A novel and practical synthesis of Iclaprim

Article abstract of DOI:10.1080/00397911.2020.1831023

A novel and facile synthesis of Iclaprim was reported. Started from trimethoprim (TMP), the amino-protection and Friedel–Crafts acetylation with acetic anhydride were simultaneously completed in CH₂Cl₂ with SnCl₄ as cataly

Full text of DOI:10.1080/00397911.2020.1831023

Synthetic Communications
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A novel and practical synthesis of Iclaprim
Weiyuan Liu , Liang Chen , Jing Pan , Ting Zhou , Kuaile Lin & Weicheng Zhou
To cite this article: Weiyuan Liu , Liang Chen , Jing Pan , Ting Zhou , Kuaile Lin & Weicheng
Zhou (2020): A novel and practical synthesis of Iclaprim, Synthetic Communications, DOI:
10.1080/00397911.2020.1831023
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https://doi.org/10.1080/00397911.2020.1831023
A novel and practical synthesis of Iclaprim
Weiyuan Liu, Liang Chen, Jing Pan, Ting Zhou, Kuaile Lin, and Weicheng Zhou
State Key Lab of New Drug & Pharmaceutical Process, Shanghai Key Lab of Anti-Infectives, Shanghai
Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai,
PR China
ABSTRACT
ARTICLE HISTORY
Received 7 June 2020
A novel and facile synthesis of Iclaprim was reported. Started from
trimethoprim (TMP), the amino-protection and Friedel–Crafts acetyl-
ation with acetic anhydride were simultaneously completed in
CH2Cl2 with SnCl4 as catalyst. The Knoevenagel condensation of 2,4-
diamino-5-(2-acetyl-3-hydroxy-4,5-dimethoxybenzyl)pyrimidine with
cyclopropyl carboxaldehyde followed by the intramolecular Michael
addition in the buffer system (pyrrolidine and acetic acid) installed
the key framework (chromanone 13). The dehydration was catalyzed
by H2SO4 so that the formation of 5-cyclopropyl-2,3-dimethoxy-
4,5,6,6a,7,12-hexahydronaphtho[1,8-bc]pyrimido[5,4-f]azepin-9-amine,
an impurity of Iclaprim reported at the first time, could be mini-
mized. In the end, Iclaprim was obtained in a total yield of 21%.
KEYWORDS
Acetylation; buffer system;
chromanone; Iclaprim;
sulfuric acid; synthesis
GRAPHICAL ABSTRACT
Introduction
Dihydrofolate reductase (DHFR) is an enzyme essential for bacterial survival that is also
an excellent target for antibacterial drug development.[1] Trimethoprim (TMP) is an
inhibitor of DHFR used as an antibacterial agent in clinic for many years.[2] Iclaprim, a
CONTACT Weicheng Zhou
zhouweicheng58@163.com
China State Institute of Pharmaceutical Industry, State Key
Lab of New Drug & Pharmaceutical Process, Shanghai Key Lab of Anti-Infectives, Shanghai Institute of Pharmaceutical
Industry, Shanghai 20122013, PR China.
Supplemental data for this article can be accessed on the publisher’s website.
ß 2020 Taylor & Francis Group, LLC

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W. LIU ET AL.
Scheme 1. Route 1.
derivative of TMP was developed by Motif Bio plc. The clinical trial demonstrated that
Iclaprim was effective for treatment of acute bacterial skin and skin structure infec-
tions.[3] Since Iclaprim is active against multi-drug resistant Gram-positive pathogens
such as methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant S.
aureus,[4,5] the synthesis has attracted much attention.
The structure of Iclaprim is composed of two heterocycle rings: 2H-chromene and pyr-
imidine. Two kinds of synthetic strategy existed in the related patents,[6–8] depending on
which heterocycle was built at first.
Strategy A (construction of the 2H-chromene first) included route 1 (Scheme 1) and
route 2 (Scheme 2). In both routes, the starting materials (compound 2 or compound
5) were expensive and there were many key bottleneck steps also. In route 1,[7]
three steps were required to establish the 2-cyclopropyl-7,8-dimethoxy-2H-chromene-5-
carbaldehyde (3) from cyclopropyl acetylene (2) in both low yield (<26%) and purity
(80%). And route 2[6] involved an essential Mitsunobu reaction between 3-hydroxy-4,5-
dimethoxybenzaldehyde and 1-cyclopropyl-3-(trimethylsilyl)prop-2-yn-1-ol (6) to gener-
ate 3-[[1-cyclopropyl-3-(trimethylsilyl)prop-2-yn-1-yl]oxy]-4,5-dimethoxybenzaldehyde
(7) in a yield of only 31%, and the removal of triphenylphosphine and its oxide in the
work-up needed column chromatography. So, these routes mentioned above are difficult
to implement in industrial production.
In strategy B (construction of the pyrimidine first), route 3[8] (Scheme 3) appeared in
the patents. It was started with TMP (8), a very cheap material. Subsequent protection
with trimethylacetic anhydride or iso-butylic anhydride, Friedel–Crafts acetylation,
demethylation, cyclization, reduction, dehydration and hydrolysis led to Iclaprim (as a
crude product) in 4.8% overall yield. According to the patent, almost all the intermedi-
ates were subjected to purification by column chromatography. From a scaleup stand-
point, it is also an undesirable method. On the basis of these limitations, it is necessary
to design a novel method to address the shortcomings. Since TMP is cheap and readily
available, we devised a new synthetic route for the Iclaprim also with TMP as the start-
ing material, based on strategy B.

