Design, synthesis and in silico insights of new 7,8-disubstituted-1,3-dimethyl-1H-purine-2,6(3H,7H)-dione derivatives with potent anticancer and multi-kinase inhibitory activities

Article abstract of DOI:10.1016/j.bioorg.2020.104569

Aiming to obtain an efficient anti-proliferative activity, structure- and ligand-based drug design approaches were expanded and utilized to design and refine a small compound library. Subsequently, thirty-two 7,8-disubstituted-1,3-dimethyl-1H-purine-2,6(3H,7H)-dione derivatives were selected for synthesis based on the characteristic pharmacophoric features required for PI3K and B-Raf oncogenes inhibition. All the synthesized compounds were evaluated for their in vitro anticancer activity. Compounds 17 and 22c displayed an acceptable potent activity according to the DTP-NCI and were further evaluated in the NCI five doses assay. To validate our design, compounds with the highest mean growth inhibition percent were screened against the target PI3Kα and B-Raf_V600E to confirm their multi-kinase activity. The tested compounds showed promising multi-kinase activity. Compounds 17 and 22c anticancer effectiveness and multi-kinase activity against PI3Kα and B-Raf_V600E were consolidated by the inhibition of B-Raf_WT, EGFR and VEGFR-2 with IC₅₀ in the sub-micromolar range. Further investigations on the most potent compounds 17 and 22c were carried out by studying their safety on normal cell line, in silico profiling and predicted ADME characteristics.

Full text of DOI:10.1016/j.bioorg.2020.104569

Bioorganic Chemistry 107 (2021) 104569
Contents lists available at ScienceDirect
Bioorganic Chemistry
journal homepage: www.elsevier.com/locate/bioorg
Design, synthesis and in silico insights of new
7,8-disubstituted-1,3-dimethyl-1H-purine-2,6(3H,7H)-dione derivatives
with potent anticancer and multi-kinase inhibitory activities
,
,
,
,d
Abdalla R. Mohameda *, Ahmed M. El Kerdawyb c, Riham F. Georgeb *, Hanan H. Georgeyb
,
Nagwa M. Abdel Gawadb
a Pharmaceutical Chemistry Department, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo 11829, Egypt
b Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
c Department of Pharmaceutical Chemistry, Faculty of Pharmacy, New Giza University, New Giza, km 22 Cairo–Alexandria Desert Road, Cairo, Egypt
d Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Heliopolis University for Sustainable Development, Cairo 11777, Egypt
A R T I C L E I N F O
A B S T R A C T
Keywords:
Anticancer
Xanthine
Aiming to obtain an efficient anti-proliferative activity, structure- and ligand-based drug design approaches were
expanded and utilized to design and refine a small compound library. Subsequently, thirty-two 7,8-disubstituted-
1,3-dimethyl-1H-purine-2,6(3H,7H)-dione derivatives were selected for synthesis based on the characteristic
pharmacophoric features required for PI3K and B-Raf oncogenes inhibition. All the synthesized compounds were
evaluated for their in vitro anticancer activity. Compounds 17 and 22c displayed an acceptable potent activity
according to the DTP-NCI and were further evaluated in the NCI five doses assay. To validate our design,
Multi-kinase targeting
B-Raf
PI3K
compounds with the highest mean growth inhibition percent were screened against the target PI3K
α and B-
RafV600E to confirm their multi-kinase activity. The tested compounds showed promising multi-kinase activity.
Compounds 17 and 22c anticancer effectiveness and multi-kinase activity against PI3Kα and B-RafV600E were
consolidated by the inhibition of B-RafWT, EGFR and VEGFR-2 with IC50 in the sub-micromolar range. Further
investigations on the most potent compounds 17 and 22c were carried out by studying their safety on normal cell
line, in silico profiling and predicted ADME characteristics.
1. Introduction
phosphorylation of phosphatidylinositol 4,5-bisphosphate to phospha-
tidylinositol 3,4,5-trisphosphate initiating a wide range of RTKs- and
Cancer is one of the leading causes of death worldwide accounting
for estimated deaths of 9.6 million in 2018 [1]. Discovering new anti-
cancer agents remains a critical challenge to overcome many tumor- and
drug-related obstacles such as side effects, systemic toxicity, and drug
resistance [2]. A general phenomenon in tumor formation is the step-
wise accumulation of genetic information changes (mutations) [3].
Several receptor tyrosine kinase (RTK) inhibitors were approved by the
FDA for treating several malignancies. However, due to many resistance
mechanisms, numerous RTK inhibitors are facing acquired resistance
and deficiency in durable efficacy [4,5]. For instance, it was reported
that hyperactivation of PI3K/AKT/mTOR signaling is often associated
with resistance to EGFR mediated endocrine chemotherapy, and other
forms of targeted therapy [6].
Ras-associated signal transduction cascades activating the oncogene Akt
and subsequently a huge number of downstream signaling events
including mammalian target of rapamycin (mTOR) activation [7]. PI3K/
Akt/mTOR pathway regulates fundamental cellular functions including
transcription, translation, proliferation, growth and survival. The
cascade was found to be dysregulated almost in all human cancers [8].
Activation of tyrosine kinase growth factor receptors or oncogenes up-
stream, loss or inactivation of the tumor suppressor PTEN (phosphatase
and tensin homolog deleted on chromosome 10), mutation and/or
amplification of PI3Ks themselves are accounting for PI3K pathway
dysregulation in a wide spectrum of human cancers [9].
The crystal structures of PI3Kγ co-crystalized with several diverse
PI3K inhibitors show common binding interactions at the ATP binding
site and the affinity pocket. These involve a hydrogen bond acceptor
PI3K family,
a lipid kinase family, is responsible for the
* Corresponding authors.
E-mail addresses: abdallaharafa@eru.edu.eg (A.R. Mohamed), riham.eskandar@pharma.cu.edu.eg (R.F. George).
https://doi.org/10.1016/j.bioorg.2020.104569
Received 25 October 2020; Received in revised form 13 December 2020; Accepted 16 December 2020
Available online 30 December 2020
0045-2068/© 2020 Elsevier Inc. All rights reserved.

A.R. Mohamed et al.
Bioorganic Chemistry 107 (2021) 104569
interaction with the hinge region Val882, and both a hydrogen-bond
on the previous approaches, using privileged structures and followed by
diverse screening, as reported for efficient lead acquirement [43]. This
was achieved through several substitutions at N-7 of the privileged 1,3-
dimethyl-2,6-purine-dione scaffold. Substitution at N-7 with benzyl
derivatives was relied on the platform of B-RafV600E mutant inhibitor
(XVII, Fig. 3B) [41,42] to afford the aimed hybrid (XIX, Fig. 3C).
Furthermore, the presence of the amide fragment, between the aryl and
N-7 methylene, affording the phenylacetamide derivatives, offers the
hydrogen bond donor and/or acceptor required for the interaction with
the target kinases. Many substitutions were explored at the phenyl-
acetamide side chain, which allowed different electronic and lipophilic
environments, rigidification and expansion of the molecular structure
(Fig. 3C).
donor with Asp841, Asp836, Asp964 and/or
a hydrogen-bond
acceptor with Lys833, Tyr867 in the affinity pocket [10–15]. The
collaboration of high-throughput screening (HTS) and structure-based
design have led to the discovery of a large set of diverse PI3K in-
hibitors (e.g., compounds I-IX, Fig. 1A) [10–18]. Furthermore, it was
found that purine ring is employed as a well-accommodated scaffold in
the development of the dual pan-PI3K/mTOR inhibitor, compound VS-
5584 VI, which was identified by using structure- and ligand-based
design. Additionally, it is involved in PI3K inhibition by strengthen
the hinge region interaction at the ATP binding site (Idelalisib VII)
[15,16].
Nevertheless, the encountered limitations of PI3K inhibitors that are
ranging from severe and occasionally fatal side effects to the adaptive
resistance and activation of compensatory pathways, are still a great
challenge to deal with [19,20]. These limitations are well reflected in
the decreased number of approved PI3K inhibitors despite of the PI3K
boosted functionality in malignancy. Moreover, it was reported that the
inhibition of the PI3K/Akt/mTOR cascade alone does not increase
apoptosis in NPA melanoma cells unless the cells are lacking B-Raf
expression or were treated with B-Raf inhibitor, where, the promoted
apoptosis is mediated through MEK/ERK-independent manner [21].
B-Raf functions in the linear Ras-Raf-MEK-ERK mitogen activated
protein kinase (MAPK) pathway [22]. Uncontrolled cellular signaling
due to oncogenic mutation in MAPK cascade members has been
considered among the most common mutations in human cancers [23].
B-Raf inhibitors show general binding interaction over the gate area
Substitutions at C-8 (X-Y, Fig. 3C) were relied on fragments from
high throughput screening results such as compound V; the imidazo
tricyclic structure with pyrimidine side chain (Fig. 1A), and also based
on the crystallographic information that led to identification of a highly
potent kinases inhibitors such as the sulfonamide derivative compound
XIV (Fig. 2) [14,38,44]. Additionally, the x-ray crystal structure of
sorafenib X bound to B-RafWT that extends over the key regions (Fig. 3D)
[45]. Subsequently, further interactions at the affinity pocket and the
hinge region of PI3K were provided, and further interactions at the gate
area of B-Raf were explored. Diversity of moieties at N-7 and C-8 in-
vestigates binding interaction at both targets regions together with 2/6-
carbonyl oxygen or N-9 of purine (Compiled library segments, Molecular
docking Supplementary Materials).
Because the construction of the compiled library was based on the
characteristics of two distinct targets (PI3K and B-Raf), two consecutive
filtration steps were applied, one step for each target. First filtration step
was based on the interpretation of the molecular docking data (binding
pattern and binding score) of the library members on PI3Kγ (PDB ID:
4GB9). An add-on pharmacophore filter was used on hinge region
Val882 and affinity pocket Lys833 during performing this docking
filtration step. 3D pharmacophore models are usually combined with
docking to reduce the number of candidate compounds for fairly com-
plex scoring calculations [34]. A second filtration step was achieved
using molecular docking in B-RafWT (PDB ID: 1UWH).
with Glu500 (Glu501 B-RafV600E) and Asp593 (Asp594 B-RafV600E
)
amino acids and in the hinge region with Cys531 (Cys532 and/or
Gln530 B-RafV600E).
The introduction of sorafenib X (Nexavar, Fig. 2), the multi-kinase
inhibitor (VEGFR1/2/3, CDK8 and B-Raf), was a breakthrough in the
treatment of hepatocellular carcinoma, advanced/metastatic renal cell
carcinoma and thyroid carcinoma [24]. However, It exhibits weak
antitumor activity in cells with mutant B-RafV600E and its clinical effi-
cacy in cancers with B-RafWT might be attributed to its multi-kinase
inhibition profile [25], which shed the light on multi-kinase inhibitors
as more efficacious alternative for drug combination [26]. The more
selective compounds towards the mutant B-RafV600E such as vemur-
afenib XI (Zelboraf) and dabrafenib XII (Tafinlar) are showing success in
melanoma harboring B-RafV600E (Fig. 2) [27,28]. However, they showed
minimal efficacy against tumors with wild-type B-Raf (B-RafWT) and can
accelerate the growth of Ras mutant tumors through paradoxical acti-
vation of Raf dimers. This vulnerability was manifested in the resistance
of B-RafWT phenotypic melanoma SK-MEL-2 cell line [29].
Compound selection from the promising set (survived the filtration
steps) was carried out such that to cover the different library segments to
be able to produce a fruitful SAR study. Noteworthy, some compounds
were chosen from the compiled library despite of their poor predicted
docking results to maintain the structural diversity in the chosen set of
compounds to obtain a comprehensive SAR results (Fig. 4). (For further
details see Molecular modeling section)
3. Results and discussion
2. Rational design of the target compounds
3.1. Chemistry
Several studies reported the potential activity of 1,3-dimethyl-1H-
purine-2,6(3H,7H)-dione derivatives (methylxanthines) on the molecu-
lar aspects of tumor cells and their growth [30–32]. The well-known
methylxanthine derivatives, theophylline and caffeine, possess the ca-
pacity to inhibit not only cell proliferation, but also the metastatic
behavior of melanoma cancer cells [33]. Subsequently, substitution at
N-7 and/or C-8 of xanthine ring attracted many researchers to identify
novel antitumor agents [34–37]. Generally, purine ring is the corner
stone in many potent PI3K inhibitors (VI-VIII, Fig. 1A) and B-Raf in-
hibitors (XIII and XIV, Fig. 2) [38,39]. Particularly, the 1,3-dimethyl-
xanthine derivative (XV, Fig. 3A) was reported to possess potent
The adopted synthetic pathways of the new 7,8-disubstituted-1,3-
dimethyl-1H-purine-2,6(3H,7H)-dione derivatives were illustrated in
Schemes 1-6. In Scheme 1, compounds 1–8 were synthesized according
to the reported methods using variety of reaction conditions [46–58]
with the exception of the new compound 4. Where, the thiazole ring
cyclization was achieved through reflux of 3f with thiourea in absolute
ethanol to produce 4, as reported by a similar reaction [59].
Scheme 2 depicted the synthetic strategies for the preparation of
compounds 9–11. Theophylline N-7 was alkylated with benzyl chloride
or 4-fluorobenzyl chloride to give compounds 9a and 9b, respectively,
via nucleophilic substitution reaction (SN2) utilizing the previously re-
ported conditions by our group [60]. Wherein, potassium carbonate was
used as a base with a catalytic amount of potassium iodide in DMF. On
the other hand, 6-(4-fluorophenyl)-4-oxo-2-thioxo-1,2,3,4-tetrahy-
dropyrimidine-5-carbonitrile 8b required strong basic conditions to
elaborate the free thiol and deprotonate it, which subsequently un-
dergoes nucleophilic aromatic substitution (SNAr) of compound 9b 4-
PI3Kα inhibitory activity [35]. Simultaneously, inspired by the scaffold-
and structure-based drug design approaches that were introduced by
Card, G. L. et al [40], which were extended to discover vemurafenib XI
through compounds XVI-XVIII (Fig. 3B) over multi-steps of sub-
structural motif identification for the oncogenic B-Raf inhibition
coupled with engineered co-crystallography [41,42].
In the current work, a small compound library was compiled relaying
2

A.R. Mohamed et al.
Bioorganic Chemistry 107 (2021) 104569
A
B
Fig. 1. A; Structures of representative PI3K inhibitors, with respect to PI3Kγ, atoms that make hydrogen bond interactions with the hinge region are illustrated by the
green squares and those that make hydrogen bonds with the affinity pocket are illustrated with blue circles. B; Representative diagram shows the general features of
PI3K inhibitor’s H-bond interactions on gamma isoform. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of
this article.)
3

A.R. Mohamed et al.
Bioorganic Chemistry 107 (2021) 104569
F
F
N
H
F
O
S
S
N
O
Cl
O
N
O
Cl
F
O
O
O
N
S
N
H
N
F
N
H
F
O
N
N
N
F
F
H
H
N
H2N
H
XII, dabrafenib, (Tafinlar)
X , sorafenib (Nexavar)
XI, vemurafenib (PLX4032)
Cl
N
NH
F
N
N
O
O
S
N
N
H
N
O
H
N
H
F
N
N
N
N
H
N
H
N
N
XIII
XIV, INU152
Fig. 2. Structures of representative B-Raf inhibitors.
fluorophenyl using sodium hydride in DMF at relatively high reaction
temperature to give compound 10. 1H NMR spectrum of compound 10
showed the additional aromatic signals at range 7.18–8.28 ppm and NH
exchangeable proton at 11.85 ppm. 13C NMR spectrum also revealed the
presence of a cyanide carbon at 115.9 and additional aromatic signals at
the range of 117.9–165.3 ppm, additional carbonyl signal at 168.6 ppm
reaction to give 15. Furthermore, sulfadiazine primary amine was
alkylated with the chlorinated derivative (15) using sodium hydride in
DMF to produce compound 16. Reaction of 6-aminouracil with 11a C-8
bromo group required an optimization of the medium pH to direct the
nucleophic attach through its primary amine, thus, sodium acetate as a
base in acetic acid prevented the de-protonation of uracil NHs, and
produced 17.
–
and disappearance of C S normally present at 175–180 ppm [61].
–
Compounds 9a and 9b were further brominated at C-8 using NBS in DMF
to produce 11a and 11b, respectively, which were confirmed by the
disappearance of C-8 purine proton signal (8.57 ppm) in their 1H NMR
spectra.
In the same context, Scheme 4 presented aromatic nucleophilic
substitution of 11a and 11b C-8 bromo group with 6-aminothiouracil
thiol group to produce 18a and 18b, respectively. The reaction was
performed using DMAP as a base in DMF, which produced optimally the
desired product in term of selectivity. Similarly to compound 10, com-
pounds 19a and 19b were afforded by reacting the thiol group of the
appropriate 4-oxo-6-phenyl-2-thioxo-1,2,3,4-tetrahydropyrimidine-5-
carbonitrile derivative 8b and 8c, respectively, with 11b C-8 bromo
group using sodium hydride in DMF, with manipulating the reaction
temperature from 0 to 80 ◦C to prevent the fluoro substitution (4-fluo-
rophenyl at N-7), which it seems easier. Interestingly, the reaction at C-8
needed lower reaction temperature compared to the 4-position of the
benzyl moiety at N-7 which could be due to steric considerations.
Scheme 5 depicted the synthesis of compounds 20–29. The 2-chloro-
N-arylacetamide derivative 3c alkylated theophylline at N-7 to afford
compound 20 according to the same previously mentioned condition to
produce compounds 9a and 9b [60,66]. Moreover, 8-bromotheophyl-
line 21 was prepared according to the reported procedure from
theophylline [67], and was subsequently alkylated at N-7 with 2-chloro-
N-arylacetamide derivatives 3a-f using potassium carbonate as a base in
DMF at room temperature to obtain compounds 22a-f, respectively
[60,66]. Compounds 22a-f were then used as premises to give the target
compounds (23–27) by aromatic nucleophilic substitution of C-8 bromo
group with amine or thiol groups of key intermediates or reagents. These
reactions produced their products exploiting their previous congener’s
strategies, taking into consideration the presence of N-7 acetamide
fragment. Wherein, compounds 22e and 22f were reacted with (1,1-
dioxo-1,2-benzothiazol-3-yl)amine 2 to give 23a and 23b, respectively,
using sodium hydride in DMF at lower reaction temperature compared
to the reaction that afforded 12a,b (utilizing potassium carbonate and
DMAP). Aniline derivatives (sulfanilamide and 4-fluoroaniline) were
also reacted with 22e and 22f under the same reaction condition to yield
24a and 24b, respectively. Additional stirring time at room temperature
In general, aromatic nucleophilic substitutions of bromo at C-8 of N-7
substituted xanthines with different secondary amines [62], or primary
aliphatic amines [63], were performed in DMF using potassium car-
bonate as a base. We directed our effort towards optimization of the
basic condition to overcome the decreased nucleophilicity of in-
termediates primary amines (2, 4, 7, 6-aminouracil and aniline de-
rivatives); due to aromaticity or being adjacent to
π bond. At the same
time, the stabilization of the produced secondary amine at C-8 could
drive the reaction forward.
In Scheme 3, substitution of the bromo substituent on 11C-8 with
different intermediates primary amines was achieved. Compounds 12a
and 12b were synthesized by substitution of the bromo substituent on
11a and 11b C-8 with the primary amine of (1,1-dioxo-1,2-benzothia-
zol-3-yl)amine 2 under basic conditions afforded by potassium carbon-
ate and catalytic amount of 4-dimethylaminopyridine (DMAP) in DMF.
1H NMR spectra showed the additional aromatic and NH signals at
7.09–8.21 ppm, and 13C NMR spectra also revealed the additional aro-
matic signals at δ 99.7–138.9 ppm.
DMAP produced better results as a base with 4-(2-aminothiazol-5-
ylamino)benzenesulfonamide 4 in DMF to afford compound 13, which
could be attributed to the suitability of the produced PKa (DMAP-PKa =
9.7) for intermediate 4 solubilization or the accessibility of DMAP to the
reaction desired nucleophile [64,65]. Compound 14 was readily affor-
ded by reaction of (Z)-2-(2-oxoindolin-3-ylidene)hydrazinecarbothioa-
mide 7 with 11a using potassium carbonate in DMF. As a more reactive
nucleophile, the primary amine of 2-chloroethylamine HCl utilized a
milder basic condition using triethylamine in DMF to neutralize the HCl
and initiate the aromatic substitution of 11a C-8 bromo group, which
was followed by addition of potassium carbonate for termination of
4

