Development of a Small Hybrid Molecule That Mediates Degradation of His-Tag Fused Proteins

Article abstract of DOI:10.1021/acs.jmedchem.7b00413

In recent years, the induction of target-protein degradation via the ubiquitin-proteasome system (UPS) mediated by small molecules has attracted attention, and this approach has applications in pharmaceutical development. However, this technique requires a ligand for the target protein that can be incorporated into tailor-made molecules, and there are many proteins for which such ligands have not been found. In this study, we developed a protein-knockdown method that recognizes a His-tag fused to a protein of interest. This strategy theoretically allows comprehensive targeting of proteins of interest by a particular molecule recognizing the tag. As expected, our hybrid molecule 10 [SNIPER(CH6)] efficiently degraded His-tagged CRABP-II and Smad2 in cells. This system provides an easy method to determine the susceptibility of proteins of interest to UPS-mediated degradation. Furthermore, we hope that this method will become an efficient tool to analyze the function of the UPS.

Full text of DOI:10.1021/acs.jmedchem.7b00413

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Article
Development of a small hybrid molecule that
mediates degradation of His-tag fused proteins
Koyo Okitsu, Takayuki Hattori, Takashi Misawa, Takuji
Shoda, Masaaki Kurihara, Mikihiko Naito, and Yosuke Demizu
J. Med. Chem., Just Accepted Manuscript • Publication Date (Web): 01 May 2017
Downloaded from http://pubs.acs.org on May 2, 2017
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Journal of Medicinal Chemistry is published by the American Chemical Society. 1155
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Development of a small hybrid molecule that
mediates degradation of His-tag fused proteins
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a,b,‡
c,‡
a
a
a
Koyo Okitsu,
Takayuki Hattori, Takashi Misawa, Takuji Shoda, Masaaki Kurihara,
c,*
a,*
Mikihiko Naito, and Yosuke Demizu
a
Division of Organic Chemistry, National Institute of Health Sciences, 1-18-1, Kamiyoga,
b
Setagaya, Tokyo 158-8501, Japan; Graduate School of Bioscience and Biotechnology, Tokyo
c
Institute of Technology, Yokohama 226-8501, Japan; Division of Molecular Target and Gene
Therapy Products, National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya, Tokyo 158-
8
501, Japan
KEYWORDS: His-tag fused protein; protein knockdown; ubiquitin-proteasome system; CRABP-
II, Smad2
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ABSTRACT. In recent years, the induction of target-protein degradation via the ubiquitin-
proteasome system (UPS) mediated by small molecules has attracted attention, and this approach
has applications in pharmaceutical development. However, this technique requires a ligand for the
target protein that can be incorporated into tailor-made molecules, and there are many proteins for
which such ligands have not been found. In this study, we developed a protein-knockdown method
that recognizes a His-tag fused to a protein of interest. This strategy theoretically allows
comprehensive targeting of proteins of interest by a particular molecule recognizing the tag. As
expected, our hybrid molecule 10 [SNIPER(CH6)] efficiently degraded His-tagged CRABP-II
and Smad2 in cells. This system provides an easy method to determine the susceptibility of
proteins of interest to UPS-mediated degradation. Furthermore, we hope that this method will
become an efficient tool to analyze the function of the UPS.
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Introduction
Understanding intracellular protein functions is crucial for elucidating living systems and
disease etiologies, and controlling the expression of proteins is useful in many aspects of biology.
In addition, the ability to control specific protein levels within a living organism using a simple
technique would be a useful strategy for pharmaceutical development. For these reasons, a variety
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of techniques for controlling protein expression have been reported, In particular, a protein-
knockdown strategy for inducing the degradation of proteins of interest (POI) using the ubiquitin-
proteasome system (UPS) has attracted attention. Small molecules called PROTACs (proteolysis-
5-15
targeting chimeras)
and SNIPERs (specific and non-genetic inhibitors of apoptosis protein
1
6-21
[IAP]-dependent protein erasers)
have been developed for use in this method. These molecules
are composed of two different ligands connected by a linker; one is a ligand for the POI, and the
other is a ligand for E3 ubiquitin ligase. Thus, these molecules are capable of crosslinking POI
and E3 ubiquitin ligase in cells, resulting in the ubiquitylation and subsequent degradation of POI
via the UPS (Figure 1a). The main advantages of this technique are that small molecules are
chemically stable and the expression of the target protein can be controlled. However, in this
method a ligand for each protein of interest is necessary to design and synthesize tailor-made
molecules, and therefore, it is difficult to comprehensively analyze which POI are most susceptible
to protein knockdown by the UPS.
