New Bacterial Targets and Computational Methods Against Bacterial Resistance

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Tarek M. Mahfouz Michael J. Young


The increasing number of resistant strains of pathogenic bacteria results in a growing number of infections becoming harder to treat. The over and misuse of antibiotics have caused the emergence and spread of multidrug resistant “superbugs” by selecting against sensitive organisms. An example that highlights the problem of multidrug resistant bacteria is the recent report by ABC news of a Nevada woman who died following septic shock caused by the bacteria K. pneumonaiae1. This bacterium was among the carbapenem-resistant Enterobacteriaceae (CRE) and was resistant to all available antibiotics in the U.S. In 2013, the CDC characterized CRE infections as an urgent threat, meaning the bacteria are an "immediate public health threat that requires urgent and aggressive action." Exacerbating the problem of drug resistance is the scaling down of funding allocated to new antibacterial development by the pharmaceutical industry due to increased cost and low return on investment compared to other groups of medications that are used for life such as cholesterol lowering medications. However, despite the growth of multidrug resistant bacteria and scaling down of funding towards it, there is still hope. The cost of developing new antibiotics can be reduced by focusing on the well validated bacterial targets and by utilizing the available computational resources to efficiently maximize the number of successful leads that make it to the market as new antibiotics. The focus in this article is on simple and cost efficient strategies to develop novel antibiotics or to revive old ones. To assist in this effort, presented in this article is a review of computational techniques and strategies that can be employed to develop safe and effective novel antibacterial therapies. This is followed by a review of resistance mechanisms in bacteria and validated bacterial targets amenable for drug design.

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MAHFOUZ, Tarek M.; YOUNG, Michael J.. New Bacterial Targets and Computational Methods Against Bacterial Resistance. Medical Research Archives, [S.l.], v. 5, n. 4, apr. 2017. ISSN 2375-1924. Available at: <>. Date accessed: 17 apr. 2024.
Antibacterial resistance, Antibacterial, Bacterial Resistance, Antibacterial Design
Review Articles


1. Bush, K.; Courvalin, P.; Dantas, G.; Davies, J.; Eisenstein, B.; Huovinen, P.; Jacoby, G. A.; Kishony, R.; Kreiswirth, B. N.; Kutter, E.; Lerner, S. A.; Levy, S.; Lewis, K.; Lomovskaya, O.; Miller, J. H.; Mobashery, S.; Piddock, L. J. V.; Projan, S.; Thomas, C. M.; Tomasz, A.; Tulkens, P. M.; Walsh, T. R.; Watson, J. D.; Witkowski, J.; Witte, W.; Wright, G.; Yeh, P.; Zgurskaya, H. I. Tackling antibiotic resistance. Nat. Rev. Microbiol. 2011, 9, 894-896.

2. Roca, I.; Akova, M.; Baquero, F.; Carlet, J.; Cavaleri, M.; Coenen, S.; Cohen, J.; Findlay, D.; Gyssens, I.; Heure, O. E.; Kahlmeter, G.; Kruse, H.; Laxminarayan, R.; Liébana, E.; López-Cerero, L.; MacGowan, A.; Martins, M.; Rodríguez-Baño, J.; Rolain, J. -.; Segovia, C.; Sigauque, B.; Tacconelli, E.; Wellington, E.; Vila, J. The global threat of antimicrobial resistance: science for intervention. New Microbe. and New Infect. 2015, 6, 22-29.

3. Holmes, A. H.; Moore, L. S. P.; Sundsfjord, A.; Steinbakk, M.; Regmi, S.; Karkey, A.; Guerin, P. J.; Piddock, L. J. V. Understanding the mechanisms and drivers of antimicrobial resistance. Lancet 2016, 387, 176-187.

4. Savage, V. J.; Chopra, I.; O'Neill, A. J. Staphylococcus aureus Biofilms Promote Horizontal Transfer of Antibiotic Resistance. Antimicrob. Agents Chemother. 2013, 57, 1968-1970.

5. National strategy for combating antibiotic-resistant bacteria. Accessed 20 September 2016. Centers for Disease Control and Prevention 2014, 1-37.

6. Anderson, A. C. The process of structure-based drug design. Chem. Biol. 2003, 10, 787-797.

7. Zoete, V.; Grosdidier, A.; Michielin, O. Docking, virtual high throughput screening and in silico fragment-based drug design. J. Cell. Mol. Med. 2009, 13, 238-248.

8. Sperandio, O.; Miteva, M. A.; Delfaud, F.; Villoutreix, B. O. Receptor-based computational screening of compound databases: the main docking-scoring engines. Curr. Protein Pept. Sci. 2006, 7, 369-393.

9. Leach, A. R.; Shoichet, B. K.; Peishoff, C. E. Prediction of protein−ligand interactions. docking and scoring:  successes and gaps. J. Med. Chem. 2006, 49, 5851-5855.

10. Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 1998, 19, 1639-1662.

11. The Scripps Research Institute. Autodock [online]. Available from URL: [Accessed 2010 Mar 24].

12. Morris, G. M.; Huey, R.; Lindstrom, W.; Sanner, M. F.; Belew, R. K.; Goodsell, D. S.; Olson, A. J. AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility. J Comput Chem 2009, 30, 2785-2791.

13. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank. Nucleic Acids Res. 2000, 28, 235-242.

14. The Research Collaboratory for Structural Bioinformatics. Protein Data Bank [online]. Available from URL: [Accessed 2010 Mar 24].

15. Irwin, J. J.; Shoichet, B. K. ZINC - A free database of commercially available compounds for virtual screening. J. Chem. Inf. Model. 2005, 45, 177-182.

16. The Bioinformatics and Chemical Informatics Research Center (BCIRC). ZINC database [online]. Available from URL: [Accessed 2010 Mar 24].

