Expanding the structural diversity of Bcr-Abl inhibitors: Hybrid molecules based on GNF-2 and Imatinib

Article abstract of DOI:10.1016/j.bmcl.2015.08.013

In order to expand the structural diversity of Bcr-Abl inhibitors, twenty hybrids (series E and P) have been synthesized and characterized based on Imatinib and GNF-2. Their biological activities were evaluated in vitro against human leukemia cells. Most compounds exhibited potent antiproliferative activity against K562 cells, especially for compounds E4, E5 and E7. Furthermore, these new hybrids were also screened for Abl kinase inhibitory activity, and some of them inhibited Abl kinase with low micromolar IC₅₀ values. In particular, compound P3 displayed the most potent activity with IC₅₀ value of 0.017 μM comparable with that of Imatinib. Molecular docking studies indicated that these novel hybrids fitted well with the active site of Bcr-Abl. These results suggested the great potential of these compounds as novel Bcr-Abl inhibitors.

Full text of DOI:10.1016/j.bmcl.2015.08.013

Bioorganic & Medicinal Chemistry Letters xxx (2015) xxx–xxx
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Expanding the structural diversity of Bcr-Abl inhibitors: Hybrid
molecules based on GNF-2 and Imatinib
⇑
Xiaoyan Pan, Jinyun Dong, Ruili Shao, Ping Su, Yaling Shi, Jinfeng Wang, Langchong He
School of Pharmacy, Health Science Center, Xi’an Jiaotong University, No. 76, Yanta West Road, Xi’an, Shaanxi Province 710061, PR China
a r t i c l e i n f o
a b s t r a c t
Article history:
In order to expand the structural diversity of Bcr-Abl inhibitors, twenty hybrids (series E and P) have been
synthesized and characterized based on Imatinib and GNF-2. Their biological activities were evaluated
in vitro against human leukemia cells. Most compounds exhibited potent antiproliferative activity
against K562 cells, especially for compounds E4, E5 and E7. Furthermore, these new hybrids were also
screened for Abl kinase inhibitory activity, and some of them inhibited Abl kinase with low micromolar
Received 11 April 2015
Revised 8 July 2015
Accepted 6 August 2015
Available online xxxx
IC50 values. In particular, compound P3 displayed the most potent activity with IC50 value of 0.017 lM
Keywords:
comparable with that of Imatinib. Molecular docking studies indicated that these novel hybrids fitted
well with the active site of Bcr-Abl. These results suggested the great potential of these compounds as
novel Bcr-Abl inhibitors.
Bcr-Abl inhibitors
Hybrid molecule
Bioactivity
Ó 2015 Elsevier Ltd. All rights reserved.
Docking
Chronic Myeloid Leukemia (CML), characterized by the clonal
expansion of cells carrying the Philadelphia (Ph) chromosome, is
a hematopoietic stem cell disease that accounts for 15–20% of all
leukemias diagnosed in adults.1 The Ph chromosome encodes the
chimeric protein Bcr-Abl with constitutively activated kinase activ-
ity.2,3 The Bcr-Abl kinase plays a critical role in the extracellular or
intracellular signal transduction pathways related to CML.4 The
Bcr-Abl kinase can phosphorylate a series of downstream sub-
strates, leading to the unlimited proliferation of mature granulo-
cytes.5 Due to the non-expression of Bcr-Abl kinase in the normal
hemopoietic stem cell, it is a well validated target for development
of small molecular inhibitors to treat CML.6
Large efforts have been devoted to the development of novel
Bcr-Abl kinase inhibitors. Imatinib is the first FDA approved Bcr-
Abl inhibitor that has been successful in treating chronic phase
CML patients.7,8 Followed by Imatinib, second generation Bcr-Abl
inhibitors including Nilotinib,9 Bafetinib,10 Dasatinib11 and
Bosutinib,12 are next developed to overcome resistance caused by
Bcr-Abl mutants. At present, the ‘third generation’ Bcr-Abl inhibi-
tor Ponatinib has been developed to overcome T315I mutation13
(Fig. 1). However, it has serious side effects like blood clotting in
cardiac valves, chambers and cerebral vessels.14 Although these
drugs have been successfully used in clinical application, novel
strategies and compounds are still in need for the treatment of
CML especially Imatinib-resistance. In this Letter, we focus our
efforts on design and synthesis of hybrid molecules as novel
Bcr-Abl inhibitors based on Imatinib and GNF-2, expanding the
structural diversity of Bcr-Abl inhibitors.
