Development of a Scalable Chiral Synthesis of MK-3281, an Inhibitor of the Hepatitis C Virus NS5B Polymerase

Abstract

The development of a scalable chiral synthesis for the HCV NS5B inhibitor MK-3281 is being reported. Several alternative routes were explored and are being described.

Key words

chiral pool - MK-3281 - HCV NS5B polymerase inhibitor - medicinal chemistry - heterocycles

References and Notes

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  WHO Factsheet No. 164: Hepatitis C, accessed 09 May 2007, http://www.who.int/mediacentre/factsheets/fs164/en/print.html.

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• 5 Narjes F. Crescenzi B. Ferrara M. Habermann J. Colarusso S. Rico Ferreira MdR. StansfieldI . Mackay A. Conte I. Ercolani C. Zaramella S. Palumbi M.-C. Meuleman P. Leroux-Roels G. Giuliano C. Fiore F. Di Marco S. Baiocco P. Koch U. Migliaccio G. Altamura S. Laufer R. De Francesco R. Rowley M. J. Med. Chem.  2011,  54:  289 
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1

New address: Stefania Colarusso, IRBM Science Park Srl, Via Pontina km. 30.600, 00040 Pomezia (Rome), Italy; Jörg Habermann, European Patent Office, Bayerstrasse 34, 80335 München, Germany.

