Synthesis of 2,4-diaminopyrimidine core-based derivatives and biological evaluation of their anti-tubercular activities

Article abstract of DOI:10.3390/molecules22101592

Tuberculosis (TB) is a chronic, potentially fatal disease caused by Mycobacterium tuberculosis (Mtb). The dihyrofolate reductase in Mtb (mt-DHFR) is believed to be an important drug target in anti-TB drug development. This enzyme contains a glycerol (GOL) binding site, which is assumed to be a useful site to improve the selectivity towards human dihyrofolate reductase (h-DHFR). There have been previous attempts to design drugs targeting the GOL binding site, but the designed compounds contain a hydrophilic group, which may prevent the compounds from crossing the cell wall of Mtb to function at the whole cell level. In the current study, we designed and synthesized a series of mt-DHFR inhibitors that contain a 2,4-diaminopyrimidine core with side chains to occupy the glycerol binding site with proper hydrophilicity for cell entry, and tested their anti-tubercular activity against Mtb H37Ra. Among them, compound 16l showed a good anti-TB activity (MIC = 6.25 μg/mL) with a significant selectivity against vero cells. In the molecular simulations performed to understand the binding poses of the compounds, it was noticed that only side chains of a certain size can occupy the glycerol binding site. In summary, the novel synthesized compounds with appropriate side chains, hydrophobicity and selectivity could be important lead compounds for future optimization towards the development of future anti-TB drugs that can be used as monotherapy or in combination with other anti-TB drugs or antibiotics. These compounds can also provide much information for further studies on mt-DHFR. However, the enzyme target of the compounds still needs to be confirmed by pure mt-DHFR binding assays.

Full text of DOI:10.3390/molecules22101592

molecules
Article
Synthesis of 2,4-Diaminopyrimidine Core-Based
Derivatives and Biological Evaluation of Their
Anti-Tubercular Activities
Yifan Ouyang 1 , Hao Yang , Peng Zhang , Yu Wang , Sargit Kaur , Xuanli Zhu , Zhe Wang ,
,†
1,†
1
1
2
1
1
1
3,
2,
1,4,
Yutong Sun , Wei Hong *, Yun Fong Ngeow * and Hao Wang
*
1
School of Pharmacy, Ningxia Medical University, Yinchuan 750004, China;
ouyang_pharmacy@163.com (Y.O.); yhao246@163.com (H.Y.); zpzzjzp@163.com (P.Z.);
wangyuxingfu@163.com (Y.W.); jf18700994479@163.com (X.Z.); 13239935127@163.com (Z.W.);
syt931115@163.com (Y.S.)
Department of Pre-Clinical Sciences, Faculty of Medicine and Health Sciences, Universiti Tunku
Abdul Rahman, Sungai Long campus, Kajang 43000, Selangor, Malaysia; sargitk3@gmail.com
School of Chemistry and Chemical Engineering, North Minzu University, Yinchuan 750021, China
KeyLaboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University,
Yinchuan 750004, China
2
3
4
*
Correspondence: hongwei136@hotmail.com (W.H.); ngeowyf@utar.edu.my (Y.F.N.); paxhw@yahoo.co.uk
(H.W.); Tel.: +86-135-1920-2157 (W.H.); +60-390-860-288 (Y.F.N.); +86-135-1929-8012 (H.W.)
†
These authors contributed equally to this work.
Received: 4 September 2017; Accepted: 20 September 2017; Published: 22 September 2017
Abstract: Tuberculosis (TB) is a chronic, potentially fatal disease caused by Mycobacterium tuberculosis (Mtb)
The dihyrofolate reductase in Mtb (mt-DHFR) is believed to be an important drug target in anti-TB drug
development. This enzyme contains a glycerol (GOL) binding site, which is assumed to be a useful site
to improve the selectivity towards human dihyrofolate reductase (h-DHFR). There have been previous
attempts to design drugs targeting the GOL binding site, but the designed compounds contain a
hydrophilic group, which may prevent the compounds from crossing the cell wall of Mtb to function
at the whole cell level. In the current study, we designed and synthesized a series of mt-DHFR
inhibitors that contain a 2,4-diaminopyrimidine core with side chains to occupy the glycerol binding
site with proper hydrophilicity for cell entry, and tested their anti-tubercular activity against Mtb
.
H37Ra. Among them, compound 16l showed a good anti-TB activity (MIC = 6.25 µg/mL) with a
significant selectivity against vero cells. In the molecular simulations performed to understand the
binding poses of the compounds, it was noticed that only side chains of a certain size can occupy the
glycerol binding site. In summary, the novel synthesized compounds with appropriate side chains,
hydrophobicity and selectivity could be important lead compounds for future optimization towards
the development of future anti-TB drugs that can be used as monotherapy or in combination with
other anti-TB drugs or antibiotics. These compounds can also provide much information for further
studies on mt-DHFR. However, the enzyme target of the compounds still needs to be confirmed by
pure mt-DHFR binding assays.
Keywords: anti-tuberculosis; 2,4-diaminopyrimidine derivatives; synthesis
1
. Introduction
There is an urgent need to develop new drugs for the treatment of tuberculosis (TB), a chronic
disabling infection caused by Mycobacterium tuberculosis (Mtb). This pathogen has developed
resistance to standard first- and second-line anti-TB drugs, leaving very few options for effective
therapy. para-Aminosalicylic acid (PAS) is a key anti-TB drug that has been in use for over 60 years.
Molecules 2017, 22, 1592; doi:10.3390/molecules22101592
www.mdpi.com/journal/molecules

Molecules 2017, 22, 1592
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Its anti-mycobacterial mechanism was not clearly understood until recently, when it was reported to be
the pro-drug of an inhibitor of the Mtb dihyrofolate reductase (mt-DHFR) [ ]. mt-DHFR catalyzes the
1
reduction of dihydrofolate to tetrahydrolate in the folate metabolic pathway that leads to the synthesis
of purines, pyrimidines and other proteins. Inhibition of the enzyme would cause cell death via the
inhibition of DNA synthesis. This association of PAS with mt-DHFR inhibition encouraged scientists
to focus once again on mt-DHFR as a potential target for anti-TB drugs.
According to their chemical structures, DHFR inhibitors can be divided into “classical” and
“
non-classical” types [
methotrexate (Figure 1), which is a commonly used anticancer drug [
non-classical inhibitors is 2,4-diaminopyrimidine, as in trimethoprim (Figure 1), an anti-bacterial
drug [ ]. The crystal structures of mt-DHFR (PDB ID: 1DF7, Figure 2) and human DHFR
h-DHFR, PDB ID: 1OHJ), show a glycerol (GOL) binding site in mt-DHFR that does not exist in
2
,
3
]. The structures of classical inhibitors are similar to that of folate, as in
4–6]. The core structure of
7–9
(
h-DHFR. To take advantage of this difference, Threadgill evaluated a group of compounds containing
glycerol-like side chains, among which one compound, El-7a (Figure 1) showed notable selectivity
for mt-DHFR inhibition over h-DHFR [10]. However, this evaluation was conducted using TB5
Saccharomyces cerevisiae carrying mt-DHFR and h-DHFR genes, therefore, there is no direct evidence
to show that El-7a can inhibit the growth of Mtb. Furthermore, the inhibition of Mtb may require
an appropriate lipophilicity in the compound [11]. Even if El-7a were able to selectively inhibit the
mt-DHFR, its low hydrophobicity may prevent it from passing through the Mtb cell wall. Hence,
we designed and synthesized a series of compounds containing more hydrophobic groups on the
6-position of 2,4-diaminopyrimidine to evaluate the ability of these compounds to inhibit Mtb
cells directly.
Figure 1. The structures of “classical” and “non-classical” DHFR inhibitors.
Figure 2. Left: the binding sites of methotrexate (MTX) and glycerol (GOL) in mt-DHFR, in which
MTX is represented as a sticks model, GOL as a ball-stick model, and protein as a molecular surface;
Right: the designed molecule is predicted to be able to occupy the GOL binding site, in which the
molecule is represented as sticks and protein as a molecular surface.

Molecules 2017, 22, 1592
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2
. Results and Discussion
2
.1. Chemistry
The synthesis of the designed compounds 10a-q or 11a-q was carried out in five
steps—chlorination, nucleophilic substitution, iodination, Suzuki reaction and deprotection—according
to our patented method [12], with 2,4-diamino-6-hydroxypyrimidine ( ) as the starting material
Scheme 1). Initially, 2,4-diamino-6-chloropyrimidine ( ) was generated from by treatment with
1
(
2
1
phosphorus oxychloride. After the reaction was quenched with ice water, the solution was hydrolyzed
◦
at 90 C to obtain a good yield (85%) of the target intermediate [13]. This procedure yields pure
without the need for chromatography.
2
NH2
NH2
OH
O
I
N
N
O
H2N
N
O
H2N
N
O
NH2
NH2
3
O
O
5
O
O
POCl3
N
N
NaH, DMSO
NIS
H N
2
N
OH
H2N
N
Cl
NH2
N
NH2
NaH, DMSO
OH
CH CN
3
I
1
2
N
N
H N
2
O
H N
2
N
O
O
O
O
O
O
O
4
6
NH2
N
R1
NH2
N
R1
N
N
H N
2
O
H N
2
O
R1
HO
HO
B
O
O
HO
OH
8
a-q
7
0.25M H2SO4
10a-q
(PPh3)4Pd, K2CO3,
EtOH/Tol/H2O
or C26H44Cl2FeP2Pd,
K2CO3, CH3CN/H2O
NH2
N
R1
NH2
R1
N
N
H2N
O
H N
2
N
O
HO OH
O
O
9
a-q
11a-q
8
8
8
8
8
8
8
8
8
8
8
8
a, 9a, 10a, 11a, R1 = 4-Cl;
m, 9m, 10m, 11m, R1 = 3-CH3-5-CH3-4-SO2NHOCH3;
8
1
b, 9b, 10b, 11b, R = 4-F;
O
c, 9c, 10c, 11c, R1 = 3,4-Cl;
1
d, 9d, 10d, 11d, R = 3-Cl-4-F;
n, 9n, 10n, 11n, R1
4
8
=
N
1
e, 9e, 10e, 11e, R = 4-CF3;
1
O
f, 9f, 10f, 11f, R = 3-CF3;
g, 9g, 10g, 11g, R1 = 4-OCF3;
O
1
h, 9h, 10h, 11h, R = 3-OCF3;
i, 9i, 10i, 11i, R1 = 4-CN
8o, 9o, 10o, 11o, R1
=
4
N
H
OCF3
j, 9j, 10j, 11j, R1 = 4-OCH ;
3
1
8p, 9p, 10p, 11p, R1 = 4-COOCH3;
8q, 9q, 10q, 11q, R1 = 3-COOCH3;
k, 9k, 10k, 11k, R = -3,4,5-OCH3;
l, 9l, 10l, 11l, R1 = 3-CH OCH CF ;
2
2
3
Scheme 1. Synthesis of 2,4-diamino-5-aryl-6-substituted pyrimidine derivatives 10a-q and 11a-q.
The treatment of (S)-2,3-isopropylidene glycerol or (R)-2,3-isopropylidene glycerol with sodium
hydride in dry DMSO generated the corresponding nucleophile, which was then reacted with to give
,4-diamino-6-substituted pyrimidines or in good yield (77%) [14]. Subsequently, the 5-positions
of or were iodinated with N-iodosuccinimide in dry acetonitrile to produce the precursor
,4-diamino-5-iodo-6-substituted pyrimidine derivatives or in 96–98% yields [15]. Initially, we used
a previously synthesized 2,4-diamino-5-bromo-6-substituted pyrimidine derivative as the starting
2
2
3
4
3
4
2
5
6

Molecules 2017, 22, 1592
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material in the model reaction of the Suzuki reactions in order to introduce a substituted aryl group in
the 5-position of the 2,4-diaminopyrimidine core. We tried several conditions, such as reacting with
phenylboronic acid, 4-chlorophenylboronic acid and 4-methoxycarbonylphenylboronic acid, different
catalysts (Pd(PPh ) [16], Pd(dbpf)Cl ) [17], different bases (K CO , K HPO ), different solvents
3
4
2
2
3
2
4
(
(
EtOH/Toluene/H O, THF/H O, CH CN/H O, Dimethoxyethane/H O), different temperatures
2 2 3 2 2
70, 80, 90, 120 C), and different heating modes (microwave or oil bath). Unfortunately, all these
◦
reactions failed. Subsequently, we realized that the iodide replacement in the 5-position of the
,4-diaminopyrimidine core in the Suzuki reaction might be easier than with a bromide. Hence,
the iodides or were allowed to react with substituted phenylboronic acids under Suzuki reaction
conditions (Pd(PPh ) as catalyst, K CO as base, and EtOH/toluene/H O as solvent). However,
2
5
6
7
3
4
2
3
2
the products 8a-o or 9a-o were only obtained in 52–78% yields. Moreover, the presence of an electron
donating (OCH ) or electron withdrawing (F, CF , OCF , ester, amide) group on the substituted
3
3
3
phenylboronic acid
7 did not show high effect of the reaction yields. However, when the products
8
p-q or 9p-q were synthesized by reacting
5
or
6
with 4- or 3-methoxycarbonylphenylboronic acids 7p
1
or 7q in EtOH/toluene/H O, the transesterification product was detected in the H-NMR sprectrum.
2
Hence, different Suzuki reaction conditions were chosen, in which
5 or 6 was reacted with 7p or 7q
with Pd(dbpf)Cl as catalyst, K CO as base and CH CN/H O as solvent, to give 8p-q or 9p-q with
2
2
3
3
2
6
3–78% yields. Subsequently, the compounds 8a-q or 9a-q were deprotected in 0.25 M H SO solution
2 4
to generate the target compounds 10a-q or 11a-q in 68–95% yields.
Subsequently 2,4-diamino-5-aryl-6-substituted pyrimidine derivatives 16a-p were synthesized
from 2,4-diamino-6-chloropyrimidine ( , Scheme 2) following our patented approach [18].
The treatment of substituted methanols 12a-d with sodium hydride in dry DMSO or THF generated the
corresponding nucleophiles, which were reacted with to give 2,4-diamino-6-substituted pyrimidines
3a-d in moderate to good yields (61–79%) [14]. Subsequently, the 5-positions of 13a-d were iodinated
with N-iodosuccinimide in dry acetonitrile to produce the precursor 2,4-diamino-5-iodo-6-substituted
pyrimidine derivatives 14a-d 15], which were used in subsequent Suzuki reactions to generate the
2
2
1
[
target compounds 16a-p in good yields (70–92%) [17].
Scheme 2. Synthesis of 2,4-diamino-5-aryl-6-substituted pyrimidine derivatives 16a-p.
A series of reactions in which iodides 14a-d were used as staring material, was investigated
as shown in Table 1. The iodides 14a-d were reacted with substituted phenylboronic acid 15 in the
◦
presence of Pd(dbpf)Cl and K CO in EtOH/toluene/H O at 90 C for 24 h (Table 1, Entries 1–14
)
2
2
3
2
◦
or in the presence of Pd(dbpf)Cl2 and K CO3 in THF/H O at 70 C for 20 h in a sealed
2
2
tube (Table 1, Entries 15, 16) to generate the desired compounds 16a-p with moderate to good

Molecules 2017, 22, 1592
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yields (51–99%). For the iodide 14a, treatment with different substituted phenylboronic acids
(Table 1, Entries 1–5) resulted in similar yields. For the iodide 14b, reaction with 15
1
5
bearing a 3-trifloromethoxy group resulted in higher yields (Table 1, Entry 7) than when 15
bore a 4-trifloromethoxy group (Table 1, Entry 6). For the iodide 14c, treatment with 15
substituted with a 3-trifloromethoxyanilinocarbonyl group or 3-(2,2,2-trifloroethoxymethyl) group
(Table 1, Entries 10, 12) resulted in higher yields than with 4-trifloromethoxy, 3-trifloromethoxy
and 3,5-dimethyl-4-(N-methoxyaminosulfonyl) groups substituted on 15 (Table 1, Entries 8, 9, 11).
Especially for the iodide 14d, reaction with 15 bearing a 4-trifloromethoxy or 3-trifloromethoxy group
(Table 1, Entries 13, 14) resulted in much higher yields than with 15 bearing a 4-methoxycarbonyl
or 3-methoxycarbonyl group (Table 1, Entries 15, 16). The presumption is that the ester group on
this Suzuki reaction could be affected by transesterification in the solvent (EtOH/toluene/H O),
2
1
which could be detected in H-NMR. Thus, in these reactions, we chose THF/H O as the solvent to
2
avoid the transesterification.
Table 1.
Synthesis of 2,4-diamino-5-aryl-6-substituted pyrimidine derivatives 16a-p via
Suzuki reactions.
Entry
R2
R3
Product
16a a
Yield c (%)
Clog P d
1
2
3
-CH OCH (14a)
-CH OCH (14a)
-CH OCH (14a)
4-OCF3
3-OCF3
3-CH OCH CF
74
74
70
2.99
2.99
2.29
2
3
a
16b
2
3
a
16c
2
3
2
2
3
3
-CH -5-CH -4-
3 3
16d a
4
-CH OCH (14a)
73
1.19
2
3
SO NHOCH
2
3
5
-CH OCH (14a)
16e a
16f a
70
3.59
2
3
6
7
-CH CH OCH (14b)
4-OCF3
3-OCF3
75
94
3.37
3.37
2
2
3
a
-CH CH OCH (14b)
16g
2
2
3
8
9
4-OCF3
3-OCF3
16h a
16i a
16j a
16k a
87
73
91
72
2.81
2.81
2.11
1.01
(
(
(
(
14c)
14c)
14c)
14c)
1
0
3-CH OCH CF
2 2 3
3
-CH -5-CH -4-
3 3
SO2NHOCH3
1
1
1
2
3
4
5
6
16l a
16m a
16n a
16o b
16p b
99
91
91
68
51
3.42
3.56
3.56
2.39
2.39
(
14c)
1
1
1
1
4-OCF3
3-OCF3
N
N
N
N
N
N
N
N
N
(14d)
N
N
N
(14d)
(14d)
(14d)
4-COOCH3
3-COOCH3
Reaction Conditions: a Pd(dbpf)Cl
0.02 mmol) and K CO
(0.02 mmol) and K
CO
in EtOH/toluene/H
O at 90 C for 24 h; Pd(dbpf)Cl
◦
b
2
2
3
2
2
◦
c
d
(
2
3
in THF/H
2
O at 70 C for 20 h in sealed tube; Isolated yields; Calculated using
ChemBioDraw (PerkinElmer, Waltham, MA, USA) 12.0.

