Design, synthesis and molecular docking study of new purine derivatives as Aurora kinase inhibitors

Article abstract of DOI:10.1016/j.molstruc.2020.129843

Nine new purine-based compounds were designed and have been synthesized through series reactions of the starting compound 8-amino-substituted purine (2) with various reagents. Full characterizations of the synthesized compounds were performed to elucidate

Full text of DOI:10.1016/j.molstruc.2020.129843

Journal of Molecular Structure 1229 (2021) 129843
Contents lists available at ScienceDirect
Journal of Molecular Structure
journal homepage: www.elsevier.com/locate/molstr
Design, synthesis and molecular docking study of new purine
derivatives as Aurora kinase inhibitors
Mohamed E. Khalifa∗
Department of Chemistry, College of Science, Taif University, P.O.Box 11099, Taif 21944, Saudi Arabia
a r t i c l e i n f o
a b s t r a c t
Article history:
Nine new purine-based compounds were designed and have been synthesized through series reactions
of the starting compound 8-amino-substituted purine (2) with various reagents. Full characterizations of
the synthesized compounds were performed to elucidate their chemical structures by means of physical
and spectroscopic methods. All products were in-vitro tested for their potent anti-cancer action against
different human cancers; leukemia (HL60), lung cancer (A549), Breast cancer (SKBR3) and Stomach can-
cer (MKN45). Upon experimental biological evaluation, synthons showed higher efficiency against SKBR3
cell lines in particular and hence were docked with anticancer enzyme (Aurora kinase) to adequately
understand the link of each entity inside the enzyme active site.
Received 2 November 2020
Revised 16 December 2020
Accepted 24 December 2020
Available online 29 December 2020
Keywords:
Purine
Antitumor activity
Molecular docking
Aurora kinase
Breast cancer
© 2020 Elsevier B.V. All rights reserved.
1. Introduction
cells’ genesis [13] and inhibiting the growth of fulvestrant resis-
tant T47D breast cancer cell lines as well [14]. Recent evidence
Among the numerous important heterocyclic compounds,
purines are the most widely distributed kind of nitrogen-
containing moieties present in nature [1]. They are consisting of
fused pyrimidine to imidazole rings and found in important bi-
suggests that the Aurora A and B (the two major types of Aurora
kinase), tend to play a key role in the regulation of chromatid di-
vergence [9,10]. More specifically, it allows the splitting cell to pro-
vide its daughter cell with its genetic material [15-18]. Inadequa-
cies genetic instability, strongly linked to tumorigenesis can occur
in this segregation [19]. Thus, the development of Aurora onco-
genic inhibitors may boost cancer patients’ clinical outcomes. In
modern drug design process, molecular docking is very important
as an optimization tool to illustrate the “best-fit” ligand orienta-
tion in binding to a specific protein and to deduce the assembly of
the intermolecular complex formed with minimum binding energy
for predicting affinity and activity [20]. The combination of two
or more pharmacophores in a single molecule is one of the major
approaches for designing of new biologically active moiety. Struc-
tural fragments with heterocyclic moieties are most obvious among
all drugs [21]. Based on the above data and our efforts to de-
velop new potent molecular anti-tumor agents [22-27], it is worth
reporting the synthesis of new derivatives incorporating purine-
imidazole core structure and in vitro investigation against various
human cancers: leukemia (HL60), lung cancer (A549), Breast can-
cer (SKBR3) and Stomach cancer (MKN45). The compounds were
also examined for their cytotoxicity against Lung normal cell lines
(WI38) in order to indicate their toxicity. The structural activity re-
lationship (SAR) study for the synthesized hybrids regarding an-
titumor activities was discussed. On the other hand, Reversine is
known as a potent inhibitor of the mitotic kinase Mps1 [28] and
has the potential to induce selectively cell death of cancer cells
ꢀ
molecules, such as adenosine triphosphate (ATP), guanosine 5 -
triphosphate (GTP), cyclic adenosine monophosphate (AMP), nicoti-
namide adenine dinucleotide hydrogen (NADH), and coenzyme
A [2]. They provide essential hydrogen bonding capabilities that
make them interesting scaffolds to target a wide range of biosyn-
thetic, regulatory and signal transduction proteins (e.g. G proteins,
cell phosphates and polymerases) [3]. Purine derivatives consti-
tute an extensive class of compounds (e.g. methylxanthine, caf-
feine, and theophylline), which are well-known for their therapeu-
tic utilities as analeptics, antiasthmatics, vasodilators, antihyper-
tensive, diuretics, anti-HIV-1, antimicrobial, bronchodilators, and
anticancer agents [4-6]. Traube synthesis was reported to prepare
most of purines by fusing pyrimidine diamines to imidazoles or
by binding the pyrimidine ring to imidazole moieties [7]. Ser-
ine/threonine kinase mammalian Aurores (Aurora-A, -B, and -C)
are the most prevalent mitotic progression regulators and are of-
ten abundantly expressed in human cancers at measured levels
[8-12]. Latest studies demonstrated their role in promoting pro-
gression of the tumor, through the activation of reprogramming
epithelial-mesenchymal transformation to lead to tumor-initiating
∗
Corresponding author.
