Dongsheng Zhu1,2, Huocong Huang3, Daniel M Pinkas4, Jinfeng Luo2, Debolina Ganguly3, Alice E Fox4, Emily Arner3, Qiuping Xiang2, Zheng-Chao Tu2, Alex N Bullock4, Rolf A Brekken3, Ke Ding1, Xiaoyun Lu1. 1. International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), School of Pharmacy , Jinan University , 601 Huangpu Avenue West , Guangzhou 510632 , China. 2. Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , 190 Kaiyuan Avenue , Guangzhou 510530 , China. 3. Division of Surgical Oncology, Department of Surgery and Hamon Center for Therapeutic Oncology Research , UT Southwestern , Dallas , Texas 75390-8593 , United States. 4. Structural Genomics Consortium , University of Oxford , Old Road Campus Research Building, Roosevelt Drive , Oxford OX3 7DQ , U.K.
Abstract
A series of 2-amino-2,3-dihydro-1H-indene-5-carboxamides were designed and synthesized as new selective discoidin domain receptor 1 (DDR1) inhibitors. One of the representative compounds, 7f, bound with DDR1 with a Kd value of 5.9 nM and suppressed the kinase activity with an half-maximal (50%) inhibitory concentration value of 14.9 nM. 7f potently inhibited collagen-induced DDR1 signaling and epithelial-mesenchymal transition, dose-dependently suppressed colony formation of pancreatic cancer cells, and exhibited promising in vivo therapeutic efficacy in orthotopic mouse models of pancreatic cancer.
A series of 2-amino-2,3-dihydro-1H-indene-5-carboxamides were designed and synthesized as new selective discoidin domain receptor 1 (DDR1) inhibitors. One of the representative compounds, 7f, bound with DDR1 with a Kd value of 5.9 nM and suppressed the kinase activity with an half-maximal (50%) inhibitory concentration value of 14.9 nM. 7f potently inhibited collagen-induced DDR1 signaling and epithelial-mesenchymal transition, dose-dependently suppressed colony formation of pancreatic cancer cells, and exhibited promising in vivo therapeutic efficacy in orthotopic mouse models of pancreatic cancer.
Pancreatic cancer,
also known as the “king of cancer”
with a 5 year survival rate less than 7%, is lacking effective therapies.[1] Intrinsic and/or acquired chemoresistance to
the first-line drug gemcitabine is a major reason for the poor prognosis.
Collective studies suggested that desmoplasia and tumor microenvironment
(TME) are the key contributors to chemoresistance of pancreatic cancerpatients. Desmoplasia (or desmoplastic reaction) is a prominent pathological
characteristic of pancreatic cancer, resulting from the rapid expansion
of cancer-associated fibroblasts and increased deposition of extracellular
matrix (ECM) components. Numerous studies have shown that ECM is heavily
involved in pancreatic cancer development, immune evasion, and therapy
resistance. Therefore, stroma-targeting therapy becomes an attractive
strategy to improve therapeutic response.[2] Collagens are the most abundant components in ECM.[3] Biological functions of collagens are mainly mediated by
two types of receptors, integrins and discoidin domain receptors (DDRs).[4,5] DDRs belong to the receptor tyrosine kinase (RTK) family. Two members
of DDRs (DDR1 and DDR2) have been identified to date.[6] DDR1 is predominantly expressed in epithelial cells, whereas
DDR2 is typically found in cells of connective tissues. Dysregulation
of DDR1 is frequently detected in a variety of humancancers and involved
in several key cellular processes, such as cell differentiation, proliferation,
adhesion, migration, and invasion.[7,8] Studies have
shown that DDR1 overexpression mediates prosurvival signals and metastasis
in breast cancer and gastric cancer and is also involved in the recurrence
of certain types of cancers.[9−11] DDR1 has also been demonstrated
to contribute to epithelial–mesenchymal transition (EMT) in
pancreatic cancer.[12,13] Pharmacological inhibition of
DDR1 by a selective DDR1 inhibitor 7rh (compound 1, Figure ) successfully slowed tumor progression and enhanced chemosensitivity
to standard-of-care pancreatic cancer regimens.[14] Therefore, DDR1 is being considered as a novel molecular
target for drug discovery against pancreatic cancer.
Figure 1
Reported selective DDRs
inhibitors.
Reported selective DDRs
inhibitors.A number of DDR inhibitors
have been reported (Figure ),[15−21] among which compound 1 (7rh)[16] represents one of the first disclosed selective
DDR1 inhibitors. This compound demonstrated promising therapeutic
potential in a variety of humancancer models including pancreatic
cancer,[14] nonsmall cell lung cancer,[22] and gastric carcinoma.[10] Most recently, tetrahydroisoquinoline-7-carboxamide derivatives
were also designed and synthesized as highly selective DDR1 inhibitors
exhibiting in vivo efficacy in mouse models of inflammation-mediated
pulmonary fibrosis and acute lung injury.[21,23] Compound 6 represents one of the most selective DDR1
inhibitors to date, which exhibited an half-maximal (50%) inhibitory
concentration (IC50) value of 15.4 nM against DDR1 kinase,
whereas it is significantly less potent for the majority of a panel
of 403 other kinases. The major “off-targets” include
tropomyosin receptor kinases B and C (TrkB and TrkC, respectively)
with corresponding binding affinities (Kd values) of 22 and 18 nM, respectively. Further kinase assay determination
confirmed that this molecule inhibited TrkA, B, and C, with IC50 values of 68.4, 36.8, and 30.2 nM, respectively. Trks are
a family of receptor tyrosine kinases (RTKs), which are activated
by neurotrophin hormones and regulate synaptic plasticity and strength
in the mammalian nervous system.[24] Lack
of Trks significantly affects the development of central and peripheral
nervous systems.[25,26] For instance, the population
of corneal sensory neurons is markedly depleted in TrkA (−/−)
mice, animals lacking TrkB in parvalbumin-positive cells displayed
sexually dimorphic behavioral phenotypes, whereas TrkC knockout mice
exhibited profound deficiencies in CNS glial cells.[27] Thus, “off-targeting” Trks may raise some
concerns about the potential neurotoxicity issues of the previously
reported DDR1 inhibitors. With the aim to improve the target specificity,
a series of 2-amino-2,3-dihydro-1H-indene-5-carboxamide
derivatives were designed and synthesized as new Trks-sparing DDR1
inhibitors. Moreover, the potential therapeutic effects on pancreatic
cancer were also investigated by utilizing in vitro and in vivo models
(Figure ).
Figure 2
Design of 2-amino-2,3-dihydro-1H-indene-5-carboxamide
derivatives 7 as new Trks-sparing selective DDR1 inhibitors.
