Synthesis of β-hydroxyphosphonate and 1,2-dihydroxy acyclic nucleoside analogs via 1,3-dipolar cycloaddition strategy

Article abstract of DOI:10.1080/15257771003597709

A convenient synthetic approach toward nucleoside analogs where β-hydroxyphosphonate- or 1,2-dihydroxy units are connected to the nucleic acid base through a triazole spacer is discussed.

Full text of DOI:10.1080/15257771003597709

This article was downloaded by: [Duke University Libraries]
On: 31 March 2013, At: 23:46
Publisher: Taylor & Francis
Informa Ltd Registered in England and Wales Registered Number: 1072954 Registered
office: Mortimer House, 37-41 Mortimer Street, London W1T 3JH, UK
Nucleosides, Nucleotides and Nucleic
Acids
Publication details, including instructions for authors and
subscription information:
http://www.tandfonline.com/loi/lncn20
Synthesis of β-Hydroxyphosphonate
and 1,2-Dihydroxy Acyclic Nucleoside
Analogs via 1,3-Dipolar Cycloaddition
Strategy
M. Ganesan a & K. M. Muraleedharan a
a Department of Chemistry, Indian Institute of Technology Madras,
Chennai, India
Version of record first published: 24 Feb 2010.
To cite this article: M. Ganesan & K. M. Muraleedharan (2010): Synthesis of β-Hydroxyphosphonate
and 1,2-Dihydroxy Acyclic Nucleoside Analogs via 1,3-Dipolar Cycloaddition Strategy, Nucleosides,
Nucleotides and Nucleic Acids, 29:2, 91-96
To link to this article: http://dx.doi.org/10.1080/15257771003597709
PLEASE SCROLL DOWN FOR ARTICLE
Full terms and conditions of use: http://www.tandfonline.com/page/terms-and-conditions
This article may be used for research, teaching, and private study purposes. Any
substantial or systematic reproduction, redistribution, reselling, loan, sub-licensing,
systematic supply, or distribution in any form to anyone is expressly forbidden.
The publisher does not give any warranty express or implied or make any representation
that the contents will be complete or accurate or up to date. The accuracy of any
instructions, formulae, and drug doses should be independently verified with primary
sources. The publisher shall not be liable for any loss, actions, claims, proceedings,
demand, or costs or damages whatsoever or howsoever caused arising directly or
indirectly in connection with or arising out of the use of this material.

Nucleosides, Nucleotides and Nucleic Acids, 29:91–96, 2010
Copyright ꢀC Taylor and Francis Group, LLC
ISSN: 1525-7770 print / 1532-2335 online
DOI: 10.1080/15257771003597709
SYNTHESIS OF β-HYDROXYPHOSPHONATE AND 1,2-DIHYDROXY
ACYCLIC NUCLEOSIDE ANALOGS VIA 1,3-DIPOLAR CYCLOADDITION
STRATEGY
M. Ganesan and K. M. Muraleedharan
Department of Chemistry, Indian Institute of Technology Madras, Chennai, India
A convenient synthetic approach toward nucleoside analogs where β-hydroxyphosphonate- or
2
1,2-dihydroxy units are connected to the nucleic acid base through a triazole spacer is discussed.
Keywords Nucleoside analogs; triazole spacer; acyclic nucleoside phosphonates
INTRODUCTION
Synthesis of nucleoside analogs with biomimetically modified “sugar” or
the “base” moieties is an area of tremendous interest due to their potential to
target pathogens such as human immunodeficiency virus (HIV), hepatitis B
virus (HBV), hepatitis C virus (HCV), and cytomegalovirus (CMV).[1,2] Ther-
apeutic effects from such molecules arise due to their interaction with targets
like DNA polymerase, reverse transcriptase, or thymidine kinase. Nucleoside
analogs with varying degrees of conformational flexibilities are known; im-
portant prototypes among these include: acyclic nucleoside phosphonates
(ANPs) where the purine base is attached to the phosphonate unit via an
acyclic linker,[1] analogs in which saturated,[3] unsaturated,[4,5] or fused[6]
carbon rings replace the furanose moiety, those with spirocyclic restriction
of furanose ring,[7] and the locked nucleoside analogs, which restricts the fu-
ranose ring to adopt either N-type or S-type puckering through appropriate
intramolecular bridging.[8–10] ANPs, the structurally simplest among these,
have emerged as one of the most important class with promising antiviral
and cytostatic activities. Of these, 9-[2-(phosphonomethoxy)ethyl]adenine
Received 17 October 2009; accepted 4 January 2010.
Financial support of this work by Council of Scientific and Industrial Research (CSIR), INDIA
(Grants 01(2121)/07/EMR-II) is gratefully acknowledged. We thank Mr. V. Ramkumar, IIT Madras, for
his help during x-ray crystallographic analysis. M.G. thanks IIT Madras for a research fellowship.
Address correspondence to K. M. Muraleedharan, Department of Chemistry, Indian Institute of
Technology Madras, Chennai 600 036, India. E-mail: mkm@iitm.ac.in
91