To solve this problem, degradation inducers for Halo-tag proteins have recently been
2
2,23
developed.
It was found that hybrid small molecules containing a Halo-tag and an E3 ligand
were able to bridge between Halo-tag and E3 ligase and facilitate the degradation of Halo-tagged
POI (Figure 1b). However, there are some concerns when a high molecular mass tag (33 KDa) is
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employed. The large tag might obstruct the function of the fused protein and Lys residues in the
tag might be ubiquitylated by degradation-inducer molecules, such as SNIPER, resulting in
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subsequent degradation of the POI. Other tags, including the His tag and dC10a tag are also
used for the imaging of intracellular proteins. The His tag generally consists of six or more His
residues attached at the N- or C-terminus of POI, and a modified His tag consisting of hexa-His
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and a Cys residue (CH6-tag) has also been reported. The CH6-tag is small and does not contain
any Lys residues and the thiol group of the Cys residue is capable of covalently binding to some
acceptors such as maleimide and chloroacetyl groups. Therefore, we speculated that the CH6-tag
might solve the above-mentioned problems found with using a high molecular mass tag (Table 1).
Herein, we describe the development of a SNIPER that bridges between CH6-tag and E3 ligase
for the knockdown of CH6-tagged POI via the UPS.
(a)
Ub
Ub
Ub
Ub
PROTAC
SNIPER
E3
POI
Protein Of
Interest
POI
E3
(b)
?
?
E3 ligase
Ubiquitin
Ub
Ub
Ub
Ub
Ub
Ub
E3
Halo
POI
Figure 1. Targeted protein knockdown by hybrid small molecules. (a) Hybrid small molecules,
such as SNIPER and PROTAC consisting of a ligand for POI and an E3 ligand, bridge between
POI and E3 ligase, and subsequently induce ubiquitylation of POI resulting in proteasomal
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degradation of POI. (b) A hybrid molecule targeting Halo-tag fused to POI mediates the
degradation of POI. However, this system cannot precisely elucidate the biological implications
of the ubiquitylation of POI because it is unclear whether Lys residues in the POI, and not those
in the tag portion, are consistently ubiquitylated by the hybrid molecules.
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Table 1. Comparison of the present system and published approaches.
PROTACs/SNIPERs Halo-tag method CH6-tag method
Comprehensive application for
proteins
Not applicable
Applicable
Applicable
Target endogenous proteins
Necessity of gene transfection
Tag size
Applicable
Not applicable
Necessary
Large
Not applicable
Necessary
Not necessary
-
-
Small
Ubiquitination of tags
Concerned
Not concerned
Results and discussion
The mechanism proposed for the degradation of CH6-tagged POI is shown in Figure 2. Two
types of molecules are essential for this technique. One is a degradation inducer 10
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[
SNIPER(CH6)] containing nickel nitrilotriacetic acid (Ni-NTA; a His-tag ligand), a maleimide
moiety conjugated to a Cys residue in a CH6-tag, and an E3 ligand. However, the degradation
inducer itself is not able to penetrate into cells because of the high polarity of Ni-NTA molecules.
Therefore, a carrier peptide conjugated with a His-tag is also required to deliver the degradation
inducer into cells. These two molecules contribute to the degradation of CH6-tagged POI in the
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following manner: 1) The degradation inducer forms a complex with the carrier peptide and then
the complex is taken into the target cells. 2) In the cells, the degradation inducer dissociates from
the carrier peptide and moves towards CH6-tagged POI, subsequently the maleimide moiety
conjugates with the Cys residue in the CH6-tag. 3) Finally, E3 ligase is recruited to the E3 ligand,
and POI are ubiquitylated and degraded by the UPS.
