An improved synthesis approach of the HIV-1 inhibitor RDEA427, a pyrrolo[2,3-d]pyrimidine derivative

Article abstract of DOI:10.24820/ark.5550190.p009.866

The diarylpyrimidine-like derivative RDEA427 is a highly potent inhibitor against wild-type and a wide range of drug-resistant HIV-1 strains and has attracted much attention. However, the yield of its reported synthesis is too low and the route is less environment-friendly and uneconomic. In order to achieve a short and more economic synthesis of RDEA427, an investigation was carried out. The optimized synthesis approach of RDEA427 was accomplished in an increased overall yield (39%). Moreover, the new route is more environment-friendly and economic. This work will accelerate the drug discovery process.

Full text of DOI:10.24820/ark.5550190.p009.866

General Papers
ARKIVOC 2016 (vi) 45-51
An improved synthesis approach of the HIV-1 inhibitor RDEA427, a
pyrrolo[2,3-d]pyrimidine derivative
Boshi Huang, Xinhao Liu, Wanzhuo Li, Zihui Chen, Dongwei Kang, Peng Zhan* and
Xinyong Liu*
Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of
Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road,
250012 Ji’nan, Shandong, PR China
E-mail: zhanpeng1982@163.com ; xinyongl@sdu.edu.cn
DOI: https://doi.org/10.24820/ark.5550190.p009.866
Abstract
The diarylpyrimidine-like derivative RDEA427 is a highly potent inhibitor against wild-type and
a wide range of drug-resistant HIV-1 strains and has attracted much attention. However, the yield
of its reported synthesis is too low and the route is less environment-friendly and uneconomic. In
order to achieve a short and more economic synthesis of RDEA427, an investigation was carried
out. The optimized synthesis approach of RDEA427 was accomplished in an increased overall
yield (39%). Moreover, the new route is more environment-friendly and economic. This work will
accelerate the drug discovery process.
Keywords: HIV-1 inhibitor, RDEA427, diarylpyrimidine-like derivative, increased overall yield,
environment-friendly
Introduction
Currently, non-nucleoside reverse transcriptase inhibitors (NNRTIs) are major components of
highly active antiretroviral therapy (HAART) to treat HIV-1 infections.1 However, the usage of the
first generation NNRTIs has been significantly compromised by the emergence of drug-resistant
HIV-1 strains. A compelling medical need still exists for novel HIV-1 NNRTIs with improved anti-
resistance profiles.2
As the second generation NNRTIs, diarylpyrimidine (DAPY) derivatives exhibit remarkable
potency against both the wild-type (wt) and mutant HIV-1 strains. Two DAPY-type drugs,
etravirine (ETR, 2008) and rilpivirine (RPV, 2011) have been approved for clinical use3. RDEA427
(1),
4-((2-((4-cyanophenyl)amino)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)oxy)-3,5-
dimethylbenzonitrile, is another representative DAPY-like NNRTI which was developed in a
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multidisciplinary structure-based drug design effort. RDEA427 inhibits wt and a wide range of
drug-resistant HIV-1 strains at subnano- or nanomole concentrations in cell-based assays4,5 (Figure
1). Besides, RDEA427 shows a lower potential for cytochrome P450 induction and improved
metabolic properties than RPV. Therefore, it has been undergone preliminary clinical evaluation
as a drug candidate.6-8
Figure 1. Structure and anti-HIV-1 profiles of RDEA427 (1).
However, only one synthetic route has been disclosed in the literature till now, with a total yield
less than 1.9% (Scheme 1):9 the starting material 2,6-diamino-2,3-dihydropyrimidin-4(1H)- one
(2) was condensed with chloroacetaldehyde (3) in the presence of NaOAc in water to provide the
intermediate 2-amino-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one (4). Chlorination of 4 in
POCl3 using N,N-dimethylaniline and triethylbenzylammonium chloride (TEBAC) as catalysts
afforded 4-chloro-7H-pyrrolo[2,3-d]pyrimidin-2-amine (5). 5 was first benzyl-protected, and then
underwent a nucleophilic reaction with 4-hydroxy-3,5-dimethylbenzonitrile (7) to give
intermediate 8. 8 passed through a Schiemann reaction in 60% HF-pyridine solution to supply the
key intermediate 9. At last, 9 underwent another nucleophilic reaction and subsequent deprotection
to afford RDEA427 (1). In the above synthesis route of RDEA427, obvious disadvantages exist as
follows: 1) the overall yield is extremely low; 2) the route contains conditions under high
temperature heating or rather low temperature cooling, which is very energy consuming; 3) the
extremely toxic HF-pyridine solution and explosive t-butylnitrite were utilized, which was not
suitable for large-scale industrialization; 4) silica gel chromatography was employed in the latter
six steps to obtain the desired products, which is less environment-friendly and uneconomic for
quantity production. Therefore, we became greatly interested in designing a more practical, more
environment-friendly synthetic approach with improved total yield.
