Chemical synthesis of cross-linked purine nucleosides

Article abstract of DOI:10.1021/ol990351m

(matrix presented) An efficient route to all of the possible cross-linked 2′-deoxypurines 1-3 has been developed by means of the Pd-mediated C-N bond formation in the key step. Utilizing this protocol, the synthesis of the first unnatural protected purine

Full text of DOI:10.1021/ol990351m

ORGANIC
LETTERS
2000
Vol. 2, No. 3
293-295
Chemical Synthesis of Cross-Linked
Purine Nucleosides
,†
,‡
Francesco De Riccardis* and Francis Johnson*
Department of Pharmacological Sciences, State UniVersity of New York at Stony
Brook, Stony Brook, New York 11794-3400, and Dipartimento di Chimica,
UniVersita` di Salerno, Via S. Allende, Baronissi, 84081 Salerno, Italy
dericca@unisa.it
Received November 10, 1999
ABSTRACT
An efficient route to all of the possible cross-linked 2′-deoxypurines 1−3 has been developed by means of the Pd-mediated C−N bond formation
in the key step. Utilizing this protocol, the synthesis of the first unnatural protected purine trimeric adduct 4 has been accomplished.
Active carcinogenic agents often are strong electrophiles
reactive enough to interact with the nucleophilic DNA
residues.1 It is known that sodium nitrite, widely used as an
additive for cured meats,2 and nitric oxide, a physiological
bioregulator,3 in the presence of acids4 or oxygen,5 respec-
tively, can induce the formation of reactive nitrosating species
such as N2O and N2O4. These oxides attack DNAs
particularly guaninessconverting the amino groups to dia-
zonium ions.6 Some of the latter may undergo nucleophilic
attack by water, giving rise to a carbonyl group, whereas
others are attacked7 by the amino group of a neighboring
nucleoside giving inter- or intrastrand or interhelical DNA
cross-links.6-8 In 1977, Shapiro reported the isolation and
partial characterization of the first coupled nucleosides 1 and
2, from nitrous acid treated DNA,8a whereas in 1992 Hopkins
showed that 1 was formed via an interstrand cross-linking
process.8b,c
† Universita` di Salerno.
‡ State University of New York at Stony Brook.
(1) Miller, E. C.; Miller, J. A. Cancer 1981, 10, 2327-2345.
(2) Handbook of Food AdditiVes, 2nd ed.; Furia, T. E., Ed.; CRC Press:
Cleveland, 1972; pp 150-155.
(3) (a) Garthwaite, J., Charles, S. L.; Chess-Williams, R. Nature 1988,
336, 385-388. (b) Bredt, D. S.; Hwang, P. M.; Snyder, S. H. Ibid. 1990,
347, 768-770.
(4) (a) Committee on Nitrite and Alternative Curing Agents in Food.
The Health Effects of Nitrate, Nitrite, and N-Nitroso Compounds; National
Academy Press: Washington, DC, 1981. (b) Zimmermann, F. K. Mutat.
Res. 1977, 39, 127-148.
(5) (a) Wink, D. A.; Kasprzac, K. S., Maragos, C. M.; Elespuru, R. K.,
Misra, M.; Dunams, T. M., Cebula, T. A.; Koch, W. H.; Andrews, A. W.;
Allen, J. S.; Keefer, L. K. Science 1991, 254, 1001-1003. (b) Tannenbaum,
S. R.; Tamir, S.; Rojas-Walker, T. D.; Wishnok, J. S. DNA Damage and
Cytotoxicity Caused by Nitric Oxide. In Nitrosamine and Related N-Nitroso
Compounds - Chemistry and Biochemistry; Loeppky, R. N., Michejda, C.
L., Eds.; ACS Symp. Ser. No. 553; American Chemical Society: Wash-
ington, DC, 1994; Chapter 10, pp 120-135. (c) Caulfield, J. L.; Wishnok,
J. S.; Tannenbaum, S. R. J. Biol. Chem. 1998, 273, 12689-12695.
(6) Glaser, R.; Rayat, S.; Lewis, M.; Son, M.-S.; Meyer, S. J. Am. Chem.
Soc. 1999, 121, 6108-6119 and references therein.
10.1021/ol990351m CCC: $19.00 © 2000 American Chemical Society
Published on Web 01/13/2000

