Improving on nature: Antibiotics that target the ribosome

Current Opinion in Microbiology

Volumn 8, Issue 5, 2005, Pages 534-542

  Sutcliffe, Joyce A ^a  

^a Rib X Pharmaceuticals Incorporated   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

A 424902; A 692345; A 72310; AMIKACIN; AMINOGLYCOSIDE ANTIBIOTIC AGENT; ANISOMYCIN; ANTIBIOTIC AGENT; CHLORAMPHENICOL; DEOXYNEGAMYCIN; FRAMYCETIN; GENTAMICIN; GYRASE INHIBITOR; HYGROMYCIN B; KANAMYCIN; LINEZOLID; MACROLIDE; MIKAMYCIN B; NAPHTHYRIDINE DERIVATIVE; NEAMINE; NEGAMYCIN; NEGAMYCIN DERIVATIVE; NUCLEOTIDE DERIVATIVE; OXAZOLIDINONE DERIVATIVE; PAROMOMYCIN; PUROMYCIN; PYRENE; QUINOLINE DERIVED ANTIINFECTIVE AGENT; SPARSOMYCIN; STREPTOGRAMIN DERIVATIVE; TYLOSIN; UNCLASSIFIED DRUG; UNINDEXED DRUG;

ANTIBACTERIAL ACTIVITY; ANTIBIOTIC RESISTANCE; CRYSTAL STRUCTURE; DRUG BINDING; DRUG BINDING SITE; DRUG CONJUGATION; NONHUMAN; PROTEIN BINDING; PROTEIN MODIFICATION; PROTEIN SYNTHESIS; REVIEW; RIBOSOME; RIBOSOME SUBUNIT; X RAY ANALYSIS;

AMINO ACIDS, DIAMINO; AMINOGLYCOSIDES; ANTI-BACTERIAL AGENTS; CRYSTALLOGRAPHY, X-RAY; DRUG DESIGN; DRUG EVALUATION, PRECLINICAL; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROTEIN BINDING; PROTEIN BIOSYNTHESIS; PROTEIN SYNTHESIS INHIBITORS; RIBOSOMES;

EID: 25144480034     PISSN: 13695274     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mib.2005.08.004     Document Type: Review

References (56)

