Chemoselective deprotection of α-indole and imidazole ribonucleosides

Article abstract of DOI:10.1080/15257770601052216

A series of 2′,3′-isopropylidene and 5′-trityl-protected α-indole and α/β-benzimidazole and imidazole ribonucleosides were deprotected with different acids. Selectivity was achieved for 5′-versus 2′,3′- deprotection by using formic acid in the α-indole ri

Full text of DOI:10.1080/15257770601052216

Nucleosides, Nucleotides, and Nucleic Acids, 26:1–8, 2007
Copyright ꢀC Taylor & Francis Group, LLC
ISSN: 1525-7770 print / 1532-2335 online
DOI: 10.1080/15257770601052216
CHEMOSELECTIVE DEPROTECTION OF α-INDOLE
AND IMIDAZOLE RIBONUCLEOSIDES
Tilak Chandra and Kenneth L. Brown
Department of Chemistry
2
and Biochemistry, Ohio University, Athens, Ohio, USA
A series of 2 ꢁ,3 ꢁ-isopropylidene and 5 ꢁ-trityl-protected α-indole and α/β-benzimidazole and
2
imidazole ribonucleosides were deprotected with different acids. Selectivity was achieved for 5 ꢁ-
versus 2 ꢁ,3 ꢁ- deprotection by using formic acid in the α-indole ribonucleoside series. Treatment
of α-indole ribonucleosides with a mixture of formic acid and ether at room temperature afforded
2 ꢁ,3 ꢁ-deprotected α-ribonucleosides, whereas treatment of the α-benzimidazole ribonucleosides with
the same acid afforded the 5 ꢁ-deprotected ribonucleoside without any 2 ꢁ, 3 ꢁ-deprotected products.
The structures of these ribonucleosides were elucidated with 2D (NOESY, COSY, and HMQC) NMR
spectroscopy.
Keywords Chemoselective; coenzyme B12; biosynthesis; glycosylation
INTRODUCTION
Semisynthesis of cobalamins[1–6] with altered axial nucleotide ligands
requires cobyric acid[7] and an α-ribonucleotide[8] as precursors. Analogs
of coenzyme B12 (5ꢁ-deoxyadenosylcobalamin, AdoCbl) with altered axial
nucleotide ligands, such as B3-deazaAdoCbl (Figure 1) are of interest as
probes of the function, if any, of the axial nucleotide in the enzymatic acti-
vation of AdoCbl for carbon-cobalt bond homolysis[9,10]. Literature reports
on the synthesis and deprotection of indole α-ribonucleosides are limited.
Deprotection is a crucial step for these unstable α-ribonucleosides,[11–18]
in order to retain the α-configuration and to achieve the synthesis of
AdoCbl. Trityl (Tr), dimethoxytrityl (DMTr), and isopropylidene groups
are commonly used for the protection of 5-hydroxyl and 2, 3-hydroxyl
groups in both carbohydrate and nucleoside chemistry.[19] Strong protic
Received 7 December 2005; accepted 15 June 2006.
This research was supported by the National Institute of General Medical Sciences, Grant GM
48858.
Address correspondence to Kenneth L. Brown, Department of Chemistry and Biochemistry, Ohio
University, Athens, OH 45701-3132. E-mail: brownk3@ohio.edu
1

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T. Chandra and K. L. Brown
FIGURE 1 Structure of AdoCbl (coenzyme B12) and the analog B3-deaza AdoCbl.
and/or Lewis acids are generally used to hydrolyze these protecting groups
with hydrochloric acid, formic acid[20] and trifluoroacetic acid (TFA)[21]
typically being used for the deprotection of trityl groups. However under
these conditions, ribonucleosides with the α-anomeric configuration may
undergo deglycosylation or decomposition. Dimethylindole, indole and
other α-ribonucleosides[13–15] when treated with neat TFA or heated for
prolonged periods in acetic acid, give a charred product without any of the
desired deprotected ribonucleosides. In addition, strong protic acids such
as TFA, HCl and others, are typically not selective under aqueous conditions
and cause the cleavage of the other acid labile groups. Since insertion of an
altered axial nucleoside into the cobalamin structure requires protection
of the 5ꢁ-hydroxyl, chemoselective deprotection at the 2ꢁ,3ꢁ positions would
be highly desirable. In this report, we describe the selective deprotection of
trityl and isopropylidene groups using different acids in organic solvents.
RESULTS AND DISCUSSION
The protected α-ribonuclesides were prepared by published meth-
ods, coupling trimethylsilyl protected indolines and protected d-ribose

