Rational Design and Synthesis of Selective PRMT4 Inhibitors: A New Chemotype for Development of Cancer Therapeutics**

Article abstract of DOI:10.1002/cmdc.202100018

Protein arginine N-methyl transferase 4 (PRMT4) asymmetrically dimethylates the arginine residues of histone H3 and nonhistone proteins. The overexpression of PRMT4 in several cancers has stimulated interest in the discovery of inhibitors as biological tools and, potentially, therapeutics. Although several PRMT4 inhibitors have been reported, most display poor selectivity against other members of the PRMT family of methyl transferases. Herein, we report the structure-based design of a new class of alanine-containing 3-arylindoles as potent and selective PRMT4 inhibitors, and describe key structure–activity relationships for this class of compounds.

Full text of DOI:10.1002/cmdc.202100018

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Rational Design and Synthesis of Selective PRMT4
Inhibitors: A New Chemotype for Development of Cancer
Therapeutics**
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Mathew Sutherland,[a] Alice Li,[b] Anissa Kaghad,[a] Dimitrios Panagopoulos,[a] Fengling Li,[b]
Magdalena Szewczyk,[b] David Smil,[b, d] Cora Scholten,[c] Léa Bouché,[c] Timo Stellfeld,[c, e]
Cheryl H. Arrowsmith,[b, f] Dalia Barsyte,[b] Masoud Vedadi,[b, g] Ingo V. Hartung,[c, h]
Holger Steuber,[c, e] Robert Britton,*[a] and Vijayaratnam Santhakumar*[b]
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Protein arginine N-methyl transferase 4 (PRMT4) asymmetrically
dimethylates the arginine residues of histone H3 and nonhi-
stone proteins. The overexpression of PRMT4 in several cancers
has stimulated interest in the discovery of inhibitors as bio-
logical tools and, potentially, therapeutics. Although several
PRMT4 inhibitors have been reported, most display poor
selectivity against other members of the PRMT family of methyl
transferases. Herein, we report the structure-based design of a
new class of alanine-containing 3-arylindoles as potent and
selective PRMT4 inhibitors, and describe key structure–activity
relationships for this class of compounds.
Introduction
proteins using the methyl group from S-adenosyl-l-methionine
(SAM).[1] These methyl transferases regulate a variety of bio-
logical processes including transcriptional activation,[2] RNA
splicing,[3] cell-cycle regulation,[4] DNA damage response,[5] and
cell differentiation,[6] while also catalyzing the methylation of a
variety of nonhistone proteins.[7] Type I arginine methyl trans-
ferases (PRMTs), PRMT1, -2, -3, -4, -6, and -8, catalyze mono and
asymmetric dimethylation. The type II PRMTs PRMT5 and -9
catalyze mono and symmetric demethylation, whereas PRMT7
catalyzes mono methylation of arginines.[8]
PRMT4 has been implicated in several malignancies and is
highly overexpressed in ~75% of colorectal cancers[9] as well as
in prostate carcinoma and androgen-independent prostate
carcinoma.[10] PRMT4 is a critical factor in the pathway of
estrogen-stimulated breast cancer growth[11] and its overexpres-
sion is associated with poor prognosis in this disease.[12]
Knockout studies in breast cancer cell lines show that PRMT4
regulates breast cancer cell migration and metastasis.[13] More-
over, pharmacological inhibition of PRMT4 with selective
inhibitors is effective in reducing the growth of multiple
myeloma cell lines[14] as well as in vivo mouse models of
multiple myeloma[15]
The majority of reported PRMT4 inhibitors shows moderate
to poor selectivity against other type I PRMTs[16,17] and/or lack of
cellular activity,[18–20] with the notable exceptions of PRMT4
selective chemical probes 1 and 2 reported by Structural
Genomics Consortium[14,21] and Epizyme,[15] respectively. Here,
we report the development of indole based, potent and PRMT4
selective inhibitors starting from a dual PRMT4/6 inhibitor
scaffold. Notably, we relied on the co-crystal structure of a hit
compound 3a (Figure 1) with PRMT6 and molecular modeling
with reported PRMT4 structures to design PRMT4 selective
inhibitors and identify key structural features relevant to PRMT4
selectivity.
Arginine methyl transferases catalyze both symmetric and
asymmetric methylation of arginine residues in the histone H3
[a] Dr. M. Sutherland, A. Kaghad, D. Panagopoulos, Dr. R. Britton
Department of Chemistry
Simon Fraser University
8888 University Drive, Burnaby, BC V5A 1S6 (Canada)
E-mail: rbritton@sfu.ca
[b] A. Li, Dr. F. Li, Dr. M. Szewczyk, Dr. D. Smil, Dr. C. H. Arrowsmith,
Dr. D. Barsyte, Dr. M. Vedadi, Dr. V. Santhakumar
Structural Genomics Consortium
University of Toronto
MaRS Centre, South Tower, Suite 700
101 College Street, Toronto, ON M5G 1L7 (Canada)
E-mail: santha.santhakumar@utoronto.ca
[c] Dr. C. Scholten, Dr. L. Bouché, Dr. T. Stellfeld, Dr. I. V. Hartung, Dr. H. Steuber
Bayer A.G. Research and Development
Pharmaceuticals
Muellerstr. 178 13442 Berlin (Germany)
[d] Dr. D. Smil
Ontario Institute for Cancer Research
661 University Ave Toronto, ON M5G 0A3 (Canada)
[e] Dr. T. Stellfeld, Dr. H. Steuber
Innovation Campus Berlin
Nuvisan ICB GmbH
Müllerstraße 178 13353 Berlin (Germany)
[f] Dr. C. H. Arrowsmith
Princess Margaret Cancer Centre and Department of Medical Biophysics
University of Toronto
610 University Ave, Toronto, ON M5G 2C1 (Canada)
[g] Dr. M. Vedadi
Department of Pharmacology and Toxicology
University of Toronto
1 King’s College Cir, Toronto, ON M5S 1A8 (Canada)
[h] Dr. I. V. Hartung
Merck Healthcare KGaA
Frankfurter Straße 250, 64293 Darmstadt (Germany)
[**] A previous version of this manuscript has been deposited on a preprint
server (https://doi.org/10.1101/2020.11.17.387233).
Supporting information for this article is available on the WWW under
https://doi.org/10.1002/cmdc.202100018
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3a with PRMT6 (PDB entry: 7NR4, Figure 2A). Based on this
structural insight, superimposition of the PRMT6-bound struc-
ture of indazole 3a in the reported PRMT4 structure[19] (Fig-
ure 2B) suggested that the corresponding indole might improve
selectivity for PRMT4. Specifically, in the PRMT6-bound structure
of 3a, H-bonding between Glu59 and the indazole NH was
identified as a key binding interaction. Thus, it was proposed
that decreasing the acidity of the NÀ H from indazole (pKa ~14)
to indole (pKa ~21) would attenuate interactions with PRMT6.
Additionally, the reduced polar surface area (PSA) of the
corresponding indole would expectedly result in improved
hydrophobic interactions with PRMT4 (Figure 2B).
To test this hypothesis, indole 4a was synthesized following
the synthetic sequence described in Scheme 1 and we were
pleased to find that this compound showed a moderate loss in
PRMT6 activity and coincident gain in PRMT4 activity compared
to 3b (Table 1, entries 2 and 3). Furthermore, replacement of
the amide with a meta-sulfonamide (entries 1 and 2) resulted in
improved PRMT4 activity. Inspired by these observations, the
corresponding meta-methyl sulfone analogue of indole 4a was
prepared (entry 4), resulting in further improved PRMT4 activity
and selectivity. Notably, the meta-methyl sulfone 4b (entry 4)
proved to be 197-fold selective against PRMT6 (PRMT4 IC50 =
40 nM) and furthermore >50-fold selective against other
arginine methyltransferases PRMT1, -3, -5 to -9. Docking studies
of the sulfonamide 3a in both PRMT4 and PRMT6 suggested
that the improved PRMT4 activity is likely due to interactions
Table 1. PRMT4 and PRMT6 activity of indazoles and indoles 3 and 4.
1
2
3
4
5
6
7
8
9
Compound
IC50 [μM][a]
PRMT4
Selectivity
PRMT4
PRMT6
1
2
3
4
3a
3b
4a
4b
0.06�0.02
>10
0.5�0.1
0.2�0.1
0.3�0.1
7.9�1.0
8.3
<0.02
0.13
197
2.30�0.20
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0.04�0.02
[a] Average�SD of three IC50 values from three experiments.
Results and Discussion
Based on the similarity with the reported PRMT inhibitors, we
selected a library of 5000 compounds from our own collection
and screened for PRMT4 and PRMT6 activity using the reported
methods[14] and identified novel indazoles as inhibitors of
PRMT4 and PRMT6. Owing to its potent PRMT4 inhibitory
activity (IC50 0.06 μM) and moderate selectivity over PRMT6
(eightfold), the indazole 3a (Table 1, entry 1) was selected as a
starting point for the development of a selective PRMT4
inhibitor.
Unfortunately, attempts to co-crystallize 3a or the structur-
ally related indazole 3b (Figure 1) with PRMT4 were unsuccess-
ful. However, we were able to obtain the co-crystal structure of
Figure 1. PRMT4 inhibitors 1 and 2 reported by the Structural Genomics
Consortium and Epizyme, respectively, and dual PRMT4/6 inhibitors identi-
fied by screening a focused library.
Figure 2. A) The PRMT6-bound structure of 3a. B) The PRMT6-bound
conformation of 3a superimposed in the binding site of PRMT4 highlights a
hydrophobic pocket (occupied by sulfonamide group) not present in PRMT6.
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entries 1 and 2) resulted in a 2.5-fold gain in PRMT4 activity
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2
3
4
5
(IC50 =0.01 μM) and a threefold improvement in selectivity
against PRMT6 (IC50 =9.1 μM, 650-fold). This result indicated
that a more lipophilic dimethyl sulfonamide better exploits the
hydrophobic binding pocket in the PRMT4 active site.
