Synthesis of Three-Dimensional (Di)Azatricyclododecene Scaffold and Its Application to Peptidomimetics

Article abstract of DOI:10.1002/chem.202101440

A novel sp³ carbon-rich tricyclic 3D scaffold-based peptide mimetic compound library was constructed to target protein-protein interactions. Tricyclic framework 7 was synthesized from 9-azabicyclo[3,3,1]nonan-3-one (11) via a gold(I)-catalyzed Conia-ene reaction. The electron-donating group on the pendant alkyne of cyclization precursor 12 b–e was the key to forming 6-endo-dig cyclized product 7 with complete regioselectivity. Using the synthetic strategy for regioselective construction of bridged tricyclic framework 7, a diazatricyclododecene 3D-scaffold 8 a, which enables the introduction of substituents into the scaffold to mimic amino acid side chains, was designed and synthesized. The peptide mimetics 21 a–u were synthesized via step-by-step installation of three substituents on diazatricyclododecene scaffold 8 a. Compounds 21 a–h were synthesized as α-helix peptide mimics of hydrophobic ZZxxZ and ZxxZZ sequences (Z=Leu or Phe) and subjected to cell-based assays: antiproliferative activity, HIF-1 transcriptional activity which is considered to affect cancer malignancy, and antiviral activity against rabies virus. Compound 21 a showed the strongest inhibitory activity of HIF-1 transcriptional activity (IC₅₀=4.1±0.8 μM), whereas compounds 21 a–g showed antiviral activity with IC₅₀ values of 4.2–12.4 μM, suggesting that the 3D-scaffold 8 a has potential as a versatile peptide mimic skeleton.

Full text of DOI:10.1002/chem.202101440

Accepted Article
Accepted Article
Title: Synthesis of Three-Dimensional (3D) (Di)azatricyclododecene
Scaffold and its Application to Peptidomimetics
Authors: Kohei Umedera, Taiki Morita, Atsushi Yoshimori, Kentaro
Yamada, Katoh Akira, Hiroyuki Kouji, and Hiroyuki Nakamura
This manuscript has been accepted after peer review and appears as an
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of the final Version of Record (VoR). This work is currently citable by
using the Digital Object Identifier (DOI) given below. The VoR will be
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the VoR from the journal website shown below when it is published
to ensure accuracy of information. The authors are responsible for the
content of this Accepted Article.
To be cited as: Chem. Eur. J. 10.1002/chem.202101440
Link to VoR: https://doi.org/10.1002/chem.202101440
01/2020

10.1002/chem.202101440
Chemistry - A European Journal
RESEARCH ARTICLE
Synthesis of Three-Dimensional (3D) (Di)azatricyclododecene
Scaffold and its Application to Peptidomimetics
Kohei Umedera,[a] Taiki Morita,[a,b] Atsushi Yoshimori,[c] Kentaro Yamada,[d,e] Akira, Katoh, [e,f] Hiroyuki
Kouji,[e,f] and Hiroyuki Nakamura*[a,b]
[a]
K. Umedera, Dr. T. Morita, Prof. Dr. H. Nakamura
School of Life Science and Technology
Tokyo Institute of Technology
Yokohama, 226-8503, Japan
[b]
Dr. T. Morita, Prof. Dr. H. Nakamura
Laboratory for Chemistry and Life Science, Institute of Innovative Research
Tokyo Institute of Technology
Yokohama, 226-8503, Japan
E-mail: hiro@res.titech.ac.jp
[c]
[d]
Dr. A. Yoshimori
Institute for Theoretical Medicine, Inc.
26-1, Muraoka-Higashi 2-chome, Fujisawa, 251-0012, Japan
Dr. K. Yamada
Faculty of Agriculture Department of Veterinary Sciences
University of Miyazaki
Miyazaki, 889-2192, Japan
[e]
[f]
Dr. H. Kouji, Dr. K. Yamada, Dr. A. Kato
Faculty of Medicine
Oita University
1-1, Idaigaoka, Hasama-machi, Yufu-city, Oita, 879-5593, Japan
Dr. H. Kouji, Dr. A. Katoh
Oita University Institute of Advanced Medcine, Inc.
17-20, Higashi kasuga-machi, Oita-city, Oita 870-0037, Japan
Supporting information for this article is provided via a link at the end of the document.((Please delete this text if not appropriate))
Abstract: A novel sp3 carbon-rich tricyclic 3D scaffold-based peptide
diversity are highly needed for targeting a wide variety of proteins.
