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Journal of Molecular Structure 1209 (2020) 127902

Contents lists available at ScienceDirect

Journal of Molecular Structure


journal homepage: http://www.elsevier.com/locate/molstruc

Synthesis, biological evaluation and molecular docking studies of


novel 2-alkylthiopyrimidino-tacrines as anticholinesterase agents and
their DFT calculations
Chamseddine Derabli a, b, Houssem Boulebd b, Ahmed B. Abdelwahab c,
Celia Boucheraine a, Sarah Zerrouki a, Chawki Bensouici d, Gilbert Kirsch e,
Raouf Boulcina b, f, *, Abdelmadjid Debache b
a
National Higher School of Biotechnology “Toufik Khaznadar” University City Ali Mendjeli, 25100, Constantine, Algeria
b
Laboratory of Synthesis of Molecules with Biological Interest, Fr
eres Mentouri Constantine 1 University, 25000, Constantine, Algeria
c
Plant Advanced Technologies (PAT), 19 avenue de la For^ et de Haye, 54500, Vandoeuvre-les-Nancy, France
d
Biotechnology Research Center, Constantine, Algeria
e
L2CM, Lorraine University, 1 Boulevard Arago, 57070, France
f
Faculty of Technology, Batna 2 University, 05000, Batna, Algeria

a r t i c l e i n f o a b s t r a c t

Article history: To search for effective and selective inhibitors of cholinesterases (AChE and BuChE), a series of poly-
Received 18 January 2020 functionalized Tacrine-derived compounds specifically 2-(alkylthio)-4-aryl-6,7,8,9-tetrahydropyrimido
Accepted 13 February 2020 [4,5-b]quinolin-5-amines were designed an synthesized via Friedlander reaction. The structures of the
Available online 14 February 2020
newly synthesized compounds were confirmed on the basis of their spectral data (1H NMR, 13C NMR) and
elemental analyses (CHNS). Compounds 3a-h were evaluated for their abilities to inhibit AChE and BChE.
Keywords:
The obtained biological results revealed that some synthesized compounds displayed higher anti-
Alzheimer’s disease
cholinesterase activity in comparison to Galantamine. Among them, compound 3d bearing S-ethyl and
2-Alkylthiopyrimidino-Tacrines
Inhibitors of cholinesterases
4-chlorophenyl moieties showed the most potent activity against AChE/BuChE with IC50s values of 4,32
Molecular docking and 15,10 mM, respectively. The anti-AChE activity of 3d was 5-fold more than that of reference drug
DFT calculations Galantamine. Moreover, molecular docking studies were performed for the most active derivatives, 3d
and 3c, in which binding mode between these compounds and the receptors were determined. Density
functional theory (DFT) method at B3LYP/6e311þþG (d,p) level of theory was employed to gain insights
into the molecular structure of the target compounds. Molecular electrostatic potential (MEP) mapping,
reactivity indices such as electronegativity, electrophilic index, softness and hardness as well as frontier
molecular orbitals HOMO-LUMO have been investigated for 3a-3c as representative compounds. In
addition, their antiradical activity has been predicted by computing bond dissociation enthalpies (BDEs).
© 2020 Elsevier B.V. All rights reserved.

1. Introduction interested in this pathology, which affects about 60e70% of elderly


people with dementia [1,2]. AD is a significant problem for old
The human brain is so complex that scientists are constantly people worldwide, it is one of the neurodegenerative diseases that
researching its anatomy, physiology and dysfunctions at the root of affects the elderly by inducing irreversible memory loss [3]. This
the various diseases that can destabilize it, the most important of disease characterized by neurofibrillary degeneration with a
which are neurodegenerative diseases. In view of the gravity and continuous, progressive and irreversible decline in cognitive func-
extent of the progression of Alzheimer’s disease (AD), scientists are tion until the ability to perform daily tasks is completely lost [4,5].
From a pathophysiological point of view, b-amyloid plaques and
neurofibrillary tangles are the major pathological signs in the brain
* Corresponding author. Laboratory of Synthesis of Molecules with Biological of AD patients [6]. Also, there is no cure for AD, only four drugs have
res Mentouri Constantine 1 University, 25000, Constantine, Algeria.
Interest, Fre been approved for AD therapy: Memantine, a N-methyl-D-aspar-
E-mail addresses: boulcinaraouf@yahoo.fr, r.boulcina@univ-batna2.dz tate receptor antagonist [7,8]; three of them are
(R. Boulcina).

https://doi.org/10.1016/j.molstruc.2020.127902
0022-2860/© 2020 Elsevier B.V. All rights reserved.
2 C. Derabli et al. / Journal of Molecular Structure 1209 (2020) 127902

