N-Substituted aminoquinoline-pyrimidine hybrids: Synthesis, in vitro antimalarial activity evaluation and docking studies

Article abstract of DOI:10.1016/j.ejmech.2018.11.021

A series of novel molecular hybrids based on 4-aminoquinoline-pyrimidine were synthesized and examined for their antimalarial activity. Most of the compounds were found to have potent in vitro antimalarial activity against both CQ-sensitive D6 and CQ-resistant W2 strains of P. falciparum. The active compounds have no considerable cytotoxicity against the mammalian VERO cell lines. Twenty three compounds displayed better antimalarial activity against CQ-resistant strain W2 with IC₅₀ values in the range 0.0189–0.945 μM, when compared with standard drug chloroquine. The best active compound 7d was studied for heme binding so as to find the primary mode of action of these hybrid molecules. Compound 7d was found to form a stable 1:1 complex with hematin as determined by its Job's plot which suggests that heme may be a probable target of these molecules. Docking studies performed with Pf-DHFR exhibited good binding interactions in the active site. The pharmacokinetic properties of some active compounds were also analysed using ADMET prediction.

Full text of DOI:10.1016/j.ejmech.2018.11.021

Accepted Manuscript
N-Substituted aminoquinoline-pyrimidine hybrids: Synthesis, in vitro antimalarial
activity evaluation and docking studies
Shiv S. Maurya, Aparna Bahuguna, Shabana I. Khan, Deepak Kumar, Rohit Kholiya,
Diwan S. Rawat
PII:
S0223-5234(18)30979-6
DOI:
https://doi.org/10.1016/j.ejmech.2018.11.021
EJMECH 10878
Reference:
To appear in: European Journal of Medicinal Chemistry
Received Date: 4 October 2018
Revised Date: 6 November 2018
Accepted Date: 8 November 2018
Please cite this article as: S.S. Maurya, A. Bahuguna, S.I. Khan, D. Kumar, R. Kholiya, D.S. Rawat,
N-Substituted aminoquinoline-pyrimidine hybrids: Synthesis, in vitro antimalarial activity evaluation
and docking studies, European Journal of Medicinal Chemistry (2018), doi: https://doi.org/10.1016/
j.ejmech.2018.11.021.
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ACCEPTED MANUSCRIPT
N-Substituted aminoquinoline-pyrimidine hybrids: Synthesis, in vitro
antimalarial activity evaluation and docking studies
Shiv S. Maurya,1 Shabana I. Khan,2 Aparna Bahuguna,1 Deepak Kumar,1 Rohit
Kholiya,1 Diwan S. Rawat1*
1Department of Chemistry, University of Delhi, Delhi-110007, India
2National Centre for Natural Products Research, University of Mississippi, MS-38677, USA
Corresponding author: dsrawat@chemistry.du.ac.in
Fax: 91-11-27667501; Tel: 91-11-27662683
Graphical Abstract

ACCEPTED MANUSCRIPT
N-Substituted aminoquinoline-pyrimidine hybrids: Synthesis, in vitro
antimalarial activity evaluation and docking studies#
Shiv S. Maurya,1+ Aparna Bahuguna,1+ Shabana I. Khan,2 Deepak Kumar,1 Rohit
Kholiya,1 Diwan S. Rawat1*
1Department of Chemistry, University of Delhi, Delhi-110007, India
2National Centre for Natural Products Research, University of Mississippi, MS-38677, USA
+Authors contributed equally to this study
#Dedicated to Dr PMS Chauhan, on the occasion of his 60th Birthday
Abstract: A series of novel molecular hybrids based on 4-aminoquinoline-pyrimidine were
synthesized and examined for their antimalarial activity. Most of the compounds were found
to have potent in vitro antimalarial activity against both CQ-sensitive D6 and CQ-resistant
W2 strains of P. falciparum. The active compounds have no considerable cytotoxicity against
the mammalian VERO cell lines. Twenty three compounds displayed better antimalarial
activity against CQ-resistant strain W2 with IC50 values in the range 0.0189-0.945 µM, when
compared with standard drug chloroquine. The best active compound 7d was studied for
heme binding so as to find the primary mode of action of these hybrid molecules. Compound
7d was found to form a stable 1:1 complex with hematin as determined by its Job’s plot
which suggests that heme may be a probable target of these molecules. Docking studies
performed with Pf-DHFR exhibited good binding interactions in the active site. The
pharmacokinetic properties of some active compounds were also analysed using ADMET
prediction.
Key Words:Aminoquinoline, pyrimidine, hybrid drugs, antimalarial Actvity, heme, docking
study, ADMET properties.
*Corresponding author:
E. Mail: dsrawat@chemistry.du.ac.in
Phone No: 91-11-27662683
Fax No: 91-11-27667501

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1. Introduction
Malaria still remains a global public health concern though there is a significant decrease
in the mortality rate during the past few years. The recent WHO report says that malaria
accounted 216 million new clinical cases and an estimated 4.5 lakh deaths worldwide in 2016
with children of age less than 5 years and the pregnant women amongst the most affected
groups [1,2].Amongst the five plasmodial species that causes malaria in human beings, P.
falciparum is the most common and virulent, responsible for more than 90% cases of malarial
deaths [1]. The conventional aminoquinoline based antimalarial drugs such as chloroquine
(CQ), amodiaquine, mefloquine and primaquine have long been used for treating the malaria
however, the efficacy of many of these quinoline based drugs has been compromised to some
extent by the spread of CQ-resistant strains of malarial parasites [3,4]. At present, the most
effective treatment for the uncomplicated malaria due to P. falciparum is the artemisinin
based combination therapy (ACT) [5]. The major advantages of ACTs are their high potency,
fast action and the less chances of development of resistance.In ACT, the fast acting
artemisinin based drugs are combined with a companion drug including amodiaquine,
mefloquine, piperaquine, lumefantrine, sulfadoxine/pyrimethamine and chlorproguanil/dapsone
[6]. Recently few cases of artemisinin resistance have been reported in five countries namely
Myanmar, Cambodia, Thailand, Vietnam and the Lao People's Democratic Republic [7,8].
Therefore, it is a dire need to develop novel antimalarial agents which are safer, affordable,
fast acting and effective against the resistant strains of P. falciparum.
In order to address the problems of drug-resistance, several strategies such as combination
therapy, hybrid drug concept, development of analogues of already existing drugs, and
incorporation of drug resistance reversers etc have been employed [9]. Of all these, the hybrid
drugs concept has attracted much attention due to its many advantages over the others [10-
12]. Hybrid drugs can exert dual mode of action and may solve the problems related to drug
resistance, drug-drug interaction, drug delivery, poor solubility etc [13]. In molecular
hybridisation two or more active pharmacophores are linked covalently resulting into one
molecule which may act on multiple targets. Further in hybrid concept more structurally
diversified compounds can be synthesized which may increase the chance of development of
a new drug. Employing the concept of hybrid drugs, our research group has developed a
variety of hybrid molecules which have shown potent antitubercular, antiamoebic, anticancer
and antimalarial activities [14-23].

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In continuation of our work on antimalarial agents, we thought to functionalize the -NH
group of our previously reported aminoquinoline-pyrimidine hybrids with the aim to study
the effect of substitution at the -NH of ethyl or propyl linker chain on the antimalarial
activity. We introduced 2-formyl thiophene and 2-formyl pyridine ring at the -NH group
through a simple reductive amination reaction (Fig. 1). These modifications may help in the
accumulation of the compounds in acidic food vacuole of the malarial parasite and also
increase the lipophilicity of the molecule which further may enhance the activity [24].Also,
thiophene and pyridine rings have been found to be the part of many antimalarial compounds
[25-28].The present article discuss the synthesis and antimalarial activity of 4-
aminoquinoline-pyrimidine based molecular hybrids against D6, CQ-sensitive and W2, CQ-
resistant strains of P. falciparum. All the compounds were also screened for their in vitro
cytotoxicity against the mammalian Vero cell lines. The molecular docking studies with Pf-
DHFR-TS and heme (monomeric and µ-oxodimeric) binding studies were also performed to
determine the probable mode of action of these hybrids. To assess the pharmacokinetic
behaviour, the ADME properties of the best active compounds were calculated.
<Insert Fig. 1 here>
2. Chemistry
The schemes 1 and 2 depict the synthesis of 4-aminoquinoline-pyrimidine hybrids. Firstly,
4,7-dichloroquinoline (1) was treated with the excess of 1,2-diaminoethane or 1,3-
diaminopropane at 120 oC to yield compounds 2a or 2b, respectively [29].The intermediates 2a
or 2b were then treated with 2-formylpyridine to give Schiff bases 3a or 3b which on reduction
with NaBH4 gave compounds 4a or 4b (Scheme 1). Compounds 4a or 4b were then treated
with 2,4-dichloro-6-methylpyrimidine in the presence of Et3N using THF as solvent at 60 oC to
give two set of regio-isomers (5a, 6a and 5b, 6b). The compounds 5a and 5b were obtained as
major products while 6a and 6b were obtained as minor products. All the four compounds (5a,
5b,6a and 6b) were finally reacted with various secondary amines at 120 °C to form the desired
products (7a-j and 8a-i) in 55-86% yield. A similar type of compounds, bearing thiophene
moiety in place of pyridine ring, were also synthesized using the similar methodology (scheme
2). All the final compounds (7a-j, 8a-i, 13a-e and 14a-e) were purified using column
chromatography and characterized through various spectroscopic techniques.
<Insert Scheme 1 here>

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<Insert Scheme 2 here>
3. Results and Discussion
The antimalarial activity results shown in table 1 indicated that all the compounds
displayed potent antimalarial activity with IC50 values in the range 0.027-.661 µM against
CQ-sensitive (D6) strain and IC50 values in the range 0.0189-1.443 µM against CQ-resistant
(W2) strain of P. falciparum. Compound 7d was the most active compound against D6 strain
with IC50 value 0.027 µM and selectivity index >351. Out of all compounds, 23 compounds
(5b, 7b, 7d, 7e, 7g, 7i, 7j, 8c-e, 8g-i, 10a, 13a-e, 14a, 14b, 14d and 14e) showed better
activity than CQ against W2 strain. Among all the compounds, 14e was found to be the best
active compound (IC50 = 0.0189 µM) against W2 strain and exhibited 22-times better activity
than CQ (IC50 = 0.4215 µM). When the activity of these compounds was compared with
artemisinin (ART), two compounds 14d and 14e showed comparable activity to ART against
the W2 strain. The regio-isomeric intermediates, 5a and 6a containing two carbon chain
linker showed better activity against the sensitive strain (IC50= 0.233 µM, 0.369 µM
respectively) as compared to activity against resistant strain. In case of regio-isomeric
intermediates 5b and 6b, containing three carbons linker exhibited better antimalarial activity
against resistant strains as compared to the activity against the sensitive strain, whereas regio-
isomers 11a and 12a showed better activity against the sensitive strain as compared to the
resistant strain. Interestingly, when the chlorine atoms of the regio-isomers 5a and 6a were
replaced by various cyclic amines, the activity of all the resulting aminoquinoline-thiophene-
pyrimidine (7a-7e and 8a-8e) hybrids against both sensitive and resistant strains got
improved with the exception of two compounds, 7e and 8a which showed little decline in the
activity against the resistant strain. Similarly compounds 7f-7j and 8f-8i showed improved
activity as compared to their corresponding intermediate regio-isomers 5b and 6b against
both the strains with the exception of three compounds 7f, 7h and 8f which displayed weaker
activity against CQ-resistant strain than their corresponding intermediates. Compounds 13a-
13e and 14a-14e containing three carbons chain linker also showed enhanced activity against
both the strains, D6 and W2, when compared the activity of their corresponding intermediate
regio-isomers 11a and 12a.
Compounds having 4-methyl piperazine (7d, 8d) and 4-ethyl piperazine (7e, 8e) were
found to show better activity than the compounds having piperidine (7a, 8a), pyrrolidine (7b,
8b) and morpholine (7c, 8c) moieties. No obvious trend of antimalarial activity was found on

