Please use this identifier to cite or link to this item:
http://hdl.handle.net/1942/21487Full metadata record
| DC Field | Value | Language |
|---|---|---|
| dc.contributor.author | KAZAKEVICH, Dzianis | - |
| dc.contributor.author | Karr, Jonathan | - |
| dc.contributor.author | Langner, Karol | - |
| dc.contributor.author | Plewczynski, Dariusz | - |
| dc.date.accessioned | 2016-06-09T13:43:18Z | - |
| dc.date.available | 2016-06-09T13:43:18Z | - |
| dc.date.issued | 2015 | - |
| dc.identifier.citation | COMPUTATIONAL BIOLOGY AND CHEMISTRY, 59, p. 91-97 | - |
| dc.identifier.issn | 1476-9271 | - |
| dc.identifier.uri | http://hdl.handle.net/1942/21487 | - |
| dc.description.abstract | Bacteria are increasingly resistant to existing antibiotics, which target a narrow range of pathways. New methods are needed to identify targets, including repositioning targets among distantly related species.We developed a novel combination of systems and structural modeling and bioinformatics to repositionknown antibiotics and targets to new species. We applied this approach to Mycoplasma genitalium, acommon cause of urethritis. First, we used quantitative metabolic modeling to identify enzymes whoseexpression affects the cellular growth rate. Second, we searched the literature for inhibitors of homologsof the most fragile enzymes. Next, we used sequence alignment to assess that the binding site is shared byM. genitalium, but not by humans. Lastly, we used molecular docking to verify that the reported inhibitorspreferentially interact with M. genitalium proteins over their human homologs. Thymidylate kinase wasthe top predicted target and piperidinylthymines were the top compounds. Further work is needed toexperimentally validate piperidinylthymines. In summary, combined systems and structural modeling isa powerful tool for drug repositioning. | - |
| dc.description.sponsorship | Polish National Science Centre (UMO-2013/09/B/NZ2/00121); Wroclaw Centre for Networking and Supercomputing (255); European Cooperation in Science and Technology (BM1405); Medical University of Bialystok; European Social Fund; National Science Foundation Graduate Fellowship; James S. McDonnell Foundation Postdoctoral Fellowship Award in Studying Complex Systems | - |
| dc.language.iso | en | - |
| dc.rights | © 2015 Elsevier Ltd. All rights reserved. | - |
| dc.subject.other | systems biology; metabolic modeling; homology modeling; drug repositioning; mycoplasma genitalium; thymidylate kinase | - |
| dc.title | A combined systems and structural modeling approach repositions antibiotics for Mycoplasma genitalium | - |
| dc.type | Journal Contribution | - |
| dc.identifier.epage | 97 | - |
| dc.identifier.spage | 91 | - |
| dc.identifier.volume | 59 | - |
| local.bibliographicCitation.jcat | A1 | - |
| dc.relation.references | Bachmair, A., Finley, D., Varshavsky, A., 1986. In vivo half-life of a protein is a function of its amino-terminal residue. Science 234 (4773), 179–186. Byun, Y., Vogel, S.R., Phipps, A.J., Carnrot, C., Eriksson, S., et al., 2008. Synthesis and biological evaluation of inhibitors of thymidine monophosphate kinase from Bacillus anthracis. Nucleosides Nucleotides Nucleic Acids 27 (3), 244–260. Cazanave, C., Manhart, L.E., B´eb´ear, C., 2012. Mycoplasma genitalium, an emerging sexually transmitted pathogen. Med. Mal. Infect. 42 (9), 381–392. Chan, J.N., Nislow, C., Emili, A., 2010. Recent advances and method develop- ment for drug target identification. Trends Pharmacol. Sci. 31 (2), 82–88. Chang, A., Schomburg, I., Placzek, S., Jeske, L., Ulbrich, M., et al., 2015. BRENDA in 2015: exciting developments in its 25th year of existence. Nucleic Acids Res. 43 (Database issue), D439–446. Chavali, A.K., Blazier, A.S., Tlaxca, J.L., Jensen, P.A., Pearson, R.D., et al., 2012. Metabolic network analysis predicts efficacy of FDA-approved drugs targeting the causative agent of a neglected tropical disease. BMC Syst. Biol. 6, 27. Choi, J.Y., Plummer, M.S., Starr, J., Desbonnet, C.R., Soutter, H., et al., 2012. Structure guided development of novel thymidine mimetics targeting Pseudomonas aeruginosa thymidylate kinase: from hit to lead generation. J. Med. Chem. 55 (2), 852–870. Citti, C., Blanchard, A., 2013. Mycoplasmas and their host: emerging and re- emerging minimal pathogens. Trends Microbiol. 