However, this modification was accompanied by a loss in
potency when more sterically hindered sulfonamides were
examined. For example, the diethyl sulfonamide 13 (entry 3,
IC50 =3.5 μM) and cyclic sulfonamide 14 (entry 4, IC50 =0.89 μM)
proved to be less active against PRMT4. While the smaller five
membered ring sulfonamide 15 (entry 5) was tolerated (IC50 =
0.18 μM), this compound was still less potent and selective than
original methyl sulfone 4b. Several analogues of the methyl
sulfone 4b were also synthesized and it was found that the
isopropyl sulfone 16 (entry 6) was a potent PRMT4 inhibitor
(IC50 =0.04 μM) and selective against PRMT6 (IC50 =8 μM). Here
again, a similar trend to that seen with sulfonamides was
observed. Specifically, increasing the size of the alkyl sulfone
led to a significant loss in potency (e.g., 17; IC50 =3.3 μM). This
data suggested that the hydrophobic binding pocket in PRMT4
could not accommodate groups larger than the dimethyl
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sulfonamide or isopropyl sulfone. As
a result, dimethyl
Scheme 1. General synthetic route for preparing indole-based PRMT4
inhibitors. a) Boc2O, THF, 52%; b) NBS, THF, 77%; c) ArB(OR)2, K2CO3,
sulfonamide 12 (entry 2) and isopropyl sulfone 16 (entry 6)
were selected as the lead molecules for further optimization.
Having identified that both the indole sulfone and sulfona-
mide confer excellent PRMT4 activity and selectivity against
PRMT6, we then turned our attention towards the amino acid
side of the molecule. Here, we aimed to increase lipophilicity to
improve cellular permeability and perhaps potency and
selectivity. With this in mind, we probed the size of the amino
acid with the l-proline methyl sulfone analogue 18 (Table 3,
entry 1) and found this compound was not active (PRMT4 IC50 >
10 μM). A similar amino acid SAR study on the isopropyl sulfone
and dimethyl sulfonamide scaffolds was undertaken through
the synthesis of compounds 19–20 and 21–25, respectively
(Table 3, entries 2–8). Here, we examined methylation and
incorporation of an azetidine for the isopropyl sulfone and in
the case of the sulfonamide, we investigated incorporation of
an azetidine, methylation, glycine incorporation, geminal
dimethylation and cyclopropanation. In the case of the
isopropyl sulfone, each modification resulted in a decrease in
PRMT4 activity (PRMT4 IC50 =0.60 to >10 μM). In general, the
dimethyl sulfonamide analogues 21–25 were more potent. In
particular, the glycine analogue 23 proved to be a low-
nanomolar inhibitor of PRMT4 (IC50 =0.01 μM) and maintained
selectivity against PRMT6. The ethyl amine and N-methyl ethyl
amine 26 and 27, respectively, were also synthesized based on
the common use of ethyl amine in PRMT inhibitors.[16,17,22]
Unfortunately, in both cases we observed a significant loss in
potency (PRMT4 IC50 >10 μM in both cases).
°
Pd(PPh3)4 or Pd(dppf)Cl2 ·CH2Cl2, THF/H2O (3:1), 80 C; d) TFA; e) N-Boc-amino
acid, DIPEA, PyBOP, DMF; f) TFA; g) phthalic anhydride, toluene, reflux; h)
K2CO3, CH3I, DMF, RT; i) H2NNH2, MeOH, RT.
within the unique hydrophobic binding pocket in PRMT4
(Figure 2B). This additional subpocket in PRMT4 is mainly
created by Gln149 and Phe153, while the corresponding less-
space-demanding residues Leu46 and Cys50 do not generate a
similar pocket in PRMT6.
To further probe the effect of modifications at the meta-
position in indole 4b, a series of sulfones and sulfonamides was
prepared in a straightforward manner as summarized in
Scheme 1 and Table 2. Here, we found that exchanging the
methyl sulfone for a dimethyl sulfonamide (e.g., compound 12,
Table 2. Biological evaluation of sulfone and sulfonamide series.
Compound
R
[IC50 μM][a]
PRMT4
At this point, we examined the cell permeability of the most
promising compounds 4b, 12, 16 and 21. The results of the
Caco-2 assay are summarized in Figure 3. From the series
methyl sulfone 4b, dimethyl sulfonamide 12 and isopropyl
sulfone 16, the dimethyl sulfonamide proved to be the most
permeable (2.13 nm/s for 12 vs 0.23 nm/s for 4b). Disappoint-
ingly, replacement of alanine for azetidine in an effort to reduce
1
2
3
4
5
6
7
4b
12
13
14
15
16
17
Me
NMe2
NEt2
N(CH2)5
N(CH2)4
iPr
0.04�0.02
0.01�0.00
3.50�0.30
0.89�0.18
0.18�0.04
0.04�0.01
3.30�0.10
C(CH2)4
[a] Average�SD of three IC50 values from three experiments.
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Table 3. SAR of the amino acid moiety.
1
2
3
4
5
6
7
8
9
Compound
R1
R2
[IC50 μM][a]
PRMT4
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1
18
Me
>10
2
3
4
5
19
20
21
22
iPr
>10
iPr
0.60�0.10
0.11�0.00
NMe2
NMe2
Figure 3. Caco-2 data for key compounds (efflux ratio in parenthesis).
4.20�0.20
this data we further explored a series of analogues that
incorporated the dimethyl sulfonamide core.
6
7
23
24
NMe2
NMe2
0.01�0.00
0.33�0.00
As the co-crystal structure of indazole 3a bound to PRMT6
indicated that the aryl ring was largely solvent exposed, we
next focused on modifications aimed to increase lipophilicity
using the most potent dimethylsulfonamide core. Thus, ana-
logues 28–30 were synthesized as summarized in Scheme 1. Of
this series, the N-methylindole 28 proved to be the most potent
and selective compound (PRMT4 IC50 = <2 nM, >500-fold
selectivity against PRMT6, Table 4, entry 1). In order to assess
the effect of attenuating the basicity of the free amine on
membrane permeability, the fluoroalanine 29 was
synthesized[23] (entry 2, Table 4), which unfortunately proved to
be approximately ten times less potent and selective. To further
reduce the total polar surface area of the molecule, we
examined the dimethyl amide 30, however, this analogue
proved also to be less active and selective. In summary, the N-
methylated derivative 28 is the most potent compound of our
series against PRMT4, indicating that H-bonding of the indole-
NH to Asn 162 is by far less relevant for PRMT4 binding, while it
is important for the charge-reinforced interaction to Glu 59 in
PRMT6. Hence, methylation of the indole-N is a key driver to
achieve selectivity against PRMT6.
8
25
NMe2
>10
9
26
27
Me
Me
>10
>10
10
[a] Average�SD of three IC50 values from three experiments.
Table 4. Evaluation of methylated indole derivatives.
Compound
R
R’
[IC50 μM][a]
PRMT4
1
2
3
28
29
30
SO2NMe2
SO2NMe2
CONMe2
Me
CH2F
Me
<0.002
0.181�0.019
0.225�0.049
Chemistry
[a] average�SD of three IC50 values from three experiments.
The general preparation of compounds described herein was
performed as shown in Scheme 1, starting from commercially
available 5-aminoindole 5. Boc protection of the amine and
indole nitrogen atoms[24] gave the bis-Boc-protected compound
6, which was exposed to NBS to furnish the corresponding 3-
brominated product 7.[25] This later material then engaged in a
H-bond donors, increased lipophilicity and maintained cellular
permeability, but increased the efflux ratio compared with
compound 11 by approximately threefold (Figure 3). Based on
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Suzuki reaction[26] with a suitable meta-substituted sulfone or Conclusion
1
2
3
4
5
6
7
8
9
sulfonamide derivative. Following the Suzuki reaction, global
deprotection was accomplished by treatment with trifluoro-
acetic acid. The 5-amino group was then coupled to a Boc-
protected amino acid using PyBOP coupling conditions.[27,28]
Finally, deprotection of the amino acid using trifluoroacetic acid
yielded the desired indole analogues as their corresponding
trifluoroacetate salts. In the case of analogues 28–30, prior to
amino acid coupling, the 5-amino group was protected as a
phthalyl group and the indole nitrogen was methylated using
methyl iodide and potassium carbonate (11, Scheme 1). Depro-
tection of the phthalimide was effected by treatment with
hydrazine and the free amine was then carried through a similar
sequence of steps as described above (i.e., peptide coupling
and Boc-deprotection).
In conclusion, we report the design, synthesis, and evaluation of
a new series of 3-arylindole alanine-based PRMT4 inhibitors that
are both potent and selective over the closely related PRMT6.
Based on the cocrystal structure of our initial hit compound 3a
with PRMT6 and comparing it with the reported PRMT4
structures, we demonstrated that selectivity for PRMT4 can be
achieved. Furthermore, methylation of the indole nitrogen
resulted in a potent and selective in-vitro PRMT4 inhibitor.
However, despite these efforts, none of the compounds
described herein achieved on-target effects in cells. Nonethe-
less, these indoles represent a new chemotype for further
development of cell active PRMT4 inhibitors, which will deepen
our understanding of the intricate biology of PRMT4 and might
engender the design of new anti-tumor PRMT4-selective
inhibitors. These compounds could possibly be used as handles
to develop PROTACs to degrade PRMT4 selectively. Linker
attachment and E3 antagonist components used for developing
PROTACs will likely influence the cellular permeability of the
PROTAC compounds and therefore the poor cellular perme-
ability of our PRMT4 inhibitors is not likely to be a hinderance
for cell active PROTAC development.
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Evaluation of cellular activity of PRMT4
inhibitors
PRMT4 has been shown to methylate BAF155 at R1064.[13] We
have evaluated key compounds 4b, 28 and 30 following the
reported methods;[14] however, none of the compounds showed
significant reduction in BAF155 methylation when tested up to
30 to 100 μM (48 h of exposure in HEK293 cells), while meth- Experimental Section
ylation of BAF155 was abrogated by 2–3 μM of the PRMT4
General chemistry: All reagents and starting materials were
selective inhibitor TP-064 (Figure 4).[14] The absence of any
significant cellular activity of compound 4b can be attributed
to its poor permeability. Even though compounds 28 and 30
were expected to show enhanced permeability because of
reduced H-bond donors (28 and 30) and reduced polar surface
area (30), the absence of cellular activity indicates these
changes were not sufficient to increase the cellular permeability
of these series of compounds.
purchased from Sigma Aldrich, TCI, Alfa Aesar, CarboSynth, and AK
Sci and were used without further purification. Dichloromethane
was distilled from CaH2 and stored under nitrogen, THF was distilled
from sodium wire/benzophenone ketyl radical and stored under
nitrogen. Column chromatography was carried out with 230–
400 mesh silica gel (Merck, Silica Gel 60). Concentration and
removal of trace solvents was done in a Buchi rotary evaporator
using acetone-dry-ice condenser and a Welch vacuum pump.
