Synthesis and biological evaluation of novel 2-Arylalkylthio-5-iodine-6- substituted-benzyl-pyrimidine-4(3H)-ones as Potent HIV-1 Non-Nucleoside reverse transcriptase inhibitors

Article abstract of DOI:10.3390/molecules19067104

A novel series of 2-arylalkylthio-5-iodine-6-substitutedbenzyl-pyrimidine- 4(3H)- ones (S-DABOs) 8a-x had been synthesized via an efficient method. Their biological activity against HIV virus and RT assay were evaluated. Some compounds, especially 8h, 8l and 8n, displayed promising activity against HIV-1 RT with IC50 values in a range of 0.41 μM to 0.71 iM, which were much better than that of nevirapine. Molecular modeling studies revealed that the binding mode would be affected via forming an additional hydrogen bond by incorporating an oxygen atom on the C-2 side chain. The biological activity was in accordance with the docking results.

Full text of DOI:10.3390/molecules19067104

Molecules 2014, 19, 7104-7121; doi:10.3390/molecules19067104
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molecules
ISSN 1420-3049
www.mdpi.com/journal/molecules
Article
Synthesis and Biological Evaluation of Novel 2-Arylalkylthio-5-
iodine-6-substituted-benzyl-pyrimidine-4(3H)-ones as Potent
HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors
Liang Zhang 1, Xiaowan Tang 1, Yuanyuan Cao 1, Shaotong Wu 1, Yu Zhang 1,
Jianxiong Zhao 1, Ying Guo 1, Chao Tian 1, Zhili Zhang 1, Junyi Liu 1,2,* and Xiaowei Wang 1,*
1
Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University,
Beijing 100191, China
2
State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
* Authors to whom correspondence should be addressed; E-Mails: jyliu@bjmu.edu.cn (J.L.);
xiaoweiwang@bjmu.edu.cn (X.W.); Tel.: +86-10-8280-5203 (X.W.); Fax: +86-10-8280-1706 (X.W.).
Received: 30 April 2014; in revised form: 26 May 2014 / Accepted: 28 May 2014 /
Published: 30 May 2014
Abstract: A novel series of 2-arylalkylthio-5-iodine-6-substitutedbenzyl-pyrimidine-4(3H)-
ones (S-DABOs) 8a–x had been synthesized via an efficient method. Their biological
activity against HIV virus and RT assay were evaluated. Some compounds, especially 8h,
8l and 8n, displayed promising activity against HIV-1 RT with IC50 values in a range of
0.41 μM to 0.71 μM, which were much better than that of nevirapine. Molecular modeling
studies revealed that the binding mode would be affected via forming an additional
hydrogen bond by incorporating an oxygen atom on the C-2 side chain. The biological
activity was in accordance with the docking results.
Keywords: HIV; NNRTIs; S-DABOs; IC50; docking
1. Introduction
The reverse transcriptase (RT) of HIV-1, being an essential enzyme in the replication of the virus, is
recognized as a great potential target for designing antiretroviral drugs [1]. In recent years, enormous
efforts have been made to develop RT inhibitors. In particular, the non-nucleoside reverse transcriptase
inhibitors (NNRTIs), a class of components of HAART, have received special attention due to their
unique antiviral potency with generally low toxicity and favorable pharmacokinetic properties [2,3].

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So far, five NNRTIs drugs—nevirapine, delavirdine, efavirenz, etravirine and rilpivirine (Figure 1)—
have been approved for clinical use [4]. However, the high mutation rate of HIV-1 RT and the rapid
emergence of drug resistance has limited the therapeutic efficacy of NNRTIs and this necessitates the
continued discovery and development of drugs with novel mechanisms of action [5].
Figure 1. Structures of NNRTI drugs.
Sulfo-dihydro-alkylthio-benzyl-oxopyrimidines (S-DABOs) as representative NNRTIs [6,7], show
their activity not only on HIV-1 wild type, but also on HIV-1 mutants [8]. By studying the crystal
structures of different kinds of NNRTIs, it’s found that S-DABOs share the same binding mode as that
of TNK-651. They interact with the binding site composed by Tyr181, Tyr188 and Trp229 residues,
which is near the catalytic site of the RT. The N-3-H of S-DABOs forms a crucial hydrogen bond with
Lys101 inside the hydrophobic pocket. In addition, the molecular may rotate to a butterfly-like
conformation so that the crucial hydrophobic forces can be formed between the aryl moiety at C-2 and
C-6 and the amino acid residues such as Tyr181, Tyr188, Phe227 [9–14].
Based on these promising results, some modifications were performed to achieve more active
S-DABO derivatives. It was anticipated that an oxygen atom on the C-2 side chain would form an
additional hydrogen bond, and extending the π-π conjugated system by introducing electron
withdrawing groups at the para position of the phenyl ring could be beneficial for the activity [15].
Moreover, optimization in the C-6 phenylmethyl ring at the meta positions would lead to closer
interactions with the non-nucleoside binding pocket (NNBP). On the basis of our previous results [16,17],
the halogen atom on C-5 position could form an interaction with the carbonyl of Tyr181, which played
an important role in improving anti-HIV-1 activity.
Herein, in order to verify the relationship between structure and activity of the target
compounds, we synthesized a series of 2-arylalkylthio-5-iodine-6-substitutedbenzyl-pyrimidine-4(3H)-
ones 8a–x (Figure 2), and evaluated their inhibitory activity on HIV-1 RT and HIV-1SF33 in TZM-bl
cell lines.

Molecules 2014, 19
Figure 2. Structures of S-DABOs, TNK-651 and target compounds.
7106
2. Results and Discussion
2.1. Chemistry
A general synthetic route to the target compounds is outlined in Scheme 1. The β-ketoesters 5 were
prepared via phenylacetyl chloride and Meldrum’s acid without substituents on the phenyl ring [18,19].
Alternatively, for the compounds with dimethyl or difluoro m-substituents on the aromatic moiety, the
corresponding compound 5 was generally obtained by reaction of the appropriate substituted benzyl
cyanide with zinc and ethyl 2-bromoacetate using the method of Hannick and Kishi [20]. Condensation
of 5 with thiourea in the presence of sodium ethoxide in boiling ethanol provided the 6-aryl thiouracils
6. The S-DABOs analogues 7a–x were prepared by S-alkylation using the appropriate substituted alkyl
halide and potassium carbonate in anhydrous DMF or sodium ethoxide in ethanol [21–23]. Subsequent
treatment of 7a–u with I2 and (NH4)2Ce(NO3)6 (CAN) in refluxing CH3CN afforded the corresponding
target compounds 8a–u [24]. Alternatively, another iodination method with NIS in DMF at 0 °C led to
target compounds 8v–x [25]. The structure assignments of these compounds were verified by NMR
and mass spectral data.
Scheme 1. Synthesis of Target Compounds 8a–x.
Reagents and conditions: (a) acetone, acetic anhydride, con.H2SO4, rt; (b) PhCH2COCl, pyridine, CH2Cl2, ice
bath; (c) EtOH, reflux; (d) m-difluoro/m-dimethyl benzyl cyanide, Zn/THF, reflux; (e) thiourea,
EtONa/EtOH, reflux; (f) substituted alkyl halide, K2CO3, rt; (g) I2, CAN, reflux; (h) substituted alkyl halide,
MeONa/MeOH, rt; (i) NIS, DMF, ice bath.

