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Volumn 31, Issue 6, 2013, Pages 561-571

Exploration of the binding of DNA binding ligands to Staphylococcal DNA through QM/MM docking and molecular dynamics simulation

Author keywords

DNA binding ligands and Staphylococcus; DNA docking; DNA gyrase; QM MM

Indexed keywords

ANTIINFECTIVE AGENT; BACTERIAL DNA; DNA BINDING LIGAND; DNA TOPOISOMERASE (ATP HYDROLYSING); UNCLASSIFIED DRUG;

EID: 84878710622     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2012.706080     Document Type: Article
Times cited : (40)

References (42)
  • 1
    • 0344438824 scopus 로고    scopus 로고
    • DNA and RNA structure (2nd ed.)
    • In, Edited by: Blackburn, G.M. and Gait, M.J. New York, NY: Oxford University Press
    • Blackburn, G.M. 1996. " DNA and RNA Structure (2nd ed.) ". In Nucleic acids in chemistry and biology, Edited by: Blackburn, G.M. and Gait, M.J. 15-81. New York, NY: Oxford University Press.
    • (1996) Nucleic Acids in Chemistry and Biology , pp. 15-81
    • Blackburn, G.M.1
  • 2
    • 0034641332 scopus 로고    scopus 로고
    • Total synthesis of distamycin A and 2640 analogues: A solution-phase combinatorial approach to the discovery of new, bioactive DNA binding agents and development of a rapid, high-throughput screen for determining relative DNA binding affinity or DNA binding sequence selectivity
    • doi: 10.1021/ja994192d
    • Boger, D.L., Fink, B.E., and, Hedrick, M.P. 2000. Total synthesis of distamycin A and 2640 analogues: A solution-phase combinatorial approach to the discovery of new, bioactive DNA binding agents and development of a rapid, high-throughput screen for determining relative DNA binding affinity or DNA binding sequence selectivity. Journal of the American Chemical Society, 122 (27): 6382-6394. doi: 10.1021/ja994192d
    • (2000) Journal of the American Chemical Society , vol.122 , Issue.27 , pp. 6382-6394
    • Boger, D.L.1    Fink, B.E.2    Hedrick, M.P.3
  • 3
    • 0003564810 scopus 로고    scopus 로고
    • Centers for Disease Control and Prevention Community associated MRSA: Frequently asked questions August Atlanta. Retrieved from
    • Centers for Disease Control and Prevention Community associated MRSA: Frequently asked questions (2003a, August). Centers for Disease Control and Prevention, Atlanta. Retrieved from http://www.cdc.gov/ncidod
    • (2003) Centers for Disease Control and Prevention
  • 4
    • 0003564810 scopus 로고    scopus 로고
    • Centers for Disease Control and Prevention. Community associated MRSA: Fact sheet February Atlanta. Retrieved from
    • Centers for Disease Control and Prevention. Community associated MRSA: Fact sheet (2003b, February). Centers for Disease Control and Prevention, Atlanta. Retrieved from http://www.cdc.gov/ncidod
    • (2003) Centers for Disease Control and Prevention
  • 5
    • 15944389483 scopus 로고    scopus 로고
    • Community-associated MRSA resistance and virulence converge
    • Chambers, H.F. 2005. Community-associated MRSA resistance and virulence converge. The New England Journal of Medicine, 352: 1485-1487. http://www.nejm.org/doi/full/10.1056/NEJMe058023
    • (2005) The New England Journal of Medicine , vol.352 , pp. 1485-1487
    • Chambers, H.F.1
  • 6
    • 0042355457 scopus 로고    scopus 로고
    • In silico prediction of drug toxicity
    • doi: 10.1023/A:1025361621494