Nuclear magnetic resonance (NMR) spectra were recorded in CDCl3,
CD3OD, CD3CN or [D6]DMSO as the solvent. Signal positions (δ) are
given in parts per million from tetramethylsilane (δ 0) and were
measured relative to the signal of the solvent (1H NMR: CDCl3: δ
7.26; CD3OD: δ3.31; CD3CN: δ1.96; [D6]DMSO: δ 2.50; 13C NMR:
CDCl3: δ 77.16; CD3OD: δ 49.00; CD3CN: δ1.32; [D6]DMSO: 39.5).
Coupling constants (J values) are given in Hertz and are reported to
1
the nearest 0.1 Hz. H NMR spectral data are tabulated in the order:
multiplicity (s, singlet; d, doublet; t, triplet; q, quartet; sept, septet;
m, multiplet; br, broad), coupling constants, number of protons.
NMR spectra were recorded on a Bruker Avance 600 equipped with
a QNP or TCI cryoprobe (600 MHz), Bruker 400 (400 MHz) or Bruker
500 (500 MHz). High performance liquid chromatography (HPLC)
analysis was performed on an Agilent 1100 HPLC, equipped with a
variable wavelength UV/Vis detector. High-resolution mass spec-
trometry was performed on an Agilent 6210 TOF LC/MS.
General procedures
Complete synthetic procedures including intermediates synthesis
are provided in the Supporting Information.
General procedure A: Suzuki-Miyaura coupling. A pressure vial
charged with a stir bar, bromoindole 7 (1.0 equiv.), boronic acid or
ester (1.0–1.6 equiv.), K2CO3 (3.0 equiv.), and Pd(PPh3)4 or Pd(dppf)
Cl2.CH2Cl2 (0.10 equiv.) was placed under vacuum and then filled
Figure 4. Effect of PRMT4-dependent BAF155 asymmetric dimethylation in
HEK293T cells upon treatment with up to 100 μM compounds 4b, 28 and 30
over 2 days.
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with nitrogen. A mixture of degassed THF and H2O (0.09 M THF/H2O
3:1 unless otherwise indicated) was then added and the resulting
dried over MgSO4, and concentrated to afford the crude aryl
thioether intermediate. To a stirred solution of the crude aryl
1
2
3
4
5
6
7
8
9
°
°
mixture was stirred under an atmosphere of nitrogen at 80 C for
thioether intermediate (1.0 equiv.) in MeOH (0.16 M) at 0 C was
18 h or until the reaction was complete as monitored by TLC
analysis. The reaction mixture was then cooled to room temper-
ature and concentrated under reduced pressure. The residue was
then dissolved in EtOAc and washed with saturated aqueous
NaHCO3 and brine. The organic layer was dried over MgSO4 and
concentrated to afford the crude aryl-indole product. Purification of
the crude product by flash chromatography (silica gel, Et2O or
EtOAc and hexanes) afforded the pure coupled product.
added oxone (potassium peroxymonosulfate; 3.0 equiv.) in H2O
(0.5 M). The resulting white suspension was warmed to room
temperature over 2 h and stirred at room temperature until
completion was observed by TLC. The reaction mixture was then
diluted with H2O and extracted with EtOAc (2×). The combined
organic layers were washed with brine, dried over MgSO4, and
concentrated to afford the aryl sulfone. The aryl sulfone was used
in subsequent reactions without further purification.
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General procedure B: Amide coupling and deprotection. To a
stirred solution of the aryl-indole intermediate (1.0 equiv.) in dry
dimethylformamide (DMF; 0.1 M) at room temperature was added
N,N-diisopropylethylamine (DIPEA; 5 equiv.), followed by benzotria-
zol-1-yl-oxytripyrrolidinophosphonium hexafluorophosphate (Py-
BOP; 1–2 equiv.) and the protected amino acid (1–2 equiv.). The
resulting solution was stirred at room temperature until completion
of the reaction as monitored by TLC. The reaction mixture was then
diluted with saturated aqueous NaHCO3 and extracted with EtOAc
(3×). The combined organic layers were washed with saturated
aqueous LiCl (3×), dried over MgSO4, and concentrated to afford
the crude product (brown gum), which was used directly in the
next step without further purification. The crude coupled product
was dissolved in TFA (neat, 0.1 M) and stirred at room temperature
until the reaction was complete as monitored by TLC analysis.
Purification of the crude indole by RP-HPLC (using a SiliCycle
SiliaChrom dtC18 semipreparative column (5 μm, 100 Å, 10×
250 mm) with a flow rate of 5 mL/min eluting with solvent (A: 0.1%
TFA in H2O B: 0.1% TFA in ACN) on gradients of 2!30%, or 2!
100% solvent B over 15 minutes as indicated afforded the final
compounds.
General procedure F: Phthalimide protection. To a stirred solution
of aminoindole intermediate (1.0 equiv.) in toluene (0.2 M) was
added phthalic anhydride (1.3 equiv.). The resultant solution was
heated to reflux until completion of the reaction was observed by
TLC. The reaction mixture was then cooled down to room temper-
ature and concentrated under reduced pressure to afford a crude
product which was used without further purification unless
otherwise indicated.
General procedure G: N-Methylation of indole scaffolds. To a
stirred solution of protected indole intermediate (1.0 equiv.) in dry
dimethylformamide (DMF; 0.2 M) was added potassium carbonate
(5 equiv.) followed by methyl iodide (3 equiv.). The resultant
°
solution was stirred at 60 C until completion of the reaction was
observed by TLC. The reaction mixture was then diluted with water
and extracted with EtOAc (3×). The combined organic layers were
washed with aqueous saturated LiCl (3×), dried over MgSO4, and
concentrated to afford the crude methylated product, which was
used directly in the next step without further purification unless
otherwise indicated.
General procedure H: Phthalimide deprotection. To a stirred
solution of N-methylindole intermediate (1.0 equiv.) in methanol
(0.06 M) was added hydrazine hydrate (1.3 equiv.). The resultant
solution was stirred at room temperature until completion of the
reaction was observed by TLC. The reaction mixture was then
concentrated, diluted in dichloromethane and filtered. The resulting
filtrate was concentrated under reduced pressure to afford the
amino indole product, which was used directly in the next step
without further purification.
General procedure C: Synthesis of sulfonamides. To a stirred
°
solution of amine (1.05 equiv.) in dry pyridine (0.2 M) at 0 C was
added dropwise (for liquids) or in small portions (for solids) the
sulfonyl chloride (1.0 equiv.). The reaction mixture was warmed to
room temperature and stirred until the reaction was complete as
monitored by TLC analysis. The reaction mixture was then
concentrated under reduced pressure and the residue was
dissolved in EtOAc and washed with 0.5 M HCl (2×). The organic
layer was then dried over MgSO4, filtered and concentrated to
afford the sulfonamide. The sulfonamide was used in subsequent
reactions without further purification.
General procedure I: Boc-deprotection.
A solution of Boc-
protected intermediate (1 equiv.) in TFA (0.1 M) was stirred at room
temperature until completion of the reaction was observed by TLC.
Concentration of the reaction mixture under reduced pressure
afforded the deprotected aryl-indole product which was used
without further purification unless otherwise indicated.
General procedure D: Boronic ester synthesis. A flask was charged
with a stir bar, aryl bromide (1.0 equiv.), B2pin2 (1.0 equiv.), NaHCO3
(2.50 equiv.), and Pd(ddpf)Cl2 (0.05 equiv.). The flask was then
placed under vacuum and filled with nitrogen. Degassed DMSO
(0.2 M) was added to the reaction vessel, and the reaction mixture
(S)-2-Amino-N-(3-(3-(N,N-dimethylsulfamoyl)phenyl)-1H-indazol-
5-yl)propenamide (3a). To a solution of 31 (57.5 mg, 0.15 mmol) in
1-methyl-2-pyrrolidinone (NMP) (1 mL), were added subsequently
[3-(dimethylsulfamoyl)phenyl]boronic acid (68.7 mg, 0.30 mmol,
°
was stirred under an atmosphere of nitrogen at 80 C for 18 h or
until the reaction was complete as monitored by TLC analysis. The
reaction mixture was then cooled to room temperature and diluted
with equal parts H2O and EtOAc, then filtered through Celite and
the Celite was rinsed with EtOAc. The filtrate was then washed with
H2O and brine, dried over MgSO4 and concentrated to afford the
crude product. Purification of the crude product by flash chroma-
tography (silica gel, Et2O or EtOAc and hexanes) afforded the aryl-
boronic ester.
dissolved
in
0.53 mL
1-methyl-2-pyrrolidinone),
[1,1’-bis
(diphenylphosphino)ferrocene] dichloropalladium(II), complex with
dichloromethane (24.5 mg, 0.03 mmol, dissolved in 1 mL NMP) and
potassium carbonate (62.2 mg, 0.45 mmol, dissolved in water
°
0.5 mL). The reaction mixture was heated to 100 C and shaken for
24 h. The crude mixture was filtered through a pad of activated MP
Alumina N (EcoChrom TM) and washed with NMP and concentrated
under vacuum. The residue was dissolved in a TFA/CH2Cl2 mixture
(1:1, 2 mL) and shaken for 24 h and finally dried using a Christ-
centrifuge to give 4.62 mg of the title compound (7% yield). LC–MS
method: Instrument MS: Waters ZQ; Instrument HPLC: Waters UPLC
Acquity; column: Acquity BEH C18 (Waters), 50 mm×2.1 mm,
1.7 μm; Solvent: A: 0.1% formic acid in water, solvent B: MeCN;
gradient: 0.0 min 99% A–1.6 min 1% A–1.8 min 1%A–1.81 min 99%
General procedure E: Sulfone synthesis from thiophenol precur-
sors. A stirred solution of substituted thiophenol (1 equiv.), K2CO3
(1.4 equiv.), and secondary bromoalkane (1.2 equiv.) in dry acetone
(0.3 M), was stirred under nitrogen at reflux until completion of the
reaction was observed by TLC (ca. 18 h). The reaction mixture was
cooled to room temperature, diluted with H2O, and extracted with
Et2O (3×). The combined organic layers were washed with brine,
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°
A–2.0 min 99% A; oven: 60 C; flow: 0.800 mL/min; UV-Detection
DMF (1.0 mL). Final Boc-deprotection of the crude mixture using
TFA (1.0 mL) and subsequent purification by RP-HPLC (using a
SiliCycle SiliaChrom dtC18 semipreparative column (5 μm, 100 Å,
10×250 mm) with a flow rate of 5 mL/min eluting with solvent (A:
0.1% TFA in water B: 0.1% TFA in MeCN) on a gradient of (2!100)
%) solvent B over 15 min, tR =6.2 min) afforded the TFA salt of 12
as a colorless solid (8 mg, 19%). 1H NMR: (400 MHz, CD3OD) δ
(ppm)=8.32 (d, J=1.9 Hz, 1H), 8.06 (br s, 1H), 7.95 (dt, J=6.7,
2.1 Hz, 1H), 7.68-7.61 (m, 3H), 7.45 (d, J=8.8 Hz, 1H), 7.26 (dd, J=
8.8, 2.1 Hz, 1H), 4.08 (q, J=7.1 Hz, 1H), 2.78 (s, 6H), 1.63 (d, J=
7.1 Hz, 3H). 13C NMR: (150 MHz, CD3OD) δ (ppm)=168.9, 138.8,
136.9, 136.2, 132.2, 132.1, 130.7, 126.6, 126.4, 125.9, 125.5, 117.2,
116.6, 113.2, 111.8, 50.89, 38.56, 17.75 HRMS: (ESI) m/z calcd for
C19H22N4O3S: 387.1491 [M+H]+; found: 387.1452.
