Identification of Thiazolidinones Spiro-Fused to IndoIin-2-ones as Potent and Selective Inhibitors of the Mycobacterium tuberculosis Protein Tyrosine Phosphatase B

Article abstract of DOI:10.1002/anie.201002138

(Figure Presented) The best of 40000: Detailed structureactivity- relationship studies revealed key structural elements of indolin-2-on-3- spirothiazolidinones (see example) and their appropriate configuration for strong inhibitory activity against the pa

Full text of DOI:10.1002/anie.201002138

Communications
DOI: 10.1002/anie.201002138
Enzyme Inhibitors
Identification of Thiazolidinones Spiro-Fused to Indolin-2-ones as
Potent and Selective Inhibitors of the Mycobacterium tuberculosis
Protein Tyrosine Phosphatase B**
Viktor V. Vintonyak, Karin Warburg, Holger Kruse, Stefan Grimme, Katja Hꢀbel, Daniel Rauh,
and Herbert Waldmann*
Mycobacterium tuberculosis protein tyrosine phosphatases A
(MptpA) and B (MptpB) mediate pathogen survival in
macrophages by the dephosphorylation of host proteins that
are involved in key pathways of the immune system.[1–3] Since
MptpB has no direct human orthologues, inhibitors active
against MptpB offer unique opportunities for the develop-
ment of new therapeutic approaches for the treatment of
tuberculosis.[3–5]
As the enzyme is secreted into the host cell by growing
mycobacteria, inhibitors would not have to pass the bacterial
cell wall. This aspect is particularly relevant, since phospha-
tase inhibitors typically contain polar acidic groups that may
be ionized at physiological pH values and can be expected to
display poor cell permeability and low oral bioavailability.
Scheme 1. Structures and IC50 values of the primary hits identified by
the screening of a compound library for the inhibition of MptpB;
positions suitable for structural modification are highlighted.
New inhibitor classes with good selectivity profiles and
improved pharmacological properties are therefore in high
demand. Herein we report the identification of indolin-2-on-
3-spirothiazolidinones as a new class of potent and selective
inhibitors of MptpB. To identify novel MptpB-inhibitor
classes, we screened a library of more than 40000 compounds
in a 384-well format with p-nitrophenyl phosphate (pNPP) as
the substrate.[5a] We identified compounds 1–3 as primary hits
with IC50 values in the mid-micromolar range (Scheme 1).
The identified inhibitors contain a 2-oxindole moiety,
which is found in a large number of natural products with a
broad spectrum of biological activity.[6] They might therefore
be biologically prevalidated starting points for further com-
pound development.[7,8] To the best of our knowledge,
spirooxindoles, such as 1–3, have not been reported as
phosphatase inhibitors before. To develop potent, selective
inhibitors and to delineate a structure–activity relationship
(SAR) for the newly identified inhibitor scaffold, we modified
the structure of the phenyl substituent on the thiazolidinone
moiety and the N-alkyl substituent on the 2-indolinone
moiety (Scheme 1).
The synthesis of indolin-2-on-3-spirothiazolidinones
(Scheme 2) commenced with the alkylation of 1H-indole-
2,3-diones 4 with different benzyl bromides. Condensation of
the products 5 or 4 itself with various anilines resulted in the
formation of isatin-3-imines, which underwent efficient cyc-
lization in the presence of mercaptoacetic acid to spirothia-
zolidinones 6. The obtained sulfides 6 were readily oxidized
with meta-chloroperbenzoic acid (mCPBA) to give a focused
library of 200 indolin-2-on-3-spirothiazolidinones 7 in greater
than 95% purity (as determined by HPLC). Further struc-
tural modifications (to produce compounds 8–12) were
carried out as depicted in Scheme 2 (see the Supporting
Information for details).