1. E.M. D'Agata Rapidly rising prevalence of nosocomial multidrug-resistant, Gram-negative bacilli: a 9-year surveillance study Infect Control Hosp Epidemiol 25 2004 842 846
2. M.R. Jacobs, D. Felmingham, P.C. Appelbaum, and R.N. Gruneberg The Alexander Project 1998-2000: susceptibility of pathogens isolated from community-acquired respiratory tract infection to commonly used antimicrobial agents J Antimicrob Chemother 52 2003 229 246
3. T.S. Naimi, K.H. LeDell, K. Como-Sabetti, S.M. Borchardt, D.J. Boxrud, J. Etienne, S.K. Johnson, F. Vandenesch, S. Fridkin, and C. O'Boyle Comparison of community- and health care-associated methicillin-resistant Staphylococcus aureus infection JAMA 290 2003 2976 2984
4. H. Wisplinghoff, T. Bischoff, S.M. Tallent, H. Seifert, R.P. Wenzel, and M.B. Edmond Nosocomial bloodstream infections in US hospitals: analysis of 24, 179 cases from a prospective nationwide surveillance study Clin Infect Dis 39 2004 309 317
5. D.J. Diekema, B.J. BootsMiller, T.E. Vaughn, R.F. Woolson, J.W. Yankey, E.J. Ernst, S.D. Flach, M.M. Ward, C.L. Franciscus, and M.A. Pfaller Antimicrobial resistance trends and outbreak frequency in United States hospitals Clin Infect Dis 38 2004 78 85
6. F. Schlunzen, J.M. Harms, F. Franceschi, H.A. Hansen, H. Bartels, R. Zarivach, and A. Yonath Structural basis for the antibiotic activity of ketolides and azalides Structure (Camb) 11 2003 329 338
7. J. Poehlsgaard, and S. Douthwaite Macrolide antibiotic interaction and resistance on the bacterial ribosome Curr Opin Investig Drugs 4 2003 140 148
8. J.L. Hansen, P.B. Moore, and T.A. Steitz Structures of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit J Mol Biol 330 2003 1061 1075
9. J.L. Hansen, J.A. Ippolito, N. Ban, P. Nissen, P.B. Moore, and T.A. Steitz The structures of four macrolide antibiotics bound to the large ribosomal subunit Mol Cell 10 2002 117 128
10. F. Schlunzen, R. Zarivach, J. Harms, A. Bashan, A. Tocilj, R. Albrecht, A. Yonath, and F. Franceschi Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria Nature 413 2001 814 821
11. B.T. Wimberly, D.E. Brodersen, W.M. Clemons Jr., R.J. Morgan-Warren, A.P. Carter, C. Vonrhein, T. Hartsch, and V. Ramakrishnan Structure of the 30S ribosomal subunit Nature 407 2000 327 339
12. N. Ban, P. Nissen, J. Hansen, P.B. Moore, and T.A. Steitz The complete atomic structure of the large ribosomal subunit at 2.4 A resolution Science 289 2000 905 920
13. D.E. Brodersen, W.M. Clemons Jr., A.P. Carter, R.J. Morgan-Warren, B.T. Wimberly, and V. Ramakrishnan The structural basis for the action of the antibiotics tetracycline, pactamycin, and hygromycin B on the 30S ribosomal subunit Cell 103 2000 1143 1154
14. D.E. Brodersen, A.P. Carter, W.M. Clemons Jr., R.J. Morgan-Warren, F.V. Murphy 4th, J.M. Ogle, M.J. Tarry, B.T. Wimberly, and V. Ramakrishnan Atomic structures of the 30S subunit and its complexes with ligands and antibiotics Cold Spring Harb Symp Quant Biol 66 2001 17 32
15. A.P. Carter, W.M. Clemons, D.E. Brodersen, R.J. Morgan-Warren, B.T. Wimberly, and V. Ramakrishnan Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics Nature 407 2000 340 348
16. V. Ramakrishnan, and P.B. Moore Atomic structures at last: the ribosome in 2000 Curr Opin Struct Biol 11 2001 144 154
17. T. Auerbach, A. Bashan, and A. Yonath Ribosomal antibiotics: structural basis for resistance, synergism and selectivity Trends Biotechnol 22 2004 570 576
18. J. Harms, F. Schluenzen, R. Zarivach, A. Bashan, S. Gat, I. Agmon, H. Bartels, F. Franceschi, and A. Yonath High resolution structure of the large ribosomal subunit from a mesophilic eubacterium Cell 107 2001 679 688
19. F. Schluenzen, A. Tocilj, R. Zarivach, J. Harms, M. Gluehmann, D. Janell, A. Bashan, H. Bartels, I. Agmon, and F. Franceschi Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution Cell 102 2000 615 623
20. F. Schlunzen, E. Pyetan, P. Fucini, A. Yonath, and J.M. Harms Inhibition of peptide bond formation by pleuromutilins: the structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with tiamulin Mol Microbiol 54 2004 1287 1294
