Synthesis of a new class of 5'-functionalized adenosines using a rh(ii)-catalyzed 1,3-dipolar cycloaddition.

Article abstract of DOI:10.1021/ol015995k

[reaction: see text] Chemically protected adenosine was functionalized at the 5' position to generate novel dipolarophiles and mesoionic dipoles. These species were found to undergo facile 1,3-dipolar cycloaddition to afford a new series of adenosine derivatives that contain a point of diversification at the 5' position of adenosine.

Full text of DOI:10.1021/ol015995k

ORGANIC
LETTERS
2001
Vol. 3, No. 15
2273-2276
Synthesis of a New Class of
5′-Functionalized Adenosines Using a
Rh(II)-Catalyzed 1,3-Dipolar
Cycloaddition
Fei Liu and David J. Austin*
Department of Chemistry, Yale UniVersity, New HaVen, Connecticut 06520
daVid.austin@yale.edu
Received April 17, 2001
ABSTRACT
Chemically protected adenosine was functionalized at the 5′ position to generate novel dipolarophiles and mesoionic dipoles. These species
were found to undergo facile 1,3-dipolar cycloaddition to afford a new series of adenosine derivatives that contain a point of diversification
at the 5′ position of adenosine.
Nucleotide-utilizing enzymes such as transferases and syn-
thases have long been recognized as playing a central role
in metabolism.1 More recently, the role of kinases and
phosphatases in signal transduction has also been recog-
nized.2 In response to this finding, small-molecule analogues
of both adenosine triphosphate (ATP) and guanosine tri-
phosphate (GTP) have been developed. While small-
molecule GTP mimicry remains a mostly underdeveloped
area, in many cases ATP analogues have shown high affinity
and inhibitory activity.3
that is characterized by high affinity yet low specificity.4 In
the few known cases where inhibitors do access the
phosphate-binding region, a greater specificity is achieved.5
In an effort to develop a molecular scaffold that will both
complement the nature of the phosphate binding site and
provide a molecular platform from which diversity can be
generated, we have developed a 1,3-dipolar cycloaddition
strategy for the construction of a series of adenosine-
derivatized bicyclic molecules (1-3). By building this feature
at the 5′ end of the adenosine, we hope to create a structure
that can replace the phosphate group of a purine nucleotide,6
thus providing a chemical diversity scaffold that is anchored
by a biologically pertinent molecule. Herein, we report the
successful rhodium(II)-catalyzed 1,3-dipolar cycloaddition
of adenosine-modified dipoles and dipolarophiles for the
Many of the traditional ATP-mimetic agents target the
hydrophobic subsite of the purine nucleotide pocket, a site
(1) (a) Richards, N. G. J. Annu. Rep. Prog. Chem., Sect. B: Org. Chem.
1999, 95, 299-334. (b) Hatse, S.; De Clercq, E.; Balzarini, J. Biochem.
Pharmacol. 1999, 58, 539-555.
(2) (a) Levine, M. A. Arch. Med. Res. 1999, 30, 522-531. (b) Stewart,
R. C.; VanBruggen, R.; Ellefson, D. D.; Wolfe, A. J. Biochemistry 1998,
37, 12269-12279.
(3) (a) Ulrich, S. M.; Buzko, O.; Shah, K.; Shokat, K. M. Tetrahedron
2000, 56, 9495-9502. (b) Kim, S.-H. Pure Appl. Chem. 1998, 70, 555-
565. (c) Gray, N. S.; Wodicka, L.; Thunnissen, A.-M. W. H.; Norman, T.
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Meijer, L.; Kim, S.-H.; Lockhart, D. J.; Schultz, P. G. Science (Washington,
D.C.) 1998, 281, 533-538.
(4) Lawrence, D. S.; Niu J. Pharmacol. Ther. 1998, 77, 81-114.
(5) (a) Setyawan, J.; Koide, K.; Diller, T. C.; Bunnage, M. E.; Taylor,
S. S.; Nicolaou, K. C.; Brunton, L. L. Mol. Pharmacol. 1999, 56,
370-376. (b) Schindler, T.; Bornmann, W.; Pellicena, P.; Miller, W. T.;
Clarkson, B.; Kuriyan, J. Science (Washington, D.C.) 2000, 289, 1938-
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Med. Chem. Lett. 1996, 6, 2411-2416. (b) Otoski, R. M.; Wilcox, C. X.
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10.1021/ol015995k CCC: $20.00 © 2001 American Chemical Society
Published on Web 06/30/2001