α-Indole and Imidazole Ribonucleosides
3
SCHEME 1 Deprotection of α-indole ribonucleosides.
using 2-fluoromethylpyridinium tosylate as a condensing reagent[22] or
by direct glycosylation.[14] 2D NMR and X-ray crystallography confirmed
the anomeric configuration of these indoline ribonucleosides.[15] Pro-
tected indole ribonucleosides[13] (1–3, Scheme 1) were prepared
from the corresponding indoline α-ribonucleosides[14,15] by manganese
dioxide oxidation[13] at elevated temperature. Benzimidazole, 5,6-
dimethylbenzimidazole and imidazole α-ribonucleosides[15] (11 & 12) and
(13 & 14) were similarly prepared using 2-fluoromethyl pyridinium tosylate
as a condensing reagent[22] (Scheme 2). These glycosylation reactions
produce mixtures of α- (70–85%) and β-ribonucleosides (15–30%).
Upon treatment with formic acid/ether (2:3) at room temperature
(Scheme 1) the indole ribonucleosides afforded the 2ꢁ,3ꢁ-deprotected
indole ribonucleoside in fairly good yield, without affecting the trityl
group. In contrast, the α-ribonucleosides of dimethylindole, indole and
5-bromoindole, on treatment with aqueous acetic acid at 50–60◦C, af-
forded the corresponding 5ꢁ-deprotected α-ribonucleoside without affecting
the isopropylidene group or causing deglycosylation. At higher temper-
ature and longer time we observed deglycosylation and charring with-
out any desired product. While it is known that 2ꢁ,3ꢁ-O-isopropylidene-
β-d-ribofuranosyl-2,5,6-trichloroindole[23] and other halogenated indole
ribonucleosides produce 2ꢁ,3ꢁ-deprotected indole ribonucleosides upon
prolonged heating with acetic acid and water (4:1), for the current α-indole
ribonucleosides we do not observe any 2ꢁ,3ꢁ-deprotected products. Instead,

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T. Chandra and K. L. Brown
SCHEME 2 Preparation and deprotection of α/ß-benzimidazole/imidazoleribunucleosides.
prolonged heating of these α-indole ribonucleosides at higher temperature
in acetic acid produced only charring.
The 1-(2,3-O-isopropylidene-5ꢁ-O-triphenylmethyl-α-d-ribofuranosyl)-
benzimidazole, and 5,6-dimethylbenzimidazole ribonucleosides (11 &
12), however, react differently (Scheme 2). The trityl group can be easily
removed by treating the protected ribonucleoside with formic acid/ether,
heating with aqueous acetic acid, or using 1% TFA in methylene chloride,
without affecting the isopropylidene.
A series of protected α and β ribosides were prepared by the
Mukaiyama[22] method and isolated in pure form and thoroughly charac-
terized by two-dimentional NMR techniques (COSY, HMQC, and NOESY).
All protected α-ribonucleosides have a NOE between the isopropylidene
methyl protons and imidazole proton, whereas the β-anomer does not have
a NOE between these protons. The methyl protons of the isopropylidene
had a NOE with the imidazole proton in 5ꢁ-deprotected α-benzimidazole
ribonucleoside 15, but the β-benzimidazole does not have a NOE between
those protons (2D NOESY).
Structural proof for the α-anomer was also confirmed with the help
of NOE difference spectroscopy. Irridation of the isopropylidene methyl
protons of 5ꢁ-deprotected benzimidazole ribonucleoside, 15, caused a 10%
positive NOE enhancement of the imidazole proton, and the precursor

