Stereoselective Syntheses of 3-Hydroxyamino- A nd 3-Methoxyamino-2,3-Dideoxynucleosides

Article abstract of DOI:10.1021/acs.orglett.9b03474

Aminonucleosides are used as key motifs in medicinal and bioconjugate chemistry; however, existing strategies toward 3-hypernucleophilic amine systems do not readily deliver deoxyribo-configured products. We report diastereoselective syntheses of deoxyribo- A nd deoxyxylo-configured 3-hydroxyamino- A nd 3-methoxyamino-nucelosides from 3-imine intermediates. The presence or absence of the 5-hydroxyl-group protection dictates facial selectivity via inter-or intramolecular delivery of hydride from BH₃ (borane). Protecting group screening gave one access to previously unknown 3-methoxyamino-deoxyguanosine derivatives.

Full text of DOI:10.1021/acs.orglett.9b03474

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Cite This: Org. Lett. XXXX, XXX, XXX−XXX
Stereoselective Syntheses of 3′-Hydroxyamino- and 3′-
Methoxyamino-2′,3′-Dideoxynucleosides
Sritama Bose* and David R. W. Hodgson*
Durham University, Department of Chemistry, Lower Mountjoy, Stockton Road, Durham, DH1 3LE, United Kingdom
S
* Supporting Information
ABSTRACT: Aminonucleosides are used as key motifs in medicinal and
bioconjugate chemistry; however, existing strategies toward 3′-hypernucleophilic
amine systems do not readily deliver deoxyribo-configured products. We report
diastereoselective syntheses of deoxyribo- and deoxyxylo-configured 3′-hydroxyami-
no- and 3′-methoxyamino-nucelosides from 3′-imine intermediates. The presence
or absence of the 5′-hydroxyl-group protection dictates facial selectivity via inter- or
intramolecular delivery of hydride from BH3 (borane). Protecting group screening
gave one access to previously unknown 3′-methoxyamino-deoxyguanosine
derivatives.
mino-functionalized nucleosides are key fragments for the
development of antiviral agents, nucleic acids technolo-
Scheme 1. Several Hydride-Transfer Agents Were Explored
and Each Delivered Deoxyxylo-Configured Product 2
Exclusively
A
gies, and bioconjugates. While the introduction of aza-
functionalities at the 5′-position is relatively straightforward
because of the limited effect of steric hindrance, 3′-
functionalization is more challenging. Modified ribo- and
deoxyribo-nucleosides with hydroxyamino and methoxyamino
groups at their 3′-positions possess antiviral, anti-leukemic, and
anti-HIV activities.1 For example, the growth of L1210 cells
was shown to be inhibited by 2′-deoxy-2′-(hydroxyamino)
cytidine with an IC50 of 1.84 μM; however, synthesis was
achieved indirectly, via a uridine derivative.1b Tronchet et al.2
explored the synthesis of 3′-methoxyamino- and 3′-hydrox-
yamino-derivatives by stereoselective reduction of 3′-imines.
They readily obtained deoxyxylo-configured systems as major
or exclusive products across a range of reduction conditions.
The deoxyribo-isomers, on the other hand, were usually minor
products or absent, where syntheses have only been achieved
via indirect, multistep methods. Richert, Szostak, and their co-
workers have also exploited the nucleophilicity of amines for
chemical primer extension studies; however, they have not
taken advantage of the enhanced nucleophilicities of hyper-
nucleophilic amines.3 Thus, we sought to develop a stereo-
selective reduction strategy to access deoxyribo-configured 3′-
hydroxyamino- and 3′-methoxyamino-nucleoside systems
directly from 3′-imine intermediates.
Sebesta et al.8 and Matsuda and co-workers1b successfully
synthesized 2′-(alkoxyamino)uridines via the intramolecular
nucleophilic substitution upon 2,2′-O-anhydrouridine deriva-
tives. Thus, we attempted nucleophilic substitution at the 3′-
position of 2,3′-anhydrothymidine with methoxylamine under
a range of reaction conditions; however, surprisingly, we only
observed a hydrolytic opening of the anhydro-linkage.