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10 [SNIPER(CH6)]
N
His
O
O
N
O
O
His
complex
1
cell surface
cytosol
) delivery
E3 Ligand
Ni-NTA
dissociation
His
CPP
N
O
O
His
His-tag
CH6-tag
E3
Ub
CH6
CH6
CH6
CH6
N
POI
O
O
N
O
O
SH
SH
SH
S
2
) bind to POI
POI
POI
Ub
3) UPS mediated degradation
proteasome
Figure 2. Delivery of 10 to ubiquitylate and degrade CH6-tagged POI. To deliver 10 into cells,
we formed a 10-carrier peptide consisting of a His-tag and a cell penetrating peptide (CPP)
complex. This complex is thought to penetrate the plasma membrane efficiently. In the cytosol,
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0 is released from the carrier peptide and forms another complex with CH6-tagged POI through
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the covalent binding of the maleimide moiety to a Cys residue. Thereafter, POI are ubiquitylated
and degraded via the UPS. See the main text for more detail.
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The chemical structure of the degradation inducer and the sequence of carrier peptides developed
in this study are shown in Figure 3. The degradation inducer 10 consists of three Ni-NTA moieties,
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which increase affinity for the His-tag; a maleimide moiety, and MV1, a pan-antagonist of
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cIAP1, cIAP2, and XIAP, as an E3 ligand. Two types of carrier peptides, 17 (R10-H4A2) and
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6 (R10-H6), which are composed of deca-arginine (R10) and His-tags, were used. The His-tag
H4A2 in the 17 carrier peptide sequence was obtained by replacing two His residues with two Ala
residues. This tag was expected to exhibit reduced affinity for Ni-NTA and to facilitate
dissociation of the degradation inducer within the target cells. To verify our method, we also
synthesized two additional molecules in which the E3 ligand moiety was replaced with a
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fluorescein molecule 5 (Fluo-triNTA) or a biotin molecule 15 (Biotin-mal-triNTA). The
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molecule 12 [SNIPER(His)] without a maleimide moiety was also synthesized. The synthetic
routes for these molecules are shown in the supporting information.
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H2O
O
2
H O
OH2
Ni2+
O
OH
2
O
O
O
O
O
Ni2+
O
N
O
O
O
O
O
O
Ni-NTA
O
O
O
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N
O
O
N
H2O
H2O
O
H
H
2
O
O
Ni2+
O
O
N
Ni2+
O
N
O
N
2
O
N
N
O
O
O
N
O
N
O
O
N
O
N
O
Ph
Ph
O
O
O
H
H
N
N
N
S
O
N
N
H
N
H
N
N
HN
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O
O
H
O
O
Ni2+O
O
O
Ni2+O
O
O
HN
O
O
H2O
O
OH2
2
O H
H
2
O
OH
N
MV1
O
O
N
HO
N
N
Maleimide
O
Fluorescein
10 [SNIPER(CH6)]
5 [Fluo-triNTA]
2
H O
OH
Ni2+
2
O
O
O
O
O
O
O
O
H2O
OH2
O
O
Ni2+
O
N
O
O
O
H
H
2
O
O
Ni2+
N
O
N
O
O
N
O
O
O
2
O
N
O
O
N
H2O
H2O
O
Ni2+
O
N
O
O
O
N
O
N
O
O
N
NH
HN
O
H
O
H
N
O
N
O
H
N
O
N
N
H
S
O
O
Ni2+O
O
O
Ph
HN
Ph
O
O
H
N
O
H
N
OH
2
N
2
O
O
O
O
N
H
N
H
Biotin
O
Ni2+
N
O
O
O
N
O
OH2
N
H2O
N
O
15 [Biotin-mal-triNTA]
12 [SNIPER(His)]
1
6 [R10-H6]
Ac-YRRRRRRRRRRGHHHHHH-NH2
Ac-YRRRRRRRRRRGHAHAHH-NH2
17 [R10-H4A2]
Figure 3. Structures of the molecules used in this study.