Imatinib is an ATP-competitive inhibitor that binds to a DFG
(AspPheGly)-out conformation of the Abl kinase domain to keep
Bcr-Abl kinase in the inactive conformation, eliminating Bcr-Abl
kinase’s capacity for phosphorylation. GNF-2 is a highly selective
inhibitor of Bcr-Abl, binding to the myristate site of Bcr-Abl located
at the N-terminus.15,16 It has been found that combining GNF-2
with ATP-competitive inhibitor such as Imatinib displayed additive
inhibitory effect in biochemical and cellular assays against native
or mutant human Bcr-Abl, and suppressed the emergence of resis-
tance mutations in vitro.16–18 Based on Imatinib and GNF-2, hybrid
strategy was applied to develop Bcr-Abl inhibitors with new
chemotypes possessing kinase inhibitory activity.
Crystallographic studies revealed that Imatinib interacted with
Bcr-Abl through four important pharmacophores (Fig. 2): the aro-
matic structure reacting with the hinge region; the phenyl ring
occupying hydrophobic pocket II; the core structure with H-bond
donor/acceptor, reacting with DFG motif; and the aromatic rings
with substituents occupying the allosteric site.19,20 Structural anal-
ysis of chemical features of GNF-2 and Imatinib revealed that they
possessed similar aromatic structure reacting with hinge region.
The phenylpyrimidine of GNF-2 (indicated in blue, Fig. 3) could
mimic pyridinylpyrimidine substructure in Imatinib. There is also
another hydrophobic pocket named as pocket I which is adjacent
to the hinge region (Fig. 2). The aniline in GNF-2 (indicated in pink,
Fig. 3) might occupy this hydrophobic pocket because of the direc-
tional effect of pyrimidine substructure. Since this introduced
⇑
Corresponding author.
http://dx.doi.org/10.1016/j.bmcl.2015.08.013
0960-894X/Ó 2015 Elsevier Ltd. All rights reserved.
Please cite this article in press as: Pan, X.; et al. Bioorg. Med. Chem. Lett. (2015), http://dx.doi.org/10.1016/j.bmcl.2015.08.013

2
X. Pan et al. / Bioorg. Med. Chem. Lett. xxx (2015) xxx–xxx
CF3
N
N
N
N
N
O
H
N
H
N
N
H
N
H
N
H
N
N
N
N
N
N
N
H
N
CF3
N
O
N
O
N
N
Imatinib
Nilotinib
Bafetinib
N
Cl
Cl
N
N
N
N
HN
O
N
N
N
O
N
OH
O
O
CN
HN
S
N
NH
H
N
N
Cl
O
CF3
N
N
Ponatinib
Bosutinib
Dasatinib
Figure 1. Chemical structures of Bcr-Abl inhibitors.
H
The synthetic route of target compounds E1–E10 and P1–P10
was outlined in Scheme 1. The synthesis details were presented
in Supplementary material.
NH
O
Hydrophobic
pocket II
NH
HO
The tris(4-methylphenyl)boroxin (1) was prepared by the for-
mation of the Grignard reagent of commercially available bromo-
toluene, followed by addition of trimethylborate.21,22 Benzylic
oxidation of (1) with KMnO4 in aqueous NaOH yielded, after acid-
ification, the carboxylic acid (2).23 The amination of 4,6-
dichloropyrimidine with p-anisidine in the presence of concd
H2SO4, refluxing in 2-propanol, yielded (3).24 Palladium-catalyzed
Suzuki–Miyaura coupling of compound (3) and carboxylic acid
(2) provided compound (4).24,25 Isobutyric anhydride, obtained
by compound (4) reacting with isobutyl chloroformate, was trea-
ted with compounds (5-1)–(5-10) or (6-1)–(6-10) to give the target
compounds E1–E10 and P1–P10.26
HN
O
N
O
O
O
Hinge
H
N
HN
H
Allosteric site
O
N
N
O
H
N
N
H3C
O
N
N
Hydrophobic
pocket I
O
D380
DFG motif
Figure 2. Interactions between Imatinib and Bcr-Abl kinase.
