Trypanoside, anti-tuberculosis, leishmanicidal, and cytotoxic activities of tetrahydrobenzothienopyrimidines

Article abstract of DOI:10.1016/j.bmc.2010.03.018

The synthesis of 2-(5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4-yl)hydrazone-derivatives (BTPs) and their in vitro evaluation against Trypanosoma cruzi trypomastigotes, Mycobacterium tuberculosis, Leishmania amazonensis axenic amastigotes, and six human cancer cell lines is described. The in vivo activity of the most active and least toxic compounds against T. cruzi and L. amazonensis was also studied. BTPs constitute a new family of drug leads with potential activity against infectious diseases. Due to their drug-like properties, this series of compounds can potentially serve as templates for future drug-optimization and drug-development efforts for use as therapeutic agents in developing countries.

Full text of DOI:10.1016/j.bmc.2010.03.018

Bioorganic & Medicinal Chemistry 18 (2010) 2880–2886
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry
journal homepage: www.elsevier.com/locate/bmc
Trypanoside, anti-tuberculosis, leishmanicidal, and cytotoxic activities
of tetrahydrobenzothienopyrimidines
José C. Aponte a, Abraham J. Vaisberg b, Denis Castillo c, German Gonzalez c, Yannick Estevez c,i
,
Jorge Arevalo c, Miguel Quiliano d, Mirko Zimic d, Manuela Verástegui b, Edith Málaga b, Robert H. Gilman e,
Juan M. Bustamante f, Rick L. Tarleton f, Yuehong Wang g, Scott G. Franzblau g, Guido F. Pauli g,h
,
Michel Sauvain b,i, Gerald B. Hammond a,
*
a Department of Chemistry, University of Louisville, Louisville, KY 40292, USA
b Departamento de Microbiología y Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
c Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
d Bioinformatics Unit—Drug Design Group, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
e Johns Hopkins University School of Public Health, USA
f Center for Tropical and Emerging Global Diseases, Coverdell Center for Biomedical Research, University of Georgia, Athens, GA 30602, USA
g Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
h Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
i Université de Toulouse;UPS;UMR 152 (Laboratoire de pharmacochimie des substances naturelles et pharmacophores redox), 118, rte de Narbonne, F-31062 Toulouse cedex 9, France
a r t i c l e i n f o
a b s t r a c t
Article history:
The synthesis of 2-(5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4-yl)hydrazone-derivatives (BTPs)
and their in vitro evaluation against Trypanosoma cruzi trypomastigotes, Mycobacterium tuberculosis,
Leishmania amazonensis axenic amastigotes, and six human cancer cell lines is described. The in vivo
activity of the most active and least toxic compounds against T. cruzi and L. amazonensis was also studied.
BTPs constitute a new family of drug leads with potential activity against infectious diseases. Due to their
drug-like properties, this series of compounds can potentially serve as templates for future drug-optimi-
zation and drug-development efforts for use as therapeutic agents in developing countries.
Ó 2010 Elsevier Ltd. All rights reserved.
Received 17 December 2009
Revised 8 March 2010
Accepted 9 March 2010
Available online 12 March 2010
Keywords:
Tetrahydrobenzothienopyrimidine
Trypanosoma cruzi
Mycobacterium tuberculosis
Leishmania amazonensis
Anticancer
1. Introduction
situation has become more acute as the number of reported cases
increased.1 Because most of the affected population live in devel-
Chagas’ disease, tuberculosis and leishmaniasis are commonly
being referred as Neglected Diseases. These infectious diseases, pre-
valent in Third World countries, lack effective, affordable, widely
accessible, and/or easy to use drug treatments. A number of factors
such as affordability, drugs resistance, poor efficacy and severe
adverse effects limit the utility of the current existing drugs. The
oping countries and cannot afford existing drugs, the pharmaceuti-
cal industry has traditionally ignored these diseases. Chagas’
disease is an endemic tropical disease that infects up to 20 million
people in Central and South America and approximately between
50,000 and 100,000 people in the United States.2 According to
the WHO, it is estimated that tuberculosis was responsible for
1.77 million deaths in 2007.3 In the case of leishmaniasis, it is esti-
mated that over 2 million people are infected, and about 57,000 die
annually.4 Current standard treatments for tuberculosis include
antibacterial drugs such as Rifampicin and Isoniazid, which require
between six to twelve month-therapies to fully eliminate mycobac-
terium from the body.5 The antifungal Amphotericin B is currently
used to treat leishmaniasis, however its high cost and elevated tox-
icity limit its use.6 Furthermore, for the treatment of leishmaniasis,
only one available drug, Miltefosine, does not accuse resistance;
however, it is contraindicated in pregnancy.7 Nifurtimox and
Abbreviations: BTP, 2-(5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4-
yl)hydrazone-derivatives; T. cruzi, Trypanosoma cruzi; M. tuberculosis, Mycobacte-
rium tuberculosis; L. amazonensis, Leishmania amazonensis; TPSA, topological polar
surface area; %ABS, percentage of absorption; n-ROTB, number of rotatable bonds;
mi Log P, logarithm of compound partition coefficient between n-octanol and
water; n-OHNH, number of hydrogen bond donors; n-ON, number of hydrogen
bond acceptors.