However, the biased use of aromatic rings in the synthesis of drugs
or their candidates tends to make the molecule sp2 carbon-rich and
planar.[1,2] Conventional small molecule libraries have been
constructed by sp2 carbon-rich planar molecules and mainly targeted
enzymes. In order to discover small molecule modulators for
promising biological targets such as protein-protein interactions
(PPIs),[3] there is a growing interest in employing sp3 carbon-rich 3D
scaffolds to access unexplored chemical spaces. Synthetic strategies
to construct structurally diverse compound collections, such as
diversity-oriented synthesis[4] and biology-oriented synthesis,[5] have
provided compounds with unique biological activities, including PPI
inhibition[6] and protein-DNA interaction inhibition.[7] Psuedo-natural
product design,[8] which combines two different natural product
scaffolds in an sp3 carbon-rich manner, has provided an autophagy
inhibitor.[9] Compound libraries based on 3D natural product scaffolds
mimetic compound library was constructed to target protein-protein
interactions. Tricyclic framework
6 was synthesized from 9-
azabicyclo[3,3,1]nonan-3-one 9 via a gold (I)-catalyzed Conia-ene
reaction. The electron-donating group on the pendant alkyne of
cyclization precursor 11b-e was the key to forming 6-endo-dig
cyclized product 6 with complete regioselectivity. Using the synthetic
strategy for regioselective construction of bridged tricyclic framework
6,
a diazatricyclododecene 3D-scaffold 7a, which enables the
introduction of substituents into the scaffold to mimic amino acid side
chains, was designed and synthesized. The peptide mimetics 20a-h
were synthesized via step-by-step installation of three substituents on
diazatricyclododecene scaffold 7a. Compounds 20a-h were
synthesized as α-helix peptide mimics of hydrophobic ZZxxZ and
ZxxZZ sequences (Z = Leu or Phe) and subjected to cell-based
assays: antiproliferative activity, HIF-1 transcriptional activity which is
considered to affect cancer malignancy, and antiviral activity against
rabies virus. Compound 20a showed the strongest inhibitory activity
of HIF-1 transcriptional activity (IC50 = 4.1 ± 0.8 μM), whereas
compounds 20a-g showed antiviral activity with IC50 values of 4.2-
12.4 μM, suggesting that the 3D-scaffold 7a has potential as a
versatile peptide mimic skeleton.
have shown
a
wide range of biological activities.[10] These
observations strongly support the high utility of 3D scaffolds in drug
discovery.
The FDA has recently approved Venetoclax (ABT-199) as a first-in-
class small molecule-based PPI inhibitor targeting the Bcl-2/Bax
interaction.[11] It was rationally designed based on the structure of
hydrophobic groove binding site in Bcl-xL.[12] Therefore, the design of
peptidomimetics targeting PPIs has been recognized as a promising
strategy for the rational development of small molecule-based
inhibitors.[13] The first small molecule-based α-helix mimetic was
reported by Rees et al.[14] They utilized 1,6-disubstituted indane as a
template for two adjacent amino acid chains of a protein α-helix motif.
Introduction
Molecular shape is one of the most fundamental factors in protein
molecular recognition. Therefore, compound libraries with structural
1
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RESEARCH ARTICLE
Pioneering work was accomplished by Hamilton et al., who reported
that an α-helix mimetic of the α-helical domain of smooth muscle
myosin light-chain kinase (smMLCK) based on the terphenyl scaffold
1 was able to inhibit PPI between calmodulin and smMLCK (Figure
1a).[15] Inspired by their simple and rational molecular design concept
of peptidomimetics based on aromatic scaffolds with peptide side-
chains, a variety of scaffolds, such as benzamide 2,[16] pyrdazine 3,[17]
and pyrroloprimidine 4,[18] have been developed to mimic the α-helix
structure. However, these scaffolds are primarily dependent on
aromatic compounds, and the biased use of aromatic rings for
designing peptidomimetics limits their therapeutic targets as other
conventional drugs. Peptides are chirality-rich and structurally
complex; therefore, sp3 carbon-rich scaffolds can be considered as
suitable scaffolds for designing small molecule-based peptide
mimetics. Arora et al. desgined an α-helix mimetic based on a non-
aromatic oligooxopiperazine scaffold 5.[19] The peptidomimetic was
found to inhibit PPI between hypoxia-inducible factor (HIF)-1α and
p300, a promising target for cancer therapy.[20] These results suggest
the importance of compound complexity in designing peptidomimetics.
