Environmentally friendly and efficient: Iron-mediated reduction of 3-methyl-5-aryl-1,2,4-oxadiazoles to benzamidines

Article abstract of DOI:10.1016/j.tetlet.2003.09.139

A new synthetic method is described for the mild and selective reduction of 3-methyl-5-aryl-1,2,4-oxadiazoles to amidines employing iron powder in aqueous medium. Its application is demonstrated in the synthesis of 1, a potent and selective urokinase-type plasminogen activator (uPA) inhibitor.

Full text of DOI:10.1016/j.tetlet.2003.09.139

TETRAHEDRON
LETTERS
Pergamon
Tetrahedron Letters 44 (2003) 8697–8700
Environmentally friendly and efficient: iron-mediated reduction of
3-methyl-5-aryl-1,2,4-oxadiazoles to benzamidines
Martin Sendzik* and Hon C. Hui
Department of Medicinal Chemistry, Celera, 180 Kimball Way, South San Francisco, CA 94080, USA
Received 21 August 2003; accepted 17 September 2003
Abstract—A new synthetic method is described for the mild and selective reduction of 3-methyl-5-aryl-1,2,4-oxadiazoles to
amidines employing iron powder in aqueous medium. Its application is demonstrated in the synthesis of 1, a potent and selective
urokinase-type plasminogen activator (uPA) inhibitor.
© 2003 Published by Elsevier Ltd.
Trypsin-like serine proteases, which include trypsin,
tryptase, factor Xa, factor VIIa, thrombin, urokinase-
type plasminogen activator (uPA), and tissue-type plas-
minogen activator (tPA), are involved or implicated in
disease states. Most known inhibitors of these enzymes
bear an amidino group as a basic group, which helps to
produce high binding affinity with the proteases due to
its interaction with Asp189 in the S1 specificity pocket.1
We required that a suitable masked amidino group was
introduced early in the synthetic sequence in order to
provide the most efficient entry to a variety of differ-
ently functionalized analogues.9 The 3-methyl-1,2,4-
oxadiazole was chosen for the protection of the
amidino group.
3-Methyl-5-aryl-1,2,4-oxadiazoles are stable to a variety
of reaction conditions and can easily be isolated and
purified by crystallization or silica gel chromatography.
Their use as masked protected amidines is diminished
somewhat by difficulties involved in unmasking the
amidine. Reduction using Raney-Ni or Pd/C under H2
atmosphere has been described in the literature.7a While
these methods are very effective and efficient, they
suffer from the disadvantage of involving reagents that
are highly reactive, toxic, or expensive, and do not
tolerate many other functionalities such as chlorine or
benzyl protecting groups.
As part of a program to develop highly potent and
selective uPA inhibitors, we have prepared a variety of
novel benzamidine-based inhibitors.2 A number of dif-
ferent methods for the preparation of amidines are
reported.3
Existing routes to benzamidines from benzonitriles
include conversion via amination of imidates (Pinner
reaction)4 or thioimidates,5 addition of aluminium
amide to nitriles,6 reduction of amidoximes,7 and reduc-
tion of 1,2,4-oxadiazoles.8
Amidine 1 is a highly potent and selective uPA-
inhibitor identified at Celera (Fig. 1).2b The correspond-
ing des-chloro analogue retains its potency but loses its
selectivity.10 In the process of synthesizing larger
amounts of 1 (>5 g), reduction of the oxadiazole was
carried out initially using Raney-Ni or Pd/C. This led
to a high level of dechlorination and resulted in a
significant amount of the nonselective uPA inhibitor
(6% and 4%, respectively). Its removal—as well as the
removal of Ni2+-ions—and purification of 1 required
several recrystallization steps, causing further loss of
material.
Figure 1. Selective uPA-inhibitor 1.
In this report we describe our studies in the mild and
chemoselective reduction of 3-methyl-5-aryl-1,2,4-oxa-
* Corresponding author. Tel.: +1-650-866-6533; fax: +1-650-866-6655;
e-mail: martin.sendzik@celera.com
0040-4039/$ - see front matter © 2003 Published by Elsevier Ltd.
doi:10.1016/j.tetlet.2003.09.139