17. Villoutreix, B. O.; Renault, N.; Lagorce, D.; Sperandio, O.; Montes, M.; Miteva, M. A. Free resources to assist structure-based virtual ligand screening experiments. Curr. Protein Pept. Sci. 2007, 8, 381-411.

18. Cavasotto, C. N.; Phatak, S. S. Homology modeling in drug discovery: current trends and applications. Drug Discov. Today 2009, 14, 676-683.

19. Hillisch, A.; Pineda, L. F.; Hilgenfeld, R. Utility of homology models in the drug discovery process. Drug Discovery Today 2004, 9, 659-669.

20. Consortium, T. U. UniProt: a hub for protein information. Nucl. Acids Res. 2015, 43, D212.

21. Arnold, K.; Bordoli, L.; Kopp, J.; Schwede, T. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 2006, 22, 195-201.

22. Swiss Institute of Bioinformatics (SIB). Available from URL: [Accessed 2010 Mar 24].

23. Sali, A.; Blundell, T. L. Comparative Protein Modelling by Satisfaction of Spatial Restraints. J. Mol. Biol. 1993, 234, 779-815.

24. MODELLER [online]. Available from URL: [Accessed 2016 Oct 14].

25. Schrodinger LLC. PRIME, version 1.5. 2005.

26. Acharya, C.; Coop, A.; Polli, J. E.; MacKerell, A. D. Recent advances in ligand-based drug design: relevance and utility of the conformationally sampled pharmacophore approach. Curr. Comput. Aided Drug Des. 2011, 7, 10-22.

27. Selick, H. E.; Beresford, A. P.; Tarbit, M. H. The emerging importance of predictive ADME simulation in drug discovery. Drug Discov. Today 2002, 7, 109-116.

28. Schrodinger LLC. QIKPROP, version 3.1 and user manual. 2008.

29. Valerio, L. G. J. In silico toxicology for the pharmaceutical sciences. Toxicol. Appl. Pharmacol. 2009, 241, 356-370.

30. Lagorce, D.; Sperandio, O.; Baell, J. B.; Miteva, M. A.; Villoutreix, B. O. FAF-Drugs3: a web server for compound property calculation and chemical library design. Nucl. Acids Res. 2015, 43, W207.

31. FAF-Drugs3 [online]. Available from URL: [Accessed 2016 Oct 14].

32. Lee, N.; Yuen, K.; Kumana, C. R. Clinical role of β-lactam/β-lactamase inhibitor combinations. Drugs 2012, 63, 1511-1524.

33. Sun, F.; Qu, F.; Ling, Y.; Mao, P.; Xia, P.; Chen, H.; Zhou, D. Biofilm-associated infections: antibiotic resistance and novel therapeutic strategies. Future Microbiol. 2013, 8, 877-886.

34. Donlan, R. M.; Costerton, J. W. Biofilms: survival mechanisms of clinically relevant microorganisms. Clin. Microbiol. Rev. 2002, 15, 167-193.

35. Lewis, K. Multidrug Tolerance of Biofilms and Persister Cells. In Bacterial Biofilms; Romeo, T., Ed.; Springer Berlin Heidelberg: 2008; pp 107-131.

36. Miller, M. B.; Bassler, B. L. Quorum sensing in bacteria. Annu. Rev. Microbiol. 2001, 55, 165-199.

37. Marquez, B. Bacterial efflux systems and efflux pumps inhibitors. Biochimie 2005, 87, 1137-1147.

38. Suci, P. A.; Mittelman, M. W.; Yu, F. P.; Geesey, G. G. Investigation of ciprofloxacin penetration into Pseudomonas aeruginosa biofilms. Antimicrob. Agents Chemother. 1994, 38, 2125-2133.

39. Souli, M.; Giamarellou, H. Effects of slime produced by clinical isolates of coagulase-negative staphylococci on activities of various antimicrobial agents. Antimicrob. Agents Chemother. 1998, 42, 939-941.

40. Gordon, C. A.; Hodges, N. A.; Marriott, C. Antibiotic interaction and diffusion through alginate and exopolysaccharide of cystic fibrosis-derived Pseudomonas aeruginosa. J. Antimicrob. Chemother. 1988, 22, 667-674.

41. Stewart, P. S. Theoretical aspects of antibiotic diffusion into microbial biofilms. Antimicrob. Agents Chemother. 1996, 40, 2517-2522.

42. Hatch, R. A.; Schiller, N. L. Alginate lyase promotes diffusion of aminoglycosides through the extracellular polysaccharide of mucoid Pseudomonas aeruginosa. Antimicrob. Agents Chemother. 1998, 42, 974-977.

43. McIntosh, M.; Stone, B. A.; Stanisich, V. A. Curdlan and other bacterial (1→3)-β-D-glucans. Appl. Microbiol. Biotechnol. 2005, 68, 163-173.

44. Walling, E.; Gindreau, E.; Lonvaud-Funel, A. A putative glucan synthase gene dps detected in exopolysaccharide-producing Pediococcus damnosus and Oenococcus oeni strains isolated from wine and cider. Int. J. Food Microbiol. 2005, 98, 53-62.

45. Qu, Y.; Daley, A. J.; Istivan, T. S.; Rouch, D. A.; Deighton, M. A. Densely adherent growth mode, rather than extracellular polymer substance matrix build-up ability, contributes to high resistance of Staphylococcus epidermidis biofilms to antibiotics. J. Antimicrob. Chemother. 2010, 65, 1405-1411.

46. Lewis, K. Programmed death in bacteria. Microbiol. Mol. Biol. Rev. 2000, 64, 503-514.

47. Spoering, A. L.; Lewis, K. Biofilms and planktonic cells of Pseudomonas aeruginosa have similar resistance to killing by antimicrobials. J. Bacteriol. 2001, 183, 6746-6751.

48. Van Melderen, L. Toxin–antitoxin systems: why so many, what for? Curr. Opin. Microbiol. 2010, 13, 781-785.

49. Fasani, R. A.; Savageau, M. A. Molecular mechanisms of multiple toxin–antitoxin systems are coordinated to govern the persister phenotype. PNAS 2013, 110, E2537.