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2.2. Biological Evaluation
All target compounds were evaluated as inhibitors of HIV-1 RT and some active compounds were
evaluated for anti-HIV-1SF33 activity in the TZM-bl cell line with nevirapine and TNK-651 as
reference compounds (Tables 1 and 2) [26]. The biological results revealed that some compounds had
potent activity and exhibited obvious structure-activity relationships.
Table 1. Inhibitory Activity of 7a–8x against HIV-1 RT a.
Compd.
7a
7b
7c
R1
H
R2
IC50b µM Compd
R1
H
R2
IC50b µM
9.20
(p-NO2)C6H5CH2
>100
3.32
8a
8b
8c
8d
8e
8f
(p-NO2)C6H5CH2
CH3
F
(p-NO2)C6H5CH2
CH3
F
(p-NO2)C6H5CH2
1.66
(p-NO2)C6H5CH2
>100
>100
29.63
15.77
55.00
17.04
33.92
>100
7.50
(p-NO2)C6H5CH2
5.50
7d
7e
H
(p-CN)C6H5CH2
H
(p-CN)C6H5CH2
10.62
4.03
CH3
F
(p-CN)C6H5CH2
CH3
F
(p-CN)C6H5CH2
7f
(p-CN)C6H5CH2
(p-CN)C6H5CH2
4.49
7g
7h
7i
H
(p-CH3CO)C6H5CH2
(p-CH3CO)C6H5CH2
(p-CH3CO)C6H5CH2
(p-CH3OOC)C6H5CH2
(p-CH3OOC)C6H5CH2
(p-CH3OOC)C6H5CH2
(p-NO2)C6H5CH2CH2
(p-NO2)C6H5CH2CH2
(p-NO2)C6H5CH2CH2
(p-NO2)C6H5OCH2CH2
(p-NO2)C6H5OCH2CH2
(p-NO2)C6H5OCH2CH2
C6H5OCH2CH2CH2
C6H5OCH2CH2CH2
C6H5OCH2CH2CH2
C6H5CH2OCH2
8g
8h
8i
H
(p-CH3CO)C6H5CH2
(p-CH3CO)C6H5CH2
(p-CH3CO)C6H5CH2
(p-CH3OOC)C6H5CH2
(p-CH3OOC)C6H5CH2
(p-CH3OOC)C6H5CH2
(p-NO2)C6H5CH2CH2
(p-NO2)C6H5CH2CH2
(p-NO2)C6H5CH2CH2
(p-NO2)C6H5OCH2CH2
(p-NO2)C6H5OCH2CH2
(p-NO2)C6H5OCH2CH2
C6H5OCH2CH2CH2
C6H5OCH2CH2CH2
C6H5OCH2CH2CH2
C6H5CH2OCH2
13.81
0.41
CH3
F
CH3
F
4.03
7j
H
8j
H
3.64
7k
7l
CH3
F
8k
8l
CH3
F
1.11
>100
67.24
1.40
0.71
7m
7n
7o
7p
7q
7r
H
8m
8n
8o
8p
8q
8r
8s
H
8.64
CH3
F
CH3
F
0.70
18.14
4.58
6.88
H
H
6.28
CH3
F
0.59
CH3
F
1.31
1.31
2.56
7s
H
16.70
2.64
H
5.88
7t
CH3
F
8t
CH3
F
12.92
18.03
10.20
8.75
7u
7v
7w
7x
14.42
12.88
1.82
8u
8v
8w
8x
H
H
CH3
C6H5CH2OCH2
CH3
C6H5CH2OCH2
F
C6H5CH2OCH2
5.46
F
C6H5CH2OCH2
1.50
a Nevirapine and TNK-651 were used as reference compounds; IC50 value for nevirapine and TNK-651 is 6.29 µM
b
and 0.14 µM respectively; Compound dose (µM) required to inhibit the HIV-1 RT activity by 50%; Data
represent mean values of three separate experiments, variation among triplicate samples was less than 15%.
In general, most of the tested compounds displayed activity against HIV-1 RT, and demonstrated a
lower IC50 than nevirapine within a range of 0.41 μM to 6.28 μM. As shown in Table 1, it was
noteworthy that the activity of compounds 8a–o, without an oxygen atom on the C-2 side chain, was
much better than that of 7a–o, especially 8h (IC50 = 0.41 µM), 8l (IC50 = 0.71 µM) and 8n (IC50 =

Molecules 2014, 19
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0.70 µM), were about 10-fold more active compared to nevirapine (IC50 = 6.29 µM). Interestingly, the
conclusion did not apply to 7p–x which had oxygen atom on the C-2 side chain. On the contrary,
7p–x revealed better activities than 8p–x, such as 7q > 8q, 7r > 8r, 7t > 8t and 7w > 8w. Therefore,
it was suggested that the oxygen atom might play a crucial role in the binding process with HIV-1 RT.
In addition, substituting electron withdrawing groups at the para position of the phenyl ring at C-2
while increasing the length of side chain, would both be beneficial for the inhibitory activity, as
exemplified by 7q > 7n > 7b, 8p > 8m > 8a, which were consistent with the previous work in our
lab [16,17]. Meanwhile, taking 8n > 8o > 8m and 8q > 8r > 8p as examples, the activities were
significantly improved by incorporating dimethyl and difluoro into the meta position of the C-6
aromatic moiety. According to the combined results, the target compounds 8h (IC50 = 0.41 µM), 8l
(IC50 = 0.71 µM), 8n (IC50 = 0.70 µM), 7q (IC50 = 0.59 µM) had the best activities.
Table 2. Antiviral Activity of Compounds on HIV-1SF33 Infection in TZM-bl Cell line.
Compd.
7n
MW
395
411
504
265
EC50 (μM)/SF33
Compd.
8n
MW EC50 (μM)/SF33
6.12
5.07
1.06
0.19
521
537
545
3.84
9.44
4.10
7q
8q
8h
NVP a
8r
a Nevirapine was used as reference compound.
Subsequently, the anti-HIV-1 activity of some active compounds was determined using nevirapine
as reference compound. As shown in Table 2, the target compounds were capable of inhibiting
wild-type virus infection by HIV-1SF33 in TZM-bl cell line. Especially, 8h showed the moderate
activity. Meanwhile, the inhibitory activity of 7n < 8n and 7q > 8q was consistent with that of the RT
assay. Moreover, the anti-HIV-1 cytotoxicity of these compounds was also determined and CC50
values above 80 µM were observed.
2.3. Computational Modeling
Furthermore, in order to explore the structure-activity relationships, docking simulations were
performed using the ChemScore program. Some target compounds were flexibly docked into the
binding site of HIV-1 RT (PDB entry1RT2, in complex with TNK-651) (Figure 3). Default parameters
were set according to the ChemScore manual, unless otherwise specified [27]. The results displayed
that these target compounds could form a hydrogen bond between N-3-H and the amino acid residues
Lys101 of RT, which was necessary for the activity. The series of compounds 7a–o and 8a–o had
similar binding modes as the complex of TNK-651/1RT2. Compared to 7a–o, 8a–o a iodo substituent
at the C-5 position could form an extra bond with the carbonyl of Tyr181, which had a significant
impact on the activity by increasing the interaction. However, when an oxygen atom was introduced on
the C-2 side chain, it could give different results. Another hydrogen bond was formed between the
oxygen atom and the Tyr318 of RT. The extra hydrogen bond could potentially function as a pivot
point to change the conformation of the compound when binding to the NNBP. Therefore, 7p–x could
interact more stronglywith RT than 7a–o, which explained the observed increase of activity.
Interestingly, as the conformation changed, the halogen bond at the C-5 position of 8p–x disappeared

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unexpectedly. Herein, by forming the additional hydrogen bond, bearing an oxygen on the C-2 side
chain could obviously affect the SAR of the traditional S-DABOs analogues. Moreover, to a certain
extent, extending the C-2 side chain for a better location at the same region as N-1 substituent of TNK-
651 was beneficial for the anti-HIV activity. Introducing substituents such as nitro, cyano, acetyl and
ester, to the para position of the phenyl ring of the C-2 side chain, could significantly improve the
inhibitory activity by forming another hydrogen bond with the Val106 residue. Meanwhile, because of
the reduction in the electron density of the benzene ring with these electron withdrawing groups, a
putative π-stacking interaction resulted with the electron rich benzene ring at the Tyr318 amino
residue. In addition, due to the double or triple bonds in these groups, the well extended π-π conjugated
system could increase the possibility of forming interactions with amino acid residues Phe227, Pro236
and so on. Considering the C-6 position, when the phenyl ring was characterized by m-dimethyl or m-
difluoro substituents, favorable π-stacking and π-σ interactions would obviously be observed with the
aromatic amino acid residues. Specifically, the dimethyl substituent could modulate the benzyl group
into the most suitable conformation for the optimal affinity to the NNIBP by providing a special steric
hindrance, where additional van der Waals contacts and π-σ interactions might be observed with the
conserved Trp229 and Phe227 residues. Introducing a difluoro substituent at the benzene ring could
reduce its electron density, which was beneficial for a better interaction by producing the
π-stacking interaction.
Figure 3. Binding mode of 8n (a), 8q (b) (blue) and TNK-651 (green) with HIV-1 RT.
Hydrogen bonds are shown as a green dashed lines, and halogen bonds are shown as a
green solid line.
8n (a)
8q (b)
3. Experimental
3.1. General Information
Melting points were measured on an X-4 apparatus and are reported without correction. NMR
spectra were recorded on a Bruker AVANCE III-400 spectrometer with TMS as an internal standard
and CDCl3 or DMSO-d6 as the solvents. The chemical shifts were expressed in parts per million
(δ ppm). Coupling constants (J) were measured in Hz. MS were taken by Bruker Apex IV FTMS with
methanol as the solvent. FTIR spectra were recorded in the solid state as KBr dispersions using a