[*] Dr. V. V. Vintonyak, Dr. K. Warburg, Dr. K. Hꢀbel,
Prof. Dr. H. Waldmann
Abteilung Chemische Biologie
Max-Planck-Institut fꢀr molekulare Physiologie
Otto-Hahn-Strasse 11, 44227 Dortmund (Germany)
Fax: (+49)231-133-2499
E-mail: herbert.waldmann@mpi-dortmund.mpg.de
Dr. K. Warburg, Prof. Dr. H. Waldmann
Fachbereich Chemische Biologie, Fakultꢁt Chemie
Technische Universitꢁt Dortmund
Otto-Hahn-Strasse 6, 44227 Dortmund (Germany)
Dr. D. Rauh
Chemical Genomics Centre der Max-Planck-Gesellschaft, Dort-
mund (Germany)
Dipl.-Chem. H. Kruse, Prof. Dr. S. Grimme
Organisch-Chemisches Institut, Westfꢁlische Wilhelms-Universitꢁt
Mꢀnster (Germany)
Investigation of the MptpB-inhibiting activity of this
family of compounds revealed a crucial role of the dihalo-
genated anilide fragment (Table 1). Compounds containing
two fluorine atoms or a fluorine and a chlorine atom in meta
and para positions of the anilide fragment (compounds 7a–
7k) were preferred over analogues bearing mono- (com-
pound 7p) or dialkyl substituents (compound 7q). The
introduction of a nitro group in the 5-position of the 2-
[**] This research was supported by the Max-Planck-Gesellschaft, the
Fonds der Chemischen Industrie, and the German Federal Ministry
for Education (Grant No. BMBF 01GS08102). We thank Dr.
Matthias Baumann, Lead Discovery Center GmbH, for physico-
chemical studies.
Supporting information for this article is available on the WWW
under http://dx.doi.org/10.1002/anie.201002138.
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Table 1: IC50 values for the inhibition of MptpB by indolin-2-on-3-
spirothiazolidinones.[a]
Compound
R1
R2
R3
IC50 [mm]
1
7a
7b
7c
7d
7e
7f
7g
7h
7i
7j
7k
7l
7m
7n
7o
7p
7q
7r
H
NO2
NO2
NO2
NO2
NO2
NO2
NO2
NO2
NO2
NO2
NO2
SO2NH2
CO2Me
OCF3
OMe
NO2
NO2
NO2
NO2
NO2
NO2
NH2
NHCO2Me
3-F
4-Br
3-F
3,4-di-F
3,4-di-F
3,4-di-F
3,4-di-F
3,4-di-F
3-Cl-4-F
3-Cl-4-F
3,4-di-F
3,4-di-F
3-Cl-4-F
3,4-di-F
3-Cl-4-F
3,4-di-F
3,4-di-F
3,4-di-F
3,4-di-F
4-Me
3,4-di-Me
3,4-di-F
3,4-di-F
3,4-di-F
3,4-di-F
3,4-di-F
3,4-di-F
20Æ2.5
1.1Æ0.3
1.2Æ0.2
1.8Æ0.4
2.1Æ0.6
2.7Æ0.4
2.7Æ0.7
3.1Æ0.4
3.2Æ0.5
3.3Æ0.3
3.6Æ0.8
3.9Æ0.8
16.4Æ1.9
18.1Æ2.1
22.3Æ2.4
27.2Æ2.2
18.4Æ2.1
n.a.[b]
4-Cl
3-Cl
3-Cl
4-Cl
4-CN
3-CF3
3,4-di-F
4-F
3-CF3
4-F
4-F
4-F
4-F
4-F
4-F
4-OH
4-OMe
–
3-F
3-F
3-F
8.2Æ1.9
22.1Æ2.1
n.a.[b]
9.6Æ1.4
31.4Æ2.5
34.7Æ2.8
7s
7t
8[c]
9
10a
[a] All IC50 values were determined with p-nitrophenyl phosphate (pNPP)
as the substrate; the release of p-nitrophenol was observed at 405 nm.
Data were derived from at least three independent measurements.
[b] n.a.=not active (no inhibition up to a concentration of 100 mm).
[c] Bisthioamide derivative.
Scheme 2. Synthesis of indolin-2-on-3-spirothiazolidinones: a) NaH,
DMF, 08C, then ArCH2Br, 6 h, 80–95%; b) 1) Ar’NH2, EtOH, reflux,
6 h; 2) mercaptoacetic acid, toluene, reflux, 16 h, 45–82%; c) mCPBA
(5 equiv), CHCl3, room temperature, 48 h, 78–92%; d) Lawesson
reagent, toluene, reflux, 2 h, 75%; e) HCO2NH4, Pd/C, EtOH, reflux,
3 h, 79%; f) RCOCl, pyridine, room temperature, 12 h, 89–92%;
g) 1) 3,4-difluoroaniline, EtOH, reflux, 6 h; 2) mercaptosuccinic acid,
toluene, reflux, 16 h, 69–77%; h) Oxone (5 equiv), MeOH/H2O (1:1),
room temperature, 24 h, 65–74%. DMF=N,N-dimethylformamide.
either lacked a substituent (in 7t) or contained alkyl
substituents at the 2-oxindole nitrogen atom were inactive
(see the Supporting Information). The moderate activity of
bisthioamide 8 highlights the importance of the carbonyl
groups in 7b. These groups may serve as hydrogen-bond
acceptors when the inhibitor is bound to the target phospha-
tase. Physicochemical studies, including parallel artificial
membrane permeability assays (PAMPA),[9] revealed that
the spirothiazolidinones 7 already displayed very appreciable
solubility. The additional introduction of a carboxylic acid
group (see 12, Scheme 2) led to a further significant increase
in compound solubility and very promising cell permeability,
whereby the high inhibitory activity was retained (Table 2).
