Asymmetric synthesis and conformational analysis of the two enantiomers of the saturated analog of the potent thrombin inhibitor MOL-376

Article abstract of DOI:10.1016/S0040-4039(02)02534-0

Asymmetric synthesis of the two enantiomers of a small molecule thrombin inhibitor is described. The key step in the synthesis is the glucose-directed chiral induction in the hetero Diels-Alder cycloaddition step. Conformational analysis indicates that th

Full text of DOI:10.1016/S0040-4039(02)02534-0

TETRAHEDRON
LETTERS
Pergamon
Tetrahedron Letters 44 (2003) 583–586
Asymmetric synthesis and conformational analysis of the two
enantiomers of the saturated analog of the potent thrombin
inhibitor MOL-376
Jessy Mathew,† Ken Farber, Hiroshi Nakanishi‡ and Maher Qabar*
Molecumetics, 2023, 120th Avenue N. E. Bellevue, WA 98005, USA
Received 6 September 2002; accepted 8 November 2002
Abstract—Asymmetric synthesis of the two enantiomers of a small molecule thrombin inhibitor is described. The key step in the
synthesis is the glucose-directed chiral induction in the hetero Diels–Alder cycloaddition step. Conformational analysis indicates
that the S-enantiomer is a better fit for the idealized b-strand conformation. © 2002 Elsevier Science Ltd. All rights reserved.
We have been working for the past several years to
develop mimetics of common secondary structure
motifs such as b-strand, reverse turns and a-helices that
can be used as novel therapeutic agents.1–3 Thrombin is
a serine protease that plays a key role in the blood
coagulation cascade leading to thrombus formation.
X-Ray crystallography studies of several proteases
including thrombin have highlighted the fact that an
extended strand motif is adapted by the inhibitor/sub-
strate in the active site.4 We have designed and synthe-
sized a number of small molecule b-strand mimetics
that adopt the bioactive conformation5 and developed
MOL-376 as a potent and selective thrombin inhibitor
(Ki=1.2 nM). The saturated analog of MOL-376 also
showed very good activity. In this paper we describe the
asymmetric synthesis of the two enantiomers 1 and 2 of
saturated analog of MOL-376 (Fig. 1).
Stoodley and co-workers have shown that (E)-1-
(2%,3%,4%,6%-tetra-O-acetyl-b- -glucopyranosyloxybuta)-1,
3-diene displayed good diastereofacial selectivity in
Diels–Alder reactions with cyclic dienophiles like ura-
zoles.6 We applied this reaction to the synthesis of
product 1 as outlined below (Scheme 1).
D
Reaction of the monosodium salt of malonaldehyde7 3
with acetobromoglucose 4 in DMSO solution8 afforded
aldehyde 5. Treatment of the aldehyde with phospho-
rane 6 at room temperature6c furnished the trans,trans-
diene 7 which was obtained as a major diastereomer in
88% yield. The diastereomerically pure diene 7 was then
obtained by crystallization from a methylene chloride–
ether–hexane system (48% yield). Diels–Alder reaction
of diene 7 with urazole 8 in the presence of iodobenzene
diacetate1 (IBD) in methylene chloride (crude dr 96:4)
Figure 1.
* Corresponding author. Present address: Aurigene Discovery Technologies, Inc., 99 Hayden Avenue, Lexington, MA 02420, USA. E-mail:
maher q@aurigene.com
–
† Present address: Chemcodes, NC.
‡ Present address: Kemia, 9390 Towne Center Dr., San Diego, CA 92121, USA.
0040-4039/03/$ - see front matter © 2002 Elsevier Science Ltd. All rights reserved.
PII: S0040-4039(02)02534-0

