Demonstration of the feasibility of a direct solid-phase split-pool Biginelli synthesis of 3,4-dihydropyrimidinones

Article abstract of DOI:10.1021/ol048946r

(Chemical Equation Presented) A direct, Lewis acid-catalyzed Biginelli synthesis of 3,4-dihydropyrimidinones has been performed on high-capacity polystyrene macrobeads with a polymer O-silyl-attached N-(3-hydroxypropyl)urea. Resin-urea was first reacted separately with either 4-bromo- or 4-chlorobenzaldehyde and LiOTf in MeCN at 80°C. After washing, the beads were pooled and reacted with ethyl acetoacetate and LiOTf in MeCN at 80°C. Formation of only one kind of Biginelli product per bead demonstrated the feasibility of a solid-phase non-Atwal two-step split-and-pool synthesis of 3,4-dihydropyrimidinones.

Full text of DOI:10.1021/ol048946r

ORGANIC
LETTERS
2004
Vol. 6, No. 19
3237-3240
Demonstration of the Feasibility of a
Direct Solid-Phase Split-Pool Biginelli
Synthesis of 3,4-Dihydropyrimidinones
,†
Michael J. Lusch* and John A. Tallarico‡
HarVard Institute of Chemistry and Cell Biology (ICCB), HarVard Medical School,
250 Longwood AVenue, Boston, Massachusetts 02115
michael.lusch@mnsu.edu
Received June 6, 2004
ABSTRACT
A direct, Lewis acid-catalyzed Biginelli synthesis of 3,4-dihydropyrimidinones has been performed on high-capacity polystyrene macrobeads
with a polymer O-silyl-attached N-(3-hydroxypropyl)urea. Resin−urea was first reacted separately with either 4-bromo- or 4-chlorobenzaldehyde
and LiOTf in MeCN at 80 °C. After washing, the beads were pooled and reacted with ethyl acetoacetate and LiOTf in MeCN at 80 °C. Formation
of only one kind of Biginelli product per bead demonstrated the feasibility of a solid-phase non-Atwal two-step split-and-pool synthesis of
3,4-dihydropyrimidinones.
Small molecules have been used in recent years to explore
many aspects of biological pathways in a systematic way, a
process termed chemical genetics,1 in a manner analogous
to classical (mutational) genetic, and more recently genomic,
approaches. Diversity-oriented2 split-(and-)pool3 synthesis
has been shown to be an effective method for synthesizing
structurally complex and diverse collections of small mol-
ecules4 for use in forward (phenotypic) or reverse (proteomic)
chemical genetics.
Recently, we have begun an exploration of the possibility
of using the three-component Biginelli reaction5 as the initial
stage in a solid-phase split-pool diversity-oriented synthesis
on high-capacity (500-600 µm) polystyrene macrobeads
whose surface has been functionalized with a carbon- and
silicon-based linker.6,7a The traditional Biginelli reaction
involves the simultaneous acid-catalyzed interaction of an
(4) Examples of diversity-oriented synthesis: (a) [Shikimic acid library]
Tan, D. S.; Foley, M. A.; Stockwell, B. R.; Shair, M. D.; Schreiber, S. L.
J. Am. Chem. Soc. 1999, 121, 9073-9087. (b) [Carpanone-like library]
Lindsley, C. W.; Chan, L. K.; Goess, B. C.; Joseph, R.; Shair, M. D. J.
Am. Chem. Soc. 2000, 122, 422-423. (c) [Ugi/Diels-Alder/RCM library]
Lee, D.; Sello, J. K.; Schreiber, S. L. Org. Lett. 2000, 2, 709-712. (d)
[THOX (tetrahydrooxazepine) library] Koide, K.; Finkelstein, J. M.; Ball,
Z.; Verdine, G. L. J. Am. Chem. Soc. 2001, 123, 398-408. (e) [1,3-Dioxane
library] Sternson, S. M.; Louca, J. B.; Wong, J. C.; Schreiber, S. L. J. Am.
Chem. Soc. 2001, 123, 1740-1747. (f) [Galanthamine library] Pelish, H.
E.; Westwood, N. J.; Feng, Y.; Kirchhausen, T.; Shair, M. D. J. Am. Chem.
Soc. 2001, 123, 6740-6741. (g) [Dihydropyrancarboxamide library]
Stavenger, R. A.; Schreiber, S. L. Angew. Chem., Int. Ed. 2001, 40, 3417-
3421. (h) [Hydroxamic acid library] Sternson, S. M.; Wong, J. C.; Grozinger,
C. M.; Schreiber, S. L. Org. Lett. 2001, 3, 4239-4242. (i) [Biaryl library]
Spring, D. R.; Krishnan, S.; Blackwell, H. E.; Schreiber, S. L. J. Am. Chem.