* Corresponding author. Tel.: +1 502 852 5998; fax: +1 502 852 3899.
E-mail address: gb.hammond@louisville.edu (G.B. Hammond).
0968-0896/$ - see front matter Ó 2010 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmc.2010.03.018

J. C. Aponte et al. / Bioorg. Med. Chem. 18 (2010) 2880–2886
2881
Benznidazole are currently used to treat Chagas’ disease, but both
are associated with major side effects and need close monitoring.8
Clearly, there is a need for a search for new types of drugs with
high selectivity, minimum side effects and low manufacturing
hydro[1]benzothieno[2,3-d]pyrimidin-4-yl)hydrazone-derivatives
(BTPs) was developed and tested for their anti-T. cruzi, anti-M.
tuberculosis, and anti-L. amazonensis potential, as well as for their
antiproliferative activity against a panel of six human cancer cell
lines and one non-tumorogenic cell line. To the best of our knowl-
edge, 13 of a total of 38 compounds (2, 3, 8, 15–17, 19, 24, 27, 32–
34, and 37) represent new chemical entities. Their structures and
in vitro bioactivities are presented in Tables 1, 2 and 4. Compound
4 exhibited the highest selectivity in the in vitro anti-T. cruzi assay
and was evaluated in a short-term in vivo assay, from which 4 re-
sulted to be inactive. Compound D and 37 BTPs were also investi-
gated for their anti-M. tuberculosis activity using the H37Rv
virulent strain in a MABA anti-TB assay. In general, this series of
compounds showed greater potential against protozoan parasites
and tumorogenic cells than against M. tuberculosis. However, when
compounds 10, 18, 24, 25 and 35 were further tested in a TB non-
replicating model, involving exposure under low-oxygen (LORA),
compounds 10, 18 and 35 showed higher anti-TB activity, while
compounds 25 and 26, exhibited the exact same inhibitory activity
in both tests (MABA and LORA). Compounds 6, 21, 28, 30 and 36
exhibited moderate-to-high degree of selectivity against L. ama-
zonensis axenic amastigotes, and were successively tested in a
macrophage-infected assay using the three most prevalent Leish-
mania species in Peru, L. amazonensis, L. brasilensis and L. peruviana
(Table 2). With in vitro anti-Leishmania bioactivity in hand, we se-
lected compounds 6, 28 and 36 for their in vivo evaluation (Table
3). It was found that 36 reduced the parasite burden in 65% after
four weeks of treatment. Table 4 shows the anti-tumor results
for BTPs; in this screening 21 exhibited antiproliferative values
costs.
2-(5,6,7,8-Tetrahydro[1]benzothieno[2,3-d]pyrimidin-4-
yl)hydrazone-derivatives (BTPs) are small molecules that have
been used as chemical probes in an image-based phenotypic
screen for inhibitors of the secretory pathway.9 Benzothienopyrim-
idines exhibit a variety of pharmacological activities, among them
anticancer,10 antimicrobial,11 and anticonvulsant.14b We selected
tetrahydrobenzothienopyrimidines in our studies because of their
structural novelty, diversity of chemical functionalities, straight-
forward synthesis and affordable starting materials.
In the present study, a series of 38 BTPs were synthesized
(Scheme 1) and evaluated in vitro against infectious pathogens Try-
panosoma cruzi, Mycobacterium tuberculosis (Table 1), and three
Leishmania strains, (Tables 1 and 2). The antiproliferative activity
of these BTPs was also studied against panel of six human cancer
cell lines and one non-tumorogenic cell line (Table 4). Based on
the in vitro study, the in vivo activity of the most active and least
toxic BTP against T. cruzi and L. amazonensis (Table 4) was evalu-
ated. The ADME properties of all molecules were calculated in sil-
ico (Table 5).
2. Chemistry
The synthesis of the BTP series is summarized in Scheme 1. It
began with the preparation of 2-amino-4,5,6,7-tetrahydrobenzo
[b]thienophene-3-carboxylic acid ethyl ester (A) using a Gewald
reaction. A reacted with an excess of formamide to obtain the cyc-
lic pyrimidinone B,12a which underwent chlorination using phos-
phorus oxychloride (POCl3), yielding C. Nucleophilic displacement
with aqueous hydrazine formed the corresponding aromatic-
hydrazine derivative D.12b The synthesis of BTPs was concluded
with the formation of a Schiff base between D and an aldehyde
or ketone. All these reactions resulted in high yield and were per-
formed in gram scale; the purification for each step was facilitated
because each intermediate in the synthesis could be recrystallized.
ranging from 0.1 to 0.5 lM against the different human cancer cell
lines, and had selectivity towards human breast and human colon
carcinomas. These results were confirmed by the NCI 60-cancer
cell line panel study.
