A General Strategy for the Preparation of Thalidomide-Conjugate Linkers

^◊ These authors contributed equally

Dedicated to Victor Snieckus on the occasion of his 80^th birthday

Abstract

The synthesis of small-molecule linkers for installation of thalidomide-based conjugates is described. Linker properties have been recognized as vital to conjugate success in drug discovery and delivery systems. These small-molecule tethers act as linkages between molecules, can also aid in cell permeability, and act as solubilizing agents. This work shows our progress in synthesizing conjugates with a variety of linker characteristics. The adaptability and manipulation of these and other linkers holds potential in improving synthetic control of chemical connectivities toward therapeutic development.

Key words

PROTAC - thalidomide - conjugates - linker - pentafluoro­phenyl ester

• References and Notes

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• 15 General Procedure for the Synthesis of 4 A solution of 3 (0.691 g, 1.64 mmol) in DMF (15 mL) was stirred with (Pd/C (0.04 g, 10 mol%) under hydrogen for 1.5 h, filtered, and concentrated in vacuo. The crude product (0.148 g, 0.45 mmol) was then redissolved in DMF (6 mL), DIPEA (0.118 g, 0.16 mL, 0.92 mmol) was added with stirring, and the solution was cooled to 0 °C. Pentafluorophenyl trifluoroacetate (0.187 g, 0.12 mL, 0.67 mmol) was then added with stirring. The reaction mixture was allowed to come to ambient temperature for 2 h. The mixture was concentrated in vacuo, and purified by trituration with Et₂O to afford 0.175 g (79%) of 4. ¹H NMR (400 MHz, CDCl₃) δ = 7.99 (s, 1 H), 7.76 (dd, J = 8.4, 7.3 Hz, 1 H), 7.63 (dd, J = 7.4, 0.7 Hz, 1 H), 7.26 (dd, J = 8.5, 0.8 Hz, 1 H), 5.34 (d, J = 1.4 Hz, 2 H), 5.04–4.97 (m, 1 H), 2.98–2.74 (m, 3 H), 2.22–2.14 (m, 1 H). ESI-HRMS: m/z calcd for [C₂₁H₁₁F₅N₂O₇ + Na]⁺: 521.0379; found: 521.0368.
• 16 No decomposition observed after 5 weeks at –20 °C.
• 17 General Procedure for Coupling to 4 To a solution of corresponding free amine (1 equiv) in DMF was added DIPEA (3 equiv) under stirring. A solution of 4 (1.1 equiv) in DMF was added to the reaction mixture at ambient temperature. After 2 h the mixture was concentrated in vacuo and purified by silica gel flash chromatography to afford the title compound.
• 18 2-[(2-(2,6-Dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl)oxy]-N-[4-oxo-4-(piperidin-1-yl)butyl]acetamide (9) Purified by silica gel flash chromatography (5% MeOH in CHCl₃) to afford 0.119 g (75%) as a colorless oil. ¹H NMR (400 MHz, CDCl₃): δ = 8.70 (s, 1 H), 7.75 (dd, J = 8.4, 7.3 Hz, 1 H), 7.71 (t, J = 5.6 Hz, 1 H), 7.57 (dd, J = 7.4, 0.7 Hz, 1 H), 7.23 (dd, J = 8.5, 0.7 Hz, 1 H), 5.00–4.92 (m, 1 H), 4.73–4.60 (m, 2 H), 3.58–3.52 (m, 2 H), 3.45 (ddd, J = 14.7, 7.4, 6.0 Hz, 1 H), 3.41–3.33 (m, 3 H), 2.98–2.70 (m, 3 H), 2.42–2.36 (m, 2 H), 2.22–2.15 (m, 1 H), 1.97–1.88 (m, 2 H), 1.66–1.60 (m, 2 H), 1.59–1.49 (m, 4 H). ¹³C NMR (400 MHz, CDCl₃): δ = 170.80, 170.42, 168.04, 166.89, 166.54, 154.97, 137.01, 133.61, 120.51, 118.56 117.68, 77.20, 69.00, 49.42, 46.61, 42.78, 39.12, 31.34, 30.66, 26.48, 25.55, 24.84, 24.54, 22.73. EIS-HRMS: m/z calcd for [C₂₄H₂₈N₄O₇ + H]⁺: 485.2031; found: 485.2047.
