Modeling of reaction steps relevant to deoxyuridylate (dUMP) enzymatic methylation and thymidylate synthase mechanism-based inhibition.
Theoretical quantum mechanical ab initio Hartree-Fock calculations on molecular systems, modeling processes related to the specificity of thymidylate synthase inactivation are reported. We considered several steps of the methylation of the substrate dUMP and 4- or 5-mono- and 4,5-bisubstituted dUMP analogs, as well. The following reactions were modeled: the cysteine residue (Cys198 in the L.casei enzyme) nucleophilic attack on the substrate and the substrate C(5)-H proton abstraction. The substrate was modeled by the 1-methyluracil molecule and its structural analogs. The cysteine Cys198 residue was modeled by the methylmercaptane molecule. The substrate-enzyme binary complex was modeled by the 1-methyl-5,6-dihydro-6-thiomethyl-uracil (P1) molecule. The present theoretical calculations suggest that the cysteine nucleophilic attack on the substrate may result in the SH-group addition to the pyrimidine C(5)=C(6) bond in the course of a weakly exothermic reaction. The formerly presumed enolate carbanion appeared to be weakly stable or unstable and it can readily split into the thiol and pyrimidine residues. The s2-thio- (P2) and s2,4-dithio- (P3) substrate analogs should form stable thiolate anions after cysteine residue attachment to the C(6) position of the pyrimidine ring. Studies of the deformed P1 molecule interacting with a water molecule bound to the pyrimidine C(4)=O carbonyl residue allow a suggestion that this water molecule may be directly involved in the C(5)-H proton abstraction and may serve as a proton transmitter between the substrate and the proton acceptor residue, possibly located on the cofactor N10-nitrogen. Interaction of the pyrimidine C(4)=O group, or its modification, with the N5,10-methylenetetrahydrofolate N(10) nitrogen atom is suggested as an additional factor influencing the inhibition process.
Leś
A
A
Department of Chemistry, University of Warsaw, Poland. ales@tiger.chem.uw.edu.pl
Adamowicz
L
L
Rode
W
W
D000465:Algorithms; D003545:Cysteine / Q000737:chemistry; D003843:Deoxycytidine Monophosphate / Q000031:analogs & derivatives / Q000737:chemistry; D003856:Deoxyuracil Nucleotides / Q000737:chemistry*; D005468:Fluorodeoxyuridylate / Q000737:chemistry; D008745:Methylation; D008956:Models, Chemical; D011789:Quantum Theory; D013438:Sulfhydryl Compounds / Q000737:chemistry; D013763:Tetrahydrofolates / Q000737:chemistry; D013940:Thymidylate Synthase / Q000037:antagonists & inhibitors*; D014498:Uracil / Q000031:analogs & derivatives / Q000737:chemistry; D014867:Water / Q000737:chemistry
D003856:Deoxyuracil Nucleotides; D013438:Sulfhydryl Compounds; D013763:Tetrahydrofolates; D014867:Water; C013123:5,10-methylenetetrahydrofolic acid; D003843:Deoxycytidine Monophosphate; D005468:Fluorodeoxyuridylate; C042920:N-4-hydroxy-2'-deoxycytidylic acid; D014498:Uracil; C002596:1-methyluracil; C007267:2'-deoxyuridylic acid; D013940:Thymidylate Synthase; D003545:Cysteine