Molecules 2014, 19
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Nicolet NEXUS 470 FTIR spectrometer. Silica gel H was used for the column chromatography and
silica gel GF254 was used for TLC plates, which were used to monitor the reactions. CH3CN and
acetone were dried with CaCl2, while other chemicals were purchased as reagent grade and used
without further purification.
3.1.1. General Procedure for the Syntheses of Compounds 7a–r
6-Substitued benzyl-2-thioxouracil (compound 6, 0.47 mmol) and K2CO3 (0.94 mmol) were
dissolved in DMSO (2 mL) and stirred at room temperature, then the corresponding substituted alkyl
bromide (0.47 mmol) was added to the solution followed by stirring for 12 h. H2O (7 mL) was added
and then the pH of solution was adjusted to 3 with 2 N hydrochloric acid. After the addition of ethyl
acetate (10 mL), the solution was stirred for another 15 min. Ethyl acetate (20 mL × 3) was used to
extract the aqueous layer and the organic phases were combined, dried over MgSO4 and concentrated
under reduced pressure with a rotary evaporator. The crude product was purified with silica gel H, and
EtOAc–petroleum ether was used as the eluting solvent, to yield the target products 7a–r.
1
2-(4-Nitrobenzylthio)-6-benzyluracil (7a). Yield: 62.61%. mp: 192–194 °C. H-NMR (DMSO-d6) δ:
3.77 (s, 2H, ArCH2), 4.40 (s, 2H, SCH2), 6.01 (s, 1H, 5-H), 7.19–7.29 (m, 5H, ArH), 7.47 (d, 2H,
o-ArH, J = 8.4 Hz), 7.80 (d, 2H, m-ArH, J = 8.4 Hz). 13C-NMR (DMSO-d6) δ: 146.85, 138.33, 130.59,
129.69, 128.88, 126.94, 123.79 (Carom), 43.12 (SCH2), 32.83 (ArCH2). HRMS calcd. for C18H16N3O3S
[M+H]+ 354.09069; found: 354.09007.
1
2-(4-Nitrobenzylthio)-6-(3,5-dimethylbenzyl)uracil (7b). Yield: 89.72%. mp: 218–220 °C. H-NMR
(DMSO-d6) δ:2.05 (s, 6H, Ar(CH3)2), 3.55 (s, 2H, (Me)2ArCH2), 4.27 (s, 2H, SCH2), 5.86 (s, 1H, 5-H),
13
6.70(s, 3H, (Me)2ArH), 7.35 (d, 2H, o-ArH, J = 8.4 Hz), 7.86(d, 2H, m-ArH, J = 8.4 Hz). C-NMR
(DMSO-d6) δ: 162.28 (C-4), 159.86 (C-2), 158.00 (C-6), 149.79, 146.78, 138.14, 137.83, 130.58,
128.36, 127.39, 123.70 (Carom), 32.93 (SCH2), 30.21 (ArCH2), 21.28 (CH3). HRMS calcd. for
C20H20N3O3S [M+H]+ 382.12199; found: 382.12142.
1
2-(4-Nitrobenzylthio)-6-(3,5-difluorobenzyl)uracil (7c). Yield: 73.05%. mp: 244–24 °C. H-NMR
(DMSO-d6) δ: 3.79 (s, 2H, F2ArCH2), 4.42 (s, 2H, SCH2), 6.07 (s, 1H, 5-H), 6.93–7.06 (m, 3H, F2ArH),
7.52 (d, 2H, o-ArH, J = 8.4 Hz), 8.03 (d, 2H, m-ArH, J = 8.4 Hz). 13C-NMR (DMSO-d6) δ: 163.98 (C-4),
163.85 (C-F), 161.54 (C-2), 161.41 (C-6), 146.84, 146.68, 142.87, 130.39, 123.70, 112.86, 112.61
(Carom), 102.43 (C-5), 42.32 (SCH2), 33.07 (ArCH2). HRMS calcd. for C18H14F2N3O3S [M+H]+
354.07184; found: 390.07125.
1
2-(4-Cyanobenzylthio)-6-benzyluracil (7d). Yield: 98.26%. mp: 190–193 °C. H-NMR (DMSO-d6) δ:
3.76 (s, 2H, ArCH2), 4.35 (s, 2H, SCH2), 6.00 (s, 1H, 5-H), 7.22–7.30 (m, 5H, ArH), 7.39 (d, 2H,
o-ArH, J = 8.4 Hz), 7.61 (d, 2H, m-ArH, J = 8.4 Hz). 13C-NMR (DMSO-d6) δ: 144.62, 138.33, 132.59,
130.34, 129.67, 128.90, 126.98, 119.21 (Carom), 110.18 (CN), 43.18 (SCH2), 33.33 (ArCH2). HRMS
calcd. for C19H16N3OS [M+H]+ 334.10086; found: 334.10041.
1
2-(4-Cyanobenzylthio)-6-(3,5-dimethylbenzyl)uracil (7e). Yield: 97.14%. mp: 193–196 °C. H-NMR
(DMSO-d6) δ: 2.18 (s, 6H, Ar(CH3)2), 3.67 (s, 2H, (Me)2ArCH2), 4.37 (s, 2H, SCH2), 5.98 (s, 1H, 5-H),

Molecules 2014, 19
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13
6.83 (d, 3H, (Me)2ArH), 7.42 (d, 2H, o-ArH, J = 8 Hz), 7.60 (d, 2H, m-ArH, J = 8 Hz). C-NMR
(DMSO-d6) δ: 144.65, 138.08, 137.813, 132.53, 130.34, 128.39, 127.39, 119.19 (Carom), 110.21 (CN),
43.08 (SCH2), 33.30 (ArCH2), 21.30 (CH3). HRMS calcd. for C21H20N3OS [M+H]+ 362.13216;
found: 362.13153.
1
2-(4-Cyanobenzylthio)-6-(3, 5-difluorobenzyl)uracil (7f). Yield: 73.05%. mp: 205–208 °C. H-NMR
(DMSO-d6) δ: 3.82 (s, 2H, F 2ArCH2), 4.44 (s, 2H, SCH2), 6.70 (s, 1H, 5-H), 6.97–7.13 (m, 3H,
13
F2ArH), 7.47 (d, 2H, o-ArH, J = 8.4 Hz), 7.66 (d, 2H, m-ArH, J = 8.4 Hz). C-NMR (DMSO-d6) δ:
164.00 (C-4), 163.86 (C–F), 161.55 (C-2), 161.42 (C-6), 144.52, 142.82, 132.52, 130.19, 119.17,
112.90, 112.66 (Carom), 110.26 (CN), 102.51 (C-5), 42.33 (SCH2), 33.32 (ArCH2). HRMS calcd. for
C19H14 F2N3OS [M+H]+ 370.08202; found: 370.08147.
1
2-(4-Acetylbenzylthio)-6-benzyluracil (7g). Yield: 83.10%. mp: 204–205 °C. H-NMR (DMSO-d6) δ:
2.38 (s, 3H, ArCOCH3), 3.65 (s, 2H, ArCH2), 4.23 (s, 2H, SCH2), 5.87 (s, 1H, 5-H), 7.08–7.18 (m, 5H,
ArH), 7.23 (d, 2H, o-ArH, J = 8.4 Hz), 7.62 (d, 2H, m-ArH, J = 8.4 Hz). 13C-NMR (DMSO-d6) δ:
197.84 (CO), 144.00, 138.36, 136.05, 129.68, 129.64, 128.88, 128.69, 126.94 (Carom), 43.22 (SCH2),
33.40 (ArCH2), 27.09 (CH3). HRMS calcd. for C20H19N2O2S [M+H]+ 351.11617; found: 351.11565.
1
2-(4-Acetylbenzylthio)-6-(3,5-dimethylbenzyl)uracil (7h). Yield: 85.18%. mp: 195–197 °C. H-NMR
(DMSO-d6) δ: 2.23 (s, 6H, Ar(CH3)2), 2.54 (s, 3H, p-ArCOCH 3), 3.73 (s, 2H, (Me)2ArCH2), 4.41 (s,
2H, SCH2), 6.01 (s, 1H, 5-H), 6.90 (s, 3H, (Me)2ArH), 7.41 (d, 2H, o-ArH, J = 7.2 Hz), 7.78 (d, 2H,
13
m-ArH, J = 7.2 Hz). C-NMR (DMSO-d6) δ: 197.78 (CO), 150.27, 138.14, 137.82, 136.04, 129.64,
128.65, 128.38, 127.44 (Carom), 44.12 (SCH2), 43.15 (ArCH2), 27.06 (COCH3), 21.32 (CH3). HRMS
calcd. for C22H23N2O2S [M+H]+ 379.14748; found: 379.14672.
1
2-(4-Acetylbenzylthio)-6-(3,5-difluorobenzyl)uracil (7i). Yield: 93.34%. mp: 251–254 °C. H-NMR
(DMSO-d6) δ: 2.50 (s, 3H, ArCOCH3), 3.80 (s, 2H, F2ArCH2), 4.36 (s, 2H, SCH2), 6.05 (s, 1H, 5-H),
6.96–7.10 (m, 3H, F 2ArH), 7.37 (d, 2H, o-ArH, J = 8 Hz), 7.76 (d, 2H, m-ArH, J = 8 Hz). 13C-NMR
(DMSO-d6) δ: 197.75 (CO), 164.02 (C-4), 163.90 (C-F), 161.58 (C-2), 161.45 (C-6), 143.97, 142.88,
136.07, 129.50, 128.62, 112.95, 112.70 (Carom), 102.49 (C-5), 42.40 (SCH2), 33.39 (ArCH2), 27.04
(COCH3). HRMS calcd. for C20H17F2N2O2S [M+H]+ 387.09733; found: 387.09703.
1
2-(4-Methoxycarbonylbenzylthio)-6-benzyluracil (7j). Yield: 93.79%. mp: 214–217 °C. H-NMR
(DMSO-d6) δ: 3.81 (s, 2H, ArCH2), 3.85 (s, 3H, ArCOOCH3), 4.40 (s, 2H, SCH2), 6.03 (s, 1H, 5-H),
13
7.25–7.34 (m, 5H, ArH), 7.39 (d, 2H, o-ArH, J = 8 Hz), 7.80 (d, 2H, m-ArH, J = 8 Hz). C-NMR
(DMSO-d6) δ: 166.52 (CO), 144.22, 138.33, 131.95, 129.71, 129.12, 128.86, 126.94 (Carom), 52.27 (OCH3),
43.04 (SCH2), 33.23 (ArCH2). HRMS calcd. for C20H19N2O3S [M+H]+ 367.11109; found: 367.11079.
2-(4-Methoxycarbonylbenzylthio)-6-(3,5-dimethylbenzyl)uracil (7k). Yield: 90.91%. mp: 221–224 °C.
1H-NMR (DMSO-d6) δ: 2.06 (s, 6H, Ar(CH3)2), 3.55 (s, 2H, (Me)2ArCH2), 3.68 (s, 3H, p-ArCO2CH3),
4.24 (s, 2H, SCH2), 5.84 (s, 1H, 5-H), 6.71 (s, 3H, (Me)2ArH), 7.23 (d, 2H, o-ArH, J = 8 Hz), 7.63 (d, 2H,
m-ArH, J = 8 Hz). 13C-NMR (DMSO-d6) δ: 166.41 (CO), 144.30, 137.81, 129.71, 129.59, 128.74,