21 (4), 196–203. Cole, S.T., 2014. Who will develop new antibacterial agents? Philos. Trans. R. Soc. Lond. B Biol. Sci. 369 (1645), 20130430. Cui, Q., Shin, W.S., Luo, Y., Tian, J., Cui, H., et al., 2013. Thymidylate kinase: an old topic brings new perspectives. Curr. Med. Chem. 20 (10), 1286–1305. D´egrange, S., Renaudin, H., Charron, A., B´eb´ear, C., B´eb´ear, C.M., 2008. Tetracycline resistance in Ureaplasma spp. and Mycoplasma hominis : preva- lence 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), 742–744. D¨onh¨ofer, A., Franckenberg, S., Wickles, S., Berninghausen, O., Beckmann, R., et al., 2012. Structural basis for tetm-mediated tetracycline resistance. Proc. Natl. Acad. Sci. U. S. A. 109 (42), 16900–16905. Duran-Frigola, M., Mosca, R., Aloy, P., 2013. Structural systems pharmacology: the role of 3D structures in next-generation drug development. Chem. Biol. 20 (5), 674–684. Focke, M., Feld, A., Lichtenthaler, K., 1990. Allicin, a naturally occurring an- tibiotic from garlic, specifically inhibits acetyl-CoA synthetase. FEBS Lett. 261 (1), 106–108. Folger, O., Jerby, L., Frezza, C., Gottlieb, E., Ruppin, E., et al., 2011. Predicting selective drug targets in cancer through metabolic networks. Mol. Syst. Biol. 7, 501. Harbarth, S., Theuretzbacher, U., Hackett, J., 2015. Antibiotic research and development: business as usual? J. Antimicrob. Chemother. pii, dkv020. Jensen, J.S., Bradshaw, C.S., Tabrizi, S.N., Fairley, C.K., Hamasuna, R., 2008. Azithromycin treatment failure in Mycoplasma genitalium -positive patients with nongonococcal urethritis is associated with induced macrolide resistance. Clin. Infect. Dis. 47 (12), 1546–1553. Karr, J.R., Sanghvi, J.C., Macklin, D.N., Gutschow, M.V., Jacobs, J.M., et al., 2012. A whole-cell computational model predicts phenotype from genotype. Cell 150 (2), 389–401. Kawatkar, S.P., Keating, T.A., Olivier, N.B., Breen, J.N., Green, O.M., et al., 2014. Antibacterial inhibitors of gram-positive thymidylate kinase: structure- activity relationships and chiral preference of a new hydrophobic binding re- gion. J. Med. Chem. 57 (11), 4584–4597. Keating, T.A., Newman, J.V., Olivier, N.B., Otterson, L.G., Andrews, B., et al., 2012. In vivo validation of thymidylate kinase (tmk) with a rationally de- signed, selective antibacterial compound. ACS Chem. Biol. 7 (11), 1866–1872. Khanna, I., 2012. Drug discovery in pharmaceutical industry: productivity chal- lenges and trends. Drug Discov. Today 17 (19–20), 1088–1102. Kim, H.U., Kim, S.Y., Jeong, H., Kim, T.Y., Kim, J.J., et al., 2011. Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery. Mol. Syst. Biol. 7, 460. Magis, C., Taly, J.F., Bussotti, G., Chang, J.M., Di Tommaso, P., et al., 2014. T-Coffee: Tree-based consistency objective function for alignment evaluation. Methods Mol. Biol. 1079, 117–129. Manhart, L.E., 2013. Mycoplasma genitalium : An emergent sexually transmit- ted disease? Infect. Dis. Clin. North Am. 27 (4), 779–792. Mart´ınez-Botella, G., Breen, J.N., Duffy, J.E., Dumas, J., Geng, B., et al., 2012. Discovery of selective and potent inhibitors of Gram-positive bacterial thymidylate kinase (TMK). J. Med. Chem. 55 (22), 10010–10021. Mart´ınez-Botella, G., Loch, J.T., Green, O.M., Kawatkar, S.P., Olivier, N.B., et al., 2013. Sulfonylpiperidines as novel, antibacterial inhibitors of Gram- positive thymidylate kinase (TMK). Bioorg. Med. Chem. Lett. 23 (1), 169– 173. Morowitz, H.J., Tourtellotte, M.E., Guild, W.R., Castro, E., Woese, C., 1962. The chemical composition and submicroscopic morphology of Mycoplasma gallisepticum, avian pplo 5969. J. Mol. Biol. 4, 93–103. Nambiar, S., Laessig, K., Toerner, J., Farley, J., Cox, E., 2014. Antibacterial drug development: challenges, recent developments, and future considera- tions. Clin. Pharmacol. Ther. 96 (2), 147–149. Orth, J.D., Thiele, I., Palsson, B.O., 2010. What is flux balance analysis? Nat. Biotechnol. 