21. Q. Vicens, and E. Westhof RNA as a drug target: the case of aminoglycosides ChemBioChem 4 2003 1018 1023
22. Q. Vicens, and E. Westhof Crystal structure of paromomycin docked into the eubacterial ribosomal decoding A site Structure (Camb) 9 2001 647 658
23. BK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance Cell 121 2005 257 270 This is the latest in a series of papers from the Steitz and Moore laboratory, which elucidates complexes of antibiotics bound to H. marismortui 50S. This paper provides the structures of Synercid (quinupristin + dalfopristin), erythromycin, clindamycin and telithromycin in 50S ribosomal subunits that have a key residue change - G2058A. A2058 is found in nearly all eubacteria and the use of a genetically modified strain as a source of 50S allowed excellent resolution of the antibiotics that were not well resolved when G2058 was present. The differences between binding modes and conformers as seen in D. radiodurans and versus the A2058 H. marismortui complexes of the same antibiotics is noted.
24. J.M. Harms, F. Schlunzen, P. Fucini, H. Bartels, and A. Yonath Alterations at the peptidyl transferase centre of the ribosome induced by the synergistic action of the streptogramins dalfopristin and quinupristin BMC Biol 2 2004 4
25. J.M. Ogle, D.E. Brodersen, W.M. Clemons Jr., M.J. Tarry, A.P. Carter, and V. Ramakrishnan Recognition of cognate transfer RNA by the 30S ribosomal subunit Science 292 2001 897 902
26. J.M. Ogle, A.P. Carter, and V. Ramakrishnan Insights into the decoding mechanism from recent ribosome structures Trends Biochem Sci 28 2003 259 266
27. V. Ramakrishnan Ribosome structure and the mechanism of translation Cell 108 2002 557 572
28. S. Shandrick, Q. Zhao, Q. Han, B.K. Ayida, M. Takahashi, G.C. Winters, K.B. Simonsen, D. Vourloumis, and T. Hermann Monitoring molecular recognition of the ribosomal decoding site Angew Chem Int Ed Engl 43 2004 3177 3182
29. Q. Han, Q. Zhao, S. Fish, K.B. Simonsen, D. Vourloumis, J.M. Froelich, D. Wall, and T. Hermann Molecular recognition by glycoside pseudo base pairs and triples in an apramycin-RNA complex Angew Chem Int Ed Engl 44 2005 2694 2700
30. S. Jana, and J.K. Deb Molecular targets for design of novel inhibitors to circumvent aminoglycoside resistance Curr Drug Targets 6 2005 353 361
31. S. Magnet, and J.S. Blanchard Molecular insights into aminoglycoside action and resistance Chem Rev 105 2005 477 498
32. D. Vourloumis, G.C. Winters, K.B. Simonsen, M. Takahashi, B.K. Ayida, S. Shandrick, Q. Zhao, Q. Han, and T. Hermann Aminoglycoside-hybrid ligands targeting the ribosomal decoding site ChemBioChem 6 2005 58 65 This is one of a series of articles in which the rationale and structural basis for the modification of aminoglycosides is proposed and tested. In this approach, the authors attempt to make chimeric antibiotics of two different types of aminoglycosides - hygromycin B and paromomycin.
33. D. Vourloumis, M. Takahashi, G.C. Winters, K.B. Simonsen, B.K. Ayida, S. Barluenga, S. Qamar, S. Shandrick, Q. Zhao, and T. Hermann Novel 2,5-dideoxystreptamine derivatives targeting the ribosomal decoding site RNA Bioorg Med Chem Lett 12 2002 3367 3372
34. K.B. Simonsen, B.K. Ayida, D. Vourloumis, M. Takahashi, G.C. Winters, S. Barluenga, S. Qamar, S. Shandrick, Q. Zhao, and T. Hermann Novel paromamine derivatives exploring shallow-groove recognition of ribosomal-decoding-site RNA ChemBioChem 3 2002 1223 1228
35. D. Vourloumis, G.C. Winters, M. Takahashi, K.B. Simonsen, B.K. Ayida, S. Shandrick, Q. Zhao, and T. Hermann Novel acyclic deoxystreptamine mimetics targeting the ribosomal decoding site ChemBioChem 4 2003 879 885
36. K.B. Simonsen, B.K. Ayida, D. Vourloumis, G.C. Winters, M. Takahashi, S. Shandrick, Q. Zhao, and T. Hermann Piperidine glycosides targeting the ribosomal decoding site ChemBioChem 4 2003 886 890
