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American Journal of Drug Discovery and Development
Year: 2014  |  Volume: 4  |  Issue: 2  |  Page No.: 121 - 133

In silico and in vivo Study the Mode of Action and Effect of Some Biurets as DNA Binding Agent

Neda Adibpour, Saeed Rezaee, Ali Khalaj, Ali Ramazani and Fakher Rahim    

Abstract: In silico biology, including computers, databases, methods and algorithms are used for statistically analyzing the data to achieve the extract information and to identify the relationships between these data sets. This study aimed to provide alternative and new drugs that connect to DNA by using in vivo, in silico and find the best option from the newly designed series of drugs. Out of 143 DNA dodecamer crystal structures available in PDB, we have selected three structures and retrieved from the Protein Data Bank (PDB), with minor/major groove or both groove biding mode. Eighteen experimental ligands were docked using AutoDock 4.3 program into the active sites of selected drug-DNA structures. We docked our experimental ligands into three modeled DNA structured and compared those to internal evaluated ligands (drug compounds include ditercalinium, adriamycin and propamidine) and observed the same binding sites in experimental ligands in comparison to internal ligands. Docking results of 6m and 6p compounds into oligonucleotide in comparison to adrimycin and propamidine showed almost same binding fashion. Our results display that the most plausible mode of action of these experimental drugs as DNA binding agents is through intercalation of AT base pairs-linker chain and azole-minor groove. Accordingly, other DNA-drug crystal structures can be used as good patterns for further improvements using in silico and structure-based drug design methods.

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