Molecules 2014, 19
7112
128.39, 127.43 (Carom), 52.52 (OCH3), 43.13 (SCH2), 33.34 (ArCH2), 21.30 (CH3). HRMS calcd. for
C22H23N2O3S [M+H]+ 395.14239; found: 395.14195.
2-(4-Methoxycarbonylbenzylthio)-6-(3,5-difluorobenzyl)uracil (7l). Yield: 70.71%. mp: 279–280 °C.
1H-NMR (DMSO-d6) δ: 3.79 (s, 2H, F2ArCH2), 3.80 (s, 3H, p-ArCO2CH3), 4.35 (s, 2H, SCH2), 6.03
(s, 1H, 5-H), 6.97–7.07 (m, 3H, F 2ArH), 7.37 (d, 2H, o-ArH, J = 8 Hz), 7.77 (d, 2H, m-ArH, J = 8
13
Hz). C-NMR (DMSO-d6) δ: 166.40 (CO), 144.21, 142.93, 129.57, 128.80, 112.96, 112.71 (Carom),
52.54 (OCH3), 42.38 (SCH2), 33.38 (ArCH2). HRMS calcd. for C20H17F2N2O3S [M+H]+ 403.09225;
found: 403.09219.
1
2-(4-Nitrophenethylthio)-6-benzyluracil (7m). Yield: 84.14%. mp: 200–204 °C. H-NMR (DMSO-d6)
δ: 3.01 (t, 2H, p-NO2ArCH2, J = 7.2 Hz), 3.34 (t, 2H, J 6.8Hz, SCH2, J = 7.2 Hz), 3.80 (s, 2H, ArCH2),
5.98 (s, 1H, 5-H), 7.20–7.32 (m, 5H, ArH), 7.43 (d, 2H, o-ArH, J = 8 Hz), 8.13 (d, 2H, m-ArH,
13
J = 8 Hz). C-NMR (DMSO-d6) δ: 148.57, 146.64, 138.41, 130.32, 129.75, 128.71, 127.02, 123.87
(Carom), 43.10 (SCH2), 35.11 (ArCH2), 30.64 (NO2ArCH2). HRMS calcd. for C19H18N3O3S [M+H]+
368.10634; found: 368.10628.
2-(4-Nitrophenethylthio)-6-(3,5-dimethylbenzyl)uracil (7n). Yield: 50.20%. mp: 212–215 °C. 1H-NMR
(DMSO-d6) δ: 2.02 (s, 6H, Ar(CH3)2), 2.88 (t, 2H, p-NO2ArCH2, J = 7.2 Hz), 3.19 (t, 2H, SCH2,
J = 7.2 Hz), 3.55 (s, 2H, (Me)2ArCH2), 5.81 (s, 1H, 5-H), 6.70 (d, 3H, (Me)2ArH), 7.28 (d, 2H, o-ArH,
J = 7.2 Hz), 7.98(d, 2H, m-ArH, J = 7.2 Hz). 13C-NMR (DMSO-d6) δ: 146.62, 137.73, 130.34, 128.32,
127.38, 123.85 (Carom), 46.63 (SCH2), 35.01 (ArCH2), 30.64 (NO2ArCH2), 21.25 (CH3). HRMS calcd.
for C21H22N3O3S [M+H]+ 396.13764; found: 396.13726. IR (KBr): 3433, 3114, 2917, 2852, 1646,
1605, 1522, 1459, 1346, 837, 756, 729 cm−1.
2-(4-Nitrophenethylthio)-6-(3,5-difluorobenzyl)uracil (7o). Yield: 79.25%. mp: 220–222 °C. 1H-NMR
(DMSO-d6) δ: 2.98 (t, 2H, p-NO2ArCH2, J = 7.6 Hz), 3.30 (t, 2H, SCH2, J = 7.6 Hz), 3.81 (s, 2H,
F2ArCH2), 6.02 (s, 1H, 5-H), 7.00–7.04 (m, 3H, F 2ArH), 7.41 (d, 2H, o-ArH, J = 8.4 Hz), 8.11 (d, 2H,
m-ArH, J = 8.4 Hz). 13C-NMR (DMSO-d6) δ: 164.00 (C-4), 163.87 (C–F), 161.42 (C-6), 148.52, 146.64,
142.92, 130.28, 123.83, 112.96, 112.71 (Carom), 102.73 (C-5), 42.41 (SCH2), 35.00 (ArCH2), 30.62
(NO2ArCH2). HRMS calcd. for C19H16F2N3O3S [M+H]+ 404.08749; found: 404.08743.
1
2-(2-(4-Nitrophenoxy)ethylthio)-6-benzyluracil (7p). Yield: 63.46%. mp: 212–213 °C. H-NMR
(DMSO-d6) δ: 3.49 (t, 2H, p-NO2ArCH2), 3.76 (s, 2H, ArCH2), 4.25 (t, 2H, SCH2), 5.99 (s, 1H, 5-H),
13
7.18 (d, 2H, o-ArH, J = 8 Hz), 7.16–7.29 (m, 5H, ArH), 8.18 (d, 2H, m-ArH, J = 8 Hz). C-NMR
(DMSO-d6) δ: 163.80 (CO), 141.46, 138.20, 129.62, 128.79, 126.90, 126.28, 115.47 (Carom), 67.30
(OCH2), 42.87 (SCH2), 28.76 (ArCH2), 21.25 (CH3). HRMS calcd. for C19H18N3O4S [M+H]+
384.10125; found: 384.10106.
2-(2-(4-Nitrophenoxy)ethylthio)-6-(3,5-dimethylbenzyl)uracil (7q). Yield: 82.12%. mp: 210–214 °C.
1H-NMR (DMSO-d6) δ: 2.16 (s, 6H, Ar(CH3)2), 3.46 (t, 2H, SCH2, J = 6.4 Hz), 3.65 (s, 2H,
(Me)2ArCH2), 4.24 (t, 2H, OCH2, J = 6.4 Hz), 5.95 (s, 1H, 5-H), 6.80 (d, 3H, (Me)2ArH), 7.08 (d, 2H, o-
13
ArH, J = 9.2 Hz), 8.15 (d, 2H, m-ArH, J = 9.2 Hz). C-NMR (DMSO-d6) δ: 163.78 (CO), 141.43,

