Structure-based discovery of C-2 substituted imidazo-pyrrolopyridine JAK1 inhibitors with improved selectivity over JAK2

Article abstract of DOI:10.1016/j.bmcl.2012.10.008

Herein we describe our successful efforts in obtaining C-2 substituted imidazo-pyrrolopyridines with improved JAK1 selectivity relative to JAK2 by targeting an amino acid residue that differs between the two isoforms (JAK1: E966; JAK2: D939). Efforts to improve cellular potency by reducing the polarity of the inhibitors are also detailed. The X-ray crystal structure of a representative inhibitor in complex with the JAK1 enzyme is also disclosed.

Full text of DOI:10.1016/j.bmcl.2012.10.008

Bioorganic & Medicinal Chemistry Letters 22 (2012) 7627–7633
Contents lists available at SciVerse ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Structure-based discovery of C-2 substituted imidazo-pyrrolopyridine JAK1
inhibitors with improved selectivity over JAK2
Sharada Labadie a, , Peter S. Dragovich a, Kathy Barrett a, Wade S. Blair a, Philippe Bergeron a,
⇑
Christine Chang a, Gauri Deshmukh a, Charles Eigenbrot a, Nico Ghilardi a, Paul Gibbons a,
Christopher A. Hurley b, Adam Johnson a, Jane R. Kenny a, Pawan Bir Kohli a, Janusz J. Kulagowski b,
Marya Liimatta a, Patrick J. Lupardus a, Rohan Mendonca b, Jeremy M. Murray a, Rebecca Pulk a,
Steven Shia a, Micah Steffek a, Savita Ubhayakar a, Mark Ultsch a, Anne van Abbema a, Stuart Ward b,
Mark Zak a
a Small Molecule Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
b Argenta, 8/9 Spire Green Centre, Flex Meadow, Harlow, Essex, CM19 5TR, United Kingdom
a r t i c l e i n f o
a b s t r a c t
Article history:
Herein we describe our successful efforts in obtaining C-2 substituted imidazo-pyrrolopyridines with
improved JAK1 selectivity relative to JAK2 by targeting an amino acid residue that differs between the
two isoforms (JAK1: E966; JAK2: D939). Efforts to improve cellular potency by reducing the polarity of
the inhibitors are also detailed. The X-ray crystal structure of a representative inhibitor in complex with
the JAK1 enzyme is also disclosed.
Received 15 August 2012
Revised 27 September 2012
Accepted 1 October 2012
Available online 11 October 2012
Ó 2012 Elsevier Ltd. All rights reserved.
Keywords:
Rheumatoid arthritis
Imidazo-pyrrolopyridines
JAK1 selective inhibitors, Structure-based
design
Rheumatoid arthritis (RA), a common chronic inflammatory
disease, affects an estimated 1% of the world’s population.1 The
disease attacks the synovial membrane and cartilage and is respon-
sible for joint destruction and severe disabilities. DMARDs
(disease-modifying anti-rheumatic drugs), DMARD combinations
large subfamily of cytokines which includes IL-6, always involves
JAK1 activation and is implicated in the pathogenesis of RA.3 The
biological agent tocilizumab is believed to exert its therapeutic ef-
fects against RA by inhibiting the activity of the JAK1 dependent
cytokine IL-6.6 In addition, a number of small molecule JAK inhibi-
tors have shown efficacy in advanced clinical trials for the treat-
ment of RA, two of which are tofacitinib/CP-690,550 (1)7,8 and
ruxolitinib/INCB018424 (2)9–11 (Fig. 1). Compound 1 is a pan-JAK
inhibitor and 2 is potent against JAK1 and JAK2 with considerably
less activity against JAK3 and TYK2. In addition to critical role
played by JAK1 in IL-6 signaling,12 a recent report suggests that
JAK1 rather than JAK3 may be dominant in driving the activity of
with glucocorticoids, and TNF-a blocker biologics (infliximab, ada-
limumab, etanercept, and the recently introduced IL-6 blocker toc-
ilizumab) have been effectively used to treat RA.2 Despite these
promising advances, new RA therapies which improve on the effi-
cacy and side-effect profiles of existing agents are still desired.