E-mail address: mohamedezzat@tu.edu.sa
https://doi.org/10.1016/j.molstruc.2020.129843
0022-2860/© 2020 Elsevier B.V. All rights reserved.

M.E. Khalifa
Journal of Molecular Structure 1229 (2021) 129843
[29]. Therefore, a molecular docking analysis was performed on the
synthesized compounds compared to Reversine to explore a cre-
ative class of Aurora inhibitors based on purine scaffold and realize
the binding modus of each molecule in the Aurora enzyme active
site.
2.4.2.2. 8-((2-Hydroxynaphthalen-1-yl)diazenyl)-1,3-dimethyl-3,7-
dihydro-1H-purine-2,6-dione (9). Scarlet red crystals (3.7 g, 53 %).
M.p. > 300°C. IR: νmax= 3341 (OH), 3059 (NH), 1688 (CO), 1649
(CO), 1540 (C=N) and 1406 (CH3) cm−1
.
1H NMR: δ/ppm= 3.29
(s, 3H, CH3–N1), 3.40 (s, 3H, CH3–N3), 6.44–7.95 (m, 6H, Ar–H),
8.85 (s, 1H, OH), 11.28 (s, 1H, NH–N7). 13C NMR: δ/ppm= 28.39
(C–N1 purine), 30.21 (C–N3 purine), 123.15, 123.45, 126.32, 126.51,
127.09, 128.70, 129.34, 140.17, (8C–naphthyl), 126.27 (C5–purine),
135.98 (C–N–naphthyl), 146.04 (C8–purine), 150.90 (C6–purine),
151.66 (C2–purine), 154.48 (C4–purine), 159.95 (C-OH–naphthyl).
MS (m/z, %): 350 (M+, 100). HRMS calc. for C17 H14 N6O3: 350.1127,
Found: 350.1181.
2. Experimental
2.1. Chemicals and instrumentations
Chemicals and instrumentations involved in this research are
fully identified and described elsewhere [30] and in supplemen-
tary file (S1).
2.4.2.3. 8-((1-Hydroxynaphthalen-2-yl)diazenyl)-1,3-dimethyl-3,7-
dihydro-1H-purine-2,6-dione (10). Reddish brick crystals (4.6 g, 66
%), M.p. > 300°C. IR: νmax= 3339 (OH), 3141 (NH), 1684 (CO),
2.2. Biological Analysis
The cultured cancer cells (DS Pharma Biomedical Co., Ltd., Os-
aka, Japan), cytotoxicity assay method and statistical analysis were
previously reported [30] and fully described in supplementary file
(S1). The relative cell viability in percentage was calculated accord-
ing to the equation (1).
1638 (CO), 1574 (C=N) and 1409 (CH3) cm−1
.