12

Experimental Procedure for the Synthesis of 1Preparation of 15
A suspension of CaCl₂ (49.9 g, 450 mmol) in dry THF (400 mL) was cooled to 0 ˚C, and NaBH₄ (34.0 g, 900 mmol) was added under stirring. To the resulting suspension, a solution of Boc-Ser(TBDMS)OMe (100 g, 300 mmol) in dry EtOH (400 mL) was added dropwise over the course of 2 h. Stirring was then continued over night. The mixture was poured onto crushed ice (600 g) and a sat. aq NH₄Cl solution (600 mL) was added. This mixture was left stirring until evolution of gas had ceased, then EtOAc was added. The phases were separated, the aqueous phase was treated with
1 N HCl to dissolve all material, then extracted twice with EtOAc. The combined organic phases were extracted with sat. aq NaHCO₃ solution and with brine, then dried over Na₂SO₄. After filtration, the volatiles were evaporated in vacuo to leave a colorless oil. The material was supported on silica gel and loaded on top of 1 kg of silica gel on a sintered frit. of CH₂Cl₂ (5 L) was allowed to flow through, then the product was eluted with of EtOAc (5 L). The solvent was evaporated in vacuo leaving 15 as clear oil (66 g, 72%). ^¹H NMR (400 MHz, CDCl₃): δ = 5.15 (br s, 1 H), 3.89-3.78 (m, 3 H), 3.75-3.63 (m, 2 H), 2.71 (br s, 1 H), 1.47 (s, 9 H), 0.92 (s, 9 H), 0.1 (s, 6 H).
Preparation of 16
A solution of Ph₃P (30.9 g, 118 mmol) in THF-MeCN (9:1, 1160 mL) was treated dropwise over 15 min with DIAD (22.91 mL, 118 mmol) at 0 ˚C. After 15 min, a solution of 15 (24 g, 79 mmol) in THF (120 mL) was added dropwise over 30 min. A white solid formed upon addition. The ice-water bath was removed and stirring continued overnight at r.t. ^¹H NMR control showed formation of product and consumption of the starting material after 24 h and represented the most unambiguous way to assess completeness of the reaction. All volatiles were evaporated in vacuo, and the residual material was treated with PE-CH₂Cl₂ (95:5) to precipitate most of the triphenylphosphine oxide. The precipitate was filtered off and washed with small portions of the same solvent mixture until no more desired product was detectable by TLC in the filtrate. The filtrate was evaporated in vacuo leaving ca. 40 g of crude product. Column chromatography on 600 g silica gel (PE-EtOAc = 95:5, 6 L) afforded after evaporation of the eluent 16.05 g (68%) of 16. ^¹H NMR (400 MHz, CDCl₃):
δ = 3.81 (dd, 1 H, J = 4.73, 11.39 Hz), 3.63 (dd, 1 H, J = 4.87, 11.39 Hz), 2.61-2.54 (m, 1 H), 2.26 (d, 1 H, J = 6.08 Hz), 2.07 (d, 1 H, J = 3.59 Hz), 1.46 (s, 9 H), 0.92 (s, 9 H), 0.09 (s, 3 H), 0.08 (s, 3 H).
Preparation of 17
A solution of 16 (25 g, 87 mmol) in THF (250 mL) and Et₂O (250 mL) was cooled to 0 ˚C and treated dropwise over 20 min with 1 M TBAF in THF (91 mL, 91 mmol). The resulting solution was stirred at 0 ˚C for 30 min. The reaction mixture was quenched by the addition of sat. aq NaHCO₃ solution (500 ml) and extracted into Et₂O-PE (4:1, 300 mL + 200 mL). The organic layers were collected, washed with brine, dried over Na₂SO₄, and after filtration evaporated in vacuo, keeping the water bath at r.t. The residual oil (ca. 42 g) was dissolved in dry CH₂Cl₂ (500 mL) and Et₃N (15.8 mL, 113 mmol) and cooled to 0 ˚C. DMAP (1.06 g, 8.7 mmol) was added, followed by 4-nitro-benzenesulfonyl chloride (21.2 g, 96 mmol). The resulting orange heterogeneous mixture was stirred at r.t. overnight. After dilution with CH₂Cl₂ the mixture was washed with sat. aq NaHCO₃ solution, H₂O, and brine. After drying over Na₂SO₄, filtration, and evaporation in vacuo a residue was obtained which was purified by chromatography (PE-EtOAc, 8:2, 750 g silica gel) to afford 19.89 g (57%) of 17 as an off-white solid. ^¹H NMR (400 MHz, CDCl₃): δ = 8.48-8.44 (m, 2 H), 8.22-8.18 (m, 2 H), 4.37 (dd, 1 H, J = 4.20, 11.30 Hz), 3.99 (dd, 1 H, J = 7.36, 11.30 Hz), 2.78-2.71 (m, 1 H), 2.30 (d, 1 H, J = 6.42 Hz), 2.05 (d, 1 H, J = 3.58 Hz), 1.35 (s, 9 H).
