The effect of 5-substitution in the pyrimidine ring of dUMP on the interaction with thymidylate synthase: Molecular modeling and QSAR

Effect of Halogen Substitutions on dUMP to Stability of Thymidylate Synthase/dUMP/mTHF Ternary Complex Using Molecular Dynamics Simulation

“…Accordingly, the dynamic property of TS in the absence of the mTHF cofactor (binary complex) may not be assumed to reasonably describe the ternary complex behavior, in contrast to a previous study. 14 The important fragments (five flexible loops, two helixes and a β sheet) involved in the binding sites for dUMP and mTHF are shown in Figure 2. To explore the effect of mTHF binding on the TS active site conformation, which may involve a change in the overall protein flexibility, the fluctuation in the conformation of these fragments was considered in terms of comparing the respective regions of the RMSD plots between the binary and ternary complexes (Figure 4A and 4B).…”

“…The substitution on the C5 position of dUMP with electron withdrawing groups was previously proposed in a QSAR study to increase the reactivity of the Michael addition reaction in TS. 14 To investigate the effect of halogen substitutions at this position on the active conformation of the binary and ternary complexes in the Michael addition, the distribution of the three intermolecular distances of (i) d 1 [S(C146)−NH2(R166)] between the reactive C146 and the stabilized R166, (ii) d 2 [S(C146)− C6(dUMP)] responsible for the focused reaction, and (iii) d 3 [O(Y94)-C5(dUMP)] that corresponds to a unique hydrogen bond with the TS Y94 residue, was monitored (see Figure 7B for the definition of d 1 −d 3 ) and is plotted in Figure 8.…”

“…This atomic charge change has been proposed to then influence the reactivity of the Michael addition reaction, which in turn indirectly effects the subsequent ternary covalent complex formation. 14 The ternary covalent intermediate formation is achieved via many simultaneous steps of conformational activation of the two substrates, dUMP, and mTHF. The description of the effect of C-5 substituents on the ternary covalent complex formation without any interference from the other intrinsic reactions has so far been limited to that derived from experimental approaches.…”

“…Molecular dynamics (MD) simulations were applied to investigate the dynamic properties as well as the intermolecular interaction between TS and the different dUMP halogen analogues using the TS/dUMP binary complex as the representative model. 14 Afterward, superimposition of the simulated binary complex to the crystal structure (static ternary complex structure) was used to broadly describe the effect of each halogen substituent on the ternary dynamics.…”

“…The fluorine substituent not only interferes with the β-elimination reaction but also directly influences the atomic charge of the C-5 atom as well. This atomic charge change has been proposed to then influence the reactivity of the Michael addition reaction, which in turn indirectly effects the subsequent ternary covalent complex formation …”