O without further purification. All solvents used for spectroscopic and


R2 NH2
synthesis studies were reagent grade and further purified by liter-
NH2 O N ature methods. Melting points were determined on an Electro-
N H
A
thermal capillary fine control apparatus. 1H and 13C NMR spectra
R1
N S N N were recorded on a Bruker Avance 400 instrument at 400 and
HO 100 MHz respectively, in CDCl3 or DMSOed6. Chemical shifts (d) are
Tacrine 3a-h
Galantamine given in part per million downfield from TMS as an internal stan-
dard for 1H and 13C NMR. Coupling constants (J) values were indi-
O NH2 cated in Hz. The chemicals were used as obtained commercially.
O O N Elemental analyses were carried out on a Microanalyzer Flash
N O
EA1112 CHNS/O Thermo Electron.
O N

Donepezil Rivastigmine Memantine 2.2. Synthesis and characterization

Fig. 1. Drugs for Alzheimer’s disease and the structure of compounds 3a-h described in 2.2.1. Synthesis of 2-(Alkylthio)-4-aryl-6,7,8,9-tetrahydropyrimido
this work. [4,5-b]quinolin-5-amine (3)
In a 100 mL round bottom flask, a mixture of 3-amino-2-
acetylcholinesterase inhibitors (AChEIs) including Donepezil, cyanopyrimidine (1, 1 mmol), aluminum chloride (2 mmol) and
Rivastigmine, and Galantamine [9], able to restore the neuro- cyclohexanone (2, 2 mmol) was added into adequate volume of dry
transmitter acetylcholine levels (Fig. 1). 1,2-dichloroethane (DCE) and stirred at reflux for 24 h (Monitored
Tacrine, the first marketed AChEI which significantly improved by TLC) After completion, water was added and the mixture was
certain functions of recognition, reasoning, perception, attention, basified with 10% sodium hydroxide solution to pH ¼ 8e9. After
decision-making and many others. stirring for 30 min, the precipitate was filtered and washed with
Indeed, it restarted brain chemistry by restoring neurotrans- water. Purification by recrystallization in ethyl acetate afforded the
mission at the synapses by protecting acetylcholine and butyr- title compounds.
ylcholine neurotransmitters. Despite the effectiveness of the
treatment, the patients who took it quickly developed rather 2.2.2. Spectral characterization
serious side effects: hepatotoxicity, heart problems, neuropsychic 4-(4-Chlorophenyl)-2-(methylthio)-6,7,8,9-tetrahydropyrimido
disorders, digestive disorders, etc [10,11], and since then many re- [4,5-b]quinolin-5-amine (3a).
searchers have been interested in the development of Tacrine an- Compound 3a was obtained as a yellow solid (41%). M.p:
alogues by minimizing adverse reactions as much as possible 251e254  C; 1H NMR (400 MHz, CDCl3) d (ppm) 7.44 (m, 4H), 4.49
[12e17]. (br s, 2H, NH2), 2.97 (t, J ¼ 6.0 Hz, 2H), 2.64 (s, 3H, SCH3), 2.32 (t,
In this context, we have recently reported the synthesis and J ¼ 6.0 Hz, 2H), 1.86e1.81 (m, 4H).13C NMR (100 MHz, CDCl3)
pharmacological studies of a series of readily available Tacrine- d (ppm) 170.3, 165.8, 165.6, 158.3, 149.1, 137.4, 136.5, 130.0, 129.8,
pyranopyrazole [18] and alkylbis(4-amino-5-cyanopyrimidine) 129.6, 129.4, 111.9, 103.7, 34.5, 23.5, 22.4, 14.4. Anal. calcd for
derivatives [19], as promising agents for AD therapy. In our efforts C18H17ClN4S: C, 60.58; H, 4.80; N, 15.70; S, 8.99; Found: C, 60.91; H,
to contribute to the development of new compounds that may be 4.67; N, 15.35, S, 9.32.
