Synthesis of bicyclic pyrimidine derivatives as ATP analogues

Article abstract of DOI:10.1021/jo015647w

A highly efficient and general solid-phase synthesis of bicyclic pyrimidine derivatives that target purine dependent proteins is reported. The synthesis of the key intermediate, 4,6-disubstituted-5-amino-pyrimidine, involved reduction of the corresponding nitro derivatives using 1,1′-dioctyl-viologen in a triphasic milieu. The mild reduction conditions enable the use of any acid labile solid support as well as a wide range of combinatorial substituents, thus enabling the synthesis of large libraries of highly diverse bicyclic pyrimidines. Alternative reduction conditions with tin(II) chloride and structure-reactivity studies are discussed as well.

Full text of DOI:10.1021/jo015647w

J . Org. Chem. 2001, 66, 5783-5789
5783
Syn th esis of Bicyclic P yr im id in e Der iva tives a s ATP An a logu es
Gergely M. Makara,* William Ewing, Yao Ma, and Edward Wintner
NeoGenesis Drug Discovery, 840 Memorial Drive, Cambridge, Massachusetts, 02139
gregm@neogenesis.com
Received March 23, 2001
A highly efficient and general solid-phase synthesis of bicyclic pyrimidine derivatives that target
purine dependent proteins is reported. The synthesis of the key intermediate, 4,6-disubstituted-
5-amino-pyrimidine, involved reduction of the corresponding nitro derivatives using 1,1′-dioctyl-
viologen in a triphasic milieu. The mild reduction conditions enable the use of any acid labile solid
support as well as a wide range of combinatorial substituents, thus enabling the synthesis of large
libraries of highly diverse bicyclic pyrimidines. Alternative reduction conditions with tin(II) chloride
and structure-reactivity studies are discussed as well.
In tr od u ction
Purines and pyrimidines are involved in a large
number of biological processes. The purine scaffold is a
component of guanine and adenine and therefore appears
in nucleic acids and cofactors that play an essential role
in the modulation of protein function and signal trans-
duction. It has been found that at least 10% of the
proteins encoded in the yeast genome appear to be
dependent on biomolecules that contain the purine scaf-
fold.1 DNA and RNA polymerases, ATPase and GTPase,
adenosine receptors, biosynthetic and metabolic enzymes,
kinases, and other ATP-dependent proteins such as heat
shock proteins are all potential targets for therapeutic
intervention. DHFR inhibitors that include pyrimidines
have antiviral, antifungal, antiprotozoan, and anticancer
activity. Adenosine and xanthine analogues have been
shown to have adenosine receptor agonist and antagonist
properties, which may be relevant in cardiovascular and
CNS therapy.2
F igu r e 1. Related scaffolds from literature.
A number of methods have been reported for the
synthesis of 2,6,9-trisubstituted purines starting from
2,6-dihalogenated purines in solution,3,4 on solid phase,1,5
and a combination thereof.6 This strategy enables the
synthesis of the purine scaffold but not that of related
ring systems. 6-aminopurine derivatives (1-3, Figure 1)
have been synthesized on solid phase using Rink resin
starting from 4,6-dichloro-5-nitropyrimidine.7 No 6-sub-
* To whom correspondence should be addressed.
(1) Chang, Y.-T.; Gray, N. S.; Rosania, G. R.; Sutherlin, D. P.; Kwon,
S.; Norman, T. C.; Sarohia, R.; Leost, M.; Meijer, L.; Schultz, P. G.
Synthesis And Application of Functionally Diverse 2,6,9-Trisubstituted
Purine Libraries as CDK Inhibitors. Chem., Biol. 1999, 6, 361-375.
(2) J acobson, K. A.; Daly, J . W.; Manganiello, V. Purines in Cellular
Signaling: Targets For New Drugs; Springer-Verlag: New York, 1990.
(3) Fiorini, M. T.; Abell, C. Solution-Phase Synthesis of 2,6,9-
Trisubstituted Purines. Tetrahedron Lett. 1998, 39, 1827-1830.
(4) Imbach, P.; Capraro, H.-G.; Furet, P.; Mett, H.; Meyer, T.;
Zimmermann, J . 2,6,9-Trisubstituted Purines: Optimization Towards
Highly Potent And Selective CDK1 Inhibitors. Bioorg. Med. Chem. Lett.
1999, 9, 919-96.