1H NMR: δ/ppm=
3.29 (s, 3H, CH3–N1), 3.44 (s, 3H, CH3–N3), 6.42–8.10 (m, 6H,
Ar–H), 8.99 (s, 1H, OH), 11.29 (s, 1H, NH–N7). 13C NMR: δ/ppm=
28.22 (C–N1), 30.17 (C–N3), 118.28 (C–N–naphthyl), 123.11, 123.42,
124.59, 125.05, 125.70, 129.34, 129.49, 135.98 (8C–naphthyl),
126.24 (C5–purine), 146.01 (C8–purine), 151.79 (C6–purine), 151.60
(C2–purine), 156.56 (C4–purine), 172.57 (C–OH–naphthyl). MS
(m/z, %): 350 (M+, 89). HRMS calc. for C17 H14 N6O3: 350.1127,
Found: 350.1181.
Abs570 treated sample
% Cell viability =
× 100.
(1)
Abs570 untreated sample
2.3. Docking methodology
The molecular docking technique was performed by using MOE
2015.10 software (The Chemical Computing Group Inc., Montreal,
Canada) [31].
2.4.2.4. 4-Amino-2-((1,3-dimethyl-2,6-dioxo-2,3,6,7-tetrahydro-
1H-purin-8-yl)diazenyl)-3-methyl-6-oxo-6,7-dihydrothieno[2,3-
b]pyridine-5-carbonitrile (11). Reddish brown crystals (4.4 g,
53 %). M.p. > 300°C. IR: νmax= 3335 (NH2), 3141 (NH), 2188
2.4. Synthesis
(CN), 1689 (CO), 1659 (CO), 1569 (C=N) and 1421 (CH3) cm−1
.
1H NMR: δ/ppm
=
2.46 (s, 3H, CH3–thienopyridine), 3.29 (s,
2.4.1. 8-Amino-1,3-dimethyl-3,4,5,7-tetrahydro-1H-purine-2,6-dione
(2)
3H, CH3–N1), 3.42 (s, 3H, CH3–N3), 4.22 (s, 2H, NH2), 10.70 (s,
1H, NH-pyridyl), 11.30 (s, 1H, NH–N7). 13C NMR: δ/ppm = 6.49
(CH3-thienopyridine), 27.89 (C-N1 purine), 30.24 (C–N3 purine),
81.42 (C5–thienopyridine), 112.69 (C2–thienopyridine), 113.21
A mixture of 8-chloro-1,3-dimethyl-3,7-dihydro-1H-purine-2,6-
dione (1; 0.43 g, 20 mmol) and excess amount of concentrated am-
monia solution (20 mL) in ethanol (20 mL) was heated at 100 °C
in a sealed tube for 2 h. The reaction mixture was allowed to cool
at room temperature and left overnight. The collected product (2)
was washed with cold spirit several times and recrystallized from
ethanol to yield colorless powder (2.4 g, 61 %). M.p. > 310 °C (Lit.
> 310 °C) [32,33].
≡
(C9–thienopyridine), 117.56 (C N), 128.14 (C5–purine), 134.32 (C3–
thienopyridine), 146.01 (C8–purine), 150.75 (C6–purine), 151.49
(C2–purine), 151.75 (C4–purine), 159.95 (C8–thienopyridine),
166.33 (C6–thienopyridine), 172.88 (C4–thienopyridine). MS (m/z,
%): 411 (M+, 34). HRMS calc. for C16 H13N9O3S: 411.0862, Found:
411.0891.
2.4.2. General method for preparation of 8-substituted
2.4.3. Synthesis of (Z)-N-(1,3-dimethyl-2,6-dioxo-2,3,6,7-tetrahydro-
1H-purin-8-yl)-2-(phenylamino)-2-thioxoacetohydrazonoyl cyanide
(13)
diazenyl-1,3-dimethyl-3,7-dihydro-1H-purine-2,6-dione derivatives
(8–11)
A soln. of 8-amino-1,3-dimethyl-3,4,5,7-tetrahydro-1H-purine-
2,6-dione 2 (3.90 g, 20 mmol) in 5% HCl soln. (20 mL) was cooled
to 0–5 °C, and then NaNO2 (1.38 g, 20 mmol) was added in four
portions. The mixture was slow stirred for 1.5 h for complete di-
azotization. Coupler components (4–7) (1.88 g, 2.88 g, 2.88 g and
4.10 g, respectively, 20 mmol) were added in small portions with
continuous slow stirring at cold condition for further 1 h. The
yielded precipitates (4–7) were filtered off, washed with cold wa-
ter, dried and recrystallized from ethanol.