A.R. Mohamed et al.
Bioorganic Chemistry 107 (2021) 104569
Fig. 3. Demonstration of the aimed approach. A; Compound XV. B; Development of vermurafenib and its binding interactions at B-RafV600E (PDB: 3OG7). Sky blue
illustrates the hybridization between PI3Kα inhibitor XV (A) and XVII (B). C; Chemical structures of the designed library segments (XIX-XXII), showing the putative
sites of binding interactions (dashed circular lines) at both targets (PI3K and B-Raf). D; Binding interactions of sorafenib at the different regions of B-RafWT (PDB:
1UWH). (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
was required for the reaction termination without the degradation or
side reaction of N-7 N-phenylacetamide group. Compounds 25 and 26
were prepared by the reaction of compound 22f with 6-aminouracil and
6-aminothiouracil, respectively, using the same conditions that were
used to afford compounds 17 and 18. Similar to its reaction with com-
pound 11b, the thiol group of 8a substituted 22e and 22f C-8 bromo
group to give 27a and 27b, respectively, in a slightly better yield, using
sodium hydride in DMF with modulation of the reaction temperature.
Several reports addressed the cyclization utilizing N-7 and C-8 of 8-
bromotheophylline 21 to produce tricyclic derivatives [68–70]. The
tricyclic imidazo[1,2-f]purine derivative 28 was afforded by the de-
protonation of the acetamide NH at N-7 of the reported compound
22a [60,66] what needed a careful gradual heating in DMF in the
presence of a strong base such as sodium hydride. Subsequently, an
intramolecular aromatic nucleophilic substitution of the C-8 bromo
group was achieved and followed by a ketone to enol tautomeric shift at
C-7. Therefore, compound 28 IR spectrum showed an OH band at 3383
cmꢀ 1. Furthermore, its 1H NMR spectrum revealed the disappearance of
the CH2 protons’ singlet signal and the exchangeable NH signal at 5.10
and 9.00 ppm, respectively. Meanwhile, it showed the presence of a
singlet signal at 9.43 ppm corresponding to the imidazole-H, and an
exchangeable signal at 11.90 ppm corresponding to the OH group.
5

A.R. Mohamed et al.
Bioorganic Chemistry 107 (2021) 104569
3.2. In vitro anticancer screening
All the newly synthesized 7,8-disubstituted-1,3-dimethyl-2,6-purine-
dione derivatives (thirty two compounds) were submitted and selected
to be examined for their antitumor activity at the NCI Developmental
Therapeutic Program (DTP), Bethesda, Maryland, USA, in accordance
with the drug evaluation branch protocol [72]. NCI cytotoxic activity
evaluation was followed by an investigation of the normal human
diploid fibroblasts (WI-38) cell line cytotoxicity, for compounds that
were selected for NCI five dose assay.
3.2.1. Growth inhibition % (in vitro single dose, 10 µM, screening)
Firstly, the novel thirty two compounds were in vitro screened in a
primary one dose (10 μM) against NCI-panel of 60 human cancer cell
lines. This panel is comprised of nine subpanels of leukemia, non-small
cell lung carcinoma (NSCLC), melanoma, and colon, CNS, ovarian,
renal, prostate, and breast cancers. Results are reported as mean-graph
of the percent growth relative to control and presented as percentage
growth inhibition (GI%, Tables 1 and 2, Supplementary Materials).
Furthermore, mean GI% of each compound in all panel cell lines is
presented in Fig. 5.
Investigation of the primary GI% data revealed that compound 17
exerted the highest activity among the newly synthesized 7-benzyl-1,3-
dimethyl-1H-purine-2,6(3H,7H)-dione derivatives (10-19a,b) with
mean GI of 41%. Compound 17 showed potent GI% and broad-spectrum
activity over all NCI subpanels except leukemia. It exhibited lethality
(100% GI or more) against COLO 205 and HT29 colon cancer cell lines,
SNB-75 CNS cancer cell line, MDA-MB-435 and SK-MEL-2 melanoma
cell lines, OVCAR-3 ovarian, A498 renal, and HS 578 T breast cancer cell
lines. Replacement of the 2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yla-
mino substitution at C-8 of compound 17 confined the activity mainly
to renal cancer cell lines (Table 1, Supplementary Materials). This is
demonstrated in compound 14 with indolin-2-one substitution at C-8
and a hydrazinecarbothioamide spacer, and compound 16 with a sul-
fadiazine moiety and an ethylamine spacer at the same position with
mean GI of 12 and 5%, respectively.
Fig. 4. Flow chart demonstrates the crucial steps that are driving to the syn-
thesized candidates.
Furthermore, 13C NMR spectrum also confirmed the disappearance of
the CH2 signal.
The N-phenylacetamide derivatives (22b-e) underwent the same
reaction conditions that were used to give 28, and subsequently reacted
with compound 8a in the same pot to produce 29a-d, respectively. The
thiol group of compound 8a was found to be capable of replacing the in
situ produced tertiary hydroxyl group under the basic condition of so-
dium hydride and DMF at relatively high temperature. This reaction
could be afforded by Newman–Kwart rearrangement [71]. Similar to
compound 28, compounds 29a-d revealed the disappearance of signals
relative to CH2 in 1H NMR, 13C NMR and DEPT-135 spectra (29b), in
addition to the presence of aromatic (include the imidazole-H) and
exchangeable protons corresponding to the 6-oxo-4-phenyl-1,6-dihydro-
pyrimidine-5-carbonitrile substitution in their 1H NMR spectra at ranges
On the other hand, replacement of N-7 benzyl side chain with N-
phenylacetamide, together with a bromo substitution at C-8, which was
investigated in a previous work [66], resulted in interesting findings.
The 4-tolyl congener with a C-8 bromo substituent, compound 22c,
showed the highest anticancer activity in this study (mean GI of 79%).
Replacement of the 4-methyl moiety with a 2,4-dichloro (22d) or a 4-
acetyl (22e) substituents resulted in a rather moderate growth inhibi-
tion. Removal of bromo at C-8 of 22c (compound 20) revealed a com-
plete loss of growth inhibition activities, which indicates the
significance of C-8 bromo for the anti-proliferative activity.
of 7.22–8.81 and 10.00–12.31 ppm, respectively. 13C NMR spectra also
The tricyclic imidazo[1,2-f]purine derivatives combined with a 6-
–
oxo-4-phenyl-1,6-dihydropyrimidine-5-carbonitrile
moiety
(com-
–
showed the presence of C N signal (115.8–119.2 ppm), additional ar-
–
–
–
pounds 29a-d) revealed a promising cytotoxic activity. The 2,4-dichloro
congener 29c showed broad and potent cytotoxic activity with mean GI
of 53%, and with the highest GI% per subpanel on CCRF-CEM (leuke-
mia; 52%), NCI-H460 (NSCLC; 86%), HCT-116 (colon cancer; 81%),
SNB-75 (CNS cancer; 106%), LOX IMVI (melanoma; 67%), OVCAR-4
(ovarian cancer; 133%), UO-31 (renal cancer; 102%), DU-145 (pros-
tate cancer; 49%), HS 578 T and T-47D (breast cancer; both are 89%)
cell lines (Table 2, Supplementary Materials). This again highlights the
significance of lipophilicity on SAR, together with structural confor-
mation; 29c mean GI% surpassed both of 2,4-dichlorophenylacetamide
derivative (22d) and other compounds bearing 6-oxo-4-phenyl-1,6-
dihydropyrimidine-5-carbonitrile moiety (19a,b and 27a,b), Fig. 5.
omatic and C O signals (91.3–171.5 and 156.0–168.7 ppm, respec-
tively). Their IR spectra revealed the presence of bands at the range of
2214–2218 cmꢀ 1 due to C N group.
–
–
–
Otherwise, Scheme 6 outlined the N-7 alkylation of 8-bromotheo-
phylline 21 with 2-chloro-N-(naphthalen-1-yl)acetamide 5 and 2-
chloro-1-(indolin-1-yl)ethanone 6 to produce 30 and 31, respectively,
using potassium carbonate in DMF (the same condition used to afford
22a-f) [60,66]. It is worth noting that the absence of the NH (N-phe-
nylacetamide) greatly enhanced the compound 31 yield (88% versus
49–70% of their acetamide derivatives). According to the previously
mentioned conditions to produce compounds 23a, 23b and 26, (1,1-
Dioxo-1,2-benzothiazol-3-yl)amine
2 and 6-aminothiouracil were
substituted compound 31C-8 bromo group by their primary amine and
thiol groups, respectively, to give compounds 32 and 33, respectively.
3.2.2. In vitro five-dose assay on full NCI-60 cell line panel
The preliminary screening results revealed that compounds 17 (NSC:
D ꢀ 821,302 / 1), 22c (NSC: D ꢀ 821,290 / 1) and 29c (NSC: D-823294
/ 1) showed prominent mean GI% (Fig. 5). Compounds 17 and 22c were
selected by the NCI for further evaluation, owing to their acceptable
6

A.R. Mohamed et al.
Bioorganic Chemistry 107 (2021) 104569
O
Cl
N
H2N
N
(a)
Cl
(b)
HN
S
S
S
O
O
O
O
O
O
1
2
sacharin
O
R1
-H
Compound
R
-H
-H
-H
-Cl
Cl
R1
R1
O
2-chloroacetyl chloride
(c) or (d)
3a
3b
3c
3d
Cl
N
H
H2N
R
aniline derivatives
-F
R
3a-f
-CH3
S
O
S
H2N
thiourea
(e)
NH2
NH2
O
S
-Cl
O
NH2
O
N
O
O
Cl
N
H2N
3e
3f
-H
-H
S
N
H
H
3f
4
O
O
NH2
S
Cl
O
Cl
O
NH2
Cl
2-chloroacetyl chloride
(f)
NH
naphthamine
5
O
Cl
Cl
O
H
N
2-chloroacetyl chloride
(g)
Cl
N
6
indoline
S
H2N
H
N
NH2
N
H
N
H
O
thiosemicarbazide
O
N
(h)
HN
O
H2N
S
isatin
7
Compound
R2
-H
O
N
8a
8b
8c
NH2
(i)
O
O
HN
N
+
+
S
NH2
-F
R2
O
S
N
H
thiourea
ethyl 2-cyanoacetate
benzaldehyde derivatives
-OCH3
R2
8a-c
Scheme 1. Synthesis of compounds 1–8, reagents and conditions: (a) PCl5, reflux 180 ◦C, 1 h; (b) ammonia, ethanol, r.t., 24 h; (c) 2 N NaOH, CH2Cl2, r.t.,1h (3a-c);
(d) DMF, TEA, r.t., 24 h (3d-f); (e) ethanol, reflux, 12 h; (f) 2 N NaOH, CH2Cl2, r.t.,1h; (g) DMF, TEA, r.t., 24 h; (h) ethanol, acetic acid, reflux, 2 h; (i) K2CO3, ethanol,
reflux, 8 h.
criteria and their anti-proliferative activities according to the Develop-
mental Therapeutic Program (DTP), at five-dose assay (0.01–100 µM).
The calculated response parameters for both compounds along with
sorafenib X , as reference standard [73], are the GI50 (50% growth in-
hibition), TGI (total growth inhibition; total cytostatic effect) and LD50
(lethal dose for 50% of cells; LC50) against 60 cell lines (Table 3, Sup-
plementary Materials). They were determined according to the estab-
lished NCI protocols [72], and the GI50 values were presented in Table 1.
The purinedione and pyrimidinedione hybrid, compound 17,
showed distinctive anti-proliferative activity against several cell lines
from different subpanels; leukemia (RPMI-8226; GI50 of 15.9 µM),
NSCLC (HOP-92; GI50 of 7.51 µM), CNS (SNB-75; GI50 of 12.5 µM) and
renal (A498; GI50 of 7.97 µM) cell lines, Table 1. Moreover, it showed
non-significant cytostatic activity and lethality toward all cell lines (TGI
and LD50 > 100 µM, Supplementary materials). Meanwhile, the puri-
nedione and tolylacetamide crossbred, compound 22c, showed a potent
growth inhibition at a single digit micromolar concentration against 43
cell lines belonging to various subpanels, Table 1.
Concerning the cytostatic and lethal (TGI and LC50) effects, com-
pound 22c was found to be superior over sorafenib on 18 and 26 cell
lines, respectively. Interestingly, OVCAR-4 ovarian cell line was 5 and
10 times more sensitive to 22c than sorafenib, regarding TGI and LC50
(4.57, 9.93 µM vs 23.17, 100.00 µM of sorafenib, respectively). In
addition, compound 22c was nearly 2.5 times more cytostatic active and
lethal than sorafenib (TGI = 9.59 µM and LC50 = 30.20 µM) on CNS
(SNB-75) with TGI and LC50 of 3.95 and 12.10 µM, respectively (Table 3,
7

A.R. Mohamed et al.
Bioorganic Chemistry 107 (2021) 104569
S
R
O
N
F
N
O
N
O
N
H
N
(a)
(b)
HN
N
N
N
N
N
N
N
O
N
O
O
O
N
theophylline
10
9 a,b
Compound
R
9a
9b
H
F
(c)
R
O
N
Compound
11a
R
-H
-F
N
N
N
Br
O
11b
11a,b
Scheme 2. Synthesis of compounds 9–11, reagents and conditions: (a) benzyl chloride or 4-fluorobenzyl chloride, K2CO3, KI, DMF, 80 ◦C, 6 h; (b) 9b, 8b, NaH, DMF,
120 ◦C, 24 h; (c) NBS, DMF, 90 ◦C, 8 h.
R
O
N
O
N
R
O
N
N
N
N
N
N
N
(a)
(f)
NH
O
NH
N
N
N
N
NH
NH
Br
O
O
O
O
S
O
Compound
12a
R
O
11a,b
12a,b
17
-H
-F
(b)
(d)
12b
(c)
O
O
N
O
N
N
NH2
N
N
NH
N
S
NH
N
O
S
O
N
O
N
Cl
N
H
O
15
13
N
N
N
(e)
O
NH
S
NH
N
O
N
NH
O
N
14
N
N
N
NH
N
O
N
O
HN
16
S
NH
O
Scheme 3. Synthesis of compounds 12–17, reagents and conditions: (a) 11a,b, 2, K2CO3, DMAP, DMF, 100 ◦C, 16 h; (b) 11a, 4, DMAP, DMF, reflux 80–90 ◦C, 6 h;
(c) 11a, 7, K2CO3, DMF, 70 ◦C, 10 h; (d) i- 11a, 2-chloroethylamine HCl, TEA, DMF, 50–60 ◦C, 2 h, ii- K2CO3, 70 ◦C, 8 h; (e) sulfadiazine, NaH, DMF, 80 ◦C, 12 h, (f)
11a, 6-aminouracil, NaOAc, acetic acid, 90 ◦C, 16 h.
Supplementary Materials).
GI50 (SI = 0.32–1.98, Table 4, Supplementary Materials). Renal,
ovarian, CNS and breast cancer subpanels were the most sensitive with
MG-MID of 2.78, 4.27, 5.28 and 5.67 µM, respectively. The greatest
activity of 22c toward the influenced cell lines were NSCL (HOP-92,
NCI-H226), CNS (SF-539, SNB-75), ovarian (OVCAR-4, SK-OV-3) and
renal (A498, UO-31) with GI50 ranging from 1.43 to 2.15 µM. Moreover,
As indicated from selectivity index conception [74], which calcu-
lated by dividing the full panel MG-MID (µM) of compounds by their
individual subpanel MG-MID (µM) which giving an average activity over
individual subpanels, compound 22c exhibited a non-selective broad
spectrum anticancer activity against all tumor subpanels with respect to
8