Molecules 2017, 22, 1592
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2
.2. Determination of In Vitro Anti-Tubercular Activity
2
Based on the different R substituents on the 2,4-diamino-5-aryl-6-substituted pyrimidine
2
derivatives, the compounds can be divided into four types: (1) the R substituents bearing hydroxy
2
2
groups (10a-q
,
11a-q); (2) the R substituents bearing alkoxy groups (16a-g); (3) the R substituents
2
bearing thiazole groups (16h-l); (4) the R substituents bearing phenyl substituted triazole groups
(
16m-p). Only compounds containing the thiazole group act as Mtb inhibitors. Among this group of
compounds, five compounds (16h-l) showed potentially useful inhibitory effects, with 16l showing the
lowest MIC (6.25 g/mL or 12.45 M) and MBC (12.5 g/mL) (Table 2). In order to see the selectivity of
6l against mammalian cells, the MTT assay was performed on vero cells, and the IC50 on cells viability
µ
µ
µ
1
was found to be around 50.22 µM. The selectivity ratio of 16l on H37Ra vs vero cells is around 4-fold.
Table 2. Minimum inhibitory concentrations (MIC) and minimum bactericidal concentrations (MBC)
of compounds 16h-l showing anti-tubercular activity.
Compound
6h
R2
R3
MIC/MBC (µg/mL)
1
4-OCF3
25/25
1
6i
6j
3-OCF3
50/50
25/25
1
3-CH OCH CF
2 2 3
3
-CH -5-CH -4-
3 3
1
6k
100/100
SO NHOCH
2
3
1
6l
6.25/12.5
Rifampicin
0.313/0.313
2
.3. Molecular Docking and Simulation
Through the structural analysis of the compounds, the Clog P of El-7a was noticed to be
which showed the compound El-7a to be very hydrophilic, and led us to assume it would not be
able to cross the Mtb cell wall. This assumption was indirectly confirmed by the observation that
−
0.17,
the hydrophilic compounds 10a-q and 11a-q (analogs of El-7a, with Clog P around
−
1 to 2), could
not inhibit the growth of Mtb. Based on the above assumption, more hydrophobic compounds were
analyzed by using molecular docking and molecular dynamic simulations, and based on the size of the
substituents on the 6-position of 2,4-diaminopyrimidine, they were divided into three groups, which
are large side chain groups (compounds 16m-p), medium side chain groups (compounds 16h-l) and
small side chain groups (compounds 16a-g). With molecular docking, it was noticed that the large side
chain group, which contains the 1-benzyl-1H-1,2,3-triazole-4-methoxy group on the 6-position, cannot
fit into the GOL binding site (Figure 3a), and this could be the reason why this group of compounds did
not show any inhibition effects on Mtb. Although the small side chain group derivatives (compounds
1
6a-g), which contain the methoxyethoxy or methoxypropoxy group on the 6-positions, can fit into the
GOL binding site (Figure 3b,c), they cannot form strong interactions or fully fill the GOL binding site.

Molecules 2017, 22, 1592
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(
a)
(b)
(
c)
Figure 3. (a) Compound 16m with large side chain group and the binding sites of glycerol (GOL) in
mt-DHFR, in which compound 16m is represented as a sticks model, GOL as a dotted line model and
protein as a molecular surface; ( ) the small side chain group of compound 16f can fit into the GOL
b,c
binding site, in which the molecule is represented as sticks and protein as a molecular surface.
The molecular docking showed that the medium side chain group (compounds 16h-l),
which contain a (thiazol-5-yl)methoxy on the 6-position, can fit into the GOL binding site properly,
and a molecular dynamics simulation was performed to understand the binding of compound 16l
to mt-DHFR. During 100 ns simulations, 16l was stable in the binding site, and the side chain of
compounds 16h-l occupied the GOL binding site along the full simulation (Figure 2). The free energy
calculation showed that the binding free energy was
−
3.47 Kcal/mol (Table 3), which indicated that
1
6l can bind with mt-DHFR tightly. The free energy contributions of each residue was calculated, and
contributions greater than
−
0.5 Kcal/mol were recorded (Ile20, Arg23, Phe31, Leu50, Pro51 and Val54)
(Figure 4 Left). Most of these residues showed a strong VDW interaction, except Phe31 and Arg23
which formed a H-bond with 16l. Arg23 could also form strong interactions with the trifluoromethoxy
group (Figure 4 Right).
Table 3. Binding free energies (Kcal/mol) of compound 16l in mt-DHFR.
Simulations ∆Evdw
42.37
0.14
∆Eele
∆Gpb
∆Gnp
∆Ggas
∆Gsolv
∆Gmmpbsa T∆S
∆Gbinding
−3.47
−
−18.16
± 0.24
37.55 ±
−5.62
± 0.01
−60.53
± 0.30
31.93 ±
−28.60
± 0.18
−25.13
± 0.73
1
6l
±
0.33
0.32

Molecules 2017, 22, 1592
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0
-
-
0.5
-
1
1.5
-
2
Figure 4. Left: The residues whose binding free energy contributions are greater than
Right: The interactions between key residues and compound 16l.
−
0.5 Kcal/mol;
Therefore, through the molecular docking and molecular dynamic simulations, we believe that
the compounds containing the (thiazol-5-yl)methoxy side chain (medium size group), can fully occupy
the GOL binding site, and have reasonable properties. Therefore, such compounds could be used as
the lead compounds for further anti-TB drug discovery studies.
3
. Materials and Methods
3
.1. General Information
All reagents and solvents were purchased from the suppliers and used directly in the experiments.
THF was dried by distillation ver sodium benzophenone. TLC was carried out using silica gel 60
pre-coated aluminium plates (0.20 mm thickness) from Macherey-Nagel (Darmstadt, Germany) with
visualisation by UV light (254 nm). Flash chromatography was performed on silica gel (particle size
4
0–63
µ
m). IR spectra were recorded on a Tensor 27 spectrometer (Bruker, Ettlingen, Germany) using
1
KBr discs. H-NMR spectra were obtained from an AVANCE III 400 spectrometer (Bruker, Fällanden
Switzerland). The chemical shifts, given as
1
δ
values, were quoted in parts per million (ppm); H-NMR
chemical shifts were measured relative to internal tetramethylsilane; Apparent coupling constants
absolute values), J, were measured in Hertz and multiplicities quoted as singlet (s), doublet (d),
triplet (t), quartet (q) or combinations thereof as appropriate. Mass spectra were obtained from an
545 Accurate-Mass Q-TOF LC/MS (Agilent Technologies, Santa Clara, CA, USA). Melting points
(
6
were determined using a WRS-1B melting point measurement instrument (Shanghai, China) and
were uncorrected.
3
.2. ChemistryIt
,4-Diamino-6-chloropyrimidine (
2
2
). 2,4-Diamino-6-hydroxypyrimidine (
1
) (1.00 g, 7.93 mmol) was
◦
added to POCl (9 mL), and stirred at 97 C for 17 h. The reaction solution was added to ice water
slowly, and then stirred at 90 C for 1 h. The pH of this solution was adjusted to 8 with NaOH,
3
◦
and then it was extracted with EtOAC (150 mL
×
3). The combined organic layers were dried with
◦
Na SO , filtered and concentrated to give white solid 0.97 g, yield 85%. m.p. 200.2–200.4 C; IR
2
4
−
1
1
(
KBr): υmax/cm 3449 (NH), 3327 (NH), 1642 (C=N), 1581 (C=C), 1551 (C=C), 795 (C-Cl); H-NMR
+
(
DMSO-d6)
δ
6.57 (s, 2H, NH ), 6.31 (s, 2H, NH ), 5.69 (s, 1H, Ar-H); ES-MS 145.0 (M + H) ; HRMS
2
2
+
Calcd. for C H ClN O 145.0281, found 145.0276.
16
20
4
3

Molecules 2017, 22, 1592
9 of 27
General Procedure for the Synthesis of Compounds 3 and 4
Under argon, to a solution of (S)-2,3-isopropylideneglycerol or (R)-2,3-isopropylideneglycerol
0
.50 mL (4.0 mmol) in dry DMSO (5 mL) was added NaH 0.20 g (60%, 5.0 mmol) and stirred at room
temperature for 1 h. 2,4-Diamino-6-chloropyrimidine (
at 90 C for 8 h. The reaction solution was quenched with sat NH Cl (20 mL) and extracted with
2
, 0.29 g, 2.0 mmol) was added and stirred
◦
4
EtOAc (30 mL
×
3), and the combined organic layers dried with Na SO , filtered and concentrated.
2 4
The residue was purified by column chromatography on silica gel using CH Cl /CH OH (50:1, v/v)
2
2
3
as the eluting solvent to give compounds 3 or 4.
(
R)-2,4-Diamino-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine (3). White solid 0.37 g, yield 77%;
◦
−1
m.p. 89.7–91.0 C; IR: υmax/cm 3474 (NH), 3452 (NH), 3373 (NH), 3359 (NH), 1668 (C=N),
1
1
627 (C=N), 1593 (C=C), 1200 (C-O-C), 1157 (C-O-C), 1082 (C-O-C), 1052 (C-O-C); H-NMR (CDCl )
3
δ
5.28 (s, 1H, Ar-H), 4.71 (s, 2H, NH ), 4.53 (s, 2H, NH ), 4.41 (q, J = 6.0, 1H, CH), 4.25 (d, J = 5.6, 2H,
2 2
OCH ), 4.11 (dd, J = 8.2, J = 6.4, 1H, OCH ), 3.81 (dd, J = 8.4, J = 6.4, 1H, OCH ), 1.44 (s, 3H, CH ),
2
1
2
2
1
2
2
3
+
+
1
.38 (s, 3H, CH ); ES-MS 241.1 (M + H) ; HRMS Calcd. for C H ClN O 241.1301, found 241.1303.
3 16 20 4 3
(
S)-2,4-Diamino-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine (4). White solid 10.32 g, yield 77%;
◦
−1
m.p. 87.6–88.9 C; IR: υmax/cm 3474 (NH), 3451 (NH), 3373 (NH), 3358 (NH), 1670 (C=N),
1
1
626 (C=N), 1592 (C=C), 1199 (C-O-C), 1159 (C-O-C), 1085 (C-O-C), 1054 (C-O-C); H-NMR (CDCl )
3
δ
5.29 (s, 1H, Ar-H), 4.67 (s, 2H, NH ), 4.50(s, 2H, NH ), 4.41 (q, J = 6.0, 1H, CH), 4.29–4.22 (m, 2H,
2 2
OCH ), 4.11 (dd, J = 8.8, J = 6.4, 1H, OCH ), 3.82 (dd, J = 8.4, J = 6.0, 1H, OCH ), 1.45 (s, 3H, CH ),
2
1
2
2
1
2
2
3
+
+
1
.38 (s, 3H, CH ); ES-MS 241.1 (M + H) ; HRMS Calcd. for C H ClN O 241.1301, found 241.1306.
3 16 20 4 3
General Procedure for the Synthesis of Compounds 5 and 6
Under argon, to a solution of or (7.18 g, 29.88 mmol) in dry CH CN (100 mL) was added
N-iodosuccinimide 10.09 g (44.83 mmol) and stirred at room temperature for 1 h. The reaction
solution was diluted with EtOAc (500 mL), washed by 5% NaHSO (500 mL), NaHCO (500 mL)
3
4
3
3
3
and H O (500 mL), and dried with Na SO , filtered and concentrated. The residue was purified by
2
2
4
column chromatography on silica gel using CH Cl /CH OH (100:1, v/v) as the eluting solvent to give
2
2
3
compounds 5 or 6.
(
9
1
R)-2,4-Diamino-5-iodo-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine (5). White solid 13.42 g, yield
◦
−1
8%; m.p. 135.5–136.8 C; IR: υmax/cm 3464 (NH), 3402 (NH), 3356 (NH), 1649 (C=N), 1627 (C=N),
1
550 (C=C), 1200 (C-O-C), 1157 (C-O-C), 1082 (C-O-C), 1052 (C-O-C), 476 (C-I); H-NMR (CDCl )
δ
3
5
.06 (s, 2H, NH ), 4.69 (s, 2H, NH ), 4.44–4.37 (m, 2H, OCH and CH), 4.30–4.25 (m, 1H, OCH ), 4.12
2
2
2
2
(
dd, J = 8.4, J = 6.4, 1H, OCH ), 3.96 (dd, J = 8.4, J = 6.0, 1H, OCH ), 1.47 (s, 3H, CH ), 1.39 (s, 3H,
1 2 2 1 2 2 3
+
+
CH ); ES-MS 367.0 (M + H) ; HRMS Calcd. for C H ClN O 367.0267, found 367.0265.
3
16 20
4
3
(
9
S)-2,4-Diamino-5-iodo-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine (
6%; m.p. 135.4–136.7 C; IR: υmax/cm 3465 (NH), 3401 (NH), 3360 (NH), 3310 (NH), 1650 (C=N),
6
). White solid 10.72 g, yield
◦
−1
1
623 (C=N), 1549 (C=C), 1200 (C-O-C), 1157 (C-O-C), 1133 (C-O-C), 1096 (C-O-C), 1071 (C-O-C), 1045
1
(C-O-C), 478 (C-I); H-NMR (CDCl )
δ
5.05 (s, 2H, NH ), 4.68 (s, 2H, NH ), 4.37–4.34 (m, 2H, OCH
2
3
2
2
and CH), 4.30–4.25 (m, 1H, CH ), 4.12 (dd, J = 8.4, J = 6.4, 1H, OCH ), 3.96 (dd, J = 8.4, J = 6.0, 1H,
2
1
2
2
1
2
+
+
OCH ), 1.47 (s, 3H, CH ), 1.39 (s, 3H, CH ); ES-MS 367.0 (M + H) ; HRMS Calcd. for C H ClN O
3
2
3
3
16 20
4
3
67.0267, found 367.0268.
General Procedure for the Synthesis of Compounds 8a-q and 9a-q
(
A) Under argon, to a mixed solution of EtOH/toluene (1:2, 60 mL) was added compound
5
or
6
−
4
(
2.73 mmol), substituted phenylboronic acid (
K CO (3 M, 3.00–5.50 mL) consecutively and then stirred at 90 C for 1–2 h. The reaction solution
7
) (3.00–5.46 mmol), Pd(PPh ) (1.38
×
10 mmol) and
3
4
◦
2
3
was extracted with EtOAc (30 mL
×
3), and the combined organic layers were washed by H O and
2

Molecules 2017, 22, 1592
10 of 27
dried with Na SO , filtered and concentrated. The residue was purified by column chromatography
2
4
on silica gel using CH Cl /CH OH (80:1, v/v) as the eluting solvent to the desired compounds.
2
2
3
(
B) In a pressure tube, to a mixed solution of CH CN/H O (1:1, 40 mL) was added compound 5 or
3 2
−
4
6
(2.73 mmol), substituted phenylboronic acid 7p or 7q (4.10 mmol), Pd(dbpf)Cl (2.73 × 10 mmol
)
2
◦
and K CO (4.10 mmol) consecutively and then stirred at 60 C for 8 h. The reaction solution was
2
3
extracted with EtOAc (30 mL
×
3), and the combined organic layers were washed by H O and dried
2
with Na SO , filtered and concentrated. The residue was purified by column chromatography on silica
2
4
gel using CH Cl /CH OH (60:1, v/v) as the eluting solvent to the desired compounds.
2
2
3
(
R)-2,4-Diamino-5-(4-chlorophenyl)-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine (8a). Method A.
◦
−1
White solid 0.64 g, yield 67%; m.p. 171.2–172.8 C; IR: υmax/cm 3475 (NH), 3454 (NH), 3305 (NH),
3
315 (NH), 1649 (C=N), 1620 (C=N), 1592 (C=C), 1549 (C=C), 1479 (C=C), 1160 (C-O-C), 1144 (C-O-C),
1
1089 (C-O-C), 794 (C-Cl); H-NMR (CDCl )
δ
7.36 (d, J = 8.4, 2H, Ar-H), 7.25 (d, J = 8.0, 2H, Ar-H), 4.69
3
(
(
s, 2H, NH ), 4.52 (s, 2H, NH ), 4.36 (dd, J = 10.8, J = 4.4, 1H, OCH ), 4.31–4.26 (m, 1H, CH), 4.20
2 2 1 2 2
dd, J = 10.8, J = 5.6, 1H, OCH ), 3.97 (dd, J = 8.4, J = 6.4, 1H, OCH ), 3.72 (dd, J = 8.4, J = 6.0, 1H,
1
2
2
1
2
2
1
2
+
+
OCH ), 1.32 (s, 3H, CH ), 1.28 (s, 3H, CH ); ES-MS 351.1 (M + H) ; HRMS Calcd. for C H ClN O
3
2
3
3
16 20
4
3
51.1224, found 351.1222.
(
R)-2,4-Diamino-5-(4-fluorophenyl)-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine (8b). Method A.
◦
−1
White solid 0.61 g, yield 74%; m.p. 162.3–163.0 C; IR: υmax/cm 3526 (NH), 3483 (NH), 3369 (NH),
3
312 (NH), 1647 (C=N), 1626 (C=N), 1593 (C=C), 1558 (C=C), 1510 (C=C), 1485(C=C), 1383 (C-F), 1160
1
(C-O-C), 1128 (C-O-C), 1105 (C-O-C), 1090 (C-O-C); H-NMR (CDCl )
δ
7.27 (dd, J = 8.8, J = 5.6,
3
1
2
2
H, Ar-H), 7.08 (t, J = 8.8, 2H, Ar-H), 4.69 (s, 2H, NH ), 4.52 (s, 2H, NH ), 4.36 (dd, J = 10.8, J = 4.0,
2 2 1 2
1
1
H, OCH ), 4.31–4.26 (m, 1H, CH), 4.20 (dd, J = 10.8, J = 5.6, 1H, OCH ), 3.96 (dd, J = 8.4, J = 6.4,
2 1 2 2 1 2
H, OCH ), 3.71 (dd, J = 8.4, J = 6.0, 1H, OCH ), 1.32 (s, 3H, CH ), 1.27 (s, 3H, CH ); ES-MS 335.2
2
1
2
2
3
3
+
+
(M + H) ; HRMS Calcd. for C H FN O 335.1519, found 335.1515.
16 20 4 3
(
R)-2,4-Diamino-5-(3,4-dichlorophenyl)-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine (8c). Method A.
◦
−1
White solid 0.55 g, yield 52%; m.p. 164.1–165.9 C; IR: υmax/cm 3487 (NH), 3378 (NH), 3316 (NH),
1
1
651 (C=N), 1624 (C=N), 1600 (C=C), 1556 (C=C), 1489 (C=C), 1154 (C-O-C), 1134 (C-O-C), 1191 (C-O-C),
1
073 (C-O-C), 795 (C-Cl); H-NMR (CDCl )
δ 7.45 (d, J = 8.0, 1H, Ar-H), 7.44 (d, J = 2.0, 1H, Ar-H),
3
7
.17 (dd, J = 8.0, J = 2.0, 1H, Ar-H), 4.73 (s, 2H, NH ), 4.56 (s, 2H, NH ), 4.35 (dd, J = 10.4, J = 4.4,
1 2 2 2 1 2
1
1
H, OCH ), 4.33–4.27 (m, 1H, CH), 4.22 (dd, J =10.4 , J = 5.2, 1H, OCH ), 3.99 (dd, J = 8.4, J = 6.0,
2 1 2 2 1 2
H, OCH ), 3.73 (dd, J = 8.4, J = 6.0, 1H, OCH ), 1.33 (s, 3H, CH ), 1.30 (s, 3H, CH ); ES-MS 385.1
2
1
2
2
3
3
+
+
(M + H) ; HRMS Calcd. for C H Cl N O 385.0834, found 385.0830.
16 19 2 4 3
(
R)-2,4-Diamino-5-(3-chloro-4-fluorophenyl)-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine
(
8d).
◦
−1
Method A. White solid 0.64 g, yield 64%; m.p. 149.1–150.1 C; IR: υmax/cm 3484 (NH), 3382 (NH),
3
320 (NH), 1650 (C=N), 1621(C=N), 1594 (C=C), 1553 (C=C), 1502 (C=C), 1372 (C-F), 1160 (C-O-C),
1
1
7
4
3
092 (C-O-C), 1065 (C-O-C), 797 (C-Cl); H-NMR (CDCl )
.20–7.14 (m, 2H, Ar-H), 4.71 (s, 2H, NH ), 4.53 (s, 2H, NH ), 4.35 (dd, J = 10.6, J = 4.2, 1H, OCH ),
.32–4.27 (m, 1H, CH), 4.22 (dd, J = 10.6, J = 5.4, 1H, OCH ), 3.98 (dd, J = 8.4, J = 6.0, 1H, OCH ),
.72 (dd, J = 8.4, J = 6.0, 1H, OCH ), 1.33 (s, 3H, CH ), 1.29 (s, 3H, CH ); ES-MS 369.1 (M + H) ;
δ
7.37 (dd, J = 7.2, J = 1.6, 1H, Ar-H),
3
1
2
2
2
1
2
2
1
2
2
1
2
2
+
1
2
2
3
3
+
HRMS Calcd. for C H ClFN O , 369.1130, found 369.1128.
16
19
4
3
(
R)-2,4-Diamino-5-(4-trifluoromethylphenyl)-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine
(
8e).
◦
−1
Method A. Light yellow solid 0.72 g, yield 69%; m.p. 126.6–127.2 C; IR: υmax/cm 3530 (NH), 3511
(
(
NH), 3444 (NH), 3420 (NH), 1649 (C=N), 1609 (C=N), 1593 (C=C), 1558 (C=C), 1491 (C=C), 1171
1
C-O-), 1128 (C-O-C), 1094 (C-O-C), 1072 (C-O-C), 1046 (C-O-C); H-NMR (CDCl )
δ
7.64 (d, J = 8.2,
3
2
H, Ar-H), 7.46 (d, J = 8.2, 2H Ar-H), 4.73 (s, 2H, NH ), 4.56 (s, 2H, NH ), 4.37 (dd, J = 11.2, J = 4.2,
2 2 1 2
1
1
H, OCH ), 4.32–4.27 (m, 1H, CH), 4.22 (dd, J = 11.2, J = 5.6, 1H, OCH ), 3.97 (dd, J = 8.4, J = 6.0,
2 1 2 2 1 2
H, OCH ), 3.71 (dd, J = 8.4, J = 6.0, 1H, OCH ), 1.32 (s, 3H, CH ), 1.24 (s, 3H, CH ); ES-MS 385.1
2
1
2
2
3
3
+
+
(M + H) ; HRMS Calcd. for C H F N O 385.1488, found 385.1485.
17 20 3 4 3