4. Discussion
The benzothienopyrimidine moiety has attracted attention due
to their wide variety of biological activities.9–11,14,15 However the
tetrahydrobenzothienopyrimidine system, containing a lipophilic
tetrahydrobenzo subunit and two biologically relevant seg-
ments—a Schiff base and hydrazone moieties, have not been inves-
tigated. The anti-trypanosome activity of BTP was evaluated by a
colorimetric method based on the reduction of the substrate chlo-
3. Results
In our continued search for biologically active compounds that
target infective parasites and cancer,13 a series of 2-(5,6,7,8-tetra-
O
CN
O
O
N
O
a
b
O
S8
+
O
NH
S
S
NH2
Gewald
reaction
A, 43.3g, 84%
B, 37.3g, 95%
c
N
N
R1
NH2
HN
HN
Cl
e
d
R2
N
N
S
S
N
S
N
N
1-37, 20-99%
D, 24.1g, 85%
C, 29.1g, 72%
Scheme 1. Synthesis of BTPs. Reagents and conditions: (a) diethyl amine, EtOH, rt, sonication, 30 min; (b) formamide, reflux, 6 h; (c) phosphorus oxychloride, reflux, 3 h; (d)
hydrazine 51% in H2O, MeOH, reflux, 3 h; (e) aldehyde or ketone, EtOH, reflux, 2–72 h.

2882
J. C. Aponte et al. / Bioorg. Med. Chem. 18 (2010) 2880–2886
Table 1
In vitro anti-T. cruzi, anti-M. tuberculosis and anti-L. amazonensis activity of compounds D and 1–37a
NH2
HN
N
N
R1
HN
N
R2
N
1-37
D
S
S
N
SIc
MIC H37Rv (
l
M) MABA (LORA)
SId
IC50 (lM)
SIe
b
Compd
R1, R2
IC50
(lM)
T. cruzi
M. tuberculosis
L. amazonensis
D
1
2
3
4
5
6
7
—
21.3
14.4
13.0
13.3
1.4
>25
>25
5.2
1.9
1.8
0.2
1.1
14.6
—
374.5
75.9
>250
>250
35.0
>250
>250
>250
>250
0.3
0.5
—
—
0.1
—
—
—
—
0.6
3.2 (8.4)
0.6
—
—
—
—
54.4
43.7
12.7
39.0
16.6
42.6
15.7
3.6
0.6
0.6
1.3
0.4
0.1
0.5
9.6
2.3
3.8
4.3
1.3
0.5
0.6
4.3
1.2
3.3
3.0
0.7
0.6
1.0
0.7
13.0
5.2
nd
4.1
2.6
1.0
3.1
85.2
5.0
8.8
5.8
5.0
1.6
5.9
5.6
8.5
0.9
—
R1 = H, R2 = C6H5
R1 = H, R2 = 1-Naphthalenyl
R1 = H, R2 = 2-Naphthalenyl
R1 = H, R2 = Cinnamyl
R1 = H, R2 = C6H4–4-CH3
R
1 = H, R2 = C6H4–4-CH2CH3
—
R1 = H, R2 = C6H4–4-CH(C2H6)
R1 = H, R2 = C6H4–4-CH(C3H9)
R1 = H, R2 = C6H4–4-OH
R1 = H, R2 = C6H4–4-OCH3
R1 = H, R2 = C6H4–3-OCH3
R1 = H, R2 = C6H3–3,4-O–CH2–O
0.5
1.2
1.1
1.1
0.9
0.7
1.8
—
0.6
—
0.4
0.6
0.1
—
8
9
11.2
11.3
16.0
16.9
22.8
18.5
>25
17.5
>25
15.4
16.1
22.9
>25
3.9
>25
>25
10.5
13.8
18.4
10.8
13.1
21.3
20.3
9.3
1.7
72.1
41.6
47.5
36.1
29.4
33.2
7.2
7.2
40.8
5.3
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
71.2 (26.9)
119.4
>250
>250
>250
>250
>250
>200
39.9 (9.7)
20.8
R
1 = H, R2 = C6H3–2,4-OCH3
R1 = H, R2 = C6H2–3,4,5-OCH3
R1 = H, R2 = C6H3–3-OCH3, 4-OH
R1 = H, R2 = C6H2–3,5-OCH3, 4-OH
R1 = H, R2 = C6H2-3,5-Allyloxy, 4-Br
R1 = H, R2 = 2-Furyl
—
—
1.0 (4.2)
0.6
—
0.2
—
—
5.5 (5.6)
1.3 (1.3)
0.6
—
—
0.7
—
0.8
—
0.3
0.5
1.4 (11.5)
0.7
—
—
1080.0
—
4.2
R1 = H, R2 = 2-Pyrrolyl
R1 = H, R2 = 4-Pyridinyl
10.1
232.6
0.5
38.5
107.8
2.0
1.2
9.7
3.3
1.7
2.2
0.9
1.3
32.3
112.6
40.6
28.5
19.0
182.3
—
>300
145.1
>250
R
1 = H, R2 = 2-Pyridinyl
—
—
—
R1 = H, R2 = C6H4-4-NO2
R1 = H, R2 = C6H4–2-NO2
R1 = H, R2 = C6H4–4-CF3
R1 = H, R2 = C6H4–2-CF3
R1 = H, R2 = C6H4–4-F
R1 = H, R2 = C6H4–2-F
R1 = H, R2 = C6H4–4-Cl
>250
0.8
0.6
1.0
1.7
1.6
0.7
0.8
0.8
—
16.2 (15.9)
15.7 (15.4)
71.1
>300
>250
124.3
>250
24.3
R
1 = H, R2 = C6H4–2-Cl
R1 = H, R2 = C6H4–4-Br
R1 = H, R2 = C6H4–2-Br
R1 = H, R2 = C6H4–4-CN
R1 = H, R2 = C(CH3)3
R1, R2 = CH3
R1 = CH3, R2 = C6H5
R1, R2 = CH2CH3
R1, R2 = C6H5
>25
>25
14.1
13.7
20.7
>25
4.5
>300
—
299.2
239.7
72.6 (8.7)
160.2
>250
2.7
0.9
1.0
—
20.8
—
Nifurtimox
Rifampin
Amphotericin B
—
—
—
0.1 (>1.9)
—
—
0.1
—
54.0
—
a
b
c
Toxicity assays on VERO cell or macrophages were performed by different research groups using independent methodologies.