92
M. Ganesan and K. M. Muraleedharan
NH2
N
NH2
N
NH2
O
N
N
HO
HO
N
O
P
N
N
O
P
O
O
HO
HO
N
HO
HO
P
O
N
O
O
N
HO
I
Adefovir
O
II
Tenofovir
O
Cidofovir III
(Vistide®)
O
NH2
N
O
NH2
N
O
N
N
O
O
N
O
O
O
P
O
P
O
O
O
N
N
O
N
COOH
COOH
O
O
Adefovir dipivoxil IV
V
Tenofovir disoproxil fumarate
(Hepsera®)
(Viread®)
FIGURE 1 Examples of therapeutically important acyclic nucleoside analogs; Vistide, Hepsera, and
Viread are marketed by Gilead Sciences, Inc., Foster City, CA, USA.
(PMEA, Adefovir) shows activity against DNA and retrovirus,[11] and its pro-
drug known as adefovir dipivoxil has been approved for hepatitis B treatment
(Figure 1).[12]
Small modification in the linker region led to the development of
tenofovir, and its prodrug, tenofovir disoproxil fumarate (Viread) is a
useful anti-HIV agent.[13,14] Another clinically useful compound from this
series is Cidofovir, which contains a hydroxymethyl group at 2-position
of 2-(phosphonomethoxy)ethyl]cytosine.[15] A plethora of information on
structure-activity relationships in ANPs is currently available[16,17] and there
is still significant research interest in identifying new skeletons with correct
balance of potency and selectivity. In this article, we report the synthesis and
crystallographic structural details of a class of nucleoside analogs in which
the terminal β-hydroxyphosphonate- or 1,2-dihydroxy groups and the nu-
cleic acid bases are linked through a triazole spacer in place of the sugar ring.
RESULTS AND DISCUSSION
The synthesis of 1,2,3-triazole-based nucleoside analogs presented here
commenced with the preparation of the azide component 3 by opening the
epoxide ring in 2.[18,19] This on Cu(I) catalyzed dipolar cycloaddition with N-
propargylated benzimidazole (4a), pyrimidines (4b,c), purines (4d,e), and
arylamines (4f–h) led to the formation of adducts 5a–h in 62–98% yields
(Scheme 1, Table 1).[20–22] Due to the lack of stereo-control during the
epoxidation step, analogs 5a–h were obtained as a mixture of enantiomers.

