Synthesis and stereospecificity of 4,5-disubstituted oxazolidinone ligands binding to T-box riboswitch RNA

Journal of Medicinal Chemistry

Volumn 54, Issue 19, 2011, Pages 6786-6795

  Orac, Crina M ^a   Zhou, Shu ^a   Means, John A ^b   Boehm, David ^a,c   Bergmeier, Stephen C ^a   Hines, Jennifer V ^a  

^a OHIO UNIVERSITY   (United States)

^b The Institute for Employee Safety   (United States)

^c UNIVERSITY OF LEIPZIG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

OXAZOLIDINONE DERIVATIVE; RNA;

ARTICLE; BINDING AFFINITY; BINDING SITE; ENANTIOMER; LIGAND BINDING; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION; RIBOSWITCH; STEREOSPECIFICITY; SURFACE PROPERTY; T BOX RIBOSWITCH;

BINDING SITES; FLUORESCENCE RESONANCE ENERGY TRANSFER; LIGANDS; MODELS, MOLECULAR; OXAZOLIDINONES; RIBOSWITCH; STEREOISOMERISM; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 80053902052     PISSN: 00222623     EISSN: 15204804     Source Type: Journal    
DOI: 10.1021/jm2006904     Document Type: Article

References (39)

1. Drysdale, M. J. RNA as a Drug Target Prog. Med. Chem. 2002, 39, 73-119
2. Foloppe, N.; Matassova, N.; Aboul-Ela, F. Towards the Discovery of Drug-like RNA Ligands? Drug Discovery Today 2006, 11, 1019-1027 (Pubitemid 44608200)
3. Gallego, J.; Varani, G. Targeting RNA with Small-Molecule Drugs: Therapeutic Promise and Chemical Challenges Acc. Chem. Res. 2001, 34, 836-843 (Pubitemid 32999608)
4. Thomas, J. R.; Hergenrother, P. J. Targeting RNA with Small Molecules Chem. Rev. 2008, 108, 1171-1224 (Pubitemid 351638813)
5. Tor, Y. Targeting RNA with Small Molecules ChemBioChem 2003, 4, 998-1007 (Pubitemid 37267588)
6. Zaman, G. J. R.; Michiels, P. J. A.; van Boeckel, C. A. A. Targeting RNA: New Opportunities To Address Drugless Targets Drug Discovery Today 2003, 8, 297-306 (Pubitemid 36332221)
7. Iorio, M. V.; Piovan, C.; Croce, C. M. Interplay between microRNAs and the Epigenetic Machinery: An Intricate Network Biochim. Biophys. Acta 2010, 1799, 694-701
8. Smith, A. M.; Fuchs, R. T.; Grundy, F. J.; Henkin, T. M. Riboswitch RNAs Regulation of Gene Expression by Direct Monitoring of a Physiological Signal RNA Biol. 2010, 7, 104-110
9. Green, N. J.; Grundy, F. J.; Henkin, T. M. The T-Box Mechanism: tRNA as a Regulatory Molecule FEBS Lett. 2010, 584, 318-324
10. Gutierrez-Preciado, A.; Henkin, T. M.; Grundy, F. J.; Yanofsky, C.; Merino, E. Biochemical Features and Functional Implications of the RNA-Based T-Box Regulatory Mechanism Microbiol. Mol. Biol. Rev. 2009, 73, 36-61
11. Anupam, R.; Nayek, A.; Green, N. J.; Grundy, F. J.; Henkin, T. M.; Means, J. A.; Bergmeier, S. C.; Hines, J. V. 4,5-Disubstituted Oxazolidinones: High Affinity Molecular Effectors of RNA Function Bioorg. Med. Chem. Lett. 2008, 18, 3541-3544 (Pubitemid 351787566)