construction of functionalized bicyclic molecules and a
computational analysis of their ability to occupy the same
relative geometric space as the phosphate portion of ATP.
Synthesis of the dipole precursor for the first adenosine-
linked 1,3-dipolar cycloaddition reaction to form scaffold 1
is shown in Scheme 1. Modification to the dipole begins
Scheme 1a
The 1,3-dipolar cycloaddition reaction is an important
transformation for the construction of polyheterocyclic
molecules.7 The concurrent formation of two carbon-carbon
bonds, yielding cyclic or even bicyclic heterocycles, makes
this reaction a good choice for diversity-oriented synthesis.
Examples of the 1,3-dipolar cycloaddition reaction for the
construction of nucleoside-like molecules include the syn-
thesis of heterocyclic aromatics such as nucleo-bases,8
synthesis of nucleoside antibiotic natural products,9 stereo-
specific generation of ribose moieties,10 and functionalization
of the 2′, 3′, and 5′ positions of nucleosides.11 While these
thermally initiated cycloadditions have proven useful, the
rhodium(II)-mediated cyclization-cycloaddition strategy is
subject to side reactivity12 and its use with molecules of this
complexity has remained elusive. We have previously
reported a diastereoselective rhodium(II) 1,3-dipolar cyclo-
addition with a class of mesoionic dipoles known as the
isomu¨nchnones.13 We sought to expand the generality of the
process and diversity of potential substrates to include
molecules of biological origin. In this example, the generation
of nucleoside-derived isomu¨nchnones and dipolarophiles will
provide adenosine-derived cycloadducts (1-3) with the
triphosphate of ATP being replaced by a polyoxygenated
bicyclic heterocycle.
a (a) (CH3CO)2O, pyridine, rt, 85%; (b) Rapoport’s reagent,
CH2Cl2, rt, 92%; (c) methyl malonyl chloride, toluene, bubbling
N2, 80 °C, 50%; (d) MsN3, Et3N, CH2Cl2, rt, 65%; (e) ethyl vinyl
ether, Rh2(pfbm)4, toluene, 60 °C, 70%; (f) TFA/H2O 10:1, 0 °C;
Pd/C, EtOH, NH4CO2H, 95%.
with amidation of 5′-aminoadenosine 414 under careful
control of both temperature and time, to protect against
overacylation of the adenine basic nitrogen. Rapoport’s Cbz-
transferring reagent,15 originally developed for deoxy-ribo-
nucleosides, was found to efficiently protect the exocyclic
amine. Imidation with methyl malonyl chloride was carried
out in refluxing toluene with nitrogen bubbling through the
reaction mixture in order to facilitate removal of HCl, which
could interfere with reaction progress and prove detrimental
to the acid-sensitive nucleoside moiety.16 The diazotransfer
step proceeded smoothly to give R-diazoimide 5 in 25% yield
over four steps from amine-nucleoside 4. Diazoimide 5 was
subjected to the tandem Rh(II)-catalyzed carbonyl-ylide
formation and cycloaddition with ethyl vinyl ether in toluene
at 60 °C. Although the potential Lewis acidity of rhodium(II)
perfluorobutyramidate [Rh2(pfbm)4] raised concerns for
possible nucleoside decomposition, the catalyst proved mild
enough to allow the reaction at elevated temperatures. While
the cycloaddition of ethyl vinyl ether proceeded with high
diastereoselectivity, providing only the endo cycloaddition
product, as previously described,17 the chiral ribose portion
of adenosine provided little facial bias for dipolarophile
approach. Deprotection of the purine exocyclic amine and
removal of the ribose acetonide furnished a 1:1 mixture of
diastereomeric products 1a and 1b.
(7) (a) Adams, D. R.; Boyd, A. S. F.; Ferguson, R.; Grierson, D. S.;
Monneret, C. Nucleosides Nucleotides 1998, 17, 1053-1075. (b) Padwa,
A.; Prein, M. J. Org. Chem. 1997, 62, 6842-6854. (c) Leggio, A.; Liguori,
A.; Procopio, A.; Siciliano, C.; Sindona, G. Nucleosides Nucleotides 1997,
16, 1515-1518. (d) Padwa, A.; Austin, D. J.; Hornbuckle, S. F. J. Org.
Chem. 1996, 61, 63-72. (e) 1,3-Dipolar Cycloaddition Chemistry; Padwa,
A., Ed.; Wiley: New York, 1984; Vols. 1 and 2.
(8) (a) De las Heras, F. G.; Tam, S. Y. K.; Klein, R. S.; Fox, J. J. J.
Org. Chem. 1976, 41, 84-90. (b) Stimac, A.; Townsend, L. B.; Kobe, J.
Nucleosides Nucleotides 1991, 10, 727-8.
(9) Merino, P.; Franco, S.; Merchan, F. L.; Tejero, T. J. Org. Chem.
2000, 65, 5575-5589.
(10) (a) Chiacchio, U.; Corsaro, A.; Gumina, G.; Rescifina, A.; Iannazzo,
D.; Piperno, A.; Romeo, G.; Romeo, R. J. Org. Chem. 1999, 64, 9321-
9327. (b) Chiacchio, U.; Rescifina, A.; Iannazzo, D.; Romeo, G. J. Org.
Chem. 1999, 64, 28-36. (c) Chiacchio, U.; Corsaro, A.; Iannazzo, D.;
Piperno, A.; Rescifina, A.; Romeo, R.; Romeo, G. Tetrahedron Lett. 2001,
42, 1777-1780.
(11) (a) Chiacchio, U.; Rescifina, A.; Corsaro, A.; Pistara, V.; Romeo,
G.; Romeo, R. Tetrahedron: Asymmetry 2000, 11, 2045-2048. (b) Lazrek,
H. B.; Engels, J. W.; Pfleiderer, W. Nucleosides Nucleotides 1998, 17,
1851-1856. (c) Xiang, Y.; Schinazi, R. F.; Zhao, K. Bioorg. Med. Chem.
Lett. 1996, 6, 1475-1478. Rong, J.; Roselt, P.; Plavec, J.; Chattopadhyaya,
J. Tetrahedron 1994, 50, 4921-36. (d) Haebich, D. Synthesis 1992, 358-
60.
Synthesis of the second adenosine scaffold, 2, begins with
the oxidized adenosine molecule 5′-carboxyadenosine (6)
(12) Padwa, A.; Austin, D. J. Angew. Chem., Int. Ed. Engl. 1994, 33,
1797-1815.
(13) (a)Whitehouse, D. L.; Nelson, K. H. Jr.; Savinov, S. N.; Lowe, R.
S.; Austin, D. J. Bioorg. Med. Chem. 1998, 6, 1273-1282. (b) Whitehouse,
D. L.; Nelson, K. H. Jr.; Savinov, S. N.; Austin, D. J. Tetrahedron Lett.
1997, 38, 7139-7142.
(14) Liu, F.; Austin, D. J. Tetrahedron Lett. 2001, 42, 3153-4.
(15) Watkins, B. E.; Kiely, J. S.; Rapoport, H. J. Am. Chem. Soc. 1982,
104, 5702-5708.
(16) See Supporting Information for details.
(17) Savinov, S. N.; Austin, D. J. Chem. Commun. (Cambridge) 1999,
1813-1814.
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Org. Lett., Vol. 3, No. 15, 2001

