A Novel Pot-Economy Approach to the Synthesis of Triantennary GalNAc-Oligonucleotide
<p>Standard approach to synthesize GalNAc-L96.</p> "> Figure 2
<p>Standard approach to synthesize GalNAc-L96.</p> "> Figure 3
<p>Standard approach to synthesize GalNAc-L96.</p> "> Figure 4
<p>New approach to synthesize GalNAc-L96. First pot.</p> "> Figure 5
<p>New approach to synthesize GalNAc-L96. Second pot.</p> "> Figure 6
<p>Synthesis of L-96 GalNAc phosphoramidite and L-96 GalNAc CPG.</p> "> Figure 7
<p>Part of synthesis in first pot.</p> "> Figure 8
<p>Part of synthesis in second pot.</p> "> Figure 9
<p>Synthesis of L-96 GalNAc phosphoramidite.</p> "> Figure 10
<p>Synthesis of L-96 GalNAc CPG.</p> ">
Abstract
:1. Introduction
2. Results and Discussion
2.1. Original Methods’ Issues
2.2. Alternative Synthesis Path
3. Materials and Methods
3.1. Materials
3.2. Methods
3.2.1. 1st Pot
- The following operations are demonstrated in Figure 7.
- To the solution of acid 11 (5.00 g, 10.61 mmol) in DCM (110 mL), CDI (1.72 g, 10.61 mmol, 1 eq.) was added by one portion, and the resulting mixture was stirred for 1 h.
- Then, tert-butyl(3-aminopropyl)carbamate (12) (1.85 g, 10.61 mmol, 1 eq.) was added, and the resulting solution was stirred for 8 h.
- After completion of the coupling reaction (TLC control), TFA (4.09 mL, 53.02 mmol, 5 eq.) was added, and the resulting solution was stirred for 24 h.
- After completion of the cleavage of protecting groups, the reaction mixture was evaporated under reduced pressure to remove the excess TFA.
- Then, the residue was dissolved in DCM (55 mL), and a solution of GalNAc acid chloride (21) in DCM (55 mL) (which was prepared from GalNAc acid (2) (14.23 g, 31.80 mmol, 3 eq.), oxalyl chloride (2.71 mL, 31.80 mmol, 3 eq.) and Et3N (4.43 mL, 31.78 mmol, 3 eq.) was added dropwise, by following the standard procedure using a catalytic amount of DMF). After stirring the reaction mixture for an additional 5 h, the resulting solution was concentrated in vacuo (55 °C, 1 h).
- Then, to the solution of crude Cbz-amine (3) (20.43 g, 10.60 mmol) in HFIP (45 mL) was added AlCl3 (4.24 g, 31.79 mmol, 3 eq.) at room temperature, and the resulting suspension was stirred at the same temperature for 6 h. After the completion of the reaction, as observed by TLC and MALDI−TOF analysis, a partial amount of HFIP was recovered by using the downward distillation method.
- The reaction mixture was diluted with DCM (100 mL). The reaction mixture was quenched with aqueous NaHCO3 (100 mL) and extracted with DCM (3 × 100 mL). The combined organic layers were washed with brine (100 mL), dried over anhydrous Na2SO4, filtered, and evaporated to give the 19.21 g crude desired product (15).
3.2.2. 2nd Pot
- The following operations are demonstrated in Figure 8.
- The crude residue of compound 15 was dissolved in DCM (55 mL), and the resulting solution was added dropwise to the solution of 12-(benzyloxy)-12-oxododecanoic acid chloride in DCM (55 mL) (which was prepared from 12-(benzyloxy)-12-oxododecanoic acid (5) (3.40 g, 10.60 mmol, 1 eq.), oxalyl chloride (902.92 µL, 10.60 mmol, 1 eq.) and Et3N (1.48 mL, 10.60 mmol, 1 eq.), by following the standard procedure using a catalytic amount of DMF). After stirring the reaction mixture for an additional 5 h, the resulting solution was concentrated in vacuo (55 °C, 1 h).
- Then, the residue was dissolved in DCM (100 mL), and to the solution of benzyl benzoate (6), dichlorodiphenylmethane (16) (3.02 g, 12.72 mmol, 1.2 eq.) was added, followed by FeCl3 (86.1 mg, 530 µmol, 5.0 mol%), and the resulting mixture was stirred at room temperature for 2 h.
- Then, (3R,5S)-5-[[bis(4-methoxyphenyl)-phenylmethoxy]methyl]pyrrolidin-3-ol (9) (5.34 g, 12.72 mmol, 1.2 eq.), DIPEA (2.77 mL, 15.90 mmol, 1.5 eq.), and DMAP (259.0 mg, 2.12 mmol, 0.2 eq.) were added to the reaction mixture and stirred for 8 h at room temperature.