1
2
3
4
5
6
7
8
9
PDA 210–400 nm. tR =0.83 min; LRMS (ESI): m/z 388 [M+H]+
(S)-4-(5-(2-Aminopropanamido)-1H-indazol-3-yl)benzamide (3b).
Carbamate 31 (57.5 mg, 0.15 mmol, dissolved in 1 mL NMP), (4-
carbamoylphenyl)boronic acid (49.5 mg, 0.30 mmol, dissolved in
0.53 mL
NMP)
and
[1,1’-Bis(diphenylphosphino)ferrocene]
dichloropalladium(II), complex with dichloromethane (24.5 mg,
0.03 mmol, dissolved in 1 mL NMP) along with potassium carbonate
(62.2 mg, 0.45 mmol, dissolved in water 0.5 mL) were heated to
°
100 C and shaken for 24 h. The microtitre plates (MTPs) were dried
by Zirbus-centrifuge and then were dissolved again in 2 mL of a
TFA/acetonitrile (1:1) mixture. The reaction mixture was further
shaken for 1 d at room temperature. The MTPs were dried again
and 2 mL NMP were added. The precipitated material was filtered
off and purified by preparative HPLC to give 4.01 mg of the title
compound (8% yield). LC-MS method: Instrument MS: Waters ZQ;
Instrument HPLC: Waters UPLC Acquity; column: Acquity BEH C18
(Waters), 50 mm×2.1 mm, 1.7 μm; Solvent A: 0.1% formic acid in
water, solvent B: MeCN; Gradient: 0.0 min 99% A–1.6 min 1% A–
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
(S)-2-Amino-N-(3-(3-(N,N-diethylsulfamoyl)phenyl)-1H-indol-5-yl)
propanamide (13). The title compound was prepared according to
the general procedures I and B using the Boc-protected-aryl-indole
39 (50 mg, 0.091 mmol) and TFA (0.9 mL) followed by treatment
with (tert-butoxycarbonyl)-l-alanine (20 mg, 0.11 mmol), PyBOP
(56 mg, 0.45 mmol), DIPEA (0.08 mL, 0.11 mmol), and dry DMF
(0.9 mL). Final Boc-deprotection of the crude mixture using TFA
(0.9 mL) and subsequent purification by RP-HPLC (using a SiliCycle
SiliaChrom dtC18 semipreparative column (5 μm, 100 Å, 10×
250 mm) with a flow rate of 5 mL/min eluting with solvent (A: 0.1%
TFA in water B: 0.1% TFA in MeCN) on a gradient of (2!100) %)
solvent B over 15 min, tR =6.6 min) afforded the TFA salt of 13 as a
colorless solid (6 mg, 16%). 1H NMR: (400 MHz, [D6]DMSO) δ
(ppm)=11.61 (s, 1H), 10.37 (s, 1H), 8.27 (s, 1H), 8.20 (br s, 2H), 7.98
(s, 1H), 7.90 (dt, J=1.6, 7.1 Hz, 1H), 7.88 (d, J=2.5 Hz, 1H), 7.68–7.59
(m, 2H), 7.47 (d, J=8.8 Hz, 1H), 7.31 (dd, J=8.8, 1.6 Hz, 1H), 4.01 (q,
J=7.0 Hz, 1H), 3.23 (q, J=7.0 Hz, 4H), 1.47 (d, J=7.0 Hz, 3H), 1.06 (t,
J=7.0 Hz, 6H). 13C NMR: (150 MHz, [D6]DMSO) δ (ppm)=167.5,
140.4, 136.8, 134.0, 131.1, 130.0, 129.7, 125.5, 124.4, 123.6, 123.1,
115.5, 114.1, 112.3, 109.4, 48.92, 41.83, 17.14, 14.03. HRMS: (ESI) m/z
calcd for C21H27N4O3S: 415.1804 [M+H]+; found: 415.
°
1.8 min 1% A–1.81 min 99% A–2.0 min 99% A; oven: 60 C; flow:
0.800 mL/min; UV-Detection PDA 210–400 nm. tR =0.50 min; LRMS
(ESI): m/z 324 [M+H]+
(S)-4-(5-(2-Aminopropanamido)-1H-indol-3-yl)benzamide
(4a).
The title compound was prepared according to general procedure
B using the aryl-indole 32 (25 mg, 0.068 mmol), (tert-butoxycarbon-
yl)-l-alanine (17 mg, 0.072 mmol), PyBOP (43 mg, 0.082 mmol),
DIPEA (0.06 mL, 0.34 mmol), and dry DMF (0.68 mL). Purification by
RP-HPLC (using
a SiliCycle SiliaChrom dtC18 semipreparative
column (5 μm, 100 Å, 10×250 mm) with a flow rate of 5 mL/min
eluting with solvent (A: 0.1% TFA in water B: 0.1% TFA in MeCN) on
a gradient of (2!100) % solvent B over 15 min, tR =4.52 min) of the
crude deprotected product afforded the TFA salt of 4a as a colorless
solid (9 mg, 32%). 1H NMR: (500 MHz, CD3OD) δ (ppm)=8.23 (d, J=
1.7 Hz, 1H), 7.94 (d, J=8.5 Hz, 2H), 7.77 (d, J=8.5 Hz, 2H), 7.64 (s,
1H), 7.43 (d, J=8.7 Hz, 1H), 7.32 (dd, J=8.7, 1.7 Hz, 1H), 4.09 (q, J=
7.1 Hz, 1H), 1.64 (d, J=7.1 Hz, 3H). 13C NMR: (125 MHz, CD3OD) δ
(ppm)=172.4, 169.0, 141.4, 136.3, 131.8, 131.4, 129.3, 127.5, 126.6,
126.0, 117.3, 117.2, 113.1, 112.5, 50.9, 17.7. HRMS: (ESI) m/z calcd for
C18H18N4O2: 323.1503 [M+H]+; found: 323.1477.
(S)-2-Amino-N-(3-(3-(piperidin-1-ylsulfonyl)phenyl)-1H-indol-5-yl)
propenamide (14). The title compound was prepared according to
the general procedures I and B using the aryl-indole 42 (49 mg,
0.088 mmol) and TFA (0.9 mL) followed by treatment with (tert-
butoxycarbonyl)-l-alanine (20 mg, 0.11 mmol), PyBOP (55 mg,
0.44 mmol), DIPEA (0.08 mL, 0.11 mmol), and dry DMF (0.9 mL).
Final Boc-deprotection of the crude mixture using TFA (0.9 mL) and
subsequent purification by RP-HPLC (using a SiliCycle SiliaChrom
dtC18 semipreparative column (5 μm, 100 Å, 10×250 mm) with a
flow rate of 5 mL/min eluting with solvent (A: 0.1% TFA in water B:
0.1% TFA in MeCN) on a gradient of (2!100) %) solvent B over
15 min, tR =6.7 min) afforded the TFA salt of 14 as a colorless solid
(S)-2-Amino-N-(3-(3-(methylsulfonyl)phenyl)-1H-indol-5-yl)
propanamide (4b). The title compound was prepared according to
general procedure
B
using the aryl-indole 33 (63.2 mg,
0.158 mmol), (tert-butoxycarbonyl)-l-alanine (60 mg, 0.32 mmol),
PyBOP (165 mg, 0.32 mmol), DIPEA (0.21 mL, 0.79 mmol), and dry
DMF (1.6 mL). Purification by RP-HPLC (using a SiliCycle SiliaChrom
dtC18 semipreparative column (5 μm, 100 Å, 10×250 mm) with a
flow rate of 5 mL/min eluting with solvent (A: 0.1% TFA in water B:
0.1% TFA in MeCN) on a gradient of (2!100) % solvent B over
15 min, tR =5.68 min) of the crude deprotected product afforded
the TFA salt of 3b as a colorless solid (11 mg, 18%). 1H NMR:
(600 MHz, CD3OD) δ (ppm)=8.24 (d, J=1.9 Hz, 1H), 8.22 (s, 1H),
7.99 (d, J=7.7 Hz, 1H), 7.80 (d, J=7.6 Hz, 1H), 7.70–7.64 (m, 2H),
7.45 (d, J=8.7 Hz, 1H), 7.33 (dd, J=8.7, 2.0 Hz, 1H), 4.10 (q, J=
7.0 Hz, 1H), 3.20 (s, 3H), 1.63 (d, J=7.1 Hz, 3H). 13C NMR: (150 MHz,
CD3OD) δ (ppm)=169.1, 142.5, 139.1, 136.2, 132.9, 132.1, 131.0,
126.4, 126.0, 126.0, 124.9, 117.2, 116.4, 113.2, 111.8, 50.9, 44.5, 17.8.
HRMS: (ESI) m/z calcd for C18H19N3O3S: 358.1220 [M+H]+; found:
358.1230.