8698
M. Sendzik, H. C. Hui / Tetrahedron Letters 44 (2003) 8697–8700
Scheme 1. Reagents and conditions: (a) 1 equiv. NIS, AcOH, 48%; (b) 2.2 equiv. Boc2O, cat. DMAP, THF; (c) 50 wt% aq. NaOH,
THF/EtOH (1/1), 90% over 2 steps; (d) 50 wt% aq. NH2OH, EtOH, reflux, 1.5 h; (e) AcCl, i-Pr2NEt, CH2Cl2, 0°C; (f) Bu4NF,
THF; >95% over 3 steps; (g) TFA, 95%; (h) CbzCl, THF, NEt3, 83%; (i) cat. Pd(PPh3)2Cl2, H-ꢀ-Ar, NEt3, cat. Cu(I)I, DMF, 72%;
(j) 20 equiv. Zn, AcOH, quant.; (k) 40 wt% aq. Bu4NOH, THF, reflux, 89%; (l) for 11: 4 M HCl/dioxane, MeOH, quant.
diazoles to benzamidines using iron powder in aqueous
solution and its application to the preparation of uPA-
inhibitor 1.11
led to a partial loss of the acid labile Boc-group. Both
acetic acid and formic acid can be used as proton
source (entries 10 to 12). Des-chloro-7a could not be
detected in any of the reactions. A variety of different
solvents were investigated (entries 13 to 23). It should
be noted that the addition of a homogenizing solvent is
essential for the reduction of oxadiazoles with limited
solubility such as 8, 10, and 12 (Table 2). Alcohols such
as methanol, ethanol, and iso-propanol in two-phase
systems worked as good as chlorinated solvents such as
dichloromethane and chloroform in three-phase sys-
tems (entries 19 and 20).
Scheme 1 outlines the chemistry employed to prepare
the oxadiazoles 4, 5, 7, 8, 10, and 12. Amino benzoni-
triles 2 and 3 were mono-Boc protected via their bis-
Boc intermediates through treatment with Boc-
anhydride followed by sodium hydroxide solution.
Conversion of the nitrile to the oxadiazole was achieved
using reported procedures providing 4 and 7.12 Simi-
larly, oxadiazole 6 was prepared from benzonitrile 2
after initial iodination with N-iodosuccinimide. Biaryl
compounds 8 and 9 were synthesized through Sono-
gashira coupling of Boc-aniline 6 with the appropriate
arylacetylenes.13,14 Following treatment of these with
aqueous tetrabutylammonium hydroxide solution,
cyclisation and concomitant Boc-deprotection provided
indoles 10 and 11. Oxadiazole 12, the direct precursor
of the uPA-inhibitor 1, was obtained by Mem-deprotec-
tion of 11 with 2M HCl in dioxane/methanol.
To extend the utility of the iron-mediated reduction,
additional oxadiazoles bearing functional groups sensi-
tive to hydrogenation were also investigated. Thus, 5
was prepared from 3 via a protecting group switch from
Boc to Cbz. The reactions were carried out with 10–20
equivalents of iron powder in methanol: acetic acid:
water (1:1:ꢀ1) at 40 to 50°C. A closed apparatus with
pressure equalization was used to avoid air-oxidation of
generated Fe2+ to Fe3+, which can complicate the isola-
tion of the product by forming Fe2+/3+-hydrates. Pro-
gression of the reactions was monitored with analytical
HPLC. The products were isolated by filtration over
C18 or by crystallization. Table 2 shows that yields of
>89% were obtained and that a number of functional
groups tolerated the reductive conditions, including:
aryl chlorides, acetylene and the Cbz-group.
In initial experiments, oxadiazole 7 was chosen as a test
system. Table 1 summarizes the reaction conditions we
examined for the reductive transformation of oxadi-
azole 7 to 2-chloro-benzamidine 7a. We found that the
reduction with iron powder15 takes place in acetic acid
(entry 1). Dilution with water reduces the reaction time
but also lowers the solubility of the oxadiazole in acetic
acid (entry 2). Addition of methanol homogenized the
reaction solution but slowed the reaction noticeably
(entries 3 and 4). Reaction times were significantly
reduced when the amount of reducing reagent was
increased (entry 9). The same effect was observed by
increasing the reaction temperature from room temper-
ature to 40°C (entry 8). Further temperature increase
General procedure: Oxadiazole 12 (4.87 g 10 mmol) was
suspended in MeOH/AcOH/H2O (90 mL/90 mL/90
mL). Iron powder (5.58 g, 100 mmol) was added and
the reaction mixture was vigorously stirred and heated
at 50°C for 5 h giving a clear light yellow solution.16
The reaction was cooled to room temperature and the

