The synthesis of 7,9-dimethoxy-3-propyl-3,4-dihydro-1H-benzo[g]isochromene- 1,5,10-trione: A potential monomer for the synthesis of the natural product xylindein

Article abstract of DOI:10.24820/ARK.5550190.P011.315

A novel synthesis of a 3-propyl-substituted-benzo[g]isochromene quinone, a potential monomer of the natural product xylindein, was accomplished in 9 steps (overall yield of 8.2%) from 2,4- dimethoxybenzaldehyde. Key steps included the use of a cross-metathesis reaction in which ethyl-3-allyl-4- (benzyloxy)-1,6,8-trimethoxy-2-naphthoate was converted into ethyl-4-(benzyloxy)-1,6,8-trimethoxy-3-(4- oxopent-2-enyl)-2-naphthoate as a mixture of (E)- and (Z)-isomers. Following an oxa-Michael addition reaction, a racemic mixture of the desired product, 5-(benzyloxy)-7,9,10-trimethoxy-3-(2-oxopropyl)-3,4- dihydro-1H-benzo[g]isochromen-1-one, the basic xylindein lactone skeleton, was obtained.

Full text of DOI:10.24820/ARK.5550190.P011.315

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Organic Chemistry
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Pyrimidine-2,4-diamines as antiplasmodial antifolates
a
a
b,c
b,c
Tswene D. Seanego, Hanna F. Klein, Natasha C. Jansen van Vuuren, Robyn L. van Zyl, and Amanda L.
a,c
Rousseau*
aMolecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Private Bag 3, PO WITS,
2
050, South Africa
b
Pharmacology Division, Department of Pharmacy and Pharmacology, Faculty of Health Sciences, University of
the Witwatersrand, 7 York Road, Parktown 2193, South Africa
WITS Research Institute for Malaria (WRIM), University of the Witwatersrand, 7 York Road, Parktown 2193,
c
South Africa
Email: Amanda.Rousseau@wits.ac.za
Received mm-dd-yyyy
Dates to be inserted by editorial office
Abstract
Accepted mm-dd-yyyy
Published on line mm-dd-yyyy
Two series of substituted pyrimidine-2,4-diamines with a flexible side chain at either the 5- or 6-position of the
pyrimdine ring were designed as potential inhibitors of P. falciparum dihydrofolate reductase (DHFR). The
compounds were synthesised and evaluated for antiplasmodial activity in vitro against a cycloguanil-resistant
strain of the P. falciparum parasite. 5-(3-(3,5-Dichlorophenoxy)propyl)-6-phenylpyrimidine-2,4-diamine was
identified as the most promising compound (IC50 0.86 µM). In general, pyrimidine-2,4-diamines substituted at
the 5-position of the pyrimidine ring showed better antiplasmodial activity (IC50 0.86 - 26.55 µM ) than those
bearing a modified side chain at the 6-position of the pyrimidine ring (IC50 4.46 – 83.45 µM).
Keywords: Pyrimidine-2,4-diamines, antifolates, dihydrofolate reductase, antiplasmodial activity
DOI: https://doi.org/10.24820/ark.5550190.p011.315
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Introduction
In 2018, approximately half of the world's population was at risk of contracting malaria, a disease
1
caused by parasitic protozoa of the genus Plasmodium. According to the most recent World Malaria
Report, 93% of the estimated 228 million malaria cases and 94% of the 405,000 deaths worldwide in
2
018 were caused by Plasmodium falciparum, one of the Plasmodium species responsible for causing
malaria in humans which is prevalent in sub-Saharan Africa. While malaria-prevention tools such as
indoor residual spraying (IRS) of insecticides, the use of insecticide-treated nets (ITNs), and
intermittent preventative therapy in pregnancy (IPTp) have played a major role in decreasing malaria
incidence and mortality over the last five years, the WHO estimates that 43% of people at risk of
contracting malaria in sub-Saharan Africa do not have access to these preventative tools.1
Furthermore, although there has been a significant decline in the number of malaria fatalities over the
last 15 years, the rate of decline has decreased, with mortality rates remaining at similar levels since
2
014.1
Folates are cellular cofactors that play an essential role in the life cycle of the malaria parasite.2
Antimalarial antifolates target two key parasitic enzymes, dihydropteroate synthase (DHPS) and
dihydrofolate reductase, which, in the parasite, is a bifunctional dimer with thymidylate synthase
(
DHFR-TS). These enzymes are responsible for maintaining adequate cellular levels of folate
3
derivatives either via a folate salvage pathway or a de novo synthetic pathway. The combination
therapy of sulfadoxine-pyrimethamine, used in IPT both in pregnancy and in infants under the age of 5
years, targets these enzymes in the parasite, with pyrimethamine (
1
) targeting DHFR (Figure 1).
), is
Unfortunately, resistance to pyrimethamine and other anti-DHFR drugs, such as cycloguanil (
2
4
-5
widespread and has limited their clinical usefulness. Point mutations in the active site of the DHFR
domains of DHFR-TS have been shown to be responsible for the development of resistance to these
6
antifolates, which contain a rigid biaryl axis. Related compounds with inherent flexibility, such as
WR99210 (
3
) and P65 (
4
) (Figure 1), however, have been shown to maintain a high binding affinity to
7
all mutant forms of P. falciparum DHFR. These compounds contain a flexible linker between the two
rings, which enables the compounds to avoid unfavourable contacts with mutant amino acid residues
in the DHFR active site.
Figure 1 Known antifolates pyrimethamine (1), cycloguanil (2), WR99210 (3) and P65 (4).
Based on these findings, we reported the synthesis of a series of novel, flexible analogues of
cycloguanil bearing a 4-atom linker between the two rings (see general structure ( ), Figure 2), with in
vitro antimalarial activity in the low nanomolar range against both drug-sensitive and drug-resistant
5
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8
strains of P. falciparum. The compounds were shown to inhibit parasitic DHFR, and were not
cytotoxic. Despite the promising biological activity of these compounds; however, they were isolated
9
as racemic mixtures in generally low yields. Furthermore, the synthesis proved challenging and could
not readily be adapted for asymmetric synthesis. Herein, we report the synthesis of pyrimidine
analogues of general structure (
whole cell Plasmodium falciparum assay. We also embarked on the synthesis of analogues of P65, of
general structure ( ), bearing a longer side chain moved to the 6-position of the pyrimidine ring in
order to assess the effect of this on biological activity in vitro.
6) of our dihydrotriazine series (5), and their biological activity in a
7
Figure 2 Dihydrotriazines (5) prepared previously, and pyrimidine analogues (6) and (7) prepared in
this work.
Results and Discussion
8
The dihydrotriazines of general structure (5) that we have prepared previously contained an atypical
phenyl substituent at the 6-position of the dihydrotriazine ring. The majority of known antifolates
targeting DHFR (such as those shown in Figure 1) contain a simple alkyl substituent at this position.
Owing to the difficulties associated with the synthesis of the dihydrotriazines (
5
) prepared
previously,8 and the fact that they were isolated as racemic mixtures, we planned to prepare the
-9
fully aromatic pyrimidine equivalents which lack the stereogenic centre.
Our approach to the pyrimidine analogues of general structure (6) began with simple alkylation of
commercially available phenols (8a-g) with 1,4-dibromobutane to afford the ethers (9a-g) in good
yields (Scheme 1). Functional-group interconversions by reacting ethers (9a-g) with potassium cyanide
gave pentanenitriles (10a-g) in reasonable yields. Reaction of 10a-g with ethyl benzoate in the
presence of base afforded α-cyanoketones (11a-g), once again in good yields.
At this stage, we envisaged utilising methodology reported for the synthesis of 5-arylpyrimidines10
on our substrates (11a-g) to afford the desired 5-alkylpyrimidines. This methodology involved
formation of an intermediate enol ether, followed by reaction with guanidine hydrochloride to afford
the desired pyrimidine products. Formation of the intermediate enol ethers was achieved by reaction
with diazomethane generated in situ from diazald (N-methyl-N-nitroso-p-toluenesulfonamide) and
potassium hydroxide. In general, the enol ethers were used as the crude products in the subsequent
1
reactions with guanidine hydrochloride, after confirmation of the formation of the enol ether by H
NMR spectroscopy.
Unfortunately, the final reaction with guanidine hydrochloride either afforded the products in low
yields or was unsuccessful, possibly due to the lack of an aromatic substituent at the α-position of our
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substrates 11a-g. Of the seven enol ethers prepared, only four were successfully converted into
pyrimidine products (6a-d), however, in disappointingly low yields.
Scheme 1 Reagents, conditions, and yields: (a) 1,4-dibromobutane, K
2
CO
3
, CH CN, reflux, 20 h, 63 –
3
t
9
8%; (b) KCN, EtOH/H
2
O, reflux, 48 h, 62 – 89%; (c) ethyl benzoate, KO Bu, THF, rt, 18 h, 63 – 94%; (d)
diazomethane, CH Cl
2
2
, rt, 18 h; (e) guanidine HCl, DMSO, NaOMe, 90°C, 24 h, 9 – 11% for 6a-d
.