1
(7 mg, 18%). H NMR: (400 MHz, CD3CN) δ 9.69 (s, 1H), 9.06 (s, 1H),
8.28 (s, 1H), 8.00 (d, J=2.0 Hz, 1H), 7.92 (d, J=7.6 Hz, 1H), 7.70–7.58
(m, 3H), 7.48 (d, J=8.7 Hz, 1H), 7.27 (dd, J=8.6, 2.0 Hz, 1H), 4.19 (q,
J=7.0 Hz, 1H), 3.03 (t, J=5.7 Hz, 4H), 1.64 (quint, J=5.7 Hz, 4H),
1.59 (d, J=7.0 Hz, 3H), 1.45-1.37 (m, 2H). 13C NMR: (150 MHz, [D6]
DMSO) δ (ppm)=167.7, 137.0, 136.0, 134.1, 131.4, 130.6, 130.0,
125.9, 124.5, 124.4, 124.0, 115.5, 114.1, 112.5, 109.3, 49.11, 46.90,
24.82, 22.98, 17.39. HRMS: (ESI) m/z calcd for C22H27N4O3S: 427.1804
[M+H]+; found: 427.1753.
(S)-2-Amino-N-(3-(3-(pyrrolidin-1-ylsulfonyl)phenyl)-1H-indol-5-yl)
propanamide (15). The title compound was prepared according to
general procedure B using the aryl-indole 45 (27 mg, 0.06 mmol),
(tert-butoxycarbonyl)-l-alanine (11 mg, 0.06 mmol), PyBOP (31 mg,
0.06 mmol), DIPEA (0.08 mL, 0.30 mmol), and dry DMF (0.6 mL). RP-
HPLC (gradient: 2–50 shortprep, tR =8.99 min) of the crude
deprotected product afforded the TFA salt of 15 as a colorless solid
(11 mg, 34%). 1H NMR: (500 MHz, CD3OD) δ (ppm)=8.29 (s, 1H),
8.10 (s, 1H), 7.94 (d, J=7.6 Hz, 1H), 7.68 (d, J=7.7 Hz, 1H), 7.644 (s,
(S)-2-Amino-N-(3-(3-(N,N-dimethylsulfamoyl)phenyl)-1H-indol-5-
yl)propenamide (12). The title compound was prepared according
to the general procedures I and B using the Boc-protected-aryl-
indole 36 (55 mg, 0.106 mmol) and TFA (1.0 mL) followed by
treatment with (tert-butoxycarbonyl)-l-alanine (24 mg, 0.13 mmol),
PyBOP (66 mg, 0.53 mmol), DIPEA (0.13 mL, 0.13 mmol), and dry
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1H), 7.636 (dd, J=7.7, 7.6 Hz, 1H), 7.45 (d, J=8.7 Hz, 1H), 7.27 (dd,
J=8.7 Hz, 1H), 4.09 (q, J=7.0 Hz, 1H), 3.34–3.30 (m, 4H), 1.79–1.75
(m, 4H), 1.63 (d, J=7.0 Hz, 3H). 13C NMR: (125 MHz, CD3OD) δ
(ppm)=169.0, 138.8, 138.3, 136.2, 132.1, 132.0, 130.7, 126.4, 126.3,
125.9, 125.3, 117.3, 116.6, 113.2, 111.9, 50.9, 49.4, 26.2, 17.8. HRMS:
(ESI) m/z calcd for C21H24N4O3S: 413.1642 [M+H]+; found: 413.1643.
(S)-N-(3-(3-(Isopropylsulfonyl)phenyl)-1H-indol-5-yl)-2-(meth-
ylamino)propanamide (19). The title compound was prepared
according to general procedure B using the aryl-indole 48 (50 mg,
0.12 mmol), N-(tert-butoxycarbonyl)-N-methyl-l-alanine (25 mg,
0.12 mmol), PyBOP (63 mg, 0.12 mmol), DIPEA (0.16 mL,
0.61 mmol), and dry DMF (1.22 mL). RP-HPLC (gradient: 2–30
shortprep, tR =11.84 min) of the crude deprotected product
1
2
3
4
5
6
7
8
9
(S)-2-Amino-N-(3-(3-(isopropylsulfonyl)phenyl)-1H-indol-5-yl)
propanamide (16). The title compound was prepared according to
general procedure B using the aryl-indole 48 (56 mg, 0.14 mmol),
(tert-butoxycarbonyl)-l-alanine (30 mg, 0.16 mmol), PyBOP (85 mg,
0.16 mmol), DIPEA (0.18 mL, 0.68 mmol), and dry DMF (1.4 mL).
Purification by RP-HPLC (using a SiliCycle SiliaChrom dtC18 semi-
preparative column (5 μm, 100 Å, 10×250 mm) with a flow rate of
5 mL/min eluting with solvent (A: 0.1% TFA in water B: 0.1% TFA in
MeCN) on a gradient of (2!100) % solvent B over 15 min, tR =
6.11 min) of the crude deprotected product afforded the TFA salt of
1
afforded the TFA salt of 18b as a colorless solid (19 mg, 30%). H
NMR: (600 MHz, CD3CN) δ (ppm)=9.86 (s, 1H), 9.39 (s, 1H), 8.19 (s,
1H), 8.07 (d, J=1.8 Hz, 1H), 7.95 (dd, J=7.6, 1.7 Hz, 1H), 7.70 (dd,
J=7.8, 1.7 Hz, 1H), 7.65 (dd, J=7.8, 7.6 Hz, 1H), 7.62 (d, J=2.5 Hz,
1H), 7.46 (d, J=8.6 Hz, 1H), 7.32 (d, J=8.7 Hz, 1H), 4.06 (q, J=
7.0 Hz, 1H), 3.33 (septet, J=6.7 Hz, 1H), 2.68 (s, 3H), 1.59 (d, J=
6.8 Hz, 3H), 1.25 (d, J=6.8 Hz, 6H). 13C NMR: (150 MHz, CD3CN) δ
(ppm)=167.8, 138.7, 137.9, 135.3, 132.7, 132.0, 130.6, 127.4, 126.6,
126.0, 125.8, 117.1, 116.0, 113.2, 111.3, 58.8, 56.0, 32.1, 16.3, 15.91,
15.90. HRMS: (ESI) m/z calcd for C21H25N3O3S: 400.1689 [M+H]+;
found: 400.1703.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
1
16 as a colorless solid (10 mg, 15%). H NMR: (600 MHz, CD3CN) δ
(ppm)=9.71 (s, 1H), 9.31 (s, 1H), 8.19 (d, J=2.0 Hz, 1H), 8.07 (t, J=
1.8 Hz, 1H), 7.95 (ddd, J=7.7, 1.5, 1.4 Hz, 1H), 7.71 (ddd, J=7.9, 1.5,
1.4 Hz, 1H), 7.65 (dd, J=7.9, 7.7 Hz, 1H), 7.63 (d, J=2.7 Hz, 1H), 7.44
(d, J=8.7 Hz, 1H), 7.33 (dd, J=8.7, 2.0 Hz, 1H), 4.24 (q, J=7.1 Hz,
1H), 3.35 (septet, J=6.8 Hz, 1H), 1.60 (d, J=7.1 Hz, 3H), 1.26 (d, J=
6.8 Hz, 6H). 13C NMR: (150 MHz, CD3CN) δ (ppm)=168.5, 138.7,
137.9, 135.2, 132.6, 132.3, 130.6, 127.4, 126.6, 125.9, 125.8, 116.9,
116.0, 113.2, 110.9, 55.9, 50.9, 17.6, 15.88, 15.87. HRMS: (ESI) m/z
calcd for C20H23N3O3S: 386.1533 [M+H]+; found: 386.1538.
(S)-N-(3-(3-(Isopropylsulfonyl)phenyl)-1H-indol-5-yl)azetidine-2-
carboxamide (20). The title compound was prepared according to
general procedure B using the aryl-indole 48 (50 mg, 0.122 mmol),
N-Boc-l-azetidine-2-carboxylic acid (25 mg, 0.122 mmol), PyBOP
(63 mg, 0.122 mmol), DIPEA (0.16 mL, 0.61 mmol), and dry DMF
(1.22 mL). Purification by RP-HPLC (using a SiliCycle SiliaChrom
dtC18 semipreparative column (5 μm, 100 Å, 10×250 mm) with a
flow rate of 5 mL/min eluting with solvent (A: 0.1% TFA in water B:
0.1% TFA in MeCN) on a gradient of (2!30) % solvent B over
15 min, tR =11.69 min) of the crude deprotected product afforded
the TFA salt of 18c as a colorless solid (14 mg, 23%). 1H NMR:
(600 MHz, CD3CN) δ (ppm)=9.81 (s, 1H), 9.36 (s, 1H), 8.21 (s, 1H),
8.08 (s, 1H), 7.96 (d, J=7.5 Hz, 1H), 7.72 (d, J=7.7 Hz, 1H), 7.66 (dd,
J=7.7, 7.5 Hz, 1H), 7.63 (s, 1H), 7.47 (d, J=8.6 Hz, 1H), 7.32 (d, J=
8.7 Hz, 1H), 5.23 (dd, J=9.4, 7.7 Hz, 1H), 4.16 (q, J=9.3 Hz, 1H), 3.96
(td, J=10.1, 6.4 Hz, 1H), 3.35 (septet, J=6.4 Hz, 1H), 2.82 (qd, J=
10.1, 6.5 Hz, 1H), 2.64 (dt, J=18.6, 8.4 Hz, 1H), 1.27 (d, J=6.5 Hz,
6H). 13C NMR: (150 MHz, CD3CN) δ (ppm)=166.4, 138.8, 138.0,
135.3, 132.7, 132.2, 130.6, 127.4, 126.6, 126.0, 125.9, 116.9, 116.1,
113.3, 111.0, 59.6, 56.0, 44.7, 24.0, 15.9. HRMS: (ESI) m/z calcd for
C21H23N3O3S: 398.1533 [M+H]+; found: 398.1564.