NH
O
F381
For synthesis of compounds (5-1)–(5-10), two methods was
used due to the different substituents on benzoic acid. Benzoic
acids were activated with isobutyl chloroformate27 to form reac-
tive anhydrides, and treated with an excess of ethylenediamine,
easily removed during aqueous work-up, to give monoacylated
ethylenediamine derivatives (5-1)–(5-5). For compounds
(5-6)–(5-10), it was found that ethylenediamine was subsequently
bis-acylated by halogenated benzoic acid using the above mixed
anhydride method. Therefore, the synthesis of compounds
(5-6)–(5-10) was carried out using CDI as mediated reagent.28,29
First, benzoic acid reacted with CDI under solvent-free condition
to form the intermediate acyl imidazole. Second, various acyl
imidazole reacted with ethylenediamine and ethylenediamine
dihydrochloride (1:1) in 20% NaCl solution which could achieve
chemoselectivity by decreasing proton exchange, yielding com-
pounds (5-6)–(5-10).
aromatic structure may have hydrophobic interaction with pocket
I, it may improve the binding affinity of these new inhibitors with
Bcr-Abl kinase.
Based on the structure analysis above, the N,6-diphenyl pyrim-
idin-4-amine substructure of GNF-2 was introduced into the novel
Bcr-Abl inhibitors to react with adenine pocket (Fig. 3). In addition,
diacylated ethylenediamine and diacylated piperazine with high
flexibility were applied to react with DFG motif to improve the sol-
ubility of designed molecules. The allosteric site was employed
with various substituted benzenes to examine the effect of
substituents on activity. Above all, we describe the design,
synthesis and biological evaluation of hybrids based on Imatinib
and GNF-2 as novel Bcr-Abl inhibitors.
O
F3CO
O
N
N
H
N
series E
H3CO
N
H
R
R
NH2
GNF-2
H
N
N
H
O
N
N
N
H
N
Imatinib
N
O
O
series P
H3CO
N
N
H
N
H
N
N
N
N
N
N
O
gatekeeper
and DFG
higne
allosteric site
Figure 3. Design strategy for Bcr-Abl inhibitors (series E and P).
Please cite this article in press as: Pan, X.; et al. Bioorg. Med. Chem. Lett. (2015), http://dx.doi.org/10.1016/j.bmcl.2015.08.013

X. Pan et al. / Bioorg. Med. Chem. Lett. xxx (2015) xxx–xxx
3
CH3
CH3
Br
CH3
COOH
a
b
c
B
O
O
B
B
N
N
O
MgBr
B
H3
C
CH3
HO
N
OH
HN
e
1
2
COOH
OCH3
Cl
N
H3CO
OCH3
d
N
N
+
4
N
Cl
Cl
H
NH2
i
3
OCH3
5-1 R=3-CF3
O
O
E1 R=3-CF3
5-2 R=3-OCH3
5-3 R=2-CH3
H
R
f
E2 R=3-OCH3
E3 R=2-CH3
R
N
NH2
+
NH
NH
H2N
H2N
H
N
5-4 R=4-C(CH3)3
5-5 R=3-N(CH3)2
R
R
HOOC
HN
E4 R=4-C(CH3)3
E5 R=3-N(CH3)2
O
(5-1)-(5-5)
N
N
N
O
O
OCH3
5-6 R=3-F
5-7 R=2-Cl
H
N
R
R
E6 R=3-F
g
5-8 R=4-F
R
E7 R=2-Cl
H2N
NH2 HCl
+
5-9 R=3,4-di-F
5-10 R=2-Cl-6-F
HOOC
HOOC
E8 R=4-F
H2N
O
H
N
E9 R=3,4-di-F
E10 R=2-Cl-6-F
HN
(5-6)-(5-10)
N
6-1 R=2-F
6-2 R=2-Cl
6-3 R=4-F
P1 R=2-F
HN
h
OCH3
HN
P2 R=2-Cl
R
6-4 R=4-OCH3
6-5 R=3-F
+
N
NH
P3 R=4-F
O
6-6 R=2,4-di-Cl
6-7 R=3,4-di-F
6-8 R=3-CF3
6-9 R=3-CH3
6-10 R=3-N(CH3)2
P4 R=4-OCH3
P5 R=3-F
O
N
(6-1)-(6-10)
R
P6 R=2,4-di-Cl
P7 R=3,4-di-F
P8 R=3-CF3
P9 R=3-CH3
P10 R=3-N(CH3)2
HN
N
N
N
O
Scheme 1. Reagents and conditions: (a) Mg, I2, THF, reflux, N2; (b) B(OMe)3, THF, À20 °C; (c) NaOH (1 M), KMnO4, TBAB, H2O; (d) concd H2SO4, i-PrOH, reflux; (e) Pd(PPh3)4,
Cs2CO3, CH3CN/H2O (V:V = 3:2), 90 °C; (f) ClCOO-iBu, NMM, DCM, 0 °C; ethylenediamine, NMM, DCM, 0 °C ? rt; (g) CDI; ethylenediamine/ethylenediamine dihydrochloride
(1:1), NaCl (20%), rt; (h) TEA, DCM, rt, 30 min; EtOH, rt; (i) ClCOO-iBu, NMM, DCM, 0 °C; (5-1)–(5-10) or (6-1)–(6-10), NMM, DCM, 0 °C ? rt.
