Mechanism of action of a novel series of naphthyridine-type ribosome inhibitors: Enhancement of tRNA footprinting at the decoding site of 16S rRNA

Antimicrobial Agents and Chemotherapy

Volumn 49, Issue 5, 2005, Pages 1890-1897

  Shen, Linus L ^a   Black Schaefer, Candace ^a   Cai, Yingna ^a   Dandliker, Peter J ^a   Beutel, Bruce A ^a  

^a ABBOTT LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

A 358816; A 362505; A 424902; A 438301; A 548501; A 692345; A 72310; APRAMYCIN; BACTERIAL PROTEIN; CHLORAMPHENICOL; FUSIDIC ACID; GENTAMICIN; HYGROMYCIN B; KANAMYCIN; KASUGAMYCIN; LINEZOLID; MOCIMYCIN; NAPHTHYRIDINE DERIVATIVE; NEOMYCIN; NOVEL RIBOSOME INHIBITOR; PAROMOMYCIN; PROTEIN INHIBITOR; PUROMYCIN; RADIOLIGAND; RIBOSOME RNA; RNA 16S; SPARSOMYCIN; SPECTINOMYCIN; STREPTOMYCIN; TETRACYCLINE; TRANSFER RNA; UNCLASSIFIED DRUG;

ARTICLE; CHEMICAL MODIFICATION; DISSOCIATION CONSTANT; DNA FOOTPRINTING; DRUG MECHANISM; ESCHERICHIA COLI; ISOTOPE LABELING; LIGAND BINDING; NONHUMAN; PRIORITY JOURNAL; PROTEIN SYNTHESIS; RIBOSOME SUBUNIT; STREPTOCOCCUS PNEUMONIAE;

AUTORADIOGRAPHY; BACTERIAL PROTEINS; DNA PRIMERS; GENE EXPRESSION REGULATION, BACTERIAL; MODELS, MOLECULAR; NAPHTHYRIDINES; PROTEIN BIOSYNTHESIS; PROTEIN FOOTPRINTING; RADIOLIGAND ASSAY; RIBOSOMES; RNA, RIBOSOMAL, 16S; RNA, TRANSFER; STREPTOCOCCUS PNEUMONIAE;

EID: 18244395053     PISSN: 00664804     EISSN: None     Source Type: Journal    
DOI: 10.1128/AAC.49.5.1890-1897.2005     Document Type: Article

References (37)