Design of 2-amino-2,3-dihydro-1H-indene-5-carboxamide
derivatives 7 as new Trks-sparing selective DDR1 inhibitors.Syntheses of the designed compounds 7a, 7b, and 7c–n are described
in Schemes S1 and , respectively. Briefly, protection of 8 and 9 with (Boc)2O gave 10 and 11, respectively. Further alkylation of 10 generated 12–14. 10–14 were converted to 15–19 by using a carbonyl-extrusion
reaction, which were deprotected by hydrochloric acid to produce intermediates 20–24. Coupling of 20–24 with 5-bromopyrimidinethrough a Buchwald–Hartwig
amination reaction provided 25–29. The ester 27 was hydrolyzed to 30. 25–30 were further reacted with 31 to produce the
final compounds 7c–n.
Scheme 1
Syntheses
of Compounds 7c–n
Reagents
and conditions: (a)
di-tert-butyl dicarbonate (Boc2O), triethylamine
(Et3N), 90–95%; (b) sodium hydride (NaH), N,N-dimethylformamide (DMF), iodomethane, 12; iodoethane, 13; 1-iodopropane, 14; 50–80%; (c) palladium(II) acetate (Pd(OAc)2),
Et3N, carbon monoxide (CO), 100 °C, 50–70%;
(d) 4 M HCl, 50 °C; (e) bis(dibenzylideneacetone)palladium (Pd(dba)2), 2-dicyclohexylphosphino-2′,6′-diisopropoxybiphenyl
(Ruphos), cesium carbonate (Cs2CO3), 5-bromopyrimidine,
80 °C, 30–40%; (f) 1 M sodium hydroxide (NaOH), dioxane,
98%; (g) potassium tert-butoxide (t-BuOK), −20 °C to room temperature (rt), 30–70%;
(h) 2-(7-aza-1H-benzotriazole-1-yl)-1,1,3,3-tetramethyluronium
hexafluorophosphate, N,N-diisopropylethylamine
(DIPEA), 20–55%.
Syntheses
of Compounds 7c–n
Reagents
and conditions: (a)
di-tert-butyl dicarbonate (Boc2O), triethylamine
(Et3N), 90–95%; (b) sodium hydride (NaH), N,N-dimethylformamide (DMF), iodomethane, 12; iodoethane, 13; 1-iodopropane, 14; 50–80%; (c) palladium(II) acetate (Pd(OAc)2),
Et3N, carbon monoxide (CO), 100 °C, 50–70%;
(d) 4 M HCl, 50 °C; (e) bis(dibenzylideneacetone)palladium (Pd(dba)2), 2-dicyclohexylphosphino-2′,6′-diisopropoxybiphenyl
(Ruphos), cesium carbonate (Cs2CO3), 5-bromopyrimidine,
80 °C, 30–40%; (f) 1 M sodium hydroxide (NaOH), dioxane,
98%; (g) potassium tert-butoxide (t-BuOK), −20 °C to room temperature (rt), 30–70%;
(h) 2-(7-aza-1H-benzotriazole-1-yl)-1,1,3,3-tetramethyluronium
hexafluorophosphate, N,N-diisopropylethylamine
(DIPEA), 20–55%.
Results and Discussion
Compound 6 is a selective DDR1 inhibitor designed
and synthesized in our laboratory. However, this compound displayed
similar off-target potency against TrkA, TrkB, and TrkC with IC50 values of 68.4, 36.8, and 30.2 nM, respectively (Table ). Off-target inhibition
against Trks may raise some concern about the potential neurotoxicity
issues of the molecule. Aiming to improve the target specificity,
we first docked compound 6 into the adenosine triphosphate
(ATP)-binding site of TrkC [Protein Data Bank (PDB) ID: 3V5Q].[28] It was shown that the compound could bind well to TrkC
with a Asp-Phe-Gly (DFG)-out conformation, which was similar to the
binding mode with DDR1 (Figure A,B).[21] The only small difference
between binding modes of 6 with DDR1 and TrkC is that
the methyl group on tetrahydroisoquinoline occupied a small hydrophobic
pocket formed by Val552, Ala570, Lys572, and Phe617 to achieve some
hydrophobic interactions in TrkC. Thus, it was predicted that diminishing
this interaction might decrease the binding with Trks and improve
DDR1 target selectivity of the molecule. Based on this hypothesis,
an isoindoline scaffold was first utilized to replace the 1-methyltetrahydroisoquinoline in 6 to generate compounds 7a and 7b. Disappointingly, both 7a and 7b lost all of the DDR1 inhibitory activity, although
the modification indeed abolished the off-target inhibition against
Trks (Table ). Further
computational investigation demonstrated that 7a failed
to fit nicely into the DDR1ATP binding pocket (PDB ID: 5FDP, data not shown),[21] whereas compound 7b could form
weak hydrogen bonds (HBs) with the hinge residue Met704, but there
was no other interaction between the isoindoline scaffold and DDR1
(Figure S1). The computational study also
indicated that the methylene moiety of 7b is accessible
to the gatekeeperThr701 residue, and it could be replaced by a hydrogen
bond donor moiety to form a hydrogen bond interaction with Thr701
to potentially improve the DDR1 inhibitory activity. To validate this
hypothesis, 2-amino-2,3-dihydro-1H-indene-5-carboxamide
enantiomers 7c and 7d were designed and
synthesized by moving the nitrogen atom out of the original isoindoline
ring. It was also predicted that the R-isomer 7c might
achieve a more favorable binding with DDR1 than that of the S-isomer 7d to form a hydrogen bond with the gatekeeper residue Thr701
(Figure S2A,B). Indeed, kinase inhibition
determination showed that compound 7c potently inhibited
DDR1 with an IC50 value of 5.6 nM, whereas the corresponding
value for 7d was 42.5 nM. Compound 7c exhibited
a similar suppressive activity against DDR2 with an IC50 value of 21.5 nM. It was also noteworthy that 7c almost
totally abolished the inhibitory potencies against Trks with IC50 values greater than 1000 nM. However, introduction of a
methyl group at the R3-position (7e) caused
an approximately 129-fold potency loss, which might be due to the
steric hindrance to interfere with potential hydrogen bond formation.
Table 1
In Vitro Kinase Inhibitory Activities
of Compounds 7a–n against DDR1, DDR2,
TrkA, TrkB, and TrkCa,b
DDR1
and DDR2 inhibition assays
were performed using
the LANCE ULTRA kinase assay.
TrkA/B/C activity was performed
using the fluorescence resonance energy transfer (FRET)-based Z′-Lyte
assay. The data are mean values from at least three independent experiments.
Figure 3
(A) Molecular
docking of 6 into DDR1 (PDB: 5FDP). (B) Molecular
docking of 6 into TrkC (PDB: 3V5Q). (C) Cocrystal structures of DDR1 and 7c (PDB: 6HP9). (D) Molecular docking of 7c into TrkC. Compounds 6 and 7c are shown in gray, purple, and blue
stick structure. The key residues of DDR1 and TrkC kinase are shown
in blue and gray stick and ribbon representation. Hydrogen bonds are
indicated by yellow dashed lines to key amino acids.