2-Phenylthiocarbamoyl derivative 7 (4.4 g, 20 mmol) was sus-
pended in 25 mL EtOH and 20% aq. KOH (30 mL). The mixture
was kept in refrigerator overnight. A freshly cooled solution of di-
azonium chloride 3 (4.2 g, 20 mmol), which freshly prepared by
adding cold sodium nitrite solution (1.38 g, 20 mmol) to cold sus-
pension of 2 (3.9 g, 20 mmol) in 12 mL concentrated HCl, was then
added dropwise with stirring to the cold suspension of (7). The re-
action mixture was allowed to stir at (0–5 °C) for additional 2 h
and kept overnight in refrigerator. The solid azo product (13) was
filtered off, dried and recrystallized from ethanol-DMF mixture as
2.4.2.1. 8-((4-Hydroxyphenyl)diazenyl)-1,3-dimethyl-3,7-dihydro-1H-
purine-2,6-dione (8). Brownish red crystals (3.4 g, 57 %). M.p. >
300°C. IR: νmax= 3165 (NH), 1687 (CO), 1651 (CO), 1550 (C=N) and
yellowish orange crystals (4.5 g, 59 %). M.p. > 300°C. IR: νmax
=
3204 (NH), 2202 (CN), 1644 (CO), 1597 (CO), 1539 (C=N) and 1442
1418 (CH3) cm−1
.
1H NMR: δ/ppm= 3.20 (s, 3H, CH3–N1), 3.41 (s,
(CH3) cm−1
.
1H NMR: δ/ppm= 3.14 (s, 3H, CH3–N1), 3.33 (s, 3H,
3H, CH3–N3), 6.79–7.91 (m, 4H, Ar–H), 9.98 (s, 1H, OH), 11.52 (s,
1H, NH–N7). 13C NMR: δ/ppm= 28.39 (C–N1), 30.21 (C–N3 purine),
116.14, 116.87, 127.09, 128.70 (4C–phenyl), 119.24 (C–N–phenyl),
126.27 (C5–purine), 146.04 (C8–purine), 150.91 (C6–purine), 151.68
(C2–purine), 154.49 (C4–purine), 159.95 (C–OH). MS (m/z, %):
300 (M+, 25.4). HRMS calc. for C13H12N6O3: 300.0971, Found:
300.0987.
CH3–N3), 7.24–7.44 (m, 5H, Ar–H), 8.64 (s, 1H, NH–purine), 9.77
(s, 1H, NH–Ph), 10.87 (s, 1H, C=N-NH). 13C NMR: δ/ppm= 28.23
(C–N1 purine), 30.21 (C–N3 purine), 108.36 (C=N-NH), 118.71 (CN),
122.34 (C5–purine), 124.17, 124.94, 125.71, 128.96, 129.31, 139.98
(6C–phenyl), 144.01 (C8–purine), 149.56 (C4–purine), 151.56 (C2–
purine), 153.08 (C6–purine), 180.15 (C=S). MS (m/z, %): 382 (M+,
51). HRMS calc. for C16 H14 N8O2S: 382.0960, Found: 382.0953.
2

M.E. Khalifa
Journal of Molecular Structure 1229 (2021) 129843
2.4.4. Synthesis of (Z)-N-(1,3-dimethyl-2,6-dioxo-2,3,6,7-tetrahydro-
1H-purin-8-yl)-benzothiazole-2-carbohydrazonoyl cyanide
(14)
A solution of purinyl azo N-phenylethanethioamide 13 (7.6 g, 20
mmol) in 20 mL of ethyl acetate was prepared and pyridine (1.6
mL) was added dropwise during 10 min with stirring. A bromine
solution was prepared (0.16 g, 20 mmol) in 10 mL ethyl acetate
and added to the mixture dropwise during another 10 min stirring.