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comparison of the activity of regio-isomeric intermediates (5a, 5b, 11a and 6a, 6b, 12a) and
their derivatives (7a-7j, 8a-8i and 13a-13e, 14a-14e), differing in the point of attachment
with pyrimidine ring. Compounds with two carbon chain linker (7a-7e and 8a-8d) were
found to be more active than the compounds with three carbon chain linker (7f-7j and 8f-8i)
against CQ-sensitive strains, whereas no particular trend was observed when compared
activity against the resistant strain. Cytotoxicity of the compounds was also analysed using
mammalian Vero cell lines (Table 1). All the compounds except four compounds 6a, 13a,
13c and 14a were found to be non-cytotoxic upto 10 µM, that is too high as compared to their
corresponding IC50 values.
<Insert Table 1 here>
In order to determine the possible mode of action of the synthesized compounds, heme
binding studies was performed with the most active compound 7d. The binding stoichiometry
was also determined using the literature reported method [30]. A band at 402 nm observed for
a solution of hematin in 40% DMSO in water at pH 7.4 (20 mM HEPES buffer) and pH 5.6
(20 mM MES buffer) indicates the presence of monomeric heme at both the pH values.
Compound 7d when titrated with the monomeric heme solution at physiological pH (HEPES
buffer, pH 7.4) and pH of parasite’s food vacuole (MES buffer, pH 5.6) displayed a
significant decrease in the absorbance of the band at 402 nm. (Fig. 2 and Fig. 3). Thus,
indicating the interaction of compound 7d with hematin. In the Job’s plot, maxima at 0.5
mole fraction indicates 1:1 stoichiometry for the binding of monomeric heme with compound
7d at pH 7.4 (Fig. 2) and pH 5.6 (Fig. 3). As chloroquine also binds to µ-oxodimericheme,
therefore we studied the binding of compound 7d with µ-oxo dimer of heme at pH 5.8. A
peak at 362 nm of heme in aqueous NaOH indicates the presence of dimeric structure of
heme as reported in literature. The intensity of absorbance at 362 nm decreases on titrating a
solution of µ-oxo dimer heme at pH 5.8 (20 mM phosphate buffer) with compound 7d (Fig.
4) indicating interaction between compound 7d and µ-oxodimericheme. The Job's plot
showed that the binding of compound 7d with µ-oxodimericheme is in 1:1 stoichiometry
(Fig. 4).
<Insert Fig. 2 here>
<Insert Fig. 3 here>
<Insert Fig. 4 here>

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To explore the pharmacokinetics of the compounds under study, ADME predictions were
done for the best active compounds using Qikprop v3.5 (Schrödinger, Inc., New York, NY,
2012) [31]. All the compounds prepared by LigPrep were used for the calculation of
pharmacokinetic properties by QikProp. Table 2 shows the results of docking studies. The
results indicate that the compounds with good antimalarial activity exhibited significant
binding affinities as is evident from their Glide energies obtained on docking with the wild
(Glide energy range -60.28 kcal mol-1 to -51.67 kcal mol-1) as well as quadruple mutant
(Glide energy range -59.11 kcal mol-1 to -52.74 kcal mol-1). The Glide Scores (GScore) have
also been shown in Table 2.
<Insert Table 2 here>
Fig. 5 and 6 show three dimensional binding pose compounds 7g, 7j and 8e with wild and
mutant Pf-DHFR-TS. All the three selected compounds (7g, 7j and 8e) showed hydrogen
bonding pattern along with cation-pi interactions with the amino acid residues at the binding
site. The protonated nitrogen of pyrimidine moiety of compound 7j, displayed cation-pi
interactions with Phe58 residue of both the mutant as well as the wild Pf-DHFR-TS and an
additional hydrogen bond interaction with Ile164 residue of wild type Pf-DHFR-TS. In both
the mutant and wild type Pf-DHFR-TS Asp54 formed a salt bridge with the nitrogen of
piperazine ring of 7j whereas Ser111 of the same compound formed a hydrogen bond with
the protonablequinoline ring nitrogen atom of aminoquinoline moiety. An additional cation-
pi interaction was also observed with protonable nitrogen of pyridine moiety of 39L and
Phe116 residue of the wild type Pf-DHFR-TS. Compound 7g showed slightly altered binding
poses in the different parasitic DHFRs, and thus the interactions with both the DHFRs were
different. The active site residues, Phe116 and Arg122 of mutant type Pf-DHFR-TS showed
cation-pi interactions with the aminoquinoline moiety and Ser111 formed hydrogen bond
with pyrimidine ring of compound 7g. The same pyrimidine moiety formed hydrogen bond
and a cation-pi interaction with Ile164 and Phe58 of the wild type Pf-DHFR-TS respectively
whereas the pyridine moiety formed cation-pi interaction with Phe116. Although the binding
poses adopted by compound 8e were dissimilar for different DHFRs, the inhibitor showed
similar interactions with both DHFRs.
<Insert Fig. 5 here>
<Insert Fig. 6 here>

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In silico assessment of pharmacokinetics and ADME predictions of the best active
compounds were carried out using Qikprop v3.5 [32].The most important of these properties
and their permissible ranges are given in Table 3 and 4. The active compounds were tested
for the Lipinski’s rule of five (Ro5), which is a set of in silico guidelines applied to predict
likelihood of high oral absorption [33]. An orally active compound must have less than 2
violations of Lipinski's Rule [32]. All the tested compounds passed the rule of five indicating
their potential to become orally active drugs. The molecular weight of some compounds was
higher than 500Da, thus violating one of the Ro5. In medicinalchemistry, an attempt to
increase the selectivity and potency of hit compounds results in increase in molecular weight
but several orally bio available drugs exist far beyond Ro5.
<Insert Table 3 here>
<Insert Table 4 here>
Results of in silico prediction of Percent Human Oral Absorption were within range (Table
4). Properties like size, polarity, lipophilicity and conformational dynamics affect the oral
bioavailability which can be assessed by additional in silico properties, the number of
rotatable bonds (<15) and polar surface area (70Å2–200 Å2) [34]. The test compounds
displayed rotatable bonds less than 15 and the polar surface area in the permissible range (7-
200 Å) (Table 4). The Caco-2 cells permeability (QPPCaco) which is a measure of intestinal
drug absorption was found to be >500 for all the tested compounds. Trans cellular absorption
occurs through passive diffusion through a cell membrane. This process is studied in vitro
using human colorectal carcinoma (Caco-2) cells model. Prediction of human serum albumin
binding (QPlogKhsa), brain/blood partition coefficient (QPlogBB) and the blood-brain
barrier mimic MDCK cell permeability (QPPMDCK) for all the active compounds were in
the permissible range.
4. Conclusions
In summary, we have reported the synthesis and antimalarial activity evaluation of 4-
aminoquinoline pyrimidine based molecular hybrids. Most of the compounds displayed good
antimalarial activity against CQ-sensitive D6 strain and CQ-resistant W2 strain of malarial
parasite in the µM range with high selectivity index. Also, these hybrids exhibited no
cytotoxicity towards the mammalian VERO cell lines up to 10 µM, the highest concentration
tested. Among all the compounds, 7d was found to be the most active compound against D6

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strain (IC50 = 0.027 µM) and compound 14e was found to be the most active compound
against W2 strain (IC50 = 0.0189 µM). The primary mode of action of these hybrids was
found to be through binding with heme as described by their heme binding studies. The
molecular docking studies showed excellent binding interactions with Pf-DHFR. The
Compounds showed good pharmacokinetic behaviour as predicted from their ADMET
parameters.
5. Experimental Protocols
All the chemicals were purchased from Sigma-Aldrich and were used without further
purification. Progress of the reactions was monitored by thin layer chromatography (Merck
Kiesel 60 F254, 0.2 mm thickness) and the compounds were purified by silica gel column
chromatography. IR spectra were recorded on Perkin-elmerFT-IR spectrophotometer using
1
13
KBr pellets and the values were expressed in cm-1. H NMR (400 MHz) and C NMR (100
MHz) spectra were recorded on Jeol ECX spectrospin instrument using CDCl3 or DMSO-d6
as solvent with TMS as internal reference. Thechemical shift values were expressed on d
scale and the coupling constant (J) in Hz. Melting points were recorded on EZ-Melt
automated melting point apparatus, Stanford Research Systems and are uncorrected. Mass
data were recorded in Jeol-Accu TOF JMS-T100LC and micromass LCT mass
spectrometer/Data system.
5.1.
General procedure for the preparation of intermediates 2a-2b
A mixture of 4,7-dichloroquinoline (1, 10.0 g, 50.49 mmol) and 1,2-diaminoethane (10.2 mL,
151.47 mmol) was heated at 110-120 oC in neat condition for 5h (Scheme 1). The progress of
the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was
cooled to room temperature and ice-cold water was added. The solid product thus obtained was
filtered and washed with excess water. Similarly, intermediate 2b was prepared by using 1,3-
diaminopropane. The crude products thus obtained were crystallized by using ethanol and all
the intermediates were characterized and matched with previously reported data [29].
5.2.
General procedure for the preparation of intermediates 3a-3b
Intermediate 2a (5.0 g, 22.55 mmol) was dissolved in ethanol at room temperature, then
pyridine-2-carboxaldehyde (2.4 g, 22.55 mmol) was added to it and the reaction mixture was
stirred at room temperature for 12-16 h. After completion of the reaction, as monitored by TLC,