(A) Molecular
docking of 6 into DDR1 (PDB: 5FDP). (B) Molecular
docking of 6 into TrkC (PDB: 3V5Q). (C) Cocrystal structures of DDR1 and 7c (PDB: 6HP9). (D) Molecular docking of 7c into TrkC. Compounds 6 and 7c are shown in gray, purple, and blue
stick structure. The key residues of DDR1 and TrkC kinase are shown
in blue and gray stick and ribbon representation. Hydrogen bonds are
indicated by yellow dashed lines to key amino acids.DDR1
and DDR2 inhibition assays
were performed using
the LANCE ULTRA kinase assay.TrkA/B/C activity was performed
using the fluorescence resonance energy transfer (FRET)-based Z′-Lyte
assay. The data are mean values from at least three independent experiments.A 2.0 Å resolution X-ray
crystallographic structure of 7c and the DDR1complex
was determined to elucidate details
of the interaction (Figure C and Table S2). It was shown that 7c fitted nicely into the ATP binding pocket of DDR1 with
a typical type II binding mode. The nitrogen atom of pyrimidine was
observed to form a hydrogen bond with hinge residue Met704, whereas
the amino group at 2-position of the indene formed a hydrogen bond
with gatekeeper residue Thr701. Two additional hydrogen bonds were
also observed, one between the amide nitrogen of 7c and
the carboxylates of Glu672 and another between the amide carbonyl
of 7c and the backbone amide nitrogen of Asp784. Additionally,
the trifluoromethyl group was observed to fit snugly into the DFG-out
pocket. A computational study was further performed to rationalize
the significant potency loss for Trks (PDB ID: 3V5Q).[18] It was shown that the pyrimidinyl moiety of 7c would still be able to form a hydrogen bond (∼3.1 Å)
with the key residue Met620 in TrkC (Figure D), but the gatekeeperPhe617 of TrkC altered
the three-dimensional (3D) structure of the ATP pocket relative to
DDR1, which would both preclude a key hydrogen bond and additionally
introduce a steric clash with 7c.Aiming to improve
DDR1 target specificity, further structural optimization
was conducted. Superposition of DDR1 (PDB: 6HP9, gray) and a homology model of DDR2 (orange)[29] indicated that DDR1 possessed a small hydrophobic
groove formed by Ile685, Thr701, and Asp703, whereas no such pocket
existed in DDR2 because of its outward shifting of Glu93 and Ile76
(Figure A). Based
on this observation, it was hypothesized that a small hydrophobic
substituent might be introduced at the nitrogen atom of 7c to improve the DDR1 selectivity. Thus, compounds 7f–h, in which a methyl, ethyl, or n-propyl group was introduced at the corresponding position, respectively,
were designed and synthesized. It was shown that the methylated compound 7i indeed significantly decreased the DDR2 inhibitory potency
with an IC50 of 933 nM, although it also caused a 2.6-fold
potency loss for DDR1 with an IC50 value of 14.9 nM (Table ). However, both 7g and 7h resulted in 26.8- and approximately
200-fold DDR1 potency decreases, respectively. Computational investigation
supported the idea that a methyl group (7f) could fit
into a small hydrophobic pocket formed by Ile685, Thr701, and Asp702,
whereas loss of a hydrogen bond with Thr701 would contribute to the
DDR1 potency decrease (Figure B).
Figure 4
(A) Superposition of DDR1 (PDB: 6HP9) and DDR2. (B) Molecular docking of 7f into DDR1 (PDB: 6HP9). The key residues of DDR1 kinase are shown in gray
stick representation and DDR2 kinase are shown in orange. Compounds 7c and 7f are shown in gray and green stick structures,
respectively. Hydrogen bonds are indicated by yellow dashed lines
to key amino acids.
(A) Superposition of DDR1 (PDB: 6HP9) and DDR2. (B) Molecular docking of 7f into DDR1 (PDB: 6HP9). The key residues of DDR1 kinase are shown in gray
stick representation and DDR2 kinase are shown in orange. Compounds 7c and 7f are shown in gray and green stick structures,
respectively. Hydrogen bonds are indicated by yellow dashed lines
to key amino acids.Further structure–activity
relationship investigation also
revealed that the trifluoromethyl of 7f could be replaced
by the ethyl (7j), isopropyl (7k), or tertiary
butyl (7l) group without obviously affecting the DDR1
inhibitory potency. For instance, compounds 7j–l exhibited IC50 values of 14.7, 15.0, and 14.4
nM, respectively. However, their potencies against DDR2 and Trks were
improved, which made the compound less selective. A replacement of
the trifluoromethyl with a methyl group (7i) caused an
approximately 43-fold decrease in DDR1 potency. When the trifluoromethyl
was replaced with a cyclohexyl group, the resulting compound 7m was also 5-fold less potent than the lead molecule 7f. Significantly, the amantadine derivative (7n) totally abolished its activity against DDR1 with an IC50 value greater than 2.0 μM. Collectively, 7f represents
one of the most potent and selective DDR1 inhibitors in the series
for further biological investigation.The binding affinity determination
showed that 7f tightly
bound to the ATP-binding sites of DDR1 with a Kd value of 5.9 nM (DiscoverX, San Diego, CA).[30] Further target specificity of 7f was investigated
by KINOMEscan profiling with a panel of 468 kinases at 1.0 μM
(Figure A). The results
indicated that 7f displayed an extraordinary target selectivity
with S (10) and S (1) scores of 0.015 and 0.007, respectively (Table S3). The major off-targets (inhibition
> 90%, ctrl% < 10) included the DDR2, ABL1, KIT, PDGFRB, and
TrkC.
The inhibitory activities (IC50) of 7f against
above-mentioned off-targets were further determined with our in-house
kinase assays (Figure B). It was shown that 7f displayed significantly less
potencies to all of the off-target kinases.
Figure 5
Target selectivity of 7f. (A) KINOMEscan profiles
for 7f. (B) Inhibitory activities (IC50) of
compound 7f against the potential off-targets.
Target selectivity of 7f. (A) KINOMEscan profiles
for 7f. (B) Inhibitory activities (IC50) of
compound 7f against the potential off-targets.To investigate the inhibitory
effects of 7f on the
biological functions of DDR1, we first examined the DDR1 signaling
pathway with the drug treatment in a mousepancreatic cancer cell
line Pan02 (Figure ). It was found that 7f dose-dependently inhibited collagen-induced
activation of DDR1 and its downstream signaling proteins, for example,
proline-rich tyrosine kinase 2 (PYK2) and pseudopodium-enriched atypical
kinase 1 (PEAK1).
Figure 6
7f inhibits DDR1 activation induced by collagen
in
vitro. Pan02 were treated with collagen I (50 μg/mL) and dimethyl
sulfoxide (DMSO) or different concentrations of 7f for
8 h. Cell lysates were harvested and subjected to western blot, probing
for p-DDR1, DDR1, p-PYK2, PYK2, p-PEAK1, PEAK1, and TUBULIN.