F igu r e 2. Synthetic routes to related scaffolds. (a) piperidine/
DMF; (b) 4,6-dichloro-5-nitropyrimidine/DIPEA/DMF; (c) amine/
DIPEA/DMF; (d) LiAlH4/AlCl3/THF; (e) FmocNHCHRCO2H/
DIC/DMAP/DMF; (f) SnCl2/EtOH/DMF (70 °C).
stituted analogues other than the 6-amino group were
enabled by this synthetic methodology (Figure 2). The
reduction of the 5-nitro group was reported to be par-
ticularly difficult. A number of methods at wide ranges
of temperatures were investigated and only a mixture of
LiAlH4 and AlCl3 was found to reduce the 4,6-dialkyl-
amino-5-nitropyrimidines to their corresponding 5-amino
derivatives. The reported synthesis does not permit the
(5) Nugiel, D. A.; Cornelius, L. A. M.; Corbett, J . W. Facile Prepara-
tion of 2,6-Disubstituted Purines Using Solid-Phase Chemistry. J . Org.
Chem. 1997, 62, 201-203.
(6) Norman, T. C.; Gray, N. S.; Koh, J . T.; Schultz, P. G. A Structure-
Based Library Approach to Kinase Inhibitors. J . Am. Chem. Soc. 1996,
118, 7430-7431.
(7) Lucrezia, R. D.; Gilbert, I. H.; Floyd, C. D. Solid-Phase Synthesis
of Purines from Pyrimidines. J . Comb. Chem. 2000, 2, 249-253.
10.1021/jo015647w CCC: $20.00 © 2001 American Chemical Society
Published on Web 07/26/2001

5784 J . Org. Chem., Vol. 66, No. 17, 2001
Ta ble 1. Red u ction Tests w ith Tin (II) Ch lor id e
Makara et al.
MS
a
a
entry
resin
Rink
Rink
Rink
Rink
Rink
Wang
Wang
Br-Wang
formyl
formyl
Rink
R1
R2
yield, %
purity, %b
16a
16b
16c
16d
16ec
16f
NH2
NH2
NH2
NH2
p-Me-benzylamine
o-anisidine
cyclohexylamine
3-Fluoroaniline
p-Me-benzylamine
p-Me-benzylamine
p-Me-benzylamine
p-Me-benzylamine
p-Me-benzylamine
p-Me-benzylamine
alanine methyl ester
p-Me-benzylamine
95+
60b
95+
95+
90
95
90
95
95
95
90
90
N/A
N/A
N/A
95
326
328
304
316
alanine
284
p-carboxybenzylamine
â-alanine
70d
95+
0
364/460
302/398
N/A
N/A
N/A
16g
16h
16h
16i
p-Me-phenethylamine
p-Me-phenethylamine
benzylamine
0
0
17a
17b
NH2
alanine
95+
0
180
N/A
Wang
N/A
a
b
R1 is site at resin; R2 is from amine replacing the second chlorine. Some 5-aminopyrimidines form the corresponding 5-trifluoroac-
etamide during cleavage. For these samples, HPLC purity was assessed as a combination of both products. c Product was found to be the
corresponding piperazinone analog. These entries were stirred (magnetic) therefore loss of some beads is expected due to crushed resin.
d
inclusion of building blocks that contain functional groups
that are labile under these harsh conditions. The prod-
ucts were also of low purity due to inorganic contami-
nants derived from the reducing cocktail. Substituted
pyrimidines have also been prepared by de novo synthesis
of the pyrimidine ring8 or from the pyrimidine core itself.9
Following the completion of experiments in our labora-
tory, a synthesis of dihydropteridinones (4 and 5, Figure
1) starting from 4,6-dichloro-5-nitropyrimidine was re-
ported.10 Either amino acids were attached to Wang resin
or diamines were linked to the Wang resin via a carbam-
ate linker (Figure 2). Reduction of the nitro group could
be effected with SnCl2 at 70 °C, a finding that is in
contrast to the results reported earlier.7 The published
methodology yielded high purities but low yields for
F igu r e 3. Scheme for premature cleavage of products with
amino acid esters. (a) Reduction.
several entries with amino acid building blocks and
limited diversity elements at the 6-position due to a need
for linkage to the resin at this position.
unrelated scaffolds using this simple reducing agent
prompted us to subject the 4-(p-methylbenzyl) derivative
(16a , Table 1) on Rink resin to SnCl2 in various solvents.
No reduction was observed at 25 °C, but complete
reduction took place at temperatures above 45 °C. Since
acid-sensitive resins are prone to premature cleavage at
low pH environments, we opted for 2 N SnCl2 in NMP at
50 °C for 24 h as an initial method. Indeed, at or above
70 °C, the product was lost during reduction when Rink
resin was used. The Wang ester type linkage (16f,g) and
other Rink attached derivatives (16b-d ) were found to
be compatible with the standard conditions, but no
product was obtained when R-amino acids were attached
as esters to Wang resin (17b). As expected, the piper-
azinone ring is closed in situ when reduction occurs (17a )
resulting in loss of the resin-bound compound. The same
phenomenon is likely to be responsible for the lower
yields reported when both pyrimidine substituents are
amino acid esters10 (Figure 3).
