Session Y45: Focus Session: Physics of Cancer II

8:00 AM–11:00 AM, Friday, March 22, 2013
Hilton Baltimore Room: Holiday Ballroom 4

Sponsoring Unit: DBIO
Chair: Larry Nagahara, National Institutes of Health

Abstract ID: BAPS.2013.MAR.Y45.12

Abstract: Y45.00012 : Computational studies on DNA recognition of novel organic and copper anti-tumor compounds

10:36 AM–10:48 AM

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Authors:

  Rafael R. Nascimento
    (Instituto de F\'isica, Universidade de S\~ao Paulo, Brazil)

  Marcos B. Gon\c{c}alves
    (Instituto de F\'isica, Universidade de S\~ao Paulo, Brazil)

  Helena M. Petrilli
    (Instituto de F\'isica, Universidade de S\~ao Paulo, Brazil)

  Ana M. D.C. Ferreira
    (Instituto de Qu\'imica, Universidade de S\~ao Paulo, Brazil)

  Emiliano Ippoliti
    (German Research School for Simulation Sciences, Forschungszentrum Juelich, Germany)

  Jens Dreyer
    (German Research School for Simulation Sciences, Forschungszentrum Juelich, Germany)

  Paolo Carloni
    (German Research School for Simulation Sciences, Forschungszentrum Juelich, Germany)

The ability of many organic and coordination compounds to bind to DNA and/or damage cellular structures has been largely exploited in anticancer research. Identifying DNA recognition mechanisms have thus important impact on the chemical biology of gene expression and the development of new drugs and therapies. Previous studies on copper(II) complexes with oxindole-Schiff base ligands have shown their potential anti-tumor activity towards different cells, inducing apoptosis through a preferential attack to DNA and/or mitochondria [SIL11]. The binding mechanism of the organic and copper(II) complexes [Cu(isaepy)2]2$+$ (1) and [Cu(isaenim)]2$+$ (2) and their modulation at DNA is investigated through theoretical studies. Here we adopted a multi-scale procedure to simulate this large system using molecular docking and classical molecular dynamics. Hybrid Car-Parrinello/Molecular Mechanics calculations were applied to parameterize the copper(II) complexes by using the force matching approach. Free energies of binding are investigated by metadynamics enhanced sampling methods[VAR08]. [SIL11] V. C. da Silveira et. al. JIB 105 (2011) 1692.[VAR08] A. V. Vargiu et. al. Nucl. Acids Res. 36 (2008) 5910.

To cite this abstract, use the following reference: http://meetings.aps.org/link/BAPS.2013.MAR.Y45.12