In this paper, we report our results on the chemical
synthesis of all of the possible N2- and N6-cross-linked 2′-
deoxypurines 1-3 and the fortuitous formation, during the
synthesis of 2, of the unique unnatural fully protected trimeric
adduct 4. Our results represent a remarkable extension of
our work on the synthesis of the N2- and N6-(o-aminoaryl)
derivatives of 2′-deoxyguanosine (dG) and 2′-deoxyadeno-
sine (dA)9 using the versatile palladium-catalyzed amination
reaction.10-12
and Cs2CO3, as the base, was efficient for the coupling of
labile biomolecules, such as nucleosides. On the basis of
these studies, we decided to evaluate the efficiency of this
protocol in the coupling between 3′,5′-bis-O-(tert-butyldi-
methylsilyl)-2′-â-deoxyguanosine (5) and 2-bromo-6-benz-
yloxy-9-[2-deoxy-3,5-bis-O-(tert-butyldimethylsilyl)-â-D-
erythro-pentofuranosyl]purine (6). We were delighted to find
that the previously reported11 713 was formed in excellent
yield (90%). The 1H NMR spectrum of the purified material
showed resonance peaks that were identical to those reported
previously.11
In his 1977 communication, Shapiro reported the isolation
of the nonsymmetrical adduct 2.8a Unfortunately, the ex-
tremely low yields obtained did not allow full spectroscopic
characterization of the product (only two UV spectra at
different pH values and a mass spectrum of a derivative were
reported). In 1991, a reinvestigation by Hopkins et al.8b,c on
the DNA interstrand cross-linked adducts, formed by treating
calf thymus DNA with nitrous acid, failed to give 2.
Described herein is the first chemical synthesis of 2, which
conclusively demonstrates that the covalent DNA lesion
found in trace amounts by Shapiro has this structure.
In our first synthetic attempt to couple 3′,5′-bis-O-(tert-
butyldimethylsilyl)-2′-deoxyadenosine (8) with 6, we used
the same reaction conditions followed for the successful
synthesis of 7. Unfortunately, from the reaction mixture we
While our synthetic studies were underway, Hopkins and
his associates reported the first synthesis of 1 using a similar
procedure.11 However, the key step of their protocolsthe
palladium-catalyzed amination reactionsgave only a moder-
ate yield (40%), probably because of the use of sodium tert-
butoxide, which is known to be detrimental in the case of
silylated nucleosides.12
obtained only low yields of 9 (24%) plus unreacted starting
material. In an endeavor to enhance the rate of the reaction,
we planned the synthesis of the more reactive 2-iodo-6-
benzyloxy-9-[2-deoxy-3,5-bis-O-(tert-butyldimethylsilyl)-â-
D-erythro-pentofuranosyl]purine (10) following the reaction
conditions described by Matsuda et al.14 and Nair et al.15
Unfortunately both procedures led to low yields of a highly
(8) (a) Shapiro, R.; Dubelman, S.; Feinberg, A. M.; Crain, P. F.;
McCloskey, J. A. J. Am. Chem. Soc. 1977, 99, 302-303. (b) Kirchner, J.
J.; Hopkins, P. B. J. Am. Chem. Soc. 1991, 113, 4681-4682. (c) Kirchner,
J. J.; Sigurdsson, S. Th., Hopkins, P. B. J. Am. Chem. Soc. 1992, 114, 4021-
4027.
(9) De Riccardis, F.; Bonala, R. R.; Johnson, F.J. Am. Chem. Soc. 1999,
121, 10453-10460.
(10) (a) Hartwig, J. F. Angew. Chem., Int. Ed. Engl. 1998, 37, 2046-
2067. (b) Wolfe, J. P.; Wagaw, S.; Marcoux, J.-F.; Buchwald, S. L. Acc.
Chem. Res. 1998, 31, 805-818. (c) Hartwig, J. F. Acc. Chem. Res. 1998,
31, 852-860. (c) Frost, C. G.; Mendonc¸a, P. J. Chem. Soc., Perkin Trans.
1 1998, 2615-2623. (d) Hartwig, J. F. Synlett 1997, 329-340.
(11) Harwood, E. A.; Sigurdsson, S. Th.; Edfeldt, N. B. F.; Reid, B. R.;
Hopkins, P. B. J. Am. Chem. Soc. 1999, 121, 5081-5082.
(12) Lakshman, M. K.; Keeler, J. C.; Hilmer, J. H.; Martin, J. Q. J. Am.
Chem. Soc. 1999, 121, 6090-6091.
In our previous work, we had found that a catalyst system
composed of 10 mol % Pd(OAc)2, 15 mol % (()-BINAP,
(13) Satisfactory analytical data (1H and 13C NMR, FAB-MS spectra
and elemental analyses) were obtained for all the new compounds (see the
Supporting Information)
(7) Burnotte, J.; Verly, W. G. J. Biol. Chem. 1971, 246, 5914-5918
and references therein.
294
Org. Lett., Vol. 2, No. 3, 2000