First, we analyzed whether the carrier peptide was able to transport compound 5 into HT1080
cells. It was found that 5 was not taken into the cells in the absence of a carrier peptide 17 after a
three-hour incubation because of the high polarity of the Ni-NTA moiety. On the other hand,
fluorescence was observed within the cells when 5 formed a complex with 17 (Figure S1),
indicating that the carrier peptide delivered 5 into the cells as expected.
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Next, a biotin pull-down assay was performed using compound 15 to confirm that 15 dissociates
from the carrier peptide and the maleimide moiety in 15 is able to covalently bind to the CH6-
tagged POI in living cells. HT1080 cells constitutively expressing 2´(CH6)-FLAG-CRABP-II
were treated with 3-µM 10/17 complex or 3-µM 15/17 complex and the cell lysate was subjected
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to a biotin pull-down assay with streptavidin beads. As shown in Figure 4, 2´(CH6)-FLAG-
CRABP-II protein was not pulled down when the cells were treated with 10/17 (lane 2). On the
other hand, treatment with 15/17 resulted in biotinylation of the 2´(CH6)-FLAG-CRABP-II
protein, which was reflected in precipitation with streptavidin beads (lane 3). These observations
suggested that 15 is released from the carrier peptide and forms a covalent bond with CH6-tagged
CRABP-II.
N- CH6
CH6
FLAG
CRABP-II
-C
2x(CH6)-FLAG-CRABP-II
1
2
3
ꢀ
50
Lane 1: none
Lane 2: 3 µM 10 / 17
Lane 3: 3 µM 15 / 17
ꢀ
37
ꢀ
25
20
15
biotin pull-down
blot: CRABP-II
ꢀ
ꢀ
Input
blot: CRABP-II
Figure 4. Compound 15 covalently attached to the 2´(CH6)-FLAG-CRABP-II protein in living
cells. HT1080 cells constitutively expressing 2´(CH6)-FLAG-CRABP-II were treated with
vehicle alone (lane 1), 3-µM 10/17 complex (lane 2), and 3-µM 15/17 complex (lane 3) for 2 h.
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Then, the cells were harvested and lysed for a biotin pull-down assay followed by immunoblotting
with anti-CRABP-II antibody. The arrow shows biotinylated 2´(CH6)-FLAG-CRABP-II protein
precipitated with streptavidin agarose.
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Then, we evaluated the effects of compound 10 on 2´(CH6)-FLAG-CRABP-II protein
degradation in HT1080 cells (Figure 5). As shown in Figure 5a, treatment with carrier peptides
alone did not affect the expression level of 2´(CH6)-FLAG-CRABP-II protein (Figure 5, lanes 4
and 5). A reduced level of the protein was observed in the cells treated with 3-µM 10/17 complex
while the use of a combination of 10 and 16 also resulted in protein degradation (Figure 5a, lanes
2
and 3), and there were no differences in activity between 17 and 16. However, compound 12
without the maleimide moiety did not promote the degradation of the protein, indicating that
covalent binding greatly influences degradation of POI (Figure 5b, lane 2). Compound 10-induced
degradation of the 2´(CH6)-FLAG-CRABP-II protein was blocked by the addition of a
proteasome inhibitor (MG132 or carfilzomib), but a lysosome inhibitor (bafilomycin A1) did not
suppress the protein degradation (Figure 5b, lanes 4-9). These findings indicate that 10 induces
the proteasomal degradation of the 2´(CH6)-FLAG-CRABP-II protein when delivered into cells
by 16 and 17.
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10 (µM)
17 (µM)
16 (µM)
(
b)
2
x(CH6)-FLAG-CRABP-II
Lane
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FLAG
CRABP-II
b-actin
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10 (µM)
12 (µM)
17 (µM)
MG132 (µM)
carfilzomib (µM)
bafilomycin (µM)
-
3
-
-
3
-
-
3
-
10 30
-
-
-
-
10 30
-
-
-
-
0.1 0.3
ꢀ
Figure 5. Degradation of 2´(CH6)-FLAG-CRABP-II by 10. (a) HT1080 cells constitutively
expressing 2´(CH6)-FLAG-CRABP-II were treated with 3-µM 10/carrier peptide complex or
carrier peptide alone for 6 h. (b) The cells were treated with 3 µM 12/17 or 10/17 complex together
with the indicated doses of MG132, carfilzomib, or bafilomycin A1 for 6 h. The lysates were
analyzed with the indicated antibodies.
