Identification of biologically active, HIV TAR RNA-binding small molecules using small molecule microarrays

Journal of the American Chemical Society

Volumn 136, Issue 23, 2014, Pages 8402-8410

  Sztuba Solinska, Joanna ^a   Shenoy, Shilpa R ^a,b   Gareiss, Peter ^c   Krumpe, Lauren R H ^a,b   Le Grice, Stuart F J ^a   O'Keefe, Barry R ^a   Schneekloth, John S ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

^b FREDERICK NATIONAL LABORATORY FOR CANCER RESEARCH   (United States)

^c YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICROARRAYS; RNA; TAR;

AMINOGLYCOSIDES; CATIONIC CHARGES; CHARGED COMPOUNDS; PRIMER EXTENSION; SMALL MOLECULE MICROARRAYS; STRUCTURE ACTIVITY RELATIONSHIPS; TRANS-ACTIVATION RESPONSE; UNTRANSLATED REGIONS;

MOLECULES;

ANTI HUMAN IMMUNODEFICIENCY VIRUS AGENT; AROMATIC COMPOUND; HETEROCYCLIC COMPOUND; THIENOPYRIDINE DERIVATIVE; TRANSACTIVATION RESPONSE RNA; UNCLASSIFIED DRUG; VIRUS RNA; MOLECULAR LIBRARY;

5' UNTRANSLATED REGION; ARTICLE; CONCENTRATION RESPONSE; CONTROLLED STUDY; DRUG CYTOTOXICITY; DRUG SCREENING; DRUG STRUCTURE; HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; HYDROPHOBICITY; MICROARRAY ANALYSIS; MOLECULAR LIBRARY; NONHUMAN; SMALL MOLECULE MICROARRAY ANALYSIS; STRUCTURE ACTIVITY RELATION; T LYMPHOCYTE; VIRUS GENOME; CHEMICAL STRUCTURE; CHEMISTRY; CYTOPATHOGENIC EFFECT; DRUG DEVELOPMENT; DRUG EFFECTS; FLUOROMETRY; GENETICS; HUMAN; LONG TERMINAL REPEAT; NUCLEOTIDE MOTIF; PATHOGENICITY; PHARMACOLOGY; TUMOR CELL LINE; VIROLOGY;

ANTI-HIV AGENTS; CELL LINE, TUMOR; CYTOPATHOGENIC EFFECT, VIRAL; DRUG DISCOVERY; FLUOROMETRY; HIV LONG TERMINAL REPEAT; HIV-1; HUMANS; MOLECULAR STRUCTURE; NUCLEOTIDE MOTIFS; RNA, VIRAL; SMALL MOLECULE LIBRARIES; T-LYMPHOCYTES;

EID: 84902274610     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja502754f     Document Type: Article

References (49)