When a â-amino acid was attached in a similar
manner, the 5-amino derivative was obtained in a good
yield (16g). The closure to the seven-membered ring
system by the â-amino acid ester is kinetically unfavor-
able compared to that of the six-membered ring created
by the R-amino acid esters. Interestingly, when alanine
was attached to Rink resin (16e), the reduced amine was
not cleaved during reduction but gave the ring-closed
piperazinone upon cleavage in good yield and purity.
When the acid-sensitive formyl (16h ,i) or Bromo-Wang
(16h ) functionalized linkers were subjected to our best
method with tin(II) chloride, no product was obtained in
subsequent cleavage. We hypothesize that these linkers
We report herein a synthetic route to substituted
bicyclic pyrimidine (and ATP) analogues such as dihy-
dropteridinones, pyrimidoimidazolones, and 6,8-diami-
nopurines starting from 4,6-dichloro-5-nitropyrimidine.
The key step is a mild reduction of the nitro group with
catalytic 1,1′-dioctyl-viologen in a mixture of water and
dichloromethane. Results and limitations for incorporat-
ing diversity elements with different solid supports are
discussed, as are our findings for reduction conditions
with SnCl2. The above reducing conditions enable the use
of all acid-sensitive solid-support types and therefore
greatly enhance the diversity of combinatorial libraries
that can be synthesized against a wide range of thera-
peutic targets. The key 5-amino intermediate opens an
avenue to the synthesis of other diverse scaffolds as well.
Resu lts a n d Discu ssion
To begin this study we set out to investigate the
reduction of the 5-nitropyrimidine moiety under various
conditions. Despite the lack of reduction reported7 with
tin(II) chloride, our earlier success in the synthesis of
(8) Obrecht, D.; Abrecht, C.; Grieder, A.; Villalgordo, J . M. A Novel
and Efficient Approach For the Combinatorial Synthesis of Structurally
Diverse Pyrimidines On the Solid Support. Helv. Chim. Acta 1997,
80, 65-72.
(9) Guiller, F.; Roussel, P.; Moser, H.; Kane, P.; Bradley, M. Solid-
Phase Synthesis of 2,4,6-Triaminopyrimidines. Chem. Eur. J . 1999,
5, 3450-3458.
(10) Baxter, A. D.; Boyd, E. A.; Cox, P. B.; Loh, V., J r.; Monteils, C.;
Proud, A. 4,6-Dichloro-5-nitropyrimidine: A Versatile Building Block
For The Solid-Phase Synthesis of Dihydropteridinones. Tetrahedron
Lett. 2000, 41, 8177-8181.

Bicyclic Pyrimidine Derivatives as ATP Analogues
J . Org. Chem., Vol. 66, No. 17, 2001 5785
are too acid sensitive to remain intact throughout the
inherently acidic reduction step at elevated temperatures.
At room temperature, the unreacted nitro derivatives
were recovered in every case. We were unable to optimize
the tin(II) chloride method to effect the reduction on the
formyl and Bromo-Wang linkers; thus, an alternative
method was sought. A literature search revealed a highly
selective but less-cited method for the reduction of
aromatic nitro groups. A catalytic amount of an electron-
transfer reagent, 1,1′-di-N-octyl-4,4′-bipyridinium dibro-
mide (1,1′-dioctyl viologen) turned over by sodium dithion-
ate under phase-transfer conditions has been shown to
effect the reduction of simple aromatic nitro groups with
very high yield and purity.11,12 It remained to be seen
whether the system could be applied to the reduction of
the problematic 4,6-dialkylamino-5-nitropyrimidine moi-
ety, and to solid-phase chemistry in general.13
F igu r e 4. Products obtained by reduction with viologen. R1,
symbolizes amines attached to resin (e.g., for formyl resin, Rr
) CH2, R1a ) amine); R2sc, side-chain of R2 amino acid esters;
(a) 1,1′-dioctyl viologen/DCM/K2CO3/Na2S2O4/H2O; (a1), amines
other than R-aminoesters; (a2), R-aminoesters.
Our initial attempts with the viologen system were
unsuccessful: no reaction was observed with revolving
shaking in a polypropylene vessel; however, our test
compound attached to Rink resin was completely reduced
with vigorous horizontal shaking in a glass vial. Simi-
larly, good results were obtained with the use of magnetic
stirring; however, the resin became pulverized and was
then difficult to filter and wash. Some viologen-related
contamination was also present in the cleaved product,
indicating ineffective wash with our standard washing
cycle (DMF, IPA, DCM). These byproducts were removed
by rapid chromatography through a silica plug in the
published solution-phase method.11 Finally, all byprod-
ucts could be removed on solid phase by an exhaustive
rinse procedure that employed five wash steps (DCM-
1% AcOH/H2O, ethyl acetate-H2O, acetone, IPA, DCM).