vaccine if the symptoms have not yet appeared. However, the fatality
rate is approximately 100% upon the appearance of the symptoms,
and no therapeutic drugs have been reported.[22] Rabies virus RNA is
known to be condensed by nucleoprotein oligomers into helical
nucleocapsids, and this nucleoprotein-RNA complex constitutes an
essential template for replication by RNA polymerase. The C-terminal
α-helix 16 of the rabies nucleoprotein, containing the FxxFL sequence
(Phe438, Phe441, and Leu442), contributes to robust oligomer
formation.[23] We also predicted that the FxxFL sequence of the rabies
virus nucleoprotein could be mimicked using a similar strategy to
design a peptidomimetic of the LLxxL sequence of HIF-1α.
Herein we report the development of azatricyclododecene 7 and
diaztricyclododecene 8 as novel 3D scaffolds (Figure 1c). Tricyclic
framwork of 7 and 8 was insipired by adding another ring to bridged
bicyclic structure 6, which was employed in our previous work[21]
.
Peptidomimetic 9 was designed based on scaffold 8, and its
compound libraries were constructed. The newly designed
peptidomimetics characterized by high threedimensionality and
precise arrangement of substitutents mimicking peptide side-chains
could expand the chemical space and discover bioactive compounds.
Cell-based assays were conducted to evaluate the antiproliferative
activity, inhibitory effect on HIF transcriptional activity, and anti-rabies
virus activity of the synthesized compounds.
Results and Discussion
A synthetic strategy for the designed bridged tricyclic is shown in
Scheme 1a. We envisioned that the the desired tricyclic framework 7
could be constructed from amine 10 via gold (I)-catalyzed Conie-ene
reaction[24]. Tertiary amine 10 was expected to be easily obtained by
propalgylation of 9-azabicyclo[3,3,1]nonan-3-one (11) which is
known to be readily prepared by Mannich cyclization.[25,26]
Figure 1. Structure of small molecule-based peptidomimetics: (a) structures of
previously designed α-helix mimetics, (b) bicyclo[3.3.1]non-2-ene scaffold (6),
(c) (di)azabicyclo scaffolds (6 and 7) and 3D scaffold-based peptidomimetic (8).
We
previously
reported
α-helix
mimetics
based
on
bicyclo[3,3,1]non-2-ene as a 3D scaffold 6 (Figure 1b).[21] In contrast
to aromatic rings, the bridged bicyclic scaffold was rich in sp3 carbons
and highly three-dimensional. The peptide mimetics were designed to
reproduce the three leucine residues (Leu818, Leu819, and Leu822)
of the C-terminal helix (helix 3) of HIF-1α. Although the mechanism of
action has not been clarified, the molecules can inhibit HIF
transcriptional activity. The design of peptidomimetics based on rigid
3D scaffolds would be an efficient strategy for exploring the chemical
space and discovering compounds with beneficial biological activities.
In addition to HIF transcriptional activity, PPI via the α-helix plays a
pivotal role replicating rabies virus. Rabies is an infectious disease
caused by the rabies virus and can be treated with a post-exposure
Scheme 1. (a) Retorosynthetic analysis of azatricyclododecen 7, (b) Synthesis
of azatricyclododecene 7a. Reaction conditions: a) propargyl bromide, K2CO3,
MeCN, rt, 2.5 h; b) TBSOTf, 2,6-lutidine, CH2Cl2, -78 ºC to 0 ºC, 40 min; c)
JohnPhosAuCl (10 mol%), AgOTf (15 mol%), toluene/MeOH = 10:1, 40 ºC, 24
h. TBS = tert-butyldimethylsilyl, Tf = trifluoromethanesulfonyl, Johnphos = (2-
biphenyl)di-t-butylphosphine
Treating 9-azabicyclo[3,3,1]nonan-3-one (10), which was
synthesized via three component coupling of 1,3-acetonedicarboxylic
acid, glutaric dialdehyde, and ammonia,[25,26] with propargyl bromide
afforded the corresponding tertiary amine 10 in 88% yield. By treating
2
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10.1002/chem.202101440
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RESEARCH ARTICLE
ketone 10 with TBSOTf and 2,6-lutidine, silyl enol ether 12a was
With a successful construction of bridged tricyclic skeleton, we
turned our attention to the synthesis of diazatricylododecene 8
(Scheme 2), which enables the introduction of substituents into the
scaffold to mimic amino acid side chains as shown in Figure 1b. To
embed one more nitrogen atom into the tricyclic framework 7, imide
14 was selected as the starting material. Reduction of imide 14 with
LiAlH4, followed by removal of the benzyl group, and subsequent
protection of the resulting secondary amine with the Cbz group
afforded diol 15 in 43% yield in three steps. The oxidative cleavage of
trans-configured diol 15 using NaIO4 afforded dialdehyde 16.[28] After
N-propargylation using propargyl iodide 18,[29] the corresponding
tertiary amine 19 was isolated in 33% yield in three steps. Cyclization
precursor 20 with a siloxymethyl group on the alkyne was prepared
quantitatively by transforming ketone 19 into silyl enol ether.