IC50: concentration that produces 50% inhibitory effect.
Assay performed at Laboratotios de Investigación y Desarrollo, UPCH; SI = IC50
cell/IC50
.
T. cruzi
VERO
d
e
Assay performed at Institute for Tuberculosis Research, UIC; SI = IC50
cell/IC50
.
VERO
M. tuberculosis
Assay performed at Instituto de Medicina Tropical Alexander von Humbolt, UPCH; SI = IC50 macrophages/IC50
.
L. amazonensis axenic amastigotes
rophenol red b-
D-galactopyranoside (CPRG) by b-galactosidase
respectively, the IC50 value for 4 being more than four times lower
resulting from the expression of the gene in T. cruzi Tulahuen C4
at the Laboratorios de Investigación y Desarrollo (UPCH). On this
study, it was noted that the presence of electron-donating (ED)
or electron-withdrawing (EW) groups on the hydrazone moiety
has a small impact on the anti-T. cruzi activity of BTPs (Table 1).
Indeed, only four compounds (4, 7, 21 and 31) showed anti-try-
than for the positive control, Benznidazole (6.5 lM). With these in
Table 2
IC50 (lM) of BTP against macrophages infected with three Leishmania species
Compd
L. amazonensis Lma
L. braziliensis
L. peruviana
CL1
PER006
LCA08
panosome activity at concentrations below 10 lM, and only 4
6
8.2
10.5
0.6
17.3
>2.0
11.1
0.1
9.5
0.7
>30.0
>2.0
7.0
was more active, with comparable toxicity to the positive control
Nifurtimox, exhibiting a moderate SI value of 15. The Selectivity
Index (SI) is the ratio of IC50 values between VERO (normal African
green monkey epithelial cells) or macrophages, and the corre-
sponding microorganism. Compounds 4 and 31 were further stud-
ied in vitro at the Center for Tropical and Emerging Global
21
28
30
36
Amp.
Ba
>2.0
>30.0
>2.0
10.9
0.4
0.1
a
Diseases (UGA), showing anti-T. cruzi activity at 1.4 and 9.3 lM,
Amphotericin B.

J. C. Aponte et al. / Bioorg. Med. Chem. 18 (2010) 2880–2886
2883
Table 3
In vivo activity of BTP on L. amazonensis-infected BALB/c mice (n = 10)a
Table 5
Physico-chemical properties of BTPsa
Compd
Lesion diameterb (mm)
After 4 weeks After 7 weeks After 4 weeks
Reduction of parasite burden (%)
ID
%ABS TPSA n-
molecular miLog P n-
n-ON
Lipinski’s
0
ROTB weight
OHNH acceptors violations
donors
(AÅ2)
After 7 weeks
Control 2.8
4.7
4.7
5.2
4.9
2.2
Rule
D
1
2
3
4
5
6
7
<500
65
<5
3
1
1
1
1
1
1
1
1
2
1
1
1
1
1
2
2
1
1
2
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
<10
4
4
4
4
4
4
4
4
4
5
5
5
6
6
7
6
7
6
5
5
5
5
7
7
4
4
4
4
4
4
4
4
5
4
4
4
4
4
61
0
0
1
1
0
0
0
1
1
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
6
28
3.0
3.6
2.8
2.1
30
46
65
2
25
17
87.0 63.8
91.7 50.2
91.7 50.2
91.7 50.2
91.7 50.2
91.7 50.2
91.7 50.2
91.7 50.2
91.7 50.2
84.7 70.4
88.5 59.4
88.5 59.4
85.3 68.6
85.3 68.6
82.1 77.9
81.5 79.6
78.3 88.9
85.3 68.6
87.2 63.3
86.2 66.0
87.2 63.1
87.2 63.1
75.9 96.0
75.9 96.0
91.7 50.2
91.7 50.2
91.7 50.2
91.7 50.2
91.7 50.2
91.7 50.2
91.7 50.2
91.7 50.2
83.5 74.0
91.7 50.2
91.7 50.2
91.7 50.2
91.7 50.2
91.7 50.2
1
3
3
3
4
3
4
4
4
3
4
4
3
5
6
4
5
9
3
3
3
3
4
4
4
4
3
3
3
3
3
3
3
3
2
3
4
4
220.3
308.4
358.5
358.5
334.4
322.4
336.5
350.5
364.5
324.4
338.4
338.4
352.4
368.5
398.5
354.4
384.5
499.4
298.4
297.4
309.4
309.4
353.4
353.4
376.4
376.4
326.4
326.4
342.9
342.9
387.3
387.3
333.4
288.4
260.4
322.4
288.4
384.5
1.84
3.89
5.05
5.07
4.65
4.34
4.80
5.40
5.60
3.41
3.95
3.92
3.78
3.93
3.52
3.23
3.24
5.96
3.15
3.04
2.60
2.72
3.85
3.80
4.78
4.74
4.05
4.00
4.57
4.52
4.70
4.65
3.64
4.00
3.12
4.34
4.12
5.55
36
Gluc.c
100
100
a
b
c
Effect of treatments after eight intralesional inoculations.
