Characterization and prediction of the mechanism of action of antibiotics through NMR metabolomics

BMC Microbiology

Volumn 16, Issue 1, 2016, Pages

  Hoerr, Verena ^a   Duggan, Gavin E ^b   Zbytnuik, Lori ^b   Poon, Karen K H ^b   Große, Christina ^a,c   Neugebauer, Ute ^a,c   Methling, Karen ^d   Löffler, Bettina ^a   Vogel, Hans J ^b  

^a JENA UNIVERSITY HOSPITAL   (Germany)

^b UNIVERSITY OF CALGARY   (Canada)

^c LEIBNIZ INSTITUTE OF PHOTONIC TECHNOLOGY   (Germany)

^d UNIVERSITY OF GREIFSWALD   (Germany)

Author keywords

1H NMR spectroscopy; Extracellular footprinting; Intracellular fingerprinting; Metabolomics; Mode of action of antibiotics; Multivariate data analysis; Prediction of antibiotic classes

Indexed keywords

AMINOGLYCOSIDE; AMPICILLIN; ANTIBIOTIC AGENT; BETA LACTAM ANTIBIOTIC; CARBENICILLIN; CEFALEXIN; CEPHALOSPORIN DERIVATIVE; CIPROFLOXACIN; DNA; DOXYCYCLINE; KANAMYCIN; OFLOXACIN; PENICILLIN DERIVATIVE; QUINOLINE DERIVED ANTIINFECTIVE AGENT; STREPTOMYCIN; TETRACYCLINE; TETRACYCLINE DERIVATIVE; ANTIINFECTIVE AGENT;

ARTICLE; BACTERICIDAL ACTIVITY; BACTERIOSTASIS; BACTERIUM CULTURE; CELL WALL; CONCENTRATION RESPONSE; CONTROLLED STUDY; DRUG DEVELOPMENT; DRUG MECHANISM; ESCHERICHIA COLI; METABOLISM; METABOLOME; METABOLOMICS; NONHUMAN; PREDICTION; PROTEIN SYNTHESIS; PROTON NUCLEAR MAGNETIC RESONANCE; CLASSIFICATION; DRUG EFFECTS; MICROBIAL SENSITIVITY TEST; MULTIVARIATE ANALYSIS; PILOT STUDY; PROCEDURES;

ANTI-BACTERIAL AGENTS; CARBENICILLIN; DRUG DISCOVERY; ESCHERICHIA COLI; METABOLOMICS; MICROBIAL SENSITIVITY TESTS; MULTIVARIATE ANALYSIS; PILOT PROJECTS; PROTON MAGNETIC RESONANCE SPECTROSCOPY; STREPTOMYCIN; TETRACYCLINE;

EID: 84969206796     PISSN: None     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/s12866-016-0696-5     Document Type: Article

References (47)