Synthesis of sulfone (17). The title compound was prepared
according to general procedure B using the aryl-indole 51 (45 mg,
0.10 mmol), (tert-butoxycarbonyl)-l-alanine (19 mg, 0.10 mmol),
PyBOP (52 mg, 0.10 mmol), DIPEA (0.14 mL, 0.50 mmol), and dry
DMF (1.0 mL). RP-HPLC (gradient: 2–50 shortprep, tR =7.52 min) of
the crude deprotected product afforded the TFA salt of 17 as a
1
colorless solid (27 mg, 50%). H NMR: (500 MHz, CD3CN) δ (ppm)=
9.74 (s, 1H), 9.18 (s, 1H), 8.17 (d, J=1.9 Hz, 1H), 8.09 (dd, J=1.8,
1.4 Hz, 1H), 7.93 (dd, J=7.8, 1.4, 1.4 Hz, 1H), 7.72 (dd, J=7.9, 1.4,
1.4 Hz, 1H), 7.64 (dd, J=7.9, 7.8 Hz, 1H), 7.62 (d, J=2.6 Hz, 2H), 7.45
(d, J=8.7 Hz, 1H), 7.30 (dd, J=8.8, 2.4 Hz, 1H), 4.23 (q, J=7.0 Hz,
1H), 3.68 (tt, J=8.9, 7.0 Hz, 1H), 2.04–1.96 (m, 2H), 1.91–1.82 (m,
2H), 1.73–1.66 (m, 2H), 1.63–1.55 (m, 5H). 13C NMR: (125 MHz,
CD3CN) δ (ppm)=168.6, 140.7, 138.1, 135.3, 132.5, 132.2, 130.7,
126.9, 126.1, 126.0, 125.9, 117.1, 116.1, 113.2, 111.2, 64.6, 51.0, 28.0,
27.9, 26.6, 17.6. HRMS: (ESI) m/z calcd for C22H25N3O3S: 412.1689 [M
+H]+; found: 412.1706.
(S)-N-(3-(3-(N,N-Dimethylsulfamoyl)phenyl)-1H-indol-5-yl)
azetidine-2-carboxamide (21). The title compound was prepared
according to general procedure B using the aryl indole 52 (58 mg,
0.14 mmol), N-Boc-l-azetidine-2-carboxylic acid (27 mg, 0.14 mmol),
PyBOP (70 mg, 0.14 mmol), DIPEA (0.179 mL, 0.68 mmol) and dry
DMF (1.45 mL). Purification by RP-HPLC (using a SiliCycle SiliaChrom
dtC18 semipreparative column (5 μm, 100 Å, 10×250 mm) with a
flow rate of 5 mL/min eluting with solvent (A: 0.1% TFA in water B:
0.1% TFA in MeCN) on a gradient of (2!50) % solvent B over
15 min, tR =8.60 min) of the crude deprotected product afforded
the TFA salt of 18d as a colorless solid (14 mg, 23%) (14 mg, 20%).
1H NMR: (400 MHz, CD3CN) δ (ppm)=δ 9.77 (s, 1H), 9.06 (s, 1H), 8.27
(d, J=1.8 Hz, 1H), 8.01 (t, J=1.7, 1H), 7.96–7.86 (m, 1H), 7.70–7.59
(m, 3H), 7.44 (d, J=8.7 Hz, 1H), 7.26 (dd, J=8.7, 2.0 Hz, 1H), 5.16 (t,
J=8.6 Hz, 1H), 4.31–3.82 (m, 2H), 2.91–2.76 (m, 1H), 2.74 (s, 6H),
2.72–2.55 (m, 1H). 13C NMR: (150 MHz, CD3CN) δ (ppm)=137.9,
136.6, 135.2, 132.3, 132.0, 130.7, 126.4, 126.0, 125.7, 116.7, 113.3,
110.7, 59.8, 44.7, 41.3, 38.7, 24.6. *13C=O not observed. HRMS: (ESI)
m/z calcd for C20H23N4O3S: 399.1485 [M+H]+; found: 399.1490.
(S)-2-Amino-N-(3-(3-(cyclopentylsulfonyl)phenyl)-1H-indol-5-yl)
propanamide (18). The title compound was prepared according to
general procedure B using the aryl-indole 33 (100 mg, 0.25 mmol),
(tert-butoxycarbonyl)-l-proline (65 mg, 0.30 mmol), PyBOP (156 mg,
0.30 mmol), DIPEA (0.33 mL, 1.25 mmol), and dry DMF (2.5 mL).
Purification by RP-HPLC (using a SiliCycle SiliaChrom dtC18 semi-
preparative column (5 μm, 100 Å, 10×250 mm) with a flow rate of
5 mL/min eluting with solvent (A: 0.1% TFA in water B: 0.1% TFA in
MeCN) on a gradient of (2!100) % solvent B over 15 min, tR =
5.88 min) of the crude deprotected product afforded the TFA salt of
18a as a pale yellow solid (21 mg, 17%). 1H NMR: (600 MHz, CD3OD)
δ (ppm)=8.25 (d, J=1.9 Hz, 1H), 8.22 (dd, J=1.9, 1.9 Hz, 1H), 7.99
(ddd, J=7.7, 1.9, 1.8 Hz, 1H), 7.80 (ddd, J=7.6, 1.9 1.8 Hz, 1H), 7.67
(s, 1H), 7.65 (dd, J=7.7, 7.6 Hz, 1H), 7.45 (d, J=8.7 Hz, 1H), 7.34 (dd,
J=8.7, 1.9 Hz, 1H), 4.43 (dd, J=7.7, 7.7 Hz, 1H), 3.48 (ddd, J=11.4,
7.1, 7.0 Hz, 1H), 3.39 (ddd, J=11.4, 71, 7.0 Hz, 1H), 3.19 (s, 3H), 2.55
(dddd, J=13.6, 7.1, 7.0, 7.0 Hz, 1H), 2.26–2.04 (m, 3H). 13C NMR:
(150 MHz, CD3OD) δ (ppm)=167.7, 142.5, 139.1, 136.2, 132.9, 132.1,
131.0, 126.3, 126.0, 126.0, 124.9, 117.2, 116.4, 113.2, 111.8, 61.7,
47.5, 44.5, 31.2, 25.2. HRMS: (ESI) m/z calcd for C20H21N3O3S:
384.1376 [M+H]+; found: 384.1386.
(S)-N-(3-(3-(N,N-Dimethylsulfamoyl)phenyl)-1H-indol-5-yl)-2-
(methylamino)propanamide (22). The title compound was pre-
pared according to general procedure B using the aryl-indole 52
(50 mg, 0.116 mmol), N-(tert-butoxycarbonyl)-N-methyl-l-alanine
(24 mg, 0.116 mmol), PyBOP (61 mg, 0.116 mmol), DIPEA (0.15 mL,
0.58 mmol), and dry DMF (1.2 mL). Purification by RP-HPLC (using a
SiliCycle SiliaChrom dtC18 semipreparative column (5 μm, 100 Å,
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10×250 mm) with a flow rate of 5 mL/min eluting with solvent (A:
0.1% TFA in water B: 0.1% TFA in MeCN) on a gradient of (2!30)
% solvent B over 15 min, tR =11.84 min) of the crude deprotected
product afforded the TFA salt of 18e as a colorless solid (20 mg,
then diluted with water and extracted with EtOAc (3x). The
remaining aqueous layer was purified by RP-HPLC (gradient: 2–30
shortprep, tR =8.33 min) to afford the TFA salt of 19a as a brown
gum (4 mg, 13%). 1H NMR: (500 MHz, CD3CN) δ (ppm)=9.47 (s, 1H),
8.17 (dd, J=1.9, 1.4 Hz, 1H), 8.01 (ddd, J=7.8, 1.4, 1.1 Hz, 1H), 7.76
(ddd, J=7.8, 1.9, 1.1 Hz, 1H), 7.67 (dd, J=7.8, 7.8 Hz, 1H), 7.57 (d,
J=2.6 Hz, 1H), 7.36 (d, J=8.5 Hz, 1H), 7.16 (s, 1H), 6.75 (d, J=8.5 Hz,
1H), 3.49 (t, J=5.9 Hz, 2H), 3.22 (t, J=5.9 Hz, 2H), 3.12 (s, 3H).
1
2
3
4
5
6
7
8
9
1
34%). H NMR: (500 MHz, CD3OD) δ (ppm)=8.31 (d, J=2.0 Hz, 1H),
8.06 (dd, J=1.8 Hz, 1H), 7.96 (ddd, J=7.2, 1.8, 1.7 Hz, 1H), 7.70–7.61
(m, 3H), 7.45 (d, J=8.7 Hz, 1H), 7.27 (dd, J=8.7, 2.0 Hz, 1H), 3.87 (q,
J=7.0 Hz, 1H), 2.77 (s, 6H), 2.70 (s, 3H), 1.60 (d, J=7.0 Hz, 3H). 13C
NMR: (150 MHz, CD3OD) δ (ppm)=169.14, 138.8, 136.8, 136.2,
132.2, 132.0, 130.7, 126.6, 126.4, 125.9, 125.6, 117.1, 116.5, 113.2,
111.8, 59.3, 38.6, 32.2, 16.9. HRMS: (ESI) m/z calcd for C20H24N4O3S:
401.1642 [M+H]+; found: 401.1655.
N1-Methyl-N2-(3-(3-(methylsulfonyl)phenyl)-1H-indol-5-yl)ethane-
1,2-diamine (27). To a stirred solution of the aryl-indole 33 (22 mg,
0.077 mmol, 1.0 equiv.) in 1,2-dichloroethane (0.77 mL, 0.1 M) was
added tert-butyl methyl(2- oxoethyl)carbamate (13 mg, 0.077 mmol,
1.0 equiv.) at room temperature. The reaction mixture was then
stirred at room temperature for 30 minutes, after which NaBH(OAc)3
(24 mg, 0.12 mmol, 1.5 equiv.) was added. The solution was then
stirred for 18 h, diluted with saturated aqueous NaHCO3 and
extracted with CH2Cl2 (3x). The combined organic layers were dried
over MgSO4 and concentrated under reduced pressure to afford the
crude protected indole (brown gum) which was used in the next
step without further purification. The crude protected product was
dissolved in TFA (neat, 0.77 mL, 0.1 M) and stirred at room
temperature for 30 min. The reaction mixture was then concen-
trated under reduced pressure to afford the crude product, which
was purified by RP-HPLC (using a SiliCycle SiliaChrom dtC18
semipreparative column (5 μm, 100 Å, 10×250 mm) with a flow
rate of 5 mL/min eluting with solvent (A: 0.1% TFA in water B: 0.1%
TFA in MeCN) on a gradient of (2!30) % solvent B over 15 min,
tR =8.95 min) to afford the TFA salt of 19b as a brown gum (3 mg,
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
2-Amino-N-(3-(3-(N,N-dimethylsulfamoyl)phenyl)-1H-indol-5-yl)
acetamide (23). The title compound was prepared according to
general procedure B using the aryl-indole 52 (45 mg, 0.10 mmol),
(tert-butoxycarbonyl)glycine (18 mg, 0.10 mmol), PyBOP (54 mg,
0.10 mmol), DIPEA (0.14 mL, 0.52 mmol), and dry DMF (1.0 mL). RP-
HPLC (gradient: 2–50 shortprep, tR =10.38 min) of the crude
deprotected product afforded the TFA salt of 18f as a colorless
solid (13 mg, 25%). 1H NMR: (500 MHz, CD3OD:CD3CN 1:1, cali-
brated to CD3OD) δ (ppm)=8.32 (d, J=2.0 Hz, 1H), 8.07 (s, 1H), 7.98
(d, J=7.2 Hz, 1H), 7.72–7.65 (m, 3H), 7.50 (d, J=8.7 Hz, 1H), 7.29
(dd, J=8.7, 2.0 Hz, 1H), 3.85 (s, 2H), 2.78 (s, 6H). 13C NMR: (125 MHz,
CD3OD:CD3CN 1:1, calibrated to CD3OD) δ (ppm)=164.9, 138.3,
136.7, 135.6, 132.13, 132.07, 130.7, 126.4, 126.12, 126.08, 125.6,
116.9, 116.2, 113.3, 111.2, 42.0, 38.6. HRMS: (ESI) m/z calcd for
C18H20N4O3S: 373.1329 [M+H]+; found: 373.1343.
