Development of Rapid and Facile Solid-Phase Synthesis of Protacs Via A Variety of Binding Styles
Development of Rapid and Facile Solid-Phase Synthesis of Protacs Via A Variety of Binding Styles
Development of Rapid and Facile Solid-Phase Synthesis of Protacs Via A Variety of Binding Styles
ChemistryOpen doi.org/10.1002/open.202200131
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Optimizing linker design is important for ensuring efficient syntheses. Herein, a solid-phase approach for convenient
degradation activity of proteolysis-targeting chimeras (PRO- PROTAC synthesis is presented. We designed azide intermedi-
TACs). Therefore, developing a straightforward synthetic ap- ates with different linker lengths to which the E3 ligand,
proach that combines the protein-of-interest ligand (POI ligand) pomalidomide, is attached and performed facile PROTACs
and the ligand for E3 ubiquitin ligase (E3 ligand) in various synthesis by forming triazole, amide, and urea bonds from the
binding styles through a linker is essential for rapid PROTAC intermediates.
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Scheme 1. Solid-phase synthesis of PROTACs(H-PGDS). (a) Synthesis of intermediate resin 1. (b) Synthesis of PROTACs 1–3 from resin 1. (c) Synthesis of
PROTAC 4 using resin 3. Abbreviations: DIC: N,N’-diisopropylcarbodiimide; HOBt: 1-hydroxybenzotriazole; HBTU: 1-[bis(dimethylamino)methylene]-1H-
benzotriazolium 3-oxide hexafluorophosphate; DIPEA: N,N-diisopropylethylamine; TFA: trifluoroacetic acid.
synthetic target. These are typical PROTACs with alkyl linkers amine were synthesized separately and used as starting linkers
that contain JQ1 as a POI ligand and degrade the target protein, (Scheme S4, Supporting Information). The synthetic route was
bromodomain-containing 4 (BRD4).[20] A number of PROTACs the same as that used for PROTAC 2, with each linker attached
targeting BRD4 have been reported for cancer therapy.[21] Most to resin 4 to obtain resins 6, 11, and 12. Subsequent
of them contain an alkyl linker,[18,19,22] while others are based on condensation with compound 7 gave the azide intermediates 1,
a PEG linker,[23] a photoswitchable azobenzene type,[24] or 13, and 14, which upon further reduction afforded resins 2, 15,
dihydropyrazine[25] formed by cyclization of trans-cyclo-octene and 16. Finally, (+)-JQ1-CO2H (17) was coupled to the resins to
with tetrazine. In the reported dBET1 and dBET6, thalidomide obtain the target PROTACs 5–7 with > 99 % purity.
was used as the E3 ligand, but the C O bond of thalidomide is We have successfully constructed azide-alkyne cycloaddi-
possibly more unstable in buffer (pH 7.4) and human plasma tions and amide bonds, which are used widely in synthesizing
than the C N bond of pomalidomide.[26] Therefore, we decided PROTACs, with efficient pathways and reaction conditions
to synthesize the pomalidomide-type dBET (PROTACs 5–7, suitable for solid-phase synthesis. Thus, the rapid and straight-
Scheme 2). For the synthesis of PROTACs 5–7, in addition to 3- forward synthesis of PROTACs by the solid-phase method
azidopropylamine, 4-azidobutan-1-amine, and 8-azidooctan-1- improves the convenience of complicated PROTACs syntheses
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Experimental Section
Conclusion
General Information
In summary, we have rapidly and easily synthesized PROTACs
All chemicals were purchased from Sigma-Aldrich Co. LLC, Kanto
by a solid-phase method using various conjugation reactions.
Chemicals Co. Inc., Tokyo Chemical Industry Co. Ltd., Wako Pure
Triazole, amide, urea, and reverse amide formation reactions Chemical Industries Ltd., and were used without further purifica-
were exploited to synthesize PROTACs (H-PGDS). We have also tion. Reactions were followed by thin-layer chromatography (TLC)
synthesized pomalidomide derivatives of dBET as PROTACs with (60 F254, Merck), and spots were visualized by UV irradiation with a
different alkyl-linker lengths and have shown that they exhibit handheld UV lamp (254/365 nm) (UVP) and iodine vapor or
potent degradation activity. The solid-phase PROTAC synthetic ninhydrin reagent. Silica gel for column chromatography was Kanto
Chemical 60 N (spherical, neutral), NH silica gel (Chromatrex NH-
method presented in this study should facilitate the rapid DM1020, Fuji Silicia), or packed columns for medium pressure
development of PROTACs targeting various proteins. column chromatography (Hi-Flash column / Inject column Yama-
zen). Resin: Aminomethyl polystyrene resin (50 mg, loading
2.5 mmol g 1). Reagent for acetaldehyde/chloranil tests: 2 %
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acetaldehyde in N,N-dimethylformamide (DMF), 2 % chloranil in the resin was suspended in a cleavage cocktail (50 % trifluoroacetic
DMF. 1H and 13C NMR spectra were measured on an ECZ 600R acid (TFA) and 50 % CH2Cl2) at room temperature for 1 h. The
spectrometer (JEOL) using deuterated solvents. Chemical shift cleavage cocktail with combined wash was evaporated under a
values (ppm) were corrected for residual solvent signals as internal stream of nitrogen, the crude products were dissolved in MeOH
standards [DMSO-d6: 2.50 for 1H NMR, 39.5 for 13C NMR; CD3OD: 3.30 (3 mL) and purified by HPLC (gradient: 40–80 % MeCN-H2O, 30 min)
for 1H NMR, 49.0 for 13C NMR; CDCl3: 7.26 for 1H NMR, 77.2 for to give PROTAC 1 (2.4 mg) in 1 % yield.