The viologen-mediated reduction method was applied
to the formyl and Wang resins as well, and high yields
and purities were attained. The pH during reduction is
kept slightly basic by the potassium carbonate; thus, all
acid-sensitive resin types are likely to be compatible with
this method. No reduction was observed without either
the dioctyl viologen or sodium dithionate, which is in
accord with findings reported for analogous solution
phase reactions.11 As in the tin(II) chloride system, in the
viologen method amino acid esters at R1 lead to cleavage,
but at R2 give the pyrimidopiperazinone compounds as
the sole products (Figure 4).
F igu r e 5. Synthetic strategy toward secondary 6-aminopy-
rimidine bicycles. (a) reductive amination; (b) 4,6-dichloro-5-
nitropyrimidine/DIPEA/NMP; (c) amine/DIPEA/NMP.
F igu r e 6. Synthetic scheme for synthesis starting from
nitrophenols. RX, phenol substituents.
Our strategy for combinatorial library development
was based on the use of the formyl linker as the primary
resin source for accessing all building blocks at the
6-position in the final bicyclic analogues possessing a
secondary amine (Figure 5). The NH at the 6-position in
these molecules preserves some of the natural H-bonding
properties of adenine and is highly conserved in most
known adenine analogues.
attached to Bromo-Wang resin (Figure 6). Using the
latter strategy, tertiary amines at the 6-position can also
be prepared if a reductive amination step is carried out
prior to nucleophilic substitution of the 4,6-dichloro-5-
nitropyrimidine by the aniline. Some of the other poten-
tial solutions for accessing tertiary amines at the 6-po-
sition by various functional groups attached to different
resins are depicted in Figure 7.
To demonstrate the utility of our approach, diary-
lamines were also made starting from nitrophenols
The 4,6-disubstituted-5-aminopyrimidines are particu-
larly versatile precursors to a wide variety of bicyclic
derivatives of the purine scaffold. In this report, we
demonstrate the synthesis of three of many possible
templates: dihydropteridinones, pyrimidoimidazolones,
and 6,8-diaminopurines (Table 2). Dihydropteridinones
were obtained if at least one of the substituents of the
pyrimidine ring was an amino acid ester (23a -d , Figure
8). In our laboratory, a number of different esters have
been employed successfully in this reaction including
methyl, ethyl, tert-butyl, and benzyl (data not shown).
(11) Park, K. K.; Oh, C. H.; J oung, W. K. Sodium Dithionate
Reduction of Nitroarenes Using Viologen as an Electron Phase-
Transfer Catalyst. Tetrahedron Lett. 1993, 34, 7445-7446.
(12) Park, K. K.; Oh, C. H.; Sim, W.-J . Chemoselective Reduction
of Nitroarenes and Nitroalkanes by Sodium Dithionate Using Octyl
viologen as an Electron-Transfer Catalyst. J . Org. Chem. 1995, 60,
6202-6204.
(13) After completion of this work, a report on the reduction of the
aryl nitro moiety with Na2S2O4 and viologen on solid support was
published; however, no reduction of the difficult pyrimidine system
was investigated. Scheuerman, R. A.; Tumelty, D. The Reduction of
Aromatic Nitro Groups on Solid Supports Using Sodium Hydrosulfite
(Na2S2O4). Tetrahedron Lett. 2000, 41, 6531-6535.

5786 J . Org. Chem., Vol. 66, No. 17, 2001
Makara et al.
R-disubstituted amines are well tolerated with high
purity, but that R-trisubstituted amines (26n ) are too
hindered for subsequent nucleophilic substitution with
dichloronitropyrimidine. Both electron-deficient (23c) and
ortho-substituted anilines (26f) are well tolerated at R1,
giving rise to products of high purity.
Nucleophilic displacement of the second, less-reactive
chlorine at R2 is brought to completion with R-disubsti-
tuted amines and anilines of nucleophilicity higher or
equal to aniline (25b, 26m ). Reaction at R2 remains
incomplete with R-trisubstituted amines (26o) or electron-
deficient anilines at ambient temperature.
Clean ring-closure with isothiocyanates at R3 was
found for unhindered aromatic and benzylic isothiocy-
anates. Aromatic isothiocyanates possessing bulky ortho-
substituents (26i) may give rise to a small amount of a
DIC adduct (observed mass equals the molecular weight
of the key aminopyrimidine intermediate plus DIC),
because thiourea formation cannot proceed to completion
before DIC is added (see experimental details). In gen-
eral, aliphatic isothiocyanates yield the desired products
albeit with less purity (26j, 80%).
The strategy described herein has been utilized in our
laboratories to generate large combinatorial libraries
with the split and pool technique for our affinity-based
screening platform, Automated Ligand Identification
System (ALIS).16 Hit-rates and activity data acquired in
screening of this compound file against ATP-dependent
and miscellaneous other targets will be detailed when
they become available.
F igu r e 7. Potential synthetic strategy toward tertiary 6-ami-
nopyrimidine bicycles. (a) 4,6-Dichloro-5-nitropyrimidine/DI-
PEA/NMP; (b) amine/DIPEA/NMP.