The Janus protein tyrosine kinases (JAK1, JAK2, JAK3, and TYK2)
mediate the intracellular signaling of numerous cytokines and
thereby play critical roles in a variety of biological processes,
including hematopoiesis and the regulation of immune and
inflammatory responses.3,4 Binding of a cytokine to its receptor
leads to the activation of receptor associated JAK family kinases
and subsequent recruitment and phosphorylation of STAT (Signal
Transducer and Activator of Transcription) proteins.5 The phos-
phorylated STATs form homo- or heterodimers, translocate to the
nucleus, and regulate transcription of target genes. Signaling by a
the immune-relevant c
c-cytokines.13 Therefore, it is believed that
JAK1 inhibition will lead to therapeutic immune modulation. JAK2
activation is required for proper signaling of erythropoietin during
hematopoiesis, and extensive JAK2 inhibition may lead to undesir-
able side effects (e.g., anemia).14,15 Therefore, we reasoned that a
JAK1 selective, JAK2 sparing inhibitor would constitute an ideal
therapeutic agent to target inflammatory disorders such as RA.
Previously, we described the discovery of tricyclic imidazo-
pyrrolopyridines 3 as potent inhibitors of the JAK1 enzyme.16,17
During these investigations utilizing hydrogen and methyl as R1
substituents, a variety of R2 groups were explored. These efforts
⇑
Corresponding author. Tel.: +1 650 467 6118; fax: +1 650 467 8382.
E-mail address: sharadal@gene.com (S. Labadie).
0960-894X/$ - see front matter Ó 2012 Elsevier Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.bmcl.2012.10.008

7628
S. Labadie et al. / Bioorg. Med. Chem. Lett. 22 (2012) 7627–7633
in Scheme 1,19 an alternate synthetic method was developed as
shown in Scheme 2. This sequence commenced with the in-situ for-
CN
mation of the imidates of amides 44 and 45 by treatment with tri-
N
N
ethyloxonium
tetrafluoroborate
in
THF.20,21
Subsequent
N
condensation with the diamine 10 in ethanol at reflux and depro-
tection of the Boc-group with 4 N HCl/1,4-dioxane afforded the
amines 46 and 47. Treatment of 46 and 47 with various acid and
sulfonyl chlorides and subsequent removal of the benzenesulfon-
amide protecting group under basic conditions provided the de-
sired compounds 48–53. Applying chemistries similar to those
depicted in Scheme 1 and 2, compounds 54–73 (Table 2) were syn-
thesized starting from the appropriate amines.22–24 Compounds
containing a chiral center were typically synthesized in racemic
form and single enantiomers were subsequently obtained by chiral
SFC separation25–27 if the racemic mixture exhibited a desirable
profile.
Compounds 33–43 generated promising data in biochemical as-
says (Table 1). Generally, a slight improvement in selectivity for
JAK1 with respect to compound 5 was observed as the methyl
group was replaced with bulkier alkyl groups (33–37) albeit with
some loss of JAK1 potency. A further increase in biochemical selec-
tivity was typically achieved by incorporation of polar atoms and
hydrogen bond donor/acceptor functionalities (39–43, 48–53) in
the C-2 substituent. Unfortunately, the cellular potency was signif-
icantly reduced in the compounds with the largest number of
hydrogen bond donor/acceptor moieties in the C-2 position
(48–53). Larger shifts between cellular and biochemical potencies
were observed as the number of polar atoms in the molecules in-
creased (e.g., compare 39 with 48). The loss of cellular potency rel-
ative to biochemical inhibition was related to increase in
compound polarity (as assessed by tPSA28 values), suggesting a
strategy of polarity reduction to optimize cellular activity.
