Benzene fused monocyclic enediynyl amides: Synthesis, reactivity and DNA-cleavage activity in comparison to the corresponding sulfonamides

Article abstract of DOI:10.1016/S0960-894X(02)00029-X

Monocyclic enediynyl amides 2a-2c have been synthesized via the corresponding free amine 5. Kinetic studies in chloroform revealed the reactivity of these amides towards Bergman cyclization to be less than that of the corresponding sulfonamides. However, differential scanning calorimetry (DSC) measurements in the solid state and DNA-cleavage studies in aqueous buffer showed higher reactivity for the amides than the sulphonamides.

Full text of DOI:10.1016/S0960-894X(02)00029-X

Bioorganic & Medicinal Chemistry Letters 12 (2002) 873–877
Benzene Fused Monocyclic Enediynyl Amides: Synthesis,
Reactivity and DNA-Cleavage Activity in Comparison to the
Corresponding Sulfonamides
Amit Basak,a,* Subrata Mandal,a Amit Kumar Dasb and Valerio Bertolasic
aDepartment of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
bDepartment of Biotechnology, Indian Institute of Technology, Kharagpur 721302, India
cDipartimento di Chimica, Universita di Ferrara, Ferrara, Italy
Received 18 September 2001;accepted 7 January 2002
Abstract—Monocyclic enediynyl amides 2a–2c have been synthesized via the corresponding free amine 5. Kinetic studies in
chloroform revealed the reactivity of these amides towards Bergman cyclization to be less than that of the corresponding sulfon-
amides. However, differential scanning calorimetry (DSC) measurements in the solid state and DNA-cleavage studies in aqueous
buffer showed higher reactivity for the amides than the sulphonamides. # 2002 Published by Elsevier Science Ltd.
During our study with N-sulfonamido enediynes 1a–1c,
we had observed1 a small but detectable dependence of
their rates of Bergman cyclization (BC)2À5 on the elec-
tronic nature of the aryl sulfonamide groups. The
presence of electron withdrawing nitro group in 1c
made the cyclization faster (ꢀ1.5 times) as compared to
the sulfonamides with electron donating methyl in 1a or
even hydrogen in 1b. We attributed this perturbation of
kinetics of BC to the greater participation of lone pair
of the ring nitrogen atom in resonance with the sulfone
when electron-withdrawing groups are present in the
aromatic ring. Considering the fact that nitrogen atom
is much more conjugated and essentially planar com-
pared to a sulfonamido nitrogen, a rate enhancement
can be expected if the sulfonamide is replaced by an
amide. With this in mind, we prepared the amido
enediynes 2a–2c and studied their rates of BC. In this
communication, we are reporting our results.
our system. No cyclic enediyne was obtained even in the
presence of strong bases like NaH or KOtBu. Carrying
out the reaction under high dilution also failed to lead
to the desired product. Same thing happened during our
attempt to cyclize the N-tBoc enediynyl mesylate 3a.
Our initial synthetic strategy is shown in Scheme 1. This
was essentially similar to the reported6 synthesis of the
sulfonamido enediynes 1a–1c. Only difference was the
intramolecular cyclization involving the amide nitrogen
and the propargylic mesylate as in 3. Although N-alky-
lation of amides is well known,7 the reaction failed in
The above experience prompted us to adopt a different
strategy. Since intramolecular cyclization worked well
with the nucleophilic sulfonamido nitrogen, it would be
better if the cyclic enediynyl sulfonamide 4a/4b is first
prepared and then deprotected under mild condition to
the free amine 5. The latter, in principle, can be con-
verted to the amides as well as to other range of deri-
vatives. Since an aromatic fused enediynyl sulfonamide
has better thermal stability as compared to the non-
aromatic ones,8 we decided to implement our strategy
*Corresponding author. Fax:+91-3222-55303;e-mail: absk@chem.
iitkgp.ernet.in
0960-894X/02/$ - see front matter # 2002 Published by Elsevier Science Ltd.
PII: S0960-894X(02)00029-X

