Chemical structural novelty: On-targets and off-targets

Journal of Medicinal Chemistry

Volumn 54, Issue 19, 2011, Pages 6771-6785

  Yera, Emmanuel R ^a   Cleves, Ann E ^a   Jain, Ajay N ^a  

^a San Francisco   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACRIVASTINE; AMITRIPTYLINE; AZATADINE; AZELASTINE; BROMODIPHENHYDRAMINE; BROMPHENIRAMINE; CARBINOXAMINE; CETIRIZINE; CHLORCYCLIZINE; CHLORPHENIRAMINE; CITALOPRAM; CLEMASTINE; CYPROHEPTADINE; DESLORATADINE; DIFENIDOL; DIMENHYDRINATE; DIPHENHYDRAMINE; EMEDASTINE; FEXOFENADINE; HYDROXYZINE; IMIPRAMINE; KETOTIFEN; LEVOCABASTINE; LORATADINE; MECLOZINE; OLOPATADINE; ORPHENADRINE; PHENINDAMINE; THIORIDAZINE; UNINDEXED DRUG;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; DRUG MECHANISM; DRUG STRUCTURE; MOLECULE; PHARMACOLOGY; PREDICTION;

BINDING SITES; COMPUTER SIMULATION; DATABASES, FACTUAL; DRUG DESIGN; LIGANDS; MODELS, MOLECULAR; PHARMACEUTICAL PREPARATIONS; PROTEINS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 80053906388     PISSN: 00222623     EISSN: 15204804     Source Type: Journal    
DOI: 10.1021/jm200666a     Document Type: Article

References (42)

