Synthesis, evaluation and molecular modelling studies of some novel 3-(3,4-dihydroisoquinolin-2(1H)-yl)-N-(substitutedphenyl)propanamides as HIV-1 non-nucleoside reverse transcriptase inhibitors

Article abstract of DOI:10.1007/s12039-010-0018-7

A novel series of fifteen 3-(3,4-dihydroisoquinolin-2(1H)-yl)-N- (substituted phenyl) propanamides 3(a-o) were synthesized by reacting the corresponding 3-chloro-N-(aryl) propanamides 2(a-o) with 1,2,3,4- tetrahydroisoquinoline 1 in acetonitrile. The compounds have been characterized on the basis of elemental analysis and spectral data. All the compounds were evaluated for their HIV-1 RT inhibitory activity. Among the synthesized compounds, 3-(3,4-dihydroisoquinolin-2(1H)-yl)-N-o-tolyl propanamide 3d and 3-(3,4-dihydroisoquinolin-2(1H)-yl)-N-(2,4,6-tribromophenyl)propanamide 3f were identified as significant inhibitors of HIV-1 reverse transcriptase with 56% and 43% residual RT activity respectively at the final concentration of 40 μM when compared with the standard drug Efavirenz. Docking studies with HIV-1 RT (PDB ID 1rt2) were also performed in order to investigate the binding pattern of these compounds. Indian Academy of Sciences.

Full text of DOI:10.1007/s12039-010-0018-7

J. Chem. Sci., Vol. 122, No. 2, March 2010, pp. 169–176. © Indian Academy of Sciences.
Synthesis, evaluation and molecular modelling studies of some
novel 3-(3,4-dihydroisoquinolin-2(1H)-yl)-N-(substituted-
phenyl)propanamides as HIV-1 non-nucleoside reverse
transcriptase inhibitors
1,
1
2
S MURUGESAN *, SWASTIKA GANGULY and GIOVANNI MAGA
1
Department of Pharmaceutical Sciences, Birla Institute of Technology, Mesra, Ranchi 835 215
2
DNA Enzymology and Molecular Virology Section, Instituto Di Genetica Molecolare, Pavia,
Italy-207-27100
e-mail: murugesaa789@yahoo.co.in, swastikaganguly@bitmesra.ac.in
MS received 2 February 2009; revised 8 May 2009; accepted 26 August 2009
Abstract. A novel series of fifteen 3-(3,4-dihydroisoquinolin-2(1H)-yl)-N-(substituted phenyl)
propanamides 3(a–o) were synthesized by reacting the corresponding 3-chloro-N-(aryl) propanamides
2(a–o) with 1,2,3,4-tetrahydroisoquinoline 1 in acetonitrile. The compounds have been characterized on
the basis of elemental analysis and spectral data. All the compounds were evaluated for their HIV-1 RT
inhibitory activity. Among the synthesized compounds, 3-(3,4-dihydroisoquinolin-2(1H)-yl)-N-o-tolyl
propanamide 3d and 3-(3,4-dihydroisoquinolin-2(1H)-yl)-N-(2,4,6-tribromophenyl)propanamide 3f were
identified as significant inhibitors of HIV-1 reverse transcriptase with 56% and 43% residual RT activity
respectively at the final concentration of 40 µM when compared with the standard drug Efavirenz. Dock-
ing studies with HIV-1 RT (PDB ID 1rt2) were also performed in order to investigate the binding pattern
of these compounds.
Keywords. HIV-1 reverse transcriptase (HIV-1 RT); non-nucleoside reverse transcriptase inhibitor
(NNRTI); docking; autodock; 1,2,3,4-tetrahydroisoquinoline.
1. Introduction
strate analogs of normal nucleotides that act com-
petitively at the catalytic site of HIV-1 RT and there
by terminating DNA synthesis, whereas NNRTIs are
a chemically diverse group of compounds that non-
competitively bind to the unique allosteric hydro-
phobic binding pocket located about 10 Å away
from the RT DNA polymerase active catalytic site
and 60 Å from the RT RNase H active site. NNRTI
binding induces rotamer conformational changes in
some residues and makes the thumb region more
Acquired immuno deficiency syndrome (AIDS) is
one of the most serious pandemic public health chal-
1
lenges since 1981. Human immuno deficiency virus
(HIV) has been identified as the probable causative
2
agent for AIDS. HIV-1 is a retrovirus and the
genome in the virion is encoded in single stranded
3
RNA. In an infected cell, the viral RNA is reverse
transcribed to produce a double stranded DNA pro-
virus by an enzyme known as DNA polymerase or
reverse transcriptase (RT) which is able to insert
rigid and thereby force the RT subunits into an inac-
14–16
tive conformation.