ꢀ
Treatment with 10/16 complex also resulted in the degradation of the 2´(CH6)-2´FLAG-Smad2
protein (Figure 6, lanes 2 and 5). The reduction in the protein level induced by 10 was abrogated
by co-treatment with MG132 (Figure 6, lanes 3, 4, 6, and 7), suggesting that the 2´(CH6)-
2
´FLAG-Smad2 protein is also degraded via the proteasome.
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N-
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CH6
FLAG
FLAG
Smad2
-C
2x(CH6)-2xFLAG-Smad2
Lane
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b-actin
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3
-
10
30
10
10
-
-
-
MG132 (µM)
10 (µM)
10
10
10
10
16 (µM)
Figure 6. Degradation of the 2´(CH6)-2´FLAG-Smad2 protein by 10/16 complex in a proteasome
activity-dependent manner. HT1080 cells constitutively expressing the 2´(CH6)-2´FLAG-
Smad2 protein were treated with the indicated doses of 10/16 complex in the presence or absence
of 10 µM or 3 µM MG132 for 6 h. The lysates were analyzed with the indicated antibodies.
ꢀ
Finally, to confirm the safety of 10 and the carrier peptides, we subjected these compounds to
cytotoxicity tests (Figure 7). HT1080 cells were treated with each compound at concentrations of
1, 3, and 10 µM for 24 h. Compounds 10, 17, 16 discrete molecules, and the compound 10/carrier
peptide complexes did not exhibit marked cytotoxicity, even at a concentration of 10 µM.
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0uM
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16
17
10
10 / 16
10 / 17
control
Figure 7. The compound 10/carrier peptide complexes are not cytotoxic at the effective
concentration. HT1080 cells were treated with 10, carrier peptides, and their complexes at
indicated concentrations. After 24 h, cell viability was assessed. 100% cell viability was
calculated from the wells without carrier peptides or 10 (control).
Conclusions
In summary, we have successfully developed a protein-knockdown method for CH6-tagged POI
using a combination of carrier peptides and 10. The compound 10/carrier peptide complexes were
capable of inducing the degradation of intracellular CH6-tagged CRABP-II and Smad2 proteins.
Our system could be an effective screening tool for finding proteins that are susceptible to
degradation via the UPS, for investigating the protein function and cellular output when forced
selective ubiquitylation of POI is induced, and for identifying target proteins for drug discovery.
Experimental Section
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General.
Chemical reagents and solvents were purchased from Aldrich Inc., Tokyo Chemical Industry
Co.,Ltd., Wako Pure Chemical Industries,Ltd., Kanto chemical co.,inc., Watanabe Chemical
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1
Industries, LTD. and Quanta BioDesign, Ltd. and used without purification. H NMR spectra were
obtained on a Varian Mercury (400 MHz). High-resolution mass spectra were recorded with
SHIMAZU LCMS-IT-TOF spectrometer.
The purified peptides and compounds were
TM
characterized using 4800 Plus MALDI TOF/TOF Analyzer (Applied Biosystems/MDS SCIEX),
and liquid chromatography-mass spectrometry-ion trap-time-of-flight (LCMS-IT-TOF)
spectroscopy (Shimadzu). Analytical thin-layer chromatography was performed on Merck Silica
Gel F254. The purity of synthesized compounds was determined by analytical RP-HPLC using a
®
Discovery Bio Wide Pore C18 column (25 cm x 4.6 mm; solvent A:0.1% TFA/water, solvent B:
−1
0
.1% TFA/MeCN, flow rate: 1.0 mL・ml , gradient: 10-60% gradient of solvent B over 30 min).
All synthesized compounds were obtained with purity ≥95%.
Synthesis and purification of peptides.