Scheme 2a
Scheme 3a
a (a) BOP reagent, HOBT, MeNH2, DMF, 84%; (b) Rapoport’s
reagent, CH3CN/CH2Cl2, rt, 66%; (c) methyl malonyl chloride,
toluene, bubbling N2, 110 °C, 50%; (d) MsN3, Et3N, CH2Cl2, rt,
86%; (e) ethyl vinyl ether, Rh2(pfbm)4, chlorobenzene, 130 °C,
37%; (f) TFA/H2O 10:1, 0 °C; Pd/C, EtOH, NH4CO2H, 60-80%.
a (a) Vinyl chloroformate, Et3N, CH2Cl2, 75%; (b) 8, Rh2(pfbm)4,
toluene, 80 °C, 69%; (c) NH3 in methanol; TFA/water 10:1, rt,
52%.
(Scheme 2). Sufficient quantities of 2′,3′-isopropylidene-
adenosine-5′-carboxylic acid (6) were obtained by oxidation
of acetonide-protected adenosine with a catalytic amount of
TEMPO and a stoichiometric amount of bis-acetoxyiodo-
benzene, as previously reported.18 Coupling of the carboxyl-
adenosine (6) with methylamine, followed by Cbz protection,
imide formation, and diazotransfer provided R-diazoimide
7. This dipole precursor behaved similarly in this synthetic
sequence as the previous diazoimide, although 7 was not as
stable under basic conditions as 5 was. Treatment of 7 with
Rh2(pfbm)4 in the presence of ethyl vinyl ether proved
somewhat sluggish, and cycloaddition in this case required
higher temperatures and proceeded with a lower yield. This
is presumably due to the higher steric congestion near the
reactive centers of the dipole. Despite the encumbered nature
of the dipole, no diastereofacial selectivity of the dipolaro-
phile was observed, again showing little facial bias from the
chiral nucleoside. However, complete endo selectivity was
observed, as in the cycloaddition of adenosine scaffold 1.
Deprotection of the Cbz and acetonide protecting groups
provided the adenosine-linked molecules (2a and 2b) at the
second position of the scaffold.
ring does not interfere with the Rh(II) catalyst. In addition,
the chiral auxiliary led to high facial selectivity, which was
not compromised at the relatively high temperature required
for the reaction. Deprotection of the resulting product yielded
adenosine scaffold 3 in 27% overall yield from adenosine
acid 4.
With the synthesis of the three modified adenosines in
hand, we sought to investigate the spatial potential for this
class of adenosine derivatives to replace an enzyme-bound
form of ATP. A Monte Carlo conformational search using
the MM2* force field, as implemented in Macromodel,20 was
performed on one of the diastereomers (1). The nucleoside
Attaching adenosine to the third position of the scaffold
required the use of an adenosine-derived dipolarophile in
the cyclization-cycloaddition strategy (Scheme 3). Dipole
8 was synthesized by treating adenosine-amine 4 with vinyl
chloroformate. R-Diazoimide 919 was treated with Rh2(pfbm)4
in toluene at 80 °C to give the facially biased isomu¨nchnone,
which underwent subsequent cycloaddition with dipolaro-
phile 8 to give a single product, cycloadduct 10. This single
product arises from an entirely diastereofacial and endo
selective cycloaddition. It is important to note that the weak
nucleophilicity of the free exo-amino group on the adenine
Figure 1. Molecular overlay of the lowest energy conformations
of diastereomer (1) with the ATP molecule from CDK2, showing
the spatial array of the diversity scaffold adjacent to adenosine.
(18) Epp, J. B.; Widlanski, T. S. J. Org. Chem. 1999, 64, 293-295.
(19) (a) Savinov, S. N. Ph.D. Dissertation, Yale University, New Haven,
CT, 2000. (b) Savinov, S. N.; Austin, D. J. Comb. Chem. High Throughput
Synth. In Press.
Org. Lett., Vol. 3, No. 15, 2001
2275