• 19 2-{4-(4-Chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl}acetic Acid (JQ1-Acid) JQ1 (0.05g, 0.1099 mmol) was dissolved in formic acid (4.5 mL) and stirred for 4 d. The solvent was removed in vacuo to afford a fine yellow powder. The product was used without purification.
• 20 Perfluorophenyl 2-{4-(4-Chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl}acetate (16) To a solution of JQ1-acid (0.055 g, 0.136 mmol) in DMF (2 mL) was added DIPEA (0.17 mL, 0.123 g, 0.952 mmol) and pentafluro­phenyl trifluoroacetate (0.05 mL, 0.076 g, 0.272 mmol). The solution was stirred for 1 h and solvent was removed in vacuo. The residue was purified by silica gel flash chromatography (EtOAc/hexanes/THF = 1:1:1) to afford 0.0432 g (56%) as a yellow oil. ¹H NMR (400 MHz, CDCl₃): δ = 7.49–7.34 (m, 4 H), 4.71 (dd, J = 9.5, 4.6 Hz, 1 H), 4.08 (dd, J = 16.9, 9.5 Hz, 1 H), 3.91 (dd, J = 16.9, 4.6 Hz, 1 H), 2.73 (s, 3 H), 2.45 (d, J = 0.9 Hz, 3 H), 1.73 (d, J = 0.9 Hz, 3 H). ¹³C NMR (151 MHz, CDCl₃): δ = 167.62, 164.38, 154.65, 150.13, 141.90 140.26, 138.70, 137.03, 136.30, 132.22, 131.00, 130.97, 130.26, 129.83, 128.76, 53.57, 36.39, 14.40, 13.11, 11.85. HRMS (MALDI): m/z calcd for [C₂₅H₁₆ClF₅N₄O₂S + H]⁺: 567.0675; found: 567.0771.
• 21 2-{4-(4-Chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl}-N-[4-(2-{[2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl]oxy}acetamido)butyl]acetamide (17) To a solution of 1,4-diaminobutane (0.03 g, 0.371 mmol) in DMF (2 mL) was added DIPEA (0.065 mL, 0.048 g, 0.371 mmol) and 16 (0.021 g, 0.0371 mmol). The mixture was stirred for 1.5 h, concentrated in vacuo, and redissolved in DMF (1 mL). DIPEA (0.026 mL, 0.019 g, 0.0148 mmol) and 4 (0.028 g, 0.0557 mmol) were added and stirred overnight, The mixture was concentrated in vacuo and purified by silica gel flash chromatography (5–10% MeOH in CHCl₃) to afford 0.014 g (48%) of the title compound as a mixture of diastereomers. ¹H NMR (600 MHz, MeOD): δ = 8.34–8.29 (*m, 1 H), 8.12 (*q, J = 5.7 Hz, 1 H), 7.80 (dd, J = 8.4, 7.3 Hz, 1 H), 7.52 (d, J = 7.3 Hz, 1 H), 7.45–7.38 (m, 5 H), 5.10 (ddd, J = 12.4, 5.5, 3.1 Hz, 1 H), 4.77 (d, J = 1.7 Hz, 2 H), 4.63 (ddd, J = 9.1, 5.4, 1.1 Hz, 1 H), 3.44–3.32 (m, 4 H), 3.30–3.25 (m, 2 H), 2.86–2.77 (m, 1 H), 2.73–2.65 (m, 5 H), 2.43 (d, J = 2.5 Hz, 3 H), 2.10 (dddd, J = 10.7, 8.0, 4.9, 2.6 Hz, 1 H), 1.70–1.60 (m, 7 H); * exchangeable protons. ¹³ NMR (151 MHz, CDCl₃): δ = 174.4, 172.77, 172.68, 171.30, 171.27, 169.91, 168.24, 167.79, 166.24, 166.21, 157.00, 156.29, 152.19, 138.23, 138.09, 137.95, 134.87, 133.53, 133.18, 132.04, 132.02, 131.96, 131.31, 129.78, 121.90, 121.87, 119.37, 118.00, 69.57, 69.55, 55.23, 50.55, 50.54, 40.21, 40.19, 40.09, 40.06, 39.84, 38.88, 38.86, 32.14, 32.12, 27.77, 27.66, 27.64, 23.63, 23.61, 14.41, 12.92, 11.62. HRMS (MALDI): m/z calcd for [C₃₈H₃₇ClN₈O₇S + H]⁺ = 785.2267; found: 785.2232.
