Fate of the C-1′ peroxyl radical in the 2′-deoxyuridine system

Article abstract of DOI:10.1039/a802375a

The mechanism of 2-deoxyribonolactone formation from the reaction of photogenerated 2′-deoxyuridin-1′-yl radical with molecular oxygen in water has been investigated.

Full text of DOI:10.1039/a802375a

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Fate of the C-1A peroxyl radical in the 2A-deoxyuridine system
Chryssostomos Chatgilialoglu*† and Thanasis Gimisis*‡
I.Co.C.E.A., Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 1-40129 Bologna, Italy
The mechanism of 2-deoxyribonolactone formation from the
O
O
reaction of photogenerated 2A-deoxyuridin-1A-yl radical with
HN
N
HN
molecular oxygen in water has been investigated.
O
O
N
O
O
A number of agents are able to react with DNA to generate
RO
RO
i
macromolecular radical species.1 These processes are of
CN
CN
considerable importance since they can lead to base modifica-
RO
RO
Br
tion or strand scissions. As research progresses in the area of the
mechanism of attack of oxidative DNA cleavers, it becomes
evident that hydrogen abstraction from the C-1A position is
involved in many cases.2,3 Evidence for the existence of these
radical species is mainly based on product studies,4,5 although
spectroscopic and theoretical studies have been reported.6,7
Furthermore, based on the b-(acyloxy)alkyl radical rearrange-
ment of a C-2A radical, we have suggested that C-1A radicals are
stabilized substantially by the presence of the base and that the
degree of stabilization is similar for purine and pyrimidine
moieties.8 Under aerobic conditions, however, C-1A radicals 1
afford 2-deoxyribonolactone 2 [eqn. (1)] through a number of
3 R = TBDMS
4 R = TBDMS
ii
O
HN
O
N
O
RO
iii
C(O)CMe3
RO
5 R = TBDMS
6 R = H
Scheme 1 Reagents and conditions: i, (TMS)3SiH, AIBN, toluene, 80 °C,
2 h, 94%; ii, 3 equiv. ButLi, THF, 278 °C, 5 min, 37%; iii, NH4F, MeOH,
60 °C, 24 h, 90%
O
O
O2
Base
O
HO
HO
(1)
H2O
HO
HO
1
2
and 5 in 15 and 85% yield, respectively. GC–MS analysis of
compound 7 showed an isotopic cluster of [M 2 57]+ as
reported in Fig. 1(a). A control experiment showed that
photolysis of the sample under anaerobic conditions gave
neither compound 2 nor uracil among the products.
currently disputed pathways.1,2,5 We report herein an ex novo
synthesis of tert-butyl ketone 69 and the mechanism of the
formation of 2 [eqn. (1)].
The recently reported synthesis of 6 has two major draw-
backs:9 (i) a known psiconucleoside triol, prepared by a low
yielding, laborious procedure, is used as the precursor,10 and (ii)
a total lack of regioselectivity in the protection step of this triol
is observed. For these reasons, we used as our precursor
compound 3, readily available in diastereomerically pure form
The oxygen source of the carbonyl in the lactone 2 was
determined by photolysis of 6 in the presence of 16O–16O and
303.0
(a)
from
the
corresponding
protected
1A,2A-didehydro-
2A-deoxyuridine by a literature procedure.11 When 3 was treated
with (TMS)3SiH12 under normal free radical conditions, the
crystalline cyanide 4 was obtained in excellent yield (94%)
(Scheme 1).13 Short treatment of 4 with excess of ButLi yielded,
after silica gel purification, the protected tert-butyl ketone 5 as
the major product (37% yield, 45% based on recovered starting
material).§ Finally, deprotection (NH4F, MeOH, 60 °C, 24 h,
90%) produced the water soluble adduct 6.
304.1
305.1
306.1
307.1
A quartz tube containing ketone 6 (23 mg; 0.073 mmol) in
H2O (200 ml) was photolyzed with a 500 W high pressure
mercury lamp at room temperature. During the photolysis,
continuous bubbling of air through the sample ensured the
presence of O2 in the reaction mixture. After 6 h of photolysis,
1H NMR analysis (CD3CN) of the lyophilized sample indicated
a product ratio of 1:0.15:0.15 for 6:2:uracil.14 The products
were derivatized with ButMe2SiCl/imidazole/DMF and isolated
by flash chromatography (hexane–ethyl acetate 9:1) to give 714
303.1
(b)
305.1
304.2
304
306.1
306
307.1
307
308.1
308
O
X
RO
302
303
305
m / z
309
Fig. 1 Isotopic clusters of [M 2 57]+ from the electron impact mass spectra
of protected 2-deoxyribonolactone obtained by GC–MS analysis. (a)
Sample isolated from the reaction in H216O (of natural isotopic distribution).
(b) Sample isolated from the reaction in H218O (95 atom% 18O).
RO
7 R = TBDMS, X = 16
8 R = TBDMS, X = 18O
O
Chem. Commun., 1998
1249