Soc. 2002, 124, 1354-1363. (j) [Ferrier/Pauson-Khand library] Kubota,
H.; Lim, J.; Depew, K. M.; Schreiber, S. L. Chem. Biol. 2002, 9, 265-
276. (k) [Benzo[b]furan library] Liao, Y.; Reitman, M.; Zhang, Y.; Fathi,
R.; Yang, Z. Org. Lett. 2002, 4, 2607-2609. (l) [Branched Diels-Alder
skeletal diversity library] Kwon, O.; Park, S. B.; Schreiber, S. L. J. Am.
Chem. Soc. 2002, 124, 13402-13404. (m) [Asymmetric azomethine ylide
1,3-dipolar cycloaddition library] Chen, C.; Li, X.; Schreiber, S. L. J. Am.
Chem. Soc. 2003, 125, 10174-10175.
† On sabbatical 2001-2002 from the Department of Chemistry and
Geology, Minnesota State University, Mankato, 242TN North Trafton
Science Center, Mankato, MN 56001.
‡ Current Address: Head of Chemogenetics, Novartis Institutes for
Biomedical Research, 100 Technology Square, Cambridge, MA 02139;
john.tallarico@pharma.novartis.com.
(1) Schreiber, S. L. Bioorg. Med. Chem. 1998, 6, 1127-1152.
(2) Schreiber, S. L. Science 2000, 287, 1964-1969.
(3) (a) Furka, A.; Sebestye´n, F.; Asgedom, M.; Dibo´, G. Int. J. Pept.
Protein Res. 1991, 37, 487-493. (b) Lam, K. S.; Salmon, S. E.; Hersh, E.
M.; Hruby, V. J.; Kazmierski, W. M.; Knapp, R. J. Nature 1991, 354, 82-84.
10.1021/ol048946r CCC: $27.50 © 2004 American Chemical Society
Published on Web 08/24/2004

aldehyde (1, usually aryl), urea or an N-monosubstituted urea
(2), and a â-ketoester (3) to produce a 3,4-dihydropyrimi-
dinone product (4) (Figure 1). Such compounds have been
found to possess a variety of biological activities.5b-f
(prepared separately by solution-phase reactions) to give
pyrimidine derivatives, which were converted to typical
Biginelli 3,4-dihydropyrimidinones only during cleavage
from the resin.
The “Atwal modification” of the Biginelli condensation
is conceptually adaptable to a solid-phase split-pool synthesis.
Marzinzik and Felder10b have described a two-step solid-
phase Atwal-like process beginning with a resin-bound
aromatic aldehyde, condensing it first with a ketone to
generate an R,â-unsaturated ketone, and then, in the one
example given, reacting this in a separate second step with
N-methylurea under basic conditions. This process, while
conceptually allowing for a solid-phase split-pool synthesis,
produced an atypical 3,4-dihydropyrimidinone product in
which the N-methyl group derived from the urea was found
at the N-3 rather than the usual N-1 position and which did
not have a carboalkoxy or other carbonyl group typically
found at the 5-position in the classical acid-catalyzed
Biginelli condensation.
Hamper et al.10c have also described a solid-phase two-
step Atwal-like process, beginning with a resin-esterified
trifluoroethyl malonate diester that was reacted with a series
of aldehydes in the first step of the synthesis. Subsequent
treatment of the resulting R,â-unsaturated resin-malonates
in a second step with amidines or S-alkylisothioureas under
basic conditions produced a series of 5,6-dihydropyrimidin-
4(3H)-ones. In these products the aldehyde-derived ring
substituent was found at the 6-carbon instead of typically at
the 4-carbon, and the pyrimidinone carbonyl, derived from
the distal malonate ester carbonyl with the loss of a
trifluoroethoxy group instead of from the urea derivative,
was found at the 4-carbon rather than the 2-carbon typical
of classical Biginelli compounds. While this Atwal-like
reaction would also be amenable to a solid-phase split-pool
process, it too does not produce the products typical of the
classical acid-catalyzed Biginelli reaction.
Figure 1. Biginelli 3,4-dihydropyrimidinone synthesis.
Wipf and Cunningham8a reported the first example of a
classical Biginelli reaction performed on solid phase by
treating a Wang resin-attached urea simultaneously with an
aldehyde and a â-ketoester to give a series of parallel solid-
phase syntheses of 3,4-dihydropyrimidin-2(1H)-ones. Kappe
and co-workers8b,c have also published solid-phase examples
of the acid-catalyzed Biginelli reaction in which resin-
attached â-ketoesters were reacted with combinations of
aldehydes and ureas in single-step parallel syntheses.