Molecules 2014, 19
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138.00, 137.72, 128.32, 127.36, 126.27, 115.45 (Carom), 67.22 (OCH2), 43.02 (SCH2), 28.84 (ArCH2),
21.25 (CH3). HRMS calcd. for C21H22N3O4S [M+H]+ 412.13255; found: 412.13196. IR (KBr): 3433,
2920, 2851, 1648, 1595, 1546, 1513, 1465, 1345, 1266, 1027, 843, 751, 652 cm−1.
2-(2-(4-Nitrophenoxy)ethylthio)-6-(3,5-difluorobenzyl)uracil (7r). Yield: 82.76%. mp: 210–212 °C.
1H-NMR (DMSO-d6) δ: 3.48 (t, 2H, SCH2, J = 6.4 Hz), 3.81 (s, 2H, F2ArCH2), 4.24 (t, 2H, OCH2,
J = 6.4 Hz), 6.07 (s, 1H, 5-H), 6.99–7.02 (m, 3H, F2ArH), 7.09 (d, 2H, o-ArH, J = 9.2 Hz), 8.18(d, 2H,
m-ArH, J = 9.2 Hz). 13C-NMR (DMSO-d6) δ: 163.94 (C-4), 163.78 (CO), 163.21 (C–F), 161.49 (C-2),
161.36 (C-6), 143.35, 142.76, 141.44, 126.27, 115.39, 112.92, 112.68 (Carom), 102.43 (C-5), 67.24
(OCH2), 43.29 (SCH2), 28.90 (ArCH2). HRMS calcd. for C19H16F2N3O4S [M+H]+ 420.08241;
found: 420.08188.
3.1.2. General Procedure for the Syntheses of Compounds 7s–x
Sodium (6.43 mmol)) was dissolved in anhydrous methanol (20 mL), 6-substitued benzyl-2-thiouracil
(compound 6, 0.92 mmol) was added, followed by addition of the appropriate substituted alkyl
halide (1.38 mmol). After completion of the reaction according to TLC analysis, the crude product
were purified by silica gel column chromatography with EtOAc–petroleum ether as eluent to afford the
white solid products 7s–x.
1
2-(Phenoxypropylthio)-6-benzyluracil (7s). Yield: 79.17%. mp: 89–91 °C. H-NMR (CDCl3) δ:
2.11–2.17 (m, 2H, ArOCH2CH2), 3.36 (t, 2H, SCH2, J = 7.2 Hz), 3.79 (s, 2H, ArCH2), 4.02 (t, 2H,
13
ArOCH2, J = 7.2 Hz), 5.99 (s, 1H, 5-H), 6.89–7.33 (m, 10H, ArH). C-NMR (DMSO-d6) δ: 158.85
(CO), 138.17, 129.95, 129.72, 128.78, 126.91, 121.03, 114.88 (Carom), 66.51 (OCH2), 43.16 (SCH2),
29.27 (ArCH2), 27.11 (CH2). HRMS calcd. for C20H21N2O2S [M+H]+ 353.13183; found: 353.13142.
1
2-(Phenoxypropylthio)-6-(3,5-dimethylbenzyl)uracil (7t). Yield: 64.57%. mp: 100–102 °C. H-NMR
(CDCl3) δ: 2.12–2.18 (m, 2H, ArOCH2CH2), 2.17 (s, 6H, Ar(CH3)2), 3.35 (t, 2H, SCH2, J = 7.2 Hz),
3.69 (s, 2H, (Me)2ArCH2), 4.01 (t, 2H, ArOCH2, J = 7.2 Hz), 5.96 (s, 1H, 5-H), 6.84–6.96 (m, 5H,
ArH), 7.29 (d, 3H, (Me)2ArH). 13C-NMR (DMSO-d6) δ: 158.97 (CO), 138.01, 137.74, 129.84, 128.32,
127.45, 121.02, 114.83 (Carom), 66.21 (OCH2), 43.17 (SCH2), 28.76 (ArCH2), 26.92 (CH2), 21.38
(CH2). HRMS calcd. for C22H25N2O2S [M+H]+ 381.16313; found: 381.16260.
1
2-(Phenoxypropylthio)-6-(3,5-difluorobenzyl)uracil (7u). Yield: 62.14%. mp: 100–101 °C. H-NMR
(CDCl3) δ: 2.09–2.16 (m, 2H, ArOCH2CH2), 3.33 (t, 2H, SCH2, J = 7.2 Hz), 3.72 (s, 2H, F2ArCH2), 4.01
13
(t, 2H, ArOCH2, J = 7.2 Hz), 5.99 (s, 1H, 5-H), 6.67–7.30 (m, 8H, ArH). C-NMR (DMSO-d6) δ:
163.91 (C-F), 161.02 (C-6), 158.78 (CO), 143.00, 129.81, 121.02, 114.83, 113.02, 102.57 (Carom),
65.87 (OCH2), 42.40 (SCH2), 29.12 (ArCH2), 27.27 (CH2). HRMS calcd. for C20H19F2N2O2S [M+H]+
389.11298; found: 389.11317.
1
2-(Benzyloxymethylthio)-6-benzyluracil (7v). Yield: 72.62%. mp: 118–120 °C. H-NMR (CDCl3) δ:
3.82 (s, 2H, ArCH2), 4.60 (s, 2H, ArCH2O), 5.43 (s, 2H, SCH2O), 5.99 (s, 1H, 5-H), 7.23–7.37 (m,
10H, ArH). 13C-NMR (DMSO-d6) δ: 176.47 (C-4), 161.01 (C-2), 156.20 (C-6), 136.03, 129.53, 129.09,

Molecules 2014, 19
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128.73, 128.26, 127.91, 127.48 (Carom), 104.14 (C-5), 70.93 (OCH2), 69.19 (SCH2), 27.56 (ArCH2).
HRMS calcd. for C19H19N2O2S [M+H]+ 339.11617; found: 339.11591.
2-(Benzyloxymethylthio)-6-(3,5-dimethylbenzyl)uracil (7w). Yield: 65.13%. mp: 134–136 °C. 1H-NMR
(CDCl3) δ: 2.17 (s, 6H, Ar(CH3)2), 3.73 (s, 2H, ArCH2), 4.58 (S, 2H, ArCH2O), 5.42 (s, 2H, SCH2O),
13
5.98 (s, 1H, 5-H), 6.83 (d, 3H, (Me)2ArH), 7.26–7.35 (m, 5H, ArH). C-NMR (DMSO-d6) δ: 156.20
(C-6), 138.07, 137.73, 128.69, 128.38, 128.16, 128.11, 127.42, 127.23 (Carom), 103.73 (C-5), 71.72
(OCH2), 70.93 (SCH2), 37.13 (ArCH2), 21.16 (CH3). HRMS calcd. for C21H23N2O2S [M+H]+
367.14748; found: 367.14662.
1
2-(Benzyloxymethylthio)-6-(3,5-difluorobenzyl)uracil (7x). Yield: 57.77%. mp: 120–122 °C. H-NMR
(CDCl3) δ: 3.78 (s, 2H, F2ArCH2), 4.62 (S, 2H, ArCH2O), 5.42 (s, 2H, SCH2O), 6.03 (s, 1H, 5-H), 6.68
(d, 3H, F 2ArH), 7.28–7.37 (m, 5H, ArH). 13C-NMR (DMSO-d6) δ: 176.47 (C-4), 163.59 (C-F), 161.34
(C-2), 154.78 (C-6), 140.83, 137.83, 128.73, 127.56, 112.98, 112.73, 102.53 (Carom), 104.55 (C-5),
71.79 (OCH2), 70.63 (SCH2), 36.49 (ArCH2). HRMS calcd. for C19H17F2N2O2S [M+H]+ 375.09733;
found: 375.09789.
3.1.3. General Procedure for the Syntheses of Compounds 8a–u
Compound 7a–u (0.30 mmol) was dissolved in dry CH3CN (20 mL) and stirred at room
temperature, then I2 (0.18 mmol) and Ce(NH4)2(NO3)6 (CAN, 0.18 mmol) were added to this solution
followed by refluxing for 4 h. After cooling to room temperature, the reaction mixture was quenched
with saturated aqueous NaHSO3 (15 mL). The CH3CN was evaporated under reduced pressure, and the
residue was extracted with CH2Cl2 (20 mL × 3). The organic phases were combined, dried over
MgSO4 and concentrated at reduced pressure with a rotary evaporator. The crude product was purified
with silica gel H, and EtOAc–petroleum ether was used as the eluting solvent, to yield products 8a–u.
2-(4-Nitrobenzylthio)-5-iodine-6-benzyluracil (8a). Yield: 75.74%. mp: 207–210 °C. 1H-NMR
(DMSO-d6) δ: 4.11 (s, 2H, ArCH2), 4.41 (s, 2H, SCH2), 7.24–7.30 (m, 5H, ArH), 7.45 (d, 2H, o-ArH,
J = 8.4 Hz), 8.01 (d, 2H, m-ArH, J = 8.4 Hz). 13C-NMR (DMSO-d6) δ: 146.87, 146.47, 137.70, 130.49,
129.36, 128.93, 127.03, 123.78 (Carom), 46.41 (SCH2), 32.02 (ArCH2). HRMS calcd. for C18H15IN3O3S
[M+H]+ 479.98733; found: 479.98704.
2-(4-Nitrobenzylthio)-5-iodine-6-(3,5-dimethylbenzyl)uracil (8b). Yield: 79.90%. mp: 224–228 °C.
1H-NMR (DMSO-d6) δ: 2.16 (s, 6H, Ar(CH3)2), 4.01 (s, 2H, (Me)2ArCH2), 4.38 (s, 2H, SCH2), 6.816
(s, 3H, (Me)2ArH),7.41 (d, 2H, o-ArH, J = 8.4 Hz), 7.95 (d, 2H, m-ArH, J = 8.4 Hz). 13C-NMR
(DMSO-d6) δ: 146.79, 146.53, 137.78, 137.50, 130.46, 128.46, 127.07, 123.66 (Carom), 46.56 (SCH2),
33.11 (ArCH2), 21.33 (CH3). HRMS calcd. for C20H19IN3O3S [M+H]+ 508.01863; found: 508.01826.
2-(4-Nitrobenzylthio)-5-iodine-6-(3,5-difluorobenzyl)uracil (8c). Yield: 69.81%. mp: 203–206 °C.
1H-NMR (DMSO-d6) δ: 4.10 (s, 2H, F2ArCH2), 4.40 (s, 2H, SCH2), 6.85–7.05 (m, 3H, F2ArH), 7.50
13
(d, 2H, o-ArH, J = 8.8 Hz), 8.04 (d, 2H, m-ArH, J = 8.8 Hz). C-NMR (DMSO-d6) δ: 163.85 (C-F),
146.83, 146.35, 142.00, 130.28, 123.68, 112.60, 112.35 (Carom), 102.51 (C-5), 47.78 (SCH2), 33.22
(ArCH2). HRMS calcd. for C18H13F2IN3O3S [M+H]+ 515.96849; found: 515.96792.