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A. Basak et al. / Bioorg. Med. Chem. Lett. 12 (2002) 873–877
with benzene fused enediynes. Regarding the choice of
protecting groups, mono or dinitro benzene sulfona-
mide derivatives were used, as these are reported9 to be
easily deprotected under mild conditions. However, due
to the extreme lability of the nitrosulfonamido group
under basic conditions, usually employed in Pd(0)-based
coupling, we had to modify the previously reported
method.6 Two successive Pd(0)-catalyzed coupling10 of
dibromobenzene, first with THP-protected propargyl
alcohol and then with 3-butyn-1-ol afforded the pro-
tected enediynyl alcohol 12 which was then elaborated
into the 4-nitro or 2,4-dinitro benzene sulfonamide 16a/
16b via the azide. Removal of THP,11 conversion to the
mesylate 18a/18b and treatment with K2CO3 in DMF
generated the cyclic enediyne 4a/4b in excellent yield.
Both the enediynes was successfully deprotected with
thiophenol and triethylamine at ambient temperature
and the amine (characterized as the p-toluene sulfonate
salt) was isolated and then converted to the various
amides 2a–2c by conventional procedure (acyl chloride
and triethylamine) (Scheme 2).
The enediynes 2a–2c appeared to be quite stable at
room temperature like the sulfonamido analogues 4a/
4b. Single crystal X-ray analysis of the nitro amide 2b
and nitrosulfonamide 4a revealed very little difference
in the 3-D-structures of the enediynes. The major dif-
ference seems to be in the orientation of the amide or
sulfonamide bearing aromatic ring. In the amide 2b,
the aromatic ring is orthogonal to the plane of the
enediynes whereas in the sulfonamide 4a, the ring is anti
to the enediynes framework (Fig. 1). In solution such as
in CDCl3, these molecules start to cyclize only when
heated to 70 ꢁC and above. Keeping a CDCl3 solution
of the enediynes 2a/2b in a thermostat maintained at
70 ꢁC and by recording the H NMR at different time
1
points the precise kinetics of cyclization could be fol-
lowed. The half-lives of all the enediynes that include
the sulfonamides and the amides were determined and
shown in Table 1 from which it was evident that the
amides were cyclizing at a slower rate as compared to the
sulfonamides. This was contrary to our expectations.
The activation energy of the amide and the sulfonamide
Scheme 1.
Scheme 2.

A. Basak et al. / Bioorg. Med. Chem. Lett. 12 (2002) 873–877
875
Figure 1. X-ray structure of 4a and 2b.
Table 1. Kinetic parameters for the cyclization of the various
enediynes in CDCl3
temperature (ꢀ75 ꢁC) than that for the sulfonamide
for which the corresponding rise started at ꢀ240 ꢁC
(Fig. 2). Thus the onset temperature for BC in solid
state is lower for the amides. Encouraged by this
observation we also checked the DNA-cleavage activity.
Again to our surprise, the amides 2a–2c were able to
cleave the plasmid DNA at micromolar concentrations
(Fig. 3). On the contrary, the sulfonamides did not
show any DNA-cleavage activity even at millimolar
level. Expectedly,the cleavage efficiency was highest
for 2c containing the DNA-bindind acridine moiety
(Fig. 4). Thus our studies indicated that the kinetics of
Bergman cyclization in organic solvents might not be
good criteria for predicting the DNA-cleavage activity,
which is done in aqueous buffer. In the absence of
DNA, both the enediynes are stable in aqueous buffer
under ambient conditions. Thus presence of DNA
somehow activates the amido enediyne towards its
cleavage.
Compd
Rate constant
(per h) at 70 ꢁC
Activation energy
E ]
(Kcal/mol)
Half life
at 70 ꢁC (h)
2a
2b
4a
4b
3.7Â10À3
5.1Â10À3
1.43Â10À2
2.44Â10À2
24
—
20
—
188
136
49
28
also followed the same trend. Thus, the amide 2a has
higher activation barrier as compared to the sulfona-
mide 4a. In a particular series, amide or sulfonamide,
the overall greater electron withdrawal facilitates the
reaction to a certain extent.12 The relative kinetics fol-
lowed the same order even in the presence of 1,4-
cyclohexadiene.
In conclusion, we have synthesized the benzene fused
amido enediynes from the amine as the intermediate.
In organic solvents the sulfonamides showed higher
reactivity whereas in the solid state and in aqueous
buffer the amides showed higher reactivity towards
cyclization as indicated by DSC and DNA-cleavage,
respectively.
The solid-state reactivity of the amides was next
studied by differential scanning calorimetry (DSC).
To our surprise, it was observed that the amides
showed the exothermic rise starting at a much lower