When compared to NRTIs,
4
itself into the host DNA. Because of the vital role
NNRTIs have the advantage of high potency, low
toxicity, high selectivity and specificity as well as
they will not interfere with the normal function of
of RT to HIV replication, inhibitor of this enzyme is
one of the major potential attractive targets in the
5–8
6
treatment of AIDS. In general, the inhibitors of
other host DNA polymerases. The efficacy of
HIV-1 RT are classified into two main categories:
NNRTIs is decreased due to emergence of drug
resistance mutations. To overcome these difficulties
novel NNRTIs are searched by modifying the exist-
ing drug classes with appropriate pharmacophoric
requirements. Earlier studies reveals that, more than
nucleoside/nucleotide inhibitors (NRTIs) and non-
9–13
nucleoside inhibitors (NNRTIs).
NRTIs are sub-
*For correspondence
169

170
S Murugesan et al
30 different classes of NNRTIs have some features phenyl propanamide (0⋅012 mol) 2a and triethyl-
in common, that is, the overall structure may be amine (0⋅024 mol) drop-wise and refluxed for 8 h.
considered reminiscent of a butterfly with hydro- The reaction mixture was then cooled, poured into
philic centre (‘body’) and two hydrophobic outskirts crushed ice and basified with solid potassium car-
17–20
(‘wings’).
bonate. The resulting precipitate was filtered, washed
Compounds having isoquinoline moiety exhibit with water, further washed with n-hexane, dried and
21–23
24–27
28–29
potent antiviral,
antiprotozoal, antimalarial,
vities since ancient days. An extensive perusal of
anti-tubercular,
antifungal,
recrystallized from ethanol to yield colourless cry-
and anticancer acti- stals of 3a.
IR (KBr) (cm ): 3298 (NH stretching of aromatic
30–45
46
–1
literatures showed that, little work has been done on secondary amide), 1662 (C=O stretching), 1323 (CN
synthetic tetrahydroisoquinolines as NNRTIs. In stretching of aliphatic amine).
1
view of these facts and our continued interest in the
H NMR (CDCl , 300 MHz): δ 6⋅9–7⋅6 (9H, m,
3
chemistry of tetrahydroisoquinolines, we report the ArH), 3⋅5 (2H, t, –N–CH –CH –CONH), 2⋅9 (2H, t,
2 2
synthesis of some novel 3-(3,4-dihydroisoquinolin- N–CH –CH –CONH), 2⋅7 (2H, t, N–CH –CH –Ar);
2 2 2 2
2(1H)-yl)-N-(substituted-phenyl)propanamides 3 with 2⋅3 (2H, t, N–CH –CH –Ar), 2⋅2 (2H, s, N–CH ).
2 2 2
+
‘butterfly-like’ congeners, evaluation for their HIV- MS: m/z 280 [M , C H N O, (18)], 281 (100), 279
18 20 2
1 reverse transcriptase inhibitory activity and dock- (25), 203 (10), 188 (15), 160 (12), 148 (18), 146
ing studies of the active compounds 3d and 3f on the (63), 134 (15), 132 (33) and 120 (18).
HIV-1-reverse transcriptase enzyme (PDB entry
1RT2). All the newly synthesized compounds were 2.1b 3-(3,4-Dihydroisoquinolin-2(1H)-yl)-N-(2-chlo-
–1
designed based on the derived pharmacophoric rophenyl)propanamide (3b): IR (KBr) (cm ):
19–20
model
with acetamide moiety (–CH2–CO–NH–) 3336 (NH stretching of aromatic secondary amide),
constituting the ‘body’ and the aryl rings of isoqui- 1680 (C=O stretching), 1350 (CN stretching of ali-
noline and substituted aromatic amines constituting phatic amine), 756 (C–Cl stretching).
the ‘wings’.
2.1c 3-(3,4-Dihydroisoquinolin-2(1H)-yl)
N-(3-
–1
chlorophenyl)propanamide (3c): IR(KBr) (cm ):
3335 (NH stretching of aromatic secondary amide),
1660 (C=O stretching), 1330 (CN stretching of ali-
phatic amine), 783 (C–Cl stretching).