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Scheme 1. Discovery route of RDEA427 (1).
Results and Discussion
The new synthesis of RDEA427 was accomplished by a relatively more environment-friendly
approach with good yields (Scheme 2). The synthesis started with the commercially available 2,4-
dichloro-7H-pyrrolo[2,3-d]pyrimidine (12), which was first
(chloromethoxy)ethyl)trimethylsilane (SEM-Cl) to afford
protected by (2-
2,4-dichloro-7-((2-
(trimethylsilyl)ethoxy)methyl)-7H-pyrrolo[2,3-d]pyrimidine (13). Compound 13 subsequently
undergone two SNAr reactions, providing the key intermediate 15. The SEM group was then
removed to give the desired product RDEA427 (1). The total yield of the new route was found to
be 39%, over 20 times better than that of the original route. With the exception of the third step,
the reactions conditions were relatively mild. In addition, no extremely toxic or explosive materials
were utilized in the optimized route, and the silica gel chromatography was only employed in three
steps, which is more economic for quantity production.
Scheme 2. The improved synthetic route of RDEA427 (1).
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At first, using a protecting-group-free strategy, it was found that the starting material 12 could
not directly afford RDEA427 after two-step SNAr reactions. Subsequently, (Boc)2O and p-
toluenesulfonyl chloride (TsCl) were applied as possible protective agents. Unfortunately, both of
the designed routes did not work out. Finally, (2-(chloromethoxy)ethyl)trimethylsilane (SEM-Cl)
was adopted to achieve the aim.
Moreover, preliminary investigations were carried out to select appropriate Pd catalysts and
ligands on the Buchwald–Hartwig reaction, since the third step reaction played a decisive role in
improving the overall yield. Pd(OAc)2/BINAP and Pd2(dba)3/Xantphos were used with different
stoichiometric ratios, and temperatures were also studied. The reaction conditions and yields were
depicted in Table 1. Considering the yield, raw material price and quantity production, the
condition using Pd2(dba)3 (0.015 eq)/Xantphos (0.015 eq)/80°C was ultimately employed.
Table 1. Explorations of Buchwald–Hartwig reaction conditions
Entry Pd catalysts (eq.)
Ligands (eq.)
BINAP (0.4)
BINAP (0.4)
BINAP (0.4)
BINAP (0.04)
Temperature (°C)
Time
4h
Yield%
10
1
2
3
4
5
6
7
8
Pd(OAc)2 (0.2)
Pd(OAc)2 (0.2)
Pd(OAc)2 (0.2)
Pd(OAc)2 (0.02)
150
140
110
140
140
4h
72
4h
0a
4h
68
Pd2(dba)3 (0.015) Xantphos (0.015)
4h
49
Pd2(dba)3 (0.015) Xantphos (0.015) 140 (microwave-assisted)b
1h
50
Pd2(dba)3 (0.015) Xantphos (0.015)
Pd2(dba)3 (0.015) Xantphos (0.015)
110
80
4h
63
4h
67
a This reaction condition did not work. b Conducted on a CEM Discover SP (0-600W) microwave
instrument.
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Conclusions
We have developed a new synthesis approach of the HIV-1 inhibitor RDEA427. The total yield of
the optimized route increased to 39%, over 20 times better than that of the original one. Protective
reagents and appropriate Pd catalysts and ligands on the Buchwald-Hartwig reaction were
preliminarily explored. Finally, SEM-Cl and Pd2(dba)3 (0.015 eq)/Xantphos (0.015 eq) were
adopted. On the whole, the reaction conditions are relatively mild, and the new route is more
environment-friendly and economic, therefore is suitable for quantity production in the future.
