Bioorganic & Medicinal Chemistry Letters 19 (2009) 279–282
Bioorganic & Medicinal Chemistry Letters
Fragment-based discovery of JAK-2 inhibitors
*
Stephen Antonysamy, Gavin Hirst , Frances Park, Paul Sprengeler, Frank Stappenbeck, Ruo Steensma,
Mark Wilson, Melissa Wong
Medicinal Chemistry, SGX Pharmaceuticals, Inc., 10505 Roselle Street, San Diego, CA 92121, USA
a r t i c l e i n f o
a b s t r a c t
Article history:
Received 7 July 2008
Revised 18 August 2008
Accepted 18 August 2008
Available online 22 August 2008
Fragment-based hit identification coupled with crystallographically enabled structure-based drug design
was used to design potent inhibitors of JAK-2. After two iterations from fragment 1, we were able to
increase potency by greater than 500-fold to provide sulfonamide 13, a 78-nM JAK-2 inhibitor.
Ó 2008 Published by Elsevier Ltd.
Keywords:
Fragment-based design
JAK-2 inhibitors
Structure-based design
Aminoindazole
Kinase inhibitors
The Janus Kinase (JAK) family comprises four cytoplasmic
receptor-associated protein tyrosine kinases, JAK-1, JAK-2, JAK-3,
and Tyk-2. Members of this enzyme family participate in signal
transduction pathways mediated by many cytokines and cyto-
kine-like hormones.1 Initial biochemical studies implicated JAK-2
in the response to receptors from the single-chain and IL-3 cyto-
lographic fragment screening can identify hits with low or unde-
tectable potency in biochemical assays. Crystallographic fragment
screening also provides unambiguous proof of binding to the target
site and reveals the details of the hit’s binding mode. This informa-
tion provides clear direction for how they may be optimized into
more potent lead compounds using efficient fragment elaboration.
We developed experimental protocols for growing JAK-2 crys-
tals that were suitable for determining inhibitor co-crystal struc-
tures by soaking. Fragments in the SGX core screening library
were chosen to be consistent with ‘lead-like’ properties, and also
to include two or more substituents to facilitate rapid analog syn-
thesis. The fragment library had a MW range of 100–220 Da and an
average MW of 160.
kine families as well as the IFN-c
receptor.2 Consistent with a crit-
ical role in erythropoiesis, knock-out of JAK-2 in mice is
embryonically lethal.3 It is noteworthy that that humans with
JAK-2 mutations exhibit myloproliferative disorders (MPD).4 Spe-
cifically, a characteristic somatic mutation, JAK-2 V617F, has re-
cently been identified in patients with polycythemia vera,
essential thrombocytosis, and myelofibrosis.5 This mutation re-
sults in a constitutively active JAK-2 tyrosine kinase. This gain-
of-function mutation has stimulated discovery and development
of inhibitors that selectively target JAK-2 as an approach toward di-
rected therapy of MPD.6 This paper describes the identification of a
series of potent JAK-2 wild-type (WT) and JAK-2 V617F inhibitors
derived from a fragment-based approach.
H
1
N
2
N
5
Br
4
H2N
1
Fragment-based lead discovery has been recently reviewed.7 In
summary, the high screening hit rate for such small, low-MW com-
pounds can often lead to the identification of novel, tractable hits
and is recognized as a tangible alternative to more traditional
high-throughput screening methods of hit identification. These
highly ligand efficient (LE) starting points can be optimized into
potent leads with good ‘drug-like’ properties. In particular, crystal-
JAK-2 IC50 = 40.9 uM
LE = 0.54
Examination of a number fragments bound to JAK-2 revealed the
bromoaminoindazole 1, a 41-lM JAK-2 inhibitor, as an attractive
starting point, particularly given its high ligand efficiency. It is note-
worthy that the corresponding 6-bromo analog is a less potent
inhibitor (131 lM). Analysis of the X-ray crystal structure of 1
bound to JAK-2 in Figure 1 revealed three hydrogen bonds between
* Corresponding author. Tel.: +1 858 228 1630; fax: +1 858 588 0642.
the aminoindazole and the hinge region. Specifically, the 3-amino
0960-894X/$ - see front matter Ó 2008 Published by Elsevier Ltd.
doi:10.1016/j.bmcl.2008.08.064