Nonetheless, we subjected compounds (6a-d) to an initial in vitro assessment of antiplasmodial
activity in a whole cell P. falciparum assay, at a single concentration of 20 μM. The compounds were
screened against a cycloguanil-resistant strain (Gambian FCR-3), for direct comparison with our
8
original series of dihydrotriazine compounds (of general structure (
5
) ) which had been screened
against this strain. At this single concentration, pyrimidines (6a-d) inhibited parasitaemia by more
than 45% in each case (Table 1). IC50 values were then determined for the compounds from the log

sigmoid dose response curves generated by GraphPad Prism software. Disappointingly, only one of
the compounds, 5-(3-(3,5-dichlorophenoxy)propyl)-6-phenylpyrimidine-2,4-diamine (6c) (entry 3,
Table 1, IC50 0.86 µM) showed activity in the nanomolar range comparable with the dihydrotriazines8
prepared previously. The remainder of the compounds displayed only moderate activity in the low
micromolar range. This could be attributed to the inflexibility of the biaryl axis now present between
the 6-phenyl substituent and the pyrimidine ring, which was not present in the original series of
3
dihydrotriazines, where the phenyl substituent was bonded to an sp hybridised carbon with
tetrahedral geometry. Notably, the DHFR inhibitor methotrexate also displayed antiplasmodial activity
in the low micromolar range against the cycloguanil-resistant strain (entry 7, Table 1, IC50 1.71 µM).
Table 1. Whole cell antiplasmodial activity of analogues (6a-d)a
Entry Inhibitor Substituent X
% Inhibition of
parasitaemia at 20 μM
59.84 ± 12.00
IC50 (µM)b
1
2
3
4
6a
6b
6c
6d
4-Cl
3,4-diCl
3,5-diCl
3-F
3.69 ± 0.35
14.80 ± 2.97
0.86 ± 0.01
26.55 ± 5.84
48.91 ± 16.49
59.94 ± 24.48
48.84 ± 17.33
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-3
-3
6
7
Control
Control
DHAc
MTXd
60.64 ± 0.17
59.69 ± 1.02
b
6.13×10 ± 1.11 ×10
1.71 0.51

a
Data are presented as the mean ± SD of three experiments. IC50 values determined by SYBR green assay
c
d
against the Gambian FCR-3 strain. DHA = Dihydroartemisinin. MTX = Methotrexate
In another aspect of this work, we wanted to assess the effect of moving the flexible side chain from C-5
to C-6 on the pyrimidine ring. This would eliminate the biaryl axis created by the presence of a phenyl
substituent at C-6 as was present in 6a-d, and preliminary modelling studies suggested that the longer flexible
chain could place the aromatic substituent at the correct binding position in the DHFR active site.11
The preparation of analogues of general structure (7) bearing a modified side chain could be achieved by
simple substitution of a 4-hydroxypyrimidine. As shown in Scheme 2, commercially available phenols (8a-d)
were alkylated with 1,3-dibromopropane, using the method described previously to afford bromoethers (12a-
d). 2,4-Diaminopyrimidin-6-ol was then reacted with bromoethers (12a-d) to give pyrimidines (7g-j) bearing a
5
-atom linker at the 6-position of the pyrimidine ring in moderate yields. 2,4-Diaminopyrimidin-6-ol was also
treated with previously-prepared bromoethers (9a-f) to afford pyrimidines (7a-f) bearing a 6-atom linker at
the 6-position of the pyrimidine ring. Pyrimidines (7a-j) prepared by this method were then assessed in the
whole cell P. falciparum screen described previously (Table 2).
Scheme 2. Reagents, conditions, and yields: (a) For 12 (n = 1); 1,3-dibromopropane, K
7 – 95%; for 9 (n = 2); 1,4-dibromobutane, reflux, 20 h, 63 – 98%; (b) 2,4-diaminopyrimidin-6-ol, K
CH CN, reflux, 20 h, 33 – 55%.
2
CO
3
, CH
3
CN, reflux, 20 h,
8
2
CO
3
,
3
Table. Whole cell antiplasmodial activity of analogues (7a-j)a
Entry Inhibitor Substituent
X
n
% Inhibition of
parasitaemia at 20 μM
66.04 ± 9.4
IC50 (µM)b
1
2
3
4
5
6
7
8
9
7a
7b
7c
7d
7e
7f
7g
7h
7i
4-Cl
3,4-diCl
3,5-diCl
3-F
2
2
2
2
2
2
1
1
1
83.45 ± 8.36
4.46 ± 0.29
22.80 ± 2.96
11.18 ± 1.06
14.96 ± 1.78
18.02 ± 2.80
44.88 ± 7.76
11.10 ± 1.71
7.66 ± 1.03
55.15 ± 5.1
40.30 ± 14.1
53.95 ± 9.4
48.18 ± 5.6
66.90 ± 3.1
57.36 ± 4.4
52.68 ± 2.8
33.95 ± 16.8
4-F
3-CF
3
4-Cl
3,4-diCl
3,5-diCl
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1
1
1
0
1
2
7j
4-F
DHA
MTXd
1
57.50 ± 8.5
60.64 ± 0.17
54.74 ± 10.91
6.13×10 ± 1.11 ×10
c
-3
-3
Control
Control
59.69 ± 1.02
1.71  0.51
a
b
Data are presented as the mean ± SD of three experiments. IC50 values determined by SYBR green assay
against the Gambian FCR-3 strain. DHA = Dihydroartemisinin. MTX = Methotrexate
c
d
The results presented in Table 2 show that moving the side chain, albeit a modified side chain, to the 6-
position of the pyrimidine ring, has a detrimental effect on antiplasmodial activity in vitro, with the majority of
pyrimidines (7a-j) being less active than pyrimidines (6a-d) against the drug-resistant strain of the P.
falciparum parasite. Although from our initial docking studies it appeared that analogues bearing a longer side
chain at the 6-position of the pyrimidine ring could adopt a suitable conformation for binding in the DHFR
active site, the biological data suggest that this could be energetically unfavourable.
Conclusions
In summary, we have prepared two series of substituted pyrimidine-2,4-diamines with a flexible side chain at
either the 5- or 6-position of the pyrimdine ring as potential inhibitors of P. falciparum dihydrofolate
reductase (DHFR). The synthesis of the first series of compounds involved construction of the pyrimidine ring
by reaction of the enol ether of a suitably substituted α-cyanoketone with guanidine hydrochloride while the
second series was prepared by substitution of the commercially available 2,4-diaminopyrimidin-6-ol. The
compounds prepared were evaluated for antiplasmodial activity in vitro against a cycloguanil-resistant strain
of the P. falciparum parasite. Compounds bearing a substituent at the 5-position of the pyrimidine ring
showed better activity, in general, than those substituted at the 6-position, with 5-(3-(3,5-
dichlorophenoxy)propyl)-6-phenylpyrimidine-2,4-diamine identified as the most active compound in the series
(IC50 0.86 µM). The remaining pyrimidine-2,4-diamines showed antiplasmodial activity in the micromolar
range.
Experimental Section
Chemistry
General. Reagents purchased from Sigma-Aldrich (Steinheim, Germany) were of reagent grade and used
without any further purification unless specified. Ethyl acetate (EtOAc) and hexane used for chromatography
or extractions were distilled prior to use. Dimethyl sulfoxide (DMSO) was distilled and stored over 4 Å
molecular sieves. Acetonitrile (CH CN) was distilled from calcium hydride and tetrahydrofuran (THF) was
3
distilled from sodium prior to use. Reactions were monitored by thin-layer chromatography (TLC) using
precoated aluminium-backed plates (Merck silica gel 60 F254) and visualised under UV light (λ = 254 nm).
Intermediates and final compounds were purified by column chromatography on Fluka silica gel 60 (70-230
mesh). NMR spectra were acquired on a Bruker 300 or 500 MHz spectrometer at room temperature, using the
specified deuterated solvent. For those compounds soluble in deuterated chloroform (CDCl
contained tetramethylsilane (TMS, 0.05% v/v) as internal standard. For others, the residual solvent signal was
used for referencing (MeOD: 3.310 ppm; DMSO-d : 2.500 ppm). Data processing was done using MestreNova
3
), the solvent
6
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Software under license from Mestrelab Research, CA, USA. Infra-red spectra were recorded on a Bruker
Tensor-27 Fourier Transform spectrometer. Mass Spectra (High Resolution) were recorded on a SYNAPT G2
HDMS mass spectrometer (ESI) at Stellenbosch University. Melting points were determined on a Stuart
SMP10 melting point apparatus and are uncorrected.
General procedure for the synthesis of (4-bromobutoxy)benzenes (9). To a solution of substituted phenol 8 in
dry acetonitrile was added 1,4-dibromobutane (3 eq) and potassium carbonate (1.5 eq). The resultant mixture
was heated at reflux overnight under a nitrogen atmosphere. After this time, TLC analysis showed
consumption of the starting material and the reaction mixture was allowed to cool to room temperature and
filtered through celite. The filtrate was concentrated on a rotary evaporator and excess 1,4-dibromobutane
was removed by distillation under high vacuum. Compounds were purified by silica gel column
chromatography (EtOAc/hexane 20:80).
9
1
-(4-Bromobutoxy)-4-chlorobenzene (9a). Prepared from 4-chlorophenol (8a) (5.00 g, 38.9 mmol), 1,4-
dibromobutane (13.9 ml, 117 mmol) and potassium carbonate (8.06 g, 58.3 mmol) in dry acetonitrile (250 ml),
-
1
isolated as a white crystalline solid (10.0 g, 98%). mp 29-30 °C. IR (vmax/cm ): 2958, 1593, 1578, 1104, 823.