The peptides were synthesized using solid phase methods on NovaPEG Rink amide resin following
the standard Fmoc chemistry. The following describes a representative coupling and deprotection
cycle at a 25 µmol scale. First, 65 mg NovaPEG Rink amide resin (loading: 0.5 mmol/g) was
2 2
soaked for 1 h in CH Cl . After the resin had been washed with DMF, Fmoc-amino acid (4 Eq)
and HBTU (4 Eq) dissolved in 1.0 ml NMP were added to the resin. Then, DIPEA (8 Eq) and
HOBt (1.0 ml, 0.1 M solution in NMP) were added for the coupling reaction. Deprotection was
carried out using 20% piperidine in NMP (2 ml). After the peptide synthesis, the resin was
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suspended in cleavage cocktail (1.9 ml TFA, 50 µl water, 50 µl TIPS; final concentration: 95%
TFA, 2.5% water, 2.5% TIPS) for 3 h at rt. The TFA solution was evaporated to a small volume
2
under a stream of N and dripped into cold ether to precipitate the peptides. The dried crude
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peptides were dissolved in 2 ml of 50% acetonitrile in water and then purified by reversed-phase
®
HPLC using a Discovery Bio Wide Pore C18 column (25 cm x 21.2 mm). After being purified,
the peptide solutions were lyophilized. Peptide purity was deterimined by analytical HPLC using
®
a Discovery Bio Wide Pore C18 column (25 cm x 4.6 mm; solvent A:0.1% TFA/water, solvent
−
1
B: 0.1% TFA/MeCN, flow rate: 1.0 mL・ml , gradient: 10-60% gradient of solvent B over 30
min), and the peptides were characterized by matrix-assisted laser desorption/ionization mass
spectrometry.
Reagents
DMEM, and Bafilomycin A1 were purchased from Sigma-Aldrich. Carfilzomib (LC Laboratories)
and MG132 (Peptide Institute) were purchased. The peroxidase-conjugated anti-FLAG (M2)
monoclonal antibody and anti-β-actin (AC-74) monoclonal antibody were from Sigma-Aldrich.
The anti-CRABP-II polyclonal antibody was form BETHYL.
Cell culture condition and transfection.
HT1080 cells were cultured in DMEM containing 10% heat-inactivated fetal bovine serum (FBS),
2
and penicillin and streptomycin mixture at 37 °C in a humidified atmosphere of 5% CO in air.
HT1080 cells were transfected with the expression vectors for CH6-tagged POI using
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Lipofectamine 2000 (Invitrogen) following the manufacturer’s instructions. After 48 h, the cells
were selected with 500 µg/ml G418 (Roche) for 2 weeks.
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Formation of SNIPER-carrier peptide complex.
2+
To load Ni to NTA moiety of SNIPERs and its derivatives, 10, 12, 15, and 5 were incubated with
2
3 equivalent of NiCl in PBS (-) for 2 h. Then, the reactant was incubated with 1 equivalent of
carrier peptide for 10 min before addition to the cell culture.
Fluorescence imaging.
HT1080 cells were seeded onto glass bottom dish (Greiner Bio-one) (10,000 cells/dish) and
incubated overnight in 2 ml of DMEM containing 10% FBS. The medium was replaced with fresh
one, and compound solution was applied to dish. After the cells had been incubated for 3 h, the
medium was removed and the cells were washed with DMEM containing 10% FBS in case of
washing the cells, and the intracellular distribution of the complexes was observed by Fluorescence
microscope. The observations were performed using a BZ-9000 (Keyence) equipped with a 40´
objective lens.
Western blotting.
Cells were treated as described in Figure legends, washed with PBS (-), lysed in SDS lysis buffer
(1% SDS, 0.1M Tris-HCl and 10% Glycerol, pH 7.4) and boiled for 10 min. Protein concentrations
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were determined using BCA Protein Assay Kit (Thermo Fisher Scientific) and normalized by total
protein concentration in each lysate. After boiling for 5 min with Laemmli buffer, each lysate was
resolved by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) with 5-20%
gradient gel and transferred onto PVDF membrane. After blocking with TBS-T (25 mM Tris-HCl,
137 mM NaCl, 2.68 mM KCl and 0.1% Tween20, pH 7.4) containing 5% skim milk, the membrane
was probed with the antibodies as described in Figure legends. The immunoblots were visualized
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TM
by enhanced chemiluminescence with Clarity Western ECL Substrate (BIO-RAD).