useful in the treatment of AD, we are focusing on the synthesis of 4-(4-Methoxyphenyl)-2-(methylthio)-6,7,8,9-
new Tacrine analogues which result from exchanging the benzene tetrahydropyrimido [4,5-b]quinolin-5-amine (3b):
ring (A) with a potentially active pharmacophore: 2- Compound 3b was obtained as a yellow solid (58%). M.p:
alkylthiopyrimidine. In fact, pyrimidine derivatives and their 176e178  C. 1H NMR (400 MHz, CDCl3) d(ppm): 7.43 (dd, J ¼ 6.8,
analog exhibit a variety of pharmacological activities, including 2.4 Hz, 2H), 6.96 (dd, J ¼ 6.8, 2.0 Hz, 2H), 4.58 (br s, 2H, NH2), 3.81 (s,
antitumoral properties [20]. They can be used as anticancer [21], 3H, OeCH3), 2.97 (t, J ¼ 6.0 Hz, 2H), 2.64 (s, 3H, SeCH3), 2.32 (t,
antimicrobial [22], antitubercular agents [23] and so forth. As our J ¼ 6.4 Hz, 2H), 1.86e1.81 (m, 4H).13C NMR (100 MHz, CDCl3):
continuous interest in the synthesis of the biologically important d (ppm): 170.3, 166.6, 165.4, 161.1, 158.4, 149.5, 132.6, 131.2, 130.2,
heterocycles, herein we describe the synthesis of a novel series of 114.9, 111.6, 103.8, 55.5, 34.4, 26.8, 23.5, 22.5, 22.4, 14.4. Anal. calcd
highly functionalized 2-(alkylthio)-4-aryl-6,7,8,9- for C19H20N4OS: C, 64.75; H, 5.72; N, 15.90; S, 9.10; Found: C, 64.35;
tetrahydropyrimido [4,5-b]quinolin-5-amines as cholinesterase H, 5.21; N, 15.45, S, 9.47.
inhibitors. In addition, molecular docking analysis was also per- 2-(Methylthio)-4-(3-nitrophenyl)-6,7,8,9-tetrahydropyrimido
formed to disclose the binding interaction template of the most [4,5-b]quinolin-5-amine (3c):
active inhibitors to the amino acid residues composing active site of Compound 3c was obtained as a orange brown solid (55%). M.p:
the AChE and BChE enzymes and the findings are presented below. 210e216  C. 1H NMR (400 MHz, CDCl3) d (ppm): 8.39 (s, 1H),
Furthermore, optimized molecular geometry, frontier molecular 8.32(dd, J ¼ 8.0, 1.6 Hz, 1H), 7.88 (dd, J ¼ 7.6, 1.2 Hz, 1H), 7.67 (t,
orbitals HOMO-LUMO, molecular electrostatic potential (MEP) J ¼ 8.0 Hz, 1H), 4.38 (br s, 2H, NH2), 3.0 (t, J ¼ 5.6 Hz, 2H), 2.63 (s,
mapping and reactivity indices (electronegativity, electrophilic in- 3H), 2.36 (t, J ¼ 6.0 Hz, 2H), 1.87e1.82 (m, 4H). 13C NMR (100 MHz,
dex, softness and hardness) have been investigated for 3a-3c as CDCl3): d (ppm): 170.5166.5, 163.9, 158.3, 148.6, 148.4, 140.5, 134.8,
representative compounds using DFT/B3LYP method. At the same 130.2, 124.9, 124.1, 112.4, 103.6, 34.5, 23.5, 22.3, 14.5. Anal. calcd for
level of theory, the antiradical properties of 3a-3c have been also C18H17N5O2S: C, 58.84; H, 4.66; N, 19.06; S, 8.73; Found: C, 58.59; H,
examined by computing bond dissociation enthalpies (BDEs). 5.03; N, 18.81, S, 8.95.
4-(4-Chlorophenyl)-2-(ethylthio)-6,7,8,9-tetrahydropyrimido
2. Experimental section [4,5-b]quinolin-5-amine (3d).
Compound 3d was obtained as an orange brown (57%). M.p
2.1. Materials and equipments 216e219  C.1H NMR (400 MHz, CDCl3) d (ppm) 7.44 (m, 4H), 4.47
(br s, 2H, NH2), 3.28 (q, J ¼ 7.2 Hz, 2H), 2.97 (t, J ¼ 6.0 Hz, 2H), 2.32 (t,
All chemicals were purchased from the Sigma-Aldrich and used J ¼ 6.0 Hz, 2H), 1.85e1.81 (m, 4H), 1.36 (t, J ¼ 7.2 Hz, 3H).13C NMR
C. Derabli et al. / Journal of Molecular Structure 1209 (2020) 127902 3

