Piperidine glycosides targeting the ribosomal decoding site

ChemBioChem

Volumn 4, Issue 9, 2003, Pages 886-890

  Simonsen, Klaus B ^a   Ayida, Benjamin K ^a   Vourloumis, Dionisios ^a   Winters, Geoffrey C ^a   Takahashi, Masayuki ^a   Shandrick, Sarah ^a   Zhao, Qiang ^a   Hermann, Thomas ^a  

^a F HOFFMANN LA ROCHE LTD   (Switzerland)

Author keywords

Aminoglycosides; Antibiotics; Drug design; Medicinal chemistry; RNA recognition

Indexed keywords

2 DEOXYSTREPTAMINE; 6' AMINOGLUCOSAMINE; AMINOGLYCOSIDE ANTIBIOTIC AGENT; FRAMYCETIN; GLUCOSAMINE DERIVATIVE; PAROMOMYCIN; PIPERIDINE DERIVATIVE; TRIACYLGLYCEROL LIPASE; UNCLASSIFIED DRUG;

ANTIBACTERIAL ACTIVITY; ARTICLE; CONTROLLED STUDY; DRUG DESIGN; DRUG SYNTHESIS; HYDROGEN BOND; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN SYNTHESIS INHIBITION; PROTON NUCLEAR MAGNETIC RESONANCE; RIBOSOME; STEREOCHEMISTRY; STRUCTURE ACTIVITY RELATION;

ANTI-BACTERIAL AGENTS; BINDING SITES; ESCHERICHIA COLI; GLYCOSIDES; INHIBITORY CONCENTRATION 50; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PIPERIDINES; RNA, BACTERIAL; RNA, RIBOSOMAL; STAPHYLOCOCCUS AUREUS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0141733703     PISSN: 14394227     EISSN: None     Source Type: Journal    
DOI: 10.1002/cbic.200300689     Document Type: Article

References (16)

1. See the preceding communication: D. Vourloumis, G.C. Winters, M. Takahashi, K. B. Simonsen, B. K. Ayida, S. Shandrick, Q. Zhao, T. Hermann, ChemBioChem 2003, 4, 879-885.
2. a) A. P. Carter, W. M. Clemons, D. E. Brodersen, R. J. Morgan-Warren, B. T. Wimberly,V. Ramakrishnan, Nature 2000, 407, 340-348;
3. b) J. M. Ogle, D. E. Brodersen, W. M. Clemons, M. J. Tarry, A. P. Carter, V. Ramakrishnan, Science 2001, 292, 897-902.
4. a) Q. Vicens, E. Westhof, Structure 2001, 9, 647-658;
5. Q. Vicens, E. Westhof, Chem. Biol. 2002, 9, 747-755.
6. Molecular modeling was performed by using published atom coordinates of the 30S ribosomal subunit-aminoglycoside complexes[2,3] and high-resolution crystal structures of synthetic RNA constructs containing the bacterial decoding-site internal loop (Q. Zhao, T. Hermann, unpublished results). Preferred conformations of the novel aminoglycoside mimetics 1 and 2 were explored by molecular dynamics simulations and energy minimization by using the Insight/Discover software (Accelrys, San Diego) and following established protocols (T. Hermann, E. Westhof, J. Mol. Biol. 1998, 276, 903-912; T. Hermann, E. Westhof, J. Med. Chem. 1999, 42, 1250-1261).
7. Molecular modeling was performed by using published atom coordinates of the 30S ribosomal subunit-aminoglycoside complexes[2,3] and high-resolution crystal structures of synthetic RNA constructs containing the bacterial decoding-site internal loop (Q. Zhao, T. Hermann, unpublished results). Preferred conformations of the novel aminoglycoside mimetics 1 and 2 were explored by molecular dynamics simulations and energy minimization by using the Insight/Discover software (Accelrys, San Diego) and following established protocols (T. Hermann, E. Westhof, J. Mol. Biol. 1998, 276, 903-912; T. Hermann, E. Westhof, J. Med. Chem. 1999, 42, 1250-1261).
8. a) K. Faber, Biotransformations in Oganic Cemistry, Springer, Berlin, 1997;
9. b) C.-H. Wong, G. M. Whiteside, Enzymes in Synthetic Organic Chemistry, Pergamon, Oxford, 1994.
10. a) B. Danieli, G. Lesma, D. Passarella, A. Silvani, J. Org. Chem. 1998, 63, 3492-3496;
11. b) B. Danieli, G. Lesma, D. Passarella, A. Silvani, N. Viviani, Tetrahedron 1999, 55, 11 871-11 878.
12. D. W. Knight, N. Lewis, A. C. Share, D. Haigh, J. Chem. Soc. Perkin Trans. 1 1998, 3673-3683.
13. X. Liang, A. Lohse, M. Bols, J. Org. Chem. 2000, 65, 7432-7437.
14. a) D. Vourloumis, M. Takahashi, G. C. Winters, K. B. Simonsen, B. K. Ayida, S. Barluenga, S. Qamar, S. Shandrick, Q. Zhao, T. Hermann, Bioorg. Med. Chem. Lett. 2002, 12, 3367-3372;
15. b) K. B. Simonsen, B. K. Ayida, D. Vourloumis, M. Takahashi, G.C. Winters, S. Barluenga, S. Qamar, S. Shandrick, Q. Zhao, T. Hermann, ChemBioChem 2002, 3, 1223-1228.
16. S. Shandrick, Q. Zhao, Q. Hau, T. Hermann, unpublished work