Molecular dynamics simulation of the physical mechanisms of the interaction of caffeine and actinocin derivatines with DNA. The role of different factors in DNA-ligand complex formation
Keywords:
actinocin derivative, caffeine, DNA, hydration, complex formation, molecular dynamicsAbstract
Molecular dynamic simulation of the complex of caffeine and the new actinocin derivative with different DNA fragments has been carried out. The molecular models of caffeine and AcII intercalating in GC-site of oligonucleotide d(AGTC)2 and of outside drug binding in the minor groove of oligonucleotide d(GATAC)2 have been obtained. Energetic and structural characteristics of investigated systems have been also defined. It was shown that complexes of actinocin derivative with DNA are more structural and energetic preferable than DNA-caffeine complexes. The analysis of the changes in the first hydration shells of interactive components after their complexation has been carried out. It has been found that the degree of destruction of the monohydrated shell of DNA double-helix after complexation is determined by the mode of ligand binding, its possibility to make the hydration bonds with water molecules and depends a little on linear sizes of ligands.
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