Benzothiazole benzimidazole (S)-isothiazolidinone derivatives as protein tyrosine phosphatase-1B inhibitors

Article abstract of DOI:10.1016/j.bmcl.2006.10.079

Benzothiazole benzimidazole (S)-isothiazolidinone ((S)-IZD) derivatives 5 were discovered through a peptidomimetic modification of the tripeptide (S)-IZD protein tyrosine phosphatase 1B (PTP1B) inhibitor 1. These derivatives are potent, competitive, and r

Full text of DOI:10.1016/j.bmcl.2006.10.079

Bioorganic & Medicinal Chemistry Letters 17 (2007) 736–740
Benzothiazole benzimidazole (S)-isothiazolidinone derivatives as
protein tyrosine phosphatase-1B inhibitors
Richard B. Sparks,a,* Padmaja Polam,a Wenyu Zhu,a Matthew L. Crawley,a
Amy Takvorian,a Erin McLaughlin,a Min Wei,b Paul J. Ala,b Lucie Gonneville,b
Nancy Taylor,c Yanlong Li,b Richard Wynn,b Timothy C. Burn,b Phillip C. C. Liub
and Andrew P. Combsa
aIncyte Corporation, Discovery Chemistry, Experimental Station, Route 141 and Henry Clay Road, Wilmington, DE 19880, USA
bApplied Technology, Experimental Station, Route 141 and Henry Clay Road, Wilmington, DE 19880, USA
cDrug Metabolism, Experimental Station, Route 141 and Henry Clay Road, Wilmington, DE 19880, USA
Received 29 September 2006; revised 25 October 2006; accepted 25 October 2006
Available online 28 October 2006
Abstract—Benzothiazole benzimidazole (S)-isothiazolidinone ((S)-IZD) derivatives 5 were discovered through a peptidomimetic
modification of the tripeptide (S)-IZD protein tyrosine phosphatase 1B (PTP1B) inhibitor 1. These derivatives are potent, compet-
itive, and reversible inhibitors of PTP1B with improved caco-2 permeability. An X-ray co-crystal structure of inhibitor 5/PTP1B at
˚
2.2 A resolution demonstrated that the benzothiazole benzimidazole forms bi-dentate H-bonds to Asp48, and the benzothiazole
interacts with the surface of the protein in a solvent exposed region towards the C-site. The design, synthesis, and SAR of this novel
series of benzothiazole benzimidazole containing (S)-IZD inhibitors of PTP1B are presented herein.
ꢀ 2006 Elsevier Ltd. All rights reserved.
Many cellular processes are controlled through phos-
phorylation and dephosphorylation of intracellular pro-
teins by protein tyrosine phosphatases (PTPs) and
protein tyrosine kinases (PTKs). Many disease states,
including diabetes, cancer, and rheumatoid arthritis,
are associated with the aberrant regulation of these sig-
naling transduction pathways.1 While the success of
PTK inhibitors is well documented, the discovery of
drug candidates for PTP drug targets remains elusive.
We recently reported a peptidomimetic strategy that
resulted in the replacement of the two N-terminal
amides with an aryl sulfonamide to afford potent benz-
imidazole sulfonamide PTP1B inhibitors.3 The ortho-
substituted derivatives, such as 2, exhibited the first
reported cellular activity (pIR) for this new class of
PTP1B inhibitors bearing the heterocyclic (S)-IZD pTyr
mimetic.
Consistent with the modest cellular activity and high po-
lar surface area (PSA = 138) was the measured low cell
permeability for this benzimidazole sulfonamide series
of compounds (caco-2 Pm 0.1–0.4 · 10À6 cm/s). We sur-
mised that further reduction in the PSA would be neces-
sary for obtaining the requisite membrane permeability
to drive cellular potency (Table 1). Analysis of the sub-
stituent contributions to the PSA of the benzimidazole
sulfonamides led us to search for replacement of the
highly polarizable sulfonamide functionality. Synthesis
of a variety of functional groups appended to the pri-
mary amine of 6 identified the benzothiazole compound
5, as a lead. Compound 5 contains the (S)-IZD as deter-
mined by X-ray crystallography studies. Consistent with
our previous report,3 compound 5 is the only active
Recently, we described the discovery of potent, compet-
itive, and reversible PTP1B peptide and non-peptide
inhibitors containing the novel heterocyclic (S)-isot-
hiazolidinone ((S)-IZD) pTyr mimetic.2 We report here-
in the design and synthesis of a less polar benzothiazole
benzimidazole scaffold containing the (S)-IZD heterocy-
clic pTyr mimetic which demonstrates improved caco-2
permeability.
Keywords: Protein tyrosine phosphatase 1B; Phosphotyrosine mimet-
ics; Phosphatase inhibitors; Isothiazolidinone heterocycle; Benzothiaz-
ole benzimidazole.
*
Corresponding author. Tel.: +1 610 547 1946; fax +1 302 425 2750;
e-mail: rsparks@incyte.com
0960-894X/$ - see front matter ꢀ 2006 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2006.10.079