1
H NMR (300 MHz, CDCl
3
): δ 7.21 (2H, d, J 8.9 Hz), 6.74 (2H, d, J 8.9 Hz), 3.93 (2H, t, J 6.0 Hz), 3.46 (2H, t, J 6.5
H
1
3
Hz), 2.14-1.97 (2H, m), 1.97-1.84 (2H, m). C NMR (75 MHz, CDCl
3
): δ 157.5, 129.3, 125.4, 115.7, 67.1, 33.5,
C
2
1
1
9.4, 27.8.
9
-(4-Bromobutoxy)-3,4-dichlorobenzene (9b). Prepared from 3,4-dichlorophenol (8b) (5.05 g, 31.0 mmol),
,4-dibromobutane (11.1 ml, 92.9 mmol) and potassium carbonate (6.42 g, 46.5 mmol) in dry acetonitrile (250
-
1
1
ml), isolated as a white solid (8.50 g, 92%). mp 25-27 °C. IR (vmax/cm ): 3041, 1578, 1145. H NMR (300 MHz,
CDCl ): δ 7.31 (1H, d, J 8.9 Hz), 6.98 (1H, d, J 2.8 Hz), 6.74 (1H, dd, J 8.9, 2.8 Hz), 3.96 (2H, t, J 5.9 Hz), 3.48 (2H,
t, J 6.4 Hz), 2.13-1.86 (4H, m). C NMR (75 MHz, CDCl
3
H
1
3
3
): δ 157.9, 132.9, 130.7, 124.0, 116.3, 114.5, 67.5, 33.2,
C
2
1
1
9.3, 27.7.
9
-(4-Bromobutoxy)-3,5-dichlorobenzene (9c). Prepared from 3,5-dichlorophenol (8c) (5.00 g, 30.7 mmol),
,4-dibromobutane (10.9 ml, 92.0 mmol) and potassium carbonate (6.36 g, 46.0 mmol) in dry acetonitrile (250
-
1
ml), isolated as a white crystalline solid (8.02 g, 88%). mp 26-28 °C. IR (vmax/cm ): 2953, 1581, 1576, 1141.
1
H NMR (300 MHz, CDCl
3
): δ 6.91 (1H, t, J 1.8 Hz), 6.75 (2H, d, J 1.8 Hz), 3.92 (2H, t, J 5.9 Hz), 3.45 (2H, t, J 6.4
H
1
3
Hz), 2.08-1.96 (2H, m), 1.96-1.84 (2H, m); C NMR (126 MHz, CDCl
3
): δ 160.2, 135.6, 121.2, 113.8, 67.8, 33.5,
C
2
1
9.6, 27.9.
-(4-Bromobutoxy)-3-fluorobenzene (9d).12 Prepared from 3-fluorophenol (8d) (5.00 g, 44.6 mmol), 1,4-
dibromobutane (15.9 ml, 134 mmol) and potassium carbonate (9.25 g, 66.9 mmol) in dry acetonitrile (250 ml),
-
1
1
isolated as an oil (9.51 g, 86%). IR (vmax/cm ): 2956, 1593, 1577, 1084. H NMR (300 MHz, CDCl
3
): δ
H
7.19 (1H,
td, J 8.2, 6.8 Hz), 6.71-6.54 (3H, m), 3.94 (2H, t, J 6.0 Hz), 3.46 (2H, t, J 6.5 Hz), 2.11-1.98 (2H, m), 1.98-1.86 (2H,
1
3
m). C NMR (75 MHz, CDCl
3
): δ
C
163.7 (d, JC-F 245.3 Hz), 160.3 (d, JC-F 10.8 Hz), 130.3 (d, JC-F 10.0 Hz), 110.3
(
1
d, JC-F 2.9 Hz), 107.6 (d, JC-F 21.3 Hz), 102.2 (d, JC-F 24.7 Hz), 67.2, 33.4, 29.5, 27.9.
-(4-Bromobutoxy)-4-fluorobenzene (9e). Prepared from 4-fluorophenol (8e) (5.02 g, 44.8 mmol), 1,4-
1
3
dibromobutane (16.0 ml, 134 mmol) and potassium carbonate (9.28 g, 67.2 mmol) in dry acetonitrile (250 ml),
-
1
1
isolated as a white solid (6.92 g, 63%). mp 32-33 °C. IR (vmax/cm ): 2930, 1599, 1578, 1133. H NMR (300 MHz,
CDCl ): δ 7.01-6.93 (2H, m), 6.86-6.75 (2H, m), 3.95 (2H, t, J 6.0 Hz), 3.48 (2H, t, J 6.6 Hz), 2.11-2.01 (2H, m),
.00-1.86 (2H, m). C NMR (75 MHz, CDCl
3.1 Hz), 115.4 (d, JC-F = 8.0 Hz), 67.4, 33.4, 29.4, 27.9. HRMS (ESI) found [M + Na] 268.9953, C10
3
H
1
3
2
2
3
): δ
C
157.3 (d, JC-F 238.3 Hz), 154.9 (d, JC-F 2.0 Hz), 115.8 (d, JC-F
+
79
H12 BrFONa
requires 268.9956.
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1
4
1
4
-(4-Bromobutoxy)-3-(trifluoromethyl)benzene (9f). Prepared from 3-(trifluoromethyl)phenol (8f) (7.00 g,
3.2 mmol), 1,4-dibromobutane (15.5 ml, 126 mmol) and potassium carbonate (8.95 g, 64.8 mmol) in dry
-
1
1
acetonitrile (250 ml), isolated as a pale-yellow oil (11.5 g, 89%). IR (vmax/cm ): 2963, 1594, 1066, 1224. H NMR
(
(
1
6
2
1
500 MHz, CDCl
2H, t, J 6.0 Hz), 3.48 (2H, t, J 6.6 Hz), 2.10-2.03 (2H, m), 2.00-1.92 (2H, m). C NMR (125 MHz, CDCl
3
): δ 7.39-7.34 (1H, m), 7.21-7.17 (1H, m), 7.13-7.09 (1H, m), 7.04 (1H, dd, J 8.4, 2.7 Hz), 4.01
H
1
3
3
): δ
59.1, 131. 9 (q, JC-F 32.2 Hz), 130.0, 124.1 (q, JC-F 272.4 Hz), 118.0, 117.4 (q, JC-F 3.8 Hz), 111.3 (q, JC-F 3.7 Hz),
C
7.2, 33.3, 29.4, 27.8.
,4-Dibromo-1-(4-bromobutoxy)benzene (9g). Prepared from 2,4-dibromophenol (8g) (5.00 g, 19.8 mmol),
,4-dibromobutane (7.11 ml, 59.5 mmol) and potassium carbonate (4.12 g, 30.0 mmol) in dry acetonitrile (260
-
1
1
ml), isolated as a light-brown solid (6.13 g, 80%). mp 30-33 °C. IR (vmax/cm ): 3042, 1583, 1095. H NMR (300
MHz, CDCl ): δ 7.65 (1H, d, J 2.4 Hz), 7.34 (1H, dd, J 8.7, 2.4 Hz), 6.73 (1H, d, J 8.7 Hz), 4.01 (2H, t, J 5.8 Hz),
.52 (2H, t, J 6.4 Hz), 2.16-2.04 (2H, m), 2.04-1.93 (2H, m). C NMR (75 MHz, CDCl
3
H
1
3
3
1
4
3
): δ
C
154.6, 135.4, 131.3,
+
79
14.3, 113.2, 113.1, 68.5, 33.6, 29.4, 27.7. HRMS (ESI): found [M + Na] 406.8266, C10
06.8258.
H11 Br
3
ONa requires
General procedure for the synthesis of 5-phenoxypentanenitriles (10). To a solution of the substituted (4-
bromobutoxy)benzene 9 in ethanol/water (3:1) was added potassium cyanide (1.1 eq). The resulting
heterogeneous mixture was stirred and heated at reflux under a nitrogen atmosphere for two days. The
reaction progress was monitored by TLC (EtOAc/hexane 40:60). When complete, the reaction mixture was
cooled to room temperature, quenched with aq. NaOH (0.1 M, 100 ml) and concentrated on a rotary
evaporator. The residue was extracted with CH
MgSO , filtered through celite and excess solvent was removed on a rotary evaporator. Products were purified
by silica gel column chromatography (EtOAc/hexane 10:90 -20:80).
2
2
Cl (3 × 100 ml), the combined organic layers were dried with
4
5
-(4-Chlorophenoxy)pentanenitrile (10a). Prepared from 1-(4-bromobutoxy)-4-chlorobenzene (9a) (4.00 g,
1
5.2 mmol) and potassium cyanide (1.10 g, 16.7 mmol) in ethanol/water (160 ml); isolated as a pale yellow oil
-
1
1
(2.85 g, 89%). IR (vmax/cm ): 3084, 2965, 2252, 1585, 1570. H NMR (300 MHz, CDCl
3
3
): δ 7.21 (2H, d, J 9.0 Hz),
H
1
6
1
C
5
.79 (2H, d, J 9.0 Hz), 3.94 (2H, t, J 5.6 Hz), 2.41 (2H, t, J 6.8 Hz), 1.97-1.77 (4H, m). C NMR (75 MHz, CDCl
3
): δ
C
+
57.3, 129.3, 125.6, 119.5, 115.7, 67.0, 28.1, 22.4, 16.9. HRMS (ESI): found [M + Na] 232.0500,
3
5
11
H
12 ClNONa requires 232.0507.
-(3,4-Dichlorophenoxy)pentanenitrile (10b). Prepared from 1-(4-bromobutoxy)-3,4-dichlorobenzene (9b)
(
5.05 g, 16.9 mmol) and potassium cyanide (1.21 g, 18.6 mmol) in ethanol/water (160 ml), isolated as pale
-1
1
yellow oil (3.55 g, 86%). IR (vmax/cm ): 3083, 2964, 2250, 1599, 1574. H NMR (300 MHz, CDCl
J 8.9 Hz), 6.97 (1H, d, J 2.8 Hz), 6.74 (1H, dd, J 8.9, 2.8 Hz), 3.97 (2H, t, J 5.8 Hz), 2.44 (2H, t, J 7.0 Hz), 2.00-1.81
3
): δ 7.31 (1H, d,
H
1
3
(4H, m). C NMR (126 MHz, CDCl
3
): δ
C
157.7, 132.9, 130.7, 124.1, 119.3, 116.3, 114.5, 67.3, 28.0, 22.3, 17.0.
