Discovery and SAR of potent, orally available 2,8-diaryl-quinoxalines as a new class of JAK2 inhibitors

Article abstract of DOI:10.1016/j.bmcl.2010.02.056

We have designed and synthesized a novel series of 2,8-diaryl-quinoxalines as Janus kinase 2 inhibitors. Many of the inhibitors show low nanomolar activity against JAK2 and potently suppress proliferation of SET-2 cells in vitro. In addition, compounds from this series have favorable rat pharmacokinetic properties suitable for in vivo efficacy evaluation.

Full text of DOI:10.1016/j.bmcl.2010.02.056

Bioorganic & Medicinal Chemistry Letters 20 (2010) 2609–2613
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Discovery and SAR of potent, orally available 2,8-diaryl-quinoxalines as a
new class of JAK2 inhibitors
*
Carole Pissot-Soldermann , Marc Gerspacher, Pascal Furet, Christoph Gaul, Philipp Holzer, Clive McCarthy,
Thomas Radimerski, Catherine H. Regnier, Fabienne Baffert, Peter Drueckes, Gisele A. Tavares,
Eric Vangrevelinghe, Francesca Blasco, Giorgio Ottaviani, Flavio Ossola, Julien Scesa, Janitha Reetz
Novartis Institutes for Biomedical Research, Novartis Pharma AG, WKL-136.4.96, CH-4002 Basel, Switzerland
a r t i c l e i n f o
a b s t r a c t
Article history:
We have designed and synthesized a novel series of 2,8-diaryl-quinoxalines as Janus kinase 2 inhibitors.
Many of the inhibitors show low nanomolar activity against JAK2 and potently suppress proliferation of
SET-2 cells in vitro. In addition, compounds from this series have favorable rat pharmacokinetic proper-
ties suitable for in vivo efficacy evaluation.
Received 18 December 2009
Revised 13 February 2010
Accepted 16 February 2010
Available online 19 February 2010
Ó 2010 Elsevier Ltd. All rights reserved.
Keywords:
Janus kinase
JAK1
JAK2
JAK3
Tyk2
Kinase inhibitors
The Janus kinase (JAK) family comprises of four non-receptor
protein tyrosine kinases, JAK1, JAK2, JAK3 and TYK2, which play
an important role in cell survival, proliferation and differentiation.1
The discovery of somatic mutations in JAK2, particularly that of
JAK2V617F, in patients with chronic myeloproliferative neoplasms
(MPNs) marked an important milestone in our understanding of
the pathogenesis of these disorders.2,3 The JAK2V617F mutation is
present in nearly every patient with polycythemia vera and in al-
most 50% of patients with essential thrombocythemia or primary
myelofibrosis.4 Thus, JAK2 represents a promising target for the
treatment of MPNs and considerable efforts are ongoing to dis-
cover and develop small molecule inhibitors of its kinase activity.
Herein, we describe the discovery of 2,8-diaryl-quinoxalines as
potent JAK2 inhibitors, and report on their JAK family selectivity,
anti-proliferative effects in JAK2V617F bearing SET-2 cells and phar-
macokinetic properties in rats.
thetical binding mode for this compound was confirmed by the
crystal structure of the active JAK2 protein kinase domain in com-
plex with 1 (Fig. 2)7 and revealed that the quinoxaline N1 atom is
involved in a critical interaction with the hinge part of the kinase
through a hydrogen-bond with the backbone amide of Leu932. In
addition, this quinoxaline ring makes hydrophobic contacts with
side chains of residues Ala880, Met929 and Leu983. Favorable
hydrophobic contacts are also observed between the aromatic ring
of the trimethoxyphenyl substituent of 1 and the side chain of
Leu855 and backbone of Gly935. The methylsulfonamide group
participates in multiple hydrogen-bond interactions with water
molecules located in the phosphate region of the ATP binding site.
The phenyl ring that links the quinoxaline core to the methylsulf-
onamide moiety, occupies a hydrophobic part of the cavity, sur-
rounded by the side chains Val863, Leu983 and backbone of
Gly993.
