A facile synthetic route to diazepinone derivatives via ring closing metathesis and its application for human cytidine deaminase inhibitors

Article abstract of DOI:10.1039/c2cc35484e

A variety of diazepinone derivatives were prepared from α-amino acids and amino alcohols by a new synthetic methodology based on ring closing metathesis as a key step. The diazepinones were coupled with ribose derivatives to afford novel diazepinone nucleosides. Among them, (4R)-1-ribosyl-4-methyl-3, 4-dihydro-1H-1,3-diazepin-2(7H)-one (3) showed a potent inhibitory effect (K_i = 145.97 ± 4.87 nM) against human cytidine deaminase.

Full text of DOI:10.1039/c2cc35484e

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COMMUNICATION
A facile synthetic route to diazepinone derivatives via ring closing
metathesis and its application for human cytidine deaminase inhibitorsw
a
a
Minkyoung Kim,z Kondaji Gajulapati,z Chorong Kim,a Hwa Young Jung,a Jail Goo,a
Kyeong Lee,b Navneet Kaur,c Hyo Jin Kang,d Sang J. Chung*d and Yongseok Choi*a
Received 29th July 2012, Accepted 6th October 2012
DOI: 10.1039/c2cc35484e
A variety of diazepinone derivatives were prepared from a-amino
acids and amino alcohols by a new synthetic methodology based
on ring closing metathesis as a key step. The diazepinones were
coupled with ribose derivatives to afford novel diazepinone
nucleosides. Among them, (4R)-1-ribosyl-4-methyl-3,4-dihydro-
1H-1,3-diazepin-2(7H)-one (3) showed a potent inhibitory effect
Fig. 1 Methyl substituted diazepinone nucleoside analogues.
(Ki = 145.97 ꢀ 4.87 nM) against human cytidine deaminase.
of enormous significance in medicinal chemistry.6 Hanson
et al. demonstrated the synthesis of unsymmetrical urea
compounds from cis-1,4-diamines and N,N0-carbonyldiimidazole
(CDI).7 They used an indirect method involving a temporary
organophosphorus reagent for making cyclic phosphorus tethers
using ring closing metathesis (RCM) reaction, which might be
limited for the synthesis of various cyclic urea compounds due to
the strong binding character of the organophosphorus reagent. In
this communication, we have developed a simple, efficient, and
direct method for these seven-membered heterocyclic compounds
via addition of allyl isocyanate to protected amino alcohol and
subsequent RCM reaction with Grubb’s 2nd generation catalyst
under mild conditions to achieve the desired 1,3-diazepinone
derivatives.
Human cytidine deaminase (hCDA) is a key enzyme to
metabolize cytidine analogues used in anticancer and antiviral
agents via a hydrated transition-state intermediate that results
from the nucleophilic attack of zinc-bound water at the active
site.1 hCDA thus catalyses the irreversible deamination
of cytidine and deoxycytidine to uridine and deoxyuridine
analogues and leads to loss of their biological activity or
possession of undesirable side-effects. Moreover, it is generally
overexpressed in cancers resistant to cytidine analogues and
has been considered as an attractive target for the development
of anticancer adjuvants.2 The crystal structure of hCDA bound
to diazepinone-1-ribose (1) showed a CH–p interaction as a key
binding interaction, which is distinguished from that of other
CDA inhibitors.4 The structure revealed a canonical CH–p-
interaction between inhibitor 1 and Phe 137 in the active site.3
To evaluate the substitution effect of the diazepinone ring on its
binding affinity, it was necessary to develop a versatile synthetic
route to generate a new class of diazepinone derivatives (Fig. 1).
Moreover, the cyclic urea moiety in the diazepinone ring is
found in many biologically active natural products and phar-
maceutically relevant compounds, and plays a key role in the
activity.5 Therefore, development of a synthetic methodology
for symmetrical and unsymmetrical diazepinone derivatives is
The synthesis of various substituted 1,3-diazepinones
was accomplished from commercially available natural and
unnatural amino acids or amino alcohols. Initially, L-alanine
was converted to the corresponding p-methoxybenzaldehyde
(PMB)-protected amino alcohol 5, which was reacted with
isocyanate to produce an inseparable mixture of the desired
urea 7 and allylcarbamate 8 in a 9 : 1 ratio. Hence, the
hydroxyl group was protected with a tert-butyldimethylsilyl
(TBS) group to give compound 6. The amine 6 was then
treated with allyl isocyanate to afford a urea compound 9 in an
excellent yield. The TBS group was then deprotected followed
by oxidation and Wittig reaction to furnish a diallyl urea
intermediate 10. Our initial attempts to cyclize 10 by RCM
reaction under various conditions i.e. change of solvents
(CH2Cl2, benzene, and toluene) and/or temperature (room
temperature and heating) were not successful as shown in
Scheme 1.8 This may be due to the unfavourable orientation of
the allyl groups. It is well documented in the literature that
trans-substituted cyclohexane derivatives undergo RCM reaction
under rigorous conditions and lower yield than the corresponding
cis-isomers is obtained.9 Thus, the NH group of the urea
a College of Life Sciences and Biotechnology, Korea University, Seoul
136-701, Korea. E-mail: ychoi@korea.ac.kr; Fax: +82-2-3290-3650;
Tel: +82-2-3290-3650
b College of Pharmacy, Dongguk University-Seoul, Seoul 100-715,
Korea
c Centre for Nanoscience and Nanotechnology, Panjab University,
Chandigarh 160014, India
d BioNanotechnology Research Center, KRIBB and NanoBio Major,
UST, Yuseong, Daejeon 305-333, Korea.
E-mail: sjchung@kribb.re.kr; Tel: +82-42-860-4362
w Electronic supplementary information (ESI) available. See DOI:
10.1039/c2cc35484e
z These authors equally contributed to this work.
c
This journal is The Royal Society of Chemistry 2012
Chem. Commun., 2012, 48, 11443–11445 11443

