The synthesis of distamycin analog containing phosphonyl group

Article abstract of DOI:10.1080/10426500701418299

In order to obtain high biological activity compound, a series of distamycin analog containing phosphonyl group were synthesized by chloroform reaction and coupling reaction using DCC/HOBT as promoting additives.

Full text of DOI:10.1080/10426500701418299

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Phosphorus, Sulfur, and Silicon
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The Synthesis of Distamycin
Analog Containing Phosphonyl
Group
Yong Ye a b c , Shang-Bin Zhong a , Ruo-Yu Liu a , Li-
Feng Cao a , Cun-Jiang Liu a , Jun-Liang Yang a & Yu-
Fen Zhao b
a Department of Chemistry, Key Laboratory
of Chemical Biology and Organic Chemistry ,
Zhengzhou University , Zhengzhou, China
b State Key Laboratory of Elemento-Organic
Chemistry , Nankai University , Tianjin, 300071,
China
c Key laboratory of Bioorganic Phosphorus Chemistry
& Chemical Biology (Ministry of Education) ,
Tsinghua University , Beijing, China
Published online: 23 Aug 2007.
To cite this article: Yong Ye , Shang-Bin Zhong , Ruo-Yu Liu , Li-Feng Cao , Cun-
Jiang Liu , Jun-Liang Yang & Yu-Fen Zhao (2008) The Synthesis of Distamycin Analog
Containing Phosphonyl Group, Phosphorus, Sulfur, and Silicon and the Related
Elements, 182:10, 2251-2257, DOI: 10.1080/10426500701418299
To link to this article: http://dx.doi.org/10.1080/10426500701418299
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Phosphorus, Sulfur, and Silicon, 182:2251–2257, 2007
Copyright © Taylor & Francis Group, LLC
ISSN: 1042-6507 print / 1563-5325 online
DOI: 10.1080/10426500701418299
The Synthesis of Distamycin Analog Containing
Phosphonyl Group
Yong Ye
Department of Chemistry, Key Laboratory of Chemical Biology and
Organic Chemistry, Zhengzhou University, Zhengzhou, China;
State Key Laboratory of Elemento-Organic Chemistry, Nankai
University, Tianjin 300071, China; Key laboratory of Bioorganic
Phosphorus Chemistry & Chemical Biology (Ministry of Education),
Tsinghua University, Beijing, China
Shang-Bin Zhong
Ruo-Yu Liu
Li-Feng Cao
Cun-Jiang Liu
Jun-Liang Yang
Department of Chemistry, Key Laboratory of Chemical Biology
and Organic Chemistry, Zhengzhou University, Zhengzhou, China
Yu-Fen Zhao
State Key Laboratory of Elemento-Organic Chemistry,
Nankai University, Tianjin 300071, China
In order to obtain high biological activity compound, a series of distamycin analog
containing phosphonyl group were synthesized by chloroform reaction and coupling
reaction using DCC/HOBT as promoting additives.
Keywords Biological activity; DNA; distamycin; polyamides
INTRODUCTION
Many research efforts have been aimed at targeting specific sequences
in DNA with synthetic ligands with the idea of designing both drugs
Received March 2, 2007; accepted April 9, 2007.
The authors would like to thank the Chinese National Science Foundation (No.
20602032), Education Department of Henan Province, and Zhengzhou University for
financial support.
Address correspondence to Yong Ye, Department of Chemistry, Key Laboratory of
Chemical Biology and Organic Chemistry, Zhengzhou University, Zhengzhou 450052,
China. E-mail: yeyong03@mail.nankai.edu.cn
2251

2252
Y. Ye et al.
and molecular probes for DNA polymorphism.1 Recently, the natural
product distamycin, netropsin and their analog have attracted consid-
erable attention on the part of synthetic and biological chemists because
they recognize and bind in the minor groove of predetermined DNA se-
quences with high affinity and specificity.2 Since these polyamides can
permeate living cell membranes, they have the potential to control spe-
cific gene expression.3 Therefore, these polyamides are one of the most
widely studied class of agents characterized by high level of sequence
specificity and they are still an interesting class of DNA ligands which
demonstrate to possess several biological activities.2−3
Our group found some amino acid containing phosphonyl group had
good biological activity.4 In order to obtain high biological activity com-
pound, a series of polyamides containing phosphonyl group are synthe-
sized. The synthetic route is shown in Scheme 1.
RESULTS AND DISSCUSION
The compounds 4 and 6 are our targeted molecule, which consist of
phosphoryl group, polyamides and amino acid methyl ester. Compounds
3 are synthesized using chloroform reaction. In this step, the choice of
SCHEME 1 Synthetic route of title compounds.