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Scheme 2. Route 2.
Scheme 3. Route 3.

4
W. LIU ET AL.
Scheme 4. New route to Iclaprim.
Results and discussion
In route 3, the amino groups were protected with the steric hindrance groups, such as
pivaloyl or isobutyryl. However, our preliminary experiment found that the following
Friedel–Crafts acetylation product was contaminated by the N-acetyl byproducts, i.e.,
one or two hindrance groups were partially replaced by acetyl group in the
Friedel–Crafts reaction. To resolve the problem, we attempted the same reagent both
for the amino-protection and for the Friedel–Crafts reaction. So, as the first step in our
new route to Iclaprim (Scheme 4), TMP was reacted with 5 equiv. of acetic anhydride
in toluene by refluxing to provide 2,4-diacetamido-5-(3,4,5-trimethoxybenzyl)pyrimidine
(9) in a 86% yield.
To screen the reaction conditions of the Friedel–Crafts acetylation of compound 9 to
form 2,4-diacetamido-5-(2-acetyl-3,4,5-trimethoxybenzyl)pyrimidine (10), two acetic
agents (acetic anhydride and acetic chloride) with different Lewis acid (AlCl3, SnCl4,
and TiCl4) in CH2Cl2 or CH2ClCH2Cl were evaluated. To our surprise, in these cases,
AlCl3 did not work at all. Finally, the best result (yield 55%) was obtained by reaction
of compound 9 with SnCl4 (2 equiv.) and acetic anhydride (5 equiv.) in dichloroethane
at refluxing.
After TMP was successfully transformed into compound 10 by two steps, the one-pot
synthesis was attempted. Initially, the conversion of TMP to compound 10 was per-
formed by 5 equiv. of acetic anhydride and 2 equiv. of SnCl4 in dichloroethane under
refluxing in a reasonable yield (46%, Table 1, entry 1), that was equivalent to the yields
from two steps. However, there was a limitation from the standpoint of largescale prep-
aration. When TMP was charged on a 100-gram scale, a severe emulsification occurred
during phase separation in the work-up, probably due to the poor solubility of com-
pound 10 in dichloroethane. Therefore, some solvents that are suitable for the
Friedel–Crafts acetylation were tested by solubility experiment. From Table 2, it was
seen that Compound 10 is much more soluble in chloroform than dichloroethane. So,

