Design, synthesis and biological evaluation of novel 5-((substituted quinolin-3-yl/1-naphthyl) methylene)-3-substituted imidazolidin-2,4-dione as HIV-1 fusion inhibitors

Article abstract of DOI:10.1016/j.bioorg.2020.103782

A series of novel 5-(substituted quinolin-3-yl or 1-naphthyl)methylene)-3-substituted imidazolidin-2,4-dione 9–26 was designed and synthesized. The prepared compounds were identified using ¹H NMR, ¹³C NMR as well as elemental analyses. The inhibitory activity of 9–26 on HIV-1_IIIB replication in MT-2 cells was evaluated. Some derivatives showed good to excellent anti-HIV activities as compounds 13, 18, 19, 20, 22 and 23. They showed EC₅₀ of 0.148, 0.460, 0.332, 0.50, 0.271 and 0.420 μM respectively being more potent than compound I (EC₅₀ = 0.70 μM) and II ( EC₅₀ = 2.40 μM) as standards. The inhibitory activity of 9–26 on infected primary HIV-1 domain, 92US657 (clade B, R5) was investigated. All the tested compounds consistently inhibited infection of this virus with EC₅₀ from 0.520 to 11.857 μM. Results from SAR studies showed that substitution on ring A with 6/7/8-methyl group resulted in significant increase in the inhibitory activity against HIV-1_IIIB infection (5- >300 times) compared to the unsubstituted analog 9. The cytotoxicity of these compounds on MT-2 cells was tested and their CC₅₀ values ranged from 11 to 85 μM with selectivity indexes ranged from 0.53 to 166. The docking study revealed nice fitting of the new compounds into the hydrophobic pocket of HIV-1 gp41 and higher affinity than NB-64. Compound 13, the most active in preventing HIV-1_IIIB infection, adopted a similar orientation to compound IV. Molecular docking analysis of the new compounds revealed hydrogen bonding interactions between the imidazolidine-2,4-dione ring and LYS574 which were missed in the weakly active derivatives.

Full text of DOI:10.1016/j.bioorg.2020.103782

BioorganicChemistry99(2020)103782
Contents lists available at ScienceDirect
Bioorganic Chemistry
journal homepage: www.elsevier.com/locate/bioorg
Design, synthesis and biological evaluation of novel 5-((substituted
quinolin-3-yl/1-naphthyl) methylene)-3-substituted imidazolidin-2,4-dione
as HIV-1 fusion inhibitors
⁎
Tarek S. Ibrahima,b, , Riham M. Bokhtiab,c, Amany M.M. AL-Mahmoudyb, Ehab S. Taherd,
Mohammed A. AlAwadha, Mohamed Elagawanye, Eatedal H. Abdel-Aalb, Siva Pandac,
⁎
Ahmed M. Goudaf, Hany Z. Asfourg, Nabil A. Alhakamyh, Bahaa G.M. Youssifi,
a Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia
b Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
c Department of Chemistry and Physics, Augusta University, Augusta, GA 30912, USA
d Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt
e Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Damanhour University, Damanhour, Egypt
f Department of Medicinal Chemistry, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt
g Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
h Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia
i Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
A R T I C L E I N F O
A B S T R A C T
Keywords:
Imidazolidine-2,4-dione
Quinoline
HIV
A series of novel 5-(substituted quinolin-3-yl or 1-naphthyl)methylene)-3-substituted imidazolidin-2,4-dione
9–26 was designed and synthesized. The prepared compounds were identified using 1H NMR, 13C NMR as well as
elemental analyses. The inhibitory activity of 9–26 on HIV-1IIIB replication in MT-2 cells was evaluated. Some
derivatives showed good to excellent anti-HIV activities as compounds 13, 18, 19, 20, 22 and 23. They showed
EC50 of 0.148, 0.460, 0.332, 0.50, 0.271 and 0.420 μM respectively being more potent than compound I
(EC50 = 0.70 μM) and II ( EC50 = 2.40 μM) as standards. The inhibitory activity of 9–26 on infected primary
HIV-1 domain, 92US657 (clade B, R5) was investigated. All the tested compounds consistently inhibited in-
fection of this virus with EC50 from 0.520 to 11.857 μM. Results from SAR studies showed that substitution on
ring A with 6/7/8-methyl group resulted in significant increase in the inhibitory activity against HIV-1IIIB in-
fection (5- > 300 times) compared to the unsubstituted analog 9. The cytotoxicity of these compounds on MT-2
cells was tested and their CC50 values ranged from 11 to 85 μM with selectivity indexes ranged from 0.53 to 166.
The docking study revealed nice fitting of the new compounds into the hydrophobic pocket of HIV-1 gp41 and
higher affinity than NB-64. Compound 13, the most active in preventing HIV-1IIIB infection, adopted a similar
orientation to compound IV. Molecular docking analysis of the new compounds revealed hydrogen bonding
interactions between the imidazolidine-2,4-dione ring and LYS574 which were missed in the weakly active
derivatives.
Inhibitors
Gp41
1. Introduction
inhibitors (PIs) resulted in the loss of cytotoxic activity of many anti-
HIV therapies counting highly active antiretroviral therapy (HAART)
Acquired immunodeficiency syndrome (AIDS) is a universal health
risk and is considered one of the foremost causes of death in many HIV-
infected patients [1]. In addition to long-term use toxicity and high
cost; drug resistance growth for many antiretroviral drugs in present
use, particularly reverse transcriptase inhibitors (RTIsa) and protease
[2-4]. Therefore, advances in drug design and modeling are urgently
needed in order to develop new compounds with potent anti-HIV ac-
tivity and new modes of action [5]. Attachment and insertion into the
host cell membrane is the most important step for human im-
munodeficiency virus type 1 (HIV-1) to begin its life cycle through the
⁎ Corresponding authors at: Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia. (T.S. Ibrahim).
Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt. (B.G.M. Youssif).
E-mail addresses: tmabrahem@kau.edu.sa (T.S. Ibrahim), bgyoussif@ju.edu.sa, bahaa.youssif@pharm.aun.edu.eg (B.G.M. Youssif).
https://doi.org/10.1016/j.bioorg.2020.103782
Received 29 December 2019; Received in revised form 19 February 2020; Accepted 19 March 2020
Availableonline24March2020
0045-2068/©2020ElsevierInc.Allrightsreserved.

T.S. Ibrahim, et al.
BioorganicChemistry99(2020)103782
Fig. 1. Small molecules with HIV-1 gp41 inhibitory activities.
use of host cell machinery [6], thereby, development of new fusion
inhibitors has been the focus of new drug discovery for many years
[7–10]. Viral envelope binding glycoprotein (Env) surface subunit
gp120 to cellular receptor CD4 and co-receptor CXCR4 or CCR5 in-
itiates HIV-1 entry by activating a sets of conformational changes in the
transmembrane subunit gp41 leading to formation of a six-helix bundle
(6-HB) core and facilitating the fusion of membranes [11–13]. Three
parallel N-terminal heptad repeat units (NHR) frequently form an in-
ternal trimeric coiled coil, and three C-terminal heptad repeat units
(CHR) are then packed into the hydrophobic grooves retained on the
central trimeric core in an anti-parallel manner [14–17]. A deep hy-
drophobic cavity in the groove substantially establishes the 6-HB and
serves as an attractive base for the development of small molecule HIV
fusion/entry inhibitors [18]. Previously, N-substituted pyrrole deriva-
tives (I) and (II) (NB-2 and NB-64) were reported [19] as small mole-
cules with low micromolar inhibitory action against HIV-1 infection,
HIV-1 Env-mediated cell-cell fusion and gp41 six-helix bundles, Fig. 1.
Docking studies showed that both (I) and (II) bind on the gp41 NHR-
trimer to the deep hydrophobic cavity, but only fill a portion of the
pocket space [19]. Later on, Katritzky et al. have reported a series of 2-
MT-2 cells (CC50 = 27.85 μM). Accordingly, the tetrazolyl analog V
exhibited a selectivity index (SI) of 1989 compared to 484 for the
parent IV. Replacement of the furan oxygen by NH group resulted in
decrease in both anti-HIV-1IIIB activity (EC50 = 0.615 μM) and se-
lectivity (SI = 48) to one-tenth of the parent IV [21]. Jiang et al also
have reported another 2,5-disubstituted furans/pyrroles series with
higher anti-HIV-1 activity than (I) and (II) [22]. Among these deriva-
tives, compound VI displayed significant inhibition against HIV-1IIIB
infection [22]. Mechanistic study revealed the ability of compound VI
to block gp41 six-helix bundle formation. Although carboxylic acid
group seems to be important for the binding to gp41, several nonacidic
compounds were reported as HIV-1 gp41 fusion inhibitors. Among
these inhibitors which lack the carboxylic acid group, SB-H02, com-
pound VII (Fig. 2) showed HIV-1 inhibitory activity with IC50 of
13.3 μM [10]. In addition, Frey et al. have developed a protein-based
assay to screen the ability of small molecules to inhibit the formation of
post fusion gp41 [23]. They have screened several library including
34800 small organic compounds for their ability to inhibit HIV infec-
tion. Among the tested compounds, four compounds have displayed the
most promising results. Of these compounds 5M038 VIII and S2986 IX
exhibited envelop-mediated membrane fusion in viral infectivity and
cell-cell fusion assay, Fig. 2. DAA-9 X was identified through a docking
protocol as potential gp41 fusion inhibitor [24]. Docking results of
DAA-9 revealed binding affinity to gp41 comparable to that of NB-64
(II). Moreover, DAA-9 also showed in vitro anti-HIV-1 activity com-
parable to that of NB-64.
aryl-5-(4-oxo-3-phenethyl-2-thioxothiazolidin-ylidene
methyl)furan
derivatives [20] with anti-HIV-1 activity. The new derivatives exhibited
higher anti-HIV-1 activity than (I) and (II). This could be suggested that
the highly bulky molecule may occupy more space in the hydrophobic
cavity, and consequently, higher binding activity and stronger in-
hibitory activity on 6-HB formation [20]. Among these derivatives,
compound III was the most selective (SI = 426), Fig. 1.
