Orthogonally protected monosaccharide building blocks for solid phase production of diversity oriented libraries

Article abstract of DOI:10.1071/CH09480

The large scale synthesis of three orthogonally protected monosaccharide scaffolds suitable for use in the solid phase preparation of large diversity libraries is presented. Scaffolds based on 2-amino-2-deoxy-d-glucopyranose, 2-amino-2-deoxy-d-allopyranos

Full text of DOI:10.1071/CH09480

Full Paper
CSIRO PUBLISHING
www.publish.csiro.au/journals/ajc
Aust. J. Chem. 2010, 63, 693–699
Orthogonally Protected Monosaccharide Building Blocks for
Solid Phase Production of Diversity Oriented Libraries
Premraj Rajaratnam,A Praveer Gupta,A Peter Katavic,A Krystle Kuipers,A
Ngoc Huyh,A Sarah Ryan,A Tania Falzun,A Gerrald B. Tometzki,A
Laurent Bornaghi,A Giang Le Thanh,A Giovanni Abbenante,A Ligong Liu,A
Wim Meutermans,A Norbert Wimmer,A and Michael L. WestA,B
AAlchemia Limited, 3 Hi Tech Court, Eight Mile Plains, Brisbane, Qld 4113, Australia.
BCorresponding author. Email: mwest@alchemia.com.au
The large scale synthesis of three orthogonally protected monosaccharide scaffolds suitable for use in the solid phase
preparation of large diversity libraries is presented. Scaffolds based on 2-amino-2-deoxy-d-glucopyranose, 2-amino-2-
deoxy-d-allopyranose, and 2,4-diamino-2,4-dideoxy-d-galactopyranose were prepared in good yield and with minimal
chromatographic purification from commercially available methyl 2-azido-2-deoxy-1-thio-β-d-glucopyranose and methyl
2-amino-2-deoxy-1-thio-β-d-glucopyranose.
Manuscript received: 9 September 2009.
Manuscript accepted: 4 January 2010.
Introduction
The anomeric position in the target libraries always bears a
substituent in order to prevent hemiacetal anomers and poten-
tial chain opening configurations of the final products, thus
precluding the use of the anomeric position as a suitable attach-
ment point to resin. An amino group at the C-2 position was
used as this simplified the selection of the orthogonal pro-
tecting groups for the scaffold. The scaffolds were designed
with the intention that the C-2 amine in the final products of
the library would be substituted with groups such as acyl or
carbamoyl moieties that restricted the rotation of the appended
groups. Consequently, theC-2positionwasunsuitableforattach-
ment to the solid support. The C-3 and C-6 positions can
be readily protected in a selective manner, leaving the least
reactive position C-4 on 2-amino-2-deoxy-d-glucopyranose and
2-amino-2-deoxy-d-allopyranose, which was used as the resin
attachment point for orthogonally protected building blocks
basedonthesemonosaccharidescaffolds.Theprotectinggroups,
outlined in Table 1, were selected for the 2-amino-2-deoxy-
d-glucopyranose and 2-amino-2-deoxy-d-allopyranose building
blocks, to allow regio-specific introduction of a wide vari-
ety of substituents. The thiomethyl glycoside[11] at C-1 allows
direct introduction of a wide variety of substituents through
glycosidation of a range of alcohols in solution phase before
resin-loading.
