From bead to flask: Synthesis of a complex β-amido-amide for probe-development studies

Summary A concise synthesis of benzimidazole-substituted β-amido-amide LLW62 is presented. The original synthesis of compounds related to LLW62 was developed on Rink resin as part of a “one-bead, one-compound” combinatorial approach for on-bead screening purposes. The current synthesis is carried out in solution and is amenable to scale-up for follow-up studies on LLW62 and investigations of related structures. The key step involves the use of a β-amino acid-forming three-component reaction (3CR), the scope of which defines its role in the synthetic strategy.


Materials and instrumentation:
Unless otherwise specified, all commercially available reagents were used as received. All reactions using dried solvents were carried out under an atmosphere of argon in flame-dried glassware with magnetic stirring. Dry solvent was dispensed from a solvent purification system that passes solvent through two columns of dry neutral alumina. 1 H NMR spectra and proton-decoupled 13 C NMR spectra were obtained on a 300, 400 or 600 MHz Varian NMR spectrometer. Chemical shifts () are reported in parts per million (ppm) relative to TMS (s, 0). Multiplicities are given as: s Abbreviations for frequently used chemicals will be seen as follows: dichloromethane (DCM), ethanol (EtOH), ethyl acetate (EtOAc), methanol (MeOH), tetrahydrofuran (THF), triethylamine (TEA).
Hexanes were added and the solid formed was filtered and then dissolved in S5 DCM, and the organic layer was washed with brine. The organic layer was dried over Na 2 SO 4 , and the solvent was removed under reduced pressure yielding 0.124 g (63%) of product as a slightly brown solid. 1 154.0,147.1,142.7,138.6,131.2,130.5,127.0,126.3,125.1,123.7,120.4,120.0,119.1,119.0,111.4,105.2,54.1,52.7,43.1,34.5,31.6,29.9,23.6;IR (neat): 2959, 2216 cm −1 . Aldehyde 4 was prepared as described in the literature [1]. Concentrated H 2 SO 4 (0.575 mL, 11 mmol) was added to a solution of 4-fluoro-3-nitrobenzoic acid (7, 1.00 g, 5.4 mmol) in MeOH (25 mL) at room temperature and the mixture was heated under reflux for 6 hours. After cooling to room temperature, EtOAc was added and MeOH was removed under reduced pressure. The resulting mixture was then diluted with water and the aqueous phase was neutralized with 1 M NaOH. The aqueous phase was extracted with DCM (2 × 20 mL), and then the combined organic extracts were dried over Na 2 SO 4 and concentrated.

S7
The aqueous layer was then basified to pH 10 with a 10% NaOH solution (15 mL). The organic layer was then separated and the aqueous layer extracted with DCM (2 × 20 mL). Combined organic extracts were washed with brine and NaHCO 3 and dried over Na 2 SO 4 . Purification by flash chromatography (5 to 10% MeOH/DCM, 0.2% TEA) afforded the title compound as a yellow oil (0.768 g, 99% Compound 16 (0.228 g, 0.74 mmol) was added to a flame-dried flask, and the flask was purged with Ar. 10% Pd on activated carbon (0.057 g) was added to the flask, followed by dry MeOH (5 mL), and the flask was further purged with Ar.
The Ar needle was removed and a balloon of H 2 (g) was added. After briefly purging with H 2 (g) to remove all Ar, the reaction was stirred under an H 2 (g) atmosphere overnight. After 17 hours, the H 2 balloon was removed and reaction contents were filtered through celite and concentrated under reduced pressure to give a crude mixture of amine compound as a red oil (0.201 g). This crude mixture appeared pure by NMR and was carried on to the following reaction without further purification.

Compound 29
The carboxylic acid compound 28 (0.366 g, 0.57 mmol) was dissolved in THF (5.7 mL) and cooled to −42 °C. TEA (0.116 g, 1.1 mmol) was added, followed by ethyl chloroformate (0.093 g, 0.86 mmol). The reaction was stirred for 1 hour, and then NH 3 (g) was bubbled into the solution for 30 minutes while coming to room temperature. The reaction mixture was stirred overnight at room temperature. The crude mixture was quenched with ethanol (5 mL) and the solvent was evaporated. The residue was taken up in H 2 O and DCM. The product was extracted with DCM, and the combined organic layers were dried, filtered and concentrated to yield 0.239 g (65%) of product as a white solid. 1 154.20, 153.62, 146.74, 143.25, 135.16, 132.19, 129.94, 126.63, 123.70, 121.54, 119.66, 119.08, 118.76, 117.07, 110.24, 79.57, 53.85, 52.85, 46.11, 42.89, 42.71, 34.28, 31.40, 28.90, 28.34, 23.47 To a solution of the compound 29 (0.118 g, 0.18 mmol) in anhydrous DCM (3 mL) at 0 °C was added trifluoroacetic acid (0.6 mL). The reaction mixture was allowed to reach room temperature and was stirred for 3 h. Then, a saturated aqueous solution of sodium bicarbonate (5 mL) was added and the crude product was extracted with DCM. The solvent was removed under reduced pressure yielding 0.087 g (87%) of product as a slightly yellow solid. The compound was submitted to the next step without further purification.