Molecules 2017, 22, 1592
11 of 27
(
R)-2,4-Diamino-5-(3-trifluoromethylphenyl)-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine
(
8f).
◦
−1
Method A. Light yellow solid 0.64 g, yield 68%; m.p. 126.0–126.8 C; IR: υmax/cm 3467 (NH), 3418
(
(
NH), 3336 (NH), 1650 (C=N), 1625 (C=N), 1593 (C=C), 1556 (C=C), 1523 (C=C), 1163 (C-O-C), 1118
1
C-O-C), 1106 (C-O-C), 1068 (C-O-C); H-NMR (CDCl )
δ
7.61 (s, 1H, Ar-H), 7.56–7.49 (m, 3H, Ar-H),
3
4
.73 (s, 2H, NH ), 4.55 (s, 2H, NH ), 4.36 (dd, J = 10.6, J = 4.2, 1H, OCH ), 4.31–4.26 (m, 1H, CH), 4.22
2 2 1 2 2
(
dd, J = 10.6, J = 5.8, 1H, OCH ), 3.96 (dd, J = 8.4, J = 6.4, 1H, OCH ), 3.70 (dd, J = 8.4, J = 6.0, 1H,
1 2 2 1 2 2 1 2
+
+
OCH ), 1.32 (s, 3H, CH ), 1.25 (s, 3H, CH ); ES-MS 385.1 (M + H) ; HRMS Calcd. for C H F N O
3
2
3
3
17 20
3
4
3
85.1488, found 385.1491.
(
R)-2,4-Diamino-5-(4-trifluoromethoxyphenyl)-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine (8g).
◦
−1
Method A. Yellow solid 0.77 g, yield 70%; m.p. 37.1–38.0 C; IR: υmax/cm 3482 (NH), 3368 (NH),
1
1
611 (C=N), 1560 (C=C), 1510 (C=C), 1374 (C-F), 1161 (C-O-C), 1092 (C-O-C), 1052 (C-O-C); H-NMR
(
CDCl3) δ 7.35 (d, J = 8.4, 2H, Ar-H), 7.24 (d, J = 8.4, 1H, Ar-H), 4.71 (s, 2H, NH ), 4.54 (s, 2H, NH ),
2 2
4
3
3
.38 (dd, J = 10.8, J = 4.0, 1H, OCH ), 4.32–4.27 (m, 1H, CH), 4.21 (dd, J = 10.8, J = 5.6, 1H, OCH ),
1 2 2 1 2 2
.96 (dd, J = 8.4, J = 6.4, 1H, OCH ), 3.72 (dd, J = 8.4, J = 6.4, 1H, OCH ), 1.32 (s, 3H, CH ), 1.23 (s,
1
2
2
1
2
2
3
+
+
H, CH ); ES-MS 401.1(M + H) ; HRMS Calcd. for C H F N O 401.1437, found 401.1434.
3
17 20
3
4
4
(
R)-2,4-Diamino-5-(3-trifluoromethoxyphenyl)-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine (8h).
◦
−1
Method A. Yellow solid 0.72 g, yield 66%; m.p. 36.2–37.1 C; IR: υmax/cm 3488 (NH), 3361 (NH),
1
1
611 (C=N), 1560 (C=C), 1379 (C-F), 1158 (C-O-C), 1082 (C-O-C), 1047 (C-O-C); H-NMR (CDCl )
δ
3
7.41 (t, J = 8.0, 1H, Ar-H), 7.28–7.26 (m, 1H Ar-H), 7.21 (s, 1H, Ar-H), 7.14 (d, J = 8.4, 1H, Ar-H), 4.73
(
(
s, 2H, NH ), 4.58 (s, 2H, NH ), 4.36 (dd, J = 10.8, J = 4.0, 1H, OCH ), 4.32–4.26 (m, 1H, CH), 4.21
2
2
1
2
2
dd, J1 = 10.8, J = 6.0, 1H, OCH ), 3.97 (dd, J = 8.4, J = 6.4, 1H, OCH ), 3.72 (dd, J = 8.4, J = 6.0, 1H,
2
2
1
2
2
1
2
+
+
OCH ), 1.32 (s, 3H, CH ), 1.27 (s, 3H, CH ); ES-MS 401.1 (M + H) ; HRMS Calcd. for C H F N O
4
2
3
3
17 20
3
4
4
01.1437, found 401.1440.
(
R)-2,4-Diamino-5-(4-cyanophenyl)-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine (8i). Method A.
◦
−1
White solid 0.62 g, yield 67%; m.p. 209.3–209.9 C; IR: υmax/cm 3482 (NH), 3456 (NH), 3370 (NH),
3
332 (NH), 2228 (CN), 1655 (C=N), 1621 (C=N), 1585 (C=C), 1564 (C=C), 1157 (C-O-C), 1091 (C-O-C),
1
1
051 (C-O-C); H-NMR (CDCl )
δ
7.68 (d, J = 8.4, 2H, Ar-H), 7.47 (d, J = 8.4, 2H Ar-H), 4.76 (s, 2H, NH2),
3
4
.57 (s, 2H, NH ), 4.36 (dd, J = 10.8, J = 4.0, 1H, OCH ), 4.32–4.27 (m, 1H, CH), 4.23 (dd, J1 = 10.8
,
2
1
2
2
J2 = 6.0, 1H, OCH ), 3.97 (dd, J = 8.4, J = 6.4, 1H, OCH ), 3.70 (dd, J = 8.4, J = 6.0, 1H, OCH ), 1.32
2
1
2
2
1
2
2
+
+
(
s, 3H, CH ), 1.28 (s, 3H, CH ); ES-MS 342.1 (M + H) ; HRMS Calcd. for C H N O 342.1566, found
3 3 17 20 5 3
3
42.1570.
(
R)-2,4-Diamino-5-(4-methoxyphenyl)-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine (8j). Method
◦
−1
A. White solid 0.64 g, yield 68%; m.p. 119.7–120.2 C; IR: υmax/cm 3456 (NH), 3348 (NH), 1643
C=N), 1617(C=N), 1594 (C=C), 1560 (C=C), 1512 (C=C), 1171 (C-O-C), 1082 (C-O-C), 1050 (C-O-C);
(
1
H-NMR (CDCl3)
δ 7.21 (d, J = 8.8, 2H, Ar-H), 6.93 (d, J = 8.8, 2H, Ar-H), 4.65 (s, 2H, NH ), 4.53 (s, 2H,
2
NH ), 4.37 (dd, J = 10.8, J = 4.0, 1H, OCH ), 4.32–4.26 (m, 1H, CH), 4.19 (dd, J = 10.8, J = 6.0, 1H,
2
1
2
2
1
2
OCH ), 3.96 (dd, J = 8.4, J = 6.4, 1H, OCH ), 3.82 (s, 3H, OCH ), 3.74 (dd, J = 8.4, J = 6.4, 1H, OCH ),
2
1
2
2
3
1
2
2
+
+
1
.32 (s, 3H, CH ), 1.28 (s, 3H, CH ); ES-MS 347.2 (M + H) ; HRMS Calcd. for C H N O 347.1719,
3 3 17 23 4 4
found 347.1723.
(
R)-2,4-Diamino-5-(3,4,5-trimethoxyphenyl)-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine
(
8k).
◦
−1
Method A. White solid 0.70 g, yield 63%; m.p. 183.8–184.1 C; IR: υmax/cm 3458 (NH), 3421 (NH),
3
339 (NH), 1661 (C=N), 1631(C=N), 1588 (C=C), 1557 (C=C), 1511 (C=C), 1164 (C-O-C), 1128 (C-O-C),
1
1
2
6
074 (C-O-C); H-NMR (CDCl )
δ
6.54 (s, 2H, Ar-H), 4.67 (s, 2H, NH ), 4.62 (s, 2H, NH ), 4.38–4.31 (m,
3
2
2
H, OCH ), 4.27–4.20 (m, 1H, CH), 4.01 (dd, J = 8.4, J = 6.4, 1H, OCH ), 3.87 (s, 3H, OCH ), 3.84 (s,
2
1
2
2
3
H, OCH3
×
2), 3.77 (dd, J = 8.0, J = 6.0, 1H, OCH ), 1.32 (s, 3H, CH ), 1.28 (s, 3H, CH ); ES-MS 407.2
1 2 2 3 3
+
+
(M + H) ; HRMS Calcd. for C H N O 407.1931, found 407.1927.
19 27 4 6
(
(
R)-2,4-Diamino-5-[3-(2,2,2-trifloroethoxymethyl)phenyl]-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]-pyrimidine
◦ −1
8l). Method A. Yellow solid 0.72 g, yield 62%; m.p. 32.2–33.2 C; IR: υmax/cm 3485 (NH), 3367

Molecules 2017, 22, 1592
12 of 27
(
NH), 1609 (C=N), 1559 (C=C), 1491 (C=C), 1373 (C-F), 1159 (C-O-C), 1093 (C-O-C), 1049 (C-O-C);
1
H-NMR (CDCl ) δ 7.40 (t, J = 7.6, 1H, Ar-H), 7.30–7.27 (m, 3H, Ar-H), 4.68 (s, 4H, CH , NH ), 4.56 (s,
3
2
2
2
H, NH ), 4.35 (dd, J = 10.8, J = 4.0, 1H, OCH ), 4.32–4.26 (m, 1H, CH), 4.22 (dd, J = 10.4, J2 = 5.6,
2 1 2 2 1
1
H, OCH ), 3.96 (dd, J = 8.4, J = 6.4, 1H, OCH ), 3.87 (q, J = 8.8, 2H, CF CH ), 3.73 (dd, J = 8.0,
2
1
2
2
3
2
+
1
J = 5.8, 1H, OCH ), 1.31 (s, 3H, CH ), 1.25 (s, 3H, CH ); ES-MS 429.2(M + H) ; HRMS Calcd. for
2
2
3
3
+
C H F N O 429.1750, found 429.1747.
19
24
3
4
4
(
R)-2,4-Diamino-5-[3,5-dimethyl-4-(N-methoxyaminosulfonyl)phenyl]-6-[4-(2,2-dimethyl-1,3-dioxolane)-
◦
methoxy]pyrimidine (8m). Method A. Light yellow solid 0.69 g, yield 56%; m.p. 157.7–158.8 C; IR:
υmax/cm 3485 (NH), 3446 (NH), 3347 (NH), 3223 (NH), 1640 (C=N), 1617 (C=N), 1591 (C=C), 1562
(
−
1
1
C=C), 1490 (C=C), 1170 (C-O-C), 1096 (C-O-C), 1053 (C-O-C); H-NMR (CDCl )
δ
7.43 (s, 1H, NH),
3
7
.18 (s, 2H, Ar-H), 4.74 (s, 2H, NH ), 4.61 (s, 2H, NH ), 4.35 (dd, J = 10.2, J = 5.0, 1H, OCH ), 4.32–4.27
2 2 1 2 2
(
(
(
m, 1H, CH), 4.24 (dd, J = 10.2, J = 5.0, 1H, OCH ), 3.99 (dd, J = 8.2, J = 6.2, 1H, OCH ), 3.75–3.72
1 2 2 1 2 2
m, 4H, OCH and OCH ), 2.69 (s, 6H, CH
×
2), 1.33 (s, 3H, CH ), 1.29 (s, 3H, CH ); ES-MS 454.2
3 3
3
2
3
+
+
M + H) ; HRMS Calcd. for C H N O S 454.1760, found 454.1756.
19
28
5
6
(
(
R)-2,4-Diamino-5-[4-(morpholine-4-carbonyl)phenyl]-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine
8n). Method A. Yellow solid 0.90 g, yield 77%; m.p. 189.4–190.5 C; IR: υmax/cm 3492 (NH), 3430
◦
−1
(
NH), 3334 (NH), 1659 (C=N), 1611(C=N), 1588 (C=C), 1560 (C=C), 1516 (C=C), 1488 (C=C), 1156
1
(C-O-C), 1114 (C-O-C), 1070 (C-O-C), 1051(C-O-C); H-NMR (CDCl )
δ
7.44 (d, J = 8.4, 2H, Ar-H), 7.38
3
(
d, J = 8.4, 2H, Ar-H), 4.71 (s, 2H, NH ), 4.57 (s, 2H, NH ), 4.35 (dd, J = 10.8, J = 4.2, 1H, OCH ),
2 2 1 2 2
4
3
.32–4.29 (m, 1H, CH), 4.22 (dd, J = 10.8, J = 5.6, 1H, OCH ), 3.97 (dd, J = 8.4, J = 6.4, 1H, OCH ),
1 2 2 1 2 2
.82–3.51 (m, 8H, CH2
×
4), 3.73 (dd, J = 8.0, J = 6.0, 1H, OCH ), 1.32 (s, 3H, CH ), 1.27 (s, 3H, CH );
1 2 2 3 3
+
+
ES-MS 430.2 (M + H) ; HRMS Calcd. for C H N O 430.2090, found 430.2092.
21
28
5
5
(
R)-2,4-Diamino-5-[4-(3-trifloromethoxyanilinocarbonyl)phenyl]-6-[4-(2,2-dimethyl-1,3-dioxolane)-methoxy]
◦
−1
pyrimidine (8o). Method A. White solid 0.73 g, yield 52%; m.p. 122.9–124.5 C; IR: υmax/cm 3496
(
(
NH), 3340 (NH), 3192 (CONH), 1655 (C=N), 1607 (C=C), 1565 (C=C), 1492 (C=C), 1156 (C-O-C), 1082
1
C-O-C); H-NMR (CDCl )
δ
8.07 (s, 1H, NH), 7.85 (d, J = 8.4, 2H, Ar-H), 7.71 (s, 1H, Ar-H), 7.54 (dd,
3
J1 = 8.0, J = 1.2, 1H, Ar-H), 7.45 (d, J = 8.4, 2H, Ar-H), 7.38 (t, J = 8.0, 1H, Ar-H), 7.02 (d, J = 8.0, 1H,
2
Ar-H), 4.74 (s, 2H, NH ), 4.58 (s, 2H, NH ), 4.35 (dd, J = 9.6, J = 3.8, 1H, OCH ), 4.32–4.29 (m, 1H,
2
2
1
2
2
CH), 4.27 (dd, J = 9.6, J = 4.6, 1H, OCH ), 3.99 (dd, J = 8.4, J = 6.0, 1H, OCH ), 3.73 (dd, J = 8.2,
1
2
2
1
2
2
1
+
J = 5.4, 1H, OCH ), 1.30 (s, 3H, CH ), 1.29 (s, 3H, CH ); ES-MS 520.2 (M + H) ; HRMS Calcd. for
2
2
3
3
+
C H F N O 520.1808, found 520.1810.
2
4
25
3
5
5
(
R)-2,4-Diamino-5-(4-methoxycarbonylphenyl)-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine (8p).
◦
−1
Method B. White solid 0.64 g, yield 63%; m.p. 151.3–152.4 C; IR: υmax/cm 3500 (NH), 3443
(
(
(
NH), 3391 (NH), 3335 (NH), 1709 (C=O), 1657 (C=N), 1608 (C=N), 1568 (C=C), 1556 (C=C), 1513
1
C=C), 1194 (C-O-C), 1180 (C-O-C), 1152 (C-O-C), 1116 (C-O-C), 1067 (C-O-C); H-NMR (CDCl )
δ 8.05
3
dd, J = 6.8, J = 1.6, 2H, Ar-H), 7.42 (dd, J = 6.8, J = 1.6, 2H, Ar-H), 4.72 (s, 2H, NH ), 4.58 (s, 2H,
1
2
1
2
2
NH ), 4.36 (dd, J = 10.4, J = 4.0, 1H, OCH ), 4.31–4.26 (m, 1H, CH), 4.22 (dd, J = 10.4, J = 6.0, 1H,
2
1
2
2
1
2
OCH ), 3.96 (dd, J = 8.0, J = 6.0, 1H, OCH ), 3.93 (s, 3H, OCH ), 3.72 (dd, J = 8.4, J = 6.0, 1H, OCH ),
2
1
2
2
3
1
2
2
+
+
1
.32 (s, 3H, CH ), 1.27 (s, 3H, CH ); ES-MS 375.2(M + H) ; HRMS Calcd. for C H N O 375.1668,
3 3 18 23 4 5
found 375.1664.
(
R)-2,4-Diamino-5-(3-methoxycarbonylphenyl)-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine (8q).
◦
−1
Method B. White solid 0.66 g, yield 65%; m.p. 181.4–181.6 C; IR: υmax/cm 3477 (NH), 3373
(
(
(
(
(
NH), 3326 (NH), 1708 (C=O), 1651 (C=N), 1626 (C=N), 1597 (C=C), 1558 (C=C), 1490 (C=C), 1158
1
C-O-C), 1115 (C-O-C), 1084 (C-O-C), 1049 (C-O-C); H-NMR (CDCl )
δ 8.00 (t, J = 1.6, 1H, Ar-H), 7.96
3
dt, J = 7.6, J = 1.6, 1H, Ar-H), 7.52 (dt, J = 7.6, J = 1.6, 1H, Ar-H), 7.47 (t, J = 7.6, 1H, Ar-H), 4.71
1
2
1
2
s, 2H, NH ), 4.54 (s, 2H, NH ), 4.37 (dd, J = 10.8, J = 4.0, 1H, OCH ), 4.30–4.25 (m, 1H, CH), 4.19
2
2
1
2
2
dd, J1 = 10.8, J = 6.0, 1H, OCH ), 3.96 (dd, J = 8.4, J = 6.0, 1H, OCH ), 3.92 (s, 3H, OCH ), 3.73 (dd,
2
2
1
2
2
3