Pyrimidoimidazolones were readily gained by cycliza-
tion with disuccinimidyl carbonate at elevated temper-
atures, a modification of the method published14 for the
synthesis of benzimidazolones (25a -e, Figure 8). Addi-
tion of isothiocyanates to the 5-amino moiety results in
thioureas that furnish 6,8-diaminopurines upon treat-
ment with dehydrating agents such as DIC (26a -r ,
Figure 8). It is noteworthy that when both the 4- and
the 6-substituent are secondary amines, cyclization can
take place in two ways to yield isomeric bicycles (Figure
9). In our experience, both isomers are obtained equally
in such cases (26q,r and Figure 10).
Con clu sion
For compounds prepared with the formyl linker, an
appreciable amount (0-30% depending on the amine
building block used in reductive amination) of a nitroso
side-product was detected by NMR and LC-MS (Figure
11). In many cases the ELSD-HPLC trace of these
samples, however, showed no peaks other than the
desired product. The commercial 4,6-dichloro-5-nitropy-
rimidine is available from a number of vendors. While
the commercial material (∼75% pure by NMR) appears
to be adequate for the synthesis of the title compounds,
some oxidated impurities, in our hypothesis, may lead
to side reactions, especially when excess amounts are
used in solid-phase reactions. To remove the byproducts,
we developed a simple purification method before the
reduction step. It has been known that tertiary amines
formed on the formyl linker are readily cleaved as
tertiary amides by acylating agents.15 Thus, 1 equiv of
o-toluoyl chloride and DIPEA were added to the resin in
dichloromethane before reduction to cleave all nitroso
side-products. No significant amount of the desired
intermediate was cleaved off the resin or acylated by this
procedure. As a result of the above purification method,
the purity of the final products can greatly be enhanced
at the expense of the yield (Table 2). It should be noted
that reaction requiring excess isothiocyanates for the
synthesis of 6,8-diaminopurines gave rise to similar
cleavage of the nitroso amines.
We have developed a versatile strategy for the solid-
phase synthesis of diverse bicyclic pyrimidines as purine
analogues. All substitution types are enabled by the
method excluding compounds containing a secondary
amine building block with no resin handle at the 4-posi-
tion and an amine with no resin handle at the 6-position
of the pyrimidine intermediate. All analogues were
obtained with good yields and purities. Additional results
of an ongoing effort in our laboratory to develop solid-
phase methodologies for the synthesis of other fused ring
systems based on the key pyrimidine intermediate will
be reported elsewhere.
Exp er im en ta l Section
Rink AM, Wang, Bromo-Wang and 4-(4-Formyl-3-methox-
yphenoxy)butyryl AM (“formyl”) resins were purchased from
Novabiochem. 4,6-Dichloro-5-nitropyrimidine was purchased
from Aldrich, Sigma and Research Plus, Inc. The substance
obtained from Sigma and Research Plus, Inc. was found about
75% pure by 1HNMR, and the one originated from Aldrich was
about 50% pure by the same technique. Amines and isothio-
cyanates were purchased from various vendors and were
verified to be 95+% pure by 1HNMR before use. All NMR
spectra were taken with a 300 MHz Brucker NMR spectrom-
eter. HPLC analyses were performed with either a Biocad
(Perceptive Biosystems) or HP-1100 Binary HPLC instru-
ments. MS spectra were recorded in positive electrospray mode
with a QTOF Tandem MS-MS mass spectrometer (Micromass).
Reactions (excluding the reductive amination and the viologen
reduction steps) at ambient temperature were carried out in
fritted polypropylene vessels (Orochem Technologies), and
were agitated by a revolving shaker (VWR). Reactions at
Structure-reactivity relationships at the site intro-
duced by reductive amination (R1) (Table 2) reveal that
(14) Wei, G. P.; Phillips, G. B. Solid-Phase Synthesis of Benzimi-
dazolones. Tetrahedron Lett. 2000, 41, 8177-8181.
(15) Miller, M. W.; Vice, S. F.; McCombie, S. W. Mild N-Dealkylation
of Tertiary Benzylic Amines With Acid Chlorides: Application to Solid-
Phase Chemistry. Tetrahedron Lett. 1998, 39, 3429-3432.
(16) For further information on the ALIS screening platform, please
go to www.neogenesis.com.

