Design and synthesis of glycolic and mandelic acid derivatives as factor Xa inhibitors

Article abstract of DOI:10.1016/S0960-894X(01)00447-4

A series of glycolic and mandelic acid derivatives was synthesized and investigated for their factor Xa inhibitory activity. These analogues are highly potent and selective inhibitors against fXa. In a rabbit deep vein thrombosis model, compound 26 showed

Full text of DOI:10.1016/S0960-894X(01)00447-4

Bioorganic & Medicinal ChemistryLetters 11 (2001) 2279–2282
Design and Synthesis of Glycolic and Mandelic Acid Derivatives
as Factor Xa Inhibitorsy
Ting Su,* Yanhong Wu, Brandon Doughan, Kim Kane-Maguire, Charles K. Marlowe,
James P. Kanter, John Woolfrey, Brian Huang, Paul Wong, Uma Sinha, Gary Park,
John Malinowski, Stan Hollenbach, Robert M. Scarborough and Bing-Yan Zhu
COR Therapeutics, Inc., 256 East Grand Avenue, South San Francisco, CA 94080, USA
Received 17 April 2001; accepted 8 June 2001
Abstract—A series of glycolic and mandelic acid derivatives was synthesized and investigated for their factor Xa inhibitory activity.
These analogues are highlypotent and selective inhibitors against fXa. In a rabbit deep vein thrombosis model, compound 26
showed significant antithrombotic effects (81% inhibition of thrombus formation) at 1.1 mM plasma concentration following
intravenous administration. # 2001 Published byElsevier Science Ltd.
Factor Xa, a trypsin-like serine protease, is located at
the convergence point of the intrinsic and extrinsic
pathways in the coagulation cascade. Once assembled in
the prothrombinase complex with factor Va and cal-
cium ions on a phospholipid surface, factor Xa converts
prothrombin to thrombin. Thrombin, in turn, converts
fibrinogen into fibrin, the insoluble matrix of blood
clots. Factor Xa’s central position in coagulation cas-
cade and the fact that thrombin has other important
functions in cellular and neurological processes2 have
made factor Xa an alternative (to thrombin) target for
design, synthesis and in vitro structure–activity rela-
tionships of glycolic and mandelic acid-based mono-
basic noncovalent factor Xa inhibitors will be discussed.
The synthesis of compounds 6–14 is exemplified in
Scheme 1. Treatment of 3-cyanophenol with tert-butyl
bromoacetate and potassium carbonate, followed by
removal of the Boc-protecting group with TFA, BOP
coupling of resulting 2-(3-cyanophenoxy) acetic acid
with methyl 4-aminobenzoate, and hydrolysis of the
methyl ester afforded key intermediate 2. Nitrile 2 was
converted to benzamidine 3 using the hydroxyl amine
3
drug discoveryfor thromboembolic diseases.
Considerable efforts are being focused on synthetic,
low-molecular-weight dibasic fXa inhibitors.3 We pre-
viouslyreported the design and synthesis of various bis-
benzamidine derivatives using hydroxymandelate as a
template (Fig. 1).4 To discover novel inhibitors with
improved bioavailabilityand duration of action, we
focused our synthetic efforts on reducing the overall
basicityand enhancing potencyof this template. During
the course of this investigation, several laboratories
published potent monobenzamidine fXa inhibitors.
Most of these inhibitors consist of one benzamidine
moietyand one neutral group linked byspacers of
appropriate length and orientation.5À8 In this report, the
*Corresponding author. Fax: +1-650-244-9287; e-mail: tsu@corr.com
yFor a preliminaryaccount of this work, see ref 1.
Figure 1. From dibenzamidine 1 to monobasic factor Xa inhibitors
using mandelic acid as a template.
0960-894X/01/$ - see front matter # 2001 Published byElsevier Science Ltd.
PII: S0960-894X(01)00447-4