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5
Table 1. Condition for amino protection and Friedel–Crafts acetylation of TMP.
Entry
Acetic anhydride (equiv.)
SnCl4 (equiv.)
Solvent
Dichloroethane (10 Va)
Chloroform (10 V)
Chloroform (10 V)
Chloroform (10 V)
Time (h)
Yield (%)
1
2
3
4
5
6
5
5
5
4.5
4
4.5
2
2
1.5
2
2
10
1
7.5
2.5
4
46
93
85
95
83
96
Chloroform (10 V)
Dichloromethane (15 V)
2
7.5
aVolume (mL)/weight (g) of compound 8.
Table 2. The solubility of compound 10.
Solvents
Chloroform
11.2
Dichloromethane
4.6
Dichloroethane
0.6
Solubility (%)
the reaction was carried out in chloroform and got an exciting yield (93%, Table 1,
entry 2). The modification on the amount of SnCl4 and acetic anhydride (Table 1,
entries 2–5) found that the best result (95%, entry 4) was achieved when acetic anhyd-
ride decreased to 4.5 equiv. Because of the concern of toxicity of chloroform in pharma-
ceutical industry, the alternative (dichloromethane) was used, and the reaction (entry 6)
gave the almost same result although the amount of solvent was increased.
For the demethylation, the preliminary experiments started with the amino-protected
compound 10 and Lewis acid (AlCl3 and BBr3) and various solvents (acetonitrile, tolu-
ene, dichloroethane, and dichloromethane) were tested, the best result was obtained
with BBr3 in dichloromethane to provide 2,4-diacetamido-5-(2-acetyl-3-hydroxy-4,5-
dimethoxybenzyl)pyrimidine in a 21% yield. The reason of a such low yield was due to
the formation of some by-products (partial de-protection in 2,4-diacetamido), that
made the purification complicated. Therefore, our attention turned to demethylation of
2,4-diamino-5-(2-acetyl-3,4,5-trimethoxybenzyl)pyrimidine (11). Compound 11 was pre-
pared by reaction of compound 10 with K2CO3 (0.1 equiv.) in methanol in 97% yield.
And then, demethylation of compound 11 with 1.5 equiv. of BBr3 in dichloromethane
gave 2,4-diamino-5-(2-acetyl-3-hydroxy-4,5-dimethoxybenzyl)pyrimidine (12) in a yield
of 65%. When the amount of BBr3 was increased or decreased (1.2 or 2 equiv.), the
yields were both declined to 50%.
The key step in the synthesis of Iclaprim is the cyclization of compound 12 with
cyclopropyl carboxaldehyde to form 2-cyclopropyl-5-[(2,4-diaminopyrimidin-5-
yl)methyl]-7,8-dimethoxychroman-4-one (13). The reaction should involve the
Knoevenagel condensation of compound 12 with cyclopropyl carboxaldehyde followed
by the intramolecular Michael addition by the ortho-phenolic group. In general, the
Knoevenagel condensation was catalyzed by organic base such as the secondary amine.
So, the reaction was carried out in the presence of pyrrolidine, and it gave a too compli-
cated mixture to purify (Table 3, entry 1), in which beside compound 13, some impur-
ities formed by the intermolecular addition of the Knoevenagel product with pyrrolidine
1
were found by the HNMR data. Therefore, diisopropylamine, the sterically hindered
base was employed, but no improvement was observed (entry 2). And then, the buffer
system (pyrrolidine 1.5 equiv./acetic acid 1 equiv.) was attempted, a 44% yield of the
compound 13 was achieved (entry 3). Addition of 1.5 equiv. of acetic acid to the reac-
tion led to a 15% raise in the reaction yield (entry 4). The other modification such as

6
W. LIU ET AL.
Table 3. Condition for cyclization of compound 12.
Cyclopropyl
carboxaldehyde
(n equiv.)
Entry
Base (n equiv.)
Solvent
Temp. (ꢀC)
Time (h)
Yield (%)
1
2
3
1.2
1.2
1.2
Pyrrolidine (1.5)
Diisopropylamine (2)
Pyrrolidine (1.5)
CH3COOH (1)
Acetonitrile
Acetonitrile
Acetonitrile
rt
Reflux
rt
3
8
36
mixture
mixture
44
4
5
6
7
8
1.2
1.2
1.2
1.5
1.2
Pyrrolidine (1.5)
CH3COOH (1.5)
Pyrrolidine (1.5)
CH3COOH (1.5)
Pyrrolidine (1.5)
CH3COOH (2)
Pyrrolidine (1.5)
CH3COOH (1.5)
Piperidine (1.5)
CH3COOH (1.5)
Acetonitrile
Acetonitrile
Acetonitrile
Acetonitrile
Acetonitrile
rt
Reflux
rt
36
1
59
44
59
58
36
36
50
rt
rt
Recovery of starting
material 12
Scheme 5. The dehydration of compound 14.
increasing the reaction temperature, the amount of acetic acid or the aldehyde did not
produce the better result (entries 5–7). Surprisingly, in the tests with piperidine, a very
similar base with pyrrolidine (entry 8), the reaction did not take place (most of the
starting material 12 was recovered).
With cyclization product 13 in hands, the 2-cyclopropyl-5-[(2,4-diaminopyrimidin-5-
yl)methyl]-7,8-dimethoxychroman-4-ol (14) was prepared by reduction with 0.5 equiv.
of NaBH4 in 80% yield.
The final step was the dehydration (Scheme 5). In the beginning, compound 14 was
heated under refluxing in methanol under the presence of TsOH.H2O (Table 4, entry

