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Abstract

5'-Phosphorylation, catalyzed by human deoxycytidine kinase (dCK), is a crucial step in the metabolic activation of anticancer and antiviral nucleoside antimetabolites, such as cytarabine (AraC), gemcitabine, cladribine (CdA), and lamivudine. Recently, crystal structures of dCK (dCKc) with various pyrimidine nucleosides as substrates have been reported. However, there is no crystal structure of dCK with a bound purine nucleoside, although purities are good substrates for dCK. We have developed a model of dCK (dCKm) specific for purine nucleosides based on the crystal structure of purine nucleoside bound deoxyguanosine kinase (dGKc) as the template. dCKm is essential for computer aided molecular design (CAMD) of novel anticancer and antiviral drugs that are based on purine nucleosides since these did not bind to dCKc in our docking experiments. The active site of dCKm was larger than that of dCKc and the amino acid (aa) residues of dCKm and dCKc, in particular Y86, Q97, D 133, R 104, R 128, and E197, were not in identical positions. Comparative docking simulations of deoxycytidine (dC), cytidine (Cyd), AraC, CdA, deoxyadenosine (dA), and deoxyguanosine (dG) with dCKm and dCKc were carried out using the FlexX (TM) docking program. Only dC (pyrimidine nucleoside) docked into the active site of dCKc but not the purine nucleosides dG and dA. As expected, the active site of dCKm appeared to be more adapted to bind purine nucleosides than the pyrimidine nucleosides. While water molecules were essential for docking experiments using dCKc, the absence of water molecules in dCKm did not affect the ability to correctly dock various purine nucleosides. (c) 2005 Elsevier Ltd. All rights reserved.

Keywords

deoxycytidine kinase; computer aided molecular design; docking simulation; homology modeling; antiviral and anticancer therapy

Published in

Bioorganic and Medicinal Chemistry
2005, volume: 13, number: 13, pages: 4160-4167
Publisher: PERGAMON-ELSEVIER SCIENCE LTD

SLU Authors

  • Eriksson, Staffan

    • Department of Molecular Biosciences, Swedish University of Agricultural Sciences

Publication identifier

  • DOI: https://doi.org/10.1016/j.bmc.2005.04.037

Permanent link to this page (URI)

https://res.slu.se/id/publ/5774