TY - JOUR
T1 - Modeling of reaction steps relevant to deoxyuridylate (dump) enzymatic methylation and thymidylate synthase mechanism-based inhibition
AU - Leś, Andrzej
AU - Adamowicz, Ludwik
AU - Rode, Wojciech
N1 - Funding Information:
Andrzej Les was partly supported by the State Committee for Scientific Research within the grant 0914/P3/94/06. Ludwik Adamowicz was partly supported by the DoE grant No. DEFG0393ER61605. The authors acknowledge Drs. W.R.Montfort, D.C.Hyatt, and F.Maley for making available their results [17] prior to publication. The computational task was parly done in the ICM computer center, University of Warsaw.
PY - 1998/2
Y1 - 1998/2
N2 - 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 methylmer-captane molecule. The substrate-enzyme binary complex was modeled by the 1-methy 1–5, 6- dihydro-6-thiomethyl-uracil (PI) 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 s24-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 PI molecule interacting with a water molecule bound to the pyrimidine C(4)=0 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)=0 group, or its modification, with the N5,10-methylenetetrahydrofolate N(10) nitrogen atom is suggested as an additional factor influencing the inhibition process.
AB - 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 methylmer-captane molecule. The substrate-enzyme binary complex was modeled by the 1-methy 1–5, 6- dihydro-6-thiomethyl-uracil (PI) 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 s24-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 PI molecule interacting with a water molecule bound to the pyrimidine C(4)=0 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)=0 group, or its modification, with the N5,10-methylenetetrahydrofolate N(10) nitrogen atom is suggested as an additional factor influencing the inhibition process.
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U2 - 10.1080/07391102.1998.10508986
DO - 10.1080/07391102.1998.10508986
M3 - Article
C2 - 9514247
AN - SCOPUS:0031943979
SN - 0739-1102
VL - 15
SP - 703
EP - 715
JO - Journal of Biomolecular Structure and Dynamics
JF - Journal of Biomolecular Structure and Dynamics
IS - 4
ER -