(100 MHz, CDCl3) d (ppm) 169.9, 165.8, 165.6, 158.3, 149.0, 137.5, the reaction of DTNB with thiocholine, released by the enzymatic
136.5, 130.0, 129.4, 111.9, 103.7, 34.5, 25.3, 23.5, 22.4, 22.3, 14.4. Anal. hydrolysis of acetylthiocholine iodide or butyrylthiocholine chlo-
calcd for C19H19ClN4S: C, 61.53; H, 5.16; N, 15.11; S, 8.65; Found: C, ride, respectively, at a wavelength of 412 nm, every 5 min for
61.87; H, 5.38; N, 14.85, S, 8.45. 15 min, utilizing a 96-well microplate reader (PerkinElmer Multi-
2-(Butylthio)-4-(4-chlorophenyl)-6,7,8,9-tetrahydropyrimido mode Plate Reader EnSpire, USA) in triplicate experiments. Gal-
[4,5-b]quinolin-5-amine (3e): anthamine was used as reference compound. The results were
Compound 3e was obtained as a yellow solid (58%). M.p: given as 50% inhibition concentration (IC50) and the percentage of
230e232  C. 1H NMR (400 MHz, CDCl3) d (ppm): 7.53 (m, 4H), 4.56 inhibition of AChE or BChE was determined by comparison of re-
(br s, 2H, NH2), 3.39 (t, J ¼ 7.2 Hz, 2H), 3.06 (t, J ¼ 6.4 Hz, 2H), 2.41 (t, action rates of samples relative to blank sample (methanol in
J ¼ 6.0 Hz, 2H), 1.95e1.90 (m, 4H), 1.77 (qt, J ¼ 7.2 Hz, 2H), 1.52 (qt, phosphate buffer, pH 8) using the formula:
J ¼ 7.6 Hz, 2H), 0.96 (t, J ¼ 7.2 Hz, 3H). 13C NMR (100 MHz, CDCl3):
d (ppm): 170.2, 165.8, 165.5, 158.3, 149.0, 137.5, 136.5, 130.1, 129.4, ES
Inhibition of AChE or BChE ð%Þ ¼  100
111.8, 103.7, 34.5, 30.9, 23.5, 22.4, 22.3, 22.1, 13.8. Anal. calcd for E
C21H23ClN4S : C, 63.22; H, 5.81; N, 14.04; S, 8.04; Found: C, 63.49; H,
Where E is the activity of enzyme without test sample, and S is the
6.09; N, 14.39, S, 7.89.
activity of enzyme with test sample.
2-(Butylthio)-4-(4-methoxyphenyl)-6,7,8,9-tetrahydropyrimido
[4,5-b]quinolin-5-amine (3f):
Compound 3f was obtained as a yellow solid (39%). M.p: 2.4. Molecular modeling
188e190  C. 1H NMR (400 MHz, CDCl3) d (ppm): 7.53 (dd, J ¼ 6.8,
2.0 Hz, 2H), 7.05 (dd, J ¼ 6.8, 2.0 Hz, 2H), 4.81 (br s, 2H, NH2), 3.90 (s, AutodockVina 1.1.1 [25] was the software of choice to generate
3H, OeCH3), 3.37 (t, J ¼ 7.2 Hz, 2H), 3.07 (t, J ¼ 6.0 Hz, 2H), 2.43 (t, the binding modes of the re-docked ligands and the tested com-
J ¼ 6.0 Hz, 2H), 1.95e1.92 (m, 4H),1.76 (qt, J ¼ 7.2 Hz, 2H), 1.50 (qt, pounds.The 2D structure was illustrated by ChemBioDraw Ultra
J ¼ 7.2 Hz, 2H), 0.95 (t, J ¼ 7.2 Hz, 3H).13C NMR (100 MHz, CDCl3): 14.0. ChemBio3D Ultra 14.0from the same package was the tool of
d (ppm): 170.3, 166.6, 164.9, 161.2, 158.2, 149.7, 131.1, 130.3, 114.6, obtaining the 3D configuration. The most stable conformers were
111.6, 104.5, 103.8, 55.5, 34.2, 30.9, 30.8, 23.5, 22.4, 22.3, 22.1, 19.7, proposed by energy minimization algorithm MOPAC which oper-
13.8. Anal. calcd for C22H26N4OS: C, 66.97; H, 6.64; N, 14.20; S, 8.13; ates inside VEGA ZZ 3.1.1.42enviroment [26]. All the crystal struc-
Found: C, 66.93; H, 6.57; N, 14.20, S, 7.40. tures were downloaded in PDB format from the Protein Data Bank
2-(Butylthio)-4-(3-nitrophenyl)-6,7,8,9-tetrahydropyrimido web site [27]. The proteins were prepared for docking by deletion of
[4,5-b]quinolin-5-amine (3g). the unwanted molecules and the water using VEGA ZZ 3.1.1.42.The
Compound 3g was obtained as a yellow solid (62%). M.p: energy minimization of proteins were performed by YASARA server
>260  C.1H NMR (400 MHz, CDCl3) d (ppm) 8.48 (d, J ¼ 2.0 Hz, 1H), [28]. The residues of the binding sites in the active site of acetyl-
8.41 (dd, J ¼ 8.4, 1.2 Hz, 1H), 7.96 (d, J ¼ 7.6 Hz 1H), 7.75 (t, J ¼ 6.0 Hz, cholinesterase were identified as Trp86, Tyr124, Ser203, Glu202,