1. Cooper, T. A.; Wan, L. L.; Dreyfuss, G. Cell 2009, 136, 777
2. Jakobovits, A.; Smith, D. H.; Jakobovits, E. B.; Capon, D. J. Mol. Cell. Biol. 1988, 8, 2555
3. Selby, M. J.; Bain, E. S.; Luciw, P. A.; Peterlin, B. M. Gene Dev 1989, 3, 547
4. Richter, S.; Cao, H.; Rana, T. M. Biochemistry 2002, 41, 6391
5. Berkhout, B.; Vastenhouw, N. L.; Klasens, B. I. F.; Huthoff, H. RNA 2001, 7, 1097
6. Thomas, J. R.; Hergenrother, P. J. Chem. Rev. 2008, 108, 1171
7. Guan, L. R.; Disney, M. D. ACS Chem. Biol. 2012, 7, 73
8. Stelzer, A. C.; Frank, A. T.; Kratz, J. D.; Swanson, M. D.; Gonzalez-Hernandez, M. J.; Lee, J.; Andricioaei, I.; Markovitz, D. M.; Al-Hashimi, H. M. Nat. Chem. Biol. 2011, 7, 553
9. Hermann, T. Curr. Opin Struct Biol. 2005, 15, 355
10. Hermann, T. Biopolymers 2003, 70, 4
11. Ogle, J. M.; Ramakrishnan, V. Annu. Rev. Biochem. 2005, 74, 129
12. Poehlsgaard, J.; Douthwaite, S. Nat. Rev. Microbiol 2005, 3, 870
13. Weeks, K. M. Curr. Opin Struct Biol. 2010, 20, 295
14. Blount, K. F.; Breaker, R. R. Nat. Biotechnol. 2006, 24, 1558
15. Parsons, J.; Castaldi, M. P.; Dutta, S.; Dibrov, S. M.; Wyles, D. L.; Hermann, T. Nat. Chem. Biol. 2009, 5, 823
16. Bradner, J. E.; McPherson, O. M.; Mazitschek, R.; Barnes-Seeman, D.; Shen, J. P.; Dhaliwal, J.; Stevenson, K. E.; Duffner, J. L.; Park, S. B.; Neuberg, D. S.; Nghiem, P.; Schreiber, S. L.; Koehler, A. N. Chem. Biol. 2006, 13, 493
17. Bradner, J. E.; McPherson, O. M.; Koehler, A. N. Nat. Protoc. 2006, 1, 2344
18. Hergenrother, P. J.; Depew, K. M.; Schreiber, S. L. J. Am. Chem. Soc. 2000, 122, 7849
19. Stanton, B. Z.; Peng, L. F.; Maloof, N.; Nakai, K.; Wang, X.; Duffner, J. L.; Taveras, K. M.; Hyman, J. M.; Lee, S. W.; Koehler, A. N.; Chen, J. K.; Fox, J. L.; Mandinova, A.; Schreiber, S. L. Nat. Chem. Biol. 2009, 5, 154
20. Miao, H.; Tallarico, J. A.; Hayakawa, H.; Munger, K.; Duffner, J. L.; Koehler, A. N.; Schreiber, S. L.; Lewis, T. A. J. Comb Chem. 2007, 9, 245
21. Koehler, A. N.; Shamji, A. F.; Schreiber, S. L. J. Am. Chem. Soc. 2003, 125, 8420
22. Kuruvilla, F. G.; Shamji, A. F.; Sternson, S. M.; Hergenrother, P. J.; Schreiber, S. L. Nature 2002, 416, 653
23. Barnes-Seeman, D.; Park, S. B.; Koehler, A. N.; Schreiber, S. L. Angew. Chem. Int. Ed. 2003, 42, 2376
24. Tran, T.; Disney, M. D. Nat. Commun. 2012, 3
25. Velagapudi, S. P.; Pushechnikov, A.; Labuda, L. P.; French, J. M.; Disney, M. D. ACS Chem. Biol. 2012, 7, 1902
26. Tran, T.; Disney, M. D. Biochemistry 2010, 49, 1833
27. Disney, M. D.; Lee, M. M.; Pushechnikov, A.; Childs-Disney, J. L. ChemBioChem 2010, 11, 375
28. Paul, D. J.; Seedhouse, S. J.; Disney, M. D. Nucleic Acids Res. 2009, 37, 5894
29. Aminova, O.; Paul, D. J.; Childs-Disney, J. L.; Disney, M. D. Biochemistry 2008, 47, 12670
30. Disney, M. D.; Labuda, L. P.; Paul, D. J.; Poplawski, S. G.; Pushechnikov, A.; Tran, T.; Velagapudi, S. P.; Wu, M.; Childs-Disney, J. L. J. Am. Chem. Soc. 2008, 130, 11185
31. Childs-Disney, J. L.; Wu, M. L.; Pushechnikov, A.; Aminova, O.; Disney, M. D. ACS Chem. Biol. 2007, 2, 745
32. Velagapudi, S. P.; Gallo, S. M.; Disney, M. D. Nat. Chem. Biol. 2014, 10, 291
33. Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Adv. Drug Delivery Rev. 1997, 23, 3
34. Hwang, S.; Tamilarasu, N.; Kibler, K.; Cao, H.; Ali, A.; Ping, Y. H.; Jeang, K. T.; Rana, T. M. J. Biol. Chem. 2003, 278, 39092
35. Chirayil, S.; Chirayil, R.; Luebke, K. J. Nucleic Acids Res. 2009, 37, 5486
36. Du, Z. H.; Lind, K. E.; James, T. L. Chem. Biol. 2002, 9, 707
37. Bradrick, T. D.; Marino, J. P. RNA 2004, 10, 1459
38. Bradrick, T. D.; Marino, J. P. Biophys. J. 2004, 86, 143A
39. Lu, J.; Kadakkuzha, B. M.; Zhao, L.; Fan, M.; Qi, X.; Xia, T. Biochemistry 2011, 50, 5042
40. Wilkinson, K. A.; Gorelick, R. J.; Vasa, S. M.; Guex, N.; Rein, A.; Mathews, D. H.; Giddings, M. C.; Weeks, K. M. PLoS Biol. 2008, 6, 883
41. Deforges, J.; Chamond, N.; Sargueil, B. Biochimie 2012, 94, 1481
42. Huthoff, H.; Berkhout, B. RNA 2001, 7, 143
43. Damgaard, C. K.; Andersen, E. S.; Knudsen, B.; Gorodkin, J.; Kjems, J. J. Mol. Biol. 2004, 336, 369
44. Renner, S.; Ludwig, V.; Boden, O.; Scheffer, U.; Gobel, M.; Schneider, G. ChemBioChem 2005, 6, 1119
45. Mitra, S.; Shcherbakova, I. V.; Altman, R. B.; Brenowitz, M.; Laederach, A. Nucleic Acids Res. 2008, 36
46. Badorrek, C. S.; Weeks, K. M. Biochemistry 2006, 45, 12664
47. Deigan, K. E.; Li, T. W.; Mathews, D. H.; Weeks, K. M. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 97
48. Darty, K.; Denise, A.; Ponty, Y. Bioinformatics 2009, 25, 1974
49. Gulakowski, R. J.; Mcmahon, J. B.; Staley, P. G.; Moran, R. A.; Boyd, M. R. J. Virol Methods 1991, 33, 87