Design, synthesis and SAR of substituted indoles as selective TrkA inhibitors

Article abstract of DOI:10.1016/j.bmcl.2017.04.045

A series of substituted indoles were examined as selective inhibitors of tropomyosin-related kinase receptor A (TrkA), a therapeutic target for the treatment of pain. An SAR optimization campaign based on ALIS screening lead compound 1 is reported.

Full text of DOI:10.1016/j.bmcl.2017.04.045

Accepted Manuscript
Design, synthesis and SAR of substituted indoles as selective TrkA inhibitors
Danielle M. Hurzy, Darrell A. Henze, Tamara D. Cabalu, Kartik Narayan,
Amanda Heller, Andrew J. Cooke
PII:
S0960-894X(17)30419-5
DOI:
http://dx.doi.org/10.1016/j.bmcl.2017.04.045
BMCL 24898
Reference:
Bioorganic & Medicinal Chemistry Letters
To appear in:
Received Date:
Revised Date:
Accepted Date:
23 February 2017
10 April 2017
12 April 2017
Please cite this article as: Hurzy, D.M., Henze, D.A., Cabalu, T.D., Narayan, K., Heller, A., Cooke, A.J., Design,
synthesis and SAR of substituted indoles as selective TrkA inhibitors, Bioorganic & Medicinal Chemistry Letters
(2017), doi: http://dx.doi.org/10.1016/j.bmcl.2017.04.045
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Bioorganic & Medicinal Chemistry Letters
journal homepage: www.els evier.com
Design, synthesis and SAR of substituted indoles as selective TrkA inhibitors
Danielle M. Hurzya,*, Darrell A. Henze b Tamara D. Cabalu c Kartik Narayand, Amanda Hellere,
,
,
Andrew J. Cooke a
a Department of Medicinal Chemistry, MRL, Merck & Co., Inc., 770 Sumneytown Pike, West Point, PA 19486, USA
b Department of Pain Research, MRL, Merck & Co., Inc., 770 Sumneytown Pike, West Point, PA 19486, USA
c Department of Drug Metabolism, MRL, Merck & Co., Inc., 770 Sumneytown Pike, West Point, PA 19486, USA
dAnalytical Process and Technology, Sanofi Pasteur, Discovery Drive, Swiftwater, PA 18370, USA
eScientific Operations, Lab Connect, LLC., 605 First Avenue, Ste. 300, Seattle, WA 98104, USA
∗ Corresponding author. Tel.: +1-215-652-2635; fax: +1-215-652-7310; e-mail: danielle_mcmaster@merck.com (D.M. Hurzy)
ARTICLE INFO
ABSTRACT
A series of substituted indoles were examined as selective inhibitors of tropomyosin-related
kinase receptor A (TrkA), a therapeutic target for the treatment of pain. An SAR optimization
campaign based on ALIS screening lead compound 1 is reported.
Article history:
Received
Received in revised form
Accepted
Available online
2009 Elsevier Ltd. All rights reserved.
Keywords:
TrkA
pain
indoles
The tropomyosin-receptor kinase (Trk) family consists of three
members: TrkA, TrkB and TrkC. Each isoform is activated by
neurotrophins, a group of soluble growth factors including nerve
growth factor (NGF) for TrkA, brain-derived neurotrophic factor
(BDNF) for TrkB, and NT-3 for TrkC.1 It has been widely
recognized that Trks play an important role in pain sensation2 and
inhibitors of the Trk/neurotrophin pathway have been validated
in numerous animal pain models.3,4
Compound 1 displayed moderate potency toward TrkA (IC50 =
607 nM) using a DiscoverX PathHunter assay, which is a
measure of activation of the TrkA receptor via phosphorylation,13
and 34-fold selectivity over TrkC. This hit was also attractive for
an optimization campaign due to its modular structure that is
amenable to rapid analog synthesis. To further optimize the ALIS
hit, our strategy was to explore SAR in the four regions of
compound 1 as shown in Figure 1. Each region was scanned
systematically to find a superior replacement with improved
potency and selectivity.
Evidence has suggested that increased levels of NGF are present
in injury, inflammation, and chronic pain states. Activation of the
TrkA receptor by NGF is believed to result in both a rapid and
long-term increased sensitivity of nociceptors leading to chronic
sensitization and pain.5 Inhibition of the NGF/TrkA pathway has
been clinically validated using anti-NGF antibodies for the
treatment of chronic pain6, 7 with on-going trials for cancer pain8,
osteoarthritis9, and chronic low back pain.10 As an alternative
approach, our efforts have focused on identifying a selective,
small molecule inhibitor of TrkA for the treatment of pain.
Automated Ligand Identification System (ALIS) screening
technology11 using the full length intracellular domain of TrkA
(residues 440-796) yielded compound 1 as a promising, selective
TrkA inhibitor. Our recent publication disclosing the crystal
structure of compound 1 binding with TrkA highlights in detail
the binding site and the key role the juxtamembrane region
(residues 440-497) plays for selectivity versus TrkB and TrkC.12
Figure 1. Design strategy for SAR campaign.