α-Indole and Imidazole Ribonucleosides
5
11 (protected ribonucleoside) shows a 12% NOE enhancement upon
irradiation of the methyl protons. The signals for the methyl pro-
tons of the isopropylidene in the benzimidazole ribonucleoside (2ꢁ,3ꢁ-O-
isopropylidene-α-d-ribofuranosyl) benzimidazole, 15, were visible at δ 1.279
and 1.382 ppm (d = 0.103). The anomeric proton signal appeared at δ 6.33
ppm with a J value of 4.5 Hz, which further confirms the α-configuration of
the ribonucleoside, whereas the anomeric proton signal for compound 17
was at δ 6.07 ppm with J value of 3.2 Hz and a methyl proton separation of
0.269 ppm. Similarly, the deprotected indole ribonucleosides also showed
the same NMR pattern as the protected α-ribonucleosides.
EXPERIMENTAL SECTION
All reactions were carried out in oven or flame-dried glassware under a
nitrogen atmosphere. Solvents were distilled prior to use. Dichloromethane,
benzene and ether were distilled from calcium hydride. Purification of
reaction products was carried out by flash chromatography using silica gel
(230–400 mesh). All reagents were commercially available and used without
further purification. All reactions were monitored by thin-layer chromatog-
raphy (TLC) using Merck silica gel 60, F-254. Column chromatography was
conducted using flash silica gel.
Physical Measurements
1H NMR and 13C NMR spectra were recorded on a Varian INOVA-500
or VXR-400 NMR spectrometers using the residual proton resonance of the
solvent as an internal reference at 25◦C. Two-dimensional NMR (COSY,
NOESY) spectra were obtained at 25◦C on a Varian INOVA-500 NMR
spectrometer using TMS as an internal reference. The multiplicities of the
13C NMR signals were determined by the HMQC and DEPT technique. Mass
data were obtained at University of Illinois using a micromass Quattro-I mass
spectrometer.
1-(5-O-Triphenylmethyl-α- d-ribofuranosyl)indole (4): A mixture of the
protected ribonucleoside 1[13] (0.700 g, 1.3 mmol) in ether:formic acid
(3:2) (10 mL) was stirred for 3–4 hours at room temperature while TLC
(ethyl acetate:hexane 1:1) was used to monitor the progress of the reaction.
Upon completion, the solvent was removed on a rotary evaporator, the
residue was dissolved in ethyl acetate, and washed with saturated sodium
bicarbonate solution. The ethyl acetate layer was concentrated and the
residue was purified by flash chromatography. Yield: 60%; Rf. 0.2; white
1
solid; H NMR (DMSO-d6): δ 3.57 (dd, J = 2.0, 5.5 Hz, 1H, 5ꢁ), 3.70 (d,
J = 7.7 Hz, 1H, 5ꢁꢁ), 3.84 (bt, 1H, 2ꢁ), 4.0 (bs, 1H), 5.0 (d, J = 3.4 Hz,
3ꢁ), 5.49 (d, J = 9.5 Hz, 1H, 1ꢁ), 6.47 (d, J = 8.0 Hz, 1H, Ar), 6.70 (t, J =
7.5 Hz, 1 H, Ar), 6.93 (s, 1H, Ar), 7.1 (d, J = 7.5 Hz, 6H, Ar), 7.2 (t, 3H,