Screening an internal proprietary kinase compound collection
resulted in the identification of a lead compound, which through
iterative scaffold morphing exercises5,6 and optimization afforded
a class of 2,8-diaryl-quinoxalines, represented by the prototype
compound (1; Fig. 1). Compound 1 is a potent inhibitor of JAK2
(IC50 = 42 nM), with a 30-fold JAK2/JAK3 selectivity in enzymatic
assays and an overall favorable kinase selectivity profile. The hypo-
N
O
N
O
O
O
S O
1
HN
* Corresponding author. Tel.: +41 61 696 18 90; fax: +41 61 696 62 46.
E-mail address: carole.pissot@novartis.com (C. Pissot-Soldermann).
Figure 1. Structure of prototype 2,8-diaryl-quinoxaline (1).
0960-894X/$ - see front matter Ó 2010 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2010.02.056

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C. Pissot-Soldermann et al. / Bioorg. Med. Chem. Lett. 20 (2010) 2609–2613
Nickel led to a mixture of the corresponding aniline derivative 5a
and the cyclized intermediate 5b. Treatment of this mixture with
KOBu-t in the presence of air (oxygen) yielded 8-bromo-1H-quin-
oxaline-2-one which was chlorinated with POCl3 to provide 8-bro-
mo-2-chloro quinoxaline (6). Intermediate (6) was a used to
introduce structural diversity in the two final steps via consecutive
selective palladium-catalyzed Suzuki coupling reactions to intro-
duce two aryl moieties.
The effects of the 2,8-diaryl-quinoxalines on JAK family mem-
bers were assessed in biochemical and JAK2-dependent cellular as-
says (Table 2).8,9 The initial SAR studies focused on variation of
substituent R2. Replacement of the methyl sulfonamide by 4-phen-
ylacetic morpholine amide (8) or 4-phenylacetic thiomorpholine
dioxide amide (9) gave a 3-8 fold gain in JAK2 potency, which also
translated into cell growth inhibition (GI50) of 228 nM and 119 nM,
respectively, in the SET-2 JAK2V617F proliferation assay. Reducing
the planar morpholine amide moiety to the more flexible and
slightly basic benzyl morpholine was tolerated (compare 13 with
14 and 15 with 16). Exploration of the effect of additional small
substituents (F or Me) on the phenyl ring in R2 showed that intro-
duction in the meta-position resulted in a fourfold increase in po-
tency (compare entry 13 with 16 and 17), whereas the same
residues in the ortho-position yielded a drastic loss of potency
(compare entries 18 and 19 with 13). In comparison to 22, intro-
duction of a 3,5-difluoro substituent further improved JAK2 inhib-
itory activity providing compound 23 with a very good inhibition
of SET-2 JAK2V617F cell proliferation (GI50 = 135 nM). This SAR is
fully supported by the crystal structure of JAK2 in complex with
1. This structure suggests that meta-substituents can provide addi-
tional favorable hydrophobic contacts with residues Val863 and
Gly856 of the P-loop on the one hand and the carbon atoms of
the side chain of Asp994 on the other hand. In contrast, ortho-sub-
stituents, by increasing the twist between the quinoxaline core and
the phenyl ring R2, lead to a steric clash of the substituent with
either Val863 or Leu983. As already mentioned, the phenyl ring
in R2 lay in proximity to the backbone of Gly993, which corre-
sponds to Ala966 in JAK3. This difference, coupled with the obser-
vation that in a structure of JAK3 recently disclosed10, Ala966
Figure 2. Crystal structure of 1 in complex with the JAK2 kinase domain solved at
2.00 Å resolution. Polar contacts between the inhibitor, solvent and the protein are
indicated with dotted lines.
The pharmacokinetic profile of 1 was evaluated in conscious rats.
After intravenous bolus administration, 1 shows a rather high total
clearance (87 mL minÀ1 kgÀ1) with a large volume of distribution
(6.75 L kgÀ1) and a moderate terminal half-life (1.69 h) and, after
oral administration (3 mg/kg as a suspension in 0.5% carboxymethyl
cellulose in bidistillated water) the AUC was 4
corresponding to 34% oral bioavailability.
l ,
g min mLÀ1
Based upon the in vitro/in vivo profile of 1, we considered this
chemotype as an attractive starting point and embarked on an
extensive medicinal chemistry program to optimize the molecule.