Molecules 2017, 22, 1592
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+
J1 = 8.4, J = 6.0, 1H, OCH ), 1.31 (s, 3H, CH ), 1.25 (s, 3H, CH ); ES-MS 375.2(M + H) ; HRMS Calcd.
2
2
3
3
+
for C H N O 375.1668, found 375.1670.
18
23
4
5
(
S)-2,4-Diamino-5-(4-chlorophenyl)-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine (9a). Method A.
◦
−1
White solid 0.58 g, yield 61%; m.p. 171.9–172.1 C; IR: υmax/cm 3475 (NH), 3454 (NH), 3396 (NH),
3
315 (NH), 1649 (C=N), 1620 (C=N), 1593 (C=C), 1549 (C=C), 1479 (C=C), 1160 (C-O-C), 1141 (C-O-C),
1
1
089(C-O-C), 794 (C-Cl); H-NMR (CDCl )
δ
7.36 (d, J = 8.2, 2H, Ar-H), 7.25 (d, J = 8.2, 2H, Ar-H), 4.69
3
(
s, 2H, NH ), 4.53 (s, 2H, NH ), 4.36 (dd, J = 10.8, J = 4.0, 1H, OCH ), 4.31–4.26 (m, 1H, CH), 4.20 (dd,
2 2 1 2 2
J = 10.8, J = 5.6, 1H, OCH ), 3.97 (dd, J = 8.4, J = 6.4, 1H, OCH ), 3.72 (dd, J = 8.4, J = 6.0, 1H,
1
2
2
1
2
2
1
2
+
+
OCH ), 1.32 (s, 3H, CH ), 1.28 (s, 3H, CH ); ES-MS 351.1 (M + H) ; HRMS Calcd. for C H ClN O
3
2
3
3
16 20
4
3
51.1224, found 351.1220.
(
S)-2,4-Diamino-5-(4-fluorophenyl)-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine (9b). Method A.
◦
−1
White solid 0.57 g, yield 62%; m.p. 164.1–164.5 C; IR: υmax/cm 3527 (NH), 3482 (NH), 3370 (NH),
3
312 (NH), 1646 (C=N), 1626 (C=N), 1593 (C=C), 1558 (C=C), 1512 (C=C), 1484 (C=C), 1380 (C-F), 1159
1
(
C-O-C), 1130 (C-O-C), 1091 (C-O-C); H-NMR (CDCl )
δ
7.26 (dd, J = 8.8, J = 5.2, 2H, Ar-H), 7.08 (t,
3
1
2
J = 8.8, 2H, Ar-H), 4.67 (s, 2H, NH ), 4.50 (s, 2H, NH ), 4.36 (dd, J = 10.8, J = 4.0, 1H, OCH ), 4.31–4.26
2
2
1
2
2
(
m, 1H, CH), 4.20 (dd, J = 10.8, J = 5.6, 1H, OCH ), 3.96 (dd, J = 8.4, J = 6.4, 1H, OCH ), 3.72 (dd,
1 2 2 1 2 2
+
J1 = 8.4, J = 6.0, 1H, OCH ), 1.32 (s, 3H, CH ), 1.27 (s, 3H, CH ); ES-MS 335.2 (M + H) ; HRMS Calcd.
for C H FN O 335.1519, found 335.1521.
2
2
3
3
+
16
20
4
3
(
S)-2,4-Diamino-5-(3,4-dichlorophenyl)-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine (9c). Method A.
◦
−1
White solid 0.58 g, yield 55%; m.p. 167.3–167.7 C; IR: υmax/cm 3487 (NH), 3434(NH), 3378 (NH),
3
318 (NH), 1650 (C=N), 1624 (C=N), 1600 (C=C), 1558 (C=C), 1487 (C=C), 1155 (C-O-C), 1093 (C-O-C),
1
1047 (C-O-C), 795 (C-Cl); H-NMR (CDCl )
δ
7.47 (d, J = 8.4, 1H, Ar-H), 7.44 (d, J = 2.0, 1H, Ar-H),
4.35 (dd, J = 10.4, J = 4.4,
3
7
.18 (dd, J = 8.4, J = 2.0, 1H, Ar-H), 4.71 (s, 2H, NH ), 4.54 (s, 2H, NH )
,
1
2
2
2
1
2
1
1
H, OCH ), 4.33–4.27 (m, 1H, CH), 4.22 (dd, J = 10.4, J = 5.2, 1H, OCH ), 3.99 (dd, J = 8.4, J = 6.0,
2 1 2 2 1 2
H, OCH ), 3.73 (dd, J = 8.4, J = 6.0, 1H, OCH ), 1.34 (s, 3H, CH ), 1.30 (s, 3H, CH ); ES-MS 385.1
2
1
2
2
3
3
+
+
(M + H) ; HRMS Calcd. for C H Cl N O 385.0834, found 385.0838.
16 19 2 4 3
(
S)-2,4-Diamino-5-(3-chloro-4-fluorophenyl)-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine
(
9d).
◦
−1
Method A. White solid 0.56 g, yield 56%; m.p. 152.4–152.6 C; IR: υmax/cm 3527 (NH), 3477 (NH),
3
377 (NH), 3355 (NH), 1626 (C=N), 1598 (C=C), 1559 (C=C), 1482 (C=C), 1376 (C-F), 1163 (C-O-C),
1
1
1
1
1
128 (C-O-C), 1093 (C-O-C), 1043 (C-O-C), 798 (C-Cl); H-NMR (CDCl )
H, Ar-H), 7.21–7.14 (m, 2H, Ar-H), 4.71 (s, 2H, NH ), 4.53 (s, 2H, NH ), 4.35 (dd, J = 10.6, J = 4.2,
H, OCH ), 4.32–4.27 (m, 1H, CH), 4.22 (dd, J = 10.6, J = 5.4, 1H, OCH ), 3.98 (dd, J = 8.4, J = 6.4,
H, OCH ), 3.72 (dd, J = 8.4, J = 6.0, 1H, OCH ), 1.33 (s, 3H, CH ), 1.29 (s, 3H, CH ); ES-MS 369.1
δ
7.37 (dd, J = 7.0, J = 1.8,
3
1
2
2
2
1
2
2
1
2
2
1
2
2
1
2
2
3
3
+
+
(M + H) ; HRMS Calcd. for C H ClFN O , 369.1130, found 369.1132.
16 19 4 3
(
S)-2,4-Diamino-5-(4-trifluoromethylphenyl)-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine
(
9e).
◦
−1
Method A. Light yellow solid 0.64 g, yield 61%; m.p. 130.0–131.6 C; IR: υmax/cm 3467 (NH), 3418
(
(
NH), 3336 (NH), 1650 (C=N), 1625 (C=N), 1593 (C=C), 1556 (C=C), 1523 (C=C), 1163 (C-O-C), 1118
1
C-O-C), 1106 (C-O-C), 1068 (C-O-C); H-NMR (CDCl )
δ 7.64 (d, J = 8.0, 2H, Ar-H), 7.46 (d, J = 8.0, 2H,
3
Ar-H), 4.72 (s, 2H, NH ), 4.55 (s, 2H, NH ), 4.37 (dd, J = 10.8, J = 4.2, 1H, OCH ), 4.32–4.27 (m, 1H,
2
2
1
2
2
CH), 4.22 (dd, J = 10.8, J = 5.6, 1H, OCH ), 3.97 (dd, J = 8.4, J = 6.0, 1H, OCH ), 3.71 (dd, J = 8.4,
1
2
2
1
2
2
1
+
J = 6.0, 1H, OCH ), 1.32 (s, 3H, CH ), 1.24 (s, 3H, CH ); ES-MS 385.1 (M + H) ; HRMS Calcd. for
2
2
3
3
+
C H F N O 385.1488, found 385.1490.
1
7
20
3
4
3
(
S)-2,4-Diamino-5-(3-trifluoromethylphenyl)-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine
(
9f).
◦
−1
Method A. Light yellow solid 0.74 g, yield 71%; m.p. 126.3–126.5 C; IR: υmax/cm 3512 (NH), 3420
(
(
(
(
NH), 3382 (NH), 3327 (NH), 1650 (C=N), 1612 (C=N), 1593 (C=C), 1559 (C=C), 1171 (C-O-C), 1128
1
C-O-C), 1094 (C-O-C), 1072 (C-O-C), 1046 (C-O-C); H-NMR (CDCl )
δ
7.61 (s, 1H, Ar-H), 7.56–7.49
3
m, 3H, Ar-H), 4.73 (s, 2H, NH ), 4.55 (s, 2H, NH ), 4.36 (dd, J = 10.8, J = 4.0, 1H, OCH ), 4.31–4.25
2
2
1
2
2
m, 1H, CH), 4.21 (dd, J = 10.8, J = 5.6, 1H, OCH ), 3.97 (dd, J = 8.2, J = 6.0, 1H, OCH ), 3.71 (dd,
1
2
2
1
2
2

Molecules 2017, 22, 1592
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+
J1 = 8.2, J = 6.0, 1H, OCH ), 1.32 (s, 3H, CH ), 1.25 (s, 3H, CH ); ES-MS 385.1 (M + H) ; HRMS Calcd.
2
2
3
3
+
for C H F N O 385.1488, found 385.1491.
17
20
3
4
3
(
S)-2,4-Diamino-5-(4-trifluoromethoxyphenyl)-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine (9g).
◦
−1
Method A. Yellow solid 0.80 g, yield 73%; m.p. 36.7–37.7 C; IR: υmax/cm 3487 (NH), 3358 (NH),
1
1
612 (C=N), 1559 (C=C), 1510 (C=C), 1374 (C-F), 1160 (C-O-C), 1092 (C-O-C), 1053 (C-O-C); H-NMR
(
CDCl3) δ 7.35 (d, J = 8.4, 2H, Ar-H), 7.24 (d, J = 8.4, 1H, Ar-H), 4.70 (s, 2H, NH ), 4.53 (s, 2H, NH ),
2 2
4
3
3
.38 (dd, J = 11.2, J = 4.0, 1H, OCH ), 4.32–4.26 (m, 1H, CH), 4.21 (dd, J = 11.2, J = 5.4, 1H, OCH ),
1 2 2 1 2 2
.96 (dd, J = 8.4, J = 6.4, 1H, OCH ), 3.72 (dd, J = 8.2, J = 6.2, 1H, OCH ), 1.32 (s, 3H, CH ), 1.24 (s,
1
2
2
1
2
2
3
+
+
H, CH ); ES-MS 401.1(M + H) ; HRMS Calcd. for C H F N O 401.1437, found 401.1440.
3
17 20
3
4
4
(
S)-2,4-Diamino-5-(3-trifluoromethoxyphenyl)-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine (9h).
◦
−1
Method A. Yellow solid 0.73 g, yield 67%; m.p. 33.7–34.7 C; IR: υmax/cm 3490 (NH), 3360 (NH),
1
1
611 (C=N), 1561 (C=C), 1379 (C-F), 1158 (C-O-C), 1082 (C-O-C), 1047 (C-O-C); H-NMR (CDCl )
δ
7.41
3
(
t, J = 8.0, 1H, Ar-H), 7.28–7.26 (m, 1H Ar-H), 7.21 (s, 1H, Ar-H) 7.14 (dt, J = 8.4, J = 1.2, 1H, Ar-H),
1 2
4
.75 (s, 2H, NH ), 4.60 (s, 2H, NH ), 4.36 (dd, J = 10.8, J = 4.2, 1H, OCH ), 4.32–4.26 (m, 1H, CH), 4.21
2 2 1 2 2
(
dd, J = 10.8, J = 5.6, 1H, OCH ), 3.97 (dd, J = 8.4, J = 6.4, 1H, OCH ), 3.72 (dd, J = 8.4, J = 6.0, 1H,
1 2 2 1 2 2 1 2
+
+
OCH ), 1.32 (s, 3H, CH ), 1.27 (s, 3H, CH ); ES-MS 401.1(M + H) ; HRMS Calcd. for C H F N O
4
2
3
3
17 20
3
4
4
01.1437, found 401.1435.
(
S)-2,4-Diamino-5-(4-cyanophenyl)-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine (9i). Method A.
◦
−1
White solid 0.66 g, yield 71%; m.p. 221.4–221.9 C; IR: υmax/cm 3482 (NH), 3456 (NH), 3371 (NH),
3
332 (NH), 2228 (CN), 1654 (C=N), 1620 (C=N), 1586 (C=C), 1564 (C=C), 1157 (C-O-C), 1091 (C-O-C),
1
1
051 (C-O-C); H-NMR (CDCl )
δ
7.67 (d, J = 8.4, 2H, Ar-H), 7.47 (d, J = 8.4, 2H Ar-H), 4.75 (s, 2H, NH2),
3
4
.57 (s, 2H, NH ), 4.36 (dd, J = 10.8, J = 4.0, 1H, OCH ), 4.32–4.27 (m, 1H, CH), 4.23 (dd, J1 = 10.4
,
2
1
2
2
J2 = 4.2, 1H, OCH ), 3.97 (dd, J = 8.4, J = 6.4, 1H, OCH ), 3.70 (dd, J = 8.4, J = 6.0, 1H, OCH ),
2
1
2
2
1
2
2
+
+
1
.32 (s, 3H, CH ), 1.28 (s, 3H, CH ); ES-MS 342.1 (M + H) ; HRMS Calcd. for C H N O 342.1566,
3 3 17 20 5 3
found 342.1564.
(
S)-2,4-Diamino-5-(4-methoxyphenyl)-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine (9j). Method A.
◦
−1
White solid 0.57 g, yield 60%; m.p. 120.1–121.3 C; IR: υmax/cm 3458 (NH), 3349 (NH), 1620 (C=N),
1
1
594 (C=C), 1558 (C=C), 1513 (C=C), 1157 (C-O-C), 1085 (C-O-C), 1046 (C-O-C); H-NMR (CDCl )
δ
3
7
.21 (d, J = 8.8, 2H, Ar-H), 6.93 (d, J = 8.8, 2H, Ar-H), 4.65 (s, 2H, NH ), 4.53 (s, 2H, NH ), 4.37 (dd,
2 2
J1 = 10.8, J = 4.0, 1H, OCH ), 4.32–4.26 (m, 1H, CH), 4.19 (dd, J = 10.8, J = 6.0, 1H, OCH ), 3.96 (dd,
2
2
1
2
2
J1 = 8.4, J = 6.0, 1H, OCH ), 3.82 (s, 3H, OCH ), 3.74 (dd, J = 8.4, J = 6.0, 1H, OCH ), 1.32 (s, 3H, CH ),
2
2
3
1
2
2
3
+
+
1
.28 (s, 3H, CH ); ES-MS 347.2 (M + H) ; HRMS Calcd. for C H N O 347.1719, found 347.1721.
3 17 23 4 4
(
S)-2,4-Diamino-5-(3,4,5-trimethoxyphenyl)-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine
(
9k).
◦
−1
Method A. White solid 0.61 g, yield 55%; m.p. 181.7–183.0 C; IR: υmax/cm 3458 (NH), 3421 (NH),
3
339 (NH), 1660 (C=N), 1631 (C=N), 1586 (C=C), 1557 (C=C), 1510 (C=C), 1163 (C-O-C), 1129 (C-O-),
1
1075 (C-O-C); H-NMR (CDCl )
δ
6.55 (s, 2H, Ar-H), 4.66 (s, 2H, NH ), 4.61 (s, 2H, NH ), 4.38–4.31 (m,
3
2
2
2
H, OCH ), 4.2–4.21 (m, 1H, CH), 4.00 (dd, J = 8.4, J = 6.4, 1H, OCH ), 3.87 (s, 3H, OCH ), 3.84 (s, 6H,
2 1 2 2 3
OCH3
×
2), 3.77 (dd, J = 8.0, J = 6.0, 1H, OCH ), 1.32 (s, 3H, CH ), 1.28 (s, 3H, CH ); ES-MS 407.2
1 2 2 3 3
+
+
(M + H) ; HRMS Calcd. for C H N O 407.1931, found 407.1933.
19 27 4 6
(
S)-2,4-Diamino-5-[3-(2,2,2-trifluoroethoxymethyl)phenyl]-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]-
◦
−1
pyrimidine (9l). Method A. Yellow solid 0.73 g, yield 62%; m.p. 32.8–33.7 C; IR: υmax/cm 3482
(
(
NH), 3372 (NH), 1611 (C=N), 1559 (C=C), 1377 (C-F), 1159 (C-O-C), 1121 (C-O-C), 1093 (C-O-C), 1049
1
C-O-C); H-NMR (CDCl )
δ 7.40 (t, J = 7.6, 1H, Ar-H), 7.30–7.27 (m, 3H, Ar-H), 4.68 (s, 4H, OCH2
3
and NH ), 4.55 (s, 2H, NH ), 4.35 (dd, J = 10.4, J = 4.0, 1H, OCH ), 4.31–4.26 (m, 1H, CH), 4.22 (dd,
2
2
1
2
2
J1 = 10.8
, J2 = 5.6, 1H, OCH ), 3.96 (dd, J = 8.4, J = 6.0, 1H, OCH ), 3.86 (q, J = 8.8, 2H, CF CH ), 3.73
2 1 2 2 3 2
+
(dd, J1 = 8.4, J = 6.0, 1H, OCH ), 1.31 (s, 3H, CH ), 1.25 (s, 3H, CH ); ES-MS 429.2(M + H) ; HRMS
2
2
3
3
+
Calcd. for C H F N O 429.1750, found 429.1752.
19
24
3
4
4