Compounds administrated at 5 mg/kg/day.
N-Methylglucamine antimoniate, administrated at 33 mg /kg/day.
8
9
Table 4
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
Cytotoxicity of compounds D and 1–37 against various cancer cell lines
Compd
GI50 (l
M) in indicated cell linea
3T3
H460
DU145
MCF-7
M-14
HT-29
K562
D
1
2
3
<4.5
21.7
16.7
27.9
4.4
9.6
13.9
20.0
24.1
24.1
5.4
>170
58.8
10.8
21.9
20.8
23.1
17.7
>250
20.0
22.5
9.9
27.2
<2.0
15.6
4.6
83.9
0.37
>170
102.9
14.8
3.5
13.9
>250
14.6
77.8
14.6
7.1
>170
25.1
11.6
16.1
15.0
>170
5.3
9.0
24.6
18.0
18.4
35.2
4.6
20.7
12.5
6.2
19.4
8.2
>170
32.2
5.9
15.7
19.5
17.3
7.4
>250
20.0
11.4
18.7
>170
3.9
11.1
13.2
4.7
6.2
1.6
7.1
11.1
4.1
18.2
19.9
20.8
2.1
133.0
28.2
5.9
11.2
6.3
9.3
2.1
4
5
6
7
37.5
36.1
9.4
12.9
18.5
5.2
>170
190.2
17.8
30.3
17.2
16.3
143.1
>250
94.4
15.6
18.8
>170
12.8
11.1
2.5
> 150
0.25
>170
>170
16.9
6.5
17.6
>250
>170
>170
33.6
15.4
>170
32.7
23.3
19.8
20.6
>170
32.4
8
9
23.2
6.6
6.4
6.3
6.4
14.9
17.1
16.2
>250
29.5
28.3
20.3
>170
3.1
17.0
12.5
14.9
117.4
21.1
10.5
13.6
>170
3.8
15.8
13.9
15.5
>250
7.9
4.7
9.0
>170
3.9
4.0
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
5FUb
14.9
17.6
>250
19.9
22.5
10.2
27.3
<2.0
7.8
7.1
1.7
1.0
0.4
8.5
3.8
2.2
1.9
83.2
0.04
>170
>170
10.8
15.8
20.5
>250
18.7
88.1
17.4
11.2
150.4
7.3
169.2
0.40
>170
52.9
15.3
5.4
83.9
0.09
>170
52.0
5.4
152.8
0.10
>170
>170
7.0
109.3
0.16
>170
>170
6.6
1.7
8.9
81.2
6.7
19.8
5.7
a
%ABS, percentage of absorption; TPSA, topological polar surface area; n-ROTB,
number of rotatable bonds; miLog P, logarithm of compound partition coefficient
between n-octanol and water; n-OHNH, number of hydrogen bond donors; n-ON,
number of hydrogen bond acceptors.
4.8
7.4
4.5
9.4
10.4
>250
15.1
56.5
12.4
8.0
>170
33.0
33.0
21.9
38.9
>170
14.9
>250
12.8
62.9
10.5
7.7
>170
24.5
9.3
15.9
15.2
>170
2.3
>250
8.4
22.0
5.9
4.5
3.0
ancy between the in vitro and in vivo assays, but we believe these
are mostly related to drug bioavailability. Although 4 shows excel-
lent ADME properties in silico (see Table 5), it may be rapidly re-
moved from the body (through the liver perhaps), or it may never
make into the circulation because is bound up in the tissue. Fur-
ther studies are needed to confirm these assumptions.