Jiang et al have also reported two series of 5-((aryl-furan/1H-pyrrol-
2-yl)methylene)-2-thioxo-3-(3-(trifluoromethyl)phenyl)-thiazolidin-4-
ones which showed effective inhibition of HIV-1 infection [21]. Among
these derivatives, compound IV blocked gp41 six-helix bundle forma-
tion and HIV-1 mediated cell-cell fusion, Fig. 1. Replacement of the
carboxylic group in compound IV with the isosteric tetrazole ring
(Compound V) resulted in significant increase in the anti-HIV-1IIIB ac-
tivity (EC50 = 0.014 μM) with slight increase in cytotoxicity against
1.1. Rational and design
Compounds IV and V were reported among a series of 4-thiazoli-
dinone-based derivatives that 6-target HB formation in HIV-1 gp41
[21]. Molecular docking analysis of this series revealed the importance
of the salt-bridge, hydrophobic, and hydrogen bond-forming groups in
their structures for inhibition of 6-HB formation. However, evaluation
of drug-likeness parameters of compounds IV and V revealed high
2

T.S. Ibrahim, et al.
BioorganicChemistry99(2020)103782
Fig. 2. HIV-1 gp41 fusion inhibitors lacking the carboxylic acid group.
Fig. 3. Rational design and structural modification of scaffold A.
lipophilicity (ClogP > 5), high molecular weight (> 500), low drug-
likeness score and 1–2 violations from Lipinski, Ghose, Egan and
Muegge rules (Supplementary data, Tables S1 and S2, Figs. S1 and S2).
Moreover, the presence of carboxylic acid group seems to be not es-
sential for the anti-HIV activity of compounds VII-X. accordingly, the
aim of the present study was to manipulate the chemical structure of
compound IV to obtain new potent antiviral agents, lacking the car-
boxylic acid group.
of TMP as a base. The prepared compounds were identified using 1
H
NMR, 13C NMR as well as elemental analyses. The inhibitory ac-
tivity of 9–26 on HIV-1IIIB replication was evaluated using an p24
measurement enzyme-linked immunosorbent assay (ELISA) in MT-2
cells against (I) and (II) (NB-2 and NB-64) as the reference com-
pounds.
Scaffold A (Fig. 3) was designed by isosteric replacement of the
two sulfur atoms in compound IV with the more polar groups (O and
NH) which can bind to the hydrophobic pocket of HIV-1 GP41 pro-
tein through hydrogen bonding interactions, Fig. 3. In addition, the
2-fluoro-3-(furan-2-yl)benzoic acid moiety in compound IV was re-
placed with quinoline nucleus, substituted with various hydrophobic
substituents (CH3, OCH3, OCH(CH3)2) that can interact hydro-
phobically with the hydrophobic residues in GP41. Position 2 of the
quinoline nucleus was substituted with either electron-donating/
withdrawing groups to evaluate the impact of their electronic effects
on the activity of the new compounds. The length of the spacer in
scaffold A was increased to two carbon atoms to extend the hydro-
phobic scaffold and increase molecular volume of the new com-
pounds which allow them to occupy larger volumes of the hydro-
2 Results and discussion
2.1 Chemistry
Synthesis of 9–26 having 5-((substituted quinolin-3-yl or 1-naph-
thyl)methylene)-3-substituted imidazolidine-2,4-diones was outlined in
Scheme 1. Imidazolidine-2,4-dione 1 was reacted with (2-bromoethyl)
benzene or benzyl bromide in dimethylformamide to afford 3-Sub-
stituted imidazolidine-2,4-dione 3a-b [25]. Refluxing of 3a-b with
substituted quinolin-3-aldehyde [26] 6a-g and 7a-d or 1-naphthalde-
hyde 8 derivatives in the presence of TMP in ethanol to yield the de-
sired target products 9–26. As a representative example of this series,
the 1H NMR spectrum of 24 demonstrated the presence of a signal at
10.95 ppm of NH, two sets of C8-H and C6-H of quinoline doublets at
7.70 and 7.40 ppm with J = 2.5 Hz each, two signals with one and six
protons integration at 3.24 (s) and 165–1.61 (m) ppm attributed to
isopropyl group and olefinic proton signal at δ 6.40 (s) as well as aro-
matic protons. The 13C NMR spectrum of compound 24 showed two
signals at 162.8 and 157.9 ppm assigned to the ketonic carbonyls of
imidazolidine-2,4-dione and all other carbons appear at their expected
chemical shifts. In addition, data from the elemental analysis further
confirmed the assigned structure.
phobic pocket.
A preliminary evaluation of physicochemical
properties of the prototype derivative (9) of scaffold A revealed an
improvement in physicochemical properties and drug-likeness score
(Supplementary data, Tables S3 and S4, Fig. S3).
The synthesis of newly designed compounds was done by
Knoevenagel condensation reaction between 3-substituted im-
midazolidin-2,4-dione 3a,b [25] and either substituted quinolin-3-
aldehyde (6a-g and 7a-d) [26] or 1-naphthaldehyde (8) in presence
3

T.S. Ibrahim, et al.
BioorganicChemistry99(2020)103782
0.460, 0.332, 0.50, 0.271 and 0.420 μM respectively being more potent
than compound I (EC50 = 0.70 μM) and II ( EC50 = 2.40 μM) but less
potent than compound IV (EC50 = 0.064 μM) as standards. The 3-
benzyl-5-((2-chloro-8-methylquinolin-3-yl) methylene) derivative 13
(R = 8-Me, X = Cl and n = 1) was the most effective of the synthesized
derivatives with an EC50 value of 0.148 µM against MT-2 cell. The
unsubstituted derivative 9 (R = H) was about 348 folds less potent than
13 showing EC50 50.61 µM. Replacement of the 8-Me group in com-
pound 13 by 6-methyl or 6-OMe or even 7-Me in compounds 10, 11 and
12 respectively resulted in a reduction in the EC50 value of a least 5
folds, indicating the importance of the 8-methyl group for HIV-1IIIB
replication in MT-2 cell inhibitory activity. Moreover, the 5-((2-chloro-
8-methylquinolin-3-yl)methylene)-3-phenethyl derivative 20 (R = 8-
Me, X = Cl and n = 2) was less potent than 13 suggesting the im-
portance of the N-benzylimidazolidine-2,4-dione architecture for the
inhibitory activity. It should be noted that compounds 21–24 with 2-
OMe in the quinoline ring were more active than their 2-Cl congeners 9,
11, 14 and 16 respectively.
Comp
R
X
n
Comp
R
X
n
9
H
Cl
Cl
Cl
Cl
Cl
Cl
Cl
Cl
1
1
1
1
1
2
2
2
17
18
19
20
21
22
23
24
7-CH3
7-OCH3
7-OCH(CH3)2
8-CH3
H
Cl
2
2
2
2
1
1
2
2
10
11
12
13
14
15
16
6-CH3
6-OCH3
7-CH3
8-CH3
H
Cl
Cl
Cl
OCH3
OCH3
OCH3
OCH3
6-OCH3
H
6-CH3
6-OCH3
6-OCH3
2.2. Biological activities
2.2.1. HIV-1 inhibitory activity
p24 ELISA assay was used to test the inhibitory effect of 9–26 on
HIV-1 IIIB replication in MT-2 cells [27] using I and II as the reference
compounds, Table 1. Most of the compounds tested substantially in-
hibited dose-dependent replication of HIV-1IIIB. Generally, 5-((sub-
stituted-quinolin-3-yl)methylene)-3-substituted imidazolidin-2,4-dione
derivatives 9–24 showed superior inhibitory activity compared to their
naphthyl counterparts 25 and 26, Table 1. The best compounds against
HIV-1IIIB are 13, 18, 19, 20, 22 and 23, which showed EC50 of 0.148,
The 9–26 inhibitory effect on primary HIV-1 isolate, 92US657 (class
B, R5), as class B is the most prevalent subtype in the United States, has
been determined. All the compounds examined reliably inhibited HIV-1
92US657 isolate infection with EC50 between 0.520 and 11.857 μM,
o
Reagents and conditions: (i) DMF, K2CO3, 80 C, overnight; (ii) Ac2O, AcOH, rt, 1h; (iii) DMF,
POCl3, 70 oC, 18h; (iv) NaOMe, EtOH, 40 oC, 3-6h; (v) EtOH, TMP, reflux, 72h.