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the reaction mixture was filtered and the solid product was used for the next step, without
further purification. Similarly, intermediate 3b was prepared and used for next step.
5.3.
General procedure for the preparation of intermediates 4a-4b
Intermediate 3a (7.0 g, 22.57 mmol) was dissolved in methanol and cooled to 0 oC then NaBH4
(2.56 g, 67.72 mmol) was added to it in fractions and reaction mixture was allowed to stir at
room temperature for 5-6 h. After completion of the reaction as monitored by TLC, the excess
methanol was evaporated using rotatory evaporator and ice-cold water was added. The solid
product thus obtained was filtered and washed with excess of water. Similarly, intermediate 4b
was obtained.
5.4.
General procedure for the preparation of compounds 5a-5b and 6a-6b
Intermediate (4a) (6.0 g, 19.18 mmol) was dissolved in THF (70 mL) and triethylamine (8.02
mL, 57.54 mmol) was added followed by the addition of 2, 4-dichloro-6-methyl-pyrimidine
o
(3.13 g, 19.18 mmol). The reaction mixture was allowed to stir at 60 C for 12 h. The
progress of reaction was monitored by TLC. On the completion of reaction, the excess THF
was evaporated and the residue was diluted with water and extracted using ethyl acetate (3 x
500 mL). The combined organic layer was washed with brine, dried over Na2SO4, and
evaporated to dryness under reduced pressure. The crude product thus obtained was purified
by silica gel column chromatography to obtain two regio-isomers 5a and 6a (5a as minor and
6a as major). Similarly, regio-isomers 5b and 6b (5b as minor and 6b as major) were
obtained from the intermediate 4b.
5.5.
General procedure for the synthesis of compounds 7a-j and 8a-i
Compound 5a, 5b, 6a or 6b (1.0 mmol) was dissolved in 5-8 mL of DMF in aRB flask and
then K2CO3 (3.0 mmol) was added to it. To this, a solution of respective amine (3.0 mmol) in
DMF (1-2 mL) was added dropwise. The reaction mixture was allowed to stir at 100-120 oC for
10 h and progress of the reaction was monitored by TLC. After completion, water (20 mL) was
added to reaction mixture and it was extracted with EtOAc (2 × 50 mL). The organic layer was
then collected, washed with water (2 × 100 mL) and brine solution, dried over Na2SO4 and
finally excess of solvent was evaporated under vacuum. The crude product thus obtained was
purified by silica gel column chromatography to yield respective compounds 7a-jand 8a-i.
Compounds 13a-13e and 14a-14e were synthesized by using the similar methodology.

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5.5.1.
N1-(2-chloro-6-methylpyrimidin-4-yl)-N2-(7-chloroquinolin-4-yl)-N1-(pyridin-2-
°
ylmethyl)ethane-1,2-diamine (5a): Off-white solid; yield 57%; mp 198–200 C; IR (KBr,
cm-1): 3230, 3055, 2943, 2362, 1732, 1666, 1570, 1539, 1510, 1421, 1367, 1288, 1242, 1207,
1174, 1130, 1085, 1045, 968, 904, 846, 813, 775, 754, 696, 619, 584, 536, 495, 464;1H-
NMR (400 MHz, CDCl3): δ (ppm) 9.55 (brs, 1H), 8.54-8.49 (m, 3H), 8.05 (s, 1H), 7.70 (brs,
2H), 7.26-7.19 (m, 2H), 6.96 (brs, 1H), 6.55 (s, 1H), 4.83 (s, 2H), 3.89-3.81 (m, 4H), 2.13 (s,
3H); HRMS Calcd for C22H20Cl2N6: 438.112, Found: 439.1218 (M + H)+, 441.1194 (MH +
2)+.
5.5.2.
N1-(2-chloro-6-methylpyrimidin-4-yl)-N3-(7-chloroquinolin-4-yl)-N1-(pyridin-2-
°
ylmethyl)propane-1,3-diamine (5b):Off-white solid; yield 52%; mp 118–120 C; IR (KBr,
cm-1): 3238, 3061, 2932, 1586, 1531, 1503, 1472, 1422, 1373, 1322, 1284, 1230, 1211, 1186,
1155, 1044, 967, 915, 880, 847, 805, 762, 541; 1H NMR (400 MHz, CDCl3): δ (ppm) 8.52 (d,
J = 3.8 Hz, 1H), 8.45 (d, J = 5.3 Hz, 1H), 8.00 (brs, 1H), 7.90 (d, J = 1.5, Hz, 1H), 7.63 (t, J =
6.1 Hz, 1H), 7.31 (d, J = 8.4 Hz, 1H), 7.22-7.15 (m, 2H), 6.35 (d, J = 5.3 Hz, 2H), 6.11 (s,
13
1H), 4.69 (s, 2H), 3.81 (s, 2H), 3.39 (q, J = 5.3 Hz, 2H), 2.18 (s, 3H), 2.00-1.95 (s, 2H); C
NMR (100 MHz, CDCl3): δ (ppm) 167.96, 159.97, 151.52, 149.94, 149.76, 149.61, 149.27,
148.80, 137.23, 135.07, 128.18, 125.21, 122.90, 121.97, 117.36, 100.23, 98.69, 53.80, 39.78,
29.67, 26.00, 23.94, HRMS Calcd for C23H22Cl2N6: 452.1289, Found: 453.1378 (M +
H)+,455.1354 (MH + 2)+.
5.5.3.
N1-(4-chloro-6-methylpyrimidin-2-yl)-N2-(7-chloroquinolin-4-yl)-N1-(pyridin-2-
°
ylmethyl)ethane-1,2-diamine (6a): Off-white solid; yield 43%; mp 198–200 C; IR (KBr,
cm-1): 3230, 3055, 2943, 2362, 1732, 1666, 1570, 1539, 1510, 1421, 1367, 1288, 1242, 1207,
1174, 1130, 1085, 1045, 968, 904, 846, 813, 775, 754, 696, 619, 584, 536, 495, 464;1H NMR
(400 MHz, CDCl3): δ (ppm) 8.53-8.49 (m, 2H), 7.92 (d, J = 2.3 Hz, 1H), 7.59 (t, J = 7.6 Hz,
1H), 7.31 (br, 2H), 7.20-7.17 (m, 1H), 6.86 (brs, 1H), 6.52 (s, 1H), 6.39 (brs, 1H), 5.00 (s,
2H), 4.15 (t, J = 4.6 Hz, 2H), 3.56-3.55 (m, 2H), 2.31 (s, 3H); HRMS Calcd for C22H20Cl2N6:
438.1126, Found: 439.1193 (M + H)+,441.1166 (MH + 2)+.
5.5.4.
N1-(4-chloro-6-methylpyrimidin-2-yl)-N3-(7-chloroquinolin-4-yl)-N1-(pyridin-2-
°
ylmethyl)propane-1,3-diamine (6b):Off-white solid; yield 71%; mp 126–128 C ; IR (KBr,
cm-1): 3790, 3663, 3238, 3061, 2967, 1582, 1547, 1467, 1433, 1368, 1319, 1294, 1235, 1137,
1
1113, 1067, 994, 899, 879, 846, 806, 778, 753, 635; H NMR (400 MHz, CDCl3): δ (ppm):
8.45 (d, J = 4.6 Hz, 1H), 8.41 (d, J = 5.3 Hz, 1H), 7.86 (d, J = 1.5 Hz, 2H), 7.57 (t, J = 7.6
Hz, 1H), 7.27-7.20 (m, 2H), 7.12 (t, J = 4.5 Hz, 1H), 6.41 (s, 1H), 6.29 (d, J = 5.3 Hz, 2H),

ACCEPTED MANUSCRIPT
13
4.94 (s, 2H), 3.79 (brs, 2H), 3.32 (q, J = 5.3 Hz, 2H), 2.14 (s, 3H), 1.93-1.89 (m, 2H); C
NMR (100 MHz, CDCl3): δ (ppm) 169.39, 161.82, 160.84, 158.16, 151.67, 150.12, 149.04,
148.90, 136.79, 134.79, 128.23, 124.90, 122.42, 122.27, 121.98, 117.39, 108.78, 98.69,
53.23, 40.37, 39.93, 26.10, 24.01; HRMS Calcd for C23H22Cl2N6: 452.1283, Found: 453.1362
(M + H)+,455.1342 (MH + 2)+.
5.5.5.
N1-(7-chloroquinolin-4-yl)-N2-(6-methyl-2-(piperidin-1-yl)pyrimidin-4-yl)-N2-
(pyridin-2-ylmethyl)ethane-1,2-diamine (7a):Off-white solid; yield 60%; mp 162–164 °C; IR
(KBr, cm-1): 3323, 3052, 2933, 2852, 1578, 1570, 1477, 1420, 1364, 1327, 1244, 1136, 1046,
1
1022, 992, 983, 879, 838, 796, 758, 619, 591, 568; H NMR (400 MHz, CDCl3): δ (ppm)
8.56 (d, J = 4.6 Hz, 1H), 8.49 (d, J = 5.3 Hz, 1H), 7.91 (d, J = 1.5 Hz, 1H), 7.54 (t, J = 6.9
Hz, 1H), 7.46 (d, J = 9.2 Hz, 1H), 7.31 (s, 1H), 7.26-7.05 (m, 3H), 6.29 (d, J = 5.3 Hz, 1H),
5.60 (s, 1H), 4.72 (s, 2H), 4.18 (s, 2H), 3.81 (s, 4H), 3.52 (d, J = 3.8 Hz, 2H), 2.14 (s, 3H),
1.60 (s, 6H), HRMS Calcd for C27H30ClN7: 487.2251, Found: 488.2325(M + H)+,490.2304
(MH + 2)+.
5.5.6.
N1-(7-chloroquinolin-4-yl)-N2-(6-methyl-2-(pyrrolidin-1-yl)pyrimidin-4-yl)-N2-
(pyridin-2-ylmethyl)ethane-1,2-diamine (7b):Off-white solid; yield 56%; mp 152–155 °C; IR
(KBr, cm-1): 3313, 2927, 2874, 2849,1578, 1457, 1331, 1243,1169, 1139, 944, 917, 876, 839,
1
801, 787, 592; H NMR (400 MHz, CDCl3): δ (ppm)8.48 (s, 1H), 8.37 (s, 1H), 8.07 (s, 1H),
7.77- 7.68(m, 2H), 7.48-7.42 (m, 2H), 7.20 (t, J = 8.4 Hz, 2H), 6.56 (s, 1H), 5.76 (brs, 1H),
4.75 (s, 2H), 3.85 (s, 2H), 3.56-3.35 (m, 6H), 2.49 (s, 3H), 1.98 (s, 4H), HRMS Calcd for
C26H28ClN7: 473.2111, Found: 474.2179 (M + H)+,476.2158 (MH + 2)+.
5.5.7. N1-(7-chloroquinolin-4-yl)-N2-(6-methyl-2-morpholinopyrimidin-4-yl)-N2-(pyridin-2-
ylmethyl)ethane-1,2-diamine (7c): Off-white solid; yield 43%; mp 178–180 °C; IR (KBr, cm-
1): 3226, 2943, 2360, 1705, 1635, 1577, 1512, 1462, 1423, 1365, 1325, 1286, 1232, 1207,
1165, 1139, 1112, 1076, 1018, 999, 945, 900, 854, 802, 788, 744, 702, 640, 615, 574, 526,
484, 420;1H-NMR (400 MHz, CDCl3): δ (ppm) 8.56 (d, J = 4.6 Hz, 1H), 8.51 (d, J = 5.3 Hz,
1H), 7.92 (s, 1H), 7.57 (t, J = 7.6 Hz, 1H), 7.46 (d, J = 9.2 Hz, 1H), 7.27 (t, J = 4.6 Hz, 1H),
7.20-7.13 (m, 3H), 6.32 (d, J = 5.3 Hz, 1H), 5.67 (s, 1H), 4.74 (s, 2H), 4.16 (s, 2H), 3.77-3.72
(m, 8H), 3.55 (d, J = 4.6 Hz, 2H), 2.13 (s, 3H); HRMS Calcd for C26H28ClN7O: 489.2043,
Found: 490.2112 (M + H)+,492.2089 (MH + 2)+.
5.5.8. N1-(7-chloroquinolin-4-yl)-N2-(6-methyl-2-(4-methylpiperazin-1-yl)pyrimidin-4-yl)-
N2-(pyridin-2-ylmethyl)ethane-1,2-diamine (7d):Off-white solid; yield 40%; mp 154–156

