Structure-based drug design meets the ribosome

Biochemical Pharmacology

Volumn 71, Issue 7, 2006, Pages 1016-1025

  Franceschi, François ^a   Duffy, Erin M ^a  

^a Rib X Pharmaceuticals Incorporated   (United States)

Author keywords

Antibacterials; Antibiotics; Computational chemistry; Ribosomes; Structure based drug design; X ray structure

Indexed keywords

AMINOGLYCOSIDE ANTIBIOTIC AGENT; AMPRENAVIR; ANISOMYCIN; ANTIBIOTIC AGENT; ANTIINFECTIVE AGENT; BACTERIAL RNA; BLASTICIDIN S; CARBOMYCIN; CELECOXIB; CHLORAMPHENICOL; CYCLOOXYGENASE 2 INHIBITOR; KETOLIDE; LINCOSAMIDE DERIVATIVE; LINEZOLID; MACROLIDE; NELFINAVIR; OXAZOLIDINONE DERIVATIVE; PACTAMYCIN; PLEUROMUTILIN; PUROMYCIN; ROFECOXIB; SPARSOMYCIN; SPECTINOMYCIN; STREPTOGRAMIN DERIVATIVE; TETRACYCLINE DERIVATIVE; ZANAMIVIR;

ACQUIRED IMMUNE DEFICIENCY SYNDROME; ANTIBIOTIC RESISTANCE; BACTERIAL CELL; BINDING SITE; CRYSTAL STRUCTURE; DEINOCOCCUS RADIODURANS; DRUG DESIGN; DRUG MECHANISM; DRUG STRUCTURE; DRUG TARGETING; HALOARCULA MARISMORTUI; INFLUENZA; MINIMUM INHIBITORY CONCENTRATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN SYNTHESIS INHIBITION; REVIEW; RIBOSOME SUBUNIT; STRUCTURE ACTIVITY RELATION;

EID: 33644610182     PISSN: 00062952     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bcp.2005.12.026     Document Type: Article

References (79)