R. B. Sparks et al. / Bioorg. Med. Chem. Lett. 17 (2007) 736–740
Table 1. Selected IZD inhibitors of PTP1B
737
HN
H
N
N
R
X
O
S
O
NH
O
Compound
R
IZD
X
H
PTP1Ba IC50 (nM)
35
pIRc (at 80 lM)
Caco-2b Pm (·10À6 cm/s)
PSA
Ph
O
1
S
Inactive
<0.1
150
O
N
H
2
3
4
5
S
Me
H
35
2.8 0.8
Inactive
Inactive
Inactive
0.4
1.3
NT
0.7
138
116
116
116
S
O
O
S
S
S
R/S
R
480
N
H
>10,000
270
N
N
S
H
a pNPP enzyme assay.
b NT, not tested.
c Fold shift versus DMSO.
isomer. This non-peptidic small molecule is a moderate-
ly potent (PTP1B IC50 = 270 nM), competitive, and
reversible inhibitor with significantly lower PSA (116).
Most notably, the reduced PSA of this derivative corre-
lated with an observed increase in cell penetration as
measured by a caco-2 assay (Pm = 0.7 · 10À6 cm/s).
Optimization of 5 by further elaboration of the benzo-
thiazole scaffold was thus warranted (Scheme 1).
Benzothiazoles containing the (S)-IZD heterocyclic
pTyr mimetic were synthesized starting from the
previously reported benzimidazole amine 6 in a two-step
process (Supporting Information). Thiourea 7 was ini-
tially formed by reacting 6 with phenylisothiocyanate.
Cyclization of 7 to give benzothiazole 8 was achieved
via bromination of the thiourea sulfur and subsequent
electrophilic addition to the ortho position of the
phenyl ring.4 Removal of the tert-butyl protecting group
on the (S)-IZD via microwave irradiation at 130 ꢁC for
1 min afforded the desired benzothiazole benzimidazole
products in high yields.
R1
R1
HN
HN
H
N
S
H2N
N
N
Synthesis of the ortho-methyl benzothiazole benzimid-
azole 32 proceeded in a similar manner from the litera-
ture bis-sem-protected intermediate 33 (Scheme 2).3 The
ortho-fluoro derivative 28 was synthesized using the
known unprotected (S)-IZD heterocycle as shown in
Scheme 3.
b
N
X
a
X
H
R2
O
O
O
S
N
S
O
N
O
O
6
7
R1
R1
Me3Si
HN
HN
R1
O
H
H
N
R1
N
S
S
N
N
HN
H
N
c
N
N
X
S
N
X
N
H2N
a, b, c
N
R2
N
Me
R2
Me
O
O
S
S
O
O
N
NH
O
O
O
O
8
O
5
S
O
NH
S
32
1 = H
33
O
N
R1, R2, X = H
O
R
O
SiMe3
Scheme 1. Synthesis of benzothiazole benzimidazole (S)-IZD inhibi-
tors. Reagents and conditions: (a) PhNCS, TEA, DCM, rt, 1 h, 57%;
chiral separation of (R/S)-IZD diastereomers was performed on a
chiral OD column; (b) benzyltrimethylammonium tribromide, HOAc,
15 min, rt, 88%; (c) TFA, 130 ꢁC, lW, 1 min, 70%.
Scheme 2. Synthesis of ortho-methyl benzothiazole benzimidazole IZD
inhibitors. Reagents and conditions: (a) PhNCS, TEA, DCM, rt, 1.5 h,
72%; (b) benzyltrimethylammonium tribromide, HOAc, 1 h, rt; (c)
TFA, 130 ꢁC, lW, 2 min, 45% (2 steps).