Molecules 2014, 19
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1
2-(4-Cyanobenzylthio)-5-iodine-6-benzyluracil (8d). Yield: 78.26%. mp: 223–226 °C. H-NMR
(DMSO-d6) δ: 4.07 (s, 2H, ArCH2), 4.34 (s, 2H, SCH2), 7.21–7.29 (m, 5H, ArH), 7.35 (d, 2H, o-ArH,
13
J = 7.2 Hz), 7.59 (d, 2H, m-ArH, J = 7.2 Hz), 13.05 (s, 1H, NH). C-NMR (DMSO-d6) δ: 144.26,
137.69, 132.55, 130.25, 129.37, 128.89, 127.08, 118.76 (Carom), 110.27 (CN), 46.79 (SCH2), 33.18
(ArCH2). HRMS calcd. for C19H15IN3OS [M+H]+ 459.99750; found: 459.99747.
2-(4-Cyanobenzylthio)-5-iodine-6-(3,5-dimethylbenzyl)uracil (8e). Yield: 65.47%. mp: 224–227 °C.
1H-NMR (DMSO-d6) δ: 2.17 (s, 6H, Ar(CH3)2), 3.99 (s, 2H, (Me)2ArCH2), 4.35 (s, 2H, SCH2), 6.83 (d,
3H, (Me)2ArH), 7.36 (d, 2H, o-ArH, J = 8 Hz), 7.57 (d, 2H, m-ArH, J = 8 Hz). 13C-NMR (DMSO-d6)
δ: 144.29, 137.76, 137.46, 132.51, 130.23, 128.48, 127.08, 119.15 (Carom), 110.25 (CN), 46.53 (SCH2),
33.41 (ArCH2), 21.34 (CH3). HRMS calcd. for C21H19IN3OS [M+H]+ 428.02880; found: 488.02855.
2-(4-Cyanobenzylthio)-5-iodine-6-(3,5-difluorobenzyl)uracil (8f). Yield: 82.17%. mp: 216–219 °C.
1H-NMR (DMSO-d6) δ: 4.06 (s, 2H, F2ArCH2), 4.32 (s, 2H, SCH2), 6.83–7.08 (m, 3H, F2ArH), 7.38 (d,
2H, o-ArH, J = 8.4 Hz), 7.60 (d, 2H, m-ArH, J = 8.4 Hz). 13C-NMR (DMSO-d6) δ: 163.83 (C-F),
161.52 (C-2), 161.38 (C-6), 144.09, 142.01, 132.50, 130.06, 119.12, 112.64, 112.39 (Carom), 110.32
(CN), 102.56 (C-5), 46.12 (SCH2), 33.49 (ArCH2). HRMS calcd. for C19H13F2IN3OS [M+H]+
495.97866; found: 495.97824.
1
2-(4-Acetylbenzylthio)-5-iodine-6-benzyluracil (8g). Yield: 86.51%. mp: 219–220 °C. H-NMR
(DMSO-d6) δ: 2.52 (s, 3H, ArCOCH3), 4.10 (s, 2H, ArCH2), 4.35 (s, 2H, SCH2), 7.24–7.30 (m, 5H,
ArH), 7.34 (d, 2H, o-ArH, J = 8 Hz), 7.76 (d, 2H, m-ArH, J = 8 Hz). 13C-NMR (DMSO-d6) δ: 197.68
(CO), 143.45, 137.64, 135.89, 129.57, 129.39, 128.88, 128.70, 127.05 (Carom), 46.45 (SCH2), 33.44
(ArCH2), 27.04 (CH3). HRMS calcd. for C20H18IN2O2S [M+H]+ 477.01282; found: 477.01248.
2-(4-Acetylbenzylthio)-5-iodine-6-(3,5-Dimethylbenzyl)uracil (8h). Yield: 79.97%. mp: 201–203 °C.
1H-NMR (DMSO-d6) δ: 2.20 (s, 6H, Ar(CH3)2), 2.53 (s, 3H, p-ArCOCH 3), 4.04 (s, 2H, (Me)2ArCH2),
4.36 (s, 2H, SCH2), 6.89 (d, 3H, (Me)2ArH), 7.33 (d, 2H, o-ArH, J = 8 Hz), 7.75 (d, 2H, m-ArH, J = 8 Hz).
13C-NMR (DMSO-d6) δ: 197.72 (CO), 143.75, 137.78, 137.49, 136.06, 129.53, 128.63, 128.49, 127.13
(Carom), 46.59 (SCH2), 33.47 (ArCH2), 27.04 (COCH3), 21.36 (CH3). HRMS calcd. for C22H22IN2O2S
[M+H]+ 505.04412; found: 505.04325. IR (KBr): 3434, 2920, 2851, 1728, 1675, 1605, 1449, 1354,
1266, 1120, 836, 776, 638, 615 cm−1.
2-(4-Acetylbenzylthio)-5-iodine-6-(3,5-difluorobenzyl)uracil (8i). Yield: 88.79%. mp: 205–206 °C.
1H-NMR (DMSO-d6) δ: 2.53 (s, 3H, ArCOCH3), 4.12 (s, 2H, F2ArCH2), 4.35 (s, 2H, SCH2), 6.93–7.11
(m, 3H, F 2ArH), 7.35 (d, 2H, o-ArH, J = 8 Hz), 7.77 (d, 2H, m-ArH, J = 8 Hz). 13C-NMR (DMSO-d6)
δ: 197.72 (CO), 164.00 (C-F), 161.54 (C-2), 161.41 (C-6), 143.59, 142.06, 136.05, 129.40, 128.60,
112.70, 112.45 (Carom), 102.57 (C-5), 46.17 (SCH2), 33.53 (ArCH2), 27.02 (COCH3). HRMS calcd. for
C20H16F2IN2O2S [M+H]+ 512.99397; found: 512.99383.
2-(4-Methoxycarbonylbenzylthio)-5-iodine-6-benzyluracil (8j). Yield: 92.59%. mp: 214–216 °C.
1H-NMR (DMSO-d6) δ: 3.85 (s, 3H, p-ArCOOCH3), 4.12 (s, 2H, ArCH2), 4.38 (s, 2H, SCH2),
7.25–7.32 (m, 5H, ArH), 7.35 (d, 2H, o-ArH, J = 7.6 Hz), 7.78 (d, 2H, m-ArH, J = 7.6 Hz), 13.07 (s,