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O
Notes and References
O
HO
7
U
† E-mail: chrys@area.bo.cnr.it
‡ E-mail: gimisis@area.bo.cnr.it
ROO
HO
§ Selected data for 5: white solid, mp (pentane) 179–181 °C. dH(200 MHz;
C6D6) 20.06, 20.04 (3 H each, s, SiMe), 20.01 (6 H, s, 2 3 SiMe), 0.86,
0.91 (9 H each, s, SiBut), 1.27 (9 H, s, But), 2.26 (1 H, dd, J 13.8, 7.4, 2Aa-
H), 3.46 (1 H, dd, J 12.3, 2.4, 5Aa-H), 3.62 (2 H, m, 4A, 5Ab-H), 3.75 (1 H,
dd, J 13.8, 8.8, 2Ab-H), 4.41 (1 H, ddd, J 8.8, 7.4, 3A-H), 5.73 (1 H, d, J 8.2,
5-H), 8.15 (1 H, d, J 8.2, 6-H), 9.29 (1 H, bs, NH); dC(50 MHz; C6D6)
25.63, 25.57, 25.02, 24.42 (each CH3), 18.0, 18.4 (each C), 25.78, 25.79,
29.0 (each 3 3 CH3), 42.5 (CH2), 43.5 (C), 60.2 (CH2), 68.5, 87.0 (each
CH), 97.5 (C), 102.0, 139.0 (each CH), 150.5, 163.2, 201.2 (each C).
10
O
O
O
HO
U
HO
9
H218O
O
+
U
1 DNA and RNA Cleavers and Chemotherapy of Cancer and Viral
Diseases, ed. B. Meunier, Kluwer, Dordrecht, 1996; for a review, see G.
Pratviel, J. Bernadou and B. Meunier, Angew. Chem., Int. Ed. Engl.,
1995, 34, 746.
2 For a recent review, see C. Chatgilialoglu and T. Gimisis, in Free
Radicals in Biology and Environment, ed. F. Minisci, Kluwer,
Dordrecht, 1997, pp. 281–292.
O
HO
8
HO
11
Scheme 2 Proposed mechanism for the formation of 2-deoxyribonol-
actone
3 For some recent work, see X. Zeng, Z. Xi, L. S. Kappen, W. Tan and I.
H. Goldberg, Biochemistry, 1995, 34, 12435; Y.-J. Xu, Z. Xi, Y.- S.
Zhen and I. H. Goldberg, Biochemistry, 1995, 34, 12451; M. Pitie´, J.
Bernadou and B. Meunier, J. Am. Chem. Soc., 1995, 117, 2935; H.
Sugiyama, K. Fujimoto and I. Saito, J. Am. Chem. Soc., 1995, 117,
2945; H. Sugiyama, K. Fujimoto, I. Saito, E. Kawashima, T. Sekine and
Y. Ishido, Tetrahedron Lett., 1996, 37, 1805; G. P. Cook and M. M.
Greenberg, J. Am. Chem. Soc., 1996, 118, 10025; T. Melvin, S. W.
Botchway, A. W. Parker and P. O’Neil, J. Am. Chem. Soc., 1996, 118,
10031; M. M. Meijler, O. Zelenko and A. S. Sigman, J. Am. Chem. Soc.,
1997, 119, 1135; H. Sugiyama, K. Fujimoto and I. Saito, Tetrahedron
Lett., 1997, 38, 8057; O. Zelenko, J. Gallagher and A. S. Sigman,
Angew. Chem., Int. Ed. Engl., 1997, 36, 2776.
4 T. Gimisis and C. Chatgilialoglu, J. Org. Chem., 1996, 61, 1908; T.
Gimisis, C. Castellari and C. Chatgilialoglu, Chem. Commun., 1997,
2089.
5 I. H. Goldberg, Acc. Chem. Res., 1991, 24, 191; B. K. Goodman and M.
M. Greenberg, J. Org. Chem., 1996, 61, 2.
6 E. G. Hole, W. H. Nelson, E. Sagstuen and D. M. Close, Radiat. Res.,
1992, 129, 119; D. M. Close, W. H. Nelson, E. Sagstuen and E. O. Hole,
Radiat. Res., 1994, 137, 300; K. Miaskiewicz and R. Osman, J. Am.
Chem. Soc., 1994, 116, 232; A.-O. Colson and M. D. Sevilla, J. Phys.
Chem., 1995, 99, 3867.
7 C. Chatgilialoglu, T. Gimisis, M. Guerra, C. Ferreri, C. J. Emanuel, J. H.
Horner, M. Newcomb, M. Lucarini and G. F. Pedulli, Tetrahedron Lett.,
in the press.
H218O. For this reason, the above experiment was performed in
H218O (95 atom% 18O) as solvent. After work-up, the protected
2-deoxyribonolactone was analyzed by GC–MS. Inspection of
the mass spectrum of the isotopic cluster of [M 2 57]+, shown
in Fig. 1(b), indicates the presence of coeluting isotopomers 7
and 8. Analysis of this isotopic cluster revealed that the product