50. Wen, Y.; Behiels, E.; Devreese, B. Toxin–antitoxin systems: their role in persistence, biofilm formation, and pathogenicity. Pathog. Dis. 2014, 70, 240-249.

51. Ramage, H. R.; Connolly, L. E.; Cox, J. S. Comprehensive functional analysis of Mycobacterium tuberculosis toxin-antitoxin systems: implications for pathogenesis, stress responses, and evolution. PLoS Genet. 2009, 5, e1000767.

52. Moyed, H. S.; Bertrand, K. P. hipA, a newly recognized gene of Escherichia coli K-12 that affects frequency of persistence after inhibition of murein synthesis. J. Bacteriol. 1983, 155, 768-775.

53. Correia, F. F.; D'Onofrio, A.; Rejtar, T.; Li, L.; Karger, B. L.; Makarova, K.; Koonin, E. V.; Lewis, K. Kinase activity of overexpressed HipA is required for growth arrest and multidrug tolerance in Escherichia coli. J. Bacteriol. 2006, 188, 8360-8367.

54. Kaspy, I.; Rotem, E.; Weiss, N.; Ronin, I.; Balaban, N. Q.; Glaser, G. HipA-mediated antibiotic persistence via phosphorylation of the glutamyl-tRNA-synthetase. Nat. Commun. 2013, 4, 3001.

55. Germain, E.; Castro-Roa, D.; Zenkin, N.; Gerdes, K. Molecular mechanism of bacterial persistence by HipA. Mol. Cell 2013, 52, 248-254.

56. Li, T.; Yin, N.; Liu, H.; Pei, J.; Lai, L. Novel inhibitors of toxin HipA reduce multidrug tolerant persisters. ACS Med. Chem. Lett. 2016, 7, 449-453.

57. Schumacher, M. A.; Piro, K. M.; Xu, W.; Hansen, S.; Lewis, K.; Brennan, R. G. Molecular mechanisms of HipA-mediated multidrug tolerance and its neutralization by HipB. Science 2009, 323, 396-401.

58. Schumacher, M. A.; Balani, P.; Min, J.; Chinnam, N. B.; Hansen, S.; Vulić, M.; Lewis, K.; Brennan, R. G. HipBA-promoter structures reveal the basis of heritable multidrug tolerance. Nature 2015, 524, 59-64.

59. Wen, Y.; Behiels, E.; Felix, J.; Elegheert, J.; Vergauwen, B.; Devreese, B.; Savvides, S. N. The bacterial antitoxin HipB establishes a ternary complex with operator DNA and phosphorylated toxin HipA to regulate bacterial persistence. Nucleic Acids Res. 2014, 42, 10134-10147.

60. Goeders, N.; Chai, R.; Chen, B.; Day, A.; Salmond, G. P. C. Structure, evolution, and functions of bacterial type III toxin-antitoxin systems. Toxins (Basel) 2016, 8, 282.

61. Fineran, P. C.; Blower, T. R.; Foulds, I. J.; Humphreys, D. P.; Lilley, K. S.; Salmond, G. P. C. The phage abortive infection system, ToxIN, functions as a protein-RNA toxin-antitoxin pair. Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 894-899.

62. Short, F. L.; Pei, X. Y.; Blower, T. R.; Ong, S.; Fineran, P. C.; Luisi, B. F.; Salmond, G. P. C. Selectivity and self-assembly in the control of a bacterial toxin by an antitoxic noncoding RNA pseudoknot. Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 241.

63. Maisonneuve, E.; Castro-Camargo, M.; Gerdes, K. (p)ppGpp controls bacterial persistence by stochastic induction of toxin-antitoxin activity. Cell 2013, 154, 1140-1150.

64. Botos, I.; Melnikov, E. E.; Cherry, S.; Tropea, J. E.; Khalatova, A. G.; Rasulova, F.; Dauter, Z.; Maurizi, M. R.; Rotanova, T. V.; Wlodawer, A.; Gustchina, A. The catalytic domain of Escherichia coli Lon protease has a unique fold and a Ser-Lys dyad in the active site. J. Biol. Chem. 2004, 279, 8140-8148.

65. Su, S.; Lin, C.; Tai, H.; Chang, M.; Ho, M.; Babu, C. S.; Liao, J.; Wu, S.; Chang, Y.; Lim, C.; Chang, C. Structural basis for the magnesium-dependent activation and hexamerization of the Lon AAA+ protease. Structure 2016, 24, 676-686.

66. Batten, L. E.; Parnell, A. E.; Wells, N. J.; Murch, A. L.; Oyston, P. C. F.; Roach, P. L. Biochemical and structural characterization of polyphosphate kinase 2 from the intracellular pathogen Francisella tularensis. Biosci. Rep. 2015, 36, e00294.

67. Mutschler, H.; Meinhart, A. ε/ζ systems: their role in resistance, virulence, and their potential for antibiotic development. J. Mol. Med. 2011, 89, 1183-1194.

68. Wanner, B. L. Phosphorus assimilation and its control of gene expression in Escherichia coli. In The Molecular Basis of Bacterial Metabolism; Hauska, P. D. G., Thauer, Professor Dr Rudolf K, Eds.; Springer Berlin Heidelberg: 1990; pp 152-163.

69. Li, Y.; Zhang, Y. PhoU Is a persistence switch involved in persister formation and tolerance to multiple antibiotics and stresses in Escherichia coli. Antimicrob. Agents Chemother. 2007, 51, 2092-2099.

70. Lee, S. J.; Park, Y. S.; Kim, S.; Lee, B.; Suh, S. W. Crystal structure of PhoU from Pseudomonas aeruginosa, a negative regulator of the Pho regulon. J. Struct. Biol. 2014, 188, 22-29.