A.R. Mohamed et al.
Bioorganic Chemistry 107 (2021) 104569
F
R
O
N
O
N
R
N
O
N
N
N
N
S
HN
O
(a)
(b)
S
HN
O
N
N
N
N
N
O
Br
N
O
N
R1
NH2
O
11a,b
N
18a,b
19a,b
Compound
11a
R
-H
-F
Compound
18a
R
-H
-F
Compound
19a
R1
-F
11b
18b
-OCH3
19b
Scheme 4. Synthesis of compounds 18 and 19, reagents and conditions: (a) 6-aminothiouracil, DMAP, DMF, reflux 80–90 ◦C, 8 h; (b) i- 11b, 8b,c, NaH, DMF, r.t.,
24 h, ii- 80 ◦C, 10 h.
compound 22c showed activity overcoming sorafenib (regarding GI50
)
3.3.2. In vitro B-RafWT, EGFR and VEGFR-2 inhibitory activity screening
The combined results of the anti-proliferative activity and enzymatic
inhibitory activity of compounds 17 and 22c, encouraged further
investigation for their in vitro effect on B-RafWT. Moreover, further
evaluation of their inhibitory activity toward EGFR and VEGFR-2 was
performed to study the effect of both of them on structurally related RTK
(see the Molecular Docking section).
on ten cell lines, attributed descendingly to renal, ovarian and CNS
cancer.
3.2.3. In vitro cytotoxicity toward human normal lung WI-38 cell line
It was reported that PI3K and B-Raf kinases are identified as having a
key role in the pathogenesis of various forms of human cancer, including
lung cancer [75,76]. Compounds 17 and 22c were further evaluated for
their cytotoxic effect against WI-38 lung cell line, as representative for
normal human cells, to investigate their general safety and selectivity
toward tumor cells using the MTT assay [77]. Sorafenib was used in this
test as an example for a safe approved targeted chemotherapy.
Table 2 showed that both compounds 17 and 22c demonstrated non-
significant cytotoxic effect toward WI-38 cell line compared to sorafenib
X.
As illustrated in Table 4, compounds 17 and 22c showed inhibitory
activity exceeding that of sorafenib X against B-RafWT (sub-micromolar
range). Furthermore, their activity on EGFR and VEGFR-2 completed
envisage of their multi-kinase inhibitory activity. Their broad multi-
kinase activities justified their potent efficacy toward the different
cancer cell lines such as NSCLC and CNS cancer.
Compound 22c is surpassing compound 17 in cellular efficiency
(Table 1) despite their comparable sub-micromolar kinases inhibitory
activities (Tables 3 and 4). This could be rationalized by the superiority
of compound 22c over compound 17 concerning the optimum lip-
ophilicity/hydrophilicity balance (logPo/w and TPSA values) as demon-
strated by the presence of compound 22c in the center of HIA region in
the BOILED-EGG plot and by its location in the pink area of the
bioavailability radar chart (Predicted ADME, Supplementary Materials).
3.3. Multi-kinase inhibitory activity evaluation
3.3.1. In vitro PI3Kα and B-RafV600E inhibitory activity screening
According to the anti-proliferative activity of the newly synthesized
compounds, 14, 16, 17, 19a, 22c, 29a-c and 30 override the remaining
congener derivatives activity on the NCI 60 cell lines, with mean GI%
ranged from 5 to 79%. To study the aimed approach regarding these
3.4. Molecular modeling
candidates, in vitro inhibitory activity on PI3Kα and the mutant B-Raf (B-
RafV600E) were assessed and reported in Table 3.
Molecular Operating Environment (MOE 2010.10) software package
was used for performing all the molecular docking studies and the 3D
diagrams were generated by using UCSF Chimera software [78,79].
As seen in Table 3, all the tested compounds showed potent inhibi-
tory activity in the nanomolar range against PI3Kα. Compound 14, with
2-(2-oxoindolin-3-ylidene)hydrazinecarbothioamide at C-8 purine
along with N-7 benzyl, was the most potent inhibitory on PI3K with
α
3.4.1. Compiled library filtration (selection stage)
IC50 of 8.46 nM. The increased hydrophobicity of phenylacetamide side
chain at N-7 along with C-8 bromo substituent that were represented in
compounds 30 and 22c, accounted for their high activity (IC50 = 9.76
and 10.3 nM, respectively). Whereas, N-phenylacetamide rigidification
into a tricyclic scaffold, in combination with the 6-oxo-4-phenyl-1,6-
dihydropyrimidine-5-carbonitrile moiety, decreased the inhibitory ac-
tivity except for the 4-tolyl congener (29b, IC50 = 10.8 nM).
The preliminary docking simulations were achieved with the aim of
filtering the compiled library segments and compounds (350 com-
pounds). Subsequently, the selected candidates for synthesis were sha-
ped into the two desired pathways (PI3K and B-Raf). Compounds’
selection was based on the previously mentioned criteria. Additionally,
structural diversity was imposed to study the effect of subtle changes in
chemical structure on the anti-proliferative activities.
On the other hand, all the tested compounds showed enhanced po-
tency with sub-micromolar range against mutant B-RafV600E. Compound
16, resembling dabrafenib XII [28], in inclusion of benzenesulfonamide
and pyrimidine moieties, was found to be the most active in term of B-
RafV600E inhibition (IC50 = 99.6 nM). Furthermore, compounds 22c,
29a, 30 and 17 exhibited a potent B-RafV600E inhibitory activity
exceeding that of sorafenib X (IC50 = 129.8–199.6 nM). It is worth
mentioning that compounds 22c and 17 were found to be the most
Docking protocols were validated by self-docking of each co-
crystallized ligand, then evaluation of the reproduced binding pattern
and the produced RMSD values between the docking pose and the co-
crystalized ligand experimental pose in each protein. These two simu-
lations successfully reproduced the binding pattern of the co-crystalized
ligand in PI3Kγ and B-RafWT binding sites with energy scores of ꢀ 13.38
and ꢀ 15.46 kcal/mol, respectively, and with RMSD of 1.112 and 0.754
Å, respectively. In addition, the docking poses reproduced all the key
interactions achieved by the co-crystallized ligands with the binding site
hot spots in PI3Kγ (Val882, Lys833) and B-RafWT (Glu500, Cys531 and
Asp593) [44,80].
correlated over the inhibitory activity of both targets (PI3K
RafV600E) along with their mean GI%.
α and B-
9

A.R. Mohamed et al.
Bioorganic Chemistry 107 (2021) 104569
R2
Compound
24a
R1
O
Compound
23a
R1
O
O
NH2
S
O
O
O
O
R1
O
N
NH2
NH2
23b
S
24b
S
-F
N
N
N
H
O
N
O
NH
O
O
O
O
R1
NH2
S
O
N
O
N
N
N
O
N
N
N
N
H
H
N
N
R2
NH
NH
24a,b
O
O
HN
O
N
S
O
NH
O
O
23a,b
25
(e)
(d)
(f)
O
O
NH2
S
O
O
O
N
O
R1
O
H
N
N
O
H
N
N
H
(g)
(b)
(c)
N
N
N
N
S
N
H
N
Br
N
N
Br
NH
N
R
O
N
O
O
N
N
N
O
O
N
Theophylline
(a)
21
H2N
22a-f
26
(j)
(h)
O
N
(i)
O
N
N
N
H
N
N
O
R1
O
O
N
N
O
N
H
N
O
N
20
OH
S
NH
N
N
N
N
N
O
N
N
HN
O
O
S
O
N
N
N
N
28
N
O
N
27a,b
R
R1
R1
-H
-F
Compound
22a
R
R1
29a-d
R
Compound
27a
-H
-H
-H
-Cl
R1
-F
Compound
29a
O
22b
-H
-CH3
22c
O
-CH3
29b
-H
NH2
22d
-Cl
O
27b
S
29c
-Cl
-Cl
O
O
22e
22f
-H
-H
29d
-H
O
NH2
S
O
Scheme 5. Synthesis of compounds 20–29, reagents and conditions: (a) 3c, K2CO3, KI, 80 ◦C, 8 h; (b) Br2, NaOAc, acetic acid, r.t., 24 h; (c) 3a-f, K2CO3, DMF, r.t., 24
h; (d) 22e,f, 2, NaH, DMF, 70 ◦C. 12 h; (e) i- 22e,f, sulfanilamide or 4-fluoroaniline, NaH, DMF, 70 ◦C, 8 h, ii- r.t., 24 h; (f) 22f, 6-aminouracil, NaOAc, acetic acid, 90
◦C, 10 h; (g) 22f, 6-aminothiouracil, DMAP, DMF, reflux 80–90 ◦C, 8 h; (h) i- 22e,f, 8a, NaH, DMF, r.t., 24 h, ii- 80 ◦C, 10 h; (i) 22a, NaH, DMF, 70–90 ◦C, 3 h; (j) i-
22b-e, NaH, DMF, 70–90 ◦C, 3 h, ii- 8a, 90 ◦C, 12 h.
The first filtration step of the designed library (350 compounds) was
based on satisfying the two key binding interactions on PI3Kγ (PDB ID:
4GB9) [44]. A set of 87 compounds survived this first filtration step. The
second filtration step relied on binding interactions of compounds to the
binding site of B-RafWT (PDB ID: 1UWH) [80], utilizing at least one key
binding interaction resulting in a set of thirty two compounds.
interactions utilizing the key amino acid Val882 residue through two H-
bonds with the carbonyl and NH groups of the uracil ring. In addition, it
shows an interaction in the affinity pocket between purine C-2 carbonyl
and the key amino acid Lys833 residue. Moreover, several hydrophobic
interactions directed different molecule fragments to fit properly in the
binding site; purine ring (Ile963, Ile831), terminal phenyl (Met804,
Met953) and uracil (Ala885, Trp812, Ile881 and Val882). (For further
details see Supplementary Materials, Fig. 8)
In PI3Kγ binding site, the N-7 benzyl derivatives 12a,b, 13, 14, 17,
18a,b, 19b showed a general binding pattern that is greatly imparted by
H-bond interactions through purine C-8 substitutions in the front cleft
(hinge region). For instance, compound 17 showed hinge region
This binding pattern was inverted upon the introduction of N-phe-
nylacetamide at purine N-7 in compounds 20, 22c-e, 23a,b, 24b, 25,
10

A.R. Mohamed et al.
Bioorganic Chemistry 107 (2021) 104569
O
N
H
N
(a)
NH
N
Br
O
O
N
O
N
N
Br
21
N
N
O
30
(b)
N
N
O
N
O
N
(d)
O
(c)
O
O
N
N
N
N
O
S
NH
N
N
N
N
NH
Br
O
N
O
N
N
O
N
O
N
S
O
O
H2N
31
32
33
Scheme 6. Synthesis of compounds 30–33, reagents and conditions: (a) 5, K2CO3, DMF, r.t., 24 h; (b) 6, K2CO3, DMF, r.t., 24 h; (c) 2, NaH, DMF, 70 ◦C, 12 h; (d) 6-
aminothiouracil, DMAP, DMF, 80–90 ◦C, 8 h.
27a,b and 30 such that the purine ring is fitted in the hinge region.
Therefore, in the docking simulation of 22c in PI3Kγ binding site, the
carbonyl group at purine C-2 formed H-bond with the key amino acid
Val882, and the acetamide moiety at N-7 is involved in H-bond inter-
action with the key amino acid Lys833. Purine ring maintained the
hydrophobic interactions with Ile963 and Ile831 residues, and addi-
tionally Ile879, Trp812, Ile881 and Val882 amino acids. (For further
details see Supplementary Materials, Figure 14)
3.4.2. Molecular docking of the selected hits from the NCI-60 panel
In order to study the binding characteristics of the best achievers on
NCI-60 panel which were selected for evaluation of their multi-kinase
inhibitory activity, 14, 16, 17, 19a, 22c, 29a-c and 30, they were
docked into the crystal structure of the target kinases; PI3Kα in complex
with alpelisib IX (NVP-BYL719, Piqray), PDB ID: 4JPS [81], and B-
RafV600E in complex with compound XIII, PDB ID: 3IDP [38].
Molecular docking protocol was initially validated by self-docking of
1H-Imidazo[1,2-f]purine derivatives (29a-d) achieved a H-bond
interaction with the key amino acid Lys833 utilizing purine N-9 (29b,c)
or pyrimidine side chain carbonyl group (29a,d). Different substitutions
at the directly attached phenyl ring at C-7 varied the H-bond interaction
with the hinge region amino acid Val882 to be switched between C-2
purine carbonyl group (29a), nitrile group (29b) or pyrimidine carbonyl
group (29c), and 4-acetylphenyl substitution (29d). Moreover, they
demonstrated hydrophobic interactions with the hydrophobic side chain
of the amino acids Ile879, Ile963, Ile831, Val882, Phe961, Met804,
Met953, Ala885, Trp812, Leu838 and Leu1090. (For further details see
Supplementary Materials, Figures 26–29)
the co-crystalized ligands in the binding sites of PI3Kα and B-RafV600E. In
PI3Kα, the docking pose reproduced the experimental binding pattern
and so the key interactions achieved by the co-crystallized ligand with
the binding site hot spots (Val851, Gln859) with energy score of ꢀ
11.05 kcal/mol and RMSD of 1.473 Å. In B-RafV600E, self-docking of the
co-crystalized ligand in the binding site reproduced the key interactions
with Glu501, Asp594 (gate area) and Cys532 (hinge region) with energy
score of ꢀ 14.66 kcal/mol and RMSD of 0.31 Å. (For further details see
Supplementary Materials)
Molecular docking in PI3Kα showed that the compounds bind in
different patterns according to their N-7 and C-8 substitutions (for
further details see Supplementary Materials). Except for the least active
compounds, 16, 19a and 29a which displayed key interactions with the
amino acids Val851 and/or Ser854, all the selected compounds showed
a key binding interaction with the amino acid Gln859 (which is reported
to be not conserved within the PI3K family), what imply the importance
Molecular docking in B-RafWT active site showed that for the ma-
jority of N-7 benzyl (12–19) and the tricyclic (29a-d) derivatives, C-8
and C-7 substitutions, respectively, are responsible for binding in-
teractions with the DFG-loop amino acid Asp593 and αC helix amino
acid Glu500. For instance, compound 17 is well accommodated in the
gate area through two H-bond interactions with Glu500 residue by its
NH at C-8 and uracil side chain NH. Moreover, the terminal phenyl and
uracil rings are involved in hydrophobic interactions with Val503 and
Leu513 residues. Interactions in the gate area with Glue500 and/or
Asp593 were also displayed by the acetamide fragment at N-7, as in
compound 22c which showed H-bond donor and acceptor at both resi-
dues, respectively. Moreover, its terminal phenyl ring maintained the
hydrophobic interactions with Val503, Leu504 and Leu596 residues
lining the hydrophobic back pocket. Additionally, its purine ring
exhibited hydrophobic interaction with Trp530, Ile462 and Val470
of the H-bond interaction with Gln859 for activity against PI3K
Molecular docking simulation of the most active compound on PI3K
14 revealed that purine N-9 accepted H-bond from the key amino acid
Gln859. The indolin-2-one terminal side chain displayed cation-
α [81].
α
π
interaction with the positively charged side chain of Lys853 residue.
Moreover, several hydrophobic interactions are achieved between the
purine ring with Ile932, Met922, Ile800, Trp780 residues and N-7 benzyl
ring with Val851 and Val850 residues. Furthermore, the thioamide
spacer formed an ionic interaction with His855 residue which could
rationalize the potent PI3Kα inhibitory activity of compound 14 (Fig. 6).
amino acids, in addition to
π-
π
stacking in the gate area with Phe594
This interaction represents a novel unique binding interaction which is
different from that of conventional PI3K inhibitors and so it could be
residue. (For further details see Supplementary Materials, Figures 41,
47)
considered in designing novel potent PI3Kα inhibitors [81].
11

A.R. Mohamed et al.
Bioorganic Chemistry 107 (2021) 104569
Table 1
Table 2
GI50 (50% growth inhibition) against full NCI-60 panel cell lines for compounds
In vitro cytotoxicity towards human normal WI-38 cell
line, expressed as mean growth inhibitory concentration
(IC50) values.
17, 22c and sorafenib X.
Cell line/Subpanel
17
22c
Sorafenib
Compound
a IC50 (µM)
GI50
(µM)
GI50
(µM)
GI50 (µM)
CCRF-CEM
HL-60(TB)
K-562
Leukemia
>100
>100
82.5
17.3
>100
18.5
27.9
3.25
8.96
5.61
10.7
2.83
1.9
2.16
1.61
2.84
2.90
1.46
3.05
2.93
2.50
1.91
1.60
1.90
1.79
2.81
2.32
2.14
2.18
3.03
1.74
2.47
2.19
1.57
2.75
2.52
1.64
1.63
3.43
2.96
2.10
1.64
2.15
2.16
1.77
1.83
2.64
1.53
2.15
1.69
2.61
2.94
3.51
2.94
2.96
2.54
2.29
3.36
2.26
2.80
2.86
3.37
2.36
4.40
2.57
2.04
3.34
2.80
1.26
17
24.9 ± 0.90
23.0 ± 0.83
14.5 ± 1.16
22c
MOLT-4
RPMI-8226
SR
>100
15.9
Sorafenib
a
>100
>100
56.6
Data were expressed as mean ± Standard error (S.E.)
A549/ATCC
EKVX
Non-Small-Cell Lung
Cancer
of three independent experiments.
HOP-62
HOP-92
NCI-H226
NCI-H23
NCI-H322M
NCI-H460
NCI-H522
COLO 205
HCC-2998
HCT-116
HCT-15
>100
7.51
bond is formed between the uracil ring substitution at C-8 and the key
amino acid Gln859. Moreover, bi-dentate H-bond interactions of both
the NH at C-8 and uracil ring NH with the key amino acid Val851 in the
hinge region. In addition, different molecule fragments are accommo-
dated in hydrophobic regions lining each of the purine ring (Il800,
Ile932 and Ile848), the uracil ring (Val851, Trp780), and the terminal
phenyl ring (Met772) (Fig. 8).
>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
12.5
2.07
6.31
3.68
3.39
9.27
5.57
15.5
2.43
12.2
13.8
13.6
13.5
8.31
9.84
1.94
7.92
1.43
2.26
6.27
2.33
5.98
9.32
13.4
11.4
2.31
13.9
11.1
5
Colon Cancer
Generally, molecular docking simulations in B-RafV600E indicated
resemblance to the binding patterns toward B-RafWT. Purine C-8 sub-
stitution of the N-7 benzyl derivatives is responsible for the binding
interaction in the gate area as H-bond donor or H-bond acceptor with
Glu501 and Asp594, respectively. Compounds 14 and 17 maintained
both interactions, while compounds 19a and 16 displayed H-bonding
interaction with Glu501 or Asp594, respectively. Compounds containing
an acetamide fragment at N-7 displayed the same interactions with
Glu501 and Asp594 (30) or with Glu501 only (22c). Fig. 9 represents
these patterns of binding interactions for 17 and 22c.
HT29
KM12
SW-620
SF-268
CNS Cancer
Melanoma
SF-295
SF-539
SNB-19
SNB-75
U251
>100
>100
>100
>100
>100
>100
>100
48
LOX IMVI
MALME-3 M
M14
The 4-tolyl and naphthyl moieties in compounds 22c and 30,
respectively, are fitted in the vicinity of the hydrophobic back pocket
amino acids Leu505, Val504 and Ile572, and involved in hydrophobic
interactions with the hydrophobic side chains of these amino acids.
MDA-MB-435
SK-MEL-2
SK-MEL-28
SK-MEL-5
UACC-257
UACC-62
IGROV1
OVCAR-3
OVCAR-4
OVCAR-5
OVCAR-8
NCI/ADR-RES
SK-OV-3
786–0
Furthermore, compound 22c achieves a cation-π interaction with the
>100
65.8
positively charged Lys483 by its purine scaffold, in addition to a hy-
drophobic interaction which is maintained by the majority of com-
pounds in the gate area with Leu514, Phe595, Val471, Ala481, Ile527
and Val482 amino acids. The high activity of compound 16 could be
attributed to its preferential binding in active site of B-RafV600E as re-
flected in its binding free energy (–16.27 kcal/mol). It exhibited further
H-bonding with Lys483 residue and additional hydrophobic interactions
with the gate area amino acids Leu505, leu597 and Ala481 through its
terminal pyrimidine ring. Moreover, the terminal phenyl ring showed a
hydrophobic interaction with Phe583 in the gate area (Fig. 10). It is
noteworthy that compounds displayed only Lys483 interaction without
achieving interaction with DFG-loop (compounds 29b and 29c)
exhibited the lowest enzyme inhibitory activity (B-RafV600E IC50 of 444
and 609 nM, respectively) compared to their 4-fluoro congener 29a (B-
RafV600E IC50 of 147 nM).
Ovarian Cancer
Renal Cancer
>100
>100
46.9
2.31
2.1
>100
>100
>100
>100
>100
7.97
3.69
4.89
9.75
2.15
2.32
2.01
2.8
A498
ACHN
>100
50.1
CAKI-1
4.32
2.29
3.16
3.2
RXF 393
SN12C
>100
>100
>100
77
TK-10
UO-31
2.13
11.5
4.64
3.91
2.44
PC-3
P.C.
>100
>100
>100
>100
DU-145
MCF7
Breast Cancer
MDA-MB-231/
ATCC
3.4.3. Modeling of 17 and 22c on EGFR and VEGFR-2
Molecular docking study was carried out to predict the possible
binding mode that could be responsible for the multi-kinase activity of
compounds 17 and 22c against EGFR and VEGFR-2. This was achieved
using EGFR (PDB ID: 1XKK) and VEGFR-2 (PDB ID: 1YWN) in complex
with lapatinib (GW572016) and 4-amino-furo[2,3-d]pyrimidine deriv-
ative (LIF), respectively [82,83]. Initially, the self-docking validation
step reproduced all the binding interactions of the co-crystallized li-
gands on EGFR and VEGFR-2 active site optimally with energy scores of
ꢀ 15.12 and ꢀ 12.09 kcal/mol, respectively, and with RMSD of 1.631
and 0.826 Å, respectively. Docking poses reproduced all the key in-
teractions that were accomplished by the co-crystallized ligands with
the hot spots in the active sites of EGFR (Met793) and VEGFR-2
(Asp1044, Glu883, Glu915 and Cys917) [84]. (For further details see
HS 578 T
BT-549
>100
69.4
3.43
11.1
3.05
10.1
2.62
3.28
1.75
2.01
T-47D
>100
54.8
MDA-MB-468
aBold values indicate superior activity than sorafenib X.
Likewise, the potent compound 22c interacted with Gln859 by its
purine N-9. The 4-tolylacetamide fragment accomplished a H-bond
interaction with the key amino acid Val851 in the hinge region, and
achieved several hydrophobic interactions with the hydrophobic side
chains of the amino acids Val851, Ile932, Phe930, Ile848, Met922 and
Ile800 (Fig. 7).
Compound 17 displayed a different binding pattern, in which a H-
12