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Scheme 4 Reagents and conditions: (a) (i) p-methoxybenzaldehyde,
CH2Cl2, Et3N, 4 A molecular sieves, for 3 h, then NaBH4, EtOH,
99%, (ii) TBSCl, Et3N, CH2Cl2, 93%; (b) (i) (Boc)2O, Et3N, THF,
reflux, 24 h, 97%, (ii) DIBAL-H, toluene, ꢁ78 1C, 65%, (iii) Tebbe’s
reagent, THF, rt, 86%; (c) TMSOTf, TEMDA, CH2Cl2, rt, 88%; (d)
(i) allyl isocyanate, THF, 0 1C, 12 h, 100%, (ii) (Boc)2O, Et3N,
DMAP, reflux, 24 h, 97%.
Scheme 1 Reagents and conditions: (a) p-methoxybenzaldehyde, 4 A
molecular sieves, CH2Cl2, then EtOH, NaBH4, 93% (over two steps);
(b) TBSCl, Et3N, CH2Cl2, 99%; (c) allyl isocyanate, THF, 0 1C, 12 h,
78%; (d) (i) HF–pyridine, pyridine, THF or PTSA, MeOH, 3 h, 62%,
(ii) DMP, CH2Cl2, 86%, (iii) CH3+PPh3Iꢁ, NaHMDS, 0 1C, dry
ether, 86%.
Scheme 5 Reagents and conditions: (a) p-methoxybenzaldehyde,
CH2Cl2, Et3N, 4 A molecular sieves, 3 h, then NaBH4, EtOH,
90–96% (over two steps); (b) (i) allyl isocyanate, THF, 0 1C–rt,
18 h, 78–80%, (ii) (Boc)2O, DMAP, Et3N, THF, reflux, 24 h, 95–97%.
Scheme 2 Reagents and conditions: (a) (Boc)2O, Et3N, DMAP, THF,
reflux, 24 h, 96%; (b) 10 mol% Grubb’s 2nd generation catalyst,
CH2Cl2, rt, 3 h, 99%.
derivative 10 was protected with tert-butyloxycarbonyl (Boc) to
afford 11, which was then subjected to RCM reaction by using
Grubb’s 2nd-generation catalyst to obtain the desired seven-
membered ring 12 in a quantitative yield (Scheme 2).
After optimization of the conditions for RCM reaction,
compound 11 was obtained from the corresponding amino
alcohol. Diallyl urea analogues 16 and 19 were also prepared
from the corresponding amino alcohols following a similar
method to that employed for 11, respectively (Scheme 3).
As shown in Scheme 4, L-serine ester was converted to an
allyl amine 21, which was also reacted with isocyanate to
afford compound 23.
Scheme 6 Reagents and conditions: (a) 15 mol% Grubb’s 2nd generation
catalyst, CH2Cl2, rt, 2–3 h; (b) TFA : CH2Cl2 (2 : 1), rt, 3–5 h, 80–95%.
analogues, respectively. Finally, PMB and Boc protecting
groups were deprotected in a single step using excess TFA to
provide the desired unsymmetrical and symmetrical cyclic urea
derivatives (Scheme 6).
In hand with diazepinones, novel diazepinone nucleosides
were synthesized as potential hCDA inhibitors. Thus,
compounds 33, 34, and 37 were coupled with bromosugar 39
via mercury-catalyzed condensation reaction to produce
exclusively single b-isomers 40, 41, and 42, respectively.10 It
was of interest that the coupling reactions produced only
4-methyl diazepinone nucleosides in the case of 41 and 42,
which might be due to the steric hindrance of the methyl
substituents. Finally, the diazepinone nucleosides 40, 41, and
42 were de-protected with liquid NH3–MeOH to furnish final
compounds 1, 2, and 3, respectively (Scheme 7).
For the preparation of the reference compound 1, allyl amine
was coupled with allyl isocyanate followed by RCM reaction to