28 (3), 245–248. Pammolli, F., Magazzini, L., Riccaboni, M., 2011. The productivity crisis in pharmaceutical R&D. Nat. Rev. Drug Discov. 10 (6), 428–438. Raman, K., Yeturu, K., Chandra, N., 2008. targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis. BMC Syst. Biol. 2, 109. Rosales-Hern´andez, M.C., Correa-Basurto, J., 2015. The importance of employ- ing computational resources for the automation of drug discovery. Expert Opin. Drug Discov. 15. Salado-Rasmussen, K., Jensen, J.S., 2014. Mycoplasma genitalium testing pat- tern and macrolide resistance: a danish nationwide retrospective survey. Clin. Infect. Dis. 59 (1), 24–30. Schr¨odinger, LLC, 2015. The pymol molecular graphics system. http://www. pymol.org/ accessed 2015-02-23. Shen, Y., Liu, J., Estiu, G., Isin, B., Ahn, Y.Y., et al., 2010. Blueprint for antimicrobial hit discovery targeting metabolic networks. Proc. Natl. Acad. Sci. U. S. A. 107 (3), 1082–1087. Shimada, Y., Deguchi, T., Nakane, K., Masue, T., Yasuda, M., et al., 2010. Emergence of clinical strains of Mycoplasma genitalium harbouring alterations in parc associated with fluoroquinolone resistance. Int. J. Antimicrob. Agents 36 (3), 255–258. Shin, J.M., Cho, D.H., 2005. PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures. Nucleic Acids Res. 33 (Database issue), D238–241. Taylor Robinson, D., 2014. Diagnosis and antimicrobial treatment of My- coplasma genitalium infection: sobering thoughts. Expert Rev. Anti. Infect. Ther. 12 (6), 715–722. Trott, O., Olson, A.J., 2010. AutoDock Vina: improving the speed and ac- curacy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 31 (2), 455–461. Vanheusden, V., Munier-Lehmann, H., Pochet, S., Herdewijn, P., Van Calen- bergh, S., 2002. Synthesis and evaluation of thymidine-5’-O-monophosphate analogues as inhibitors of Mycobacterium tuberculosis thymidylate kinase. Bioorg. Med. Chem. Lett. 12 (19), 2695–2698. Webb, B., Sali, A., 2014. Protein structure modeling with MODELLER. Meth- ods Mol. Biol. 1137, 1–15. Weiner 3rd, J., Zimmerman, C.U., G¨ohlmann, H.W., Herrmann, R., 2003. Tran- scription profiles of the bacterium Mycoplasma pneumoniae grown at different temperatures. Nucleic Acids Res. 31 (21), 6306–6320. Weinstein, S.A., Stiles, B.G., 2012. Recent perspectives in the diagnosis and evidence-based treatment of Mycoplasma genitalium . Expert Rev. Anti. In- fect. Ther. 10 (4), 487–499. Wittig, U., Kania, R., Golebiewski, M., Rey, M., Shi, L., et al., 2012. SABIO-RK–database for biochemical reaction kinetics. Nucleic Acids Res. 40 (Database issue), D790–796. Zarei, O., Rezania, S., Mousavi, A., 2013. Mycoplasma genitalium and cancer: a brief review. Asian Pac. J. Cancer Prev. 14 (6), 3425–3428. | - |
| local.type.refereed | Refereed | - |
| local.type.specified | Article | - |
| dc.identifier.doi | 10.1016/j.compbiolchem.2015.07.007 | - |
| dc.identifier.isi | 000367634000009 | - |
| item.fulltext | With Fulltext | - |
| item.accessRights | Restricted Access | - |
| item.fullcitation | KAZAKEVICH, Dzianis; Karr, Jonathan; Langner, Karol & Plewczynski, Dariusz (2015) A combined systems and structural modeling approach repositions antibiotics for Mycoplasma genitalium. In: COMPUTATIONAL BIOLOGY AND CHEMISTRY, 59, p. 91-97. | - |
| item.validation | ecoom 2017 | - |
| item.contributor | KAZAKEVICH, Dzianis | - |
| item.contributor | Karr, Jonathan | - |
| item.contributor | Langner, Karol | - |
| item.contributor | Plewczynski, Dariusz | - |
| crisitem.journal.issn | 1476-9271 | - |
| crisitem.journal.eissn | 1476-928X | - |
| Appears in Collections: | Research publications | |
Files in This Item:
| File | Description | Size | Format | |
|---|---|---|---|---|
| 1-s2.0-S147692711530089X-main.pdf Restricted Access | Published version | 898.68 kB | Adobe PDF | View/Open Request a copy |
SCOPUSTM
Citations
6
checked on Sep 3, 2020
WEB OF SCIENCETM
Citations
11
checked on May 8, 2024
Page view(s)
54
checked on Sep 6, 2022
Download(s)
42
checked on Sep 6, 2022
Google ScholarTM
Check
Altmetric
Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.