All indolin-2-on-3-spirothiazolidinones discussed above
were initially synthesized and assayed as racemates. To shed
light on the relevance of the configuration of the spiro center
for inhibitory activity against MptpB, we separated the 10
most potent sulfones into their pure enantiomers by prepa-
rative HPLC on a chiral phase (see the Supporting Informa-
tion for details) and determined their individual IC50 values
(Table 3). In all cases, the (À) enantiomer (F2) was 7–20 times
as potent as the corresponding (+) enantiomer (F1). Notably,
the most active compounds displayed IC50 values in the
nanomolar range (Table 3).
oxindole core (in 7b) significantly enhanced potency (17-fold)
against MptpB over that of our primary hit 1. Replacement of
the nitro group with a sulfonamide (in 7l), methyl ester (in
7m), trifluoromethoxy (in 7n), or methoxy group (in 7o) led
to loss of inhibitory activity. In the same way, analogues with
amine (in 9) or carbamate groups (in 10a) were essentially
inactive.
To investigate the role of the substituted N-benzyl frag-
ment for activity against MptpB, we synthesized 13 analogues
of 7b with different substituents on the phenyl ring. Replace-
ment of the fluorine substituent with chlorine (in 7d) or a
trifluoromethyl group (in 7h), or relocation of the fluorine
substituent to the para position of the phenyl ring (in 7j) did
not improve potency in comparison to that of 7b. Replace-
ment of the para fluorine substituent with a cyano group (in
7g) was well-tolerated, whereas the introduction of a para
hydroxy (in 7r) or methoxy groups (in 7s) resulted in a 6- to
18-fold decrease in activity. Furthermore, compounds that
For determination of the absolute configuration of the
spiro center, various crystallization procedures were explored
but failed to deliver crystals suitable for X-ray diffraction
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Table 2: IC50 values, solubility, and cell permeability of indolin-2-on-3-
spirothiazolidinones 7 and 12.[a]
R2
IC50 [mm] Sol.
[mm][b]
R2
IC50 [mm] Sol.
[mm][b]
flux
[%][c]
7a 4-Br 1.1Æ0.3 250
7c 4-Cl 1.8Æ0.6 225
7d 3-Cl 2.1Æ0.6 240
12a 4-Br 2.6Æ0.2 376
12b 4-Cl 2.9Æ0.4 412
12c 3-Cl 2.3Æ0.2 425
20
20
22
21
7h 3-
CF3
7j 4-F 3.6Æ0.8 205
3.2Æ0.4 139
12d 3-
CF3
12e 4-F 4.8Æ0.6 430
2.4Æ0.3 421
13
[a] All IC50 values were determined from at least three independent
measurements. [b] Kinetic solubility, as determined by a direct UV
assay.[10] [c] Cell permeability, as determined by a parallel artificial
membrane permeability assay (PAMPA). Flux [%] denotes concentration
(test well)/concentration (control well)ꢂ100.
Figure 1. Comparison of the theoretical CD spectra of a model
compound (COSMO-PBE0/TZVP’ structure shown) with the CD spec-
trum of (À)-7e. The theoretical spectra were obtained with B2PLYP
and PBE0 by using the def2-TZVPP basis set. Bars indicate the
positions and rotational strengths of electronic transitions calculated
with B2PLYP. Dots mark transitions with small rotational strengths.
Table 3: IC50 values of enantiomerically pure compounds 7a–k for the
inhibition of MptpB.[a]
IC50 [mm]
IC50 [mm]
F1 (+)[b]
F2 (À)[b]
F1 (+)[b]
F2 (À)[b]
7a
7b
7d
7e
7 f
2.9Æ0.5
3.9Æ0.6
9.6Æ1.4
8.9Æ0.8
9.5Æ0.5
0.28Æ0.06
0.32Æ0.05
0.94Æ0.12
0.51Æ0.08
1.24Æ0.15
7g
7h
7i
7j
7k
8.8Æ0.6
7.9Æ0.4
11Æ1.2
5.8Æ1.1
9.1Æ0.4
1.3Æ0.1
0.38Æ0.06
1.3Æ0.2
of six different phosphatases, including the mycobacterial
phosphatase MptpA and the mammalian phosphatases
PTP1B, SHP-2, PTPN2, h-PTPb, and VHR (see the Support-
ing Information for details), which are involved in a variety of
important biological processes in mammalian cells and the
establishment of different diseases.[4] All tested compounds
showed excellent selectivity in favor of MptpB; the other
phosphatases were not inhibited significantly by the com-
pounds at a concentration of 50 mm.