1H), 4.45 (br s, 2H, NH2), 3.39 (t, J ¼ 7.2 Hz, 2H), 3.08 (t, J ¼ 6.0 Hz, Tyr337, Phe338, His447, and Tyr449.The backbone of the binding
2H), 2.44 (t, J ¼ 6.0 Hz, 2H), 1.95e1.88 (m, 4H), 1.68 (qt, J ¼ 7.2 Hz, cavity of butyrylcholinesterase has the following flexible amino
2H), 1.27 (qt, J ¼ 7.2 Hz, 2H), 0.99 (t, J ¼ 7.2 Hz, 3H). 13C NMR acids, Asn68, Ile69, Asp70, Trp82, Gln119, Thr120, Ser198, Trp231,
(400 MHz, CDCl3) d (ppm) 170.3, 166.4, 163.9, 158.3, 148.5, 148.3, leu286, Ser287, Val288, phe329, Tyr332, phe398, Trp430, Met437,
140.5, 134.9, 130.1, 124.8, 124.1, 112.3, 103.6, 34.5, 30.8, 23.5, 22.3, His438 and Tyr440. The flexible residues were allowed to move
14.2. Anal.calcd for C212H23N5O2S: C, 61.59; H, 5.66; N, 17.10; S, 7.83; freely during the processed flexible docking. The docking grid was
Found: C, 61.87; H, 5.92; N, 17.85, S, 7.54. sized to enclose the co-crystallized molecule and the flexible resi-
4-(4-Chlorophenyl)-2-(octylthio)-6,7,8,9-tetrahydropyrimido dues. For acetylcholinesterase (4ey6) [29] the center of the grid box
[4,5-b]quinolin-5-amine (3h): was: X ¼ 8.2, Y ¼ 61.5, Z ¼ 23.8 and the size was 17 *17 *17 Å.
Compound 3h was obtained as a yellow solid (51%). M.p: Crystal structure AchE (4bdt) [30] has the following spatial center
164e167  C. 1H NMR (400 MHz, CDCl3) d(ppm7.44 (m, 4H), 4.46 (br of the docking box X ¼ 2.22, Y ¼ 34.6, Z ¼ 52.3 and the size was
s, 2H, NH2), 3.29 (t, J ¼ 7.2 Hz, 2H), 2.97 (t, J ¼ 6.0 Hz, 2H),2.32 (t, 17*20*18 Å. For butyrylcholinesterase (5dyw) [31] the grid box size
J ¼ 6.0 Hz, 2H), 1.86e1.81 (m, 4H), 1.68 (qt, J ¼ 7.6 Hz, 2H), 1.40 (qt, was 28 *22*22 Å and the center of box: X ¼ 137.1 Y ¼ 114.3, Z ¼ 39.9.
J ¼ 7.6 Hz, 2H),1.24e1.18 (m, 8H), 0.80 (t, J ¼ 6.8 Hz, 3H).13C NMR Pymol software was the visualization tool for the ligands/protein
(400 MHz, CDCl3): d(ppm): 170.3, 165.8, 165.5, 158.3, 149.0, 137.5, complex [32].
136.5, 130.1, 129.4, 111.8, 103.8, 34.5, 31.8, 31.1, 29.2, 29.0, 28.8, 23.5,
22.7, 22.4, 22.3, 14.1. Anal. calcd for C25H31ClN4S: C, 65.98; H, 6.87; 2.5. Computational details
N, 12.31; S, 7.05; Found: C, 66.23; H, 6.54; N, 12.70, S, 6.73.
Density functional theory (DFT) calculations have been carried
2.3. Method for cholinesterase activity assay out using Gaussian09software [33]. The B3LYP functional [34,35]
and the 6e311þþG(d,p) basis set have been used for all calcula-
Acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) tions. All the ground states were confirmed by vibrational fre-
inhibitory activity was measured, by the spectrophotometric quency analysis (no imaginary frequency). Electronegativity,
method developed by Ellman, G.L., et al. [24] Briefly, 150 ml of chemical softness, chemical hardness and electrophilic indexwere
100 mM sodium phosphate buffer (pH 8.0), 10 ml of sample solution calculated based on HOMO and LUMO energiesas reported in the
dissolved in methanol at different concentrations and 20 ml AChE literature [36e40]. Thebond dissociation enthalpy (BDE) have been
(5.32  10-3 U) or BChE (6.85  10-3U) solution were mixed and calculated as reported in our previous works [41,42].
incubated for 15 min at 25  C, and 10 ml of 0.5 mM DTNB[5,50 -
dithio-bis(2-nitrobenzoic) acid] were added. The reaction was then 3. Results and discussion
initiated by the addition of 10 ml of acetylthiocholine iodide
(0.71 mM) or butyrylthiocholine chloride (0.2 mM). The hydrolysis 3.1. Chemistry
of these substrates were monitored spectrophotometrically by the
formation of yellow 5-thio-2-nitrobenzoate anion, as the result of The target compounds 3a-h were synthesized via Friedlander
4 C. Derabli et al. / Journal of Molecular Structure 1209 (2020) 127902