13
C NMR]. The splitting modes of the signals are as follows (singlet
(s), doublet (d), triplet (t), quartet (q), double of doublets (dd), Procedure for the synthesis of PROTAC 2 by amidation: Resin 2
multiplet (m), broad (br)). High-resolution mass spectrometry (50 mg, loading 2.5 mmol g 1) was swollen in CH2Cl2 (2 mL) for
(HRMS) was measured by electrospray ionization using Shimadzu 30 min, and washed with DMF (3 × 2 mL). The mixture of compound
IT-TOF MS (Shimadzu). 9 (204 mg, 0.375 mmol), HOBt (124 mg, 0.375 mmol), HBTU
(143 mg, 0.375 mmol) and N,N-diisopropylethylamine (97 mg,
0.75 mmol) in DMF was added to the resin and shaken overnight at
Solid-Phase Organic Synthesis room temperature, followed by washing with DMF (3 × 2 mL). The
resin was suspended in a cleavage cocktail (50 % TFA and 50 %
CH2Cl2) at room temperature for 1 h. The cleavage cocktail with
Procedure for loading of the amide linker and combined wash was evaporated under a stream of nitrogen, the
3-azidopropylamine onto a resin (synthesis of resin 6) crude products were dissolved in MeOH (3 mL) and purified by
Loading of amide linker: Aminomethyl polystyrene resin (50 mg, HPLC (gradient: 10–90 % MeCN-H2O containing 0.1 % TFA, 30 min)
loading 2.5 mmol g 1) was swollen in CH2Cl2 (2 mL) for 30 min, to give PROTAC 2 (2.1 mg) in 1 % yield.
washed with DMF (3 × 2 mL), neutralized in DMF/piperidine (5 : 1, Procedure for the synthesis of PROTAC 3 by urea formation: Resin
2 mL) for 30 min and washed with DMF (3 × 2 mL). Backbone amide 2 (50 mg, loading 2.5 mmol g 1) was swollen in CH2Cl2 (2 mL) for
linker of 4-(4-formyl-3-methoxyphenoxy)butanoic acid (90 mg, 30 min, and washed with DMF (3 × 2 mL). 4-Nitrophenyl chlorofor-
0.375 mmol), 1-hydroxybenzotriazole (HOBt, 51 mg, 0.375 mmol) mate was dissolve in THF (1 mL) and stirred at 40 °C for 30 min
were dissolved in DMF/CH2Cl2 (1 : 1, 2 mL, v/v) and N,N’-diisopropyl- and then added to the resin with N,N-diisopropylethylamine
carbodiimide (DIC, 59 μL, 0.375 mmol) was added. The resulting (97 mg, 0.75 mmol) and stirred for 24 h at room temperature. The
solution was added to resin. The reaction slurry was shaken at mixture of compound 10 (182 mg, 0.375 mmol), N,N-diisopropyle-
room temperature overnight, followed by wash with DMF (3 × 2 mL) thylamine (97 mg, 0.75 mmol) and 4-dimethylaminopyridine
and CH2Cl2 (3 × 2 mL). Acetaldehyde/Chloranil test confirmed the (DMAP, 10 mg, 0.075 mmol) in THF/DMF (1 mL) was added to the
absence of amino groups. resin and stirred for 16 h at room temperature, followed by washing
Loading of 3-azidopropylamine: The resin intermediate was swollen with DMF (3 × 2 mL). The resin was suspended in a cleavage cocktail
in CH2Cl2 (2 mL) for 30 min, and washed with DMF (3 × 2 mL). The (50 % TFA and 50 % CH2Cl2) at room temperature for 1 h. The
solution of 3-azidopropylamine (38 mg, 0.375 mmol) in DMF/AcOH cleavage cocktail with combined wash was evaporated under a
(10 : 1, 2 mL, v/v) was added to resin and shaken overnight at room stream of nitrogen, the crude products were dissolved in MeOH
temperature. NaBH(OAc)3 (80 mg, 0.375 mmol) in DMF/AcOH (20 : 1, (3 mL) and purified by HPLC (gradient: 40–80 % MeCN-H2O, 30 min)
2 mL, v/v) was added to the reaction mixture for 4 h, followed by to give PROTAC 3 (3.3 mg) in 1 % yield.
