A facile synthetic approach to 7-deazaguanine nucleosides via a boc protection strategy

Article abstract of DOI:10.1021/ol9007537

An efficient route to the preparation of 5-substituted 2-amino-7-((2R,4R, 5R)-tetrahydro-4-hydroxy-5-(hydroxymethyl)furan-2-yl)-3H-pyrrolo[2,3- d]pyrimidin-4(7H)-one compounds has been developed by the condensation of ω-substituted aldehydes with 2,6-diaminopyrimidin-4(3H)-one, followed by Boc protection to afford the corresponding N²,N²,N ⁷-tris-Boc-O4-t-Bu-5-substituted 2-amino-3H-pyrrolo[2,3-d]pyrimidin- 4(7H)-one, which is amenable to direct condensation with 1-chloro-2-deoxy-3,5- di-O-p-toluoyl-r-D-erythro-pentofuranose. This route affords an efficient synthesis to 2-amino-3H-pyrrolo[2,3-d]pyrimidin-4(7H)-one, 2-amino-5-alkyl-3H- pyrrolo[2,3-d]pyrimidin-4(7H)-one, and guanine nucleosides.

Full text of DOI:10.1021/ol9007537

ORGANIC
LETTERS
2009
Vol. 11, No. 11
2465-2468
A Facile Synthetic Approach to
7-Deazaguanine Nucleosides via a Boc
Protection Strategy
Ruo-Wen Wang and Barry Gold*
Department of Pharmaceutical Sciences, UniVersity of Pittsburgh, 512 Salk Hall,
3501 Terrace Street, Pittsburgh, PennsylVania 15261
goldbi@pitt.edu
Received April 7, 2009
ABSTRACT
An efficient route to the preparation of 5-substituted 2-amino-7-((2R,4R,5R)-tetrahydro-4-hydroxy-5-(hydroxymethyl)furan-2-yl)-3H-pyrrolo[2,3-
d]pyrimidin-4(7H)-one compounds has been developed by the condensation of ω-substituted aldehydes with 2,6-diaminopyrimidin-4(3H)-one,
followed by Boc protection to afford the corresponding N2,N2,N7-tris-Boc-O4-t-Bu-5-substituted 2-amino-3H-pyrrolo[2,3-d]pyrimidin-4(7H)-one,
which is amenable to direct condensation with 1-chloro-2-deoxy-3,5-di-O-p-toluoyl-r-D-erythro-pentofuranose. This route affords an efficient
synthesis to 2-amino-3H-pyrrolo[2,3-d]pyrimidin-4(7H)-one, 2-amino-5-alkyl-3H-pyrrolo[2,3-d]pyrimidin-4(7H)-one, and guanine nucleosides.
The 5-position of 2-amino-3H-pyrrolo[2,3-d]pyrimidin-
4(7H)-one (aka, 7-deazaguanine) is well-suited to introduce
functionalized appendages into the major groove of DNA
for the purposes of structural and stability studies,1 DNA
fluorescence labeling,2 DNA sequencing,3 and the production
of DNA-based nanoarrays.4 There are also a number of
naturally occurring 5-substituted 2-amino-3H-pyrrolo[2,3-
d]pyrimidin-4(7H)-one nucleosides, including Queuosine (I),
and related glycosylated analogues,5 and Archaeosine (II)6
Figure 1. Queuosine (I) and Archaeosine (II).
(1) Rosemeyer, H.; Ramzaeva, N.; Becker, E. M.; Feiling, E.; Seela, F.
Bioconjugate Chem. 2002, 13, 1274–1285.
found in tRNA (Figure 1). Accordingly, there have been
numerous studies on routes to the synthesis of 2-amino-3H-
pyrrolo[2,3-d]pyrimidin-4(7H)-one modified nucleosides.7
There are several barriers to the synthesis of 5-substituted
2-amino-3H-pyrrolo[2,3-d]pyrimidin-4(7H)-one nucleosides.
(2) Ju, J.; Kim, D. H.; Bi, L.; Meng, Q.; Bai, X.; Li, Z.; Li, X.; Marma,
M. S.; Shi, S.; Wu, J.; Edwards, J. R.; Romu, A.; Turro, N. J. Proc. Natl.
Acad. Sci. U.S.A. 2006, 103, 19635–19640.
