10.1002/chem.202003387
Chemistry - A European Journal
FULL PAPER
was evaporated under reduced pressure. The resultant crude product
was purified by flash column chromatography (CH2Cl2-MeOH, 98:2) to
give the intermediate N-Alloc-protected AMBA-N-acylated nucleosyl
amino acid as a white foam (245 mg, 94%). To a solution of the N-Alloc-
protected AMBA-N-acylated nucleosyl amino acid (152 mg, 0.166 mmol)
in CH2Cl2 (5 mL), phenylsilane (95 L, 1.0 mmol) and tetrakis(triphenyl-
phosphine)palladium(0) (19 mg, 17 mol) were added under the
exclusion of light. The reaction mixture was stirred at rt for 6 h.
Subsequently, EtOAc (40 mL) was added and the mixture was washed
with NaHCO3 solution (40 mL), dried over Na2SO4 and the solvent was
evaporated under reduced pressure. The resultant crude product was
purified by flash column chromatography (CH2Cl2-MeOH, 98:2 95:5
9:1) to give 30 as a white foam (100 mg, 73%, 69% over 2 steps from 17).
[α]2D0 = +52.4 (c = 1.0, CH2Cl2). 1H NMR§ (500 MHz, CDCl3): = 0.04 (s,
3H, SiCH3), 0.04 (s, 3H, SiCH3), 0.05 (s, 3H, SiCH3), 0.06 (s, 3H, SiCH3),
0.86 (s, 9H, SiC(CH3)3), 0.87 (s, 9H, SiC(CH3)3), 1.23 (d, J = 7.3 Hz, 1H,
AMBA-H-4), 1.43 (s, 9H, OC(CH3)3), 1.85-2.08 (m, 2H, H-5'a, H-5'b),
2.90 (s, 3H, AMBA-NCH3), 3.56-3.59 (m, 1H, AMBA-H-2), 3.64-3.69 (m,
1H, H-3'), 4.14-4.21 (m, 2H, H-4', AMBA-H-3), 4.40-4.48 (m, 2H, H-2',
H-6'), 5.13-5.15 (m, 2H, Cbz-H-1), 5.39-5.49 (m, 1H, H-1'), 5.74 (d,
J = 8.1 Hz, 1H, H-5), 7.25-7.38 (m, 5H, aryl-H), 7.50 (m, 1H, H-6), 7.65 (d,
J = 5.8 Hz, 1H, NH) ppm. 13C NMR§ (126 MHz, CDCl3): = -4.72 (SiCH3),
-4.67 (SiCH3), -4.48 (SiCH3), -4.11 (SiCH3), 13.01 (AMBA-C-4), 18.07
(SiC(CH3)3), 18.16 (SiC(CH3)3), 25.90 (SiC(CH3)3), 25.92 (SiC(CH3)3),
28.08 (OC(CH3)3), 32.05 (AMBA-NCH3), 35.40 (C-5'), 51.89 (C-6'), 56.07
(AMBA-C-3), 58.38 (AMBA-C-2), 67.47 (Cbz-C-1), 73.78 (C-2'), 75.71
(C-3'), 82.48 (OC(CH3)3, C-4'), 93.88 (C-1'), 102.46 (C-5), 127.94, 128.08,
128.61 (Cbz-C-3-7), 136.85 (Cbz-C-2), 142.01 (C-6), 150.97 (C-2),
157.02 (Cbz-C=O), 163.35 (C-4), 170.80 (C-7'), 172.97 (AMBA-C-1) ppm.
MS (ESI): m/z = 834.66 [M+H]+. HRMS (ESI): calcd. for C40H68N5O10Si2
[M+H]+ 834.4499, found 834.4486. IR (ATR): = 2931, 2857, 1683, 1457,
1255, 1154, 866, 835, 776, 730 cm-1. UV (MeCN): max = 260 nm.