Scheme 1. Synthetic route of novel (Z)-5-((substituted quinolin-3-yl or 1-naphthyl) methylene)-3-substituted imidazolidine-2,4-diones 9–26. Reagents and con-
ditions: (i) DMF, K2CO3, 80 °C, overnight; (ii) Ac2O, AcOH, rt, 1 h; (iii) DMF, POCl3, 70 °C, 18 h; (iv) NaOMe, EtOH, 40 °C, 3–6 h; (v) EtOH, TMP, reflux, 72 h.
4

T.S. Ibrahim, et al.
BioorganicChemistry99(2020)103782
Table 1
compound 12. However, a slight increase in anti-HIV-1 activity and a
significant increase in selectivity was observed on replacement of the 6-
methyl group in compound 10 by methoxy group. In addition, in-
creasing the length of the spacer between the phenyl and the imida-
zolidine ring by one carbon resulted in reduction of the inhibitory ac-
tivity and selectivity against HIV-1. The resulting compound 20 was
more than three times less potent than compound 13. The removal of
the 8-methoxy group in compound 20 decreased both activity and se-
lectivity against HIV-1. The 8-desmethoxy analog 14 (EC50 = 2.92 μM,
SI = 29.25) was nearly 6 times less potent than compound 20, Fig. 4.
An increase in activity of compound 14 was observed on replace of
the 2-Cl by OCH3 group. Moreover, substitution on quinoline ring of
compound 14 by 7-OCH3, 7-OCH(CH3)2, or 8-CH3 also resulted in in-
Anti-HIV-1IIIB Activity, Cytotoxicity and Selectivity Indexes of compounds
9–26.
SIc
EC50 (μM)
a
b
d
Compound
EC50 (μM)
CC50 (μM)
crease in activity (EC50
=
0.33–0.5 μM) and selectivity
9
50.61
5.54
1.96
0.72
0.148
2.92
22.76
1.01
2.55
0.46
0.33
0.50
1.41
0.27
0.42
1.51
1.52
1.93
0.70
2.4
0.01
26.91
56.23
97.26
41.68
17.37
85.43
58.88
19.05
14.12
32.36
54.95
43.51
11.22
42.65
43.65
28.84
35.48
19.05
133.4
335.7
30.96
1.80
0.53
1.66
1.16
0.70
10.86
8.70
1.05
0.52
1.23
1.004
1.05
11.85
1.32
2.49
0.75
6.87
1.42
2.80
1.39
–
0.21
(SI = 70.34–166.50) where compound 19 was the most selective
10
0.01
0.004
0.007
0.006
0.004
0.002
0.01
1.23
5.36
1.16
0.99
4.66
4.23
0.57
1.66
2.47
4.31
6.22
2.13
6.33
6.74
5.49
6.39
3.94
5.42
6.68
10.15
49.62
57.88
117.36
29.25
2.58
0.02
0.12
11
among all the new compounds, Fig. 4.
12
1.29
13
2.14
0.11
0.04
0.24
2.3. Docking study into HIV-1 gp41
14
15
In the last two decades, several small molecules were reported as
HIV-1 fusion inhibitors [21,29,30]. The ability of these compounds to
interfere with the six-helix bundle (6-HB) formation was evaluated in
several reports [21,29,30]. Of these inhibitors, the reference compound
IV was reported among a series of 4-thiazolidinone-based derivatives
that target HIV-1 gp41 and inhibit 6-HB formation [21]. The results of
the docking study of these compounds into the hydrophobic pocket of
HIV-1 gp41 revealed a noticeable correlation with the experimental
results [21].
16
18.86
5.54
17
0.004
0.002
0.001
0.004
0.008
0.003
0.002
0.002
0.004
0.005
0.002
0.008
0.003
18
70.34
166.50
87.02
7.95
0.01
3.24
19
20
0.41
0.45
0.12
0.22
0.11
0.61
0.42
21
22
157.96
103.92
19.09
23.34
9.87
23
24
25
26
In this work, a molecular docking study was performed to evaluate
binding affinities, modes, and interactions of compounds 9–26 hydro-
phobic pocket of HIV-1 gp41. The study was performed considering the
previously reported docking protocols [21,31]. The study was per-
formed using AutoDock 4.2 [32]. The core structure of HIV-1 gp41
(PDB code: 1AIK) [15] was obtained from the protein data bank
(https://www.rcsb.org/). Ligands, protein, grid parameter, and docking
parameter files were prepared according to the previous reports [31,33-
36]. Validation of the docking results was done by comparing the
binding modes and interactions of compounds IV and NB-64 (II) with
those in the previous reports [21,31]. discovery studio visualizer [37]
was used to generate the 2/3D binding modes of the new compound.
The results of this study were represented in Figs. 5–8.
NB-2 (I)
NB-64 (II)
Compound IVe
191
140
–
0.064
484
a
EC50 to prevent of HIV-1IIIB infection. Each compound has been measured
in triplicates and the data is shown as the mean
SD.
b
c
CC50 for MT-2 cells.
SI was determined to inhibit HIV-1IIIB infection on the basis of CC50 for
MT-2 cells and EC50
.
d
e
Primary HIV-1 Isolate inhibitory function, 92US657 (R5, Class B).
All data have been obtained from previous publication [21] for comparison
purposes.
Table 1. The best inhibitory activity was shown by Compound 15.
Table 1 results showed that the newly synthesized 9–26 compounds are
effective against both laboratory and primary HIV-1 strains.
The results of the docking study revealed nice fitting of compounds
IV and BN-64 (II) into the hydrophobic pocket of HIV-1 gp41 protein.
Molecular docking analyses of compound IV and NB-64 (II) revealed
the formation of an important salt-bridge interaction with LYS574.
Moreover, the two compounds exhibited different types of hydrophobic
interactions with the key amino acids (GLN567, LEU568, VAL570,
TRP571, LYS574, GLN575, and TRP631) in the hydrophobic pocket.
The 2D binding modes of compounds IV and BN-64 (II) showing dif-
ferent types of interactions were provided in Fig. 5.
2.2.2. Detection of in vitro cytotoxicity
A colorimetric XTT assay [28] was used to determine the cytotoxi-
city of 9–26 on MT-2 cells. Their CC50 (50% cytotoxicity concentration)
ranged from 11 to 85 μM and their selectivity index ranged from 0.53 to
166 (Table 1). Two of the best HIV-1 IIIB inhibitors are 13 and 19 with
EC50 of 0.148 and 0.33 μM and SI of 117 and 166 in comparison to
compound IV (SI = 484).
The new compounds 9–26 exhibited higher affinities (ΔGb = −6.06
to −6.93 kcal/mol) compared to NB-64 (ΔGb = −4.89 kcal/mol for).
The higher affinities of the new compounds could be attributed to their
extended hydrophobic scaffold which allowed them to interact more
hydrophobically with amino acids in the hydrophobic pocket. The large
molecular volumes of the new compounds allowed them also to occupy
more space in the hydrophobic pocket. On the other hand, the lower
affinities of the new compounds compared to compound IV
(ΔGb = −7.02 kcal/mol) could be attributed to the absence of the salt-
bridge with LYS574.
2.2.3. Structure activity relationship (SAR)
The impact of different substituents in compounds 9–26 on both
anti-HIV-1 inhibitory activity and selectivity was evaluated in this
section based on the biological results, Table 1. Based on these results,
compound 13 exhibited the highest inhibitory activity against HIV-1
infection. Removal of the 8-methyl group in compound 13 resulted in
sharp decrease in both inhibitory activity and selectivity against HIV-1
as indicated by the results of compound 9. Moreover, the other hand,
replacement of the 8-methyl-2-chloro-quinoline by 1-naphthalenyl re-
sulted in 10 times decrease in activity and 2 times decrease in se-
lectivity against HIV-1, Fig. 4.
The relationship between docking results of the new compounds
9–26 and their biological data (Table 1), could be explained on the
basis of their binding affinities, orientations, and types of interactions
into the hydrophobic pocket in comparison with compounds II and
reference IV. Molecular docking analyses of the best-fit conformations
of the new compounds revealed different orientations of the new
The movement of the 8-methyl group in compound 13 or C6 or C7
(compounds 10 and 12) resulted also in reduction in the activity and
selectivity toward HIV-1, where compound 10 was less active than
5

T.S. Ibrahim, et al.
