Pyrimidines protonation site

Since a knowledge of the correct tautomeric form of the pyrimidines is a requisite for understanding the mode of binding to active sites, as well as nucleic acid structure and modification, the formulae of the conventionally-named 2- and 4-hydroxypyrimidines are presented in the correct lactam, or pyrimidone, form in this chapter. Other physical properties of the pyrimidines, such as dissociation constants, protonation sites, and distribution coefficients, are presented in cases where there is a known relation to drug activity. Biogenesis and enzyme control mechanisms are discussed where they relate to an understanding of inhibitor action. 

C-NMR studies on l-isopropyl-4-aminopyrazolo[3,4-4]pyrimidine(240, R = i-Pr) and the isomeric 2-isopropyl derivative 241 (R = i-Pr) indicate that N-5 and N-7 are the respective protonation sites (77JA7257). 

The reduction of the pyrimidine to dihydropyrimidine is the reverse of the oxidation reaction carried out by DHODs. The structure of the FMN/pyrimidine-binding site is very similar to the structure of L. lactis DHODs. Three Asn residues form hydrogen bonds with the nitrogens and carbonyls of the pyrimidine analogous to DHODs. DPD has an active site cysteine proposed to act in acid/base chemistry similar to Class 1 DHODs. When mutated to alanine, only 1% of the wild-type activity was retained, indicating the importance of this residue in catalysis. Secondary tritium isotope effects using 5- H-uracil were determined in both H2O and D2O an inverse isotope effect was observed in H2O and the value became more inverse in D20. " This was taken as evidence of a stepwise mechanism in which hydride transfer to C6 is followed by protonation at C5. 

Fig. 7 QM models used to calculate the proton affinity of all protonation sites in the pyrimidine ring. This series of models shows the effects of extensions to the substrate model and of residues hydrogen bonding to the ring. Extensions made to a previous model in the series are shaded to facilitate comparison between models. Models 10 and 11 contain atoms that are kept frozen during the optimization and each of these atoms are marked with an asterisk...

The coordination properties of pyrimidine bases seem to be less versatile than those of purine derivatives. Various Pt(II) and Pt(IV) compounds, including cis- and rrans-DDP, preferentially bind to the N3 site in N1-substituted cytosine derivatives (Figure 7), as verified by a variety of methods [7]. Simultaneous binding to N3 and to the exocyclic amino group C(4)-NH2 upon loss of a proton has been observed in a bridged Pt(II) system and in a chelated Pt(IV) system [7]. With 1,3-di-methyluracil, Pt(II) coordination to the C5 atom has been ascertained by X-ray crystallography [22]. 

Platination of the N3 position in 1-substituted uracil and thymine derivatives requires proton abstraction and usually occurs only at high pH, but the Pt-N3 bond, once formed, is thermodynamically stable (log K 9.6) [7]. Platinum binding to N3 increases the basicity of 04, which becomes an additional binding site leading to di- and trinuclear complexes. A list of X-ray structurally characterized species is given by Lippert [7]. Pt complexes of uracil and thymine can form intensely colored adducts (e.g. platinum pyrimidine blues), which show anticar-cinogenic activity analogously to the monomeric species [7]. 

The emission from [Ru(bpz)3] is quenched by carboxylic acids the observed rate constants for the process can be rationalized in terms of the protonation of the non-coordinated N atoms on the bpz ligands. The effects of concentration of carboxylate ion on the absorption and emission intensity of [Ru(bpz)3] have been examined. The absorption spectrum of [Ru(bpz)(bpy)2] " shows a strong dependence on [H+] because of protonation of the free N sites the protonated species exhibits no emission. Phosphorescence is partly quenched by HsO" " even in solutions where [H+] is so low that protonation is not evidenced from the absorption spectrum. The lifetime of the excited state of the nonemissive [Ru(Hbpz)(bpy)2] " is 1.1ns, much shorter than that of [Ru(bpz)(bpy)2] (88 nm). The effects of complex formation between [Ru(bpz)(bpy)2] and Ag on electronic spectroscopic properties have also been studied. Like bpz, coordinated 2,2 -bipyrimidine and 2-(2 -pyridyl)pyrimidine also have the... 

There is one binding site on RNase with a high association constant for pyrimidine nucleotides. This was demonstrated by difference spectra for 2 -CMP by Nelson and Hummel (457) and confirmed by Barnard and Ramel (458) by sedimentation. No evidence for a second binding site was seen. With l-CM-His-119-RNase no interaction with 2 -CMP was seen spectrally, and the sedimentation studies indicated that if any interaction occurred the dissociation constant was greater than 10 3 M compared to 10-6 M for the native enzyme. A close relationship between the phosphate group and a histidine residue is thus implied as it was in the proton uptake studies referred to above. 

Deeble DJ, von Sonntag C (1985) TheUV absorption spectra of theC(5) and C(6) OH adduct radicals of uracil and thymine derivatives. A pulse radiolysis study. Z Naturforsch 40c 925-928 Deeble DJ, von Sonntag C (1987) Radioprotection of pyrimidines by oxygen and sensitization by phosphate a feature of their electron adducts. Int J Radiat Biol 51 791-796 Deeble DJ, Das S, von Sonntag C (1985) Uracil derivatives sites and kinetics of protonation of the radical anions and the UV spectra of theC(5) and C(6) H-atom adducts. J Phys Chem 89 5784-5788... 

Overlap Geometry A schematic representation of the proposed overlap geometry for proflavine intercalated into a deoxy pyrimidine(3 -5 )purine site is presented below with the (o) symbols representing the location of the phenanthridine ring protons. The mutual overlap of the two base pairs at the intercalation site involves features observed in the crystal structures of a platinum metallointercalator miniature dC-dG duplex complex (55) and the more recent proflavine miniature dC-dG duplex complex (48), as well as features derived in a linked-atom conformational calculation of the intercalation site in the proflavine DNA complex (51). [4]... 

Again we allow for competition between the proton and metal ion for the basic N(l) sites on purine and N(3) sites on pyrimidine 5 -nucleoside monophosphates to find for neutral solutions at pH 7.4 the sequence... 

Suzuki and co-workers <68CPB750> have correlated chemical shift values of protons attached to the carbon at different sites in thiazolo[5,4-J]pyrimidine with the ease of substitution of halogen in 2,5,7-trichlorothiazolo[5,4-J]pyrimidine. The order of reactivity of chlorine was thus concluded to be C-2 > C-5 > C-7 which is the order of chemical shift protons at C-2 resonate at lower field than those at C-5, and C-7 protons resonate at highest field. It seems, however, that the reactivity at C-5 and C-2 is very similar as compound (175) reacts with hydrazine hydrate to yield a mixture of the isomers (176) and (177) (Equation (15)) <79IJC307>. 

When there is an N-oxide function present in an azine, another site becomes available for proton attack. Although pyridazine iV-oxides often react at the free nitrogen, pyrimidine oxides frequently form the hydroxy salts (83CHE1012). 

In general the pyrimidines show a much lower reactivity towards the metal ions. Apparently no reaction was observed with uracil while the stability constants of Cu-cytosine are even lower than the lgJCi and gK% values of Cu(NH3)62+ (79). The high stability of the purine metal complexes can be attributed to the binding site at the imidazole residue. There the imino proton competes with the metal ion. Fig. 1 presents a model of the 2 1 complex of Cu-(adenine)%. 

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