of interest contains 65 and 35% oxygen-16 and oxygen-18,
respectively. A control experiment showed that the product
lactone 2 does not exchange oxygen with the solvent under the
conditions employed.
The mechanism we envisage for the formation of the
18O-labelled 2-deoxyribonolactone is outlined in Scheme 2.
Reaction of C-1A radical 1 with O2 gives the peroxyl radical 9.
Laser flash photolysis studies showed that rate constant for
oxygen trapping of the C-1A radical is about 1 3 109 m21 s21 7
.
The peroxyl radical 9 decays either via a bimolecular reaction
with another peroxyl radical to generate the alkoxyl radical 10
or via a unimolecular path (heterolytic cleavage) to generate the
carbocation 11 and superoxide radical anion.15a The heterolytic
cleavage of peroxides or alternatively the reaction of electron-
rich carbon-centered radicals to give superoxide and carboca-
tions is not without precedent.15 The cationic intermediate 11
was trapped by H218O, thus demonstrating the partition between
the two channels.
8 T. Gimisis, G. Ialongo, M. Zamboni and C. Chatgilialoglu, Tetrahedron
Lett., 1995, 36, 6781; T. Gimisis, G. Ialongo and C. Chatgilialoglu,
Tetrahedron, 1998, 54, 573.
9 M. M. Greenberg, D. J. Yoo and B. K. Goodman, Nucleosides
Nucleotides, 1997, 16, 33.
An important consequence of the mechanism in Scheme 2 is
that the C-1A peroxyl radical generated on DNA, in the absence
of good hydrogen donors, should mainly undergo heterolytic
cleavage since the probability that two macromolecular peroxyl
radicals meet is low. This finding accentuates the different
chemical reactivity exhibited by the C-1A radical species when
compared with the one observed in the more studied C-5A and
C-4A positions,1 a reactivity which is mainly due to the presence
of the two a-heteroatoms present in the anomeric position.
Further work on the reactions of compounds 3 and 4 with a
variety of electrophiles and on the kinetics of radical reactions
associated with the C-1A position is in progress.
10 A. Holy, Nucleic Acids Res., 1974, 1, 289.
11 K. Haraguchi, Y. Itoh, H. Tanaka, K. Yamaguchi and T. Miyasaka,
Tetrahedron Lett., 1993, 34, 6913; Y. Itoh, K. Haraguchi, H. Tanaka, E.
Gen and T. Miyasaka, J. Org. Chem., 1995, 60, 656.
12 C. Chatgilialoglu, Acc. Chem. Res., 1992, 25, 118; C. Chatgilialoglu,
Chem Rev., 1995, 95, 1229.
13 The reduction using Bu3SnH was reported to give 77% yield, see Y.
Yoshimura, F. Kano, S. Miyazaki, N. Ashida, S. Sakata, K. Haraguchi,
Y. Itoh, H. Tanaka and T. Miyasaka, Nucleosides Nucleotides, 1996, 15,
305.
14 For compounds 2 and 7, see F. J. Lopez-Herrera, M. Valpuesta-
Fernandez and S. Garcia-Claros, Tetrahedron, 1990, 46, 7165; A. P.
Kozikowski and A. K. Ghosh, J. Org. Chem., 1984, 49, 2762.
15 (a) C. von Sonntag and H.-P. Schuchmann, Angew. Chem., Int. Ed.
Engl., 1991, 30, 1229; (b) K. U. Ingold, T. Paul, M. J. Young and L.
Doiron, J. Am. Chem. Soc., 1997, 119, 12364.
We are grateful to the European Commission for a ‘Marie
Curie’ post-doctoral fellowship to T. G., to NATO for a
Collaborative Research Grant, and to Drs C. Ferreri and M.
Lucarini for helpful discussions.
Received in Glasgow, UK, 25th March 1998; 8/02375A
1250
Chem. Commun., 1998