1. NIAID. The Problem of Antibiotic Resistance, NIAID Fact Sheet. April 2004, http://www.niaid.nih.gov/factsheets/antimicro.htm.
2. K.L. LaPlante, and M.J. Rybak Daptomycin-a novel antibiotic against Gram-positive pathogens Expert Opin Pharmacother 5 2004 2321 2331
3. D.H. Batts Linezolid - a new option for treating gram-positive infections Oncology 14 2000 23 29
4. J.F. Barrett Linezolid Pharmacia Corp Curr Opin Investig Drugs 1 2000 181 187
5. A.H. Mutnick, V. Enne, and R.N. Jones Linezolid resistance since 2001: SENTRY Antimicrobial Surveillance Program Ann Pharmacother 37 2003 769 774
6. S. Tsiodras, H.S. Gold, G. Sakoulas, G.M. Eliopoulos, C. Wennersten, and L. Venkataraman Linezolid resistance in a clinical isolate of Staphylococcus aureus Lancet 358 2001 207 208
7. L.S. Munoz-Price, K. Lolans, and J.P. Quinn Emergence of resistance to daptomycin during treatment of vancomycin-resistant Enterococcus faecalis infection Clin Infect Dis 41 2005 565 566
8. T. Terasaka, T. Kinoshita, M. Kuno, N. Seki, K. Tanaka, and I. Nakanishi Structure-based design, synthesis, and structure-activity relationship studies of novel non-nucleoside adenosine deaminase inhibitors J Med Chem 47 2004 3730 3743
9. J.J. Parlow, B.L. Case, T.A. Dice, R.L. Fenton, M.J. Hayes, and D.E. Jones Design, parallel synthesis, and crystal structures of pyrazinone antithrombotics as selective inhibitors of the tissue factor VIIa complex J Med Chem 46 2003 4050 4062
10. R.S. Rowland Using X-ray crystallography in drug discovery Curr Opin Drug Discov Devel 5 2002 613 619
11. R.C. Jackson Contributions of protein structure-based drug design to cancer chemotherapy Semin Oncol 24 1997 164 172
12. N.A. Roberts, J.A. Martin, D. Kinchington, A.V. Broadhurst, J.C. Craig, and I.B. Duncan Rational design of peptide-based HIV proteinase inhibitors Science 248 1990 358 361
13. J. Erickson, D.J. Neidhart, J. VanDrie, D.J. Kempf, X.C. Wang, and D.W. Norbeck Design, activity, and 2.8 Å crystal structure of a C2 symmetric inhibitor complexed to HIV-1 protease Science 249 1990 527 533
14. B.D. Dorsey, R.B. Levin, S.L. McDaniel, J.P. Vacca, J.P. Guare, and P.L. Darke L-735,524: the design of a potent and orally bioavailable HIV protease inhibitor J Med Chem 37 1994 3443 3451
15. E.F. Gale, P.E. Reynolds, M.J. Richmond, and M.J. Waring The molecular basis of antibiotic action 1981 John Wiley and Sons London
16. C. Walsh Molecular mechanisms that confer antibacterial drug resistance Nature 406 2000 775 781
17. M.M. Yusupov, G.Z. Yusupova, A. Baucom, K. Lieberman, T.N. Earnest, and J.H. Cate Crystal structure of the ribosome at 5.5 Å resolution Science 292 2001 883 896
18. E. Cundliffe Recognition sites for antibiotics within rRNA W.E. Hill The ribosome: structure function and evolution 1990 ASM Washington, DC 479 490
19. D. Tu, G. Blaha, P.B. Moore, and T.A. Steitz Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance Cell 121 2005 257 270
20. F. Schluenzen, A. Tocilj, R. Zarivach, J. Harms, M. Gluehmann, and D. Janell Structure of functionally activated small ribosomal subunit at 3.3 Å resolution Cell 102 2000 615 623
21. B.T. Wimberly, D.E. Brodersen, W.M. Clemons Jr., R.J. Morgan-Warren, A.P. Carter, and C. Vonrhein Structure of the 30S ribosomal subunit Nature 407 2000 327 339
22. J. Harms, F. Schluenzen, R. Zarivach, A. Bashan, S. Gat, and I. Agmon High resolution structure of the large ribosomal subunit from a mesophilic eubacterium Cell 107 2001 679 688
23. 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 Å resolution Science 289 2000 905 920
24. H.M. Berman, W.K. Olson, D.L. Beveridge, J. Westbrook, A. Gelbin, and T. Demeny The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids Biophys J 63 1992 751 759
25. Q. Vicens, and E. Westhof Crystal structure of paromomycin docked into the eubacterial ribosomal decoding A site Structure 9 2001 647 658
26. 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
27. D.E. Brodersen, A.P. Carter, W.M. Clemons Jr., R.J. Morgan-Warren, F.V.t. Murphy, and J.M. Ogle Atomic structures of the 30S subunit and its complexes with ligands and antibiotics Cold Spring Harb Symp Quant Biol 66 2001 17 32