A.R. Mohamed et al.
Bioorganic Chemistry 107 (2021) 104569
Fig. 5. Mean growth inhibition percent (Mean GI%) of the tested compounds over NCI-60 cell line panel.
derivative compound XV (PI3K inhibitor) cores, through the replace-
Supplementary Materials)
α
Hisham et al [37], reported some C-8 substituted xanthine de-
rivatives with potent inhibitory activity against EGFR. Moreover,
purine-based compounds revealed potent activity toward EGFR and
considerable inhibitory activity against some other related kinases,
including VEGFR-2 [85]. Binding of these purine derivatives depends on
a clamp like hydrophobic interaction through N-9 hydrophobic side
chain with the hydrophobic side chains of Leu844, Leu718 and Val726
residues [85].
ment of 1H-pyrrolo[2,3-b]pyridine scaffold in vemurafenib with the 1,3-
dimethyl-1H-purine-2,6(3H,7H)-dione scaffold in XV. This was followed
by diverse molecular structure modifications including purine ring N-7
methylene replacement with acetamide and further, N-7 terminal
phenyl substitutions increasing bulkiness of this arm. Furthermore,
substitution at C-8 with diverse privileged moieties, such as integration
with N-7 phenylacetamide in elaboration of novel tricyclic molecules
based on the purine ring. In other words, several lead identification and
optimization strategies such as hybridization, bio-isosteric replacement,
ring fusion and extension were adopted. Finally, a fruitful small library
was compiled and subjected to refinement processes based on the crystal
structures of PI3Kγ and B-RafWT binding sites. Essence of this effort was
demonstrated by a distinct and broad anti-proliferative activity of
several compounds of the designed library and a potent multi-kinase
targeting efficacy. Particularly, the effect of compounds 17 and 22c
on B-RafWT phenotypic melanoma SK-MEL-2 and B-RafV600E phenotypic
colon carcinoma HT-29 cell lines. Compound 17 Showed GI of 103% and
104% at 10 µM, respectively, whereas compound 22c exhibited GI50 of
Substitutions at N-7 and C-8 of compounds 17 and 22c fitted the
purine ring itself into the hydrophobic clamp when they were docked
into EGFR crystal structure. Furthermore, the uracil ring at C-8 in
compound 17 participated in three H-bonding interactions through its
carbonyl groups with Arg841, Lys745 and Phe723 residues. On the other
hand, compound 22c formed H-bond interaction with Thr854 through
the acetamide oxygen at N-7. Moreover, its terminal 4-tolyl ring
involved in hydrophobic interactions with the hydrophobic side chains
of Phe856 and Leu777 residues. (For further details see Supplementary
Materials, Figures 88, 89)
The reported VEGFR-2 inhibitory activity of xanthine congeners
[34], along with the broad and potent in vitro anticancer activity of
compounds 17 and 22c encouraged us to explore their experimental
enzyme activity, as well as, their binding to VEGFR-2 active site. Com-
pounds 17 and 22c formed H-bond interactions with the key amino acid
Asp1044 through NH of uracil side chain at C-8 and oxygen of acetamide
fragment at N-7, respectively. Both compounds are fitted properly by
hydrophobic interactions with Leu887, Leu1017, Ile890, Ile1042 and
Ile886. Additionally, compound 17 showed two H-bond interactions
(donor and acceptor) by its uracil ring and purine C-2 carbonyl with
Ile1023 and Lys866, respectively. Moreover, compound 22c showed
further H-bond interaction between NH of acetamide fragment and the
13.4 µM and 13.8 µM, respectively. Moreover, PI3Kα and B-RafV600E
inhibitory activities of compound 17 (IC50 = 12.2 and 199.6 nM,
respectively) and compound 22c (IC50 = 10.3 and 129.8 nM, respec-
tively) are augmented by their binding characteristics in the active sites
of both targets. Furthermore, in silico and in vitro biological studies
revealed the extension of both compounds’ activities toward two ki-
nases, EGFR (17 and 22c; IC50 = 124 and 277 nM, respectively) and
VEGFR-2 (17 and 22c; IC50 = 152 and 301 nM, respectively). Interest-
ingly, compound 22c showed renal MG-MID of 2.78 µM vs 3.00 µM of
sorafenib. Compound 22c surpassed sorafenib regarding growth inhi-
bition, cytostatic effect, and cytotoxicity on several NCI-60 panel cell
lines. The most sensitive cell lines to compound 17 are NSCLC (HOP-92;
α
C helix Glu883 residue. Also, a hydrophobic interaction was exhibited
GI50 = 7.51
7.97 M) cancers. Whereas the most sensitive cell lines to compound 22c
are NSCLC (HOP-92; GI50 = 1.90 M), CNS (SNB-75; GI50 = 1.43 M, SF-
539; GI50 = 1.94 M), ovarian (OVCAR-4; GI50 = 2.10 M, SK-OV-3;
GI50 = 2.15 M) and renal (A498; GI50 = 2.01 M, UO-31; GI50
2.13 μM) cancers. Both compounds 17 and 22c exhibited a non-
μM), CNS (SNB-75; GI50 = 12.5 μM) and renal (A498; GI50 =
between terminal phenyl ring and the hydrophobic side chains of
Val914, Leu1033, Val846, and Val896 residues. (For further details see
Supplementary Materials, Figures 91, 92)
μ
μ
μ
μ
μ
μ
μ
=
4. Conclusion
significant in vitro cytotoxicity toward normal WI-38 cell line. Finally,
it can be concluded that the 1,3-dimethylxanthine scaffold is open for
manipulation to afford compounds with promising physicochemical and
The molecular hybridization approach was applied between both of
vemurafenib (selective B-RafV600E inhibitor) and the methylxanthine
13

A.R. Mohamed et al.
Bioorganic Chemistry 107 (2021) 104569
Table 3
PI3Kα and B-RafV600E inhibitory activities of the selected compounds and the
reference compounds (IC50, nM).
Compound
PI3K
α
IC50 (nM)a
B-RafV600E IC50 (nM)a
8.46 0.3
403.8 ± 13
14
16
44.8 ± 1.5
12.2 ± 0.4
99.61 3.3
199.6 6.6
17
19.1 ± 0.6
401.1 ± 13
Fig. 6. 2D representation of molecular docking of compound 14 on PI3K
α
19a
22c
crystal structure (PDB ID: 4JPS) (Distances in Å).
10.3 0.3
129.8 4.3
147 4.8
pharmacokinetic properties such as 22c, in addition to their potent
anticancer activity.
25.7 ± 0.8
5. Experimental
5.1. Chemistry
29a
29b
Starting materials, reagents and solvents were obtained from com-
mercial suppliers and used without further purification. Melting points
were carried out by the open capillary tube method using a Stuart (Stone
Staffordshire ST/50SA UK) apparatus and they were uncorrected.
Infrared Spectra were performed on Schimadzu FT-IR 8400 S spec-
trometer Affinity A1 using potassium bromide discs, and expressed in
wave number (cmꢀ 1). NMR spectra were recorded on a Bruker Ascend
400/R (1H: 400 MHz, 13C and DEPT-135: 100 MHz) spectrophotometer.
Chemical shift values (δ) were given in parts per million (ppm) down-
field from tetramethylsilane (TMS) as an internal reference. Elemental
analyses were carried out using FLASH 2000 CHNS/O analyzer, Thermo
Scientific at the Regional Centre for Mycology and Biotechnology
(RCMB), Al-Azhar University, Nasr City, Cairo.Mass spectra were carried
out on Direct Inlet part to mass analyzer in Thermo Scientific GCMS
model ISQ at the Regional Centre for Mycology and Biotechnology
(RCMB), Al-Azhar University, Nasr City, Cairo. All the reactions were
monitored by thin layer chromatography silica gel F 254, Aluminium
sheets 20 × 20 cm (Sigma-Aldrich) were used. Dichlomethane: methanol
(1: 0.1) was the adopted elution system. Compounds 1, 2 [46,47], 3a-f
[48–53], 5 [54], 6 [55], 7 [56], 8a-c [57,58], 9a,b [86,87], 21 [67], and
22a,b,f [60,66] were synthesized according to reported procedures.
10.8 ± 0.4
15.9 ± 0.5
444.1 ± 15
609.4 ± 20
29c
9.76 0.3
156.5 5.1
30
LY294002
Sorafenib
10.6 ± 0.3
–
–
244.5 ± 8
Bold values indicate superior activity on PI3K
α
or BRAFV600E than LY294002 or
sorafenib, respectively.
a
Data were expressed as Mean ± Standard error (S.E.) of three independent
experiments.
5.1.1. 4-(2-Aminothiazol-5-ylamino)benzenesulfonamide (4).
A mixture of 2-chloro-N-(4-sulfamoylphenyl)acetamide 3f (2.71 g,
10.90 mmol) and thiourea (0.83 g, 10.90 mmol) in absolute ethanol (25
ml) was refluxed for 12 h. The reaction mixture was poured into ice
water, the formed precipitate was filtered, washed with water, dried and
recrystallization from methanol to give dark green solid, yield 38%, mp
179–182 ◦C, 1H NMR (DMSO‑d6) δ: 7.11 (s, 1H, Ar-H), 7.22 (s, 2H, NH2
exchanged with D2O), 7.35 (s, 2H, NH2 exchanged with D2O), 7.47,7.49
(d, 2H, J = 7.32 Hz, Ar-H), 7.81, 7.83 (d, 2H, J = 7.8 Hz, Ar-H), 11.89 (s,
1H, NH exchanged with D2O), 13C NMR (DMSO‑d6) δ: 113.7, 120.4,
121.8, 127.5 (Ar-C), 127.9, 131.4, 140.1 (thiazole-C). MS, m/z (%):
Table 4
B-RafWT, EGFR and VEGFR-2 in vitro inhibitory activity (IC50, nM).
Compound
IC50 (nM) a
B-RafWT
EGFR
VEGFR-2
17
170.6 5.6
115.1 3.8
186.5 ± 6.1
124 ± 2.6
277 ± 5.8
78.4 ± 1.6
152 ± 4.53
301 ± 8.98
65.7 ± 1.96
22c
Sorafenib X
Bold values indicate higher activity than sorafenib.
a
Data were expressed as mean ± Standard error (S.E.) of three independent
270.30 (M+, 8.87), 271.38 (M+
+
1, 19.36); Anal. Calcd for
experiments.
C9H10N4O2S2: C, 39.99; H, 3.73; N, 20.73; found C, 39.51; H, 3.42; N,
14

A.R. Mohamed et al.
Bioorganic Chemistry 107 (2021) 104569
Fig. 8. 2D diagram (A) and 3D representation (B) of molecular docking of
compound 17 on PI3K
α
crystal structure (PDB ID: 4JPS) (Distances in Å).
ꢀ 1
solid, yield 39%, mp 257–258 ◦C, IR (KBr) ѵ (cm ): 3148 (N H), 3090
–
–
–
–
–
–
(C H aromatic), 2955 (C H aliphatic), 2207 (C N), 1700–1650 (3C
= O), 1612, 1601 (N H bending), 1539–1505 (C C aromatic), 1H
–
–
–
NMR (DMSO‑d6) δ: 3.22 (s, 3H, CH3), 3.42 (s, 3H, CH3), 5.47 (s, 2H,
CH2), 7.18 (t, 2H, J = 8.86 Hz, Ar-H), 7.35–7.44 (m, 2H, Ar-H),
7.94–7.97 (m, 4H, Ar-H), 8.28 (s, 1H, Ar-H), 11.85 (s, 1H, NH
exchanged with D2O), 13C NMR (DMSO‑d6) δ: 28.0 (CH3), 29.9 (CH3),
Fig. 7. 2D diagram (A) and 3D representation (B) of molecular docking of
compound 22c on PI3Kα crystal structure (PDB ID: 4JPS) (Distances in Å).
–
–
38.1 (CH2), 83.2, 107.5, 115.7 (Ar-C), 115.9 (C N), 117.9, 130.3,
–
–
–
20.43.
130.4, 131.3, 131.4, 133.5, 133.6, 143.2 (Ar-C) 151.5 (C O), 155.0
–
–
–
–
(C O), 162.9, 163.6, 165.3 (Ar-C), 168.6 (C O) . MS, m/z (%): 515.47
(M+, 14.11); Anal. Calcd for C25H18FN7O3S: C, 58.25; H, 3.52; N, 19.02;
found C, 58.61; H, 3.19; N, 19.28.
5.1.2. 2-(4-[(1,3-Dimethyl-2,6-dioxo-2,3-dihydro-1H-purin-7(6H)-yl)
methyl]phenylthio)-4-(4-fluorophenyl)-6-oxo-1,6-dihydropyrimidine-5-
carbonitrile (10).
Sodium hydride 60% (0.28 g, 6.94 mmol) was added to a mixture of
7-(4-fluorobenzyl)-1,3-dimethyl-1H-purine-2,6(3H,7H)-dione 9b (0.5 g,
1.73 mmol) and 6-(4-fluorophenyl)-4-oxo-2-thioxo-1,2,3,4-tetrahy-
dropyrimidine-5-carbonitrile 8b (0.47 g, 1.91 mmol) in DMF (6 ml) and
stirred at 120 ◦C for 24 h. The reaction mixture was cooled to room
temperature then poured onto ice water and adjusted at pH 4–5 with
hydrochloric acid (1 N). The produced precipitate was filtered, washed
with water, dried and recrystallized from ethanol/DMF to give yellow
5.1.3. General procedure for synthesis of 11a,b
A
mixture of 7-benzyl-1,3-dimethyl-1H-purine-2,6(3H,7H)-dione
derivative 9a,b (14.81 mmol) and NBS (3.95 g, 22.20 mmol) in DMF (35
ml) was refluxed at 90 ◦C for 8 h. Then the reaction mixture was cooled
down to room temperature and poured onto ice water. The formed
precipitate was filtered, washed with water, dried and recrystallized
from ethanol 95%.
15

A.R. Mohamed et al.
Bioorganic Chemistry 107 (2021) 104569
Fig. 9. 2D diagram and 3D representation of molecular docking of compound 17 (A and B, respectively) and compound 22c (C and D, respectively) on B-RafV600E
crystal structure (PDB ID: 3IDP) (Distances in Å).
5.1.3.1. 7-Benzyl-8-bromo-1,3-dimethyl-1H-purine-2,6(3H,7H)-dione
(11a).. The titled compound was synthesized using compound 9a (4.00
ꢀ 1
g), yield 85%, mp 141–143 ◦C, IR (KBr) ѵ (cm ): 3179 (N H),
–
–
–
3032–3009 (C H aromatic), 2951 (C H aliphatic), 1709, 1667 (2C =
1
–
–
O), 1539 (C C aromatic), H NMR (CDCl ) δ: 3.41 (s, 3H, CH ), 3.48 (s,
3H, CH3), 5.70 (s, 2H, CH2), 7.24–7.29 (m, 5H, Ar-H), 313C NMR
3
(DMSO‑d6) δ: 28.1 (CH3), 29.9 (CH3), 49.7 (CH2), 109.5, 127.5, 128.2,
–
–
–
–
128.8, 135.2, 141.2, 148.1 (Ar-C), 151.2 (C O), 154.6 (C O).
5.1.3.2. 8-Bromo-7-(4-fluorobenzyl)-1,3-dimethyl-1H-purine-2,6
(3H,7H)-dione (11b).. The titled compound was synthesized using
compound 9b (4.27 g), yield 83%, mp 168–171 ◦C, 1H NMR (CDCl3) δ:
3.22 (s, 3H, CH3), 3.32 (s, 3H, CH3), 5.59 (s, 2H, CH2), 7.08 (t, 2H, J =
8.80 Hz, Ar-H), 7.22 (dd, 2H, J = 5.44, 8.24 Hz, Ar-H).
5.1.4. General procedure for synthesis of 12a,b
7-Benzyl-8-bromo-1,3-dimethyl-1H-purine-2,6(3H,7H)-dione deriv-
ative 11a,b (1.08 mmol) was added to a mixture of potassium carbonate
(0.30 g, 2.16 mmol), DMAP (0.03 g, 0.22 mmol) and (1,1-dioxo-1,2-
benzothiazol-3-yl)amine 2 (0.24 g, 1.31 mmol) in DMF (6 ml). The re-
action mixture was stirred at 100 ◦C for 16 h then was cooled to room
Fig. 10. 2D representation of molecular docking of compound 16 on B-RafV600E
crystal structure (PDB ID: 3IDP) (Distances in Å).
16