reaction as shown in Scheme 1. First, the straightforward conden- Table 1


sation between 2-alkylthiouronium halides and arylidenemalono- Cholinesterase inhibition efficacy of compounds 3a-h.

nitriles in the presence of potassium carbonate afforded the Compound IC50 (mM) ± SD/% inhibitiona Selectivity index
corresponding alkylthiopyrimidine derivatives 1a-h, as previously AChE BuChE AChEc BuChEd
investigated in our laboratory [43]. Condensation of the starting
3a 8,76 ± 0,22 19,97 ± 0,86 2,28 0,44
pyrimidines 1a-h with cyclohexanone 2 in the presence of AlCl3 in
3b 5,85 ± 0.28 6,78 ± 0,51 1,16 0,86
dry 1,2 dichloromethane gave eight new compounds 3a-h, with 3c 4,68 ± 0,73 21,71 ± 0,41 4,64 0,21
moderate to good yields (39e62%). These compounds were purified 3d 4,32 ± 0,87 15,10 ± 0,19 3,49 0,29
by recrystallization in ethyl acetate and characterized by 1H NMR, 3e 13,16 ± 0,14 115,82 ± 5,95 8,80 0,11
13 3f 4,94 ± 0,42 2,74 ± 0,74 0,55 1,80
C NMR, and elemental analyses (CHNS).
3g 69,19 ± 4,99 121,24 ± 1,40 1,75 0,57
3h 48,94 ± 4,05 151,38 ± 22,2 3,09 0,32
3.2. Biological evaluation Galantamineb 21,81 ± 1,15 40,72 ± 2,85 1,87 0,53
a
IC50 values represent the means ± SD of three parallel measurements (p < 0.05).
The inhibitory proprieties of target compounds 3a-h were per- b
Reference compound.
formed by the spectroscopic method described by Ellman’s [24] c
Selectivity for AChE is defined as IC50 BuChE (mM)/IC50 AChE (mM).
using Galantamine as the standard. Most of the compounds showed
d
Selectivity for BuChE is defined as IC50 AChE (mM)/IC50 BuChE (mM).

potent inhibitory activity against AChE with IC50s values ranging


from 4,32 to 69,19 mM. Compound 3d with IC50 value of 4.32 mM
compared to BuChE with a factor ranging from 1.16 to 8.80 except
was found to be the most potent compound against AChE, this
3c which on the contrary has an affinity for BChE.
compound was 5-fold more potent than reference drug Galant-
amine with IC50 value of 21.81 mM (Table 1). For comparison pur-
poses, among compounds 3a, 3b and 3c having all the S-methyl 3.3. In silico studies
group, with IC50s values of 8,76, 5,85 and 4,68 mM respectively,
molecule 3c with a 4-nitro group on the benzene ring is more active The suggested binding modes of the active candidates were
than the other two compounds 3a and 3b with 4-chloro and 4- proposed by molecular docking study. The protein data bank was
methoxy groups on the benzene ring respectively. On the other accessed for obtaining the 3D structure of the enzymes [27]. Two
hand, compounds 3e, 3f and 3g with IC50s values of 13,16, 4,94 and proteins of human acetylcholinesterase were downloaded for the
69,19 mM respectively which have the S-ethyl group, it was noticed purpose of achieving a comparative study. One of them (pdb code:
that compound 3f with a 4-methoxy group on the benzene ring is 4ey6) [29] has Galantamine as a native ligand which was the
more active than compounds 3e and 3g with 4-chloro and 4-nitro reference for the biological study. The other one (pdb code: 4bdt)
substituents respectively. In addition, compound 3d was more [30] was co-crystallized with the Tacrine like compound (huprine
potent than 3h with IC50 value of 48,94 mM by 11-fold improve- w), so it could offer a model for protein interaction with our com-
ment. The difference in efficacy is due probably to the length of S- pounds which have Tacrine core in their structures. As a conse-
alkyl chain attached to the thiopyrimidine motiey. quence we can identify the residues which may be involved in the
The BChE results revealed IC50 values ranging from 2.74 to stabilization of the tested compounds. The spatial distribution of
151.38 mM. The most active compounds are 3f and 3b with IC50s of the amino acids within the active sites was different between the
2.74 mM and 6.78 mM respectively which are more potent than two proteins. It was evident that the amino acids move freely to
Galanthamine with value of 40.72 mM. Both compounds have a 4- give a maximum fitting of the ligands. Energy minimization of the
methoxy group linked to the phenyl, which leads to deduce that protein to restore the original distribution of the amino acids in the
it is responsible for improving BChE’s inhibitory activity. By binding site to their supposed natural orientation was essential.
comparing compounds having the same S-alkyl chain, 3a, 3b and 3c After the energy minimization of the two proteins, the active sites
with IC50s values of 19,97, 6,78 and 21,71 mM respectively, are showed a good matching of the orientation inside the pocket be-
molecule 3b with a 4-methoxy group is more effective than the tween each other.
other two compounds 3a and 3c with 4-chloro and 4-nitro groups The noticed difference in the orientation of the amino acids in
respectively. The calculation of the selectivity index allows the the binding pocket which provoked by the interaction with the
evaluation of the degree of affinity that the synthesized compounds bound structure implied the importance of the allowance the free
have with AChE and BChE. Experimental results revealed that all rotation of the flexible amino acids inside the protein gorge.
compounds showed relatively more inhibitory activity to AChE as Henceforth the flexible docking was the technique of choice to
calibrate the process and for the docking of the tested compounds.
It was postulated that the resulted orientation of the ligand and the
R2 O R2 surrounding environment of the flexible amino acids residues may
superimposed with that of the non-minimized protein.
The validation of the docking process was conducted by drawing
NH2 the native ligand using in 2D form. The 2D structure was trans-
CN 2
formed into 3D and the best conformer was picked up. The re-
N N
R1 AlCl3, DCE R1 docking of the native molecules for both examples was per-
S N NH2 S N N
reflux, 24h formed by AutodockVina [25]. The output of the theoretical inter-
1a-h 3a-h action between Galantamine and the protein showed a pattern
similarity to that of the crystal structure. The ligand was super-
3a (R1 = CH3, R2 = Cl) (41%) 3e (R1 = C4H9, R2 = Cl) (58%) imposed over the co-crystallized one as well as the surrounding
3b (R1 = CH3, R2 = OCH3) (58%) 3f (R1 = C4H9, R2 = OCH3) (39%) amino acids with a narrow margin of deviation (Fig. 2 a). For
3c (R1 = CH3, R2 = NO2) (55%) 3g (R1 = C4H9, R2 = NO2) (62%) huprine w, although the orientation of the ligand and the flexible
3d (R1 = C2H5, R2 = Cl) (57%) 3h (R1 = C8H17, R2 = Cl) (51%)
amino acid backbone of the pocket wasn’t superimposed, we could
notice that the spatial interaction between the ligand and the
Scheme 1. The structures of reported Tacrine-derived AChE/BChE inhibitors. amino acids was preserved. The hydrophobic interactions between
C. Derabli et al. / Journal of Molecular Structure 1209 (2020) 127902 5