(3) Kawate, T.; Allerson, C. R.; Wolfe, J. L. Org. Lett. 2005, 7, 3865–
3868.
(4) (a) Seeman, N. C. J. Theor. Biol. 1982, 99, 237–247. (b) Feldkamp,
U.; Niemeyer, C. M. Angew. Chem., Int. Ed. 2006, 45, 1856–1876. (c)
Seeman, N. C. Nature 2003, 421, 427–431.
(7) (a) Seela, F.; Winkeler, H. D. J. Org. Chem. 1983, 48, 3119–3122.
(b) Ramasamy, K.; Joshi, R. V.; Robins, R. K.; Revankar, G. R. J. Chem.
Soc., Perkin Trans. 1 1989, 2375–2384. (c) Ramasamy, K.; Robins, R. K.;
Revankar, G. R. J. Chem. Soc., Chem. Commun. 1989, 560–562. (d) Seela,
F.; Peng, X. J. Org. Chem. 2006, 71, 81–90. (e) Meng, Q.; Kim, D. H.;
Bai, X.; Bi, L.; Turro, N. J.; Ju, J. J. Org. Chem. 2006, 71, 3248–3252. (f)
Vorbru¨ggen, H.; Ruh-Polenz, C. Org. React. 2000, 55, 1–630.
(5) Okada, N.; Noguchi, S.; Nishimura, S.; Ohgi, T.; Goto, T.; Crain,
P. F.; McCloskey, J. A. Nucleic Acids Res. 1977, 7, 2289–2296. (b) Okada,
N.; Yasuda, T.; Nishimura, S. Nucleic Acids Res. 1977, 4, 4063–4075.
(6) Gregson, M.; Crain, P. F.; Edmonds, C. G.; Gupta, R.; Hashizume,
T.; Phillipson, D. W.; McCloskey, J. A. J. Biol. Chem. 1993, 268, 10076–
10086.
10.1021/ol9007537 CCC: $40.75
Published on Web 05/07/2009
 2009 American Chemical Society

Unlike the N1 of pyrimidines and the N9 of adenine, the
N9-position of guanine, which is incorporated into a number
of antiviral and anticancer nucleoside compounds,8 and the
5-position of 2-amino-3H-pyrrolo[2,3-d]pyrimidin-4(7H)-one
derivatives are not sufficiently activated for direct glycosyl-
ation.9 The classic solution to the preparation of 2-amino-
3H-pyrrolo[2,3-d]pyrimidin-4(7H)-one nuclosides is to
convert the 5-functionalized-2-amino-3H-pyrrolo[2,3-d]py-
rimidin-4(7H)-one to the 4-chloro compound, which is
suitable for reaction with an activated sugar (e.g., 1-chloro-
2-deoxy-3,5-di-O-p-toluoyl-R-D-erythro-pentofuranose).10 The
4-chloro nucleoside is then converted back to the keto
derivative by hydrolysis.7 In addition to the extra synthetic
steps, the 4-chloro derivatives have very poor solubility
characteristics,11 which confounds their functionalization.7b,8b
If the synthesis of 5-substituted 2-amino-3H-pyrrolo[2,3-
d]pyrimidin-4(7H)-one starts with 4-chloro-2-amino-3H-
pyrrolo[2,3-d]pyrimidin-4(7H)-one, it must be first converted
to the 5-iodo compound prior to the introduction of modi-
fications to the 5-position by metal-mediated Sonoga-
shira,7e,12 Stille,13 or related cross-coupling reactions.
In an effort to prepare a series of 5-substituted 2-amino-
7-((2R,4R,5R)-tetrahydro-4-hydroxy-5-(hydroxymethyl)-fu-
ran-2-yl)-3H-pyrrolo[2,3-d]pyrimidin-4(7H)-one modified
DNAs (Figure 2) to (1) extend studies on how cationic and
We report herein the synthesis of 5-aminomethyl- and
5-hydroxymethyl-2-amino-7-((2R,4R,5R)-tetrahydro-4-hydroxy-
5-(hydroxymethyl)furan-2-yl)-3H-pyrrolo[2,3-d]pyrimidin-
4(7H)-ones as examples of a convenient, efficient, and
general route to 5-substituted 2-amino-7-((2R,4R,5R)-tet-
rahydro-4-hydroxy-5-(hydroxymethyl)furan-2-yl)-3H-pyrro-
lo[2,3-d]pyrimidin-4(7H)-ones that involves mild reaction
conditions. It is also demonstrated that the approach is
amenable to the preparation of guanine nucleosides.