With five functionalized chiral centres in a cyclic arrange-
ment, monosaccharides represent versatile and compact scaf-
folds that provide the medicinal chemist plenty of scope to
custom design molecules to a pharmacophore model.[1,2] Highly
diverse molecules can be envisaged and new bioactives identi-
fied by appending suitable substituents at various positions on
the monosaccharide scaffold.[3–6] For close to 20 years, this
has been explored by many laboratories and that work is well
reviewed.[7,8]
We have been interested in employing the sugar scaffold to
produce libraries of systematic diversity.[9] In order to produce
such libraries, the need for a series of orthogonally protected
monosaccharide scaffolds was identified. It was apparent that
these building blocks must be readily synthesized at the 100 g
scale with potential to be prepared at the kilogram scale. The
building blocks needed to be protected with groups that are stable
to the wide variety of chemical conditions required to introduce
and elaborate the substituent groups. Here we report the design
and large scale synthesis of three such building blocks based on
d-glucopyranose, d-allopyranose, and d-galactopyranose, that
we have successfully used as the starting points in the production
of our diversity oriented libraries.[10]
A third monosaccharide scaffold was based on a 2,4-diamino-
2,4-dideoxy-d-galactopyranose core. This scaffold contained
a masked axial C-4-amino group and a protected equatorial
C-2 amino group resulting in a building block containing two
nitrogen atoms. The protecting groups selected for this building
block were a thiomethyl glycoside for C-1, a 5ꢀ-methylene-1ꢀ,3ꢀ-
dimethypyrimidine-2,4,6-(1H,3H,5H)trione (DTPM) for C-2, a
benzoate ester for C-3, and an azide for C-4, with a masked resin-
linking position at C-6 (Table 2). The resin linking position in
the scaffold is masked with a tert-butyldiphenylsilyl ether to
Results and Discussion
Building Block Design and Synthesis
It was anticipated that a series of large diversity libraries would
be prepared from a small number of orthogonally protected
monosaccharide scaffolds. Efficient production of these libraries
required a solid phase approach necessitating one resin attach-
ment position on the carbohydrate building block. The choice
of the attachment position was governed by several other requi-
site characteristics of the target molecules within the library.
© CSIRO 2010
10.1071/CH09480
0004-9425/10/040693

694
P. Rajaratnam et al.
Table 1. 2-Amino-2-deoxy-d-glucopyranose and 2-amino-2-deoxy-d-allopyranose building block design
OTBDPS
OTBDPS
O
O
HO
HO
SMe
SMe
BzO
N3
N3
OBz
1
2
Order of reaction
1.
Protecting or masking group
SMe – thiomethyl
Chemistry for removal or conversion
Dimethyl(methylthio)-sulfonium trifluoromethanesulfonate
in anhydrous diethyl ether
2.
3.
4.
Bz – benzoate ester
TBDPS – tert-butyldiphenylsilyl ether
N3 – azide
Sodium methoxide in anhydrous methanol
Pyridine/HF
Dithiothreitol
Table 2. 2,4-Diamino-2,4-dideoxy-d-galactopyranose building block design
OTBDPS
N3
O
SMe
BzO
3
HN
O
O
N
N
Me
Me
O
Order of reaction
1.
Protecting or masking group
SMe – thiomethyl
Chemistry for removal or conversion
Dimethyl(methylthio)-sulfonium trifluoromethanesulfonate
in anhydrous diethyl ether
2.
3.
4.
TBDPS – tert-butyldiphenylsilyl ether
Pyridine/HF followed by immobilization on solid support
Sodium methoxide in anhydrous methanol
Hydrazine hydrate in dichloromethane
Bz – benzoate ester
DTPM – 5ꢀ-methylene-1ꢀ,3ꢀ-dimethypyrimidine-
2,4,6-(1H,3H,5H)trione
5.
N3 – azide
Dithiothreitol
OH
PhCH(OMe)2
p-TsOH·H2O, ACN
BzCl
Pyridine
O
O
Ph
Ph
O
O
O
O
O
HO
HO
SMe
SMe
SMe
HO
BzO
N3
N3
N3
4
5
6
OTBDPS
O
OH
TBDPSCl
Imidazole, DCM
p-TsOH·H2O
MeOH, ACN
O
HO
BzO
HO
BzO
SMe
SMe
N3
N3
7
1
Scheme 1. Synthesis of building block 1.
allow clean glycoside formation at the anomeric position. Once
the anomeric glycosides are formed, the tert-butyldiphenylsilyl
ether is removed with HF/pyridine to reveal the free hydroxyl
group at C-6 ready for linking to the solid support.
