Discovery of potent poly(ADP-ribose) polymerase-1 inhibitors from the modification of indeno[1,2-c]isoquinolinone

Article abstract of DOI:10.1021/jm0502891

Novel indeno[1,2-c]isoquinolinone derivatives were synthesized and evaluated as inhibitors of the nuclear enzyme poly(ADP-ribose) polymerase-1 (PARP-1). These potent non-mutagenic PARP-1 inhibitors possess an additional five-membered ring between the B an

Full text of DOI:10.1021/jm0502891

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5100
J. Med. Chem. 2005, 48, 5100-5103
Discovery of Potent Poly(ADP-ribose)
Polymerase-1 Inhibitors from the
Modification of
Indeno[1,2-c]isoquinolinone
Prakash G. Jagtap,* Erkan Baloglu,
Garry J. Southan, Jon G. Mabley, Hongshan Li,
Jing Zhou, John van Duzer, Andrew L. Salzman, and
Csaba Szabo´
Inotek Pharmaceuticals Corporation, 100 Cummings Center,
Suite 419E, Beverly, Massachusetts 01915
Received March 31, 2005
Figure 1. Design of novel PARP-1 inhibitors.
Abstract: Novel indeno[1,2-c]isoquinolinone derivatives were
synthesized and evaluated as inhibitors of the nuclear enzyme
poly(ADP-ribose) polymerase-1 (PARP-1). These potent non-
mutagenic PARP-1 inhibitors possess an additional five-
membered ring between the B and C rings of 6(5H)-phenan-
thridinone. The most potent PARP-1 inhibitors were obtained
from the substitution of the D ring at the C-9 position, in
particular sulfonamide and N-acyl analogues (6 and 11). The
9-sulfonamide analogues 11a and 12a exhibited IC50 values
of 1 and 10 nM, respectively.
Scheme 1. Synthesis of C-8 Substituted
Indeno[1,2-c]isoquinolinonesa
Poly(ADP-ribose) polymerase (PARP) activation plays
a role in the pathogenesis of various cardiovascular and
inflammatory diseases.1 At the same time, PARP acti-
vation is also relevant for the ability of cells to repair
injured DNA. Thus, depending on the circumstances,
pharmacological inhibitors of PARP may be able to
attenuate ischemic and inflammatory cell and organ
injury or may be able to enhance the cytotoxicity of
antitumor agents. Both aspects of the “double-edged
sword” role of PARP can be exploited for the experi-
mental therapy of many diseases (overviewed in ref 1).
Recent articles2 suggest a new mechanism-based ap-
proach for the treatment of patients with BRCA2-
associated cancers with PARP inhibitors.
Extensive investigations have been conducted in the
identification of novel PARP-1 inhibitors.2 Various ap-
proaches to design the scaffolds for PARP inhibitors
based on the prototypical PARP inhibitor 3-aminoben-
zamide have been developed.2 Structure-activity rela-
tionship studies have provided insight into the struc-
tural requirements that are important for the inhibition
of PARP. One of the commonly used techniques is to
lock the amide group of benzamide in the anti confor-
mation. With this tool, several bi-, tri-, and tetracyclic
lactam scaffolds were investigated and modified to
achieve potent PARP-1 inhibitory activity.2,3 Previous
reports4,5 showed that the modifications at the C-2
position of 6(5H)-phenanthridinone are well-tolerated
(Figure 1). Introduction of appropriate side chains,
which carry a terminal amino group, at the C-2 position
showed improved PARP-1 inhibition compared to the
unsubstituted 6(5H)-phenanthridinone. Because of its
structural similarity to the prototypical PARP inhibi-
tors6 6(5H)-phenanthridinone and isoquinolinone, in-
a (a) Ammonium formate, Pd-C (10%), DMF, heat, 95%; (b)
ClCOCH2Cl, saturated NaHCO3, EtOAc, DMF, 67%; (c) HNR1R2,
EtOH or DMF, 5a 75%, 5b 66%, 5c 67%; (d) ClCO(CH2)3Cl,
saturated NaHCO3, EtOAc, DMF, 97%; (e) morpholine, DMF,
Et3N, 82%.
deno[1,2-c]isoquinolinone was chosen as a scaffold for
further chemical modifications (Figure 1). In addition
and in contrast to the 6(5H)-phenanthridinones, the
methylene group of the five-membered C ring of indeno-
[1,2-c]isoquinolinone disrupts the planarity of the basic
structure so that it is not a DNA intercalator.7
Indeno[1,2-c]isoquinolinones have been known for
topoisomerase-I inhibitory activity.8 Cushman et al.7,8
have synthesized a series of 11-keto derivatives of
indeno[1,2-c]isoquinolinone starting from homophthalic
anhydride and benz[d]indeno[1,2-b]pyran-5,11-dione.
The starting compounds 1a-e required in this study
were obtained as reported elsewhere.9 The synthetic
routes for the newly synthesized C-8 and C-9 substi-
tuted indeno[1,2-c]isoquinolinone analogues are outlined
in Schemes 1 and 2.
* To whom correspondence should be addressed. Phone: (978) 232
9660, extension 2295. Fax: (978) 232 8975. E-mail: pjagtap@
inotekcorp.com.
10.1021/jm0502891 CCC: $30.25 © 2005 American Chemical Society
Published on Web 07/16/2005