Bicyclic Pyrimidine Derivatives as ATP Analogues
J . Org. Chem., Vol. 66, No. 17, 2001 5787
Ta ble 2. Selected Bicyclic P yr im id in e Der iva tive
yield, purity,
a
a
a
entry
resin
R1
R2
lysine(Boc)-OMe
R3
%
%
MS
23a
23b
23c
23d
25a
25b
25c
25d
25e
26a
26b
26c
26d
26e
26f
26g
26h
26i
formyl
formyl
formyl
formyl
Rink
Br-Wang 3-Nitrophenol
formyl
Rink
3-(1-morpholino)propylamine
3-benzyloxyaniline
4-chloroaniline
3-(1-morpholino)propylamine
alanine
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
90
95+
364
390
362
337
327
338
372
256
234
457
483
549
518
518
529
439
465
497
429
522
541
535
N/A
517
475
505
533
valine-OMe
60
50
50
70
75
70
95
95
90
glutamic acid(OMe)-OMe
threonine(OtBu)-OMe
p-Me-benzylamine
3-fluoroaniline
95+
95+
90
90
95+
95
p-Me-benzylamine
NH2
2-aminoindane
p-Me-benzylamine
cyclohexylamine
p-Me-benzylamine
p-Me-benzylamine
Rink
NH2
90
formyl
formyl
formyl
formyl
formyl
formyl
formyl
formyl
formyl
formyl
formyl
formyl
cyclohexylamine
N-aminopropylimidazole
trans-2-benzyloxycyclopropylamine p-Me-benzylamine
Boc-lysine-OMe
4-(1,2,4-triazolyl)phenylamine
o-anisidine
3,4-methylenedioxyphenylSCN 70
3,4-methylenedioxyphenylSCN 50
3,4-methylenedioxyphenylSCN 70
3,4-methylenedioxyphenylSCN 70
3,4-methylenedioxyphenylSCN 45
95+
95
95+
95+
95+
95+
95
95
80
80
90
90
95
N/A
45
40
p-Me-benzylamine
p-Me-benzylamine
phenethylamine
p-Me-benzylamine
p-Me-benzylamine
p-Me-benzylamine
p-Me-benzylamine
4-amino-1-ethylcarboxypiperidine
4-phenoxyphenylSCN
3-fluorophenylSCN
4-methoxybenzylSCN
2-biphenylSCN
γ-butyrolactone-2-SCN
2-naphthylSCN
70
85
85
50
85
70
75
75
0
50
45
70
80
benzylamine
benzylamine
benzylamine
benzylamine
benzylamine
benzylamine
benzylamine
26j
26k
26l
trans-2-benzyloxycyclopropylamine 2-naphthylSCN
26m formyl
4-phenoxyaniline
2-naphthylSCN
2-naphthylSCN
2-naphthylSCN
2-naphthylSCN
26n
26o
26p
26q
26r
formyl
formyl
formyl
p-F-R-dimethylphenethylamine
p-Me-benzylamine
benzylamine
benzylamine
p-F-R-dimethylphenethylamine
N-(3-aminopropyl)imidazole
3-fluoroaniline
Br-Wang 3-nitrophenol
4-phenoxyphenylSCN
4-phenoxyphenylSCN
90
90
Br-Wang 5-fluoro-2-nitrophenol
phenethylamine
a
R1 is site at resin, R2 is from amine replacing the second chlorine, and R3 is from isothiocyanates.
F igu r e 9. Possible cyclization routes to isomeric bicycles. (a)
R3SCN/DMF/DIC/80 °C.
shown in Table 2 for every step that involves resin transfer.
This according to our calibration is approximately the average
amount lost in a single transfer of polystyrene beads.
Purity of all compounds was established by HPLC, high-
resolution mass spectroscopy and LC-MS. In addition, repre-
sentative compounds in every product class were confirmed
1
by H NMR spectroscopy.
F igu r e 8. Bicycles from 5-nitropyrimidines (resin connection
symbolizes all resin linkers used). R2sc, side-chain of amino acid
esters; (a) 1,1′-dioctyl viologen/DCM/K2CO3/Na2S2O4/H2O; (b)
DSC/DMF/80 °C; (c) R3SCN/DMF/DIC/80 °C.
Rep r esen ta tive P r oced u r e for th e 5-Nitr op yr im id in e
In ter m ed ia tes Sta r tin g fr om Rin k AM Resin . Rink AM
resin (0.1 mmol) was shaken with 50% piperidine in DMF (2
mL) for 30 min. The resin was filtered off and washed with
DMF (4×), IPA (3×), and DCM (3×). To the resin were added
NMP (1.5 mL), DIPEA (174 µL, 1.0 mmol), and 4,6-dichloro-
5-nitropyrimidine (97 mg, 0.5 mmol). The mixture was shaken
for 2h at room temperature. The resin was filtered and washed
with DMF (3×), IPA (3×), and DCM (3×). To the resin were
added NMP (1.0 mL), DIPEA (88 µL, 0.5 mmol), and amine
building block (0.5 mmol). The mixture was shaken for 16h at
room temperature. The resin was filtered, washed with DMF
(3×), IPA (3×), and DCM (3×), and dried.