The syntheses of the 2-amino-2-deoxy-d-glucopyranose
building block 1, and the 2-amino-2-deoxy-d-allopyranose
building block 2 are shown in Schemes 1 and 2. These building
blocks were prepared in solution and the procedures developed
were amenable to large-scale synthesis.
methyl 2-azido-2-deoxy-1-thio-β-d-glucopyranoside 4. Subse-
quently the hydroxyl group at C-3 of 5 was benzoylated
using benzoyl chloride in pyridine to yield the fully pro-
tected d-glucopyranose 6. The benzylidene deprotection of
6 was accomplished with 4-toluenesulfonic acid hydrate in
methanol and acetonitrile to yield diol 7. In the first purifi-
cation of the synthesis, diol 7 was substantially purified
by precipitation from a dichloromethane solution by addi-
tion of petroleum ether. Selective protection of the pri-
mary alcohol with tert-butyldiphenylchlorosilane in anhydrous
dichloromethane furnished building block 1, which was purified
The synthesis of building block 1 (Scheme 1) started with the
benzylidene protection at C-4,6 of the commercially available

Building Blocks for Diversity Libraries
695
MsCl
DMAP, pyridine, DCM
O
O
Ph
O
Ph
O
O
O
SMe
SMe
MsO
HO
N3
N3
5
8
OH
OTBDPS
O
p-TsOH·H2O
MeOH, ACN, H2O
TBDPSCl
Imidazole, DCM
NaOBz
DMF
O
O
Ph
O
O
HO
HO
SMe
SMe
SMe
N3
N3
N3
OBz
OBz
OBz
9
10
2
Scheme 2. Synthesis of building block 2.
OH
Bz2O
Pyridine
PhCH(OMe)2
CSA, ACN
O
O
Ph
Ph
O
O
O
O
HO
O
SMe
NHDTPM
11
SMe
NHDTPM
12
SMe
NHDTPM
HO
HO
BzO
13
OH
O
OTBDPS
O
OTBDPS
O
p-TsOH·H2O
MeOH, ACN, H2O
Tf2O
Pyridine, DCM
TBDPSCl
Imidazole, DCM
HO
BzO
HO
BzO
TfO
BzO
SMe
SMe
NHDTPM
SMe
NHDTPM
NHDTPM
14
15
16
OTBDPS
O
N3
BzO
NaN3
DMF
SMe
3
HN
O
O
O
O
N
N
Me
Me
N
N
O
Me
Me
DTPM ꢀ 5ꢁ-methylene-1ꢁ,3ꢁ-dimethypyrimidine-2,4,6-(1H,3H,5H)trione
O
Scheme 3. Synthesis of building block 3.
by column chromatography on silica gel. Despite the need for a
chromatographic purification, building block 1 was prepared on
100–200 g scale in 66% overall yield.
The product 11 precipitated from the methanolic solution and
was collected by vacuum filtration. Benzylidene formation was
accomplished using the standard procedures described above,
and the free hydroxyl group at C-3 of product 12 was benzoylated
with benzoic anhydride in pyridine. Deprotection of benzylidene
13 and selective silylation of diol 14 gave intermediate 15. The
hydroxyl group at C-4 was then converted to a triflate 16 using
triflic anhydride, and nucleophilic displacement of the triflate
using sodium azide furnished the d-galactopyranose building
block 3, which was purified by silica gel chromatography. The
d-galactopyranose derived building block 3 was prepared in 41%
overall yield on a 100 g scale.
The described methods allow the preparation of three
monosaccharide scaffolds on a large laboratory scale in good
yield. Chromatographic purifications are restricted to simple
separations, which are amenable to further scale-up. The scaf-
folds prepared in this manner have been employed in the
preparation of large diversity libraries[12] and have been shown
to be amenable to a wide array of solid phase chemistries. Addi-
tionally, the orthogonally protected scaffolds have been used in
the solution phase preparation of gram quantities of biologically
active compounds identified through screening of the diversity
libraries.[12] Thus the building blocks described allow the medic-
inal chemist to rapidly prepare compounds from diversity library
based discovery to pre-clinical assessment.
Building block 2 (Scheme 2) was prepared from benzyli-
dene 5. Mesylation of the C-3 hydroxyl group on 5 proceeded
cleanly and the resultant mesylate 8 was used directly in the
next reaction step. Mesylate displacement with inversion of
stereochemistry at C-3 was achieved by reaction with sodium
benzoate in N,N-dimethyl formamide at 140◦C for 24 h to afford
the benzoate-protected 2-azido-4,6-O-benzylidene-2-deoxy-d-
allopyranose derivatived 9 as a black oil, which was effectively
decolourized by the addition of activated charcoal. Removal of
the benzylidene group from 9 by 4-toluenesulfonic acid hydrate
in methanolic acetonitrile was followed by selective protection
of the primary alcohol in 10 with tert-butyldiphenylchlorosilane
giving building block 2, which was purified by silica gel col-
umn chromatography. Building block 2 was prepared from
intermediate 5 in 29% overall yield on 100 g scale.