166.24 (C-4), 173.62, 173.71‡, 173.78 (C-7', C-1'') ppm. 19F NMR
(376 MHz, D2O): = -75.56 (TFA-CF3) ppm. HRMS (ESI): calcd. for
C24H32N5O10 [M+H]+ 550.2144, found 550.2126. IR (ATR): = 1669,
1542, 1401, 1190, 1133, 808, 724, 557 cm-1. UV (HPLC, MeCN/H2O):
max = 216, 261 nm. HPLC (method 2): tR = 16.0 min.
Additional urea dipeptide target compound (33): Protected urea
dipeptide 18 (11 mg, 22 mol) was dissolved in TFA and water (4:1,
2.5 mL). The reaction mixture was stirred at rt for 26 h. Water (5 mL) was
added and the solvent was evaporated by lyophilisation. The resultant
crude product was purified by semi-preparative HPLC (method 1) to give
33 as a yellowish fluffy solid (4.1 mg, 51%). 1H NMR (500 MHz, CD3OD):
= 0.93 (d, J = 6.4 Hz, 3H, Leu-H-5a), 0.95 (d, J = 6.6 Hz, 3H, Leu-H-5b),
1.50 (ddd, J = 13.7, 9.8, 5.5 Hz, 1H, Leu-H-3a), 1.58 (ddd, J = 13.7, 8.7,
5.0 Hz, 1H, Leu-H-3b), 1.67-1.78 (m, 1H, Leu-H-4), 3.23 (ddd, J = 14.7,
5.9, 0.6 Hz, 1H, Trp-H-3a), 3.23 (ddd, J = 14.7, 5.6, 0.6 Hz, 1H, Trp-H-
3b), 4.28 (dd, J = 9.8, 5.0 Hz, 1H, Leu-H-2), 4.61 (dd, J = 5.8, 5.6 Hz, 1H,
Trp-H-2), 7.00 (ddd, J = 8.0, 7.0, 1.0 Hz, 1H, Trp-indole-H-6), 7.00 (ddd,
J = 8.1, 7.0, 1.1 Hz, 1H, Trp-indole-H-5), 7.12 (s, 1H, Trp-indole-H-2),
7.31 (ddd, J = 8.1, 8.0, 1.0 Hz, 1H, Trp-indole-H-4), 7.58-7.60 (m, 1H,
Trp-indole-H-7) ppm. 13C NMR (126 MHz, CD3OD): = 22.01 (Leu-C-5a),
23.39 (Leu-C-5b), 25.93 (Leu-C-4), 29.07 (Trp-C-3), 42.49 (Leu-C-3),
52.65 (Leu-C-2), 54.95 (Trp-C-2), 110.57 (Trp-indole-C-3), 112.07 (Trp-
indole-C-4), 119.63 (Trp-indole-C-7), 119.80 (Trp-indole-C-6), 122.28
(Trp-indole-C-5), 124.71 (Trp-indole-C-2), 129.09 (Trp-indole-C-3a),
137.99 (Trp-indole-C-7a), 159.98 (urea-C=O), 176.10 (Trp-C-1), 177.27
(Leu-C-1) ppm. MS (ESI): m/z = 362.15 [M+H]+. HRMS (ESI): calcd. for
C18H24N3O5 [M+H]+ 362.1710, found 362.1703. IR (ATR): = 3380, 2958,
1640, 1556, 1449, 1192, 746 cm-1. UV (HPLC, MeCN/H2O): max = 221,
280 nm. HPLC (method 1): tR = 16.0 min.