ACCEPTED MANUSCRIPT
°C; IR (KBr, cm-1): 3199, 3062, 2917, 2787, 2373, 2345, 1578, 1449, 1381, 1325, 1297,
1
1270, 1234, 1188, 1139, 1009, 944, 901, 851, 767, 614; H NMR (400 MHz, CDCl3): δ
(ppm) 8.56 (d, J = 4.6 Hz, 1H), 8.51 (d, J = 5.3 Hz, 1H), 7.92 (s, 1H), 7.56 (t, J = 7.2 Hz,
1H), 7.44 (d, J = 9.2 Hz, 1H), 7.26-7.12 (m, 4H), 6.31 (d, J = 4.6 Hz, 1H), 5.64 (s, 1H), 4.73
(s, 2H), 4.17 (s, 2H), 3.85 (s, 4H), 3.54 (d, J = 3.8 Hz, 2H), 2.44 (s, 4H), 2.31 (s, 3H), 2.14 (s,
3H); HRMS Calcd for C27H31ClN8: 502.2360, Found: 503.2437 (M + H)+,505.2410 (MH +
2)+.
5.5.9. N1-(7-chloroquinolin-4-yl)-N2-(2-(4-ethylpiperazin-1-yl)-6-methylpyrimidin-4-yl)-N2-
°
(pyridin-2-ylmethyl)ethane-1,2-diamine(7e):Off-white solid; yield 57%; mp 106–108 C; IR
(KBr, cm-1): 3309, 2931, 2849, 2801, 2372, 2345, 1578, 1420, 1364, 1331, 1272, 1237, 1203,
1
1165, 1150, 1127, 1079, 1027, 995, 875, 838, 802, 788, 763, 604; H NMR (400 MHz,
CDCl3): δ (ppm) 8.56 (d, J = 5.3 Hz, 1H), 8.50 (d, J = 5.3 Hz, 1H), 7.91 (d, J = 1.5 Hz, 1H),
7.56 (t, J = 7.6 Hz, 1H), 7.44 (d, J = 9.2 Hz, 1H), 7.27-7.12 (m, 4H), 6.31 (d, J = 5.3 Hz, 1H),
5.64 (s, 1H), 4.73 (s, 2H), 4.18 (s, 2H), 3.86 (s, 4H), 3.53 (d, J = 4.6 Hz, 2H), 2.49-2.40 (m,
6H), 2.14 (s, 3H), 1.10 (t, J = 7.2 Hz, 3H); HRMS Calcd for C28H33ClN8: 516.2516, Found:
517.2601 (M + H)+,519.2562 (MH + 2)+.
5.5.10.
N1-(7-chloroquinolin-4-yl)-N3-(6-methyl-2-(piperidin-1-yl)pyrimidin-4-yl)-N3-
°
(pyridin-2-ylmethyl)propane-1,3-diamine (7f):Off-white solid; yield 63%; mp 174–176 C;
IR (KBr, cm-1): 3216, 3063, 2921, 2853, 1580, 1479, 1447, 1431, 1371, 1330, 1279, 1247,
1
1229, 1186, 1138, 1084, 1027, 995, 897, 846, 803, 782, 761, 640, 599, 465; H NMR (400
MHz, CDCl3): δ (ppm) 8.42 (d, J = 5.3 Hz, 2H), 7.85 (s, 1H), 7.58-7.40 (m, 2H), 7.18-7.05
(m, 3H), 6.28 (d, J = 5.3 Hz, 1H), 5.77 (s, 1H), 5.51 (s, 1H), 4.70 (s, 2H), 3.72 (s, 2H), 3.60
(t, J = 5.0 Hz, 4H), 3.34 (q, J = 5.8 Hz, 2H), 2.02-1.98 (m, 5H), 1.52 (d, J = 3.8 Hz, 2H), 1.42
13
(d, J = 3.8 Hz, 4H); C NMR (100 MHz, CDCl3): δ (ppm) 166.36, 162.62, 161.50, 158.35,
151.88, 149.84, 149.14, 149.07, 136.58, 134.66, 128.47, 124.96, 122.27, 121.38, 117.27,
98.72, 90.83, 53.65, 46.67, 44.75, 41.60, 26.59, 25.72, 24.90, 24.51,HRMS Calcd for
C28H32ClN7: 501.2407, Found: 502.2491 (M + H)+,504.2471 (MH + 2)+.
5.5.11.
N1-(7-chloroquinolin-4-yl)-N3-(6-methyl-2-(pyrrolidin-1-yl)pyrimidin-4-yl)-N3-
°
(pyridin-2-ylmethyl)propane-1,3-diamine (7g):Off-white solid; yield 56%; mp 178–180 C;
IR (KBr, cm-1): 3212, 3062, 2957, 2957, 2869, 1574, 1470, 1455, 1433, 1360, 1324, 1279,
1245, 1203, 1178, 1138, 1082, 1050, 996, 965, 898, 862, 847, 802, 784, 762, 696, 639, 603,
562, 464 ; 1H NMR (400 MHz, CDCl3): δ (ppm) 8.45-8.41 (m, 2H), 7.85 (d, J = 1.9 Hz, 1H),
7.53-7.44 (m, 2H), 7.19-7.09 (m, 2H), 6.28 (d, J = 5.3 Hz, 1H), 5.79 (brs, 1H), 5.52 (s, 1H),

ACCEPTED MANUSCRIPT
4.71 (s, 2H), 3.75 (brs, 2H), 3.38-3.34 (m, 6H), 2.04 (s, 3H), 1.78-1.74 (m, 6H);HRMS Calcd
for C27H30ClN7: 487.2251, Found: 488.2335 (M + H)+,490.2316 (MH + 2)+.
5.5.12. N1-(7-chloroquinolin-4-yl)-N3-(6-methyl-2-morpholinopyrimidin-4-yl)-N3-(pyridin-
2-ylmethyl)propane-1,3-diamine (7h): Off-white solid; yield 68%; mp 158–160 °C; IR (KBr,
cm-1): 3211, 3061, 2960, 2846, 2362, 1734, 1577, 1475, 1425, 1363, 1328, 1274, 1232, 1178,
1114, 1047, 995, 964, 896, 852, 790, 756, 634, 599, 555, 462; 1H-NMR (400 MHz, CDCl3): δ
(ppm) 8.43 (d, J = 4.2 Hz, 2H), 7.85 (s, 1H), 7.55-7.48 (m, 2H), 7.19-7.12 (m, 3H), 6.27 (d, J
= 4.6 Hz, 1H), 5.80 (s, 1H), 5.59 (s, 1H), 4.73 (s, 2H), 3.71 (s, 2H), 3.56 (s, 4H), 3.34-3.32
13
(m, 2H), 2.00 (s, 5H), 1.79 (s, 4H); C NMR (100 MHz, CDCl3): δ (ppm) 166.31, 162.53,
161.46, 158.16, 151.75, 149.89, 149.16, 148.91, 136.90, 134.72, 128.38, 124.97, 122.35,
121.38, 117.21, 98.70, 91.87, 66.77, 53.71, 46.83, 44.24, 41.64, 26.57, 24.34, HRMS Calcd
for C27H30ClN7O: 503.2197,Found: 504.2269 (M + H)+,506.2254 (MH + 2)+.
5.5.13. N1-(7-chloroquinolin-4-yl)-N3-(6-methyl-2-(4-methylpiperazin-1-yl)pyrimidin-4-yl)-
N3-(pyridin-2-ylmethyl)propane-1,3-diamine(7i):Off-white solid; yield 52%; mp 144–146
°C; IR (KBr, cm-1): 2914, 2788, 1578, 1485, 1426, 1366, 1325, 1250, 1139, 1008, 842, 768;
1H NMR (400 MHz, CDCl3): δ (ppm) 8.42 (d, J = 5.3 Hz, 2H), 7.85 (d, J = 1.5 Hz, 1H), 7.53
(t, J = 7.6 Hz, 1H), 7.47 (d, J = 9.1 Hz, 1H), 7.19-7.09 (m, 3H), 6.27(d, J = 5.3 Hz, 1H), 5.76
(s, 1H), 5.55 (s, 1H), 4.72 (s, 2H), 3.72 (s, 2H), 3.62 (s, 4H), 3.34 (q, J = 5.3 Hz, 2H), 2.25 (t,
J = 4.6 Hz, 2H), 2.20 (s, 3H), 2.01 (s, 3H), 1.88 (s, 4H); 13C NMR (100 MHz, CDCl3): δ
(ppm) 166.37, 162.58, 161.43, 158.23, 151.93, 149.81, 149.19, 149.10, 136.89, 134.69,
128.56, 125.03, 122.33, 121.43, 121.31, 117.27, 98.76, 91.53, 54.92, 53.70, 46.73, 46.20,
43.66, 41.64, 26.61, 24.43 ; HRMS Calcd for C28H33ClN8: 516.2516, Found: 517.2595 (M +
H)+,519.2572 (MH + 2)+.
5.5.14. N1-(7-chloroquinolin-4-yl)-N3-(2-(4-ethylpiperazin-1-yl)-6-methylpyrimidin-4-yl)-
N3-(pyridin-2-ylmethyl)propane-1,3-diamine(7j):Off-white solid; yield 50%; mp 120–123
°C; IR (KBr, cm-1): 3320, 2932, 2842, 2360, 1581, 1485, 1475, 1441, 1414, 1370, 1347,
1
1331, 1266, 1238, 1167, 1136, 996, 967, 873, 853, 790, 760, 620; H NMR (400 MHz,
CDCl3): δ (ppm) 8.42 (d, J = 4.6 Hz, 2H), 7.85 (d, J = 1.1 Hz, 1H), 7.54-7.46 (m, 2H), 7.19-
7.09 (m, 3H), 6.27 (d, J = 5.3 Hz, 1H), 5.76 (s, 1H), 5.55 (s, 1H), 4.71 (s, 2H), 3.72 (brs, 2H),
3.63 (brs, 4H), 3.32 (t, J = 5.3 Hz, 2H), 2.34-2.28 (m, 6H), 2.01-1.92 (m, 6H), 1.02 (t, J = 6.8
Hz, 2H); 13C NMR (100 MHz, CDCl3): δ (ppm) 166.32, 162.55, 161.39, 158.40, 151.86,
149.84, 149.15, 149.02, 136.88, 134.68, 128.46, 124.99, 122.31, 121.35, 117.25, 98.73,