BioorganicChemistry99(2020)103782
∼
∼
∼
Fig. 4. SAR of the anti-HIV-1IIIB activity and selectivity of compounds 9–26.
compounds from compound IV, Fig. 6. Compounds 12, 13, 16 and 23
(EC50 values ≤ 1) adopted a quite similar orientation to compound IV.
Among these four compounds, compound 13 was most active
(EC50 = 0.148) and exhibited the highest affinity. On the other hand,
compounds 9, 10, 15, 17 and 26 which have weakest antiviral activity
(EC50 values = 1.93–50.61 μM) exhibited different orientations from
that of compound IV.
preventing HIV-1IIIB infection (EC50 = 0.27 μM), exhibited also higher
binding free energy than that of NB-64, but lower than those of com-
pound IV and 13. These results were also matched with the EC50 values
of these compounds, Table 1. However, the molecular docking analysis
of compound 22 revealed a different orientation from compounds IV
and 13 which could account for the observed decrease in the antiviral
activity of compound 22 compared to compounds IV and 13. However,
the orientation of compound 22 was still able to form two hydrogen
bonds with key amino acids, LYS574 and GLN575, Fig. 7.
Compound 13, the most active in preventing HIV-1IIIB infection,
exhibited a binding affinity of −6.84 kcal/mol which was higher than
that NB-64 and comparable to compound IV. These results were in
concordance with the EC50 values of these three compounds (II, IV, and
13), Table 1. Moreover, the best-fit conformation of compound 13
adopted an orientation similar to compound IV, Fig. 7. This orientation
allowed the two oxygen atoms of the imidazolidine-2,4-dione ring in
compound 13 to form a cluster of hydrogen bonds with LYS574 and
GLN575. These hydrogen bonds could compensate for the absence of
the salt-bridge observed with compounds II and IV. These hydrogen
bonds, together with the high affinity and orientation of compound 13
could account for its highest antiviral activity.
In addition, compounds 18, 19 and 23 exhibited nearly equal
binding affinities toward the hydrophobic pocket (ΔGb = −6.06 to
−6.19 kcal/mol). These results were quite matched with the biological
results of the three compounds (EC50 values = 0.33–0.46 M). Among
these compounds, compound 19 displayed the highest affinity and
antiviral activity, Table 1. Moreover, compounds 21 and 25 exhibited
nearly equal binding affinities toward the hydrophobic pocket and
displayed similar antiviral activity with EC50 values of 1.41 and
1.52 μM, respectively.
On the other hand, compound 26 exhibited higher binding affinity
than compound 13. Hoverer, compound 26 was about ten times less
Moreover, compound 22, the second most active compound in
Fig. 5. Binding interactions of compounds IV and II into the hydrophobic pocket of HIV-1 gp41 protein (PDB: 1AIK) A) 2D binding mode of compound II; B) 2D
binding mode of compound IV, showing one salt bridge with LYS574 and different types of hydrophobic interactions, hydrogen atoms were omitted for clarity.
6

T.S. Ibrahim, et al.
BioorganicChemistry99(2020)103782
Fig. 6. The new compounds 9–24 overlaid with compound IV: A) Overlay of the best fit conformation of compounds 9–13, 21 and 22 (n = 1, shown as yellow lines)
with compound IV (shown as sticks colored by element); B) Overlay of the best fit conformation of compounds 14–20, 23, 24 (n = 2, shown as blue lines) with
compound IV (shown as sticks colored by element). Receptor is shown as hydrophobicity surface; hydrogen atoms were omitted for clarity. (For interpretation of the
references to colour in this figure legend, the reader is referred to the web version of this article.)
active than compound 13, Table 1. The molecular docking analysis of
compound 26 revealed a different orientation from that of compound
IV and 13. This orientation prevented the formation of the critical
hydrogen bonds with LYS574 which could account for the weak anti-
viral activity of compound 26. In addition, investigation of the binding
interactions of this compound revealed the presence of one unfavorable
acceptor-acceptor interaction with the imidazolidine-2,4-dione oxygen,
Fig. 8.
B). SAR study revealed a significant increase in anti-HIV-1 activity and
selectivity of the parent compound 9 was observed on elongation of the
spacer between phenyl and imidazolidine rings from one to two car-
bons. Moreover, substitution with 7-methoxy group on the quinoline
ring resulted in significant increase in the anti-HIV-1 activity and se-
lectivity. In addition, replacement of the 2-chloro group in compounds
9, 11, 14 and 15 with methoxy resulted in increased activity and se-
lectivity. The results of the docking study of the new compounds re-
vealed nice fitting into the hydrophobic pocket of HIV-1 gp41. Due to
their extended hydrophobic scaffold, all the new compounds 9–26 ex-
hibited higher affinities than NB-64. Compound 13, the most active in
preventing HIV-1IIIB infection, adopted a similar orientation to com-
pound IV and exhibited a comparable affinity. Molecular docking
analysis of the new compounds revealed hydrogen bonding interactions
between imidazolidine-2,4-dione ring of the new compounds and
LYS574. These interactions were missed in most of the weakly active
derivatives 9, 10, 15, 17 and 26.
Similarly, compounds 9, 10, 15 and 17, the least active in pre-
venting HIV-1IIIB infection (Table 1), adopted different orientations
from compounds IV and 13 and missed the hydrogen bonding inter-
actions with LYS574.
3. Conclusion
In this study, a series of 5-((substituted quinolin-3-yl/1-naphthyl)
methylene)-3-substituted imidazolidine-2,4-diones derivatives 9–26
were designed and synthesized. Spectral and elemental analyses con-
firmed the chemical structure of the new compounds. The ability of
9–26 to inhibit HIV-1IIIB replication in MT-2 was assessed using a p24
ELISA assay. Cytotoxicity of these compounds against MT-2 cells was
also evaluated. The results revealed the ability of most of the new
compounds to significantly inhibit HIV-1IIIB replication in a dose-de-
pendent manner. Among the new derivatives, compound13was the
most potent in inhibiting the HIV-1IIIB infection with EC50 value of
0.148 µM and selectivity index of 117.36. compound 13 exhibited EC50
value of 8.7 µM against the primary HIV-1 Isolate, 92US657 (R5, Clade
4. Experimental
4.1. Chemistry
4.1.1. General details [See Appendix A]
4.1.1.1. General method for synthesis of (Z)-5-((substituted quinolin-3-yl
or 1-naphthyl) methylene)-3-substituted imidazolidin-2,4-dione (9–26). A
mixture of 2,6,7,8-tetrasubstituted quinolin-3-aldehyde 6a-g and 7a-d
(2.5 mmol) or 1-naphthaldehyde
8 (2.5 mmol), 3-substituted
Fig. 7. Binding modes/interactions of compound 13 and 22 into the hydrophobic pocket of HIV-1 gp41 protein: A) 3D binding mode of compound 13 (shown as
sticks colored by element) overlaid with compound IV (shown as pink lines); B) 3D binding mode of compound 22 (shown as sticks colored by element) overlaid with
compound IV (shown as pink lines), hydrogen atoms were omitted for clarity. (For interpretation of the references to colour in this figure legend, the reader is
referred to the web version of this article.)
7

T.S. Ibrahim, et al.
BioorganicChemistry99(2020)103782
Fig. 8. Binding modes of compound 26 into the hydrophobic pocket of HIV-1 gp41 protein: A) 3D binding mode, receptor is shown as hydrophobicity surface; B) 2D
binding mode of compound 26 (shown as sticks colored by element), hydrogen atoms were omitted for clarity.
imidazolidin-2,4-dione 3a,b (0.5 g, 2.5 mmol) and 2–5 drops of 2,2,6,6-
tetramethyl piperidine in 7 ml ethanol was heated under reflux for 72 h.
After cooling the solid obtained was filtered and washed with cold
ethanol to give compounds 9–26.
C21H16ClN3O2: C, 66.76; H, 4.27; N, 11.12. Found: C, 66.88; H, 4.39;
N 11.06.
4.1.1.1.5. (Z)-3-benzyl-5-((2-chloro-8-methylquinolin-3-yl)methylene)
imidazolidine-2,4-dione (13). Yellow micro crystals from ethanol, yield:
45% (0.45 g), mp: 242–244 °C, 1H NMR (500 MHz, DMSO‑d6) δ: 11.09
(s, 1H, NH, D2O exchangeable), 8.36 (s, 1H, C4-H of quinoline),
7.91–7.85 (m, 1H, C5-H of quinoline), 7.68–7.63 (m, 1H, C7-H of
quinoline), 7.59–7.48 (m, 1H, C6-H of quinoline), 7.38–7.17 (m, 5H,
ArH), 6.73 (s, 1H, olefinic CH]C), 4.69 (s, 2H, CH2), 2.60 (s, 3H, CH3);
13C NMR (125 MHz, DMSO‑d6) δ:163.7, 158.7, 154.7, 144.7, 138.1,
136.5, 134.3, 130.0, 128.6, 127.6, 125.7, 123.9, 119.4, 105.9, 51.1,
17.2. Anal. Calcd. for C21H16ClN3O2: C, 66.76; H, 4.27; N, 11.12.
Found: C, 66.92; H, 4.48; N 11.34.
