Bartiromo, M., Sessa, F., Villa, F., Musacchio, A., and Cortese, R. (2008) Reversine, a novel Aurora kinases inhibitor, inhibits colony formation of human acute myeloid leukemia cells Mol. Cancer Ther. 7, 1140-1149
41. Vijay Kumar, D., Hoarau, C., Bursavich, M., Slattum, P., Gerrish, D., Yager, K., Saunders, M., Shenderovich, M., Roth, B. L., McKinnon, R., Chan, A., Cimbora, D. M., Bradford, C., Reeves, L., Patton, S., Papac, D. I., Williams, B. L., and Carlson, R. O. (2012) Lead optimization of purine based orally bioavailable Mps1 (TTK) inhibitors Bioorg. Med. Chem. Lett. 22, 4377-4385
42. Anastassiadis, T., Deacon, S. W., Devarajan, K., Ma, H., and Peterson, J. R. (2011) Comprehensive assay of kinase catalytic activity reveals features of kinase inhibitor selectivity Nat. Biotechnol. 29, 1039-1045
43. Wang, Y., Xiao, J., Suzek, T. O., Zhang, J., Wang, J., Zhou, Z., Han, L., Karapetyan, K., Dracheva, S., Shoemaker, B. A., Bolton, E., Gindulyte, A., and Bryant, S. H. (2012) PubChem's BioAssay database Nucleic Acids Res. 40, D400-412
44. Krejsa, C. M., Horvath, D., Rogalski, S. L., Penzotti, J. E., Mao, B., Barbosa, F., and Migeon, J. C. (2003) Predicting ADME properties and side effects: the BioPrint approach Curr. Opin. Drug Discovery Dev. 6, 470-480 (Pubitemid 36975350)
45. Wassermann, A. M., Lounkine, E., and Glick, M. (2013) Bioturbo similarity searching: combining chemical and biological similarity to discover structurally diverse bioactive Molecules J. Chem. Inf. Model. 53, 692-703