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A. Basak et al. / Bioorg. Med. Chem. Lett. 12 (2002) 873–877
Figure 2. DSC curve of 2b and 4a.
Selected Spectral Data
1-[4-Nitrophenylsulfonyl]-[5,6]-benz-1-aza-cyclodec-3,7-
diyne (4a). White solid;mp 220 ꢁC dec); dH 2.78 (2H, t,
J=5.22 Hz, N–CH2CH2), 3.74 (2H, t, J=5.25 Hz, N–
CH2–CH2), 4.33 (2H, s, N–CH2–CC), 7.25–7.29 (4H, m,
Ar–H), 8.11 (2H, d, J=8.98 Hz, Ar–H), 8.25 (2H, d,
J=8.94 Hz, Ar–H); dC 21.60, 43.41, 51.25, 86.49, 93.66,
98.14, 100.34, 122.92, 124.38, 127.50, 127.63, 127.81,
128.19, 128.77, 133.02, 144.0, 152.43.
Figure 3. Interaction of supercoiled DNA (in Tris–acetate buffer, pH
8.0) and various enediynes in acetonitrile;incubation was continued
up to 48 h and analyzed by agarose (0.7%) gel electrophoresis using
ethidium bromide stain: Lanes 1: DNA;2: DNA+enediyne 2b (40
mmol);3: DNA+enediyne 2a (40 mmol).
1-[2,4-Dinitrophenylsulfonyl]-[5,6]-benz-1-aza-cyclodec-
3,7-diyne (4b). Yellow solid;mp 160 ꢁC (dec); dH 2.76
(2H, t, J=5.22 Hz, N–CH2–CH2), 3.88 (2H, t, J=5.25
Hz, N–CH2–CH2), 4.43 (2H, s, N–CH2–CC), 7.30–7.38
(4H, m, Ar–H), 8.32 (H, dd, J=8.61 Hz, J=2.1 Hz, Ar–
H), 8.50 (H, dd, J=8.77 Hz, J=3.42 Hz, Ar–H), 8.52
(H, d, J=8.77, one signal is obscured); dC 22.32, 43.51,
52.48, 83.93, 87.82, 94.15, 98.75, 120.92, 127.54, 128.56,
128.67, 128.88, 129.28, 130.17, 133.03, 137.44, 151.31.
1 - Benzoyl - [5,6] - benz - 1 - aza - cyclodec - 3,7 - diyne (2a).
Brown solid;mp 78 ꢁC; dH 2.96 (2H, t, J=5.03 Hz, N–
CH2–CH2), 3.92 (2H, t, J=5.01, N–CH2–CH2), 4.21
(2H, s, N–CH2–CC), 7.26–7.42 (7H, m, Ar–H), 7.61
(2H, d, J=2.44 Hz, Ar–H); dC 18.76, 44.23, 50.33,
82.38, 88.04, 93.84, 98.89, 126.25, 126.85, 127.24,
127.37, 127.71, 128.05, 128.20, 128.35, 128.53, 129.06,
129.81, 130.35, 135.56, 171.60.
Figure 4. Interaction of supercoiled DNA (in Tris–acetate buffer, pH
8.0) and various enediynes in acetonitrile: Lanes 1: DNA;2:
DNA+enediyne 4a (1 mmol);3: DNA+enediyne 2c (40 mmol);4:
DNA+enediyne 2b (40 mmol).
Relevant parameters from X-ray structures:
1-[4-Nitrobenzoyl]-[5,6]-benz-1-aza-cyclodec-3,7-diyne
(2b). Pale brown solid;mp 110 ꢁC; dH 2.98 (2H, t,
J=5.29 Hz, N–CH2–CH2), 3.95 (2H, t, J=5.24 Hz, N–
CH2–CH2), 4.16 (2H, s, N–CH2–CC), 7.24–7.36 (4H, m,
Ar–H), 7.77–7.82 (2H, m, Ar–H), 8.26–8.30 (2H, m, Ar–
H); dC 18.56, 44.17, 50.66, 82.56, 88.91, 92.76, 98.19,
123.59, 123.90, 127.57, 127.83, 128.33, 128.51, 129.73,
131.19, 139.40, 140.84, 169.44.
Compd Bond
Bond
C3–C8
distance (A)
distance (A) angle (ꢁ)
2b
4a
N–CO 1.36 C2–N–C10 118.12 3.29
N–C2 1.47 N–C10–C9 113.2
N–C10 1.47 N–C2–C3 111.1
N–S 1.69
C2–N–C10 118.31 3.29
N–C2 1.49 N–C10–C9 115.0
N–C10 1.47 N–C2–C3 119.8
1-[9-Acridinoyl]-[5,6]-benz-1-aza-cyclodec-3,7-diyne (2c).
Brown solid;mp >220 ꢁC; dH 3.35 (2H, t, J=5.21 Hz,