Thereafter, the substrate 20 was subjected to the gold(I)-catalyzed
Conia-ene reaction. As a result, an alkyl group on the alkyne
expectedly enabled the selective formation of the 6-endo-dig cyclized
product. The subsequent removal of the Cbz group produced the
desired diazatricyclododecene 8a in 79% yield in two steps.
obtained as
a precursor for the bridged tricyclic skeleton in
quantitative yield. Thereafter, 12a was subjected to gold (I)-catalyzed
Conia-ene reaction.[24] The desired 6-endo-dig cyclization proceeded
in the presence of a catalytic amount of JohnphosAuCl and AgOTf to
provide azatricyclododecene 7a in 44% yield with the generation of 5-
exo-dig cyclized product 13a in 17% yield.
To improve the yield of 6-endo-cyclized product 7 in a highly
regioselective manner, we investigated the gold (I)-catalyzed
cyclization of 12. Screening of ligands and silver salts did not
significantly improve regioselectivity (see Table S1). Thereafter, the
effects of substituent R on the pendant alkyne were examined (Table
1). It has been reported that the regioselectivity of the gold(I)-
catalyzed intramolecular cyclization depends on the electronic effect
of the substituents.[27] Therefore, we tested various types of
precursors 12a-i with different substituents on the alkyne moiety.
When substrate 12b, which has 4-methoxyphenyl group on alkyne
was treated with cationic gold catalyst, the desired 6-endo-dig
cyclized product 7b was obtained in good yield (75%) with complete
regioselectivity (entry 2). Similarly, the use of alkyl groups, such as
the siloxymethyl group (entry 3), phthalimidylmethyl group (entry 4),
and methyl group (entry 5), led to the selective formation of six-
membered rings to provide the corresponding products in good yields
(7c: 67%, 7d: 55%, 7e: 66%). In contrast, electron-withdrawing
groups such as the trifluoromethyl group (entry 6), ethoxycarbonyl
group (entry 7), and amide group (entry 8) selectively induced 5-exo-
dig cyclization to give products 13f-h as a single diastereomer.
Iodoalkyne 12i was not converted into the corresponding cyclized
products 7i and 13i; however, it resulted in a complex mixture (entry
9). These results suggest that electron-donating groups on the alkyne
prefer the 6-endo cyclization mode.
Table 1. Investigation of regioselectivity of the gold(I)-catalyzed cyclizationa
Scheme 2. Synthesis of diazatricyclododecene 8a. Reaction conditions: a)
Yieldb (%) of
LiAlH4, THF, 90 °C, 3.5 h; b) Pd/C, H2, MeOH, 50 °C, 4 h; c) CbzOSu, Na2CO3,
Products
entry
substrate
R
H2O, 1,4-dioxane,
0 °C, 2.5 h; d) NaIO4, H2O, Et2O, rt, 19 h; e) 1,3-
7/13
acetonedicarboxylic acid, NH3, H2O, 0 °C to rt, 46 h; f) 19, K2CO3, MeCN, rt, 7.5
h; g) TBSOTf, Et3N, CH2Cl2, −78 °C to 0 ºC, 10 min; h) JohnPhosAuCl, AgOTf,
toluene/MeOH = 10:1, 40 °C 1.5 h; i) Rh/Al2O3, H2, MeOH, 50 °C, 11 h. Cbz =
Carbobenzyloxy, OSu = oxysuccinimide.