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T. Su et al. / Bioorg. Med. Chem. Lett. 11 (2001) 2279–2282
addition route. PyBOP coupling of various amines with
carboxylic acid 3 afforded inhibitors 6–14. Compound
17 was synthesized employing similar procedures using
3-hydroxy-4-(phenylmethoxy)benzenecarbonitrile.
In the first series, a varietyof amides of the 2-(3-cyano-
phenoxy) acetic acid were prepared to explore the P4
binding element. Pyrrolidine-containing analogue such
as 7 appeared to be optimal since contracting the ring
(6) decreased fXa inhibitoryactivity3-fold, and enlar-
gement of the ring (8–11) decreased fXa inhibitory
activity17- to 20-fold. The bulkyrings apparentlycan-
not enter the S4 binding site. The placement of a
hydrogen acceptor group O– in the ring (10) does not
influence the affinity. Placement of a tertiary nitrogen
group within the ring (11) is also unfavorable for fXa
inhibition. Introduction of a double bond in pyrrolidine
ring (12) resulted in a 10-fold increase in potency
toward fXa. Addition of a t-butyl ester (14) to the pyr-
rolidine ring reduced potencytoward fXa by44-fold.
More significantly, substitution of pyrrolidine ring with
a carboxylic acid group (13) reduced potencytoward
fXa by >166-fold. This and the observed ring size effect
demonstrate the strict steric requirements in the P4 ele-
ment in this series. In a second series, compounds con-
taining biaryl or heteroaryl amides were prepared based
The synthesis of compounds 23–25 is exemplified in
Scheme 2. Methyl a-bromophenylacetate was treated
with 3-cyanophenol and potassium carbonate to yield 4.
Weinreb9 amidation of ester 4 and substituted or non-
substituted 3,40-amino[1,10-biphenyl]-2-tert-butylsulfon-
10
amide,7 followed byamidine formation
and final
removal of t-butyl group afforded free sulfonamides 23–
25. Compounds 19–22 were synthesized employing
similar procedures using commerciallyavailable biaryl-
aniline. Compound 15 was synthesized using tert-butyl-
bromoacetate. Compound 16 was synthesized using 3-
hydroxy-4-(phenylmethoxy) benzenecarbonitrile and
tert-butylbromoacetate.
The synthesis of pyrrolamide 27 is shown in Scheme 3.
The keyintermediate 5 was prepared bytreating pyrro-
lidine with 4-nitrobenzoyl chloride followed by reduc-
tion of nitro group and bromination of the phenyl ring.
7
on reports byQuan et al., in which biphenylsulfona-
mide moietyof their potent fXa inhibitors were
designed to interact with the S4 aryl-binding domain of
the fXa active site. Incorporation of biphenylsulfona-
mide in our series resulted in 15 with an IC50 of 0.022
mM. Analogues 7 and 15 were chosen for further optimi-
zation due to their good potencyand ease of synthesis.
10
Weinreb amidation, followed bystandard Pinner
conditions gave 27. All mandelic acids derivatives
described above were prepared as racemates.
When preparing 18, several attempts failed when treat-
ing 3-cyanophenol with 3-bromopropionic acid. The
alternative procedure shown in Scheme 4 afforded the
desired product.
Addressing the P1 element, several groups have descri-
bed the potencyenhancing effects of incorporating a
hydroxyl group para to the amidino group on the
phenyl ring.6 Introduction of a hydroxyl group in our
two most potent compounds 7 and 15 increased potency
by10-fold in 16 and 94-fold in 17. Homologation of 15
The enzyme inhibition constants of compounds 6–27
toward fXa and the structurallyrelated serine proteases
thrombin and trypsin are summarized in Tables 1–2.11,12
Scheme 3. Synthesis of 27: (a) pyrrolidine, Et3N, DCM; (b) H2,
10%Pd/C; (c) pyridinium tribromide, AcOH; (d) 4, AlMe3, DCM, (e)
HCl, MeOH; (f) NH4OAc, MeOH.
Scheme 1. Synthesis of compounds 6–14. (a) BrCH2CO2tBu, K2CO3;
(b) TFA; (c) methyl 4-aminobenzoate, BOP, DIEA, DMF, rt.; (d) aq
.
LiOH; (e) NH2OH HCl, TEA; (f) AcOH, Ac2O; (g) 10% Pd/C, H2; (h)
amine, PyBOP, DIEA, DMF.
Scheme 2. Synthesis of compound 23: (a) 3-cyanophenol, K2CO3,
CH3CN, reflux; (b) 3,40-amino[1,10-biphenyl]-2-tert-butylsulfonamide,
AlMe3, DCM; (c) H2S, TEA/Pry; (d), MeI, acetone, reflux; (e)
NH4OAc, MeOH, reflux; (f) neat TFA, rt.
Scheme 4. Synthesis of 18: (a) 3-cyanophenol, Cs2CO3, DMF; (b)
PDC, DMF; (c) 3,40-amino[1,10-biphenyl]-2-tert-butylsulfonamide,
AlMe3, DCM; AlMe3, DCM, (d) HCl, MeOH; (e) NH4OAc, MeOH;
(f) TFA.