2. Experimental
2.1 Materials, methods and instruments
Melting points were taken in open capillaries on
Thomas Hoover melting point apparatus and are
uncorrected. Infrared spectra were recorded on KBr
disks on a Shimadzu FTIR series1020 spectrometer.
2.1d 3-(3,4-Dihydroisoquinolin-2(1H)-yl)-N-o-tolyl
–1
propanamide (3d): IR(KBr) (cm ): 3228 (NH
stretching of aromatic secondary amide), 1653 (C=O
1
stretching), 1303 (CN stretching of aliphatic amine),
1
H NMR spectra were recorded on a Jeol D-
2980 and 1498 (C–CH stretching). H NMR
3
300 MHz Bruker FT-NMR spectrometer using
(CDCl , 300 MHz): δ 8⋅8 (s, 1H, NH), 6⋅8–7⋅7
3
CDCl as solvent. Mass spectral data were obtained
3
(m, 9H, ArH), 3⋅8 (s, 2H, N–CH –Ar), 2⋅9 (t, 4H,
2
on a Jeol D-300 spectrometer using Fast Atom
Bombardment (FAB positive). Elemental analysis
was performed on a Vario Elementor C, H, N ana-
lyser. Compounds 2a–o were prepared according to
N–CH –CH –Ar), 3⋅0 (t, 2H, CH ), 2⋅7 (t, 2H, CH ),
2 2 2 2
+
1⋅9 (s 3H Ar-CH ), MS: m/z 294 [M , C H N O,
3 19 22 2
(30)], 295 (100), 293 (75), 146 (82), 132 (70) and 91
(30).
47
the literature method. The reactions were moni-
tored by thin layer chromatography (TLC) carried
out on activated silica gel coated plates and the
solvent system used was chloroform : benzene :
methanol (3 : 0⋅3 : 0⋅1).
2.1e 3-(3,4-Dihydroisoquinolin-2(1H)-yl)-N-(4-chlo-
–1
rophenyl)propanamide (3e): IR(KBr) (cm ): 3483
(NH stretching of aromatic secondary amide), 1640
(C=O stretching), 1338 (CN stretching of aliphatic
1
amine), 742 (C–Cl stretching). H NMR (CDCl ,
3
2.1a Preparation of 3-(3,4-dihydroisoquinolin-
2(1H)-yl)-N-phenyl propanamide (3a): To a solu-
tion of 1,2,3,4-tetrahydroisoquinoline (0⋅012 mol) 1
in 16⋅7 ml of acetonitrile was added 3-chloro-N-
300 MHz): δ 11⋅10 (1H, s, NH), 7⋅70–7⋅32 (9H, m,
Ar-H), 3⋅80 (2H, s, N–CH –Ar), 2⋅94–2⋅89 (4H, m,
2
N–CH –CH –Ar), 3⋅03–3⋅00 (2H, t, N–CH –CH –
2 2 2 2

Studies of some novel 3-(3,4-dihydroisoquinolin-2(1H)-yl)-N-(substituted-phenyl)propanamides
171
CO), 2⋅65–2⋅61 (2H, t, N–CH –CH –CO). MS: m/z 2887 (C–CH stretching), 1647 (C=O stretching),
2 2 3
+
315 [M , C H N OCl, (100)], 316 (30), 314 (20), 1379 (CN stretching of aliphatic amine).
18 19 2
155 (20), 146 (90) and 132 (80).
2.1n 3-(3,4-Dihydroisoquinolin-2(1H)-yl)-N-(4-
–1
2.1f 3-(3,4-Dihydroisoquinolin-2(1H)-yl)-N-(2,4,6-
–1
methoxyhenyl)propanamide (3n): IR (KBr) (cm ):
tribromophenyl)propanamide (3f): IR(KBr) (cm ): 3306 (NH stretching of aromatic secondary amide),
3282 (NH stretching of aromatic secondary amide), 1660 (C=O stretching), 1354 (CN stretching of
1664 (C=O stretching), 1360 (CN stretching of ali- aliphatic amine), 1160 and 1031 (C–O–C stretch-
phatic amine), 601 (C–Br stretching).
ing).