    • Dearden, J.C. 2003. In silico prediction of drug toxicity. Journal of Computer-Aided Molecular Design, 17: 119-127. doi: 10.1023/A:1025361621494
    • (2003) Journal of Computer-Aided Molecular Design , vol.17 , pp. 119-127
    • Dearden, J.C.1
  • 7
    • 0027956736 scopus 로고
    • Cloning and primary structure of Staphylococcus aureus DNA topoisomerase IV: A primary target of fluoroquinolones
    • doi: 10.1111/j.1365-2958.1994.tb00458.x
    • Ferrero, L., Cameron, B., Manse, B., Lagneaux, D., Crouzet, J., Famechon, A., and, Blanche, F. 1994. Cloning and primary structure of Staphylococcus aureus DNA topoisomerase IV: A primary target of fluoroquinolones. Molecular Microbiology, 13 (4): 641-653. doi: 10.1111/j.1365-2958.1994.tb00458.x
    • (1994) Molecular Microbiology , vol.13 , Issue.4 , pp. 641-653
    • Ferrero, L.1    Cameron, B.2    Manse, B.3    Lagneaux, D.4    Crouzet, J.5    Famechon, A.6    Blanche, F.7
  • 8
    • 0032551901 scopus 로고    scopus 로고
    • Staphylococcus aureus infections
    • Franklin, D., and, Lowy, M.D. 1998. Staphylococcus aureus infections. The New England Journal of Medicine, 339: 520-532. http://www.nejm.org/doi/full/10. 1056/NEJM199808203390806
    • (1998) The New England Journal of Medicine , vol.339 , pp. 520-532
    • Franklin, D.1    Lowy, M.D.2
  • 9
    • 12144289984 scopus 로고    scopus 로고
    • Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
    • doi: 10.1021/jm0306430
    • Friesner, R.A., Banks, J.L., Murphy, R.B., Halgren, T.A., Klicic, J.J., Mainz, D.T.,., and, Shenkin, P.S. 2004. Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of Medicinal Chemistry, 47 (7): 1739-1749. doi: 10.1021/jm0306430
    • (2004) Journal of Medicinal Chemistry , vol.47 , Issue.7 , pp. 1739-1749
    • Friesner, R.A.1    Banks, J.L.2    Murphy, R.B.3    Halgren, T.A.4    Klicic, J.J.5    Mainz, D.T.6    Shenkin, P.S.7
  • 10
    • 0036784340 scopus 로고    scopus 로고
    • In vitro antimicrobial activity of GSQ1530, a new heteroaromatic polycyclic compound
    • doi: 10.1128/AAC.46.10.3168-3174.2002
    • Ge, Y., Difuntorum, S., Touami, S., Critchley, I., Bürli, R., Jiang, V.,., and, Moser, H. 2002. In vitro antimicrobial activity of GSQ1530, a new heteroaromatic polycyclic compound. Antimicrobial Agents and Chemotherapy, 46 (10): 3168-3174. doi: 10.1128/AAC.46.10.3168-3174.2002
    • (2002) Antimicrobial Agents and Chemotherapy , vol.46 , Issue.10 , pp. 3168-3174
    • Ge, Y.1    Difuntorum, S.2    Touami, S.3    Critchley, I.4    Bürli, R.5    Jiang, V.6    Moser, H.7
  • 11
    • 0034899540 scopus 로고    scopus 로고
    • ADMET-turning chemicals into drugs
    • doi: 10.1038/90761
    • Hodgson, J. 2001. ADMET-turning chemicals into drugs. Nature Biotechnology, 19 (8): 722-726. doi: 10.1038/90761
    • (2001) Nature Biotechnology , vol.19 , Issue.8 , pp. 722-726
    • Hodgson, J.1
  • 12
    • 1442281404 scopus 로고    scopus 로고
    • Partial rigid-body dynamics in NPT, NPAT and NPgammaT ensembles for proteins and membranes
    • doi: 10.1002/jcc.10402
    • Ikeguchi, M. 2004. Partial rigid-body dynamics in NPT, NPAT and NPgammaT ensembles for proteins and membranes. Journal of Computational Chemistry, 25 (4): 529-541. doi: 10.1002/jcc.10402
    • (2004) Journal of Computational Chemistry , vol.25 , Issue.4 , pp. 529-541
    • Ikeguchi, M.1
  • 14
    • 84878683431 scopus 로고    scopus 로고
    • Jaguar version 7.8, Schrödinger, LLC. New York, NY
    • Jaguar version 7.8, Schrödinger, LLC., New York, NY.