738
R. B. Sparks et al. / Bioorg. Med. Chem. Lett. 17 (2007) 736–740
R1
A variety of substitutions at the 4-, 5-, and 6-positions of
R1
HN
HN
the benzothiazole were synthesized and tested in the
PTP1B enzyme assay. The SAR revealed only minor
substitution effects on enzyme potency (Table 2). An
X-ray co-crystal structure of benzothiazole benzimid-
H
N
H2N
S
N
N
a,b
N
F
F
O
O
˚
azole 5/PTP1B solved to 2.2 A resolution (PDB deposi-
O
S
NH
28
R1 = H
O
S
O
34
NH
O
tion number 2CNF) confirmed the presence of the bi-
dentate H-bonding mode with Asp48 and the position
of the benzimidazole in the, so-called E-site of PTP1B
(Fig. 1). The benzothiazole binds toward the C-site
above Tyr46. The nitrogen lone pair of the benzothiaz-
ole forms a hydrogen bond to a water molecule, but is
otherwise solvent exposed on the surface of the enzyme.
Scheme 3. Synthesis of ortho-fluoro benzothiazole benzimidazole IZD
inhibitors. Reagents and conditions: (a) PhNCS, TEA, DCM, rt, 1 h,
70%; (b) benzyltrimethylammonium tribromide, HOAc, 1.5 h, rt, 62%.
Synthesis of the ortho-bromo derivatives 30 and ortho-
chloro derivatives 29 required the development of a
new synthetic route as shown in Scheme 4. Previously,
we reported a novel chemoselective and regioselective
Heck reaction that was used on the methylester of 37
to access the ortho-halogenated IZD intermediate 41.
In our new strategy, the Heck coupling is performed lat-
er in the synthesis with the bis-Boc-protected benzimid-
azole 39 to afford the requisite aminobenzimidazole
after deprotection.
Caco-2 permeability was significantly enhanced for this
series of non-peptidic benzothiazole benzimidazole
IZD inhibitors. The most permeable compounds were
the fluoro substituted benzothiazoles (12, 13, and 14)
with caco-2 Pm values of 0.9, 1.3, and 1.7 · 10À6 cm/s,
respectively.
A representative set of substituted benzimidazoles is
shown in Table 3. Again, only small changes in the en-
zyme potency were achieved. This SAR is consistent
with the binding mode observed in the X-ray structure
in which the benzimidazole binds in the solvent exposed
E-site. Indeed, similar SAR was observed for the benz-
imidazole sulfonamide series 3 where the benzimidazole
was shown to bind in an identical conformation3
(Table 4).
The synthesis of the ortho-chloro derivative 29 was per-
formed in an analogous fashion, in similar yields, using
NCS in the halogenation step (c). The ortho-cyano
derivative 31 was obtained through Negishi coupling
to the ortho-bromo derivative 30.
BocHN
CO2H
BocHN
CO2Bn
BocHN
c, d, e
CO2 H
a, b
NO2
Br
I
NH2
36
35
37
Table 2. Benzothiazole SAR of IZD inhibitors of PTP1B
R1
HN
H
BocN
i,j, k
f, g, h
N
S
BocHN
7
N
N
O
N
6
H2N
H2N
X
R1
5
R2 4
N
S
O
40
I
O
O
39
38
O
S
NH
O
R1
R1
HN
Compound
R2
H
PTP1Ba IC50
Caco-2b Pm
HN
H
N
(lM)
(·10À6 cm/s)
H2N
N
S
N
l, m, n
X
N
X
3
9
0.48
0.33
1.3
0.1
NT
0.1
0.9
1.3
1.7
0.8
0.8
NT
0.5
1.0
0.4
NT
0.2
1.3
NT
6-CF3
5-CF3
4-CF3
6-F
O
O
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
1.30
0.74
O
S
O
N
S
O
NH
41
O
0.49
29 X = Cl, R1 = H
30 X = Br, R1 = H
5-F
4-F
0.42 (0.34)c
0.66
0.44
o
31 X = CN, R1 = H
6-Cl
5-Cl
0.97
2.40
Scheme 4. Synthesis of ortho-bromo benzothiazole benzimidazole IZD
inhibitors. Reagents and conditions: (a) BnBr, DBU, THF, 60 ꢁC, 2 h,
80%; (b) Zn0, NH4Cl, MeOH, H2O, 78%; (c) NBS, DMF, rt, 30 min,
51%; (d) NaNO2, 1 N aq. HCl, KI, 44%; (e) NaOH, H2O, CH3CN, rt,
2 h; (f) BOPCl, i-Pr2NEt, 38, DMF, rt, 2 h, 98% (2 steps); (g) AcOH,
40 ꢁC, 2 h; (h) Boc2O, NaOH, H20, THF, 35 ꢁC, 2 h, 68% (2 steps); (i)
Pd(OAc)2, Bu4NCl, 40, Et3N, DMF, 70 ꢁC, 2.5 h, 34%; (j)
L-Selectride, THF, À78 ꢁC, 10 min, 78%; (k) TFA, DCM, 1:4, rt,
1 h, 58%; (l) PhNCS, TEA, DCM, rt, 1 h; (m) benzyltrimethylammo-
nium tribromide, HOAc, 16 h, rt; (n) TFA, 130 ꢁC, lW, 1 min, 36% (3
steps); (o) tetrakis(triphenylphosphine)Pdꢁ, Zn(CN)2, DMF, 175 ꢁC,
lW, 4 min.
4-Cl
6-OMe
4-OMe
6-CN
5-CN
6-Br
0.35
0.55
0.47
1.10
0.50
0.62
5-Br
4-Br
1.10
a pNPP enzyme assay.
b NT, not tested.
c The pNPP data for the separated single diastereomer.