71. Dwyer, D. J.; Belenky, P. A.; Yang, J. H.; MacDonald, I. C.; Martell, J. D.; Takahashi, N.; Chan, C. T. Y.; Lobritz, M. A.; Braff, D.; Schwarz, E. G.; Ye, J. D.; Pati, M.; Vercruysse, M.; Ralifo, P. S.; Allison, K. R.; Khalil, A. S.; Ting, A. Y.; Walker, G. C.; Collins, J. J. Antibiotics induce redox-related physiological alterations as part of their lethality. Proc. Natl. Acad. Sci. U. S. A. 2014, 111, 2100.

72. Courcelle, J.; Hanawalt, P. C. RecA-dependent recovery of arrested DNA replication forks. Annu. Rev. Genet. 2003, 37, 611-646.

73. Kohanski, M. A.; Dwyer, D. J.; Hayete, B.; Lawrence, C. A.; Collins, J. J. A common mechanism of cellular death induced by bactericidal antibiotics. Cell 2007, 130, 797-810.

74. Peterson, E. J. R.; Janzen, W. P.; Kireev, D.; Singleton, S. F. High-throughput screening for RecA inhibitors using a transcreener adenosine 5'-O-diphosphate assay. Assay Drug Dev. Technol. 2012, 10, 260-268.

75. Bernier, S. P.; Lebeaux, D.; DeFrancesco, A. S.; Valomon, A.; Soubigou, G.; Coppée, J.; Ghigo, J.; Beloin, C. Starvation, together with the SOS response, mediates high biofilm-specific tolerance to the fluoroquinolone ofloxacin. PLoS Genet. 2013, 9, 1-14.

76. Van Acker, H.; Sass, A.; Bazzini, S.; De Roy, K.; Udine, C.; Messiaen, T.; Riccardi, G.; Boon, N.; Nelis, H. J.; Mahenthiralingam, E.; Coenye, T. Biofilm-grown Burkholderia cepacia complex cells survive antibiotic treatment by avoiding production of reactive oxygen species. PLoS ONE 2013, 8, e58943.

77. Shinohara, T.; Ikawa, S.; Iwasaki, W.; Hiraki, T.; Hikima, T.; Mikawa, T.; Arai, N.; Kamiya, N.; Shibata, T. Loop L1 governs the DNA-binding specificity and order for RecA-catalyzed reactions in homologous recombination and DNA repair. Nucleic Acids Res. 2015, 43, 973-986.

78. Wigle, T. J.; Singleton, S. F. Directed molecular screening for RecA ATPase inhibitors. Bioorg. Med. Chem. Lett. 2007, 17, 3249-3253.

79. Wiseman, B.; Carpena, X.; Feliz, M.; Donald, L. J.; Pons, M.; Fita, I.; Loewen, P. C. Isonicotinic acid hydrazide conversion to isonicotinyl-NAD by catalase-peroxidases. J. Biol. Chem. 2010, 285, 26662-26673.

80. Jha, V.; Chelikani, P.; Carpena, X.; Fita, I.; Loewen, P. C. Influence of main channel structure on H(2)O(2) access to the heme cavity of catalase KatE of Escherichia coli. Arch. Biochem. Biophys. 2012, 526, 54-59.

81. Loewen, P. C.; Carpena, X.; Rovira, C.; Ivancich, A.; Perez-Luque, R.; Haas, R.; Odenbreit, S.; Nicholls, P.; Fita, I. Structure of Helicobacter pylori catalase, with and without formic acid bound, at 1.6 A resolution. Biochemistry 2004, 43, 3089-3103.

82. Whittaker, M. M.; Lerch, T. F.; Kirillova, O.; Chapman, M. S.; Whittaker, J. W. Subunit dissociation and metal binding by Escherichia coli apo-manganese superoxide dismutase. Arch. Biochem. Biophys. 2011, 505, 213-225.

83. Krauss, I. R.; Merlino, A.; Pica, A.; Rullo, R.; Bertoni, A.; Capasso, A.; Amato, M.; Riccitiello, F.; Vendittis, E. D.; Sica, F. Fine tuning of metal-specific activity in the Mn-like group of cambialistic superoxide dismutases. RSC Adv. 2015, 5, 87876-87887.

84. Zhang, Y.; Heym, B.; Allen, B.; Young, D.; Cole, S. The catalase-peroxidase gene and isoniazid resistance of Mycobacterium tuberculosis. Nature 1992, 358, 591-593.

85. Credito, K.; Lin, G.; Koeth, L.; Sturgess, M. A.; Appelbaum, P. C. Activity of levofloxacin alone and in combination with a DnaK inhibitor against Gram-negative rods, including levofloxacin-resistant strains. Antimicrob. Agents Chemother. 2009, 53, 814-817.

86. Leu, J. I.; Zhang, P.; Murphy, M. E.; Marmorstein, R.; George, D. L. Structural basis for the inhibition of HSP70 and DnaK chaperones by small-molecule targeting of a C-terminal allosteric pocket. ACS Chem. Biol. 2014, 9, 2508-2516.

87. Britton, K. L.; Abeysinghe, I. S.; Baker, P. J.; Barynin, V.; Diehl, P.; Langridge, S. J.; McFadden, B. A.; Sedelnikova, S. E.; Stillman, T. J.; Weeradechapon, K.; Rice, D. W. The structure and domain organization of Escherichia coli isocitrate lyase. Acta Crystallogr. D Biol. Crystallogr. 2001, 57, 1209-1218.

88. Ahmer, B. M. M. Cell-to-cell signalling in Escherichia coli and Salmonella enterica. Mol. Microbiol. 2004, 52, 933-945.

89. Kalia, V. C. Quorum sensing inhibitors: an overview. Biotechnol. Adv. 2013, 31, 224-245.

90. O’Loughlin, C. T.; Miller, L. C.; Siryaporn, A.; Drescher, K.; Semmelhack, M. F.; Bassler, B. L. A quorum-sensing inhibitor blocks Pseudomonas aeruginosa virulence and biofilm formation. PNAS 2013, 110, 17981-17986.