4.1.1.1.1. (Z)-3-benzyl-5-((2-chloroquinolin-3-yl)methylene)
imidazolidine-2,4-dione (9). Yellow crystals from ethanol, yield: 56%
(0.54 g), m.p: 203–205 °C, 1H NMR (500 MHz, DMSO‑d6) δ: 11.03 (s,
1H, NH, D2O exchangeable), 8.35 (s, 1H, C4-H of quinoline), 7.66 (d,
J = 7.5 Hz, 2H, C5,8-H of quinoline), 7.53 (t, J = 8.0, 7.0 Hz, 2H, C6,7-H
of quinoline), 7.36–7.21 (m, 5H, ArH), 6.68 (s, 1H, olefinic CH]C),
4.68 (s, 2H, CH2); 13CNMR (125 MHz, DMSO‑d6) δ: 163.6, 161.0, 154.1,
140.0, 138.2, 136.4, 131.2, 128.6, 128.4, 127.5, 127.4, 124.9, 122.5,
119.4, 115.1, 104.0, 41.4. Anal. Calcd. for C20H14ClN3O2: C, 66.03; H,
3.88; N, 11.55. Found: C, 66.36; H, 4.12; N 11.83.
4.1.1.1.6. (Z)-5-((2-chloroquinolin-3-yl)methylene)-3-
4.1.1.1.2. (Z)-3-benzyl-5-((2-chloro-6-methylquinolin-3-yl)methylene)
imidazolid-ine-2,4-dione (10). Fine yellow crystals from ethanol, yield:
36% (0.36 g), m.p: 217–219 °C, IR: νmax/cm−1; 3468 (OH), 3104 (NH),
3021 (CH, aromatic), 2921, 2853 (CH, aliphatic), 1706 (C]O), 1591
(C]N), 1453 (C]C), 1182 (C-O), 700 (C-Cl); 1H NMR (500 MHz,
DMSO‑d6) δ: 8.45 (s, 1H, C4-H of quinoline), 7.93–7.85 (m, 2H, C5,8-H
of quinoline), 7.65 (d, J = 8.5 Hz, 1H, C6-H of quinoline), 7.32–7.25
(m, 5H, ArH), 6.32 (s, 1H, NH, D2O exchangeable), 4.63–4.60 (m, H,
olefinic CH]C), 4.54–4.51 (m, 2H, CH2), 2.49 (s, 3H, CH3); 13C NMR
(125 MHz, DMSO‑d6) δ: 172.3, 157.3, 146.4, 145.1, 137.8, 136.9,
136.6, 132.7, 132.6, 128.3, 127.3, 127.2, 127.1, 127.0, 60.5, 21.1.
Anal. Calcd. for C21H16ClN3O2: C, 66.76; H, 4.27; N, 11.72. Found: C,
67.00; H, 4.36; N 11.92.
phenethylimidazolidine-2,4-dione (14). Yellow crystals from ethanol,
yield: 54% (0.50 g), mp: 194–196 °C, 1H NMR (500 MHz, DMSO‑d6)
δ: 10.89 (s, 1H, NH, D2O exchangeable), 8.32 (s, 1H, C4-H of quinoline),
7.66 (d, J = 7.0 Hz, 2H, C5,8-H of quinoline), 7.54–7.50 (m, 2H, C6,7-H
of quinoline), 7.32–7.19 (m, 5H, ArH), 6.61 (s, 1H, olefinic CH]C),
3.71 (t, 2H, CH2), 2.91 (t, 2H, CH2); 13C NMR (125 MHz, DMSO‑d6) δ:
163.6, 161.0, 154.1, 139.8, 138.2, 138.1, 131.1, 128.6, 128.5, 128.3,
127.5, 126.5, 124.9, 122.5, 119.4, 115.1, 103.5, 33.2. Anal. Calcd. For
C
21H16ClN3O2: C, 66.76; H, 4.27; N, 11.12. Found: C, 67.03; H, 4.66; N
11.52.
4.1.1.1.7. (Z)-5-((2-chloro-6-methylquinolin-3-yl)methylene)-3-
phenethylimidazolidine-2,4-dione (15). Off white micro crystals from
ethanol, yield: 44% (0.42 g), mp: 203–205 °C, IR: νmax/cm−1; 3106
(NH), 3028 (CH, aromatic), 2942, 2855 (CH, aliphatic), 1701 (C]O),
1592 (C]N), 1454 (C]C), 1133 (CeO), 702 (C-Cl); 1H NMR
(500 MHz, DMSO‑d6) δ: 8.42 (s, 1H, C4-H of quinoline), 7.89–7.85
(m, 2H, C5,8-H of quinoline), 7.65 (d, J = 8.5 Hz, 1H, C7-H of
quinoline), 7.32–7.29 (m, 2H, ArH), 7.24–7.20 (m, 3H, ArH), 6.25 (s,
1H, NH, D2O exchangeable), 5.32 (s, 1H, olefinic CH] C), 3.60–3.55
4.1.1.1.3. (Z)-3-benzyl-5-((2-chloro-6-methoxyquinolin-3-yl)
methylene)imidazoli-dine-2,4-dione (11). Shiny yellowish white micro
crystals from ethanol, yield: 75% (0.78 g), mp: 197–199 °C, 1H NMR
(500 MHz, DMSO‑d6) δ: 8.47 (s, 1H, C4-H of quinoline), 7.92–7.85 (m,
2H, C7,8-H of quinoline), 7.57 (d, J = 3.0 Hz, 1H ArH), 7.45–7.43 (m,
1H, ArH), 7.34–7.31 (m, 3H, ArH), 7.28–7.2 (m, 1H, C5-H of quinoline),
6.32 (s, 1H, NH, D2O exchangeable), 4.64–4.60 (m, 1H, olefinic
CH]C), 4.55–4.52 (m, 2H, CH2), 3.89 (s, 3H, OCH3); 13C NMR
(125 MHz, DMSO‑d6) δ: 172.6, 158.1, 157.7, 144.9, 142.7, 137.6,
136.8, 133.0, 129.1, 128.8, 128.7, 127.5, 127.2, 123.2, 106.5, 67.7,
56.0. Anal. Calcd. for C21H16ClN3O3: C, 64.05; H, 4.09; N, 10.67.
Found: C, 64.28; H, 4.42; N 11.03.
(m, 2H, CH2), 2.81 (t, J = 7.5, 8.0 Hz, 2H, CH2), 2.53 (s, 3H, CH3); 13
C
NMR (125 MHz, DMSO‑d6) δ: 172.1, 157.3, 146.4, 145.1, 138.3, 137.7,
136.9, 132.7, 132.6, 128.6, 128.5, 127.2, 127.0, 126.4, 67.6, 60.2,
33.5, 21.1. Anal. Calcd. for C22H18ClN3O2: C, 67.43; H, 4.63; N, 10.72.
Found: C, 67.70; H, 4.87; N 11.09.
4.1.1.1.8. (Z)-5-((2-chloro-6-methoxyquinolin-3-yl)methylene)-3-
phenethylimidazolidine-2,4-dione (16). White crystals from ethanol,
yield: 68% (0.68 g), mp: 216–218 °C, IR: νmax/cm−1; 3409 (OH),
3105 (NH), 3032 (CH, aromatic), 2935, 2875 (CH, aliphatic), 1700
(C]O), 1626 (C]N), 1456 (C]C), 701 (CeCl); 1H NMR (500 MHz,
DMSO‑d6) δ: 8.43 (s, 1H, C4-H of quinoline), 7.87–7.82 (m, 2H, C7,8-H
of quinoline), 7.56 (s, 1H, ArH), 7.45–7.43 (m, 1H, ArH), 7.32–7.29 (m,
1H, ArH), 7.24–7.20 (m, 3H, 2ArH + C5-H of quinoline), 6.23 (s, 1H,
NH, D2O exchangeable), 5.32 (s, 1H, olefinic CH]C), 3.90 (s, 3H,
4.1.1.1.4. (Z)-3-benzyl-5-((2-chloro-7-methylquinolin-3-yl)methylene)
imidazo-lidine-2,4-dione (12). Pale brown micro crystals from ethanol,
yield: 38% (0.38 g), mp: 218–220 °C, 1H NMR (500 MHz, DMSO‑d6) δ:
11.26 (s, 1H, NH, D2O exchangeable), 8.45 (s, 1H, C4-H of quinoline),
7.98–7.95 (m, 2H C5,8-H of quinoline), 7.75 (s, 1H, C6-H of quinoline),
7.32–7.24 (m, 5H, ArH), 6.71 (s, 1H, olefinic CH]C), 4.69–4.46 (m,
2H, CH2), 2.49 (s, 3H, CH3); 13C NMR (125 MHz, DMSO‑d6) δ: 172.3
(C]O), 170.9, 157.4, 147.5, 146.8, 140.9, 138.4, 136.6, 130.9, 128.3,
128.2, 127.5, 127.0, 126.8, 124.8, 60.2, 21.4. Anal. Calcd. for
OCH3), 3.59–3.55 (m, 2H, CH2), 2.82 (t, J = 7.5, 8.0 Hz, 2H, CH2); 13
C
8

T.S. Ibrahim, et al.
