The first synthesis of a novel 5:7:5-fused diimidazodiazepine ring system and some of its chemical properties

Article abstract of DOI:10.1021/ol8020176

(Chemical Equation Presented) The first synthesis of a novel 5:7:5-fused heterocyclic ring system, a diimidazodiazepine, is reported. The propensity of the ring system to undergo facile, acid-catalyzed nucleophilic addition reactions by neutral carbon and

Full text of DOI:10.1021/ol8020176

ORGANIC
LETTERS
2008
Vol. 10, No. 20
4681-4684
The First Synthesis of a Novel
5:7:5-Fused Diimidazodiazepine Ring
System and Some of Its Chemical
Properties
Raj Kumar, Ravi K. Ujjinamatada, and Ramachandra S. Hosmane*
Laboratory For Drug Design and Synthesis, Department of Chemistry and
Biochemistry, UniVersity of Maryland, Baltimore County (UMBC), 1000 Hilltop Circle,
Baltimore, Maryland 21250
hosmane@umbc.edu
Received August 28, 2008
ABSTRACT
The first synthesis of a novel 5:7:5-fused heterocyclic ring system, a diimidazodiazepine, is reported. The propensity of the ring system to
undergo facile, acid-catalyzed nucleophilic addition reactions by neutral carbon and nitrogen nucleophiles has been explored. The ring system
has potential future applications in mechanistic studies of formation and repair of DNA interstrand cross-links.
Mechanistic studies of formation and repair of DNA inter-
strand cross-links have elicited considerable interest of
chemists, biochemists, and biophysicists alike for decades.1-5
Many bifunctional organic reagents like nitrogen mustards,6
organometallic compounds such as cis-platin,7 and natural
products such as psoralen8 and mitomycin C9 are long known
to cause interstrand cross-links in DNA, and this property
has been extensively explored in cancer chemotherapy.10
A
major problem in using these molecules for mechanistic
studies at the molecular level is the formation of a host of
products that are often unstable, making the isolation and
purification of a specific cross-linked product difficult and
cumbersome.2 Therefore, the challenge is to chemically
synthesize a DNA duplex containing a single cross-link at a
defined site.2 Most of the known work in this area involves
the synthesis of a single-stranded oligonucleotide covalently
linked to one side of a cross-link, which would then be
hybridized with a cDNA strand, and further subjected to
chemical or phtochemical reaction to produce interstrand
(1) Swenson, M. C.; Paranawithana, S. R.; Miller, P. S.; Kielkopf, C. L.
Biochemistry 2007, 46, 4545
.
(2) Noll, D. M.; McGregor Mason, T.; Miller, P. S Chem. ReV. 2006,
106, 277
.
(3) Wilds, C. J.; Noronha, A. M.; Robidoux, S.; Miller, P. S. J. Am.
Chem. Soc. 2004, 126, 9257
(4) Noll, D. M.; Noronha, A. M.; Wilds, C. J.; Miller, P. S. Front. Biosci.
2004, 9, 421
(5) Noronha, A. M.; Noll, D. M.; Wilds, C. J.; Miller, P. S. Biochemistry
2002, 41, 760
(6) Ojwang, J. O.; Grueneberg, D. A.; Loechler, E. L. Cancer Res. 1989,
.
.
.
(9) Remers, W. A. In Anticancer Agents from Natural Products; Cragg,
G. M. K., David G. I., Newman, D. J., Eds.; CRC Press LLC: Boca Raton,
FL, 2005; p 475.
49, 6529.
(7) Kerpel-Fronius, S. Analogue-Based Drug DiscoV. 2006, 385.
(8) Morison, W. L.; Honigsmann, H. Basic Clin. Dermatol. 2007, 38,
(10) McHugh, P. J.; Spanswick, V. J.; Hartley, J. A. Lancet Oncol. 2001,
2, 483.
347.
10.1021/ol8020176 CCC: $40.75
Published on Web 09/25/2008
2008 American Chemical Society

cross-links.4 In this regard, another novel strategy would be
to start from a tricyclic heterocycle such as 1, serving as a
single interstrand cross-link, from which the two DNA
strands could be extended via (deoxy)ribosylation of each
imidazole ring to produce 2, followed by conversion to
phosphoramidite derivatives and oligomerization with a DNA
synthesizer. The presence of four nitrogen atoms in two
imidazole rings offers an additional scope for synthesis of a
variety duplexes extending from different nitrogen atoms.
These duplexes have potential applications for biochemical
and biophysical explorations of DNA formation, structure,
stability, and conformation in addition to DNA repair of
interstrand cross-links.
Scheme 2
An examination of the literature revealed that the target
5:7:5 heterocyclic ring system is yet unknown. We report
here our first entry into such a ring system employing a
representative example 3, containing a removable p-meth-
oxybenzyl (PMB) group attached to each of the two
imidazole rings. Heating diaminomaleonitrile 4 (Scheme 1)
with triethyl orthoformate in dioxane yielded formimidate
5.11 The reaction of 5 with p-methoxybenzylamine catalyzed
by aniline hydrochloride formed formimidine 6,12 which
Scheme 3
Scheme 1
underwent intramolecular cyclization in the presence of DBU
to form imidazole derivative 7.13 The treatment of latter with
p-methoxybenzyl isocyanate resulted into a mixture of 8 and
9.14 The complete coversion of 8 into 9 was achieved by
treating the mixture with DBU in acetonitrile.14 The reaction
of isolated 9 with triethyl orthoformate yielded the target
heterocycle 3. We did not observe the reported rearrangement
of compound such as 8 into an oxopurine such as 10.14 Such
Figure 1. Selected HMBCs of 12.
4682
Org. Lett., Vol. 10, No. 20, 2008