0.52Æ0.08
1.4Æ0.2
[a] All IC50 values were determined from at least three independent
measurements. [b] F1 (+) and F2 (À) were assigned the S and R
configuration, respectively.
experiments. We therefore decided to use circular dichroism
(CD) spectroscopy in combination with time-dependent
density functional theory (TDDFT) calculations to assign
absolute configuration.[11] The combination of experimental
CD investigations with quantum-chemical CD calculations
has proven to be an efficient and reliable method for the
assignment of the absolute configuration of various chiral
organic molecules.[12] The CD spectra of both enantiomers of
7e were recorded in acetonitrile and compared with spectra
obtained from quantum-chemical calculations at the TD-
B2PLYP and TD-PBE0 levels for a model compound in which
two of the phenyl rings were replaced with methyl groups to
reduce conformational complexity and computing time (see
the Supporting Information for details).[13] The almost
quantitative agreement between the experimental and simu-
lated spectra revealed that (À)-7e (F2) has the R configura-
tion (Figure 1).
In conclusion, indolin-2-on-3-spirothiazolidinones were
identified as a novel class of potent and selective substrate-
competitive inhibitors of MptpB and could serve as promising
starting points for the development of antibiotics directed
against Mycobacterium tuberculosis.
Received: April 12, 2010
Published online: July 14, 2010
Keywords: chemical biology · circular dichroism ·
.
enzyme inhibitors · phosphatases · tuberculosis
[1] A. Koul, T. Herget, B. Klebl, A. Ullrich, Nat. Rev. Microbiol.
2004, 2, 189 – 202.
[2] R. Singh, V. Rao, H. Shakila, R. Gupta, A. Khera, N. Dhar, A.
Singh, A. Koul, Y. Singh, M. Naseema, P. R. Narayanan, C. N.
Paramasivan, V. D. Ramanathan, A. K. Tyagi, Mol. Microbiol.
2003, 50, 751 – 762.
[3] a) N. J. Beresford, D. Mulhearn, B. Szczepankiewicz, G. Liu,
M. E. Johnson, A. Fordham-Skelton, C. Abad-Zapatero, J. S.
Cavet, L. Tabernero, J. Antimicrob. Chemother. 2009, 63, 928 –
936; b) B. Zhou, Y. He, X. Zhang, J. Xu, Y. Luo, Y. Wang, S. G.
Franzblau, Z. Yang, R. J. Chan, Y. Liu, J. Zheng, Z.-Y. Zhang,
Proc. Natl. Acad. Sci. USA 2010, 107, 4573 – 4578.
[4] For recent reviews, see: a) V. V. Vintonyak, A. P. Antonchick, D.
Rauh, H. Waldmann, Curr. Opin. Chem. Biol. 2009, 13, 272 –
283; b) L. Bialy, H. Waldmann, Angew. Chem. 2005, 117, 3880 –
3906; Angew. Chem. Int. Ed. 2005, 44, 3814 – 3839.
To characterize the inhibition mode of the spirothiazoli-
dinones, we performed detailed kinetic analysis, including
Lineweaver–Burk analysis (see the Supporting Information
for details). The indolin-2-on-3-spirothiazolidinones (R)-(À)-
7a, (R)-(À)-7b, (R)-(À)-7h, and (R)-(À)-7j were thus found
to be reversible substrate-competitive inhibitors of MptpB
with Ki values of (260 Æ 30), (250 Æ 10), (750 Æ 180), and
(200 Æ 50) nm, respectively.
Finally, we addressed the selectivity of inhibition for
different phosphatases. To this end, we performed phospha-
tase profiling for the 15 most potent inhibitors against a panel
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[5] For selected examples, see: a) A. Nꢀren-Mꢁller, I. Reis-Cor-
rÞa, Jr., H. Prinz, C. Rosenbaum, K. Saxena, H. J. Schwalbe, D.
Vestweber, G. Cagna, S. Schunk, O. Schwarz, H. Schiewe, H.
Waldmann, Proc. Natl. Acad. Sci. USA 2006, 103, 10606 – 10611;
b) I. R. CorrÞa, Jr., A. Nꢀren-Mꢁller, H.-D. Ambrosi, S. Jaku-
povic, K. Saxena, H. Schwalbe, M. Kaiser, H. Waldmann, Chem.
