A combined systems and structural modeling approach repositions antibiotics for Mycoplasma genitalium

Computational Biology and Chemistry

Volumn 59, Issue , 2015, Pages 91-97

  Kazakiewicz, Denis ^a,b,c   Karr, Jonathan R ^d,e   Langner, Karol M ^f,i   Plewczynski, Dariusz ^a,g,h  

^a Center for Innovative Research   (Poland)

^b HASSELT UNIVERSITY   (Belgium)

^c Interuniversity Institute for Biostatistics and Statistical Bioinformatics   (Belgium)

^d MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^e STANFORD UNIVERSITY   (United States)

^f UNIVERSITY OF VIRGINIA   (United States)

^g UNIVERSITY OF WARSAW   (Poland)

^h JACKSON LABORATORY   (United States)

ⁱ GOOGLE INC   (United States)

Author keywords

Drug repositioning; Homology modeling; Metabolic modeling; Mycoplasma genitalium; Systems biology; Thymidylate kinase

Indexed keywords

ANTIBIOTICS; BINDING SITES; BIOINFORMATICS; METABOLISM;

DRUG REPOSITIONING; HOMOLOGY MODELING; METABOLIC MODELING; MYCOPLASMA GENITALIUM; SYSTEMS BIOLOGY; THYMIDYLATE KINASE;

ENZYMES;

ANTIINFECTIVE AGENT; DTMP KINASE; NUCLEOSIDE MONOPHOSPHATE KINASE; PIPERIDINE DERIVATIVE; THYMINE;

ALGORITHM; ANALOGS AND DERIVATIVES; ANTAGONISTS AND INHIBITORS; BINDING SITE; BIOLOGICAL MODEL; CHEMISTRY; DRUG EFFECTS; DRUG REPOSITIONING; ENZYMOLOGY; HUMAN; METABOLISM; MICROBIAL SENSITIVITY TEST; MYCOPLASMA GENITALIUM; PROCEDURES; SYSTEMS BIOLOGY;

ALGORITHMS; ANTI-BACTERIAL AGENTS; BINDING SITES; DRUG REPOSITIONING; HUMANS; MICROBIAL SENSITIVITY TESTS; MODELS, BIOLOGICAL; MYCOPLASMA GENITALIUM; NUCLEOSIDE-PHOSPHATE KINASE; PIPERIDINES; SYSTEMS BIOLOGY; THYMINE;

EID: 84939864747     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2015.07.007     Document Type: Article

References (62)