2-Amino-N-(3-(3-(N,N-dimethylsulfamoyl)phenyl)-1H-indol-5-yl)-2-
methylpropanamide (24). The title compound was prepared
according to general procedure B using the aryl-indole 52 (50 mg,
0.116 mmol), N-Boc-α-methyl alanine (24 mg, 0.116 mmol), PyBOP
(601 mg, 0.116 mmol), DIPEA (0.15 mL, 0.58 mmol), and dry DMF
(1.2 mL). RP-HPLC (gradient: 2–50 shortprep, tR =8.50 min) of the
crude deprotected product afforded the TFA salt of 18g as a
1
8%). H NMR: (600 MHz, CD3OD) δ (ppm)=8.26 (s, 1H), 7.99 (d, J=
8.0 Hz, 1H), 7.79 (d, J=7.8 Hz, 1H), 7.68 (dd, J=7.8, 7.8 Hz, 1H), 7.58
(s, 1H), 7.34 (d, J=8.7 Hz, 1H), 7.23 (d, J=2.1 Hz, 0H), 6.80 (dd, J=
8.7, 2.1 Hz, 1H), 3.53 (t, J=6.0 Hz, 2H), 3.31 (t, J=6.1 Hz, 2H), 3.19 (s,
3H), 2.78 (s, 3H). 13C NMR: (150 MHz, CD3OD) δ (ppm)=143.0, 142.4,
139.7, 133.6, 132.6, 131.0, 127.1, 125.8, 125.1, 124.5, 115.4, 113.9,
113.8, 102.5, 49.6, 44.4, 42.9, 33.7. HRMS: (ESI) m/z calcd for
C18H21N3O2S: 344.1427 [M+H]+; found: 344.1427.
1
colorless solid (17 mg, 28%). H NMR: (500 MHz, CD3CN) δ (ppm)=
9.75 (s, 1H), 8.75 (s, 1H), 8.20 (d, J=1.9 Hz, 1H), 8.01 (dd, J=1.7,
1.6 Hz, 1H), 7.95 (ddd, J=7.3, 1.7, 1.6 Hz, 1H), 7.71–7.60 (m, 3H),
7.50 (d, J=8.7 Hz, 1H), 7.34 (dd, J=8.7, 1.9 Hz, 1H), 2.73 (s, 6H), 1.72
(s, 6H). 13C NMR: (125 MHz, CD3CN) δ (ppm)=170.6, 137.8, 136.5,
135.4, 131.9, 131.8, 130.6, 126.3, 125.9, 125.8, 125.6, 117.9, 116.2,
113.1, 112.2, 59.2, 38.6, 24.1. HRMS: (ESI) m/z calcd for C20H24N4O3S:
401.1642 [M+H]+; found: 401.1652.
(S)-2-Amino-N-(3-(3-(N,N-dimethylsulfamoyl)phenyl)-1-methyl-1H-
indol-5-yl)propanamide (28). The title compound was prepared
according to general procedure B using the aryl-indole 55 (28 mg,
0.080 mmol), (tert-butoxycarbonyl)-l-alanine (18 mg, 0.095 mmol),
PyBOP (50 mg, 0.38 mmol), DIPEA (0.070 mL, 0.095 mmol), and dry
DMF (0.8 mL) followed by Boc-deprotection using TFA (0.7 mL).
Purification by RP-HPLC (using a SiliCycle SiliaChrom dtC18 semi-
preparative column (5 μm, 100 Å, 10×250 mm) with a flow rate of
5 mL/min eluting with solvent (A: 0.1% TFA in water B: 0.1% TFA in
MeCN) on a gradient of (2!100) %) solvent B over 15 min, tR =
6.5 min) of the crude deprotected product afforded the TFA salt of
1-Amino-N-(3-(3-(N,N-dimethylsulfamoyl)phenyl)-1H-indol-5-yl)
cyclopropane-1-carboxamide (25). The title compound was pre-
pared according to general procedure B using the aryl-indole 52
(50 mg, 0.116 mmol), 1-((tert-butoxycarbonyl)amino)cyclopropane-
1-carboxylic acid (23 mg, 0.116 mmol), PyBOP (61 mg, 0.116 mmol),
DIPEA (0.15 mL, 0.58 mmol), and dry DMF (1.16 mL). RP-HPLC
(gradient: 2–50 shortprep, tR =8.43 min) of the crude deprotected
product afforded the TFA salt of 18h as a colorless solid (16 mg,
1
20 as a colorless solid (10 mg, 15%). H NMR: (400 MHz, CD3CN) δ
(ppm)=9.23 (s, 1 H), 8.23 (d, J=1.6 Hz, 1H), 7.96 (br s, 1H), 7.87 (dt,
J=7.4, 1.6 Hz, 1H), 7.63 (t, J=7.4 Hz, 1H), 7.60 (t, J=1.6 Hz, 1H),
7.55 (s, 1H), 7.35 (dq, J=8.9, 0.8 Hz, 1H), 7.29 (dd, J=8.9, 1.9 Hz,
1H), 4.24 (q, J=7.0 Hz, 1H), 3.79 (s, 3H), 2.71 (s, 6H), 1.58 (d, J=
7.0 Hz, 3H). 13C NMR: (150 MHz, CD3CN) δ (ppm)=168.6, 137.7,
136.6, 136.0, 132.2, 131.6, 130.6, 130.2, 126.2, 126.1, 125.4, 116.8,
114.9, 111.4, 111.3, 50.96, 38.60, 33.47, 17.62. HRMS: (ESI) m/z calcd
for C21H24N4O3S: 401.1647 [M+H]+; found: 401.1602.
1
27%). H NMR: (500 MHz, CD3CN) δ (ppm)=9.68 (s, 1H), 8.12 (d, J=
1.9 Hz, 1H), 8.01 (dd, J=1.7, 1.7 Hz, 1H), 7.93 (ddd, J=7.2, 1.8,
1.7 Hz, 1H), 7.89 (s, 1H), 7.70–7.62 (m, 3H), 7.49 (d, J=8.7 Hz, 1H),
7.26 (dd, J=8.8, 2.0 Hz, 1H), 2.74 (s, 6H), 1.74–1.68 (m, 2H), 1.60–
1.54 (m, 2H). 13C NMR: (125 MHz, CD3CN) δ (ppm)=167.1, 136.9,
135.8, 134.6, 131.0, 130.3, 129.7, 125.4, 125.0, 124.9, 124.7, 118.2,
115.3, 112.2, 111.7, 37.6, 36.6, 12.4. HRMS: (ESI) m/z calcd for
C20H22N4O3S: 399.1485 [M+H]+; found: 399.1495.
(R)-2-Amino-N-(3-(3-(N,N-dimethylsulfamoyl)phenyl)-1-methyl-1H-
indol-5-yl)-3-fluoropropanamide (29). To a solution of 61 (12 mg,
0.02 mmol, 1 equiv.) in dry CH2Cl2 (200 μL), TFA (200 μL, 2.6 mmol,
131 equiv.) was added. After 1 h at room temperature, the solvents
N1-(3-(3-(Methylsulfonyl)phenyl)-1H-indol-5-yl)ethane-1,2-dia-
mine (26). To a stirred solution of the aryl-indole 33 (35 mg,
0.12 mmol, 2.0 equiv.) in water (ca. 0.15 mL, 2.0 M) was added 2-
bromoethan-1-amine hydrochloride (13 mg, 0.061 mmol, 1.0 equiv.)
were evaporated. Purification by RP-HPLC (using
a SiliCycle
SiliaChrom dtC18 semipreparative column (5 μm, 100 Å, 10×
250 mm) with a flow rate of 5 mL/min eluting with solvent (A: 0.1%
TFA in water B: 0.1% TFA in MeCN) on a gradient of (2!100) %)
solvent B over 15 min, tR =6.60 min) afforded the TFA salt of 29 as a
°
at room temperature. The reaction mixture was then stirred at 95 C
for 22 h and cooled to room temperature. The reaction mixture was
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1
[5] Y. H. Lee, M. R. Stallcup, Cell Cycle 2011, 10, 1343–1344.
[6] S. L. Chen, K. A. Loffler, D. Chen, M. R. Stallcup, G. E. Muscat, J. Biol.
Chem. 2002, 277, 4324–4333.
[7] H. Wei, R. Mundade, K. C. Lange, T. Lu, Cell Cycle 2014, 13, 32–41.
[8] J. Fuhrmann, K. W. Clancy, P. R. Thompson, Chem. Rev. 2015, 115, 5413–
5461.
colourless solid (3 mg, 24%). H NMR: (400 MHz, CD3CN) δ (ppm)=
9.44 (s, 1H), 8.24 (s, 1H), 7.98 (s, 1H), 7.91–7.89 (m, 1H), 7.66–7.58 (m,
3H), 7.40 (d, J=8.7 Hz, 1H), 7.32 (d, J=8.8 Hz, 1H), 4.96 (d, J=
46.5 Hz, 2H), 4.46 (s, 1H), 3.82 (s, 3H), 2.72 (s, 6H). 19F NMR:
(376 MHz, CD3CN) δ (ppm)=À 231.3 (s, 1F). HRMS: (ESI) m/z calcd
for C20H23FN4O3S: 419.1548 [M+H]+; found: 419.1565.