The compounds were readily synthesized via the sequence out-
lined in Scheme 1, starting from 2-bromo-6-fluoro-aniline (2). Oxi-
dation of the aniline in two steps yielded the nitro compound (3)
and fluoride displacement with ethyl glycinate afforded (4). Reduc-
tion of the nitro group via hydrogenation in the presence of Raney–
adopts a
w backbone conformation of opposite direction compared
to that of Gly993 in JAK2 provides a rationale to explain the selec-
tivity for JAK2 against JAK3 obtained with our analogs. The R2 phe-
nyl ring and its substituents appear to be better accommodated by
the less sterically demanding Gly993 residue of JAK2. Introduction
of small R1 groups (F or Me) resulted in significant loss of potency
(entry 11 and 12). As expected from the structure, this R1 position
is too close to the carbonyl group of Glu930 to tolerate any
substituent.
Br
O
F
F
O
N+
NH2
Br
N+
c
a,b
O
O
O
N
H
Br
O
4
3
2
Br
Br
Br
H
N
N
Cl
NH2
e, f
O
d
Exploration of the R3 substituent was pursued to optimize the
physicochemical properties of the compounds as well as to im-
prove JAK2 affinity (compare 10 with 20 and 15 with 21). The R3
substituent is located in the hydrophobic channel formed by resi-
dues Gly935 and Leu855 at the entrance of the cavity. Compounds
20 to 23, in which the trimethoxyphenyl moiety is replaced by
carboxamide-substituted phenyl residues, show potent cellular
+
O
N
N
H
N
H
O
5a
5b
6
mixture 1:1
NH
O
S O
O
O
O
O
Br
g
h
N
N
N
N
O
Table 1
O
Comparison of measured molecular properties of compounds11,12
Compounds
Log 1/S0 (M)
Log P
D
SL
MP
pKa
7
1
20
24
25
26
4.80
4.60
5.06
3.98
2.80
4.00
3.80
3.20
2.00
0.60
1.26
0.78
204.03
168.41
227.28
137.30
3.9/6.5
4.5/7.2
3.6/6.9
5.5/9.1
Scheme 1. Reagents and conditions: (a) mCPBA, CH2Cl2, reflux, 30 min 93%; (b)
H2O2 30% AcOH, fuming HNO3, rt then 90 °C, 30 min 66% (crude); (c) ethylglyci-
nateÁHCl, DMA, DIEA, 80 °C, 18 h, 62%; (d) H2, RaNi, EtOH, THF 1:1, quant. (crude);
(e) KOBu-t, THF, MeOH, air, rt, 16 h, 66%; (f) POCl3, 55 °C, 3 h, 88%; (g) 3,4,5-
trimethoxyphenylboronic acid, Pd(PPh3)4, Na2CO3, DMF, 105 °C, 68%; (h) S-Phos,
Pd2(dba)3, K3PO4, 1,2-DME, 4-N-methyl (aminosulfonylphenyl) boronic acid, 110 °C,
15 h, 71%.
S0, intrinsic aqueous solubility, Log P logarithm of the partition coefficient P, based
on experimental Log P,
SL = Log 1/S0 À Log P, MP: melting point, pKa: (minus)
logarithm of the ionization constant Ka, measured by potentiometry.
D

C. Pissot-Soldermann et al. / Bioorg. Med. Chem. Lett. 20 (2010) 2609–2613
2611
Table 2
Effects of compounds 1, and 8–26 on enzymatic activity of JAK family kinases and on cell proliferation in SET-2 JAK2V617F cells8,9
R2
R3
N
R1
N
Compds
R1
H
H
H
R2
R3
JAK1 IC50
(nM)
JAK2 IC50
(nM)
JAK3 IC50
(nM)
TYK2 IC50
(nM)
Inhibition of
SET-2 JAK2
proliferation GI50 (nM)
V617F
O
O
1
8
9
130
91
42
13
5.1
1300
1300
280
640
640
340
n.d.
S
N
O
*
*
*
*
*
H
O
O
O
O
228
119
N
O
O
O
O
*
O
O
O
35
N
S
O
O
O
O
*
N
*
10
H
98
14
360
520
n.d.
S
O
O
O
O
O
*
O
11
12
13
14
Me
F
>10,000
940
4200
101
72
>10,000
>10,000
2500
>10,000
>10,000
2900
n.d.
n.d.
n.d.
n.d.