1. R. Adadi, B. Volkmer, R. Milo, M. Heinemann, and T. Shlomi Prediction of microbial growth rate versus biomass yield by a metabolic network with kinetic parameters PLoS Comput. Biol. 8 7 2012 e1002575
2. A. Bachmair, D. Finley, and A. Varshavsky In vivo half-life of a protein is a function of its amino-terminal residue Science 234 4773 1986 179 186
3. S.A. Becker, and B.O. Palsson Context-specific metabolic networks are consistent with experiments PLoS Comput. Biol. 4 5 2008 e1000082
4. Y. Byun, S.R. Vogel, A.J. Phipps, C. Carnrot, S. Eriksson, and et al. Synthesis and biological evaluation of inhibitors of thymidine monophosphate kinase from Bacillus anthracis Nucleosides Nucleotides Nucleic Acids 27 3 2008 244 260
5. C. Cazanave, L.E. Manhart, and C. Bébéar Mycoplasma genitalium, an emerging sexually transmitted pathogen Med. Mal. Infect. 42 9 2012 381 392
6. J.N. Chan, C. Nislow, and A. Emili Recent advances and method development for drug target identification Trends Pharmacol. Sci. 31 2 2010 82 88
7. S. Chandrasekaran, and N.D. Price Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis Proc. Natl. Acad. Sci. U.S.A 107 41 2010 17845 17850
8. A. Chang, I. Schomburg, S. Placzek, L. Jeske, M. Ulbrich, and et al. BRENDA in 2015: exciting developments in its 25th year of existence Nucleic Acids Res. 2015 D439 D446
9. A.K. Chavali, A.S. Blazier, J.L. Tlaxca, P.A. Jensen, R.D. Pearson, and et al. Metabolic network analysis predicts efficacy of FDA-approved drugs targeting the causative agent of a neglected tropical disease BMC Syst. Biol. 6 2012 27
10. J.Y. Choi, M.S. Plummer, J. Starr, C.R. Desbonnet, H. Soutter, and et al. Structure guided development of novel thymidine mimetics targeting Pseudomonas aeruginosa thymidylate kinase: from hit to lead generation J. Med. Chem. 55 2 2012 852 870
11. C. Citti, and A. Blanchard Mycoplasmas and their host: emerging and reemerging minimal pathogens Trends Microbiol. 21 4 2013 196 203
12. S.T. Cole Who will develop new antibacterial agents? Philos. Trans. R. Soc. Lond. B Biol. Sci. 369 1645 2014 20130430
13. C. Colijn, A. Brandes, J. Zucker, D.S. Lun, B. Weiner, and et al. Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production PLoS Comput. Biol. 5 8 2009 e1000489
14. M.W. Covert, E.M. Knight, J.L. Reed, M.J. Herrgard, and B.O. Palsson Integrating high-throughput and computational data elucidates bacterial networks Nature 429 6987 2004 92 96
15. M.W. Covert, N. Xiao, T.J. Chen, and J.R. Karr Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli Bioinformatics 24 18 2008 2044 2050
16. Q. Cui, W.S. Shin, Y. Luo, J. Tian, H. Cui, and et al. Thymidylate kinase: an old topic brings new perspectives Curr. Med. Chem. 20 10 2013 1286 1305
17. S. Dégrange, H. Renaudin, A. Charron, C. Bébéar, and C.M. Bébéar Tetracycline resistance in Ureaplasma spp. and Mycoplasma hominis: prevalence in Bordeaux, France, from 1999 to 2002 and description of two tet(M)-positive isolates of M. hominis susceptible to tetracyclines Antimicrob. Agents Chemother. 52 2 2008 742 744
18. A. Dönhöfer, S. Franckenberg, S. Wickles, O. Berninghausen, R. Beckmann, and et al. Structural basis for TetM-mediated tetracycline resistance Proc. Natl. Acad. Sci. U.S.A. 109 42 2012 16900 16905
19. M. Duran-Frigola, R. Mosca, and P. Aloy Structural systems pharmacology: the role of 3D structures in next-generation drug development Chem. Biol. 20 5 2013 674 684
20. M. Focke, A. Feld, and K. Lichtenthaler Allicin, a naturally occurring antibiotic from garlic, specifically inhibits acetyl-CoA synthetase FEBS Lett. 261 1 1990 106 108
21. O. Folger, L. Jerby, C. Frezza, E. Gottlieb, E. Ruppin, and et al. Predicting selective drug targets in cancer through metabolic networks Mol. Syst. Biol. 7 2011 501
22. J.I. Glass, N. Assad-Garcia, N. Alperovich, S. Yooseph, M.R. Lewis, and et al. Essential genes of a minimal bacterium Proc. Natl. Acad. Sci. U.S.A. 103 2 2006 425 430
23. Google, 2015. Google Scholar. (accessed 23.02.15).
24. S. Harbarth, U. Theuretzbacher, and J. Hackett Antibiotic research and development: business as usual? J. Antimicrob. Chemother. 2015 pii, dkv020
25. J.S. Jensen, C.S. Bradshaw, S.N. Tabrizi, C.K. Fairley, and R. Hamasuna Azithromycin treatment failure in Mycoplasma genitalium -positive patients with nongonococcal urethritis is associated with induced macrolide resistance Clin. Infect. Dis. 47 12 2008 1546 1553
26. J.R. Karr, J.C. Sanghvi, D.N. Macklin, M.V. Gutschow, J.M. Jacobs, and et al. A whole-cell computational model predicts phenotype from genotype Cell 150 2 2012 389 401
27. Karr, J.R., Sanghvi, J.C., Macklin, D.N., Jacobs, J.M., Covert, M.W., 2015. Mycoplasma genitalium whole-cell model version 1.1. figshare.1321518 (accessed 03.03.15).
28. S.P. Kawatkar, T.A. Keating, N.B. Olivier, J.N. Breen, O.M. Green, and et al. Antibacterial inhibitors of gram-positive thymidylate kinase: structure-activity relationships and chiral preference of a new hydrophobic binding region J. Med. Chem. 57 11 2014 4584 4597
29. T.A. Keating, J.V. Newman, N.B. Olivier, L.G. Otterson, B. Andrews, and et al. In vivo validation of thymidylate kinase (TMK) with a rationally designed, selective antibacterial compound ACS Chem. Biol. 7 11 2012 1866 1872