The mixture was stirred continuously for further 3 h. The prod-
uct was collected and recrystallized from ethanol as faint brown
crystals (5.5 g, 73 %). M.p. > 300°C. IR: νmax= 3292 (NH), 2175
(CN), 1731 (CO), 1628 (CO), 1548 (C=N purine) and 1389 (CH3)
Scheme 1. Synthesis of 8-amino-substituted purine (2).
cm−1
.
1H NMR: δ/ppm= 3.21 (s, 3H, CH3–N1), 3.41 (s, 3H, CH3–
N3), 7.21–8.02 (m, 4H, Ar–H), 10.47 (s, 1H, C=N-NH), 11.13 (s, 1H,
NH–purine). 13C NMR: δ/ppm= 28.20 (C–N1 purine), 30.27 (C–
N3 purine), 117.66 (CN), 119.95 (C5–purine), 116.14, 116.87, 126.27,
127.09, 132.47, 136.71 (C=N-NH), 150.91 (6C–benzothiazole), 141.51
(C8–purine), 149.33 (C4–purine), 152.07 (C2–purine), 154.48 (C6–
purine), 159.95 ((C(S) benzothiazole)). MS (m/z, %): 380 (M+, 18).
HRMS calc. for C16 H12N8O2S: 380.0804, Found: 380.0799.
(Scheme 1) was very useful to produce prospective bioactive in-
gredients against malignant cell lines. The starting component was
produced in high yield and in agreement with literature [32,33].
The target anticancer agents were planned to be synthesized
through creating diazenyl derivatives of the starting 8-amino
purine (2) and hence implementing imidazo and benzothiazolyl
purines upon cyclization ability of active terminals. Diazotization of
acidic solution of 8-amino purine (2) with sodium nitrite afforded
the corresponding diazonium chloride (3) [32], which underwent
coupling with aryl and/or hetaryl aromatic amines to afford the
diazenyl derivatives (8–11) as described in Schemes 2 and 3. The
products were structurally elucidated with various spectral analy-
ses (c.f. experimental part).
2.4.5. General method for synthesis of
1,3-dimethyl-7substituted-1H-imidazo[2,1-f]purine-2,4(3H,8H)-dione
derivatives (16a-c)
A
mixture of equimolar quantities (20 mmol) of 8-amino-
1,3-dimethyl-3,4,5,7-tetrahydro-1H-purine-2,6-dione 2 (3.9 g, 20
mmol) in warm DMF (50 mL) and α-halo carbonyl compounds
15a–c (3.8 g phenacyl chloride, 2.2 g chloroacetyl chloride and 2.4
g ethyl chloroacetate, respectively) in presence of anhydrous potas-
sium carbonate (4.2 g, 30 mmol) was refluxed for 10 h (monitored
by TLC using ethyl acetate as eluent). The mixtures were then con-
centrated under vacuum and poured onto acidified ice-cold water.
The collected precipitates were recrystallized from ethanol-DMF
mixture.
Accomplishing different hydroxyl derivatives (4–6) was per-
formed upon coupling with different hydroxyl couplers (i.e. phe-
nol, α- and β- naphthols) yielding derivatives (8–10), respectively,
under cold condition (0–5 °C) and in presence of sodium acetate
and ethanol (Scheme 2).
Inserting nitrile and amino functions could be achieved by cou-
pling of diazonium salt (3) with thieno pyridine scaffold (7) to af-
ford the diazenylthieno pyridine-5-carbonitrile compound (11). The
pyridine coupler (7) was exclusively pre-synthesized in our lab by
the reaction of 2-aminothiophene derivative with ethyl cyanoac-
etate followed by ethoxide cyclization [35].
2.4.5.1. 1,3-Dimethyl-7-phenyl-1H-imidazo[2,1-f]purine-2,4(3H,8H)-
dione (16a). Greenish yellow crystals (4.6 g, 78 %). M.p. > 300°C
(Lit. > 310 °C) [34].