Preparation of 20
A solution of 2 ⁵ (19 g, 54.4 mmol) in DMF (360 mL) was treated with CsF (33.0 g, 218 mmol) in one portion. The resulting fluorescent yellow mixture was stirred 20 min at r.t. then a solution of 17 (24.9 g, 69.6 mmol in 130 mL of DMF) was added dropwise over 30 min. The resulting orange clear solution was stirred at 30 ˚C overnight. The reaction mixture was cooled to 0 ˚C, and powdered KOt-Bu (8.54 g, 76 mmol) was added slowly to the reaction mixture. After 1.5 h the reaction was quenched by the addition of sat. aq NH₄Cl solution and the product extracted into EtOAc. The combined organic layers were washed with H₂O and brine, dried over Na₂SO₄, filtered, and evaporated in vacuo. The residual material was purified by chromatography (PE-EtOAc, 80:20, 600-700 g silica gel) affording 23.2 g (85%) of 20. C₃₀H₃₆N₂O₅; MS (ES⁺): m/z = 527 [M + Na]⁺. ^¹H NMR (400 MHz, DMSO-d ₆): δ = 8.36 (s, 1 H), 7.93-7.86 (m, 1 H), 7.73-7.62 (m, 1 H), 7.58-7.46 (m, 1 H), 7.35-7.11 (m, 3 H), 4.40-4.25 (m, 2 H), 3.90-3.65 (m, 6 H), 2.75-2.64 (m, 1 H), 2.03-1.28 (m, 20 H).
Preparation of 6
Compound 20 (14 g, 27.7 mmol) was treated with CH₂Cl₂-TFA (220 mL, 9:1) at r.t. for 1 h. The reaction was diluted with CH₂Cl₂, and sat. aq NaHCO₃ was slowly added. The mixture was extracted exhaustively with CH₂Cl₂. The combined organic phases were washed with brine, dried over Na₂SO₄, and filtered. After evaporation in vacuo 11.21 g (quant.) of off-white 6 were obtained which were used without further purification. C₂₅H₂₈N₂O₃; MS (ES⁺):
m/z = 405 [M + H]⁺.
Preparation of 21
A solution of 6 (18.4 g, 45 mmol) in THF (131 mL) was treated dropwise with 2,2,2-trifluoroethyl formate (7 mL, 55 mmol) and stirred overnight at r.t. All volatiles were evaporated in vacuo, and the residual material was dissolved in THF (400 mL). Borane dimethylsulfide complex in THF (114 mL, 228 mmol) was added dropwise. The resulting yellow solution was stirred at r.t. for 20 h. The reaction was quenched by the careful addition of HCl-MeOH (1.25 M, 100 mL), and the resulting solution was heated in an open flask for 2 h to destroy all the boron adducts and remove B(OMe)₃. All remaining volatiles were then evaporated in vacuo. The residual material was partitioned between sat. aq NaHCO₃ and EtOAc. The combined organic layers were washed with brine, dried over Na₂SO₄, and evaporated to afford a residue which was purified by chromatography (EtOAc-PE, 8:2 + 1% Et₃N). After evaporation of the eluents in vacuo 21 was obtained as a colorless solid (14.9 g, 79%). C₂₆H₃₀N₂O₃; MS (ES⁺): m/z = 419 [M + H]⁺. ^¹H NMR (400 MHz, DMSO-d ₆): δ = 8.15 (s, 1 H), 7.89 (d, 1 H, J = 8.49 Hz), 7.68 (dd, 1 H, J = 1.35, 8.49 Hz), 7.55-7.49 (m, 1 H), 7.34-7.24 (m, 3 H), 4.51 (d, 1 H, J = 15.23 Hz), 4.27 (dd, 1 H, J = 4.33, 12.13 Hz), 3.88 (s, 3 H), 3.73 (dd, 1 H, J = 8.42, 12.13 Hz), 3.50 (dd, 1 H, J = 10.28, 15.23 Hz), 2.87-2.77 (m, 1 H), 2.74-2.63 (m, 1 H), 2.48 (s, 3 H), 2.14-1.50 (m, 8 H), 1.44-1.10 (m, 3 H).
Preparation of 22
To a solution of Boc-amino acetaldehyde (5.7 g, 35.5 mmol) in dry MeOH (93 mL) was added a mixture of 21 (14.9 g, 35.5 mmol), AcOH (4.1 mL, 71.0 mmol), and NaOAc (2.9 g, 35.5 mmol) in dry MeOH (260 mL), and the mixture was stirred at r.t. for 15 min. Then Pd/C (10 mol%, 5.67 g, 5.34 mmol) was added, the mixture was degassed thoroughly, and H₂ atmosphere was applied. The resulting mixture was stirred under H₂ atmosphere at 63 ˚C for 5 h, then at 55 ˚C overnight. The mixture was cooled to r.t., degassed, and flushed with argon. Filtration through Celite with MeOH and EtOAc as solvent afforded after evaporation in vacuo a residue (26.9 g) that was purified by chromatography (PE-EtOAc = 2.5:1 to 1.5:1) to give 22 (16.4 g, 82%). C₃₃H₄₃N₃O₅; MS (ES⁺): m/z = 562 [M + H]⁺. ^¹H NMR (400 MHz, CDCl₃): δ = 8.11 (s, 1 H), 7.90 (d, 1 H, J = 8.36 Hz), 7.68 (d, 1 H, J = 8.36 Hz), 7.57-7.51 (m, 1 H), 7.34-7.26 (m, 3 H), 6.70-6.63 (m, 1 H), 4.56 (d, 1 H, J = 14.78 Hz), 4.26 (dd, 1 H, J = 4.86, 12.26 Hz), 3.97 (dd, 1 H, J = 9.92, 12.26 Hz), 3.88 (s, 3 H), 3.74-3.62 (m, 1 H), 3.06-2.94 (m, 3 H), 2.75-2.56 (m, 3 H), 2.41 (s, 3 H), 2.01-1.63 (m, 7 H), 1.44-1.32 (m, 3 H), 1.37 (s, 9 H).