Synthesis of the 2,4-diamino-2,4-dideoxy-d-galactoyranose
based building block is described in Scheme 3. Methyl 2-[amino-
5ꢀ-methylene-1ꢀ,3ꢀ-dimethypyrimidine-2,4,6-(1H,3H,5H)trione]-
2-deoxy-1-thio-β-d-glucopyranoside 11 was prepared from
commercially available methyl 2-amino-2-deoxy-1-thio-β-d-
glucopyranosidebyreactionwith5-((dimethylamino)methylene)-
1,3-dimethylpyrimidine-2,4,6-(1H,3H,5H)trione in methanol.

696
P. Rajaratnam et al.
Table 3. Reactions monitored by reverse phase HPLC
Methyl 2-Azido-3-O-benzoyl-4,6-O-benzylidene-
2-deoxy-1-thio-β-D-glucopyranoside (6)
Column: Zorbax SB-C18 5 µm 4.6 × 50 mm; flow rate: 1 mL min−1; sol-
vent A: acetonitrile/10 mM ammonium formate in water (1:9); solvent B:
acetonitrile/10 mM ammonium formate in water (9:1), gradient cycle
Crude acetal (5) (143.5 g) was dissolved in anhydrous pyridine
(1.0 L) and the resultant solution cooled in an ice water bath with
stirring under nitrogen. Benzoyl chloride (60 mL, 0.517 mol)
was added in a dropwise manner over 5 min to the solution of 5.
The resulting suspension was allowed to warm to room tem-
perature and stirring continued for 2 h. After this time, water
(20 mL) was added to the suspension and stirred for a further
1 h. Pyridine was removed under reduced pressure to give a yel-
low solid.The yellow solid was dissolved in DCM (1.2 L) and the
organic phase was washed with 10% citric acid (3 × 800 mL),
saturated sodium bicarbonate (2 × 800 mL), and brine (800 mL).
The organic phase was dried over anhydrous magnesium sul-
fate and the solvent removed under reduced pressure to give the
ester (6) as a white solid (172.5 g crude). HPLC Rt 7.18 min. δH
(300 MHz CDCl3): 8.18 & 7.70–7.37 (10H, m, Ar-H), 5.58 (1H,
t, J 9.5), 5.52 (1H, s), 4.68 (1H, d, J 10.1, H1), 4.43 (1H, dd, J
Time [min]
%B
0
1
0
0
12
15
16
20
70
70
0
0
Materials and Methods
NMR spectra of intermediate compounds were recorded on a
Varian AM300 spectrometer (1H at 300 MHz and 13C NMR
spectra at 75 MHz). 1D and 2D NMR spectra of final products
were recorded on a Varian spectrometer (1H at 500 MHz, 13C
at 125 MHz, gCOSY at 500/125 MHz). Electrospray mass spec-
tra were recorded on a micromass LCZ single quadrupole mass
spectrometer. High resolution mass spectra were recorded on a
Brucker microTOF-Q 70.
All chromatographic separations were performed by the ‘dry
column vacuum chromatography’ technique[13] with silica gel
60 for flash chromatography 0.04–0.06 mm (230 to 400 mesh)
purchased from Scharlau Chemie SA. An 11 cm diameter sinter
funnel was employed.
ꢀ
10.5, 6.8, H4), 3.84 (1H, t, J 10., H6), 3.74 (1H, t, J 10.0, H6 ),
3.63 (1H, m), 3.60 (1H, t, J 9.8), 2.41 (3H, s). m/z (ES MS) 428
[M + H]+.
