Synthesis of C-methyl chalcones as HIV-integrase inhibitors - Computational approach

Article abstract of DOI:10.1007/s00044-013-0687-0

Eight new 3-methyl chalcones (3a-h) were synthesized for active inhibition against HIV-integrase basing on docking studies on a series of titled compounds. The selected integrase (IN) enzyme is taken as an attractive target for therapeutic drug design. Th

Full text of DOI:10.1007/s00044-013-0687-0

MEDICINAL
CHEMISTRY
RESEARCH
Med Chem Res
DOI 10.1007/s00044-013-0687-0
ORIGINAL RESEARCH
Synthesis of C-methyl chalcones as HIV-integrase
inhibitors—computational approach
•
•
•
A. Vasu Babu Ramesh Navudu G. Trimurtulu
B. Hari Babu
Received: 6 April 2013 / Accepted: 26 July 2013
Ó Springer Science+Business Media New York 2013
Abstract Eight new 3-methyl chalcones (3a–h) were
synthesized for active inhibition against HIV-integrase
basing on docking studies on a series of titled compounds.
The selected integrase (IN) enzyme is taken as an attractive
target for therapeutic drug design. The protease, reverse
transcriptase, and IN were the three viral enzymes encoded
within the HIV pol gene and translated as a polyprotein.
Retroviral IN is an enzyme produced by a retrovirus (such
as HIV) that enables its genetic material to be integrated
into the DNA of the infected cell. Basing on the literature
and computational study new analogs of C-methyl chal-
cones were identified as antiretroviral drugs. Prominent
G-score was obtained for compounds 3e (-6.86604), 3g
(-6.8236), and 3h (-6.58996) out of the estimated series
of analogs.
Davies, 2004). The HIV genome consists of single-stan-
dard RNA like other retroviruses. The viral RNA is
released into the host cell following fusion of the viral
particles to the cell membrane during infection (Sierra
et al., 2005). This viral RNA serves as a template for the
synthesis of a double-stranded DNA copy of the viral RNA
(cDNA) bearing long terminal repeats by the HIV-encoded
reverse transcriptase. The conversion of the viral RNA into
cDNA is necessary for making new viral RNA copies and
for transcribing the virally encoding genes. Transcription
of the viral cDNA also requires its insertion into a host
chromosome (Semenova et al., 2010). In recent years drug
discovery inventions are now turning toward allosteric IN
inhibitors which should be devoid of cross-resistance with
IN strand transfer inhibitors. An attempt was made to
evaluate their mechanism of action basing on docking
studies of these molecules in the IN pocket.
Keywords C-methyl chalcones ꢀ HIV-integrase ꢀ
Docking studies
One of the chalcone (2-methoxy-3-methyl-4,6-dihy-
droxy-5-(30-hydroxy)-cinnamoyl benzaldehyde) isolated
from the Desmos spp. (Wu et al., 2003) had showed potent
anti-HIV activity with EC50 values of 0.022 and 2.30 lg/mL
and therapeutic indexes of 489 and 45.2, respectively. Basing
on this report, in the present investigation an attempt was
made to develop a new series of chalcone compounds by
docking approach and was also aimed to synthesize the
compounds.
Introduction
HIV-1 integrase (IN) is a multidomain enzyme which is
required for the integration of viral DNA into the host
genome. It is one of the three enzymes of HIV, the others
being the Reverse Transcriptase and the Protease. It is an
attractive target for therapeutic drug design (Chiu and
Results and discussions
A. Vasu Babu ꢀ R. Navudu ꢀ B. Hari Babu (&)
Department of Chemistry, Acharya Nagarjuna University,
Nagarjunanagar, Guntur 522510, Andhra Pradesh, India
e-mail: drharibabuanu@gmail.com
From the G-score (Table 1) it was clearly understood that
when there was only an m-substitution (either ?I group)
without any other substitutions or any halogen substitution
on ligand, the ligand interacts more effectively with the
protein. The molecule 3e with ethoxy group at m-position
G. Trimurtulu
Laila Impex R&D Center, Jawahar Autonagar,
Vijayawada 520007, Andhra Pradesh, India
123

Med Chem Res
got the best dock pose with G-score -6.86. No regular
hydrogen bonds were identified in this pose with any of
binding site residues of 3OAY. Interestingly the molecule
was able to coordinate with metal cofactor of the enzyme
by its suitable positioned carbonyl and hydroxyl oxygen
atoms (Fig. 1). These interactions satisfactorily drew the
molecule inside the binding pocket for better fit which can
be seen in the surface view of ligand–target binding site
complex (Fig. 2). The compounds (3g) with hydroxyl
group at m-position also got G-score -6.82, similarly the
compound 3h also showed dock score -6.58996 that may
be due to hydroxyl group at p-position.