A.R. Mohamed et al.
Bioorganic Chemistry 107 (2021) 104569
temperature and poured onto ice water, medium was neutralized with
acetic acid (1 N). The resulted precipitate was filtered, washed with
water, dried and recrystallized from ethanol/DMF.
precipitate was filtered, washed with water, dried and recrystallized
from ethanol/DMF to give red solid, yield 42%, mp 185–186 ◦C, IR (KBr)
ѵ (cmꢀ 1): 3399 (N H amine), 3275 (N H amide), 3090–3071 (C
–
H
H
–
–
–
–
aromatic), 2951 (C H aliphatic), 1701, 1651 (3C = O), 1612 (N
aromatic), 1180 (C S), 1H NMR
–
–
–
bending), 1539–1497 (C
C
–
5.1.4.1. 7-Benzyl-8-[(1,1-dioxo-1,2-benzothiazol-3-yl)amino]-1,3-
(DMSO‑d6) δ: 3.18, 3.26 (2 s, 3H, CH3), 3.41, 3.48 (2 s, 3H, CH3), 5.46,
5.64 (2 s, 2H, CH2), 6.84–6.97 (m, 2H, Ar-H), 7.24–7.39 (m, 5H, Ar-H),
7.97(d, 1H, J = 7.04 Hz, Ar-H), 8.30 (d, 1H, J = 7.28 Hz, 1H, Ar-H),
10.43 (s, 1H, NH exchanged with D2O), 10.57 (2 s, 2H, 2NH
exchanged with D2O), 13C NMR (DMSO‑d6) δ: 28.2 (CH3), 30.2 (CH3),
49.4 (CH2), 109.3, 110.1, 110.5, 111.3, 120.7, 122.8, 127.1, 127.4,
dimethyl-purine-2,6-dione (12a).. The titled compound was synthesized
using compound 11a (0.38 g) to give yellow solid, yield 46%, mp
ꢀ 1
242–245 ◦C, IR (KBr) ѵ (cm ): 3179 (N H), 3086–3032 (C H aro-
–
–
–
–
H
matic), 2920 (C H aliphatic), 1701, 1667 (2C = O), 1636 (N
bending), 1600–1543 (C C aromatic), 1335, 1157 (SO ). 1H NMR
–
–
(DMSO‑d6) δ: 3.26 (s, 3H, CH3), 3.49 (s, 3H, CH3), 5.58 (2s, 2H, CH2),
–
–
127.9, 128.3, 131.0, 137.0, 141.9, 148.8 (Ar-C), 151.2 (C O), 154.6
–
7.25 (s, 6H, Ar-H, N H), 7.88 (t, 2H, J = 5.56 Hz, Ar-H), 8.09 (d, 1H, J
= 6.68 Hz, Ar-H), 8.16 (d, 1H, J = 6.64 Hz, Ar-H), 13C NMR (DMSO‑d6)
–
–
–
–
–
–
(C O), 155.7, 163.2 (Ar-C), 165.9 (C O), 167.6 (C S). MS, m/z (%):
488.19 (M+, 14.87), 488.83 (M+ + 1, 9.03), 491.01, (M+ + 3, 10.69);
Anal. Calcd for C23H20N8O3S: C, 56.55; H, 4.13; N, 22.94; found C,
56.91; H, 4.38; N, 22.63.
δ: 27.9 (CH3), 30.1 (CH3), 41.5 (CH2), 109.2, 120.7, 123.7, 126.5, 127.9,
–
–
127.9, 128.1, 128.9, 129.1, 133.0, 138.0 (Ar-C), 151.5 (C O), 154.2
(C O). MS, m/z (%): 450.92 (M , 26.01), 451.48 (M+ + 1, 9.69); Anal.
+
–
–
Calcd for C21H18N6O4S: C, 55.99; H, 4.03; N, 18.66; found C, 55.87; H,
5.1.7. 7-Benzyl-8-(2-chloroethylamino)-1,3-dimethyl-1H-purine-2,6
(3H,7H)-dione (15).
3.84; N, 18.53.
Triethylamine (0.42 ml, 5.73 mmol) was added to a mixture of 7-
benzyl-8-bromo-1,3-dimethyl-1H-purine-2,6(3H,7H)-dione 11a (2 g,
5.73 mmol) and 2-chloroethylamine HCl (1.33 g, 11.47 mmol) in DMF
(20 ml). The resulted mixture was stirred at 50–60 ◦C for 2 h then po-
tassium carbonate (0.4 g, 2.86 mmol) was added, stirring was then
continued for 8 h at 70 ◦C. The reaction mixture was cooled to room
temperature and poured onto ice water, the formed precipitate was
5.1.4.2. 8-[(1,1-Dioxo-1,2-benzothiazol-3-yl)amino]-7-[(4-fluorophenyl)
methyl]-1,3-dimethyl-purine-2,6-dione (12b).. The titled compound was
synthesized using compound 11b (0.4 g) to give yellow solid, yield 42%,
ꢀ 1
mp > 300 ◦C, IR (KBr) ѵ (cm ): 3179 (N H), 3086 (C H aromatic),
–
–
–
–
2928 (C H aliphatic), 1697, 1667 (2C = O), 1636 (N H bending),
1
–
–
1601–1543 (C C aromatic), 1335, 1157 (SO ). H NMR (DMSO‑d ) δ:
3.26 (s, 3H, CH3), 3.49 (s, 3H, CH3), 5.57 (s, 2H, CH2), 7.09 (t, 2H,6J =
2
filtered, washed with water, petroleum ether and dried to give pale
–
8.56 Hz, Ar-H), 7.31 (br.s, 2H, Ar-H), 7.91–7.93 (m, 3H, Ar-H, N H),
ꢀ 1
yellow solid, yield 49%, mp 161–162 ◦C IR (KBr) ѵ (cm ): 3345 (N H),
8.12 (d, 1H, J = 6.36 Hz, Ar-H), 8.21 (d, 1H, J = 5.36 Hz, Ar-H), 13C
NMR (DMSO‑d6) δ: 27.7 (CH3), 29.9 (CH3), 46.1 (CH2), 102.8, 115.4,
115.6, 120.3, 130.5, 130.6, 131.7, 132.4, 134.8, 134.9, 143.0, 148.6
–
–
–
3067–3032 (C H aromatic), 2994–2947 (C H aliphatic), 1697–1667
1
–
–
–
(2C = O), 1612 (N H bending), 1535 (C C aromatic), H NMR (CDCl )
δ: 3.42 (s, 5H, CH3, CH2), 3.57 (s, 2H, CH2), 3.58 (s, 3H, CH3), 5.57 (3s,
2H, CH2), 7.29 (s, 1H, 1NH exchanged with D2O), 7.34–7.39 (m, 5H, Ar-
H), 13C NMR (CDCl3) δ: 28.1 (CH3, CH2), 29.9 (CH3, CH2), 50.3 (CH2),
–
–
–
–
(Ar-C), 151.5 (C O), 154.0 (C O), 158.7, 160.7, 163.1 (Ar-C). MS, m/z
(%): 468.91 (M+, 24.65), 471.86 (M+ + 2, 14.11); Anal. Calcd for
C
21H17FN6O4S: C, 53.84; H, 3.66; N, 17.94; found C, 54.11; H, 3.94; N,
–
–
108.9, 127.9, 128.5, 128.9, 134.9, 148.4 (Ar-C), 151.3 (C O), 154.3
18.17.
(C O). MS, m/z (%): 347.73 (M , 36.92), 349.21 (M+ + 1, 46.39); Anal.
+
–
–
Calcd for C16H18ClN5O2: C, 55.25; H, 5.22; N, 20.14; found C, 55.28; H,
5.1.5. 4-[2-(7-Benzyl-1,3-dimethyl-2,6-dioxo-2,3,6,7-tetrahydro-1H-
purin-8-ylamino)thiazol-5-ylamino]benzenesulfonamide (13).
4.85; N, 20.07.
A mixture of 7-benzyl-8-bromo-1,3-dimethyl-1H-purine-2,6(3H,7H)-
dione 11a (0.5 g, 1.43 mmol), 4-(2-aminothiazol-5-ylamino)benzene-
sulfonamide 4 (0.43 g, 1.58 mmol) and DMAP (0.175 g, 1.43 mmol) in
DMF (6 ml) was stirred at 80–90 ◦C for 6 h. The reaction mixture was
cooled to room temperature, poured onto ice water and adjusted at pH
4–5 using hydrochloric acid (1 N). The formed precipitate was filtered,
5.1.8. 4-[2-(7-Benzyl-1,3-dimethyl-2,6-dioxo-2,3,6,7-tetrahydro-1H-
purin-8-ylamino)ethylamino]-N-(pyrimidin-2-yl)benzenesulfonamide (16).
A mixture of 7-benzyl-8-(2-chloroethylamino)-1,3-dimethyl-1H-pu-
rine-2,6(3H,7H)-dione 15 (0.5 g, 1.44 mmol), sulfadiazine (0.4 g, 1.59
mmol) and sodium hydride 60% (0.17 g, 4.31 mmol) in DMF (5 ml) was
stirred at 80 ◦C for 12 h. The reaction mixture was cooled to room
temperature then poured onto ice water and adjusted at pH 4–5 with
hydrochloric acid (1 N). The produced precipitate was filtered, washed
with water, dried and recrystallized from ethanol/DMF to give yellow
solid, yield 44%, mp 188–190 ◦C, IR (KBr) ѵ (cmꢀ 1): 3426, 3356, 3260
washed with water and recrystallized from ethanol/DMF to give dark
ꢀ 1
grey solid, yield 39%, mp 265–267 ◦C, IR (KBr) ѵ (cm ): 3352 (N
H
H
–
–
–
amine), 3256, 3210 (NH2), 3063–3009 (C H aromatic), 2951 (C
–
aliphatic), 1709, 1670 (2C = O), 1605 (N H bending), 1539–1501
1
–
–
(C C aromatic), 1350, 1157 (SO ), H NMR (DMSO‑d ) δ: 3.22 (s, 3H,
CH3), 3.32 (s, 3H, CH3), 5.60 (s, 2H, CH2), 7.12–7.26 (m6, 7H, Ar-H), 7.35
(br.s, 3H, NH, NH2 exchanged with D2O), 7.85–7.87 (m, 3H, Ar-H), 7.96
(br.s, 1H, NH exchanged with D2O), 13C, DEPT-135 NMR, (DMSO‑d6) δ:
28.1 (CH3), 30.0 (CH3), 49.4 (CH2), 109.3 (Ar-C), 127.1, 127.5, 127.9,
2
–
–
(N-Hs), 3102–3036 (C H aromatic), 2940 (C H aliphatic), 1697–1651
–
–
= O), 1605 (N H bending), 1582–1528 (C C aromatic),
–
(2C
1323–1153 (SO2), 1H NMR (DMSO‑d6) δ: 2.91 (s, 4H, 2CH2), 3.18 (s, 3H,
CH3), 3.40 (s, 3H, CH3), 5.46 (s, 2H, CH2), 6.00 (s, 2H, 2NH exchanged
with D2O), 6.57 (d, 2H, J = 8.72 Hz, Ar-H), 7.01 (t, 1H, J = 4.82 Ar-H),
7.11–7.35 (m, 5H, Ar-H), 7.62 (d, 2H, J = 8.68, Ar-H), 8.48 (d, 2H, J =
4.84, Ar-H), 11.28 (s, 1H, NH exchanged with D2O), 13C NMR
(DMSO‑d6) δ: 27.8 (CH3), 29.9 (CH3), 41.5 (2CH2), 48.5 (CH2), 104.1,
112.7, 116.0, 125.3, 126.5, 127.3, 127.4, 127.8, 128.0, 128.7, 129.0,
–
–
–
–
128.8 (Ar-CH), 135.9, 141.2, 147.9 (Ar-C), 151.0 (C O), 154.4 (C O).
MS, m/z (%): 538.06 (M+, 32.79), 541.36 (M+ + 3, 49.28); Anal. Calcd
for C23H22N8O4S2: C, 51.29; H, 4.12; N, 20.80; found C, 51.52; H, 3.96;
N, 20.59.
–
–
–
–
130.3, 138.0, 148.2 (Ar-C), 151.5 (C O), 153.5 (Ar-C), 153.9 (C O),
5.1.6. (Z)-N-(7-Benzyl-1,3-dimethyl-2,6-dioxo-2,3,6,7-tetrahydro-1H-
purin-8-yl)-2-(2-oxoindolin-3-ylidene)hydrazinecarbothioamide (14).
A mixture of 7-benzyl-8-bromo-1,3-dimethyl-1H-purine-2,6(3H,7H)-
dione 11a (0.50 g, 1.43 mmol), (Z)-2-(2-oxoindolin-3-ylidene)hydrazi-
necarbothioamide 7 (0.35 g, 1.58 mmol) and potassium carbonate (0.4
g, 2.86 mmol) in DMF (6 ml) was stirred at 70 ◦C for 10 h. The reaction
mixture was cooled to room temperature then was poured onto ice
water. Medium was neutralized with acetic acid (1 N) and the resulted
157.7, 158.7 (Ar-C). MS, m/z (%): 561.15 (M+, 17.69); Anal. Calcd for
C
26H27N9O4S: C, 55.60; H, 4.85; N, 22.45; found C, 55.49; H, 4.59; N,
23.13.
5.1.9. 7-Benzyl-8-(2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-ylamino)-1,3-
dimethyl-1H-purine-2,6(3H,7H)-dione (17).
A mixture of 7-benzyl-8-bromo-1,3-dimethyl-1H-purine-2,6(3H,7H)-
dione 11a (0.42 g, 1.06 mmol), 6-aminouracil (0.15 g, 1.16 mmol) and
17