584
J. Mathew et al. / Tetrahedron Letters 44 (2003) 583–586
Scheme 1.
followed by crystallization (methylene chloride–hexane
system) afforded the cycloadduct 9 in 84% yield ([h]D20
−15.8, c 1.0, CHCl3). The diastereoselection in this type
of Diels–Alder reaction involving cyclic aza dienophiles
was reported by Stoodley to be higher than their
olefinic counterparts and was rationalized by Stoodley
and co-workers6d to arise by an endo attack of the
cyclic dienophile to the less hindered top face of the
solution preferred conformer, as depicted in Fig. 2.
The enantiomeric ratio of the product was determined
by chiral HPLC10 and compared with a racemic mix-
ture prepared without using the sugar auxiliary.
In order to obtain 2, the trans cycloadduct 14 must be
synthesized. For this the cis,trans-diene 13 was synthe-
sized from aldehyde 5 using a procedure reported by
Still.11 The crude diene, containing a trace of the
trans,trans-diene 7, was crystallized (methylene chlo-
ride–ether–hexane system) to obtain diastereomerically
pure diene 13 which underwent cycloaddition with
compound 8 (crude dr 92:8) to afford the trans product
14 (95% yield, [h]2D0 +113.1, c 1.0, CHCl3). Removal of
the sugar auxiliary as described above followed by
hydrogenation of the double bond, hydrolysis of the
methyl ester (0.2N LiOH, THF), coupling with trans-
amine 12 and removal of the Boc group afforded
product 2 with traces of 1 in the ratio 95:5 (90% ee,
[h]2D0 +30.7, c 1.0, CH3OH) (Scheme 2).11
When 9 was treated with triethyl silane and TFA in
methylene chloride overnight it underwent a reductive
cleavage reaction to afford the desired compound 10 in
81% yield ([h]2D0 −200.9, c 1.0, CHCl3). Hydrogenation
of the cycloadduct 10 afforded the acid 11, which was
further purified by crystallization (methylene chloride–
hexane system). The crystallized acid 11 ([h]2D0 −61.5, c
1.0, CH3OH) was then coupled with the trans-
monoBoc protected diamine 12 in the presence of BOP,
HOBt and DIEA followed by purification and removal
of Boc group to give enantiomers 1 and 29 in the ratio
98:2 (96% ee) in 62% yield ([h]2D0 −31.0, c 1.0, CH3OH).
Monte Carlo conformational analysis for the core
bicyclic templates in Mol-376, 1, and 2 was carried out
using MMFF94/GBSA-water12 as implemented in
MacroModel (Version 7.1, Schrodinger, Inc.).13 The
overlay of the energy-minimized structures was based
on X-ray data of MOL-376 bound to thrombin, where
the anchoring of the cyclohexyl amine P1 to Asp-189 in
the thrombin specificity pocket, was preserved. Two
hydrogen-bond formations involved in binding to
thrombin were also taken into account for the overlay
of the templates. Overlay of the lowest energy confor-
mations of MOL-376 with S configuration at C5 posi-
tion and 1 (Fig. 3) shows the differences in the template
conformation and in the positioning of the P3 methyl
group. The P3 substituent differed in the directions by
approximately 15°. While this difference may be small
at the urazole moiety, the distance is significant at the
Figure 2.

J. Mathew et al. / Tetrahedron Letters 44 (2003) 583–586
585
Scheme 2.
far end of the P3 group as it extends along the hydro-
phobic cleft of thrombin. S-Isomer 1 was also com-
pared with an idealized b-strand conformation (in
green) at nine heavy atom positions along with the
,
strand backbone with RMSD value of 0.47 A (Fig. 4).
In contrast, the R-isomer, 2, did not fit very well
with the idealized b-strand conformation, as shown
in Figure 5. From this analysis, we expect that the
bioactive enantiomer of the saturated template is the
S-isomer, 1.
In summary, a facile asymmetric synthesis of both
enantiomers of saturated MOL-376 was accomplished.
The enantiomer 1 was synthesized from diene 7 in five
steps and 30% overall yield while enantiomer 2 from
diene 15 in six steps and 27% overall yield.
Figure 3. Comparison of the lowest energy conformations of
MOL-376 (with P1 and P3 truncated for clarity) in cyan and
saturated b-strand template
1 with S configuration in
magenta. Superposition was carried out at three heavy atom
positions to preserve the hydrogen-bonds and P1 binding to
the thrombin active site (see text). Nitrogens and oxygens are
color coded as blue and red, respectively.
Acknowledgements
The authors thank Tom Little and Minh Nguyen for
technical assistance, Dr Hwa-Ok Kim for support and
Drs Doug Boatman and Mark Blaskovich for stimulat-
ing discussions.
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