The anti-TB activity is presented in Table 1. There is no direct
correlation between the presence of ED or EW groups on the
hydrazone moiety; however, BTPs containing EW groups gave a
slightly higher number of active compounds. Initially, BTPs were
tested using the Microwell Alamar Blue Assay (MABA)19a,b against
H37Rv, a virulent strain of M. tuberculosis. With the exception of 24
and 25—which were the only compounds exhibiting minimum
101.7
26.0
12.2
16.5
15.1
>170
4.5
>170
27.5
13.6
10.9
11.6
>170
89.9
>3.5
5.4
4.8
>170
<3.0
a
3T3, BALB/3T3 clone A31 embryonic mouse fibroblast cells; H460, human large
cell lung cancer; DU145, human prostate carcinoma; MCF-7, human breast ade-
nocarcinoma; M-14, human melanoma; HT-29, human colon adenocarcinoma;
K562, human chronic myelogenous leukemia cells.
b
5FU, 5-Fluoruracil.
inhibitory concentration (MIC) values below 20
15.7 M, respectively)—BTPs exhibited only very moderate anti-
TB potential under MABA conditions. A significant number of BTPs
had MICs below 100 M (1, 4, 9, 10, 18, 19, 26, 31 and 35), but only
10, 18, 24, 25 and 35 were relatively non-toxic in a VERO cell assay.
Only those compounds with anti-M. tuberculosis selectivity indices
(SI values) ranging from 1 to 6-fold were further tested in the Low
Oxygen Recovery Assay (LORA),19c also using the H37Rv strain of
M. tuberculosis. Interestingly, compounds 10, 18 and 35 were 2–8
lM (16.2 and
vitro information in hand, and aware of the lower cytotoxicity of 4,
we selected it for a short-term in vivo treatment assay. Compound
4 was suspended in 1% DMSO and administered daily to mice
through intraperitoneal injection on days 6–11 post-infection at
a concentration of 20 mg/kg/day. Treatment with Benznidazole
using this protocol resulted in a marked decrease in parasite rep-
lication over the 6-day treatment period but administration of 4
had no effect.16a There are several possible reasons for the discrep-
l
l

2884
J. C. Aponte et al. / Bioorg. Med. Chem. 18 (2010) 2880–2886
times more active in LORA than in MABA, whereby 18 and 35
exhibited the highest MICs in LORA (MIC = 9.7 and 8.7 M, respec-
tively). The same three compounds showed a greater SI in the LORA
system as well. On the other hand, compounds 24 and 25 exhibited
identical MICs and SI values in both bioassay panels.
The in vitro activity of BTPs against axenic amastigotes of L.
amazonensis is presented on Table 1. From these results, a direct
correlation between BTPs bearing ED or EW groups on the hydra-
zone moiety can be found. With exception of the moieties contain-
ing a nitrile or a nitro group on the aromatic moiety, it appears that
EW groups increase the in vitro anti-L. amazonensis activity and
selectivity of BTPs. With the exception of 26, aromatic systems
containing halogens (24, 25, 27–31) exhibited low IC50 values
(NCI) to be further tested in a 60 cell line panel; the results are
shown on Table S1 (in the Supplementary data). The NCI screening
confirmed the activity against human breast and human colon can-
l
cer, with GI50 values of 0.33 and 0.18 lM against MCF-7 and HT-29,
respectively. Furthermore, 21 was much more selective towards
HL-60 (TB) leukemia cell, HCT-116 colon cancer cell and OVCAR-
3 ovarian cancer cell lines than to the rest of cancer cell lines, its
GI50 values ranging from 0.11 to 0.17 lM. Recently a series of thi-
eno[2,3-d]pyrimidin-4-yl] hydrazones were found to be cyclin-
dependent kinase 4 (CDK4) inhibitors.10a Inhibition of CDK4 in-
duces G1 cell cycle arrest.
A computational study designed to predict the ADME properties
of our BTPs was performed, and the results are presented in Table
5. Topological polar surface area (TPSA) is a good indicator of drug
absorbance in the intestines, Caco-2 monolayers penetration, and
blood–brain barrier crossing.17a TPSA was used to calculate the
percentage of absorption (%ABS) according to the equation:
%ABS = 109 ꢀ 0.345 ꢁ TPSA, as reported by Zhao et al.17b In addi-
tion, the number of rotatable bonds (n-ROTB), and Lipinski’s rule
of five,17c were also calculated. All of the most active and selective
compounds found for each specific bioassay (compounds 4, 18, 21,
35 and 36) showed high percentages of intestinal absorption, with
values above 87%, and an excellent n-ROTB, ranging only from 3 to
4.17d None of these compounds violated any of the Lipinski’s
parameters, an important characteristic for future drug-devel-
opment.
(ranging from 0.9 to 2.0 lM) and high SIs (ranging from 3 to 85).