Experimental Section
General. All melting points (mp) were determined on a micromelting point apparatus and are
uncorrected. Mass spectra were performed on a LC Autosampler Device: Standard G1313A
1
instrument by electrospray ionization. H NMR and 13C NMR spectra were obtained on a Bruker
AV-400 spectrometer (Bruker BioSpin, Fällanden, Switzerland) in the indicated solvent DMSO-
d6. Chemical shifts were expressed in δ units (ppm), using TMS as an internal standard, and J
values were reported in hertz (Hz). TLC was performed on Silica Gel GF254. Spots were visualized
by irradiation with UV light (λ 254 nm). Flash column chromatography was carried out on columns
packed with silica gel 60 (200–300 mesh). Solvents were of reagent grade and, if needed, were
purified and dried by standard methods. The key reagents were purchased from commercial
suppliers and with no further purification when used. Rotary evaporators were served in
concentration of the reaction solutions under reduced pressure.
2,4-Dichloro-7-((2-(trimethylsilyl)ethoxy)methyl)-7H-pyrrolo[2,3-d]pyrimidine (13). To a
suspension of NaH (60% in oil, 234 mg, 5.85 mmol) in anhydrous DMF (3 mL) was dropwise
added a solution of 12 (1.00 g, 5.32 mmol) in DMF (5 mL) at 0 °C. Additional DMF (2 mL) was
used to rinse the flask and then was added to the solution. The resulting mixture was stirred for
15 min and then treated with SEM-Cl (1 mL, 5.85 mmol) slowly. After the mixture was stirred at
room temperature for 4 h, the reaction was quenched with water (150 mL), and extracted with
EtOAc (3 × 40 mL). The organic layers were combined, washed with saturated brine (50 mL),
dried over anhydrous Na2SO4, filtered and concentrated under reduced pressure. Finally, the
residue was further purified by silica gel chromatography with EtOAc/petroleum ether =1/4 to
afford the title compound as a colorless oil (1.35 g). Yield: 80%. 1H NMR (400 MHz, DMSO-d6)
δ: 7.99 (d, JHH 3.68 Hz, 1H, pyrrole-H), 6.82 (d, JHH 3.68 Hz, 1H, pyrrole-H), 5.72 (s, 2H, NCH2),
3.64 (d, JHH 8.08 Hz, 2H, OCH2), 0.94 (d, JHH 8.08 Hz, 2H, SiCH2), 0.00 (s, 9H, CH3×3). 13C NMR
(100 MHz, DMSO-d6) δ: 153.26, 152.33, 151.77, 133.38, 117.24, 100.82, 74.17, 67.08, 18.13, -
0.50. ESI-MS: m/z 318.2 (M+H)+, C12H17Cl2N3OSi (317.05).
4-((2-Chloro-7-((2-(trimethylsilyl)ethoxy)methyl)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)oxy)-3,5-
dimethylbenzonitrile (14). K2CO3 (0.70 g, 5.04 mmol) was added to a solution of 4-hydroxy-3,5-
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dimethylbenzonitrile (0.37 g, 2.52 mmol) in anhydrous DMF (6 mL). The mixture was stirred at
room temperature for 10 min, then intermediate 13 (0.80 g, 2.52 mmol) in DMF (3 mL) was slowly
added. The reaction was heated at 60 °C for 3 h until its completion. 50 mL H2O was added, and
the resultant precipitate was filtered, washed with water and dried in vacuo to obtain the crude
product 14 (1.00 g) as a white solid, which could be used in the next step without further
purification. Yield: 92%, mp 139.5-140.1 °C. ESI-MS: m/z 429.4 (M+H)+, 451.4 (M+Na)+,
C21H25ClN4O2Si (428.14).