A.R. Mohamed et al.
Bioorganic Chemistry 107 (2021) 104569
sodium acetate (0.13 g, 2.07 mmol) in glacial acetic acid (8 ml) was
stirred at 90 ◦C for 16 h. The reaction mixture was cooled to room
temperature then poured onto ice water. The formed precipitate was
filtered, washed with water, dried and recrystallized from ethanol/DMF
to give grey solid, yield 51%, mp 176–177 ◦C, IR (KBr) ѵ (cmꢀ 1): 3345,
precipitate was filtered, washed with water, dried and recrystallized
from ethanol/water.
5.1.11.1. 2-[7-(4-Fluorobenzyl)-1,3-dimethyl-2,6-dioxo-2,3,6,7-tetrahy-
dro-1H-purin-8-ylthio]-4-(4-fluorophenyl)-6-oxo-1,6-dihydropyrimidine-5-
carbonitrile (19a).. The titled compound was synthesized using com-
pound 8b (0.40 g) to give dark green solid, yield 40%, mp, IR (KBr) ѵ
–
–
3171 (N-Hs), 3067–3032 (C H aromatic), 2951 (C H aliphatic),
–
–
1697–1667 (4C = O), 1612 (N H bending), 1535–1443 (C C aro-
–
matic), 1H NMR (DMSO‑d6) δ: 3.23 (s, 3H, CH3), 3.41 (s, 3H, CH3), 5.53
(s, 2H, CH2), 6.67 (s, 1H, NH exchanged with D2O), 7.25–7.38 (m, 6H,
Ar-H, pyrimidine-H), 9.89 (s, 1H, NH exchanged with D2O), 12.80 (s,
1H, NH exchanged with D2O), 13C NMR (DMSO‑d6) δ: 28.1 (CH3), 30.0
(CH3), 49.8 (CH2), 89.5, 108.8, 127.5, 128.0, 128.4, 128.6, 128.7,
–
–
–
aromatic), 2924 (C H
(cmꢀ 1): 3287 (N H), 3075–3009 (C
H
–
–
–
aliphatic), 2222 (C N), 1700–1663 (3C = O), 1605 (N H bending),
–
1539–1512 (C C aromatic), 1H NMR (DMSO‑d6) δ: 3.29 (s, 3H, CH3),
–
–
3.32 (s, 3H, CH3), 4.54 (s, 2H, CH2), 7.13–7.47 (m, 7H, Ar-H, NH
exchanged with D2O), 8.04 (dd, 2H, J = 4.75, 8.72 Hz, Ar-H), 13C NMR
–
–
–
–
–
–
128.9, 129.2, 136.0, 148.3 (Ar-C), 151.2 (C O), 154.2 (C O), 165.8
(DMSO‑d6) δ: 28.1 (CH3), 30.0 (CH3), 41.6 (CH2), 93.5 (C N), 109.2,
–
+
–
–
–
–
(C O), 165.9 (C O). MS, m/z (%): 394.80 (M , 15.21), 396.55 (M+ +
109.7, 115.4, 115.9, 116.3, 122.3, 129.3, 130.7, 131.3, 131.5, 131.9,
–
–
–
–
1, 15.25); Anal. Calcd for C18H17N7O4: C, 54.68; H, 4.33; N, 24.80; found
132.1, 133.1, 141.2, 147.9 (Ar-C), 151.4 (C O), 154.8 (C O), 160.7,
–
–
C, 54.76; H, 4.78; N, 25.17.
161.5, 163.2, 163.3, 165.8, 166.1(Ar-C), 166.6 (C O). MS, m/z (%):
533.75 (M+, 9.84); Anal. Calcd for C25H17F2N7O3S: C, 56.28; H, 3.21; N,
18.38; found C, 56.73; H, 3.53; N, 18.26.
5.1.10. General procedure for synthesis of 18a,b
A mixture of 7-benzyl-8-bromo-1,3-dimethyl-1H-purine-2,6(3H,7H)-
dione derivative 11a,b (1.15 mmol), 6-aminothiouracil (0.18 g, 1.26
mmol) and DMAP (0.14 g, 1.15 mmol) in DMF (6 ml) was stirred at
80–90 ◦C for 8 h. The reaction mixture was cooled to room temperature,
poured onto ice water and adjusted at pH 4–5 using hydrochloric acid (1
N). The formed precipitate was filtered, washed with water and
recrystallized from ethanol/DMF to give the product.
5.1.11.2. 2-[7-(4-Fluorobenzyl)-1,3-dimethyl-2,6-dioxo-2,3,6,7-tetrahy-
dro-1H-purin-8-ylthio]-4-(4-methoxyphenyl)-6-oxo-1,6-dihydropyrimidine-
5-carbonitrile (19b).. The titled compound was synthesized using com-
pound 8c (0.42 g) to give yellow solid, yield 39%, mp 268–269 ◦C, IR
(KBr) ѵ (cmꢀ 1): 3151 (N H), 3094–3028 (C H aromatic), 2951, 2913
–
–
–
–
–
–
–
(C
H
aliphatic), 2218 (C N), 1694–1636 (C O), 1605 (N
H
–
–
bending), 1539–1512 (C C aromatic), 1H NMR (DMSO‑d6) δ: 3.30 (s,
–
–
5.1.10.1. 8-(4-Amino-6-oxo-1,6-dihydropyrimidin-2-ylthio)-7-benzyl-1,3-
3H, CH3), 3.46 (s, 3H, CH3), 3.83 (s, 3H, OCH3), 5.64 (s, 2H, CH2),
dimethyl-1H-purine-2,6(3H,7H)-dione (18a).. The titled compound was
6.95–7.02 (m, 5H, Ar-H, NH exchanged with D2O), 7.30 (t, 2H, J = 6.8
Hz, Ar-H), 7.64 (d, 2H, J = 8.76 Hz, Ar-H), 13C NMR (DMSO‑d6) δ: 28.3
synthesized using compound 11a (0.4 g) to give white solid, yield 42%,
ꢀ 1
mp 271–274 ◦C, IR (KBr) ѵ (cm ): 3360, 3194 (N-Hs), 3090–3009(C
–
–
–
H
(CH3), 30.1 (CH3), 48.9 (CH2), 56.0 (OCH3), 91.4 (C N), 109.8, 114.5,
–
–
aromatic), 2951 (C H aliphatic), 1709, 1667, 1651 (3C = O), 1605
115.5, 115.7, 116.4, 127.0, 130.2, 130.3, 130.9, 132.4, 139.0, 148.2
(N H bending), 1539–1443 (C C aromatic), 1H NMR (DMSO‑d6) δ:
–
–
–
–
–
–
(Ar-C), 151.1 (C O), 154.8 (C O), 160.8, 162.7, 163.2, 164.4, 164.6
–
+
+
–
3.22 (s, 3H, CH3), 3.42 (s, 3H, CH3), 5.60 (s, 2H, CH2), 7.06–7.35 (m, 7H,
Ar-H, NH2 exchanged with D2O), 9.02 (d, 1H, J = 9.40 Hz, pyrimidine-
H), 11.88 (s, 1H, NH exchanged with D2O), 13C, DEPT-135 NMR,
(DMSO‑d6) δ: 28.1 (CH3), 30.0 (CH3), 49.4 (CH2), 109.3 (Ar-C), 127.1,
(Ar-C), 166.8 (C O). MS, m/z (%): 545.02 (M , 29.01), 547.54 (M
+
–
2, 51.68); Anal. Calcd for C26H20FN7O4S: C, 57.24; H, 3.70; N, 17.97;
found C, 57.68; H, 3.53; N, 17.68.
127.3, 127.9, 128.9, 129.4 (Ar-CH), 136.0, 141.2, 147.9 (Ar-C), 151.0
5.1.12. 2-[1,3-Dimethyl-2,6-dioxo-2,3-dihydro-1H-purin-7(6H)-yl]-N-p-
tolylacetamide. (20).
+
–
–
–
–
–
–
(C O), 154.4 (C O), 159.9 (C O). MS, m/z (%): 411.12 (M , 9.33),
413.64 (M+ + 2, 12.42); Anal. Calcd for C18H17N7O3S: C, 52.55; H, 4.16;
Theophylline (0.5 g, 2.78 mmol) was added to a suspension of po-
tassium carbonate (0.96 g, 6.93 mmol) in DMF (8 ml) and stirred at 100
◦C for 2 h. A mixture of 2-chloro-N-p-tolylacetamide 3c (1.02 g, 5.55
mmol) and potassium iodide (0.23 g, 1.38 mmol) in DMF (4 ml) was
added to the previous mixture, and was stirred at 80 ◦C for 8 h. The
reaction mixture was cooled to room temperature, poured onto ice water
and adjusted at pH 6 by hydrochloric acid (1 N). The formed precipitate
was filtered, washed with water, dried and recrystallized from ethanol/
water to give brown solid, yield 46%, mp 120 ◦C , IR (KBr) ѵ (cmꢀ 1):
N, 23.83; found C, 53.03; H, 4.13; N, 24.05.
5.1.10.2. 8-(4-Amino-6-oxo-1,6-dihydropyrimidin-2-ylthio)-7-(4-fluo-
robenzyl)-1,3-dimethyl-1H-purine-2,6(3H,7H)-dione (18b).. The titled
compound was synthesized using compound 11b (0.42 g) to give buff
solid, yield 46%, mp 287–288 ◦C, IR (KBr) ѵ (cmꢀ 1): 3352, 3321, 3190
–
–
(N-Hs), 3082–3017 (C H aromatic), 2955 (C H aliphatic), 1705–1656
–
–
–
(3C = O), 1605 (N H bending), 1539–1443 (C C aromatic), 1H NMR
–
–
–
aromatic), 2951, 2920 (C H
(DMSO‑d6) δ: 3.21 (s, 3H, CH3), 3.40 (s, 3H, CH3), 5.57 (s, 2H, CH2),
7.05–7.35 (m, 6H, Ar-H, NH2 exchanged with D2O), 9.02 (t, 1H, J =
7.42 Hz, pyrimidine-H), 11.88 (s, 1H, NH exchanged with D2O), 13C
NMR (DMSO‑d6) δ: 28.1 (CH3), 30.0 (CH3), 48.7 (CH2), 107.3, 107.5,
109.2, 115.5, 115.8, 129.5, 129.5, 132.1, 136.9, 141.2, 147.9 (Ar-C),
3264 (N
H
amide), 3075 (C
H
–
aliphatic), 1701–1655 (3C = O), 1609 (N H bending), 1547–1512
1
–
–
(C C aromatic), H NMR (DMSO‑d ) δ: 2.14 (s, 3H, CH ), 2.26 (s, 3H,
6
3
CH3), 2.52 (s, 3H, CH3), 3.22 (s, 2H, CH2), 7.31–7.77 (m, 5H, Ar-H),
10.73 (s, 1H, NH exchanged with D2O), 13C NMR (DMSO‑d6) δ: 20.9
(2CH3), 21.0 (CH2, CH3), 118.6, 119.6, 120.8, 129.6, 129.7, 134.2,
–
–
–
–
151.0 (C O), 154.4 (C O), 160.7 (C O), 163.2, 166.9 (Ar-C). MS, m/z
–
–
(%): 429.99 (M+, 6.24); Anal. Calcd for C18H16FN7O3S: C, 50.34; H,
3.76; N, 22.83; found C, 50.59; H, 4.02; N, 22.68.
135.6 (Ar-C), 159.0 (C O), 159.8 (2C = O). MS, m/z (%): 327.14 (M ,
+
–
–
41.00), 328.97 (M+ + 1, 16.79); Anal. Calcd for C16H17N5O3: C, 58.71;
H, 5.23; N, 21.39; found C, 59.02; H, 5.50; N, 21.65.
5.1.11. General procedure for synthesis of 19a,b
Sodium hydride 60% (0.17 g, 4.3 mmol) was added to a mixture of 8-
bromo-7-(4-fluorobenzyl)-1,3-dimethyl-1H-purine-2,6(3H,7H)-dione
11b (0.53 g, 1.43 mmol) and the appropriate 4-oxo-6-phenyl-2-thioxo-
1,2,3,4-tetrahydropyrimidine-5-carbonitrile derivative 8b,c (1.61
mmol) in DMF (6 ml). The mixture was stirred at 0–5 ◦C for 1 h then
stirred at room temperature for 24 h and at 80 ◦C for 10 h. The reaction
mixture was cooled to room temperature then poured onto ice water and
adjusted at pH 4–5 with hydrochloric acid (1 N). The produced
5.1.12.1. General procedure for synthesis of 22a-f. 8-Bromotheophylline
21 (1 g, 3.86 mmol) was added to a suspension of potassium carbonate
(1.34 g, 9.70 mmol) in DMF (10 ml) and the mixture was stirred at 100
◦C for 2 h. The appropriate 2-chloro-N-(substituted phenyl)acetamide
derivative 3a-f (5.80 mmol) was dissolved in DMF (4 ml) and then added
to the previous mixture. The resulted mixture was stirred at room
temperature for 24 h. The reaction mixture was poured onto ice water
and adjusted at pH 6 by hydrochloric acid (1 N). The formed precipitate
18

A.R. Mohamed et al.
Bioorganic Chemistry 107 (2021) 104569
was filtered, washed with water, dried and recrystallized from ethanol/
water to give the product.
D2O), 10.13 (s, 1H, NH exchanged with D2O). 13C NMR (DMSO‑d6) δ:
–
26.0 (CH -C O), 26.8 (CH ), 27.8 (CH ), 30.0 (CH ), 102.8, 116.5,
–
3
3
117.3, 127.5, 128.4, 129.3,3130.0, 130.2, 130.5, 1332.9, 135.5, 136.7,
–
–
–
142.9, 147.0, 147.6, 149.1, 150.6 (Ar-C), 151.5 (C O), 154.0 (C O),
–
5.1.12.2. 2-[8-Bromo-1,3-dimethyl-2,6-dioxo-2,3-dihydro-1H-purin-7
+
–
–
–
–
170.5 (C O), 197.5 (CH -C O). MS, m/z (%): 535.46 (M , 13.76);
Anal. Calcd for C24H21N73O6S: C, 53.83; H, 3.95; N, 18.31; found C,
(6H)-yl]-N-p-tolylacetamide (22c).. The titled compound was synthe-
sized using compound 3c (1.07 g) to give white solid, yield 62%, mp
ꢀ 1
290–293 ◦C, IR (KBr) ѵ (cm ): 3310 (N H), 3078–3032 (C H aro-
–
–
53.62; H, 4.02; N, 18.52.
–
–
H
matic), 2920 (C H aliphatic), 1701–1643 (3C = O), 1601 (N
bending), 1558–1501 (C C aromatic). 1H NMR (DMSO‑d6) δ: 2.27 (s,
5.1.12.7. 2-(8-[(1,1-Dioxo-1,2-benzothiazol-3-yl)amino]-1,3-dimethyl-
–
–
3H, CH3), 3.19 (s, 3H, CH3), 3.42 (s, 3H, CH3), 5.03 (s, 2H, CH2), 7.13 (d,
2H, J = 8.36 Hz, Ar-H), 7.56 (d, 2H J = 8.44 Hz, Ar-H), 9.17 (s, 1H, NH
exchanged with D2O). 13C NMR (CDCl3) δ: 25.6 (CH3), 32.3 (CH3), 34.5
(CH3), 51.4 (CH2), 107.2, 123.6, 124.1, 134.1, 134.2, 135.9, 137.5,
2,6-dioxo-purin-7-yl)-~(N)-(4-sulfamoylphenyl)acetamide
(23b).. The
titled compound was synthesized using compound 22f (0.5 g) to give
brown solid, yield 43%, mp, IR (KBr) ѵ (cmꢀ 1): 3441, 3333, 3291, 3198
–
–
–
(NH2, N H), 3067–3028 (C H aromatic), 2990–2909 (C H aliphatic),
–
–
–
–
–
–
141.3, 142.4 (Ar-C), 152.9 (C O), 155.8 (C O), 156.2, 158.5 (Ar-C),
1697–1650 (3C = O), 1601 (N H bending), 1555–1489 (C C aro-
–
+
170.1 (C O). MS, m/z (%): 406.60 (M , 7.87); Anal. Calcd for
matic), 1339, 1161 (SO2), 1H NMR (DMSO‑d6) δ: 3.24 (s, 3H, CH3), 3.37
(s, 3H, CH3), 4.85 (s, 1H, NH exchanged with D2O), 4.98 (s, 2H, CH2),
7.17 (s, 1H, NH exchanged with D2O), 7.49 (s, 2H, NH2 exchanged with
D2O), 7.65, (d, 1H, J = 8.48 Hz, Ar-H), 7.75 (dd, 2H, J = 8.52, 12.12 Hz,
Ar-H), 7.84 (d, 1H, J = 8.48 Hz, Ar-H), 7.96–8.04 (m, 4H, Ar-H), 13C
NMR (DMSO‑d6) δ: 28.1 (CH3), 29.9 (CH3), 50.2 (CH2), 104.0, 117.6,
123.3, 124.1, 125.4, 127.3, 128.0, 133.8, 135.5, 136.6, 143.2, 143.7,
–
–
C16H16BrN5O3: C, 47.31; H, 3.97; N, 17.24; found C, 47.66; H, 3.83; N,
17.49.
5.1.12.3. 2-[8-Bromo-1,3-dimethyl-2,6-dioxo-2,3-dihydro-1H-purin-7
(6H)-yl]-N-(2,4-dichlorophenyl)acetamide (22d).. The titled compound
was synthesized using compound 3d (0.78 g) to give white solid, yield
ꢀ 1
–
–
–
70%, mp 141–142 ◦C, IR (KBr) ѵ (cm ): 3256 (N H amide),
–
147.4, 149.3 (Ar-C), 151.3 (C O), 152.7 (Ar-C), 153.6 (C O), 162.8
–
+
–
–
–
(Ar-C), 170.8 (C O). MS, m/z (%): 572.72 (M , 23.33); Anal. Calcd for
–
3075–3021 (C H aromatic), 2970, 2951 (C H aliphatic), 1697–1659
1
–
–
–
C22H20N8O7S2: C, 46.15; H, 3.52; N, 19.57; found C, 46.49; H, 3.52; N,
(3C = O), 1624 (N H bending), 1589–1520 (C C aromatic). H NMR
19.63.
(CDCl3) δ: 3.46 (s, 3H, CH3), 3.61 (s, 3H, CH3), 5.09 (s, 2H, CH2), 7.44
(dd, 1H, J = 2.04 Hz, J = 8.96 Hz, Ar-H), 8.23–8.38 (m, 2H, Ar-H), 9.11
(s, 1H, NH exchanged with D2O). 13C NMR (DMSO‑d6) δ: 27.9 (CH3),
30.1 (CH3), 49.2 (CH2), 106.2, 119.5, 123.3, 127.6, 127.9, 129.0, 129.2,
5.1.12.8. General procedure for synthesis of 24a,b. To a mixture of so-
dium hydride 60% (0.14 g, 3.45 mmol) and aniline derivative (sulfa-
nilamide, 4-fluoroaniline) in DMF (7 ml), 2-(8-bromo-1,3-dimethyl-2,6-
dioxo-2,3-dihydro-1H-purin-7(6H)-yl)-N-substituted phenylacetamide
derivative 22e,f was added. The resulted mixture was stirred at 70 ◦C for
8 h then at room temperature for 24 h. The reaction mixture was poured
onto ice water and neutralized with acetic acid (1 N). The formed pre-
cipitate was filtered, washed with hot ethanol several times to remove
the excess aniline derivative and dried. The crude was recrystallized
from ethanol/DMF to give the product.
–
–
–
–
–
135.4, 148.7 (Ar-C), 151.1 (C O), 154.2 (C O), 165.6 (C O). MS, m/z
–
(%): 460.20 (M+, 5.27), 461.50 (M+ + 1, 14.53), 462.18 (M+ + 2,
30.51), 462.72 (M+ + 3, 9.89); Anal. Calcd for C15H12BrCl2N5O3: C,
39.07; H, 2.62; N, 15.19; found C, 39.25; H, 2.93; N, 15.64.
5.1.12.4. N-(4-Acetylphenyl)-2-[8-bromo-1,3-dimethyl-2,6-dioxo-2,3-
dihydro-1H-purin-7(6H)-yl]acetamide (22e).. The titled compound was
synthesized using compound 3e (1.23 g) to give white solid, yield 57%,
ꢀ 1
mp 244–245 ◦C, IR (KBr) ѵ (cm ): 3217 (N H), 3063–3001 (C
H
–
–
H
–
–
aromatic), 2978 (C H aliphatic), 1713–1651 (3C = O), 1601 (N
5.1.12.9. N-(4-Acetylphenyl)-2-[1,3-dimethyl-2,6-dioxo-8-(4-sulfamoyl-
bending), 1555–1504 (C C aromatic). 1H NMR (DMSO‑d6) δ: 2.52 (s,
phenylamino)-2,3-dihydro-1H-purin-7(6H)-yl]acetamide
(24a).. The
–
–
3H, CH3), 3.19 (s, 3H, CH3), 3.49 (s, 3H, CH3), 5.27 (s, 2H, CH2),
titled compound was synthesized by reaction of compound 22e (0.50 g,
1.15 mmol) with sulfanilamide (0.40 g, 2.32 mmol) to give brown solid,
yield 43%, mp 243–245 ◦C, IR (KBr) ѵ (cmꢀ 1): 3441, 3418, 3318, 3217
7.72–7.96 (m, 4H, Ar-H), 9.67 (s, 1H, NH exchanged with D2O). 13C
–
–
NMR (CDCl ) δ: 26.8 (CH -C O), 28.1 (CH ), 30.5 (CH ), 50.1 (CH ),
102.7, 117.4, 118.8, 123.34, 129.7, 130.1, 132.4, 143.4, 144.7 (Ar-C),
(NH2, N H), 3078–3001 (C H aromatic), 2959 (C H aliphatic),
3
3
3
2
–
–
–
–
–
–
–
–
–
–
–
–
–
–
151.3 (C O), 166.1 (C O), 170.8 (C O), 197.8 (C O). MS, m/z (%):
1697–1651 (4C = O), 1601 (N H bending), 1555–1447 (C C aro-
434.19 (M+, 55.26); Anal. Calcd for C17H16BrN5O4: C, 47.02; H, 3.71; N,
16.13; found C, 47.34; H, 3.72; N, 16.82.
matic), 1362, 1184 (SO2), 1H NMR (DMSO‑d6) δ: 2.63 (s, 3H, CH3), 3.24
(s, 3H, CH3), 3.45 (s, 3H, CH3), 4.97 (s, 2H, CH2), 6.89 (s, 1H, NH
exchanged with D2O), 7.55 (s, 2H, NH2 exchanged with D2O), 7.71 (d,
2H, J = 8.6 Hz, Ar-H), 7.78–8.00 (m, 2H, Ar-H), 7.98 (d, 2H, J = 8.60 Hz,
Ar-H), 8.16 (d, 2H, J = 8.60 Hz, Ar-H), 10.71 (s, 1H, NH exchanged with
5.1.12.5. General procedure for synthesis of 23a,b. The appropriate 2-(8-
bromo-1,3-dimethyl-2,6-dioxo-2,3-dihydro-1H-purin-7(6H)-yl)-N-
substituted phenylacetamide derivative 22e,f (1.06 mmol) was added to
a mixture of (1,1-dioxo-1,2-benzothiazol-3-yl)amine 2 (0.21 g, 1.16
mmol) and sodium hydride 60% (0.12 g, 3.18 mmol) in DMF (6 ml). The
resulted mixture was stirred at 70 ◦C for 12 h. The reaction mixture was
cooled to room temperature then poured onto ice water and neutralized
with acetic acid (1 N). The produced precipitate was filtered, washed
with water, dried and recrystallized from ethanol/DMF.
D2O), 13C NMR (DMSO‑d ) δ: 26.7 (CH -C O), 27.2 (CH ), 28.1 (CH ),
–
–
30.3 (CH3), 95.0, 103.26, 104.4, 113.2, 116.5, 117.3, 3123.2, 129.8,
3
2
–
–
130.0, 130.2, 137.0, 145.5, 149.3, 151.4 (Ar-C), 151.6 (C O), 153.8
–
–
–
–
–
–
(C O), 156.2 (Ar-C), 171.1 (C O), 197.4 (CH -C O). MS, m/z (%):
525.06 (M+, 16.92), 527.57 (M+ + 2, 18.391); Anal. Calcd for
C
23H23N7O6S: C, 52.56; H, 4.41; N, 18.66; found C, 52.88; H, 4.55; N,
18.35.
5.1.12.10. 2-[8-(4-Fluorophenylamino)-1,3-dimethyl-2,6-dioxo-2,3-dihy-
5.1.12.6. 2-(8-[(1,1-Dioxo-1,2-benzothiazol-3-yl)amino]-1,3-dimethyl-
2,6-dioxo-purin-7-yl)-~(N)-(4-acetylphenyl)acetamide (23a).. The titled
compound was synthesized using compound 22e (0.46 g) to give brown
solid, yield 42%, mp , IR (KBr) ѵ (cmꢀ 1): 3441, 3287 (N-Hs), 3086–3001
dro-1H-purin-7(6H)-yl]-N-(4-sulfamoylphenyl)acetamide
(24b).. The
titled compound was synthesized by reaction of compound 22f (0.50 g,
1.06 mmol) with 4-fluoroaniline (1 ml, 10.56 mmol) to give dark brown
solid, yield 42%, mp 265–267 ◦C, IR (KBr) ѵ (cmꢀ 1): 3441, 3395, 3333,
–
–
(C H aromatic), 2959 (C H aliphatic), 1697–1651 (4C = O), 1605
(N H bending), 1597–1497 (C C aromatic), 1366–1161 (SO ), 1H
–
–
–
–
–
3271 (NH2, N H), 3090 (C H aromatic), 2909 (C H aliphatic),
–
NMR (DMSO‑d6) δ: 2.51 (s, 3H, CH3), 3.20 (s, 3H, CH3), 3.46 (2s, 3H,
CH3), 4.97 (s, 2H, CH2), 7.68–7.94 (m, 9H, Ar-H, NH exchanged with
–
–
–
1697–1650 (3C = O), 1601 (N H bending), 1555–1493 (C C aro-
matic), 1327, 1157 (SO2), 1H NMR (DMSO‑d6) δ: 3.24 (s, 3H, CH3), 3.46
19

