5-Selenocyanato and 5-trifluoromethanesulfonyl derivatives of 2'-deoxyuridine: synthesis, radiation and computational chemistry as well as cytotoxicity

Abstract

5-Selenocyanato-2'-deoxyuridine (SeCNdU) and 5-trifluoromethanesulfonyl-2'-deoxyuridine (OTfdU) have been synthesized and their structures have been confirmed with NMR and MS methods. Both compounds undergo dissociative electron attachment (DEA) when irradiated with X-rays in an aqueous solution containing a hydroxyl radical scavenger. The DEA yield of SeCNdU significantly exceeds that of 5-bromo-2'-deoxyuridine (BrdU), remaining in good agreement with the computationally revealed profile of electron-induced degradation. The radiolysis products indicate, in line with theoretical predictions, Se-CN bond dissociation as the main reaction channel. On the other hand, the DEA yield for OTfdU is slightly lower than the degradation yield measured for BrdU, despite the fact that the calculated driving force for the electron-induced OTfdU dissociation substantially overpasses the thermodynamic stimulus for BrdU degradation. Moreover, the calculated DEA profile suggests that the electron attachment induced formation of 5-hydroxy-2'-deoxyuridine (OHdU) from OTfdU, while 2'-deoxyuridine (dU) is mainly observed experimentally. We explained this discrepancy in terms of the increased acidity of OTfdU resulting in efficient deprotonation of the N3 atom, which brings about the domination of the OTfdU(N3-H)^- anion in the equilibrium mixture. As a consequence, electron addition chiefly leads to the radical dianion, OTfdU(N3-H)˙^2-, which easily protonates at the C5 site. As a result, the C5-O rather than O-S bond undergoes dissociation, leading to dU, observed experimentally. A negligible cytotoxicity of the studied compounds toward the MCF-7 cell line at the concentrations used for cell labelling calls for further studies aiming at the clinical use of the proposed derivatives.

Fig. 1. Structures used for calculations. Bonds that were tested for breakage upon electron attachment are marked with the green dotted lines. The pyrimidine ring atoms numbering is shown on the OTfdU structure.

Fig. 2. DEA pathway for OTfdU along with the names of particular stationary points. The neutral molecule (NEU) becomes anion radical (AR) after electron attachment, and then, via transition state (TS) is transformed into the product complex (COM). ISOL stands for the non-interacting fragments, separated to infinity.

Fig. 3. Gibbs free energy changes during DEA for the selected uracil and 2′-deoxyuridine derivatives calculated at the M06-2X/6-31++G(d,p) level. DEA for BrdU, calculated at the same level of theory, is shown for comparison.

Fig. 4. HPLC analysis of a solution of BrdU (A), CH₂CNU (B), SeCNdU (C) and OTfdU (D) before (black chromatograms) and after irradiation with a dose of 140 Gy (red chromatograms).

Fig. 5. OTfdU electron induced degradation paths. Normal arrows lead to the main, while dotted arrows lead to the side products of each path. Final products of each path are framed.

Fig. 6. Viability of MCF-7 cells after 24 and 48 h treatment with SeCNdU (A) and OTfdU (B) in a range of concentrations from 0 to 2 × 10⁻⁴ M. Results are shown as mean ± SD of three independent experiments performed in triplicate. *statistically significant difference is present between treated samples compared with control (untreated sample).