Direct monoacylation of piperazine was carried out using
trimethylacetic arylcarboxylic anhydride.30 Various benzoic acids
were allowed to react with trimethylacetyl chloride in dichloro-
methane in the presence of triethylamine, giving trimethylacetic
arylcarboxylic anhydride. Then the generated anhydrides were fur-
ther treated with piperazine in ethanol to provide monoacylated
piperazine derivatives (6-1)–(6-10).
For series P, compound P3 was the most potent with IC50 value
of 0.017 M. Compounds with F atom or CF3 group at 3-position of
phenyl ring (P5, IC50 = 23.51 M; P8, IC50 = 12.41 M) exhibited
higher inhibitory potency than compound with CH3 (P9,
IC50 > 100 M). Compound P3 (R = 4-F) was also more potent than
compound P4 (R = 4-OCH3, IC50 > 100 M). The results confirmed
that the introduction of electron withdrawing groups such as F,
Cl into phenyl ring was beneficial for activity. Furthermore, com-
pound P3 (R = 4-F) displayed higher potency than compounds P1
l
l
l
l
l
All compounds were preliminarily evaluated31,32 for their inhi-
bitory potency against Abl kinase with Imatinib as positive control
(Table 1) (Experimental procedures see Supplementary material).
Most compounds showed moderate to significant inhibition activ-
(R = 2-F, IC50 = 8.95 lM) and P5 (R = 3-F, IC50 = 23.51 lM). It was
indicated that incorporation of F at the 4-position of phenyl ring
ity, with IC50 values ranging from 0.017
Compound P3 was the most potent with IC50 value of 0.017
comparable to that of Imatinib (IC50 = 0.074 M).
Preliminary structure–activity relationships (SARs) were
explored when various R groups were introduced into the ter-
minal phenyl ring. As shown in Table 1, compound E4 showed
no inhibition activity toward Abl, suggesting that the introduc-
tion of bulky group into phenyl ring was not beneficial.
l
M
to 23.51
l
l
M.
M,
was favorable for the bioactivity.
The antiproliferative activities of synthesized compounds were
evaluated against K562 cell line by MTT assay33 (Experimental
procedures see Supplementary material). The bioactivity data
was presented as IC50 values derived from the average of three
independent experiments (Table 1).
As illustrated in Table 1, most target compounds showed mod-
erate to excellent antiproliferative activity against K562 cell line.
The IC50 values for the tested leukaemia cell line (K562) ranged
l
Compound E2 (R = 2-CH3, IC50 = 14.55
against Abl than compound E7 (R = 2-Cl, IC50 = 9.24
E10 (R = 2-Cl-6-F, IC50 = 6.20 M). The results revealed that the
lM) was less potent
lM) and
from 0.64 to 73.91
lM. Compounds E4, E5, E7 displayed excellent
l
activities with IC50 values of 0.83
l
M, 0.85 M, 0.64 M, respec-
l
l
introduction of electron withdrawing groups was better than
electron donating groups into 2-position of phenyl ring.