4-((2-((4-Cyanophenyl)amino)-7-((2-(trimethylsilyl)ethoxy)methyl)-7H-pyrrolo[2,3-
d]pyrimidin-4-yl)oxy)-3,5-dimethylbenzonitrile (15). A mixture of 14 (1.00 g, 2.34 mmol), 4-
aminobenzonitrile (0.28 g, 2.34 mmol), Cs2CO3 (1.14 g, 3.51 mmol), Pd2(dba)3 (32.1 mg, 0.0351
mmol) and Xantphos (20.3 mg, 0.0351 mmol) was dissolved in 40 mL 1,4-dioxane, and then the
solution was refluxed at 80°C for 4h under N2 atmosphere. Subsequently, the solution was filtered
and concentrated under reduced pressure. Finally, the residue was further purified by silica gel
chromatography with EtOAc/petroleum ether =1/8 and recrystallized from absolute ethanol to give
1
15 (0.80 g) as a white solid. Yield: 67%, mp 190.0-191.0 °C. H NMR (400 MHz, DMSO-d6) δ:
10.03 (s, 1H, NH), 7.93 (s, 2H, OPh-H), 7.83 (d, JHH 8.72 Hz, 2H, CN-Ph-H), 7.63 (d, JHH 8.84
Hz, 2H, CN-Ph-H), 7.55 (d, JHH 3.64 Hz, 1H, pyrrole-H), 6.69 (d, JHH 3.60 Hz, 1H, pyrrole-H),
5.69 (s, 2H, NCH2), 3.70 (d, JHH 8.08 Hz, 2H, OCH2), 2.27 (s, 6H, CH3×2), 0.97 (d, JHH 8.08 Hz,
13
2H, SiCH2), 0.00 (s, 9H, CH3×3). C NMR (100 MHz, DMSO-d6) δ: 161.63, 155.59, 155.20,
154.77, 146.22, 133.87, 133.74, 133.59, 127.63, 120.64, 119.66, 118.76, 109.57, 102.68, 99.85,
99.79, 73.66, 66.57, 18.11, 16.83, -0.50. ESI-MS: m/z 511.4 (M+H)+, 533.4 (M+Na)+,
C28H30N6O2Si (510.22).
4-((2-((4-Cyanophenyl)amino)-7H-pyrrolo[2,3-d]pyrimidin-4-yl)oxy)-3,5-
dimethylbenzonitrile (RDEA427, 1). To a solution of 15 (0.50 g, 0.98 mmol) in dichloromethane
(6 mL) was added 4 mL trifluoroacetic acid, and then the mixture was stirred at room temperature
for 2h. The extra solvent was removed under reduced pressure to provide a greyish white solid,
which was redissolved in methanol/2N NaOH(aq) (1/1, 5 mL). The reaction mixture was then
stirred at room temperature for 4 h. Water (100 mL) was added and the solution was extracted
using EtOAc (3 × 30 mL), washed with saturated brine (50 mL), dried over anhydrous Na2SO4,
filtered and concentrated under reduced pressure. Futher, the residue was purified by silica gel
chromatography with EtOAc/petroleum ether =1/2 and recrystallized from absolute methanol to
afford the pure target compound 1 (0.29 g) as a white solid. Yield: 79%, mp: 280.3-282.2 °C. 1H
NMR (400 MHz, DMSO-d6) δ: 11.87 (s, 1H, pyrrole-NH), 9.75 (s, 1H, NH), 7.79 (s, 2H, OPh-H),
7.66 (d, JHH 8.80 Hz, 2H, CN-Ph-H), 7.49 (d, JHH 8.84 Hz, 2H, CN-Ph-H), 7.25 (dd, J HH-1 3.44 Hz,
JHH-2 2.32 Hz, 1H, pyrrole-H), 6.46 (dd, JHH-1 3.40 Hz, JHH-2 1.76 Hz, 1H, pyrrole-H), 2.14 (s, 6H,
13
CH3×2). C NMR (100 MHz, DMSO-d6) δ: 160.87, 155.29, 154.35, 154.34, 145.88, 133.38,
133.11, 132.98, 123.63, 120.16, 119.13, 117.91, 108.86, 101.74, 99.04, 98.60, 16.31. ESI-MS: m/z
379.5 (M-H)-, C22H16N6O (380.14).
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Acknowledgements
Financial support from the National Natural Science Foundation of China (NSFC Nos. 81273354,
81573347), Key Project of NSFC for International Cooperation (No. 81420108027), Young
Scholars Program of Shandong University (YSPSDU No. 2016WLJH32, to P.Z.), the Science and
Technology Development Project of Shandong Province (No. 2014GSF118175, 2014GSF118012)
and Major Project of Science and Technology of Shandong Province (No. 2015ZDJS04001) is
gratefully acknowledged.
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