Physical insights into permeation of and resistance to antibiotics in bacteria

Current Drug Targets

Volumn 9, Issue 9, 2008, Pages 779-788

  Ceccarelli, Matteo ^a   Ruggerone, Paolo ^a,b  

^a UNIVERSITY OF CAGLIARI   (Italy)

^b DEMOCRITOS NATIONAL SIMULATION CENTER   (Italy)

Author keywords

Antibiotics in Bacteria; Gram negative bacteria; Metadynamics; Porins; Water filled membrane protein channels

Indexed keywords

AMOXICILLIN; AMPICILLIN; ANTIBIOTIC AGENT; BETA LACTAM ANTIBIOTIC; CARBENICILLIN; CEPHALOSPORIN DERIVATIVE; OUTER MEMBRANE PROTEIN F; PENICILLIN DERIVATIVE; PORIN; QUINOLINE DERIVED ANTIINFECTIVE AGENT;

ANTIBIOTIC RESISTANCE; BACTERIAL METABOLISM; BACTERIAL OUTER MEMBRANE; CELL MEMBRANE PERMEABILITY; CELL MEMBRANE TRANSPORT; DRUG DESIGN; DRUG PENETRATION; DRUG TRANSPORT; GENE MUTATION; GRAM NEGATIVE BACTERIUM; MOLECULAR DYNAMICS; NONHUMAN; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEIN SYNTHESIS INHIBITION; REVIEW; SIMULATION;

ANTI-BACTERIAL AGENTS; BIOLOGICAL TRANSPORT; CELL MEMBRANE PERMEABILITY; COMPUTER SIMULATION; DRUG DESIGN; DRUG RESISTANCE, BACTERIAL; GRAM-NEGATIVE BACTERIA; PORINS;

EID: 52449131735     PISSN: 13894501     EISSN: None     Source Type: Journal    
DOI: 10.2174/138945008785747770     Document Type: Review

References (80)