However, a solid-phase split-(and-)pool process mandates
that the resin-bound reactant be subjected to separate reaction
steps to introduce each of the other components of the
reaction sequence (and the variation therein). Biginelli
products have been prepared in solution in a stepwise fashion
via separate generation of R,â-unsaturated ketoesters (by
reacting â-ketoesters 3 with aldehydes 1), and then treatment
of these Knoevenagel condensation products with O(or S)-
alkylated ureas under basic conditions to give 1,4-dihydro-
pyrimidine derivatives of the traditional Biginelli 3,4-
dihydropyrimidinone products (the “Atwal modification” of
the Biginelli reaction).9 Kappe10a has reported a solid-phase
version of this method in which a resin-attached (via sulfur)
isothiourea was reacted with Knoevenagel compounds
For the generation of large libraries of Biginelli structures
without massive (parallel) synthetic effort, a split-and-pool
solid-phase synthetic strategy would be desirable. This
process would require that the classical acid-catalyzed three-
component Biginelli reaction be carried out in two discrete
steps on a solid-phase resin, first combining one resin-bound
reactant (e.g., resin-linked urea) separately with a number
of examples of a second reactant (e.g., aldehydes), followed
by pooling of the resins and splitting of the collection into
separate vessels for reaction with a variety of examples of
the third component (e.g., â-ketoesters) in a discrete second
step. To our knowledge, a non-Atwal solid-phase two-step
Biginelli reaction has not previously been demonstrated. We
herein report that such a protocol can be implemented on
high-capacity polystyrene macrobeads with a resin-bound
urea in a stepwise fashion that would be compatible with
split-and-pool techniques.
(5) (a) Biginelli, P. Gazz. Chim. Ital. 1893, 23, 360-416. Recent
reviews: (b) Kappe, C. O.; Stadler, A. Org. React. 2004, 63, 1-116. (c)
Kappe, C. O. QSAR Comb. Sci. 2003, 22, 630-645. (d) Kappe, C. O. Eur.
J. Med. Chem. 2000, 35, 1043-1052. (e) Kappe, C. O. Acc. Chem. Res.
2000, 33, 879-888. (f) Kappe, C. O. Tetrahedron 1993, 49, 6937-6963.
(6) Tallarico, J. A.; Depew, K. M.; Pelish, H. E.; Westwood, N. J.;
Lindsley, C. W.; Shair, M. D.; Schreiber, S. L.; Foley, M. A. J. Comb.
Chem. 2001, 3, 312-318.
(7) (a) Blackwell, H. E.; Pe´rez, L.; Stavenger, R. A.; Tallarico, J. A.;
Cope-Eatough, E.; Foley, M. A.; Schreiber, S. L. Chem. Biol. 2001, 8,
1167-1182. (b) Clemons, P. A.; Koehler, A. N.; Wagner, B. K.; Sprigings,
T. G.; Spring, D. R.; King, R. W.; Schreiber, S. L.; Foley, M. A. Chem.
Biol. 2001, 8, 1183-1195.
(8) (a) Wipf, P.; Cunningham, A. Tetrahedron Lett. 1995, 36, 7819-
7822. (b) Valverde, M. G.; Dallinger, D.; Kappe, C. O. Synlett 2001, 741-
744. (c) Pe´rez, R.; Beryozkina, T.; Zbruyev, O. I.; Haas, W.; Kappe, C. O.
J. Comb. Chem. 2002, 4, 501-510.
(9) (a) O’Reilly, B. C.; Atwal, K. S. Heterocycles 1987, 26, 1185-1188.
(b) Atwal, K. S.; O’Reilly, B. C.; Gougoutas, J. Z.; Malley, M. F.
Heterocycles 1987, 26, 1189-1192. (c) Atwal, K. S.; Rovnyak, G. C.;
O’Reilly, B. C.; Schwartz, J. J. Org. Chem. 1989, 54, 5898-5907.
(10) (a) Kappe, C. O. Bioorg. Med. Chem. Lett. 2000, 10, 49-51. (b)
Marzinzik, A. L.; Felder, E. R. J. Org. Chem. 1998, 63, 723-727. (c)
Hamper, B. C.; Gan, K. Z.; Owen, T. J. Tetrahedron Lett. 1999, 40, 4973-
4976.