ACCEPTED MANUSCRIPT
91.46, 53.65, 52.67, 52.38, 46.69, 43.64, 41.58, 26.58, 24.40, 11.87;HRMS Calcd for
C29H35ClN8: 530.2673, Found: 531.2757 (M + H)+,533.2735 (MH + 2)+.
5.5.15.
N1-(7-chloroquinolin-4-yl)-N2-(4-methyl-6-(piperidin-1-yl)pyrimidin-2-yl)-N2-
(pyridin-2-ylmethyl)ethane-1,2-diamine (8a):Off-white solid; yield 31%; mp 138–141 °C; IR
(KBr, cm-1):3290, 3005, 2931, 2850, 2362, 1573, 1541, 1475, 1415, 1367, 1321, 1249, 1219,
1130, 1076, 1031, 975, 916, 875, 840, 792, 758, 702, 642, 601, 534, 486, 428; 1H NMR (400
MHz, CDCl3): δ (ppm) 8.52-8.50 (m, 1H), 8.47 (d, J = 5.0 Hz, 1H), 7.90 (d, J = 1.8 Hz, 1H),
7.57-7.46 (m, 3H), 7.24-7.21 (m, 2H), 7.13-7.10 (m, 1H), 6.26 (d, J = 5.5 Hz, 1H), 5.89 (s,
1H), 4.98 (s, 2H), 4.15 (t, J = 4.6 Hz, 2H), 3.49-3.43 (m, 6H), 2.36 (s, 3H), 1.61-1.49 (m,
13
6H); C NMR (100 MHz, CDCl3): δ (ppm) 162.57, 159.63, 152.11, 150.51, 149.07, 148.88,
136.53, 134.45, 128.38, 124.43, 122.28, 121.87, 121.35, 117.34, 98.12, 92.29, 53.32, 46.13,
45.11, 44.23, 25.41, 24.65, 24.55; HRMS Calcd for C27H30ClN7: 487.2251, Found: 488.2324
(M + H)+,490.2304 (MH + 2)+.
5.5.16.
N1-(7-chloroquinolin-4-yl)-N2-(4-methyl-6-(pyrrolidin-1-yl)pyrimidin-2-yl)-N2-
(pyridin-2-ylmethyl)ethane-1,2-diamine (8b):Off-white solid; yield 38%; mp 153–155 °C; IR
(KBr, cm-1):3325, 2951, 2866, 2362, 1730, 1587, 1546, 1479, 1417, 1363, 1327, 1296, 1246,
1213, 1170, 1136, 1083, 1043, 1002, 968, 902, 844, 794, 761, 698, 636, 596, 545, 486, 449,
1
414; H NMR (400 MHz, CDCl3): δ (ppm)8.52-8.50 (m, 1H), 8.46 (d, J = 5.5 Hz, 1H), 7.89
(d, J = 2.3 Hz, 1H), 7.59-7.53 (m, 1H), 7.50-7.45 (m,1H), 7.28-7.26 (m, 1H), 7.20 (d, J = 8.2
Hz, 1H), 7.13-7.10 (m, 1H), 6.25 (d, J = 5.0 Hz, 1H), 5.69 (s, 1H), 5.02 (s, 2H), 4.16 (t, J =
5.0 Hz, 2H), 3.45-3.37 (m, 6H), 2.36 (s, 3H), 2.00-1.91 (m, 4H);13C NMR (100 MHz,
CDCl3): δ (ppm)162.47, 160.99, 159.74, 152.06, 150.55, 149.03, 148.84, 136.51, 134.45,
128.33, 124.35, 122.23, 121.87, 121.52, 117.35, 98.09, 93.14, 53.06, 46.16, 45.87, 44.21,
25.30, 24.36; HRMS Calcd for C26H28ClN7: 473.2094, Found: 474.2161 (M + H)+,476.2142
(MH + 2)+.
5.5.17. N1-(7-chloroquinolin-4-yl)-N2-(4-methyl-6-morpholinopyrimidin-2-yl)-N2-(pyridin-
°
2-ylmethyl)ethane-1,2-diamine (8c): Off-white solid; yield 36%; mp 181–183 C; IR (KBr,
cm-1): 3226, 2932, 1586, 1531, 1503, 1472, 1422, 1373, 1322, 1284, 1230, 1211, 1186,
1155, 1044, 967, 915, 880, 847, 805, 762, 541;1H-NMR (400 MHz, CDCl3): δ (ppm) 8.52-
8.47 (m, 2H), 7.93 (d, J = 1.6 Hz, 1H), 7.58-7.48 (m, 3H), 7.26-7.19 (m, 2H), 7.14-7.11 (m,
1H), 6.30 (d, J = 5.5 Hz, 1H), 5.86 (s, 1H), 4.97 (s, 2H), 4.17 (t, J = 4.8 Hz, 2H), 3.65(brs,
4H), 3.47 (brs, 6H), 2.38 (s, 3H); 13C NMR (100 MHz, CDCl3): δ (ppm) 162.39, 159.36,
151.81, 150.58, 148.97, 148.74, 136.59, 134.66, 134.56, 128.47, 128.24, 124.85, 124.63,

ACCEPTED MANUSCRIPT
122.09, 121.96, 117.25, 98.20, 92.30, 66.45, 53.27, 46.18, 44.23, 44.10, 24.55; HRMS Calcd
for C26H28ClN7O: 489.2043, Found: 490.2112 (M + H)+,492.2089 (MH + 2)+.
5.5.18. N1-(7-chloroquinolin-4-yl)-N2-(4-methyl-6-(4-methylpiperazin-1-yl)pyrimidin-2-yl)-
N2-(pyridin-2-ylmethyl)ethane-1,2-diamine (8d):Off-white solid; yield 41%; mp 89–90°C;
IR (KBr, cm-1): 3277, 3010, 2968, 2939, 2852, 2360, 1739, 1575, 1417, 1367, 1294, 1218,
1224, 1170,1082, 1045, 997, 887, 842, 821, 773, 696, 619, 586, 545, 482, 428; 1H NMR (400
MHz, CDCl3): δ (ppm) 8.51 (d, J = 4.6 Hz, 1H), 8.46 (d, J = 5.1 Hz, 1H), 7.90 (d, J = 1.8 Hz,
1H), 7.56 (d, J = 7.3 Hz, 1H), 7.49 (t, J = 7.8 Hz, 2H), 7.27-7.22 (m, 2H), 7.13 (t, J = 5.5 Hz,
1H), 6.27 (d, J = 5.5 Hz, 1H), 5.88 (s, 1H), 4.98 (s, 2H), 4.15 (t, J = 4.8 Hz, 2H), 3.52 (brs,
4H), 3.46-3.45 (m, 2H), 2.36 (brs, 4H), 2.27 (s, 3H), 2.10 (s, 3H);13C NMR (100 MHz,
CDCl3): δ (ppm) 162.84, 162.43, 160.64, 159.44, 152.09, 150.43, 148.91, 136.56, 134.47,
128.40, 124.54, 122.15, 121.91, 121.28, 117.30, 98.16, 92.37, 54.55, 53.36, 46.09, 44.11,
43.80, 24.53;HRMS Calcd for C27H31ClN8: 502.2360, Found: 503.2425 (M + H)+,505.2378
(MH + 2)+.
5.5.19. N1-(7-chloroquinolin-4-yl)-N2-(4-(4-ethylpiperazin-1-yl)-6-methylpyrimidin-2-yl)-
°
N2-(pyridin-2-ylmethyl)ethane-1,2-diamine (8e):Off-white solid; yield 31%; mp 92–94 C;
1
IR (KBr, cm-1): 2914, 2788, 2362, 1739, 1575, 1417, 1367, 1222, 1139, 997, 889, 773; H
NMR (400 MHz, CDCl3): δ (ppm) 8.51 (d, J = 4.6 Hz, 1H), 8.46 (d, J = 4.6 Hz, 1H), 7.90 (s,
1H), 7.57 (d, J = 6.1 Hz, 1H), 7.49 (t, J = 7.6 Hz, 2H), 7.23 (d, J = 7.6 Hz, 3H), 7.13 (t, J =
6.1 Hz, 1H), 6.27 (d, J = 4.6 Hz, 1H), 5.88 (s, 1H), 4.98 (s, 2H), 4.15 (s, 2H), 3.53-3.46 (m,
6H), 2.40-2.37 (m, 8H), 1.07 (t, J = 7.6 Hz, 3H);HRMS Calcd for C28H33ClN8: 516.2516,
Found: 517.2587 (M + H)+,519.2562 (MH + 2)+.
5.5.20.
N1-(7-chloroquinolin-4-yl)-N3-(4-methyl-6-(piperidin-1-yl)pyrimidin-2-yl)-N3-
(pyridin-2-ylmethyl)propane-1,3-diamine(8f): Off-white solid; yield 61%; mp 98–100 °C; IR
(KBr, cm-1): 3226, 2940, 2872, 1583, 1550, 1475, 1433, 1369, 1321, 1282, 1210, 1131, 1183,
1083, 973, 874, 853, 788, 754;1H-NMR (400 MHz, CDCl3): δ (ppm) 8.42 (d, J = 4.5 Hz, 1H),
8.39 (d, J = 5.3 Hz, 1H), 7.84 (s, 1H), 7.76 (d, J = 8.4 Hz, 1H), 7.48 (t, J = 7.6 Hz, 1H), 7.19-
7.16 (m, 2H), 7.05 (t, J = 6.1 Hz, 1H), 6.64 (brs, 1H), 6.30 (d, J = 4.6 Hz, 1H), 5.66 (s, 1H),
4.86 (s, 2H), 3.79 (t, J = 5.3 Hz, 2H), 3.33 (s, 6H), 2.16 (s, 3H), 1.87-1.76 (m, 2H), 1.52-1.51
(m, 2H), 1.36 (brs, 4H); 13C NMR (100 MHz, CDCl3): δ (ppm)165.56, 162.47, 161.88,
159.92, 151.91, 150.27, 149.21, 148.76, 136.47, 134.55, 128.35, 124.57, 122.17, 121.75,
121.52, 117.69, 98.81, 91.73, 53.24, 44.91, 40.22, 26.59, 25.36, 24.84, 24.71;HRMS Calcd
for C28H32ClN7: 501.2389, Found: 502.2468 (M + H)+,504.2458 (MH + 2)+.