BioorganicChemistry99(2020)103782
NMR (125 MHz, DMSO‑d6) δ: 172.2 (C]O), 157.8 (C]O), 157.4,
144.6, 142.5, 138.3, 137.3, 132.8, 128.9, 128.7, 128.5, 126.4, 122.9,
106.3, 67.5, 60.2, 55.7. Anal. Calcd. for C22H18ClN3O3: C, 64.79; H,
4.45; N, 10.30. Found: C, 64.66; H, 4.62; N 11.43.
4.1.1.1.14. (Z)-3-benzyl-5-((2,6-dimethoxyquinolin-3-yl)methylene)
imidazolidine-2,4-dione (22). Pale brown crystals from ethanol, yield:
49% (0.50 g), mp: 172–174 °C, 1H NMR (500 MHz, DMSO‑d6) δ: 11.09
(s, 1H, NH, D2O exchangeable), 8.47 (s, 1H, C4-H of quinoline), 7.67 (d,
J = 9.5 Hz, 1H, C8-H of quinoline), 7.37–7.25 (m, 7H, C5,7-H of
quinolone + 5ArH), 6.72 (s, 1H, olefinic CH]C), 4.69 (s, 2H, CH2),
4.00 (s, 3H, OCH3), 3.86 (s, 3H, OCH3); 13C NMR (125 MHz, DMSO‑d6)
δ: 163.6, 157.7, 155.8, 154.9, 140.5, 136.7, 136.4, 128.6, 128.4, 127.8,
127.5, 127.4, 125.4, 121.8, 117.4, 106.7, 102.2, 55.3, 53.6, 41.4. Anal.
Calcd. for C22H19N3O4: C, 67.86; H, 4.92; N, 10.79. Found: C, 67.96; H,
5.09; N 10.99.
4.1.1.1.9. (Z)-5-((2-chloro-7-methylquinolin-3-yl)methylene)-3-
phenethylimidazolidine-2,4-dione (17). Light brown micro crystals from
ethanol, yield: 78% (0.75 g), mp: 206–208 °C. 1H NMR (500 MHz,
DMSO‑d6) δ: 11.22 (s, 1H, NH, D2O exchangeable), 8.38 (s, 1H, C4-H of
quinoline), 7.98–7.95 (m, 2H C5,6-H of quinoline), 7.39 (s, 1H, C8-H of
quinoline), 7.31–7.19 (m, 5H, ArH), 6.61 (s, 1H, olefinic CH]C),
4.46–4.37 (m, 2H, CH2), 2.99–2.83 (m, 2H, CH2), 2.44 (s, 3H, CH3); 13
C
NMR (125 MHz, DMSO‑d6) δ: 160.8, 157.8, 149.1, 146.7, 140.2, 139.4,
135.1, 130.6, 130.2, 129.9, 128.6, 127.9, 127.5, 125.9, 122.4, 50.3,
42.9, 20.6. Anal. Calcd. for C22H18ClN3O2: C, 67.43; H, 4.63; N, 10.72.
Found: C, 67.49; H, 4.77; N 11.02.
4.1.1.1.15. (Z)-5-((2-methoxyquinolin-3-yl)methylene)-3-
phenethylimidazolidine-2,4-dione (23). Yellowish brown micro crystals
from DMF, yield: 46% (0.42 g), mp: 315–317 °C, IR: νmax/cm−1; 3170
(NH), 3022 (CH, aromatic), 2955, 2895 (CH, aliphatic), 1640 (C]O),
1559 (C]N), 1449 (C]C), 1213 (CeO); 1H NMR (500 MHz, DMSO‑d6)
δ: 10.91 (s, 1H, NH, D2O exchangeable), 8.38 (s, 1H, C4-H of quinoline),
7.67 (d, J = 7.2 Hz, 1H, C8-H of quinoline), 7.53 (t, J = 6.0, 7.6 Hz,
1H, C5-H of quinoline), 7.35–7.24 (m, 7H, C6,7-H of quinoline + 5ArH),
6.61 (s, 1H, olefinic CH]C), 3.74 (t, J = 7.8 Hz, 2H, CH2), 3.34 (s, 3H,
OCH3), 2.94 (t, 2H, CH2), ; 13C NMR (125 MHz, DMSO‑d6) δ: 164.3,
161.1, 139.1, 139.0, 138.2, 137.9, 130.7, 128.6, 128.4, 128.1, 126.4,
125.4, 122.4, 119.6, 115.0, 102.3, 33.3. Anal. Calcd. for C22H19N3O3:
C, 70.76; H, 5.13; N, 11.25. Found: C, 70.50; H, 4.88; N 11.37.
4.1.1.1.16. (Z)-5-((2,6-dimethoxyquinolin-3-yl)methylene)-3-
4.1.1.1.10. (Z)-5-((2-chloro-7-methoxyquinolin-3-yl)methylene)-3-
phenethylimidazolidine-2,4-dione (18). Pale brown micro crystals from
ethanol, yield: 36% (0.36 g), mp: 263–265 °C, 1H NMR (500 MHz,
DMSO‑d6) δ: 10.81 (s, 1H, NH, D2O exchangeable), 8.25 (s, 1H, C4-H of
quinoline), 7.57 (d, J = 9.0 Hz, 1H, C5-H of quinoline), 7.30–7.27 (m,
2H, C6,8-H of quinoline), 7.22–7.18 (m, 3H, ArH), 6.87–6.82 (m, 2H,
ArH), 6.57 (s, 1H, olefinic CH]C), 3.82 (s, 3H, OCH3), 3.71 (t, J = 7.0,
8.0 Hz, 2H, CH2), 2.90 (t, J = 7.5, 7.5 Hz, 2H, CH2); 13C NMR
(125 MHz, DMSO‑d6) δ: 172.3, 163.4, 157.4, 154.9, 148.2, 146.4,
145.6, 139.0, 138.8, 136.6, 135.2, 132.4, 128.6, 128.3, 127.5, 127.0,
126.4, 125.0, 103.1, 67.5, 60.5. Anal. Calcd. for C22H18ClN3O3: C,
64.79; H, 4.45; N, 10.30. Found: C, 64.33; H, 4.62; N 11.56.
phenethylimidazolidine-2,4-dione (24). Yellowish white crystals from
ethanol, yield: 52% (0.52 g), mp: 185–187 °C, 1H NMR (400 MHz,
DMSO‑d6) δ: 10.96 (s, 1H, NH, D2O exchangeable), 8.46 (s, 1H, C4-H of
quinoline), 8.19 (d, J = 14.0 Hz, 1H C8-H of quinoline), 7.75–7.67 (m,
2H, C5,7-H of quinoline), 7.33–7.16 (m, 5H, ArH), 6.66 (s, 1H, olefinic
CH]C), 4.02–3.98 (m, 2H, CH2), 3.87 (s, 3H, OCH3), 3.86 (s, 3H,
OCH3), 2.85–2.81 (m, 2H, CH2); 13C NMR (125 MHz, DMSO‑d6) δ:
172.5, 157.3, 155.7, 140.4, 138.3, 136.5, 135.7, 128.6, 128.4, 127.6,
126.4, 125.9, 125.5, 120.5, 107.0, 65.9, 60.2, 55.4, 53.3. Anal. Calcd.
for C23H21N3O4: C, 68.47; H, 5.25; N, 10.42. Found: C, 68.65; H, 4.96;
N 10.74.
