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Y. Wang et al. / European Journal of Medicinal Chemistry 133 (2017) 197e207
at room temperature for 2 h. Oligonucleotides were purified by 20%
denaturing polyacrylamide gel electrophoresis. Radiolabeling was
carried out according to the standard protocols. Quantification of
radiolabeled oligonucleotides was carried out using a Phosphor-
image equipped with ImageQuant Version 5.2 software. For all
Phosphorimage autoradiogram, the top dark spot that migrated
slowest is considered as DNA cross-link product and the bottom
dark spot considered as the single-stranded ODN, which were
determined using molecular ladder [15,19]. All cross-linking yields
were subtracted from the control experiment with DNA and drug
4.1.4. 4,4,5,5-Tetramethyl-2-(3,4,5-trimethoxy-2,6-
dimethylphenyl)-1,3,2-dioxaborolane (14)
To a stirred solution of 13 (3.88 g, 14.2 mmol) in anhydrous THF
(40 mL) was added dropwise a 2.2 M solution of n-BuLi (7.7 mL,
ꢀ
17 mmol) at ꢂ78 C via cannula over a 2 min period under argon.
ꢀ
The cloudy solution was stirred at ꢂ78 C for 30 min. Then, iso-
propoxyboronic acid pinacol ester (3.47 mL, 17 mmol) was added
ꢀ
ꢀ
at ꢂ78 C under argon via syringe. The mixture was allowed to stir
at ꢂ78 C for 30 min, warm slowly to room temperature, and stirred
for 6 h. The mixture was quenched with aqueous 1 M HCl solution,
extracted with 3 ꢃ 30 mL EtOAc, the organic layer was washed with
water and brine, dried over sodium sulfate, and concentrated under
reduced pressure then purified through column chromatography
1
13
2 2
without addition of H O . H NMR and C NMR spectra were taken
on 300 MHz or 500 MHz spectrophotometer. High resolution masss
pectrometry was performed at the University of California-
Riverside and University of Wisconsin-Milwaukee Mass Spec-
trometry Lab on an atmospheric-pressure chemical ionization
1
(5% EtOAc/Hexane) to give 14 (3.32 g 73%) as colorless oil. H NMR
(300 MHz, CDCl
12H). C NMR (75 MHz, CDCl
3
):
d 3.91 (s, 3H), 3.79 (s, 6H), 2.28 (s, 6H), 1.41 (s,
13
(
APCI) TOF mass spectrometer or electron spray injection mass
spectrometer (ESI). The purity was determined by RP-HPLC on a
.6 ꢃ 250 mm RP-C18 column with 254 nm detection, which
confirmed that all compounds had ꢁ95% purity.
3
):
d
149.7,147.2,130.3, 83.9, 60.7, 60.5,
þ
25.0, 15.1. HRMS (ESI): m/z calcd. for C17
H
27
O
5
B [M] 321.1982,
4
found 321.1983.
4
.1.5. 2-(2,6-Bis(bromomethyl)-3,4,5-trimethoxyphenyl)-4,4,5,5-
tetramethyl-1,3,2-dioxaborolane (4a)
A solution of 14 (1.28 g, 4 mmol), NBS (1.71 g 9.6 mmol) and
AIBN (65.6 mg 0.4 mmol) in anhydrous CCl (30 mL) was stirred to
4.1.1. 2-(2,6-Bis(bromomethyl)-4-methoxyphenyl)-4,4,5,5-
tetramethyl-1,3,2-dioxaborolane (2a)
A solution of 7 (1.31 g, 5 mmol), NBS (1.87 g 10.5 mmol), and
4
AIBN (82.1 mg 0.5 mmol) in anhydrous CCl
reflux with a light for 2 h. The mixture was allowed to cool to room
temperature. The solvent was evaporated and 50 mL CH Cl added.
4
(30 mL) was stirred to
reflux under a light for 2 h. The mixture was allowed to cool to
room temperature. After evaporation of the solvent followed by
addition of 20 mL CH Cl , the organic layer was washed with water
2 2
2
2
The organic layer was washed with water and brine, dried over
sodium sulfate, and concentrated under reduced pressure then
purified through column chromatography (30% DCM/Hexane) to
and brine, dried over sodium sulfate, and concentrated under
reduced pressure then purified through column chromatography
(2.5% EtOAc/Hexane) to give 4a (0.53 g 28%) as white solid: mp
ꢀ
1
ꢀ
1
give 2a (0.63 g 30%) as white solid: mp 103e104 C; H NMR
300 MHz, CDCl ): 6.85 (s, 2H), 4.84 (s, 4H), 3.84 (s, 3H), 1.46 (s,
2H). C NMR (125 MHz, CDCl
96e98 C; H NMR (300 MHz, CDCl
(s, 3H), 1.48 (s, 12H). C NMR (75 MHz, CDCl ): 152.7, 147.4, 132.8,
3
)
d
4.90 (s, 4H), 3.99 (s, 6H), 3.91
13
(
1
3
d
3
d
13
3
):
d
160.7, 146.4, 115.7, 84.0, 55.3,
84.5, 61.2, 60.6, 27.6, 25.1. HRMS (ESI): m/z calcd. For C17
[M] 477.0193, found 477.0179.
25
H O
5
BBr
2
[MþH]þ
þ
3
4.1, 25.1. IT-TOF-MS (APCI): m/z calcd. for C15
H
21
O
3
BBr
2
419.0026, found 419.0022.