Accordingly, we focused our efforts on tPSA reduction by
decreasing the number of polar atoms in the molecules. Since
C-2 amides and sulfonamide moieties provided improved bio-
chemical potency and JAK1 selectivity relative to other hydrogen
bond donor/acceptor functionalities, we attempted to combine
these groups with non-polar cyanoethylpiperidyl replacements.
Details of this investigation are shown in Table 2 (54–73). In gen-
eral, compounds bearing N-acetyl moieties at C-2 were weaker and
less selective JAK1 inhibitors than the corresponding N-sulfonyl
containing molecules (compare 54 with 55 and 62 with 64). In
addition, a one carbon linker between the sulfonamide moiety
and the tricyclic core afforded improved JAK1 selectivity relative
to a two carbon linker (compare 64 with 65 and 69 with 70). As
suggested by the data in Table 2, cellular potencies improved as
the polarity of the compounds diminished (compare 48 with 54
and 50 with 55). Further boosts in biochemical/cellular potencies
N
N
CN
O
N
N
N
H
N
H
N
2
1
Figure 1. JAK inhibitors in advance clinical evaluation.
identified the highly potent and moderately JAK1 selective com-
pounds 4 and 5 (Fig. 2). Analysis of the X-ray structure of a related
inhibitor 6 in complex with JAK1 (Fig. 3a) revealed that the C-2
methyl group of 6 approached within 3.4 Å of the JAK1 E966 side
chain.16 In contrast, a crystal structure of 6 in complex with the
JAK2 isoform showed the same methyl group to be further re-
moved from the corresponding JAK2 residue (D939, Fig. 3b). Simi-
lar observations were made with another related compound which
exhibited 5.6 fold selectivity for JAK1 over JAK2.16 Presumably, the
proximity of the methyl group in these molecules to the E966 side
chain contributes to the observed selectivity. We therefore postu-
lated that replacement of the C-2 methyl group present in 5 and/or
6 with more bulky/polar moieties might afford compounds which
display improved interaction with the JAK1 E966 side chain. Here-
in, we describe our successful efforts in obtaining such molecules
and also detail their enhanced selectivity for JAK1 over JAK2 rela-
tive to 4 and 5.
Although the inhibitor 6 showed high JAK1 selectivity relative to
JAK2, it exhibited modest biochemical and cellular potencies and
extremely poor cell permeability16 relative to compounds 4 and 5.
Therefore, the initial C-2 modifications to improve selectivity were
explored using template 5 bearing the 4-cyanoethylpiperidine moi-
ety as the R2 substituent. The synthesis of compounds with varying
alkyl groups at C-2 is described in Scheme 1 and commenced as pre-
viously described.16,17 SNAr displacement of the chloride present in
7
17 with 818 in the presence of a tertiary amine provided the nitro
intermediate 9. The reduction of the nitro group in 9 with H2/Pd-
C followed by HATU coupling of the diamine 10 with various acids
generated the amide intermediates 11–21. After several failed at-
tempts to affect cyclization, heating the intermediates in acetic acid
at 100 °C afforded the cyclization products 22–32 in poor to moder-
ate yields. Base mediated benzenesulfonamide hydrolysis then
afforded final compounds 33–43. Because of the difficulties
encountered in the cyclization step to form the tricyclic ring system
CN
CN
NH
N
N
CH3
CH3
R1
N
R2
N
2
N
N
N
N
N
N
1
NH
N
NH
N
NH
N
NH
N
6
5
3
4
JAK1 Ki = 0.6 nM
JAK1 Ki = 0.9 nM
JAK1 Ki = 10 nM
JAK2/JAK1 = 1.8
JAK1 Cell EC50 = 43 nM
JAK2/JAK1 = 2.3
JAK2/JAK1 = 20
JAK1 Cell EC50 = 250 nM
JAK1 Cell EC50 = 26 nM
MDCK Papp A:B = 5.1x10-6 cm/s MDCK Papp A:B = 0.4x10-6 cm/s
Figure 2. Previously described imidazo-pyrrolopyridines.