a
1
Table 1. H NMR (δ, DMSO-d6, J in Hz in Parentheses) Data of Compounds 3 and 11-14
compd
H-2
H-5
H-12
H-14 and H-18
H-1′
H-3′ and H-7′
H-9 (N)
H-2′′and H-6′′
3
8.92 s
8.75 s
5.51 s
7.33 d
(8.7)
-
5.08 s
7.29 d
(8.7)
7.19 d
(8.6)
7.33 d
(8.6)
7.20 d
(8.72)
7.22 d
(8.72)
-
-
11
7.87 s
7.69 s
7.83
7.53 s
7.65 s
7.50 s
7.50 s
-
4.63 dd
(15.1, 18.3)
4.72 s
9.82 s
9.47 s
9.68 s
9.4 s
6.68 d
(8.6)
6.72 d
(8.6)
6.56 d
(9.2)
5.80 d (H-2′′)
(8.72)
12
(CDCl3)
13
5.13 q
(14.2)
-
7.08 d
(8.6)
-
s
4.62 dd
(15.1, 18.3)
4.60 dd
14
7.85 s
-
-
(15.1, 18.3)
a Assignments are based on DEPT, HMQC, and HMBC experiments.
a rearrangement, however, has been limited to the use of
N-tosylisocyanate, but not other isocyanates.14 This was
further corroborated by the facile ring-closure of 9 to form
3. All intermediates and final product were fully characterized
by spectroscopic and analytical data.15
analytical data. Interestingly, 12 was converted into 11 when
heated with TFA at 60 °C for 1 h. This suggests that the
reaction proceeds by first addition of anisole, followed by
selective cleavage of the N-3 PMB group. As TFA is often
used to remove the PMB group from heterocyclic rings,17
the observed deprotection of one of the imidazole rings under
these conditions is not totally surprising.
The generality of the above reaction was studied using
two other electron-rich carbon nucleophiles, including N,N-
dimethylaniline and 1,2,3-trimethoxybenzene. Thus, when
3 (1 mmol) was heated separately (Scheme 3) at 60 °C for
6 h with N,N-dimethylaniline (5 mL) or 1,2,3-trimethoxy
benzene (5 mL) in TFA (10 mL), compounds 13 (78%) or
14 (80%) were formed, respectively.
The structures of 3 and 11-14 were determined by 1D
and 2D NMR experiments (some important peaks and
correlations are presented in Figure 1 with an example of
12; and Tables 1-3), including HMQC, HMBC and DEPT
experiments. In the HMBC spectra, H-5 showed the cor-
relations with C-6a and C-11; H-1′ showed correlation with
C-8, C-3,′ and C-7′; C-8 showed correlations with H-1′. The
addition of anisole/1,2,3-trimethoxybenzene/N,N-dimethy-
laniline at position 9a was determined by the correlation of
H-2′′ (or/and) and H-6′′ with C-9a; two-bond coupling
enhancement between C-9a and H-9 (N) and H-9 (N) and
C-8.
The above reactions failed to proceed at room temperature
as well as at 60 °C in the absence of acid catalysis by TFA.
The attempted reactions with nitrogen nucleophiles, including
benzylamine and n-butylamine, failed to produce any prod-
ucts at room temperature with or without TFA even after
6 h. However, intractable multiple products were formed
upon heating the reaction mixture at 60 °C in the presence
The core tricyclic structure of 3 containing 14 π electrons
is aromatic by the Hu¨ckel rule. Nevertheless, with six
nitrogen atoms and a conjugated carbonyl group present in
the heterocyclic ring system, compound 3 is anticipated to
be considerably electrophilic. To explore this aspect a little
further, we set out to treat 3 with a few carbon and nitrogen
nucleophiles. The carbon nucleophiles attempted include
anisole, N,N-dimethylaniline, and 1,2,3-trimethoxybenzene,
all of which contain electron-donating substituent(s) on their
aromatic rings. Thus, the reaction of a mixture of 3 (1 mmol),
anisole (5 mL), and TFA (10 mL) at 60 °C for 3 h (Scheme
2) formed a novel product 11 that was isolated, purified
(81%), and characterized.
To throw more light on the pathway of formation of 11
from 3, the latter (1 mmol) was treated with a mixture of
TFA (10 mL) and anisole (5 mL)16 at rt for 12 h (Scheme
2), which yielded a mixture of 11 (10%) and 12 (60%) that
was found to be an adduct of anisole by spectroscopic and
Table 2. 13C NMR (δ, DMSO-d6) Data of Compounds 3 and
11-14a
C
3
11
12 (CDCl3)
13
14
C-2
C-5
148.9 137.5
150.3 145.9
160.2 154.3
166.3 155.8
138.3
146.6
154.6
156.2
64.2
121.0
134.4
46.9
129.0
43.4
129.9
127.4
137.2 137.2
145.9 146.0
154.7 154.2
155.8 156.6
64.7 63.4
121.3 122.0
134.7 134.9
C-6a
C-8
C-9a
C-10
C-11
C-12
-
-
-
64.6
121.0
134.8
-
(11) Sun, Z.; Hosmane, R. S. Synth. Commun. 2001, 31, 549.
(12) Yahya-Zadeh, A.; Booth, B. L. Synth. Commun. 2001, 31, 3225.
(13) Yahyazadeh, A.; Sharifi, Z. Phosphorus, Sulfur, Silicon, Relat. Elem.
2006, 181, 1339.
47.0
-
-
-
-
C-14 and C-18 129.8
C-1′
C-3′ and C-7′ 129.7 129.4
C-2′′ and C-6′′ 127.7
-
(14) Dias, A. M.; Cabral, I.; Proenca, M. F.; Booth, B. L. J. Org. Chem.
2002, 67, 5546.
43.4 40.6
42.8 42.9
129.4 129.9
127.1 122.8 (C-2′′)
(15) See Supporting Information.
(16) Buenadicha, F. L.; Bartolome, M. T.; Aguirre, M. J.; Avendano,
C.; Sollhuber, M. Tetrahedron: Asymmetry 1998, 9, 483.
(17) Miki, Y.; Hachiken, H.; Kashima, Y.; Sugimura, W.; Yanase, N.
Heterocycles 1998, 48, 1.
-
a Assignments are based on DEPT, HMQC, and HMBC experiments.
Org. Lett., Vol. 10, No. 20, 2008
4683