1. Page, M. (2005) Europ. BioPharm. Rev. Spring Issue, 40-45.
2. See www.idsociety.org/badbugsnodrugs.
3. Brad Spellberg, B., Powers, J. H.; Brass, E. P.; Miller, L.G.; Edwards Jr. J.E. (2004) Clin. Infect. Dis., 38, 1279-1286.
4. D'Costa, V.; McGrann, K. M.; Hughes, D. W.; Wright, G. D. (2006) Science, 311, 374-377.
5. Davies, J. (1994) Science, 264, 375-382.
6. Hermann, J. C.; Hensen, C.; Ridder, L.; Mulholland, A. J.; Höltje, H.-D (2005) J. Am. Chem. Soc., 127, 4454-4465.
7. Nikaido, H. (1989) Antimicrob. Agents Chemother., 33, 1831-1836.
8. Webber, M. A.; Piddock, L. J. (2003) J. Antimicrob. Chemother., 51, 9-11.
9. Delcour, A. H. (2003) Front. Biosci., 8, 1055-1071.
10. Koronakis, V.; Sharff, A.; Koronakis, E.; Luisi, B.; Hughes, C. (2000) Nature, 405, 914-919.
11. Murakami, S.; Nakashima, R.; Yamashita, E.; Yamaguchi, A. (2002) Nature, 419, 587-593.
12. Pos, K. M.; Schieffier, A.; Seeger, M. A.; Diedrichs, K. (2004) FEBS Lett., 564, 333-339.
13. Nikaido, H. (1994) Science, 264, 382-388.
14. Simonet V.; Malléa, M.; Pagès, J.-M. (2000) Antimicrob. Agents Chemother., 44, 311-315.
15. Piddock L. J. (2006) Clin. Microbiol. Rev., 19, 382-402.
16. Barker, J. J. (2006) Drug. Discov. Today, 11, 391-404.
17. Nestorovich, E. M.; Danelon, C.; Winterhalter, M.; Bezrukov, S. M. (2002) Proc. Natl. Acad. Sci. USA., 99, 9789-9794.
18. Schwarz, G. C.; Danelon, C.; Winterhalter, M. (2003) Biophys. J., 84, 2990-2998.
19. Berezhkovskii, A. M.; Bezrukov, S. M. (2005) Biophys. J., 104, L17-L19.
20. Bauer, W. R.; Nadler, W. (2006)Proc. Natl. Acad. Sci. USA, 103, 11446-11451.
21. Ceccarelli, M.; Danelon, C.; Laio, A.; Parrinello, M. (2004) Biophys. J., 87, 58-64.
22. Luckey, M.; Nikaido, H. (1980) Proc. Natl. Acad. Sci. USA, 77, 165-171.
23. Benz, R.; Schmid, A.; Vos-Sheperkeuter, G. H. (1987) J. Membr. Biol., 100, 21-29.
24. Dutzler, R.; Wang, Y. F.; Rizkallah, P. J.; Rosenbusch, J. P.; Schirmer, T. (1996) Structure, 4, 127-134.
25. Dutzler, R.; Schirmer, T.; Karplus, M.; Fischer, S. (2002) Structure, 10, 1273-1284.
26. Danelon, C.; Brando, T.; Winterhalter, M. (2003) J. Biol. Chem., 278, 35542-35551.
27. Jacoby, G. A. (2005) Clin. Infect. Dis., 41, S120-S126.
28. Cowan. S. W.; Schirmer, T.; Rummel, G.; Steiert, M.; Pauptit, R.A.; Jansonius, J. N.; Rosenbusch, J. P. (1992) Nature, 358, 727-733.
29. Karshikoff, A.; Spassov, V.; Cowan, S. W.; Ladenstein, R.; Schirmer, T. (1994) J. Mol. Biol., 240, 372-384.
30. Vidal, S.; Bredin, J.; Pagès, J.-M.; Barbe, J. (2005) J. Med. Chem., 48, 1395-1400.
31. Hanke, W.; Schlue, W. R. Planar lipid bilayers: methods and applications. Academic Press, San Diego, CA (1993).
32. Benz, R.; Janko, K.; Boos, W.; Lager, P. (1978) Biochim. Biophys. Acta, 511, 305-319.
33. Schindler, H.; Rosenbusch, J. P. (1981)Proc. Natl. Acad. Sci. USA., 78, 2302-2306.
34. Nikaido, H.; Rosenberg, E. Y. (1983) J. Bacteriol., 153, 241-252.
35. Yoshimura, F.; Nikaido, H. (1985) Antimicrob. Agents Chemother., 27, 84-92.
36. Winterhalter, M. (1999) Colloide Surf A., 149, 547-551.
37. Bezrukov, S. M. (2000) J. Membr. Biol., 174, 1-13.
38. Bezrukov, S. M.; Winterhalter, M. (2000) Phys. Rev. Lett., 85, 202-205.
39. Hilly, C.; Winterhalter, M. (2001) Phys. Rev. Lett., 86, 5624-5627.
40. Benz, R.; Schmid, A.; Nakae, T.; Vos-Scheperkeuter, G. H. (1986) J. Bacteriol., 165, 978-986.
41. Andersen, C.; Jordy M.; Benz, R. (1995) J. Gen. Physiol., 105, 385-401.
42. Kullman, L.; Winterhalter, M.; Bezrukov, S. M. (2002) Biophys. J., 82, 803-812.
43. Kolomeisky, A. B. (2007) Phys. Rev. Lett., 98, 048105.
