485
Views
20
CrossRef citations to date
0
Altmetric
Research Articles

Dynamics of fluoroquinolones induced resistance in DNA gyrase of Mycobacterium tuberculosis

, , , , , , & show all
Pages 362-375 | Received 06 Jul 2016, Accepted 22 Dec 2016, Published online: 27 Jan 2017

References

  • Abraham, M. J. , Murtola, T. , Schulz, R. , Páll, S. , Smith, J. C. , Hess, B. , & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX , 1–2 , 19–25.10.1016/j.softx.2015.06.001
  • Aldred, K. J. , Blower, T. R. , Kerns, R. J. , Berger, J. M. , & Osheroff, N. (2016). Fluoroquinolone interactions with Mycobacterium tuberculosis gyrase: Enhancing drug activity against wild-type and resistant gyrase. Proceedings of the National Academy of Sciences , 113 , E839–E846.10.1073/pnas.1525055113
  • Arias-Gonzalez, J. R. (2012). Entropy involved in fidelity of DNA replication. PLoS ONE , 7 , e42272.10.1371/journal.pone.0042272
  • Ascone, A. T. , & Sakidja, R. (2016). MDM2 case study: Computational protocol utilizing protein flexibility improves ligand binding mode predictions. bioRxiv , 054239.
  • Beard, H. , Cholleti, A. , Pearlman, D. , Sherman, W. , & Loving, K. A. (2013). Applying physics-based scoring to calculate free energies of binding for single amino acid mutations in protein-protein complexes. PLoS ONE , 8 , e82849.10.1371/journal.pone.0082849
  • Blower, T. R. , Williamson, B. H. , Kerns, R. J. , & Berger, J. M. (2016). Crystal structure and stability of gyrase–fluoroquinolone cleaved complexes from Mycobacterium tuberculosis. Proceedings of the National Academy of Sciences , 113 , 1706–1713.10.1073/pnas.1525047113
  • Costantini, S. , Colonna, G. , & Facchiano, A. M. (2008). ESBRI: A web server for evaluating salt bridges in proteins. Bioinformation , 3 , 137–138.10.6026/bioinformation
  • Cuzzolin, A. , Sturlese, M. , Malvacio, I. , Ciancetta, A. , & Moro, S. (2015). DockBench: An integrated informatic platform bridging the gap between the robust validation of docking protocols and virtual screening simulations. Molecules , 20 , 9977–9993.10.3390/molecules20069977
  • David, C. C. , & Jacobs, D. J. (2014). Principal component analysis: A method for determining the essential dynamics of proteins. In Dennis R. Livesay (Ed.), Protein dynamics (pp. 193–226). New York: Springer.
  • Dundas, J. , Ouyang, Z. , Tseng, J. , Binkowski, A. , Turpaz, Y. , & Liang, J. (2006). CASTp: Computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Research , 34 (Web Server), W116–W118.10.1093/nar/gkl282
  • Forli, S. , Huey, R. , Pique, M. E. , Sanner, M. F. , Goodsell, D. S. , & Olson, A. J. (2016). Computational protein–ligand docking and virtual drug screening with the AutoDock suite. Nature Protocols , 11 , 905–919.10.1038/nprot.2016.051
  • Goyal, M. , Grover, S. , Dhanjal, J. K. , Goyal, S. , Tyagi, C. , Chacko, S. , & Grover, A. (2013). Novel natural structure corrector of ApoE4 for checking Alzheimer’s disease: Benefits from high throughput screening and molecular dynamics simulations. BioMed Research International , 2015 , 1–8.
  • Goyal, S. , Jamal, S. , Shanker, A. , & Grover, A. (2015). Structural investigations of T854A mutation in EGFR and identification of novel inhibitors using structure activity relationships. BMC Genomics , 16 (Suppl. 5), S8.10.1186/1471-2164-16-S5-S8
  • Gupta, A. , Jamal, S. , Goyal, S. , Jain, R. , Wahi, D. , & Grover, A. (2015). Structural studies on molecular mechanisms of Nelfinavir resistance caused by non-active site mutation V77I in HIV-1 protease. BMC Bioinformatics , 16 (Suppl. 19), S10.10.1186/1471-2105-16-S19-S10
  • Hess, B. , Kutzner, C. , van der Spoel, D. , & Lindahl, E. (2008). GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation , 4 , 435–447.10.1021/ct700301q
  • Hevener, K. E. , Zhao, W. , Ball, D. M. , Babaoglu, K. , Qi, J. , White, S. W. , & Lee, R. E. (2009). Validation of molecular docking programs for virtual screening against dihydropteroate synthase. Journal of Chemical Information and Modeling , 49 , 444–460.10.1021/ci800293n
  • Humphrey, W. , Dalke, A. , & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics , 14 , 33–38.10.1016/0263-7855(96)00018-5