S. Labadie et al. / Bioorg. Med. Chem. Lett. 22 (2012) 7627–7633
7629
Figure 3. X-ray structure of 6 in complex with (a) JAK1 at 2.2 Å and (b) JAK2 at 2.4 Å. Compound 6 is depicted in orange. Hydrogen bonds to the ligand are shown as dashed
black lines. Backbone hinge atoms contacting 6 are highlighted (JAK1: E957 and L959; JAK2: E930 and L932). Notable crystallographic waters are denoted as red spheres
(waters modeled into electron density peaks >1.5
r). A molecule of ethylene glycol (teal) is observed in Figure 3a. The double-headed black arrows highlight the proximity of
the C-2 methyl substituent to a key residue difference between JAK1 (E966) and JAK2 (D939).
CN
CN
N
CN
N
HN
N
Cl
N
HN
N
H2N
O2N
O2N
i
ii
iii
+
N
SO2Ph
N
N
SO2Ph
N
SO2Ph
NH2
10
9
7
8
CN
CN
CN
N
N
N
R1
N
R1
O
R1
HN
N
N
HN
N
v
iv
N
SO2Ph
N
H
N
N
N
N
SO2Ph
11-21
33-43
22-32
Scheme 1. Reagents and conditions: See Table 1 for descriptions of R substituents. (i) DIPEA, i-PrOH, 65–120 °C; (ii) Pd-C, H2, THF-ethanol, 50 °C; (iii) R1COOH, HATU, DIPEA,
DMF, rt, 20 h; (iv) acetic acid, 100 °C, 0.5–20 h; (v) 1 N NaOH, ethanol or isopropanol, 50 °C, 20 h.
CN
CN
examined, the exo-norbornyl group produced the best potency
and selectivity results (69). In general, when a chiral center was
present in the R2 substituent of the molecules one enantiomer
was always more potent and more selective (compare 56 with
57, 59 with 60 and 72 with 73). The (R, R, S) enantiomer (72) of
the exo-norbornane analog was 15 fold more potent and superior
in selectivity than the corresponding ( S, S, R) enantiomer (73).29
Compound 72 also showed excellent cellular JAK1 potency
(EC50 = 118 nM) in a human whole blood assay.30 Because of its
excellent biochemical, cell, and whole blood potencies and attrac-
tive JAK1 selectivity relative to JAK2, compound 72 was progressed
to in vitro DMPK and rat in vivo PK studies.
N
N
N
NH2
( )n
R1
N
NHBoc
( )n
N
i, ii, iii
iv, v
N
NH2
N
O
N
H
N
N
SO2Ph
44 n = 1
45 n = 2
46 n = 1
47 n = 2
48-53
Scheme 2. Reagents and conditions: See Table 1 for description of R1 substituents.
(i) triethyloxonium tetrafluoroborate, THF or DCM, rt, 2 h; (ii) 10, ethanol, reflux;
(iii) 4 N HCl-1,4-dioxane, DCM; (iv) R1COCl, R1OCOCl, or R1SO2Cl, DIPEA, THF; (v)
1 N NaOH, i-PrOH, 50 °C, 20 h.
Inhibitor 72 displayed excellent in vitro DMPK properties. The
compound had low human liver microsomal clearance (CL = 4.2 mL
/min/kg), moderate human hepatocyte clearance (CL = 7.0 mL/min/
kg), good aqueous solubility (71 lM) and permeability (MDCK Papp
and JAK1 selectivity were observed when sulfonamide moieties
with one carbon C-2 linkers were combined with cycloalkyl R2 sub-
stituents (64–67, 69–73). Among the cycloalkyl R2 substituents
A:B = 8.2x10À6 cm/s). The compound did not inhibit Cytochrome-
P450 (CYP) enzymes (1A2, 3A4, 2C9, 2C19, and 2D6; IC50 val-
ues = >10 lM), and did not exhibit any time dependent inhibition

7630
S. Labadie et al. / Bioorg. Med. Chem. Lett. 22 (2012) 7627–7633
Table 1
SAR of compounds 5, 33–43 and 48–53
CN
N
R1
N
N
N
H
N
Ex.