91. Norizan, S. N. M.; Yin, W.; Chan, K. Caffeine as a potential quorum sensing inhibitor. Sensors 2013, 13, 5117-5129.

92. Castang, S.; Chantegrel, B.; Deshayes, C.; Dolmazon, R.; Gouet, P.; Haser, R.; Reverchon, S.; Nasser, W.; Hugouvieux-Cotte-Pattat, N.; Doutheau, A. N-sulfonyl homoserine lactones as antagonists of bacterial quorum sensing. Bioorg. Med. Chem. Lett. 2004, 14, 5145-5149.

93. Frezza, M.; Castang, S.; Estephane, J.; Soulère, L.; Deshayes, C.; Chantegrel, B.; Nasser, W.; Queneau, Y.; Reverchon, S.; Doutheau, A. Synthesis and biological evaluation of homoserine lactone derived ureas as antagonists of bacterial quorum sensing. Bioorg. Med. Chem. 2006, 14, 4781-4791.

94. Morohoshi, T.; Shiono, T.; Takidouchi, K.; Kato, M.; Kato, N.; Kato, J.; Ikeda, T. Inhibition of quorum sensing in Serratia marcescens AS-1 by synthetic analogs of N-acylhomoserine lactone. Appl. Environ. Microbiol. 2007, 73, 6339-6344.

95. Lewis, H. A.; Furlong, E. B.; Laubert, B.; Eroshkina, G. A.; Batiyenko, Y.; Adams, J. M.; Bergseid, M. G.; Marsh, C. D.; Peat, T. S.; Sanderson, W. E.; Sauder, J. M.; Buchanan, S. G. A structural genomics approach to the study of quorum sensing: crystal structures of three LuxS orthologs. Structure 2001, 9, 527-537.

96. Chen, X.; Schauder, S.; Potier, N.; Van Dorsselaer, A.; Pelczer, I.; Bassler, B. L.; Hughson, F. M. Structural identification of a bacterial quorum-sensing signal containing boron. Nature 2002, 415, 545-549.

97. Miller, S. T.; Xavier, K. B.; Campagna, S. R.; Taga, M. E.; Semmelhack, M. F.; Bassler, B. L.; Hughson, F. M. Salmonella typhimurium recognizes a chemically distinct form of the bacterial quorum-sensing signal AI-2. Mol. Cell 2004, 15, 677-687.

98. Pereira, C. S.; McAuley, J. R.; Taga, M. E.; Xavier, K. B.; Miller, S. T. Sinorhizobium meliloti, a bacterium lacking the autoinducer-2 synthase, responds to AI-2 supplied by other bacteria. Mol. Microbiol. 2008, 70, 1223-1235.

99. Koch, B.; Liljefors, T.; Persson, T.; Nielsen, J.; Kjelleberg, S.; Givskov, M. The LuxR receptor: the sites of interaction with quorum-sensing signals and inhibitors. Microbiology 2005, 151, 3589-3602.

100. Kvist, M.; Hancock, V.; Klemm, P. Inactivation of efflux pumps abolishes bacterial biofilm formation. Appl. Environ. Microbiol. 2008, 74, 7376-7382.

101. Baugh, S.; Ekanayaka, A. S.; Piddock, L. J. V.; Webber, M. A. Loss of or inhibition of all multidrug resistance efflux pumps of Salmonella enterica serovar Typhimurium results in impaired ability to form a biofilm. J. Antimicrob. Chemother. 2012, 67, 2409-2417.

102. Baugh, S.; Phillips, C. R.; Ekanayaka, A. S.; Piddock, L. J. V.; Webber, M. A. Inhibition of multidrug efflux as a strategy to prevent biofilm formation. J. Antimicrob. Chemother. 2014, 69, 673-681.

103. Imuta, N.; Nishi, J.; Tokuda, K.; Fujiyama, R.; Manago, K.; Iwashita, M.; Sarantuya, J.; Kawano, Y. The Escherichia coli efflux pump TolC promotes aggregation of enteroaggregative E. coli 042. Infect. Immun. 2008, 76, 1247-1256.

104. Putman, M.; Veen, H. W. v.; Konings, W. N. Molecular properties of bacterial multidrug transporters. Microbiol. Mol. Biol. Rev. 2000, 64, 672-693.

105. Handzlik, J.; Matys, A.; Kieć-Kononowicz, K. Recent advances in multi-drug resistance (MDR) efflux pump inhibitors of Gram-positive bacteria S. aureus. Antibiotics 2013, 2, 28-45.

106. Thaker, M.; Spanogiannopoulos, P.; Wright, G. D. The tetracycline resistome. Cell. Mol. Life Sci. 2009, 67, 419-431.

107. Sun, J.; Deng, Z.; Yan, A. Bacterial multidrug efflux pumps: mechanisms, physiology and pharmacological exploitations. Biochem. Biophys. Res. Commun. 2014, 453, 254-267.

108. Van Bambeke, F.; Pagès, J.; Lee, V. J. Inhibitors of bacterial efflux pumps as adjuvants in antibiotic treatments and diagnostic tools for detection of resistance by efflux. Recent Pat Antiinfect Drug Discov 2006, 1, 157-175.

109. Eicher, T.; Seeger, M. A.; Anselmi, C.; Zhou, W.; Brandstätter, L.; Verrey, F.; Diederichs, K.; Faraldo-Gómez, J. D.; Pos, K. M. Coupling of remote alternating-access transport mechanisms for protons and substrates in the multidrug efflux pump AcrB. Elife 2014, 3, 03145.