More interestingly, on compounds 28–29 and 30–31, the isomer
containing a halide substituent on the para-position of the phenyl
ring is more selective than the ortho-isomer. Compounds 6, 21, 28,
30 and 36 exhibited SIs greater than 8; they were selected for an
in vitro screening under a macrophage-infected model using three
of the most prevalent Leishmania strains in Peru, namely L. amazon-
ensis, L. brasilensis and L. peruviana. The results of this in vitro
screening are summarized in Table 2. Although there is no direct
correlation between the activity of the compounds on the axenic
amastigotes model and the macrophage-infected model, it can be
observed from this second screening that compounds 6 and 36
exhibited better and more congruent IC50 values on the macro-
phage-infected model than in the values obtained on the axenic
amastigote model, while compound 21, was only congruent in
the case of macrophages infected with L. brasilensis and L. peruvi-
ana. Aware of the toxicity of compounds 21 and 30, and consider-
ing their structural characteristics, we choose compounds 6, 28
and 36 for an in vivo assay; the results are presented in Table 3.
From this study, we can conclude that none of the tested com-
pounds was as effective as the positive control (N-methylgluca-
mine antimoniate, Gluc.) in reducing the lesion diameter.
Because the lesion diameter depends on various factors, such as
immune response, the inflammation process and parasite viru-
lence—which are not proportional to the parasite load and the par-
asite burden—the measure of percentage of reduction of the
parasite burden was completed by counting the L. amazonensis
amastigotes in the foot tissue using a fluorescent probe. From this
count, 36 (administered to the infected mice in a concentration al-
most seven times lower than the positive control) showed a 65%
reduction of the parasite burden, after 4 weeks; and a reduction
of its antiparasitic potential after completion of the in vivo assay.
None of the in vivo-assayed compounds exhibited any cutaneous
toxicity at the tested doses and the fact that they did not exhibit
a reduction of the lesion diameter is probably due to their lack of
anti-inflammatory activity.
The anti-tumor activity of BTPs is presented on Table 4. It can be
observed that the activity of this series of compounds is indepen-
dent of the presence of ED or EW substituents on the phenyl ring
of the hydrazone moiety. Compound 5 was found selective against
MCF-7 and K562 cell lines (human breast adenocarcinoma and hu-
man chronic myelogenous leukemia cell, respectively), while 12
and 18 were selective against MCF-7. Also, 17 was selective against
DU145, human prostate carcinoma. Three of the screened com-
pounds (4, 19 and 21) exhibited cytotoxicity below 5
lM to all cell
lines; indeed, compound 21 was found to be not only the most
cytotoxic compound of the entire series, (GI50 values ranged from
0.04 to 0.37 lM) but it also showed selectivity towards MCF-7
and HT-29 cell lines. In isomers 26–27 and 28–29, compounds con-
taining the halogen on the para-position were more active than
their ortho counterparts. Compound 21 was at least a threefold
more cytotoxic than its structural isomer 20. Because of its high
cytotoxicity, 21 was submitted to the National Cancer Institute
5. Conclusion
The collaborative effort of a multidisciplinary and international
network of scientist led to the synthesis and biological evaluation
of 38 tetrahydrobenzothienopyrimidines for their potential activ-
ity against three neglected diseases and several tumorogenic cell
lines. Compound 4 was effective in vitro against T. cruzi parasites;
compounds 18 and 35 were mildly selective towards the LORA for
M. tuberculosis; compound 28 was highly selective in vitro against
L. amazonensis, while compound 36 showed a 65% reduction of the
same parasitic burden on an in vivo assay; finally, compound 21
was the most cytotoxic against human cancer cell lines and has
been further screened at the NCI. These compounds contained a
variety of chemical functionalities and exhibited moderate to good
selectivity in the tested disease models. BTPs are easy to prepare
and exhibited promising drug-like properties. These are important
characteristics for future drug-optimization studies and possible
use in developing countries.
6. Experimental procedures
6.1. General methods
1H and 13C NMR spectra were recorded at 500 and 125 MHz,
respectively, using DMSO-d6 as a solvent on a Varian Inova 500.
The chemical shifts are reported in ppm values relative to DMSO-
d6 (2.62 ppm for 1H NMR and 40.76 ppm for 13C NMR). Coupling
constants (J) are reported in hertz (Hz). Melting points were mea-
sured on a Thomas Hoover capillary melting point apparatus and
are uncorrected. Elemental analysis was performed at Atlantic
Microlab, Inc., Norcross, GA. Reactions were monitored on Merck
silica gel 60 F254 aluminum sheets. TLC spots were visualized by
inspection of plates under UV light (254 and 365 nm) and after
submersion in 4% phosphomolybdic acid and heating (110 °C). All
commercial reagents were obtained either from Aldrich, Acros or
Alfa Aesar and used without any further purification. 3,5-Bisallyl-
oxy-4-bromobenzaldehyde was available from our laboratory.18

J. C. Aponte et al. / Bioorg. Med. Chem. 18 (2010) 2880–2886
2885
6.2. Synthesis of BTPs
G.B.H.), to the FINCYT-BID (Banco Interamericano para el Desarrol-
lo) Program in Peru (grant #PIBAB03-084 to M.S.), to the Infectious
Diseases Training Program in Peru # 5D43 TW006581 (R.H. G) and
to the NIH grant P01-044979 (to R.L.T.) for their financial support.