Conjugate gradient protocol. Partial atomic charges were
computed using the OPLS-2005 force field. The LigPrep is
a utility in Schrodinger software suite that combines tools
for generating 3D structures from 1D (Smiles) and 2D
(SDF) representation, searching for tautomers and steric
isomers, and geometry minimization of ligands. Finally, 32
poses had been prepared with different tautomeric and
steric features for docking studies.
Docking
Docking studies were performed using Docking protocol of
¨
GLIDE v5.5 from Schrodinger Suite 2009 (Glide, Version
5.5, 2009). GLIDE scoring function was used to calculate
the binding affinity. The prepared target structure was used
for docking simulations. Initially a receptor grid, where the
ligand has to be docked with the receptor was set by
picking the centroid of the co-crystallized inhibitor present
at the active site. It creates a grid box and the size of the
Experimental
Protein preparation
X-ray crystal structure of HIV IN (PDB id: 3OAY) was
downloaded from www.rcsb.org. The protein (PDB: 3OAY
Chain B) was prepared using the Protein Preparation
Wizard. Preprocessed bond orders were assigned, hydro-
gens were added, metals were treated, and water molecules
were deleted. Heterostate for co-crystallized ligand was
generated using Epik, protonation state and optimization of
H-bonding of the protein side chains were assigned using
Protassign. Energy minimization was done (impref mini-
mization) using Optimized Potentials for Liquid Simula-
tions (OPLS) 2001 force field (Jorgensen et al., 1996).
˚
grid box was limited to 20 A. The output of different
conformations of the docked complexes (poses) was set to
a maximum of 20. Then the molecules were docked at the
active site of 3OAY. The poses generated were ranked
based on G-score. The poses with better G-score were
further analyzed for interactions. The best docked pose was
selected as the one with the lowest G-score; the more
negative the G-score, the more favorable the binding.
Further, the dock score was compared with that of the
reference substrate.
Ligand preparation
Synthesis of chalcones
The structure of the compounds were drawn by using
chemsketch (ACDLABS 12.0) and converted to 3D struc-
ture with the help of 3D optimization tool. By using the
LigPrep (2.3) module (Ligprep, Version 2.3, 2009), the
drawn ligand was geometry optimized by using the OPLS-
2005 (Cornell et al., 1995; Duan et al., 2003) force field
with the Steepest Descent followed by truncated Newton
Chemicals and equipment
Acetophenone (synthesized in our laboratory) and other
chemicals used were of AR grade (Merck). Melting points
were taken in open glass capillary by using Remi melting
1
point apparatus and were uncorrected. H NMR spectra
were recorded on Brucker 400 MHz and 13C NMR was on
Table 1 Synthesized chalcones (3a–h)
Compound
R1
R2
R3
R4
R5
G-score
a
b
c
d
e
f
OCH3
Cl
H
OCH3
H
H
H
H
H
H
H
H
H
H
-5.83644
-6.73129
-6.50991
-6.46386
-6.86604
-6.41563
-6.8236
H
H
OCH3
H
H
OCH3
OCH3
H
–O–CH2–O–
H
OC2H5
H
H
H
H
OC2H5
H
H
g
h
H
OH
H
H
H
OH
H
-6.58996
All these compounds were first time prepared by us
123

Med Chem Res
Fig. 1 Ligand (3e) interactions
with protein (3OAY)
Fig. 2 3D-view of ligand (3e)
interactions with protein
(3OAY)
Brucker 100 MHz. Mass spectra were recorded on LC/MS
Agilent LC1100 series.
(6H, s, OCH3 at C-4, 6), 3.84 (3H, s, OCH3 at C-20), 3.35
(3H, s, OCH3 at C-60), 2.30 (3H, s, CH3 at C-3). 13C NMR
(CDCl3, 100 MHz, d in ppm): 193.4 (C=O), 164.2 (C-2),
163.1 (C-4), 162.7 (C-6), 160.9 (C-40), 160.1 (C-20), 137.8
(C-b), 130.2 (C-10), 125.8 (C-a), 117.8 (C-60), 106.5 (C-50),
106.1 (C-3), 105.5 (C-1), 98.4 (C-30), 86.4 (C-5), 55.7, 55.5
(OCH3 at C-4, 6), 55.4, 55.3 (OCH3 at C-40, 20), 7.28 (CH3
at C-3). MS: m/z (M-H)- at 357.2, mass-358.2. M.F.