Synthesis of Distamycin Analog
2253
solvent is important. The hydrochloric acid salt of amino acid methyl
ester is diffluent in water or methol. But in these solvents, compound
1 will be transfer to relevant carboxylic acid (NO2PyCOOH) or ester
(NO2PyCOOMe). Compared to DMF and acetone, chloroform is best
solvent for this reaction. After Et3N is added, the hydrochloric acid salt
of amino acid methyl ester can well solved in chloroform at ultrasonic.
In the synthesis of compounds 4, TLC is needed to monitor the
progress of the hydrogenation. After this step is finished, phospho-
rochloridic acid alkyl ester is dropwised into it. The coupling reaction
finished in 24 h and compounds 4 can be easily obtained by column
chromatography.
There were two elements in the synthesis of compound 5. One is
the qualitative reduction of the nitro group of 3 to an amino group.
The termination of hydrogenation in time is very important. Although
the hydrogenation is fulfilled almost quantitatively, the amino products
are rather unstable. To achieve the optimum result, TLC are employed
to monitor the progress of the hydrogenation. The other one is the prepa-
ration of an active ester of the carboxyl component. Adding excess of
DCC facilitated the formation of the active ester. In this step, methanol
and ethanol are better solvent than other solvent.
Similar to the synthesis of 5, TLC is needed to monitor the progress
of the hydrogenation in the syntheisis of 6. However, alcohol can not
used as solvent in this step due to the alcoholysis of phosphorochloridic
acid alkyl ester. After compared to other solvent, CH2Cl2 and acetic acid
ethyl ester are good solvent for this step.
1H NMR, IR, and ESI-MS spectra of the obtained compounds are
recorded. Compounds 3 and 4 exhibit one N-Me signal and one O-Me
signal, which appears a single peak at ca. 3.9 and 3.8, respectively.
31P NMR and 1H–31P HMQC spectra of the obtained compounds 4 also
are recorded. From the 31P NMR, a single peak is observed arround
3.9 ppm. There are two kind of amide signals appears at ca. 5.0 and
1
ca. 6.2 ppm in H NMR. The peak observed at δ = 5 ppm assign to
the H atom on P NH bond, due to its interaction with P resonance at
δ = 3.9 ppm. Compounds 5 and 6 exhibit three N–Me signals and one
O-Me, all of them appears at ca. 4.18 ppm. ESI mass spectra for all
compounds showed both [M+H]+ and [M+Na]+ ion.
CONCLUSION
In conclusion, we developed a good route for the synthesis of distamycin
analog containing phosphonyl group. The significant feature of this pro-
cedure is that there is no need of protecting and deprotecting amino