110. Sjuts, H.; Vargiu, A. V.; Kwasny, S. M.; Nguyen, S. T.; Kim, H.; Ding, X.; Ornik, A. R.; Ruggerone, P.; Bowlin, T. L.; Nikaido, H.; Pos, K. M.; Opperman, T. J. Molecular basis for inhibition of AcrB multidrug efflux pump by novel and powerful pyranopyridine derivatives. PNAS 2016, 113, 3509-3514.

111. Ababou, A.; Koronakis, V. Structures of gate loop variants of the AcrB drug efflux pump bound by erythromycin substrate. PLoS One 2016, 11, e0159154.

112. Lei, H.; Chou, T.; Su, C.; Bolla, J. R.; Kumar, N.; Radhakrishnan, A.; Long, F.; Delmar, J. A.; Do, S. V.; Rajashankar, K. R.; Shafer, W. M.; Yu, E. W. Crystal structure of the open state of the Neisseria gonorrhoeae MtrE outer membrane channel. PLoS One 2014, 9, e97475.

113. Hinchliffe, P.; Greene, N. P.; Paterson, N. G.; Crow, A.; Hughes, C.; Koronakis, V. Structure of the periplasmic adaptor protein from a major facilitator superfamily (MFS) multidrug efflux pump. FEBS Lett. 2014, 588, 3147-3153.

114. Bugg, T. D.; Wright, G. D.; Dutka-Malen, S.; Arthur, M.; Courvalin, P.; Walsh, C. T. Molecular basis for vancomycin resistance in Enterococcus faecium BM4147: biosynthesis of a depsipeptide peptidoglycan precursor by vancomycin resistance proteins VanH and VanA. Biochemistry 1991, 30, 10408-10415.

115. Handwerger, S.; Pucci, M. J.; Volk, K. J.; Liu, J.; Lee, M. S. The cytoplasmic peptidoglycan precursor of vancomycin-resistant Enterococcus faecalis terminates in lactate. J. Bacteriol. 1992, 174, 5982-5984.

116. Bugg, T. D.; Dutka-Malen, S.; Arthur, M.; Courvalin, P.; Walsh, C. T. Identification of vancomycin resistance protein VanA as a D-alanine:D-alanine ligase of altered substrate specificity. Biochemistry 1991, 30, 2017-2021.

117. Arthur, M.; Molinas, C.; Dutka-Malen, S.; Courvalin, P. Structural relationship between the vancomycin resistance protein VanH and 2-hydroxycarboxylic acid dehydrogenases. Gene 1991, 103, 133-134.

118. Reynolds, P. E.; Depardieu, F.; Dutka-Malen, S.; Arthur, M.; Courvalin, P. Glycopeptide resistance mediated by enterococcal transposon Tn1546 requires production of VanX for hydrolysis of D-alanyl-D-alanine. Mol. Microbiol. 1994, 13, 1065-1070.

119. Arthur, M.; Depardieu, F.; Gerbaud, G.; Galimand, M.; Leclercq, R.; Courvalin, P. The VanS sensor negatively controls VanR-mediated transcriptional activation of glycopeptide resistance genes of Tn1546 and related elements in the absence of induction. J. Bacteriol. 1997, 179, 97-106.

120. Evers, S.; Sahm, D. F.; Courvalin, P. The vanB gene of vancomycin-resistant Enterococcus faecalis V583 is structurally related to genes encoding D-Ala:D-Ala ligases and glycopeptide-resistance proteins VanA and VanC. Gene 1993, 124, 143-144.

121. Fines, M.; Perichon, B.; Reynolds, P.; Sahm, D. F.; Courvalin, P. VanE, a new type of acquired glycopeptide resistance in Enterococcus faecalis BM4405. Antimicrob. Agents Chemother. 1999, 43, 2161-2164.

122. Evers, S.; Reynolds, P. E.; Courvalin, P. Sequence of the vanB and ddl genes encoding d-alanine:d-lactate and d-alanine:d-alanine ligases in vancomycin-resistant Enterococcus faecalis V583. Gene 1994, 140, 97-102.

123. Meziane-Cherif, D.; Saul, F. A.; Moubareck, C.; Weber, P.; Haouz, A.; Courvalin, P.; Périchon, B. Molecular basis of vancomycin dependence in VanA-type Staphylococcus aureus VRSA-9. J. Bacteriol. 2010, 192, 5465-5471.

124. Roper, D. I.; Huyton, T.; Vagin, A.; Dodson, G. The molecular basis of vancomycin resistance in clinically relevant enterococci: crystal structure of d-alanyl-d-lactate ligase (VanA). PNAS 2000, 97, 8921-8925.

125. Kuzin, A. P.; Sun, T.; Jorczak-Baillass, J.; Healy, V. L.; Walsh, C. T.; Knox, J. R. Enzymes of vancomycin resistance: the structure of D-alanine-D-lactate ligase of naturally resistant Leuconostoc mesenteroides. Structure 2000, 8, 463-470.

126. Fan, C.; Moews, P. C.; Walsh, C. T.; Knox, J. R. Vancomycin resistance: structure of D-alanine:D-alanine ligase at 2.3 A resolution. Science 1994, 266, 439-443.

127. Meziane-Cherif, D.; Saul, F. A.; Haouz, A.; Courvalin, P. Structural and functional characterization of VanG D-Ala:D-Ser ligase associated with vancomycin resistance in Enterococcus faecalis. J. Biol. Chem. 2012, 287, 37583-37592.

128. Bussiere, D. E.; Pratt, S. D.; Katz, L.; Severin, J. M.; Holzman, T.; Park, C. H. The structure of VanX reveals a novel amino-dipeptidase involved in mediating transposon-based vancomycin resistance. Mol. Cell 1998, 2, 75-84.

129. Meziane-Cherif, D.; Stogios, P. J.; Evdokimova, E.; Savchenko, A.; Courvalin, P. Structural basis for the evolution of vancomycin resistance D,D-peptidases. PNAS 2014, 111, 5872-5877.