Asian J. 2007, 2, 1109 – 1126; c) A. Nꢀren-Mꢁller, W. Wilk, K.
Saxena, H. Schwalbe, M. Kaiser, H. Waldmann, Angew. Chem.
2008, 120, 6061 – 6066; Angew. Chem. Int. Ed. 2008, 47, 5973 –
5977; d) C. Grundner, D. Perrin, R. Hooft van Huijsduijnen, D.
Swinnen, J. Gonzalez, C. L. Gee, T. N. Wells, T. Alber, Structure
2007, 15, 499 – 509; e) M. B. Soellner, K. A. Rawls, C. Grundner,
T. Alber, J. A. Ellman, J. Am. Chem. Soc. 2007, 129, 9613 – 9615;
f) L. P. Tan, H. Wu, P. Y. Yang, K. A. Kalesh, X. Zhang, M. Hu,
R. Srinivasan, S. Q. Yao, Org. Lett. 2009, 11, 5102 – 5105.
[6] a) J. S. Bindra in The Alkaloids, Vol. 14 (Eds.: R. H. F. Manske),
Academic Press, New York, 1973, pp. 84 – 121; b) R. T. Brown in
The Chemistry of Heterocyclic Compounds, Part 4, Vol. 25 (Ed.:
J. E. Saxton), John Wiley and Sons, New York, 1983; c) C. V.
Galliford, K. A. Scheidt, Angew. Chem. 2007, 119, 8902 – 8912;
Angew. Chem. Int. Ed. 2007, 46, 8748 – 8758.
[9] M. Kansy, F. Senner, K. Gubernator, J. Med. Chem. 1998, 41,
1007 – 1010.
[10] A. Avdeef in Pharmacokinetic Optimization in Drug Research
(Eds.: B. Testa, H. van de Waterbeemd, G. Folkers, R. Guy),
Verlag Helvetica Chimica Acta, Zꢁrich and Wiley-VCH,
Weinheim, 2001, pp. 305 – 326.
[11] M. A. Marques, C. A. Ullrich, F. Nogueira, A. Rubio, K. Burke,
E. K. U. Gross, Time-Dependent Density Functional Theory,
Springer, Berlin, 2006.
[12] For a recent review, see: G. Bringmann, T. Bruhn, K. Maksi-
menka, Y. Hemberger, Eur. J. Org. Chem. 2009, 2717 – 2727; for
representative applications, see: a) P. J. Stephens, J.-J. Pan, F. J.
ˇ
Devlin, M. Urbanovꢂ, J. Hꢂjꢃcek, J. Org. Chem. 2007, 72, 2508 –
2524; b) P. J. Stephens, J.-J. Pan, F. J. Devlin, M. Urbanovꢂ, O.
ˇ
Julꢃnek, J. Hꢂjꢃcek, Chirality 2008, 20, 454 – 470; c) S. Grimme, A.
Bahlmann in Modern Cyclophane Chemistry (Eds.: R. Gleiter,
H. Hopf), Wiley, Chichester, 2004, p. 311; d) T. Mori, Y. Inoue, S.
Grimme, J. Phys. Chem. A 2007, 111, 7995 – 8006; e) C. Diedrich,
S. Grimme, J. Phys. Chem. A 2003, 107, 2524 – 2539; f) L.
Autschbach, J. Jensen, G. C. Schatz, Y. C. E. Tse, M. Krykunov,
J. Phys. Chem. A 2006, 110, 2461 – 2473; g) T. D. Crawford, M. C.
Tam, M. L. Abrams, Mol. Phys. 2007, 105, 2607 – 2617; h) M. C.
Tam, M. L. Abrams, T. D. Crawford, J. Phys. Chem. A 2007, 111,
11232 – 11241.
[7] M. A. Koch, L. O. Wittenberg, S. Basu, D. A. Jeyaraj, E.
Gourzoulidou, K. Reinecke, A. Odermatt, H. Waldmann,
Proc. Natl. Acad. Sci. USA 2004, 101, 16721 – 16726.
[8] M. A. Koch, A. Schuffenhauer, M. Scheck, S. Wetzel, M.
Casaulta, A. Odermatt, P. Ertl, H. Waldmann, Proc. Natl.
Acad. Sci. USA 2005, 102, 17272 – 17277.
[13] L. Goerigk, S. Grimme, J. Phys. Chem. A 2009, 113, 767 – 776.
Angew. Chem. Int. Ed. 2010, 49, 5902 –5905
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