C20H22O6.
General method for synthesis of chalcones
Chalcones (3a–d) were synthesized by using Claisen con-
densation (Scheme 1-Ia) and chalcones (3e–h) were pre-
pared by using the hot condensation process (Scheme 1-Ib).
To a solution of acetophenone (0.5 g, 0.00238 mol) and
substituted benzaldehydes (2a–h) (1 eq) in ethanol (10 mL),
aqueous potassium hydroxide (0.599 g, 4.5 eq in 0.5 mL
water) is added. The mixture is stirred at room temperature
for 24 h. To this, ice-cold water was added and the separated
solid was filtered and dissolved in ethyl acetate, dried over
sodium sulfate, and concentrated under vacuum.
3-(2-Chlorophenyl)-1-(2-hydroxy-4,6-dimethoxy-3-methyl-
phenyl)prop-2-en-1-one (3b) This compound was
obtained as a yellow solid, mp. 184–185 °C, yield 55 %.
1H NMR (CDCl3, 400 MHz, d in ppm): 13.95 (1H, s,
OH at C-2), 8.12 (1H, d, J = 15.6 Hz, H-b), 7.84 (1H, d,
J = 16.0 Hz, H-a), 7.685 (1H, m, H-40), 7.43 (1H, m,
H-50), 7.32 (2H, m, H-30, 60), 5.99 (1H, s, H-5), 3.93 (3H, s,
OCH3 at C-4), 3.90 (3H, s, OCH3 at C-6), 2.03 (3H, s, CH3
at C-3). 13C NMR (CDCl3, 100 MHz, d in ppm): 192.7
(C=O), 164.3 (C-2), 163.8 (C-4), 161.1 (C-6),137.4 (C-b),
135.3 (C-20), 134.1 (C-10), 130.5 (C-60), 130.2 (C-40), 127.8
(C-30), 127.6 (C-50), 126.9 (C-a), 106.4 (C-3), 106.3 (C-1),
86.4 (C-5), 55.8, 55.5 (OCH3 at C-4, 6), 7.2 (CH3 at C-3).
MS: m/z (M?H)? at 333.1, mass-332.1, M.F. C18H17O4Cl.
3-(2,4-Dimethoxyphenyl)-1-(2-hydroxy-4,6-dimethoxy-3-
methylphenyl)prop-2-en-1-one (3a) This compound was
obtained as a yellow solid. mp. 195–197 °C, yield 75 %.
1H NMR (CDCl3, 400 MHz, d in ppm): 14.29 (1H, s,
OH at C-2), 8.10 (1H, d, J = 15.6 Hz, H-b), 7.89 (1H, d,
J = 15.6 Hz, H-a), 7.54 (1H, d, J = 8.4 Hz, H-60), 6.52
(1H, m, H-50), 6.4 (1H, s, H-30), 5.97 (1H, s, H-5), 3.88
123

Med Chem Res
R2
Scheme 1 Synthesis of
chalcones (3a–h). Reagents and
conditions: Ia KOH/EtOH,
24 h. Ib KOH/EtOH, 24 h, D at
50 °C
R1
CH3
CHO
R3
3′
CH3
R5
OH
4′
H3CO
R3
′
R1
R2
3
2
2
OH
Ia/Ib
H3CO
5′
+
4
5
β
α
′
1
1
6′
R4
R4
R5
6
OCH3 O
OCH3O
2a-h
3a-h
1
CH3). 13C NMR (CDCl3, 100 MHz, d in ppm): 192.5
(C=O), 163.7 (C-2), 162.7 (C-4),161.1(C-6), 158.9 (C-30),
141.7 (C-b), 136.3 (C-10), 130.1 (C-60), 127.1 (C-a), 120.4
(C-50), 116.6 (C-40), 114.1 (C-20), 105.6 (C-1), 104.2 (C-3),
87.6 (C-5), 63.1 (O–CH2–CH3), 56.2, 55.8 (OCH3 at C-4,
6), 14.5 (–CH2–CH3), 7.2 (CH3 at C-3). MS: m/z at 343.2;
mass-342.2, M.F. C20H22O5.