1. Blaha, G., U. Stelzl, C. M. Spahn, R. K. Agrawal, J. Frank, and K. H. Nierhaus. 2000. Preparation of functional ribosomal complexes and effect of buffer conditions on tRNA positions observed by cryoelectron microscopy. Methods Enzymol. 317:292-309.
2. Brodersen, D. E., W. M. Clemons, Jr., A. P. Carter, R. J. Morgan-Warren, B. T. Wimberly, and V. Ramakrishnan. 2000. The structural basis for the action of the antibiotics tetracycline, pactamycin, and hygromycin B on the 30S ribosomal subunit. Cell 103:1143-1154.
3. Carter, A. P., W. M. Clemons, D. E. Brodersen, R. J. Morgan-Warren, B. T. Wimberly, and V. Ramakrishnan. 2000. Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature 407:340-348.
4. Clark, R. F., S. Wang, Z. Ma, M. Weitzberg, C. Motter, M. Tufano, R. Wagner, Y. G. Gu, P. J. Dandliker, C. G. Lerner, L. E. Chovan, Y. Cai, C. L. Black-Schaefer, L. Lynch, D. Kalvin, A. M. Nilius, S. D. Pratt, N. Soni, T. Zhang, X. Zhang, and B. A. Beutel. 2004. Novel inhibitors of bacterial protein synthesis; structure-activity relationships for 1,8-naphthyridine derivatives incorporating position 3 and 4 variants. Bioorg. Med. Chem. Lett. 14:3299-3302.
5. Dandliker, P. J., S. D. Pratt, A. M. Nilius, C. Black-Schaefer, X. Ruan, D. L. Towne, R. F. Clark, E. E. Englund, R. Wagner, M. Weitzberg, L. E. Chovan, R. K. Hickman, M. M. Daly, S. Kakavas, P. Zhong, Z. Cao, C. A. David, X. Xuei, C. G. Lerner, N. B. Soni, M. Bui, L. L. Shen, Y. Cai, P. J. Merta, A. Y. Saiki, and B. A. Beutel. 2003. Novel antibacterial class. Antimicrob. Agents Chemother. 47:3831-3839.
6. Fourmy, D., M. I. Recht, S. C. Blanchard, and J. D. Puglisi. 1996. Structure of the A site of Escherichia coli 16S rRNA complexed with an aminoglycoside antibiotic. Science 274:1367-1371.
7. Fourmy, D., M. I. Recht, and J. D. Puglisi. 1998. Binding of neomycin-class aminoglycoside antibiotics to the A-site of 16 S rRNA. J. Mol. Biol. 277: 347-362.
8. Klotz, I. M. 1974. Protein interactions with small molecules. Acc. Chem. Res. 7:162-168.
9. Lodmell, J. S., W. E. Tapprich, and W. E. Hill. 1993. Evidence for a conformational change in the exit site of the Escherichia coli ribosome upon tRNA binding. Biochemistry 32:4067-4072.
10. Mascaretti, O. A. 2003. Bacteria versus antibacterial agents: an integrated approach. ASM Press, Washington, D.C.
11. Matassova, N. B., M. V. Rodnina, R. Endermann, H. P. Kroll, U. Pleiss, H. Wild, and W. Wintermeyer. 1999. Ribosomal RNA is the target for oxazolidinones, a novel class of translational inhibitors. RNA 5:939-946.
12. Miyaguchi, H., H. Narita, K. Sakamoto, and S. Yokoyama. 1996. An antibiotic-binding motif of an RNA fragment derived from the A-site-related region of Escherichia coli 16S rRNA. Nucleic Acids Res. 24:3700-3706.
13. Moazed, D., and H. F. Noller. 1987. Chloramphenicol, erythromycin, carbomycin and vernamycin B protect overlapping sites in the peptidyl transferase region of 23S ribosomal RNA. Biochimie 69:879-884.
14. Moazed, D., and H. F. Noller. 1987. Interaction of antibiotics with functional sites in 16S ribosomal RNA. Nature 327:389-394.
15. Moazed, D., and H. F. Noller. 1989. Interaction of tRNA with 23S rRNA in the ribosomal A, P, and E sites. Cell 57:585-597.
16. Moazed, D., and H. F. Noller. 1986. Transfer RNA shields specific nucleotides in 16S ribosomal RNA from attack by chemical probes. Cell 47:985-994.
17. Moazed, D., S. Stern, and H. F. Noller. 1986. Rapid chemical probing of conformation in 16S ribosomal RNA and 30 S ribosomal subunits using primer extension. J. Mol. Biol. 187:399-416.
18. Pioletti, M., F. Schlunzen, J. Harms, R. Zarivach, M. Gluhmann, H. Avila, A. Bashan, H. Bartels, T. Auerbach, C. Jacobi, T. Hartsch, A. Yonath, and F. Franceschi. 2001. Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine, and IF3. EMBO J. 20:1829-1839.