2.1g 3-(3,4-Dihydroisoquinolin-2(1H)-yl)-N-(2-
2.1o 3-(3,4-Dihydroisoquinolin-2(1H)-yl)-N-(4-
–1
–1
hydroxyphenyl)propanamide (3g): IR (KBr) (cm ): ethoxyphenyl)propanamide (3o): IR (KBr) (cm ):
3650 (Phenolic –OH stretching), 3360 (NH stretching 3480 (NH stretching of aromatic secondary amide),
of aromatic secondary amide), 1635 (C=O stretch- 1680 (C=O stretching), 1360 (CN stretching of ali-
ing), 1440 (OH stretching), 1360 (CN stretching of phatic amine), 1219 and 1040 (C–O–C stretching).
aliphatic amine).
2.2 HIV-1 RT RNA dependent DNA polymerase
2.1h 3-(3,4-Dihydroisoquinolin-2(1H)-yl)-N-(3-
activity assay
–1
hydroxhphenyl)propanamide (3h): IR (KBr) (cm ):
3566 (phenolic –OH stretching), 3481 (NH stretching
All the synthesized compounds were evaluated for
of aromatic secondary amide), 1660 (C=O stretch-
HIV-1 RT inhibitory activity by using HIV-1 RT
48
ing), 1400 (OH stretching), 1320 (CN stretching of
RNA dependent DNA polymerase activity assay.
aliphatic amine).
Efavirenz was used as the standard. Poly(rA)/
oligo(dT) was used as a template for the RNA-
2.1i 3-(3,4-Dihydroisoquinolin-2(1H)-yl)-N-(2-nitro-
dependent DNA polymerase reaction by HIV-1 RT,
–1
phenyl)propanamide (3i): IR(KBr) (cm ): 3320
either wt or carrying the mutations. For the activity
(NH stretching of aromatic secondary amide), 1680
assay, a 25 μl final reaction volume contained TDB
(C=O stretching), 1579 (C–NO stretching), 1305
2
buffer (50 mM Tris-HCl (pH 8⋅0), 1 mM dithiothrei-
(CN stretching of aliphatic amine).
tol (DTT), 0⋅2 mg/ml bovine serum albumin (BSA),
2% glycerol), 10 mM MgCl , 0⋅5 mg of poly(rA):
2
3
2.1j 3-(3,4-Dihydroisoquinolin-2(1H)-yl)-N-(4-nitro-
–1
oligo(dT)
(0⋅3 mM 3′ –OH ends), 10 mM [H]-
10 : 1
phenyl)propanamide (3j): IR(KBr) (cm ): 3473
dTTP (1Ci/mmol) and finally, introduced into tubes
containing aliquots of different enzyme concentra-
tions (5 to 10 nM RT). After incubation at 37°C for
indicated time, 20 μL from each reaction tube were
spiked on glass fibre filters GF/C and immediately,
immersed in 5% ice-cold trichloroacetic acid (TCA)
(AppliChem GmbH, Darmstadt). Filters were washed
three times with 5% TCA and once with ethanol for
5 min, then dried and, finally, added with EcoLume®
Scintillation cocktail (ICN, Research Products Divi-
sion, Costa Mesa, CA USA), to detect the acid-
precipitable radioactivity by PerkinElmer® Trilux
MicroBeta 1450 Counter.
(NH stretching of aromatic secondary amide), 1680
(C=O stretching), 1560 (C–NO stretching), 1336
2
(CN stretching of aliphatic amine).
2.1k 3-(3,4-Dihydroisoquinolin-2(1H)-yl)-N-m-tolyl
–1
propanamide (3k): IR(KBr) (cm ): 3309 (NH
stretching of aromatic secondary amide), 2891
(C–CH stretching), 1670 (C=O stretching), 1332
3
(CN stretching of aliphatic amine).
2.1l 3-(3,4-Dihydroisoquinolin-2(1H)-yl)-N-p-tolyl
–1
propanamide (3l): IR (KBr) (cm ): 3284 (NH
stretching of aromatic secondary amide), 2821
(C-CH stretching), 1653 (C=O stretching), 1320
3
2.3 Computational studies
(CN stretching of aliphatic amine).
All computational studies were carried out using
49–52
2.1m 3-(3,4-Dihydroisoquinolin-2(1H)-yl)-N-(2,4-
–1
Autodock 4.0.1
installed in a single machine
dimethyphenyl)propanamide (3m): IR (KBr) (cm ): running on a 3⋅4 GHz Pentium 4 processor with
3290 (NH stretching of aromatic secondary amide), 512 MB RAM and 80 GB hard disk with Red Hat

172
S Murugesan et al
Table 1. Physical characterization data of compounds 3a–o.