Additional full-length target compound (34): Protected intermediate
31 (20 mg, 15 mol) was dissolved in TFA and water (4:1, 2.5 mL). The
reaction mixture was stirred at rt for 42 h. Water (6 mL) was added and
the solvent was evaporated by lyophilisation. The resultant crude product
was purified by semi-preparative HPLC (method 3) to give 34 as a white
fluffy solid (4.3 mg, 31%). 1H NMR (500 MHz, CD3OD): = 0.91 (d, J =
6.6 Hz, 3H, Leu-H-5a), 0.95 (d, J = 6.9 Hz, 3H, Leu-H-5b), 1.13‡, 1.18 (d,
J = 6.8 Hz, 3H, AMBA-H-4), 1.42-1.49 (m, 1H, Leu-H-3a), 1.50-1.57 (m,
1H, Leu-H-3b), 1.61-1.72 (m, 1H, Leu-H-4), 2.06-2.16 (m, 1H, H-5'a),
2.23-2.31 (m, 1H, H-5'b), 2.83 (s, 3H, NCH3), 3.19 (dd, J = 14.8, 6.7 Hz,
1H, Trp-H-3a), 3.27 (dd, J = 14.8, 5.1 Hz, 1H, Trp-H-3b), 3.88 (dd,
J = 5.5, 5.1 Hz, 1H, H-3'), 4.00-4.08 (m, 1H, H-4'), 4.10 (dd, J = 4.8,
4.8 Hz, 1H, H-2'), 4.21 (dd, J = 9.8, 4.8 Hz, 1H, Leu-H-2), 4.34-4.43,
4.46-4.55‡ (m, 1H, AMBA-H-3), 4.56-4.65 (m, 2H, H-6', Trp-H-2), 4.66-
4.72 (m, 1H, AMBA-H-2), 5.06 (d, J = 12.4 Hz, 1H, Cbz-H-1a), 5.10 (d,
J = 12.4 Hz, 1H, Cbz-H-1b), 5.68 (d, J = 8.1 Hz, 1H, H-5), 5.78 (d, J =
4.8 Hz, 1H, H-1'), 7.00 (ddd, J = 8.0, 7.0, 1.0 Hz, 1H, Trp-indole-H-6),
7.03-7.08 (m, 1H, Trp-indole-H-5), 7.11‡, 7.13 (s, 1H, Trp-indole-H-2),
7.23-7.42 (m, 6H, Cbz-aryl-H, Trp-indole-H-4), 7.56 (d, J = 8.0 Hz, 1H,
Trp-indole-H-7), 7.60 (d, J = 8.1 Hz, 1H, H-6), 8.08-8.17 (m, 1H, 6'-NH or
Trp-NH), 8.21-8.30 (m, 1H, AMBA-NH) ppm. 13C NMR (126 MHz,
CD3OD): = 14.42, 14.96‡ (AMBA-C-4), 22.02 (Leu-C-5), 23.53 (Leu-
C-5), 25.85 (Leu-C-4), 29.02 (Trp-C-3), 30.75 (NCH3), 36.02 (C-5'), 42.17
(Leu-C-3), 50.96 (Trp-C-2), 53.87 (Leu-C-2), 54.86 (C-6'), 54.86‡, 54.93
(AMBA-C-3), 56.92 (AMBA-C-2), 68.37 (Cbz-C-1), 74.59 (C-2'), 74.88
(C-3'), 81.74 (C-4'), 91.74 (C-1'), 102.95 (C-5), 110.63 (Trp-indole-C-3),
112.20 (Trp-indole-C-4), 119.50 (Trp-indole-C-7), 119.83 (Trp-indole-C-6),
122.34 (Trp-indole-C-5), 124.77 (Trp-indole-C-2), 128.66, 128.91, 128.98
(Cbz-C-3-7), 129.49 (Trp-indole-C-3a), 137.99 (Trp-indole-C-7a), 138.18
(Cbz-C-2), 142.76 (C-6), 152.25 (C-2), 158.15 (Cbz-C=O), 159.89 (urea-
C=O), 166.14 (C-4), 171.49 (AMBA-C-1), 174.10 (C-7'), 175.91 (Trp-C-1),
176.22 (Leu-C-1) ppm. HRMS (ESI): calcd. for C42H53N8O14 [M+H]+
893.3676, found 893.3659. IR (ATR): = 2955, 1663, 1549, 1456, 1192,
1129, 745 cm-1. UV (HPLC, MeCN/H2O): max = 220, 260 nm. HPLC
(method 3): tR = 28.5 min.
