Cytosine, alkylation

FIGURE 2.2 Optimized TS geometries of the cytosine alkylation reaction by o-QM, without and with water assistance. Bond lengths (in A) and activation Gibbs free energies (in kcal/mol) in the gas phase and in aqueous solution (in parentheses) at the B3LYP/6-311 +G(d,p)// B3LYP/6-31G(d) level of theory with respect to the reactants have been taken from Ref. [14]. 

Chemotherapeutic agents are grouped by cytotoxic mechanism. The alkylating agents, such as cyclophosphamide [50-18-0] and melphalan [148-82-3] interfere with normal cellular activity by alkylation deoxyribonucleic acid (DNA). Antimetabohtes, interfering with complex metaboHc pathways in the cell, include methotrexate [59-05-2] 5-fluorouracil [51-21-8] and cytosine arabinoside hydrochloride [69-74-9]. Antibiotics such as bleomycin [11056-06-7] and doxombicin [23214-92-8] h.a.ve been used, as have the plant alkaloids vincristine [57-22-7] and vinblastine [865-21-4]. 

Alkylation of Adenine and Cytosine Residues can Accelerate Deamination 341... 

Deamination, the hydrolytic loss of exocyclic amino groups on the DNA bases, is typically a very slow reaction. For example, deamination of cytosine residues in dnplex DNA occnrs with a half-life of about 30,000 years under physiological conditions, and the deamination of adenine residues is still more sluggish. " Alkylation at the N3-position of cytosine (Scheme 8.5) greatly increases the rate of deamination (ty2 = 406 h). Deamination of 3-methyl-2 -deoxycytidine proceeds 4000 times faster than the same reaction in the unalkylated nucleoside. Alkylation of the N3-position in cytosine residues also facilitates deglycosylation (Jy2 = 7700 h, lower pathway in Scheme 8.5), but the deamination reaction is 20 times faster and, therefore, predominates. ... 

Solomon JJ, Segal A. 1985. Direct alkylation of calf thymus DNA by acrylonitrile. Isolation of cyanoethyl adducts of guanine and thymine and carboxyethyl adducts of adenine and cytosine. Environ Health Perspect 62 227- 230. 

Potentially tautomeric pyrimidines and purines are /V-alkylated under two-phase conditions, using tetra-n-butylammonium bromide or Aliquat as the catalyst [75-77], Alkylation of, for example, uracil, thiamine, and cytosine yield the 1-mono-and 1,3-dialkylated derivatives [77-81]. Theobromine and other xanthines are alkylated at N1 and/or at N3, but adenine is preferentially alkylated at N9 (70-80%), with smaller amounts of the N3-alkylated derivative (20-25%), under the basic two-phase conditions [76]. These observations should be compared with the preferential alkylation at N3 under neutral conditions. The procedure is of importance in the derivatization of nucleic acids and it has been developed for the /V-alkylation of nucleosides and nucleotides using haloalkanes or trialkyl phosphates in the presence of tetra-n-butylammonium fluoride [80], Under analogous conditions, pyrimidine nucleosides are O-acylated [79]. The catalysed alkylation reactions have been extended to the glycosidation of pyrrolo[2,3-r/]pyrimidines, pyrrolo[3,2-c]pyridines, and pyrazolo[3,4-r/]pyrimidines (e.g. Scheme 5.20) [e.g. 82-88] as a route to potentially biologically active azapurine analogues. 

Synthesis of Lipophilic Arabinofuranosyl Cytosine N" -Alkyl Derivatives and Heterodinucleoside Phosphate Duplex Drugs... 

Deprotonation provides the necessary electron push to kick out the electron pair joining C(6) with the nitrobenzene oxygen. If, however, N(l) is alkylated (as with the nucleosides and nucleotides), OH catalysis is much less efficient since it now proceeds by deprotonation from N(3) (with the uracils) or from the amino group at C(4) (with the cytosines). In these cases the area of deprotonation is separated from the reaction site by a (hydroxy)methylene group which means that the increase in electron density that results from deprotonation at N(3) is transferable to the reaction site only through the carbon skeleton (inductive effect), which is of course inefficient as compared to the electron-pair donation from N(l) (mesomeric effect) [26]. Reaction 15 is a 1 1 model for the catalytic effect of OH on the heterolysis of peroxyl radicals from pyrimidine-6-yl radicals (see Sect. 2.4). 

P-Propiolactone is a direct-acting alkylating agent that reacts with polynucleotides and DNA, mainly at N7 of guanine and NI of adenine, to form carboxyethyl derivatives. It also forms adducts with the N of cytosine and thymine (Hemminki, 1981 Lawley, 1984). It is genotoxic to a wide range of organisms in vitro and in vivo. 

Alkylating agents can alter certain bases of DNA For example, the highly reactive chemical dimethylsul-fate (Fig. 8—35b) can methylate a guanine to yield O6-methylguanine, which cannot base-pair with cytosine. 

FIGURE 25-27 Direct repair of alkylated bases by AlkB. The AlkB protein is an a-ketoglutarate-Fe2+-dependent dioxygenase. It catalyzes the oxidative demethylation of 1-methyladenine and 3-methyl-cytosine residues. 

Ogilvie et al.ls0 have described facile alkylation of purines and pyrimidines in THF, using tetrabutylammonium fluoride (TBAF) at room temperature. Uracil, cytosine, and adenine give mainly 1,3-dialkylation. 

UV spectroscopy is a sensitive tool for the elucidation of structures of molecules only if the different tautomers have distinct spectra. In some cases, cytosine or cytidine and their alkylated analogs have similar spectra with seriously overlapping bands, and thus the application of UV spectroscopy to the elucidation of the tautomeric structures of the molecules is inconclusive. In particular, the method is unreliable for the determination of tautomeric equilibria of cytosine (see below). Nevertheless the UV absorption spectra confirm the conclusions drawn from other studies as to the main form of cytosine and cytidine in aqueous solution at room temperature. 

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