30. I. Khanna Drug discovery in pharmaceutical industry: productivity challenges and trends Drug Discov. Today 17 19-20 2012 1088 1102
31. H.U. Kim, S.Y. Kim, H. Jeong, T.Y. Kim, J.J. Kim, and et al. Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery Mol. Syst. Biol. 7 2011 460
32. D. Machado, and M. Herrgård Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism PLoS Comput. Biol. 10 4 2014 e1003580
33. C. Magis, J.F. Taly, G. Bussotti, J.M. Chang, P. Di Tommaso, and et al. T-coffee: tree-based consistency objective function for alignment evaluation Methods Mol. Biol. 1079 2014 117 129
34. L.E. Manhart Mycoplasma genitalium: an emergent sexually transmitted disease? Infect. Dis. Clin. North Am. 27 4 2013 779 792
35. G. Martínez-Botella, J.N. Breen, J.E. Duffy, J. Dumas, B. Geng, and et al. Discovery of selective and potent inhibitors of Gram-positive bacterial thymidylate kinase (TMK) J. Med. Chem. 55 22 2012 10010 10021
36. G. Martínez-Botella, J.T. Loch, O.M. Green, S.P. Kawatkar, N.B. Olivier, and et al. Sulfonylpiperidines as novel, antibacterial inhibitors of Gram-positive thymidylate kinase (TMK) Bioorg. Med. Chem. Lett. 23 1 2013 169 173
37. A. Merino, A.K. Bronowska, D.B. Jackson, and D.J. Cahill Drug profiling: knowing where it hits Drug Discov. Today 15 17-18 2010 749 756
38. C. Merlot Computational toxicology-a tool for early safety evaluation Drug Discov. Today 15 1-2 2010 16 22
39. H.J. Morowitz, M.E. Tourtellotte, W.R. Guild, E. Castro, and C. Woese The chemical composition and submicroscopic morphology of Mycoplasma gallisepticum, avian PPLO 5969 J. Mol. Biol. 4 1962 93 103
40. S. Nambiar, K. Laessig, J. Toerner, J. Farley, and E. Cox Antibacterial drug development: challenges, recent developments, and future considerations Clin. Pharmacol. Ther. 96 2 2014 147 149
41. National Center for Biotechnology Information, 2015. PubMed. (accessed 23.02.15).
42. J.D. Orth, I. Thiele, and B.O. Palsson What is flux balance analysis Nat. Biotechnol. 28 3 2010 245 248
43. F. Pammolli, L. Magazzini, and M. Riccaboni The productivity crisis in pharmaceutical R&D Nat. Rev. Drug Discov. 10 6 2011 428 438
44. K. Raman, K. Yeturu, and N. Chandra TargetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis BMC Syst. Biol. 2 2008 109
45. M.C. Rosales-Hernández, and J. Correa-Basurto The importance of employing computational resources for the automation of drug discovery Expert Opin. Drug Discov. 2015 15
46. K. Salado-Rasmussen, and J.S. Jensen Mycoplasma genitalium testing pattern and macrolide resistance: a Danish nationwide retrospective survey Clin. Infect. Dis. 59 1 2014 24 30
47. F. Schmidt, H. Matter, G. Hessler, and A. Czich Predictive in silico off-target profiling in drug discovery Future Med. Chem. 6 3 2014 295 317
48. Schrödinger, LLC, 2015. The PyMOL Molecular Graphics System. (accessed 23.02.15).
49. Y. Shen, J. Liu, G. Estiu, B. Isin, Y.Y. Ahn, and et al. Blueprint for antimicrobial hit discovery targeting metabolic networks Proc. Natl. Acad. Sci. U.S.A. 107 3 2010 1082 1087
50. Y. Shimada, T. Deguchi, K. Nakane, T. Masue, M. Yasuda, and et al. Emergence of clinical strains of Mycoplasma genitalium harbouring alterations in ParC associated with fluoroquinolone resistance Int. J. Antimicrob. Agents 36 3 2010 255 258
51. J.M. Shin, and D.H. Cho PDB-ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures Nucleic Acids Res. 33 Database issue 2005 D238 D241
52. P.F. Suthers, M.S. Dasika, V.S. Kumar, G. Denisov, J.I. Glass, and et al. A genome-scale metabolic reconstruction of Mycoplasma genitalium, iPS189 PLoS Comput. Biol. 5 2 2009 e1000285
53. D. Taylor-Robinson Diagnosis and antimicrobial treatment of Mycoplasma genitalium infection: sobering thoughts Expert Rev. Anti Infect. Ther. 12 6 2014 715 722
54. O. Trott, and A.J. Olson AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading J. Comput. Chem. 31 2 2010 455 461
55. V. Vanheusden, H. Munier-Lehmann, S. Pochet, P. Herdewijn, and S. Van Calenbergh Synthesis and evaluation of thymidine-5′-O-monophosphate analogues as inhibitors of Mycobacterium tuberculosis thymidylate kinase Bioorg. Med. Chem. Lett. 12 19 2002 2695 2698
56. B. Webb, and A. Sali Protein structure modeling with MODELLER Methods Mol. Biol. 1137 2014 1 15
57. J. Weiner 3rd, C.U. Zimmerman, H.W. Göhlmann, and R. Herrmann Transcription profiles of the bacterium Mycoplasma pneumoniae grown at different temperatures Nucleic Acids Res. 31 21 2003 6306 6320
58. S.A. Weinstein, and B.G. Stiles Recent perspectives in the diagnosis and evidence-based treatment of Mycoplasma genitalium Expert Rev. Anti Infect. Ther 10 4 2012 487 499
59. U. Wittig, R. Kania, M. Golebiewski, M. Rey, L. Shi, and et al. SABIO-RK-database for biochemical reaction kinetics Nucleic Acids Res. 40 Database issue 2012 D790 796
60. L. Xie, L. Xie, and P.E. Bourne Structure-based systems biology for analyzing off-target binding Curr. Opin. Struct. Biol. 21 2 2011 189 199
61. O. Zarei, S. Rezania, and A. Mousavi Mycoplasma genitalium and cancer: a brief review Asian Pac. J. Cancer Prev. 14 6 2013 3425 3428
62. H. Zur, E. Ruppin, and T. Shlomi iMAT: an integrative metabolic analysis tool Bioinformatics 26 24 2010 3140 3142