130. Ellsworth, B. A.; Tom, N. J.; Bartlett, P. A. Synthesis and evaluation of inhibitors of bacterial D-alanine: D-alanine ligases. Chem. Biol. 1996, 3, 37-44.

131. Yang, K.; Brandt, J. J.; Chatwood, L. L.; Crowder, M. W. Phosphonamidate and phosphothioate dipeptides as potential inhibitors of VanX. Bioorg. Med. Chem. Lett. 2000, 10, 1085-1087.

132. Jia, C.; Yang, K.; Liu, C.; Feng, L.; Xiao, J.; Zhou, L.; Zhang, Y. Synthesis, characterization and activity of new phosphonate dipeptides as potential inhibitors of VanX. Bioorg. Med. Chem. Lett. 2012, 22, 482-484.

133. Sauvage, E.; Kerff, F.; Terrak, M.; Ayala, J. A.; Charlier, P. The penicillin-binding proteins: structure and role in peptidoglycan biosynthesis. FEMS Microbiol. Rev. 2008, 32, 234-258.

134. Fuda, C.; Suvorov, M.; Vakulenko, S. B.; Mobashery, S. The basis for resistance to beta-lactam antibiotics by penicillin-binding protein 2a of methicillin-resistant Staphylococcus aureus. J. Biol. Chem. 2004, 279, 40802-40806.

135. Lim, D.; Strynadka, N. C. J. Structural basis for the beta lactam resistance of PBP2a from methicillin-resistant Staphylococcus aureus. Nat. Struct. Biol. 2002, 9, 870-876.

136. Powell, A. J.; Tomberg, J.; Deacon, A. M.; Nicholas, R. A.; Davies, C. Crystal structures of penicillin-binding protein 2 from penicillin-susceptible and -resistant strains of Neisseria gonorrhoeae reveal an unexpectedly subtle mechanism for antibiotic resistance. J. Biol. Chem. 2009, 284, 1202-1212.

137. Sainsbury, S.; Bird, L.; Rao, V.; Shepherd, S. M.; Stuart, D. I.; Hunter, W. N.; Owens, R. J.; Ren, J. Crystal structures of penicillin-binding protein 3 from Pseudomonas aeruginosa: comparison of native and antibiotic-bound forms. J. Mol. Biol. 2011, 405, 173-184.

138. Contreras-Martel, C.; Job, V.; Di Guilmi, A. M.; Vernet, T.; Dideberg, O.; Dessen, A. Crystal structure of penicillin-binding protein 1a (PBP1a) reveals a mutational hotspot implicated in β-lactam resistance in Streptococcus pneumoniae. J. Mol. Biol. 2006, 355, 684-696.

139. Contreras-Martel, C.; Dahout-Gonzalez, C.; Martins, A. D. S.; Kotnik, M.; Dessen, A. PBP active site flexibility as the key mechanism for β-lactam resistance in pneumococci. J. Mol. Biol. 2009, 387, 899-909.

140. Pernot, L.; Chesnel, L.; Gouellec, A. L.; Croizé, J.; Vernet, T.; Dideberg, O.; Dessen, A. A PBP2x from a clinical isolate of Streptococcus pneumoniae exhibits an alternative mechanism for reduction of susceptibility to β-lactam antibiotics. J. Biol. Chem. 2004, 279, 16463-16470.

141. Hooper, D. C. Mechanisms of action of antimicrobials: focus on fluoroquinolones. Clin. Infect. Dis. 2001, 32 Suppl 1, S15.

142. Willmott, C. J.; Maxwell, A. A single point mutation in the DNA gyrase A protein greatly reduces binding of fluoroquinolones to the gyrase-DNA complex. Antimicrob. Agents Chemother. 1993, 37, 126-127.

143. Blondeau, J. M. Fluoroquinolones: mechanism of action, classification, and development of resistance. Surv. Ophthalmol. 2004, 49 Suppl 2, S78.

144. Hearnshaw, S. J.; Edwards, M. J.; Stevenson, C. E.; Lawson, D. M.; Maxwell, A. A new crystal structure of the bifunctional antibiotic simocyclinone D8 bound to DNA gyrase gives fresh insight into the mechanism of inhibition. J. Mol. Biol. 2014, 426, 2023-2033.

145. Miles, T. J.; Hennessy, A. J.; Bax, B.; Brooks, G.; Brown, B. S.; Brown, P.; Cailleau, N.; Chen, D.; Dabbs, S.; Davies, D. T.; Esken, J. M.; Giordano, I.; Hoover, J. L.; Jones, G. E.; Kusalakumari Sukmar, S. K.; Markwell, R. E.; Minthorn, E. A.; Rittenhouse, S.; Gwynn, M. N.; Pearson, N. D. Novel tricyclics (e.g., GSK945237) as potent inhibitors of bacterial type IIA topoisomerases. Bioorg. Med. Chem. Lett. 2016, 26, 2464-2469.

146. Mariam, D. H.; Mengistu, Y.; Hoffner, S. E.; Andersson, D. I. Effect of rpoB mutations conferring rifampin resistance on fitness of Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 2004, 48, 1289-1294.

147. Molodtsov, V.; Nawarathne, I. N.; Scharf, N. T.; Kirchhoff, P. D.; Showalter, H. D. H.; Garcia, G. A.; Murakami, K. S. X-ray crystal structures of the Escherichia coli RNA polymerase in complex with benzoxazinorifamycins. J. Med. Chem. 2013, 56, 4758-4763.

148. Lambert, P. A. Bacterial resistance to antibiotics: modified target sites. Adv. Drug Deliv. Rev. 2005, 57, 1471-1485.

149. Hansen, J. L.; Ippolito, J. A.; Ban, N.; Nissen, P.; Moore, P. B.; Steitz, T. A. The structures of four macrolide antibiotics bound to the large ribosomal subunit. Mol. Cell 2002, 10, 117-128.

