Synthesis and biological evaluation of novel small non-peptidic HIV-1 PIs: The benzothiophene ring as an effective moiety

Article abstract of DOI:10.1016/j.bmcl.2012.02.046

Synthesis and biological evaluation of a new series of potential HIV-1 protease inhibitors incorporating different heterocycles are described. The variation of heteroatom in such molecules has displayed totally different biological activities and a benzothiophene containing inhibitor has shown high potency against wild type HIV-1 protease with IC₅₀ = 60 nM, thanks to the lower desolvation penalty to be payed by such hydrophobic moiety.

Full text of DOI:10.1016/j.bmcl.2012.02.046

Bioorganic & Medicinal Chemistry Letters 22 (2012) 2948–2950
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Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Synthesis and biological evaluation of novel small non-peptidic HIV-1 PIs:
The benzothiophene ring as an effective moiety
Lucia Chiummiento a, Maria Funicello a, , Paolo Lupattelli a, Francesco Tramutola a, Federico Berti b,
⇑
Francesca Marino-Merlo c
a Dipartimento di Chimica ‘Antonio Mario Tamburro’, Università degli Studi della Basilicata, Viale dell’ Ateneo Lucano 10, 85100 Potenza, Italy
b Dipartimento di Scienze Chimiche, Università degli Studi di Trieste, Via Giorgieri 1, 34127 Trieste, Italy
c Dipartimento di Scienze della Vita, Sez. Scienze Microbiologiche Genetiche e Molecolari, Università degli Studi di Messina, Via F. Stagno d’Alcontres 31, Messina 98166, Italy
a r t i c l e i n f o
a b s t r a c t
Article history:
Synthesis and biological evaluation of a new series of potential HIV-1 protease inhibitors incorporating
different heterocycles are described. The variation of heteroatom in such molecules has displayed totally
different biological activities and a benzothiophene containing inhibitor has shown high potency against
wild type HIV-1 protease with IC50 = 60 nM, thanks to the lower desolvation penalty to be payed by such
hydrophobic moiety.
Received 5 January 2012
Revised 10 February 2012
Accepted 15 February 2012
Available online 23 February 2012
Ó 2012 Elsevier Ltd. All rights reserved.
Keywords:
HIV protease
Inhibitor
Heterocycles
Synthesis
The devastating effect of the AIDS epidemic is a reality we are
currently still dealing with.1 However, since the highly active anti-
retroviral therapy (HAART), protease inhibitors (PIs) in combination
with reverse transcriptase inhibitors (RTIs), has been employed to
combat the illness, HIV infection has definitely become more
manageable.2 Hence HIV protease has been a very attractive target
to develop new HIV drugs3 but despite the already marketed PIs
have an evident crucial role into HAART regimen, some complex
issues associated with these drugs remain unsolved.4 These include
poor bioavailability, side effects, treatment cost and the most
worrying problem, drug resistance. This emergency has led scien-
tists to seek novel structures able to overcome such problems.5
Working on this direction, we recently demonstrated the bene-
ficial effect of a heteroaromatic group in a series of new thienyl
ring containing analogues of two approved PIs, nelfinavir and
saquinavir.6 Indeed such molecules were able to maintain or even
increase the activity of the original drugs against either wild type
or mutant HIV protease. Moreover, we also reported the facile
synthesis and biological evaluation of new non-peptidic heteroaro-
matic molecules as PIs, which displayed modest activities.7 Among
were suitable moieties to be linked to a stereochemically defined
isopropanolic core, to obtain biological activity.
On the basis of this result, we have therefore been really intri-
gued by understanding the actual importance of the indole NH
function regarding the efficiency of 1. Thus, our initial intention
was to protect the nitrogen with a methyl or a benzyl group and
then to switch the heteroatom to oxygen or sulfur in order to check
any variation of antiviral activity with the resulting structures 2–5
(Fig. 1).
The synthesis of molecules 2–5 is depicted in Scheme 1. Com-
mercially available (S)-glycidol (98% ee) was reacted with 3-nitro-
benzenesulfonyl chloride (NsCl) and triethylamine (Et3N) in dry
dichloromethane (DCM) at À10 °C to afford 6 in 80% yield. Glycidyl
nosylate 6, which represents a versatile building block in total
synthesis,8 was subjected to a regioselective displacement of the
nosylate with the appropriate 5-hydroxyheteroarene and K2CO3
in dry dimethylformamide (DMF) at room temperature (rt) to pro-
vide the corresponding epoxides 7, 10 and 11 in 70%, 78% and 82%
OMe
them the best one (1) showed an IC50 of 1 lM. Despite the moder-
OMe
ate potency, this small molecule represented a reference structure,
considering the ease of its preparation. Therein we determined that
5-hydroxyindolic ring and 3,4-dimethoxy-benzenesulfonamide
OH
O
N
O
S
O
X
1 X= NH
2 X= NMe
3 X= NBn
4 X= O
⇑
Corresponding author. Tel.: +39 0971 205490; fax: +39 0971 205678.
E-mail address: maria.funicello@unibas.it (M. Funicello).
5
X= S
0960-894X/$ - see front matter Ó 2012 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2012.02.046
Figure 1. Inhibitors 1–5.