28. J.F. Blake, and E.R. Laird Recent advances in virtual ligand scoring Ann Rep Med Chem 38 2003 305 314
29. G. Klebe Recent developments in structure-based drug design J Mol Med 78 2000 269 281
30. W.L. Jorgensen The many roles of computation in drug discovery Science 303 2004 1813 1818
31. NIGMS. NIGMS-Supported Structure-Based Drug Design Saves Lives. 2003, http://www.nigms.nih.gov/news/facts/structure_drugs.html.
32. A.I. Su, D.M. Lorber, G.S. Weston, W.A. Baase, B.W. Matthews, and B.K. Shoichet Docking molecules by families to increase the diversity of hits in database screens: computational strategy and experimental evaluation Proteins 42 2001 279 293
33. R.D. Taylor, P.J. Jewsbury, and J.W. Essex A review of protein-small molecule docking methods J Comput Aided Mol Des 16 2002 151 166
34. R. Taylor Life-science applications of the Cambridge Structural Database Acta Crystallogr D Biol Crystallogr 58 2002 879 888
35. T. Hermann, and E. Westhof RNA as a drug target: chemical, modeling, and evolutionary tools Curr Opin Biotechnol 9 1998 66 73
36. T. Hermann Rational ligand design for RNA: the role of static structure and conformational flexibility in target recognition Biochimie 84 2002 869 875
37. M.J. Drysdale, G. Lentzen, N. Matassova, A.I. Murchie, F. Aboul-Ela, and M. Afshar RNA as a drug target Prog Med Chem 39 2002 73 119
38. C.A. Lipinski Drug-like properties and the causes of poor solubility and poor permeability J Pharmacol Toxicol Methods 44 2000 235 249
39. C.A. Lipinski, F. Lombardo, B.W. Dominy, and P.J. Feeney Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings Adv Drug Deliv Rev 46 2001 3 26
40. W.P. Walters, and M.A. Murcko Prediction of 'drug-likeness' Adv Drug Deliv Rev 54 2002 255 271
41. W.J. Egan, W.P. Walters, and M.A. Murcko Guiding molecules towards drug-likeness Curr Opin Drug Discov Devel 5 2002 540 549
42. W.L. Jorgensen, and E.M. Duffy Prediction of drug solubility from structure Adv Drug Deliv Rev 54 2002 355 366
43. S. Jana, and J.K. Deb Molecular targets for design of novel inhibitors to circumvent aminoglycoside resistance Curr Drug Targets 6 2005 353 361
44. S. Magnet, and J.S. Blanchard Molecular insights into aminoglycoside action and resistance Chem Rev 105 2005 477 498
45. T. Hermann, and E. Westhof Docking of cationic antibiotics to negatively charged pockets in RNA folds J Med Chem 42 1999 1250 1261
46. D.J. Knowles, N. Foloppe, N.B. Matassova, and A.I. Murchie The bacterial ribosome, a promising focus for structure-based drug design Curr Opin Pharmacol 2 2002 501 506
47. D. Johansson, C.H. Jessen, J. Pohlsgaard, K.B. Jensen, B. Vester, and E.B. Pedersen Design, synthesis and ribosome binding of chloramphenicol nucleotide and intercalator conjugates Bioorg Med Chem Lett 15 2005 2079 2083
48. 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
49. 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
50. Q. Vicens, and E. Westhof Crystal structure of a complex between the aminoglycoside tobramycin and an oligonucleotide containing the ribosomal decoding a site Chem Biol 9 2002 747 755
51. K.B. Simonsen, B.K. Ayida, D. Vourloumis, M. Takahashi, G.C. Winters, and S. Barluenga Novel paromamine derivatives exploring shallow-groove recognition of ribosomal-decoding-site RNA Chembiochem 3 2002 1223 1228
52. D. Vourloumis, M. Takahashi, G.C. Winters, K.B. Simonsen, B.K. Ayida, and S. Barluenga Novel 2 5-dideoxystreptamine derivatives targeting the ribosomal decoding site RNA Bioorg Med Chem Lett 12 2002 3367 3372
53. D. Vourloumis, G.C. Winters, K.B. Simonsen, M. Takahashi, B.K. Ayida, and S. Shandrick Aminoglycoside-hybrid ligands targeting the ribosomal decoding site Chembiochem 6 2005 58 65
54. D. Vourloumis, G.C. Winters, M. Takahashi, K.B. Simonsen, B.K. Ayida, and S. Shandrick Novel acyclic deoxystreptamine mimetics targeting the ribosomal decoding site Chembiochem 4 2003 879 885
55. J.A. Sutcliffe Improving on nature: antibiotics that target the ribosome Curr Opin Microbiol 8 2005 534 542