Compounds (E1, E2, and E9) bearing substituents on 3-position
of phenyl ring showed similar potency against Abl with the IC50
tively. Conversely, compounds P4, P9 and P10 exhibited very little
activity. Compared with series P compounds, the series E com-
pounds displayed higher inhibition activity against K562 cell line
overall. We suspected that it may be contributed to the better sol-
ubility of series E compounds than series P compounds. Compound
values at 2.59 lM, 8.53 lM, and 4.40 lM, respectively. These
results indicated that electron withdrawing or donating groups
at the C-3 position of phenyl ring had little influence on
activity.
E4 (IC50 = 0.83
cell line, but no inhibitory potency toward Abl kinase
(IC50 > 100 M). This suggested that compound E4 may had
lM) displayed good inhibition activity against K562
l
Please cite this article in press as: Pan, X.; et al. Bioorg. Med. Chem. Lett. (2015), http://dx.doi.org/10.1016/j.bmcl.2015.08.013

4
X. Pan et al. / Bioorg. Med. Chem. Lett. xxx (2015) xxx–xxx
Table 1
In vitro biological activities of target compounds E1–E10 and P1–P10
OCH3
OCH3
O
O
H
N
R
N
H
N
R
HN
O
HN
N
N
N
N
N
O
a
b
a
b
Compd
R
Abl IC50
(
lM)
K562 IC50
(lM)
CLogP
Compd
R
Abl IC50
(l
M)
K562 IC50
(l
M)
CLogP
E1
E2
E3
E4
E5
E6
E7
E8
3-CF3
2.59
8.53
14.55
>100
9.25
11.30
9.24
ND
65.33
11.18
38.48
0.83
0.85
33.88
0.64
10.94
6.20
8.50
4.31
2.89
3.72
4.94
3.47
3.56
3.43
3.98
4.20
2.62
P1
P2
P3
P4
P5
P6
P7
P8
2-F
2-Cl
4-F
4-OCH3
3-F
2,4-Di-Cl
3,4-Di-F
3-CF3
8.95
ND
8.96
1.51
2.99
2.11
2.41
2.14
3.77
2.27
2.94
2.34
2.09
3-OCH3
2-CH3
4-C(CH3)3
3-N(CH3)2
3-F
2-Cl
4-F
3,4-Di-F
2-Cl-6-F
—
73.91
35.66
>100
42.17
35.04
15.32
51.92
>100
>100
4.12
0.017
>100
23.51
16.84
17.62
12.41
>100
3.32
E9
E10
Imatinib
4.40
6.20
0.074
P9
P10
Imatinib
3-CH3
3-N(CH3)2
—
4.12
0.074
ND: not determined.
a
Values were the average of three experiments, SD <10%.
Values were the average of two experiments, SD <10%.
b
alternative biological target other than Abl. Compound P10, with
high potency toward Abl kinase, exhibited low activity against
K562 cell line. It may attribute to their poor capability to pass
through the cell membrane. As MTT assay was carried out
in vitro, the inhibitory effect variance among these compounds
could be attributed to the hydrophobicity and permeability
changes resulting from different substituents on the terminal phe-
nyl ring.
To elucidate the binding mode of two series compounds with
Bcr-Abl kinase and to guide further SARs, a detailed docking anal-
ysis was performed on representative compounds E1 and P3
(Docking procedures see Supplementary material). The docking
analysis was conducted using the Surflex-Dock module, a fully
automatic docking tool available on SYBYL version X 2.0 (Tripos
Inc.).
In docking of target compounds with Abl kinase in ATP binding
site, the crystal structure of Abl–Imatinib complex was collected
from the Protein Data Bank under code 1IEP.34 In order to validate
the docking protocol, co-crystallized ligand, Imatinib, was
re-docked to its target protein Abl. Because the nitrogen of
N-methylpiperazine in the ligand was protonated, an indirect
docking method was used in this docking analysis.35 Compounds
E1 and P3 were separately docked into the ATP pocket using the
same method validated. The docking results are displayed in
Figure 4. Further analysis on the interactions between Abl and
compounds E1 and P3 is performed.
Compound E1 makes four hydrogen bonds with the receptor:
the pyrimidine–N with the back-bone-NH of Met318, the
amide-CO (closed to heterocyclic biphenyl structure) with the side
chain of Thr315, the amide–NH (closed to the terminal phenyl
ring) to the side chain of Glu286, the amide–CO (closed to the ter-
minal phenyl ring) with back-bone-NH of Asp381. As shown in
Figure 4a, compound E1 has a binding mode similar to that of
Imatinib as we expected. The binding conformation of
phenylpyrimidine is similar to pyridinyl-pyrimidine in Imatinib.