R. B. Sparks et al. / Bioorg. Med. Chem. Lett. 17 (2007) 736–740
739
We reported earlier3 that the benzimidazole sulfon-
amide series afforded cellular active PTP1B inhibitors
only when they were substituted ortho to the (S)-IZD
heterocyclic pTyr mimetic on the aryl ring. A series
of ortho substituted benzothiazole derivatives were
therefore synthesized and assayed in the PTP1B en-
zyme and pIR cellular assays. The ortho-fluoro deriv-
ative 28 and the ortho-chloro derivative 29 were the
most potent of the benzothiazole benzimidazole
inhibitors, but gave modest increases in enzyme
potency (2-fold) as compared to the unsubstituted
parent. Unfortunately, unlike the benzimidazole sul-
fonamide series, no improvements in the caco-2 per-
meability or pIR cellular activity were observed.
This is believed to be due to the modest potencies
of these derivatives.
In summary, optimization of the tripeptidic (S)-IZD
protein tyrosine phosphatase 1B (PTP1B) inhibitors
1 led to the discovery of novel non-peptidic benzo-
thiazole benzimidazoles 5 with reduced PSA. These
derivatives are potent, competitive, and reversible
inhibitors of PTP1B. A co-crystal structure revealed
that the benzothiazole binds in the solvent exposed
C-site while the benzimidazole binds in the E-site.
As a result of the solvent exposed nature of the
E- and C-sites, substitution of the benzothiazole and
benzimidazole gave only modest improvement in
potency for this new series. Caco-2 permeability was
significantly enhanced for this series of non-peptidic
benzothiazole benzimidazole IZD inhibitors presum-
ably due to the lower PSA. Although no activity
was observed in our cellular pIR assay these results
demonstrate that non-peptidic compounds bearing
the (S)-IZD pTyr mimetic with low PSAs can have
improved caco-2 permeabilities.
Figure 1. Co-crystal structure of 5/PTP1B showing the (S)-IZD
heterocycle in the active site, the bi-dentate hydrogen bonding to
Asp-48, the benzimidazole in the E-site, and the benzothiazole in the
C-site. PDB deposition number 2CNF.
Table 3. Benzimidazole SAR of IZD inhibitors of PTP1B
Compound
R1
PTP1Ba IC50
Caco-2 Pm
(·10À6 cm/s)
(lM)
3
25
26
27
H
0.48
0.15
0.41
0.47
1.3
0.4
0.8
0.4
5-CF3
5-Cl
5-CN
Supplementary data
a pNPP enzyme assay.
Supplementary data associated with this article can be
found, in the online version, at doi:10.1016/
j.bmcl.2006.10.079.
Table 4. IZD inhibitors of PTP1B
HN
H
References and notes
N
S
N
N
X
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O
O
S
NH
O
Compound
X
PTP1Ba
pIRc
Caco-2 Pmb PSA
IC50 (lM) (at 80 lM) (·10À6 cm/s)
3
H
F
0.48
0.23
Inactive
Inactive
Inactive
Inactive
Inactive
Inactive
1.3
0.8
0.7
NT
0.5
0.5
116
116
116
116
140
116
28
29
30
31
32
Cl 0.28
Br 1.60
CN 0.40
Me 0.46
a pNPP enzyme assay.
b NT, not tested.
c Fold shift versus DMSO.

740
R. B. Sparks et al. / Bioorg. Med. Chem. Lett. 17 (2007) 736–740
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