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Journal of Medicinal Chemistry, 2005, Vol. 48, No. 16 5101
Scheme 2. Synthesis of C-9 Substituted
Indeno[1,2-c]isoquinolinonesa
Scheme 3. Synthesis of C-9 Sulfonamide Derivatives of
Indeno[1,2-c]isoquinolinonesa
a (a) Concentrated H2SO4, 0 °C to room temperature, then
NaOH; (b) ClSO3H, 0 °C to room temperature, 9 92%; (c)
H2N(CH2)nNR1R2 or H2N(CH2)nPh, 4-aminomorpholine or imida-
i
zole, CH2Cl2, Et3N or Pr2EtN, room temp, 11a 44%.
appropriate amines in the presence of triethylamine.
Similarly, the 12a, 12b, and 12c were prepared by
treating 10 with 4-(3-aminopropyl)morpholine, 4-ami-
nomorpholine, and imidazole, respectively. Compound
13 was obtained from the reaction of 1a with concen-
trated H2SO4 followed by treatment with NaOH. Qua-
ternary ammonium salt 14 was prepared from 11a and
MeI.
The inhibition of purified PARP-1 enzyme by selected
compounds was subsequently determined. The assay
was performed in 96-well ELISA plates according to
instructions provided with a commercially available
PARP inhibition assay kit (Trevigen, Gaithersburg,
MD). The inhibitory effect of the compounds on PARP
activity is summarized in Table 1. An IC50 value of the
prototypical PARP-1 inhibitor, 3-aminobenzamide (3-
AB), is included in Table 1 as a reference. The unsub-
stituted indeno[1,2-c]isoquinolinone core molecule 1a
showed poor PARP-1 inhibitory activity. The C-8 and
C-9 nitro and fluoro derivatives (1b-e) exhibited mod-
erate activity. The 9-amino compound 2b showed a
3-fold increase in potency compared to the 8-amino
analogue 2a.
The C-8 N-substituted amide compounds (5b and 5c),
which carry morpholine and piperazine groups on the
side chain, also showed weak PARP-1 inhibition. How-
ever, the dimethylamino derivative 5a, which contains
a one methylene unit linker, and the morpholine deriva-
tive 5d with a three methylene linker exhibited IC50
values of 0.8 and 0.4 µM, respectively. The correspond-
ing C-9 substituted derivatives 6a and 6c (both camphor
sulfonic acid salts) exhibited EC50 values of 0.028 and
0.009 µM, respectively. The C-9 analogues with the
amine separated from the carbonyl by one or three
methylene groups showed increased PARP-1 inhibitory
potency. The nature of the linker and the size of the
a (a) Ammonium formate, Pd-C (10%), DMF, heat, 68%; (b)
ClCOCH2Cl, saturated NaHCO3, EtOAc, DMF, 82%; (c) ClCO-
(CH2)3Cl, saturated NaHCO3, EtOAc, DMF; (d) HNR1R2, EtOH
or DMF, 6a 92%; (e) morpholine, DMF, Et3N, 6c 85%; (f)
ClCOCH2OAc, saturated NaHCO3, EtOAc, DMF, 72%; (g) NH2-
NH2‚H2O, EtOH, reflux, 7 82%; (h) n-propylisocyanate, DMF, 100
°C, 6 h, 8 42%.
Our initial attempts to make 1b or 1c from the
nitration of 1a were not successful, resulting in mixed
nitration products. The nitro derivatives (1b and 1c)
obtained from the alternative synthesis9 were reduced
to 8- and 9-aminoindeno[1,2-c]isoquinolinones 2a and
2b using Pd-C (10%) and ammonium formate in DMF.
Schotten-Baumann acylation reaction of 2a and 2b
with chloroacetyl chloride in ethyl acetate and in the
presence of saturated NaHCO3 provided chloroacetyl
derivatives 3a and 4a, respectively. Following similar
reaction conditions, 3b and 4b were prepared from 2a
and 2b using 3-chlorobutyl chloride. Amination of 3a
with dimethylamine, morpholine, and 4-methylpipera-
zine provided the amino-substituted compounds 5a, 5b
and 5c respectively. Under similar conditions, 3b and
morpholine produced 5d. Similarly, the 8-chloroacetyl
derivative 4a was treated with dimethylamine and 1-(4-
fluorophenyl)piperazine in ethanol to produce the amino
derivatives 6a and 6b, respectively. Compound 6c was
prepared from chlorobutyryl derivative 4b and morpho-
line using triethylamine. The analogues 7 and 8 were
prepared from 2b as depicted in Scheme 2.
The synthesis of 9-sulfonamide derivatives is outlined
in Scheme 3. Selective C-9 chlorosulfonation of the
indeno[1,2-c]isoquinolinones 1a and 1d was achieved
using chlorosulfonic acid. The resulting cholorosulfonyl
compounds 9 and 10 were contaminated with corre-
sponding sulfonic acid derivatives. The sulfonamides
11a-c were then obtained by reacting 9 with the