5
R1
JAK1 Ki (nM)a,b
0.9
Biochemical JAK1 Selectivityc
2.3
IL-6-pSTAT3 JAK1 EC50 (nM)a,b
26
Cell JAK1 Selectivityd
3.7
Cell_Shifte
29
tPSAf
73
Me
33
4.6
2.9
9.1
2.1
1.8
4.2
275
160
410
5.7
4.3
16
60
55
45
73
73
73
34g
35
36
37
4.3
16
3.6
4.5
430
6.2
5.1
100
125
73
73
2000
O
38h
39h
40
24
8.7
43
1.5
5.4
4.8
1300
570
7.2
9.2
3.8
54
65
60
82
82
82
O
2600
O
N
N
41
9.3
5.5
5200
1.9
559
91
N
42
43
14
13
2.6
7.6
1800
2600
5.6
3.9
128
200
91
91
N
N
N
O
48g
49
16
5.4
3.6
5.5
>3800
625
2.6
10
>238
74
102
111
119
N
H
O
8.4
7.3
O
N
H
O
O
O
S
50
>3500
2.9
>479
N
H
O
O
S
51
5.4
11
1200
8.6
222
119
N
H
O
52
53
3.7
1.7
5.6
7.0
>6500
>6000
1.5
1.7
>1756
>3529
102
119
N
H
O
S
N
H
a
Unless otherwise noted, all biochemical and cell-based assay results are reported as the arithmetic mean of at least 3 separate runs (n = 3). On average, the coefficients of
variation were less than 0.3 times the mean for biochemical assays and less than 0.5 times the mean for cell-based assays.
b
For biochemical and cell based assay details see Ref. 16
c
Biochemical JAK1 selectivity vs JAK2 = JAK2 Ki Ä JAK1 Ki.
d
Cell based JAK1 selectivity vs JAK2 = EPO-pSTAT5 EC50 Ä IL6-pSTAT3 EC50.
e
Cell-Shift = IL6-pSTAT3 EC50 Ä JAK1 Ki.
f
Topological polar surface area. see Ref. 28
g
Biochemical data from a single run.
Racemate.
h

S. Labadie et al. / Bioorg. Med. Chem. Lett. 22 (2012) 7627–7633
7631
Table 2
SAR of compounds 54–73
R1
N
R2
N
N
H
N
Ex.
54
R1
R2
JAK1 Ki (nM)a,b Biochemical JAK1 Selectivityc IL-6 pSTAT3-JAK1 EC50 (nM)a,b JAK1 Cell Selectivityd Cell-Shifte tPSAf
O
12
6.7
10
1500
325
2.8
20
125
65
78
F3C
N
N
N
H
O
S
O
O
O
O
O
O
O
55g
56h
57h
58
5.0
5.8
97
95
F3C
O
N
H
O
S
23
1300
>5300
2200
86
7.6
1.9
4.5
43
224
>54
523
41
101
101
112
92
N
H
O
O
S
7.6
18
N
H
O
S
4.2
2.1
18
N
H
HO
S
O
S
59h
60h
61
27
N
H
S
O
S
7.6
8.0
1600
4200
3.0
1.8
89
92
N
H
O
S
O
28
150
101
N
H
Exo-racemate
O
O
62
63
64
65
66
10
8.5
12
18
14
26
670
210
190
180
815
9.6
19
27
13
11
67
75
75
92
92
92
N
H
2.6
2.6
2.1.
5.3
81
N
H
O
S
O
73
N
H
O
S
O
85
N
H
O
S
O
154
N
H
O
S
O
67
68
69
70i
71
72
3.3
3.0
0.3
0.6
3.2
0.2
4.4
8.4
28
130
160
30
13
19
41
9.0
9.7
40
39
92
92
92
92
92
92
N
H
O
53
N
H
Exo-racemate
Exo-racemate
Exo-racemate
Endo-racemate
O
S
O
O
100
83
N
H
O
S
N
H
10
50
O
S
O
O
7.1
27
355
13
110
65
N
H
O
S
N
H
(continued on next page)

7632
S. Labadie et al. / Bioorg. Med. Chem. Lett. 22 (2012) 7627–7633
Table 2 (continued)
Ex.