7f inhibits DDR1 activation induced by collagen
in
vitro. Pan02 were treated with collagen I (50 μg/mL) and dimethyl
sulfoxide (DMSO) or different concentrations of 7f for
8 h. Cell lysates were harvested and subjected to western blot, probing
for p-DDR1, DDR1, p-PYK2, PYK2, p-PEAK1, PEAK1, and TUBULIN.The activation of DDR1–PYK2–PEAK1
signaling has been
shown to mediate the tumor-promoting functions of collagen, including
an important process of EMT called cadherin switching,[31] in which cancer cells specifically upregulate
the mesenchymal cell adhesion protein N-cadherin, whereas the epithelial
cell adhesion protein E-cadherin may or may not be affected. As a
result of N-cadherin upregulation, cancer cells become substantially
more motile and aggressive.[32] Therefore,
we performed immunofluorescence staining for E-cadherin and N-cadherin
in Pan02 and another mousepancreatic cancer cell line BMF-A3 derived
from KPfC (Kras; Trp53; Ptf1a) mice, a genetically engineered mouse model of pancreatic
cancer, to explore the effects of 7f on inhibiting DDR1-mediated
cadherin switching (Figure A). Consistently, 7f markedly inhibited cadherin
switching in each cell line regardless of the different genetic background.
Moreover, we also found that 7f significantly inhibited
the migratory capability of the cells in a wound-healing assay (Figure B).
Figure 7
7f inhibits
collagen-induced cadherin switching and
migration in pancreatic cancer. (A) Pan02 and primary mouse pancreatic
cancer cell line BMF-A3 were treated with collagen I (50 μg/mL)
and DMSO or 1 μM 7f for 24 h. Cells were fixed
with methanol and stained with E-cadherin (green), N-cadherin (red),
and 4′,6-diamidino-2-phenylindole (DAPI, blue). Fluorescent
images were captured at 20× magnification. (B) Wound-healing
assay was performed with Pan02 cells. Cells were treated with collagen
I (50 μg/mL) and DMSO or 1 μM 7f for 24 h,
and relative rates of migration were measured after a 24 h period
of time. **** P < 0.0001.
7f inhibits
collagen-induced cadherin switching and
migration in pancreatic cancer. (A) Pan02 and primary mouse pancreatic
cancer cell line BMF-A3 were treated with collagen I (50 μg/mL)
and DMSO or 1 μM 7f for 24 h. Cells were fixed
with methanol and stained with E-cadherin (green), N-cadherin (red),
and 4′,6-diamidino-2-phenylindole (DAPI, blue). Fluorescent
images were captured at 20× magnification. (B) Wound-healing
assay was performed with Pan02 cells. Cells were treated with collagen
I (50 μg/mL) and DMSO or 1 μM 7f for 24 h,
and relative rates of migration were measured after a 24 h period
of time. **** P < 0.0001.Cell heterogeneity is a major cause of therapy resistance
in most
types of cancers.[33] To understand whether 7f had similar effects on inhibiting cadherin switching in
different cancer cell populations derived from the same tumor, we
performed a 3D culture experiment with two different cancer cell clones
derived from a KPfC tumor (BMF-A3 and CT1A-C11).
In the presence of ECM that mimics the in vivo tumor microenvironment.[34] We found that BMF-A3 represented a more epithelial
phenotype, which remained as clusters under 3D culture, whereas CT1A-C11
was more mesenchymal and aggressive, with an elongated and fibroblastic
morphology. However, we found that 7f strongly inhibited
such a mesenchymal phenotype (Figure A). We also examined the effect of 7f on
DDR1-induced cadherin switching in the two cell lines by probing for
E-cadherin and N-cadherin expressions in cell lysates. We found that
although the two cell lines had different phenotypes in 3D culture, 7f inhibited the upregulation of N-cadherin similarly in a
dose-dependent manner (Figure B). This suggests that 7f may have effects on
many cancer cell populations despite cellular heterogeneity.
Figure 8
7f inhibits collagen-induced cadherin switching in
different cancer cell clones from KPfC mice. (A)
BMF-A3 and CT1A-C11 were embedded in ECM consisting of 5 mg/mL matrigel
and 2.1 mg/mL collagen I. Cultures were overlaid with Dulbecco’s
modified Eagle’s medium (DMEM) + 10% fetal bovine serum (FBS)
containing 2% matrigel. After 48 h, cells were fixed with methanol
and stained with phalloidin (red) and DAPI (blue). Fluorescent images
were captured at 20× magnification. (B) Primary mouse pancreatic
cancer cell lines BMF-A3 and CT1A-C11 were treated with collagen I
(50 μg/mL) and DMSO or different concentrations of 7f for 18 h. Cell lysates were harvested and subjected to western blot,
probing for N-cadherin, E-cadherin, and ACTIN.
7f inhibits collagen-induced cadherin switching in
different cancer cell clones from KPfC mice. (A)
BMF-A3 and CT1A-C11 were embedded in ECM consisting of 5 mg/mL matrigel
and 2.1 mg/mL collagen I. Cultures were overlaid with Dulbecco’s
modified Eagle’s medium (DMEM) + 10% fetal bovine serum (FBS)
containing 2% matrigel. After 48 h, cells were fixed with methanol
and stained with phalloidin (red) and DAPI (blue). Fluorescent images
were captured at 20× magnification. (B) Primary mouse pancreatic
cancer cell lines BMF-A3 and CT1A-C11 were treated with collagen I
(50 μg/mL) and DMSO or different concentrations of 7f for 18 h. Cell lysates were harvested and subjected to western blot,
probing for N-cadherin, E-cadherin, and ACTIN.In addition, we examined the effects of 7f on
the
tumorigenicity of pancreatic cancer cells using an in vitro colony
formation assay. As shown in Figure A,B, 7f dose-dependently inhibited colony
formation significantly in BMF-A3 and Pan02 cells. However, the direct
effect against proliferation of 7f seemed to be moderate,
measured by cell proliferation in two-dimensional with BMF-A3 and
Pan02 cells showing IC50s values of 4.26 and 11.92 μM,
respectively (Figure S4).
Figure 9
7f inhibits
colony formation in BMF-A3 (A) and Pan02
(B) pancreatic cancer cells. Colony formation for cells was grown
in DMEM with 10% FBS ± 7f at the indicated doses
for 10 days. Mean ± standard deviation (S.D.) colonies are shown.
** P < 0.01, **** P < 0.001,
***** P < 0.0001 by Student’s t-test vs DMSO.
7f inhibits
colony formation in BMF-A3 (A) and Pan02
(B) pancreatic cancer cells. Colony formation for cells was grown
in DMEM with 10% FBS ± 7f at the indicated doses
for 10 days. Mean ± standard deviation (S.D.) colonies are shown.
** P < 0.01, **** P < 0.001,
***** P < 0.0001 by Student’s t-test vs DMSO.Given the effects of 7f on pancreatic cancer cells
in vitro, we further studied its effects in vivo. First, we profiled
the in vivo pharmacokinetics (PK) of 7f in Sprague-Dawley
(SD) rats (Table ).
7f displayed an ideal PK profile with an oral area under
curve (AUC) value of 80 535 μg/(L h), a T1/2 value of 1.7 h, and an oral bioavailability of 89.9%,
which provides the foundation for an in vivo dosing regimen.