On the other hand, the 2-phenylthiocarbamoyl derivative (12)
[36] was freshly prepared through the catalyzed base addi-
tion of phenyl isothiocyanate to cyanoacetamide as active cou-
pler for Japp-Klingemann reaction. Therefore, coupling of 2-
phenylthiocarbamoyl derivative (12) with appropriate diazonium
salt (3) in potassium hydroxide proceeded in Japp-Klingemann
reaction regime, causing amide cleavage [36] to afford the cor-
responding cyano-purine hydrazonoyl-N-phenylethanethioamide
derivative (13) as indicated in Scheme 3. The IR spectrum of com-
pound (13) showed disappearance of acetyl carbonyl at 1713 cm−1
and the singlet signal affiliated to methyl group at δ 2.2 ppm in the
1H NMR spectrum. While cyano function at 2202 cm−1 was ap-
peared. Extensively, cyclization of purin-2-thioxoacetohydrazonoyl
cyanide compound (13) in bromine solution (Br2 in ethyl ac-
etate) in pyridine gave benzothiazolyl acetonitrile derivative (14)
(Scheme 3). 1H NMR spectrum displayed two signals (D2O ex-
changeable) at δ 10.47 and 11.13 ppm due to two NH protons in
addition to multiplet signal in the region of δ 7.21–8.02 ppm at-
tributed to 4 aromatic protons.
2.4.5.2. 1,3,7-Trimethyl-1H-imidazo[2,1-f]purine-2,4(3H,8H)-dione
(16b). Light brown crystals (2.8 g, 60 %). M.p. > 300°C. IR: νmax
=
3150 (NH), 1688 (CO), 1539 (CO), 1489 (C=N purine) and 1406
(CH3) cm−1
.
1H NMR: δ/ppm= 1.86 (s, 3H, CH3), 3.19 (s, 3H,
CH3–N1), 3.31 (s, 3H, CH3–N3), 6.44 (s, 1H, CH=) and 11.28 (s,
1H, NH). 13C NMR: δ/ppm= 13.92 (CH3 imidazole), 28.23 (C–N1
purine), 30.26 (C–N3 purine), 100.84 (C5–purine), 104.26, 147.29
(2C–imidazole), 148.69 (C4–purine), 151.68 (C8–purine), 152.14
(C2–purine), 153.45 (C6–purine). MS (m/z, %): 233 (M+, 18). HRMS
calc. for C10H11 N5O2: 233.0913, Found: 233.0902.
2.4.5.3. 1,3-Dimethyl-1H-imidazo[2,1-f]purine-2,4,7(3H,6H,8H)-trione
(16c). Faint brown crystals (2.8 g, 54 %). M.p. > 300°C. IR: νmax
=
3292 (NH), 1628 (CO), 1588 (CO), 1548 (CO), 1478 (C=N purine),
1389 (CH2) and 1349 (CH3) cm−1
.
1H NMR: δ/ppm= 3.32 (s, 6H,
2CH3), 4.18 (s, 2H, CH2) and 11.12 (s, 1H, NH). 13C NMR: δ/ppm=
28.23 (C–N1 purine), 30.26 (C–N3 purine), 50.26 (CH2, imidazole),
100.84 (C5–purine), 148.69 (C4–purine), 151.68 (C8–purine), 152.14
(C2–purine), 153.45 (C6–purine), 181.08 (C=O, imidazole). MS (m/z,
%): 263 (M+, 24). HRMS calc. for C9H19N5O3: 235.0718, Found:
235.0711.
Accordingly, 8-amino purine (2) underwent successful cycliza-
tion reaction on treatment with active α-halo carbonyl compounds
(15a-c) (namely; phenacyl chloride, chloroacetyl chloride and ethyl
chloroacetate) in presence of anhydrous potassium carbonate to
yield the imidazo purine derivative (16a-c) as shown in Scheme 4.
The structure is elucidated by the disappearance of characteristic
signals of NH2 (δ = 6.45 ppm) and purine NH (δ = 11.56 ppm) in
the 1HNMR spectrum, while presence of singlet signal at δ = 6.44
ppm and 11.12–11.28 ppm attributed to CH= and NH protons of
imidazole ring, respectively.