R1
R2
JAK1 Ki (nM)a,b Biochemical JAK1 Selectivityc IL-6 pSTAT3-JAK1 EC50 (nM)a,b JAK1 Cell Selectivityd Cell-Shifte tPSAf
O
O
S
73
3.8
9.5
160
14
42
92
N
H
a
Unless otherwise noted, all biochemical and cell-based assay results are reported as the arithmetic mean of at least 3 separate runs (n = 3). On average, the coefficients of
variation were less than 0.3 times the mean for biochemical assays and less than 0.5 times the mean for cell-based assays.
b
For biochemical and cellular assay details see Ref.16
c
Biochemical JAK1 selectivity vs JAK2 = JAK2 Ki Ä JAK1 Ki.
d
Cell JAK1 selectivity vs JAK2 = EPO-pSTAT5 EC50 Ä IL6-pSTAT3 EC50
Cell-Shift = IL6-pSTAT3 EC50 Ä JAK1 Ki.
.
e
f
Topological polar surface area, see Ref. 28
g
h
i
Biochemical data is the average of two runs.
Single enantiomer of unknown absolute configuration.
Biochemical data from a single run.
Table 3
Rat in vivo PK parameters of compound 72
IV CL (mL/min/kg)a
IV Vss (L/kg)
4.0
IV T1 (h)
PO AUC (
l
M⁄h)b
PO%F
79
2
33
1.5
2.2
a
Intravenous bolus dose (0.4 mg/kg) as a solution in DMSO/PEG/water (5/55/40).
Oral dose (2 mg/kg) formulated as a suspension in MCT.
b
(TDI) against the same CYP isoforms. Only two out of 284 kinases
(CSF-1R, LRRK2) were inhibited greater than 50% when the com-
pound was tested in the Invitrogen screening panel at 0.10 lM
(625 fold above the JAK1 Ki value). The in vivo DMPK profile of com-
pound 72 in rat is detailed in Fig. 4 and Table 3. The inhibitor dis-
played moderate IV-clearance and excellent oral exposure/
bioavailability suggesting it was appropriate for oral delivery.
In order to better understand the excellent selectivity of 72 for
JAK1 over JAK2, the crystal structure of the inhibitor bound to the
JAK1 enzyme was obtained (Fig. 5). As expected, the pyrrolopyri-
dine ring of 72 makes two H-bond interactions in the hinge region
of the JAK1 protein similar to those observed for compound 6.16
The tricyclic moiety of 72 makes van der Waals contacts with
JAK1 residues L881, V889, A906, and V938 of the N-terminal lobe
and L1010 of the C-terminal lobe. The norbornyl methylene group
is buried in the hydrophobic region of the C-terminal residue
(L1010) and also makes hydrophobic interactions with V889 of
Fig. 4. Plasma concentration vs. time profiles following IV (0.4 mg/kg) and oral
(2 mg/kg) administration of compound 72 to male Sprague Dawley rats (n = 2).
Fig. 5. X-ray structure of 72 in complex with JAK1 at 2.2 Å resolution (deposited in the PDB under accession code 4FK6). Figures 5a and 5b provide two visual perspectives. 5b
is rotated approximately 90 degrees relative 5a. Compound 72 is depicted in orange. Hydrogen bonds between the ligand and hinge are shown as dashed purple lines.
Hydrogen bonds between the ligand and side chain residues R879 and E966 are shown as dashed red lines.