Table 2
Pharmacokinetic Profile of Compound 7f in Ratsa
po (25 mg/kg)
iv (5 mg/kg)
AUC(0–∞) μg/(L h)
80 535.0
16 855.5
T1/2 (h)
1.7
0.9
Tmax (h)
4.0
0.083
Cmax (μg/L)
15 352.5
14 746.0
BA (%)
89.9
SD rats (male,
three animals per
group) weighted 180–220 g were used for the study.
SD rats (male,
three animals per
group) weighted 180–220 g were used for the study.We then established syngeneic models
of pancreatic cancer by orthotopically
implanting the BMF-A3 and Pan02 cells in C57BL/6 mice and evaluated
the efficacy of 7f on pancreatic cancer progression.
The animals were orally (po) administered vehicle or 7f [twice per day (bid), 25 and 50 mg(kg day)] for 3 weeks. In both
tumor models, 7f inhibited the progression of the tumors
significantly without obviously caused animal body weight loss (Table S4), highlighting the in vivo efficacy
of the molecule in pancreatic cancer (Figure ).
Figure 10
7f inhibits pancreatic cancer
progression in vivo.
Mouse pancreatic cancer cell lines BMF-A3 and Pan02 were implanted
orthotopically in C57BL/6 mice. 10 days after implantation, mice (n = 4–5 per group) were orally administered with
vehicle or 7f (25 and 50 mg/kg) twice per day for 3 weeks.
Data were analyzed by analysis of variance (ANOVA) and presented as
the mean ± S.D. * P < 0.05.
7f inhibits pancreatic cancer
progression in vivo.
Mousepancreatic cancer cell lines BMF-A3 and Pan02 were implanted
orthotopically in C57BL/6 mice. 10 days after implantation, mice (n = 4–5 per group) were orally administered with
vehicle or 7f (25 and 50 mg/kg) twice per day for 3 weeks.
Data were analyzed by analysis of variance (ANOVA) and presented as
the mean ± S.D. * P < 0.05.
Conclusions
In summary, a series
of 2-amino-2,3-dihydro-1H-indene-5-carboxamide derivatives
were designed and synthesized as
novel highly selective DDR1 inhibitors with a structure-based drug
design method. Compound 7f strongly suppressed DDR1 with
an IC50 value of 14.9 nM, but it was significantly less
potent against a panel of other 403 nonmutated kinases at 1.0 μM. 7f also potently inhibited the collagen-induced cadherin switching
event induced by DDR1 and dose-dependently suppressed colony formation
of pancreatic cancer cells. Moreover, 7f demonstrated
good pharmacokinetic properties and promising therapeutic effect by
oral administration in orthotopic syngenic models of pancreatic cancer.
Notably, several somatic mutations of DDR1 had been clinically identified,
but most of them are located out of the kinase domain.[35] Thus, 7f may achieve similar inhibition
against these disease-related mutants. Extensive biological investigation
is undergoing to validate 7f as a lead molecule for further
development.
Experimental Section
General
Chemistry
Reagents and solvents were purchased
from commercial sources and used directedly. Flash chromatography
was performed using 300-mesh silica gel. Reactions were monitored
by thin-layer chromatography using silica gel plates with fluorescence
F254 and UV light visualization. Low-resolution electrospray
ionization mass spectrometry (ESI-MS) was performed on an Agilent
1200 high-performance liquid chromatography (HPLC)-mass selective
detector mass spectrometer and high-resolution ESI-MS on an Applied
Biosystems Q-STAR Elite ESI-LC-MS/MS mass spectrometer. 1H NMR spectra were performed on a Bruker AV-400 spectrometer at 400
MHz or a Bruker AV-500 spectrometer at 500 MHz. 13C NMR
spectra were performed on a Bruker AV-500 spectrometer at 125 MHz.
Coupling constants (J) were expressed in hertz (Hz).
Chemical shifts (δ) of NMR were reported in parts per million
units relative to an internal standard (tetramethylsilane). Purity
of the compounds was determined by reverse-phase high-performance
liquid chromatography (HPLC) analysis to be >95%. HPLC instrument:
Dionex Summit HPLC (column: Diamonsil C18, 5.0 μm, 4.6 ×
250 mm2 (Dikma Technologies); detector: PDA-100 photodiode
array; injector: ASI-100 autoinjector; pump: p-680A). A flow rate
of 1.0 mL/min was used with mobile phase of MeOH in H2O
with a 0.1% modifier (ammonia, v/v).
To a mixture
of (R)-5-bromo-2,3-dihydro-1H-inden-2-amine 8 (40 mg, 0.19 mmol) and Et3N (39 μL, 0.28
mmol) in 1 mL of dichloromethane (DCM) was added (Boc)2O (131 μL, 0.57 mmol). The reaction mixture was stirred at
room temperature overnight. The mixture was then poured into water
and extracted three times with dichloromethane. The combined organic
phase was dried over Na2SO4 and purified by
column chromatography to give 10 (53 mg, 90%). 1H NMR (400 MHz, DMSO-d6), 7.38 (s, 1H),
7.29 (d, J = 8.0 Hz, 1H), 7.17 (s, 1H), 7.14 (d, J = 8.0 Hz, 1H), 4.22–4.17 (m, 1H), 3.14–3.02
(m, 2H), 2.79–2.68 (m, 2H), 1.38 (s, 9H). MS (ESI) m/z 335.3 [M + Na]+.
tert-Butyl (R)-(5-bromo-2,3-dihydro-1H-inden-2-yl)carbamate 10 (600 mg, 1.92 mmol)
was dissolved in 2 mL of DMF, and sodium hydride (89 mg, 2.22 mmol,
in 60% mineral oil) was added. The reaction was stirred for 40 min,
and then CH3I (0.13 mL, 2.12 mmol) was added dropwise in
an ice bath. The reaction was stirred overnight at room temperature.
The mixture was quenched by water and extracted with ethyl acetatethree times. The combined organic layer was dried over magnesium sulfate,
filtered, evaporated, and purified by silica gel column chromatography
to give 12 (501 mg, 80%). 1H NMR (500 MHz,
DMSO-d6), δ 7.41 (s, 1H), 7.32 (d, J = 1.6 Hz, 1H), 7.31 (d, J = 1.5 Hz, 1H),
7.17 (d, J = 8.0 Hz, 1H), 4.85 (s, 1H), 3.09–2.99
(m, 2H), 2.96–2.85 (m, 2H), 2.64 (s, 3H), 1.39 (s, 9H). MS
(ESI) m/z 348.3 [M + Na]+.
A
mixture of methyl (R)-2-((tert-butoxycarbonyl)amino)-2,3-dihydro-1H-indene-5-carboxylate 15 (126 mg, 0.43 mmol)
and 4 M HCl (1 mL) in dioxane (1 mL) was stirred at 60 °C for
2 h. The reaction mixture was concentrated to give the amine, which
was used directly for the next step without further purification.