44. Danelon, C.; Nestorovich, E. M.; Winterhalter, M.; Ceccarelli, M.; Bezrukov, S. M. (2006) Biophys. J., 90, 1617-1627.
45. Frenkel, D.; Smit, B. Understanding Molecular Simulations: From Algorithms to Applications. Academic Press, San Diego, CA, 2 edition (2002).
46. Cornell, W. D.; Cieplak, P.; Bavly, C. I.; Gould, I. R.; Merz, K. M. Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollmann, P. (1995) J. Am. Chem. Soc., 117, 5179-5197.
47. Mackerell A. D. (2004) J. Comp. Chem., 25, 1584-1604.
48. Ceccarelli, M.; Marchi, M. (2003) J. Phys. Chem. B., 107, 1423-1431.
49. Perez, A.; Marchan, I.; Svozil, D.; Sponer, J.; Cheatham, T. E. III; Laughton, C. A.; Orozco, M. (2007) Biophys. J., 92(11), 3817-3829.
50. Karplus, M.; Petsko, G. A. (1990) Nature, 347, 631-639.
51. Chandler, D. Introduction to modern statistical mechanics. Oxford University Press (1987).
52. Hanggi, P.; Talkner, P.; Borkovec, M. (1990) Rev. Mod. Phys., 62, 251-341.
53. Chandler, D. Computer simulations of rare events and the dynamics of classical and quantum condensed matter systems, Lecture 3. Proceedings of the Enrico Fermi Summer School (1997).
54. Carter, E. A.; Ciccotti, G.; Hynes, J. T.; Kapral, R. (1989) Chem. Phys. Lett., 156(5), 472-477.
55. Torrie, G. M.; Valleau, J. P. (1977) J. Chem. Phys., 23, 187-199.
56. Kumar, S.; Rosenberg, J. M.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A. (1995) J. Comp. Chem.; 16(11), 1339-1350.
57. Roux, B. (1995) Comput. Phys. Comm., 91, 275-282.
58. Babin, V.; Roland, C.; Darden, T.A.; Sagui, C. (2006) J. Chem. Phys., 125, 204909.
59. Hummer, G.; Szabo, A. (2001) Proc. Natl. Acad. Sci. USA, 98, 3658-3661.
60. Park, S.; Schulten, K. (2004) J. Chem. Phys., 120, 5946- 5948.
61. Kostzin, I.; Barz, B.; Janosi, L. (2006) J. Chem. Phys., 124, 064106.
62. Jarzynsky, C. (1997) Phys. Rev. Lett., 78, 2690-2693.
63. Darve, E.; Pohorille, A. (2001) J. Chem. Phys., 115(20), 9169-9183.
64. Dellago, C.; Bolhuis, P. G.; Csajka, F. S.; Chandler, D. (1998) J. Chem. Phys., 108(5), 1964-1977.
65. Laio, A.; Parrinello, M. (2002) Proc. Natl. Acad. Sci. USA, 99, 12562-12566.
66. Laio, A.; Rodriguez-Fortea, A.; Gervasio, F. L.; Ceccarelli, M.; Parrinello, M. (2005) J. Phys. Chem. B., 109, 6714-6721.
67. Ensing, B.; De Vivo, M.; Liu, Z.; Moore, P.; Klein, M.L. (2006) Acc. Chem. Res., 39(2), 73-81.
68. Gervasio, F.L.; Laio, A.; Parrinello, M. (2005) J. Am. Chem. Soc., 127, 2600-2607.
69. Branduardi, D.; Gervasio, F.L.; Cavalli, A.M. (2005) J. Am. Chem. Soc., 127, 9147-9155.
70. Barducci, A.; Chelli, R.; Procacci, P.V.; Schettino, F.L. (2006) J. Am. Chem. Soc., 128, 2705-2710.
71. Ceccarelli, M.; Anedda, R.; Casu, M.; Ruggerone, P. (2008) Proteins, 71, 1231-1236.
72. Robertson, K. M.; D. P. (2002) FEBS Lett., 528, 53-57.
73. Phale, P. S.; Philippsen, A.C.; Widmer, V. P.; Phale, J. P. (2001) Biochemistry, 40, 6319-6325.
74. Bredin, J.; Saint, N.; Malléa, M.; Dé, E.; Molle, G.; Pagès, J.-M.; Simonet, V. (2002) Biochem. J., 363, 521-528.
75. Tong, J.; McIntosh, T. J. (2004) Biophys. J., 86, 3759-3771.
76. Lins, R. D.; Straatsma, T. P. (2001) Aeruginosa Biophys. J., 81, 1037-1046.
77. Baslé, A.; Rummel, G.; Storici, P.; Rosenbusch, J. P.; Schirmer, T (2006) J. Mol. Biol., 362, 933-942.
78. Duret, G.; Delcour, A. H. (2006) J. Biol. Chem., 281, 19899-19905.
79. Simonet, V. C.; Baslé, A.; Klose, K. E.; Delcour A. H. (2003) J. Biol. Chem., 278, 17539-17545.
80. Hu, W. S.; Li, P.-C.; Cheng, C.-Y. (2005) Antimicrob. Agents Chemother., 49, 3955-3958.