12. Means, J. A.; Katz, S.; Nayek, A.; Anupam, R.; Hines, J. V.; Bergmeier, S. C. Structure-Activity Studies of Oxazolidinone Analogs as RNA-Binding Agents Bioorg. Med. Chem. Lett. 2006, 16, 3600-3604 (Pubitemid 43777113)
13. Means, J. A.; Hines, J. V. Fluorescence Resonance Energy Transfer Studies of Aminoglycoside Binding to a T Box Antiterminator RNA Bioorg. Med. Chem. Lett. 2005, 15, 2169-2172 (Pubitemid 40445487)
14. Anupam, R.; Denapoli, L.; Muchenditsi, A.; Hines, J. V. Identification of Neomycin B-Binding Site in T-Box Antiterminator Model RNA Bioorg. Med. Chem. 2008, 16, 4466-4470 (Pubitemid 351539035)
15. Acquaah-Harrison, G.; Zhou, S.; Hines, J. V.; Bergmeier, S. C. Library of 1,4-Disubstituted 1,2,3-Triazole Analogs of Oxazolidinone RNA-Binding Agents J. Comb. Chem. 2010, 12, 491-496
16. Grundy, F. J.; Moir, T. R.; Haldeman, M. T.; Henkin, T. M. Sequence Requirements for Terminators and Antiterminators in the T-Box Transcription Antitermination System: Disparity between Conservation and Functional Requirements Nucleic Acids Res. 2002, 30, 1646-1655 (Pubitemid 34679740)
17. Maciagiewicz, I.; Zhou, S.; Bergmeier, S. C.; Hines, J. V. Structure Activity Studies of RNA-Binding Oxazolidinone Derivatives Bioorg. Med. Chem. Lett. 2011, 4524-4527
18. Bergmeier, S. C.; Katz, S. J. A Method for the Parallel Synthesis of Multiply Substituted Oxazolidinones J. Comb. Chem. 2002, 4, 162-166
19. Bergmeier, S. C.; Stanchina, D. M. Synthesis of Vicinal Amino Alcohols via a Tandem Acylnitrene Aziridination-Aziridine Ring Opening J. Org. Chem. 1997, 62, 4449-4456 (Pubitemid 127491360)
20. Bergmeier, S. C.; Stanchina, D. M. Acylnitrene Route to Vicinal Amino Alcohols. Application to the Synthesis of (-)-Bestatin and Analogues J. Org. Chem. 1999, 64, 2852-2859
21. Schaus, S. E.; Brandes, B. D.; Larrow, J. F.; Tokunaga, M.; Hansen, K. B.; Gould, A. E.; Furrow, M. E.; Jacobsen, E. N. Highly Selective Hydrolytic Kinetic Resolution of Terminal Epoxides Catalyzed by Chiral (salen)Co-III Complexes. Practical Synthesis of Enantioenriched Terminal Epoxides and 1,2-Diols J. Am. Chem. Soc. 2002, 124, 1307-1315 (Pubitemid 34169137)
22. Dale, J. A.; Dull, D. L.; Mosher, H. S. α-Methoxy-α- trifluoromethylphenylacetic Acid, a Versatile Reagent for Determination of Enantiomeric Composition of Alcohols and Amines J. Org. Chem. 1969, 34, 2543-2549
23. Rottger, S.; Waldmann, H. Solid-Phase Synthesis of Decalin Scaffolds by Robinson Annulation with Immobilised Nazarov Reagents Eur. J. Org. Chem. 2006, 2093-2099
24. Nelson, W. L.; Freeman, D. S.; Vincenzi, F. F. Stereochemical Analogs of a Muscarinic, Ganglionic Stimulant. 2. Cis and Trans Olefinic, Epoxide, and Cyclopropane Analogs Related to 4-[ n -(3-Chlorophenyl)carbamoyloxy]-2- butynyltrimethylammonium Chloride (McN-A-343) J. Med. Chem. 1976, 19, 153-158