1c
2c
3c
4
12a
12b
12c
12d
12e
12f
H
4-MeOC6H5
TBSOCH2
PhthNCH2
Me
7a/13a
7b/13b
7c/13c
7d/13d
7e/13e
7f/13f
44/17
75 d/0
67 d/0
55 d/0
66d/0
With
a
novel diazatricyclo scaffold 8a, we designed
peptidomimetics by introducing three substituents, mimicking the
leucine residue (R = i-Bu) or phenylalanine residue (R = Bn), on the
tricyclic scaffold (Figure 2a). The validity of the designed molecule 21
as a mimetic of helix 3 was evaluated by pharmacophore modeling
using LigandScout 4.4.[30] Conformers of the designed molecules
were generated using ‘iCon Fast’ option and screened to assess
whether the generated structures could achieve three hydrophobic
features derived from the target peptides. Compound 21a was found
to reproduce the spatial orientation of the LLxxL sequence in HIF-1α
(Figure 2b). Similarly, compound 21b mimicked the spatial
arrangement of the FxxFL sequence in the nucleoprotein of the rabies
virus (Figure 2c). These results suggest that the designed skeletal
molecule 21 may serve as a versatile peptide mimic.
5
6
F3C
0/25d (45)f
0/50d
7
12g
12h
12i
EtOCO
n-BuNHCO
I
7g/13g
7h/13h
7i/13i
8
0/36d
9
0/0e
[a] Standard conditions: JohnPhosAuCl (10 mol%), AgOTf (15 mol%),
toluene/MeOH = 10:1, 80 °C, 13.5–24 h. [b] Isolated yield. [c] The reaction was
performed at 40 °C. [d] Single diastereomer. [e] Complex mixture. [f] Recovery
of 13g in parentheses. Ph
phthalimidyl methyl, Et = ethyl, Bu = butyl.
= phenyl, TMS = trimethylsilyl, PhthNCH2 =
3
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Due to its the potential as a peptidomimetic, a compound library of
mimetics 21 was constructed via step-by-step installation of three
substituents on the diazatricyclododecene scaffold 8a (Scheme 3A).
For diazatricyclododecene 8a, the first substituents were introduced
to secondary amine moiety by reductive amination to afford tertiary
amines 22a and 22b. Thereafter, azides 23a and 23b were prepared
through carbonyl reduction with LiAlH4, mesylation of the resulting
alcohol, and azidation using NaN3. Subsequent Staudinger reduction
furnished amines 24a and 24b. The second substituents were
introduced by condensation with the corresponding carboxylic acids
to afford amides 25a-d. The structure of amide 25b was
unambiguously determined by X-ray crystallographic analysis, and
the stereoselective installation of an azide group was confirmed.
Finally, the third substituent was introduced through a sequence of
TBS deprotection and esterification to provide the desired
peptidomimetics 21a-h.
Figure 2. Design of peptidomimetics based on diazatricyclododecene scaffold.
(a) Structure of designed peptidomimetic 21, (b) Superimposition of 21a and
helix 3 of HIF-1α (PDB ID: 1L8C), (c) Superimposition of 21b and rabies virus
nucleoprotein (PDB ID: 2GTT).
4
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RESEARCH ARTICLE
Scheme 3. Construction of compound library. (A) Synthesis of helix 3 mimetics. (B) Derivatization of R3 group. (C) Derivatization of R2 group. (D) Derivatization of
R1 group.. Trt = trityl; Boc = tert-butoxycarbonyl; PMB = p-methoxybenzyl, Bn = benzyl, Ac = acetyl, DCE = 1,2-dichloroethane, Ms = methanesulfonyl, NMM = N-
methylmorpholine, EDCI = 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide, HOBt = 1-hydroxybenzotriazole, DMF = N,N-dimethylformamide, TFA = trifluoroacetic
acid, TBAF = tetrabutylammonium fluoride, DMAP = 4-dimethylaminopyridine.