Stereoselective reduction of 3′-keto nucleosides to ribonu-
cleosides via intramolecular delivery of hydride, tethered
through a free 5′-hydroxyl group, has been reported.9
Moreover, Matsuda and co-workers1b reported that 3′-
(hydroxyamino) uridine with a ribo-configuration 5a can be
obtained from the corresponding 3′-hydroxyiminouridine 4a
by treatment with NaBH4/AcOH (Scheme 2). Thus, we
Our initial investigations centered on thymidine systems
because they do not require nucleobase protection and show
reasonable solubility properties. We chose 5′-O-TBDMS-2,3-
dideoxy-3-N-methoxyimino-thymidine 1 as our starting ma-
terial, and it was prepared according to reported procedur-
es.4,2a Tronchet et al.2a reported the use of NaBH3CN to
reduce 1, albeit with low levels of conversion; thus, we
explored the use of Bu3SnH/BF3·Et2O,5 L-selectride,6 and
NaBH4;7 however, in all cases, we were unable to obtain the
desired ribo-configured compound 3 (Scheme 1), and the xylo-
product was formed instead.
Received: October 1, 2019
© XXXX American Chemical Society
A
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attempted the reduction of imine 4b under similar conditions;
however, poor conversion to 5b was observed (Scheme 2).
This result aligns with the findings of Tronchet et al.,2 who
used NaBH3CN upon 1 under acidic conditions to obtain low
levels of the deoxyribomethoxyamino-product 5b as part of a
complex mixture that prevented the isolation of pure material.
We then explored the application of the borane−
tetrahydrofuran complex for the reduction of 4b, which we
expected to show higher reactivity and higher levels of
conversion. To our delight, we obtained 3′-methoxyamino-
thymidine 5b with the desired deoxyribo-configuration
exclusively in 72% yield (Scheme 3). We were also able to
reduce protected imine 1 with BH3·THF to give deoxyxylo-
configured product 2 in a yield of 70%. We sought to confirm
the absolute configurations of the deprotected 3′-methox-
yamino-products 5b and 6 by 2D NMR spectroscopy.
Unfortunately, the signals arising from the 3′-H [NCH-
(OMe)], 4′-H (OCH), and the 5′-H (OCH2OTBS) protons
were overlapping in the 1H NMR spectra, thus preventing clear
assignments by NOESY correlations. We also attempted
Scheme 2. Stereoselective Reduction of Uridine-Based
Oxime 4a1b Is Observed but Not for the Thymidine Analog
4b
a
Scheme 3. Stereoselective Syntheses of Deoxyribo- and Deoxyxylo-Configured 3′-Methoxyamino-Thymidines
a
Arrows on structures 7 and 8 indicate observed NOESY correlations.
B
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similar analyses using the 5′-TBS-protected systems 2 and 3;
however, we encountered the same signal overlap problems.
Thus, in order to increase the chemical shifts of the 5′-H
signals and, to a lesser extent, 4′-H signals, we prepared 5′-
tosyl derivatives 7 and 8. This strategy allowed us to
distinguish and assign each of the proton signals around the
sugar rings. The deoxyribo-isomer 7 did not show NOESY
correlation between the 3′- and the 1′-protons, whereas
correlations were clearly observed for the deoxyxylo-isomer 8.