37. S. Barluenga, K.B. Simonsen, E.S. Littlefield, B.K. Ayida, D. Vourloumis, G.C. Winters, M. Takahashi, S. Shandrick, Q. Zhao, and Q. Han Rational design of azepane-glycoside antibiotics targeting the bacterial ribosome Bioorg Med Chem Lett 14 2004 713 718
38. R.J. Russell, J.B. Murray, G. Lentzen, J. Haddad, and S. Mobashery The complex of a designer antibiotic with a model aminoacyl site of the 30S ribosomal subunit revealed by X-ray crystallography J Am Chem Soc 125 2003 3410 3411
39. J. Haddad, L.P. Kotra, B. Llano-Sotelo, C. Kim, E.F. Azucena Jr., M. Liu, S.B. Vakulenko, C.S. Chow, and S. Mobashery Design of novel antibiotics that bind to the ribosomal acyltransfer site J Am Chem Soc 124 2002 3229 3237
40. N. Foloppe, I.J. Chen, B. Davis, A. Hold, D. Morley, and R. Howes A structure-based strategy to identify new molecular scaffolds targeting the bacterial ribosomal A-site Bioorg Med Chem 12 2004 935 947
41. P.J. Dandliker, S.D. Pratt, A.M. Nilius, C. Black-Schaefer, X. Ruan, D.L. Towne, R.F. Clark, E.E. Englund, R. Wagner, and M. Weitzberg Novel antibacterial class Antimicrob Agents Chemother 47 2003 3831 3839
42. R.F. Clark, S. Wang, Z. Ma, M. Weitzberg, C. Motter, M. Tufano, R. Wagner, Y.G. Gu, P.J. Dandliker, and C.G. Lerner 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 2004 3299 3302
43. S.D. Pratt, C.A. David, C. Black-Schaefer, P.J. Dandliker, X. Xuei, U. Warrior, D.J. Burns, P. Zhong, Z. Cao, and A.Y. Saiki A strategy for discovery of novel broad-spectrum antibacterials using a high-throughput Streptococcus pneumoniae transcription/translation screen J Biomol Screen 9 2004 3 11
44. L.L. Shen, C. Black-Schaefer, Y. Cai, P.J. Dandliker, and B.A. Beutel Mechanism of action of a novel series of naphthyridine-type ribosome inhibitors: enhancement of tRNA footprinting at the decoding site of 16S rRNA Antimicrob Agents Chemother 49 2005 1890 1897
45. Y. Uehara, M. Hori, and H. Umezawa Specific inhibition of the termination process of protein synthesis by negamycin Biochim Biophys Acta 442 1976 251 262
46. Y. Uehara, S. Kondo, H. Umezawa, K. Suzukake, and M. Hori Negamycin, a miscoding antibiotic with a unique structure J Antibiot (Tokyo) 25 1972 685 688
47. M. Arakawa, M. Shiozuka, Y. Nakayama, T. Hara, M. Hamada, S. Kondo, D. Ikeda, Y. Takahashi, R. Sawa, and Y. Nonomura Negamycin restores dystrophin expression in skeletal and cardiac muscles of mdx mice J Biochem (Tokyo) 134 2003 751 758
48. B. Raju, K. Mortell, S. Anandan, H. O'Dowd, H. Gao, M. Gomez, C. Hackbarth, C. Wu, W. Wang, and Z. Yuan N- and C-terminal modifications of negamycin Bioorg Med Chem Lett 13 2003 2413 2418
49. B. Raju, S. Anandan, S. Gu, P. Herradura, H. O'Dowd, B. Kim, M. Gomez, C. Hackbarth, C. Wu, and W. Wang Conformationally restricted analogs of deoxynegamycin Bioorg Med Chem Lett 14 2004 3103 3107
50. Steitz TA, Moore PB, Sutcliffe JA, Oyelere A, Ippolito JA: Ribosome structure and protein synthesis inhibitors. Yale University and Rib-X Pharmaceuticals, Inc. Accession number US 2005/0036997; 2005.
51. R. Berisio, J. Harms, F. Schluenzen, R. Zarivach, H.A. Hansen, P. Fucini, and A. Yonath Structural insight into the antibiotic action of telithromycin against resistant mutants J Bacteriol 185 2003 4276 4279
52. T.A. Mukhtar, and G.D. Wright Streptogramins, oxazolidinones, and other inhibitors of bacterial protein synthesis Chem Rev 105 2005 529 542
53. J. Sutcliffe, and R. Leclercq Mechanisms of resistance to macrolides, lincosamides, and ketolides W. Schonfeld H.A. Kirst Macrolide Antibiotics 2002 Birkhauser Verlag 281 317
54. T.A. Mukhtar, K.P. Koteva, and G.D. Wright Chimeric streptogramin- tyrocidine antibiotics that overcome streptogramin resistance Chem Biol 12 2005 229 235
55. N.V. Sumbatyan, G.A. Korshunova, and A.A. Bogdanov Peptide derivatives of antibiotics tylosin and desmycosin, protein synthesis inhibitors Biochemistry (Mosc) 68 2003 1156 1158
56. D. Johansson, C.H. Jessen, J. Pohlsgaard, K.B. Jensen, B. Vester, E.B. Pedersen, and P. Nielsen Design, synthesis and ribosome binding of chloramphenicol nucleotide and intercalator conjugates Bioorg Med Chem Lett 15 2005 2079 2083