For drug development, the modular synthesis of derivatives with
various substituents on a scaffold is highly required. Therefore, the
compound library was further expanded by assembling various
functional groups rather than isobutyl or benzyl group. As a result,
the derivatization of R3 was first demonstrated as shown in Scheme
3B. After TBS deprotection of intermediate 25a, eight more
substituents were introduced as R3 via esterification. Diverse
functional groups, including carboxylic acid, amide, heterocycles,
amine, and phenol were tolerated, and 21i-p were obtained. To
diversify the R2 group (Scheme 3C), amine 24a was coupled with
carboxylic acids 28 and 26 to afford 25f and 25g, respectively. It was
also possible to introduce the Boc group into the R2 group, and the
corresponding carbamate 25h was obtained. Following the same
protocols as in Scheme 3A, trisubstituted 21q-s with the Bn group
as R3 were provided. As a variation of the R1 group, a phenoxy group
was introduced (Scheme 3D). Conjugation of diazatricyclododecene
8a and 4-tert-butoxybenzaldehyde via reductive amination afforded
tertiary amine 22c, which was converted to primary amine 24c
through 23c following the established procedure shown in Scheme
3A. After introducing isobutyl group to afford 25i, acidic removal of
both TBS and tert-Bu groups, followed by condensation with
isovaleric acid afforded diester 21t, was performed. Instead of
diester, the treatment of amide 25j with TBAF, followed by a
sequence of esterification and acidic removal of the tert-Bu group
presented phenol 21u.
antiviral activity (Table 2). Prior to the following luciferase reporter
gene assay, the MTT assay was conducted to evaluate the
antiproliferative activity of helix 3 mimetics 21a-h against human
epithelioid cervical carcinoma HeLa cells and Neuro 2a (N2a) cells.
All compounds inhibited the growth of N2a cells more significantly
compared to HeLa cells (entries 3-10). Compound 21a was the most
potent to inhibit the growth of both HeLa and N2a cells with IC50
values of 10.3 ± 0.8 μM and 2.1 ± 0.6 μM, respectively (entry 3).
To verify the α-helix mimic strategy, the inhibitory effect on HIF
transcriptional activity was evaluated using a cell-based reporter
gene assay. HeLa cells transfected with a hypoxic response element
(HRE)-dependent luciferase reporter gene were incubated under
hypoxic conditions in the presence of compounds, and their IC50
values were determined (Table 2). YC-1,[32] an inhibitor of HIF-1
activity, was used as a positive control. Among the compounds
synthesized, compound 21a (entry 1) showed the strongest
inhibitory activity (IC50 = 4.1 ± 0.8 μM), with a level similar to YC-1
(entry 9). However, 21a also inhibited the growth of HeLa cells with
IC50 value of 10.3 ± 0.8 μM. Therefore, the cytotoxicity of 21a may
affect the inhibition of HIF transcriptional activity. Among compounds
with low cytotoxicity against HeLa cells (MTT IC50 > 30 μM),
compound 21c (entry 5) was the most potent inhibitor of HIF
transcriptional activity (IC50 = 9.1 ± 1.8 μM).
Antirabies viral activity was also examined. Rabies virus RNA
fused with Gaussia luciferase reporter was incubated with N2a cells
in the presence of compounds up to 18 μM. IC50 values were
determined by measuring the luciferase activity in the cell
supernatant secreted extracellularly. Favipiravir (T-705),[33] an
antiviral agent, was used as a positive control. Compounds 21a-g
were found to exhibit antiviral activity with IC50 values of 4.2–12.4 μM
(entries 3–9), suggesting that these compounds are more potent
than the known antiviral T-705. Since the antiproliferative inhibitory
activities of 21a-g against N2a cells are comparable to the inhibition
of anti-rabies viral activity, the observed antiviral activity may be
attributed to cytotoxicity against host cells. However, there was no
correlation between the IC50 values of the MTT assay against N2a
cells and the luciferase reporter gene assay for antiviral activity.
Therefore, at least part of the inhibitory effect could be attributed to
the antiviral effect, indicating the potential of peptidomimetics to be
developed as antiviral drugs.
Molecular shape of synthesized compounds were compared with
approved drugs in DrugBank database (v.5.1.7) using principle
moment of inertia (PMI)[31] based on their lowest-energy
conformations generated by ‘iCon Fast’ option of LigandAcout4.4.
(Figure 3). While approved drugs were congested along the rod or
disc-like axis, our synthesized compounds were widely distributed
around the right center field of the triangle. The analysis suggests
that compared to conventional drugs, our compounds are more
three-dimensional, which has been a highly demanded feature for a
bioactive compound library.