Additionally, in the case of deoxyribo-isomer 7, NOESY signals
were observed between the 3′-proton and thymine nucleobase,
along with the expected NOESY correlation between the 4′-
and the 1′-protons. The xylo-isomer 8 also showed the
expected 4′−1′ NOESY correlations.
cytidine systems. Reduction with BH3·THF was successfully
performed on 5′-OH- and 5′-OTBS-3′-methoxyimino-2′,3′-
dideoxycytidine systems12 to afford deoxyribo-product (9a)
and deoxyxylo-product (9b), respectively, in 71% and 68%
yields (Figure 2). The 5′-OH-3′-methoxyimino-2′,3′-dideox-
In order to gain mechanistic insights into the proposed
intramolecular hydride delivery via complexation of the boron
to the free hydroxyl group at the 5′-position, we carried out 11
B
NMR experiments.10 The 5′-TBS protected thymidine imine 1
and deprotected 3′-methoxyimino thymidine 4b were treated
with B(OMe)3 in THF-d8. Starting with the addition of 0.5
equiv of B(OMe)3, 11B NMR spectra were recorded for
multiple additions of 0.5 equiv of B(OMe)3 up to 2.5 equiv.
Figure 1 gives evidence for B−N complexation via the imine
Figure 2. Product scope for deoxycytidine and deoxyadenosine
systems.
yadenosine system12 afforded the deoxyribomethoxylamine
product 10 exclusively, which was derivatized at the 5′-position
(Figure 2) to minimize conformational changes and, thus,
confirm configuration (see the Supporting Information).14,2b
We then moved on to explore the application of our BH3·
THF reduction strategies toward guanosine systems. Guano-
sine systems present significant synthetic challenges because of
their poor solubility properties.13 With this in mind, we
attempted reductions on the 5′-OTBS-N-isobutyroyl-protected
methoxyimino-derivative of deoxyguanosine and the analogous
5′-OH system12 using BH3·THF. These reactions resulted in
the reduction of the imines to the desired deoxyxylo-product
(11b) and deoxyribo-product (11a) in 85% and 70% yield,
respectively, but the isobutyroyl group was also reduced. Thus,
we moved to a N-DMT-protected substrate, which tolerated
BH3·THF to yield the deoxyribo-product 12 after TBS
protection, as its tosic acid salt in 80% yield upon deprotection
of the DMT group (Figure 3). The configurations of the
derivatives of all guanosine products were confirmed by
NOESY analysis of the 5′-derivatives (see the Supporting
Information).
Next, we explored the BH3·THF reductions of 3′-
hydroxyimino systems. The unprotected 3′-hydroxyimino-
thymidine derivative4 13a was reduced by BH3·THF stereo-
selectively to give deoxyribo-configured 14a15 as the major
product alongside the deoxyxylo-derivative 14b1c in a 4:1 ratio,
where the mixture could be separated by column chromatog-
raphy. On the other hand, the 5′-TBS-protected 3′-
hydroxyimino-thymidine derivative 13b2b afforded the deoxy-
xylo-product 152b exclusively. The NMR spectra of the TBS-
protected deoxyribo-derivative 16 and deoxyxylo-isomer 15
matched NMR data reported by Tronchet et al.2b (Scheme 4).
This strategy was also successfully applied to deoxycytidine
and deoxyadenosine systems to afford mixtures of deoxyribo-
and deoxyxylo-isomers, in ∼4:1 ratios, which could also be
isolated by chromatography. The products were derivatized to
17a, 17b, and 18 to minimize conformational equilibration14
Figure 1. 11B NMR studies in THF-d8. (A) 5′-OH imine 4b (1.0
equiv) mixed with B(OMe)3 (1.5 equiv). (B) 5′-OTBS imine 1 (1.0
equiv) mixed with B(OMe)3 (1.5 equiv). (C) B(OMe)3 alone.
nitrogen of 5′-TBS-protected 3′-methoxyimino-thymidine 1
via a signal at 19.19 ppm, which persists even after overnight
incubation with 2.5 equiv of B(OMe)3. In the case of the 5′-
hydroxy 3′-methoxyimino-thymidine 4b, we observed two
distinct signals at 22.98 ppm (RO−B−N) and 19.20 ppm that
indicate the complexation of boron with the free hydroxyl
group at the 5′-position and B−N complex, respectively
(Figure 1).11 Taken together, these simple experiments
support the idea of a critical role for 5′-OH complexation in
the reduction of 4b to deliver the deoxyribo-configuration
observed in 5b.