The terminal aniline slides right to occupy hydrophobic pocket I.
Compound P3 makes two hydrogen bonds with the receptor:
the pyrimidine–N with the side chain of Thr315, the F atom with
the side chain of Arg362. Compound P3 docks into the ATP site
of Abl kinase well, but a little different from what we had expected
(Fig. 4b). The binding model of P3 with Bcr-Abl was slightly differ-
ent with Imatinib. We speculate that diacylated piperazine has no
H-bond donor, resulting in loss of key interactions with DFG motif
which can anchor compound in the position as Imatinib.
We also docked compounds E1 and P3 into the myristate site of
Abl kinase. The crystal structure of Abl–GNF-2 complex was col-
lected from the Protein Data Bank under code 3K5V.19 In order to
validate the docking protocol, co-crystallized ligand, GNF-2, was
Figure 4. PyMOL cartoon representation of docking result for compound E1 (a) and P3 (b) in Bcr-Abl ATP binding site. Imatinib (cyan) is used as reference molecule. For the
sake of clarity, only polar hydrons are displayed; and only the amino acids that generate H-bonds are shown as lines.
Please cite this article in press as: Pan, X.; et al. Bioorg. Med. Chem. Lett. (2015), http://dx.doi.org/10.1016/j.bmcl.2015.08.013

X. Pan et al. / Bioorg. Med. Chem. Lett. xxx (2015) xxx–xxx
5
References and notes
1. Sawyers, C. L. N. Eng. J. Med. 1999, 340, 1330.
2. Schiffer, C. A. N. Eng. J. Med. 2007, 357, 258.
3. Deininger, M. W.; Goldman, J. M.; Melo, J. V. Blood 2000, 96, 3343.
4. Miyazawa, K.; Toyama, K. Nihon. Naika. Gakkai. Zasshi. 1995, 84, 965.
5. Nakamura, S.; Yokota, D.; Tan, L.; Nagata, Y.; Takemura, T.; Hirano, I.; Shigeno,
K.; Shibata, K.; Fujisawa, S.; Ohnishi, K. Int. J. Cancer 2012, 30, 1046.
6. Deininger, M.; Buchdunger, E.; Druker, B. J. Blood 2005, 105, 2640.
7. Habeck, M. Lancet Oncol. 2002, 3, 6.
8. Breccia, M.; Alimena, G. Cancer Lett. 2012, 322, 127.
9. Weisberg, E.; Manley, P. W.; Breitenstein, W.; Brueggen, J.; Cowan-Jacob, S. W.;
Ray, A.; Huntly, B.; Fabbro, D.; Fendrich, G.; Hall-Meyers, E.; Kung, A. L.;
Mestan, J.; Daley, G. Q.; Callahan, L.; Catley, L.; Cavazza, C.; Azam, M.; Neuberg,
D.; Wright, R. D.; Gilliland, D. G.; Griffin, J. D. Cancer Cell 2005, 7, 129.
10. Kimura, S.; Naito, H.; Segawa, H.; Kuroda, J.; Yuasa, T.; Sato, K.; Yokota, A.;
Kamitsuji, Y.; Kawata, E.; Ashihara, E.; Nakaya, Y.; Naruoka, H.; Wakayama, T.;
Nasu, K.; Asaki, T.; Niwa, T.; Hirabayashi, K.; Maekawa, T. Blood 2005, 106,
3948.
11. Lombardo, L. J.; Lee, F. Y.; Chen, P.; Norris, D.; Barrish, J. C.; Behnia, K.;
Castaneda, S.; Cornelius, L. A.; Das, J.; Doweyko, A. M.; Fairchild, C.; Hunt, J. T.;
Inigo, I.; Johnston, K.; Kamath, A.; Kan, D.; Klei, H.; Marathe, P.; Pang, S.;
Peterson, R.; Pitt, S.; Schieven, G. L.; Schmidt, R. J.; Tokarski, J.; Wen, M. L.;
Wityak, J.; Borzilleri, R. M. J. Med. Chem. 2004, 47, 6658.