4
.1.6. (3,5-Bis(bromomethyl)-4-(4,4,5,5-tetramethyl-1,3,2-
dioxaborolan-2-yl)phenoxy) (tert-butyl) dimethylsilane (18)
A solution of 17 (4.1 g, 11.8 mmol), NBS (5.11 g, 28.4 mmol) and
AIBN (194 mg, 0.118 mmol) in anhydrous CCl (100 mL) was stirred
4.1.2. 2-(3,5-Dimethoxy-2,6-dimethylphenyl)-4,4,5,5-tetramethyl-
1,3,2-dioxaborolane (11)
To a stirred solution of 10 (1.88 g, 7.7 mmol) in anhydrous THF
4
(
9
40 mL) was added dropwise a 2.5 M solution of n-BuLi (3.7 mL,
to reflux under a light for 2 h. The mixture was allowed to cool to
room temperature. After evaporation of the solvent followed by
addition of 100 mL CH Cl , the organic layer was washed with
2 2
ꢀ
.25 mmol) at ꢂ78 C via cannula over a 2 min period under argon.
ꢀ
The cloudy solution was stirred at ꢂ78 C for 30 min. Iso-
propoxyboronic acid pinacol ester (1.89 mL, 9.25 mmol) was added
water and brine, dried over sodium sulfate, and concentrated under
reduced pressure then purified through column chromatography
(20% DCM/Hexane) to give 18 (2.67 g 44%) as white solid: mp
ꢀ
ꢀ
at ꢂ78 C under argon via syringe. The mixture was allowed to stir
at ꢂ78 C for 30 min, then warmed slowly to room temperature and
ꢀ
1
stirred for 6 h. The mixture was quenched with aqueous 1 M HCl
solution and extracted with 3 ꢃ 30 mL EtOAc. The organic layer was
washed with water and brine, dried over sodium sulfate, concen-
trated under reduced pressure, and purified through column
chromatography (5% EtOAc/Hexane) to give 11 (1.92 g 85%) as white
81e82 C; H NMR (300 MHz, CDCl
3
): d 6.79 (s, 2H), 4.80 (s, 4H),
13
1.47 (s, 12H), 1.00 (s, 9H), 0.23 (s, 6H). C NMR (125 MHz, CDCl
3
):
d
157.1,146.3,121.9, 84.0, 34.0, 25.7, 25.1,18.2. IT-TOF-MS (APCI): m/z
calcd. for C20
H O
33 3
BSiBr
2
[MþH]þ 519.0736, found 519.0736.
ꢀ
1
solid: mp 140e141 C; H NMR (300 MHz, CDCl
3
d
3
):
d
6.46 (s, 1H),
):
4.1.7. 3,5-Bis(bromomethyl)-4-(4,4,5,5-tetramethyl-1,3,2-
dioxaborolan-2-yl)phenol (5a)
13
.81 (s, 6H), 2.21 (s, 6H), 1.42 (s, 12H). C NMR (75 MHz, CDCl
3
156.1, 121.2, 97.2, 83.9, 56.0, 25.1, 14.7. HRMS (ESI): m/z calcd. for
A solution of 18 (2.6 g, 5.0 mmol) and TBATB (0.24 g, 0.5 mmol)
in MeOH (50 mL) was stirred for one day, then another portion of
TBATB (0.24 g, 0.5 mmol) was added to the solution. The mixture
was stirred for one more day, evaporated, and purified through
column chromatography (20% DCM/Hexane) to give 5a (0.72 g 36%)
þ
C
H
16 25
O
4
B [M] 291.1877, found 291.1872.
4
.1.3. 2-(2,6-Bis(bromomethyl)-3,5-dimethoxyphenyl)-4,4,5,5-
tetramethyl-1,3,2-dioxaborolane (3a)
ꢀ
1
A solution of 11 (584 mg, 2 mmol), NBS (854 mg, 4.8 mmol), and
as white solid: mp 195-195 C; H NMR (300 MHz, CDCl
3
):
d
6.78 (s,
156.8,
BBr
13
AIBN (32.8 mg, 0.2 mmol) in anhydrous CCl
reflux under a light for 2 h. The mixture was allowed to cool to
room temperature and the solvent evaporated. Then, 20 mL CH Cl
4
(10 mL) was stirred to
3
2H), 4.79 (s, 4H), 1.46 (s, 12H). C NMR (125 MHz, CDCl ): d
146.7, 117.1, 84.1, 33.7, 25.1. HRMS (ESI): m/z calcd. for C14
[M] 402.9825, found 402.9814.
H
19
O
3
2
þ
2
2
was added. The organic layer was washed with water and brine,
dried over sodium sulfate, and concentrated under reduced pres-
4.1.8. (2-Bromo-1,3-phenylene)bis(methylene) diacetate (21)
To a solution of 20 (1.08 g, 5 mmol) in CH Cl (25 mL) was added
1
sure to give 3a (120 mg 13%). H NMR (300 MHz, CDCl
3
):
d
6.47 (s,
2
2
1
H), 4.9 (s, 4H), 3.92 (s, 6H), 1.49 (s, 12H). 3a is not stable enough for
C NMR and MS.
Et
3
N (2.02 g, 20 mmol), pyridine (1.58 g, 20 mmol), and acetyl
1
3
ꢀ
chloride (1.56 g, 20 mmol) at 0 C. The mixture was allowed to