2254
Y. Ye et al.
group. The reactions are convenient and efficient. The biological activ-
ity of compounds 4 and 6 are currently being examined.
EXPERIMENTAL
General
1H NMR and 31P NMR spectra were measured by using a Bruker AC-
P400 spectrometer with TMS and 85% H3PO4 as the internal and exter-
nal reference respectively and with CDCl3 or DMSO as the solvent. IR
spectra was recorded as KBr pellets on a BRUCK spectrometer. Mass
spectra was acquired in positive ion mode using a Bruker ESQUIRE-
LCTM ion trap spectrometer equipped with a gas nebulizer probe, ca-
pable of analyzing ions up to m/z 20000. Solvents were purified and
dried by standard procedures. Compounds 1 and 2 were synthesized
according to Refs,5,6 respectively.
The Synthesis of Compound 3
To a solution of compound 2c 1.010 2 g (5.0 mmol) in 20 ml of CH2Cl2
was added Et3N (0.8 mL). After stirred 1/2 h and filtrated, the active
amino acid solution was obtained. Separately, a solution of compound 1
1.3110 g (4.8 mmol) in 5 ml of CH2Cl2 was dropped to the active amino
acid solution, followed by stirring 24 h. Then the mixture solution was
concentrated in vacuo. Column chromatography of the residue (eluant
with CHCl3 and MeOH 40:1) provided light yellow power of compound
3c in 70%.
3a. Yield: 83%; m.p. 147–148◦C; 1H NMR (400MHz,CDCl3) :7.56 (d,
1H, J = 1.4Hz), 7.16 (d, 1H, J = 1.7Hz),6.48 (d, 1H, J = 6.4Hz) (-NH),
4.68 (m, 1H) (-CH),3.98 (s, 3H),3.80 (s, 3H),1.50 (d, 3H, J = 7.1H) (-CH3)
; IR υ/cm−1: 3354, 3125, 2966, 1720, 1665, 1526, 1373, 1314, 1212, 750;
ESI-MS: 255.8 [M+H]+, 277.8[M+Na]+.
3b. Yield: 84%; m.p. 153–154◦C; 1H NMR : 7.58 (d, 1H, J =
1.7Hz),7.18 (d, 1H, J = 1.9Hz), 6.49 (br, 1H,) (-NH), 4.17 (d, 2H, J
= 5.3Hz) (-CH2), 3.98 (S, 3H), 3.82 (S, 3H); IR υ/cm−1: 3399, 3135,
2958, 1724, 1665, 1520, 1324, 1231, 755; 241.5; ESI-MS: [M+H]+, 263.3
[M+Na]+,
3c. Yield: 70%; m.p. 96–97◦C; 1H NMR: 7.57 (d, 1H, J = 2.0Hz), 7.18
(d, 1H, J = 2.0 Hz), 6.43 (d, 1H, J = 8.4 Hz) (-NH), 4.64 (m, 1H) (-CH),
3.97 (S, 3H), 3.79 (S, 3H), 2.25 (m, 1H) (-CH), 1.0 (d, 3H, J = 9.6 Hz),
0.98 (d, 3H, J = 10Hz); IR υ/cm−1:3367, 3138, 2945, 1747, 1645, 1522,
1315, 752; ESI-MS: 284.6 [M+H]+,306.6[M+Na]+.

