A molecular modeling study of the interaction of 2'-fluoro-substituted analogues of dUMP/FdUMP with thymidylate synthase.

Adam Jarmuła, Anna Dowierciał, Wojciech Rode

Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura 3, 02-093 Warszawa, Poland. a.jarmula@nencki.gov.pl

Bioorganic & medicinal chemistry letters 2008 Apr 15

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Molecular dynamics simulations and free energy calculations are presented, exploring previously described experimentally studied interactions of a series of 2'-fluoro-substituted dUMP/FdUMP analogues with thymidylate synthase (TS). The results show the inhibitory behaviors of 2'-F-ara-UMP, 2',2''-diF-dUMP and 2',5-diF-ara-UMP to be dependent upon the binding positions and orientations adopted by the molecules of these compounds in the active site of TS. The binding mode of 2',5-diF-ara-UMP suggests a novel role of the active site residue Trp 80, stabilizing through hydrophobic stacking the binding position of the pyrimidine ring in 2',5-diF-ara-UMP.

Citation

Adam Jarmuła, Anna Dowierciał, Wojciech Rode. A molecular modeling study of the interaction of 2'-fluoro-substituted analogues of dUMP/FdUMP with thymidylate synthase. Bioorganic & medicinal chemistry letters. 2008 Apr 15;18(8):2701-8