MS (ESI) m/z 192.2 [M + H]+.
A mixture
of methyl (R)-2-((tert-butoxycarbonyl)(methyl)amino)-2,3-dihydro-1H-indene-5-carboxylate 17 (1.9 g, 6.22 mmol)
and 4 M HCl (13 mL) in dioxane (13 mL) was stirred at 50 °C for
4 h. The solvent was evaporated in vacuum. The residue was diluted
with H2O and extracted with dichloromethanethree times.
The combined organic phase was washed with saturated NaHCO3. The aqueous layer was extracted twice with dichloromethane. The
combined organic layer was washed with brine and dried over anhydrous
Na2SO4. The solvent was evaporated in vacuo
to give the free amine 22 (1.0 g, 78%), which was used
directly in the next step without further purification.
To
a solution of methyl (R)-2-(methyl(pyrimidin-5-yl)amino)-2,3-dihydro-1H-indole-5-carboxylate 27 (1 g, 3.5 mmol) in
dioxane was added 1 M sodium hydroxide solution. The reaction mixture
was stirred at 50 °C overnight. The solvent was evaporated under
vacuo, and the resulting residue was dissolved in water. The solution
was acidified to pH 4, and a white precipitate was formed, which was
collected, washed with water, and dried to give 30 (772.9
mg, 82%). 1H NMR (400 MHz, DMSO-d6) δ 12.78 (s, 1H), 8.50 (s, 1H), 8.43 (s, 2H), 7.82
(s, 1H), 7.78 (d, J = 7.6 Hz, 1H), 7.36 (d, J = 8.0 Hz, 1H), 5.09–4.89 (m, 1H), 3.25 (dd, J = 17.6, 8.0 Hz, 2H), 3.12–2.98 (m, 2H), 2.74 (s,
3H).Compounds 33–37 were prepared
according to the published methods.[36]
5-Bromoisoindoline-1,3-dione (33)
4-bromophthalic
anhydride 32 (1 g, 4.4 mmol) and formamide were combined
in a sealed tube. The reaction mixture was stirred overnight at 200
°C. After cooling to room temperature, 10 mL of water was added
to the reaction mixture. The precipitate was filtered, washed with
methanol, and dried in a vacuum oven to give 33 (788
mg, 79%). 1H NMR (500 MHz, DMSO-d6) δ 11.46 (s, 1H), 8.04–8.00 (m, 1H), 8.01 (d, J = 3.0 Hz, 1H), 7.75 (d, J = 8.0 Hz, 1H).
MS (ESI) m/z 247.2 [M + Na]+.
5-Bromoisoindoline (34)
To a solution
of 5-bromoisoindoline-1,3-dione 33 (788 mg, 3.5 mmol)
in THF (20 mL) was added the brane–THFcomplex (1 M, 14 mL).
The reaction was heated to reflux overnight. After cooling to room
temperature, the solvent was concentrated in vacuo. Water was added
to the residue. The aqueous phase was extracted with DCMthree times.
The combined organic phase was dried over Na2SO4, filtered, and concentrated in vacuo to give 34 (282
mg, 41%), which was used for the next step without further purification.
MS (ESI) m/z 198.4 [M + H]+.
tert-Butyl 5-Bromoisoindoline-2-carboxylate
(35)
To 5-bromoisoindoline 34 (282
mg, 1.42 mmol) in 6 mL of THF were added (Boc)2O (1 mL,
4.3 mmol) and NaHCO3 (360.8 mg, 4.29 mmol). The reaction
mixture was stirred at room temperature overnight. The reaction was
quenched by water and extracted three times with CH2Cl2. The combined organic phase was washed with brine, dried
over Na2SO4, concentrated in vacuo, and purified
by silica gel column chromatography to give 35 (238 mg,
56%). 1H NMR (400 MHz, DMSO-d6) δ 7.55 (d, J = 4.4 Hz, 1H), 7.46 (d, J = 8.0 Hz, 1H), 7.28 (dd, J = 8.0, 4.0
Hz, 1H), 4.55 (dd, J = 14.8, 9.2 Hz, 4H), 1.45 (s,
9H). MS (ESI) m/z 320.3 [M + Na]+.
2-(tert-Butyl)
5-methylisoindoline-2,5-dicarboxylate 36 (154 mg, 0.2
mmol) was stirred in a mixture of 4 M HCl
(1.5 mL) and dioxane (1.5 mL) at 50 °C for 4 h. The reaction
mixture was concentrated in vacuo to give 37, which was
used directly for the next step without further purification. MS (ESI) m/z 178.1 [M + H]+.
To methyl isoindoline-5-carboxylate hydrochloride 37 (90 mg, 0.42 mmol) in DMF were added 5-chloromethylpyrimidine
(65 mg, 0.41 mmol) and potassium carbonate (145 mg, 1.05 mmol). The
reaction was stirred overnight at 50 °C. Then, water (10 mL)
was added to the reaction mixture and extracted with ethyl acetatethree times. The combined organic phase was dried over Na2SO4, concentrated in vacuo, and purified by column chromatography
to give 39 (44 mg, 41%). 1H NMR (500 MHz,
CDCl3) δ 9.17 (s, 1H), 8.79 (s, 2H), 7.95–7.90
(m, 1H), 7.87 (s, 1H), 7.25 (s, 1H), 4.00 (s, 4H), 3.95 (s, 2H), 3.90
(s, 3H). MS (ESI) m/z 270.3 [M +
H]+.
In Vitro Kinase Assay
Inhibition
activity of compounds
against TrkA/TrkB/TrkC was determined using the FRET-based Z′-Lyte
assay system according to the manufacturer’s instructions (Invitrogen).
Tyr1 peptide was used as the substrate. The reactions were carried
out in 384-well plates in a 10 μL reaction volume with appropriate
amount of kinases in 50 mM N-(2-hydroxyethyl)piperazine-N′-ethanesulfonic acid (HEPES) (pH 7.5), 10 mM MgCl2, 1 mM ethylene glycol–bis(β-aminoethyl ether)-N,N,N′,N′-tetraacetic acid (EGTA), and 0.01% Brij-35. TrkA/TrkB/TrkC
kinase reactions were incubated 1.5 h at room temperature in the presence
of 2 μM of substrate with 400, 25, and 50 μM ATP, respectively,
and in the presence of various concentrations of the compounds; then,
5 μL of the development reagent was added for further 1 h room-temperature
incubation followed by the addition of 5 μL of the stop solution.
The fluorescence-to-signal ratio of 400 nm (excitation)/445 nm and
520 nm (emission) was examined with an EnVision Multilabel Reader
(PerkinElmer, Inc.). Data analysis and curve fitting were performed
using GraphPad Prism5 (GraphPad Software, Inc).The effects
of compounds on the kinases DDR1 and DDR2 were assessed using a LanthaScreen
Eu kinase activity assay technology (Invitrogen). Kinase reactions
are performed in a 10 μL volume in low-volume 384-well plates.