Preparation of 23
TFA (120 mL) was added at r.t. to a solution of 22 (16.4 g, 15.3 mmol) in dry CH₂Cl₂ (370 mL), and the mixture was stirred for 1.5 h. Evaporation to dryness gave a residue that was dissolved in CH₂Cl₂ (450 mL), treated with 2 M HCl-Et₂O (65 mL) and evaporated again. This treatment was repeated twice. The residue obtained was dried under high vacuum for 2 h. The light brown powder (23, 13.3 g, 87%) was used as such. C₂₈H₃₅N₃O₂˙2HCl; MS (ES⁺): m/z = 462 [M + H]⁺.
Preparation of 24
NaOAc (6.15 g, 75 mmol) and 37% aq HCHO (4.3 mL, 57.5 mmol) were added to a stirred solution of 29 (13.36 g, 25 mmol) in dry MeOH (200 mL), and the mixture was stirred at r.t. for 10 min. Pd/C (10 mol%, 2.66 g, 2.5 mmol) was added portionwise. The mixture was thoroughly degassed and H₂ atmosphere (balloon) was applied. The reaction was stirred for 20 h at r.t. The catalyst was filtered off over Celite, and the filtrate was concentrated in vacuo. The residual material was dissolved in EtOAc, washed with sat. aq NaHCO₃ and brine, dried over Na₂SO₄, and concentrated in vacuo to give 29 g of crude product. Chromatography (silica gel, EtOAc-MeOH-Et₃N = 100:6:2) afforded a main fraction that was triturated with Et₂O-pentane. After filtration a pale yellow solid was obtained which was dried in vacuo to yield pure methyl ester 24 (9.8 g, 80%). C₃₀H₃₉N₃O₃; MS (ES⁺): m/z = 490 [M + H]⁺. ^¹H NMR (400 MHz, DMSO-d ₆): δ = 8.12 (s, 1 H), 7.90 (d, 1 H, J = 8.48 Hz), 7.68 (d, 1 H, J = 8.48 Hz), 7.58-7.51 (m, 1 H), 7.36-7.26 (m, 3 H), 4.56 (d, 1 H, J = 14.96 Hz), 4.29 (dd, 1 H, J = 4.91, 12.06 Hz), 4.05-3.96 (m, 1 H), 3.87 (s, 3 H), 3.76-3.67 (m, 1 H), 3.07-2.98 (m, 1 H), 2.81-2.63 (m, 3 H), 2.36 (s, 3 H), 2.38-2.32 (m, 2 H), 2.17 (s, 6 H), 2.04-1.64 (m, 6 H), 1.60-1.12 (m, 4 H).
Preparation of 1
Freshly prepared 1 M aq NaOH (85 mL, 85 mmol) was added dropwise under N₂ atmosphere to a solution of 24 (20.38 g, 41.6 mmol) in THF (100 mL) and MeOH (100 mL), and the mixture was stirred at 60 ˚C for 4 h. The mixture was concentrated in vacuo to ca. 10% of its volume, then H₂O (200 mL) was added, followed by dropwise addition of 1 N aq HCl (85 mL). The aqueous layer was extracted with n-BuOH (1 × 500 mL, then 2 × 250 mL), and the organic layer was washed twice with small amounts of ice-cold water, dried over Na₂SO₄, and concentrated to give a residue which was dissolved in CH₂Cl₂ and filtered. Evaporation to dryness afforded a residue that was taken into MeCN, and 1 N aq HCl (100 mL) was added. The resulting solution was evaporated to dryness, and this operation was repeated twice, using 40 mL of 1 N HCl each time. The material was dried under high vacuum overnight to remove H₂O, then was triturated with hot MeCN, and filtered to give 20.8 g (91%) of 1 (bishydrochloride salt, 20.8 g, >99% ee, 99.2% purity). C₂₉H₃₇N₃O₃˙2HCl. MS (ES⁺): m/z = 476 [M + H]⁺; [α]_D ^²0 +55.5 (c 1.0, MeCN:H₂O, 1:1). ^¹H NMR (free base, 400 MHz, DMSO-d ₆): δ = 8.11 (s, 1 H), 7.86 (d, 1 H, J = 8.45 Hz), 7.66 (d, 1 H, J = 8.45 Hz), 7.56-7.49 (m, 1 H), 7.34-7.25 (m, 3 H), 4.54 (d, 1 H, J = 14.69 Hz), 4.28 (dd, 1 H, J = 4.62, 12.27 Hz), 4.00 (dd, 1 H, J = 9.65, 12.27 Hz), 3.71 (dd, 1 H, J = 10.06, 15.09 Hz), 3.08-2.97 (m, 1 H), 2.81-2.63 (m, 3 H), 2.43-2.37 (m, 2 H), 2.37 (s, 3 H), 2.20 (s, 6 H), 2.04-1.64 (m, 6 H), 1.58-1.09 (m, 5 H). Anal. Calcd for C₂₉H₃₉Cl₂N₃O₃: C, 63.50; H, 7.17; N, 7.66. Found: C, 63.04; H, 6.89; N, 7.24.