  • 15
    • 0041418315 scopus 로고    scopus 로고
    • DNA binding ligands targeting drug-resistant bacteria: Structure, activity, and pharmacology
    • doi: 10.1021/jm030097a
    • Kaizerman, J.A., Gross, M.I., Ge, Y., White, S., Hu, W., Duan, J.X.,., and, Bürli, R.W. 2003. DNA binding ligands targeting drug-resistant bacteria: Structure, activity, and pharmacology. Journal of Medicinal Chemistry, 46 (18): 3914-3929. doi: 10.1021/jm030097a
    • (2003) Journal of Medicinal Chemistry , vol.46 , Issue.18 , pp. 3914-3929
    • Kaizerman, J.A.1    Gross, M.I.2    Ge, Y.3    White, S.4    Hu, W.5    Duan, J.X.6    Bürli, R.W.7
  • 17
    • 46149120143 scopus 로고    scopus 로고
    • Implementations of Nosé-Hoover and Nosé-Poincaré thermostats in mesoscopic dynamic simulations with the united-residue model of a polypeptide chain
    • doi: 10.1063/1.2943146
    • Kleinerman, D.S., Czaplewski, C., Liwo, A., and, Scheraga, H.A. 2008. Implementations of Nosé-Hoover and Nosé-Poincaré thermostats in mesoscopic dynamic simulations with the united-residue model of a polypeptide chain. Journal of Chemical Physics, 128 (24): 245103-1-245103-16. doi: 10.1063/1.2943146
    • (2008) Journal of Chemical Physics , vol.128 , Issue.24 , pp. 2451031-24510316
    • Kleinerman, D.S.1    Czaplewski, C.2    Liwo, A.3    Scheraga, H.A.4
  • 18
    • 0031571640 scopus 로고    scopus 로고
    • Defining GC-specificity in the minor groove: Side-by-side binding of the di-imidazole lexitropsin to C-A-T-G-G-C-C-A-T-G
    • doi: 10.1016/S0969-2126(97)00255-4
    • Kopka, M.L., Goodsell, D.S., Han, G.W., Chiu, T.K., Lown, J.W., and, Dickerson, R.E. 1997. Defining GC-specificity in the minor groove: Side-by-side binding of the di-imidazole lexitropsin to C-A-T-G-G-C-C-A-T-G. Structure, 5 (8): 1033-1046. doi: 10.1016/S0969-2126(97)00255-4
    • (1997) Structure , vol.5 , Issue.8 , pp. 1033-1046
    • Kopka, M.L.1    Goodsell, D.S.2    Han, G.W.3    Chiu, T.K.4    Lown, J.W.5    Dickerson, R.E.6
  • 19
    • 84878683053 scopus 로고    scopus 로고
    • LigPrep (2.5) [Schrödinger, LLC]. New York, NY
    • LigPrep (2.5) [Schrödinger, LLC]. New York, NY.
  • 20
    • 33745081753 scopus 로고    scopus 로고
    • Understanding the rise of the superbug: Investigation of the evolution and genomic variation of Staphylococcus aureus
    • doi: 10.1007/s10142-005-0019-7
    • Lindsay, J.A., and, Holden, M.T. 2006. Understanding the rise of the superbug: Investigation of the evolution and genomic variation of Staphylococcus aureus. Functional & Integrative Genomics, 6 (3): 186-201. doi: 10.1007/s10142-005-0019-7
    • (2006) Functional & Integrative Genomics , vol.6 , Issue.3 , pp. 186-201
    • Lindsay, J.A.1    Holden, M.T.2
  • 21
    • 0035289779 scopus 로고    scopus 로고
    • Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
    • Lipinski, C.A., Lombardo, F., Dominy, B.W., and, Feeney, P.J. 2001. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 46: 3-26. http://dx.doi.org/10.1016/S0169-409X(96)00423-1
    • (2001) Advanced Drug Delivery Reviews , vol.46 , pp. 3-26
    • Lipinski, C.A.1    Lombardo, F.2    Dominy, B.W.3    Feeney, P.J.4
  • 22
    • 0018039318 scopus 로고
    • DNA-DNA gyrase complex: The wrapping of the DNA duplex outside the enzyme
    • 10.1016/0092-8674(78)90281-7
    • Liu, L.F., and, Wang, J.C. 1978. DNA-DNA gyrase complex: The wrapping of the DNA duplex outside the enzyme. Cell, 979-984. 10.1016/0092-8674(78)90281-7
    • (1978) Cell , pp. 979-984
    • Liu, L.F.1    Wang, J.C.2
  • 23
    • 84878733967 scopus 로고    scopus 로고
    • Maestro (9.2) [Schrödinger, LLC]. New York, NY
    • Maestro (9.2) [Schrödinger, LLC]. New York, NY.
  • 24
    • 84878738768 scopus 로고    scopus 로고
    • Marvin Draw (5.1.5) [Chemaxon Ltd]. Budapest
    • Marvin Draw (5.1.5) [Chemaxon Ltd]. Budapest.