+
35
HRMS (ESI): found [M + Na] 266.011, C11
H11 Cl
2
NONa requires 266.0118.
5
-(3,5-Dichlorophenoxy)pentanenitrile (10c). Prepared from 1-(4-bromobutoxy)-3,5-dichlorobenzene (9c)
(
4.20 g, 14.1 mmol) and potassium cyanide (1.01 g, 15.5 mmol) in ethanol/water (160 ml), isolated as a white
-
1
1
solid (2.45 g, 71%). mp 52-53 °C. IR (vmax/cm ): 3083, 2966, 2253, 1585, 1570. H NMR (300 MHz, CDCl
6
3
): δ
H
1
3
.96 (1H, t, J 1.8 Hz), 6.78 (2H, d, J 1.8 Hz), 3.98 (2H, t, J 5.6 Hz), 2.45 (2H, t, J 6.8 Hz), 2.0-1.80 (4H, m). C NMR
(75 MHz, CDCl
3
): δ
C
159.7, 135.5, 121.3, 119.3, 113.6, 67.3, 28.0, 22.3, 17.0. HRMS (ESI): found [M + Na]+
NONa requires 266.0118.
2
5
2
66.0115, C11
H
11 5Cl
3
2
-(3-Fluorophenoxy)pentanenitrile (10d). Prepared from 1-(4-bromobutoxy)-3-fluorobenzene (9d) (5.00 g,
0.2 mmol) and potassium cyanide (1.58 g, 24.3 mmol) in ethanol/water (160 ml), isolated as a brown oil (3.22
-
1
1
g, 72%). IR (vmax/cm ): 2961, 2932, 2239, 1596, 1503. H NMR (300 MHz, CDCl
6
3
): δ 7.26 -7.14 (1H, m), 6.70-
H
1
3
.55 (3H, m), 3.95 (2H, t, J 5.6 Hz), 2.41 (2H, t, J 6.8 Hz), 1.99-1.75 (4H, m). C NMR (75 MHz, CDCl
3
): δ 163.7
C
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(
2
d, JC-F = 245.7 Hz), 160.1 (d, JC-F = 10.8 Hz), 130.4 (d, JC-F = 10.1 Hz), 119.5, 110.3 (d, JC-F = 3.0 Hz), 107.8 (d, JC-F
=
+
1.4 Hz), 102.2 (d, JC-F = 24.8 Hz), 67.0, 28.2, 22.5, 17.1. HRMS (ESI): found [M +Na] 216.0807, C11
H12FNONa
requires 216.0803.
5
-(4-Fluorophenoxy)pentanenitrile (10e). Prepared from 1-(4-bromobutoxy)-4-fluorobenzene (9e) (4.00 g,
1
6.2 mmol) and potassium cyanide (1.20 g, 17.8 mmol) in ethanol/water (160 ml), isolated as a white solid
-
1
1
(1.93 g, 62%). mp 26-27 °C. IR (vmax/cm ): 2960, 2933, 2240, 1596, 1503. H NMR (300 MHz, CDCl
3
): δ
H
7.09-
13
6
.88 (2H, m), 6.88-6.71 (2H, m), 3.96 (2H, t, J 5.5 Hz), 2.44 (2H, t, J 6.6 Hz), 2.04-1.76 (4H, m). C NMR (75
MHz, CDCl
3
): δ
C
157.3 (d, JC-F 238.3 Hz), 154.8 (d, JC-F 2.1 Hz), 119.5, 115.8 (d, JC-F 23.1 Hz), 115.4 (d, JC-F 8.0
+
Hz), 67.3, 28.2, 22.5, 17.0. HRMS (ESI): found [M + Na] 216.0809, C11
H
12FNONa requires 216.0803.
Prepared from 1-(4-bromobutoxy)-3-
trifluoromethyl)benzene (9f) (6.00 g, 20.2 mmol) and potassium cyanide (1.45 g, 22.2 mmol) in ethanol/water
5
(
(
-(3-(Trifluoromethyl)phenoxy)pentanenitrile
(10f).
-
1
1
160 ml), isolated as a yellow oil (3.65 g, 74%). IR (vmax/cm ): 3039, 2930, 2239, 1599. H NMR (300 MHz,
): δ 7.37 (1H, t, J 8.1 Hz), 7.23-7.16 (1H, m), 7.12 (1H, br s), 7.05 (1H, dd, J 8.3, 2.6 Hz), 4.01 (2H, t, J 5.7
Hz), 2.42 (2H, t, J 6.8 Hz), 2.04-1.73 (4H, m). C NMR (75 MHz, CDCl
24.0 (q, JC-F 272.3 Hz), 119.5, 118.0, 117.7 (q, JC-F 3.9 Hz), 111.3 (q, JC-F 3.9 Hz), 67.0, 28.2, 22.5, 17.1. HRMS
CDCl
3
H
1
3
3
): δ 158.9, 132.0 (q, JC-F 32.3 Hz), 130.1,
C
1
+
(
5
(
ESI): found [M + Na] 266.0773, C12
-(2,4-Dibromophenoxy)pentanenitrile (10g). Prepared from 2,4-dibromo-1-(4-bromobutoxy)benzene (9g)
5.00 g, 12.9 mmol) and potassium cyanide (1.01 g, 15.5 mmol, 1.2 eq) in ethanol/water (160 ml), isolated as
H
12
F
3
NONa requires 266.0771.
-
1
1
white solid (3.12 g, 73%). mp 49-50 °C. IR (vmax/cm ): 3091, 2948, 2253, 1580, 1480. H NMR (300 MHz, CDCl
3
):
δ
H
7.66 (1H, d, J 2.4 Hz), 7.36 (1H, dd, J 8.8, 2.4 Hz), 6.74 (1H, d, J 8.8 Hz), 4.04 (2H, t, J 5.4 Hz), 2.50 (2H, t, J 6.7
1
3
Hz), 2.03-1.89 (4H, m). C NMR (75 MHz, CDCl
3
): δ
C
154.4, 135.5, 131.2, 119.5, 114.2, 113.2, 113.1, 68.3, 27.9,
+
79
2
2.5, 17.1. HRMS (ESI): found [M + Na] 353.9108, C11
H11 Br
2
NONa requires 353.9107.
General procedure for the synthesis of 2-benzoyl-5-phenoxypentanenitriles (11). To a solution of the
substituted 5-phenoxypentanenitrile 10 (1 eq) in dry THF was added potassium tert-butoxide (3 eq) and ethyl
benzoate (4 eq). The reaction mixture was stirred at room temperature under a nitrogen atmosphere
overnight. After consumption of the starting material, the reaction was quenched with sat. aq. NH
4
Cl and THF
removed under reduced pressure. The remaining aqueous residue was washed with EtOAc (3 × 100 ml) and
the organic layers were combined, dried over MgSO
by column chromatography (EtOAc/hexane 20:80).
4
and filtered through celite. Crude products were purified
2
-Benzoyl-5-(4-chlorophenoxy)pentanenitrile (11a). Prepared from 5-(4-chlorophenoxy)pentanenitrile (10a)
(
2.32 g, 11.1 mmol), potassium tert-butoxide (3.72 g, 33.2 mmol) and ethyl benzoate (6.33 ml, 44.3 mmol) in
-
1
dry THF (50 ml), isolated as yellow crystals (2.82 g, 81%). mp 124-126 °C. IR (vmax/cm ): 2878, 2253, 1694,
1
1
596, 1580. H NMR (300 MHz, CDCl
3
): δ 7.97 (2H, d, J 7.2 Hz), 7.65 (1H, t, J 7.4 Hz), 7.52 (2H, dd, J 8.3, 6.9
H
Hz), 7.21 (2H, d, J 9.0 Hz), 6.77 (2H, d, J 9.0 Hz), 4.48 (1H, dd, J 8.4, 5.7 Hz), 4.04-3.99 (2H, m), 2.37-1.99 (4H,
1
3
m). C NMR (75 MHz, CDCl
3
2
3
): δ
9.4, 26.7, 26.5. HRMS (ESI): found [M + Na] 336.0757, C18
-Benzoyl-5-(3,4-dichlorophenoxy)pentanenitrile (11b). Prepared from 5-(3,4-dichlorophenoxy)pentanenitrile
C
190.4, 157.1, 134.6, 133.9, 129.4, 129.2, 128.8, 125.9, 117.1, 115.7, 67.0,
+
35
H
16 ClNO Na requires 336.0770.
2
(
10b) (2.50 g, 10.2 mmol), potassium tert-butoxide (3.45 g, 30.7 mmol) and ethyl benzoate (5.89 ml, 40.9
-
1
mmol) in dry THF (60 ml), isolated as a white solid (3.34 g, 94%). mp 43-44 °C. IR (vmax/cm ): 3041, 2954, 2252,
1
7
1
695, 1586, 1574. H NMR (500 MHz, CDCl
3
): δ 7.96 (2H, d, J 6.9 Hz), 7.69-7.61 (1H, m), 7.51 (2H, t, J 8.0 Hz),
H
.28 (1H, dd, J 8.7, 2.9 Hz), 6.91 (1H, s), 6.73-6.67 (1H, m), 4.64-4.40 (1H, m), 4.07-3.92 (2H, m), 2.34-2.12 (2H,
13
m), 2.12-1.95 (2H, m). C NMR (126 MHz, CDCl
3
): δ 190.6, 157.6, 134.6, 133.9, 132.8, 130.7, 129.2, 128.8,
C
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1535Cl
NO Na
+
1
24.1, 117.3, 116.4, 114.4, 67.3, 39.5, 26.6, 26.4. HRMS (ESI): found [M + Na] 370.0377, C18
requires 370.0380.