portion of the molecule was obtained from a crystallographic
structure of cyclin dependent kinase 2 (CDK2).21 The energy
minimizations were performed with the GB/SA solvation
model for water22 with the adenosine rigidified. All confor-
mations within 5 kcal/mol of the global minimum conforma-
tion were kept, and all other conformers were rejected. Figure
1 shows an atomic overlay of those structures within 3 kcal/
mol (MM2 energy) of the global minimum, with the
adenosine held constant. It is easy to see that the bicyclic
structure is free to sample conformational space adjacent to
the adenosine nucleus. To assess the ability of any indiVidual
isomer to approximate the phosphate backbone, a second
conformational analysis was performed, in which the ad-
enosine was also allowed to explore conformational space.
Figure 2 shows an overlay of one of these conformers with
the enzyme-bound ATP from a cyclin-bound CDK2.23 Even
with a flexible adenosine, the displacement of the scaffold
relative to the adenosine can be maintained.
Figure 2. Atomic overlay of a single conformational isomer of
diastereomer (1) with the bound conformation of ATP in CDK2.
In conclusion, we have shown that the Rh(II)-catalyzed
tandem cyclization-cycloaddition sequence can be used in
a general and versatile strategy for the synthesis of complex
substrates containing adenosine. In addition, we have shown
that the synthetic attachment of the diversity core is within
the geometric space of the phosphate portion of an enzyme-
bound ATP molecule. Evaluation of the biological activity
for this new class of molecules and their ability to interact
with ATP-binding proteins and ATP-utilizing enzymes is
currently underway.
Acknowledgment. The authors thank Yale Corporation
and the National Cancer Institute (P01 CA49639) for
financial support.
(20) Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.;
Lipton, M.; Caufield, C.; Chang, G.; Hendrickson, T.; Still, W. C. J. Comput.
Chem. 1990, 11, 440-67.
(21) Adenosine taken from PDB 1b38, Cyclin Dependent Kinase (CDK2)
at 2.4 Å resolution. Brown, N. R.; Noble, M. E.; Lawrie, A. M.; Morris,
M. C.; Tunnah, P.; Divita, G.; Johnson, L. N.; Endicott, J. A. J. Biol. Chem.
1999, 274, 8746-56.
(22) Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. J. Am.
Chem. Soc. 1990, 112, 6127-9.
(23) ATP taken from PDB 1jst, Cyclin Dependent Kinase (CDK2) at
2.6 Å resolution. Russo, A. A.; Jeffrey, P. D.; Pavletich, N. P. Nat. Struct.
Biol. 1996, 3, 696-700.
Supporting Information Available: Experimental details
of the synthesis and characterization of compounds 1-10.
This material is available free of charge via the Internet at
http://pubs.acs.org.
OL015995K
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Org. Lett., Vol. 3, No. 15, 2001