1-(2-Hydroxy-4,6-dimethoxy-3-methylphenyl)-3-(2,4,6-tri-
methoxyphenyl)prop-2-en-1-one (3c) This compound was
obtained as a yellow solid, mp. 187–190 °C, yield 72 %.
1H NMR (CDCl3, 400 MHz, d in ppm): 14.42 (1H, s,
OH at C-2), 8.32 (1H, d, J = 15.6 Hz, H-b), 8.21 (1H, d,
J = 15.6 Hz, H-a), 6.13 (2H, s, H-30, 50), 5.98 (1H, s, H-5),
3.92 (3H, s, OCH3 at C-40), 3.90 (6H, s, OCH3 at C-20,
C-60), 3.88 (3H, s, OCH3 at C-4), 3.85 (3H, s, OCH3 at
C-6), 2.02 (3H, s, CH3 at C-3). 13C NMR (CDCl3,
100 MHz, d in ppm): 194.5 (C=O), 164.2 (C-2), 162.8
(C-4), 162.8 (C-6), 161.6 (C-20, 60),160.9 (C-40), 133.8
(C-b), 127.5 (C-a), 107.3 (C-10), 106.9 (C-1), 106.1 (C-3),
90.7 (C-30, 50), 86.5 (C-5), 55.7 (OCH3 at C-20, 60), 55.6,
55.4, 55.3 (OCH3 at C-40, 4, 6), 7.3 (CH3 at C-3). MS:
m/z (M?H)? at 389.2, mass-388.15, M.F. C21H24O7.
3-(4-Ethoxyphenyl)-1-(2-hydroxy-4,6-dimethoxy-3-methyl-
phenyl)prop-2-en-1-one (3f) This compound was
obtained as a yellow solid, mp. 96–98 °C, yield 85 %.
1H NMR (CDCl3, 400 MHz, d in ppm): 13.94 (1H, s,
OH at C-2), 7.81 (1H, d, J = 16.0 Hz, H-b), 7.73 (1H, d,
J = 15.6 Hz, H-a), 7.69 (2H, d, J = 8.8 Hz, H-20, 60), 7.62
(2H, d, J = 8.4 Hz, H-30, 50), 6.28 (1H, s, H-5), 4.12 (2H,
q, J = 7.8 Hz, –OCH2–CH3), 3.92 (3H, s, OCH3 at C-4),
3.90 (3H, s, OCH3 at C-6), 1.99 (3H, s, CH3 at C-3), 1.37
(3H, t, J = 6.8 Hz, –OCH2–CH3), 13C NMR (CDCl3,
100 MHz, d in ppm): 192.3 (C=O), 163.5 (C-2), 162.9
(C-4), 161.5 (C-6), 160.4 (C-40), 142.3 (C-b), 135.3 (C-10),
130.3 (C-20, 60), 127.3 (C-a), 120.4 (C-30, 50), 106.6 (C-3),
105.0 (C-1), 87.5 (C-5), 63.3 (–OCH2–CH3), 55.9, 55.8
(OCH3 at C-4, 6), 14.5 (–CH2–CH3), 7.1 (CH3 at C-3).
MS: m/z (M?H)? at 343.2; mass-342.2, M.F. C20H22O5.
3-(Benzo[d][1,3]dioxol-5-yl)-1-(2-hydroxy-4,6-dimethoxy-
3-methylphenyl)prop-2-en-1-one (3d) This compound
was obtained as a yellow solid, mp. 188–190 °C, yield
85 %.
1H NMR (CDCl3, 400 MHz, d in ppm): 14.12 (1H, s,
OH at C-2), 7.71 (2H, brs, H-a, b), 7.35 (1H, m,
H-50), 7.10 (1H, s, H-80), 7.02 (1H, m, H-60), 6.82 (1H, s,
H-5), 6.01 (2H, brs, H-20), 3.90 (6H, s, OCH3 at C-4, 6),
2.03 (3H, s, CH3 at C-3). 13C NMR (CDCl3, 100 MHz, d in
ppm): 192.8 (C=O), 164.2 (C-2), 163.4 (C-4), 161.0
(C-6), 149.4 (C-40), 148.3 (C-90),141.9 (C-b), 130.2
(C-70), 126.1 (C-a), 124.8 (C-60), 108.6 (C-50), 106.6 (C-
80), 106.3 (C-1), 106.1 (C-3), 101.4 (C-20), 86.4 (C-5), 55.8,
55.4 (OCH3 at C-4, 6), 7.2 (CH3 at C-3). MS: m/z (M?H)?
at 343.2; mass-342.2, M.F. C19H18O6.