-Benzoyl-5-(3,5-dichlorophenoxy)pentanenitrile (11c). Prepared from 5-(3,5-dichlorophenoxy)pentanenitrile
10c) (1.98 g, 8.11 mmol), potassium tert-butoxide (2.73 g, 24.3 mmol) and ethyl benzoate (4.64 ml, 32.4
H
2
2
2
(
-
1
mmol) in dry THF (40 ml), isolated as a light yellow solid (2.80 g, 91 %). mp 45-46 °C. IR (vmax/cm ): 2889, 2255,
1
1
697, 1582, 1570. H NMR (300 MHz, CDCl
3
): δ 7.97 (2H, d, J 7.1 Hz), 7.74-7.61 (1H, m), 7.53 (2H, dd, J 8.3, 7.0
H
Hz), 6.95 (1H, t, J 1.8 Hz), 6.72 (2H, d, J 1.8 Hz), 4.46 (1H, dd, J 8.1, 5.9 Hz), 4.06-3.88 (2H, m), 2.36-1.82 (4H, m).
1
3
C NMR (75 MHz, CDCl
): δ
3 C
190.2, 159.5, 135.5 (2C), 134.7, 133.9, 129.2, 128.8, 121.3, 117.0, 113.6, 113.5,
+
35
6
7.3, 39.3, 26.5, 26.4. HRMS (ESI): found [M + Na] 370.0381, C18
H15 Cl
2
NO Na requires 370.0380.
2
2
-Benzoyl-5-(3-fluorophenoxy)pentanenitrile (11d). Prepared from 5-(3-fluorophenoxy)pentanenitrile (10d)
(
4.88 g, 25.3 mmol), potassium tert-butoxide (8.50 g, 75.8 mmol) and ethyl benzoate (14.4 ml, 101 mmol) in
-
1
dry THF (70 ml), isolated as a yellow solid (6.53 g, 87%). mp 32 °C. IR (vmax/cm ) 2876, 2254, 1689, 1596, 1576.
1
H NMR (300 MHz, CDCl
3
): δ 7.96 (2H, d, J 7.1 Hz), 7.70-7.59 (1H, m), 7.51 (2H, dd, J 8.4, 7.1 Hz), 7.28-7.12
H
1
3
(1H, m), 6.73-6.46 (3H, m), 4.50 (1H, dd, J 8.4, 5.7 Hz), 4.04-3.92 (2H, m), 2.36-1.99 (4H, m). C NMR (75 MHz,
CDCl ): δ 190.5, 163.6 (d, JC-F 245.3 Hz), 159.9 (d, JC-F 10.8 Hz), 134.6, 133.9, 130.3 (d, JC-F 10.0 Hz), 129.1,
3
C
1
28.8, 117.2, 110.2 (d, JC-F 2.9 Hz), 107.8 (d, JC-F 21.3 Hz), 102.2 (d, JC-F 24.8 Hz), 66.9, 39.4, 26.7, 26.4. HRMS
+
(ESI): found [M + Na] 320.1063, C18
H
16FNO Na requires 320.1065.
2
2
-Benzoyl-5-(4-fluorophenoxy)pentanenitrile (11e). Prepared from 5-(4-fluorophenoxy)pentanenitrile (10e)
(
1.55 g, 8.02 mmol), potassium tert-butoxide (2.70 g, 24.1 mmol) and ethyl benzoate (4.60 ml, 32.1 mmol) in
-
1
dry THF (45 ml), isolated as a yellow solid (1.99 g, 83%). mp 86-87 °C. IR (vmax/cm ): 2956, 2930, 2252, 1703,
1
7
1
586, 1577. H NMR (300 MHz, CDCl
3
): δ 8.04-7.90 (2H, m), 7.72-7.57 (1H, m), 7.51 (2H, dd, J 8.4, 7.1 Hz),
H
1
3
.03-6.90 (2H, m), 6.87-6.70 (2H, m), 4.50 (1H, dd, J 8.5, 5.7 Hz), 4.08-3.93 (2H, m), 2.34-1.78 (4H, m). C NMR
(
75 MHz, CDCl
3
): δ
C
190.4, 157.4 (d, JC-F 238.7 Hz), 154.6 (d, JC-F 2.1 Hz), 134.6, 133.9, 129.1, 128.8, 117.2,
+
1
C
2
15.8 (d, JC-F 23.1 Hz), 115.4 (d, JC-F 8.0 Hz), 67.3, 39.4, 26.8, 26.6. HRMS (ESI): found [M + Na] 320.1100,
18
H16FNO
2
Na requires 320.1065.
-Benzoyl-5-(3-(trifluoromethyl)phenoxy)pentanenitrile
(11f).
Prepared
from
5-(3-
(
trifluoromethyl)phenoxy)pentanenitrile (10f) (2.50 g, 10.3 mmol), potassium tert-butoxide (3.46 g, 30.8
mmol) and ethyl benzoate (5.88 ml, 41.1 mmol) in dry THF (60 ml), isolated as a yellow viscous oil (2.24 g,
-
1
1
6
3%). IR (vmax/cm ): 2941, 2249, 1696, 1592, 1571. H NMR (300 MHz, CDCl
3
): δ
H
7.97 (2H, d, J 7.3 Hz), 7.66
(
1H, t, J 7.4 Hz), 7.52 (2H, t, J 7.7 Hz), 7.38 (1H, t, J 7.9 Hz), 7.21 (1H, d, J 7.7 Hz), 7.08-6.96 (2H, m), 4.49 (1H,
1
3
dd, J 8.2, 5.8 Hz), 4.16-4.00 (2H, m), 2.40-2.00 (4H, m). C NMR (75 MHz, CDCl
31.9 (q, JC-F 32.3 Hz), 130.1, 129.2, 128.8, 123.9 (q, JC-F 272.4 Hz), 117.8, 117.7 (q, JC-F 3.9 Hz), 117.1, 111.3
3
): δ
C
190.3, 158.6, 134.6, 134.0,
1
+
(q, JC-F 3.8 Hz), 67.0, 39.3, 26.7, 26.5. HRMS (ESI): found [M + H] 348.1227, C19
H
17
F
3
NO
2
requires 348.1213.
from 5-(2,4-
2
-Benzoyl-5-(2,4-dibromophenoxy)pentanenitrile (11g). Prepared
dibromophenoxy)pentanenitrile (10g) (2.94 g, 8.83 mmol), potassium tert-butoxide (2.97 g, 26.5 mmol) and
ethyl benzoate (5.05 ml, 35.3 mmol) in dry THF (50 ml), isolated as a yellow solid (3.03 g, 79%). mp 35-36 °C. IR
-
1
1
(v
max/cm ): 3010, 2255, 1699, 1578, 1569. H NMR (500 MHz, CDCl
3
): δ
H
8.00 (2H, d, J 7.0 Hz), 7.70-7.61 (2H,
m), 7.56-7.47 (2H, m), 7.37 (1H, d, J 7.9 Hz), 6.76 (1H, dd, J 8.9, 2.9 Hz), 4.66 (1H, p, J 3.8 Hz), 4.19-4.00 (2H, m),
1
3
2
1
C
.43-2.18 (2H, m), 2.19-2.06 (2H, m). C NMR (126 MHz, CDCl
3
): δ
C
190.7, 154.2, 135.5, 134.6, 133.9, 131.3,
+
29.1, 128.9, 117.3, 114.2, 113.3, 113.0, 68.4, 39.8, 26.9, 26.3. HRMS (ESI): found [M + Na] 457.9370,
7
9
18
H
15 Br
2
NO Na requires 457.9270.