T. Su et al. / Bioorg. Med. Chem. Lett. 11 (2001) 2279–2282
2281
at the central unit also afforded a 3-fold more potent
analogue 18. SAR studies with various side-chain sub-
stitution groups in our amino acid-based mono-
benzamidine fXa inhibitors13 demonstrated that a
phenyl group is optimal for the inhibitory activity. A
36-fold increase in potencyoccurred when the glycolic
acid central unit of 15 was replaced with mandelic acid
unit in 23. More significantly, 366-fold increase in
potencywas achieved in 26 when a phenyl group was
incorporated into 7. Further optimization at P4 did not
improve the activityin analogues 19–22. Interestingly,
halogen substitution at the R3 position of the proximal
phenyl ring (see Fig. 1), which increased the activity in
other series, reduced potencyin our series (analogues
24, 25, and 27).
As shown in Tables 1 and 2, all compounds displayed
good selectivityfor fXa over thrombin and trpysin.
High selectivityagainst a panel of serine proteases
including tissue plasminogen activator (tPA), activated
protein C (APC) and plasmin, was also observed for
these compounds (data not shown). For example, com-
pound 23 has IC50 values of 0.55 nM for Xa, 21.2 mM
for tPA, 181 mM for APC and 83.4 mM for plasmin. 26
has IC50 values of 0.18 nM for Xa, >11 mM for tPA,
>11 mM for APC and >11 mM for plasmin. In a rabbit
deep vein thrombosis model,11 compound 23 showed
significant antithrombotic effects (56% inhibition of
thrombus formation) at 0.132 mM plasma concentration
following intravenous administration. Compound 26
also showed significant antithrombotic effects (81%
inhibition of thrombosis formation) at 1.1 mM plasma
Table 1. In vitro activityfor compounds 6–18
Compd
R4
n
R1
IC50 (mM)
fXa
Thromb
Tryp
2.05
Table 2. In vitro activityfor compounds 19–27
6
7
1
1
H
H
0.227
>10
>10
0.066
1.37
1.19
1.12
2.7
8
1
1
1
1
1
1
H
H
H
H
H
H
>10
>10
>10
>10
>10
>10
>10
Compd
R
IC50 (mM)
fXa
Thromb
Tryp
9
>10
>10
>10
19
20
21
22
23
0.093
0.014
0.17
4.09
>10
8.78
5.33
10
11
12
13
>10
>10
>10
0.0063
0.875
0.0044
0.00055
>10
>10
>10
>10
>10
1.25
14
1
H
2.93
>10
6.64
24
0.013
>10
9.82
15
16
17
18
1
1
1
2
H
OH
OH
H
0.021
>10
>10
>10
>10
3.37
2.29
0.283
2.57
0.0022
0.0007
0.0064
25
26
27
0.0032
8.64
>10
4
0.00018
0.00099
0.174
0.521
>10

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T. Su et al. / Bioorg. Med. Chem. Lett. 11 (2001) 2279–2282
concentration following intravenous administration.
The anticoagulant activityof compounds 23 and 26 is
also demonstrated bythe results of the plasma coagu-
lation assays since they doubled the activated partial
thromboplastin time (aPTT) at 1.03 and 1.6 mM,
respectively.
4. Wu, Y.; Yang, W.; Doughan, B.; Tran, K.; Sinha, U.;
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National Meeting of the American Chemical Society, San
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The pharmacokinetic properties of analogues 23 and 26
were evaluated in Sprague–Dawleyrats. The oral bio-
availabilityof 23 and 26 were found to be less than 5%.
Although we were not successful in identifying oral fXa
inhibitors with high bioavailabilitywithin this series of
compounds, the glycolic and especially the mandelic
acid templates have afforded potent and selective fXa
inhibitors. Further SAR studies on improving pharma-
cokinetic properties of these inhibitors will be the subject
of additional communications from our laboratories.
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