Calculated (found)
Molecular
formula
Compound
Mol. wt.
m.p. (°C) Yield (%)
C
H
N
3a
3b
3c
3d
3e
3f
C H N O
18 20 2
280⋅37
314⋅82
314⋅82
294⋅40
314⋅82
517⋅06
296⋅37
296⋅37
325⋅37
325⋅37
294⋅40
294⋅40
308⋅42
310⋅52
324⋅42
165–170
80–88
65–70
98–104
78–82
90–94
82–90
108–112
84–90
78–82
58–64
90–96
108–112
90–96
70–74
82
97
95
75
89
84
98
98
82
82
90
91
97
96
78
77⋅11 (77⋅13)
68⋅67 (68⋅70)
68⋅67 (68⋅66)
77⋅52 (77⋅50)
68⋅67 (68⋅68)
41⋅81 (41⋅84)
72⋅95 (72⋅93)
72⋅95 (72⋅98)
66⋅45 (66⋅46)
66⋅45 (66⋅42)
77⋅52 (77⋅54)
77⋅52 (77⋅50)
77⋅89 (77⋅92)
73⋅52 (73⋅51)
74⋅04 (74⋅06)
7⋅19 (7⋅16)
6⋅08 (6⋅06)
6⋅08 (6⋅09)
7⋅53 (7⋅56)
6⋅08 (6⋅10)
3⋅31 (3⋅29)
6⋅80 (6⋅82)
6⋅80 (6⋅79)
5⋅89 (5⋅91)
5⋅89 (5⋅90)
7⋅53 (7⋅51)
7⋅53 (7⋅55)
7⋅84 (7⋅82)
7⋅14 (7⋅17)
7⋅46 (7⋅50)
9⋅79 (9⋅77)
8⋅90 (8⋅89)
8⋅90 (8⋅94)
9⋅52 (9⋅48)
8⋅90 (8⋅91)
5⋅42 (5⋅39)
9⋅45 (9⋅42)
9⋅45 (9⋅47)
12⋅91 (12⋅90)
12⋅91 (12⋅88)
9⋅52 (9⋅50)
9⋅52 (9⋅51)
9⋅08 (9⋅11)
9⋅03 (9⋅00)
8⋅64 (8⋅60)
C H N OCl
18 19 2
C H N OCl
18 19 2
C H N O
19 22 2
C H N OCl
18 19 2
C H N OBr
18 17 2 3
3g
3h
3i
C H N O
18 20 2
2
2
3
3
C H N O
18 20 2
C H N O
18 19 3
3j
C H N O
18 19 3
3k
3l
C H N O
19 22 2
C H N O
19 22 2
3m
3n
3o
C H N O
20 24 2
C H N O
19 22 2
3
2
C H N O
20 24 2
a; Ar = C H , b; Ar = 2-ClC H , c; Ar = 3-ClC H , d;
6 5 6 4 4
6
Ar = o-CH C H , e; Ar = 4-ClC H , f; Ar = 2,4,6-Br C H ,
3 4 3 6 2
6
4
6
g; Ar = 2-OHC H , h; Ar = 3-OHC H , i; Ar = 2-NO C H ,
6 4 6 4 4
2
6
j; Ar = 4-NO C H , k; Ar = m-CH C H , l; Ar = p-
6 4 3 6 4
2
CH C H , m; Ar = 2,4-(CH ) C H , n; Ar = p-OCH C H ,
3 6 4 3 2 6
3
3
6
4
o; Ar = p-OC H C H .
2 5 6 4
Scheme 1. Synthetic protocol of the compounds.
49–52
Autodock 4.0.1
was used to explore the bind-
ing conformation of TNK 651 4 and active test
molecules. The AutodockTools package version
1.4.6 was employed to generate the docking input
files and to analyse the docking results. All the non-
polar hydrogens were merged and the water mole-
cules were removed. For the docking, a grid spacing
of 0⋅375 Å and 60 × 60 × 60 number of points was
used. The grid was centered on the mass center of the
experimental bound TNK 651 coordinates. Auto-
dock generated 50 possible binding conformations,
i.e. 50 runs for each docking by using genetic algo-
Linux Enterprise version 3.0 as the operating sys-
tem.