Protected intermediate (31): To a solution of protected urea dipeptide
18 (40 mg, 76 mol) in DMF (3 mL), DIPEA (32 L, 0.18 mmol) and
benzotriazol-1-yl-oxytripyrrolidinophosphonium
hexafluorophosphate
(PyBOP) (58 mg, 0.11 mmol) were added. The resultant solution was
stirred at rt for 3 h. Then a solution of N-deprotected AMBA-N-acylated
nucleosyl amino acid 30 (62 mg, 74 mol) in DMF (3.5 mL) was added
and the reaction mixture was stirred at rt for further 17 h. EtOAc (40 mL)
was added and the mixture was washed with HCl (1 M, 30 mL) and brine
(30 mL), dried over Na2SO4 and the solvent was evaporated under
reduced pressure. The resultant crude product was purified by flash
column chromatography (CH2Cl2-MeOH, 98:2) to give 31 as a white foam
(62 mg, 64%). Due to pronounced rotamer formation of the title
compound that resulted in very complex NMR spectra, 31 was analysed
by LC-MS only. Purity was confirmed based on the UV chromatogram of
the LC-MS analysis. MS (ESI): m/z = 1334.24 [M+H]+. TLC (CH2Cl2-
MeOH, 98:2): Rf = 0.15.
Additional nucleosyl amino acid-AMBA target compound (32):
N-Deprotected AMBA-N-acylated nucleosyl amino acid 30 (16 mg,
19 mol) was dissolved in TFA and water (4:1, 2.5 mL). The reaction
mixture was stirred at rt for 25 h. Water (5 mL) was added and the
solvent was evaporated by lyophilisation. The resultant crude product
was purified by semi-preparative HPLC (method 2) to give 32 as a white
fluffy solid (9.3 mg, 74%). 1H NMR (500 MHz, D2O): = 1.41 (d, J =
6.9 Hz, 3H, AMBA-H-4), 2.12-2.29 (m, 1H, H-5'a), 2.30-2.44 (m, 1H,
H-5'b), 2.83‡, 2.87 (brs, 3H, AMBA-NCH3), 4.02-4.21 (m, 3H, H-3', H-4',
AMBA-H-2), 4.36 (dd, J = 5.2, 4.1 Hz, 1H, H-2'), 4.40-4.52 (m, 1H,
AMBA-H-3), 4.56-4.69 (m, 2H, H-6', AMBA-H-3‡), 5.06-5.17 (m, 2H, Cbz-
H-1), 5.75-5.83 (m, 1H, H-1'), 5.87 (d, J = 8.1 Hz, 1H, H-5), 7.36-7.50 (m,
5H, aryl-H), 7.63 (d, J = 8.1 Hz, 1H, H-6) ppm. 13C NMR (126 MHz, D2O):
= 13.65, 14.23‡ (AMBA-C-4), 29.59‡, 30.52 (AMBA-NCH3), 34.04 (C-5'),
50.57 (AMBA-C-3), 52.19‡, 53.14 (C-6), 55.32‡, 55.61 (AMBA-C-2),
67.98, 68.15‡ (Cbz-C-1), 72.98 (C-2'), 73.14 (C-3'), 79.82 (C-4'), 90.48
(C-1'), 102.29 (C-5), 116.41 (q, JCF = 291.6 Hz, TFA-CF3), 127.89,
128.26, 128.54, 128.83 (Cbz-C-3-7), 136.15 (Cbz-C-2), 142.05 (C-6),
151.54 (C-2), 157.84 (Cbz-C=O), 163.06 (q, JCF = 35.5 Hz, TFA-C=O),
10
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