12. Puttini, M.; Coluccia, A. M.; Boschelli, F.; Cleris, L.; Marchesi, E.; Donella-Deana,
A.; Ahmed, S.; Redaelli, S.; Piazza, R.; Magistroni, V.; Andreoni, F.; Scapozza, L.;
Formelli, F.; Gambacorti-Passerini, C. Cancer Res. 2006, 66, 11314.
13. O’Hare, T.; Shakespeare, W. C.; Zhu, X.; Eide, C. A.; Rivera, V. M.; Wang, F.;
Adrian, L. T.; Zhou, T.; Huang, W. S.; Xu, Q.; Metcalf, C. A., 3rd; Tyner, J. W.;
Loriaux, M. M.; Corbin, A. S.; Wardwell, S.; Ning, Y.; Keats, J. A.; Wang, Y.;
Sundaramoorthi, R.; Thomas, M.; Zhou, D.; Snodgrass, J.; Commodore, L.;
Sawyer, T. K.; Dalgarno, D. C.; Deininger, M. W.; Druker, B. J.; Clackson, T.
Cancer Cell 2009, 16, 401.
Figure 5. PyMOL cartoon representation of docking result for compounds E1
(yellow), P3 (magenta) and GNF-2 (lime green) in Bcr-Abl myristate binding site.
The surface of amino acids around active site is displayed; and its cut plane is given
in order to see the match between compounds and Bcr-Abl myristate site more
clearly.
also re-docked to its target protein Abl. Compounds E1 and P3
were docked into the binding pocket using the same method vali-
dated. As shown in Figure 5, the binding modes of the two com-
pounds were consistent with that of GNF-2. This suggests that
series E and P compounds may also act in a similar way of GNF-2.
In summary, we have designed two series of N,6-diphenyl-
pyrimidin-4-amine derivatives as novel Bcr-Abl inhibitors, and
described an efficient method for their synthesis. The target com-
pounds were investigated for their in vitro antiproliferative activity
against K562 cell line and screened for Abl kinase inhibitory activ-
ity. Most compounds exhibit potent Bcr-Abl inhibitory activity and
antiproliferation effect on K562 cells. Among them, compound P3
exhibits significant inhibition of Abl kinase comparable with
Imatinib. Compounds (E1, E2, E3, E9 and P10) exhibit micromolar
inhibition of the Abl kinase. In addition, the activities of series E
compounds are better than those of series P compounds overall.
The docking results show that series E and P compounds have
the similar binding mode as that of Imatinib, and the two series
compounds docked well with Bcr-Abl kinase. These compounds
represent new scaffolds for Bcr-Abl kinase inhibitors, which are
still needed in oncological drug discovery. Further studies aimed
at optimizing the structures of the hits in order to increase their
potency against Bcr-Abl kinase and cancer cell lines in vitro are
underway in our laboratories.
14. Cancer Disc. 2014, 4, 6.
15. Pluk, H.; Dorey, K.; Superti-Furga, G. Cell 2002, 108, 247.
16. Adrian, F. J.; Ding, Q.; Sim, T.; Velentza, A.; Sloan, C.; Liu, Y.; Zhang, G.; Hur, W.;
Ding, S.; Manley, P.; Mestan, J.; Fabbro, D.; Gray, N. S. Nat. Chem. Biol. 2006, 2,
95.
17. Zhang, J.; Adrian, F. J.; Jahnke, W.; Cowan-Jacob, S. W.; Li, A. G.; Iacob, R. E.; Sim,
T.; Powers, J.; Dierks, C.; Sun, F.; Cuo, G. R.; Ding, Q.; Okram, B.; Choi, Y.;
Wojciechowski, A.; Deng, X.; Liu, G.; Fendrich, G.; Strauss, A.; Vajpai, N.;
Grzesiek, S.; Tuntland, T.; Liu, Y.; Bursulaya, B.; Azam, M.; Manley, P. W.; Engen,
J. R.; Daley, G. Q.; Warmuth, M.; Gray, N. S. Nature 2010, 463, 501.
18. Iacob, R. E.; Zhang, J.; Gray, N. S.; Engen, J. R. PLoS One 2011, 6, e15929.
19. Manley, P. W.; Cowan-Jacob, S. W.; Buchdunger, E.; Fabbro, D.; Fendrich, G.;
Furet, P.; Meyer, T.; Zimmermann, J. Eur. J. Cancer 2002, 38, S19.