The geometry of the NNBS of the wt RT strain was
taken from the structure of HIV-1 RT/TNK 651
complex filed in the Brookhaven Protein Data
53
Bank (entry code 1rt2). All the residues within
20 Å core from TNK 651 4 were used to define the
NNBS. The starting conformations for docking
studies were obtained using molecular dynamics
with simulated annealing as implemented in SYBYL
7.1.

Studies of some novel 3-(3,4-dihydroisoquinolin-2(1H)-yl)-N-(substituted-phenyl)propanamides
173
rithm (GA-LS) searches. A default protocol was 3. Results and discussion
applied, with an initial population of 150 randomly
5
3.1 Synthesis of 3-(3,4-dihydroisoquinolin-2(1H)-
placed individuals, a maximum number of 2⋅5 × 10
yl)-N-(substituted-phenyl) propanamides
energy evaluations, and a maximum number of
4
2⋅7 × 10 generations. A mutation rate of 0⋅02 and a
Synthesis of title compound is effected by reacting
the corresponding 3-chloro-N-(aryl) propanamide
with 1,2,3,4-tetrahydroisoquinoline in presence of
triethylamine by using acetonitrile as solvent. In this
reaction, the liberated HCl is neutralized with solid
anhydrous potassium carbonate, repeated washings
with water and finally with n-hexane.
crossover rate of 0⋅8 were used.
To validate the use of the Autodock program, re-
docking was performed on the reference compound
TNK 651 and for comparison purpose, cross docking
was performed on the standard NNRTI Efavirenz 5.
Autodock successfully reproduced the experimental
binding conformations of the reference drug TNK
651 with acceptable root-mean-square deviation
(RMSD) of 0⋅56 Å. The structures of the newly syn-
thesized 3-(3,4-dihydroisoquinolin-2(1H)-yl)-N-(sub-
stituted phenyl)propanamides were drawn and
The FT–IR spectra of all the synthesized com-
1
pounds and H NMR spectra of the compounds 3a,
3d and 3e were in complete agreement with the as-
signed structure. In case of IR spectral analysis, broad
–1
band in the region between 3228 and 3298 cm con-
54
optimized using PRODRG online server and saved
firms the presence of NH stretching of aromatic sec-
ondary amide in the title compounds. The carbonyl
group appeared as sharp band in the region between
in PDB format. These structures were used for
the docking studies and the interactions of the
active compounds 3d and 3f as shown in figures 1a
and b.
–1
–1
1653 and 1662 cm . Another band around 744 cm
was appeared in the compound 3d is mainly due to
the presence of mono chloroalkanes. Appearance of
–1
absorbance band around 3650–3560 cm indicates
the presence of phenolic hydroxyl group in the com-
pounds 3g and 3h. A sharp absorbance band around
–1
1579–1560 cm confirms the presence of C–NO
2
stretching in the compounds 3i and 3j. The com-
pounds 3n and 3o showed absorbance band around
–1
1219–1031 cm indicates the presence of C–O–C
1
stretching. H NMR spectral analysis of the com-
pounds 3d and 3e exhibited a broad singlet at δ 8⋅80
and 11⋅10 ppm respectively confirming the presence
of NH group. Aromatic protons were appeared in the
expected range of δ 6⋅80–7⋅30 ppm as multiplet
which confirms the presence of aromatic functional
group. A triplet in the range between δ 2⋅90 and
3⋅50 ppm is mainly due to the presence of N–CH –
2
CH –CONH group. Compound 3d exhibited singlet
2
at δ 1⋅90 ppm assigned to methyl group at ortho
position in the aromatic amino phenyl ring.
The FAB mass spectra of the compounds 3a, 3d
and 3e showed a molecular ion peak at m/z 280, 294
and 315 respectively confirming the molecular
weight of the appropriate title compounds.
Figure 1. (a) interaction between the compound 3d
(ball and stick model) and residues (coloured line model
with three letter codes) within the HIV-1 RT NNBP ob-
tained by the docking procedure. The rest of the protein
structure was suppressed for clarification purposes. (b)
Interaction between the compound 3f (ball and stick
model) and residues (coloured line model with three letter
codes) within the HIV-1 RT NNBP obtained by the dock-
ing procedure. The rest of the protein structure was sup-
pressed for clarification purposes.
The elemental analysis data of the all synthesized
compounds were within 0⋅4% of the theoretical values.