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5102 Journal of Medicinal Chemistry, 2005, Vol. 48, No. 16
Table 1. PARP-1 Activity Data of Indeno[1,2-c]isoquinolinones
Letters
a Assay performed using the commercially available PARP inhibition assay kit (Trevigen, Gaithersburg, MD). b EC50 values determined
using the cell protection assay (see Supporting Information for the assay procedures). nd: not determined. c An average of EC50 and IC50
values measured from three cellular or cell-free assays. d Reference 10.
amino group appear to play a major role in the PARP-1
activity in C-8 and C-9 substituted indeno[1,2-c]-
isoquinolinones.
fied above, the C-8 derivatives generally showed weaker
PARP-1 inhibition than the corresponding C-9 substi-
tuted compounds. However, the C-8 and C-9 disubsti-
tuted 12a was 25-fold more potent than the 9-fluoroin-
deno[1,2-c]isoquinolinone (1d). An increase in potency
of the disubstituted compound 12a could be explained
by the presence of the sulfonamide linker of 11a at the
C-8 position.
The 9-sulfonic acid sodium salt (13) showed an IC50
of 0.7 µM. However, the 9-sulfonamide derivative 11a
mesylate salt exhibited excellent PARP-1 inhibition in
both assays (IC50 and EC50 of 1 and 10 nM, respectively).
Replacement of the morpholino group of 11a with a
phenyl ring (11c) resulted in deleterious effects on the
activity. Compound 14 with the N-methylmorpholinium
group showed a large decrease in activity. As exempli-
In conclusion, we have synthesized a novel series of
potent PARP-1 inhibitors from the modification of
indeno[1,2-c]isoquinolinones. It is of interest to note that

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Letters
Journal of Medicinal Chemistry, 2005, Vol. 48, No. 16 5103
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and clinical data will be published in due course.
Acknowledgment. This work was supported by the
National Institutes of Health (Grants R44DK054099
and R44GM058986).
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Supporting Information Available: Experimental pro-
cedures and spectral data for the new and known products
and detailed PARP-1 assay procedures. This material is
available free of charge via the Internet at http://pubs.acs.org.
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JM0502891