Molecules 2017, 22, 1592
15 of 27
(
S)-2,4-Diamino-5-[3,5-dimethyl-4-(N-methoxyaminosulfonyl)phenyl]-6-[4-(2,2-dimethyl-1,3-dioxolane)-
◦
methoxy]pyrimidine (9m). Method A. Light yellow solid 0.75 g, yield 61%; m.p. 160.5–160.8 C; IR:
υmax/cm 3484 (NH), 3446 (NH), 3347 (NH), 3223 (SO NH), 1641 (C=N), 1619 (C=N), 1591 (C=C),
1
−
1
2
1
562 (C=C), 1492 (C=C), 1173 (C-O-C), 1149 (C-O-C), 1099 (C-O-C), 1054 (C-O-C); H-NMR (CDCl )
δ
3
7
.42 (s, 1H, NH), 7.18 (s, 2H, Ar-H), 4.73 (s, 2H, NH ), 4.60 (s, 2H, NH ), 4.35 (dd, J = 10.4, J = 4.0, 1H,
2 2 1 2
OCH ), 4.32–4.27 (m, 1H, CH), 4.24 (dd, J = 10.4, J = 4.8, 1H, OCH ), 3.99 (dd, J = 8.2, J = 6.2, 1H,
2
1
2
2
1
2
OCH ), 3.75–3.72 (m, 4H, OCH and OCH ), 2.69 (s, 6H, CH
×
2), 1.33 (s, 3H, CH ), 1.29 (s, 3H, CH );
3 3
2
3
2
3
+
+
ES-MS 454.2 (M + H) ; HRMS Calcd. for C H N O S 454.1760, found 454.1762.
19
28
5
6
(
(
(
(
S)-2,4-Diamino-5-[4-(morpholino-4-carbonyl)phenyl]-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine
9n). Method A. White solid 0.64 g, yield 55%; m.p. 186.1–187.2 C; IR: υmax/cm 3492 (NH), 3430
◦
−1
NH), 3332 (NH), 1659 (C=N), 1610 (C=N), 1588 (C=C), 1558 (C=C), 1516 (C=C), 1488 (C=C), 1156
1
C-O-C), 1114 (C-O-C), 1070 (C-O-C), 1050 (C-O-C); H-NMR (CDCl )
δ 7.45 (d, J = 8.4, 2H, Ar-H),
3
7
4
3
.38 (d, J = 8.4, 2H, Ar-H), 4.82 (s, 2H, NH ), 4.67 (s, 2H, NH ), 4.38 (dd, J = 10.8, J = 4.4, 1H, OCH ),
2 2 1 2 2
.32–4.28 (m, 1H, CH), 4.23 (dd, J = 10.8, J = 5.6, 1H, OCH ), 3.97 (dd, J = 8.2, J = 6.2, 1H, OCH ),
1
2
2
1
2
2
.82–3.51 (m, 8H, CH2
×
4), 3.72 (dd, J = 8.4, J = 6.0, 1H, OCH ), 1.32 (s, 3H, CH ), 1.28 (s, 3H, CH );
1 2 2 3 3
+
+
ES-MS 430.2 (M + H) ; HRMS Calcd. for C H N O 430.2090, found 430.2088.
21
28
5
5
(
S)-2,4-Diamino-5-[4-(3-trifluoromethoxyanilinocarbonyl)phenyl]-6-[4-(2,2-dimethyl-1,3-dioxolane)-methoxy]
◦
−1
pyrimidine (9o). Method A. White solid 0.74 g, yield 52%; m.p. 83.7–85 C; IR: υmax/cm 3488 (NH),
3
351 (NH), 3202 (CONH), 1657 (C=N), 1606 (C=C), 1565 (C=C), 1548 (C=C), 1492 (C=C), 1156 (C-O-C),
1
1082 (C-O-C); H-NMR (CDCl )
δ
8.04 (s, 1H, NH), 7.85 (d, J = 8.4, 2H, Ar-H), 7.71 (s, 1H, Ar-H),
3
7
.54 (dd, J = 8.0, J = 1.2, 1H, Ar-H), 7.45 (d, J = 8.4, 2H, Ar-H), 7.39 (t, J = 8.0, 1H, Ar-H), 7.02 (dt,
1 2
J1 = 8.0, J2 = 1.0, 1H, Ar-H), 4.74 (s, 2H, NH ), 4.59 (s, 2H, NH ), 4.35 (dd, J = 10.0, J = 4.0, 1H, OCH ),
2 2 1 2 2
4
3
.32–4.29 (m, 1H, CH), 4.26 (dd, J = 10.0, J = 4.8, 1H, OCH ), 3.99 (dd, J = 8.4, J = 6.0, 1H, OCH ),
1 2 2 1 2 2
+
.73 (dd, J = 8.2, J = 5.4, 1H, OCH ), 1.30 (s, 3H, CH ), 1.29 (s, 3H, CH ); ES-MS 520.2 (M + H) ;
1
2
2
3
3
+
HRMS Calcd. for C H F N O 520.1808, found 520.1811.
2
4
25
3
5
5
(
S)-2,4-Diamino-5-(4-methoxycarbonylphenyl)-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine (9p).
◦
−1
Method B. White solid 0.70 g, yield 69%; m.p. 146.3–147.4 C; IR: υmax/cm 3501 (NH), 3442
(
(
NH), 3392 (NH), 3336 (NH), 1708 (C=O), 1658 (C=N), 1610 (C=N), 1555 (C=C), 1515 (C=C), 1153
1
C-O-C), 1115 (C-O-C), 1067 (C-O-C); H-NMR (CDCl )
δ 8.05 (d, J = 8.4, 2H, Ar-H), 7.29 (d, J = 8.4, 2H,
3
Ar-H), 4.72 (s, 2H, NH ), 4.58 (s, 2H, NH ), 4.36 (dd, J = 10.6, J = 4.2, 1H, OCH ), 4.31–4.26 (m, 1H,
2
2
1
2
2
CH), 4.22 (dd, J = 10.6, J = 5.8, 1H, OCH ), 3.96 (dd, J = 8.4, J = 6.0, 1H, OCH ), 3.93 (s, 3H, OCH ),
1
2
2
1
2
2
3
+
3
.71 (dd, J = 8.0, J = 6.0, 1H, OCH ), 1.32 (s, 3H, CH ), 1.27 (s, 3H, CH ); ES-MS 375.2(M + H) ; HRMS
1 2 2 3 3
+
Calcd. for C H N O 375.1668, found 375.1670.
18
23
4
5
(
S)-2,4-Diamino-5-(3-methoxycarbonylphenyl)-6-[4-(2,2-dimethyl-1,3-dioxolane)methoxy]pyrimidine (9q).
◦
−1
Method B. White solid 0.80 g, yield 78%; m.p. 179.2–180.3 C; IR: υmax/cm 3480 (NH), 3371
(
(
(
(
(
NH), 3326 (NH), 1708 (C=O), 1652 (C=N), 1626 (C=N), 1601 (C=C), 1592 (C=C), 1557 (C=C), 1158
1
C-O-C), 1115 (C-O-C), 1084 (C-O-C), 1049 (C-O-C); H-NMR (CDCl )
δ 8.00 (t, J = 1.6, 1H, Ar-H), 7.96
3
dt, J = 7.6, J = 1.6, 1H, Ar-H), 7.52 (dt, J = 7.6, J = 1.6, 1H, Ar-H), 7.47 (t, J = 7.6, 1H, Ar-H), 4.71
1
2
1
2
s, 2H, NH ), 4.54 (s, 2H, NH ), 4.37 (dd, J = 10.8, J = 4.0, 1H, OCH ), 4.30–4.25 (m, 1H, CH), 4.19
2
2
1
2
2
dd, J1 = 10.8, J = 6.0, 1H, OCH ), 3.96 (dd, J = 8.4, J = 6.4, 1H, OCH ), 3.92 (s, 3H, OCH ), 3.72 (dd,
2
2
1
2
2
3
+
J1 = 8.4, J = 6.0, 1H, OCH ), 1.31 (s, 3H, CH ), 1.25 (s, 3H, CH ); ES-MS 375.2(M + H) ; HRMS Calcd.
for C H N O 375.1668, found 375.1666.
2
2
3
3
+
18
23
4
5
General Procedure for the Synthesis of Compounds 10a-q and 11a-q
The compounds 8a-q or 9a-q (1.42 mmol) was added to 0.25 M H SO (20 mL) and stirred at room
2
4
temperature overnight. After the completion of the reaction as indicated by TLC analysis, the reaction
solution was adjusted the pH to 9 and extracted with EtOAc (30 mL 3). The combined organic layers
were washed by H O and dried with Na SO , filtered and concentrated. The residue was purified by
×
2
2
4

Molecules 2017, 22, 1592
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column chromatography on silica gel using CH Cl /CH OH (80:1, v/v) as the eluting solvent to the
2
2
3
desired compounds.
(
R)-2,4-Diamino-5-(4-chlorophenyl)-6-(1,2-dihydroxypropyl)pyrimidine (10a). White solid 0.37 g, yield 84%;
◦
−1
m.p. 164.4–166.3 C; IR: υmax/cm 3443 (OH), 3396 (OH), 3335 (NH), 3224 (NH), 1658 (C=N), 1627
(
1
C=N), 1604 (C=C), 1591 (C=C), 1569 (C=C), 1555 (C=C), 1503 (C=C), 1483 (C=C), 796 (C-Cl); H-NMR
(
DMSO-d6)
δ 7.38 (d, J = 8.4, 2H, Ar-H), 7.27 (d, J = 8.4, 2H, Ar-H), 6.02 (s, 2H, NH ), 5.63 (s, 2H, NH ),
2 2
4
.72 (d, J = 4.8, 1H, CHOH), 4.50 (t, J = 5.8, 1H, CH OH), 4.08 (d, J = 5.2, 2H, OCH ), 3.62–3.56 (m, 1H,
2
2
+
+
CH), 3.29–3.23 (m, 2H, OCH ); ES-MS 311.1 (M + H) ; HRMS Calcd. for C H ClN O 311.0911,
2
13 16
4
3
found 311.0909.
(
R)-2,4-Diamino-5-(4-fluorophenyl)-6-(1,2-dihydroxypropyl)pyrimidine (10b). White solid 0.30 g, yield 68%;
◦
−1
m.p. 122.4–122.8 C; IR: υmax/cm 3520 (OH), 3472 (OH), 3407 (NH), 3349 (NH), 1651 (C=N), 1617
(
1
C=N), 1592 (C=C), 1570 (C=C), 1484 (C=C), 1397 (C-F); H-NMR (DMSO-d )
δ
7.28 (dd, J = 8.8,
6
1
J2 = 5.6, 2H, Ar-H), 7.15 (t, J = 8.8, 2H, Ar-H), 5.99 (s, 2H, NH ), 5.57 (s, 2H, NH ), 4.72 (d, J = 4.8, 1H,
2
2
CHOH), 4.49 (t, J = 5.6, 1H, CH OH), 4.08 (d, J = 5.6, 2H, OCH ), 3.63–3.55 (m, 1H, CH), 3.31–3.24 (m,
2
2
+
+
2
H, OCH ); ES-MS 295.1 (M + H) ; HRMS Calcd. for C H FN O 295.1206, found 295.1204.
2 13 16 4 3
(
7
1
R)-2,4-Diamino-5-(3,4-dichlorophenyl)-6-(1,2-dihydroxypropyl)pyrimidine (10c). White solid 0.32 g, yield
◦
−1
1%; m.p. 159.5–160.2 C; IR: υmax/cm 3504 (OH), 3476 (OH), 3344 (NH), 3229 (NH), 1650 (C=N),
1
619(C=N), 1593 (C=C), 1570 (C=C), 1490 (C=C), 792 (C-Cl); H-NMR (DMSO-d )
δ
7.56 (d, J = 8.0, 1H,
6
Ar-H), 7.47 (d, J = 2.0, 1H, Ar-H), 7.24 (dd, J =8.0, J = 2.0, 1H, Ar-H), 6.07 (s, 2H, NH ), 5.79 (s, 2H,
1
2
2
NH ), 4.74 (d, 1H, J = 4.8, CHOH), 4.52 (t, J = 5.8, 1H, CH OH), 4.14–4.06 (m, 2H, OCH ), 3.63–3.57 (m,
2
2
2
+
+
1
H, CH), 3.28–3.31 (m, 2H, OCH ); ES-MS 345.1 (M + H) ; HRMS Calcd. for C H Cl N O 345.0521,
2 13 15 2 4 3
found 345.0519.
(
R)-2,4-Diamino-5-(3-chloro-4-fluorophenyl)-6-(1,2-dihydroxypropyl)pyrimidine (10d). White solid 0.39 g,
◦
−1
yield 88%; m.p. 158.0–159.9 C; IR: υmax/cm 3484 (OH), 3437 (OH), 3318 (NH), 3209 (NH), 1627
(
1
C=N), 1586 (C=C), 1560 (C=C), 1349 (C-F), 801 (C-Cl); H-NMR (DMSO-d )
δ
7.40 (dd, J = 7.6, J2 = 2.4
,
6
1
1
H, Ar-H), 7.36 (t, J = 9.0, 1H, Ar-H), 7.23 (ddd, J = 8.4, J = 4.8, J = 2.0, 1H, Ar-H), 6.04 (s, 2H,
1 2 3
NH ), 5.74 (s, 2H, NH ), 4.74 (d, J = 4.8, 1H, CHOH), 4.51 (t, J = 5.8, 1H, CH OH), 4.13–4.05 (m, 2H,
2
2
2
+
OCH ), 3.63–3.56 (m, 1H, CH), 3.30–3.26 (m, 2H, OCH ); ES-MS 329.1(M + H) ; HRMS Calcd. for
C H ClFN O 329.0817, found 329.0820.
2
2
+
13
15
4
3
(
R)-2,4-Diamino-5-(4-trifluoromethylphenyl)-6-(1,2-dihydroxypropyl)pyrimidine (10e). White solid 0.37 g,
◦
−1
yield 83%; m.p. 170.5–171.0 C; IR: υmax/cm 3587 (OH), 3506 (OH), 3378 (NH), 3226 (NH), 1631
(
1
C=N), 1591 (C=C), 1559 (C=C), 1520 (C=C), 1322 (C-F); H-NMR (DMSO-d )
δ
7.67 (d, J = 8.4, 2H,
6
Ar-H), 7.50 (d, J = 8.0, 2H, Ar-H), 6.09 (s, 2H, NH ), 5.75 (s, 2H, NH ), 4.74 (d, J = 5.2, 1H, CHOH), 4.52
2
2
(
t, J = 5.8, 1H, CH OH), 4.15–4.07 (m, 2H, OCH ), 3.64–3.57 (m, 1H, CH), 3.24–3.30 (m, 2H, OCH );
2
2
2
+
+
ES-MS 345.1 (M + H) ; HRMS Calcd. for C H F N O 345.1175, found 345.1173.
14
16
3
4
3
(
R)-2,4-Diamino-5-(3-trifluoromethylphenyl)-6-(1,2-dihydroxypropyl)pyrimidine (10f). White solid 0.41 g,
◦
−1
yield 92%; m.p. 137.8–138.9 C; IR: υmax/cm 3521 (OH), 3474 (OH), 3349 (NH), 3235 (NH), 1650
(
1
C=N), 1621 (C=N), 1594 (C=C), 1569 (C=C), 1495 (C=C), 1341 (C-F); H-NMR (DMSO-d )
δ
7.58–7.55
6
(
m, 4H, Ar-H), 6.08 (s, 2H, NH ), 5.74 (s, 2H, NH ), 4.72 (d, 1H, J = 5.2, CHOH), 4.50 (t, J = 5.8, 1H,
2
2
CH OH), 4.11 (d, J = 4.8, 2H, OCH ), 3.62–3.56 (m, 1H, CH), 3.31–3.26 (m, 2H, OCH ); ES-MS 345.1
2
2
2
+
+
(
M + H) ; HRMS Calcd. for C H F N O 345.1175, found 345.1172.
14 16 3 4 3
(
R)-2,4-Diamino-5-(4-trifluoromethoxyphenyl)-6-(1,2-dihydroxypropyl)pyrimidine (10g). White solid 0.42 g,
◦
−1
yield 85%; m.p. 181.4–182.1 C; IR: υmax/cm 3579 (OH), 3457 (OH), 3341(NH), 3231 (NH), 1636
(
1
C=N), 1590 (C=C), 1557 (C=C), 1549 (C=C), 1501 (C=C), 1316 (C-F); H-NMR (DMSO-d )
δ
7.38 (d,
6
J = 8.4, 2H, Ar-H), 7.31 (d, J = 8.4, 2H, Ar-H), 6.06 (s, 2H, NH ), 5.69 (s, 2H, NH ), 4.77 (d, J = 5.2, 1H,
2
2
CHOH), 4.53 (t, J = 5.8, 1H, CH OH), 4.10 (d, J = 5.2, 2H, OCH ), 3.63–3.57 (m, 1H, CH), 3.32–3.23 (m,
2
2
+
+
2
H, OCH ); ES-MS 361.1 (M + H) ; HRMS Calcd. for C H F N O 361.1124, found 361.1120.
2 14 16 3 4 4

Molecules 2017, 22, 1592
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(
R)-2,4-Diamino-5-(3-trifluoromethoxyphenyl)-6-(1,2-dihydroxypropyl)pyrimidine (10h). White solid 0.44 g,
◦
−1
yield 89%; m.p. 58.5–59.6 C; IR: υmax/cm 3467 (OH), 3379 (OH), 3350 (NH), 1612 (C=N), 1562
(
1
C=C), 1495 (C=C), 1348 (C-F); H-NMR (DMSO-d )
δ
7.46 (t, J = 8.0, 2H, Ar-H), 7.31 (d, J = 8.0, 2H,
6
Ar-H), 7.23 (s, 1H, Ar-H), 7.20 (d, J = 8.0, 1H, Ar-H), 6.09 (s, 2H, NH ), 5.73 (s, 2H, NH ), 4.75 (d, J = 4.8,
2
2
1
H, CHOH), 4.52 (t, J = 5.6, 1H, CH OH), 4.10 (d, J = 5.2, 2H, OCH ), 3.63–3.56 (m, 1H, CH), 3.31–3.24
2
2
+
+
(m, 2H, OCH ); ES-MS 361.1 (M + H) ; HRMS Calcd. for C H F N O 361.1124, found 361.1128.
2 14 16 3 4 4
(
R)-2,4-Diamino-5-(4-cyanophenyl)-6-(1,2-dihydroxypropyl)pyrimidine (10i). White solid 0.39 g, yield 88%;
◦
−1
m.p. 199.7–200.8 C; IR: υmax/cm 3459 (OH), 3382 (NH), 2228(CN), 1658 (C=N), 1624(C=N), 1592
(
1
C=C), 1563 (C=C), 1549 (C=C), 1510 (C=C); H-NMR (DMSO-d )
δ
7.77 (d, J = 8.4, 2H, Ar-H), 7.48
6
(
d, J = 8.0, 2H, Ar-H), 6.15 (s, 2H, NH ), 5.82 (s, 2H, NH ), 4.77 (d, J = 4.8, 1H, CHOH), 4.55 (t, J = 5.6,
2 2
1
H, CH OH), 4.14–4.06 (m, 2H, OCH ), 3.63–3.57 (m, 1H, CH), 3.31–3.25 (m, 2H, OCH ); ES-MS 302.1
2
2
2
+
+
(M + H) ; HRMS Calcd. for C H N O 302.1253, found 302.1250.
14 16 5 3
(
8
1
2
4
3
R)-2,4-Diamino-5-(4-methoxyphenyl)-6-(1,2-dihydroxypropyl)pyrimidine (10j). White solid 0.37 g, yield
◦
−1
4%; m.p. 188.4–188.9 C; IR: υmax/cm 3544 (OH), 3497 (OH), 3466 (NH), 3339 (NH), 1639 (C=N),
1
621 (C=N), 1591 (C=C), 1557 (C=C); H-NMR (DMSO-d )
δ
7.16 (d, J = 8.8, 2H, Ar-H), 6.92 (d, J = 8.8,
6
H, Ar-H), 5.94 (s, 2H, NH ), 5.46 (s, 2H, NH ), 4.73 (d, 1H, J = 4.8, CHOH), 4.49 (t, J = 5.8, 1H, CH OH),
2
2
2
.11–4.04 (m, 2H, OCH ), 3.76 (s, 3H, OCH ), 3.62–3.55 (m, 1H, CH), 3.33–3.24 (m, 2H, OCH ); ES-MS
2
3
2
+
+
07.1 (M + H) ; HRMS Calcd. for C H N O 307.1406, found 307.1404.
14
19
4
4
(
R)-2,4-Diamino-5-(3,4,5-trimethoxyphenyl)-6-(1,2-dihydroxypropyl)pyrimidine (10k). White solid 0.34 g,
◦
−1
yield 75%; m.p. 198.6–199.7 C; IR: υmax/cm 3489 (OH), 3439 (OH), 3356 (NH), 3208 (NH), 1626
(
1
C=N), 1589 (C=C), 1569 (C=C), 1489 (C=C); H-NMR (DMSO-d )
δ
6.55 (s, 2H, Ar-H), 5.96 (s, 2H,
6
NH ), 5.69 (s, 2H, NH ), 4.76 (d, J = 5.2, 1H, CHOH), 4.53 (t, J = 5.6, 1H, CH OH), 4.16–4.05 (m, 2H,
2
2
2
OCH ), 3.75 (s, 6H, OCH
ES-MS 367.2 (M + H) ; HRMS Calcd. for C H N O 367.1618, found 367.1616.
×
2), 3.68 (s, 3H, OCH ), 3.67–3.60 (m, 1H, CH), 3.38–3.28 (m, 2H, OCH );
2
3
3
2
+
+
16
23
4
6
(
R)-2,4-Diamino-5-[3-(2,2,2-trifluoroethoxymethyl)phenyl]-6-(1,2-dihydroxypropyl)pyrimidine
(
10l).
◦
−1
White solid 0.41 g, yield 82%; m.p. 48.2–49.3 C; IR: υmax/cm 3478 (OH), 3347 (NH), 3215 (NH),
1
1
612 (C=N), 1562 (C=C), 1492 (C=C), 1348(C-F); H-NMR (DMSO-d )
δ
7.36 (t, J = 7.8, 1H, Ar-H),
6
7
.20–7.23 (m,3H, Ar-H), 6.02 (s, 2H, NH ), 5.59 (s, 2H, NH ), 4.74 (d, J = 5.2, 1H, CHOH), 4.65 (s, 2H,
2 2
CH ), 4.51 (t, J = 5.6, 1H, CH OH), 4.09 (dd, J = 18.8 , J = 9.6 , 2H, CF CH ), 4.08 (d, J = 5.2, 2H,
2
2
1
2
3
2
+
OCH ), 3.62–3.55 (m, 1H, CH), 3.34–3.23 (m, 2H, OCH ); ES-MS 389.1(M + H) ; HRMS Calcd. for
C H F N O 389.1437, found 389.1435.
2
2
+
16
20
3
4
4
(
(
(
(
R)-2,4-Diamino-5-[3,5-dimethyl-4-(N-methoxyaminosulfonyl)phenyl]-6-(1,2-dihydroxypropyl)pyrimidine
◦
−1
10m). White solid 0.40 g, yield 88%; m.p. 98.3–99.3 C; IR: υmax/cm 3475 (OH), 3378 (NH), 3216
1
NH), 1610 (C=N), 1594 (C=C), 1562 (C=C), 1482(C=C); H-NMR (DMSO-d )
δ 10.29 (s, 1H, NH), 7.18
6
s, 2H, Ar-H), 6.12 (s, 2H, NH ), 5.80 (s, 2H, NH ), 4.79 (d, J = 4.8, 1H, CHOH), 4.56 (t, J = 5.8, 1H,
2
2
CH OH), 4.15–4.07 (m, 2H, OCH ), 3.64–3.58 (m, 1H, CH and OCH ), 3.33–3.27 (m, 2H, OCH ), 2.59 (s,
2
2
3
2
+
+
6
H, CH ); ES-MS 414.1(M + H) ; HRMS Calcd. for C H N O S 414.1447, found 414.1450.
3 16 24 5 6
(
0
(
R)-2,4-Diamino-5-[4-(morpholine-4-carbonyl)phenyl]-6-(1,2-dihydroxypropyl)pyrimidine (10n). White solid
◦
−1
.53 g, yield 90%; m.p. 210.1–211.3 C; IR (KBr): υmax/cm 3446 (OH), 3343 (NH), 3220 (NH), 1630
1
C=N), 1606 (C=C), 1591 (C=C), 1569 (C=C), 1511 (C=C); H-NMR (DMSO-d )
δ
7.36 (d, J = 8.4, 2H,
6
Ar-H), 7.32 (d, J = 8.4, 2H, Ar-H), 6.04 (s, 2H, NH ), 5.69 (s, 2H, NH ), 4.77 (d, J = 5.2, 1H, CHOH),
2
2
4
.53 (t, J = 5.6, 1H, CH OH), 4.10 (d, J = 5.6, 2H, OCH ), 3.63–3.59 (m, 1H, CH), 3.76–3.42 (m, 8H,
2
2
+
+
CH × 4), 3.30–3.27 (m, 2H, OCH ); ES-MS 390.2 (M + H) ; HRMS Calcd. for C H N O 390.1777,
2
2
18 24
5
5
found 390.1774.
(
R)-2,4-Diamino-5-[4-(3-trifluoromethoxyanilinocarbonyl)phenyl]-6-(1,2-dihydroxypropyl)pyrimidine (10o).
◦
−1
White solid 0.46 g, yield 91%; m.p. 142.0–143.6 C; IR: υmax/cm 3346 (OH), 3228 (NH), 1656 (C=N),
1
1
632 (C=N), 1607 (C=C), 1549 (C=C), 1490 (C=C), 1349(C-F); H-NMR (DMSO-d )
δ
10.49 (s, 1H, NH),
6