M. Sendzik, H. C. Hui / Tetrahedron Letters 44 (2003) 8697–8700
Table 1. Optimization conditions for the iron-mediated reduction of 7 to 7aa
8699
Entry
Conditions
H2O (mL)
Conversion (%)b
5 h 20 h
Fe (equiv.)
Acid (1 mL)
Solvent
Temp.
1
2
3
4
5
6
7
8
20
20
20
20
20
20
10
10
30
20
20
20
20
20
20
20
20
20
20
20
20
20
20
AcOH
AcOH
AcOH
AcOH
AcOH
AcOH
AcOH
AcOH
AcOH
HCOOH
HCOOH
HCOOH
AcOH
AcOH
AcOH
AcOH
AcOH
AcOH
AcOH
AcOH
AcOH
AcOH
AcOH
0
1
0
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
–
–
rt
rt
rt
rt
rt
rt
rt
40°C
rt
rt
rt
rt
rt
rt
rt
rt
rt
rt
rt
rt
rt
rt
rt
13
48
16
41
31
32
14
100
47
42
55
55
21
27
24
19
14
14
35
24
28
14
20
81
100
59
100
88
1 mL MeOH
0.5 mL MeOH
1 mL MeOH
2 mL MeOH
1 mL MeOH
1 mL MeOH
1 mL MeOH
1 mL MeOH
1 mL CH2Cl2
–
1 mL EtOH
1 mL i-PrOH
1 mL acetone
1 mL EtOAc
1 mL THF
1 mL dioxane
1 mL CH2Cl2
1 mL CHCl3
1 mL AcCN
1 mL DMSO
1 mL DMF
83
67
c
9
100
84
100
89
87
72
84
79
46
48
100
81
79
51
52
10
11
12
13
14
15
16
17
18
19
20
21
22
23
a The reactions were carried out in a 0.2 mmol scale.
b Determined by analytical HPLC.
c Partial loss of Boc-group.
elemental iron was removed. 1 M HCl (ꢀ100 mL) was
added until the solution became light yellow. The solu-
tion was extracted with diethylether (5×) giving a white
precipitate in the aqueous layer. The aqueous phase
was concentrated to half of its volume and the precipi-
tate was filtered and washed with 1 M HCl. The white
solid was dissolved in a minimum amount of hot etha-
nol and precipitated by the slow addition of 1 M HCl
Table 2. Examples for iron-mediated reduction
a
Isolated as its HCl salt.
b Isolated by recrystallization.