The synthesis started with 5-substituted 2-amino-3H-
pyrrolo[2,3-d]pyrimidin-4(7H)-one compounds (1 and 2) that
were prepared by condensation of the ω-substituted alde-
hydes16 with 2,6-diaminopyrimidin-4(3H)-one.17 As men-
tioned above, normally, the 5-substituted 2-amino-3H-
pyrrolo[2,3-d]pyrimidin-4(7H)-one would be transformed to
the 4-halo derivative to activate the 7-position for reaction
with a protected 1-chloro-2-deoxy-R-D-erythro-pentofura-
nose.10 Attempts to convert 1 and 2 to the 4-chloro
compounds were unsuccessful.
It was envisioned that the tetra-Boc derivatives of 1 and
2 could be prepared and then selectively deprotected to reveal
the pyrrole NH-7 for coupling with a reactive Cl sugar
(Figure 3).
Figure 3. Design of 5-substituted 2-amino-3H-pyrrolo[2,3-d]pyri-
midin-4(7H)-one as new coupling precusors with improved solubil-
ity.
Figure 2. 5-Aminomethyl- (left) and 5-hydroxymethyl- (right)
2-amino-7-((2R,4R,5R)-tetrahydro-4-hydroxy-5-(hydroxymethyl)fu-
ran-2-yl)-3H-pyrrolo[2,3-d]pyrimidin-4(7H)-ones in DNA.
Compounds 1 and 2 have very limited solubility, so they
were treated as a suspension in MeCN with excess Boc2O.
After several days at rt, all of the solid starting material had
gone into solution. Instead of the anticipated tetra-Boc
derivative, it was found that 1 and 2 afforded the tris-Boc-
protected O4-t-Bu ether compounds 7 and 8, respectively
(Scheme 1). Fortuitously, formation of the O-t-Bu ethers
negates the need to convert the 2-amino-3H-pyrrolo[2,3-
d]pyrimidin-4(7H)-one nucleus into the 4-chloro derivative
prior to sugar coupling.
polar groups located near the floor of the major groove affect
the thermodynamic stability, reactivity, and structure of
DNA14 and (2) generate stable interstrand cross-links,15 we
found that the existing synthetic schemes were not suitable.
(8) (a) Sims, K. A.; Woodland, A. M. Pharmacotherapy 2006, 12, 1745–
1757. (b) Field, A. K.; Tuomari, A. V.; McGeever-Rubin, B.; Terry, B. J.;
Mazina, K. E.; Haffey, M. L.; Hagen, M. E.; Clark, J. M.; Braitman, A.;
Slusarchyk, W. A. AntiViral Res. 1990, 13, 41–52. (c) Brigden, D.; Fiddian,
P.; Rosling, A. E.; Ravenscroft, T. AntiViral Res. 1981, 1, 203–212. (d)
Vere Hodge, R. A.; Sutton, D.; Boyd, M. R.; Harnden, M. R.; Jarvest, R. L.
Antimicrob. Agents Chemother. 1989, 33, 1765–7173. (e) Lee, J.; Chuang,
T.-H.; Redecke, V.; She, L.; Pitha, P. M.; Carson, D. A.; Raz, E.; Cottam,
H. B. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 6646–6651.
To elucidate the origin of the O4-t-Bu ethers 7 and 8, the
reactions were monitored by TLC and LC/MS analysis. Time
(14) (a) Manning, G. S. Q. ReV. Biophys. 1978, 2, 179–246. (b) Record,
M. T.; Anderson, C. F.; Lohman, T. M. Q. ReV. Biophys. 1978, 2, 103–
179. (c) Honig, B.; Nicholls, A. Science 1995, 268, 1144–1149. (d) Gold,
B. Biopolymers 2002, 65, 173–179. (e) Gold, B.; Marky, L. M.; Stone,
M. P.; Williams, L. D. Chem. Res. Toxicol. 2006, 19, 1402–1414.
(15) (a) Wilds, C. J.; Noronha, A. M.; Robidoux, S.; Miller, P. S.