The chemistry utilized to prepare the target molecules in Tables
1-4 is depicted in Schemes 1-4. Commercially available
carboxylic acid 2 served as a starting point for several desired
targets. Amides 14 and 20-34 were synthesized via HATU
mediated coupling of 2 with an array of commercially available
amines. Acid 2 was subsequently converted to aldehyde 4 under
Scheme 3. Reagents and conditions: (a) R2-X or R2-B(OH)2, Pd(PPh3)2Cl2,
2M Na2CO3, Dioxane, 120 oC; (b) (i) methyl chloroacetate, Cs2CO3, DMF, 60
oC; (ii) 1 M NaOH, MeOH, 100 oC; (c) 2-aminomethylpyridine, HATU,
DIEA, DMF, rt.
standard conditions. Reductive amination of
4 and 2-
(aminomethyl)pyridine affords compound 16. Amine 5 was
obtained via Ti(OEt)4 mediated condensation of 4 under Ellman
conditions14 followed by HCl deprotection. Amine 5 was
subsequently functionalized as described to afford amide 17 and
sulfonamide 18. In Scheme 2, 2-thiophen-2-yl-indole 6 was
treated with triphosgene to afford carbamoyl chloride 7 which
was converted to ureas 15 and 19 using the appropriate amine.
Scheme 4. Reagents and conditions: (a) (i) oxalyl chloride, DCM, DMF, rt;
(ii) 1H-1,2,3-triazole, K2CO3, sulfolane, 140 oC; (b) (i) methylchloroacetate,
Cs2CO3, DMF, 60 oC; (ii)
1 M
NaOH, MeOH, 100 oC; (c) 2-
aminomethyl)pyridine, HATU, iPr2NEt, DMF, rt.
Initial medicinal chemistry efforts focused on exploration of
linker region C while maintaining the indole, thiophene and 2-
pyridyl portions of 1 as shown in Table 1. To determine TrkA
and TrkC activity, analogs were evaluated using a DiscoverX
Pathhunter assay and expressed as IC50 values. Removal of a
methylene spacer either on the 2-pyridyl side (14) or on the
indole side (15) led to a loss of both potency and selectivity.
Reduction of the carbonyl group to a methylene group to form
compound 16 was also detrimental to TrkA activity. Shifting the
amide toward the 2-pyridyl moiety (17) or replacing the amide
with a sulfonamide (18) was not tolerated. Urea compound 19
showed a complete loss of activity. Methylation of the NH to
NMe (20) also resulted in lack of activity. All changes to the
linker portion displayed inferior potency and selectivity as
compared to compound 1. These findings are in agreement with
the X-ray crystal structure recently disclosed by Su et al. which
identified key interactions of the central amide of 1 with Asp-668
and Ile-490 residues,12 and thus remained fixed for further SAR
studies.
Scheme 1. Reagents and conditions: (a) RNH2, HATU, DIEA, DMF, rt; (b)
LiAlH4, THF, 0 oC; (c) Dess-Martin, DCM, rt; (d) 2-(aminomethyl)pyridine,
NaBH(OAc)3, AcOH, DCM, rt; (e) (i) 2-methyl-2-propanesulfinamide,
Ti(OEt)4, THF; (ii) NaBH4, 0 oC; (iii) 4N HCl, DCM, rt; (f) picolinic acid,
HATU, DIEA, DMF, rt; (g) pyridine-2-sulfonyl chloride, NEt3, DCM, rt.
Table 1
SAR of linker region C
N
S
Scheme 2. Reagents and conditions: (a) triphosgene, NEt3, DCM, 0 oC;
(b) RNH2, NEt3, DCM, rt.
R
Compound
R
TrkA IC50 (nM)
>81010
TrkC IC50 (nM)
> 9001
Selectivity (C/A)
-
O
14
N
H
N
N
In Scheme 3, Suzuki coupling of the corresponding boronic
esters and arylhalides 8 gives compound 9. Subsequent alkylation
and saponification affords carboxylic acid 10 which was readily
converted to analogs 35-40 and 42-53 via HATU coupling as
described. In Scheme 4, indole-2-carboxylic acid 11 was
converted to the acid chloride, then treated with 1-H-1,2,3-
triazole in sulfolane to afford oxazole 12 in a one-pot procedure.
Alkylation of 12 and hydrolysis of the intermediate ester affords
13 which is converted to 41 as previously described. Compounds
54 and 55 were prepared in similar fashion to Scheme 4.
H
N
15
16
64320
81160
25140
1.2
O
H
N
>81010
-
N
N
H
N
17
18
74020
80020
1.1
-
O
H
N
O
S
>81010
> 81010
N
N
O
O
19
20
>81010
47300
80270
-
N
H
N
> 81010
1.7
N
O