the benzene ring of the pyrimidine scaffold and Tyrosine 337 and result in preserving the hydrophobic interaction. The hydrogen
the fused alicyclic ring with the tryptophan 86 were maintained bonding interaction between the sulfite moiety and Thr120 was
while the hydrogen bond interaction was shifted from Ser203 to identical in both crystallized and re-docked models. One binding
Trp86 (Fig. 2 b). mode from the docking of the compounds under investigation was
The same docking parameter was applied for the assayed proposed. This pose was selected as it afforded the maximum
compound. Rigid and flexible dockings were performed where the number of hydrogen bonds between the most active inhibitor 3f
flexible docking introduced more reliable results than the rigid and and the protein. On the other hand it was the most frequent binding
more compatible with biological study. The orientation of Tacrine mode between all poses generated by the automated flexible
core of all compounds (with exception of 3c and 3g) was found to docking. In the selected binding mode the phenyl ring directed
be well oriented to give a good hydrophobic field toward Trp86 in toward the outside of the binding cavity and pi-interaction with the
addition to hydrogen bonds with Tyr124 (Fig. 3 c). phenyl ring of Tyr332 represented a possibility. Another stabiliza-
The presence of the nitro group on 3c and 3g may lead to an tion could be provided by hydrogen bond interaction with Asp70.
inverse orientation in which the nitro group made hydrogen bonds The hydrophobic interaction of the compounds with the protein
with Gly121. Trp86 was parallel in this case to the phenyl ring seemed to be more limited in comparison with the native ligand
which offered a reduced surface area for the hydrophobic interac- which may describe the high IC50 of most of them obtained from
tion which might be compensated by the hydrogen bond interac- the in vitro assay.
tion from the nitro group and pi-interaction. This effect is suggested
to potentiate the efficacy of 3c while it might have a negative 3.4. Theoretical investigations
impact on 3g. The decrease in the inhibitory action could be
attributed to the hindrance between the long side chain of the After having successfully synthesized and evaluated in vitro the
compound and the inner wall of the pocket. This Impact could be biological activity of the target Tacrine analogues, we next envis-
seen also in case of 3h which showed the lowest affinity in both aged to gain insights about the reactive nature and reactivity in-
rigid and flexible models. The length of side chain seemed to have a sights of tacrines 3a-3c, as representative compounds, by using
key role in the interaction which may be repulsive in case of 3g and density functional theory (DFT) calculations. Optimized molecular
3h while might be an additive hydrophobic site in case of 3f (Fig. 3 geometries obtained by theoretical methods are useful to explain
d). the three-dimensional structures of the investigated compounds.
The pocket of BuChE (Pdb code: 5dyw) [31] is larger than that of The molecular structures of 3a, 3b and 3c have been optimized at
AChE, and the docking was a challenge. The rigid docking modeling B3LYP/6-311Gþþ(d,p) level of theory. The obtained structures are
provided results not correlated to the biological studies. The flex- shown in Fig. 5. As can be seen, the structures of 3a-3c are non-
ible docking still the better choice in this case. The binding affinity planar due to the presence of the NH2 group of the pyridine ring.
provided by flexible docking was more reasonable in a relative to The substituted benzenes are inclined by 53.67, 46.45 and 50.85
the biological study comparing to the rigid one. The interesting for 3a, 3b and 3c, respectively. The fused pyridine and pyrimidine
result obtained from the calibration of the docking tool was satis- rings adopt quasi-planar geometries for all the studied compounds.
factory to consider the docking results as consistent. Fig. 4. Reactivity indices such as electronegativity, electrophilic index,
The native ligand oriented in a similar binding mode displayed softness and hardness are excellent tools that characterize the
by the non-minimized crystal structure of the enzyme. Some reactivity of the target compounds [44,45]. Electronegativity is a
displacement in the position of Trp82 could be noticed which measure of the tendency to attract electrons in a chemical bond.
possibly occurred to maintain the hydrophobic and the pi-inter- Electrophilicity index is related to the energy lowering associated
action toward the lateral benzene ring. Similarly Tyr440 was moved with a maximum amount of electron flow between a donor and an
in to adjust the new position of the same benzene ring which could acceptor [39,46]. The chemical softness and hardness are measures