Nucleosides Nucleotides Nucleic Acids 2005, 4, 965–969. (b) Ra¨schle, M.;
Knipsheer, P.; Enoiu, M.; Angelov, T.; Sun, J.; Griffith, J. D.; Ellenberger,
T. E.; Scha¨rer, O. D.; Walter, J. C. Cell 2008, 134, 969–980.
(16) De Luca, L.; Giacomelli, G.; Porcheddu, A. Org. Lett. 2001, 3,
3041–3043.
(9) (a) Tolman, R. L.; Tolman, G. L.; Robins, R. K.; Townsend, L. B.
J. Heterocycl. Chem. 1970, 7, 799–806. (b) Seela, F.; Westermann, B.;
Bindig, U. J. Chem. Soc., Perkin Trans. 1 1988, 697–702.
(10) Ramasamy, K.; Imamura, N.; Robins, R. K.; Revankar, G. R.
Tetrahedron Lett. 1987, 43, 5107–5100.
(11) Dey, S.; Garner, P. J. Org. Chem. 2000, 65, 7697–7699.
(12) (a) Jager, S.; Rasched, G.; Kornreich-Leshem, H.; Engeser, M.;
Thum, O.; Famulok, M. J. Am. Chem. Soc. 2005, 127, 15071–15082. (b)
Seela, F.; Shaikh, K. I. Tetrahedron 2005, 61, 2675–2681
(13) Angelov, T.; Guainazzi, A.; Scharer, O. D. Org. Lett. 2009, 11,
661–664.
.
(17) (a) Klepper, F.; Polborn, K.; Carell, T. HelV. Chim. Acta 2005, 88,
2610–2616. (b) Barnett, C. J.; Grubb, L. M. Tetrahedron Lett. 2000, 41,
9741–9745.
2466
Org. Lett., Vol. 11, No. 11, 2009

Scheme 1
.
Preparation of O-t-Bu Ethers
Scheme 2. Synthesis of 16
course studies clearly showed the buildup of the tetra-Boc
derivatives (presumably 3 and 4) and subsequent loss of CO2
with ether formation to give 7 and 8, respectively (Figure
4).
The toluoyl groups were selectively removed with Mg(OMe)2
to give trifluoroacetamide 15.18 The N2-amino group in 15
was selectively protected to give isobutyric amide 16. The
overall yield from 1 to 16 is 6.2%.
Compound 16 was converted into the O3′-(2-cyanoet-
hoxy)(diisopropylamino)phosphino]-5′-O-(4,4′-dimethoxytri-
tyl) derivative 18 (Scheme 3) by standard procedures to
Figure 4. Products 7 and 8 formed from the reactions of 1 and 2
with t-Boc2O, respectively, that arise via intermediates 3 and 4.
In terms of the scope of the reaction, the tetra-Boc
intermediate and the butyl ether product were also observed
in the reaction of unsubstituted 2-amino-3H-pyrrolo[2,3-
d]pyrimidin-4(7H)-one, indicating that the functionality
attached to the 5-position does not play a role in the
conversion of the carbamate to the ether (9). The reaction
with guanine was explored despite previous reports on the
difficulty of protecting guanine with Boc2O.10 After 96 h,
the N2,N2,N7-tris-Boc-O4-t-Bu ether derivative of guanine was
isolated and characterized. Earlier time points in the reaction
were analyzed by LC/MS and clearly showed that formation
of ether product (10) proceeds through the initial formation
of the tetra-Boc derivative.
Scheme 3. Syntheses of Phosphamidite 18
The conversion of 7 to the protected 2′-deoxynucleoside
is shown in Scheme 2. To reveal the pyrrole NH-7, the N7-
Boc was selectively deprotected by sodium methoxide to give
pyrrolo[2,3-d]pyrimidinone 12, which is an efficient precur-
sor, with good solubility, for the sugar coupling reaction.