*
*
*
*
N
S
O
O
O
O
*
O
O
O
N
O
O
O
O
O
H
390
*
*
N
N
O
O
O
H
1500
120
>10,000
>10,000
O
O
O
O
*
15
H
1850
195
8300
7130
n.d.
*
N
O
O
O
O
N
*
16
17
18
19
H
H
H
H
460
20
1500
4900
2700
9900
1400
2200
4200
9300
n.d.
n.d.
n.d.
O
O
O
O
*
*
*
*
O
O
O
O
N
250
20
*
*
*
F
O
O
O
O
O
O
N
1200
4700
685
501
O
O
O
N
n.d.
F
O
(continued on next page)

2612
C. Pissot-Soldermann et al. / Bioorg. Med. Chem. Lett. 20 (2010) 2609–2613
Table 2 (continued)
Compds
R1
R2
R3
JAK1 IC50
(nM)
JAK2 IC50
(nM)
JAK3 IC50
(nM)
TYK2 IC50
(nM)
Inhibition of
SET-2 JAK2
V617F
proliferation GI50 (nM)
O
O
*
N
N
N
20
H
89
7.1
232
330
96
N
*
*
S
O
O
*
*
21
22
H
H
362
190
13
408
630
439
520
n.d.
226
N
O
O
O
O
N
N
N
N
12.5
O
F
F
*
O
*
*
23
24
H
H
60
28
3.1
4.3
130
166
120
135
152
O
N
*
*
F
O
F
N
94
N
F
O
F
N
N
N
*
*
*
N
25
26
H
H
82
6.8
7.3
230
610
86
98
88
F
S
O
O
F
N
NH
N
303
384
*
N
F
O
Table 3
activity, but have similar poor water solubility as the prototype
compound 1. In order to understand the main factor causing the
low aqueous solubility, we examined the molecular properties of
the compounds (Table 1),11 and it appears that the high crystal lat-
tice energy of compound 20 (mp = 204 °C), limits its solubility.
Introducing solubilizing groups, as in compounds 24 and 25, main-
tained good potency and selectivity, but did not afford good aque-
ous solubility (0.004 mg mLÀ1 at pH 6.8 for both compounds).
However, the solubility of 24 is limited by lipophilicity, whereas
a high crystal lattice energy limits the solubility of 25.11 Introduc-
tion of a piperidinyl-pyrazole residue afforded 26 which has very
good solubility (>1.5 mg/mL at pH 6.8) and maintains very good
cellular potency (GI50 = 51 nM), together with attractive JAK2 ki-
nase selectivity (at least 40-fold over JAK1, 80-fold over JAK3 and
50-fold over TYK2) and good overall kinase selectivity (the only
other kinase in a panel of 36 kinases inhibited with IC50 values
<100 nM was ABL (IC50 = 80 nM)).
Effects of compounds 24–26 on pharmacokinetic parameters following administra-
tion to ratsa,13
Parameters
Compounds
24
25
26
Thermodynamic solubility (g/L) pH 6.8
CL (iv) (mL/min/kg)
Vss (L/kg)
0.004
19
0.004
39
13.2
4.8
760
912
8
>1.5
23
33
18.4
1472
449
7.0
18.9
13.4
1653
1981
5.8
74
ꢀ100
t
(h)
½
AUC (iv) nmol h LÀ1 dnb
AUC (po) nmol h LÀ1 dnb
Tmax (h)
Cmax (nM) dnb
Oral %F
47
ꢀ100
16
31
a
Mean of four animals.
Dose-normalized, that is, calculated to a dose of 1 mg/kg.
b
As the most promising compounds, 24, 25 and 26 were selected
for pharmacokinetic studies in rats (Table 3),13 and showed low to
moderate clearance, a high volume of distribution and a long elim-
ination half-life after administration of 1 mg/kg iv. After oral
administration of 3 mg/kg, all three compounds 24-26 exhibited
a low Cmax, a late Tmax and an absolute oral bioavailability ranging
from 31% to 100%.