2
General procedure for the synthesis of 6-phenylpyrimidine-2,4-diamines (6). Carbitol, diethyl ether and
aqueous potassium hydroxide (10.7 M, 20.0 eq) were placed in a diazomethane apparatus fitted with a
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condenser and a dropping funnel containing diazald (3.0 eq) dissolved in diethyl ether. The diazomethane
apparatus was lowered into a water bath at 70-80 °C. Diazomethane gas, generated from the reaction of
diazald and the above reaction mixture was passed into a flask containing the starting material 11a-g (1.0 eq),
in dry dichloromethane (50 ml). Diethyl ether (10 ml) was used to rinse the dropping funnel. After distillation
was complete, the reaction mixture was left to stir at room temperature overnight. Any excess diazomethane
was quenched with glacial acetic acid. The reaction was evaporated to dryness in vacuo to give the crude
product, which was taken to the next step without further purification. Partial characterisation of the
1
13
intermediate enol ethers was done by H and C NMR spectroscopy (exemplified in the synthesis of 6a
below). In the subsequent step, guanidine hydrochloride was treated with sodium methoxide (2.0 eq) in
methanol (20 ml) to furnish free guanidine after filtration and removal of methanol in vacuo. The enol ether
prepared in the first step (1.0 eq) was dissolved in dry DMSO and then added to the flask containing free
guanidine. The reaction mixture was then heated at 80-100 °C overnight. After formation of a new product
spot visible by TLC, the reaction mixture was heated to 120 °C to remove DMSO under vacuum. The resulting
solid residue was dissolved in a methanol-ethyl acetate mixture and purified by column chromatography
(EtOAc/hexane 20:80) to give the desired pyrimidine product 6.
5
-(3-(4-Chlorophenoxy)propyl)-6-phenylpyrimidine-2,4-diamine (6a). Diazomethane gas, produced from the
reaction of diazald (2.05 g, 9.56 mmol) with potassium hydroxide solution (10.7 M, 6 ml), in a mixture of
carbitol (4 ml) and diethyl ether (20 ml) was passed through a solution of 2-benzoyl-5-(4-chlorophenoxy)-
pentanenitrile (11a) (2.10 g, 3.19 mmol), in dry DCM. The resulting enol ether was isolated as a mixture of E
1
and Z isomers in a ratio of 1.4:1. Major isomer: H NMR (300 MHz, CDCl
3
): δ 7.56-7.33 (4H, m), 7.23-7.18 (1H,
H
m), 7.23 (2H, d, J 9.1 Hz), 6.84 (2H, d, J 9.0 Hz), 4.00 (2H, t, J 6.1 Hz), 3.43 (3H, s), 2.57 (2H, dd, J 8.2, 6.7 Hz),
1
3
2
1
.11-2.01 (2H, m). C NMR (75 MHz, CDCl
3
): δ
C
168.9, 157.6, 131.5, 130.5, 129.3, 128.9, 128.8, 125.5, 120.1,
1
15.8, 94.2, 67.1, 58.3, 28.1, 25.0. Minor isomer: H NMR (300 MHz, CDCl
3
): δ 7.56-7.33 (4H, m), 7.23-7.18
H
(
1H, m), 7.18 (2H, d, J 9.1 Hz), 6.66 (2H, d, J 8.9 Hz), 3.85 (2H, t, J 5.9 Hz), 3.47 (3H, s), 2.23 (2H, dd, J 8.1, 6.5
13
Hz), 1.99-1.87 (2H, m). C NMR (75 MHz, CDCl
18.2, 115.6, 91.9, 66.1, 58.1, 27.7, 23.8. The enol ether (0.55 g, 1.68 mmol) was treated with free guanidine
0.32 g, 3.36 mmol) in dry DMSO (5.0 ml) as described to afford 6a as a yellow solid (0.065 g, 11%). mp 130-
3
): δ
C
168.7, 157.2, 130.7, 130.3, 129.2, 128.8, 128.7, 125.5,
1
(
-
1
1
1
7
1
1
5
32 °C. IR (vmax/cm ): 3328, 3140, 2929, 1637, 1583, 1555. H NMR (300 MHz, CDCl
3
): δ
H
7.43-7.33 (5H, m),
.21 (2H, d, J 8.9 Hz), 6.74 (2H, d, J 8.9 Hz), 5.29 (2H, s), 5.15 (2H, s), 3.84 (2H, t, J 5.6 Hz), 2.53 (2H, t, J 8.6 Hz),
1
3
.93-1.84 (2H, m). C NMR (75 MHz, CDCl
3
): δ
C
165.6, 163.3, 160.4, 157.1, 129.7, 129.4, 128.4, 128.3, 128.0,
+
35
25.9, 115.7, 104.8, 67.1, 28.6, 22.2. HRMS (ESI): found [M + H] 355.1326, C19
-(3-(3,4-Dichlorophenoxy)propyl)-6-phenylpyrimidine-2,4-diamine
H20 ClN
4
O requires 355.1327.
2-Benzoyl-5-(3,4-
(6b).
dichlorophenoxy)pentanenitrile (11b) (499 mg, 1.38 mmol) was treated with diazomethane as described. The
resulting enol ether was treated with free guanidine (0.26 g, 2.76 mmol) in dry DMSO (5.0 ml) to afford a light-
-
1
1
yellow solid (0.057 g, 11%). mp 102-104 °C. IR (vmax/cm ): 3430, 3164, 2866, 1636, 1582, 1554. H NMR (500
MHz, MeOD): δ 7.52 – 7.35 (5H, m), 6.97 (1H, t, J 1.8 Hz), 6.65 (2H, d, J 1.8), 3.81 (2H, t, J 5.7 Hz), 2.60 (2H, t, J
H
1
3
7
1
.4 Hz), 1.91-1.83 (2H, m). C NMR (126 MHz, MeOD): δ
28.1, 120.2 (2C), 116.7, 113.2, 105.9, 66.7, 27.0, 20.9. HRMS (ESI): found [M + H] 389.0936, C19
C
171.6, 165.1, 160.0 (2C), 135.0 (2C), 129.7, 128.5,
+
35
H
19 Cl
2
4
N O
requires 389.0938.
-(3-(3,5-Dichlorophenoxy)propyl)-6-phenylpyrimidine-2,4-diamine
5
(6c).
2-Benzoyl-5-(3,5-
dichlorophenoxy)pentanenitrile (11c) (607 mg, 1.68 mmol) was treated with diazomethane as described. The
resulting enol ether was treated with free guanidine (0.32 g, 3.36 mmol) in dry DMSO (5.0 ml) to afford a
-
1
1
brown solid (0.048 g, 9%). mp 105-107 °C. IR (vmax/cm ): 3430, 3164, 2956, 1637, 1599, 1575. H NMR (300
MHz, MeOD): δ 7.98 (2H, d, J 7.5 Hz), 7.56-7.30 (5H, m), 6.98 (1H, t, J 1.8 Hz), 6.68 (2H, d, J 1.8 Hz), 3.83 (2H,
H
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1
3
t, J 5.8 Hz), 2.60 (2H, t, J 7.4 Hz), 1.98-1.72 (2H, m). C NMR (126 MHz, MeOD): δ
C
164.7, 159.9, 157.7, 135.0,
+
1
C
5
30.8, 129.1, 128.2, 128.1, 127.5, 120.2, 113.2, 105.3, 66.9, 27.2, 21.1. HRMS (ESI): found [M + H] 389.0936,
3
5
19
H
19 Cl
2
N
4
O requires 389.0938.
-(3-(3-Fluorophenoxy)propyl)-6-phenylpyrimidine-2,4-diamine
(6d).
2-Benzoyl-5-(3-
fluorophenoxy)pentanenitrile (11d) (450 mg, 1.45 mmol) was treated with diazomethane as described. The
resulting enol ether was treated with free guanidine (0.28 g, 2.89 mmol) in dry DMSO (5.0 ml) to afford a
-
1
1
creamy-white solid (0.043 g, 9%). mp 104-105 °C. IR (vmax/cm ): 3479, 3112, 2875, 1612, 1576, 1505. H NMR
300 MHz, MeOD): δ 7.57-7.33 (4H, m), 7.29-7.09 (1H, m), 6.73-6.29 (3H, m), 3.82 (2H, t, J 5.9 Hz), 2.56 (2H,
dd, J 8.6, 6.6 Hz), 1.99-1.83 (2H, m). C NMR (75 MHz, CDCl 175.04, 163.7 (d, JC-F 245.0 Hz), 163.4, 160.6,
(
H
1
3
3
): δ
60.3 (d, JC-F 10.9 Hz), 130.24, 130.1, 128.3, 128.29, 128.0, 110.3 (d, JC-F 3.0 Hz), 107.4 (d, JC-F 21.3 Hz), 104.7,
02.2 (d, JC-F 24.7 Hz), 67.8, 28.6, 22.1. HRMS (ESI) found [M + H] 339.1621, C19
C
1
1
+
H
20FN O requires 339.1703.
4
General procedure for the synthesis of (4-bromopropoxy)benzenes (12). (4-Bromopropoxy)benzenes (12)
were prepared using the same method described for the synthesis of (4-bromobutoxy)benzenes 9 described
above.
9
1
-(3-Bromopropoxy)-4-chlorobenzene (12a). Prepared from 4-chlorophenol (8a) (6.50 g, 50.6 mmol), 1,3-
dibromopropane (15.4 ml, 152 mmol) and potassium carbonate (10.5 g, 75.8 mmol) in dry acetonitrile (300
-
1
ml), isolated as a white crystalline solid (12.5 g, 99%). mp 28-29 °C. IR (vmax/cm ): 2959, 1596, 1578, 1102.
1
H NMR (300 MHz, CDCl
3
3
): δ 7.23 (2H, d, J 8.9 Hz), 6.81 (2H, d, J 8.9 Hz), 4.02 (2H, t, J 5.7 Hz), 3.46 (2H, t, J 6.5
H
1
Hz), 2.19-1.95 (2H, m). C NMR (75 MHz, CDCl
4
3
): δ
C
157.3, 129.3, 125.6, 115.7, 67.2, 33.3, 27.8.
