Nucleotides phosphoramidates

The formation of a phosphorimidazolide intermediate provides better reactivity toward amine nucleophiles than the EDC phosphodiester intermediate if EDC is used without added imidazole. The EDC phosphodiester intermediate also has a shorter half-life in aqueous conditions due to hydrolysis than the phosphorimidazolide. Although EDC alone will create nucleotide phosphoramidate conjugates with amine-containing molecules (Shabarova, 1988), the result of forming the secondary phosphorimidazolide-activated species is increased derivatiza-tion yield over carbodiimide-only reactions. 

Cyclophosphamide (Cytoxan) is the most versatile and useful of the nitrogen mustards. Preclinical testing showed it to have a favorable therapeutic index and to possess the broadest spectrum of antitumor activity of all alkylating agents. As with the other nitrogen mustards, cyclophosphamide administration results in the formation of cross-links within DNA due to a reaction of the two chloroethyl moieties of cyclophosphamide with adjacent nucleotide bases. Cyclophosphamide must be activated metabofically by microsomal enzymes of the cytochrome P450 system before ionization of the chloride atoms and formation of the cyclic ethylenimmonium ion can occur. The metabolites phosphoramide mustard and acrolein are thought to be the ultimate active cytotoxic moiety derived from cyclophosphamide. 

The first application of this reaction for the synthesis of sugar nucleotides was reported in 1958, when Moffatt and Khorana269 prepared uridine 5 -(a-D-glucopyranosyl pyrophosphate) (5) in 59% yield from uridine 5 -phosphoramidate (58). Other examples of similar... 

In all of the foregoing examples, an activated derivative of the nucleotide has been employed for generating the pyrophosphate link. An attempt to use an activated glycosyl phosphate failed 311 the only product identified from the reaction between /3-D-glucopyranosyl phosphoramidate (68) and uridine 5 -phosphate was the cyclic phosphate 69. The ease of participation of the sterically accessible, C-2 hydroxyl group probably accounts for this result. The usual procedure... 

BNA (also known as LNA) has been used in TFOs in a pyrimidine motif at neutral pH. The binding constant of the BNA TFO was about 20 times larger than that of DNA as a result of a large decrease in the dissociation rate constant. A 3 -amino-2, 4 -BNA nucleotide has been prepared to introduce N3 -P5 phosphoramidate linkages. It is introduced as a dinucleotide unit (61), and in thermal stability studies was shown to exhibit superior duplex and triplex stability compared to either BNA or DNA, and shows enhanced resistance to digestion by SVPDE. These properties have previously been observed for N3 -P5 phosphoramidate linkages in DNA. ... 

Symmetrical dinucleoside phosphoramidates and iV-substituted phosphora-midates (63) and (64) were obtained after oxidative coupling of the symmetrical //-phosphonate diester of AZT with the appropriate amine Biological evaluation on HIV-infected TK-deficient cell lines suggested that such dinucleoside phosphoramidates could not be regarded as pronucleotides, as they were unable to deliver the corresponding 5 -nucleotide inside the cells. 

Phosphorylation. Chambers et al. found the reagent useful for the preparation of nucleoside diphosphoric acids (3, R —adenine, uracil, etc.). A nucleotide (I) is converted into the 5 -phosphoramidate (2) by reaction with ammonia and dicyclo-hexylcarbodiimide (DCC), and the amidate (2) is treated with dioxane diphosphate in o-chlorophenol (3 hrs..0 ). The diphosphoric acid (3) is precipitated with petroleum ether and purified as the ammonium salt. Yields are around 90%, whereas when 8.5% phosphoric add was used yields were in the order of 50-60%. However, anhydrous... 

The synthesis of a nucleotide-like phosphoramidite building block in which the nucleic base has been replaced by a tert-butyldimethylsilyl-protected styrene glycol (47) has been described. After its incorporation in an oligonucleotide by automated synthesis, the terminal alcohol has been oxidized with NaI04 after fluoride deprotection. A similar phosphoramidate in which the nucleic base has been replaced by an alkyl diol (48) has been incorporated in an oligonucleotide and further conjugated with biotin after oxidation to the aldehydic functional-ity. ... 

The conformationally-locked 3 -amino thymidine derivative (47) was prepared and incorporated into DNA as a dimer unit, attaching the amino group via a carbamate or phosphoramidate linkage.Both modifications were found to be destabilising towards both RNA and DNA targets. The hybridisation properties of an amino-modified bicyclic thymine nucleotide (48) have been exam-ined. Using alternate T and (48) residues there is an increase in duplex stability with d(A)io, with no pH dependence. When the amino group is acetylated, the duplex stability is decreased. The locked C-nucleoside oxazole derivative (49) has been incorporated into TFOs where it was found to selectively enhance the stability with a C.G base pair. ... 

The reaction of 5 -amino-5 -deoxyadenosine with trimetaphosphate affords the 5 -Af-triphosphate (23). When (23) is employed as substrate with glucose in the hexokinase-catalysed reaction, the 5 -AT-diphosphate (24) is obtained the latter is cleaved by snake venom phosphodiesterase to the 5 -phosphoramidate, and hydrolyses in acid to the amino-nucleoside. It does not appear to be polymerized by polynucleotide phosphorylase. In this context it is noteworthy that uridine 5 -5-thiopyrophosphate (25) is a competitive inhibitor for polynucleotide phosphorylase from E. coli, but not a substrate, and that the 5 -S-thiotriphosphates (26) and (27) show neither substrate nor inhibitory properties for RNA polymerase or DNA polymerase I, respectively. However, (23) can be polymerized using the latter enzyme, showing that the introduction of a 5 -heteroatom does not completely exclude these modified nucleotides as substrates for the polymerizing enzymes. 

Nucleotides in aqueous solution can be alkylated at the phosphate (and in some cases the nucleoside also) by the action of l-oxidopyridin-2-yldiazo-methane (33). - The protecting group may be removed from the phosphate with snake venom phosphodiesterase, or generally by acetic anhydride treatment, followed by ammonia. Phosphoramidates have been described previously as phosphate-protecting groups, and if 2-naphthylamine is used as its anilidate for this purpose, organic solvent extraction (as above) is possible. A variation on this theme is to use dianilidophosphochloridate (34) as a... 

Nucleoside S -phosphoramidates have proved to be useful intermediates in the synthesis of nucleoside 5 -pyrophosphates and nucleotide coenzymes. Nucleoside phosphoramidates may also be prepared by treatment of a nucleoside 5 -phosphate with ammonia in the presence of N, IV -dioyclohexylcarbodiimide [R. W. Chambers and J. G. Moffatt, J. Am. Chem. Soc., 80, 3752 (1958)]. 

As pointed out in section 9.6.5, insertion of 3 -0-(N,N-diisopropylamino)methoxyphos-phine nucleotide monomers and subsequent amidation using 1,5-diaminopentane/iodine leads to aminoalkylated phosphoramidates, which may act as linkers for functional moieties (Fig. 33). 

A/ A -Dimethyl-p-phenylenediamine (30) has been attached to nucleotides to form basic phosphoramidates. These have been polymerized and the products purified by using a cationic rather than an anionic ion-exchange... 

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