20. Zhang, J.; Yang, P. L.; Gray, N. S. Nat. Rev. Cancer 2009, 9, 28.
21. Seaman, W.; Johnson, J. R. J. Am. Chem. Soc. 1931, 53, 711.
22. Matsubara, H.; Seto, K.; Tahara, T.; Takahashi, S. Bull. Chem. Soc. Jpn. 1989, 62,
3896.
23. Ma, S.; Sun, D.; Forster, P. M.; Yuan, D.; Zhuang, W.; Chen, Y. S.; Parise, J. B.;
Zhou, H. C. Inorg. Chem. 2009, 48, 4616.
24. Hartung, C. G.; Backes, A. C.; Felber, B.; Missio, A.; Philipp, A. Tetrahedron 2006,
62, 10055.
25. Deng, X.; Okram, B.; Ding, Q.; Zhang, J.; Choi, Y.; Adrian, F. J.; Wojciechowski,
A.; Zhang, G.; Che, J.; Bursulaya, B.; Cowan-Jacob, S. W.; Rummel, G.; Sim, T.;
Gray, N. S. J. Med. Chem. 2010, 53, 6934.
26. Pan, X.; Wang, F.; Zhang, Y.; Gao, H.; Hu, Z.; Wang, S.; Zhang, J. Bioorg. Med.
Chem. 2013, 21, 2527.
27. Beaulieu, P. L.; Lavallee, P.; Abraham, A.; Anderson, P. C.; Boucher, C.; Bousquet,
Y.; Duceppe, J. S.; Gillard, J.; Gorys, V.; Grand-Maıtre, C.; Grenier, L.; Guindon,
Y.; Guse, I.; Plamondon, L.; Soucy, F.; Valois, S.; Wernic, D.; Yoakim, C. J. Org.
Chem. 1997, 62, 3440.
Acknowledgments
28. Verma, S. K.; Ghorpade, R.; Pratap, A.; Kaushik, M. P. Green Chem. 2012, 14, 326.
29. Verma, S. K.; Acharya, B. N.; Kaushik, M. P. Org. Lett. 2010, 12, 4232.
30. Lai, L.; Wang, E.; Luh, B. J. Synthesis 2001, 2001, 361.
31. Zhang, C.; Tan, C.; Zu, X.; Zhai, X.; Liu, F.; Chu, B.; Ma, X.; Chen, Y.; Gong, P.;
Jiang, Y. Eur. J. Med. Chem. 2011, 46, 1404.
32. Li, H.; Totoritis, R. D.; Lor, L. A.; Schwartz, B.; Caprioli, P.; Jurewicz, A. J.; Zhang,
G. Assay Drug Dev. Technol. 2009, 7, 598.
33. Pan, X.; Dong, J.; Gao, H.; Wang, F.; Zhang, Y.; Wang, S.; Zhang, J. Chem. Biol.
Drug Des. 2014, 83, 592.
This work was supported by the National Natural Science
Foundation of China (NSFC) (Grant Nos. 81227802 and
81230079), the Natural Science Basic Research Plan in Shaanxi
Province of China (Program No. 2015JQ8312), and the
Fundamental Research Funds for the Central Universities.
34. Cowan-Jacob, S. W.; Fendrich, G.; Floersheimer, A.; Furet, P.; Liebetanz, J.;
Rummel, G.; Rheinberger, P.; Centeleghe, M.; Fabbro, D.; Manley, P. W. Acta
Crystallogr., D: Biol. Crystallogr. 2007, 63, 80.
35. Lü, S.; Luo, Q.; Hao, X.; Li, X.; Ji, L.; Zheng, W.; Wang, F. Bioorg. Med. Chem. Lett.
2011, 21, 6964.
Supplementary data
Supplementary data (synthetic procedures, spectral characteri-
zation, biological assay procedures and molecular modeling proce-
dures) associated with this article can be found, in the online
version, at http://dx.doi.org/10.1016/j.bmcl.2015.08.013.
Please cite this article in press as: Pan, X.; et al. Bioorg. Med. Chem. Lett. (2015), http://dx.doi.org/10.1016/j.bmcl.2015.08.013