  • 25
    • 0031105464 scopus 로고    scopus 로고
    • DNA gyrase as a drug target
    • Maxwell, A. 1997. DNA gyrase as a drug target. Trends in Microbiology, 5 (3): 102-109. http://dx.doi.org/10.1016/S0966-842X(96)10085-8
    • (1997) Trends in Microbiology , vol.5 , Issue.3 , pp. 102-109
    • Maxwell, A.1
  • 26
    • 34547112538 scopus 로고    scopus 로고
    • Mycobacterium tuberculosis DNA gyrase as a target for drug discovery
    • Mdluli, K., and, Ma, Z. 2007. Mycobacterium tuberculosis DNA gyrase as a target for drug discovery. Infectious Disorders-Drug Targets, 2: 159-168. http://www.benthamdirect.org/pages/content.php?IDDT/2007/00000007/00000002/ 0008S.SGM
    • (2007) Infectious Disorders-Drug Targets , vol.2 , pp. 159-168
    • Mdluli, K.1    Ma, Z.2
  • 27
    • 73749087528 scopus 로고    scopus 로고
    • Computational toxicology - A tool for early safety evaluation
    • Merlot, C. 2010. Computational toxicology-a tool for early safety evaluation. Drug Discovery Today, 15: 16-22. http://dx.doi.org/10.1016/j.drudis. 2009.09.010
    • (2010) Drug Discovery Today , vol.15 , pp. 16-22
    • Merlot, C.1
  • 28
    • 0036493160 scopus 로고    scopus 로고
    • Protein and drug interactions in the minor groove of DNA
    • doi: 10.1093/nar/30.5.1182
    • Morávek, Z., Neidle, S., and, Schneider, B. 2002. Protein and drug interactions in the minor groove of DNA. Nucleic Acids Research, 30 (5): 1182-1191. doi: 10.1093/nar/30.5.1182
    • (2002) Nucleic Acids Research , vol.30 , Issue.5 , pp. 1182-1191
    • Morávek, Z.1    Neidle, S.2    Schneider, B.3
  • 29
    • 35948967317 scopus 로고    scopus 로고
    • Design of DNA minor groove binding diamidines that recognize GC base pair sequences: A dimeric-hinge interaction motif
    • doi: 10.1021/ja074560a
    • Munde, M., Ismail, M.A., Arafa, R., Peixoto, P., Collar, C.J., Liu, Y.,., and, Wilson, W.D. 2007. Design of DNA minor groove binding diamidines that recognize GC base pair sequences: A dimeric-hinge interaction motif. Journal of the American Chemical Society, 129 (44): 13732-13743. doi: 10.1021/ja074560a
    • (2007) Journal of the American Chemical Society , vol.129 , Issue.44 , pp. 13732-13743
    • Munde, M.1    Ismail, M.A.2    Arafa, R.3    Peixoto, P.4    Collar, C.J.5    Liu, Y.6    Wilson, W.D.7
  • 30
    • 84863641465 scopus 로고    scopus 로고
    • NABI Biopharmaceuticals Key facts about S. aureus infections April 10 Miami. Retrieved from
    • NABI Biopharmaceuticals Key facts about S. aureus infections (2007, April 10) NABI Biopharmaceuticals, Miami. Retrieved from http://www.nabi.com
    • (2007) NABI Biopharmaceuticals
  • 31
    • 37549056566 scopus 로고    scopus 로고
    • DNA as a target for anticancer compounds: Methods to determine the mode of binding and the mechanism of action
    • Palchaudhuri, P., and, Hergenrother, P.J. 2007. DNA as a target for anticancer compounds: Methods to determine the mode of binding and the mechanism of action. Current Opinion in Biotechnology, 6: 497-503. http://dx.doi.org/10. 1016/j.copbio.2007.09.006
    • (2007) Current Opinion in Biotechnology , vol.6 , pp. 497-503
    • Palchaudhuri, P.1    Hergenrother, P.J.2
  • 32
    • 0035144211 scopus 로고    scopus 로고
    • Evaluation of the TOPKAT system for predicting the carcinogenicity of chemicals
    • doi: 10.1002/1098-2280(2001) 37:1<55: AID-EM1006>3.0.CO;2-5
    • Prival, M.J. 2001. Evaluation of the TOPKAT system for predicting the carcinogenicity of chemicals. Environmental and Molecular Mutagenesis, 37 (1): 55-69. doi: 10.1002/1098-2280(2001) 37:1<55::AID-EM1006>3.0.CO;2-5
    • (2001) Environmental and Molecular Mutagenesis , vol.37 , Issue.1 , pp. 55-69
    • Prival, M.J.1
  • 33
    • 84878700599 scopus 로고    scopus 로고
    • QikProp (3.4) [Schrödinger, LLC]. New York, NY
    • QikProp (3.4) [Schrödinger, LLC]. New York, NY.
  • 34
    • 84878714502 scopus 로고    scopus 로고
    • QM-Polarized Ligand Docking protocol; Glide version 5.7, Schrödinger, LLC. New York, NY
    • QM-Polarized Ligand Docking protocol; Glide version 5.7, Schrödinger, LLC., New York, NY.