a b

Fig. 2. The molecular docking study of AChE a)The re-docking result of the native ligand (inside the blue mesh) with crystallized Galantamine (salmon color) is showing the near
positioning between the generated orientation of the flexible amino acids residues (blue sticks) and the crystallized one (salmon sticks) of AchE (Pdb code: 4ey6) b) in silico
proposed binding mode of huprine w and with the free rotated amino acids of the gorge relatively to the crystallized structure (salmon color) of AchE pdb code: 4bdt.
6 C. Derabli et al. / Journal of Molecular Structure 1209 (2020) 127902

c d

Fig. 3. The molecular docking study of AChE c) 3c binding mode (blue) within the flexible amino acid residues of the binding site (salmon) d) 3d (blue) interaction with the flexible
amino acids backbone of the pocket (salmon color).

Fig. 4. Docking results of BuChE (5dyw) a) Re-docked native ligand (blue) and the flexible amino acid in comparison with the original orientation (salmon color). b) Docking result
of 3f showing the interaction with the movable amino acid residues of the active site (salmon stick).

Table 2
Reactivity indices of 3a-3c obtained at B3LYP/6e311þþG(d,p)level of theory.

Reactivity indices 3a 3b 3c

Electronegativity 4.20 3.98 4.91


Softness 0.27 0.25 0.38
Hardness 1.87 1.97 1.31
Electrophilic index 4.72 4.04 9.24

Fig. 5. Optimized geometries of 3a-3c obtained at B3LYP/6-311Gþþ(d,p) level of act as electron donor rather than electron acceptor. In terms of
theory.
electrophilic index, the least reactive compound as electron donor
is 3c, whereas the other compounds have a comparable reactivity.
of resistance to charge transfer. The reactivity indices of compounds Molecular electrostatic potential (MEP) mapping is a very useful
3a-3c were calculated in the gas-phase and are given in Table 2. approach to explore the reactivity of the investigated compounds.
An examination of the obtained results reveals that 3a-3c have MEP mapping results for 3a, 3b and 3c are illustrated in Fig. 6. The
comparable values of electronegativity, softness and hardness in nucleophilic and electrophilic sites are expressed in term of
the range of 3.98e4.91, 1.31e1.97 and 0.25e0.38, respectively. 3c different color codes; a deep red color indicates an electron-rich
has the highest electrophilicity index value (9.24), whereas 3a and site, whereas deep blue indicates an electron-deficient site. As
3b have comparable values (4.04 and 4.72, respectively).These ob- shown in Fig. 6, the most electron-rich sites of 3a-3c are located
servations clearly shown that all the studied compounds prefer to around the two adjacent nitrogen atoms of the pyridine and py-
rimidine rings, where as the most electron-deficient sites are one
C. Derabli et al. / Journal of Molecular Structure 1209 (2020) 127902 7

with HOMOs results.

4. Conclusion

In the present study, we report the development of a novel se-


ries of substituted 2-alkylthiopyrimidino-Tacrines 3a-h carried out
by applying Friedlander reaction of 3-amino-2-cyanopyrimidines
1a-h with cyclohexanone in the presence of AlCl3 in 1,2 dichloro-
ethane. All compounds were evaluated for their potential to inhibit
commercially available electric eel. acetylcholinesterase (AChE) and
horse serum butyrylcholinesterase (BChE). The experimental re-
sults showed that most compounds were highly active towards
AChE (IC50s ranging from 4.32 to 69.19 mM) and few towards BChE
with IC50s in the range of 2.74e151.38 mM. Also, molecular docking
studies was in parallel to the in vitro results, for the purpose of
assisted in explaining the structure-activity relationships of this
type of compounds. Finally, theoretical calculations by means of
DFT/B3LYP method have been carried out in order to gain insights
about the molecular structure and reactivity insights of tacrines 3a-
3c as representative compounds.

Acknowledgments
Fig. 6. Lowest unoccupied molecular orbital (a), highest occupied molecular orbital (b)
and molecular electrostatic potential (c) of 3a-3c calculated at B3LYP/6-311Gþþ(d,p) We thank MESRS (Ministe re de l’Enseignement Supe rieur et de
level of theory. la Recherche Scientifique) and DGRST (Direction Ge  ne
rale de la
Recherche Scientifique et Technologique), Algeria for financial
support. H.B. thanks the HPC resources of UCI (Unite  de Calcul
the NH2 groups. These results suggest that these sites are the res Mentouri Constantine 1 University for the used
Intesif) of the Fre
preferred sites for electrophilic and nucleophilic attacks, computational resources.
respectively.
Highest occupied molecular orbital (HOMO) and lowest unoc-
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