Probing mechanism of metal catalyzed hydrolysis of Thymidylyl (3'-O, 5'-S) thymidine phosphodiester derivatives.

Mahboobeh Rahimian, Shridhar P Gejji

Journal of molecular modeling 2013 Mar

filter terms:

Hydrolysis of nucleic acids is of fundamental importance in biological sciences. Kinetic and theoretical studies on different substrates wherein the phosphodiester bond combined with alkyl or aryl groups and sugar moiety have been the focus of attention in recent literature. The present work focuses on understanding the mechanism and energetics of alkali metal (Li, Na, and K) catalyzed hydrolysis of phosphodiester bond in modeled substrates including Thymidylyl (3'-O, 5'-S) thymidine phosphodiester (Tp-ST) (1), 3'-Thymidylyl (1-trifluoroethyl) phosphodiester (Tp-OCH(2)CF(3)) (2), 3'-Thymidylyl (o-cholorophenyl) phosphodiester (Tp-OPh(o-Cl)) (3) and 3'-Thymidylyl(p-nitrophenyl) phosphodiester (Tp-OPh(p-NO(2))) (4) employing density functional theory. Theoretical calculations reveal that the reaction follows a single-step (A(N)D(N)) mechanism where nucleophile attack and leaving group departure take place simultaneously. Activation barrier for potassium catalyzed Tp-ST hydrolysis (12.0 kcal mol(-1)) has been nearly twice as large compared to that for hydrolysis incorporating lithium or sodium. Effect of solvent (water) on activation energies has further been analyzed by adding a water molecule to each metal ion of the substrate. It has been shown that activation barrier of phosphodiester hydrolysis correlates well with basicity of leaving group.

Citation

Mahboobeh Rahimian, Shridhar P Gejji. Probing mechanism of metal catalyzed hydrolysis of Thymidylyl (3'-O, 5'-S) thymidine phosphodiester derivatives. Journal of molecular modeling. 2013 Mar;19(3):1027-37