150. Hansen, J. L.; Moore, P. B.; Steitz, T. A. Structures of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit. J. Mol. Biol. 2003, 330, 1061-1075.

151. Tu, D.; Blaha, G.; Moore, P. B.; Steitz, T. A. Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance. Cell 2005, 121, 257-270.

152. Borovinskaya, M. A.; Pai, R. D.; Zhang, W.; Schuwirth, B. S.; Holton, J. M.; Hirokawa, G.; Kaji, H.; Kaji, A.; Cate, J. H. D. Structural basis for aminoglycoside inhibition of bacterial ribosome recycling. Nat. Struct. Mol. Biol. 2007, 14, 727-732.

153. Basso, L. A.; Zheng, R.; Musser, J. M.; Jacobs, W. R.; Blanchard, J. S. Mechanisms of isoniazid resistance in Mycobacterium tuberculosis: enzymatic characterization of enoyl reductase mutants identified in isoniazid-resistant clinical isolates. J. Infect. Dis. 1998, 178, 769-775.

154. Mestdagh, M.; Fonteyne, P. A.; Realini, L.; Rossau, R.; Jannes, G.; Mijs, W.; De Smet, K. A.; Portaels, F.; Van den Eeckhout, E. Relationship between pyrazinamide resistance, loss of pyrazinamidase activity, and mutations in the pncA locus in multidrug-resistant clinical isolates of Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 1999, 43, 2317-2319.

155. Bertrand, T.; Eady, N. A. J.; Jones, J. N.; Jesmin, n.; Nagy, J. M.; Jamart-Grégoire, B.; Raven, E. L.; Brown, K. A. Crystal structure of Mycobacterium tuberculosis catalase-peroxidase. J. Biol. Chem. 2004, 279, 38991-38999.

156. Zhao, X.; Hersleth, H.; Zhu, J.; Andersson, K. K.; Magliozzo, R. S. Access channel residues Ser315 and Asp137 in Mycobacterium tuberculosis catalase-peroxidase (KatG) control peroxidatic activation of the pro-drug isoniazid. Chem. Commun. (Camb. ) 2013, 49, 11650-11652.

157. Petrella, S.; Gelus-Ziental, N.; Maudry, A.; Laurans, C.; Boudjelloul, R.; Sougakoff, W. Crystal structure of the pyrazinamidase of Mycobacterium tuberculosis: insights into natural and acquired resistance to pyrazinamide. PLoS ONE 2011, 6, e15785.

158. Connell, S. R.; Tracz, D. M.; Nierhaus, K. H.; Taylor, D. E. Ribosomal protection proteins and their mechanism of tetracycline resistance. Antimicrob. Agents Chemother. 2003, 47, 3675-3681.

159. Anokhina, M. M.; Barta, A.; Nierhaus, K. H.; Spiridonova, V. A.; Kopylov, A. M. Mapping of the second tetracycline binding site on the ribosomal small subunit of E.coli. Nucleic Acids Res. 2004, 32, 2594-2597.

160. Trieber, C. A.; Burkhardt, N.; Nierhaus, K. H.; Taylor, D. E. Ribosomal protection from tetracycline mediated by Tet(O): Tet(O) interaction with ribosomes is GTP-dependent. Biol. Chem. 1998, 379, 847-855.

161. Brodersen, D. E.; Clemons Jr., W. M.; Carter, A. P.; Morgan-Warren, R. J.; Wimberly, B. T.; Ramakrishnan, V. The structural basis for the action of the antibiotics tetracycline, pactamycin, and hygromycin B on the 30S ribosomal subunit. Cell 2000, 103, 1143-1154.

162. Li, W.; Atkinson, G. C.; Thakor, N. S.; Allas, Ü; Lu, C.; Chan, K.; Tenson, T.; Schulten, K.; Wilson, K. S.; Hauryliuk, V.; Frank, J. Mechanism of tetracycline resistance by ribosomal protection protein Tet(O). Nat. Commun. 2013, 4, 1477-1485.

163. Wright, G. D. Bacterial resistance to antibiotics: enzymatic degradation and modification. Adv. Drug Deliv. Rev. 2005, 57, 1451-1470.

164. Birnbaum, J.; Kahan, F. M.; Kropp, H.; MacDonald, J. S. Carbapenems, a new class of beta-lactam antibiotics. Discovery and development of imipenem/cilastatin. Am. J. Med. 1985, 78, 3-21.

165. Pozzi, C.; De Luca, F.; Benvenuti, M.; Poirel, L.; Nordmann, P.; Rossolini, G. M.; Mangani, S.; Docquier, J. Crystal structure of the Pseudomonas aeruginosa BEL-1 extended-spectrum β-lactamase and its complex with moxalactam and imipenem. Antimicrob. Agents Chemother. 2016, 60, 7189-7199.

166. Schwarz, S.; Kehrenberg, C.; Doublet, B.; Cloeckaert, A. Molecular basis of bacterial resistance to chloramphenicol and florfenicol. FEMS Microbiology Reviews 2004, 28, 519-542.

167. Ramirez, M. S.; Tolmasky, M. E. Aminoglycoside modifying enzymes. Drug Resist. Updat. 2010, 13, 151-171.

168. Biswas, T.; Houghton, J. L.; Garneau-Tsodikova, S.; Tsodikov, O. V. The structural basis for substrate versatility of chloramphenicol acetyltransferase CATI. Protein Sci. 2012, 21, 520-530.

169. Vetting, M. W.; Park, C. H.; Hegde, S. S.; Jacoby, G. A.; Hooper, D. C.; Blanchard, J. S. Mechanistic and structural analysis of aminoglycoside N-acetyltransferase AAC(6')-Ib and its bifunctional, fluoroquinolone-active AAC(6')-Ib-cr variant. Biochemistry 2008, 47, 9825-9835.

170. Andersson, D. I. Improving predictions of the risk of resistance development against new and old antibiotics. Clin. Microbiol. Infect. 2015, 21, 894-898.