Molecules 2017, 22, 1592
18 of 27
7
.98–7.96 (m, 3H, Ar-H), 7.80 (dd, J = 8.0, J = 1.2, 1H, Ar-H), 7.51–7.45 (m, 3H, Ar-H), 7.09 (dt, J = 8.4,
1 2 1
J = 1.2, 1H, Ar-H), 6.10 (s, 2H, NH ), 5.71 (s, 2H, NH ), 4.77 (d, J = 5.2, 1H, CHOH), 4.55 (t, J = 5.6, 1H,
2
2
2
CH OH), 4.12 (d, J = 5.2, 2H, OCH ), 3.65–3.59 (m, 1H, CH), 3.33–3.26 (m, 2H, OCH ); ES-MS 480.1
2
2
2
+
+
(
M + H) ; HRMS Calcd. for C H F N O 480.1495, found 480.1492.
21 21 3 5 5
(
R)-2,4-Diamino-5-(4-methoxycarbonylphenyl)-6-(1,2-dihydroxypropyl)pyrimidine (10p). White solid 0.40 g,
◦
−1
yield 90%; m.p. 186.7–188.2 C; IR: υmax/cm 3449 (OH), 3330 (NH), 3219 (NH), 1705 (C=O), 1631
(
1
C=N), 1592 (C=C), 1514 (C=C); H-NMR (DMSO-d )
δ
7.91 (d, J = 8.4, 2H, Ar-H), 7.44 (d, J = 8.4, 2H,
6
Ar-H), 6.10 (s, 2H, NH ), 5.73 (s, 2H, NH ), 4.75 (d, J = 4.8, 1H, CHOH), 4.53 (t, J = 5.8, 1H, CH OH),
2
2
2
4
3
.09 (d, J = 5.2, 2H, OCH ), 3.86 (s, 3H, OCH ), 3.63–3.55 (m, 1H, CH), 3.30–3.25 (m, 2H, OCH ); ES-MS
2 3 2
+
+
35.1 (M + H) ; HRMS Calcd. for C H N O 335.1355, found 335.1350.
15
19
4
5
(
R)-2,4-Diamino-5-(3-methoxycarbonylphenyl)-6-(1,2-dihydroxypropyl)pyrimidine (10q). White solid 0.40 g,
◦
−1
yield 90%; m.p. 140.6–141.5 C; IR: υmax/cm 3457 (OH), 3336 (NH), 3224 (NH), 1705 (C=O), 1658
(
1
C=N), 1600 (C=C), 1560 (C=C), 1490 (C=C); H-NMR (DMSO-d )
δ
7.84 (t, J = 1.2, 1H, Ar-H), 7.81 (dt,
6
J = 7.6, J = 1.6, 1H, Ar-H), 7.54 (dt, J = 8.0, J = 1.6, 1H, Ar-H), 7.49 (t, J = 7.6, 1H, Ar-H), 6.06 (s, 2H,
1
2
1
2
NH ), 5.68 (s, 2H, NH ), 4.72 (d, J = 5.2, 1H, CHOH), 4.50 (t, J = 5.6, 1H, CH OH), 4.09 (d, J = 5.6, 2H,
2
2
2
+
OCH ), 3.85 (s, 3H, OCH ), 3.61–3.54 (m, 1H, CH), 3.30–3.24 (m, 2H, OCH ); ES-MS 335.1 (M + H) ;
HRMS Calcd. for C H N O 335.1355, found 335.1358.
2
3
2
+
15
19
4
5
(
S)-2,4-Diamino-5-(4-chlorophenyl)-6-(1,2-dihydroxypropyl)pyrimidine (11a). White solid 0.36 g, yield 85%;
◦
−1
m.p. 169.8–169.9 C; IR: υmax/cm 3446 (OH), 3396 (OH), 3336 (NH), 3214 (NH), 1606 (C=N), 1589
(
1
C=C), 1569 (C=C), 1556 (C=C), 1503(C=C), 797 (C-Cl); H-NMR (DMSO-d )
δ
7.38 (d, J = 8.4, 2H,
6
Ar-H), 7.27 (d, J = 8.4, 2H, Ar-H), 6.03 (s, 2H, NH ), 5.65 (s, 2H, NH ), 4.74 (d, J = 5.2, 1H, CHOH), 4.51
2
2
(
t, J = 5.6, 1H, CH OH), 4.08 (d, J = 5.6, 2H, OCH ), 3.63–3.56 (m, 1H, CH), 3.31–3.23 (m, 2H, OCH );
2
2
2
+
+
ES-MS 311.1 (M + H) ; HRMS Calcd. for C H ClN O 311.0911, found 311.0908.
13
16
4
3
(
S)-2,4-Diamino-5-(4-fluorophenyl)-6-(1,2-dihydroxypropyl)pyrimidine (11b). White solid 0.42 g, yield 95%;
◦
−1
m.p. 111.7–113.7 C; IR: υmax/cm 3482 (OH), 3343 (NH), 3212 (NH), 1614 (C=N), 1593 (C=C), 1562
(
1
C=C), 1509 (C=C), 1398 (C-F); H-NMR (DMSO-d )
δ
7.27 (dd, J = 8.8, J = 6.0, 2H, Ar-H), 7.16 (t,
6
1
2
J = 8.8, 2H, Ar-H), 6.00 (s, 2H, NH ), 5.57 (s, 2H, NH ), 4.73 (d, J = 5.2, 1H, CHOH), 4.50 (t, J = 5.8, 1H,
2
2
CH OH), 4.08 (d, J = 5.2, 2H, OCH ), 3.62–3.55 (m, 1H, CH), 3.33–3.23 (m, 2H, OCH ); ES-MS 295.1
2
2
2
+
+
(
M + H) ; HRMS Calcd. for C H FN O 295.1206, found 295.1208.
13 16 4 3
(
8
1
S)-2,4-Diamino-5-(3,4-dichlorophenyl)-6-(1,2-dihydroxypropyl)pyrimidine (11c). White solid 0.35 g, yield
◦
−1
7%; m.p. 160.6–160.8 C; IR: υmax/cm 3504 (OH), 3476 (OH), 3383 (NH), 3346 (NH), 1649 (C=N),
1
617 (C=N), 1592 (C=C), 1569 (C=C), 1491 (C=C), 793 (C-Cl); H-NMR (DMSO-d )
δ
7.56 (d, J = 8.0, 2H,
6
Ar-H), 7.47 (d, J = 2.0, 1H, Ar-H), 7.24 (dd, J = 8.0, J = 2.0, 1H, Ar-H), 6.08 (s, 2H, NH ), 5.81 (s, 2H,
1
2
2
NH ), 4.75 (d, 1H, J = 5.2, CHOH), 4.53 (t, J = 5.6, 1H, CH OH), 4.14–4.06 (m, 2H, OCH ), 3.63–3.57 (m,
2
2
2
+
+
1
H, CH), 3.31–3.25 (m, 2H, OCH ); ES-MS 345.1 (M + H) ; HRMS Calcd. for C H Cl N O 345.0521,
2 13 15 2 4 3
found 345.0523.
(
S)-2,4-Diamino-5-(3-chloro-4-fluorophenyl)-6-(1,2-dihydroxypropyl)pyrimidine (11d). White solid 0.37 g,
◦
−1
yield 90%; m.p. 157.7–158.1 C; IR: υmax/cm 3484 (OH), 3329 (NH), 3210 (NH), 1622 (C=N), 1605
(
1
C=C), 1590 (C=C), 1561 (C=C), 1347 (C-F), 799 (C-Cl); H-NMR (DMSO-d )
δ
7.40 (dd, J = 7.2, J2 = 2.0
,
6
1
1
H, Ar-H), 7.36 (t, J = 8.8, 1H, Ar-H), 7.25–7.21 (ddd, J = 8.8, J = 4.8, J = 2.0, 1H, Ar-H), 6.05 (s, 2H,
1 2 3
NH ), 5.74 (s, 2H, NH ), 4.74 (d, J = 5.2, 1H, CHOH), 4.52 (t, J = 5.6, 1H, CH OH), 4.13–4.06 (m, 2H,
2
2
2
+
OCH ), 3.63–3.56 (m, 1H, CH), 3.30–3.26 (m, 2H, OCH ); ES-MS 329.1(M + H) ; HRMS Calcd. for
C H ClFN O 329.0817, found 329.0821.
2
2
+
13
15
4
3
(
S)-2,4-Diamino-5-(4-trifluoromethylphenyl)-6-(1,2-dihydroxypropyl)pyrimidine (11e). White solid 0.37 g,
◦
−1
yield 83%; m.p. 170.8–171.5 C; IR: υmax/cm 3620 (OH), 3512 (OH), 3334 (NH), 3225 (NH), 1661
(
1
C=N), 1632 (C=N), 1598 (C=C), 1554 (C=C), 1493 (C=C), 1339 (C-F); H-NMR (DMSO-d )
δ
7.67 (d,
6
J = 8.0, 2H, Ar-H), 7.50 (d, J = 8.0, 2H, Ar-H), 6.10 (s, 2H, NH ), 5.77 (s, 2H, NH ), 4.75 (d, J = 5.2, 1H,
2
2

Molecules 2017, 22, 1592
19 of 27
CHOH), 4.53 (t, J = 5.6, 1H, CH OH), 4.15–4.07 (m, 2H, OCH ), 3.64–3.57 (m, 1H, CH), 3.31–3.26 (m,
2
2
+
+
2
H, OCH ); ES-MS 345.1 (M + H) ; HRMS Calcd. for C H F N O 345.1175, found 345.1180.
2 14 16 3 4 3
(
S)-2,4-Diamino-5-(3-trifluoromethylphenyl)-6-(1,2-dihydroxypropyl)pyrimidine (11f). White solid 0.37 g,
◦
−1
yield 83%; m.p. 144.2–144.3 C; IR: υmax/cm 3474 (OH), 3389 (OH), 3348 (NH), 3224 (NH), 1617
(
1
C=N), 1594 (C=C), 1564 (C=C), 1496 (C=C), 1336 (C-F); H-NMR (DMSO-d )
δ
7.59–7.55 (m, 4H, Ar-H),
6
6
.09 (s, 2H, NH ), 5.74 (s, 2H, NH ), 4.72 (d, J = 4.8, 1H, CHOH), 4.50 (t, J = 5.8, 1H, CH OH), 4.12 (d,
2
2
2
+
J = 5.2, 2H, OCH ), 3.63–3.54 (m, 1H, CH), 3.31–3.25 (m, 2H, OCH ); ES-MS 345.1 (M + H) ; HRMS
Calcd. for C H F N O 345.1175, found 345.1177.
2
2
+
14
16
3
4
3
(
S)-2,4-Diamino-5-(4-trifluoromethoxyphenyl)-6-(1,2-dihydroxypropyl)pyrimidine (11g). White solid 0.44 g,
◦
−1
yield 90%; m.p. 141.7–143.2 C; IR: υmax/cm 3345 (OH), 3216 (NH), 1614 (C=N), 1595 (C=C), 1561
(
1
C=C), 1349 (C-F); H-NMR (DMSO-d )
δ
7.39 (d, J = 8.4, 2H, Ar-H), 7.31 (d, J = 8.4, 2H, Ar-H), 6.05 (s,
6
2
2
H, NH ), 5.68 (s, 2H, NH ), 4.76 (d, J = 4.8, 1H, CHOH), 4.52 (t, J = 5.6, 1H, CH OH), 4.10 (d, J = 5.2,
2 2 2
+
H, OCH ), 3.64–3.57 (m, 1H, CH), 3.31–3.24 (m, 2H, OCH ); ES-MS 361.1 (M + H) ; HRMS Calcd. for
2
2
+
C H F N O 361.1124, found 361.1127.
14
16
3
4
4
(
S)-2,4-Diamino-5-(3-trifluoromethoxyphenyl)-6-(1,2-dihydroxypropyl)pyrimidine (11h). White solid 0.44 g,
◦
−1
yield 90%; m.p. 120.5–122.0 C; IR: υmax/cm 3621 (OH), 3340 (OH), 3224 (NH), 1656 (C=N), 1629
(
1
C=N), 1609 (C=C), 1563 (C=C), 1499 (C=C), 1354 (C-F); H-NMR (DMSO-d )
δ
7.46 (t, J = 7.8, 2H, Ar-H),
6
7
.31 (d, J = 7.8, 2H, Ar-H), 7.23 (s, 1H, Ar-H), 7.19 (d, J = 7.8, 1H, Ar-H), 6.09 (s, 2H, NH ), 5.73 (s, 2H,
2
NH ), 4.74 (d, J = 4.8, 1H, CHOH), 4.51 (t, J = 5.6, 1H, CH OH), 4.10 (d, J = 5.2, 2H, OCH ), 3.63–3.56 (m,
2
2
2
+
+
1
H, CH), 3.31–3.25 (m, 2H, OCH ); ES-MS 361.1 (M + H) ; HRMS Calcd. for C H F N O 361.1124,
2
14 16
3
4
4
found 361.1122.
(
S)-2,4-Diamino-5-(4-cyanophenyl)-6-(1,2-dihydroxypropyl)pyrimidine (11i). White solid 0.38 g, yield 86%;
◦
−1
m.p. 201.6–203.0 C; IR: υmax/cm 3458 (OH), 3359 (NH), 2230 (CN), 1631 (C=N), 1604 (C=C) 1586
(
1
C=C), 1563 (C=C), 1550 (C=C); H-NMR (DMSO-d )
δ
7.77 (d, J = 8.8, 2H, Ar-H), 7.48 (d, J = 8.8, 2H,
6
Ar-H), 6.15 (s, 2H, NH ), 5.83 (s, 2H, NH ), 4.76 (d, J = 5.2, 1H, CHOH), 4.54 (t, J = 5.6, 1H, CH OH),
2
2
2
+
4
.14–4.07 (m, 2H, OCH ), 3.62–3.58 (m, 1H, CH), 3.31–3.3124 (m, 2H, OCH ); ES-MS 302.1 (M + H) ;
2
2
+
HRMS Calcd. for C H N O 302.1253, found 302.1251.
14
16
5
3
(
9
1
S)-2,4-Diamino-5-(4-methoxyphenyl)-6-(1,2-dihydroxypropyl)pyrimidine (11j). White solid 0.36 g, yield
◦
−1
1%; m.p. 187.4–188.7 C; IR: υmax/cm 3542 (OH), 3496 (OH), 3467 (NH), 3339 (NH), 1639 (C=N),
1
621 (C=N), 1608 (C=C), 1591 (C=C), 1558 (C=C); H-NMR (DMSO-d )
δ
7.15 (d, J = 8.8, 2H, Ar-H),
6
6
.92 (d, J = 8.8, 2H, Ar-H), 5.94 (s, 2H, NH ), 5.46 (s, 2H, NH ), 4.73 (d, J = 4.8, 1H, CHOH), 4.50 (t,
2
2
J = 5.6, 1H, CH OH), 4.11–4.04 (m, 2H, OCH ), 3.76 (s, 3H, OCH ), 3.62–3.56 (m, 1H, CH), 3.32–3.25 (m,
2
2
3
+
+
2
H, OCH ); ES-MS 307.1 (M + H) ; HRMS Calcd. for C H N O 307.1406, found 307.1408.
2 14 19 4 4
(
S)-2,4-Diamino-5-(3,4,5-trimethoxyphenyl)-6-(1,2-dihydroxypropyl)pyrimidine (11k). White solid 0.40 g,
◦
−1
yield 89%; m.p. 199.1–200.3 C; IR: υmax/cm 3489 (OH), 3439 (OH), 3356 (NH), 3208 (NH), 1626
(
1
C=N), 1589 (C=C), 1569 (C=C), 1489 (C=C); H-NMR (DMSO-d )
δ
6.55 (s, 2H, Ar-H), 5.96 (s, 2H,
6
NH ), 5.64 (s, 2H, NH ), 4.76 (d, J = 4.8, 1H, CHOH), 4.53 (t, J = 5.8, 1H, CH OH), 4.14–4.07 (m, 2H,
2
2
2
OCH ), 3.75 (s, 6H, OCH ), 3.68 (s, 3H, OCH ), 3.65–3.60 (m, 1H, CH), 3.38–3.28 (m, 2H, OCH ); ES-MS
2
3
3
2
+
+
3
67.2 (M + H) ; HRMS Calcd. for C H N O 367.1618, found 367.1620.
16 23 4 6
(
S)-2,4-Diamino-5-[3-(2,2,2-trifluoroethoxymethyl)phenyl]-6-(1,2-dihydroxypropyl)pyrimidine
(11l).
◦
−1
White solid 0.38 g, yield 84%; m.p. 42.7–43.5 C; IR: υmax/cm 3477 (OH), 3346 (NH), 3215 (NH), 1613
1
(
(
(
C=N), 1561 (C=C), 1495 (C=C), 1346 (C-F); H-NMR (DMSO-d )
δ
7.36 (t, J = 7.8, 1H, Ar-H), 7.23–7.20
6
m,3H, Ar-H), 6.01 (s, 2H, NH ), 5.57 (s, 2H, NH ), 4.73 (d, J = 5.2, 1H, CHOH), 4.66 (s, 2H, OCH ), 4.50
2
2
2
t, J = 5.6, 1H, CH OH), 4.13–4.06 (m, 4H, OCH and CF CH ), 3.62–3.55 (m, 1H, CH), 3.31–3.23 (m, 2H,
2
2
3
2
+
+
OCH ); ES-MS 389.1(M + H) ; HRMS Calcd. for C H F N O 389.1437, found 389.1440.
2
16 20
3
4
4
(
(
S)-2,4-Diamino-5-[3,5-dimethyl-4-(N-methoxyaminosulfonyl)phenyl]-6-(1,2-dihydroxypropyl)pyrimidine
◦ −1
11m). White solid 0.31 g, yield 85%; m.p. 93.0–93.8 C; IR: υmax/cm 3463 (OH), 3379 (NH), 3215