9
-(3-Bromopropoxy)-1,2-dichlorobenzene (12b). Prepared from 3,4-dichlorophenol (8b) (5.40 g, 33.1 mmol),
1
,3-dibromopropane (10.1 ml, 99.4 mmol) and potassium carbonate (6.87 g, 49.7 mmol) in dry acetonitrile
-
1
1
(
250 ml), isolated as a white solid (8.96 g, 95%). mp 29-30 °C. IR (vmax/cm ): 3041, 1578, 1145. H NMR (300
MHz, CDCl ): δ 7.31 (1H, d, J 8.9 Hz), 6.97 (1H, d, J 2.9 Hz), 6.73 (1H, dd, J 8.9, 2.9 Hz), 4.00 (2H, t, J 5.8 Hz),
.45 (2H, t, J 6.4 Hz), 2.18-1.99 (2H, m). C NMR (75 MHz, CDCl
6.0, 25.2, 14.1.
3
H
1
3
3
6
1
1
3
): δ 157.4, 132.7, 130.7, 124.2, 116.4, 114.5,
C
9
-(3-Bromopropoxy)-3,5-dichlorobenzene (12c). Prepared from 3,5-dichlorophenol (8c) (5.00 g, 30.7 mmol),
,3-dibromopropane (9.34 ml, 92.0 mmol) and potassium carbonate (6.36 g, 46.0 mmol) in dry acetonitrile
-
1
1
(
(
200 ml), isolated as a white solid (8.46 g, 97%). mp 27-28 °C. IR (vmax/cm ): 2953, 1581, 1576, 1141. H NMR
300 MHz, CDCl ): δ 6.91 (1H, t, J 1.8 Hz), 6.75 (2H, d, J 1.9 Hz), 3.92 (2H, t, J 5.9 Hz), 3.45 (2H, t, J 6.4 Hz),
3
H
1
3
1
1
.90-1.77 (2H, m). C NMR (75 MHz, CDCl
3
): δ
C
159.7, 135.5 (2C), 121.3, 114.0 (2C), 67.3, 28.0, 22.3.
1
5
-(3-Bromopropoxy)-4-fluorobenzene (12d). Prepared from 4-fluorophenol (8f) (4.00 g, 35.7 mmol), 1,3-
dibromopropane (10.9 ml, 107 mmol) and potassium carbonate (7.40 g, 53.5 mmol) in dry acetonitrile (200
-
1
1
ml), isolated as a pale solid (7.26 g, 87%). mp 30-31 °C. IR (vmax/cm ): 2956, 1593, 1577, 1084. H NMR (300
MHz, CDCl ): δ 7.08-6.94 (2H, m), 6.85-6.81 (2H, m), 4.02 (2H, t, J 5.6 Hz), 3.45 (2H, t, J 6.4 Hz), 2.15-2.07 (2H,
m). C NMR (75 MHz, CDCl ): δ 157.3 (d, JC-F 238.3 Hz), 154.9 (d, JC-F 2.0 Hz), 115.8 (d, JC-F 23.1 Hz), 115.4 (d,
C-F 8.0 Hz), 66.0, 30.8, 14.2.
3
H
1
3
3
C
J
General procedure for the synthesis of 6-(4-(4-chlorophenoxy)butoxy)pyrimidine-2,4-diamine (7a) and
analogues. To a stirred solution of 2,4-diamino-6-hydroxy pyrimidine in dry acetonitrile (20 ml) was added
potassium carbonate (1.5 eq), followed by a suitably substituted bromoether 9 or 12 (1.0 eq) in dry
acetonitrile (30 ml). The reaction was heated to reflux under an atmosphere of nitrogen overnight. The
reaction mixture was allowed to cool to room temperature, filtered through celite and the filtrate was
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concentrated in vacuo. The crude product was purified by column chromatography (EtOAc/hexane 60:40) to
furnish the desired product.
6
-(4-(4-Chlorophenoxy)butoxy)pyrimidine-2,4-diamine (7a). Prepared from 2,4-diamino-6-hydroxy
pyrimidine (0.48 g, 3.79 mmol), potassium carbonate (0.79 g, 5.69 mmol) and 9a (1.00 g, 3.79 mmol) in dry
-
1
acetonitrile, isolated as a white solid (0.58 g, 50%). mp 97-98 °C. IR (vmax/cm ): 3520, 3359, 3011, 1576, 1124,
1
7
(
1
C
6
91. H NMR (300 MHz, DMSO-d
6
): δ 7.31 (2H, d, J 8.9 Hz), 6.95 (2H, d, J 9.0 Hz), 5.98 (2H, s), 5.82 (2H, s), 5.04
H
1
3
1H, s), 4.15-4.11 (2H, m), 3.98 (2H, t, J 3.5 Hz), 1.81-1.68 (4H, m). C NMR (75 MHz, DMSO-d
6
): δ
C
170.1,
65.9, 162.9, 157.4, 129.2, 124.1, 116.2, 76.1, 67.5, 64.1, 25.3 (2C). HRMS (ESI): found [M + H] 309.1117,
requires 309.1120.
-(4-(3,4-Dichlorophenoxy)butoxy)pyrimidine-2,4-diamine (7b). Prepared from 2,4-diamino-6-hydroxy
+
14
H
18ClN
O
4 2
pyrimidine (0.43 g, 3.42 mmol), potassium carbonate (0.71 g, 5.13 mmol) and 9b (1.02 g, 3.42 mmol) in dry
-
1
acetonitrile, isolated as a white solid (0.53 g, 45%). mp 136-137 °C. IR (vmax/cm ): 3520, 3359, 3011, 1576,
1
1
124, 791. H NMR (300 MHz, DMSO-d
6
): δ 7.50 (1H, d, J 8.9 Hz), 7.22 (1H, d, J 2.9 Hz), 6.95 (1H, dd, J 8.9, 2.9
H
1
3
Hz), 5.99 (2H, s), 5.82 (2H, s), 5.04 (1H, s), 4.15-4.11 (2H, m), 4.05-4.01 (2H, m), 1.78-1.74 (4H, m). C NMR (75
MHz, DMSO-d
HRMS (ESI): found [M + H] 343.0729, C14
6
): δ
C
170.6, 166.5, 163.4, 158.6, 132.1, 131.4, 122.7, 116.8, 115.9, 76.6, 68.5, 64.6, 25.7 (2C).
+
H17Cl
2
N
4
2
O requires 343.0730.
6
-(4-(3,5-Dichlorophenoxy)butoxy)pyrimidine-2,4-diamine (7c). Prepared from 2,4-diamino-6-hydroxy
pyrimidine (0.40 g, 3.15 mmol), potassium carbonate (0.65 g, 4.73 mmol) and 9c (0.94 g, 3.15 mmol) in dry
-
1
acetonitrile, isolated as a white solid (0.59 g, 55%). mp 106-107 °C. IR (vmax/cm ): 3440, 3327, 3008, 1560,
1
1
(
1
3
6
141, 828, 791. H NMR (300 MHz, DMSO-d
6
): δ 7.13 (1H, t, J 1.8 Hz), 7.03 (2H, d, J 1.8 Hz), 5.98 (2H, s), 5.82
H
1
3
2H, s), 5.04 (1H, s), 4.15-4.10 (2H, m), 4.06-4.00 (2H, m), 1.83-1.68 (4H, m). C NMR (75 MHz, DMSO-d
6
): δ
C
+
70.1, 165.9, 163.0, 160.1, 134.5 (2C), 120.1, 113.8 (2C), 76.1, 68.2, 25.2, 25.1, HRMS (ESI): found [M + H]
43.0724, C14 requires 343.0730.
-(4-(3-fluorophenoxy)butoxy)pyrimidine-2,4-diamine (7d). Prepared from 2,4-diamino-6-hydroxy pyrimidine
H
17Cl
2
N
O
4 2
(
0.27 g, 2.14 mmol), potassium carbonate (0.44 g, 3.22 mmol) and 9d (0.53 g, 2.14 mmol) in dry acetonitrile,
-
1
1
isolated as an off-white solid (0.25 g, 40%). mp 98-99 °C. IR (vmax/cm ): 3512, 3344, 2939, 1569, 1145, 1016. H
NMR (300 MHz, DMSO-d ): δ 7.34-7.26 (1H, m), 6.83-6.71 (3H, m), 6.02 (2H, s), 5.86 (2H, s), 5.04 (1H, s), 4.15
2H, t, J 6.0 Hz), 4.01 (2H, t, J 3.7 Hz), 1.79-1.77 (4H, m). C NMR (75 MHz, DMSO-d
6
H
1
3
(
(
6
): δ 170.1, 165.9, 163.0
C
d, JC-F 245.3 Hz), 162.8, 160.1 (d, JC-F 10.8 Hz), 130.6 (d, JC-F 10.0 Hz), 110.8 (d, JC-F 2.9 Hz), 106.9 (d, JC-F 21.3
+
Hz), 101.9 (d, JC-F 24.8 Hz), 76.1, 67.6, 64.2, 25.33, 25.31. HRMS (ESI): found [M + H] 293.1413, C14
H18FN
O
4 2
requires 293.1416.