  • 35
    • 0032435458 scopus 로고    scopus 로고
    • Commercial toxicology prediction systems: A regulatory perspective
    • Richard, A.M. 1998. Commercial toxicology prediction systems: A regulatory perspective. Toxicology Letters, 102-103: 611-616. http://dx.doi.org/10.1016/S0378-4274(98)00257-4
    • (1998) Toxicology Letters , vol.102-103 , pp. 611-616
    • Richard, A.M.1
  • 36
    • 37449022029 scopus 로고    scopus 로고
    • Docking mode of delvardine and its analogues into the p66 domain of HIV-1 reverse transcriptase: Screening using molecular mechanics-generalized born/surface area and absorption, distribution, metabolism and excretion properties
    • Sengupta, D., Verma, D., and, Naik, P.K. 2007. Docking mode of delvardine and its analogues into the p66 domain of HIV-1 reverse transcriptase: Screening using molecular mechanics-generalized born/surface area and absorption, distribution, metabolism and excretion properties. Journal of Biosciences, 32 (7): 1307-1316. http://www.springerlink.com/content/d323x7865421j4g0/
    • (2007) Journal of Biosciences , vol.32 , Issue.7 , pp. 1307-1316
    • Sengupta, D.1    Verma, D.2    Naik, P.K.3
  • 37
    • 84878689788 scopus 로고    scopus 로고
    • Sitemap (2.5) [Schrödinger, LLC]. New York, NY
    • Sitemap (2.5) [Schrödinger, LLC]. New York, NY.
  • 38
    • 70449435306 scopus 로고    scopus 로고
    • Staphylococcus aureus nasal carriage and its contributing factors
    • doi: 10.2217/fmb.09.79
    • Sivaraman, K., Venkataraman, N., and, Cole, A.M. 2009. Staphylococcus aureus nasal carriage and its contributing factors. Future Microbiology, 4 (8): 999-1008. doi: 10.2217/fmb.09.79
    • (2009) Future Microbiology , vol.4 , Issue.8 , pp. 999-1008
    • Sivaraman, K.1    Venkataraman, N.2    Cole, A.M.3
  • 39
    • 0026517408 scopus 로고
    • An epidemiological study of burn patients hospitalized in Valencia, Spain, during 1989
    • Tejerina, C., Reig, A., Codina, J., Safont, J., Baena, P., and, Mirabet, V. 1992. An epidemiological study of burn patients hospitalized in Valencia, Spain, during 1989. Burns, 18: 15-18. http://dx.doi.org/10.1016/0305-4179(92) 90112-8
    • (1992) Burns , vol.18 , pp. 15-18
    • Tejerina, C.1    Reig, A.2    Codina, J.3    Safont, J.4    Baena, P.5    Mirabet, V.6
  • 40
    • 0037364162 scopus 로고    scopus 로고
    • ADMET in silico modelling: Towards prediction paradise
    • doi: 10.1038/nrd1032
    • Van de Waterbeemd, H., and, Gifford, E. 2003. ADMET in silico modelling: Towards prediction paradise. Nature Reviews Drug Discovery, 2: 192-204. doi: 10.1038/nrd1032
    • (2003) Nature Reviews Drug Discovery , vol.2 , pp. 192-204
    • Van De Waterbeemd, H.1    Gifford, E.2
  • 41
    • 0024022068 scopus 로고
    • The partition locus of plasmid pSC101 is a specific binding site for DNA gyrase
    • Wahle, E., and, Kornberg, A. 1988. The partition locus of plasmid pSC101 is a specific binding site for DNA gyrase. The EMBO Journal, 7 (6): 1889-1895. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC457182/pdf/emboj00143-0313.pdf
    • (1988) The EMBO Journal , vol.7 , Issue.6 , pp. 1889-1895
    • Wahle, E.1    Kornberg, A.2
  • 42
    • 77956931884 scopus 로고    scopus 로고
    • Molecular dynamics in physiological solutions: Force fields, alkali metal ions, and ionic strength
    • doi: 10.1021/ct9006579
    • Zhang, C., Rauge, S., Eisenberg, B., and, Carloni, P. 2010. Molecular dynamics in physiological solutions: Force fields, alkali metal ions, and ionic strength. Journal of Chemical Theory and Computation, 6: 2167-2175. doi: 10.1021/ct9006579
    • (2010) Journal of Chemical Theory and Computation , vol.6 , pp. 2167-2175
    • Zhang, C.1    Rauge, S.2    Eisenberg, B.3    Carloni, P.4


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