The kinases in the reaction buffer consist of 50 mM HEPES pH 7.5,
0.01% Brij-35, 10 mM MgCl2, and 1 mM EGTA; the concentration
of the fluorescein–poly-GAT substrate (Invitrogen) in the assay
is 100 nM. Kinase reactions were initiated with the addition of 100
nM ATP in the presence of serials of dilutions of compounds. The reactions
were allowed to proceed for 1 h at room temperature before a 10 μL
preparation of EDTA (20 mM) and Eu-labeled antibody (4 nM) in time-resolved
(TR)-FRET dilution buffer are added. The final concentration of antibody
in the assay well is 2 nM, and the final concentration of EDTA is
10 mM. The plate is allowed to incubate at room temperature for one
more hour before the TR-FRET emission ratios of 665/340 nm were acquired
on a PerkinElmer EnVision multilabel reader (Perkin-Elmer, Inc.).
Data analysis and curve fitting were performed using GraphPad Prism
7 software.
KINOMEscan
Kinase-tagged T7 phage
strains were prepared
in an Escherichia coli host derived
from the BL21 strain. E. coli were
grown to log-phase and infected with the T7 phage and incubated with
shaking at 32 °C until lysis. The lysates were centrifuged and
filtered to remove cell debris. The remaining kinases were produced
in HEK-293 cells and subsequently tagged with DNA for quantitative
polymerase chain reaction (qPCR) detection. Streptavidin-coated magnetic
beads were treated with biotinylated small-molecule ligands for 30
min at room temperature to generate affinity resins for kinase assays.
The liganded beads were blocked with excess biotin and washed with
blocking buffer [SeaBlock (Pierce), 1% bovine serum albumin (BSA),
0.05% Tween 20, 1 mM dithiothreitol (DTT)] to remove the unbound ligand
and to reduce nonspecific binding. Binding reactions were assembled
by combining kinases, liganded affinity beads, and compound 7i in 1× binding buffer [20% SeaBlock, 0.17× phosphate-buffered
saline (PBS), 0.05% Tween 20, 6 mM DTT]. All reactions were performed
in polystyrene 96-well plates in a final volume of 0.135 mL. The assay
plates were incubated at room temperature with shaking for 1 h, and
the affinity beads were washed with wash buffer (1× PBS, 0.05%
Tween 20). The beads were then resuspended in an elution buffer (1×
PBS, 0.05% Tween 20, 0.5 μM nonbiotinylated affinity ligand)
and incubated at room temperature with shaking for 30 min. The kinase
concentration in the eluates was measured by qPCR. For primary screening,
compound 6j was screened at the concentration of 1 μM,
and the results are reported as “% Ctrl”.For Kd determination, an 11-point 3-fold serial dilution
of compound 7f was prepared in 100% DMSO at 100×
final test concentration and subsequently diluted to 1× in the
assay (final DMSOconcentration = 1%). Binding constants (Kd values) were calculated with a standard dose–response
curve using the Hill equation.
Western Blot Analysis
Pan02, BMF-A3, and CT1A-C11 cells
were cultured in DMEM (Corning) containing 10% fetal bovine serum
(FBS) and maintained at 37 °C in a humidified incubator with
5% CO2 and 95% air. For the collagen and 7f treatment, cells were cultured in 10 mL of complete media with 50
μg/mL collagen and indicated concentration of 7f for 8 or 18 h. Cells were lysed, supernatants were recovered by
centrifugation at 13 000 rpm, protein concentration was measured,
and equal amounts of total protein were separated by sodium dodecyl
sulfate-polyacrylamide gel electrophoresis. Proteins were transferred
to poly(vinylidene difluoride) membranes (Bio-Rad, Hercules, CA) followed
by blockade for 1 h in 5% bovine serum albumin in TBS-T. Membranes
were incubated overnight at 4 °C with primary antibody phospho-DDR1
(Tyr792, Cell Signaling #11994), DDR1 (Santa Cruz SC-532), phospho-PYK2
(Tyr402, Cell Signaling #3291), PYK2 (Cell Signaling #3292), PEAK1
(Millipore 09-274), phospho-PEAK1 (Tyr665, Millipore #ABT52), E-cadherin
(24E10, Cell Signaling #3195), N-cadherin (13A9, Cell Signaling #3195),
and TUBULIN α (Biorad, MCA77D800). Membranes were incubated
with the corresponding horseradish peroxidase-conjugated secondary
antibody (Pierce Biotechnologies, Rockford, IL) for 1 h. Specific
bands were detected using the enhanced chemiluminescence reagent (ECL,
PerkinElmer Life Sciences, Boston, MA) on an autoradiographic film.
Epithelial–Mesenchymal Transition Assay
For
immunofluorescent staining, cells were treated with 50 μg/mL
collagen and indicated concentration of 7f for 24 h.
Cells were fixed with methanol and stained with E-cadherin (24E10,
Cell Signaling #3195), N-cadherin (13A9, Cell Signaling #3195), and
DAPI. Fluorescent images were captured with a Photometric CoolSNAP
HQ camera using NIS Elements AR 2.3 Software (Nikon).For 3D
culture, cells were embedded in ECM consisting of 5 mg/mL matrigel
(BD Biosciences) and 2.1 mg/mL collagen I (BD Biosciences). Cultures
were overlaid with DMEM + 10% FBS containing 2% matrigel. For analysis
of spheroid morphology, 48 h after plating onto ECM, cells were fixed
with methanol and stained with phalloidin and DAPI. Fluorescent images
were captured with a Photometric CoolSNAP HQ camera using NIS Elements
AR 2.3 Software (Nikon).
Colony Formation Assay
Cells were
cultured in six-well
tissue culture plates at low density (1000 cells per well) in 2 mL
of media with 10% FBS ± 7f at the indicated doses
for 10 days. A DMSOcontrol was added to the respective wells to demonstrate
the vehicle-independent effect. Cells were then stained with crystal
violet.
Cells were plated at 2000 cells/well in tissue-culture-treated
96-well plates. The following day, different concentration of 7f was added to each plate in a dilution series across the
plate. On day 5, 20 μL of thiazolyl blue tetrazolium blue was
added, followed by a 3 h incubation at 37 °C, and then the medium
was removed, and 100 μL of DMSO was added to each well. The
absorbance was read at 540 nm on a plate reader.
Wound-Healing
Assay
Cells were cultured in six-well
tissue culture plates at high density (∼90% confluence) in
2 mL of media with 5% FBS. Uniform scratches were made down the center
of each well with a p20 pipette tip, cells were gently washed with
PBS to remove the loose cell debris, and drug was added in media containing
5% FBS. Each condition was in triplicates. Images from the center
of each well were taken at 0 and 24 h. The wound width (μm)
was measured using NIS Elements AR 2.30 software. The initial wound
width was used to verify consistency in scratches.