elevated temperatures were double coupled in tightly capped
13 × 100 mm Pyrex tubes and were carried out in heating
blocks (VWR) tightened on an orbital shaker. Reductive
aminations were performed in 4 mL Teflon capped glass vials
shaken with a revolving shaker (VWR) The viologen reductions
were done in 4 mL Teflon capped glass vials shaken horizon-
tally with a reciprocating shaker. Cleavage of products from
the beads for formyl resins was effected by a dilute TFA
cocktail (TFA:H2O ) 7:3) while that for Wang, Bromo-Wang
and Rink resins was achieved by a concentrated TFA cocktail
(TFA:H2O ) 95:5). A dilute cleavage condition was found to
produce products of high purity for all batches of formyl resin,
while 95% TFA led to lower purity for some (but not all) of
the batches. Cleavages were carried out for 1 h at room
temperature. 10% bead loss was calculated into all yields
Rep r esen ta tive P r oced u r e for th e 5-Nitr op yr im id in e
In ter m ed ia tes Sta r tin g fr om Rin k AM Resin a n d Am in o
Acid s. Rink AM resin (0.1 mmol) was shaken with 50%
piperidine in DMF (2 mL) for 30 min. The resin was filtered
off and washed with DMF (4×), IPA (3×), and DCM (3×). To
the resin were added DMF (1.5 mL), Fmoc-protected amino
acid (0.3 mmol), a mixture of TBTU (86 mg, 0.3 mmol) and

5788 J . Org. Chem., Vol. 66, No. 17, 2001
Makara et al.
F igu r e 10. Typical HPLC profiles of crude 6,8-diaminopurines.
(210 µL, 1.2 mmol), and 4,6-dichloro-5-nitropyrimidine (48 mg,
0.25 mmol). The mixture was shaken for 2 h at room temper-
ature. The resin was filtered and washed with DMF (3×), IPA
(3×), and DCM (3×). To the resin were added NMP (1.0 mL),
DIPEA (87 µL, 0.5 mmol), and amine building block (0.5
mmol). The mixture was shaken for 16 h at room temperature.
The resin was filtered, washed with DMF (3×), IPA (3×), and
DCM (3×), and dried. To the resin were added DCM (1.5 mL),
DIPEA (35 µL, 0.2 mmol), and o-toluoyl chloride (13 µL, 0.1
mmol). The mixture was shaken for 2 h at room temperature
and filtered. The resin was washed with DCM (3×), IPA (3×),
and DCM (3×).
F igu r e 11. Proposed side reaction observed with formyl
linkers.
HOBt monohydrate (46 mg, 0.3 mmol) in DMF (0.5 mL), and
DIPEA (105 µL, 0.6 mmol). The mixture was shaken for 16 h
at room temperature. The resin was filtered and washed with
DMF (3×), IPA (3×), and DCM (3×). The resin (0.1 mmol) was
then shaken with 50% piperidine in DMF (2 mL) for 30 min.
The resin was filtered off and washed with DMF (4×), IPA
(3×), and DCM (3×). To the resin were added NMP (1.5 mL),
DIPEA (174 µL, 1.0 mmol), and 4,6-dichloro-5-nitropyrimidine
(97 mg, 0.5 mmol). The mixture was shaken for 2 h at room
temperature. The resin was filtered and washed with DMF
(3×), IPA (3×), and DCM (3×). To the resin were added NMP
(1.0 mL), DIPEA (88 µL, 0.5 mmol), and amine building block
(0.5 mmol). The mixture was shaken for 16 h at room
temperature. The resin was filtered, washed with DMF (3×),
IPA (3×), and DCM (3×), and dried.
Rep r esen ta tive P r oced u r e for th e 5-Nitr op yr im id in e
In ter m ed ia tes Sta r tin g fr om Wa n g Resin . Amino acid
attached to Wang resin (0.1 mmol) was shaken with 50%
piperidine in DMF (2 mL) for 30 min to remove the Fmoc
group. The resin was filtered and washed with DMF (4×), IPA
(3×), and DCM (3×). To the resin were added NMP (1.5 mL),
DIPEA (174 µL, 1.0 mmol), and 4,6-dichloro-5-nitropyrimidine
(97 mg, 0.5 mmol). The mixture was shaken for 2 h at room
temperature. The resin was filtered and washed with DMF
(3×), IPA (3×), and DCM (3×). To the resin were added NMP
(1.0 mL), DIPEA (88 µL, 0.5 mmol), and amine building block
(0.5 mmol). The mixture was shaken for 16 h at room
temperature. The resin was filtered, washed with DMF (3×),
IPA (3×), and DCM (3×), and dried.