1. Jones KE, Patel NG, Levy MA, Storeygard A, Balk D, Gittleman JL, Daszak P. Global trends in emerging infectious diseases. Nature. 2008;451:990-3.
2. Boucher HW, Talbot GH, Bradley JS, Edwards JE, Gilbert D, Rice LB, Scheld M, Spellberg B, Bartlett J. Bad bugs, no drugs: no ESKAPE! An update from the Infectious Diseases Society of America. Clin Infect Dis. 2009;48:1-12.
3. Spellberg B. The future of antibiotics. Crit Care. 2014;18:228-35.
4. Wright GD. The antibiotic resistome: the nexus of chemical and genetic diversity. Nat Rev Microbiol. 2007;5:175-86.
5. Fair RJ, Tor Y. Antibiotics and bacterial resistance in the 21st century. Perspect Medicin Chem. 2014;6:25-64.
6. Coates AR, Hu Y. Novel approaches to developing new antibiotics for bacterial infections. Br J Pharmacol. 2007;152:1147-54.
7. Coates AR, Hu Y. Targeting non-multiplying organisms as a way to develop novel antimicrobials. Microbiology. 2009;155:2664-75.
8. Walsh C. Molecular mechanisms that confer antibacterial drug resistance. Nature. 2000;406:775-81.
9. Kohanski MA, Dwyer DJ, Hayete B, Lawrence CA, Collins JJ. A common mechanism of cellular death induced by bactericidal antibiotics. Cell. 2007;130:797-810.
10. Walsh C. Where will new antibiotics come from? Nat Rev Microbiol. 2003;1:65-70.
11. Miller JR, Waldrop GL. Discovery of novel antibacterials. Expert Opin Drug Discov. 2010;5:145-54.
12. Coates RM, Halls G, Hu Y. Novel classes of antibiotics or more of the same? Br J Pharmacol. 2011;163:184-94.
13. Lewis K. Platforms for antibiotic discovery. Nat Rev Drug Discov. 2013;12:371-87.
14. Payne DJ, Miller LF, Findlay D, Anderson J, Marks L. Time for a change: addressing R&D and commercialization challenges for antibacterials. Philos Trans R Soc Lond B Biol Sci. 2015;370:20140086.
15. Bajorath J. Integration of virtual and high-throughput screening. Nature Rev Drug Discov. 2002;1:882-93.
16. National Committee for Clinical Laboratory Standards. Methods for dilution antimicrobial susceptibility tests for bacteria that grow aerobically, Approved Standard M7-A4. 4th ed. Villanova, PA: National Committee for Clinical Laboratory Standards; 1997.
17. National Committee for Clinical Laboratory Standards. Development of in vitro susceptibility testing criteria and quality control parameters, Approved Guideline M23-A. Villanova, PA: National Committee for Clinical Laboratory Standards; 1994.
18. National Committee for Clinical Laboratory Standards. Performance standards for antimicrobial disk susceptibility tests, Approved standard M2-A6. Villanova, PA: National Committee for Clinical Laboratory Standards; 1997.
19. Kinnings SL, Liu N, Buchmeier N, Tonge PJ, Xie L, Bourne PE. Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis. PLoS Comput Biol. 2009;5:e1000423.
20. Tiwari V, Tiwari M. Quantitative proteomics to study carbapenem resistance in Acinetobacter baumannii. Front Microbiol. 2014;5:512.
21. Bandow JE, Brötz H, Leichert LI, Labischinski H, Hecker M. Proteomic approach to understanding antibiotic action. Antimicrob Agents Chemother. 2003;47:948-55.
22. Navid A. Applications of system-level models of metabolism for analysis of bacterial physiology and identification of new drug targets. Brief Funct Genomics. 2011;10:354-64.
23. Hartman HB, Fell DA, Rossell S, Jensen PR, Woodward MJ, Thorndahl L, Jelsbak L, Olsen JE, Raghunathan A, Daefler S, Poolman MG. Identification of potential drug targets in Salmonella enterica sv. Typhimurium using metabolic modelling and experimental validation. Microbiology. 2014;160:1252-66.
24. Panjkovich A, Gibert I, Daura X. antibacTR: dynamic antibacterial-drug-target ranking integrating comparative genomics, structural analysis and experimental annotation. BMC Genomics. 2014;15:36.
25. Bleicher KH, Böhm HJ, Müller K, Alanine AI. A guide to drug discovery: Hit and lead generation: beyond high-throughput screening. Nature Rev Drug Disc. 2003;2:369-78.
