Relative binding free energy calculations of DNA to daunomycin and its 13-dihydro analogue.
We present the results of thermodynamic integration/molecular dynamics on the 13-dihydrodaunomycin.d(CGTACG) complex and 13-dihydrodaunomycin in vacuo based on the GROMOS force field. The objective is to calculate the binding free energy differences between two complexes--13-dihydrodaunomycin.d(CGTACG) and daunomycin.d(CGTACG). The results are in agreement with the experimental data, i.e. the theoretical binding free energy difference of 13-dihydrodaunomycin.d(CGTACG) and daunomycin.d(CGTACG) is 2.1 +/- 1.6 kcal/mol which accords well with the experimental value of 0.6 kcal/mol. The free energy contributions of different interactions and different groups have also been analysed.
Department of Biology, University of Science and Technology of China, Hefei, Anhui.
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Shi
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Zhao
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Wang
D004247:DNA / Q000378:metabolism*; D003630:Daunorubicin / Q000031:analogs & derivatives* / Q000378:metabolism*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry / Q000378:metabolism; D013816:Thermodynamics
D009838:Oligodeoxyribonucleotides; D004247:DNA; C000847:daunorubicinol; D003630:Daunorubicin