ACCEPTED MANUSCRIPT
5.5.21.
N1-(7-chloroquinolin-4-yl)-N3-(4-methyl-6-(pyrrolidin-1-yl)pyrimidin-2-yl)-N3-
°
(pyridin-2-ylmethyl)propane-1,3-diamine(8g): Off-white solid; yield 68%; mp 130–132 C;
IR (KBr, cm-1): 3226, 2947, 2872, 1583, 1551, 1475, 1432, 1414, 1367, 1348, 1319, 1242,
1169, 1139, 974, 875, 853, 804, 789, 764;1H NMR (400 MHz, CDCl3): δ (ppm) 8.43 (d, J =
4.6 Hz, 1H), 8.38 (d, J = 6.1 Hz, 1H), 7.83(d,J = 1.5 Hz, 1H), 7.73(d, J = 9.1Hz, 1H), 7.49 (t,
J = 7.6 Hz, 1H), 7.22-7.10 (m, 1H), 7.15 (ddJ = 1.5, 2.6 Hz, 1H), 7.08-7.05(m, 1H), 6.67(brs,
1H) 6.29 (d, J = 5.3 Hz, 1H), 5.40 (s, 1H), 4.90 (s, 2H), 3.79 (t, J = 6.1 Hz, 2H), 3.34 (q, J =
13
5.3 Hz, 2H), 3.19 (s, 4H), 2.13 (s, 3H), 1.88-1.81 (m, 6H); C NMR (100 MHz, CDCl3): δ
(ppm) 164.65, 161.72, 160.82, 160.06, 151.77, 150.36, 149.08, 148.71, 136.48, 134.53,
128.16, 124.48, 122.25, 121.78, 117.65, 98.75, 92.51, 53.04, 45.88, 44.95, 40.50, 26.52,
25.12, 24.57; HRMS Calcd for C27H30ClN7: 487.2251, Found: 488.2348 (M + H)+,490.2330
(MH + 2)+.
5.5.22. N1-(7-chloroquinolin-4-yl)-N3-(4-methyl-6-morpholinopyrimidin-2-yl)-N3-(pyridin-
°
2-ylmethyl)propane-1,3-diamine(8h): Off-white solid; yield 50%; mp 120–122 C; IR (KBr,
cm-1): 3226, 2932, 2853, 1582, 1557, 1503, 1472, 1409, 1367, 1321, 1245, 1187, 1122, 992,
873, 853, 791, 757, 594;1H NMR (400 MHz, CDCl3): δ (ppm) 8.43 (d, J =4.5 Hz, 1H), 8.40
(d, J =5.5 Hz, 1H),7.84 (d, J =2.3, Hz, 1H), 7.74 (d, J = 9.1, Hz, 1H), 7.51 (t, J =7.8 Hz, 1H),
7.19-7.15 (m, 2H), 7.08 (t, J =5.0 Hz, 1H), 6.61 (brs, 1H), 6.30 (d, J = 5.5 Hz, 1H), 5.59 (s,
1H), 4.86 (s, 2H), 3.81 (t, J = 6.0 Hz, 2H), 3.54 (t, J = 5.0 Hz, 4H), 3.35-3.30 (m, 6H), 2.15
(s, 3H), 1.89 (q, J = 5.6 Hz, 2H);HRMS Calcd for C27H30ClN7O: 503.2215, Found: 504.2293
(M + H)+,506.2274 (MH + 2)+.
5.5.23. N1-(7-chloroquinolin-4-yl)-N3-(4-methyl-6-(4-methylpiperazin-1-yl)pyrimidin-2-yl)-
N3-(pyridin-2-ylmethyl)propane-1,3-diamine(8i):Off-white solid; yield52%; mp 97–99°C; IR
(KBr, cm-1): 2940, 2797, 1583, 1553, 1473, 1410, 1368, 1322, 1284, 1252, 1232, 1199, 1169,
1138, 1000, 879, 853, 789, 751, 621;1H NMR (400 MHz, CDCl3): δ (ppm) 8.48 (d, J = 8.4
Hz, 2H), 7.92 (s, 1H) 7.82 (d, J= 8.4, 1H), 7.57(s, 1H), 7.23-7.14 (m, 2H),6.76 (s, 1H), 6.37
(s, 1H), 5.69 (s, 1H), 4.94 (s, 2H), 3.87(s, 2H), 3.43 (brs, 6H), 2.31-2.12 (m, 10H), 1.96 (s,
13
2H); C NMR (100 MHz, CDCl3): δ (ppm) 165.92, 162.69, 161.69, 159.74, 151.59, 150.40,
148.74, 136.55, 134.67, 128.02, 124.65, 122.15, 121.85, 121.50, 117.56, 98.72, 91.76, 54.47,
53.27, 46.04, 45.21, 43.53, 40.41, 26.54, 24.76; HRMS Calcd for C28H33ClN8: 516.2524,
Found: 517.2600(M + H)+,519.2575 (MH + 2)+.
5.5.24.
(10a):White solid; yield: 89%; mp 112–114 oC; IR (KBr, cm-1): 3199, 3061, 2937, 1573, 1442,
N1-(7-Chloroquinolin-4-yl)-N3-(thiophen-2-ylmethyl)propane-1,3-diamine

ACCEPTED MANUSCRIPT
1
1363, 1211, 1076, 848, 705, 567, 478; H NMR (400 MHz; CDCl3):δ (ppm) 8.49 (d, J = 5.3
Hz, 1H), 7.91 (d, J = 2.2 Hz, 1H), 7.65 (d, J = 9.1 Hz, 1H), 7.44 (brs, 1H), 7.28-7.26 (m, 2H),
7.23 (dd, J= 9.1, 2.2 Hz, 1H), 7.01-6.96 (m, 2H), 6.31 (d, J = 5.3 Hz, 1H), 4.06 (s, 2H), 3.42-
13
3.38 (m, 2H), 2.98 (t, J = 5.7 Hz, 2H), 1.97-1.91 (m, 2H); C NMR (100 MHz, CDCl3):δ
(ppm) 151.91, 150.40, 148.93, 142.74, 134.59, 128.36, 126.82, 125.56, 124.86, 124.77, 122.24,
117.43, 98.25, 48.83, 48.59, 43.76, 27.36; HRMS calcd for C17H18ClN3S: 331.0910, found:
332.0984 (M + H)+, 334.0956 (MH + 2)+.
5.5.25. N1-(2-Chloro-6-methylpyrimidin-4-yl)-N3-(7-chloroquinolin-4-yl)-N1-(thiophen-2-
ylmethyl)propane-1,3-diamine (11a):White solid; yield: 60%; mp 117–119 oC; IR (KBr, cm-1):
1
3236, 2956, 1735, 1583, 1500, 1423, 1365, 1220, 893, 696, 538, 470; H NMR (400 MHz;
CDCl3):δ (ppm) 8.50 (d, J = 5.3 Hz, 1H), 8.01 (brs, 1H), 7.96-7.95 (m, 1H), 7.40-7.37 (m,
1H), 7.25-7.23 (m, 1H), 6.97-6.92 (m, 2H), 6.39 (d, J= 5.3 Hz, 1H), 6.30 (s, 1H), 5.98 (brs,
1H), 4.76 (s, 2H), 3.81-3.74 (m, 2H), 3.41-3.37 (m, 2H), 2.32 (s, 3H), 2.00-1.95 (m, 2H); 13C
NMR (100 MHz, CDCl3):δ (ppm) 172.09, 167.32, 162.38, 158.98, 151.57, 150.25, 148.98,
139.77, 133.64, 127.12, 126.64, 125.95, 124.26, 124.17, 117.43, 100.34, 98.92, 45.30, 25.27,
23.17, 21.12; HRMS calcd for C22H21Cl2N5S: 457.0895, found: 458.0936 (M + H)+, 460.0910
(MH + 2)+.
5.5.26.
N1-(4-Chloro-6-methylpyrimidin-2-yl)-N3-(7-chloroquinolin-4-yl)-N1-(thiophen-2-
o
ylmethyl)propane-1,3-diamine (12a):White solid; yield: 26%; mp 154–156 C; IR (KBr, cm-
1): 3242, 2929, 1737, 1571, 1431, 1363, 1286, 1220, 1116, 1068, 891,842, 702, 430;1H NMR
(400 MHz; CDCl3) δ(ppm): 8.49 (d, J = 5.3 Hz, 1H), 7.96 (brs, 1H), 7.93 (d, J = 2.2 Hz, 1H),
7.35 (dd, J = 9.1, 2.2 Hz, 1H), 7.20-7.18 (m, 1H), 7.01 (d, J = 3.81 Hz, 1H), 6.92 (dd, J = 5.3,
3.8 Hz, 1H), 6.51 (s, 1H), 6.38 (d, J = 5.3 Hz, 1H), 5.96-5.93 (m, 1H), 4.97 (s, 2H), 3.75 (t, J =
6.1 Hz, 2H), 3.36-3.32 (m, 2H), 2.37 (s, 3H), 1.97-1.91 (m, 2H); 13C NMR (100 MHz, CDCl3)
δ (ppm): 169.45, 161.48, 160.90, 151.71, 149.77, 148.98, 140.28, 134.81, 128.33,
126.65, 126.21, 125.45, 124.91, 121.86, 117.36, 108.95, 98.72, 45.80, 43.63, 39.39,
26.13, 24.05; HRMS calcd for C22H21Cl2N5S: 457.0895, found: 458.0942 (M + H)+, 460.0916
(MH + 2)+.
5.5.27.
N1-(7-Chloroquinolin-4-yl)-N3-(6-methyl-2-(piperidin-1-yl)pyrimidin-4-yl)-N3-
(thiophen-2-ylmethyl)propane-1,3-diamine (13a):Off white solid; yield: 89%; mp 194–196
oC; IR (KBr, cm-1): 3226, 2924, 2858, 1571, 1469, 1433, 1367, 1236, 1141, 850, 796, 696,
464; 1H NMR (400 MHz; CDCl3) δ (ppm): 8.50 (d, J = 5.3 Hz, 1H), 7.94 (d, J = 2.2 Hz, 1H),
7.45 (d, J = 9.1 Hz, 1H), 7.31 (dd, J = 9.1, 2.2 Hz, 1H), 7.18-7.17 (m, 1H), 6.90-6.89 (m, 2H),