To begin, the macrobeads were functionalized with an
O-silyl-attached 3-aminopropanol group (Scheme 1), by
activating the silyl-linker in 56 with triflic acid (TfOH,
trifluoromethanesulfonic acid) and then treating the resulting
silyl triflate with 3-FMOC-aminopropanol (6). Removal of
the FMOC protecting group11a from 7 analytically with 20%
piperidine in DMF11b-d showed a loading of 0.88 mmol per
3238
Org. Lett., Vol. 6, No. 19, 2004

MeCN, PhMe, Dioxane, EtOAc, NMP, DMF). Acetic acid/
morpholine12e in THF or ClCH2CH2Cl was also found to be
ineffective.
Scheme 1. Synthesis of Resin-Attached Urea 10
Eventually, the mild Lewis acids LiClO4,14 LiOTf,14 and
Yb(OTf)315 were tested in MeCN and THF solvents (0.1 M
Lewis acid, 0.5 M 11a and 13, 75 °C, 40 h) (Scheme 2).
Scheme 2. Solid-Phase Split-and-Pool Synthesis of
3,4-Dihydropyrimidinones
gram of resin (79.5%; 132.5 nmol/bead), and bulk depro-
tection under similar conditions gave the 3-silyloxypropyl-
amine-functionalized resin 8. This amino-resin was converted
into urea-resin 10 by treatment with TMSNCO (trimeth-
ylsilylisocyanate, 9) and pyridine in CH2Cl2.12
Since the strong protonic acid catalyst of the classical
Biginelli reaction would not be compatible with the O-silyl
linker on the polystyrene macrobeads, it was first necessary
to identify an appropriate catalyst for use with the beads.
Polyphosphate ester (PPE), which was quite effective as a
catalyst for solution-phase Biginelli reactions,13 was found
to produce no on-bead Biginelli product when used as a
catalyst in the reaction of urea-resin 10 with 4-bromoben-
zaldehyde (11a) and ethyl acetoacetate (13) in a wide variety
of solvents (THF, ClCH2CH2Cl, 100% EtOH, CF3CH2OH,
The Yb(OTf)3 catalyst produced no on-bead Biginelli product
14 at all in either solvent, as judged by subsequent HF/
pyridine cleavage and LC/MS analysis for the free hydrox-
ypropyl Biginelli adduct 15a. Both LiClO4 and LiOTf
catalysts gave on-bead product in either solvent, but the best
results appeared to be with LiOTf/MeCN, which gave the
greatest amount of desired product 15a with the least amount
of impurities upon cleavage from the solid support. LiOTf/
MeCN was therefore chosen as the catalyst/solvent for
subsequent studies.
(11) (a) Carpino, L. A.; Han, G. Y. J. Org. Chem. 1972, 37, 3404-
3409; 1973, 38, 4218. (b) Atherton, E.; Fox, H.; Harkiss, D.; Logan, C. J.;
Sheppard, R. C.; Williams, B. J. J. Chem. Soc., Chem. Commun. 1978,
537-539. (c) Atherton, E.; Logan, C. J.; Sheppard, R. C. J. Chem. Soc.,
Perkin Trans. 1 1981, 538-546. (d) NoVabiochem Catalog and Peptide
Synthesis Handbook; Novabiochem, 2000; Technical Notes Section, Method
6P, p P4.
(12) (a) Neville, R. G. J. Org. Chem. 1958, 23, 937-938. (b) Neville,
R. G.; McGee, J. J. Can. J. Chem. 1963, 41, 2123-2129. (c) Goubeau, J.;
Heubach, E. Chem. Ber. 1960, 93, 1117-1125. (d) Boger, D. L.; Coleman,
R. S.; Invergo, B. J. J. Org. Chem. 1987, 52, 1521-1530. (e) McDonald,
A. I.; Overman, L. E. J. Org. Chem. 1999, 64, 1520-1528.
(13) Kappe, C. O.; Falsone, S. F. Synlett 1998, 718-720.
(14) Yadav, J. S.; Subba Reddy, B. V.; Srinivas, R.; Venugopal, C.;
Ramalingam, T. Synthesis 2001, 1341-1345.
(15) Ma, Y.; Qian, C.; Wang, L.; Yang, M. J. Org. Chem. 2000, 65,
3864-3868.
Org. Lett., Vol. 6, No. 19, 2004
3239

The identity of the on-bead Biginelli product was con-
firmed by alternate solution-phase synthesis (Scheme 3).
remaining two six-bead vials were treated with 100 µL each
of the same solution. These three vials were then heated
under N2 at 80 °C for 69 h.