Methyl 2-Azido-3-O-benzoyl-2-deoxy-1-thio-
β-D-glucopyranoside (7)
4-Toluenesulfonic acid monohydrate (700 mg, 3.68 mmol pH 4)
was added to a solution of the benzoate (6) (172.5 g, crude) in
methanol (1.2 L) and acetonitrile (400 mL). The resulting solu-
tion was heated at 60◦C for 1 h then allowed to cool to room
temperature. The reaction was neutralized with triethylamine
and the solvent was removed under reduced pressure to give the
diol (7) as a viscous yellow oil. The crude oil was dissolved
in DCM (500 mL), washed with water (3 × 500 mL), and the
organic layer evaporated under reduced pressure. The resultant
oil was re-dissolved in DCM (80 mL) and (7) was precipitated
by the portion wise addition of petroleum ether (500 mL). The
precipitate was collected by vacuum filtration, dried under high
vacuum to yield pure 7 (124.3 g, 86.2% over three steps). HPLC
Rt 4.26 min. δH (300 MHz CDCl3): 8.18 & 7.70–7.15 (5H, Ar-
H), 5.18 (1H, t, J 9.5), 4.57 (1H, d, J 10.1, H1), 3.92 (1H, m),
3.82 (1H, m), 3.74 (1H, t, J 9.5), 3.47 (2H, m), 2.36 (3H, s). m/z
(ES MS) 340 [M + H]+.
Anhydrous solvents were purchased from Aldrich chemical
company as Sure/Seal™ solvents. All other solvents were LR
grade reagents supplied by Ajax.
Reactions were monitored by reverse phase HPLC under
the following conditions (Table 3). Column: Zorbax SB-
C18 5 µm 4.6 × 50 mm, flow rate: 1 mL min−1 solvent A:
acetonitrile/10 mM ammonium formate (1:9) in water, solvent
B: acetonitrile/10 mM ammonium formate in water (9:1), gra-
dient cycle: t = 0 min 0% B; t = 2 min 0% B; t = 12 min 80%
B; t = 13 min 100% B; t = 15 min 100% B; t = 17 min 0% B;
t = 20 min 0% B.
Experimental
Methyl 2-Azido-4,6-O-benzylidene-2-deoxy-1-thio-
β-D-glucopyranoside (5)
Methyl 2-Azido-3-O-benzoyl-6-O-tert-butyldiphenylsilyl-
2-deoxy-1-thio-β-D-glucopyranoside (1)
Benzaldehydedimethylacetal(96 mL, 0.640 mol)wasaddedtoa
solution of methyl 2-azido-2-deoxy-1-thio-β-d-glucopyranoside
(4) (100 g, 0.425 mol) in dry acetonitrile (1.0 L) followed by
p-toluenesulfonic acid monohydrate (670 mg, 3.5 mmol). The
resulting solution (pH ∼4) was stirred at 60◦C under nitrogen
for 1.5 h then quenched by the dropwise addition of triethyl-
amine until a pH of ∼8–9 was reached (∼10 mL). The solvent
was removed under reduced pressure and the residue was dis-
solved in dichloromethane (DCM) (1.2 L). The organic phase
was washed with brine (1.0 L) followed by water (2 × 1.0 L),
dried over anhydrous magnesium sulphate, and filtered. The sol-
vent was removed under reduced pressure and the crude product
was evaporated from dry acetonitrile (2 × 600 mL) to give crude
acetal (5) as a yellow solid (143.5 g). HPLC Rt 4.90 min. δH
(300 MHz CDCl3): 7.48 (4H, m, Ar-H), 5.50 (1H, s), 4.43 (1H,
The diol (7) (124 g, 0.366 mol) was dissolved in dry DCM (1.5 L)
and the solution was stirred at room temperature under nitro-
gen. Imidazole (41 g, 0.602 mol) was added, followed by tert-
butylchlorodiphenylsilane (TBDPS-Cl, 116 mL, 0.446 mol).
The resulting mixture was heated at reflux for 2 h, and then
allowed to cool to room temperature before further cooling in
an ice water bath to effect precipitation of the imidazole salts.
The salts were removed by vacuum filtration and the filtrate was
washed with 10% citric acid (2 × 1.5 L) and water (1.5 L), and
then dried over anhydrous magnesium sulfate and filtered. The
solvent was removed under reduced pressure to give a viscous
oil (283.3 g), which was purified by column chromatography
(silica gel 300 g, eluent: 5–20% EtOAc/petrol) to yield the
desired product (1) 122.2 g (57.7%) from the initial chromato-
graphy and a further 40 g (19%) from re-chromatography of
mixed fractions. The overall yield of (1) was 162.2 g (76.7%)
ꢀ
d, J 10.1, H1), 4.34 (1H, dd, J 10.4, 6.8, H4), 3.95 (2H, m, H6,6 ),
3.42 (1H, m), 3.38 (1H, m), 3.29 (1H, m), 2.37 (3H, s). m/z (ES
MS) 324 [M + H]+.