1. Cleves, A. E.; Jain, A. N. Effects of inductive bias on computational evaluations of ligand-based modeling and on drug discovery J. Comput.-Aided Mol. Des. 2008, 22, 147-159
2. Cleves, A. E.; Jain, A. N. Robust ligand-based modeling of the biological targets of known drugs J. Med. Chem. 2006, 49, 2921-2938
3. Keiser, M. J.; Roth, B. L.; Armbruster, B. N.; Ernsberger, P.; Irwin, J. J.; Shoichet, B. K. Relating protein pharmacology by ligand chemistry Nature Biotechnol. 2007, 25, 197-206 (Pubitemid 46227119)
4. 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.; Roth, B. L. Predicting new molecular targets for known drugs Nature 2009, 462, 175-181
5. Muchmore, S. W.; Debe, D. A.; Metz, J. T.; Brown, S. P.; Martin, Y. C.; Hajduk, P. J. Application of belief theory to similarity data fusion for use in analog searching and lead hopping J. Chem. Inf. Model. 2008, 48, 941-948
6. Taboureau, O.; Nielsen, S. K.; Audouze, K.; Weinhold, N.; Edsgärd, D.; Roque, F. S.; Kouskoumvekaki, I.; Bora, A.; Curpan, R.; Jensen, T. S. ChemProt: A disease chemical biology database Nucleic Acids Res. 2011, 39, D367-D372
7. 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.; Wishart, D. S. DrugBank 3.0: a comprehensive resource for "omics" research on drugs Nucleic Acids Res. 2011, 39, 1035-1041
8. Eyre, T. A.; Ducluzeau, F.; Sneddon, T. P.; Povey, S.; Bruford, E. A.; Lush, M. J. The HUGO Gene Nomenclature Database, 2006 Updates Nucleic Acids Res. 2006, 34, 319-321
9. Nidhi; Glick, M.; Davies, J. W.; Jenkins, J. L. Prediction of biological targets for compounds using multiple-category Bayesian models trained on chemogenomics databases J. Chem. Inf. Model. 2006, 46, 1124-1133 (Pubitemid 43999157)
10. Yildirim, M. A.; Goh, K. I.; Cusick, M. E.; Barabasi, A. L.; Vidal, M. Drug-target network Nature Biotechnol. 2007, 25, 1119-1126 (Pubitemid 47538114)
11. Chen, X.; Lin, Y.; Liu, M.; Gilson, M. K. The Binding Database: data management and interface design Bioinformatics 2002, 18, 130-139 (Pubitemid 34145041)
12. Kuhn, M.; Campillos, M.; Letunic, I.; Jensen, L. J.; Bork, P. A side effect resource to capture phenotypic effects of drugs Mol. Syst. Biol. 2010, 6, 343
13. Largent, B. L.; Wikstrom, H.; Gundlach, A. L.; Snyder, S. H. Structural determinants of sigma receptor affinity Mol. Pharmacol. 1987, 32, 772-784 (Pubitemid 18008346)
14. Silvestrini, B. Beyond the limits of typical antidepressants Psychopharmacology (Berlin) 1988, 95 (Suppl) S1-S2
15. Chenard, B. L.; Shalaby, I. A.; Koe, B. K.; Ronau, R. T.; Butler, T. W.; Prochniak, M. A.; Schmidt, A. W.; Fox, C. B. Separation of alpha 1 adrenergic and N -methyl- d -aspartate antagonist activity in a series of ifenprodil compounds J. Med. Chem. 1991, 34, 3085-3090
16. Jain, A. N. Morphological similarity: a 3D molecular similarity method correlated with protein-ligand recognition J Comput.-Aided Mol. Des. 2000, 14, 199-213 (Pubitemid 30110675)
17. Jain, A. N. Ligand-based structural hypotheses for virtual screening J. Med. Chem. 2004, 47, 947-961 (Pubitemid 38176797)
18. Nicholls, A.; McGaughey, G. B.; Sheridan, R. P.; Good, A. C.; Warren, G.; Mathieu, M.; Muchmore, S. W.; Brown, S. P.; Grant, J. A.; Haigh, J. A.; Nevins, N.; Jain, A. N.; Kelley, B. Molecular shape and medicinal chemistry: a perspective J. Med. Chem. 2010, 53, 3862-386
19. Pham, T. A.; Jain, A. N. Parameter estimation for scoring protein-ligand interactions using negative training data J. Med. Chem. 2006, 49, 5856-5868 (Pubitemid 44484932)
20. Pham, T. A.; Jain, A. N. Customizing scoring functions for docking J. Comput.-Aided Mol. Des. 2008, 22, 269-286
21. Sneader, W. Drug Discovery: A History; John Wiley & Sons Inc: New York, 2005.
22. Horn, F.; Vriend, G.; Cohen, F. E. Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems Nucleic Acids Res. 2001, 29, 346-349 (Pubitemid 32054489)
23. Coupet, J.; Fisher, S. K.; Rauh, C. E. Interaction of amoxapine with muscarinic cholinergic receptors: an in vitro assessment Eur. J. Pharmacol. 1985, 112, 231-235 (Pubitemid 15038027)
24. Lin, S. C.; Olson, K. C.; Okazaki, H.; Richelson, E. Studies on muscarinic binding sites in human brain identified with [3H] pirenzepine J. Neurochem. 1986, 46, 274-279 (Pubitemid 16185458)