S. Labadie et al. / Bioorg. Med. Chem. Lett. 22 (2012) 7627–7633
7633
http://dx.doi.org/10.1002/art.29936.; (b) Fridman, J. S.; Scherle, P. A.; Collins,
R.; Burn, T. C.; Li, Y.; Li, J.; Covington, M. B.; Thomas, B.; Collier, P.; Favata, M. F.;
Wen, X.; Shi, J.; McGee, R.; Haley, P. J.; Shepard, S.; Rodgers, J. D.; Yaleswaram,
G. H.; Newton, R. C.; Metcalf, B.; Friedman, S. M.; Vaddi, K. J. Immunol. 2010,
184, 5298.
the N-terminal lobe. The NH- of the methanesulfonamide makes a
2.7 Å H-bond interaction with the O-atom of the carboxylic group
of the E966 side chain residue. In addition, an O-atom of the sulfon-
amide group in 72 forms a 3.0 Å H-bond with the guanidine NH of
the R879 JAK1 side chain residue. To date, we have been unsuc-
cessful in obtaining a crystal structure of 72 bound to the JAK2 iso-
form. However, we hypothesize that, as observed in the crystal
structure of inhibitor 6 bound to JAK2 (Fig. 3b), the D939 JAK2 side
chain is likely too far away from the ligand 72 to be involved in a
direct H-bond interaction. A similar situation may also apply in the
case of the Q853 JAK2 side chain location relative to the R879 JAK1
side chain. We therefore speculate that the two strong hydrogen
bond interactions observed in JAK1 with the E966 and R879 resi-
dues (which differ between JAK1 and JAK2 isoforms) are responsi-
ble for the observed selectivity of the inhibitor 72.
In summary, we utilized structure-based design techniques to
discover very potent and JAK1 selective tricyclic imidazo-pyrrolo-
pyridine inhibitors bearing polar substituents at the C-2 position.
We also demonstrated that balancing the polarity of the molecule
was essential to obtain desired cellular activity. The excellent
selectivity for JAK1 relative to JAK2 exhibited by the inhibitor 72
was clarified by the crystal structure of the compound bound to
JAK1. This structure revealed two direct H-bond interactions be-
tween the sulfonamide moiety at the C-2 position of the ligand
and the side chains of two residues which differ between JAK1
and JAK2. Additional efforts to exploit similar interactions to gain
selectivity for JAK1 relative to JAK2 will be reported in future
disclosures.
12. Parganas, E.; Wang, D.; Stravopodis, D.; Topham, D. J.; Marine, J. C.; Teglund, S.;
Vanin, E. F.; Bodner, S.; Colamonici, O. R.; van Deursen, J. M.; Grosveld, G.; Ihle,
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19. The cyclization of the amides 11–21 to form 22–32 proceeded with poor yields
(10–30%). The main side reaction was the loss of the benzenesulfonamide
protecting group prior to cyclization. The unprotected intermediate amides
failed to undergo cyclization even with extended reaction times.
20. In some instances, when the imidate formation with triethyloxonium
tetrafluoroborate was performed in THF, polymerization of the solvent
occurred to form a viscous mass and the reaction could not be continued.
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References and notes
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11. (a) A related small molecule JAK1/2 inhibitor (INCB028050/LY3009104) is
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25. Chiral separation of 56 and 57 was performed by SFC using Chiralpak OJ
column and 20% methanol 80% CO2 as mobile phase.
26. Chiral separation of 59 and 60 was performed by SFC using Chiralpak IC
column and 35% methanol w/0.1% NH4OH/65% CO2 as mobile phase.
27. Chiral separation of 72 and 73 was performed by SFC using Phenomenex
Cellulose-1column and 40% methanol w/0.1% NH4OH/60% CO2 as mobile phase.
28. Ertl, P.; Rohde, B.; Selzer, P. J. Med. Chem. 2000, 43, 3714.
29. Compound 73 was synthesized using norbornyl amine of known chirality
(obtained as described in Ref. 24). The chirality of the corresponding
enantiomer 72 was inferred from the configuration of 73 and was supported
by the co-crystal structure with JAK1.
30. In vitro IL6-pSTAT3 cell-based assay conducted in TF-1 cells in the presence of
human whole blood. See supporting information in Ref. 16.