Rep r esen ta tive P r oced u r e for th e 5-Nitr op yr im id in e
In ter m ed ia tes Sta r tin g fr om F or m yl Resin . To formyl
resin (0.1 mmol) in a vial were added 1% acetic acid in DMF
(1.3 mL), DIPEA (30 µL, 0.172 mmol), and amine building
block (0.55 mmol). The mixture was shaken for 6 h at room
temperature. when NaBH(OAc)3 (117 mg, 0.55 mmol) was
added. The mixture was shaken for 36 h when methanol (1
mL) was added to help dissolve the borate salts. The mixture
was transferred to a polypropylene vessel, and the resin was
filtered and washed with MeOH (3×), DMF (3×), IPA (3×),
and DCM (3×). To the resin were added NMP (1.5 mL), DIPEA
Rep r esen ta tive P r oced u r e for th e 5-Nitr op yr im id in e
In ter m ed ia tes Sta r tin g fr om Br om o-Wa n g Resin . To
Bromo-Wang resin (0.1 mmol) in DMF (1.0 mL) were added
Cs2CO3 (98 mg, 0.30 mmol), KI (17 mg, 0.1 mmol), and
nitrophenol building block (0.5 mmol). The mixture was
shaken for 16 h at 80 °C. The mixture was cooled to room
temperature and the resin was transferred to a polypropylene
vessel, filtered, and washed with DMF (3×), H2O (3×), DMF
(2×), IPA (3×), and DCM (3×). To the resin was added a
solution of SnCl2 (500 mg, 2.64 mmol) in a mixture of NMP
(1.0 mL) and ethanol (50 µL), and the mixture was shaken for

Bicyclic Pyrimidine Derivatives as ATP Analogues
J . Org. Chem., Vol. 66, No. 17, 2001 5789
16,h at room temperature. The resin was filtered and washed
with DMF (3×), IPA (3×), and DCM (3×). To the resin were
added NMP (1.5 mL), DIPEA (174 µL, 1.0 mmol), and 4,6-
dichloro-5-nitropyrimidine (97 mg, 0.5 mmol). The mixture was
shaken for 2 h at room temperature. The resin was filtered
and washed with DMF (3×), IPA (3×), and DCM (3×). To the
resin were added NMP (1.0 mL), DIPEA (88 µL, 0.5 mmol),
and amine building block (0.5 mmol). The mixture was shaken
for 16 h at room temperature. The resin was filtered, washed
with DMF (3×), IPA (3×), and DCM (3×), and dried.
Rep r esen ta tive P r oced u r e for Red u ction w ith Sn Cl2.
To the resin (0.1 mmol) was added a solution of SnCl2 in NMP
(2 N, 2.0 mL), and the mixture was shaken for 20 h at 50 °C.
The mixture was transferred to a fritted polypropylene vessel,
and the solvent was drained. The resin was rinsed with DMF
(3×), IPA (3×), and DCM (3×).
Rep r esen ta tive P r oced u r e for th e Syn th esis of P y-
r im id oim id a zolon es. 5-Aminopyrimidine resin (obtained in
reduction, 0.1 mmol) in a mixture of THF (1.1 mL) and DMF
(0.4 mL) was treated with disuccinimidyl carbonate (43 mg,
0.168 mmol). The mixture was shaken for 16 h at 80 °C and
then cooled to room temperature. The mixture was transferred
to a polypropylene vessel, and the resin was filtered off and
washed with THF (3×), DMF (3×), IPA (3×), and DCM (3×).
The procedure was repeated one more time.
Rep r esen ta tive P r oced u r e for th e Syn th esis of 6,8-
Dia m in op u r in es. To 5-aminopyrimidine resin (obtained in
reduction, 0.1 mmol) in DMF (1.5 mL) was added the isothio-
cyanate building block (1.0 mmol). The mixture was heated
to 80 °C for 20-25 min (prolonged heating before DIC is added
results in decreased purity of the final products), DIC (156
µL, 1.0 mmol) was injected, and the mixture was shaken for
16 h at 80 °C. The mixture was cooled to room temperature
and was transferred to a polypropylene vessel, and the resin
was filtered off and washed with DMF (3×), IPA (3×), and
DCM (3×). The procedure was repeated one more time.
Rep r esen ta tive P r oced u r e for Red u ction w ith Violo-
gen (a n d for th e syn th esis of d ih yd r op ter id in on es). To
the resin (0.1 mmol) in a vial in DCM (2 mL) was injected a
mixture of K2CO3 (138 mg, 1.0 mmol) and Na2S2O4 (156 mg,
0.896 mmol) in H2O (0.8 mL). 1,1-Dioctyl-viologen dihydro-
bromide (20 mg, 0.037) was added, and the deep blue mixture
was vigorously shaken for 20 h at room temperature. The
mixture was transferred to a fritted polypropylene vessel, and
the solvent was drained. The resin was rinsed with DCM-1%
AcOH/H2O (1:1, 3×), ethyl acetate-H2O (1:1, 3×), acetone
(3×), IPA (3×), and DCM (3×).
Ack n ow led gm en t. The authors are grateful to
J ean-Paul Orminati for helping develop production scale
synthesis using the methodology described in this paper.
J O015647W