56. 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
57. J. Haddad, L.P. Kotra, B. Llano-Sotelo, C. Kim, E.F. Azucena, and M.Z. Liu Design of novel antibiotics that bind to the ribosomal acyltransfer site J Am Chem Soc 124 2002 3229 3237
58. 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
59. Lawrence L, Danese P, Sutcliffe J. In vitro activity of designer oxazolidinones against Gram-positive hospital pathogens. In: Proceedings of the 45th Interscience Conference on Antimicrobial Agents and Chemotherapy, Abstract A-3434. Washington, DC; 2005.
60. Lawrence L, Sutcliffe J. In vitro activity of designer oxazolidinones against respiratory pathogens. In: Proceedings of the 45th Interscience Conference on Antimicrobial Agents and Chemotherapy, Abstract A-3432. Washington, DC; 2005.
61. Ippolito J, Kanyo Z, Wimberly B, Wang D, Skripkin E, Devito J, et al. Structural Basis for the Binding Rx-01, a Novel Oxazolidinone Class, to Bacterial Ribosomes. In: Proceedings of the 45th Interscience Conference on Antimicrobial Agents and Chemotherapy, Abstract A-3445. Washington, DC; 2005.
62. E.M. Duffy, and W.L. Jorgensen Prediction of properties from simulations: free energies of solvation in hexadecane, octanol, and water J Am Chem Soc 122 2000 2878 2888
63. Skripkin E, McConnell T, King B, Devito J, Franceschi F, Sutcliffe J. Designer oxazolidinones bind to the 50S peptidyl-transferase region and can overcome ribosome-based linezolid resistance. In: Proceedings of the 45th Interscience Conference on Antimicrobial Agents and Chemotherapy, Abstract A-3440. Washington, DC; 2005.
64. Chen S, Wu Y, Lou R, Oyelere A, Bhattacharje A, Wang D, et al. Design at the atomic level: synthesis of biaryloxazolidinones as potent, orally active antibiotics. In: Proceedings of the 45th Interscience Conference on Antimicrobial Agents and Chemotherapy, Abstract A-3428. Washington, DC; 2005.
65. Oyelere A, Bhattacharje A, Wang D, Lou R, Tran J, Wu Y, et al. Structure-based design and synthesis of novel amino acid amide-oxazolidinones. In: Proceedings of the 45th Interscience Conference on Antimicrobial Agents and Chemotherapy, Abstract A-3404 2005. Washington, DC; 2005.
66. Q. Han, Q. Zhao, S. Fish, K.B. Simonsen, D. Vourloumis, and J.M. Froelich Molecular recognition by glycoside pseudo base pairs and triples in an apramycin-RNA complex Angew Chem Int Ed Engl 44 2005 2694 2700
67. Q. Vicens, and E. Westhof Crystal structure of geneticin bound to a bacterial 16S ribosomal RNA A site oligonucleotide J Mol Biol 326 2003 1175 1188
68. 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
69. M. Pioletti, F. Schlunzen, J. Harms, R. Zarivach, M. Gluhmann, and H. Avila Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3 EMBO J 20 2001 1829 1839
70. 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
71. F. Schlunzen, J.M. Harms, F. Franceschi, H.A. Hansen, H. Bartels, and R. Zarivach Structural basis for the antibiotic activity of ketolides and azalides Structure 11 2003 329 338
72. F. Schlunzen, R. Zarivach, J. Harms, A. Bashan, A. Tocilj, and R. Albrecht Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria Nature 413 2001 814 821
73. R. Berisio, F. Schluenzen, J. Harms, A. Bashan, T. Auerbach, and D. Baram Structural insight into the role of the ribosomal tunnel in cellular regulation Nat Struct Biol 10 2003 366 370
74. R. Berisio, J. Harms, F. Schluenzen, R. Zarivach, H.A. Hansen, and P. Fucini Structural insight into the antibiotic action of telithromycin against resistant mutants J Bacteriol 185 2003, Aug 4276 4279 erratum appears in J Bacteriol. 2003 185(16):5027
75. 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
76. 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
77. 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
78. P. Nissen, J. Hansen, N. Ban, P.B. Moore, and T.A. Steitz The structural basis of ribosome activity in peptide bond synthesis Science 289 2000 920 930
79. D.N. Wilson, J.M. Harms, K.H. Nierhaus, F. Schlünzen, and P. Fucini Species-specific antibiotic-ribosome interactions: implications for drug development Biol Chem 386 2005 1239 1252