photosensitive compound, which decomposed within few
hours. An alternative to these unsuccessful approaches was
the procedure of Richardson,16b we were able to raise the
yield of this coupling step to a satisfying 51%.
Having the iodonucleoside 13 available, we reinvestigated
the coupling reaction with the protected dG (5), in an attempt
to increase further the yield of adduct 9. To our surprise,
the cross-coupling reaction gave a lower yield (45%). Careful
investigation of the reaction products led to the isolation of
a less polar compound. Its spectral data (particularly 1H and
13C NMR) showed the presence of two different resonance
patterns in a 2:1 ratio. The preeminent one was assigned to
a 2′-deoxyadenosine residue, the other to a 2′-deoxygua-
nosine. The absence, in the 1H NMR, of an N-H signal and
a molecular weight of 1510 Da (FAB-MS spectrum) suggests
structure 4 for the new compound (formed in 17% yield).
The ultimate acquisition of 2 and 3 required only standard
deprotection chemistry (Scheme 1). Compound 9 was
the palladium-catalyzed nucleophilic displacement of the
6-bromo-9-[2-deoxy-3,5-bis-O-(tert-butyldimethylsilyl)-â-D-
erythro-pentofuranosyl]purine (11) [easily synthesized through
light-catalyzed bromination of 3′,5′-bis-O-(tert-butyldimeth-
ylsilyl)-2′-deoxyadenosine (8)12,16a] with the more reactive
N2-amino group of the protected dG, 5. A similar coupling,
using compound 11, has been reported by the Lakshman
group for the synthesis of the simpler N6-aryl-2′-deoxy-
adenosine analogues.12 The nucleophilic displacement of the
6-bromo group occurred with considerable ease and gave
the nonsymmetrical adduct 9 in 60% yield (75% yield based
on unrecovered starting material).
Scheme 1
subjected to hydrogenolysis using palladium-on-charcoal
catalyst, at 60 psi, to give 14 in quantitative yield. We were
also gratified to observe that 14 was easily desilylated with
HF and pyridine18 to give the cross-linked nucleoside 2 in
97% yield.19 Desilylation of compound 12 was similarly
accomplished to give the symmetrical so far nonnatural
adduct 3 in quantitative yield.
The further extension of this type of coupling reaction to
other nucleosides including both purine and pyrimidine
classes is under investigation.
In view of this success, we decided, prior to deprotecting
9, to investigate the potential of this method for the synthesis
of the symmetrical, adduct 3, which has never been reported.
Thus, a reaction between the less nucleophilic 8 and the
bromonucleoside 11 was attempted under the usual reaction
conditions. As expected, this reaction gave only a low yield
of 12 (21%), contaminated with a minor but inseparable
impurity. Increasing the temperature (120 °C), the reaction
times (24 h, 48 h), and the amount of Pd(OAc)2 and ligand
(20 mol % and 30% mol, respectively) or replacing the Pd
species (Pd2(dba)3) and the base (K3PO4)17 did not induce
any increase in the yield or of the rate of conversion. Finally,
using our standard amination conditions, but replacing the
bromopurine 11 with the more reactive, light-stable 6-iodo-
9-[2-deoxy-3,5-bis-O-(tert-butyldimethylsilyl)-â-D-erythro-
pentofuranosyl]purine (13), conveniently available through
Acknowledgment. We thank Mr. Robert A. Rieger for
the mass spectral data. This research was supported by a
grant (ES04068) from the National Institute for Environ-
mental Health Sciences, a division of the National Institutes
of Health.
Supporting Information Available: Experimental pro-
cedures and full characterization for compounds 2-4, 7, 9,
1
12, and 14; H and 13C NMR spectra of 2-4, 7, 9, 12, and
(14) Matsuda, A.; Shinozaki, M.; Yamaguchi, T.; Homma, H.; Nomoto,
R.; Miyasaka, T.; Watanabe, Y.; Abiru, T. J. Med. Chem. 1992, 35, 241-
252.
(15) Nair, V.; Young, D. A.; DeSilva, R. J. Org. Chem. 1987, 52, 1344-
1347.
(16) (a) Nair, V.; Richardson, S. G. J. Org. Chem. 1980, 45, 3969-
3974. (b) Cosstick, R.; Douglas, M. E. J. Chem. Soc., Perkin Trans. 1 1991,
1035-1040.
(17) Old, D. W.; Wolfe, J. P., Buchwald, S. L. J. Am. Chem. Soc. 1998,
120, 9722-9723.
14; UV spectra (pH ) 5.7 and 10.5) of 2. This material is
available free of charge via the Internet at http://pubs.acs.org.
OL990351M
(18) Nicolaou, K. C., Webber, S. E. Synthesis 1986, 453-461.
(19) The UV spectra of this product were almost identical to those
reported by Shapiro et al.8a in 1977 (see the Supporting Information).
Org. Lett., Vol. 2, No. 3, 2000
295