8700
M. Sendzik, H. C. Hui / Tetrahedron Letters 44 (2003) 8697–8700
and cooling to room temperature. The precipitate was
filtered and the dissolving–precipitation process
repeated. The solid was dried in vacuo to afford the
hydrochloride salt of 1 (4.46 g, 9.23 mmol, 92%)17 as a
white solid with a purity of >99%. The iron content was
determined to be 33 ppm (Robertson Microlit Labora-
tories, Inc.). Alternatively, the aqueous layer was
lyophilized, dissolved in a small amount of acetonitrile/
1 M HCl, filtered through a short plug of C18 to remove
iron salts and re-lyophilized to provide pure amidine
hydrochloride salt.
Lepore, S. D.; Schacht, A. L.; Wiley, M. R. Tetrahedron
Lett. 2002, 43, 8777–8779.
8. Eloy, F. Fortschr. Chem. Forsch Bd. 1965, 4, 807–876.
9. Unpublished results.
10. (a) Katz, B. A.; Sprengeler, P. A.; Luong, C.; Verner, E.;
Elrod, K.; Kirtley, M.; Janc, J.; Spencer, J. R.; Breiten-
bucher, J. G.; Hui, H. C.; McGee, D.; Allen, D.; Martelli,
A.; Mackman, R. L. Chem. Biol. 2001, 8, 1107–1121; (b)
Mackman, R. L.; Katz, B. A.; Breitenbucher, J. G.; Hui,
H. C.; Verner, E.; Luong, C.; Sprengeler, P. A. J. Med.
Chem. 2001, 44, 3856–3871.
11. Examples for reduction of the NꢁO bond in NO2 using
iron: (a) Desai, D. G.; Swami, S. S.; Hapase, S. B. Synth.
Comm. 1999, 29, 1033–1036; (b) Koch, V.; Schnatterer, S.
Synthesis 1990, 499–501.
12. Gangloff, A. R.; Litvak, J.; Shelton, E. J.; Sperandio, D.;
Wang, V. R.; Rice, K. D. Tetrahedron Lett. 2001, 42,
1441–1443.
13. (a) Sonogashira, K. In Metal-Catalyzed Cross-Coupling
Reactions; Diederich, F.; Stang, P. J., Eds.; Wiley-VCH:
New York, 1998; Chapter 5; (b) Yasuhara, A.;
Kanamori, Y.; Kaneko, M.; Numata, A.; Kondo, Y.;
Sakamoto, T. J. Chem. Soc., Perkin Trans. 1 1999, 529–
534.
In conclusion, we have described a new synthetic
method for the chemoselective reduction of 5-aryl-
1,2,4-oxadiazoles to benzamidines employing iron pow-
der in acidic aqueous solution. The conditions are
sufficiently mild to be compatible with functional
groups such as chlorine, benzyl ether, and alkynes. The
method was successfully applied in the synthesis of the
potent and selective uPA-inhibitor 1.
Acknowledgements
14. (a) The alkyne, which is required for the synthesis of 11,
with R1=OMem, R2=Ph, R3=CH2CONMe2 was pre-
pared from methyl p-hydroxyphenyl acetate in 7 steps;
(b) See also: Young. W. B.; Kolesnikov, A.; Rai, R.;
Sprengeler, P. A.; Leahy, E. M.; Shrader, W. D.;
Sanalang, J.; Burgess-Henry, J.; Spencer, J. R.; Elrod, K.;
Cregar, L. Bioorg. Med. Chem. Lett. 2001, 11, 2253–2256.
15. Iron, powder, −325 mesh, 97%; commercially available
from Acros Organics.
We would like to thank Dr R. L. Mackman for helpful
discussions and Dr. K. E. Wesson for the review of this
manuscript.
References
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1
(s, 1H), 7.57–7.33 (m, 7H), 7.11 (d, 1H, J=2.0 Hz), 7.04
(d, 1H, J=0.7 Hz), 3.71 (s, 2H), 3.06 (s, 3H), 2.84 (s,
3H), 2.68 (s, 3H). 13C NMR (68 MHz, DMSO-d6) l
176.2, 170.4, 149.2, 138.3, 138.1, 137.6, 131.6, 131.3,
129.3, 128.3, 127.1, 127.0, 124.1, 123.2, 121.5, 116.4,
113.0, 101.8, 37.2, 35.0, 11.9; MS ESI (m/z) 487 (MH+).
HPLC (Polaris 5m 50×2.0 mm; 2–95% in 5 min with 1
mL/min, MeCN/H2O, 0.05% TFA), retention time: 3.97
1
min, purity >99%. 1: H NMR (270 MHz, DMSO-d6) l
11.83 (s, 1H), 9.34 (s, 2H), 9.21 (s, 2H), 8.94 (s, 1H), 7.84
(s, 1H), 7.66 (s, 1H), 7.58 (s, 1H), 7.53–7.32 (m, 5H), 7.07
(s, 2H), 3.68 (s, 2H), 3.04 (s, 3H), 2.81 (s, 3H). 13C NMR
(68 MHz, DMSO-d6) l 185.0, 153.6, 136.9, 126.2, 125.9,
125.5, 119.4, 119.1, 116.9, 116.1, 116.0, 114.8, 114.1,
109.8, 109.4, 108.9, 107.8, 100.0, 89.39, 24.87, 22.69. MS
ESI (m/z) 447 (MH+). HPLC (Polaris 5m 50×2.0 mm;
2–95% in 5 min with 1 mL/min, MeCN/H2O, 0.05%
TFA), retention time: 3.02 min, purity >99%. Anal.
(C25H23ClN4O2–HCl), C, H, N, Cl. Fe detection (Robert-
son Microlit Laboratories, Inc.)=33 ppm.