  • Karkare, S. , Chung, T. T. , Collin, F. , Mitchenall, L. A. , McKay, A. R. , Greive, S. J. , … Maxwell, A. (2013). The naphthoquinone diospyrin is an inhibitor of DNA gyrase with a novel mechanism of action. Journal of Biological Chemistry , 288 , 5149–5156.10.1074/jbc.M112.419069
  • Locher, C. P. , Jones, S. M. , Hanzelka, B. L. , Perola, E. , Shoen, C. M. , Cynamon, M. H. , … Betoudji, F. (2015). A novel inhibitor of gyrase B is a potent drug candidate for treatment of tuberculosis and nontuberculosis mycobacterial infections. Antimicrobial Agents and Chemotherapy , 59 , 1455–1465.10.1128/AAC.04347-14
  • Longo, D. L. , Horsburgh, C. R., Jr ., Barry, C. E., III , & Lange, C. (2015). Treatment of tuberculosis. New England Journal of Medicine , 373 , 2149–2160.
  • Lou, H. , & Cukier, R. I. (2006). Molecular dynamics of apo-adenylate kinase: A principal component analysis. The Journal of Physical Chemistry B , 110 , 12796–12808.10.1021/jp061976m
  • Maruri, F. , Sterling, T. R. , Kaiga, A. W. , Blackman, A. , van der Heijden, Y. F. , Mayer, C. , … Aubry, A. (2012). A systematic review of gyrase mutations associated with fluoroquinolone-resistant Mycobacterium tuberculosis and a proposed gyrase numbering system. Journal of Antimicrobial Chemotherapy , 67 , 819–831.10.1093/jac/dkr566
  • Mashiach, E. , Schneidman-Duhovny, D. , Andrusier, N. , Nussinov, R. , & Wolfson, H. J. (2008). FireDock: A web server for fast interaction refinement in molecular docking. Nucleic Acids Research , 36 (Web Server), W229–W232.10.1093/nar/gkn186
  • Nagpal, N. , Goyal, S. , Wahi, D. , Jain, R. , Jamal, S. , Singh, A. , … Grover, A. (2015). Molecular principles behind Boceprevir resistance due to mutations in hepatitis C NS3/4A protease. Gene , 570 , 115–121.10.1016/j.gene.2015.06.008
  • Patel, K. , Tyagi, C. , Goyal, S. , Jamal, S. , Wahi, D. , Jain, R. , … Grover, A. (2015). Identification of chebulinic acid as potent natural inhibitor of M. tuberculosis DNA gyrase and molecular insights into its binding mode of action. Computational Biology and Chemistry , 59 , 37–47.10.1016/j.compbiolchem.2015.09.006
  • Piton, J. , Petrella, S. , Delarue, M. , André-Leroux, G. , Jarlier, V. , Aubry, A. , & Mayer, C. (2010). Structural insights into the quinolone resistance mechanism of Mycobacterium tuberculosis DNA gyrase. PLoS ONE , 5 , e12245.10.1371/journal.pone.0012245
  • Repasky, M. P. , Shelley, M. , & Friesner, R. A. (2007). Flexible ligand docking with Glide. Current Protocols in Bioinformatics , 8.12. 11-18.12. 36.
  • Sastry, G. M. , Adzhigirey, M. , Day, T. , Annabhimoju, R. , & Sherman, W. (2013). Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments. Journal of Computer-Aided Molecular Design , 27 , 221–234.10.1007/s10822-013-9644-8
  • Schneidman-Duhovny, D. , Inbar, Y. , Nussinov, R. , & Wolfson, H. J. (2005). PatchDock and SymmDock: Servers for rigid and symmetric docking. Nucleic Acids Research , 33 (Web Server), W363–W367.10.1093/nar/gki481
  • Schrodinger, L. (2009). Prime [version 2.1]. New York, NY: Schrödinger, LLC.
  • Schrodinger, L. (2011). Schrodinger software suite . New York, NY : Schrödinger, LLC.
  • Stanger, F. V. , Dehio, C. , & Schirmer, T. (2014). Structure of the N-terminal gyrase B fragment in complex with ADP⋅ P i reveals rigid-body motion induced by ATP hydrolysis. Plos ONE , 9 , e107289.
  • Tretter, E. M. , & Berger, J. M. (2012). Mechanisms for defining supercoiling set point of DNA gyrase orthologs II. The shape of the gyra subunit C-terminal domain (CTD) is not a sole determinant for controlling supercoiling efficiency. Journal of Biological Chemistry , 287 , 18645–18654.10.1074/jbc.M112.345736
  • Tyagi, C. , Grover, S. , Dhanjal, J. K. , Goyal, S. , Goyal, M. , & Grover, A. (2013). Mechanistic insights into mode of action of novel natural cathepsin L inhibitors. BMC Genomics , 14 (Suppl. 8), S10.10.1186/1471-2164-14-S8-S10
  • Vats, C. , Dhanjal, J. K. , Goyal, S. , Gupta, A. , Bharadvaja, N. , & Grover, A. (2015). Mechanistic analysis elucidating the relationship between Lys96 mutation in Mycobacterium tuberculosis pyrazinamidase enzyme and pyrazinamide susceptibility. BMC Genomics , 16 (Suppl. 2), S14.10.1186/1471-2164-16-S2-S14

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.