After cooling, the reaction solutions were removed and
the beads in each vial were rinsed with MeCN (2 × 30 min)
and THF (2 × 30 min) with vortex agitation. The resins were
then transferred into separate small fritted chromatography
columns and washed sequentially with tumbler agitation 2
× 30 min in each of the following solvents: THF; 3:1 THF/
IPA (IPA ) isopropyl alcohol); 3:1 THF/H2O; 3:1 THF/
IPA; THF; DMF; and finally THF again. Each of the 12
beads from the pooled Br/Cl vial was then placed in a
separate 0.5 mL Eppendorf vial, while the 6 beads from the
Br- or Cl-only reactions were placed in their own 1.5 mL
vials. Each of these samples was cleaved with HF/pyridine/
THF and quenched with TMSOEt, and the cleavage solutions
were evaporated in vacuo and analyzed by LC/MS.
The 6 pure 4-bromobenzaldehyde beads formed 4-bro-
mophenyl Biginelli product 15a, while the 6 pure 4-chlo-
robenzaldehyde beads formed 4-chlorophenyl Biginelli prod-
uct 15b. Significantly, of the 12 pooled beads, 6 of the
indiVidually analyzed beads showed only bromo product 15a,
while the other 6 showed only chloro product 15b, indicating
that there was no cross-reaction between chloro- and bromo-
beads in the pooled reaction.
Scheme 3. Alternate Solution-Phase Synthesis of 15a
This finding suggests that the presumed acylimine inter-
mediate 12 derived from the resin-attached N-alkylurea and
an aldehyde is sufficiently stable on the polystyrene mac-
robead support to allow the beads to be washed to remove
excess aldehyde, pooled, and then split into collections of
beads for subsequent reaction with a â-ketoester. The
generation of the final 3,4-dihydropyrimidinone product can
therefore be accomplished without crossoVer of the aldehyde
reactant from one bead to another, thus preserving the
integrity of the split-(and-)pool process. No other report of
which we are aware has yet demonstrated the above-
described process. We therefore conclude that it should be
possible to conduct a direct solid-phase split-and-pool
synthesis of a collection of Biginelli compounds on poly-
styrene macrobeads using a variety of aryl aldehydes in the
first stage of acylimine formation, followed by a variety of
â-ketoesters in the second stage. Efforts will continue to
implement such a solid-phase split-and-pool synthesis of
Biginelli compounds, as well as subsequent studies of the
further elaboration of these products, as a beginning point
in a diversity-oriented synthesis of collections of small
molecules.
3-Aminopropanol (16) was selectively protected on the
hydroxyl-oxygen by treatment with triisopropylsilyl trifluo-
romethanesulfonate (TIPSOTf) and 2,6-lutidine in CH2Cl2.
The resulting 3-TIPSO-propylamine 17 was then converted
to urea 18 with TMSNCO and pyridine/CH2Cl2 at rt or
DMAP/THF12d at reflux. Biginelli reaction of 18 with 11a
and 13 catalyzed by LiOTf in MeCN gave crude 19
containing a small amount of desilylated product 15a. Silyl
cleavage with HF/pyridine in THF, followed by quenching
with methoxytrimethylsilane (TMSOMe), gave 1-(3-hydrox-
ypropyl)-3,4-dihydropyrimidinone 15a identical with the on-
bead product by LC/MS.
Demonstration of the feasibility of a solid-phase split-pool
stepwise Biginelli 3,4-dihydropyrimidinone synthesis was
carried out in the following manner. Four reaction vials, each
containing six beads of resin 10, were prepared. Into each
of two vials was placed 100 µL of a MeCN solution 0.1 M
in LiOTf and 0.5 M in 4-bromobenzaldehyde (11a). Into each
of the other two vials was placed 100 µL of a MeCN solution
0.1 M in LiOTf and 0.5 M in 4-chlorobenzaldehyde (11b).
These four vials were then heated under N2 at 80 °C for 43
h, presumably to generate the acylimines 12 from the on-
bead urea and the aldehydes. The reaction solutions were
then removed from each of the vials; the beads in each vial
were rinsed briefly with fresh MeCN (2 × 100 µL), and
one set of 4-bromobenzaldehyde beads was pooled with one
set of 4-chlorobenzaldehyde beads. The pooled set of 12
beads was treated with 200 µL of a MeCN solution 0.1 M
in LiOTf and 0.5 M in ethyl acetoacetate (13), while the
Acknowledgment. We thank Max Narovlyanski for
synthesizing the silyl-linker resin 5 used in this study and
Kerry Pierce and Jennifer Tee for assistance with the LC/
MS. Harvard ICCB is financially supported by Merck & Co.,
Merck KGaA, the Keck Foundation, and the National Cancer
Institutes.
Supporting Information Available: Experimental de-
tails. This material is available free of charge via the Internet
at http://pubs.acs.org.
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