Synthesis of Distamycin Analog
2255
1
3d. Yield: 87%; m.p. 99100◦C; H NMR: 7.56 (d, 1H, J = 1.6Hz),
7.16 (d, 1H, J = 1.8Hz) 6.41 (d, 1H, J = 8.1Hz) (-NH) 4.68 (m, 1H) (-
CH) 3.96 (S, 3H) 3.78 (S, 3H) 1.97 (m, 1H), 1.48 (m, 1H), 1.26 (m, 1H),
0.96(m,6H,2-CH3); IR υ/cm−1: 3312, 3130, 2953, 1742, 1642, 1527, 1313,
1207, 754; ESI-MS: 298.6 [M+H]+320.6 [M+Na]+.
3e. Yield: 66%; m.p. 118–119◦C; 1H NMR: 7.54 (S, 1H), 7.30 (m, 3H)
(ph-H), 7.13 (m, 2H,) (ph-H) 6.99 (d, 1H, J = 2.0Hz) 6.30 (d, 1H, J =
7.6Hz) (-NH) 4.97 (m, 1H) (-CH), 3.95 (S, 3H) 3.77 (S, 3H) 3.21 (m, 2H)
(-CH2-ph); IR υ/cm−1: 3344, 3131, 1738, 1635, 1527, 1403, 1313, 751;
ESI-MS: 330.1 [M-H]−.
The Synthesis of Compound 4
To a solution of compound 3 (0.31 mmol) in 15 ml of CH2Cl2 was added
Pd/C catalyst (10%), and the mixture was stirred under a slight posi-
tive pressure of H2 at room temperature for 18 h. The catalyst was re-
moved by filtration through Celite and the filtrate was added 1 ml Et3N.
The solution was cooled to −10◦C and 0.2 ml (EtO)(n-C4H9O)POCl was
dropped. The result solution was stirred for 24 h at this temperature.
After filtrated and concentrated in vacuo, a yellow oil was obtained. Pu-
rification by column chromatography (CHCl3:CHOH = 20:1), compound
4 was obtained in oil.
4a. 1H NMR (400 MHz,CDCl3): δ6.50 (s,1H), 6.35 (s,1H), 6.34 (d, 1H),
5.13 (d, 1H, J = 10.4 Hz) 4.67 (m,1H) (-CH), 4.08 (m,4H) (2-OCH2), 3.84
(s,3H), 3.75 (s,3H), 1.66 (m,2H) (-CH2), 1.47 (d,3H, J = 7.2Hz) (-CH3),
1.37(m,5H) (-CH2-CH3), 0.92 (t, 3H, J = 7.4Hz) (-CH3); 31P NMR: 3.96;
IR υ/cm−1: 3272, 2959, 1743, 1648, 1526, 1457, 1206, 1024; ESI-MS:
390.3 [M+H]+, 412.3 [M+Na].
4c. 1H NMR: 6.52 (s,1H), 6.35 (s,1H), 6.24 (d,1H,J = 8.8 Hz) (-NH),
4.98 (d,1H,J = 10.4 Hz), 4.64 (m,1H) (-CH), 4.09 (m,4H) (2-OCH2), 3.84
(s,3H), 3.76 (s,3H), 2.22 (m,1H) (-CH), 1.67 (m,2H) (-CH2), 1.37 (m,5H)
(-CH2-CH3), 0.94 (m,9H) (3-CH3); 31P NMR:3.91; IR υ/cm−1: 3436, 3268,
2962, 1741, 1653, 1509, 1462, 1239, 1025; ESI-MS: 418.3 [M+H]+, 440.3
[M+Na]+.
4d. 1H NMR: 6.50 (s,1H), 6.34 (s,1H), 6.12 (d,1H,J = 8.4 Hz) (-NH),
4.83 (d, 1H, J = 7.4 Hz), 4.71 (m,1H) (-CH), 4.12(m,4H) (2-OCH2), 3.84
(s,3H), 3.75 (s,3H), 1.67 (m,6H) (3-CH2), 1.37 (m,5H) (-CH2-CH3), 0.94
(m,9H) (3-CH3); 31P NMR: 3.98; IR υ/cm−1: 3423, 2959, 1741, 1652,
1581, 1526, 1440, 1204, 1025; ESI-MS: 432.4 [M+H]+.