26. Lindon JC, Holmes E, Nicholson JK. Metabonomics Techniques and Applications to Pharmaceutical Research & Development. Pharm Res. 2006;23:1076-88.
27. Dörries K, Schlueter R, Lalk M. Impact of antibiotics with various target sites on the metabolome of Staphylococcus aureus. Antimicrob Agents Chemother. 2014;58:7151-63.
28. Han PP, Jia SR, Sun Y, Tan ZL, Zhong C, Dai YJ, Tan N, Shen SG. Metabolomic approach to optimizing and evaluating antibiotic treatment in the axenic culture of cyanobacterium Nostoc flagelliforme. World J Microbiol Biotechnol. 2014;30:2407-18.
29. Su YB, Peng B, Han Y, Li H, Peng XX. Fructose restores susceptibility of multidrug-resistant Edwardsiella tarda to kanamycin. J Proteome Res. 2015;14:1612-20.
30. Wharfe ES, Winder CL, Jarvis RM, Goodacre R. Monitoring the effects of chiral pharmaceuticals on aquatic microorganisms by metabolic fingerprinting. Appl Environ Microbiol. 2010;76:2075-85.
31. Jung GB, Nam SW, Choi S, Lee GJ, Park HK. Evaluation of antibiotic effects on Pseudomonas aeruginosa biofilm using Raman spectroscopy and multivariate analysis. Biomed Opt Express. 2014;5:3238-51.
32. Schröder UC, Beleites C, Assmann C, Glaser U, Hübner U, Pfister W, Fritzsche W, Popp J, Neugebauer U. Detection of vancomycin resistances in enterococci within 3 (12) hours. Sci Rep. 2015;5:8217.
33. López-Díez EC, Winder CL, Ashton L, Currie F, Goodacre R. Monitoring the mode of action of antibiotics using Raman spectroscopy: investigating subinhibitory effects of amikacin on Pseudomonas aeruginosa. Anal Chem. 2005;77:2901-6.
34. Halouska S, Fenton RJ, Barletta RG, Powers R. Predicting the in Vivo Mechanism of Action for Drug Leads Using NMR Metabolomics. ACS Chem Biol. 2012;7:166-71.
35. Deutsches Institut für Normierung e.V. Methoden zur Empfindlichkeitsprüfung von bakteriellen Krankheitserregern (ausser Mykobakterien) gegen Chemotherapeutika-Mikrodilution. Deutsches Institut für Normierung e.V., DIN 58940 Teil 8, 1990.
36. Jennifer MA. Determination of minimum inhibitory concentrations. J Antimicrob Chemother. 2001;48(Suppl S1):5-16.
37. Stocks SM. Mechanism and use of the commercially available viability stain, BacLight. Cytometry, Part A. 2004;61:189-95.
38. Molecular Probes. Molecular Probes LIVE/DEAD BacLight Bacterial Viability Kits Product Information Molecular Probes Inc. Göttingen, Germany: Mobitec; 1997.
39. Moat AG, Foster JW, Spector MP. Microbial Physiology. New York: John Wiley & Sons; 2003.
40. Kempf B, Bremer E. Uptake and synthesis of compatible solutes as microbial stress responses to high-osmolality environments. Arch Microbiol. 1998;170:319-30.
41. Feehily C, Karatzas KA. Role of glutamate metabolism in bacterial responses towards acid and other stresses. J Appl Microbiol. 2013;114:11-24.
42. Aghatabay NM, Baş A, Kircali A, Sen G, Yazicioǧlu MB, Gücin F, Dülger B. Synthesis, Raman, FT-IR, NMR spectroscopic characterization, antimicrobial activity, cytotoxicity and DNA binding of new mixed aza-oxo-thia macrocyclic compounds. Eur J Med Chem. 2009;44:4681-9.
43. Svensson M, Lohmeier-Vogel E, Waak E, Svensson U, Rådström P. Altered nucleotide sugar metabolism in Streptococcus thermophilus interferes with nitrogen metabolism. Int J Food Microbiol. 2007;113:195-200.
44. Kumar A, Ernst RR, Wüthrich K. A two-dimensional nuclear Overhauser enhancement (2D NOE) experiment for the elucidation of complete proton-proton cross-relaxation networks in biological macromolecules. Biochem Biophys Res Commun. 1980;95:1-6.
45. Nicholson JK, Foxall PJ, Spraul M, Farrant RD, Lindon JC. 750 MHz 1H and 1H-13C NMR spectroscopy of human blood plasma. Anal Chem. 1995;67:793-811.
46. Weljie AM, Newton J, Mercier P, Carlson E, Slupsky CM. Targeted profiling: quantitative analysis of 1H NMR metabolomics data. Anal Chem. 2006;78:4430-42.
47. Dieterle F, Ross A, Schlotterbeck G, Senn H. Probabilistic quotient normalization as robust method to account for dilution of complex biological mixtures. Application in 1H NMR metabonomics. Anal Chem. 2006;78:4281-90.