25. Katoh, T.; Itoh, E.; Yoshino, T.; Terashima, S. Total Synthesis of an Enantiomeric Pair of FR900482. 1. Synthetic and End-Game Strategies Tetrahedron 1997, 53, 10229-10238 (Pubitemid 27303831)
26. Calderon, F.; Doyaguez, E. G.; Fernandez-Mayoralas, A. Synthesis of Azasugars through a Proline-Catalyzed Reaction J. Org. Chem. 2006, 71, 6258-6261 (Pubitemid 44200301)
27. SanchezSancho, F.; Valverde, S.; Herradon, B. Stereoselective Syntheses and Reactions of Chiral Oxygenated alpha,beta-Unsaturated-gamma- and delta-Lactones Tetrahedron: Asymmetry 1996, 7, 3209-3246 (Pubitemid 26394371)
28. Fadnavis, N. W.; Sharfuddin, M.; Vadivel, S. K. Porcine Pancreatic Lipase Mediated Regio- and Stereoselective Hydrolysis: Chemoenzymatic Synthesis of (2 S,3 S)-2-Amino-3,4-dihydroxybutyric Acid Tetrahedron: Asymmetry 2001, 12, 691-693 (Pubitemid 32497079)
29. Nicolaou, K. C.; Reddy, K. R.; Skokotas, G.; Sato, F.; Xiao, X. Y.; Hwang, C. K. Total Synthesis of Hemibrevetoxin-b and (7a-α)-epi- Hemibrevetoxin-b J. Am. Chem. Soc. 1993, 115, 3558-3575
30. Jorgensen, W. L.; Maxwell, D. S.; TiradoRives, J. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids J. Am. Chem. Soc. 1996, 118, 11225-11236 (Pubitemid 26399746)
31. Eldridge, M. D.; Murray, C. W.; Auton, T. R.; Paolini, G. V.; Mee, R. P. Empirical Scoring Functions. 1. The Development of a Fast Empirical Scoring Function To Estimate the Binding Affinity of Ligands in Receptor Complexes J. Comput.-Aided Mol. Des. 1997, 11, 425-445 (Pubitemid 127505895)
32. First Discovery 2.7 Technical Notes; Schrodinger: Portland, OR, 2003.
33. Litovchick, A.; Rando, R. R. Stereospecificity of Short Rev-Derived Peptide Interactions with RRE IIB RNA RNA 2003, 9, 937-948 (Pubitemid 36899237)
34. Paulsen, R. B.; Seth, P. P.; Swayze, E. E.; Griffey, R. H.; Skalicky, J. J.; Cheatham, T. E. I.; Davis, D. R. Inhibitor-Induced Structural Change in the HCV IRES Domain IIa RNA Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 7263-7268
35. Gerdeman, M. S.; Henkin, T. M.; Hines, J. V. Solution Structure of the Bacillus subtilis T-Box Antiterminator RNA: Seven Nucleotide Bulge Characterized by Stacking and Flexibility J. Mol. Biol. 2003, 326, 189-201 (Pubitemid 36284724)
36. Regulski, E. E.; Breaker, R. R. In-Line Probing Analysis of Riboswitches Methods Mol. Biol. 2008, 419, 53-67
37. Gerdeman, M. S.; Henkin, T. M.; Hines, J. V. In Vitro Structure-Function Studies of the Bacillus subtilis tyrS mRNA Antiterminator: Evidence for Factor-Independent tRNA Acceptor Stem Binding Specificity Nucleic Acids Res. 2002, 30, 1065-1072 (Pubitemid 34679676)
38. Hehre, W. J.; Yu, J.; Klunzinger, P. E. A Guide to Molecular Mechanics and Molecular Orbital Calculations in Spartan; Wavefunction, Inc.: Irvine, CA, 1997.
39. Sanner, M. F. Python: A Programming Language for Software Integration and Development J. Mol. Graphics Mod. 1999, 17, 57-61 (Pubitemid 30029318)