Biotin pull-down assay.
HT1080 cells were transiently transfected with pcDNA3-2´(CH6)-FLAG-CRABP-II in 6-well
plate. The following day, the cells were trypsinized and divided into 3 wells. 48 h after transfection,
cells were treated as described in Figure legend, harvested, and lysed with SDS lysis buffer. After
boiling for 10 min, the lysate was diluted 10 times with pull-down buffer (0.3 M NaCl, 50 mM
Tris-HCl (pH 7.5), 0.5% TritonX-100) and incubated with Streptavidin-Agarose (Upstate Biotech)
at 4 °C for 3 h. The agarose beads were washed with pull-down buffer 4 times, eluted with
2
´Laemmli buffer, and then subjected to SDS-PAGE followed by Western blot analysis.
Cytotoxicity.
HT1080 cells were seeded onto 96-well culture plate (5,000 cells/well) and incubated for 24 h in
DMEM containing 10% FBS. Compound solution in fresh medium was added at each
concentration (1-30 µM). After 24 h, cell viability was evaluated using cell counting kit-8
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(
DOJINDO) following to the manufacture’s protocol. 100% cell viability was calculated from the
wells without peptides 16, 17 and 10. The results were presented as the mean and standard error
values obtained from three independent cultures.
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Supporting Information
Experimental data for the ligands and peptides, and construction of expression plasmids. This
material is available free of charge via the Internet at http:// pubs.acs.org.
Corresponding Author
*
Corresponding authors: Tel: +81-3-3700-1141, Fax: +81-3-3707-6950, E-mail: miki-
naito@nihs.go.jp (M. Naito), demizu@nihs.go.jp (Y. Demizu)
Author Contributions
‡
These authors contributed equally.
T.H., M.N. and Y.D. designed the research and wrote the paper. K.O., T.M., T.S., and M.K.
performed the experiments and analyzed results. All authors discussed the results and commented
on the manuscript.
Funding Sources
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This study was supported, in part, by the Japan Society for the Promotion of Science KAKENHI
grant numbers 26460169 (Y.D.), 16H05090, and 16K15121 (M.N.); by a Grant-in-Aid from the
Research Foundation for Pharmaceutical Sciences (Y.D.); by the Shorai Foundation for Science
and Technology (Y.D.); and by grants for the Project for Cancer Research And Therapeutic
Evolution (P-CREATE) (Y.D.) and Research on the Development of New Drugs (M.N.) from the
Japan Agency for Medical Research and Development (AMED).
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ABBREVIATIONS USED
CRABP-II, cellular retinoic acid-binding protein II; CPP, cell penetrating peptide; DIPEA, N,N-
diisopropylethylamine; DMF, N,N-dimethylformamide; FBS, fetal bovine serum; HBTU, 2-(1H-
benzotriazol-1-yl)-1,1,3,3-tetramethyluronium
hexafluorophosphate;
HOBt,
1-
hydroxybenzotriazole; HPLC, high performance liquid chromatography; IAP, inhibitors of
apoptosis proteins; MeCN, acetonitrile; Ni-NTA, nickel-nitrilotriacetic acid; NMP, N-methyl-2-
pyrrolidone; POI, protein of interest; SDS, sodium dodecyl sulfate; TFA, trifluoroacetic acid; TIPS,
triisopropylsilane; UPS, ubiquitin-proteasome system
Authors will release the atomic coordinates and experimental data upon article publication.
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1
1
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1
1
1
1
1
1
2
2
2
2
2
2
2
2
2
2
3
3
3
3
3
3
3
3
3
3
4
4
4
4
CH6
POI
CH6
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
N
O
O
SH
E3
SH
CH6
N
O
O
S
N
POI
O
O
POI
Ub
Ub
H2O
O
OH2
Ni2+
O
Ub
O
O
O
N
O
O
N
O
O
H2O
H2O
O
O
N
Ni2+
O
N
O
O
O
N
O
N
O
proteasome
Ph
Ph
O
O
O
H
N
H
N
N
N
N
H
N
H
N
H
O
O
O
O
O
O
Ni2+
O
H2O
OH2
N
O
N
N
N
O
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