Molecules 2017, 22, 1592
20 of 27
1
(
NH), 1612 (C=N), 1594 (C=C), 1563 (C=C); H-NMR (DMSO-d )
δ
10.29 (s, 1H, NH), 7.18 (s, 2H, Ar-H),
6
6
.11 (s, 2H, NH ), 5.78 (s, 2H, NH ), 4.77 (d, J = 5.2, 1H, CHOH), 4.55 (t, J = 5.6, 1H, CH OH), 4.15–4.07
2
2
2
(
m, 2H, OCH ), 3.62–3.58 (m, 4H, OCH and CH), 3.32–3.28 (m, 2H, OCH ), 2.59 (s, 6H, CH
×
2);
2
3
2
3
+
+
ES-MS 414.1(M + H) ; HRMS Calcd. for C H N O S 414.1447, found 414.1449.
16
24
5
6
(
0
1
S)-2,4-Diamino-5-[4-(morpholino-4-carbonyl)phenyl]-6-(1,2-dihydroxypropyl)pyrimidine (11n). White solid
◦
−1
.35 g, yield 86%; m.p. 209.6–210.2 C; IR: υmax/cm 3443 (OH), 3342 (NH), 3220 (NH), 1629 (C=N),
1
609 (C=C), 1590 (C=C), 1568 (C=C), 1511 (C=C); H-NMR (DMSO-d )
δ
7.36 (d, J = 8.4, 2H, Ar-H), 7.34
6
(
d, J = 8.4, 2H, Ar-H), 6.04 (s, 2H, NH ), 5.69 (s, 2H, NH ), 4.77 (d, J = 5.2, 1H, CHOH), 4.53 (t, J = 5.6,
2 2
1
H, CH OH), 4.10 (d, J = 5.2, 2H, OCH ), 3.63–3.59 (m, 1H, CH), 3.74–3.38 (m, 8H, CH
2
×
4), 3.32–3.25
2
2
+
+
(m, 2H, OCH ); ES-MS 390.2 (M + H) ; HRMS Calcd. for C H N O 390.1777, found 390.1779.
2 18 24 5 5
(
S)-2,4-Diamino-5-[4-(3-trifluoromethoxyanilinocarbonyl)phenyl]-6-(1,2-dihydroxypropyl)pyrimidine (11o).
◦
−1
White soilid 0.44 g, 87%; m.p. 143.2–145.0 C; IR: υmax/cm 3336 (OH), 3225 (NH), 1658 (C=N), 1606
(
1
C=C), 1549 (C=C), 1491 (C=C), 1350 (C-F); H-NMR (DMSO-d )
δ
10.49 (s, 1H, NH), 7.98–7.96 ( m,
6
3
H, Ar-H), 7.80 (dd, J = 8.2, J = 1.0, 1H, Ar-H), 7.51–7.45 (m, 3H, Ar-H), 7.09 (dt, J = 8.4, J = 1.2, 1H,
1 2 1 2
Ar-H), 6.10 (s, 2H, NH ), 5.70 (s, 2H, NH ), 4.77 (d, J = 5.2, 1H, CHOH), 4.55 (t, J = 5.8, 1H, CH OH),
2
2
2
+
4
.12 (d, J = 5.2, 2H, CH ), 3.58–3.65 (m, 1H, CH), 3.28–3.33 (m, 2H, OH); ES-MS 480.1 (M + H) ; HRMS
2
+
Calcd. for C H F N O 480.1495, found 480.1497.
21
21
3
5
5
(
S)-2,4-Diamino-5-(4-methoxycarbonylphenyl)-6-(1,2-dihydroxypropyl)pyrimidine (11p). White solid 0.32 g,
◦
−1
yield 90%; m.p. 211.3–212.4 C; IR: υmax/cm 3562 (OH), 3450 (NH), 3227 (NH), 3217 (NH), 1712
(
1
C=O), 1629 (C=N), 1592 (C=C), 1573 (C=C), 1555 (C=C), 1515 (C=C); H-NMR (DMSO-d )
δ
7.92 (d,
6
J = 8.4, 2H, Ar-H), 7.44 (d, J = 8.4, 2H, Ar-H), 6.10 (s, 2H, NH ), 5.74 (s, 2H, NH ), 4.74 (d, J = 5.2,
2
2
1
H, CHOH), 4.52 (t, J = 5.6, 1H, CH OH), 4.13–4.06 (m, 2H, OCH ), 3.86 (s, 3H, OCH ) 3.6–3.57 (m,
2 2 3
+
+
1H, CH), 3.3–3.24 (m, 2H, OCH ); ES-MS 335.1 (M + H) ; HRMS Calcd. for C H N O 335.1355,
2 15 19 4 5
found 335.1357.
(
S)-2,4-Diamino-5-(3-methoxycarbonylphenyl)-6-(1,2-dihydroxypropyl)pyrimidine (11q). White solid 0.38 g,
◦
−1
yield 85%; m.p. 181.4–182.3 C; IR: υmax/cm 3577 (OH), 3525 (OH), 3453 (NH), 3338 (NH), 1705
(
1
C=O), 1637 (C=N), 1590 (C=C), 1558 (C=C), 1501 (C=C); H-NMR (DMSO-d )
δ
7.84 (s, 1H, Ar-H), 7.81
6
(
d, J = 7.2, 1H, Ar-H) 7.54 (d, J = 7.6, 1H, Ar-H), 7.49 (t, J = 7.6, 1H, Ar-H), 6.06 (s, 2H, NH ), 5.69 (s,
2
2
3
H, NH ), 4.72 (d, J = 4.8, 1H, CHOH), 4.50 (t, J = 5.8, 1H, CH OH), 4.09 (d, J = 5.2, 2H, OCH ), 3.85 (s,
2 2 2
+
H, OCH ) 3.61–3.54 (m, 1H, CH), 3.30–3.22 (m, 2H, OCH ); ES-MS 335.1 (M + H) ; HRMS Calcd. for
3
2
+
C H N O 335.1355, found 335.1353.
15
19
4
5
General Procedure for the Synthesis of 2,4-Diamino-6-substituted Pyrimidine Derivatives 13a-d
Under argon, to a solution of substituted methanol 12a-d (17.45 mmol) in dry DMSO or
THF (30 mL) was added NaH (60%, 21.82 mmol) and stirred at room temperature for 1 h.
2,4-Diamino-6-chloropyrimidine (2) (8.73 mmol) was added and stirred at room temperature for 11 h.
The reaction solution was quenched with sat NH Cl (50 mL) and extracted with EtOAc (150 mL × 3),
4
and the combined organic layers dried with Na SO , filtered and concentrated. The residue was
2
4
purified by column chromatography on silica gel using CH Cl /CH OH (50:1, v/v) as the eluting
2
2
3
solvent to give compounds 13a-d.
◦
2
,4-Diamino-6-(2-methoxyethoxy)pyrimidine (13a). White solid 1.04 g, yield 65%. m.p. 152.9–153.9 C; IR:
−
1
1
υmax/cm 3440 (NH), 3368 (NH), 1636 (C=N), 1563 (C=C), 1118 (C-O-C); H-NMR (DMSO-d )
δ
6.00
6
(
(
s, 2H, NH ), 5.85 (s, 2H, NH ), 5.02 (s, 1H, Ar-H), 4.23–4.17 (m, 2H, CH ), 3.59–3.51 (m, 2H, CH ), 3.27
2 2 2 2
+
+
s, 3H, CH ); ES-MS 185.1 (M + H) ; HRMS Calcd. for C H ClN O 185.1039, found 185.1040.
3
16 20
4
3
◦
2
,4-Diamino-6-(3-methoxylpropoxy)pyrimidine (13b). White solid 1.07 g, yield 62%. m.p. 104.2–104.8 C;
−
1
1
IR: υmax/cm 3456 (NH), 3343 (NH), 1656 (C=N), 1572 (C=C), 1207 (C-O-C); H-NMR (DMSO-d )
6
δ
5.98 (s, 2H, NH ), 5.84 (s, 2H, NH ), 5.02 (s, 1H, Ar-H), 4.11 (t, J = 6.6, 2H, CH ), 3.40 (t, J = 6.3, 2H,
2 2 2

Molecules 2017, 22, 1592
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+
+
CH ), 3.23 (s, 3H, CH ), 1.84 (m, 2H, CH ); ES-MS 199.1 (M + H) ; HRMS Calcd. for C H ClN O
2
3
2
16 20
4
3
1
99.1195, found 199.1198.
◦
2
,4-Diamino-6-(thiazole-5-methoxy)pyrimidine (13c). Yellow solid 1.44 g, yield 74%. m.p. 156.8–161.3 C;
−
1
IR: υmax/cm 3466 (NH), 3320 (NH), 1625 (C=N), 1570 (C=C), 1454 (C=C), 1138 (C-O-C), 1061 (C-O-C);
δ 9.06 (s, 1H, Ar-H), 7.97 (s, 1H, Ar-H), 6.07 (s, 2H, NH ), 5.98 (s, 2H, NH ), 5.44
2 2
s, 2H, CH ), 5.04 (s, 1H, Ar-H); ES-MS 224.0 (M + H) ; HRMS Calcd. for C H ClN O 224.0606,
1
H-NMR (DMSO-d6)
+
+
(
2 16 20 4 3
found 224.0608.
2
,4-Diamino-6-(1-benzyl-1H-1,2,3-triazole-4-methoxy)pyrimidine (13d). White solid 2.05 g, yield 79%.
◦
−1
m.p.131.4–135.7 C; IR: υmax/cm 3421 (NH), 3333 (NH), 1631 (C=N), 1588 (N=N), 1451 (C=C), 1422
1
(
C=C), 1197 (C-O-C); H-NMR (DMSO-d )
δ
8.20 (s, 1H, Ar-H), 7.36 (m, 5H, Ar-H), 6.04 (s, 2H, NH ),
6
2
+
5
.96 (s, 2H, NH ), 5.59 (s, 2H, CH ), 5.20 (s, 2H, CH ), 5.02 (s, 1H, Ar-H); ES-MS 298.1 (M + H) ; HRMS
2
2
2
+
Calcd. for C H ClN O 298.1416, found 298.1412.
16
20
4
3
General Procedure for the Synthesis of 2,4-Diamino-5-iodine-6-substitutedpyrimidine Derivatives
4a-d
1
Under argon, to a solution of 13-d (6.06 mmol) in dry CH CN (35 mL) was added
3
N-iodosuccinimide (9.09 mmol) and stirred at room temperature for 12 h. The reaction solution
was extracted with EtOAc (150 mL 3), and the combined organic layers were washed by NaHSO3,
sat. NaHCO and sat. NaCl, and dried with Na SO , filtered and concentrated. The residue was
×
3
2
4
purified by column chromatography on silica gel using CH Cl /CH OH (80:1, v/v) as the eluting
2
2
3
solvent to give compounds 14a-d.
◦
2
,4-Diamino-5-iodo-6-(2-methoxyethoxy)pyrimidine (14a). Yellow solid 1.50 g, 80%. m.p. 109.7–111.0 C;
−
1
1
IR: υmax/cm 3424 (NH), 3345 (NH), 1705 (C=N), 1554 (C=C), 1116 (C-O-C), 523 (C-I); H-NMR
DMSO-d6) 6.10 (s, 4H, NH ), 4.31–4.27 (m, 2H, CH ), 3.61–3.57 (m, 2H, CH ), 3.31 (s, 3H, CH );
ES-MS 310.9 (M + H) ; HRMS Calcd. for C H ClN O 311.0005, found 311.0003.
(
δ
2
2
2
3
+
+
16
20
4
3
◦
,4-Diamino-5-iodo-6-(3-methoxypropoxy)pyrimidine (14b). Yellow solid 1.37 g, 70%. m.p. 124.0–125.8 C;
2
−
1
1
IR: υmax/cm 3472 (NH), 3357 (NH), 1631 (C=N), 1553 (C=C), 1145 (C-O-C), 532 (C-I); H-NMR
DMSO-d6) 6.09 (s, 4H, NH ), 4.20 (t, J = 6.4, 2H, CH ), 3.45 (t, J = 6.3, 2H, CH ), 3.24 (s, 3H, CH ),
(
1
δ
2
2
2
3
+
+
.86 (m, 2H, CH ); ES-MS 325.0 (M + H) ; HRMS Calcd. for C H ClN O 325.0161, found 325.0159.
2 16 20 4 3
2
,4-Diamino-5-iodo-6-(thiazole-5-methoxy)pyrimidine (14c). Yellow solid 1.90 g, yield 90%. m.p.
◦
−1
178.0–179.9 C; IR: υmax/cm 3436 (NH), 3305 (NH), 1624 (C=N), 1541 (C=C), 1442 (C=C), 1127
1
(C-O-C), 1103 (C-O-C), 545 (C-I); H-NMR (DMSO-d )
δ
9.08 (d, J = 0.5, 1H, Ar-H), 8.01 (d, J = 0.6, 1H,
6
+
+
Ar-H), 6.24 (s, 4H, NH ), 5.51 (s, 2H, CH ); ES-MS 349.9 (M + H) ; HRMS Calcd. for C H ClN O
2
2
16 20
4
3
3
49.9572, found 349.9572.
2
9
,4-Diamino-5-iodo-6-(1-benzyl-1H-1,2,3-triazole-4-methoxy)pyrimidine (14d). Yellow solid 2.38 g, yield
◦
−1
3%. m.p. 156.4–159.1 C; IR: υmax/cm 3441 (NH), 3340 (NH), 1618 (C=N), 1552 (N=N), 1446 (C=C),
1
1280 (C-O-C); H-NMR (DMSO-d )
δ
8.51 (s, 1H, Ar-H), 7.86–7.74 (m, 5H, Ar-H), 6.28 (s, 2H, NH ),
6
2
+
6
.20 (s, 2H, NH ), 6.08 (s, 2H, CH ), 5.81 (s, 2H, CH ); ES-MS 424.0 (M + H) ; HRMS Calcd. for
2
2
2
+
C H ClN O 424.0383, found 424.0380.
16
20
4
3
General Procedure for the Synthesis of 2,4-Diamino-5-aryl-6-substitutedpyrimidine Derivatives 16a-p
A) Under argon, to a mixed solution of EtOH/toluene/H O (1:2:1, 60 mL) was added compounds
(
2
1
4a-d (2.36 mmol), substituted phenylboronic acid 15 (3.55 mmol), Pd(dbpf)Cl (0.02 mmol) and K CO
2 2 3
◦
(
3.55 mmol) consecutively and then stirred at 90 C for 24 h. The reaction solution was extracted with
EtOAc (150 mL 3), and the combined organic layers were washed by H O and dried with Na SO ,
×
2
2
4
filtered and concentrated. The residue was purified by column chromatography on silica gel using
CH Cl /CH OH (80:1, v/v) as the eluting solvent to the desired compounds.
2
2
3

Molecules 2017, 22, 1592
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(
B) In a pressure tube, to a mixed solution of THF/H O (1:1, 50 mL) was added compounds 14a-d
2
(
(
2.40 mmol), substituted phenylboronic acid 15 (3.60 mmol), Pd(dbpf)Cl (0.03 mmol) and K CO
2 2 3
◦
3.60 mmol) consecutively and then stirred at 70 C for 20 h. The reaction solution was extracted with
3), and the combined organic layers were washed by H O and dried with Na SO ,
EtOAc (150 mL
×
2
2
4
filtered and concentrated. The residue was purified by column chromatography on silica gel using
CH Cl /CH OH (60:1, v/v) as the eluting solvent to the desired compounds.
2
2
3
2
0
,4-Diamino-5-(4-trifluoromethoxyphenyl)-6-(2-methoxyethoxy)pyrimidine (16a). Method A. White solid
◦
−1
.60 g, yield 74%. m.p. 178.3–179.0 C; IR: υmax/cm 3477 (NH), 3349 (NH), 1619 (C=N), 1553 (C=C),
1
1
4
3
486 (C=C), 1447 (C=C), 1275 (C-F), 1222 (C-O-C), 1143 (C-O-C); H-NMR (DMSO-d )
δ
7.38–7.29 (m,
6
H, Ar-H), 6.04 (s, 2H, NH ), 5.67 (s, 2H, NH ), 4.28–4.23 (m, 2H, CH ), 3.52–3.46 (m, 2H, CH ), 3.18 (s,
2
2
2
2
+
+
H, CH ); ES-MS 345.1 (M + H) ; HRMS Calcd. for C H ClN O 345.1175, found 345.1176.
3
16 20
4
3
2
0
,4-Diamino-5-(3-trifluoromethoxyphenyl)-6-(2-methoxyethoxy)pyrimidine (16b). Method A. White solid
◦
−1
.60 g, yield 74%. m.p. 80.1–81.7 C; IR: υmax/cm 3347 (NH), 3393 (NH), 1620 (C=N), 1561 (C=C),
1
1451 (C=C), 1292 (C-F), 1207 (C-O-C), 1157 (C-O-C); H-NMR (DMSO-d ) 7.49–7.44 (m, 1H, Ar-H),
6
7
.29 (d, J = 7.8, 1H, Ar-H), 7.20 (d, J = 6.4, 2H, Ar-H), 6.08 (s, 2H, NH ), 5.73 (s, 2H, NH ), 4.28–4.23
2 2
+
(m, 2H, CH ), 3.51–3.46 (m, 2H, CH ), 3.18 (s, 3H, CH ); ES-MS 345.1 (M + H) ; HRMS Calcd. for
2 2 3
+
C H ClN O 345.1175, found 345.1177.
16
20
4
3
2
,4-Diamino-5-[3-(2,2,2-trifluoroethoxymethyl)phenyl]-6-(2-methoxyethoxy)pyrimidine (16c). Method A.
−
1
Colorless oil 0.61 g, yield 70%; IR: υmax/cm 3480 (NH), 3383 (NH), 1607 (C=N), 1558 (C=C), 1437
1
(
C=C), 1279 (C-F), 1160 (C-O-C), 1121 (C-O-C); H-NMR (DMSO-d )
δ
7.40–7.34 (m, 1H, Ar-H), 7.25–7.17
6
(
m, 3H, Ar-H), 6.01 (s, 2H, NH ), 5.57 (s, 2H, NH ), 4.65 (s, 2H, CH ), 4.27–4.22 (m, 2H, CH ), 4.09 (q,
2
2
2
2
+
J = 9.4, 2H, CH ), 3.51–3.45 (m, 2H, CH ), 3.18 (s, 3H, CH ); ES-MS 373.1 (M + H) ; HRMS Calcd. for
C H ClN O 373.1488, found 373.1486.
2
+
2
3
16
20
4
3
2
,4-Diamino-5-[3,5-dimethyl-4-(N-methoxyaminosulfonyl)phenyl]-6-(2-methoxyethoxy)pyrimidine (16d).
◦
−1
Method A. White solid 0.68 g, yield 73%. m.p. 167.3–171.4 C; IR: υmax/cm 3466 (NH), 3364
1
(
NH), 1633 (C=N), 1587 (C=C), 1507 (NH), 1435 (C=C), 1157 (SO ), 1078 (SO ), 1014 (SO ); H-NMR
2
2
2
(
DMSO-d6)
δ 10.26 (s, 1H, NH), 7.15 (s, 2H, Ar-H), 6.09 (s, 2H, NH ), 5.77 (s, 2H, NH ), 4.29–4.23 (m,
2 2
2
H, CH ), 3.62 (s, 3H, CH ), 3.53–3.47 (m, 2H, CH ), 3.22 (s, 3H, CH ), 2.59 (s, 6H, CH ); ES-MS 398.1
2
+
3
2
3
3
+
(M + H) ; HRMS Calcd. for C H ClN O 398.1498, found 398.1497.
16 20 4 3
2
,4-Diamino-5-[4-(3-trifluoromethoxyanilinoformoxyl)phenyl)-6-(2-methoxyethoxy)pyrimidine
(16e).
◦
−1
Method A. White solid 0.77 g, yield 70%. m.p. 96.50–100.1 C; IR: υmax/cm 3424 (NH), 3345 (NH),
1
1705 (C=N), 1554 (C=C), 1116 (C-O-C), 523 (C-I); H-NMR (DMSO-d )
δ
10.48 (d, J = 10.3, 1H, NH),
6
7.94 (dd, J = 17.0, 4.9, 4H, Ar-H), 7.49 (t, J = 8.2, 1H, Ar-H), 7.43 (d, J = 8.4, 2H, Ar-H), 7.09 (d, J = 8.3,
1
3
H, Ar-H), 6.09 (s, 2H, NH ), 5.70 (s, 2H, NH ), 4.31–4.25 (m, 2H, CH ), 3.53–3.48 (m, 2H, CH ), 3.21 (s,
2
2
2
2
+
+
H, CH ); ES-MS 464.1 (M + H) ; HRMS Calcd. for C H ClN O 464.4252, found 464.4250.
3
16 20
4
3
2
0
,4-Diamino-5-(4-trifluoromethoxyphenyl)-6-(3-methoxypropoxy)pyrimidine (16f). Method A. White solid
◦
−1
.63 g, yield 75%. m.p. 189.3–190.9 C; IR: υmax/cm 3471 (NH), 3365 (NH), 1632 (C=N), 1557 (C=C),
1
1
451 (C=C), 1276 (C-F), 1207 (C-O-C), 1160 (C-O-C); H-NMR (DMSO-d )
δ
7.33 (m, 4H, Ar-H), 6.02 (s,
6
2
H, NH ), 5.64 (s, 2H, NH ), 4.15 (t, J = 6.5, 2H, CH ), 3.27 (t, J = 6.3, 2H, CH ), 3.16 (s, 3H, CH ), 1.74
2
2
2
2
3
+
+
(m, 2H, CH ); ES-MS 359.1 (M + H) ; HRMS Calcd. for C H ClN O 359.1331, found 359.1333.
2 16 20 4 3
2
0
,4-Diamino-5-(3-trifluoromethoxyphenyl)-6-(3-methoxypropoxy)pyrimidine (16g). Method A. White solid
◦
−1
.79 g, yield 94%. m.p. 165.1–165.4 C; IR: υmax/cm 3470 (NH), 3364 (NH), 1633 (C=N), 1559 (C=C),
1
1454 (C=C), 1283 (C-F), 1205 (C-O-C), 1154 (C-O-C); H-NMR (DMSO-d )
δ
7.47 (t, J = 8.0, 1H, Ar-H),
6
7
.27 (d, J = 7.8, 1H, Ar-H), 7.21 (dd, J = 8.3, 1.0, 1H, Ar-H), 7.17 (s, 1H, Ar-H), 6.06 (s, 2H, NH ), 5.70
2
(
s, 2H, NH ), 4.15 (t, J = 6.4, 2H, CH ), 3.29 (t, J = 6.3, 2H, CH ), 3.17 (s, 3H, CH ), 1.74 (m, 2H, CH );
2 2 2 3 2
+
+
ES-MS 359.1 (M + H) ; HRMS Calcd. for C H ClN O 359.1331, found 359.1330.
16
20
4
3