On the basis of our promising results with the thymidine
system, we applied the same strategies to the adenosine and
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Figure 3. Deoxyguanosine systems. (A) The protecting groups of the
isobutyroyl-protected imine substrates were also reduced. (B) DMT-
protected imine substrate afforded the desired deoxyribo-configured
methoxyamino-nucleoside upon DMT deprotection (pTSA = para-
toluenesulfonate).
Figure 4. Product scope for deoxycytidine and deoxyadenosine
systems.
Scheme 5. Synthesis of 3′-Aminonucleoside Systems via
Catalytic Reductions of Hydroxylamines
and thus allow differentiation between the deoxyribo- and
deoxyxylo-products through NOESY assignments. Bis-TBS-
protected 3′-hydroxyamino-cytidine derivative 17a exhibited
NOESY correlations between the 3′-proton and the 6-
(nucleobase)-proton, whereas the debenzoylated-deoxyxylo-
derivative 17b exhibited 1′-H to 3′-H NOESY correlation.
Similarly, the TBS-protected-deoxyribo-3′-hydroxyamino-ad-
enosine 18 exhibited NOESY correlations between the protons
3′- and 8-H of the nucleobase (Figure 4).
Kojima et al. demonstrated that 3′-hydroxylamine systems
can be further reduced to 3′-amines by Pd/C and hydrogen to
afford 3′-amino-ribonucleoside analogs.16 We applied the same
methodology to hydroxylamino-systems 14a and 15, and we
were pleased to observe clean conversion to the corresponding
amine systems 19 and 20 in 89% and 75% yield, respectively
(Scheme 5).
In conclusion, we have developed efficient, direct strategies
to obtain deoxyribo- and deoxyxylo-isomers of 3′-methoxyami-
no- and 3′-hydroxyamino-deoxynucleosides, from common
Scheme 4. Synthesis of Deoxyribo- and Deoxyxylo-Configured 3′-Hydroxyamino Thymidine Derivative
D
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intermediates, via stereoselective reductions of the correspond-
ing 3′-imino deoxynucleosides using BH3·THF. Our approach
has delivered ribo-configured deoxynucleosides in good yields,
which are otherwise difficult to obtain. To the best of our
knowledge, the ribo-deoxycytidine derivative 9a, deoxyadeno-
sine derivative 10, and ribo- and xylo-deoxyguanosine
derivatives 11a−c and 12 containing the 3′-methoxyamino-
functionality are novel compounds.
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ASSOCIATED CONTENT
* Supporting Information
The Supporting Information is available free of charge on the
ACS Publications website at DOI: 10.1021/acs.or-
glett.9b03474.
■
S
́
M. C.; Trmcic, M.; Hodgson, D. R. W. Chem. Commun. 2009, 4980.
(d) Hodgson, D. R. W. Adv. Phys. Org. Chem. 2017, 51, 187.
(14) (a) Dudycz, L.; Stolarski, R.; Pless, R.; Shugar, D. A. Z.
Naturforsch., C: J. Biosci. 1979, 34C, 359. (b) Stolarski, R.; Dudycz, L.;
Shugar, D. Eur. J. Biochem. 1980, 108, 111.
Experimental procedures and characterizations (PDF)
(15) Schreiber, S. L.; Ikemoto, N. Tetrahedron Lett. 1988, 29, 3211.
(16) (a) Kojima, N.; Szabo, I. E.; Bruice, T. C. Tetrahedron 2002, 58,
867. (b) Kojima, N.; Bruice, T. C. Org. Lett. 2000, 2, 81.
AUTHOR INFORMATION
Corresponding Authors
■
*E-mail: d.r.w.hodgson@durham.ac.uk.
*E-mail: bonsaibose@yahoo.com.
ORCID
Sritama Bose: 0000-0002-9007-4964
David R. W. Hodgson: 0000-0003-4517-9166
Notes
The authors declare no competing financial interest.
ACKNOWLEDGMENTS
■
We are grateful to BBSRC for funding this research through
grant number BB/P02145X/1.
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