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Table 4. Condition for dehydration.
Monitoring the reaction process by HPLC
Entry Acid (n equiv.)
Solvent
Temp. (ꢀC) Time (h) Yield (%)
1 (%)
14 (%)
1a (%)
1
2
3
4
5
6
7
8
9
TsOH.H2O (1.5) Methanol Reflux
TsOH.H2O (1.5) THF
CH3SO3H (1.5) THF
CF3COOH (5)
H2SO4 (1.2)
H2SO4 (1.2)
H2SO4 (1.2)
H2SO4 (1.5)
H2SO4 (1)
1
4
7
2
2
4
8
4
4
67a
34
43
42b
64
73
–
–
–
2.53
2.30
–
10.04
2.03
2.25
–
–
15.50
12.20
–
1.92
1.95
2.36
–
Reflux
Reflux
Reflux
Reflux
Reflux
Reflux
Reflux
Reflux
54.02
77.63
–
84.28
92.53
89.98
–
Toluene
THF
THF
THF
THF
THF
69
67
–
–
–
aCompound 14a was the main product in the reaction.
bImpurity 1a was isolated in the reaction.
1), and 2-cyclopropyl-4-methoxyl-5-[(2,4-diaminopyrimidin-5-yl)methyl]-7,8-dimethoxy-
chroman (14a) instead of Iclaprim was obtained as the main product. It was seen that
methanol worked as a nucleophilic reagent to attack the benzyl position of chroman in
compound 14. So, the solvent was changed into tetrahydrofuran (THF) and the reaction
produced Iclaprim in a low yield (34%, entry 2). Different acids as the catalyst were
evaluated for this reaction, and the results were listed in Table 4. The best condition
was achieved using H2SO4 (1.2 equiv.) in THF (entry 6). Although the reactions with
CF3COOH as a catalyst gave disappointing yields, an unknown impurity was isolated in
the reaction with toluene as the solvent (entry 4). It was identified as 5-cyclopropyl-2,3-
dimethoxy-4,5,6,6a,7,12-hexahydronaphtho[1,8-bc]pyrimido[5,4-f]azepin-9-amine
(1a)
by HNMR, 13CNMR, elemental analysis and MS data. With compound 1a in hands, an
HPLC method was established to monitor the process. Under the presence of H2SO4,
the best refluxing time was 4 h. At this point, although ca 2% of compound 14 was
retained, the formation of impurity 1a was controlled under 2%. Finally, Iclaprim was
obtained with 73% yield and with a satisfactory purity of >99% after recrystallization
with 95% ethanol (Table 4 entry 6).
1
Conclusion
In summary, the novel and practical synthesis of Iclaprim was accomplished. Compared
with the route 3 in the literature, our new way only included six reaction steps with an
overall yield of 21%, which was almost four times as much as the route 3. The one-step
synthesis of amino-protection and Friedel–Crafts acetylation was the highlight in this
paper, which not only shortened the reaction steps, but also improved the yield greatly
(92% vs. 24%). Additionally, the new synthesis was suitable for scaling-up, all purifica-
tion only involved recrystallization without any column chromatography.
Experimental
General
Solvents and reagents from vendors were used as received unless otherwise indicated.
Melting points were determined on a capillary melting point apparatus and were

8
W. LIU ET AL.
uncorrected. NMR spectra were taken on a Bruker Avance III instrument operated at
400 or 600 MHz for 1H-NMR and 100 MHz for 13C-NMR with tetramethylsilane
(Me4Si) as an internal standard. HPLC was performed on a YMC-Pack ODS-AQ col-
umn (150 ꢁ 3.0 mm, 3 lm silica) with mobile phase A: 0.02 M KH2PO4 aqueous solu-
tion; mobile phase B: acetonitrile; flow rate: 0.6 mL/min.
2-Cyclopropyl-5-[(2,4-diaminopyrimidin-5-yl)methyl]-7,8-dimethoxychromen (1)
To a suspension of 14 (26.3 g, 70.7 mmol) in THF (260 mL) was added concentrated sul-
furic acid (8.3 g, 84.7 mmol) at room temperature, and the whole was stirred for 4 h at
refluxing. After the reaction was completed, the pH of the solution was adjusted to
9–10 with saturated aqueous Na2CO3. Evaporation of the THF under vacuum and the
crude product 1 (24.0 g) was collected by filtration. The crude was recrystallized from
1
ethanol-water to give 1 (18.3 g, 73%, HPLC purity 99.41%). H-NMR and melting point
data were in accordance with published patents.[7,8] M.p. 215–217 ꢀC. 1H-NMR
(600 MHz, DMSO-d6): d 7.07 (s, 1H), 6.46–6.45 (d, 1H), 6.42 (s, 1H), 6.19 (brs, 2H),
5.72–5.70 (m, 1H), 5.68 (brs, 2H), 4.26–4.24 (m, 1H), 3.71 (s, 3H),3.70 (s, 3H), 3.52 (d,
2H), 1.15–1.11 (m, 1H), 0.43–0.51 (m, 2H), 0.35–0.39 (m, 1H), 0.30–0.33 (m, 1H); 13C-
NMR (100 MHz, DMSO-d6): d 162.06, 161.94, 154.76, 152.51, 146.77, 135.47, 129.98,
122.36, 121.00, 114.83, 106.23, 105.09, 77.54, 60.10, 55.67, 29.43, 14.84, 2.55, 1.09; MS
(ESIþ): m/z, 355 ([M þ H]þ).
Experimental procedures and NMR, MS HPLC Spectra and characterization data of
10, 11, 12, 13, 14, 14a, 1, and 1a. This material can be found via the “Supplementary
Material” section of this article’s webpage.
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