β-Hydroxyphosphonate and 1,2-Dihydroxy Acyclic Nucleoside Analogs
93
OH
O
P
O
P
O
P
c
OEt
OEt
a
O
OEt
OEt
b
OEt
OEt
N3
R
N
O
P
OH
N
N
EtO
EtO
3
1
2
5a-h
R
4a-h
R
N
N
OH
HO
N
OH
O
d
e
c
O
D-Mannitol
HO
N3
N3
9a-h
6
7
8
SCHEME 1 Synthesis of 1,2,3-triazole-based nucleoside analogs; R groups in 4a–h correspond to the
substituents (R) shown in Table 1. Reagents and conditions: (a) mCPBA, CH2Cl2, 0◦C, 45%; (b) NaN3,
NH4Cl, MeOH-H2O (4:1), 80◦C, 6 h, 89%; (c) CuSO4 (5 mol%), Na-ascorbate (20 mol%), Ethanol-H2O
(2:1), rt; (d) (i) ZnCl2, acetone, 18hrs, 35%; (ii) NaIO4, NaHCO3, CH2Cl2, 1hr; (iii) NaBH4, ethanol,
0◦C (59%, two steps); (iv) MsCl, Et3N, 0◦C, 2hrs, quantitative; (v) NaN3, DMF, 90◦C, 73%; (e) 20%
TFA-CH2Cl2, 80%.
In order to prepare optically pure hydroxylated analogs, we redesigned the
reaction sequence by including (D)-mannitol-derived isopropylidene-azide
(7)[23] in the cycloaddition step to generate another series of nucleoside
analogs 9a–h in 67–92% yields.
TABLE 1 β-hydroxyphosphonate- and 1,2-dihydroxy nucleoside analogs prepared via dipolar
cycloaddition strategy
Reaction
time (h)
Reaction
time (h)
%
Yield
R
Compounds
% Yield
R
Compounds
Cl
5a
9a
26
8
62
67
5e
9e
9
6
76
73
N
N
N
N
N
N
O
N
5b
9b
9
18
78
67
5f
9f
28
27
78
92
NH
HN
O
NO2
5c
9c
30
16
98
71
5g
9g
18
12
67
83
NH
NH
O
HN
O
N
NH2
N
5d
9d
10
18
81
64
5h
9h
24
10
68
81
N
N
N

94
M. Ganesan and K. M. Muraleedharan
Bond parameter
5c
9f
OH
1N
C7-N9 (Ao )
6.32
6.581
7
H
R2
R1
8
5
C5-N1-C6-C7
N
6
−95.57
130.29
9
(torsion)
R3
4
N3
N
C5-C4-C8-N9
107.24
−3.60
2
(torsion)
5c
9f
FIGURE 2 X-ray crystallographic structures and relevant details of compounds 5c and 9f.
Crystals suitable for x-ray diffraction studies were obtained by slow evap-
oration of a solution of compound 5c in methanol. This belonged to the
triclinic form under the space group P-1 with Z = 2. In the solid state, the
molecule adopted a conformation with C7-N9 distance of 6.32 A◦. The di-
hedral angles of −95.57o and 107.24◦, respectively, across C5-N1-C6-C7 and
C5-C4-C8-N9 bonds led to a syn-orientation of the thymine and phosphonate
groups with respect to the central triazole ring as shown in Figure 2.
Although the dihydroxy-analogs from nucleic acid bases (9a–e) did not
give crystals suitable for diffraction studies, we were successful in getting
crystals of the nitro-derivative 9f by slow evaporation of its chloroform so-
lution. Molecules in this case, crystallized in rhombohedral form under the
space group R3, had Z = 2. The C7-N9 distance in this case was 6.581 A◦, a
value very close to that observed in 5c. The dihedral angles across C5-N1-C6-
C7 and C5-C4-C8-N9 bonds were however notably different from that in 5c
(130.29◦ and −3.60◦, respectively), which shows the greater conformational
flexibility of the terminal moieties with respect to the triazole ring.
There have been a number of reports on the biological activities of
phosphonate-based nucleoside analogs which carry chemically and enzy-
maticaly stable P-C linkage instead of P-O.[24,25] Herein, we have demon-
strated a useful approach that can give such compounds in minimum
number of reaction steps. Dipolar cycloaddition approach, particularly