1
2
3
4
[9] Y. R. Kim, B. K. Lee, R. Y. Park, N. T. Nguyen, J. A. Bae, D. D. Kwon, C.
5
6
7
8
Jung, BMC Cancer 2010, 10, 197.
(S)-3-(5-(2-Aminopropanamido)-1-methyl-1H-indol-3-yl)-N,N-
dimethylbenzamide (30). The title compound was prepared
according to general procedure B using the aryl-indole 64 (14 mg,
0.048 mmol), (tert-butoxycarbonyl)-l-alanine (11 mg, 0.057 mmol),
PyBOP (30 mg, 0.24 mmol), DIPEA (0.041 mL, 0.057 mmol), and dry
DMF (0.5 mL) followed by Boc-deprotection using TFA (0.5 mL).
Purification by RP-HPLC (using a SiliCycle SiliaChrom dtC18 semi-
preparative column (5 μm, 100 Å, 10×250 mm) with a flow rate of
5 mL/min eluting with solvent (A: 0.1% TFA in water B: 0.1% TFA in
MeCN) on a gradient of (2!100) %) solvent B over 15 min, tR =
5.95 min) of the crude deprotected product afforded the TFA salt of
[10] H. Hong, C. Kao, M. H. Jeng, J. N. Eble, M. O. Koch, T. A. Gardner, S.
Zhang, L. Li, C. X. Pan, Z. Hu, G. T. MacLennan, L. Cheng, Cancer 2004,
101, 83–89.
[11] S. Frietze, M. Lupien, P. A. Silver, M. Brown, Cancer Res. 2008, 68, 301–
9
306.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
[12] H. O. Habashy, E. A. Rakha, I. O. Ellis, D. G. Powe, Breast Cancer Res. Treat.
2013, 140, 307–316.
[13] L. Wang, Z. Zhao, M. B. Meyer, S. Saha, M. Yu, A. Guo, K. B. Wisinski, W.
Huang, W. Cai, J. W. Pike, M. Yuan, P. Ahlquist, W. Xu, Cancer Cell 2014,
25, 21–36.
[14] K. Nakayama, M. M. Szewczyk, C. Dela Sena, H. Wu, A. Dong, H. Zeng, F.
Li, R. F. de Freitas, M. S. Eram, M. Schapira, Y. Baba, M. Kunitomo, D. R.
Cary, M. Tawada, A. Ohashi, Y. Imaeda, K. S. Saikatendu, C. E. Grimshaw,
M. Vedadi, C. H. Arrowsmith, D. Barsyte-Lovejoy, A. Kiba, D. Tomita, P. J.
Brown, Oncotarget 2018, 9, 18480–18493.
[15] A. E. Drew, O. Moradei, S. L. Jacques, N. Rioux, A. P. Boriack-Sjodin, C.
Allain, M. P. Scott, L. Jin, A. Raimondi, J. L. Handler, H. M. Ott, R. G.
Kruger, M. T. McCabe, C. Sneeringer, T. Riera, G. Shapiro, N. J. Waters,
L. H. Mitchell, K. W. Duncan, M. P. Moyer, R. A. Copeland, J. Smith, R.
Chesworth, S. A. Ribich, Sci. Rep. 2017, 7, 17993.
[16] Y. Shen, M. M. Szewczyk, M. S. Eram, D. Smil, H. U. Kaniskan, R. F.
de Freitas, G. Senisterra, F. Li, M. Schapira, P. J. Brown, C. H. Arrowsmith,
D. Barsyte-Lovejoy, J. Liu, M. Vedadi, J. Jin, J. Med. Chem. 2016, 59,
9124–9139.
[17] M. S. Eram, Y. Shen, M. Szewczyk, H. Wu, G. Senisterra, F. Li, K. V. Butler,
H. U. Kaniskan, B. A. Speed, C. Dela Sena, A. Dong, H. Zeng, M. Schapira,
P. J. Brown, C. H. Arrowsmith, D. Barsyte-Lovejoy, J. Liu, M. Vedadi, J. Jin,
ACS Chem. Biol. 2016, 11, 772–781.
[18] H. Hu, K. Qian, M. C. Ho, Y. G. Zheng, Expert Opin. Invest. Drugs 2016, 25,
335–358.
[19] J. S. Sack, S. Thieffine, T. Bandiera, M. Fasolini, G. J. Duke, L. Jayaraman,
K. F. Kish, H. E. Klei, A. V. Purandare, P. Rosettani, S. Troiani, D. Xie, J. A.
Bertrand, Biochem. J. 2011, 436, 331–339.
[20] R. Ferreira de Freitas, M. S. Eram, D. Smil, M. M. Szewczyk, S. Kennedy,
P. J. Brown, V. Santhakumar, D. Barsyte-Lovejoy, C. H. Arrowsmith, M.
Vedadi, M. Schapira, J. Med. Chem. 2016, 59, 6838–6847.
[21] X. C. Cai, T. Zhang, E. J. Kim, M. Jiang, K. Wang, J. Wang, S. Chen, N.
Zhang, H. Wu, F. Li, C. C. Dela Sena, H. Zeng, V. Vivcharuk, X. Niu, W.
Zheng, J. P. Lee, Y. Chen, D. Barsyte, M. Szewczyk, T. Hajian, G. Ibanez, A.
Dong, L. Dombrovski, Z. Zhang, H. Deng, J. Min, C. H. Arrowsmith, L.
Mazutis, L. Shi, M. Vedadi, P. J. Brown, J. Xiang, L. X. Qin, W. Xu, M. Luo,
eLife 2019, 8, e47110.
[22] L. H. Mitchell, A. E. Drew, S. A. Ribich, N. Rioux, K. K. Swinger, S. L.
Jacques, T. Lingaraj, P. A. Boriack-Sjodin, N. J. Waters, T. J. Wigle, O.
Moradei, L. Jin, T. Riera, M. Porter-Scott, M. P. Moyer, J. J. Smith, R.
Chesworth, R. A. Copeland, ACS Med. Chem. Lett. 2015, 6, 655–659.
[23] C. Carpentier, R. Godbout, F. Otis, N. Voyer, Tetrahedron Lett. 2015, 56,
244–1246.
[24] C. B. De Koning, J. P. Michael, A. L. J. Rousseau, Chem. Soc. Perkin Trans.
1 2000, 1705–1713.
[25] B. E. Blough, A. Landavazo, J. S. Partilla, A. M. Decker, K. M. Page, M. H.
Baumann, R. B. Rothman, Bioorg. Med. Chem. Lett. 2014, 24, 4754–4758.
[26] M. Livendahl, J. Jamroskovic, S. Ivanova, P. Demirel, N. Sabouri, E.
Chorell, Chem. Eur. J. 2016, 22, 13004–13009.
1
22 as a colorless solid (7 mg, 40%). H NMR: (400 MHz, CD3CN) δ
(ppm)=9.10 (s, 1H), 8.22 (s, 1H), 7.67 (d, J=7.3, 2H), 7.49 (s, 1H),
7.46 (t, J=7.9 Hz, 1H), 7.38 (d, J=8.8 Hz, 1H), 7.29 (br d, J=8.8 Hz,
1H), 7.25 (br d, J=7.6 Hz, 1H), 4.19 (q, J=6.4 Hz, 1H), 3.80 (s, 3H),
3.05 (br s, 3H), 2.99 (br s, 3H), 1.58 (d, J=6.4 Hz, 3H). 13C NMR:
(150 MHz, CD3CN) δ (ppm)=172.1, 168.6, 138.4, 136.7, 135.9, 131.9,
129.8, 129.6, 128.5, 126.4, 126.0, 125.0, 116.6, 116.0, 111.6, 111.3,
51.02, 39.89, 35.39, 33.50, 30.20, 17.57. HRMS: (ESI) m/z calcd for
C21H24N4O2 365.4565 [M+H]+; found: 365.1915.
Acknowledgements
This work was supported by a Natural Sciences and Engineering
Research Council (NSERC) Discovery Grant (RB 2019-06368), and
NSERC CREATE Grant (432008-2013). The SGC is a registered
charity (no. 1097737) that receives funds from AbbVie, Bayer
Pharma AG, Boehringer Ingelheim, Canada Foundation for
Innovation, Eshelman Institute for Innovation, Genome Canada
through Ontario Genomics Institute [OGI-055], Innovative Medi-
cines Initiative (EU/ EFPIA) [ULTRA-DD grant no. 115766], Janssen,
Merck KGaA, Darmstadt, Germany, MSD, Novartis Pharma AG,
Ontario Ministry of Research, Innovation and Science (MRIS),
Pfizer, São Paulo Research Foundation-FAPESP, Takeda, and
Wellcome [106169/ZZ14/Z].
Conflict of Interest
The authors declare no conflict of interest.
Keywords: co-crystal structures · methylation · protein arginine
methyl transferases · structure-based drug design
[27] M. Taddei, E. Cini, L. Giannotti, G. Giannini, G. Battistuzzi, D. Vignola, L.
Vesci, W. Cabri, Bioorg. Med. Chem. Lett. 2014, 24, 61–64.
[28] E. Valeur, M. Bradley, Chem. Soc. Rev. 2009, 38, 606–631.
[1] B. T. Schurter, S. S. Koh, D. Chen, G. J. Bunick, J. M. Harp, B. L. Hanson, A.
Henschen-Edman, D. R. Mackay, M. R. Stallcup, D. W. Aswad, Biochemis-
try 2001, 40, 5747–5756.
[2] W. An, J. Kim, R. G. Roeder, Cell 2004, 117, 735–748.
[3] D. Cheng, J. Cote, S. Shaaban, M. T. Bedford, Mol. Cell 2007, 25, 71–83.
[4] S. El Messaoudi, E. Fabbrizio, C. Rodriguez, P. Chuchana, L. Fauquier, D.
Cheng, C. Theillet, L. Vandel, M. T. Bedford, C. Sardet, Proc. Natl. Acad.
Sci. USA 2006, 103, 13351–13356.
Manuscript received: January 8, 2021
Accepted manuscript online: January 29, 2021
Version of record online: March 4, 2021
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