afford compound 25. Compound 27 was also obtained from
methylallyl amine with the same method (Scheme 5).
The prepared diallyl urea analogues shown in Schemes 3–5
were subjected to RCM reactions to afford the cyclic urea
The high regioselectivity for the 4-methyl isomer of 41 was
confirmed by its 2D NOESY experiment as shown in Fig. 2.
We could observe a correlation between signals of 20H
(5.64 ppm) and 7Hb (3.69 ppm) and no correlation between
signals of 20H (5.48 ppm) and 4H (4.28 ppm).
Scheme 3 Reagents and conditions: (a) p-methoxybenzaldehyde,
CH2Cl2, Et3N, 4 A molecular sieves, for 3 h, then NaBH4, EtOH,
92–98%; (b) (i) allyl isocyanate, THF, 0 1C, 12 h, 78–80% and (ii)
(Boc)2O, Et3N, DMAP, THF, reflux, 24 h, 90–97%; (c) (i) HF–
pyridine, pyridine, THF or PTSA, MeOH, 3 h, 62–75%, (ii) DMP,
CH2Cl2, 85–90%, (iii) CH3+PPh3Iꢁ, NaHMDS, 0 1C, dry ether, 70–78%.
The newly synthesized compounds 2 and 3 were evaluated
for their activities against hCDA in comparison with compound
c
11444 Chem. Commun., 2012, 48, 11443–11445
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Notes and references
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Scheme 7 Reagents and conditions: (a) BSTFA, CH3CN; 39, HgO/
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Fig. 2 2D NOESY experiment of 41.
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Inhibitor
1
2 (Me, S)
3 (Me, R)
Ki
35.3 ꢀ 0.49 (nM) 2.56 ꢀ 0.18 (mM) 146 ꢀ 4.87 (nM)
a
Human cytidine deaminase activity was determined by a direct
spectrophotometric assay based on the decrease in absorbance at
282 nm upon cytidine deamination.
1 (Table 1). Among them, 4R-isomer 3 (Ki = 146 nM) was
more potent than 4S-isomer 2 (Ki = 2.56 mM), which might be
due to the stereochemical preference of 4R-configuration to 4S-
configuration in the active site of hCDA. Both isomers were
found to show competitive inhibition against cytidine deamination
by hCDA, i.e. the compounds bind to the active site of hCDA.
In summary, novel diazepinone derivatives were successfully
synthesized from the corresponding a-amino acids and amino
alcohols by a new and efficient synthetic method using ring
closing metathesis. In addition, novel 4-methyl diazepinone
derivatives were successfully employed for the synthesis of
diazepinone nucleosides, which showed interesting inhibitory
activity against hCDA depending on their stereochemistry of
4-methyl substituents. Further work in this regard is underway
in our laboratory.
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This work was supported by Basic Science Research Program
through the National Research Foundation of Korea (NRF)
funded by the Ministry of Education, Science and Technology
(Grant 313-2007-2-E00642 to Y. C.), a Korea University grant
(K0618131 to Y. C.), and GRRC program (Dongguk 2012-B02
to K. L.) by Gyeonggido, Korea.
c
This journal is The Royal Society of Chemistry 2012
Chem. Commun., 2012, 48, 11443–11445 11445