Determination
of Pharmacokinetic Parameters in Rats
All animal studies
were performed according to the protocols and
guidelines of the institutional care and use committee. The 4–6
week old male Sprague-Dawley rats were purchased from the Shanghai
Laboratory Animal Research Center (Shanghai, China). All of the procedures
related to animal handling, care, and treatment in this article were
performed in compliance with Agreement of the Ethics Committee on
Laboratory Animal Care and the Guidelines for the Care and Use of
Laboratory Animals in Shanghai, China. Animals were maintained on
standard animal chow and water ad libitum, in a climate-controlled
room (23 ± 1 °C, 30–70% relative humidity, a minimum
of 10 exchanges of room air/h and a 12 h light/dark cycle) for one
week prior to experiments. The compound was dissolved in the solution
containing 2% DMSO, 4% ethanol, 4% castor oil, and 90% ddH2O. Pharmacokinetic properties of SD rats (male) were determined following
intravenous (iv) and oral administration. Animals were randomly distributed
into two experimental groups (n = 3). The oral groups
were given 25 mg/kg by gastric gavage. The other group was dosed by
injection into the tail vein (5 mg/kg). After a single administration,
whole blood samples (100–200 μL) were obtained from the
orbital venous plexus at the following time points after dosing: 5,
10, and 30 min and 1, 2, 3, 4, 6, 8, 11, and 24 h (po); 2, 10, and
30 min and 1, 2, 3, 4, 6, 8, 11, and 24 h (iv). Whole blood samples
were collected in heparinized tubes. The plasma fraction was immediately
separated by centrifugation (8000 rpm, 6 min, 4 °C) and stored
at −20 °C until liquid chromatography–mass spectrometry
analysis. The rats were humanely euthanized by carbon dioxide 24 h
after experiment without pain. The pharmacokinetics parameters were
calculated by analyzing the compound concentration in plasma samples
using the pharmacokinetic software DAS.2.0.
In Vivo Anticancer Activity
Assay
All animals were
housed in a pathogen-free facility with access to food and water ad
libitum. C57BL/6 mice were purchased from the UT SouthwesternMouse
Breeding Core. Pan02 and BMF-A3 cells (5 × 105) were
injected orthotopically in 6–8 week-old C57BL/6 mice. Fourteen
days after tumor cell injection, mice were randomized to receive treatment.
Experiments were approved and performed in accordance with the Institutional
Animal Care and Use Committee at UT Southwestern. Experiments were
stopped after the designated time post tumor cell implantation. Tumors
were harvested, and tumor weight was measured. Data sets were analyzed
by ANOVA.
Molecular Modeling
All of the procedures
were performed
in Maestro 11.2 (version 11.2, Schrödinger, LLC, New York,
NY, 2017). The DDR1 (PDB code: 5FDP and 6HP9) and TrkC (PDB code: 3V5Q) proteins were processed
using the “Protein Preparation Wizard” workflow in Maestro
9.4 (version 11.2, Schrödinger, LLC, New York, NY, 2017) to
add bond orders and hydrogens. All hetatm residues and crystal water
molecules beyond 5 Å from the het group were removed. Compounds
were built by the LigPrep module using the OPLS-2005 force field.
The glide module was used as the docking program. The grid-enclosing
box was placed on the centroid of the 0LI, which was extracted from
the crystal structures of DDR1 and TrkC separately. The standard precision
approach of Glide was adopted to dock compounds 6 and 7a–n to DDR1 and compound 7c to TrkC with the default parameters.
Crystallization and Structure
Determination
The kinase
domain of humanDDR1 (Uniprot Q08345, residues 601–913) was
expressed as an N-terminal 6× His fusion in Sf9 cells and purified
by nickel affinity chromatography followed by tag cleavage with tobacco
etch virus protease and then size exclusion chromatography on an S200
column (GE Healthcare). Protein at 12 mg/mL in 50 mM HEPES pH 7.5,
300 mM NaCl, 0.5 mM tris(2-carboxyethyl)phosphine, 2% DMSO was incubated
with 1 mM compound 7c for 3 h on ice and then filtered
to 0.22 μm. Then, 150 nL of sitting drops was set up with diffracting
crystals being obtained from a 1:2 ratio of protein to mother liquor
(10% ethylene glycol, 0.2 M sodium sulfate, 25% poly(ethylene glycol)
1500, 0.1 M bis–tris–propane pH 7.1). Crystals were
cryoprotected in the mother liquor supplemented with 25% ethylene
glycol and flash-frozen in liquid nitrogen. Diffraction was carried
out at Diamond Light Source beamline I04 at 100 K. Data were indexed
and integrated using XDS[37] and scaled using
AIMLESS.[38] Initial phases were identified
using molecular replacement in PHASER.[39] The structure was refined using iterative rounds of manual building
using COOT[40] and refinement using PHENIX.REFINE.[41] The refined structure was validated with MolProbity,[42] and the atomic coordinate files were deposited
in the Protein Data Bank with Autodep.[43]
Authors: André Richters; Hoang D Nguyen; Trang Phan; Jeffrey R Simard; Christian Grütter; Julian Engel; Daniel Rauh Journal: J Med Chem Date: 2014-05-05 Impact factor: 7.446
Authors: Paul D Adams; Pavel V Afonine; Gábor Bunkóczi; Vincent B Chen; Ian W Davis; Nathaniel Echols; Jeffrey J Headd; Li-Wei Hung; Gary J Kapral; Ralf W Grosse-Kunstleve; Airlie J McCoy; Nigel W Moriarty; Robert Oeffner; Randy J Read; David C Richardson; Jane S Richardson; Thomas C Terwilliger; Peter H Zwart Journal: Acta Crystallogr D Biol Crystallogr Date: 2010-01-22
Authors: Vincent B Chen; W Bryan Arendall; Jeffrey J Headd; Daniel A Keedy; Robert M Immormino; Gary J Kapral; Laura W Murray; Jane S Richardson; David C Richardson Journal: Acta Crystallogr D Biol Crystallogr Date: 2009-12-21
Authors: Hyung-Gu Kim; Li Tan; Ellen L Weisberg; Feiyang Liu; Peter Canning; Hwan Geun Choi; Scott A Ezell; Hong Wu; Zheng Zhao; Jinhua Wang; Anna Mandinova; James D Griffin; Alex N Bullock; Qingsong Liu; Sam W Lee; Nathanael S Gray Journal: ACS Chem Biol Date: 2013-08-13 Impact factor: 5.100
Authors: Zhen Wang; Huan Bian; Sergio G Bartual; Wenting Du; Jinfeng Luo; Hu Zhao; Shasha Zhang; Cheng Mo; Yang Zhou; Yong Xu; Zhengchao Tu; Xiaomei Ren; Xiaoyun Lu; Rolf A Brekken; Libo Yao; Alex N Bullock; Jin Su; Ke Ding Journal: J Med Chem Date: 2016-06-03 Impact factor: 7.446
Authors: Justin F Creeden; Khaled Alganem; Ali S Imami; Nicholas D Henkel; F Charles Brunicardi; Shi-He Liu; Rammohan Shukla; Tushar Tomar; Faris Naji; Robert E McCullumsmith Journal: Int J Mol Sci Date: 2020-11-21 Impact factor: 5.923