Molecules 2017, 22, 1592
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2
0
,4-Diamino-5-(4-trifluoromethoxyphenyl)-6-(thiazole-5-methoxy)pyrimidine (16h). Method A. Yellow solid
◦
−1
.79 g, yield 87%. m.p. 188.3–189.6 C; IR: υmax/cm 3429 (NH), 3327 (NH), 1601 (C=N), 1556 (C=C),
1
1449 (C=C), 1245 (C-F), 1105 (C-O-C), 1025 (C-O-C); H-NMR (DMSO-d )
δ
9.03 (s, 1H, Ar-H), 7.91
6
(
(
s, 1H, Ar-H), 7.30 (s, 4H, Ar-H), 6.16 (s, 2H, NH ), 5.75 (s, 2H, NH ), 5.45 (s, 2H, CH ); ES-MS 384.0
2 2 2
+
+
M + H) ; HRMS Calcd. for C H ClN O 384.0742, found 384.0745.
16
20
4
3
2
0
,4-Diamino-5-(3-trifluoromethoxyphenyl)-6-(thiazole-5-methoxy)pyrimidine (16i). Method A. Yellow solid
◦
−1
.66 g, yield 73%. m.p. 142.8–143.2 C; IR (KBr): υmax/cm 3467 (NH), 3361 (NH), 1628 (C=N),
1
1556 (C=C), 1452 (C=C), 1261 (C-F), 1106 (C-O-C), 1042 (C-O-C); H-NMR (DMSO-d )
δ
9.01 (s, 1H,
6
Ar-H), 7.87 (s, 1H, Ar-H), 7.50–7.45 (m, 1H, Ar-H), 7.30 (d, J = 7.8, 1H, Ar-H), 7.21 (d, J = 6.4, 2H,
+
Ar-H), 6.20 (s, 2H, NH ), 5.79 (s, 2H, NH ), 5.45 (s, 2H, CH ); ES-MS 384.0 (M + H) ; HRMS Calcd. for
2
2
2
+
C H ClN O 384.0742, found 384.0740.
16
20
4
3
2
,4-Diamino-5-[3-(2,2,2-trifluoroethoxymethyl)phenyl]-6-(thiazole-5-methoxy)pyrimidine (16j). Method A.
◦
−1
Yellow solid 0.88 g, yield 91%. m.p. 126.3–129.0 C; IR: υmax/cm 3478 (NH), 3316 (NH), 1624 (C=N),
1
1
553 (C=C), 1442 (C=C), 1282 (C-F), 1158 (C-O-C); H-NMR (DMSO-d )
δ
9.02 (s, 1H, Ar-H), 7.90 (s, 1H,
6
Ar-H), 7.35 (t, J = 7.6, 1H, Ar-H), 7.21 (d, J = 7.7 , 1H, Ar-H), 7.14 (d, J = 8.6, 2H, Ar-H), 6.12 (s, 2H, NH ),
2
+
5
.64 (s, 2H, NH ), 5.44 (s, 2H, CH ), 4.64 (s, 2H, CH ), 4.08 (q, J = 9.4, 2H, CH ); ES-MS 412.1 (M + H)
;
2
2
+
2
2
HRMS Calcd. for C H ClN O 412.1055, found 412.1056.
16
20
4
3
2
,4-Diamino-5-[3,5-dimethyl-4-(N-methoxyaminosulfonyl)phenyl]-6-(thiazole-5-methoxy)pyrimidine (16k).
◦
−1
Method A. White solid 0.74 g, yield 72%. m.p. 139.2–142.6 C; IR: υmax/cm 3463 (NH), 3358
1
(
NH), 1616 (C=N), 1589 (C=C), 1490 (C=C), 1448 (C=C), 1168 (SO ), 1076 (SO ), 1009 (SO ); H-NMR
2
2
2
(
DMSO-d6)
δ
10.26 (s, 1H, NH), 9.05 (s, 1H, Ar-H), 7.92 (s, 1H, Ar-H), 7.07 (s, 2H, Ar-H), 6.21 (s, 2H,
+
NH ), 5.84 (s, 2H, NH ), 5.46 (s, 2H, CH ), 3.61 (s, 3H, CH ), 2.57 (s, 6H, CH ); ES-MS 437.1 (M + H) ;
HRMS Calcd. for C H ClN O 437.1066, found 437.1065.
2
2
2
3
3
+
16
20
4
3
2
,4-Diamino-5-[4-(3-trifluoromethoxyanilinocarbonyl)phenyl]-6-(thiazole-5-methoxy)pyrimidine
(16l).
◦
−1
Method A. Yellow solid 1.17 g, yield 99%. m.p. 180.9–182.9 C; IR: υmax/cm 3430 (NH), 3340
1
(
(
NH), 3200 (NH), 1654 (C=O), 1608 (C=N), 1551 (C=C), 1484 (C=C), 1442 (C=C), 1257 (C-F); H-NMR
DMSO-d6)
δ 10.46 (s, 1H, NH), 9.04 (s, 1H, Ar-H), 7.94 (d, J = 8.6, 4H, Ar-H), 7.79 (d, J = 8.2, 1H, Ar-H),
7
.48 (t, J = 8.2, 1H, Ar-H), 7.36 (d, J = 8.4, 2H, Ar-H), 7.09 (d, J = 8.2, 1H, Ar-H), 6.20 (s, 2H, NH ), 5.77
2
+
+
(s, 2H, NH ), 5.47 (s, 2H, CH ); ES-MS 503.1 (M + H) ; HRMS Calcd. for C H ClN O 503.1113,
2 2 16 20 4 3
found 503.1111.
2
,4-Diamino-5-(4-trifluoromethoxyphenyl)-6-(1-benzyl-1H-1,2,3-triazole-4-methoxy)pyrimidine
(16m).
◦
−1
Method A. White solid 0.98 g, yield 91%. m.p.159.5–160.6 C; IR: υmax/cm 3489 (NH), 3371 (NH),
1
1608 (C=N), 1556 (N=N), 1492 (C=C), 1439 (C=C), 1261 (C-O-C), 1219 (C-F); H-NMR (DMSO-d )
δ
6
8
.15 (s,1H, Ar-H), 7.40–7.23 (m, 9H, Ar-H), 6.17 (s, 2H, NH ), 5.73 (s, 2H, NH ), 5.57 (s, 2H, CH ), 5.24
2 2 2
+
+
(s, 2H, CH ); ES-MS 458.1 (M + H) ; HRMS Calcd. for C H ClN O 458.1552, found 458.1555.
2 16 20 4 3
2
,4-Diamino-5-(3-trifluoromethoxyphenyl)-6-(1-benzyl-1H-1,2,3-triazole-4-methoxy)pyrimidine
(
16n).
◦
−1
Method A. White solid 0.98 g, yield 91%. m.p. 171.9–173.0 C; IR: υmax/cm 3495 (NH), 3376 (NH),
1
1607 (C=N), 1556 (N=N), 1491 (C=C), 1431 (C=C), 1278 (C-O-C), 1219 (C-F); H-NMR (DMSO-d )
δ
6
8
.15 (s, 1H, Ar-H), 7.40–7.23 (m, 9H, Ar-H), 6.17 (s, 2H, NH ), 5.73 (s, 2H, NH ), 5.57 (s, 2H, CH ), 5.24
2 2 2
+
+
(s, 2H, CH ); ES-MS 458.1 (M + H) ; HRMS Calcd. for C H ClN O 458.1552, found 458.1553.
2 16 20 4 3
2
,4-Diamino-5-(4-methoxycarbonylphenyl)-6-(1-benzyl-1H-1,2,3-triazole-4-methoxy)pyrimidine
(
16o).
◦
−1
Method B. Gray solid 0.70 g, yield 68%. m.p. 218.6–222.3 C; IR: υmax/cm 3487 (NH), 3440 (NH),
1
1709 (C=O), 1616 (C=N), 1555 (N=N), 1483 (C=C), 1440 (C=C), 1285 (C-O-C); H-NMR (DMSO-d ):
6
8
.16 (s, 1H, Ar-H), 7.87 (d, J = 8.4, 2H, Ar-H), 7.39–7.25 (m, 7H, Ar-H), 6.20 (s, 2H, NH ), 5.77 (s, 2H,
2
+
NH ), 5.57 (s, 2H, CH ), 5.24 (s, 2H, CH ), 3.86 (s, 3H, CH ); ES-MS 432.1 (M + H) ; HRMS Calcd. for
C H ClN O 432.1784, found 432.1786.
2
2
2
3
+
16
20
4
3

Molecules 2017, 22, 1592
24 of 27
2
,4-Diamino-5-(3-methoxycarbonylphenyl)-6-(1-benzyl-1H-1,2,3-triazole-4-methoxy)pyrimidine
(16p).
◦
−1
Method B. Yellow solid 0.53 g, yield 51%. m.p. 210.4–213.7 C; IR: υmax/cm 3432 (NH), 3351 (NH),
1
1
706 (C=O), 1619 (C=N), 1564 (N=N), 1485 (C=C), 1442 (C=C), 1252 (C-O-C); H-NMR (DMSO-d )
δ
6
8
.13 (s, 1H, Ar-H), 7.80 (dd, J = 8.8, 4.4, 2H, Ar-H), 7.44 (d, J = 5.1, 2H, Ar-H), 7.34 (dd, J = 9.1, 6.9, 3H,
Ar-H), 7.28–7.24 (m, 2H, Ar-H), 6.16 (s, 2H, NH ), 5.71 (s, 2H, NH ), 5.56 (s, 2H, CH ), 5.24 (s, 2H, CH ),
2
2
2
2
+
+
3
.82 (s, 3H, CH ); ES-MS 432.1 (M + H) ; HRMS Calcd. for C H ClN O 432.1784, found 432.1785.
3
16 20
4
3
3
.3. Determination of Anti-Mycobacterial Activity
The minimum inhibitory concentrations (MIC) and minimum bactericidal concentrations (MBC)
of the test compounds were determined as described previously [19] with minor modifications.
In brief, the MIC was determined using the microbroth dilution method in 96-well microtitre plates.
Mycobacterium tuberculosis H37Ra (ATCC 25177) was used as the test strain, at a final inoculum of
5
approximately 10 cfu/mL. The compounds were dissolved in DMSO and diluted in 1% DMSO in 7H9
broth to obtain concentrations ranging from 100
sealed with Parafilm and incubated at 36 C for 28 days. On days 14 and 28, all wells were observed
µ
g/mL to 1.56
µ
g/mL. All inoculated plates were
◦
for visible growth, and 10
µ
L was removed from each well for subculturing on compound-free 7H10
◦
agar plates which were incubated for six weeks at 36 C. For each compound, the lowest concentration
to inhibit the growth of H37Ra in broth culture was taken to be the MIC. The MBC was the lowest
concentration to inhibit the formation of colonies on the agar subculture, up to six weeks of incubation.
3
.4. Molecular Docking
The crystal structure of mt-DHFR in complex with NADPH and MTX (PDB ID: 1DF7) [20] was
used as the receptor for molecular docking, which was performed by GOLD Docking: GOLD (v 5.2.2
Genetic Optimization for Ligand Docking) [21]. The bound ligand, MTX was used as a reference to
indicate the binding site, and each molecule was docked 10 times with the default automatic genetic
algorithm parameter settings and the results were evaluated by Gold Score.
3
.5. Molecular Dynamic Simulation
The geometry of the docked ligand was optimized by using the B3LYP 6–31 G* basis set within
Gaussian09 [22], and the atom-centered point charges were calculated to fit the electrostatic potential
using RESP [23]. The parameters of NADPH were obtained from AMBER parameter database (http:
/
/www.pharmacy.manchester.ac.uk/bryce/amber/, uploaded by U. Ryde).
The docked compound and mt-DHFR complex was explicitly solvated in a truncated octahedral
box of TIP3P model water (at least 12 Å from the complex to avoid periodic artifacts from occurring)
by using Amber 16 with the amber ff14SB force field. The system charges were neutralized by
+
adding enough K ions by using the tleap module (AmberTools 16). The explicit solvent models
and the NPT ensemble (T = 300 K; P = 1 atm) were performed on all molecular dynamic simulations.
Periodic boundary conditions (PBC) and particle-mesh-Ewald method (PME) [24] were used to treat
long-range electrostatic effects, with the temperature coupled to an external bath using a weak coupling
algorithm [25]. The non-bonded interaction cutoff was set as 8 Å. The bond interactions involving
H-atoms were constrained by using the SHAKE algorithm. The time step necessary to solve the
Newton’s equations was chosen to be equal to 2 fs and the trajectory files were collected every 10 ps.
All trajectory analysis was performed with the Ptraj module in the AmberTools 16 and examined
visually using VMD software [26].
The whole system was first optimized by energy minimization, followed by 110 ns molecular
dynamic simulation, including 10 ns equilibration and 100 ns production simulations. The last
80 ns (1000 snapshots, 80 ps intervals) stable, equilibrated trajectories of the production simulation
were taken for binding free energy calculations performed by using MM-PBSA [27
–29] (included in
AMBERTOOLS 16).

Molecules 2017, 22, 1592
25 of 27
The entropy was estimated by using the Normal Mode program [28
,
29] within the AMBER16
suite. Because the entropy calculations are computationally intensive, only 100 snapshots from the last
8
0 ns trajectories were used for the normal-mode analysis.
4
. Conclusions
In conclusion, in order to occupy the GOL binding site on mt-DHFR and maintain proper
hydrophobicities to allow the compounds to function in the Mtb whole cell assay, we designed
and synthesized three series of compounds which contain a hydrophobic side chain. Among them,
the compounds with a thiazole side chain significantly inhibited the growth of Mtb, and the best
inhibition effect was observed on compound 16l. More interestingly, this compound showed selectivity
for Mtb over vero cells, which makes it potentially useful as a lead compound for future studies on
anti-TB drugs. Unfortunately, we are currently unable to confirm 16l as an mt-DHFR inhibitor by
performing the binding assay on the pure mt-DHFR enzyme.
Sulfonamides were the first anti-bacterial agents to be used for the treatment of tuberculosis [30].
They were subsequently replaced by the standard first-line anti-TB drugs rifampicin, isoniazid,
ethambutol and pyrazinamide, which had greater anti-TB activity. With the increase of multidrug
resistant TB in the past two decades, and the therapeutic failures with standard anti-TB drugs,
respiratory physicians have to resort the treatment with other antibiotics and chemotherapeutic agents
including the trimethoprim-sulfamethoxazole combination [31]. While sulfamethoxazole competes
with para-aminobenzoic acid (PABA) for the enzyme dihydropteroate synthetase, trimethoprim directly
inhibits the dihydrofolate reductase for the reduction of dihydrofolic acid to tetrahydrofolic acid.
This combination was found to have in vitro activity for up to 98% of Mtb isolates [32]. However, both
drugs are bacteriostatic, and are associated with drug resistance. Sulfonamide resistance has been
reported to result from a point mutation or the acquisition of a plasmid which enables the synthesis
of a dihydropteroic synthetase that has poor affinity for sulfonamides. Similarly, trimethoprim can
be rendered ineffective by plasmid- and transposon-mediated production of an altered dihydrofolate
reductase that has markedly reduced affinity for the drug. In some studies, trimethoprim, when used
by itself, has been shown to have little activity on some strains of Mtb [33]. The new compounds
we synthesized appear to be bactericidal against Mtb, making it a better drug for TB therapy in
immunocompromised patients. Further studies are required to test for the frequency of mutation to
resistance among clinical strains of Mtb and whether the compounds can be used in combination with
other anti-TB drugs or antibiotics for synergistic activity or to retard the development of resistance.
Acknowledgments: This work was supported by National Natural Science Foundation of China (81773582)
given to H.W.; National Natural Science Foundation of China (81460538, 81660588) given to W.H.;
IPSR/RMC/UTARRF/2015-C1/NO3 awarded to Y.F.N. by Universiti Tunku Abdul Rahman (UTAR),
Kuala Lumpur, Malaysia.
Author Contributions: Wei Hong, Hao Wang and Yun Fong Ngeow conceived and designed the experiments;
Yifan Ouyang, Hao Yang, Peng Zhang, Yu Wang, Sargit Kaur, Xuanli Zhu, Zhe Wang, and Yutong Sun performed
the experiments; Wei Hong and Hao Wang analyzed the data; Wei Hong, Hao Wang and Yun Fong Ngeow wrote
the paper.
Conflicts of Interest: All authors declare no conflict of interest.
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Sample Availability: Samples of the compounds 10a-q, 11a-q and 16a-p are available from the authors.
©
2017 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access
article distributed under the terms and conditions of the Creative Commons Attribution
CC BY) license (http://creativecommons.org/licenses/by/4.0/).
(