Building Blocks for Diversity Libraries
697
as a white solid on removal of solvents. HPLC Rt 7.19 min. impu-
rity corresponding to methyl 2-azido-4-O-benzoyl-6-O-tert-
butyldiphenylsilyl-2-deoxy-1-thio-β-d-glucopyranoside HPLC
Rt 7.14 min. 0.2 area%. δH (500 MHz, CDCl3): 8.12 (2H, d,
Ar-H), 7.71 (4H, t, Ar-H), 7.62 (1H, t, Ar-H), 7.37–7.51 (8H, m,
Ar-H), 5.19 (1H, t, JH3,H4 = 9.4, JH2,H3 9.4, H-3), 4.37 (1H, d,
JH1,H2 10.1, H-1), 3.97 (2H, m, H-6a, H-6b), 3.92 (1H, t, H-4),
3.62 (1H, t, JH2,H3 9.98, H-2), 3.52 (1H, m, H-5), 3.10 (1H, bs,
OH-4), 2.26 (3H, s, SMe), 1.07 (9H, s, tBu). δH (100.6 MHz,
CDCl3): 166.9 (C=O), 135.65, 135.57, 133.63, 132.93, 132.84,
130.02, 129.86, 129.15, 128.53, 127.78, 127.75 (allAr-C), 84.27
(C-1), 79.47 (C-5), 78.21 (C-3), 70.60 (C-4), 64.12 (C-6), 63.48
(C-2), 26.81 (tBuC), 19.23 (tBuC), 12.35 (SMe). m/z (ES MS)
578 [M + H]+. m/z (HRMS, ESI +ve) m/z [M + Na]+ Anal.
Calc. for C30H35N3NaO5SSi, 600.1964. Found: 600.1959.
yellow compound (41 g, 45% yield over three steps). HPLC
Rt 4.30 min. m/z (ESMS) 340 [M + H]+.
Methyl 2-Azido-3-O-benzoyl-6-O-tert-butyldiphenylsilyl-
2-deoxy-1-thio-β-D-allopyranoside (2)
Diol (10) (40 g, 118 mmol) was dissolved in anhydrous DCM
(2.5 L). Imidazole (9.62 g, 141 mmol) was added to the solu-
tion of diol (10), followed by tert-butyldiphenylchlorosilane
(28.2 mL, 108 mmol). The mixture was refluxed at 40◦C under
nitrogen for 1 h. The reaction mixture was cooled to 0◦C and
stirred for a further 30 min during which time a fine white
precipitateofimidazolehydrochloridesettledout.Thewhiteimi-
dazole salt was removed by filtration and rinsed with cold DCM
(300 mL).Thefiltratewaswashedwithwater(1 L)anddriedover
anhydrous magnesium sulfate. The solvent was removed under
reduced pressure to give a dark yellow syrup, which was purified
by column chromatography (silica gel 400 g; eluent petroleum
ether 2 L; Pet/EtOAc 10:1 3 L; Pet/EtOAc 8:1 3 L; Pet/EtOAc
4:1 3 L) to give a white foam (45 g, 66%). The chromatographed
product was further recrystallized with 2.5% EtOAc in hex-
ane to yield (2) as pure white crystals. HPLC Rt 7.15 min. δH
(500 MHz, CDCl3): 8.07 (2H, d, J 7.7, Ar-H), 7.35–7.74 (13H,
m, Ar-H), 5.19 (1H, t, JH3,H4 9.4, JH2,H3 9.4, H-3), 5.93 (1H,
t, H-3), 4.83 (1H, d, JH1,H2 10.1, H-1), 4.03 (1H, dd, JH3,H4
2.5, JH4,H5 9.6, H-4), 3.95 (2H, m, H-6a, H-6b), 3.83 (1H,
ddd, H-5), 3.57 (1H, dd, JH2,H3 10., H-2), 2.72 (1H, bs, 4-OH),
2.26 (3H, s, SMe), 1.06 (9H, s, tBu). δC (100.6 MHz, CDCl3):
166.31 (C=O), 135.64, 135.56, 133.53, 132.94, 132.84, 129.93,
129.87, 129.38, 128.5, 127.774, 127.75 (all Ar-C), 81.14 (C-1),
76.21 (C-5), 71.98 (C-3), 68.48 (C-4), 64.31 (C-6), 60.43(C-
2), 26.80 (tBuC), 19.23 (tBuC), 11.73 (SMe). m/z (ESMS) 578
[M + H]+. m/z (HRMS, ESI +ve) [M + Na]+ Anal. Calc. for
C30H35N3NaO5SSi, 600.1964. Found: 600.1953.