ACCEPTED MANUSCRIPT
6.34 (d, J = 5.3 Hz, 1H), 5.67 (s, 1H), 5.12 (brs, 1H), 4.78 (s, 2H), 3.76 (t, J = 5.3 Hz., 4H),
3.65 (t, J = 6.1 Hz, 2H), 3.37-3.33 (m, 2H), 2.17 (s, 3H), 2.06-1.99 (m, 2H), 1.65-1.59 (m, 2H),
13
1.57-1.51 (m, 4H); C NMR (100 MHz, CDCl3) δ (ppm): 165.06, 161.68, 160.68, 151.90,
149.94, 149.12, 141.63, 133.37, 127.52, 126.34, 126.18, 125.61, 125.50, 124.07, 117.53, 98.87,
90.58, 45.07, 44.07, 25.80, 25.37, 24.54, 24.04; HRMS calcd. for C27H31ClN6S: 506.2019,
found: 507.2053 (M + H)+, 509.2024 (MH + 2)+.
5.5.28.
N1-(7-Chloroquinolin-4-yl)-N3-(6-methyl-2-(pyrrolidin-1-yl)pyrimidin-4-yl)-N3-
(thiophen-2-ylmethyl)propane-1,3-diamine (13b):Off white solid; yield: 82%; mp 217–219
oC; IR (KBr, cm-1): 3207, 2954, 2858, 1564, 1462, 1327, 1242, 1139, 854, 769, 694, 559, 462;
1H NMR (400 MHz; CDCl3) δ (ppm): 8.49 (d, J = 5.3 Hz, 1H), 7.94 (d, J = 2.2 Hz, 1H), 7.45
(d, J = 9.1 Hz, 1H), 7.29 (dd, J = 9.1, 2.2 Hz, 1H), 7.18-7.16 (m, 1H), 6.90-6.89 (m, 2H), 6.34
(d, J = 5.3 Hz, 1H), 5.70 (s, 1H), 5.21 (brs, 1H), 4.78 (s, 2H), 3.68 (t, J = 6.8 Hz, 2H), 3.55-3.52
(m, 4H), 3.39-3.34 (m, 2H), 2.19 (s, 3H), 2.06-2.00 (m, 2H), 1.90-1.87 (m, 4H); HRMS calcd.
for C26H29ClN6S: 492.1863, found: 493.1892 (M + H)+, 495.1864 (MH + 2)+.
5.5.29. N1-(7-Chloroquinolin-4-yl)-N3-(6-methyl-2-morpholinopyrimidin-4-yl)-N3-(thiophen-
2-ylmethyl)propane-1,3-diamine (13c):White solid; yield: 79%; mp 196–198 oC; 1H NMR (400
MHz; CDCl3) δ (ppm): 8.49 (d, J = 5.3 Hz, 1H), 7.95 (d, J = 2.2 Hz, 1H), 7.51 (d, J = 9.1 Hz,
1H), 7.33 (dd, J = 9.1, 2.2 Hz, 1H), 7.19-7.17 (m, 1H), 6.91-6.90 (m, 2H), 6.32 (d, J = 5.3 Hz,
1H), 5.74 (s, 1H), 5.17 (brs, 1H), 4.81 (s, 2H), 3.77-3.74 (m, 4H), 3.71-3.68 (m, 4H), 3.64 (t, J
= 6.1 Hz, 2H), 3.37-3.32 (m, 2H), 2.16 (s, 3H), 2.07-2.00 (m, 2H); 13C NMR (100 MHz,
CDCl3) δ (ppm): 166.50, 162.27, 161.56, 151.77, 149.51, 148.86, 141.02, 134.96, 128.62,
126.46, 125.79, 125.35, 125.32, 120.80, 117.04, 99.08, 91.76, 66.91, 46.34, 45.24, 44.38,
41.01, 26.69, 24.48; HRMS calcd. for C26H29ClN6OS: 508.1812, found: 509.1920 (M + H)+,
511.1900 (MH + 2)+.
5.5.30. N1-(7-Chloroquinolin-4-yl)-N3-(6-methyl-2-(4-methylpiperazin-1-yl)pyrimidin-4-yl)-
N3-(thiophen-2-ylmethyl)propane-1,3-diamine (13d): White solid; yield: 76%; mp 127–129 oC;
IR (KBr, cm-1): 3356, 3072, 2935, 1581, 1546, 1473, 1431, 1365, 1315, 1234, 999, 794, 599,
549; 1H NMR (400 MHz; CDCl3) δ (ppm): 8.50 (d, J = 5.3 Hz, 1H), 7.95 (d, J = 2.2 Hz, 1H),
7.48 (d, J = 9.1 Hz, 1H), 7.32 (dd, J = 9.1, 2.2 Hz, 1H), 7.19-7.17 (m, 1H), 6.91-6.90 (m, 2H),
6.33 (d, J = 5.3 Hz, 1H), 5.72 (s, 1H), 5.07 (brs, 1H), 4.79 (s, 2H), 3.80 (t, J = 4.5 Hz, 4H), 3.64
(t, J = 6.1 Hz, 2H), 3.36-3.32 (m, 2H), 2.38 (t, J = 4.5 Hz, 4H), 2.29 (s, 3H), 2.16 (s, 3H), 2.06-
1.99 (m, 2H); 13C NMR (100 MHz, CDCl3) δ (ppm): 166.46, 162.25, 161.45, 151.92, 149,43,
149.02, 141.07, 134.82, 128.69, 126.43, 125.73, 157.26, 120.83, 117.09, 98.99, 91.38, 55.00,

ACCEPTED MANUSCRIPT
46.27, 46.21, 45.18, 43.72, 41.02, 26.65, 24.53; HRMS calcd. for C27H32ClN7S: 521.2128,
found: 522.2159 (M + H)+, 524.2119 (MH + 2)+.
5.5.31. N1-(7-Chloroquinolin-4-yl)-N3-(2-(4-ethylpiperazin-1-yl)-6-methylpyrimidin-4-yl)-
N3-(thiophen-2-ylmethyl)propane-1,3-diamine (13e):Off white solid; yield: 79 %; mp
o
114–116 C; IR (KBr, cm-1): 3215, 2958, 1564, 1431, 1365, 1238, 1134, 1004, 781,
702;1H NMR (400 MHz; CDCl3)
7.47 (d, = 9.1 Hz, 1H), 7.33-7.31 (m, 1H), 7.19-7.17 (m, 1H), 6.91-6.90 (m, 2H), 6.34
(d, = 5.3 Hz, 1H), 5.72 (s, 1H), 5.06 (brs, 1H), 4.79 (s, 2H), 3.81 (t, = 5.3 Hz, 4H),
3.65 (t, = 6.10 Hz, 2H), 3.37-3.32 (m, 2H), 2.46-2.39 (m, 6H), 2.17 (s, 3H), 2.06-1.99
(m, 2H), 1.10 (t, (ppm): 166.50, 162.31,
= 6.8 Hz, 3H); 13C NMR (100 MHz, CDCl3)
δ (ppm): 8.51 (d, J = 5.3 Hz, 1H), 7.96-7.94 (m, 1H),
J
J
J
J
J
δ
161.47, 151.90, 149.48, 149.00, 141.10, 134.88, 128.71, 126.46, 125.74, 125.32, 125.25,
120.80, 117.09, 99.08, 91.39, 52.79, 52.42, 46.34, 4524, 43.75, 41.09, 26.71, 24.54,
11.88; HRMS calcd. for C28H34ClN7S: 535.2285; found: 536.2321 (M + H)+, 538.2287
(MH + 2)+.
5.5.32.
N1-(7-Chloroquinolin-4-yl)-N3-(4-methyl-6-(piperidin-1-yl)pyrimidin-2-yl)-N3-
o
(thiophen-2-ylmethyl)propane-1,3-diamine (14a):White solid; yield: 89%; mp 142–144 C; IR
(KBr, cm-1): 3215, 2927, 2854, 1564, 1463, 1423, 1361, 1238, 1207, 1126, 852, 692, 466 cm-1;
1H NMR (400 MHz; CDCl3) δ (ppm): 8.46 (d, J = 5.3 Hz, 1H), 7.92-7.91 (m, 1H), 7.81 (d, J =
9.1 Hz, 1H), 7.30-7.27 (m, 1H), 7.15-7.14 (m, 1H), 6.96-6.95 (m, 1H), 6.90-6.88 (m, 1H), 6.50
(brs, 1H), 6.38 (d, J = 5.3 Hz, 1H), 5.81 (s, 1H), 4.91 (s, 2H), 3.76 (t, J = 6.1 Hz, 2H), 3.58 (d, J
= 5.3 Hz, 4H), 3.37-3.33 (m, 2H), 2.28 (s, 3H), 1.88 (t, J = 6.1 Hz, 2H), 1.66-1.65 (m, 2H),
13
1.57-1.56 (m, 4H); C NMR (100 MHz, CDCl3) δ (ppm): 165.60, 162.34, 161.65, 151.94,
150.11, 149.25, 142.21, 134.58, 128.42, 125.89, 125.86, 125.12, 124.59, 122.03, 117.69, 98.91,
91.80, 45.67, 45.02, 43.18, 39.51, 26.51, 25.57, 24.96, 24.76; HRMS calcd. for C27H31ClN6S:
506.2019, found: 507.2042 (M + H)+, 509.2019 (MH + 2)+.
5.5.33.
N1-(7-Chloroquinolin-4-yl)-N3-(4-methyl-6-(pyrrolidin-1-yl)pyrimidin-2-yl)-N3-
(thiophen-2-ylmethyl)propane-1,3-diamine (14b): Off white solid; yield: 86%; mp 140–142
oC; IR (KBr, cm-1): 3217, 2960, 2856, 1570, 1463, 1419, 1352, 1234, 1138, 854, 769, 688,
460; 1H NMR (400 MHz; CDCl3) δ (ppm): 8.46 (d, J = 5.3 Hz, 1H), 7.93 (d, J = 2.2 Hz, 1H),
7.80 (d, J = 9.1 Hz, 1H), 7.28 (dd, J = 9.1, 2.2 Hz, 1H), 7.15-7.13 (m, 1H), 6.97 (d, J = 3.8 Hz,
1H), 6.89 (dd, J = 5.3, 3.8 Hz, 1H), 6.55 (brs, 1H), 6.38 (d, J = 5.3 Hz, 1H), 5.59 (s, 1H), 4.94
(s, 2H), 3.77 (t, J = 6.1 Hz, 2H), 3.58-3.34 (m, 6H), 2.28 (s, 3H), 1.94-1.87 (m, 6H); 13C NMR
(100 MHz, CDCl3) δ (ppm): 164.74, 161.19, 160.99, 152.47, 150.58, 149.73, 143.05, 133.91,