washing with DMF (3 × 2 mL). Acetaldehyde/Chloranil test con- Procedure for the synthesis of carboxylic acid resin 3: Resin 3 was
firmed the absence of amino groups. synthesized same manner as resin 1 via compound 5 condensation
Procedure for loading of pomalidomide onto a resin (synthesis of to the resin 4, reductive amination, compound 7 condensation, and
resin 1): Resin 6 (50 mg, loading 2.5 mmol g 1) was swollen in following allyl deprotection by Pd(OAc)2 catalyst with phenylsilane.
CH2Cl2 (2 mL) for 30 min, and washed with DMF (3 × 2 mL). The The procedure for allyl deprotection is as follows; Resin after the
mixture of compound 7 (124 mg, 0.375 mmol), HOBt (61 mg, compound 7 condensation (50 mg, loading 2.5 mmol g 1) was
0.375 mmol), 1-[bis(dimethylamino)methylene]-1H-benzotriazolium swollen in CH2Cl2 (2 mL) for 30 min, and washed with DMF (3 ×
3-oxide hexafluorophosphate (HBTU, 143 mg, 0.375 mmol) and N,N- 2 mL). The mixture of palladium(II) acetate (5.6 mg, 0.025 mmol)
diisopropylethylamine (DIPEA, 97 mg, 0.75 mmol) in DMF was and phenylsilane (270.5 mg, 2.5 mmol) in CH2Cl2 was added to the
added to the resin and shaken overnight at room temperature, resin and shaken overnight at room temperature, followed by
followed by washing with DMF (3 × 2 mL). washing with DMF (3 × 2 mL) for 2 times.
Procedure for reduction of the azide group of resin 1 (synthesis Procedure for the synthesis of PROTAC 4 by amidation: Resin 3
of resin 2): Resin 1 (50 mg, loading 2.5 mmol g 1) was swollen in (50 mg, loading 2.5 mmol g 1) was swollen in CH2Cl2 (2 mL) for
CH2Cl2 (2 mL) for 30 min, and washed with DMF (3 × 2 mL). 30 min, and washed with DMF (3 × 2 mL). The mixture of compound
Tris(hydroxypropyl)phosphine (THPP, 78 mg, 0.375 mmol) was dis- 10 (182.5 mg, 0.375 mmol), HOBt (124 mg, 0.375 mmol), HBTU
solved in water/DMF (1 : 9, 2 mL, v/v) and added to the resin shaken (143 mg, 0.375 mmol) and N,N-diisopropylethylamine (97 mg,
overnight at room temperature, followed by washing with DMF (3 × 0.75 mmol) in DMF was added to the resin and shaken overnight at
2 mL). room temperature, followed by washing with DMF (3 × 2 mL). The
resin was suspended in a cleavage cocktail (50 % TFA and 50 %
The resin 15 and 16 were synthesized from resin 4 in the same CH2Cl2) at room temperature for 1 h. The cleavage cocktail with
manner as resin 2, using 4-azidobutan-1-amine for resin 15 and 8- combined wash was evaporated under a stream of nitrogen, the
azidooctan-1-amine for resin 16 instead of 3-azidopropylamine. crude products were dissolved in MeOH (3 mL) and purified by
HPLC (gradient: 30–70 % MeCN-H2O, 30 min) to give PROTAC 4
Procedure for the synthesis of PROTAC 1 by CuAAC: Resin 1
(1.2 mg) in 1 % yield.
(50 mg, loading 2.5 mmol g 1) was swollen in CH2Cl2 (2 mL) for
30 min, and washed with DMF (3 × 2 mL). The mixture of 8 (202 mg, Procedure for the synthesis of PROTACs 5–7: The PROTACs 5–7
0.375 mmol), CuI (24 mg, 0.125 mmol) and N,N-diisopropylethyl- were synthesized in the same manner as PROTAC 2 synthesis by
amine (97 mg, 0.75 mmol) in DMF was added to the resin and using compound 17 instead of compound 7.
shaken for 24 h at room temperature, followed by washing with
DMF (3 × 2 mL). After performing the above coupling reaction twice,
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Keywords: BRD4 · H-PGDS · PROTAC · protein degradation · K. G. Wagner, J. Krönke, I. Sosič, M. Gütschow, C. Steinebach, ACS Med.
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solid-phase synthesis
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