4.1.1.1.11. (Z)-5-((2-chloro-7-isopropoxyquinolin-3-yl)methylene)-3-
phenethylimidazolidine-2,4-dione (19). Fine yellow micro crystals from
ethanol, mp: 186–188 °C, yield: 78% (0.83 g). 1H NMR (500 MHz,
DMSO‑d6) δ: 10.95 (s, 1H, NH, D2O exchangeable), 8.33 (s, 1H, C4-H of
quinoline), 7.82–7.81 (m, 1H, C5-H of quinoline), 7.70 (d, J = 2.5 Hz,
1H, C8-H of quinoline), 7.40 (dd, J = 2.5, 2.5 Hz, 1H, C6-H of
quinoline), 7.30–7.27 (m, 2H, ArH), 7.22–7.19 (m, 3H, ArH), 6.40 (s,
1H, olefinic CH]C), 3.73 (t, J = 7.0, 8.0 Hz, 2H, CH2), 3.24 (s, 1H,
isopropyloxy CH), 2.92 (t, J = 8.0, 7.0 Hz, 2H, CH2), 1.65–1.61 (m, 6H,
isopropyloxy 2CH3). 13C NMR (125 MHz, DMSO‑d6) δ: 162.8, 157.9,
159.6, 152.6, 146.8, 138.1, 137.5, 130.6, 128.6, 127.7, 125.6, 124.8,
105.9, 119.4, 105.9, 80.3, 50.4, 43.2, 22.2. Anal. Calcd. for
4.1.1.1.17. (Z)-3-benzyl-5-(naphthalen-1-ylmethylene)imidazolidine-
2,4-dione (25). White crystals from ethanol, yield: 72% (0.62 g), mp:
210–212 °C, IR: νmax/cm−1; 3428 (OH), 3212 (NH), 3036 (CH, aromatic),
2924 (CH, aliphatic), 1672 (C]O), 1442 (C]C), 1156 (CeO); 1H NMR
(500 MHz, DMSO‑d6) δ: 10.92 (s, 1H, NH, D2O exchangeable), 8.07 (d,
J = 8.0 Hz, 1H, C5-H of naphthyl), 7.99–7.93 (m, 2H, C4,8-H of naphthyl),
7.74 (d, J = 7.5 Hz, 1H, C2-H of naphthyl), 7.62–7.54 (m, 3H, C3,6,7-H of
naphthyl), 7.38–7.29 (m, 5H, ArH), 7.14 (s, 1H, olefinic CH]C), 4.70 (s,
2H, CH2); 13C NMR (125 MHz, DMSO‑d6) δ: 163.6, 154.9, 136.5, 133.2,
131.0, 129.2, 129.0, 128.8, 128.7, 128.6, 127.5, 126.9, 126.3, 125.7,
123.7, 106.3, 41.4. Anal. Calcd. for C21H16N2O2: C, 76.81; H, 4.91; N,
8.53. Found: C, 77.06; H, 4.76; N 8.87.
C24H22ClN3O3: C, 66.13; H, 5.09; N, 9.64. Found: C, 66.45; H, 4.89;
N 9.93.
4.1.1.1.12. (Z)-5-((2-chloro-8-methylquinolin-3-yl)methylene)-3-
phenethylimidazolidine-2,4-dione (20). Fine lemon yellow micro crystals
from ethanol, yield: 82% (0.79 g), mp: 260–262 °C, 1H NMR (500 MHz,
DMSO‑d6) δ: 11.17 (s, 1H, NH, D2O exchangeable), 8.64 (s, 1H, C4-H of
quinoline), 7.92–7.85 (m, 1H, C5-H of quinoline), 7.69–7.48 (m, 2H,
C6,7-H of quinoline), 7.31–7.15 (m, 5H, ArH), 6.67 (s, 1H, olefinic
CH]C), 3.75–3.71 (m, 2H, CH2), 2.92 (t, J = 8.0, 7.0 Hz, 2H, CH2),
2.65 (s, 3H, CH3); 13C NMR (125 MHz, DMSO‑d6) δ: 163.3, 158.7,
154.9, 148.2, 144.9, 138.8, 138.0, 135.4, 134.3, 131.3, 129.7, 128.6,
128.5, 127.4, 126.5, 124.8, 119.4, 102.5, 51.0, 17.2. Anal. Calcd. for
4.1.1.1.18. (Z)-5-(naphthalen-1-ylmethylene)-3-
phenethylimidazolidine-2,4-dione (26). Fine yellow micro crystals from
ethanol, yield: 52% (0.44 g), mp: 170–172 °C, IR: νmax/cm−1; 3466
(OH), 3265 (NH), 3028 (CH, aromatic), 2939 (CH, aliphatic), 1659 (C]
O), 1505 (C]N), 1451 (C]C), 1155(CeO); 1H NMR (400 MHz,
DMSO‑d6) δ: 10.78 (s, 1H, NH, D2O exchangeable), 8.07–7.23 (m,
12H, ArH), 7.09 (s, 1H, olefinic CH]C), 3.75 (t, J = 6.8, 6.4 Hz, 2H,
CH2), 2.95 (t, J = 6.4 Hz, 2H, CH2); 13C NMR (125 MHz, DMSO‑d6) δ:
163.6, 154.9, 138.1, 133.2, 131.0, 129.2, 128.9, 128.6, 128.5, 127.4,
126.9, 126.5, 126.3, 125.7, 123.6, 105.7, 67.3, 61.7. Anal. Calcd. for
C22H18ClN3O2: C, 67.43; H, 4.63; N, 10.72. Found: C, 67.72; H, 4.79; N
11.02.
4.1.1.1.13. (Z)-3-benzyl-5-((2-methoxyquinolin-3-yl)methylene)
imidazolidine-2,4-dione (21). Dark yellow micro crystals from ethanol,
yield: 68% (0.64 g), mp: 330–332 °C, IR: νmax/cm−1; 3163 (NH), 3026
(CH, aromatic), 2958, 2906 (CH, aliphatic), 1639 (C]O), 1554 (C]N),
1437(C]C), 1207(CeO); 1H NMR (500 MHz, DMSO‑d6) δ: 11.04 (s,
1H, NH, D2O exchangeable), 8.36 (s, 1H, C4-H of quinoline), 7.66 (d,
J = 7.0 Hz, 1H, C8-H of quinoline), 7.51 (t, J = 7.6 Hz, 1H, C5-H of
quinoline), 7.34–7.22 (m, 7H, C6,7-H of quinolone + 5ArH), 6.67 (s,
1H, olefinic CH]C), 4.66 (s, 2H, CH2), 3.68 (s, 3H, OCH3) ; 13C NMR
(125 MHz, DMSO‑d6) δ: 163.8, 161.1, 154.4, 139.9, 138.2, 136.5,
131.1, 128.6, 128.4, 127.5, 127.4, 125.0, 122.5, 119.5, 115.1, 103.8,
41.4. Anal. Calcd. for C21H17N3O3: C, 70.18; H, 4.77; N, 11.69. Found:
C, 70.37; H, 4.48; N 11.77.
C
22H18N2O2: C, 77.17; H, 5.30; N, 8.18. Found: C, 77.27; H, 5.48; N
8.33.
4.2. Biological evaluation
4.2.1. HIV-1 inhibitory activity
The inhibitory activity of compounds on HIV-1IIIB replication in MT-
2 cells was determined at Department of Biochemistry and Molecular
9

T.S. Ibrahim, et al.
BioorganicChemistry99(2020)103782
Biology, Drexel University, College of Medicine, Philadelphia,
Pennsylvania 19,102 United States as previously described [27]. See
Appendix A.
[15] D.C. Chan, D. Fass, J.M. Berger, P.S. Kim, Core structure of gp41 from the HIV
envelope glycoprotein, Cell 89 (1997) 263–273.
[16] W. Weissenhorn, A. Dessen, S.C. Harrison, J.J. Skehel, D.C. Wiley, Atomic structure
of the ectodomain from HIV-1 gp41, Nature 387 (1997) 426–428.
[17] K. Tan, J. Liu, J.-H. Wang, S. Shen, M. Liu, Atomic structure of a thermostable
subdomain of HIV-1 gp41, Proc. Natl. Acad. Sci. U.S.A. 94 (1997) 12303–12308.
[18] D.C. Chan, C.T. Chutkowski, P.S. Kim, Evidence that a prominent cavity in the
coiled coil of HIV type 1 gp41 is an attractive drug target, Proc. Natl. Acad. Sci.
U.S.A. 95 (1998) 15613–15617.
4.2.2. Detection of in vitro cytotoxicity
The in vitro cytotoxicity of compounds on MT-2 cells was measured
by XTT assay as previously described [28]. See Appendix A.
[19] S. Jiang, H. Lu, S. Liu, Q. Zhao, Y. He, A.K. Debnath, N-substituted pyrrole deri-
vatives as novel human immunodeficiency virus type 1 entry inhibitors that in-
terfere with the gp41 six-helix bundle formation and block virus fusion, Antimicrob.
Agents Chemother. 48 (2004) 4349–4359.
4.3. Docking study
[20] A.R. Katritzky, S.R. Tala, H. Lu, A.V. Vakulenko, Q.Y. Chen, J. Sivapackiam,
K. Pandya, S. Jiang, A.K. Debnath, Design, synthesis and structure-activity re-
lationship of a novel series of 2-aryl 5-(4-oxo-3-phenethyl-2-thiox-
othiazolidinylidenemethyl) furans as HIV-1 entry inhibitors, J. Med. Chem. 52
(2009) 7631–7639.
In the preparation of the HIV-1 gp41 protein for docking, all CHR
residues were removed except Trp631and Asp632 amino acids which
were reported to have important role in formation of 6-HB [21]. The
ligand [29,30] and core structure of HIV-1 gp41 was prepared ac-
cording to the previous report [31]. The grid parameters and docking
parameters were prepared following the previously reported proce-
dures [32–37].