ACCEPTED MANUSCRIPT
128.10, 126.69, 126.63, 126.02, 124.65, 124.54, 118.15, 99.20, 92.56, 46.13, 45.64, 44.94,
40.80, 26.85, 25.26, 24.64; HRMS calcd. for C26H29ClN6S: 492.1863, found: 493.1887 (M +
H)+, 495.1862 (MH + 2)+.
5.5.34. N1-(7-Chloroquinolin-4-yl)-N3-(4-methyl-6-morpholinopyrimidin-2-yl)-N3-(thiophen-
o
2-ylmethyl)propane-1,3-diamine (14c):White solid; yield: 81%; mp 142–144 C; IR (KBr, cm-
1): 3226, 2956, 2850, 1570, 1415, 1363, 1242, 1188, 1118, 993, 852, 794, 711, 636, 462 cm-1;
1H NMR (400 MHz; CDCl3) δ (ppm): 8.46 (d, J = 5.3 Hz, 1H),7.96-7.95 (m, 1H), 7.81 (d, J =
9.1 Hz, 1H), 7.31-7.29 (m, 1H), 7.16-7.15 (m, 1H), 6.96-6.95 (m, 1H), 6.91-6.88 (m, 1H), 6.53
(brs, 1H), 6.38 (d, J = 5.3 Hz, 1H), 5.79 (s, 1H), 4.91 (s, 2H), 3.78-3.72 (m, 6H), 3.59 (t, J = 5.3
13
Hz, 4H), 3.38-3.34 (m, 2H), 2.29 (s, 3H), 1.92-1.89 (m, 2H); C NMR (100 MHz, CDCl3) δ
(ppm): 166.27, 162.95, 161.52, 151.71, 150.16, 148.98, 141.94, 134.79, 128.33, 125.98,
125.19, 124.77, 121.86, 117.57, 98.93, 91.83, 66.60, 43.83, 44.26, 43.39, 39.68, 26.59, 24.94;
HRMS calcd. for C26H29ClN6OS: 508.1812, found: 509.1924 (M + H)+, 511.1906 (MH + 2)+.
5.5.35. N1-(7-Chloroquinolin-4-yl)-N3-(4-methyl-6-(4-methylpiperazin-1-yl)pyrimidin-2-yl)-
o
N3-(thiophen-2-ylmethyl)propane-1,3-diamine (14d):White solid; yield: 76%; mp 108–110 C;
IR (KBr, cm-1): 3228, 2924, 2787, 1570, 1458, 1417, 1363, 1207, 1138, 995, 788, 696, 462; 1H
NMR (400 MHz; CDCl3) δ (ppm): 8.47 (d, J = 5.3 Hz, 1H), 7.92 (d, J = 2.2 Hz, 1H), 7.79 (d, J
= 9.1 Hz, 1H), 7.29 (dd, J = 9.1, 2.2 Hz, 1H), 7.16-7.14 (m, 1H), 6.96-6.95 (m, 1H), 6.90-6.88
(m, 1H), 6.38-6.37 (m, 2H), 5.81 (s, 1H), 4.91 (s, 2H), 3.76 (t, J = 6.1 Hz, 2H), 3.65-3.61 (m,
13
4H), 3.37-3.32 (m, 2H), 2.43-2.29 (m, 12H); C NMR (100 MHz, CDCl3) δ (ppm): 166.05,
162.67, 161.58, 151.87, 150.13, 149.17, 142.08, 134.70, 128.43, 125.95, 125.17, 124.73,
121.89, 117.64, 98.94, 91.92, 54.70, 46.13, 45.80, 43.80, 43.40, 39.71, 26.60, 24.92; HRMS
calcd. for C27H32ClN7S: 521.2128, found: 522.2190 (M + H)+, 524.2133 (MH + 2)+.
5.5.36. N1-(7-Chloroquinolin-4-yl)-N3-(4-(4-ethylpiperazin-1-yl)-6-methylpyrimidin-2-yl)-N3-
o
(thiophen-2-ylmethyl)propane-1,3-diamine (14e):Off white solid; yield: 80%; mp 96–98 C;
IR (KBr, cm-1): 3230, 2922, 1568, 1462, 1419, 1363, 1244, 1203, 1134, 997, 773, 696, 460; 1H
NMR (400 MHz; CDCl3) δ (ppm): 8.47 (d, J = 5.3 Hz, 1H), 7.93-7.92 (m, 1H), 7.80 (d, J = 9.1
Hz, 1H), 7.30-7.28 (m, 1H), 7.15-7.14 (m, 1H), 6.97-6.96 (m, 1H), 6.90-6.88 (m, 1H), 6.46-
6.32 (m, 2H), 5.81 (s, 1H), 4.91 (s, 2H), 3.76 (t, J = 6.1 Hz, 2H), 3.66-3.61 (m, 4H), 3.35-3.34
(m, 2H), 2.49-2.41 (m, 8H), 2.29 (s, 3H), 1.11 (t, J = 6.8 Hz, 3H); 13C NMR (100 MHz, CDCl3)
δ (ppm): 166.00, 162.67, 161.58, 151.81, 150.16, 149.11, 142.09, 134.74, 128.38, 125.95,
125.17, 124.74, 121.90, 117.63, 98.92, 91.92, 52.48, 52.34, 45.81, 43.83, 43.41, 39.71, 26.60,

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24.92, 11.89; HRMS calcd. for C28H34ClN7S: 535.2285; found: 536.2355 (M + H)+, 538.2318
(MH + 2)+.
Acknowledgements
DSR thanks SERB [EMR/2014/001127] New Delhi, Govt. of India, for financial support.
SSM, RK and DK are thankful to CSIR India for JRF and SRF. For analytical data authors
are thankful to USIC-CIF, University of Delhi. SIK is thankful to Department of Agriculture
(USDA), United States Agricultural Research Service Specific Cooperative Agreement No.
58-6408-2-0009 for partial support of this work.
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Table 1: In vitroantimalarial activity and cytotoxicity of the 4-aminoquinoline-pyrimidine
molecular hybrids
P. falciparum
(D6 strain)
IC50
P. falciparum
(W2 strain)
IC50
Cytotoxicity
(VERO cells)
IC50 (µM)
Comp.
R
n
SI
SI
(µM)
(µM)
0.492
0.319
1.006
0.804
Cl
2
3
2
3
2
2
2
2
2
3
3
3
3
3
2
2
2
2
2
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
0.233
1.391
0.369
1.661
0.065
0.030
0.152
0.027
0.028
0.093
0.036
0.114
0.426
0.028
0.252
0.140
0.311
0.040
0.034
1.193
1.039
1.144
0.551
0.4239
0.2461
0.1190
0.0837
0.0420
0.0552
0.0370
0.0358
0.0446
0.0359
0.0558
>46.6
>7.6
23.2
>6.3
>22
NC
5a
Cl
>33.5
8.5
NC
5b
6a
Cl
3763.1
NC
Cl
>13
6b
7a
Piperidin-1-yl
Pyrrolidin-1-yl
Morpholin-1-yl
4-Methyl-piperazin-1-yl
4-Ethyl-piperazin-1-yl
Piperidin-1-yl
Pyrrolidin-1-yl
Morpholin-1-yl
4-Methyl-piperazin-1-yl
4-Ethyl-piperazin-1-yl
Piperidin-1-yl
Pyrrolidin-1-yl
Morpholin-1-yl
4-Methyl-piperazin-1-yl
4-Ethyl-piperazin-1-yl
Piperidin-1-yl
Pyrrolidin-1-yl
Morpholin-1-yl
4-Methyl-piperazin-1-yl
-
>150.9 0.494
>19.7
>70
NC
>331
>64.2
>351
>326
0.143
0.526
0.142
0.093
NC
7b
7c
>18.5
>67
NC
NC
7d
7e
>98
NC
>101.9 0.819
>11.6
>69
NC
7f
>274
>82.5
>21.6
>321
>38.6
>71.7
>31.2
>238
>270
>7.9
0.140
0.511
0.243
0.137
1.443
0.855
0.248
0.139
0.039
0.945
0.389
0.334
0.189
0.0751
0.6057
0.4621
0.2351
NC
7g
>18.5
>37.8
>66
NC
7h
7i
NC
NC
7j
>6.8
>11.7
>39.1
>68
NC
8a
NC
8b
8c
NC
NC
8d
8e
>273
>10
NC
NC
8f
>9.4
>25.1
>28.3
>48.5
>19.1
>17.1
>22.5
38.9
NC
8g
>8.3
NC
8h
8i
>16.7
>33.8
>42.2
>87.2
109.4
NC
NC
10a
11a
12a
13a
13b
13c
13d
13e
14a
14b
14c
Cl
NC
Cl
NC
Piperidin-1-yl
Pyrrolidin-1-yl
Morpholin-1-yl
4-Methyl-piperazin-1-yl
4-Ethyl-piperazin-1-yl
Piperidin-1-yl
Pyrrolidin-1-yl
Morpholin-1-yl
9.1549
NC
>229.4 0.2023
>47.7
22.7
168.3
>24.6
>24.8
161.3
>26.8
0.4091
0.0387
0.0312
0.1852
0.0401
9.2993
NC
>23.5
>28.4
38.9
NC
7.1973
NC
>24
>167.4 0.5423
>17.2
NC

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4-Methyl-piperazin-1-yl
3
3
-
0.0389
0.0328
0.0204
0.0171
>23.4
>27
0.0199
0.0189
0.4215
0.0162
>45.8
>46.8
>1.8
NC
NC
NC
NC
14d
14e
4-Ethyl-piperazin-1-yl
-
-
>36.5
>49.2
CQ
-
>52
ART
IC50: concentration of drug that results 50% growth inhibition; S.I. Selectivity index = (IC50 for cytotoxicity /
IC50 for antimalarial activity); NC: No cytotoxicity up to 10 µM; Vero: Monkey kidney fibroblasts

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Table 2:Glide docking scores (kcal mol-1) and glide energies of best active compounds
Docking results with wild Pf-DHFR
Docking results with mutant Pf-DHFR
Compounds
XP GScore
Glide Energy
XP GScore
Glide Energy
-8.27
-9.24
-8.00
-7.98
-7.74
-7.95
-7.40
-9.12
-9.17
-9.48
-10.43
-60.28
-51.67
-54.13
-52.11
-55.35
-56.41
-55.51
-40.42
-40.67
-52.71
-57.71
-6.96
-7.59
-7.10
-7.09
-7.56
-7.61
-7.77
-9.05
-8.97
-9.62
-11.15
-53.13
-55.95
-52.74
-55.84
-53.30
-53.84
-59.11
-40.38
-40.24
-53.09
-67.66
7b
7d
7e
7g
7j
8d
8e
Pyrimethamine
Cycloguanil
WR99210
Dihydrofolate

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Table 3: Prediction of Lipinski's rule of 5’ for the most active compounds
mol_MW
(<500)
DonorHB
(<5)
Compounds
AccptHB (<10) QPlogPo/w (<5) RuleOfFive (<4)
474.007
503.048
517.075
488.034
531.102
503.048
517.075
248.71
1
1
1
1
1
1
1
4
4
6
8
6.475
5.494
5.868
6.633
6.188
5.289
5.909
1.82
1
2
2
1
2
2
2
0
0
7b
7d
8
7e
6
7g
8
7j
8d
8
8
8e
3
Pyrimethamine
Cycloguanil
251.72
3.5
1.63