Modeling of reaction steps relevant to deoxyuridylate (dUMP) enzymatic methylation and thymidylate synthase mechanism-based inhibition

Combined computational and experimental studies on cysteine-sulfadiazine adduct formation

The electrochemical characterization of sulfadiazine-cysteine (SD-CYS) adduct formation was performed in phosphate buffer (pH 7) on the basis of voltammetric current and peak potential measurements. Due to the association of cysteine with sulfadiazine, the reduction peak currents of mercuric and mercurous cysteine thiolates decreased and their peak potentials simultaneously shifted to less negative potentials. By using the current changes of mercurous cysteine thiolate, it was determined that cysteine and sulfadiazine are associated with a 1:1 stoichiometry with a conditional association constant of 1.99 ×104 M-1 . In addition to experimental studies, a computational approach was carried out to study the geometrical parameters, electron densities, and UV-Vis absorption spectra of sulfadiazine and SDCYS adduct in water. Calculated (B3LYP/6-311++G(d,p) level) and experimental UV-Vis absorption spectra of the compounds were found to be in good agreement in water. The computational study suggests that cysteine bound to the C(5) on the pyrimidine ring via SH-group nucleophilic attack. Computational results reveal that sulfadiazine and its derivatives effectively bind cysteine and may lead to new molecules/drugs to target cysteine.

Crystal structure of YecO from Haemophilus influenzae (HI0319) reveals a methyltransferase fold and a bound S-adenosylhomocysteine

The crystal structure of YecO from Haemophilus influenzae (HI0319), a protein annotated in the sequence databases as hypothetical, and that has not been assigned a function, has been determined at 2.2-A resolution. The structure reveals a fold typical of S-adenosyl-L-methionine-dependent (AdoMet) methyltransferase enzymes. Moreover, a processed cofactor, S-adenosyl-L-homocysteine (AdoHcy), is bound to the enzyme, further confirming the biochemical function of HI0319 and its sequence family members. An active site arginine, shielded from bulk solvent, interacts with an anion, possibly a chloride ion, which in turn interacts with the sulfur atom of AdoHcy. The AdoHcy and nearby protein residues delineate a small solvent-excluded substrate binding cavity of 162 A(3) in volume. The environment surrounding the cavity indicates that the substrate molecule contains a hydrophobic moiety and an anionic group. Many of the residues that define the cavity are invariant in the HI0319 sequence family but are not conserved in other methyltransferases. Therefore, the substrate specificity of YecO enzymes is unique and differs from the substrate specificity of all other methyltransferases sequenced to date. Examination of the Enzyme Commission list of methyltransferases prompted a manual inspection of 10 possible substrates using computer graphics and suggested that the ortho-substituted benzoic acids fit best in the active site.

Different Activities of 5-Hydroxy-dUMP and 5-Hydroxymethyl-dUMP in Thymidylate Synthase-Catalyzed Reaction in View of Molecular Modeling and Structural Studies

In order to explain different activities shown by 5-hydroxy-dUMP (substrate) and its close analogue 5-hydroxymethyl-dUMP (slow-binding inhibitor) in the reaction catalyzed by thymidylate synthase, studies have been undertaken involving (i) ab initio RHF simulations, (ii) comparative analysis of crystallographic structures available from CSD, and (iii) QSAR analysis of experimental results describing thymidylate synthase interaction with various 5-substituted dUMP analogues. Assuming substrate activity of 5-hydroxy-dUMP to be associated with proton release from the C(5) hydroxyl in the enzyme-catalyzed reaction, acidities of 5-hydroxy and 5-hydroxymethyl substituents in dUMP molecule were compared. The results indicate the 5-hydroxyl deprotonation to be easier and supported by resonance electronic effect, pointing to a probable mechanism of different activities of the two dUMP analogues in thymidylate synthase reaction. The possibility is discussed that 5-mercapto-dUMP and 5-hydroseleno-dUMP, previously assumed to be inhibitors, could be also substrates for thymidylate synthase, as the 5-mercaptyl and 5-hydroselenidyl appear to be deprotonated even more easily than the 5-hydroxyl. Copyright 2000 Academic Press.