Practical Synthetic Method for Ogipeptin Derivatives

Abstract

In synthesizing novel derivatives of the natural cyclic peptides the ogipeptins, we established a simple and practical solid-phase peptide synthesis and macrocyclization method. By using this method, it became possible to obtain skeleton-modified ogipeptin derivatives with dehydroxylation of the β-hydroxy-α,γ-diaminobutyric acid, replacement of the (Z)-dehydrobutyrine residue, or replacement of the arginine residue.

Key words

ogipeptins - antibiotics - medicinal chemistry - cyclic peptides - solid-phase peptide synthesis - macrocyclization

Publikationsverlauf

Eingereicht: 01. November 2022

Angenommen nach Revision: 17. November 2022

Accepted Manuscript online:
17. November 2022

Artikel online veröffentlicht:
05. Dezember 2022

• References and Notes

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• 17 tert-Butyl (2S,3R)-2-({(2S)-2-[(tert-butoxycarbonyl)amino]-4-[9H-fluoren-9-yl(methoxycarbonyl)amino]butanoyl}amino)-3-hydroxybutanoate (3a): Typical Procedure To a solution of Boc-Dab(Fmoc)-OH (1.00 g, 2.27 mmol) in DMF (23 mL) were added l-threonine tert-butyl ester hydrochloride (0.53 g, 2.50 mmol), HATU (1.29 g, 3.41 mmol), and DIPEA (1.56 mL, 9.08 mmol). The mixture was stirred for 1.5 h at rt, then diluted with EtOAc (50 mL), brine (25 mL), and water (25 mL). The organic layer was separated and the aqueous layer was extracted with EtOAc (50 mL). The combined organic layer was washed with sat. aq NaHCO₃ (50 mL) and brine (50 mL), dried (Na₂SO₄), filtered, and concentrated. The resulting residue was purified by flash column chromatography (silica gel, hexane to 50% EtOAc–hexane) to afford a white solid; yield: 1.21 g (89%). ¹H NMR (400 MHz, DMSO-d ₆): δ = 7.89 (d, J = 7.3 Hz, 2 H), 7.73 (d, J = 8.5 Hz, 1 H), 7.69 (dd, J = 7.6, 2.1 Hz, 2 H), 7.41 (t, J = 7.3 Hz, 2 H), 7.35–7.30 (m, 3 H), 7.02 (d, J = 7.9 Hz, 1 H), 4.96 (d, J = 4.9 Hz, 1 H), 4.30–4.20 (m, 3 H), 4.17–4.04 (m, 3 H), 3.11–3.02 (m, 2 H), 1.86–1.79 (m, 1 H), 1.64–1.59 (m, 1 H), 1.38 (overlapped, 18 H), 1.05 (d, J = 6.1 Hz, 3 H). ¹³C NMR (100 MHz, DMSO-d ₆): δ = 172.2, 169.6, 156.0, 155.3, 143.9, 140.7, 127.6, 127.1, 125.1, 120.1, 80.5, 78.1, 66.4, 65.3, 58.0, 52.0, 46.7, 37.3, 32.0, 28.2, 27.7, 20.2. HRMS (ESI): m/z [M + H]⁺ calcd for C₃₂H₄₄N₃O₈: 598.3123; found: 598.3141. tert-Butyl (2Z)-2-[((2S)-2-[(tert-Butoxycarbonyl)amino]-4-{[(9H-fluoren-9-ylmethoxy)carbonyl]amino}butanoyl)amino]but-2-enoate (4) A solution of the Martin sulfurane (966 mg, 1.44 mmol) in anhydrous CH₂Cl₂ (4.5 mL) was added dropwise to a solution of compound 3a (477 mg, 0.80 mmol) in anhydrous CH₂Cl₂ (9.5 mL) at 0 ℃ under a N₂ atmosphere. The mixture was stirred for 30 min at 0 ℃ under N₂, diluted with sat. aq NaHCO₃ (30 mL), and extracted with CH₂Cl₂. The organic layer was washed with brine, dried (Na₂SO₄), filtered, and concentrated. The residue was purified by flash column chromatography (silica gel, hexane to 40% EtOAc–hexane) to give a colorless solid; yield: 387 mg (84%). ¹H NMR (400 MHz, DMSO-d ₆): δ = 9.07 (s, 1 H), 7.89 (d, J = 7.3 Hz, 2 H), 7.69 (d, J = 7.3 Hz, 2 H), 7.42 (t, J = 7.3 Hz, 2 H), 7.35–7.27 (m, 3 H), 6.99 (d, J = 7.9 Hz, 1 H), 6.42 (q, J = 6.9 Hz, 1 H), 4.31 (br d, J = 6.1 Hz, 2 H), 4.22 (t, J = 7.0 Hz, 1 H), 4.04 (q, J = 7.3 Hz, 1 H), 3.08 (m, 2 H), 1.83 (m, 1 H), 1.68 (m, overlapped, 1 H), 1.65 (d, J = 6.3 Hz, 3 H), 1.40–1.38 (overlapped, 18 H). ¹³C NMR (100 MHz, DMSO-d ₆): δ = 170.8, 163.3, 156.1, 155.3, 143.9, 140.7, 130.9, 128.9, 127.6, 127.3, 127.1, 125.1, 121.4, 120.1, 120.0, 80.2, 78.1, 65.3, 52.2, 46.7, 37.4, 32.0, 28.2, 27.6, 13.3. HRMS (ESI): m/z [M + H]⁺ calcd for C₃₂H₄₂N₃O₇: 580.3017; found: 580.3053. (2Z)-2-({(2S)-2-(Decanoylamino)-4-[9H-fluoren-9-yl(methoxycarbonyl)amino]butanoyl}amino)but-2-enoic acid (6a): Typical Procedure Compound 4 (500 mg, 0.86 mmol) was treated with 30% TFA in CH₂Cl₂ (10 mL) at rt, and the mixture was stirred for 3 h. The mixture was then concentrated and dried in vacuo. The residue was dissolved in THF (9 mL), and compound 5 (350 mg, 1.04 mmol) and DIPEA (1.48 mL, 8.63 mmol) were added at 0 ℃. The mixture was stirred overnight at rt, then diluted with EtOAc and water. The diluted mixture was adjusted to pH 1 with 1 N HCl, then extracted with EtOAc. The organic layer was washed with brine, dried (Na₂SO₄), filtered, and concentrated. The residue was purified by reverse-phase HPLC (0.1% HCOOH in 60% MeCN–H₂O to 0.1% HCOOH in 90% MeCN–H₂O), and the collected fractions were concentrated and dried in vacuo to give a white solid; yield: 275 mg (55%). ¹H NMR (400 MHz, DMSO-d ₆): δ = 9.06 (s, 1 H), 8.02 (d, J = 8.5 Hz, 1 H), 7.89 (d, J = 7.3 Hz, 2 H), 7.69 (d, J = 7.3 Hz, 2 H), 7.41 (t, J = 7.3 Hz, 2 H), 7.33 (t, J = 7.6 Hz, 2 H), 7.26 (t, J = 5.5 Hz, 1 H), 6.57 (q, J = 7.1 Hz, 1 H), 4.43 (dd, J = 14.0, 8.5 Hz, 1 H), 4.30–4.20 (m, 3 H), 3.08 (q, J = 6.5 Hz, 2 H), 2.13 (ddd, J = 15.7, 8.4, 6.0 Hz, 2 H), 1.88 (m, 1 H), 1.69 (m, 1 H), 1.64 (d, J = 7.3 Hz, 3 H), 1.48 (br t, J = 5.8 Hz, 2 H), 1.22 (overlapped, 12 H), 0.83 (t, J = 6.7 Hz, 3 H). ¹³C NMR (100 MHz, DMSO-d ₆): δ = 172.4, 170.3, 165.5, 156.0, 143.9, 140.7, 132.2, 128.1, 127.6, 127.1, 125.1, 120.1, 65.3, 50.4, 46.7, 37.3, 35.1, 32.3, 31.3, 28.9, 28.8, 28.7, 28.6, 25.2, 22.1, 13.9, 13.7. HRMS (ESI): m/z [M + H]⁺ calcd for C₃₃H₄₄N₃O₆: 578.3225; found: 578.3227. Macrocyclic peptide 11a: Typical Procedure A mixture of compound 10a (59 mg, 0.040 mmol) and DIPEA (41 μL, 0.24 mmol) in 1:1 MeCN–THF (10 mL) was added dropwise to a solution of COMU (51 mg, 0.12 mmol) in 1:1 MeCN–THF (30 mL), and the mixture was stirred overnight at 40 ℃, then concentrated. The residue was purified by reversed-phase HPLC (0.1% HCOOH in 65% MeCN–H₂O to 0.1% HCOOH in MeCN), then lyophilized to afford the cyclic form of compound 10a as a yellowish solid; yield: 24 mg (40%). LRMS (ESI): m/z [M + H]⁺ calcd for C₇₀H₁₁₉N₁₄O₁₇S: 1459.8593; found: 1460.4. The cyclic compound was treated with a deprotection cocktail of 95:2.5:2.5 TFA–TIPS–H₂O (1 mL) at rt, and the mixture was stirred for 3.5 h. The mixture was concentrated, purified by reversed-phase HPLC (0.1% HCOOH in 5% MeCN–H₂O to 0.1% formic acid in MeCN), then lyophilized to afford compound 11a as a white solid; yield: 20 mg (quant, four formic acid salts). ¹H NMR (400 MHz, D₂O): δ = 6.67 (q, J = 7.1 Hz, 1 H), 4.53 (dd, J = 10.1, 5.2 Hz, 1 H), 4.36–4.25 (m, 6 H), 3.56 (m, 1 H), 3.26–3.01 (m, 12 H), 2.35 (t, J = 7.3 Hz, 2 H), 2.30–1.82 (m, 2 H), 1.77 (d, J = 6.7 Hz, 3 H), 1.62 (m, overlapped, 8 H), 1.29 (overlapped, 17 H), 0.96 (d, J = 6.1 Hz, 3 H), 0.91 (d, J = 6.1 Hz, 3 H), 0.86 (t, J = 6.7 Hz, 3 H); HRMS (ESI): m/z [M–H]^– calcd for C₄₂H₇₇N₁₄O₈: 905.6054; found: 905.6017.