[21] S. Jiang, S.R. Tala, H. Lu, N.E. Abo-Dya, I. Avan, K. Gyanda, L. Lu, A.R. Katritzky,
A.K. Debnath, Design, synthesis, and biological activity of novel 5-((arylfuran/1H-
pyrrol-2-yl)methylene)-2-thioxo-3-(3-(trifluoromethyl)phenyl)thi azolidin-4-ones
as HIV-1 fusion inhibitors targeting gp41, J. Med. Chem. 54 (2011) 572–579.
[22] S. Jiang, S.R. Tala, H. Lu, P. Zou, I. Avan, T.S. Ibrahim, N.E. Abo-Dya,
A. Abdelmajeid, A.K. Debnath, A.R. Katritzky, Design, synthesis and biological
activity of a novel series of 2,5-disubstituted furans/pyrroles as HIV-1 fusion in-
hibitors targeting gp41, Bioorg. Med. Chem. Lett. 21 (2011) 6895–6898.
[23] G. Frey, S. Rits-Volloch, X.Q. Zhang, R.T. Schooley, B. Chen, S.C. Harrison, Small
molecules that bind the inner core of gp41 and inhibit HIV envelope-mediated
fusion, Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 13938–13943.
Acknowledgment
This project was funded by the Deanship of Scientific Research
(DSR), King Abdulaziz University, Jeddah, under Grant No. (RG-8-166-
41). The authors, therefore, gratefully acknowledge DSR technical and
financial support.
[24] S. Sardari, K. Azadmanesh, F. Mahboudi, A. Davood, R. Vahabpour, R. Zabihollahi,
H. Gomari, Design of small molecules with HIV fusion inhibitory property based on
Gp41 interaction assay, Avicenna J. Med. Biotechnol. 5 (2013) 78–86.
[25] A. Srivastava, R.M. Singh, Vilsmeier-Haack reagent: A facile synthesis of 2-chloro-3-
formyl quinolones from N-aryl acetamides and transformation into different func-
tionalities, Indian J. Chem. 44B (2005) 1868–1875.
Declaration of Competing Interest
The authors declare no conflict of interest
Appendix A. Supplementary material
[26] R.N. Comber, R.C. Reynolds, J.D. Friedrich, R.A. Manguikian, R.W. Buckheit,
J.J.W. Truss, W.M. Shannn, J.A. Secrist, 5,5- Di substituted Hydantoins and anti-
HIV activity, J. Med. Chem. 35 (1992) 3567–3572.
[27] C.A. Lipinski, F. Lombardo, B.W. Dominy, P.J. Feeney, Experimental and compu-
tational approaches to estimate solubility and permeability in drug discovery and
development settings, Adv. Drug Del. Rev. 23 (1997) 3–25.
Supplementary data to this article can be found online at https://
doi.org/10.1016/j.bioorg.2020.103782.
[28] Q. Zhao, L. Ma, S. Jiang, H. Lu, S. Liu, Y. He, N. Strick, N. Neamati, A.K. Debnath,
Identification of N-phenyl-N'-(2,2,6,6- tetramethyl-piperidin-4-yl)-oxalamides as a
new class of HIV-1 entry inhibitors that prevent gp120 binding to CD4, Virology
339 (2005) 213–225.
References
[29] H. Wang, Z. Qi, A. Guo, Q. Mao, H. Lu, X. An, C. Xia, X. Li, A.K. Debnath, S. Wu,
S. Liu, S. Jiang, ADS-J1 inhibits human immunodeficiency virus type 1 entry by
interacting with the gp41 pocket region and blocking fusion-active gp41 core for-
mation, Antimicrob. Agents Chemother. 53 (2009) 4987–4998.
[1] AIDS Epidemic Update UNAIDS (http://www.unaids.org), 2009.
[2] V.A. Johnson, F. Brun-Vezinet, B. Clotet, B. Conway, R.T. D’Aquila, L.M. Demeter,
D.R. Kuritzkes, D. Pillay, J.M. Schapiro, A. Telenti, D.D. Richman, Drug resistance
mutations in HIV-1, Top. HIV Med. 11 (2003) 215–221.
[30] S. Sepehri, S. Soleymani, R. Zabihollahi, M.R. Aghasadeghi, M. Sadat, L. Saghaie,
A. Fassihi, Synthesis, biological evaluation, and molecular docking studies of Novel
4-[4-Arylpyridin-1(4H)-yl]benzoic acid derivatives as Anti-HIV-1 agents, Chem.
Biodivers. 1–14 (2017).
[3] D.D. Richman, S.C. Morton, T. Wrin, N. Hellmann, S. Berry, M.F. Shapiro,
S.A. Bozzette, The prevalence of antiretroviral drug resistance in the United States,
AIDS. 18 (2004) 1393–1401.
[31] R. Munnaluri, S.K. Sivan, V. Manga, Molecular docking and MM/GBSA integrated
protocol for designing small molecule inhibitors against HIV-1 gp41, Med. Chem.
Res. 24 (2015) 829–841.
[4] A. Carr, D.A. Cooper, Adverse effects of antiretroviral therapy, Lancet. 356 (2000)
1423–1430.
[32] G.M. Morris, R. Huey, W. Lindstrom, M.F. Sanner, R.K. Belew, D.S. Goodsell,
A.J. Olson, AutoDock4 and AutoDockTools4: Automated docking with selective
receptor flexibility, J. Comput. Chem. 30 (2009) 2785–2791.
[5] P. Yves, A.J. Allison, M. Christophe, Nat. Rev. Drug Disc. 4 (2005) 236.
[6] C.B. Wilen, J.C. Tilton, R.W. Doms, HIV: cell binding and entry, Cold Spring Harbor
Perspect. Med. 2 (2012).
[33] A.M. Gouda, F.A. Almalki, Carprofen : a theoretical mechanistic study to investigate
the impact hydrophobic interactions of alkyl groups on modulation of COX – 1/2
binding selectivity, SN Appli. Sci. (2019), https://doi.org/10.1007/s42452-019-
0335-5.
[7] M. Caffrey, HIV envelope: challenges and opportunities for development of entry
inhibitors, Trends Microbiol. 19 (2011) 191–197.
[8] C.A. Didigu, R.W. Doms, Novel approaches to inhibit HIV entry, Viruses 4 (2012)
309–324.
[34] F.A. Almalki, A.M. Gouda, M.H. Bin Ali, O.M. Almehmadi, Profens: a comparative
molecular docking study into cyclooxygenase-1/2, Drug Invent Today 11 (2019)
480–487.
[9] F. Yu, L. Lu, L. Du, X. Zhu, A.K. Debnath, S. Jiang, Approaches for identification of
HIV-1 entry inhibitors targeting gp41 pocket, Viruses 5 (2013) 127–149.
[10] L. Lu, F. Yu, L. Cai, A.K. Debnath, S. Jiang, Development of small-molecule HIV
entry inhibitors specifically targeting gp120 or gp41, Curr. Top. Med. Chem. 16
(2016) 1074–1090.
[35] A.M. Shawky, M.A.S. Abourehab, A.N. Abdalla, A.M. Gouda, Optimization of pyr-
rolizine-based Schiff bases with 4-thiazolidinone motif: Design, synthesis and in-
vestigation of cytotoxicity and anti-inflammatory potency, Eur. J. Med. Chem.
(2020), https://doi.org/10.1016/j.ejmech.2019.111780.
[11] D.M. Eckert, P.S. Kim, Mechanisms of viral membrane fusion and its inhibition,
Annu. Rev. Biochem. 70 (2001) 777–810.
[36] K.M. Attalah, A.N. Abdalla, A. Aslam, M. Ahmed, M.A.S. Abourehab, N.A. ElSawy,
A.M. Gouda, Ethyl benzoate bearing pyrrolizine/indolizine moieties: Design,
synthesis and biological evaluation of anti-inflammatory and cytotoxic activities,
Bioorg. Chem. (2019), https://doi.org/10.1016/j.bioorg.2019.103371.
[37] Dassault systems BIOVIA, Discovery Studio Visualizer, v16.1.0.15350, San Diego:
Dassault systems, 2016.
[12] J.P. Moore, R.W. Doms, The entry of entry inhibitors: a fusion of science and
medicine, Proc. Natl. Acad. Sci. U.S.A. 100 (2003) 10598–10602.
[13] S. Liu, S. Wu, S. Jiang, HIV entry inhibitors targeting gp41: from polypeptides to
small-molecule compounds, Curr. Pharm. Des. 13 (2007) 143–162.
[14] M. Lu, S.C. Blacklow, P.S. Kim, Atrimeric structural domain of the HIV-1 trans-
membrane glycoprotein, Nat. Struct. Biol. 2 (1995) 1075–1082.
10