L. Chiummiento et al. / Bioorg. Med. Chem. Lett. 22 (2012) 2948–2950
2949
M)
Table 1
O
O
b
NsO
O
Anti-HIV activity against wild type protease
a
6
Entry
Inhibitor
IC50
1
(l
X
1
2
3
4
5
6
1
2
3
4
c
a
8 X= NMe
9 X= NBn
>1000
>1000
130
7
X= NH
X= O
d
(S)-glycidol
10
5
0.06
11 X= S
Nelfinavir
0.009b
a
e
IC50 values were obtained by measuring the initial rates of hydrolysis of the
fluorogenic substrate Abz-Thr-Ile-Nle-Phe(NO2)-Gln-Arg. Results are the mean of at
least three independent experiments.
12 X= NMe
13 X= NBn
14
b
The IC50 for nelfinavir has been measured as a reference in the same assay.
OH
O
NH
X= O
15 X= S
X
activity. The benzofuran containing compound 4 was significantly
less potent than 1, but in contrast compound 5, bearing a
f
benzothiophene, exhibited a 16-fold improvement, reaching a
12
OMe
60 nM IC50
.
2 X= NMe
3 X= NBn
X= O
OMe
Alkylation at indole nitrogen leads to inactive compounds, most
likely due to steric reasons, and the replacement of nitrogen with
oxygen is not effective. However, the more hydrophobic ben-
zothiophene containing compound is significantly more active
than the parent indole molecule, and the enhanced activity is
consistent with a reduced desolvation penalty. We have calculated
the free energy of solvation of compounds 1 and 5 with the IEF
polarizable continuum model13 with the b3lyp density functional
at the 6-3111++g(3d,3p) level of theory (Table 2), and we have
found that solvation of the indole derivative is more favourable
by about 5 kcal/mol. This difference fully explains the nanomolar
activity of 5 in comparison with the micromolar activity of 1, as
the more polar compound is going to lose solvent stabilization
upon entering the hydrophobic catalytic site, while 5 is already
lacking of such stabilization.
OH
O
N
O
4
S
O
5 X= S
X
Scheme 1. Reagents and conditions: (a) NsCl, Et3N, DCM, À10 °C, 5 h, 80%; (b) Het-
OH, K2CO3, DMF, rt, 14 h, 70–82%; (c) MeI, NaH, DMF, rt, 1 h, 90%; (d) BnCl, NaH,
DMF, rt, 1 h, 86%; (e) i-BuNH2, i-PrOH, rt, 24 h, quantitative; (f) 3,4-diMeO–C6H3–
SO2Cl, Et3N, DCM, rt, 24 h, 89–92%.
yields, respectively.9 Indole derivative 7 was alkylated with methyl
iodide (MeI) and benzyl chloride (BnCl) in the presence of NaH in
dry DMF to furnish 8 and 9 in 90% and 86% yields. Oxiranyl ring
opening reaction on 8–11 with i-BuNH2 in i-PrOH at rt provided
aminoalcohols 12–15 in quantitative yields. These compounds
were subsequently reacted with 3,4-dimethoxybenzenesulfonyl
chloride and Et3N in dry DCM to afford target compounds 2–5 in
89%, 90%, 92% and 90% yields, respectively.
We have carried out several attempts to obtain a crystal
structure of the HIV protease–5 complex, but the crystallization
trials were not successful.
5-Hydroxybenzothiophene was prepared according to our re-
ported procedure for the synthesis of 5-hydroxybenzofuran10
(Scheme 2). Thus, 4-methoxythiophenol 16 was reacted with
bromoacetaldehyde diethyl acetal and K2CO3 in dry DMF at reflux
to furnish 17 in 86% yield which was directly used in the next
reaction without further purification. Compound 17 was converted
to 5-methoxybenzothiophene11 18 by treatment with polypho-
sphoric acid (PPA) in toluene at reflux in 24% yield. Demethylation
of 18 with BBr3ÁSMe2 in dry chlorobenzene at reflux provided
5-hydroxybenzothiophene (19) in 81% yield.
Table 2
Free energy of solvation of 1 and 5
a
Inhibitor
D
Gsol (Kcal/mol)
1
5
À17.69
À12.84
a
b3lyp/6-3111++g(3d,3p)/IEFPCM free energy of
solvation: Gsol Gsol(polarized G(cavi-
G(dispersion) G(repulsion) solvent = water.
D
=
D
+ D
+ D
solvent)
solute
À
+
D
tation)
With these new potential inhibitors in hand, we could finally
evaluate their potency against wild type HIV-1 protease: these
results are shown in Table 1. Alkylation of the indole NH function
with a methyl (2) or benzyl (3) group led to a complete loss of
MeO
MeO
EtO
S
OEt
a
SH
17
16
b
HO
MeO
c
S
S
19
18
Scheme 2. Reagents and conditions: (a) BrCH2CH(OEt)2, K2CO3, DMF. reflux, 3 h,
Figure 2. Overlay of the two most favourable docking poses of inhibitor 1 inside wt
HIV protease. The indole system is placed in S1 subsite in both cases, with different
orientation.
86%; (b) PPA, toluene, reflux, 2 h, 24%; (c) BBr3ÁSMe2, chlorobenzene, reflux, 8 h,
81%.