In summary, we have discovered a series of selective and potent
JAK2 inhibitors. Optimization of the 2,8-diaryl-quinoxalines led to
analogs such as 26, an orally bioavailable small molecule ATP-com-

C. Pissot-Soldermann et al. / Bioorg. Med. Chem. Lett. 20 (2010) 2609–2613
2613
measured using the colorimetric WST-1 (catalog number 1644807, Roche
Diagnostics GmbH, Penzberg, Germany) cell viability readout. Of each triplicate
treatment the mean was calculated and these data were plotted in XLfit 4 (XLfit
4 curve fitting software for Microsoft Exel, ID business Solutions Ltd, Guildford,
Surrey, United Kingdom) to determine the respective GI50 values.
petitive inhibitor of V617F mutant and wild type JAK2 protein hav-
ing reduced clearance, improved half-life and superior oral bio-
availability compared to the prototype compound 1.
10. Boggon, T. J.; Li, Y.; Manley, P. W.; Eck, M. J. Blood 2005, 106, 996.
11. Faller, B.; Ertl, P. Adv. Drug Delivery Rev. 2007, 59, 533.
References and notes
12. Box, K. J.; Cromer, J. E. A. Curr. Drug Metab. 2008, 9, 869.
13. Pharmacokinetic properties were determined in conscious, fed, permanently
cannulated female rats. For po administration by gavage, aq solutions of
1. Rane, S. G.; Reddy, E. P. Oncogene 2000, 19, 5662.
2. Levine, R. L.; Pardanani, A.; Tefferi, A.; Gilliland, D. G. Nat. Rev. Cancer 2007, 673.
3. Tefferi, A.; Vardiman, J. W. Leukemia 2008, 22, 14.
compounds 24–26 in PEG200 (50%) were used as
a vehicle (2.5 mL/kg),
4. Tefferi, A.; Gilliland, D. G. Cell Cycle 2005, 4, 1053.
whereas for the iv route compounds 24–26 were administered into the femoral
5. Furet, P.; Gerspacher, M.; Pissot-Soldermann, C. Bioorg. Med. Chem. Lett. 2010,
20, 1858.
vein as a solution in NMP (30%) in PEG 200 (0.5 mL/kg). Blood samples (approx.
70 lL) were collected from the femoral artery 48 h after iv administration and
6. Gerspacher, M.; Furet, P.; Pissot-Soldermann, C.; Gaul, C.; Holzer, P.;
Vangrevelinghe, E.; Lang, M.; Erdmann, D.; Radimerski, T.; Regnier, C. H.;
Chene, P.; De Pover, A.; Hofmann, F.; Baffert, F.; Buhl, T.; Aichholz, R.; Blasco, F.;
Endres, R.; Trappe, J.; Drueckes, P. Bioorg. Med. Chem. Lett. 2010, 20, 1724.
7. Structure deposited in the RCSB Protein Data Bank under PDB ID: 3LPB.
8. Detailed description of the biochemical assays: Gerspacher, M.; Furet, P.;
Vangrevelinghe, E.; Pissot-Soldermann, C.; Gaul, C.; Holzer, P. PCT Int. Appl. WO
2008148867, 2008; Chem Abstr. 2008, 150, 56197.
for 24 h after oral dosing. Iv and po administration was in the same animals
with a 48 h washout period between administrations (cross-over design). After
CH3CN precipitation of blood samples (50 lL), dried residues were re-dissolved
in methanol/water, separated by HPLC on a C18 reversed-phase HPLC column,
followed by MS/MS analysis on a triple quadrupole mass analyzer (Finnigan
TSQ Quantum). The compound was detected as a fragment of its protonated
quasi-molecular ion [M+H]+. A structurally closely related compound was used
as analytical standard. Quantification of blood levels of the parent compound
was based on a seven-level calibration curve (in triplicate) using blank rat
blood samples spiked with stock solutions of external and internal standards.
9. Human megakaryoblastic SET-2 cells (number ACC608), DSMZ, Braunschweig,
Germany) were cultured in standard RPMI medium supplemented with 10% of
fetal calf serum (FCS), 2 mM
L
-glutamine and 1% (v/v) penicillin/streptomycin.
Pharmacokinetic parameters were estimated using a non compartmental
To determine the anti-proliferative activity of candidate JAK2 inhibitors, SET-2
cells were incubated for 72 h with an 8 point concentration range of compound
and cell proliferation relative to DMSO vehicle control treated cells was
approach. AUCs iv and po were calculated using the trapezoidal rule, then
extrapolated to infinity using the terminal half-life calculated by log-linear
regression from the last three (measurable) blood levels after iv administration.