1-(2-Hydroxy-4,6-dimethoxy-3-methylphenyl)-3-(3-
hydroxyphenyl)prop-2-en-1-one (3g) This compound was
obtained as a yellow solid, mp. 160–165 °C, yield 76 %.
1H NMR (CDCl3, 400 MHz, d in ppm): 13.99 (1H, s,
OH at C-2), 9.67 (1H, s, OH at C-30), 7.82 (1H, d,
J = 15.6 Hz, H-b), 7.62 (1H, d, J = 15.6 Hz, H-a), 7.28
(1H, t, J = 8.0 Hz, H-50), 7.16 (1H, d, J = 7.6 Hz, H-60),
7. 09 (1H, s, H-20), 6.87 (1H, d, J = 7.6 Hz, H-40), 6.30
(1H, s, H-5), 4.0 (3H, s, OCH3 at C-4), 3.93 (3H, s, OCH3
at C-6), 1.93 (3H, s, CH3 at C-3). 13C NMR (CDCl3,
100 MHz, d in ppm): 192.4 (C=O), 163.6 (C-2), 162.9
(C-4), 161.1 (C-6), 157.7 (C-30), 142.1 (C-b), 136.1 (C-10),
130.1 (–C-60), 127.2 (C-a), 119.6 (C-50), 117.6 (C-40),
114.3 (C-20), 105.5 (C-3), 104.2 (C-1), 87.6 (C-5), 56.2,
55.8 (OCH3 at C-4, 6), 7.3 (CH3 at C-3). MS: m/z
(M-H)-at 313.2; mass-314.2, M.F. C18H18O5.
3-(3-Ethoxyphenyl)-1-(2-hydroxy-4,6-dimethoxy-3-methylphenyl)
prop-2-en-1-one (3e) This compound was obtained as a
yellow solid, mp. 92–94 °C, yield 80 %.
1H NMR (CDCl3, 400 MHz, d in ppm): 13.9 (1H, s, OH
at C-2), 7.8 (1H, d, J = 15.6 Hz, H-b), 7.6 (1H, d,
J = 16.0 Hz, H-a), 7.36 (1H, m, H-50), 7.24 (1H, s, H-20),
7.30 (1H, d, J = 7.2 Hz, H-60), 7.01 (1H, d, J = 7.6 Hz,
H-40), 6.29 (1H, s, H-5), 4.11 (2H, q, J = 7.2 Hz, O–CH2–
CH3), 3.98 (3H, s, OCH3 at C-4), 3.93 (3H, s, OCH3 at C6),
1.93 (3H, s, CH3 at C-3), 1.37 (3H, t, J = 6.8 Hz, –CH2–
123

Med Chem Res
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1-(2-Hydroxy-4,6-dimethoxy-3-methylphenyl)-3-(4-
hydroxyphenyl)prop-2-en-1-one (3h) This compound was
obtained as a yellow solid, mp. 105–110 °C, yield 75 %.
1H NMR (CDCl3, 400 MHz, d in ppm): 13.94 (1H, s, OH at
C-2), 10.09 (1H, s, OH at C-40), 7.80 (1H, d, J = 15.6 Hz,
H-b), 7.60 (1H, d, J = 15.6 Hz, H-a), 7.28 (2H, d,
J = 8.0 Hz, H-20, 60), 6.86 (2H, d, J = 7.6 Hz, H-30, 40), 6.27
(1H, s, H-5), 3.92 (3H, s, OCH3 at C-4), 3.90 (3H, s, OCH3 at
C-6), 1.92 (3H, s, CH3 at C-3). 13C NMR (CDCl3, 100 MHz, d
in ppm): 192.4 (C=), 163.5 (C-2), 162.5 (C-4), 161.5(C-6),
157.9 (C-40), 142.2 (C-b), 136.3 (C-10), 130.1 (C-20,60), 127.2
(C-a), 119.6 (C-30,50), 105.1 (C-3), 103.8 (C-1), 87.1 (C-5),
55.9, 55.8 (OCH3 at C-4, 6), 7.1 (CH3 at C-3). MS:
m/z (M?H)? at 315.2; mass-314.2 M.F. C18H18O5.
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