3. Results and discussion
3.1. Chemistry
Successful preparation of 8-amino-substituted purine (2) by
treatment of 8-chloro analogue (1) with ethanolic ammonia
3

M.E. Khalifa
Journal of Molecular Structure 1229 (2021) 129843
Scheme 2. Synthesis of 8-substituted diazenyl-purine derivatives (8–11).
Scheme 3. Synthesis of cyano-purine diazenyl-N-phenylethanethioamide compound (13) and purine-diazenyl benzothiazolyl acetonitrile derivative (14).
3.2. Impact on the growth of human tumor cell lines
cell growth (Table 1). The more decrease of the IC50 value indicates
higher efficiency against tumor cell.
Evaluation of synthons in vitro for possible potential antitu-
mor agents against different human cancers; Leukemia (HL60),
Lung cancer (A549), Breast cancer (SKBR3) and Stomach can-
cer (MKN45), was performed after continuous exposure of 48 h.
Cytotoxicity function has been determined by their cell growth
inhibitory effect using the tetrazolium (3-(4,5-dimethylthiazol-2-
yl)-2,5-diphenyltetrazolium bromide (MTT) assay [37]. IC50 values
were then recorded as concentrations that inhibit 50% of tumor
Recorded data in Tale 1 indicates that derivatives (9-11) have
high to moderate antitumor action in relatively low concentrations
especially for Breast cancer cell lines (SKBR3). Although deriva-
tive (9) has high activity in low concentration (IC50= 26.16 μM),
but it’s still not safe to normal cell lines along with compounds
(13, 14, 16b and 16c; IC50= < 3- 33.15 μM). Most of other tested
compounds seem to be safe to normal cell lines in higher concen-
trations > 100 μM. These findings agree well with the molecular
docking analysis.
4

M.E. Khalifa
Journal of Molecular Structure 1229 (2021) 129843
Scheme 4. Synthesis of imidazo[2,1-f]purine-2,4(3H,8H)-dione derivatives (16a-c).
Table 1
Effect of the synthesized compounds (8-11, 13, 14 and 16a-c) on the growth of different tumor cell lines under investigation (In
vitro Cytotoxicity IC50
)
In vitro Cytotoxicity IC50 (μM)
Cpd. No.
8
Leukemia HL60
> 100
Lung cancer A549
Breast cancer SKBR3
53.73 3.8
Stomach cancer MKN45
58.07 3.9
87.48 4.7
62.61 3.8
79.62 4.7
96.48 4.6
99.03 2.5
> 100
Lung normal WI38
> 100
87.48 4.7
36.78 3.1
64.54 3.7
80.22 4.1
95.17 3.1
88.71 4.3
99.25 5.1
85.80 4.1
89.57 3.2
9
> 100
26.16 2.1
< 3
10
> 100
25.11 1.9
> 100
11
64.60 3.8
83.41 3.4
88.12 3.2
> 100
42.96 3.2
> 100
13
98.09 2.7
33.15 1.2
23.41 3.8
> 100
14
92.70 2.2
16a
16b
16c
52.21
3.7
83.05 1.6
78.21 3.1
93.51 3.3
77.19 1.1
89.13 3.1
85.73 4.5
18.60 4.7
32.14 1.8
Means
SEM of three-independent experiments
Table 2
3.4. Structural activity relationship (SAR)
Validation table energy score (kcal/mol) and rmsd
All compounds are capable to inhibit the growth of the tested
human tumor cell lines with variable activities regarding to their
chemical structure (Table 1). Inserting of hydroxyl phenyl feature
showed superior tumor inhibition in lower concentrations espe-
Compound
Energy score (kcal/mol)
rmsd
1.89
1.41
2.61
0.849
0.732
1.60
1.80
1.47
1.00
0.90
Reversine
-6.90
-5.32
-6.81
-6.54
-6.95
-7.01
6.99
8
9
10
11
13
14
16a
16b
16c
cially for Breast cancer cell lines (e.g. Purine derivative 10, IC50
=
25.11 μM). This phenomenon could be explained by its higher an-
tioxidant and free radical scavenging action [38,39].