19. Poulsen, S. M., C. Kofoed, and B. Vester. 2000. Inhibition of the ribosomal peptidyl transferase reaction by the mycarose moiety of the antibiotics car-bomycin, spiramycin, and tylosin. J. Mol. Biol. 304:471-481.
20. Pratt, S. D., C. A. David, C. Black-Schaefer, P. J. Dandliker, X. Xuei, U. Warrior, D. Burns, P. Zhong, Z. Cao, A. Y. C. Saiki, C. G. Lerner, L. E. Chovan, N. B. Soni, A. M. Nilius, F. L. Wagenaar, P. J. Merta, L. M. Traphagen, and B. A. Beutel. 2004. A strategy for discovery of novel broad-spectrum antibacterials using a high-throughput Streptococcus pneumoniae transcription/translation screen. J. Biomol. Screening 9:3-11.
21. Purohit, P., and S. Stern. 1994. Interactions of a small RNA with antibiotic and RNA ligands of the 30S subunit. Nature 370:659-662.
22. Rasmussen, B., H. F. Noller, G. Daubresse, B. Oliva, Z. Misulovin, D. M. Rothstein, G. A. Ellestad, Y. Gluzman, F. P. Tally, and I. Chopra. 1991. Molecular basis of tetracycline action: identification of analogs whose primary target is not the bacterial ribosome. Antimicrob. Agents Chemother. 35:2306-2311.
23. Recht, M. I., S. Douthwaite, and J. D. Puglisi. 1999. Basis for prokaryotic specificity of action of aminoglycoside antibiotics. EMBO J. 18:3133-3138.
24. Recht, M. I., D. Fourmy, S. C. Blanchard, K. D. Dahlquist, and J. D. Puglisi. 1996. RNA sequence determinants for aminoglycoside binding to an A-site rRNA model oligonucleotide. J. Mol. Biol. 262:421-436.
25. Schlunzen, F., R. Zarivach, J. Harms, A. Bashan, A. Tocilj, R. Albrecht, A. Yonath, and F. Franceschi. 2001. Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria. Nature 413: 814-821.
26. Shen, L. L., J. Baranowski, J. Fostel, D. A. Montgomery, and P. A. Lartey. 1992. DNA topoisomerases from pathogenic fungi: targets for the discovery of antifungal drugs. Antimicrob. Agents Chemother. 36:2778-2784.
27. Shen, L. L., J. Baranowski, and A. G. Pernet. 1989. Mechanism of inhibition of DNA gyrase by quinolone antibacterials: specificity and cooperativity of drug binding to DNA. Biochemistry 28:3879-3885.
28. Shen, L. L., W. E. Kohlbrenner, D. Weigl, and J. Baranowski. 1989. Mechanism of quinolone inhibition of DNA gyrase. Appearance of unique norfloxacin binding sites in enzyme-DNA complexes. J. Biol. Chem. 264:2973-2978.
29. Shen, L. L., L. A. Mitscher, P. N. Sharma, T. J. O'Donnell, D. W. Chu, C. S. Cooper, T. Rosen, and A. G. Pernet. 1989. Mechanism of inhibition of DNA gyrase by quinolone antibacterials: a cooperative drug-DNA binding model. Biochemistry 28:3886-3894.
30. Shen, L. L., and A. G. Pernet. 1985. Mechanism of inhibition of DNA gyrase by analogues of nalidixic acid: the target of the drugs is DNA. Proc. Natl. Acad. Sci. USA 82:307-311.
31. Stern, S., D. Moazed, and H. F. Noller. 1988. Structural analysis of RNA using chemical and enzymatic probing monitored by primer extension. Methods Enzymol. 164:481-489.
32. Sypherd, P. S., and J. W. Wireman. 1974. Preparation of ribosomal subunits by large-scale zonal centrifugation. Methods Enzymol. 30:349-354.
33. Vicens, Q., and E. Westhof. 2002. Crystal structure of a complex between the aminoglycoside tobramycin and an oligonucleotide containing the ribosomal decoding a site. Chem. Biol. 9:747-755.
34. Vicens, Q., and E. Westhof. 2003. Crystal structure of Geneticin bound to a bacterial 16S ribosomal RNA A site oligonucleotide. J. Mol. Biol. 326:1175-1188.
35. Vicens, Q., and E. Westhof. 2001. Crystal structure of paromomycin docked into the eubacterial ribosomal decoding A site. Structure 9:647-658.
36. Vicens, Q., and E. Westhof. 2003. Molecular recognition of aminoglycoside antibiotics by ribosomal RNA and resistance enzymes: an analysis of x-ray crystal structures. Biopolymers 70:42-57.
37. Walsh, C. 2003. Antibiotics: action, origins, resistance. ASM Press, Washington, D.C.