SAR studies then focused on the 2-pyridyl portion of the lead
compound as illustrated in Table 2. Movement of nitrogen to the
meta and para positions resulted in a ~15-fold and ~7-fold
decrease in potency for the 3-pyridyl 21 and 4-pyridyl 22 analogs
as compared to 1. Complete removal of the nitrogen heteroatom
to give compound 25 resulted in a loss of activity and selectivity.
These results indicate that the preferred position for a heteroatom
is the ortho position.
opportunity to mitigate the toxicophore nature of the thiophene
moiety15 while reducing the lipophilicity to improve metabolic
stability.16,17 A range of other heterocyclic systems were explored
as shown with compounds 35-44. Methylthiophene (35) and
isothiazole (40) analogs displayed a ~2-fold boost in selectivity,
while thiazole (39) and oxazole (41) derivatives showed a similar
selectivity with reduced cLogP (2.59 and 1.94 vs. 3.87) as
compared to lead compound 1. All other 5-member heterocyclic
modifications (36-38) were not tolerated as well as the pyridyl
analogs (42-44). Replacement of the thiophene with a phenyl
(45) was very comparable to 1.
Table 2
SAR of 2-pyridyl region D
Table 3
SAR of thiophene region B
N
S
O
NH
R
R
N
Compound
R
TrkA IC50 (nM)
9085
TrkC IC50 (nM)
>81010
Selectivity (C/A)
9
O
NH
21
N
N
N
22
23
24
4394
8829
36600
> 81010
58440
18
7
N
Compound
R
TrkA IC50 (nM)
662
TrkC IC50 (nM)
47860
Selectivity (C/A)
72
N
35
N
N
>27000
-
S
12970
3944
73070
70240
5.6
17
36
37
38
O
S
25
26
>9001
1300
> 3000
>81010
-
NH
N
N
N
>62
N
N
49000
>81010
>1.6
27
28
> 81010
210
> 81010
>81010
-
S
N
NH
NH
2400
961
>81010
> 81010
> 34
>84
39
40
>386
S
N
N
29
70
>81010
>1157
S
N
N
O
N
N
2114
53490
> 81010
> 81010
-
25
>7
-
30
31
3163
7310
>81010
38500
>25
5
41
42
43
44
S
11890
>81010
30870
O
N
N
32
33
9400
3388
120000
>81010
13
NH
N
N
>24
-
N
NH
N
34
218
71720
328
1424
25960
18
45
N
Replacement of the 2-pyridyl moiety with other heterocyclic
systems led to variable effects as compared to 1. Pyrimidine 23
displayed a decrease in both potency and selectivity, while
pyrazine 24 exhibited a ~60-fold decrease in potency.
Methylimidazole 27 was not tolerated, while thiazole (30),
oxazole (31), and imidazoles (32 and 33) were tolerated but did
not display any appreciable improvements over 1. However,
imidazole analog 26 did show a 2-fold increase in selectivity over
TrkC. Further probing of imidazole moieties led to
phenylimidazole (28) and imidazole (34) analogs which both
showed a ~3-fold increase in potency and a ~ 10-fold increase in
selectivity. Benzimidazole 29 was the most potent compound
thus far in this series with a TrkA potency of 70 nM and >1157-
fold selective over TrkC.
While maintaining the 2-phenyl moiety, SAR on the indole
region of the molecule was examined (Table 4). Azaindole
analogs 46-49 showed a moderate decrease in potency and
selectivity relative to the phenyl counterpart (45). However,
substitution on the indole moiety proved to be an acceptable
modification in terms of potency and selectivity, as shown by the
4- and 5-fluoro substituted analogs 50 and 51. This substitution
provides a ~2.5-fold boost in selectivity while reducing the
electron rich nature of the indole ring system.
Combining the most successful modifications from each region
of the molecule provided compounds 54 and 55, potent and
selective TrkA inhibitors as shown in Figure 2. Compound 54
showed a potency of 215 nM and 316-fold selective over TrkC.
The introduction of the 5-fluoro substitutent (55) provided an
even greater jump in potency toward TrkA (IC50 = 113 nM) and
In a concurrent effort, SAR of thiophene region B was also
investigated (Table 3). This modification provides an