6
-(4-(4-Fluorophenoxy)butoxy)pyrimidine-2,4-diamine (7e). Prepared from 2,4-diamino-6-hydroxy pyrimidine
(
0.23 g, 1.86 mmol), potassium carbonate (0.39 g, 2.79 mmol) and 9e (0.46 g, 1.86 mmol) in dry acetonitrile,
-
1
1
isolated as a white solid (0.18 g, 33%). mp 138-139 °C. IR (vmax/cm ): 3478, 2957, 1577, 1216, 1199, 1075. H
NMR (300 MHz, DMSO-d ): δ 7.12-7.06 (2H, m), 6.99-6.84 (2H, m), 5.99 (2H, s), 5.81 (2H, s), 5.06 (1H, s), 4.13
2H, t, J 3.1 Hz), 3.98-3.94 (2H, m), 1.78-1.74 (4H, m). C NMR (75 MHz, DMSO-d
6
H
1
3
(
6
): δ 170.1, 165.9, 162.9,
C
1
2
6
56.4 (d, JC-F 227.9 Hz), 154.8 (d, JC-F 2.0 Hz), 115.8 (d, JC-F 23.1 Hz), 115.6 (d, JC-F 8.0 Hz), 76.1, 67.7, 64.2,
+
5.4, 25.3. HRMS (ESI): found [M + H] 293.1411, C14
H18FN
4
2
O requires 293.1416.
-(4-(3-(Trifluoromethyl)phenoxy)butoxy)pyrimidine-2,4-diamine (7f). Prepared from 2,4-diamino-6-hydroxy
pyrimidine (0.51 g, 4.04 mmol), potassium carbonate (0.84 g, 6.06 mmol) and 9f (1.20 g, 4.04 mmol) in dry
-
1
acetonitrile, isolated as a white solid (0.64 g, 46%). mp 100-101 °C. IR (vmax/cm ): 3512, 2939, 1569, 1216,
1
1
7
(
141, 1015. H NMR (500 MHz, DMSO-d
6
): δ 7.35 (1H, t, J 8.0 Hz), 7.17 (1H, d, J 7.8 Hz), 7.11 (1H, t, J 2.1 Hz),
H
.04 (1H, dd, J 8.3, 2.5 Hz), 5.27-5.13 (2H, m), 4.97 (2H, s), 4.26-4.13 (2H, m), 4.00 (2H, t, J 3.8 Hz), 1.97-1.74
4H, m). C NMR (125 MHz, DMSO-d
1
3
6
): δ 170.6, 166.4, 163.4, 159.4, 130.8 (q, J 31.7 Hz), 124.5 (q, JC-F 272.4
C
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Hz), 119.2, 117.4 (q, JC-F = 3.8 Hz), 111.4 (q, J 3.7 Hz), 76.6, 68.2, 64.6, 25.8 (2C). HRMS (ESI): found [M + H]+
3
43.1377, C15
H
18
F
3
N
4
O
2
requires 343.1384.
6
-(3-(4-Chlorophenoxy)propoxy)pyrimidine-2,4-diamine (7g). Prepared from 2,4-diamino-6-hydroxy
pyrimidine (0.51 g, 4.01 mmol), potassium carbonate (0.83 g, 6.01 mmol) and 12a (1.00 g, 4.01 mmol) in dry
-
1
acetonitrile, isolated as a white solid (0.41 g, 35%). mp 81-82 °C. IR (vmax/cm ): 3520, 3359, 3011, 1576, 1125,
1
7
(
1
C
6
91. H NMR (300 MHz, DMSO-d
6
): δ 7.31 (2H, d, J 9.0 Hz), 6.96 (2H, d, J 9.0 Hz), 6.00 (2H, s), 5.85 (2H, s), 5.06
H
1
3
1H, s), 4.22 (2H, t, J 6.4 Hz), 4.05 (2H, t, J 6.3 Hz), 2.07 (2H, p, J 6.3 Hz). C NMR (75 MHz, DMSO-d
6
+
): δ
C
170.0,
65.9, 163.0, 157.3, 129.3, 124.2, 116.2, 76.1, 64.8, 61.4, 28.5. HRMS (ESI): found [M + H] 295.0956,
requires 295.0964.
-(3-(3,4-Dichlorophenoxy)propoxy)pyrimidine-2,4-diamine (7h). Prepared from 2,4-diamino-6-hydroxy
13
H
16ClN
O
4 2
pyrimidine (0.44 g, 3.52 mmol), potassium carbonate (0.73 g, 5.28 mmol) and 12b (1.00 g, 3.52 mmol) in dry
-
1
acetonitrile, isolated as a light yellow solid (0.43 g, 37%). mp 134-135 °C. IR (vmax/cm ): 3529, 3343, 3010,
1
1
2
581, 1101. H NMR (300 MHz, DMSO-d
6
): δ 7.50 (1H, d, J 8.9 Hz), 7.22 (1H, d, J 2.9 Hz), 6.95 (1H, dd, J 8.9,
H
.9 Hz), 5.99 (2H, s), 5.82 (2H, s), 5.04 (1H, s), 4.22 (2H, t, J 6.4 Hz), 4.12 (2H, t, J 6.2 Hz), 2.06 (2H, p, J 6.3 Hz).
1
3
C NMR (75 MHz, DMSO-d
8.9. HRMS (ESI): found [M + H] 329.0565, C13
-(3-(3,5-Dichlorophenoxy)propoxy)pyrimidine-2,4-diamine (7i). Prepared from 2,4-diamino-6-hydroxy
6
): δ 170.4, 166.5, 163.4, 158.5, 132.1, 131.4, 122.8, 116.8, 115.9, 76.6, 65.8, 61.8,
H
+
2
6
H15Cl
2
N
4
2
O requires 329.0574.
pyrimidine (0.89 g, 7.04 mmol), potassium carbonate (1.46 g, 10.6 mmol) and 12c (2.00 g, 7.04 mmol) in dry
-1
acetonitrile, isolated as a creamy white solid (1.26 g, 54%). mp 105-107 °C. IR (vmax/cm ): 3541, 3362, 3035,
1
1
(
δ
3
6
588, 1144, 799. H NMR (300 MHz, DMSO-d
6
): δ 7.14 (1H, t, J 1.8 Hz), 7.06 (2H, d, J 1.8 Hz), 6.00 (2H, s), 5.84
H
1
3
2H, s), 5.05 (1H, s), 4.21 (2H, t, J 6.4 Hz), 4.12 (2H, t, J 6.2 Hz), 2.11-2.02 (2H, m). C NMR (75 MHz, DMSO-d
6
):
+
C
170.0, 166.0, 163.0, 160.0, 134.6 (2C), 120.3, 113.9 (2C), 76.1, 65.5, 61.2, 28.3, HRMS (ESI): found [M + H]
29.0572, C13 requires 329.0574.
-(3-(4-Fluorophenoxy)propoxy)pyrimidine-2,4-diamine (7j). Prepared from 2,4-diamino-6-hydroxy
H
15Cl
2
N
O
4 2
pyrimidine (0.27 g, 2.15 mmol), potassium carbonate (0.44 g, 3.22 mmol) and compound 12d (0.50 g, 2.15
-
1
mmol) in dry acetonitrile, isolated as a white solid (0.20 g, 34%). mp 69-71 °C. IR (vmax/cm ): 3539, 3332, 3032,
1
1
5
1
6
586, 1153. H NMR (300 MHz, DMSO-d
6
): δ 7.18-7.01 (2H, m), 6.99-6.87 (2H, m), 5.99 (2H, s), 5.85 (2H, s),
H
1
3
.04 (1H, s), 4.22 (2H, t, J 6.3 Hz), 4.03 (2H, t, J 6.3 Hz), 2.06 (2H, p, J 6.3 Hz). C NMR (75 MHz, DMSO-d
70.0, 166.0, 163.0, 159.7 (d, JC-F 225.5 Hz), 154.8 (d, JC-F 3.0 Hz), 115.8 (d, JC-F 15.7 Hz), 115.6, 76.1, 65.0,
1.4, 28.6. HRMS (ESI): found [M + H] 279.1252, C13
6
): δ
C
+
H16FN
4
2
O requires 279.1310.
Biology
SYBR green assay against Gambian FCR-3 strain.
P. falciparum (FCR-3) strain was cultured in vitro at 37 °C in 3% O
2
, 5% CO
2
, 92% N and adjusted to a 0.625%
2
parasitaemia/1.25% haematocrit before being incubated along with the analogues for 72 h. The plates were
frozen overnight and, once thawed, incubated in the dark for 1 h at room temperature with buffered SYBR
green I. The fluorescence was read in a microplate reader with excitation and emission wavelength bands
centred at 485 and 528 nm, respectively. The percentage inhibition was calculated taking the untreated and
dihydroartemisinin control into account. Dihydroartemisinin (DHA) and methotrexate (MTX) were used as
positive controls. At least three independent experiments were conducted for each analogue. The
concentration that inhibited 50% of parasite growth (IC50 value) was determined from the log sigmoid dose

response curves generated by GraphPad Prism software. Each experiment was repeated in triplicate.
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Acknowledgements
Research reported in this publication was supported by the Medical Research Council (South Africa) under a
Self-Initiated Research Grant. HFK and TDS thank the National Research Foundation (South Africa) for funding.
Supplementary Material
1
13
Readers will be able to access supporting information ( H and C NMR spectra of synthesized compounds)
using the link "Supplementary Material" in the journal issue contents.
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