Methyl 2-Azido-4,6-O-benzylidene-2-deoxy-3-
methanesulfonyl-1-thio-β-D-glucopyranoside (8)
4-Dimethylaminopyridine (DMAP) (40.4 g, 331 mmol) and
anhydrous pyridine (50 mL) were added to a pre-cooled (0◦C)
solution of the alcohol (5) (107 g of crude product prepared in the
cognate preparation, ∼331 mmol) in DCM (2 L). Methanesul-
fonyl chloride (31 mL, 402 mmol) was then added in a dropwise
manner over 15 min. The resulting slurry was stirred at room
temperature for 4 h and then water (1.1 L) was added and the sus-
pension was stirred for a further 10 min. The organic phase was
separated and washed with a cold HCl solution (0.54 M, 1.1 L)
followed by water (2 × 1.1 L) before being dried over anhydrous
magnesium sulfate. Removal of the magnesium sulfate by filtra-
tion and evaporation of the solvents under reduced pressure gave
(8) as a white solid (118.5 g), which was used without further
purification; HPLC Rt 5.34 min. m/z (ESMS) 402.06 [M + H]+.
Methyl 2-Azido-3-O-benzoyl-4,6-O-benzylidene-
2-deoxy-1-thio-β-D-allopyranoside (9)
5-((Dimethylamino)methylene)-1,3-dimethylpyrimidine-
2,4,6-(1H,3H,5H)trione
The mesylate (8) (118.5 g, 295 mmol) and sodium benzoate
(63.80 g, 443 mmol) in DMF (2 L) was stirred under nitrogen
at 140◦C for 24 h, then cooled to room temperature, and diluted
with water (2 L). The product was extracted with chloroform
(3 × 2 L) and the organic phase washed with water (2 × 4 L),
brine (3 L), dried over anhydrous magnesium sulfate, filtered,
and evaporated to give a thick black residue. This black residue
was re-dissolved in EtOAc (2 L), heated to 73◦C, and decoloured
by the addition of activated charcoal (100 g) at this tempera-
ture. After filtration, the light yellow solution was evaporated
under reduced pressure to give a yellow solid (9) (105 g),
which was used directly for the next step without further purifi-
cation. HPLC Rt 6.09 min. m/z (ESMS) 428 [M + H]+, 491
[M + Na+CH3CN]+.
N,Nꢀ-dimethylformamide dimethyl acetal (560 mL, 4.08 mol)
was stirred at 0◦C in chloroform (2 L). 1,3-Dimethylbarbituric
acid (600 g, 3.76 mol) was dissolved in chloroform (3.3 L)
and added to the reaction mixture dropwise over 1.5 h. When
the addition was complete, the reaction mixture was allowed
to warm to room temperature and stirred until the reaction
was judged to be complete by tlc (EtOAc/AcOH, 20:1), after
approximately 2 h. The reaction mass was washed with cold
water (3 × 4 L) followed by brine (2 L) and the organic layer
dried over magnesium sulfate and filtered. The solvents were
removed under vacuum to yield 5-[(dimethylamino)methylene]-
1,3-dimethylpyrimidine-2,4,6-(1H,3H,5H)trione (470 g, 58%).
Methyl 2-[Amino-5ꢀ-methylene-1ꢀ,3ꢀ-dimethypyrimidine-
2,4,6-(1H,3H,5H)trione]-2-deoxy-1-thio-β-D-
glucopyranoside (11)
Methyl 2-Azido-3-O-benzoyl-2-deoxy-1-thio-
β-D-allopyranoside (10)
Methyl 2-amino-2-deoxy-1-thio-β-d-glucopyranoside (355 g,
1.79 mol) was suspended in methanol (3 L) and the pH adjusted
to ∼9 by the addition of triethylamine. 5-[(Dimethylamino)
methylene-1,3-dimethylpyrimidine]-2,4,6-(1H,3H,5H )trione
(360 g, 1.70 mol) was dissolved in methanol (5 L) and added
to the stirred solution of methyl 2-deoxy-2-amino-1-thio-β-d-
glucopyranoside. The reaction was warmed to 50◦C for 2 h after
which time the solvents were removed under vacuum to furnish
crude (11) suitable for use in the next stage.