selectivity against TrkC (607x). Both of these compounds have
reduced cLogP values of 2.86 and 3.02 vs. compound 1 (3.87)
which were expected to contribute favorably to the
physiochemical and pharmacokinetic profiles of these
compounds.
In summary, a series of substituted indoles were prepared and
evaluated as selective TrkA inhibitors. An SAR campaign of the
4 regions of ALIS hit 1 provided new analogs with improved
potency, selectivity and pharmacokinetic profile. Additional SAR
optimization and in vivo studies are ongoing and will be reported
in a later publication.
Table 4
SAR of indole region A
Table 5
Pharmacokinetic profiles in rats
a,b
R
F
Compound
(%)
Cl (mL/min/kg)c,d
Cmax M)a,b
0.515
1/2 (h)c,d
t
O
1
5
24
25
0.4
1.3
2.3
NH
29
34
34
2.325
N
54
38
2.265
a
Compound
R
TrkA IC50 (nM)
>81010
TrkC IC50 (nM)
>81010
Selectivity (C/A)
-
Compound 1 dosed at 10 mpk for PO in 20% Vit E TPGS.
b Compounds 29 and 54 dosed at 10 mpk for PO in 40:10:50
PEG400/Tween80/H2O.
N
46
N
N
N
N
c Compound 1 dosed at 2 mpk in 1:1 DMSO/PEG400.
d Compounds 29 and 54 dosed at 2 mpk in 20:60:20 DMSO/PEG400/H2O.
N
N
47
48
22000
14000
> 81010
51000
> 4
References
4
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49
99820
38550
-
N
F
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N
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52
53
2552
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>32
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>27000
-
N
F
http://clinicaltrials.gov/show/NCT02609828 NLM Identifier:
NCT02609828
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protein binding in rat was 99.1%. Benzimidazole 29 showed an
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N
N
O
O
NH
NH
NH
NH
N
N
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54
55
TrkA IC50 = 215 nM
TrkC IC50 = 68160 nM
Selectivity (C/A) = 316
TrkA IC50 = 113 nM
TrkC IC50 = 68750 nM
Selectivity (C/A) = 607
cLog = 2.86
P
cLog = 3.02
P
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Figure 2. Compounds 54 and 55

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Design, synthesis and SAR of substituted
indoles as selective TrkA inhibitors
Danielle M. Hurzya,*, Darrell A. Henze b Tamara D. Cabalu c Kartik Narayand, Amanda Hellere,
,
,
Andrew J. Cooke a
a Department of Medicinal Chemistry, MRL, Merck & Co., Inc., 770 Sumneytown Pike, West Point, PA 19486, USA
b Department of Pain Research, MRL, Merck & Co.,Inc., 770 Sumneytown Pike, West Point, PA 19486, USA
c Department of Drug Metabolism, MRL, Merck & Co., Inc., 770 Sumneytown Pike, West Point, PA 19486, USA
dAnalytical Process and Technology, Sanofi Pasteur, Discovery Drive, Swiftwater, PA 18370, USA
eScientific Operations, Lab Connect, LLC., 605 First Avenue, Ste. 300, Seattle, WA 98104, USA
A
B
N
S
N
S
O
O
C
NH
N
NH
N
D
1
TrkA IC50 = 607 nM
TrkC IC50 = 20690 nM
Selectivity (A/C) = 34
cLogP = 3.87
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