-6.21
-5.84
-5.66
3.5. Molecular docking
The study of molecular docks is an important technique to as-
sess the potentially interactive relationship between the binding
molecules and the target enzyme as well as receptor. On the basis
of MOE 2015.10 device protocol [31], the validation of the docking
of the synthesized purine derivatives (8-11, 13, 14 and 16a-c) and
Reversine (reference molecule) was achieved [40]. A new class of
Aurora inhibitors was identified as purine moeity [8-12] comparing
drug validity between the synthesized purines and Reversine as a
new category of pan-Aurora kinase blockers with strong emphasis
viability against tumor in mice to propose a new platform for drug
evolution. The validation of Aurora kinase in purine-derived com-
plex based on measured ligand-protein interactive energies.
All the synthesized derivatives and reference molecule were vir-
tually screened and analyzed. The selection of purine derivatives
for potential inhibitors in the Aurora kinase pharmacopoeia was
based on their effectiveness against SKBR3 cell lines. Docking the
comparable molecules at the binding position of Aurora A led to a
measured binding energy score of kcal/ mol (Table 2).
Reversine was used as a reference molecule and interaction
with aurora kinase enzyme explained a very good drug ligand in-
teraction (Fig. 1a,b) but gave bad drug ligand suitability, (rmsd=
1.89). This value was considered as a higher value compared with
the synthesized purine molecules (Table 2).
It’s of interest to discuss ligand interaction diagrams of the
most active compounds (10 and 11) with Aurora kinase enzyme
based on their experimental potency, while the rest diagrams will
be included in Figures file (attached).
The dynamic 2D Aurora pocket with a purine derivative (10)
describes how three electrostatic bonds interact (Fig. 2a). The 3D-
crysyallophy structure explains the interaction between (10) as a
ligand and Aurora pocket residues in which the hydrogen in the
azepine ring attached with Leu99 and Lys180 (Fig. 2a).
The superposition of purine (11) generated a pharmacophore
with H-bond with the active site of enzyme (Fig. 3a). Active site
protein analysis was conducted from the same amino acid residue
database, Leu223, Val107, Ala120, Lys101, Leu154, Leu170, Pro174,
5

M.E. Khalifa
Journal of Molecular Structure 1229 (2021) 129843
Fig. 1. a 2D interaction diagrams of Reversine (reference molecule) with Aurora kinase enzyme. b 3D interaction diagrams of Reversine with Aurora kinase enzyme.
6

M.E. Khalifa
Journal of Molecular Structure 1229 (2021) 129843
Fig. 2. a 2D interaction diagrams of compound (10) with Aurora kinase enzyme. b 3D interaction diagrams of compound (10) with Aurora kinase enzyme.
7

M.E. Khalifa
Journal of Molecular Structure 1229 (2021) 129843
Fig. 3. a 2D interaction diagrams of compound (11) with Aurora kinase enzyme. b 3D interaction diagrams of compound (11) with Aurora kinase enzyme.
Gly176, Glu171, Phe172, Gly100, Leu99, Ala173, Arg97, Glu181,
Lys184, Lys180, Arg175. The 2D pocket of Aurora kinase in a lig-
and complex with purine (11) explains that four hydrogen bonds
and two π-π stacking. (Fig. 3b) Fig. 4.
3.5.1. The drug-ligand electrostatic force distance measurements
The drug-ligand electrostatic force distances represent the good
drug-ligand interaction. For example, compound (11) presented 7
intramolecular forces indicating high drug ligand interaction (i.e.
H- bond distances between lys218 and cyano group= 2.23; Asp234
8

M.E. Khalifa
Journal of Molecular Structure 1229 (2021) 129843
Fig. 4. The drug-ligand electrostatic force distance measurements for compound (11).
and NH, S= 2.23, 3.41; Gly 177 and NH= 2.08 and Ala 173 and
carbonyl group= 2.42). The π-π stacking also is existed between
Val 107 and the two aromatic rings.
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Mohamed E Khalifa: Conceptualization, Methodology, Software
interpretation, Data curation, Visualization, Investigation, Writing
Manuscript, Reviewing and Editing.
Declaration of Competing Interest
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