6
T. Chandra and K. L. Brown
trityl), 7.27 (t, J = 7.7 Hz, 6H, trityl), 7.44 (d, 1H, J = 8.0 Hz, Ar); 13C NMR
(DMSO-d6): 65.0, 66.64, 68.45, 71.43, 81.98 (C1ꢁ), 110.8 (CH), 119.0 (CH),
121.1 (CH), 121.7 (CH), 121.8 (Cquat), 126.0 (CH), 126.48, 127.48 (CH),
128.0 (Cquat), 130.1 (CH), 137.25, 145.9 (Cquat); HRMS: m/z: 492.2166
(calcd for C32H30NO4; 492.2174) (M + H); MS: (FAB) m/z 492, 394, 324,
243.
1-(2, 3-isopropylidene-α- d-ribofuranosyl)5,6-dimethylindole (8): Com-
pound 2[13] (150 mg, 0.26 mmol) was dissolved in aqueous acetic acid
(5 mL) and heated for 5 hours at 50–60◦C in a oil bath. After complete
conversion of the starting material, the reaction mixture was cooled and
then concentrated to dryness to give a residue. The residue was purified
by flash column chromatography (benzene:ether; 50:50) to give 70 mg of
1
compound 8 as a viscous oil. Yield: 80%; Rf. 0.7; H NMR (CDCl3): δ 1.38
(s, 3H, CH3, isopropylidene), 1.64 (s, 3H, CH3, isopropylidene), 2.35 (s, 3H,
CH3), 2.40 (s, 3H, CH3), 3.73 (dd, J = 4.0, 8.0Hz, 1H, 5ꢁ), 3.82 (dd, J = 3.24,
8.9Hz, 1H, 5ꢁ), 4.22 (q, 1H, CH, 4ꢁ), 4.93–4.95 (m, 1H, CH, 3ꢁ), 5.03–5.05
(m, 1H, CH, 2ꢁ), 6.06 (d, J = 3.5 Hz, 1H, CH, 1ꢁ), 6.46 (d, J = 3.0 Hz, 1H,
indole), 7.10 (d, J = 3.0 Hz, 1H, indole), 7.27 (s, 1H, Ar), 7.39 (s, 1H, Ar);
13C NMR (CDCl3): δ 19.97 (CH3), 20.70 (CH3), 25.36 (CH3), 27.26 (CH3),
62.52 (CH2, 5ꢁ), 80.18 (C 3ꢁ), 84.03 (C 2ꢁ), 84.83 (C 4ꢁ), 91.15 (C 1ꢁ), 103.13
(CH, Ar), 110.52 (CH), 114.70 (Cquat, isoprop), 121.25 (CH), 123.72 (CH),
126.01 (Cquat), 127.35 (Cquat), 130.75 (Cquat), 146.22 (Cquat); HRMS:
m/z: 318.1704 (calcd for C18H24NO4; 318.1704) (M + H).
1-(2,3-O-isopropylidene-α-d-ribofuranosyl)benzimidazole (15): The ben-
zimidazole ribonucleoside[15,17] 11, was similarly deprotected as described
for the indole nucleoside 4 using either the mixture of (formic acid:ether)
or aqueous acetic acid (method described for the compound 8) Yield:
1
80–90%; Rf. 0.3; White foam; H NMR (CDCl3): δ 1.279 (s, 3H, CH3,
isopropylidene), 1.382 (s, 3H, CH3, isopropylidene), 3.85 (dd, J = 3.5, 8.5
Hz, 1H, 5ꢁ), 3.96 (dd, J = 2.0, 9.5 Hz, 1H, 5ꢁꢁ), 4.42 (bt, 1H, CH, 4ꢁ), 4.92 (t,
J = 6.5 Hz, 1H, CH, 2ꢁ), 5.01 (d, J = 6 Hz, 1H, CH, 3ꢁ), 6.33 (d, J = 4.5 Hz,
1H, CH, 1ꢁ), 7.21–7.28 (m, 3H, Ar), 7.76 (d, J = 7.5 Hz, 1H, Ar), 8.24 (s, 1H,
imidazole); 13C NMR (CDCl3): δ 24.18 (CH3), 25.65 (CH3), 63.87 (CH2, 5ꢁ),
80.06 (C 2ꢁ), 82.35 (C 3ꢁ), 83.45 (C 4ꢁ), 87.21 (C 1ꢁ), 109.90 (CH, Ar), 113.34
(Cquat, isoprop), 119.61 (CH), 122.47 (CH), 123.06 (CH), 132.69 (Cquat),
142.30 (CH), 142.58 (Cquat); HRMS: m/z: 291.1344 (calcd for C15H19N2O4;
291.1343) (M + H); MS: (FAB) m/z 291, 195, 152, 119.
1-(2, 3-O-isopropylidene-β -d-ribofuranosyl)benzimidazole (17): Yield:
1
80–90%; Rf. 0.3; White crystalline solid; H NMR (CDCl3): δ 1.40 (s, 3H,
CH3, isopropylidene), 1.67 (s, 3H, CH3, isopropylidene), 3.85 (dd, J = 2.83,
8.91Hz, 1H, 5ꢁ), 4.01 (dd, J = 2.43, 9.72Hz, 1H, 5ꢁꢁ), 4.51 (d, 1H, CH, 4ꢁ),
4.65 (bs, 1H, OH), 4.98–4.99 (m, 1H, CH, 2ꢁ), 5.05 (dd, J = 2.43, 3.64 Hz,
1H, CH, 3ꢁ), 6.07 (d, J = 3.24 Hz, 1 H, CH, 1ꢁ), 7.29–7.32 (m, 2H, Ar),
7.52 (d, J = 7.29 Hz, 1H, Ar), 7.75 (d, 1H, J = 6.89Hz, 1H, Ar), 8.39 (s, 1H,

α-Indole and Imidazole Ribonucleosides
7
imidazole); 13C NMR (CDCl3): δ 25.25 (CH3), 27.28 (CH3), 62.05 (CH2, 5ꢁ),
81.50 (C 3ꢁ), 85.36 (C 2ꢁ), 86.52 (C 4ꢁ), 92.81 (C 1ꢁ), 110.46 (CH, Ar), 114.18
(Cquat, isoprop), 119.87 (CH), 122.82 (CH), 123.44 (CH), 132.41 (Cquat),
142.83 (CH), 143.33 (Cquat); HRMS: m/z: 291.1346 (calcd for C15H19N2O4;
291.1343) (M + H); MS: (FAB) m/z 291, 195, 152, 119.
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