Promiscuity and the conformational rearrangement of drug-like molecules: Insight from the protein data bank

ChemMedChem

Volumn 10, Issue 2, 2015, Pages 238-244

  He, Michael W ^a   Lee, Patrick S ^a   Sweeney, Zachary K ^a  

^a NOVARTIS INSTITUTES FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

Conformation flexibility; Ligand design strategy; PDB; Polypharmacology; Selectivity

Indexed keywords

LIGAND; BENZAMIDE DERIVATIVE; HUMAN IMMUNODEFICIENCY VIRUS PROTEINASE; IMATINIB; INDINAVIR; INDIRUBIN-5-SULFONIC ACID; INDOLE DERIVATIVE; P16 PROTEASE, HUMAN IMMUNODEFICIENCY VIRUS 1; PIPERAZINE DERIVATIVE; PROTEIN; PROTEIN BINDING; PROTOZOAL PROTEIN; PYRIMIDINE DERIVATIVE; STEM CELL FACTOR RECEPTOR; SULFONIC ACID DERIVATIVE;

AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; CONFORMATION; CRYSTAL STRUCTURE; DRUG DESIGN; DRUG RECEPTOR BINDING; LIGAND BINDING; POLYPHARMACOLOGY; PRIORITY JOURNAL; PROTEIN DATA BANK; CHEMISTRY; KINETICS; METABOLISM; PROTEIN DATABASE; PROTEIN TERTIARY STRUCTURE;

BENZAMIDES; DATABASES, PROTEIN; DRUG DESIGN; HIV PROTEASE; INDINAVIR; INDOLES; KINETICS; LIGANDS; PIPERAZINES; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; PROTO-ONCOGENE PROTEINS C-KIT; PROTOZOAN PROTEINS; PYRIMIDINES; SULFONIC ACIDS;

EID: 84921731597     PISSN: 18607179     EISSN: 18607187     Source Type: Journal    
DOI: 10.1002/cmdc.201402389     Document Type: Article

References (36)