1
Table 3. Three-Bond H-C13 Coupling (HMBC) in Compounds 3 and 11-14
H
3
11
12
13
14
H-2
H-5
H-12
H-14 and C-18
H-1′
H-3′ and H-7′
H-9(N)
H-2′′ and H-6′′
C-12
C-6a
C-10 and C-11
C-6a and C-11
-
-
C-10 and C-11
C-6a and C-11
C-2, C-14 and C-18
C-12
C-10 and C-11
C-6a and C-11
-
-
C-10 and C-11
C-6a and C-11
-
C-2, C-14 and C-18
C-12
C-6a, C-8, C-3′ and C-7′
C-1′
-
-
C-8, C-3′ and C-7′
C-1′
C-8, C-3′ and C-7′
C-1′
C-8, C-3′ and C-7′
C-1′
C-8, C-3′ and C-7′H-
C-1′
C-8a, C-9aa
C-9a
C-8a, C-9aa
C-9a
C-8a, C-9aa
C-9a
C-8a, C-9aa
C-9a (H-2′′)
-
a Two-bond coupling enhancement observed.
or absence of TFA. The results were no different when
stoichiometric amounts of nucleophiles were employed for
the reactions.
The attempts to induce reaction of 3 (1 mmol) with a
mixture of phenol (5 mL) and TFA (10 mL) resulted in the
formation of o- and p-phenol adducts (see Supporting
Information) and were not separated, whereas reaction of 3
(1 mmol) with aniline (5 mL)-TFA (10 mL) mixture led to
multiple products (>8) as detected by TLC.
have explored the electrophilicity of the ring system employ-
ing carbon and amine nucleophiles. The system is reasonably
stable toward both carbon and nitrogen nucleophiles under
physiological temperature and pH, but undergoes facile acid-
catalyzed Michael-type conjugate addition reactions. While
neutral, electron-rich carbon nucleophiles produce relatively
clean products, those with nitrogen nucleophiles were found
intractable.
No reaction occurred when 3 (1 mmol) was treated with
nitrobenzene (5 mL)-TFA (10 mL) mixtue proving that the
reaction is feasible only with nucleophiles bearing electron
donating substiuents with partcipation in resonance.
In conclusion, we have synthesized a novel 5:7:5-fused
heterocycle containing a diimidazodiazepine system that has
potential applications in mechanistic studies of DNA inter-
strand cross-links and repair in addition to explorations of
DNA structure, function, stability, and conformation. We
Acknowledgment. This research was supported by grants
(#1 R01 GM087738-01A1 and #1 R21 AI071802) from the
National Institutes of Health.
Supporting Information Available: Experimental details,
spectra, and spectral data of all compounds. This material is
available free of charge via the Internet at http://pubs.acs.org.
OL8020176
4684
Org. Lett., Vol. 10, No. 20, 2008