Molecules 2014, 19
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1H, NH). 13C-NMR (DMSO-d6) δ: 166.40 (CO), 143.82, 137.62, 129.64, 129.61, 129.40, 128.84,
127.03 (Carom), 52.69 (OCH3), 46.79 (SCH2), 33.53 (ArCH2). HRMS calcd. for C20H18IN2O3S [M+H]+
493.00773; found: 493.00702.
2-(4-Methoxycarbonylbenzylthio)-5-iodine-6-(3,5-dimethylbenzyl)uracil (8k). Yield: 80.18%. mp:
1
208–211 °C. H-NMR (DMSO-d6) δ: 2.16 (s, 6H, Ar(CH3)2), 3.81 (s, 3H, p-ArCO2CH3), 4.01 (s, 2H,
(Me)2ArCH2), 4.34 (s, 2H, SCH2), 6.84 (s, 3H, (Me)2ArH), 7.29 (d, 2H, o-ArH, J = 8 Hz), 7.72 (d, 2H,
m-ArH, J = 8 Hz). 13C-NMR (DMSO-d6) δ: 166.37 (CO), 143.95, 137.77, 129.60, 129.58, 128.78,
128.49, 127.13 (Carom), 52.54 (OCH3), 46.60 (SCH2), 33.46 (ArCH2), 21.35 (CH3). HRMS calcd. for
C22H22IN2O3S [M+H]+ 521.03903; found: 521.03770.
2-(4-Methoxycarbonylbenzylthio)-5-iodine-6-(3,5-difluorobenzyl)uracil (8l). Yield: 41.41%. mp:
1
210–213 °C. H-NMR (DMSO-d6) δ: 3.81(s, 3H, p-ArCO2CH3), 4.09 (s, 2H, F2ArCH2), 4.32 (s, 2H,
SCH2), 6.88–7.08 (m, 3H, F2ArH), 7.32 (d, 2H, o-ArH, J = 8.4 Hz), 7.75 (d, 2H, m-ArH, J = 8.4 Hz).
13C-NMR (DMSO-d6) δ: 166.34 (CO), 163.86 (C-F), 161.54 (C-2), 161.41 (C-6), 143.80, 142.08,
129.53, 129.46, 128.81, 112.71, 112.46 (Carom), 52.53 (OCH3), 46.18 (SCH2), 33.49 (ArCH2). HRMS
calcd. for C20H16F2IN2O3S [M+H]+ 528.98889; found: 528.98826.
1
2-(4-Nitrophenethylthio)-5-iodine-6-benzyluracil (8m). Yield: 75.83%. mp: 209–212 °C. H-NMR
(DMSO-d6) δ: 2.93 (t, 2H, p-NO2ArCH2, J = 7.2 Hz), 3.28 (t, 2H, SCH2, J = 7.2 Hz), 4.09 (s, 2H,
ArCH2), 7.18–7.30 (m, 5H, ArH), 7.35 (d, 2H, o-ArH, J = 8.4 Hz), 8.10 (d, 2H, m-ArH, J = 8.4 Hz),
13
12.99 (s, 1H, NH). C-NMR (DMSO-d6) δ: 148.36, 146.64, 137.87, 130.32, 129.28, 128.85, 127.02,
123.84 (Carom), 46.78 (SCH2), 34.84 (ArCH2), 30.80 (NO2ArCH2). HRMS calcd. for C19H17IN3O3S
[M+H]+ 494.00298; found: 494.00270.
2-(4-Nitrophenethylthio)-5-iodine-6-(3,5-dimethylbenzyl)uracil (8n). Yield: 74.15%. mp: 220–221 °C.
1H-NMR (DMSO-d6) δ: 2.17 (s, 6H, Ar(CH3)2), 2.25 (t, 2H, p-NO2ArCH2, J = 7.6 Hz), 3.00 (t, 2H,
SCH2, J = 7.6 Hz), 4.05 (s, 2H, (Me)2ArCH2), 6.88 (d, 3H, (Me)2ArH), 7.40 (d, 2H, o-ArH,
J = 8.4 Hz), 8.12 (d, 2H, m-ArH, J = 8.4 Hz). 13C-NMR (DMSO-d6) δ: 148.47, 146.62, 137.72, 130.31,
128.43, 127.03, 126.49, 123.82 (Carom), 46.57 (SCH2), 34.81 (ArCH2), 30.86 (NO2ArCH2), 21.31
(CH3). HRMS calcd. for C21H21IN3O3S [M+H]+ 522.03428; found: 522.03387. IR (KBr): 3433, 2923,
2853, 1640, 1560, 1555, 1515, 1453, 1341, 1230, 1030, 995, 848, 711, 684, 596 cm−1.
2-(4-Nitrophenethylthio)-5-iodine-6-(3,5-difluorobenzyl)uracil (8o). Yield: 74.73%. mp: 220–221°C.
1H-NMR (DMSO-d6) δ: 2.94 (t, 2H, p-NO2ArCH2, J = 7.6 Hz), 3.27 (t, 2H, SCH2, J = 7.6 Hz), 4.14 (s,
2H, F2ArCH2), 6.98–7.08 (m, 3H, F 2ArH), 7.39 (d, 2H, o-ArH, J = 8.8 Hz), 8.11 (d, 2H, m-ArH,
J = 8.8 Hz). 13C-NMR (DMSO-d6) δ: 163.99 (C-4), 163.86 (C-F), 161.55 (C-6), 148.33, 146.63, 130.26,
123.79, 112.71, 112.46 (Carom), 102.53 (C-5), 46.20 (SCH2), 34.71 (ArCH2), 30.79 (NO2ArCH2).
HRMS calcd. for C19H15F2IN3O3S [M+H]+ 529.98414; found: 529.98365.
2-(2-(4-Nitrophenoxy)ethylthio))-5-iodine-6-benzyluracil (8p). Yield: 63.64%. mp: 204–205 °C.
1H-NMR (DMSO-d6) δ: 3.44 (t, 2H, p-NO2ArOCH2, J = 6.4 Hz), 4.06 (s, 2H, ArCH2), 4.16 (t, 2H,
SCH2, J = 6.4 Hz), 7.05 (d, 2H, o-ArH, J = 9.2 Hz), 7.16–7.29 (m, 5H, ArH), 8.16 (d, 2H, m-ArH,

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13
J = 9.2 Hz). C-NMR (DMSO-d6) δ: 163.91 (CO), 141.46, 137.86, 129.32, 128.31, 126.97, 126.14,
115.49 (Carom), 67.34 (OCH2), 46.80 (SCH2), 29.10 (ArCH2). HRMS calcd. for C19H17IN3O4S [M+H]+
509.99791; found: 509.99834.
2-(2-(4-Nitrophenoxy)ethylthio))-5-iodine-6-(3,5-dimethylbenzyl)uracil (8q). Yield: 60.48%. mp:
1
215–218 °C. H-NMR (DMSO-d6) δ: 2.16 (s, 6H, Ar(CH3)2), 3.42 (t, 2H, SCH2, J = 6.8 Hz), 3.96 (s,
2H, (Me)2ArCH2), 4.18 (t, 2H, OCH2, J = 6.8 Hz), 6.81 (d, 3H, (Me)2ArH), 7.09 (d, 2H, o-ArH,
J = 9.2 Hz), 8.15 (d, 2H, m-ArH, J = 9.2 Hz). 13C-NMR (DMSO-d6) δ: 163.72 (CO), 141.44, 137.68,
137.51, 128.41, 127.06, 126.23 (Carom), 115.39 (C-5), 67.02 (OCH2), 46.50 (SCH2), 29.18 (ArCH2),
21.31 (CH3). HRMS calcd. for C21H21IN3O4S [M+H]+ 538.02920; found: 538.02847. IR (KBr): 3433,
2920, 2851, 1633, 1596, 1554, 1513, 1464, 1347, 1258, 1231, 1030, 840, 750, 651, 596 cm−1.
2-(2-(4-Nitrophenoxy)ethylthio)-5-Iodine-6-(3,5-difluorobenzyl)uracil (8r). Yield: 75.52%. mp:
1
224–226 °C. H-NMR (DMSO-d6) δ: 3.41 (t, 2H, SCH2, J = 6.4 Hz), 4.09 (s, 2H, F2ArCH2), 4.15 (t,
2H, OCH2, J = 6.4 Hz), 6.98 (d, 3H, F2ArH), 7.05 (d, 2H, o-ArH, J = 9.2 Hz), 8.16 (d, 2H, m-ArH,
13
J = 9.2 Hz). C-NMR (MHz, DMSO-d6) δ: 163.92 (CO), 163.73 (C-F), 161.48 (C-2), 161.34 (C-6),
141.43, 126.23, 115.36, 112.74, 112.49 (Carom), 102.49 (C-5), 67.03 (OCH2), 46.18 (SCH2), 29.17
(ArCH2). HRMS calcd. for C19H14F2IN3NaO4S [M+Na]+ 567.96100; found: 567.96056. IR (KBr):
3435, 2924, 2853, 1644, 1592, 1557, 1516, 1461, 1343, 1261, 1241, 1116, 1033, 851, 751, 656, 603 cm−1.
1
2-(Phenoxypropylthio)-5-iodine-6-benzyluracil (8s). Yield: 68.26%. mp: 135–137 °C. H-NMR
(CDCl3) δ: 1.95–2.00 (m, 2H, ArOCH2CH2), 3.19–3.20 (m, 2H, SCH2), 3.82–3.90 (m, 2H, ArOCH2),
4.10 (s, 2H, ArCH2), 6.58–7.51 (m, 10H, ArH). 13C-NMR (DMSO-d6) δ: 158.85 (CO), 138.43, 129.95,
129.44, 128.90, 127.01, 121.04, 117.70 (Carom), 114.79 (C-5), 66.51 (OCH2), 46.73 (SCH2), 29.07
(ArCH2), 27.39 (CH2). HRMS calcd. for C20H20IN2O2S [M+H]+ 479.02847; found: 479.02956.
2-(Phenoxypropylthio)-5-iodine-6-(3,5-dimethylbenzyl)uracil (8t). Yield: 60.11%. mp: 165–167 °C.
1H-NMR (CDCl3) δ: 2.04–2.10 (m, 2H, ArOCH2CH2), 2.27 (s, 6H, Ar(CH3)2), 3.27 (t, 2H, SCH2,
J = 7.2 Hz), 3.93 (t, 2H, ArOCH2, J = 7.2 Hz), 4.08 (s, 2H, (Me)2ArCH2), 6.86–7.04 (m, 5H, ArH),
7.27 (q, 3H, (Me)2ArH). 13C-NMR (DMSO-d6) δ: 158.80 (CO), 138.37, 137.63, 129.80, 128.28,
127.09, 120.98, 117.65 (Carom), 114.35 (C-5), 66.21 (OCH2), 46.04 (SCH2), 29.13 (ArCH2), 27.26
(CH2), 21.38 (CH2). HRMS calcd. for C22H24IN2O2S [M+H]+ 507.05977; found: 507.06077.
2-(Phenoxypropylthio)-5-iodine-6-(3,5-difluorobenzyl)uracil (8u). Yield: 62.40%. mp: 156–158 °C.
1H-NMR (CDCl3) δ: 2.05–2.11 (m, 2H, ArOCH2CH2), 3.26 (t, 2H, SCH2, J = 7.2 Hz), 3.99 (t, 2H,
ArOCH2, J = 7.2 Hz), 4.10 (s, 2H, F2ArCH2), 6.66–6.97 (m, 5H, ArH), 7.28 (q, 3H, F2ArH). 13C-NMR
(DMSO-d6) δ: 161.62 (C-F), 160.28 (C-6), 158.52 (CO), 142.26, 129.56, 120.79, 112.32, 112.03,
102.25 (Carom), 114.73 (C-5), 65.47 (OCH2), 46.36 (SCH2), 29.11 (ArCH2), 27.69 (CH2). HRMS calcd.
for C20H18F2IN2O2S [M+H]+ 515.00962; found: 515.01071.
3.1.4. General Procedure for the Syntheses of Compounds 8v–x
Compound 7v–u (0.10 mmol) and NIS (0.12 mmol) were dissolved in dry DMF (15 mL)
after cooling to 0 °C of ice bath, then stirred to room temperature for another 10 h, the reaction