3.2 HIV-1 RT inhibitory activity
All the synthesized compounds were evaluated for
HIV-1 RT inhibitory activity using HIV-1 RT RNA

174
S Murugesan et al
48
dependent DNA polymerase activity assay. Efavirenz ties of the compounds 3d and 3f at the NNIBP of
was used as the standard. The screening results indi- HIV-1-RT. From these docking studies, it was pre-
cate that compounds 3d and 3f were significantly dicted that both the active analogs 3d and 3f adopt a
active against HIV-1 reverse transcriptase at the common type of ‘butterfly-like’ confirmation within
final concentration of 40 μM with 56% and 43% the active site of NNIBP of HIV-1 RT which resem-
residual RT activity respectively.
bles the same binding confirmation as that of first
generation NNRTIs (i.e. nevirapine, delavirdine and
efavirenz).
3.3 Molecular docking and binding mode analysis
4. Conclusion
The binding mode of the active compounds 3d and
3f were investigated. Ligand structures were drawn
and optimized using PRODRG online server and
saved in PDB format. Autodock 4.0.1 program was
used to dock 3d and 3f into the RT non-nucleoside
inhibitor binding pocket (NNIBP). The NNIBP was
obtained using the coordinates of HIV-1-RT/TNK
651 taken from the Protein Brookehaven Database
(PDB entry code 1rt2).
In this study, some novel analogs of 3-(3,4-
dihydroisoquinolin-2(1H)-yl)-N-(substituted phenyl)
propanamide were synthesized based on common
pharmacophoric requirements for NNRTIs and has
been confirmed by spectral and elemental analysis.
All the analogs were screened for HIV-1 RT inhibi-
tory assay. Docking studies of the most active ana-
logs 3d and 3f were carried out to understand their
exact binding mode in the active site of HIV-1 RT
as well as to study their interaction with amino acid
residues of HIV-1 RT. This led us to conclude that,
the active analogs 3d and 3f adopt a similar ‘butter-
fly-like’ orientation like some classical NNRTIs
(nevirapine, delavirdine and efavirenz) within the
active site of NNIBP of HIV-1 RT. Further modifi-
cations in the phenyl portion of the tetrahydroiso-
quinoline nucleus in the two active analogs 3d and
3f could be carried out, which may lead to signifi-
cantly active compounds with improved in vitro
potency and in vivo efficacy against both wild and
resistant strains of HIV-1.
The docking experiments were carried out using
the Lamarckian genetic algorithm with local search
(GA-LS) hybrid formalism of the docking program
Autodock 4.0.1. Initially, the docking of TNK 651 4,
which is extracted, previously from 1rt2 receptor
complex into the RT was performed to test the reli-
ability and reproducibility of the docking protocol
for our study. Secondly similar docking experiment
was performed using standard molecule Efavirenz 5
for comparison purpose.
Autodock was able to reproduce the experimental
binding conformation of 4 within a minimal root
mean square deviation (RMSD = 0⋅56 Å). The esti-
mated binding free energy and predicted inhibitory
constant value for the compound 3d was –10⋅48 and
20⋅86 nM respectively. From the figure 1a, it was
observed that, the tetrahydroisoquinoline moiety of
Acknowledgements
3d was oriented towards the hydrophobic pocket One of the authors S M thankfully acknowledges the
formed by the side chains of TYR 318, PRO 236, financial help in form of Quality Improvement Pro-
HIS 235 and PHE 227 and the phenyl group substi- gramme (QIP) Fellowship provided by All India
tuted at the ortho position with methyl group is sur- Council of Technical Education (AICTE), New
rounded by the residues VAL 106, LEU 100 and Delhi, India during the course of study. We are
GLY 190 of HIV-1 RT NNIBP. For the compound grateful to the Sophisticated Analytical Instrument
3f, the estimated binding free energy and predicted Facility, Central Drug Research Insitute (CDRI),
inhibitory constant value was –10⋅36 and 25⋅62 nM Lucknow, India) for providing NMR and Mass spec-
respectively. From the figure 1b, it was observed tral data. We are also thankful to the Central Instru-
that, the tetrahydroisoquinoline moiety of 3f was mentation Facility (CIF, Birla Institute of
oriented towards the side chains of TRP 229, TYR Technology, Mesra) for providing IR spectral data.
181 and PRO 96 and the phenyl group substituted
with three bromine atoms at 2nd, 4th and 6th posi-
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