J.M.B and R.L.T. thank Adriana M. C. Canavaci at the CTEGD-Univer-
sity of Georgia for her technical assistance with the in vitro testing
of drugs for T. cruzi. The skillful technical assistance of Mrs. Baojie
Wan and Yuehong Wang, ITR, UIC College of Pharmacy, Chicago
(IL), is gratefully acknowledged.
Cyanoacetic acid ethyl ester (0.23 mol), diethyl amine
(1.0 equiv) and cyclohexanone (1.5 equiv) were dissolved in EtOH
(75 mL) and placed in an ice bath; after 5 min, elemental sulfur
(0.23 mol) was added and the mixture was sonicated at room
temperature for 30 min. After cooling inside a fridge for 1 h,
the pale yellow solid (A, 2-amino-4,5,6,7-tetrahydro-3-eth-
oxycarbonylbenzothiophene, 43.3 g, 84%) was filtered and washed
with a cold solution of 60% EtOH in H2O. After drying under vac-
uum overnight, A was suspended in formamide (400 mL) and re-
fluxed for 6 h. After cooling to room temperature, the dark
solution was placed inside a fridge overnight, and the dark brown
needles (B, 4-hydroxy-5,6-tetramethylenethieno[2,3-d]pyrimidine,
37.3 g, 95%) were filtered and washed with a cold solution of 40%
EtOH in H2O. After drying under vacuum overnight, B was sus-
pended in POCl3 (400 mL) and refluxed for 3 h. After cooling to
room temperature, the excess of POCl3 was removed under re-
duced pressure, and then 300 mL of CHCl3 were added and the
homogeneous solution was poured over iced deionized water
(500 mL). The resulting bilayer mixture was separated and the
aqueous layer was adjusted to pH 8 using NH4OH (concd) and then
extracted with CHCl3. The organic fractions were pooled and dried
over anhydrous MgSO4. The CHCl3 was removed under reduced
pressure and the remaining yellow solid was re-dissolved in hot
MeOH. Afterwards, the solution was allowed to cool to room tem-
perature and placed inside a fridge overnight. The precipitated
white crystals (C, 4-chloro-5,6,7,8-tetrahydro-[1]benzothieno[2,3-
d]pyrimidine, 29.1 g, 72%) were filtered, washed with a cold solu-
tion of 80% EtOH in H2O and dried overnight under vacuum. C
was suspended in MeOH (400 mL) and hydrazine hydrate 80%
(hydrazine 51%) in H2O (16 mL) and refluxed for 2 h; immediately
after, hydrazine (8 mL) was added to complete the reaction and the
mixture was allowed to reflux for 1 h. After cooling to room tem-
perature, it was placed in a fridge overnight. The resulting
yellow precipitate (D, 4-hydrazinyl-5,6,7,8-tetrahydro-[1]benzo-
thieno[2,3-d]pyrimidine, 24.1 g, 85%) was filtered and washed with
a cold solution of 40% EtOH in H2O. An aliquot of D (1 mmol) was
mixed with 1.2 equiv of the corresponding aldehyde or ketone and
dissolved in EtOH (10 to 15 mL), and the mixture was then refluxed
from 2 to 48 h. After cooling to room temperature, it was placed
overnight in a fridge and the colored-formed solid (1–38, 2-
(5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4-yl)hydra-
zone-derivative, 20–99%) was filtered, washed with a solution of
cold 80% EtOH in H2O, and recrystallized from EtOH.
Supplementary data
Supplementary data (1H and 13C NMR), elemental analysis, indi-
vidual tables for each test with cell/microorganism control, NCI re-
sults for 21, different Log P calculations of all tested compounds
and a brief description of the anti-M. tuberculosis and anti-L. ama-
zonensis bioassays) associated with this article can be found, in the
online version, at doi:10.1016/j.bmc.2010.03.018.
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6.3. In vitro, in vivo bioassays and calculation of physico-
chemical parameters
BTPs were evaluated against T. cruzi trypomastigotes in vitro,13a
and in vivo;16 against L. amazonensis axenic amastigotes in vitro
and in vivo;20 against tumorogenic cell lines in vitro,13b and against
M. tuberculosis in vitro under (MABA)19a,b and (LORA)19c assays,
using previously reported methodologies. BTPs physicochemical
properties were calculated using literature methods.13a,17
Acknowledgments
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G.B.H. and J.C.A. wish to acknowledge the early contribution of
Mr. Devin Pantess (University of Louisville) and Dr. Rosario Rojas
(Universidad Peruana Cayetano Heredia) in the synthesis of BTPs
and their anti-tuberculosis screening. The authors are grateful to
the USA Department of Defense Prostate Cancer Research Program
(PCRP) of the Office of the Congressionally Directed Medical Re-
search Programs (CDMRP) (Grant #W81XWH-07-1-0299 to

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