Compound 12 was condensed with 1-chloro-2-deoxy-3,5-
di-O-p-toluoyl-R-D-erythro-pentofuranose (30) to give the
desired ꢀ-anomer of the protected 2′-deoxynucleoside 13.
The phthalimide and Boc protecting groups were sequentially
removed with hydrazine and TFA, and the primary amine
was then protected as the trifluoroacetamide 14. From
compound 7, compound 14 was prepared in five steps in
42% yield, and only one column purification was required.
provide the required intermediate for solid phase DNA
synthesis.19
Similarly, the conversion of 8 to the deoxynucleoside 27
involved its coupling to the chlorosugar after selective
removal of the N7-Boc group with NaOMe (Scheme 4).
(18) Xu, Y.-C.; Lebeau, E.; Walker, C. Tetrahedron Lett. 1994, 35,
6207–6210.
(19) (a) BeaucageS. L. In Protocols for Oligonucleotides and Analogs;
Agrawal, S., Ed.; Humana Press: Totowa, NJ, 1993; pp 33-62. (b)
Bleasdale, B.; Ellwood, S. B.; Golding, B. T. J. Chem. Soc., Perkin Trans.
1 1990, 803–805.
Org. Lett., Vol. 11, No. 11, 2009
2467

Boc and O4-t-butyl groups were removed by heating at 80
°C in vacuo on silica.20 The N2-position was reprotected with
i-PrCOCl and the silyl protection removed with TBAF. The
overall yield of 27 from 2 is 6.4% via 14 steps. The primary
alcohol 23 can, if desired, be further reduced to give
5-methyl-2-amino-3H-pyrrolo[2,3-d]pyrimidin-4(7H)-one, a
useful isosteric analogue of 7-methylguanine. The Bz group
of ester 24 can also be removed in acidic conditions used
for removal of N-Boc groups. The synthesis of compound
27 illustrated that Boc protection strategy provides an
efficient route to the preparation of those 5-substituted
2-amino-7-((2R,4R,5R)-tetrahydro-4-hydroxy-5-(hydroxym-
ethyl)furan-2-yl)-3H-pyrrolo[2,3-d]pyrimidin-4(7H)-one with
senstive functionalities since Boc and O4-t-butyl groups can
be efficiently removed under mild condition.
Scheme 4. Syntheses of Compound 27
In conclusion, we have synthesized 5-aminomethyl-2-
amino-7-((2R,4R,5R)-tetrahydro-4-hydroxy-5-(hydroxymeth-
yl)furan-2-yl)-3H-pyrrolo[2,3-d]pyrimidin-4(7H)-one (16)
and 5-hydroxymethyl-2-amino-7-((2R,4R,5R)-tetrahydro-4-
hydroxy-5-(hydroxymethyl)furan-2-yl)-3H-pyrrolo[2,3-d]py-
rimidin-4(7H)-one (27) from 1 and 2, respectively, in 6%
yield via key O4-t-Bu ether intermediates 7 and 8. These
syntheses illustrate an efficient and general route to the
preparation of 5-substituted 2-amino-7-((2R,4R,5R)-tetrahy-
dro-4-hydroxy-5-(hydroxymethyl)furan-2-yl)-3H-pyrrolo[2,3-
d]pyrimidin-4(7H)-ones. Time course studies showed that
the tetra-Boc derivatives were converted to the O4-t-Bu ethers
via intramolecular transformation.
Acknowledgment. This work was supported by NIH RO1
CA29088.
Supporting Information Available: Experimental pro-
cedure and spectral data for synthesized compounds. This
material is available free of charge via the Internet at
http://pubs.acs.org.
The O3′- and O5′-toluoyl protection was converted to
TBDMS protection by sequential treatment with NaOMe and
TBSMSCl. Reaction with Boc2O restored the bis-N2-Boc
protection, and the O-Bn group was then reductively removed
by Pd(OH)2-catalyzed hydrogenation. The free primary
alcohol 23 was reprotected as the benzoate 24, and the N2-
OL9007537
(20) Apelqvist, T.; Wensbo, D. Tetrahedron Lett. 1996, 37, 1471–1472.
2468
Org. Lett., Vol. 11, No. 11, 2009