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L. Chiummiento et al. / Bioorg. Med. Chem. Lett. 22 (2012) 2948–2950
M. N. L.; Anjum, S. G.; Cao, H.; Chellappan, S.; Kairys, V.; Fernandes, M. X.;
Docking of the inhibitors, carried out with Autodock Vina,14
suggests a S1 placement for the heterocyclic moiety of the mole-
cule (Fig. 2), and the system is in contact with Ile50, Pro81 and
Val82, in an overall hydrophobic environment.
Pleased to have found a really promising inhibitory activity for
compound 5 we also evaluated its in vitro cytotoxicity which re-
sulted minimal, indeed the concentration that reduced the meta-
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bolic activity of target cells by 50% (CC50) was greater than 90 lM.
In summary we have reported synthesis and biological evalua-
tion of a series of novel compounds bearing a heteroarene moiety.
We have discussed about the relation between heteroatom nature
and inhibitory effectiveness of corresponding molecules. The ben-
zothiophene containing compound 5 has displayed a potent anti-
viral activity which is worth to be underlined especially in view
of its small structure with resulting short and cheap synthesis.
We anticipate that further elaborations of this molecule are cur-
rently ongoing in our laboratory.
Acknowledgments
6. Bonini, C.; Chiummiento, L.; De Bonis, M.; Di Blasio, N.; Funicello, M.; Lupattelli,
P.; Pandolfo, R.; Tramutola, F.; Berti, F. J. Med. Chem. 2010, 53, 1451.
7. Chiummiento, L.; Funicello, M.; Lupattelli, P.; Tramutola, F.; Campaner, P.
Tetrahedron 2009, 65, 5984.
Support has been provided by MIUR (Italian Ministry of Univer-
sity) - PRIN 2008 and Università degli Studi della Basilicata.
8. Hanson, R. M. Chem. Rev. 1991, 91, 437.
Supplementary data
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11. For other synthesis of 5-methoxybenzothiophene see: (a) Pérez-Silanes, S.;
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Tetrahedron 2003, 59, 4767. and references cited therein.
Supplementary data associated with this article can be found, in
the online version, at doi:10.1016/j.bmcl.2012.02.046.
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