- The mixture was poured into water (150 mL) and extracted with DCM (2 × 100 mL). The combined organic layers were washed with brine (200 mL), dried over anhydrous Na2SO4, filtered, and concentrated.
- The resulting residue was purified by flash column chromatography on silica gel with DCM-EtOH-Et3N (3%) as an eluent from 20:1 to 5:1 (5:1 Rf = 0.6) to afford 15.59 g. of the desired product (10). Total yield: 61%.
3.2.3. Chemical Modification for Further Oligonucleotide Synthesis
- Alcohol (10) (2.407 g, 1 mmol, 1 eq) was dissolved in DCM (20 mL), and to a clear solution in an argon atmosphere, 3-((bis(diisopropylamino)phosphaneyl)oxy)propanenitrile (18) (0.7525 g, 2.5 mmol, 2.5 eq) and DCI (0.118 g, 1 mmol, 1 eq) in 10 mL of MeCN were added. The reaction mixture was stirred in an argon atmosphere for 12 h. Then, the reaction mixture was poured into water, extracted with DCM, and dried over sodium sulfate. The organic phase was evaporated under reduced pressure. The crude material was precipitated with ethyl acetate and dried in vacuo to afford 2.1 g, a yield of 81% with 98.5% purity.
- 3.
- We charged (1.0 g, 0.4 mmol, 10 eq) compound 10 in a 25 mL round bottom flask and dissolved it in 8 mL of a 1:1 v/v pyridine-DMF mixture. Sequentially, we added (12 mg, 0.1 mmol, 2.5 eq) of DMAP, 1.0 g of succinylated LCAA-CPG 40 μmol/g, and diisopropylcarbodiimide (62 μL, 0.4 mmol, 10 eq), under stirring. We left the mixture at ambient temperature for 48 h and gently shook the mix daily. We gently shook the mix and immediately took a small portion, 150 μL, of the CPG suspension into a 1.5 mL tube and separated the CPG by decanting. We washed the CPG twice with 1 mL of DCM, twice with 2 mL of acetonitrile, and 5 times with 1 mL of diethyl ether. We dried the CPG in high vacuo for 1 h.
- 4.
- We accurately transferred ~15 mg of CPG 20 into a 25 mL flask and added 10 mL 5% TFA in DCM to it. After 15 min of exposure, we measured the absorbance of the mixture at 505 nm using a UV–Vis spectrophotometer, with DCM used as a blank, and we calculated the loading of GalNAc CPG using the following equation: L (μmol/g) = (V × 1000 × Abs)/78 × m, where m is the mass of 20 (in mg), Abs is the absorbance of the mixture at 505 nm, V is the total volume of the solution (mL), and 78 is the extinction coefficient of dimethoxytrityl cation (ml/μmol). The loading of the solid support 20 was calculated at ~32 μmol/g CPG. The yield of this step is over 80%. In addition, we set up the synthesis using a PolyGen oligo synthesizer, using 5 mg of the obtained CPG.
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Gusev, A.E.; Ivanov, V.N.; Dmitriev, N.A.; Kholstov, A.V.; Vasilichin, V.A.; Kofiadi, I.A.; Khaitov, M.R. A Novel Pot-Economy Approach to the Synthesis of Triantennary GalNAc-Oligonucleotide. Molecules 2024, 29, 5959. https://doi.org/10.3390/molecules29245959
Gusev AE, Ivanov VN, Dmitriev NA, Kholstov AV, Vasilichin VA, Kofiadi IA, Khaitov MR. A Novel Pot-Economy Approach to the Synthesis of Triantennary GalNAc-Oligonucleotide. Molecules. 2024; 29(24):5959. https://doi.org/10.3390/molecules29245959
Chicago/Turabian StyleGusev, Artem Evgenievich, Vladimir Nikolaevich Ivanov, Nikolai Andreevich Dmitriev, Aleksandr Viktorovich Kholstov, Vladislav Aleksandrovich Vasilichin, Ilya Andreevich Kofiadi, and Musa Rakhimovich Khaitov. 2024. "A Novel Pot-Economy Approach to the Synthesis of Triantennary GalNAc-Oligonucleotide" Molecules 29, no. 24: 5959. https://doi.org/10.3390/molecules29245959
APA StyleGusev, A. E., Ivanov, V. N., Dmitriev, N. A., Kholstov, A. V., Vasilichin, V. A., Kofiadi, I. A., & Khaitov, M. R. (2024). A Novel Pot-Economy Approach to the Synthesis of Triantennary GalNAc-Oligonucleotide. Molecules, 29(24), 5959. https://doi.org/10.3390/molecules29245959