A.R. Mohamed et al.
Bioorganic Chemistry 107 (2021) 104569
(s, 3H, CH3), 4.98 (s, 2H, CH2), 7.20 (s, 2H, NH2 exchanged with D2O),
7.45–8.02 (m, 8H, Ar-H), 9.97 (s, 1H, NH exchanged with D2O), 12.29
(s, 1H, NH exchanged with D2O), 13C NMR (DMSO‑d6) δ: 28.1 (CH3),
28.7 (CH2), 30.3 (CH3), 102.6, 117.1, 119.6, 124.2, 126.8, 127.3, 127.4,
and then stirred at room temperature for 24 h and at 80 ◦C for 10 h. The
reaction mixture was cooled to room temperature then poured onto ice
water and adjusted at pH 4–5 with hydrochloric acid (1 N). The pro-
duced precipitate was filtered, washed with water, dried and recrystal-
lized from ethanol/water.
–
128.0, 136.6, 143.6, 148.5, 149.1, 151.3 (Ar-C), 151.6 (C O), 153.6
–
+
–
–
–
(C O), 162.0 (Ar-C), 163.0 (C O). MS, m/z (%): 501.07 (M , 27.15),
–
502.57 (M+ + 1, 1.95); Anal. Calcd for C21H20FN7O5S: C, 50.29; H, 4.02;
5.1.12.14. N-(4-Acetylphenyl)-2-[8-(5-cyano-6-oxo-4-phenyl-1,6-dihy-
dropyrimidin-2-ylthio)-1,3-dimethyl-2,6-dioxo-2,3-dihydro-1H-purin-7
(6H)-yl]acetamide (27a).. The titled compound was synthesized using
compound 22e (0.50 g) to give brown solid, yield 46%, mp 267–268 ◦C,
–
N, 19.55; found C, 50.66; H, 4.19; N, 19.89.
5.1.12.11. 2-[8-(2,6-Dioxo-1,2,3,6-tetrahydropyrimidin-4-ylamino)-1,3-
dimethyl-2,6-dioxo-2,3-dihydro-1H-purin-7(6H)-yl]-N-(4-sulfamoyl-
phenyl)acetamide (25).. A mixture of 2-[8-bromo-1,3-dimethyl-2,6-
dioxo-2,3-dihydro-1H-purin-7(6H)-yl]-N-(4-sulfamoylphenylphenyl)
acetamide 22f (0.50 g, 1.06 mmol), 6-aminouracil (0.15 g, 1.16 mmol)
and sodium acetate (0.13 g, 2.07 mmol) in glacial acetic acid (8 ml) was
stirred at 80 ◦C for 10 h. The reaction mixture was cooled to room
temperature then poured onto ice water. The formed precipitate was
filtered, washed with water, dried and recrystallized from ethanol/DMF
to give red solid, yield 41%, mp 272–273 ◦C, IR (KBr) ѵ (cmꢀ 1): 3414,
IR (KBr) ѵ (cmꢀ 1): 3329, 3202 (N-Hs), 3063 (C
H aromatic),
–
–
–
–
2994–2955 (C H aliphatic), 2214 (C N), 1697–1655 (5C = O), 1601
(N H bending), 1555–1493 (C C aromatic), 1H NMR (DMSO‑d6) δ:
–
–
–
2.52 (s, 3H, CH3), 3.19 (s, 3H, CH3), 3.44 (s, 3H, CH3), 5.05 (s, 2H, CH2),
7.53 (s, 2H, Ar-H, NH exchanged with D2O), 7.73–8.03 (m, 8H, Ar-H),
9.73, 11.73 (2 s, 1H, NH/OH exchanged with D2O), 13C, DEPT-135
–
NMR (DMSO‑d ) δ: 26.8 (CH -C O), 27.7 (CH ), 28.7 (CH ), 45.6
–
6
–
3
3
3
–
–
(CH2), 102.6 (C N), 117.4, 118.0, 128.7, 129.1, 130.0, 130.2, 130.7,
–
–
131.5 (Ar-CH), 144.7, 147.5, 148.8, 150.2 (Ar-C), 151.3 (C O), 154.0
–
–
–
–
–
3
–
–
3391, 3333, 3175 (NH2, N H), 3067–3032 (C H aromatic), 2990,
(C O), 166.9 (C O), 169.5 (C O), 196.6 (CH -C O). MS, m/z (%):
– – –
2909 (C H aliphatic), 1712–1667 (5C = O), 1601 (N H bending),
582.28 (M+, 17.45); Anal. Calcd for C28H22N8O5S: C, 57.72; H, 3.81; N,
19.23; found C, 57.81; H, 4.21; N, 19.18.
–
–
1
–
1555–1485 (C C aromatic), 1339, 1161 (SO ), H NMR (DMSO‑d ) δ:
–
2
6
3.25 (s, 3H, CH3), 3.44 (s, 3H, CH3), 4.42 (s, 1H, NH exchanged with
D2O), 4.98 (s, 2H, CH2), 6.22 (s, 1H, NH exchanged with D2O),
7.17–7.20 (br.s, 1H, NH exchanged with D2O), 7.49 (s, 2H, NH2
exchanged with D2O), 7.64–7.85 (m, 3H, 2Ar-H, pyrimidine-H), 8.01
(dd, 2H, J = 4.72, 8.73 Hz, Ar-H), 10.08, 10.11 (2 s, 1H, NH/OH
exchanged with D2O), 13C, DEPT-135 NMR (DMSO‑d6) δ: 28.1 (CH3),
5.1.12.15. 2-[8-(5-Cyano-6-oxo-4-phenyl-1,6-dihydropyrimidin-2-ylthio)-
1,3-dimethyl-2,6-dioxo-2,3-dihydro-1H-purin-7(6H)-yl]-N-(4-sulfamoyl-
phenyl)acetamide (27b).. The titled compound was synthesized using
compound 22f (0.54 g) to give brown solid, yield 62%, mp 251–253 ◦C,
IR (KBr) ѵ (cmꢀ 1): 3476, 3441, 3325 (NH2, N H), 3090 (C H aro-
–
–
–
–
–
30.5 (CH3), 50.2 (CH2), 74.6 (CH = C), 104.0, 117.8 (Ar-C), 124.1, 127.3
–
matic), 2955, 2928 (C H aliphatic), 2226 (C N), 1697–1650 (4C = O),
–
–
–
(Ar-CH), 135.5, 143.2, 149.3, 151.3 (Ar-C), 151.5 (C O), 152.7, 153.6
–
–
1632 (N H bending), 1555–1489 (C C aromatic), 1335, 1157 (SO ),
1H NMR (DMSO‑d6) δ: 3.18 (s, 3H, CH3), 3.24 (s, 3H, CH3), 5.06 (s, 22H,
CH2), 7.22 (s, 2H, NH2 exchanged with D2O), 7.52–7.95 (m, 9H, Ar-H),
9.62 (s, 1H, NH exchanged with D2O), 10.66, 12.34 (2 s, 1H, NH/OH
exchanged with D2O), 13C NMR (DMSO‑d6) δ: 27.8 (CH3), 30.0 (CH2),
–
–
–
–
–
–
–
–
(C O), 155.7 (C O), 164.8 (C O), 170.8 (C O). MS, m/z (%): 516.69
(M+, 37.05), 518.52 (M+ + 1, 24.51), 519.71 (M+ + 2, 13.95), 520.65
(M+ + 3, 11.09); Anal. Calcd for C19H19N9O7S: C, 44.10; H, 3.70; N,
24.36; found C, 43.84; H, 4.12; N, 23.57.
–
–
31.2 (CH3), 97.5 (C N), 117.1, 117.9, 126.2, 127.1, 127.3, 127.7,
–
5.1.12.12. 2-[8-(4-Amino-6-oxo-1,6-dihydropyrimidin-2-ylthio)-1,3-
dimethyl-2,6-dioxo-2,3-dihydro-1H-purin-7(6H)-yl]-N-(4-sulfamoyl-
phenyl)acetamide (26).. A mixture of 2-(8-bromo-1,3-dimethyl-2,6-
dioxo-2,3-dihydro-1H-purin-7(6H)-yl)-N-(4-sulfamoylphenyl)acet-
amide 22f (0.5 g, 1.06 mmol), 6-aminothiouracil (0.15 g, 1.16 mmol)
and DMAP (0.13 g, 1.06 mmol) in DMF (8 ml) was stirred at 70 ◦C for 8
h. The reaction mixture was cooled to room temperature, poured onto
ice water and adjusted at pH 4–5 using hydrochloric acid (1 N). The
formed precipitate was filtered, washed with water and recrystallized
128.5, 128.7, 128.8, 128.9, 129.6, 131.5, 132.7, 141.0 (Ar-C), 151.5
+
–
–
–
–
(C O), 154.3 (C O), 162.9 (2C = O). MS, m/z (%): 619.01 (M ,
12.31); Anal. Calcd for C26H21N9O6S2: C, 50.87; H, 3.63; N, 20.34; found
C, 50.82; H, 3.68; N, 20.26.
5.1.12.16. 7-Hydroxy-1,3-dimethyl-8-phenyl-1H-imidazo[1,2-f]purine-
2,4(3H,8H)-dione (28).. 2-[8-bromo-1,3-dimethyl-2,6-dioxo-2,3-dihy-
dro-1H-purin-7(6H)-yl]-N-phenylacetamide 22a (0.42 g, 1.06 mmol)
was added to sodium hydride 60% (0.12 g, 3.18 mmol) in DMF (6 ml).
The resulted mixture was stirred at gradually increased temperature
70–90 ◦C for 3 h. The reaction mixture was cooled to room temperature
then poured onto ice water and neutralized with acetic acid (1 N). The
produced precipitate was filtered, washed with water, dried and
from ethanol/DMF to give reddish brown solid, yield 56%, mp 283–285
ꢀ 1
◦C, IR (KBr) ѵ (cm ): 3329, 3194, 3140, 3109 (NH2, N H), 3090 (C
H
–
–
H
–
–
aromatic), 2913 (C H aliphatic), 1697–1667 (4C = O), 1605 (N
bending), 1556–1457 (C C aromatic), 1327, 1157 (SO ), 1H NMR
–
–
(DMSO‑d6) δ: 3.24 (s, 3H, CH3), 3.45 (s, 3H, CH3), 4.892 (s, 1H, NH
exchanged with D2O), 4.98 (s, 2H, CH2), 7.20 (s, 2H, NH2 exchanged
with D2O), 7.48 (s, 1H, NH exchanged with D2O), 7.68–7.89 (m, 3H, Ar-
H, pyrimidine-H), 7.97–8.04 (m, 2H, Ar-H), 10.08, 10.11 (2 s, 2H, NH2
exchanged with D2O), 13C NMR (DMSO‑d6) δ: 28.1 (CH3), 30.3 (CH3),
50.2 (CH2), 82.0 (CH = C), 104.0, 117.1, 124.2, 127.3, 128.1, 135.5,
recrystallized from ethanol/DMF to give brownish green solid, yield
ꢀ 1
42%, mp 281–282 ◦C, IR (KBr) ѵ (cm ): 3383 (O H), 3094, 3055
–
–
–
H
(C
H
aromatic), 2995 (C
aliphatic), 1694–1660 (2C = O),
1566–1497 (C C aromatic), 1H NMR (DMSO‑d6) δ: 3.23 (s, 3H, CH3),
–
–
3.44 (s, 3H, CH3), 6.96 (t, 1H, J = 7.32 Hz, Ar-H), 7.30 (t, 2H, J = 7.86
Hz, Ar-H), 7.57 (d, 2H, J = 7.88 Hz, Ar-H), 9.43 (s, 1H, imidazole-H),
11.90 (s, 1H, OH exchanged with D2O), 13C NMR (DMSO‑d6) δ: 28.0
(CH3), 30.2 (CH3), 102.2, 118.0, 121.9, 129.3, 140.5, 148.8, 150.2 (Ar-
–
–
136.6, 143.2, 147.4, 149.1 (Ar-C), 151.3 (C O), 152.7 (Ar-C), 153.6
+
–
–
–
–
–
(C O), 163.8 (C O), 170.8 (C O). MS, m/z (%): 533.26 (M , 24.55);
–
+
–
–
Anal. Calcd. for C19H19N9O6S2: C, 42.77; H, 3.59; N, 23.63; found C,
C), 151.7 (C O), 153.4 (Ar-C). MS, m/z (%): 311.27 (M , 13.53); Anal.
42.46; H, 3.39; N, 23.54.
Calcd for C15H13N5O3: C, 57.87; H, 4.21; N, 22.50; found C, 57.63; H,
4.01; N, 22.91.
5.1.12.13. General procedure for synthesis of 27a,b. Sodium hydride
60% (0.14 g, 3.45 mmol) was added to a mixture of appropriate 2-(8-
bromo-1,3-dimethyl-2,6-dioxo-2,3-dihydro-1H-purin-7(6H)-yl)-N-
substituted phenylacetamide derivative 22e,f (1.15 mmol) and 4-oxo-6-
phenyl-2-thioxo-1,2,3,4-tetrahydropyrimidine-5-carbonitrile 8a (0.29
g, 1.27 mmol) in DMF (6 ml). The mixture was stirred at 0–5 ◦C for 1 h,
5.1.12.17. General procedure for synthesis of 29a-d. 2-(8-Bromo-1,3-
dimethyl-2,6-dioxo-2,3-dihydro-1H-purin-7(6H)-yl)-N-substituted phe-
nylacetamide derivative 22b-e (1.22 mmol) was added to sodium hy-
dride 60% (0.15 g, 3.67 mmol) in DMF (6 ml). The resulted mixture was
stirred at gradually increased temperature 70–90 ◦C for 3 h. 4-Oxo-6-
20

