Bioorganic & Medicinal Chemistry Letters
Discovery of novel benzo[b][1,4]oxazin-3(4H)-ones
as poly(ADP-ribose)polymerase inhibitors
a
a
a
a
Anthony R. Gangloff a, , Jason Brown , Ron de Jong , Douglas R. Dougan , Charles E. Grimshaw ,
Mark Hixon a, Andy Jennings a, Ruhi Kamran a, Andre Kiryanov a, Shawn O’Connell b, Ewan Taylor a
Phong Vu a
⇑
a Takeda California, 10410 Science Center Dr, San Diego, CA 92121, USA
b Quanticel Pharmaceuticals, 9393 Towne Center Dr #110, 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:
Structure based drug design of a series of novel 1,4-benzoxazin-3-one derived PARP-1 inhibitors are
described. The synthesis, enzymatic & cellular activities and pharmacodynamic effects are described.
Optimized analogs demonstrated inhibition of poly-ADP-ribosylation in SW620 tumor bearing nude mice
through 24 h following a single dose.
Received 18 April 2013
Revised 13 June 2013
Accepted 17 June 2013
Available online 24 June 2013
Ó 2013 Elsevier Ltd. All rights reserved.
Keywords:
Poly(ADP-ribose)polymerase inhibitors
PARP-1
Structure-based drug design
1,4-Benzoxazin-3-one
Chemopotentiation
The enzyme poly(ADP-ribose)polymerase (PARP), previously
known as poly(ADP-ribose)synthase and poly(ADP-ribosyl)trans-
ferase, constitutes a super family of proteins containing PARP cat-
alytic domains involved in the repair of DNA, the regulation of
cellular energy pools, and the transcription of inflammatory
genes.1 PARP-1 is a nuclear enzyme which catalyzes DNA repair
through cleavage of NAD+ to nicotinamide and ADP-ribose to form
long, branched ADP-ribose polymers on target proteins.2 PARP-1
inhibition leads to sustained DNA damage and ultimately apopto-
sis when used in combination with DNA damaging agents such
as temozolomide (TMZ), thus providing for chemopotentiation
in vitro and in vivo.3 PARP-1 inhibitors have also been shown to
act as single agents through a form of synthetic lethality4 by
exploiting a DNA repair flaw seen in tumors expressing defective
BRCA1/2-genes.5 Therefore, inhibition of PARP-1 (which is over-ex-
pressed in tumors) is expected to hinder intracellular DNA repair
and enhance the antitumor effects of cancer therapies.6
inhibitors, from which the 1,4-benz-oxazin-3-one core emerged
as a promising chemotype. Using a published PARP-1 X-ray crystal
structure,8 benzoxazinone 2a was overlaid onto the bound ligand
present in the crystal structure (Fig. 2). Our analysis based on
alignment of the cis-amide indicated the 6-position of the benzox-
azinone to be a suitable initial starting point for extension into the
back pocket to pick up interactions with the protein, although the
7-position could offer an additional vector. In addition, we antici-
pated that interactions with the hydrophobic shelf could be
achieved through substitution on the 2- and 8-position of the ben-
zoxazinone core.
The initial compounds were synthesized as outlined in
Scheme 1. Alkylation of substituted o-nitrophenols was accom-
plished in >70% yield using
a-bromoacetates in DMF with K2CO3.
Reduction of the nitro group and subsequent cyclization of the
resultant amine was achieved in a single step using iron dust in
AcOH at 80 °C. Reductive amination when R3 is a formyl group
introduced substituents which could extend into the back pocket.
A notable observation was that a methyl group at the 2-position
increased both binding potency against PARP-1 and ligand-lipo-
philic efficiency10 (LLE) as demonstrated by the benzoxazinone
fragments 2a and 2d where the 2-methyl group confers an order
of magnitude improvement in inhibitory activity (Table 1). In the
case of 3d and 3e, the Kd was increased by two log units and LLE
by 1.5 log units. These observations can be explained by the
presence of a proximal narrow hydrophobic cleft (defined by
A key feature of PARP inhibitors is the ability to mimic nicotin-
amide binding to the backbone carbonyl and amide N–H of Gly202
as well as the O–H of Ser243 in the NAD pocket of PARP-1 (Fig. 1).7
Hence, inhibitors containing a cis-amide capable of competing with
NAD+ were considered to be a good starting point. A screening
campaign identified several small fragments as weak PARP
⇑
Corresponding author. Tel.: +1 858 731 3531; fax: +1 858 550 0526.
0960-894X/$ - see front matter Ó 2013 Elsevier Ltd. All rights reserved.