β-Hydroxyphosphonate and 1,2-Dihydroxy Acyclic Nucleoside Analogs
95
that involving an azide and alkyne for preparing therapeutically impor-
tant chemical entities is well documented in literature and has benefited
the area of nucleoside analogs as well.[26] Lazrek et al., has previously
adopted this method to prepare acyclic nucleoside analogs by reacting 4-
azidobutyl acetate and 2-(azidomethoxy)ethyl acetate with propargylated
nucleo-bases.[27,28] In the present work, we have explored the possibility of
connecting β-hydroxyphosphonate and 1,2-dihydroxy units to the nucleic
acid bases through the “click” protocol. X-ray diffraction studies involving
crystals of 5c and 9f (CCDC numbers 749638 and 750866, respectively) have
given useful information on the preferred orientations of terminal hydroxyl-
or hydroxyphosphonate units and the nucleic acid bases with respect to the
triazole ring. Biological activities of these phosphonates (as phosphonic
acids)17 and diols will be evaluated and reported in due course.
REFERENCES
1. De Clercq, E.; Holy, A. Case history: Acyclic nucleoside phosphonates: A key class of antiviral drugs.
Nat. Rev. Drug Discovery 2005, 4, 928–940.
2. Bonate, P.L.; Arthaud, L.; Cantrell, W.R., Jr.; Stephenson, K.; Secrist, J.A., III; Weitman, S. Discovery
and development of clofarabine: A nucleoside analogue for treating cancer. Nat. Rev. Drug Discovery
2006, 5, 855–863.
3. Zhu, X.-F. The latest progress in the synthesis of carbocyclic nucleosides. Nucleoside Nucleotides Nucleic
Acids 2000, 19, 651–690.
4. Canoa, P.; Gonzalez-Moa, M.J.; Teijeira, M.; Teran, C.; Uriarte, E.; et al. Synthesis and anti-HIV activity
of novel cyclopentenyl nucleoside analogs of 8-azapurine. Chem. Pharm. Bull. 2006, 54, 1418–1420.
5. Yin, X.-Q.; Schneller, S.W. Isomers of neplanocin A and 2ꢁ-deoxyneplanocin A possessing a C-1ꢁ/C-6ꢁ
double bond. Tetrahedron Lett. 2005, 46, 1927–1929.
6. Lescop, C.; Huet, F. Synthesis of novel nucleosides with a fused cyclopropane ring substituted by a
hydroxymethyl group. Tetrahedron 2000, 56, 2995–3003.
7. Paquette, L.A.; Owen, D.R.; Bibart, R.T.; Seekamp, C.K. Spirocyclic restriction of nucleosides. An
analysis of protecting group feasibility while accessing prototype anti-1-oxaspiro[4.4]nonanyl mimics.
Org. Lett. 2001, 3, 4043–4045.
8. Obika, S.; Andoh, J.-I.; Sugimoto, T.; Miyashita, K.; Imanishi, T. Synthesis of a conformationally
locked AZT analog, 3ꢁ-azido-3ꢁ-deoxy-2ꢁ-O,4ꢁ-C-methylene-5-methyluridine. Tetrahedron Lett. 1999, 40,
6465–6468.
9. Osaki, T.; Obika, S.; Harada, Y.; Mitsuoka, Y.; Sugaya, K.; et al. Development of a novel nucleoside
analog with S-type sugar conformation: 2ꢁ-Deoxy-trans-3ꢁ,4ꢁ-bridged nucleic acids. Tetrahedron 2007,
63, 8977–8986.
10. Kim, H.S.; Jacobson, K.A. Synthesis of a novel conformationally locked carbocyclic nucleoside ring
system. Org. Lett. 2003, 5, 1665–1668.
11. De Clercq, E.; Holy´, A.; Rosenberg, I.; Sakuma, T.; Balzarini, J.; et al. A novel selective broad-spectrum
anti-DNA virus agent. Nature 1986, 323, 464–467.
12. Marcellin, P.; Chang, T.-T.; Lim, S.G.; Tong, M.J.; Sievert, W.; et al. Adefovir Dipivoxil for the
treatment of hepatitis B e Antigen–positive chronic hepatitis B. N. Engl. J. Med. 2003, 348, 808–816.
13. Balzarini, J.; Holy, A.; Jindrich, J.; Naesens, L.; Snoeck, R.; et al. Differential antiherpesvirus and
antiretrovirus effects of the (S) and (R) enantiomers of acyclic nucleoside phosphonates: Potent
and selective in vitro and in vivo antiretrovirus activities of (R)-9-(2-phosphonomethoxypropyl)-2,6-
diaminopurine. Antimicrob. Agents Chemother. 1993, 37, 332–338.
14. De Clercq, E. Acyclic nucleoside phosphonates: Past, present and future Bridging chemistry to
HIV, HBV, HCV, HPV, adeno-, herpes-, and poxvirus infections: The phosphonate bridge. Biochem.
Pharmacol. 2007, 73, 911–922.

