Organic Process Research & Development 2009, 13, 807–811
Practical Synthesis of 5-Fluoro-2-(piperidin-4-yloxy)pyrimidin-4-amine, a Key
Intermediate in the Preparation of Potent Deoxycytidine Kinase Inhibitors
Haiming Zhang, Jie Yan,† Ramanaiah C. Kanamarlapudi,‡ Wenxue Wu,* and Philip Keyes
Chemical DeVelopment, Lexicon Pharmaceuticals, 350 Carter Road, Princeton, New Jersey 08540, U.S.A.
Scheme 1. Preparation of dCK inhibitors from 1
Abstract:
A practical synthesis of 5-fluoro-2-(piperidin-4-yloxy)pyrimidin-
4-amine, a key intermediate in the preparation of a new class of
potent deoxycytidine kinase (dCK) inhibitors, is described. The
commercially available 2,4-dichloro-5-fluoropyrimidine (12) is
converted in four telescoped steps to tert-butyl 4-(4-amino-5-
fluoropyrimidin-2-yloxy)piperidine-1-carboxylate (6a) which upon
deprotection gives 5-fluoro-2-(piperidin-4-yloxy)pyrimidin-4-amine
dihydrochloride (1a) in about 68% overall yield. This process
proved to be an economical alternative to a Mitsunobu-based
synthesis.
Scheme 2. Medicinal chemistry synthesis of 1a
Introduction
Deoxycytidine kinase (dCK) is an enzyme that catalyzes
phosphorylation of pyrimidine and purine deoxynucleosides,
one of the initial biochemical steps in the deoxynucleoside
salvage pathway that supplies precursors for DNA synthesis.1
Human dCK is known to be involved in the activation of several
chemotherapeutically important nucleoside analogues.2 Through
phenotypical analysis of knockout (KO) mice, Lexicon identi-
fied dCK as a potential drug target in multiple therapeutic areas
within cancer, immunological disorders, and infectious diseases.3
Internal medicinal chemistry research led to a class of O-linked
pyrimidin-4-amine-based compounds as potent inhibitors of
dCK.4 We report herein a scalable synthesis of a key intermedi-
ate for the preparation of this class of compounds, 5-fluoro-2-
(piperidin-4-yloxy)pyrimidin-4-amine (1, Scheme 1).
Results and Discussion
The medicinal chemistry group used a synthesis based on
the Mitsunobu reaction5 of commercially available 5-fluorocy-
tosine (2)6 and N-Boc-4-piperidinol (3) (Scheme 2).4 The
resulting iminophosphorane7 4 is then treated with HCl to give
the 5-fluoro-2-(piperidin-4-yloxy)pyrimidin-4-amine dihydro-
chloride (1a) in about 60% yield. While this synthesis worked
well on small scale and provided rapid access to gram quantities
of 1 for early investigations of structure activity relationships
(SAR), it gave inconsistent yields on scale-up. As a process, it
also suffers several major shortcomings in addition to the usual
issues associated with Mitsunobu reactions. Up to 2 equiv of 2
are required to fully convert the piperidinol 3 at a reasonable
reaction rate. The low solubility of 2 as well as that of 4
necessitates a very large volume of reaction solvent (100 mL
THF/g of 3). Additionally, the unreacted 2 remaining in the
reaction mixture poses significant purification challenges. As a
result, the iminophosphorane 4 had to be purified by chroma-
tography to remove large amounts of 2 and side products prior
to deprotection in order to produce 1a of acceptable purity.
Although a vendor was able to use this chemistry to produce
500 g of 1a in about 40% overall yield to support lead
* To whom correspondence should be addressed. E-mail: wwu@
lexpharma.com.
† Current address: Amgen, Inc., One Kendall Square, Building 1000,
Cambridge, MA 02139. E-mail: yanj@amgen.com.
‡ Current address: Concert Pharmaceuticals, Inc., 99 Hayden Ave, Suite 500,
Lexington, MA 02421. E-mail: rkanamarlapudi@concertpharma.com.
(1) (a) Arner, E. S. J.; Eriksson, S. Pharmacol. Ther. 1995, 67, 155–186,
and references cited therein. (b) Chottiner, E. G.; Shewach, D. S.;
Datta, N. S.; Ashcraft, E.; Gribbin, D.; Ginsburg, D.; Fox, I. H.;
Mitchell, B. S. Proc. Natl. Acad. Sci. U.S.A. 1991, 88, 1531–1535.
(2) (a) Van Rompay, A. R.; Johansson, M.; Karlsson, A. Pharmacol. Ther.
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Biochemistry 2003, 42, 14711–14719.
(5) For a review of the Mitsunobu reaction, see: Hughes, D. L. Org. React.
1992, 42, 335–656.
(3) Some deoxycytidine kinase inhibitors have been reported. For
examples, see: (a) Krenitsky, T. A.; Tuttle, J. V.; Koszalka, G. W.;
Chen, I. S.; Beacham, L. M., III.; Rideout, J. L.; Elion, G. B. J. Biol.
Chem. 1976, 251, 4055–4061. (b) Ward, A. D.; Baker, B. R. J. Med.
Chem. 1977, 20, 88–92.
(6) (a) 5-Fluorocytosine is an antifungal with the generic drug name of
flucytosine. For a recent review on this prodrug, see: (b) Vermes, A.;
Guchelaar, H.-J.; Dankert, J. J. Antimicrob. Chemother. 2000, 46, 171–
179.
(4) Augeri, D. J.; Carlsen, M.; Carson, K. G.; Fu, Q.; Healy, J. P.; Heim-
Riether, A.; Jessop, T. C.; Keyes, P. E.; Shen, M.; Tarver, J. E.; Taylor,
J. A.; Xu, X. U.S. Pat. Appl. Publ 20080146571 A1, 2008.
(7) For recent reviews on iminophosphorane, see: (a) Wamhoff, H.;
Richardt, G.; Stoelben, S. AdV. Heterocl. Chem. 1995, 64, 159–249.
(b) Molina, P.; Vilaplana, M. J. Synthesis 1994, 1197, 218.
10.1021/op900060u CCC: $40.75 2009 American Chemical Society
Published on Web 04/30/2009
Vol. 13, No. 4, 2009 / Organic Process Research & Development
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