2256
Y. Ye et al.
The Synthesis of Compound 5
To a solution of NO2PyPyCOOH (0.513 g, 1.7 mmol) in 18 ml of
DMFwas added HOBt (0.2254 g, 1.7 mmol) and DCC solution (0.4326 g,
2.1 mmol DCC in 3 ml CH2Cl2). The solution was stirred for 4 h at room
temperature. After filtrated, the active ester solution was obtained.
Separately, a solution of compound 3a 0.4271 g (1.7 mmol) in 20 ml
of CH3OH was mixed with Pd/C catalyst (10%), and the mixture was
stirred under a slight positive pressure of H2 at room temperature for
12 h. The catalyst was removed by filtration through Celite and the
filtrate was added to the active ester. Then 1 ml Et3N was added to
the mixture solution, followed by stirring 24 h. The desiccator was re-
moved by filtration, and the filtrate was concentrated in vacuo. Column
chromatography of the residue (eluant with CHCl3 and MeOH 20:1)
provided compound 5a 0.4589 g (0.92 mmol) in 54%.
1
5a. Yield: 54%; m.p. 142–144◦C; H NMR (400MHz,CDCl3): δ8.65
(s,1H), 8.04 (s, 1H), 7.58 (s, 2H), 7.47 (s, 1H), 7.27 (s, 1H), 7.17 (s, 1H),
6.69 (s, 1H), 6.46 (s, 1H), 4.75 (d, 1H, J = 8.8Hz) (-CH), 4.03 (s, 3H),
3.90 (s, 3H), 3.81 (s, 3H), 3.75 (s, 3H), 1.52 (d, 3H, J = 7.2Hz) (-CH3);
IR υ/cm−1: 3398, 3130, 2930, 1738, 1649, 1527, 1400, 1309, 1206, 1112,
812; ESI-MS: 497.7 [M-H]− 522.3[M+Na]+.
5b. Yield: 44%; m.p. 237–239◦C; 1H NMR: 10.30 (s, 1H), 9.99 (s, 1H),
8.43 (t, 1H), 8.17 (s, 1H), 7.59 (s, 1H), 7.28 (s, 1H), 7.25 (s, 1H), 7.04 (s,
1H), 6.94 (s, 1H), 3.96 (s, 3H), 3.92 (s, 2H) (-CH2), 3.86 (s, 3H), 3.80 (s,
3H), 3.66 (s, 3H); IR υ/cm−1: 3124, 2925, 1740, 1657, 1555, 1438, 1406,
1307, 810, 774, 747; ESI-MS: 484.2 [M-H]−.
1
5c. Yield: 51%; m.p. 141–43◦C; H NMR: 8.69 (s, 1H), 7.52 (s, 1H),
7.60 (s, 1H,) ,7.42 (s, 1H), 7.38 (s, 1H), 7.18 (s,1H), 6.68 (s, 1H), 6.65 (s,
1H), 6.38 (s, 1H), 4.73 (m, 1H,) (-CH) , 4.04 (s, 3H), 3.91 (s, 3H) ,3.81 (s,
3H) ,3.75 (s, 3H), 2.25 (m, 1H) (-CH) ,1.01 (d, 3H, J = 7Hz),0.99 (d, 3H,
J = 7 Hz); IR υ/cm−1: 3422, 3286, 3138, 3114, 2961, 1739, 1652, 1589,
1523, 1465, 1311; ESI-MS: 526.3 [M-H]− 550.3[M+Na]+.
1
5d 7. Yield: 57%; m.p. 135–137◦C; H NMR: 10.31 (s, 1H) , 9.98 (s,
1H), 8.32 (s, 1H), 8.20 (d, 1H, J = 1.64Hz), 7.60 (s, 1H), 7.28 (s, 1H), 7.23
(s, 1H), 7.05 (s, 2H), 4.43 (m, 1H) (-CH), 3.97 (s, 3H), 3.87 (s, 3H), 3.79 (s,
3H), 3.64 (s, 3H), 1.52 (m, 1H), 1.71 (m, 1H), 1.61 (m, 1H), 0.91 (d, 3H,
J = 4.9 Hz),0.87 (d, 3H, J = 6.4Hz); IR υ/cm−1: 3450, 3351, 3308, 3130,
2953, 1737, 1648, 1526, 1367, 1311, 1225; ESI-MS: 540.2 [M-H]−542.3
[M+H]+ 564.3[M+Na]+.

Synthesis of Distamycin Analog
2257
The Synthesis of Compound 6
To a solution of compound 4a 0.1530 g (0.31 mmol) in 15 ml of CH2Cl2
was added Pd/C catalyst (10%), and the mixture was stirred under a
slight positive pressure of H2 at room temperature for 18 h. The cat-
alyst was removed by filtration through Celite and the filtrate was
added 1 ml Et3N. The solution was cooled to −10◦C and 0.2 ml (EtO)(n-
C4H9O)POCl was dropped. The result solution was stirred 24 h at this
temperature. After filtrated and concentrated in vacuo, a yellow oil
was obtained. Purification by column chromatography (CHCl3:CHOH
= 20:1), 0.0823 g (1.29 mmol) compound 6a was obtained in 41% yield.
6a. 1H NMR (400MHz,CDCl3): :8.70 (s, 1H), 8.11 (s,1H), 7.28 (m,2H),
6.82 (s,1H), 6.76 (s,1H), 6.64 (d, 1H, J = 7.3Hz), 6.47 (s, 2H), 6.22 (d,
1H, J = 9.3Hz) (-NH), 4.70 (m, 1H0) (-CH), 4.02 (m, 4H) (2-OCH2),
3.92(s, 3H), 3.87 (s, 6H), 3.74 (s, 3H), 1.58 (m, 2H) (-CH2), 1.49 (d, 3H,
J = 7.1Hz) (-CH3), 1.29 (m, 5H) (-CH2-CH3), 0.84 (t, 3H, J=7.4Hz) (-
CH3);31P NMR: -6.82; IR υ/cm−1: 3285, 2956, 1738, 1643, 1529, 1463,
1256, 1022, 777; ESI-MS: 634.3 [M+H]+,656.3 [M+Na]+.
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