96
M. Ganesan and K. M. Muraleedharan
15. De Clercq, E.; Sakuma, T.; Baba, M.; Pauwels, R.; Balzarini, J.; et al. Antiviral activity of phosphonyl-
methoxyalkyl derivatives of purine and pyrimidines. Antiviral Res. 1987, 8, 261–272.
16. Tan, X.; Chu, C.K.; Boudinot, F.D. Development and optimization of anti-HIV nucleoside analogs
and prodrugs: A review of their cellular pharmacology, structure-activity relationships and pharma-
cokinetics. Adv. Drug Delivery Rev. 1999, 39, 117–151.
17. Holy, A.N.; Gunter, J.G.; Dvorakova, H.; Masojıdkova, M.; Andrei, G.; et al. Structure-Antiviral ac-
tivity relationship in the series of pyrimidine and purine N-[2-(2-Phosphonomethoxy)ethyl] nu-
cleotide analogues. 1. Derivatives substituted at the carbon atoms of the base. J. Med. Chem. 1999, 42,
2064–2086.
18. Nesterov, V.V.; Kolodiazhnyi, O.I. Efficient method for the asymmetric reduction of alpha- and
beta-ketophosphonates. Tetrahedron 2007, 63, 6720–6731.
19. Nagase, T.; Kawashima, T.; Inamoto, N. A new synthetic route of beta-hydroxyalkylphosphonates
from beta,gamma-epoxyalkylphosphonates. Chem. Lett. 1984, 1997–2000.
20. Rostovtsev Vsevolod, V.; Green Luke, G.; Fokin Valery, V.; Sharpless, K.B. A stepwise huisgen cycload-
dition process: Copper(I)-catalyzed regioselective “ligation” of azides and terminal alkynes. Angew
Chem Int Ed. 2002, 41, 2596–2599.
21. Hakimelahi, G.H.; Gassanov, G.S.; Hsu, M.-H.; Hwu, J.R.; Hakimelahi, S. A Novel Approach towards
studying non-genotoxic enediynes as potential anticancer therapeutics. Bioorg. Med. Chem. 2002, 10,
1321–1328.
22. Joshi, R.V.; Zemlicka, J. Alkylation of adenine with tert-propargyl chlorides: Acetylene/allene ratio
and N9/N7 regioselectivity. Tetrahedron 1993, 49, 2353–2360.
23. Gibson, F.S.; Park, M.S.; Rapoport, H. Bis[[4-(2,2-dimethyl-1,3-dioxolyl)]methyl]- carbodiimide
(BDDC) and its application to residue-free esterifications, peptide couplings, and dehydrations.
J. Org. Chem. 1994, 59, 7503–7507.
24. Gallier, F.; Peyrottes, S.; Perigaud, C. Ex-chiral-pool synthesis of beta-hydroxyphosphonate nucleoside
analogues. Eur. J. Org. Chem. 2007, 925–933.
25. Kralikova, S.; Budesinsky, M.; Masojidkova, M.; Rosenberg, I. Geminal hydroxy phosphonate deriva-
tives of nucleosides: A novel class of nucleoside 5ꢁ-monophosphate analogues. Tetrahedron Lett. 2000,
41, 955–958.
26. Amblard, F.; Cho, J.H.; Schinazi, R.F. Cu(I)-Catalyzed Huisgen Azide-alkyne 1,3-dipolar cycloaddition
reaction in nucleoside, nucleotide, and oligonucleotide chemistry. Chem. Rev. 2009, 109, 4207–4220.
27. Lazrek, H.B.; Taourirte, M.; Oulih, T.; Barascut, J.L.; Imbach, J.L.; et al. Synthesis and anti-HIV
activity of new modified 1,2,3-triazole acyclonucleosides. Nucleoside Nucleotides Nucleic Acids 2001, 20,
1949–1960.
28. Lazrek, H.B.; Taourirte, M.; Oulih, T.; Lebtoumi, M.; Barascut, J.L.; et al. Synthesis of new 1,2,3-
triazole acylonucleoside analogs of ACV and HBG. Nucleoside Nucleotides Nucleic Acids 1997, 16,
1115–1118.