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completed according to TLC analysis. The mixture was added to EtOAc (50 mL) and washed by saturated
brine (50 mL × 3). The organic phase was dried over MgSO4 and concentrated at reduced pressure with
a rotary evaporator. The crude product was purified with silica gel H, and EtOAc–petroleum ether was
used as the eluting solvent, to yield products 8v–x.
1
2-(Benzyloxymethylthio)-5-iodine-6-benzyluracil (8v). Yield: 91.25%. mp: 133–135 °C. H-NMR
(CDCl3) δ: 4.14 (s, 2H, ArCH2), 4.47 (s, 2H, ArCH2O), 5.35 (s, 2H, SCH2O), 7.15–7.33 (m, 8H, ArH).
13C-NMR (DMSO-d6) δ: 175.23 (C-4), 160.50 (C-2), 156.39 (C-6), 138.60, 129.12, 129.06, 128.80,
128.45, 127.49, 127.43 (Carom), 104.14 (C-5), 71.53 (OCH2), 69.84 (SCH2), 29.43 (ArCH2). HRMS
calcd. for C19H18IN2O2S [M+H]+ 465.01282; found: 465.01307.
2-(Benzyloxymethylthio)-5-iodine-6-(3,5-dimethylbenzyl)uracil (8w).Yield: 78.90%. mp: 200–202 °C.
1H-NMR (CDCl3) δ: 2.20 (s, 6H, Ar(CH3)2), 4.07 (s, 2H, ArCH2), 4.47 (s, 2H, ArCH2O), 5.34 (s, 2H,
SCH2O), 6.80–6.95 (m, 5H, ArH), 7.26–7.33 (m, 3H, (Me)2ArH). 13C-NMR (DMSO-d6) δ: 156.39 (C-6),
138.97, 137.49, 129.36, 129.02, 128.58, 128.06, 127.52, 126.96 (Carom), 103.73 (C-5), 71.72 (OCH2),
70.93 (SCH2), 37.13 (ArCH2), 21.16 (CH3). HRMS calcd. for C21H22IN2O2S [M+H]+ 493.04412;
found: 493.04508.
2-(Benzyloxymethylthio)-5-iodine-6-(3,5-difluorobenzyl)uracil (8x).Yield: 78.93%. mp: 196–198 °C.
1H-NMR (CDCl3) δ: 4.12 (s, 2H, F2ArCH2), 4.59 (s, 2H, ArCH2O), 5.35 (s, 2H, SCH2O), 6.63–6.90
(m, 3H, F ArH), 7.26–7.36 (m, 5H, ArH). 13C-NMR (DMSO-d6) δ: 176.62 (C-4), 163.46 (C-F),
2
161.48 (C-2), 154.41 (C-6), 141.21, 138.27, 128.83, 127.77, 112.99, 111.94, 102.59 (Carom), 105.25
(C-5), 72.22 (OCH2), 70.92 (SCH2), 35.53 (ArCH2). HRMS calcd. for C19H16F2IN2O2S [M+H]+
500.99397; found: 500.99365.
3.2. Biological Assays
3.2.1. Assay for Measuring the Inhibitory Activity of Compounds against HIV-1 RT
Oligo(dT) (TaKaRa Co., Otsu, Japan) was immobilized via its 5'-terminal phosphate to Covalink-
NH microtiter plates (NUNC Co., Roskilde, Denmark). The biotin-dUTP was incorporated by reverse
transcriptase (Sigma, St. Louis, MO, USA). Briefly, a serial concentration of inhibitor was added to the
mixture, which contained 50 mmol/L Tris-HCl (pH 8.3), 3 mmol/L MgCl2, 75 mmol/L KCl, 5 mmol/L
DTT, 0.13 mg/mL BSA, 10 μg/mL poly (A), 0.75 μM biotin-11-Dutp, 1.5 μM dTTP and HIV-1 RT.
After incubation at 37 °C for 1h, washing buffer, which contained 50 mmol/L Tris-HCl (pH 7.5),
0.15 mol/L NaCl, 0.05 mmol/L MgCl2 and 0.02% Tween20, was used to wash the plate. Then each
well of the plate was added 100 mL 1% BSA and incubated at room temperature for another 30 min.
The plate was washed with the same buffer for 3 times. Before further incubation at 37 °C for 1 h, 50 μL
of alkaline phosphatase streptavidin (SA-ALP) solution (100 ng/mL) was added to each well and
washed again as above. Finally, 50 μL of p-nitrophenyl phosphate, disodium (PNPP, 1 mg/mL, pH 9.5)
was added and incubated at 37 °C for 30 min. 0.5 mol/L NaOH was added to stop the reaction
and a colorimetric streptavidin-alkaline phosphatase reporter system was used to detect and quantify
the result.

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3.2.2. Assay for Measuring the Inhibitory Activity of Compounds on HIV-1SF33 Infectious
TZM-bl cells, HIV-1SF33 were obtained from the NIH AIDS Research and Reference
Reagent Program (Germantown, MD, USA). The inhibitory activity of the compounds on infection by
a laboratory-adapted HIV-1 strain SF33 was tested in TZM-bl cells. Briefly, TZM-bl cells (4 × 104/well)
were infected by addition of 200 TCID50 of HIV-1, followed by incubation for 2 h at 37 °C before addition
of compounds at serial dilutions. After further incubation at 37 °C for 7 days, p24 was measured using
a commercial enzyme-linked immunosorbent assay (ELISA) kit (Vironostika HIV-1 Microelisa
system; BioMérieux; Marcy l’Etoile, France).The concentration of a compound for inhibiting 50%
viral replication (EC50) was determined by nonlinear regression using GraphPad Prism 5.01.
3.3. Molecular Modeling
The docking studies were conducted by using software GOLD3.0.1 and protein crystal structures of
wildtype RT/1 complex (PDB ID: 1RT2). Following the default settings of Chemscore in the software
tool, top scored docked poses were visually inspected for each ligand in the DS 2.5 based on relevant
molecules. The radius of the binding site sphere was defined by the original ligand as 8.9 Å, thus
ensuring that the docking method was reliable.
4. Conclusions
In summary, a series of novel 2-arylalkylthio-5-iodine-6-substitutedbenzyl-pyrimidine-4(3H)-ones
(S-DABOs) were synthesized as inhibitors of HIV-1 RT. We evaluated their anti-HIV activity on
the HIV-1 RT and HIV-1SF33 in TZM-bl cell lines. Biological results revealed that the target
compounds displayed good activity. It was noteworthy that compounds bearing an oxygen atom on the
C-2 side chain demonstrated a new SAR, and the differences in biological results seen between 7a–x
and 8a–x were discussed. From this study, useful information was obtained for designing HIV-1
inhibitors with great efficiency and low toxicity.
Acknowledgments
We thank the Foundation of China (20972011, 21042009, 21172014) and grants from the Ministry
of Science and Technology of China (2009ZX09301-010) for financial support.
Author Contributions
The listed authors contributed to this work as described in the following: J.L. and W.X. designed
research; L.Z., X.T., Y.C., S.W., Y.Z., J.Z. and Y.G. performed research and analyzed the dara; L.Z.,
C.T., Z.Z., J.L. and W.X. wrote the paper. All authors read and approved the final manuscript.
Conflicts of Interest
The authors declare no conflict of interest.

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Sample Availability: Samples of the compounds are not available from the authors.
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