• 22 2-{4-(4-Chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl}-N-[4-(2-{[2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl]oxy}acetamido)butyl]acetamide (17) To a solution of the free amine 4 linker (0.021 g, 0.052 mmol) in DMF (1.5 mL) was added DIPEA (0.09 mL, 0.067 g, 0.5 mmol) and 16 (0.022 g, 0.039 mmol) and stirred overnight. The reaction mixture was stirred with K₂CO₃ (0.021 g) for 30 min, filtered, concentrated in vacuo, and purified by silica gel flash chromatography (5–10% MeOH in CHCl₃) to afford 0.025 g (81%) of the title compound as a mixture of diastereomers. Data are identical to ref. 22.
• 23 N-(1-{[2-(2,6-Dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl]oxy}-2-oxo-7,10,13-trioxa-3-azahexadecan-16-yl)-4-oxo-4-(piperidin-1-yl)butanamide (12) Purified by flash chromatography (5% MeOH in CHCl₃) to afford 0.011 g (79%) as a colorless oil. ¹H NMR (600 MHz, CDCl₃): δ = 9.43 (s, 1 H), 7.74 (dd, J = 8.4, 7.4 Hz, 1 H), 7.60 (t, J = 5.8 Hz, 1 H), 7.55 (dd, J = 7.5, 0.7 Hz, 1 H), 7.21 (dd, J = 8.4, 0.6 Hz, 1 H), 6.66 (t, J = 5.6 Hz, 1 H), 5.03–4.96 (m, 1 H), 4.65 (d, J = 2.7 Hz, 2 H), 3.67–3.64 (m, 4 H), 3.64–3.61 (m, 2 H), 3.58 (tt, J = 6.5, 2.7 Hz, 3 H), 3.53 (td, J = 5.7, 1.8 Hz, 4 H), 3.50–3.44 (m, 2 H), 3.43–3.39 (m, 2 H), 3.31 (qd, J = 6.4, 4.9 Hz, 2 H), 2.91–2.75 (m, 3 H), 2.66 (td, J = 6.7, 1.3 Hz, 2 H), 2.49 (t, J = 6.8 Hz, 2 H), 2.18–2.13 (m, 1 H), 1.87 (p, J = 6.4 Hz, 2 H), 1.82 (s, 1 H), 1.75 (q, J = 6.3 Hz, 2 H), 1.62 (td, J = 6.9, 4.9 Hz, 2 H), 1.58–1.48 (m, 4 H).¹³C NMR (600 MHz, CDCl₃): δ = 172.57, 171.34, 170.13, 168.33, 166.69, 166.62, 154.61, 136.93, 133.62, 119.68, 117.33, 70.41, 70.40, 70.15, 70.06, 69.39, 68.73, 68.22, 49.35, 46.40, 42.90, 37.31, 36.49, 31.59, 31.46, 29.23, 28.97, 28.80, 26.30, 25.54, 24.48, 22.69. ESI-HRMS: m/z calcd for [C₃₄H₄₇N₅O₁₁ + Na]⁺: 724.3163; found: 724.3168.
• 24 2-{[2-(2,6-Dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl]oxy}-N-[4-(piperidin-1-ylsulfonyl)butyl]acetamide (15) Purified by flash chromatography (5% MeOH in CHCl₃) to afford 0.016 g (47%) as a white solid. ¹H NMR (400 MHz, CDCl₃): δ = 8.08 (s, 1 H), 7.75 (dd, J = 8.4, 7.4 Hz, 1 H), 7.67 (s, 1 H), 7.56 (dd, J = 7.3, 0.7 Hz, 1 H), 7.20 (dd, J = 8.4, 0.7 Hz, 1 H), 5.05–4.98 (m, 1 H), 4.65 (d, J = 2.3 Hz, 2 H), 3.43 (sept, J = 6.9 Hz, 2 H), 3.29–3.12 (m, 4 H), 2.97–2.89 (m, 3 H), 2.89–2.71 (m, 2 H), 2.23–2.14 (m, 1 H), 1.99–1.87 (m, 2 H), 1.74 (dt, J = 14.4, 6.9 Hz, 2 H), 1.67–1.53 (m, 6 H). ¹³C NMR (400 MHz, CDCl₃): δ = 170.82, 168.00, 166.95, 166.55, 154.65, 137.10, 133.55, 120.08, 118.46, 117.64, 77.21, 68.49, 49.38, 48.51, 46.64, 38.44, 31.40, 28.27, 25.67, 23.81, 22.57, 20.55. ESI-HRMS: m/z calcd for [C₂₄H₃₀N₄O₈S + H]⁺: 535.1857; found: 535.1853.