Table 2. Evaluation of bioactivity of helix 3 mimetics 21a-h
Inhibition of HIF
Anti-rabies
Antiproliferative activity: transcriptional
entry
compound
viral activity:
IC50 (μM)[a]
IC50 (μM)[a]
activity:
IC50 (μM)[a]
HeLa
N2a
Figure 3. PMI analysis of synthesized compounds and approved drugs in
DrugBank database.
1
2
3
4
21a
21b
21c
21d
10.3 ± 0.8
15.9 ± 2.6
> 30
2.1 ± 0.6
3.4 ± 1.0
9.2 ± 2.0
5.6 ± 0.4
4.1 ± 0.8
11.0 ± 0.1
9.1 ± 1.8
21.2 ± 2.2
11.0 ± 3.6
4.2 ± 1.2
12.4 ± 4.3
9.7 ± 3.0
We selected compounds 20a-h as mimics of hydrophobic ZZxxZ
and ZxxZZ sequences (Z = Leu or Phe), which exist in helix 3 and
rabies nucleoprotein, respectively, and performed cell-based
assays: anti-proliferative activity, HIF-1 transcriptional activity, and
> 30
5
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RESEARCH ARTICLE
[4]
[5]
a) S. L. Schreiber, Science 2000, 287, 1964-1969; b) W. R. J. D.
Galloway, A. Isidro-Llobet, D. R. Spring, Nat. Commun. 2010, 1, 1-13;
c) C. J. Gerry, S. L. Schreiber, Curr. Opin. Chem. Biol. 2020, 56, 1-9.
a) S. Wetzel, R. S. Bon, K. Kumar, H. Waldmann, Angew. Chem. Int.
Ed. 2011, 50, 10800-10826; Angew. Chem. 2011, 123, 10990-11018;
b) H. van Hattum, H. Waldmann, J. Am. Chem. Soc. 2014, 136, 11853–
11859.
5
21e
16.9 ± 4.3
25.7 ± 0.4
> 30
3.9 ± 1.2
4.8 ± 0.1
11.8 ± 1.6
17.8 ± 1.7
12.5 ± 2.7
18.9 ± 6.0
11.7 ± 4.2
> 30
11.6 ± 0.9
12.1 ± 0.5
8.3 ± 3.3
> 18
6
21f
7
21g
8
21h
> 30
[6]
[7]
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[b]
[b]
[b]
9
YC-1
T-705
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2.9 ± 1.3
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[b]
[b]
[b]
10
-
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-
37.7
[a] Indicated values are mean ± SD of single experiment conducted
in triplicate. [b] Not determined.
[8]
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We
have
developed
a
novel
3D-shaped
diazatricyclododecene scaffold featuring a constrained bridging
tricyclic core. Synthetic studies on the gold(I)-catalyzed
cyclization of monoaza substrate 12 revealed that the electron-
donating group on the pendant alkyne is the key to the formation
of 6-endo-dig cyclized product 7 with complete regioselectivity.
The established synthetic strategy allowed the generation of the
diazatricyclododecne scaffold 8a, and the stepwise assembly of
the three substituents resulted in the generation of diversely
functionalized compounds 21a-u. Biological assays of designed
mimics of helix-3 of HIF-1α and the α-helix 16 of rabies virus
nucleoprotein indicated that some helix-mimetic compounds of
the hydrophobic ZZxxZ and ZxxZZ sequences (Z = Leu or Phe)
inhibited HIF transcriptional activity and/or anti-rabies viral
activity, revealing that our designed diazatricyclododecene 3D-
scaffold 8a has potential to be a versatile peptide mimic skeleton.
We believe that peptide mimicry based on rigid 3D scaffolds can
provide a new perspective for generating bioactive compounds.
Further development of novel 3D scaffolds and bioactive
compounds based on these scaffolds is currently being
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Conflict of interest
The authors declare no conflict of interest.
Keywords: 3D scaffold • chemical space • gold catalysis •
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RESEARCH ARTICLE
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7
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RESEARCH ARTICLE
Entry for the Table of Contents
Three-dimensional (3D) scaffolds have the potential to provide unique bioactivity, which cannot be achieved by conventional flat
aromatic ring- based compounds. (Di)azatricyclododecene scaffold with a bridged tricyclic system was developed and applied to design
peptidomimetics with a 3D scaffold. The designed peptidomimetics showed inhibition of HIF transcription activity and antiviral activity
toward rabies virus, both of which α-helix peptide mediated interaction play a pivotal role.
8
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