25. Syvalahti, E. K.; Kunelius, R.; Lauren, L. Effects of antiparkinsonian drugs on muscarinic receptor binding in rat brain, heart and lung Pharmacol. Toxicol. 1988, 62, 90-94 (Pubitemid 18046375)
26. + channel J. Mol. Cell. Cardiol. 2004, 36, 151-160 (Pubitemid 38084800)
27. Brown, E. G.; Wood, L.; Wood, S. The medical dictionary for regulatory activities (MedDRA) Drug Saf. 1999, 20, 109-117 (Pubitemid 29101275)
28. Shafer, G. The combination of evidence Int. J. Intell. Syst. 1986, 1, 155-179
29. Rush, T. S., III; Grant, J. A.; Mosyak, L.; Nicholls, A. A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction J. Med. Chem. 2005, 48, 1489-1495 (Pubitemid 40364556)
30. Flower, D. R. On the properties of bit string-based measures of chemical similarity J. Chem. Inf. Comput. Sci. 1998, 38, 379-386 (Pubitemid 128594448)
31. Healy, D. Obituary: Roland Kuhn (1912-2005) Hist. Psychiatry 2006, 17, 253-255
32. Kuhn, R. The treatment of depressive states with G 22355 (imipramine hydrochloride) Am. J. Psychiatry 1958, 115, 459-464
33. Hagihara, K.; Kashima, H.; Iida, K.; Enokizono, J.; Uchida, S.; Nonaka, H.; Kurokawa, M.; Shimada, J. Novel 4-(6,7-dimethoxy-1,2,3,4- tetrahydroisoquinolin-2-yl)methylbenzofuran derivatives as selective alpha(2C)-adrenergic receptor antagonists Bioorg. Med. Chem. Lett. 2007, 17, 1616-1621 (Pubitemid 46274346)
34. Jablonowski, J. A.; Grice, C. A.; Chai, W.; Dvorak, C. A.; Venable, J. D.; Kwok, A. K.; Ly, K. S.; Wei, J.; Baker, S. M.; Desai, P. J.; Jiang, W.; Wilson, S. J.; Thurmond, R. L.; Karlsson, L.; Edwards, J. P.; Lovenberg, T. W.; Carruthers, N. I. The first potent and selective non-imidazole human histamine H4 receptor antagonists J. Med. Chem. 2003, 46, 3957-3960 (Pubitemid 37122442)
35. Efange, S. M.; Kamath, A. P.; Khare, A. B.; Kung, M. P.; Mach, R. H.; Parsons, S. M. N -Hydroxyalkyl derivatives of 3 beta-phenyltropane and 1-methylspiro[1 H -indoline-3,4′-piperidine]: vesamicol analogues with affinity for monoamine transporters J. Med. Chem. 1997, 40, 3905-3914 (Pubitemid 27512307)
36. Wright, J. L.; Downing, D. M.; Feng, M. R.; Hayes, R. N.; Heffner, T. G.; MacKenzie, R. G.; Meltzer, L. T.; Pugsley, T. A.; Wise, L. D. Identification, characterization and pharmacological profile of three metabolites of (R)-(+)-1,2,3,6-tetrahydro-4-phenyl-1-[(3-phenylcyclohexen-1- yl)methyl]pyridine (CI-1007), a dopamine autoreceptor agonist and potential antipsychotic agent J. Med. Chem. 1995, 38, 5007-5014 (Pubitemid 26018407)
37. Thomas, J. B.; Mascarella, S. W.; Rothman, R. B.; Partilla, J. S.; Xu, H.; McCullough, K. B.; Dersch, C. M.; Cantrell, B. E.; Zimmerman, D. M.; Carroll, F. I. Investigation of the N-substituent conformation governing potency and mu receptor subtype-selectivity in (+)-(3 R,4 R)-dimethyl-4-(3- hydroxyphenyl)piperidine opioid antagonists J. Med. Chem. 1998, 41, 1980-1990 (Pubitemid 28248672)
38. Zimmerman, D. M.; Leander, J. D.; Cantrell, B. E.; Reel, J. K.; Snoddy, J.; Mendelsohn, L. G.; Johnson, B. G.; Mitch, C. H. Structure-activity relationships of trans -3,4-dimethyl-4-(3-hydroxyphenyl)piperidine antagonists for mu- and kappa-opioid receptors J. Med. Chem. 1993, 36, 2833-2841 (Pubitemid 23315385)
39. De Matos, P.; Alcántara, R.; Dekker, A.; Ennis, M.; Hastings, J.; Haug, K.; Spiteri, I.; Turner, S.; Steinbeck, C. Chemical entities of biological interest: an update Nucleic Acids Res. 2010, 38, D249-D254
40. Whittemore, E. R.; Ilyin, V. I.; Woodward, R. M. Antagonism of N -methyl- d -aspartate receptors by sigma site ligands: potency, subtype-selectivity and mechanisms of inhibition J. Pharmacol. Exp. Ther. 1997, 282, 326-338 (Pubitemid 27425558)
41. Hollister, L. E. O. E.; Overall, J. E.; Johnson, M.; Pennington, V.; Katz, G.; Shelton, J. Controlled comparison of amitriptyline, imipramine and placebo in hospitalized depressed patients J. Nerv. Ment. Dis. 1964, 139, 370-375
42. Scheiber, J.; Chen, B.; Milik, M.; Sukuru, S. C.; Bender, A.; Mikhailov, D.; Whitebread, S.; Hamon, J.; Azzaoui, K.; Urban, L.; Glick, M.; Davies, J. W.; Jenkins, J. L. Gaining insight into off-target mediated effects of drug candidates with a comprehensive systems chemical biology analysis J. Chem. Inf. Model. 2009, 49, 308-317