Investigation of reactions postulated to occur during inhibition of ribonucleotide reductases by 2′-azido-2′-deoxynucleotides

Abstract

Model 3′-azido-3′-deoxynucleosides with thiol or vicinal dithiol substituents at C2′ or C5′ were synthesized to study reactions postulated to occur during inhibition of ribonucleotide reductases by 2′-azido-2′-deoxynucleotides. Esterification of 5′-(tert-butyldiphenylsilyl)-3′-azido-3′-deoxyadenosine and 3′-azido-3′-deoxythymidine (AZT) with 2,3-S-isopropylidene-2,3-dimercaptopropanoic acid or N-Boc-S-trityl-L-cysteine and deprotection gave 3′-azido-3′-deoxy-2′-O-(2,3-dimercaptopropanoyl or cysteinyl)adenosine and the 3′-azido-3′-deoxy-5′-O-(2,3-dimercaptopropanoyl or cysteinyl)thymidine analogs. Density functional calculations predicted that intramolecular reactions between generated thiyl radicals and an azido group on such model compounds would be exothermic by 33.6-41.2 kcal/mol and have low energy barriers of 10.4-13.5 kcal/mol. Reduction of the azido group occurred to give 3′-amino-3′-deoxythymidine, which was postulated to occur with thiyl radicals generated by treatment of 3′-azido-3′-deoxy-5′-O-(2,3-dimercaptopropanoyl)thymidine with 2,2′-azobis-(2-methyl-2-propionamidine) dihydrochloride. Gamma radiolysis of N2O-saturated aqueous solutions of AZT and cysteine produced 3′-amino-3′-deoxythymidine and thymine most likely by both radical and ionic processes.

Nitrogen-Centered Radicals Derived from Azidonucleosides

“…Moreover, the γ-radiolysis of N 2 O-saturated aqueous solutions of AZT and cysteine produced 3 ′ -amino-3 ′ -deoxythymidine and thymine. The DFT-calculated predictions and results with radical-initiated intramolecular azido substituent reduction with model compounds, such as 9 and 11, bearing azido and thiol substituents might be in harmony with the enzymatic positioning of azido-containing substrates in close proximity with thiol functionalities that exist in the active sites of RNRs [71].…”

“…Thao and coworkers designed model 3 ′ -azido-3 ′ -deoxynucleosides with thiol or vicinal dithiol substituents at C2 ′ or C5 ′ to study reactions postulated to occur during the inhibition of ribonucleotide reductases (RNRs) by N 3 UDP (9-11, Figure 2) [71]. It was presumed that the intramolecular addition of the thiyl radical in 12 (generated from 9) to the azido group via an eight-membered TS would produce the transient triazenyl radical 13.…”

“…A loss of N 2 would generate nitrogen-centered radical 14 (similar to sulfinylimine radical of type 7; vide supra), and an abstraction of a hydrogen atom by 14 should give a cyclic sulfenamide, which might undergo ring opening to give 3 ′ -amino-3 ′ -deoxy products. Density functional theory calculations predicted that intramolecular reactions between the generated thiyl radicals and azido group on the model compounds 9-11 will be exothermic by 33.6-41.2 kcal/mol with low energy barriers of 10.4-13.5 kcal/mol [71]. The heating of 3′-azido-3′-deoxy-5-O-(2,3-dimercaptopropanoyl)thymidine 11 in H2O with 2′-azobis-(2-methyl-2-propionamidine) dihydrochloride (AAPH) as an initiator for the production of thiyl radicals gave 3′-amino-3′-deoxythymidine, whereas the analogous treatment of 3′-azido-3′-deoxythymidine (AZT, a control substrate lacking a thiol substituent) resulted in the isolation of major quantities of unchanged AZT.…”

“…29, x FOR PEER REVIEW 4 of vide supra), and an abstraction of a hydrogen atom by 14 should give a cyclic sulfenamide, which might undergo ring opening to give 3′-amino-3′-deoxy products. Density functional theory calculations predicted that intramolecular reactions between the generated thiyl radicals and azido group on the model compounds 9-11 will be exothermic by 33.6-41.2 kcal/mol with low energy barriers of 10.4-13.5 kcal/mol[71].…”

End-processing nucleases and phosphodiesterases: An elite supporting cast for the non-homologous end joining pathway of DNA double-strand break repair

“…Inhibitors of RNRs such as gemcitabine prevent this process and the mechanism of action involves a variety of intermediate components, one of them being 3′-keto-2′-deoxynucleotide [46] which can then be incorporated into DNA (Figure 1d). Although this lesion is not formed directly during double-strand cleavage, it can still be construed as a modified DNA end and that would need to be processed.…”