A.R. Mohamed et al.
Bioorganic Chemistry 107 (2021) 104569
–
phenyl-2-thioxo-1,2,3,4-tetrahydropyrimidine-5-carbonitrile 8a (0.31
g, 1.34 mmol) was dissolved in DMF (2 ml) and was added to previous
mixture. The resulted reaction mixture was stirred for 12 h at 90 ◦C, then
cooled to room temperature, poured onto ice water and neutralized with
acetic acid (1 N). The produced precipitate was filtered, washed with
water, dried and recrystallized from ethanol/DMF
(DMSO‑d ) δ: 26.8 (CH -C O), 28.1 (CH ), 30.3 (CH ), 102.7 (Ar-C),
–
6 3 3 3
–
–
116.7 (C N), 128.9, 130.2, 145.0, 148.4, 148.9, 151.6 (Ar-C), 151.7
–
–
–
–
–
–
–
–
(C O), 153.6 (C O), 166.8 (C O), 196.5 (C O). MS, m/z (%): 564.05
–
(M+, 40.32); Anal. Calcd for C28H20N8O4S: C, 59.57; H, 3.57; N, 19.85;
found C, 59.34; H, 3.63; N, 19.92.
5.1.12.22. 2-(8-Bromo-1,3-dimethyl-2,6-dioxo-2,3-dihydro-1H-purin-7
(6H)-yl)-N-(naphthalen-1-yl)acetamide (30).. The titled compound was
synthesized according to general procedure for synthesis of compounds
22a-f using 8-bromotheophylline 21 (1.00 g, 3.86 mmol) and 2-chloro-
5.1.12.18. 2-(8-(4-Fluorophenyl)-1,3-dimethyl-2,4-dioxo-2,3,4,8-tetrahy-
dro-1H-imidazo[1,2-f]purin-7-ylthio)-6-oxo-4-phenyl-1,6-dihydropyr-
imidine-5-carbonitrile (29a).. The titled compound was synthesized
using compound 22b (0.50 g) to give white solid, yield 38%, mp 296 ◦C,
N-(naphthalen-1-yl)acetamide 5 (1.27 g, 5.80 mmol) to give brown
ꢀ 1
IR (KBr) ѵ (cmꢀ 1): 3225 (N H), 3063, 3005 (C H aromatic),
solid, yield 49%, mp 199–202 ◦C, IR (KBr) ѵ (cm ): 3271 (N H),
–
–
–
–
–
–
–
–
2959–2928 (C H aliphatic), 2218 (C N), 1709, 1653 (3C = O), 1601
3055–3013 (C H aromatic), 2947 (C H aliphatic), 1701–1651 (3C =
–
1
(N H bending), 1566–1493 (C C aromatic), 1H NMR (DMSO‑d6) δ:
O), 1559 (N H bending), 1550–1443 (C C aromatic). H NMR (CDCl )
–
–
–
–
–
–
3
3.26 (s, 3H, CH3), 3.47 (s, 3H, CH3), 7.22 (t, 2H, J = 8.80 Hz, Ar-H),
7.51–7.53 (m, 4H, 3Ar-H, imidazole-H), 7.66–7.69 (m, 2H, Ar-H),
8.02 (dd, 2H, J = 2.86, 17.40 Hz, Ar-H), 11.45 (s, 1H, NH exchanged
with D2O), 13C NMR (DMSO‑d6) δ: 28.6 (CH3), 30.2 (CH3), 91.3, 101.3
δ: 3.22 (s, 3H, CH3), 3.36 (s, 2H, CH2), 3.44 (s, 3H, CH3), 7.48–7.56 (m,
3H, Ar-H), 7.65 (d, 1H, J = 8.12 Hz, Ar-H), 7.94 (t, 1H, J = 4.52 Hz, Ar-
H), 8.03 (d, 1H, J = 7.44 Hz, Ar-H), 8.30 (t, 1H, J = 4.22 Hz, Ar-H), 9.85
(s, 1H, NH exchanged with D2O). 13C NMR (DMSO‑d6) δ: 28.0 (CH3),
30.2 (CH3, CH2), 102.1, 116.7, 122.5, 123.5, 126.2, 126.5, 126.6, 128.7,
–
–
(Ar-C), 116.0 (C N), 116.3, 119.5, 120.7, 128.7, 129.1, 130.8, 135.1,
–
–
–
–
–
–
–
137.5, 150.5, 151.0 (Ar-H), 151.5 (C O), 152.9 (Ar-H), 156.5 (C O),
134.4, 135.5, 148.7 (Ar-C), 151.7 (C O), 151.8 (C O), 153.3 (C O).
– –
–
–
+
–
157.1 (Ar-C), 168.6 (C O), 171.5 (Ar-C). MS, m/z (%): 539.66 (M ,
MS, m/z (%): 442.63 (M+, 30.76), 443.13 (M+ + 1, 35.17); Anal. Calcd
for C19H16BrN5O3: C, C, 51.60; H, 3.65; N, 15.84; found C, 51.73; H,
3.71; N, 15.72.
–
34.88), 540.85 (M+ + 1, 26.72); Anal. Calcd for C26H17FN8O3S: C,
57.77; H, 3.17; N, 20.73; found C, 57.86; H, 3.19; N, 21.36.
5.1.12.19. 2-(1,3-Dimethyl-2,4-dioxo-8-p-tolyl-2,3,4,8-tetrahydro-1H-
imidazo[1,2-f]purin-7-ylthio)-6-oxo-4-phenyl-1,6-dihydropyrimidine-5-
carbonitrile (29b).. The titled compound was synthesized using com-
pound 22c (0.50 g) to give white solid, yield 39%, mp > 300 ◦C, IR (KBr)
5.1.12.23. 8-Bromo-7-[2-(indolin-1-yl)-2-oxoethyl]-1,3-dimethyl-1H-pu-
rine-2,6(3H,7H)-dione (31).. The titled compound was synthesized ac-
cording to general procedure for synthesis of compounds 22a-f using 8-
bromotheophylline 21 (1 g, 3.86 mmol) and 2-chloro-1-(indolin-1-yl)
ethanone 6 (1.13 g, 5.80 mmol) to give white solid, yield 88%, mp
ѵ (cmꢀ 1): 3271, 3194 (N H), 3028 (C H aromatic), 2955–2924 (C
–
–
–
H
–
ꢀ 1
aliphatic), 2214 (C N), 1709–1662 (3C = O), 1635 (N H bending),
268–269 ◦C. IR (KBr) ѵ (cm ): 3067 (C H aromatic), 2936 (C
–
–
–
–
H
–
1553–1489 (C C aromatic), 1H NMR (DMSO‑d6) δ: 2.29 (s, 3H, CH3),
aliphatic), 1697–1670 (3C = O), 1597–1485 (C C aromatic). H NMR
1
–
–
–
–
3.26 (s, 3H, CH3), 3.49 (s, 3H, CH3), 7.20 (d, 2H, J = 8.32 Hz, Ar-H),
7.50–7.56 (m, 6H, Ar-H, imidazole-H), 8.02 (dd, 2H, J = 4.40, 7.32
Hz, Ar-H), 11.41 (s, 1H, NH exchanged with D2O), 13C, DEPT-135 NMR
(DMSO‑d6) δ: 20.9 (CH3), 28.5 (CH3), 30.3 (CH3), 91.1, 101.2 (Ar-C),
(DMSO‑d6) δ: 3.20 (s, 3H, CH3), 3.27 (t, 2H, J = 8.28 Hz, CH2), 3.44 (s,
3H, CH3), 4.30 (t, 2H, J = 8.32 Hz, CH2), 5.36 (s, 2H, CH2), 7.05 (t, 1H, J
= 7.32 Hz, Ar-H), 7.16 (t, 1H, J = 7.62 Hz, Ar-H), 7.30 (d, 1H, J = 7.28
Hz, Ar-H), 7.95 (d, 1H, J = 8.00 Hz, Ar-H). 13C NMR (DMSO‑d6) δ: 27.8
(CH3), 28.0 (CH2), 30.0 (CH3), 47.1 (CH2), 49.4 (CH2), 109.0, 116.3,
–
–
119.2 (CH = C), 119.7 (C N), 128.6, 129.1, 130.0, 130.7 (Ar-CH),
–
–
–
–
–
132.3, 136.2, 137.7, 150.7, 151.1 (Ar-C), 151.7 (C O), 152.8 (Ar-C),
124.5, 125.5, 127.6, 130.1, 132.3, 142.7, 147.9 (Ar-C), 151.1 (C O),
+
+
–
–
–
–
–
–
–
156.8 (C O), 168.7 (C O), 171.3 (Ar-C). MS, m/z (%): 536.86 (M ,
154.2 (C O), 163.6 (C O). MS, m/z (%): 418.40 (M , 100), 420.18
–
17.62); Anal. Calcd for C27H20N8O3S: C, 60.44; H, 3.76; N, 20.88; found
(M+ + 2, 20.94); Anal. Calcd for C17H16BrN5O3: C, 48.82; H, 3.86; N,
C, 59.98; H, 3.55; N, 20.97.
16.74; found C, 49.06; H, 3.60; N, 16.69.
5.1.12.20. 2-[8-(2,4-Dichlorophenyl)-1,3-dimethyl-2,4-dioxo-2,3,4,8-tet-
rahydro-1H-imidazo[1,2-f]purin-7-ylthio]-6-oxo-4-phenyl-1,6-dihydropyr-
imidine-5-carbonitrile (29c).. The titled compound was synthesized
using compound 22d (0.56 g) to give greyish white solid, yield 36%, mp
> 300 ◦C, 1H NMR (DMSO‑d6) δ: 3.22 (s, 3H, CH3), 3.42 (s, 3H, CH3),
7.41–7.65 (m, 5H, Ar-H, imidazole-H), 7.86 (d, 1H, J = 6.88 Hz, Ar-H),
8.21 (d, 2H, J = 8.84 Hz, Ar-H), 8.81 (s, 1H, Ar-H), 11.80 (s, 1H, NH
5.1.12.24. 8-[(1,1-Dioxo-1,2-benzothiazol-3-yl)amino]-7-(2-indolin-1-yl-
2-oxo-ethyl)-1,3-dimethyl-purine-2,6-dione (32).. The titled compound
was synthesized according to general procedure for synthesis of com-
pounds 23a,b using 8-bromo-7-(2-(indolin-1-yl)-2-oxoethyl)-1,3-
dimethyl-1H-purine-2,6(3H,7H)-dione 31 (0.44 g, 1.05 mmol) and (1,1-
dioxo-1,2-benzothiazol-3-yl)amine 2 (0.21 g, 1.16 mmol) to give yellow
ꢀ 1
solid, yield 41%, mp > 300 ◦C, IR (KBr) ѵ (cm ): 3244 (N H),
–
–
exchanged with D2O), 13C NMR (DMSO‑d6) δ: 28.0 (CH3), 30.3 (CH3),
3067–3028 (C H aromatic), 2943 (C H aliphatic), 1705–1660 (C O),
–
–
–
–
–
–
–
1628 (N H bending), 1551–1485 (C C aromatic), 1331, 1161 (SO ).
–
2
92.5, 98.8, 102.3 (Ar-C), 115.8 (C N), 122.0, 123.9, 126.9, 128.5,
–
128.9, 129.1, 129.3, 135.7, 141.8, 147.3, 148.3, 149.5 (Ar-C), 151.6
1H NMR (DMSO‑d6) δ: 3.21 (br.s, 5H, CH3, CH2), 3.51 (s, 3H, CH3), 4.22
(t, 2H, J = 7.96 Hz, CH2), 5.34 (s, 2H, CH2), 7.01 (t, 1H, J = 7.20 Hz, Ar-
H), 7.13 (t, 1H, J = 7.46 Hz, Ar-H), 7.26 (d, 1H, J = 7.04 Hz, Ar-H),
7.76–7.83 (m, 2H, Ar-H), 7.94 (d, 1H, J = 7.92 Hz, Ar-H), 8.00 (d,
1H, J = 7.04 Hz, Ar-H), 8.20 (d, 1H, J = 6.76 Hz, Ar-H), 13C, DEPT-135
NMR (DMSO‑d6) δ: 27.8 (CH3), 28.0 (CH2), 30.1 (CH3), 47.0 (CH2), 47.1
(CH2), 104.7 (Ar-C), 116.3, 120.9, 124.1, 125.4, 127.5, 132.1, 132.9,
+
–
–
–
–
(C O), 153.5 (C O), 156.0 (C O). MS, m/z (%): 591.04 (M , 31.86);
–
–
Anal. Calcd for C26H16Cl2N8O3S: C, 52.80; H, 2.73; N, 18.95; found C,
52.67; H, 3.22; N, 18.93.
5.1.12.21. 2-(8-(4-Acetylphenyl)-1,3-dimethyl-2,4-dioxo-2,3,4,8-tetrahy-
dro-1H-imidazo[1,2-f]purin-7-ylthio)-6-oxo-4-phenyl-1,6-dihydropyr-
imidine-5-carbonitrile (29d).. The titled compound was synthesized
–
–
–
133.0 (Ar-CH), 142.0, 143.1, 147.4 (Ar-C), 151.5 (C O), 154.3 (C O),
–
+
–
–
158.3 (Ar-C), 165.2 (C O). MS, m/z (%): 519.85 (M , 12); Anal. Calcd
using compound 22e (0.53 g) to give red solid, yield 42%, mp 297–298
ꢀ 1
◦C, IR (KBr) ѵ (cm ): 3321 (N H), 3063 (C H aromatic), 2951 (C
–
–
–
H
for C24H21N7O5S: C, 55.48; H, 4.07; N, 18.87; found C, 55.82; H, 4.53; N,
–
–
–
18.59.
aliphatic), 2214 (C N), 1694–1650 (3C = O), 1632 (N H bending),
–
1555–1504 (C C aromatic), 1H NMR (DMSO‑d6) δ: 2.11 (s, 3H, CH3),
–
–
3.24 (s, 3H, CH3), 3.46 (s, 3H, CH3), 7.54–7.58 (m, 4H, Ar-H, imidazole-
H), 7.69 (d, 2H, J = 8.20 Hz, Ar-H), 7.91 (d, 4H, J = 8.28 Hz, Ar-H),
10.00, 12.31 (2 s, 1H, NH/OH exchanged with D2O), 13C NMR
5.1.12.25. 8-(4-Amino-6-oxo-1,6-dihydropyrimidin-2-ylthio)-7-[2-(indo-
lin-1-yl)-2-oxoethyl]-1,3-dimethyl-1H-purine-2,6(3H,7H)-dione
(33)..
The titled compound was synthesized according to the adopted
21

A.R. Mohamed et al.
Bioorganic Chemistry 107 (2021) 104569
procedure for synthesis of compound 26 using 8-bromo-7-(2-(indolin-1-
yl)-2-oxoethyl)-1,3-dimethyl-1H-purine-2,6(3H,7H)-dione 31 (0.5 g,
1.2 mmol), 6-aminothiouracil (0.19 g, 1.32 mmol), and DMAP (0.15 g,
1.2 mmol) to give off white solid, yield 59%, mp 268–270 ◦C, IR (KBr) ѵ
solution without phenol red and serum. Reconstituted MTT was added in
an amount equal to 10% of the culture medium volume. Cultures were
incubated for 2–4 h depending on cell type and maximum cell density.
MTT Solubilization Solution [M ꢀ 8910] was added to cultures to
dissolve the resulting formazan crystals and dissolution was enhanced
by mixing in gyratory shaker. Moreover, trituration was helpful for
complete dissolution. ROBONIK P2000 was used to measure the color
intensity at wavelength of 450 nM. To draw the survival curve for WI-38
cell line after specified time, surviving fraction was plotted versus the
(cmꢀ 1): 3391, 3364, 3194 (NH2, N H), 3067–3028 (C H aromatic),
–
–
–
–
H
2951, 2909 (C H aliphatic), 1701–1657 (4C = O), 1612 (N
1
–
–
bending), 1539–1485 (C C aromatic), H NMR (DMSO‑d ) δ: 3.14–3.26
6
(m, 5H, CH2, CH3), 3.46 (s, 3H, CH3), 4.26 (t, 2H, J = 8.22 Hz, CH2),
5.45 (s, 2H, CH2), 7.03–7.30 (m, 5H, 2Ar-H, pyrimidine-H, NH2
exchanged with D2O), 7.72 (d, 1H, J = 6.36 Hz, Ar-H), 7.92 (d, 1H, J =
8.04 Hz, Ar-H), 12.02 (s, 1H, NH exchanged with D2O), 13C NMR
(DMSO‑d6) δ: 27.6 (CH3), 28.1 (2CH2), 30.3 (CH3), 51.0 (CH2), 90.0 (CH
= C), 102.6, 107.4, 117.1, 127.4, 136.6, 143.6, 148.4, 149.1 (Ar-C),
drug concentration. The half maximal inhibitory concentration (IC50
)
was calculated to the test compounds 17, 22c and the reference drug
sorafenib. The surviving fractions were expressed as means ± S.E.
–
–
–
–
–
151.6 (C O), 153.6 (C O), 162.3 (Ar-C), 164.1 (C O), 166.1 (C O).
–
–
–
5.3. Multi-kinase inhibitory activity screening
MS, m/z (%): 480.65 (M+, 32.41); Anal. Calcd for C21H20N8O4S: C,
52.49; H, 4.20; N, 23.32; found C, 52.33; H, 4.06; N, 22.97.
5.3.1. PI3Kα inhibitory activity screening
Assay was carried out using PI3K kit [88], which is used for deter-
mination of the degree of (general and isoform-specific) class I PI3 Ki-
5.2. In vitro anticancer screening
nase inhibition. Screening of the selected compounds against PI3Kα was
achieved in accordance to instruction manual for PI3 kinase activity/
inhibitor assay kit, PI3K, p110 (Part No. CS203304).
5.2.1. Anti-proliferative assay
α
The antitumor assay of the targeted compounds was performed at the
Drug Evaluation Branch, NCI, Bethesda (Maryland, USA), using sulfo-
rhodamine B (SRB) assay to assess the cell growth and viability [72]. In
accordance with Drug Evaluation Branch protocol, the levels of cellular
protein were determined after 48 h of drug exposure by using the seven
absorbance measurements [time zero (Tz), control growth (C), and test
growth in the presence of drug at the five concentration levels (Ti)], the
percentage growth was calculated at each of the drug concentration
levels. Percentage growth inhibition was calculated as:
5.3.2. B-RafV600E, B-RafWT, EGFR and VEGFR-2 inhibitory assays
These assays were carried out using B-RafV600E, B-RafWT [89,90]
EGFR [91], and VEGFR-2 [92], (Bioscience) kinase assay kits and
employing Kinase-Glo Plus luminescence (Promega) kit as detection
reagent in accordance to Data Sheet B-Raf(V600E) Kinase Assay Kit
(Catalog # 48688), bpsbioscience.com . A stock solution of the tested
compounds and sorafenib in DMSO e.g. 10% was initially prepared.
Serial dilutions were carried out and 5 ml of the dilution was added to a
50 ml reaction mixture. After the enzymatic reaction, 50 ml of Kinase-
Glo Plus Luminescence kinase assay solution was added to each reac-
tion and the plate was incubated for 15 min at room temperature.
Luminescence signal was measured using Promega multimode micro-
plate reader. The difference between luminescence intensities in the
absence of Kinase (Lut) and in the presence of Kinase (Luc) was defined
as 100% activity (Lut e Luc). Using luminescence signal (Lu) in the
presence of the compound, % activity was calculated as: % activity =
[(Lut - Lu) / (Lut - Luc)] X 100%, where Lu = the luminescence intensity
in the presence of the compound. The luminescence data were analyzed
using Graphpad Prism and IC50 values were calculated as the average
value from two independent experiments.
[(Ti – Tz) / (C – Tz)] X 100 for concentrations for which Ti ≥ Tz
[(Ti – Tz) / Tz] X 100 for concentrations for which Ti < Tz
Three dose response parameters were calculated for each tested
compound (17 and 22c): Growth inhibition of 50% (GI50) was calcu-
lated when [(Ti – Tz) / (C – Tz)] X 100 = 50. The compound concen-
tration resulting in total growth inhibition (TGI) was calculated when Ti
= Tz. The LC50 indicating a net loss of cells following treatment was
calculated when [(Ti – Tz) / Tz] X 100 = -50.
5.2.2. In vitro cytotoxicity toward human normal WI-38 cell line
Cell culture protocol of normal human diploid fibroblasts (WI-38)
which was obtained from American Type Culture Collection, cells were
cultured using Dulbecco’s modified Eagle medium (DMEM) (Invitrogen/
Life Technologies) supplemented with 10% fetal bovine serum (FBS)
(Hyclone), 10 mg/ml of insulin (Sigma-Aldrich), and 1% penicillin
streptomycin. All of the other chemicals and reagents were purchased
from Sigma-Aldrich, or Invitrogen. The culture medium was transferred
to a centrifuge tube. In order to remove any traces of serum, the cell
layer was washed with 0.25% (w/v) Trypsin 0.53 mM EDTA solution.
Trypsin EDTA solution (2.0–3.0 ml) was added and cells were examined
under an inverted microscope until cell layer was dispersed (5–15 min).
Complete growth medium (6.0–8.0 ml) was added and cells were aspi-
rated by gentle pipetting. The cell suspension in addition to the medium
and cells from previous step was centrifuged (5–10 min) at 125 X g. The
supernatant was thrown out then fresh growth medium was added to the
cell pellet and the cell suspension was transferred to new culture vessels.
To induce hypoxia, 25 mM stock solution was prepared in sterile water
(prepared immediately before use). Culture was incubated for 24 h at 37
◦C. Cells were treated with serial concentrations of the test compounds
17, 22c and sorafenib then incubated for 48 h at 37 ◦C, then, proceeded
for the MTT assay.
5.4. Modeling studies
All molecular docking studies were performed using Molecular
Operating Environment (MOE 2010.10) software package. The X-ray
crystal structures of the target kinases were obtained from RSCB protein
data bank [93]. Namely; the molecular docking study of the compiled
library (selection stage) in the binding sites of PI3Kγ (PDB ID: 4 GB9)
and B-RafWT (PDB ID: 1UWH), and the newly synthesized compounds in
the binding sites of PI3Kα (PDB ID: 4JPS), B-RafV600E (PDB ID: 3IDP),
EGFR (PDB ID: 1XKK) and VEGFR-2 (PDB ID: 1YWN).
For the preparation of the crystal structures for the intended mo-
lecular docking studies, water molecules and ligands that are not
involved in binding were removed from each protein. In B-RafWT, chain
B was removed. All proteins were prepared for the docking study using
Protonate 3D protocol with default options. For docking protocol vali-
dation, the prepared PDB crystal structures were validated by self-
docking of each co-crystallized ligand, then evaluation of the repro-
duced binding pattern. All molecular docking protocols proved suit-
ability in the validation step with produced RMSD values of 1.112 and
0.754 Å in PI3Kγ and B-RafWT, respectively, in the selection stage and
MTT cytotoxic assay protocol; cells were plated in a volume of 100
ml complete growth medium (cells density 1.2–1.8 X 10,000 cells/well)
and 100 ml of the tested compound per well in a 96-well plate for 24 h
before the MTT assay. Cultures from incubator were removed into
laminar flow hood or other sterile work area. Each vial of MTT [M ꢀ
5655] to be used was reconstituted with 3 ml of medium or balanced salt
1.473, 0.310, 1.631 and 0.826 Å in PI3Kα, B-RafV600E, EGFR and VEGFR-
2, respectively. (For further details see Supplementary Materials)
Chemical structures of the compiled library compounds were
22

A.R. Mohamed et al.
Bioorganic Chemistry 107 (2021) 104569
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Declaration of Competing Interest
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Acknowledgement
Our sincere thanks to the National Cancer Institute (NCI), Bethesda
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