1. S. K. Mencher, L. G. Wang, BMC Clin. Pharmacol. 2005, 5, 3.
2. A. J. Brown, B. T. Korber, J. H. Condra, AIDS Res. Hum. Retroviruses 1999, 15, 247-253.
3. J. Bauer, S. Spanton, R. Henry, J. Quick, W. Dziki, W. Porter, J. Morris, Pharm. Res. 2001, 18, 859-866.
4. J. M. Goldman, J. V. Melo, N. Engl. J. Med. 2003, 349, 1451-1464.
5. J. S. Tokarski, J. A. Newitt, C. Y. J. Chang, J. D. Cheng, M. Wittekind, S. E. Kiefer, K. Kish, F. Y. F. Lee, R. Borzillerri, L. J. Lombardo, D. L. Xie, Y. Q. Zhang, H. E. Klei, Cancer Res. 2006, 66, 5790-5797.
6. X. Wang, N. Greene, Mol. Inf. 2012, 31, 145-159.
7. T. Force, K. L. Kolaja, Nat. Rev. Drug Discovery 2011, 10, 111-126.
8. J. U. Peters, J. Med. Chem. 2013, 56, 8955-8971.
9. M. E. Bunnage, E. L. P. Checkler, L. H. Jones, Nat. Chem. Biol. 2013, 9, 195-199.
10. K. Azzaoui, J. Hamon, B. Faller, S. Whitebread, E. Jacoby, A. Bender, J. L. Jenkins, L. Urban, ChemMedChem 2007, 2, 874-880.
11. J. U. Peters, J. Hert, C. Bissantz, A. Hillebrecht, G. Gerebtzoff, S. Bendels, F. Tillier, J. Migeon, H. Fischer, W. Guba, M. Kansyet, Drug Discovery Today 2012, 17, 325-335.
12. Á. Tarcsay, G. M. Keseru{combining double acute accent}, J. Med. Chem. 2013, 56, 1789-1795.
13. A. L. Hopkins, Nature 2009, 462, 167-168.
14. Y. Hu, J. Bajorath, Drug Discovery Today 2013, 18, 644-650.
15. F. Lovering, MedChemComm 2013, 4, 515-519.
16. C. Schärfer, T. Schulz-Gasch, H.-C. Ehrlich, W. Guba, M. Rarey, M. Stahl, J. Med. Chem. 2013, 56, 2016-2028.
17. B. S. Safina, Z. K. Sweeney, J. Li, B. K. Chan, A. Bisconte, D. Carrera, G. Castanedo, M. Flagella, R. Heald, C. Lewis, J. M. Murray, J. Nonomiya, J. Pang, S. Price, K. Reif, L. Salphati, E. M. Seward, B. Q. Wei, D. P. Sutherlin, Bioorg. Med. Chem. Lett. 2013, 23, 4953-4959.
18. M. D. Cowart, R. J. Altenbach, H. Liu, G. C. Hsieh, I. Drizin, I. Milicic, T. R. Miller, D. G. Witte, N. Wishart, S. R. Fix-Stenzel, M. J. McPherson, R. M. Adair, J. M. Wetter, B. M. Bettencourt, K. C. Marsh, J. P. Sulliva, P. Honore, T. A. Esbenshade, J. D. Brioni, J. Med. Chem. 2008, 51, 6547-6557.
19. M. W. Harrold, Am. J. Pharm. Educ. 1996, 60, 192-197.
20. D. P. Sutherlin, D. Sampath, M. Berry, G. Castanedo, Z. Chang, I. Chuckowree, J. Dotson, A. Folkes, L. Friedman, R. Goldsmith, T. Heffronet, L. Lee, J. Lesnick, C. Lewis, S. Mathieu, J. Nonomiya, A. Olivero, J. Pang, W. W. Prior, L. Salphati, S. Sideris, Q. P. Tian, V. Tsui, N. C. Wan, S. M. Wang, C. Wiesmann, S. Wong, B. Y. Zhu, J. Med. Chem. 2010, 53, 1086-1097.
21. S. A. Wacowich-Sgarbi, D. R. Bundle, J. Org. Chem. 1999, 64, 9080-9089.
22. A. Mann in The Practice of Medicinal Chemistry (Ed.: C. G. Wermuth), Elsevier, Amsterdam, 2003, pp. 233-250.
23. M. R. Berthold, N. Cebron, F. Dill, T. R. Gabriel, T. Kotter, T. Meinl, P. Ohl, C. Sieb, K. Thiel, B. Wiswedel in Studies in Classification, Data Analysis, and Knowledge Organization (Eds.: H.-H. Bock, W. Gaul, M. Vichi, C. Weihs), Springer, Heidelberg, 2008, 319-326.
24. F. Milletti, L. Storchi, G. Sforna, G. Cruciani, J. Chem. Inf. Model. 2007, 47, 2172-2181.
25. A. Gaulton, L. J. Bellis, A. P. Bento, J. Chambers, M. Davies, A. Hersey, Y. Light, S. McGlinchey, D. Michalovich, B. Al-Lazikani, J. P. Overington, Nucleic Acids Res. 2012, 40, D1100-D1107.
26. T. Liu, Y. Lin, X. Wen, R. N. Jorissen, M. K. Gilson, Nucleic Acids Res. 2007, 35, D198-D201.
27. R. Wang, X. Fang, Y. Lu, S. Wang, J. Med. Chem. 2004, 47, 2977-2980.
28. A. L. Hopkins, C. R. Groom, A. Alex, Drug Discovery Today 2004, 9, 430-431.
29. S. Günther, C. Senger, E. Michalsky, A. Goede, R. Preissner, BMC Bioinf. 2006, 7, 293-304.
30. N. Sturm, J. Desaphy, R. J. Quinn, D. Rognan, E. Kellenberger, J. Chem. Inf. Model. 2012, 52, 2410-2421.
31. V. J. Haupt, S. Daminelli, M. Schroeder, PLoS One 2013, 8, e65894.
32. UniProt Consortium, Nucleic Acids Res. 2012, 40, D71-75.
33. M. I. Davis, J. P. Hunt, S. Herrgard, P. Ciceri, L. M. Wodicka, G. Pallares, M. Hocker, D. K. Treiber, P. P. Zarrinkar, Nat. Biotechnol. 2011, 29, 1046-1051.
34. C. Farenc, P. H. N. Celie, C. P. Tensen, I. J. P. De Esch, G. Siegal, FEBS Lett. 2011, 585, 3593-3599.
35. B. Mahalingam, Y. F. Wang, P. I. Boross, J. Tozser, J. M. Louis, R. W. Harrison, I. T. Weber, Eur. J. Biochem. 2004, 271, 1516-1524.
36. I. Pichová, L. Pavlícková, J. Dostál, E. Dolejsí, O. Hrusková-Heidingsfeldová, J. Weber, T. Ruml, M. Soucek, Eur. J. Biochem. 2001, 268, 2669-2677.