A. Basak et al. / Bioorg. Med. Chem. Lett. 12 (2002) 873–877
877
N–CH2–CH2), 3.97 (2H, s, N–CH2–CC), 4.19 (2H, t,
J=5.2 Hz, N–CH2–CH2), 7.07–7.45 (6H, m, Ar–H),
7.75 (2H, t, J=7.69 Hz, Ar–H), 8.03 (2H, d, J=8.64
Hz, Ar–H), 8.29 (2H, d, J=8.78 Hz, Ar–H); dC 18.55,
43.02, 50.36, 83.32, 88.13, 92.23, 97.86, 122.0, 125.34,
126.92, 127.49, 127.69, 127.96, 128.85, 129.31, 131.19,
140.54, 147.76, 168.23.
2. (a) Jones, R. P.;Bergman, R. G. J. Am. Chem. Soc. 1972,
94, 660. (b) Bergman, R. G. Acc. Chem. Res. 1973, 6, 25. (c)
Lockhart, T. P.;Comita, P. B.;Bergman, R. G. J. Am. Chem.
Soc. 1981, 103, 4082.
3. Semmelhack, M. F.;Neu, T.;Foubelo, F. Tetrahedron Lett.
1992, 33, 3227.
4. Moss, D. K.;Spence, J. D.;Nantz, M. H. J. Org. Chem.
1999, 64, 4339.
5. (a) Nicolaou, K. C.;Zuccarello, G.;Rimer, C.;Estevez,
V. A.;Dai, M. K. J. Am. Chem. Soc. 1992, 114, 7360. (b)
Nicolaou, K. C.;Zuccarello, G.;Ogawa, Y.;Schewiger, E. J.;
Kumazawa, J. J. Am. Chem. Soc. 1988, 110, 4866.
6. Basak, A.;Shain, J. C.;Khamrai, U. K.;Rudra, K. R.;
Basak, A. J. Chem. Soc., Perkin Trans. 1 2000, 1955.
7. (a) Knapp, S.;Gibson, F. S. J. Org. Chem. 1992, 57, 4802.
(b) Luh, T.-Y.;Fung, S. H. Synth. Commun. 1979, 9, 757.
8. (a) Semmelhack, M. E.;Neu, T.;Foubelo, F. Tetrahedron
Lett. 1992, 33, 3277. (b) Nicolaou, K. C.;Liu, A.;Zheng, Z.;
McComb, S. J. Am. Chem. Soc. 1992, 114, 9279.
9. Fukuyama, T.;Cheung, M.;Jow, C.-K.;Hidai, Y.;Kan, T.
Tetrahedron Lett. 1997, 38, 5831.
[5,6]-Benz-1-aza-cyclodec-3,7-diyne (5) 4-toluene sulfo-
nate. dH 2.25 (3H, s, Ar–CH3), 2.79 (2H, t, J=5.51 Hz,
N–CH2–CH2), 3.55 (2H, t, J=5.23 Hz, N–CH2–CH2),
4.05 (2H, s, N–CH2–CC), 7.00 (2H, d, J=7.88 Hz, Ar–
H), 7.60 (2H, d, J=8.08 Hz, Ar–H), 9.77 (2H, bs, NH2).
Acknowledgements
The authors wish to thank DST, Government of India
for funding the project. S.M. thanks CSIR, Government
of India for a fellowship.
10. Sonogashira, K.;Tohda, Y.;Hagihara, N.
Lett. 1975, 17, 4467.
11. Miyashita, N.;Yoshokoshi, A.;Grieco, P. A.
Chem. 1977, 42, 3772.
12. Schmittel, M.;Kiau, S. Chem. Lett. 1995, 953.
Tetrahedron
References and Notes
J. Org.
1. Basak, A.;Bdour, H. M.;Shain, J. C. J. Indian Chem. Soc.
1999, 76, 679.