4-Toluenesulfonic acid monohydrate (4.67 g) was added to
a solution of benzoate (9) (105 g) in acetonitrile (1100 mL),
methanol (370 mL) and water (75 mL). The clear solution was
stirred under nitrogen at 50◦C for 11 h. The reaction mixture
was cooled down in an ice bath and neutralized with triethyl-
amine.The solvents were evaporated under reduced pressure and
the residue was purified by column chromatography (silica gel
400 mL; eluent: EtOAc/Pet 1:2 to 1:1) to yield (10) as a pale

698
P. Rajaratnam et al.
Methyl 2-[Amino-5ꢀ-methylene-1ꢀ,3ꢀ-dimethypyrimidine-
2,4,6-(1H,3H,5H)trione]-4,6-O-benzylidene-2-deoxy-
1-thio-β-D-glucopyranoside (12)
dried over anhydrous sodium sulfate. The solvent was evapo-
rated under reduced pressure and the residue purified by column
chromatography (silica gel 200 g; eluent: petroleum ether 4 L,
petroleum ether/DCM (1:1) 3 L, DCM 3 L, and 2% MeOH/DCM
3 L) to give the title compound (15) (49.63 g, 79%). HPLC Rt
6.88 min. m/z (ESMS) 718 [M + H]+, 1435 [2M + H]+.
A mixture containing methyl 2-[amino-5ꢀ-methylene-1ꢀ,3ꢀ-
dimethypyrimidine-2,4,6-(1H,3H,5H)trione]-2-deoxy-1-thio-β-
d-glucopyranoside (11) (265 g, 0.706 mol), dimethyl benzalde-
hyde acetal (116 mL, 776 mmol), and (1S)-(+)-Camphor-10-
sulfonic acid (53.44 g, 212 mmol) in acetonitrile (2.6 L) was
stirred on the rotary evaporator (65◦C bath temperature,
650 mbar) for 4 h. The mixture was then basified to pH 8 with
Et3N. Crude compound (12) (278 g) was taken directly to the
next step without further purification. HPLC Rt 4.61 min. m/z
(ESMS) 464 [M + H]+, 927 [2M + H]+.
Methyl 2-[Amino-5ꢀ-methylene-1ꢀ,3ꢀ-dimethypyrimidine-
2,4,6-(1H,3H,5H)trione]-3-O-benzoyl-6-O-tert-
butyldiphenylsilyl-2-deoxy-1-thio-4-O-
trifluoromethanesulfonyl-β-D-glucopyranoside (16)
A solution of methyl 2-[amino-5ꢀ-methylene-1ꢀ,3ꢀ-dimethy-
pyrimidine-2,4,6-(1H,3H,5H)trione]-3-O-benzoyl-6-O-tert-butyl-
diphenylsilyl-2-deoxy-1-thio-β-d-glucopyranoside (15) (99 g,
125 mmol) and pyridine (25 mL, 312 mmol) in anhydrous DCM
(500 mL) was stirred under nitrogen and cooled in an iced water
bath for 20 min. Triflic anhydride (36.7 mL, 218 mmol) was
added dropwise over 10 min. The mixture was warmed to room
temperature and stirring was continued for a further 30 min.
The reaction mixture was diluted with DCM (2 L) and washed
with 5% citric acid solution (2 × 1 L) followed by brine (1 L),
dried over anhydrous magnesium sulphate, and then evaporated
under reduced pressure to give the title compound (16) as a
golden syrup (115.3 g). The crude residue 16 was used imme-
diately in the following step without further purification. HPLC
Rt 7.39 min. m/z (ESMS) 850 [M + H]+, 1699 [2M + H]+.
Methyl 2-[Amino-5ꢀ-methylene-1ꢀ,3ꢀ-dimethypyrimidine-
2,4,6-(1H,3H,5H)trione]-3-O-benzoyl-4,6-O-benzylidene-
2-deoxy-1-thio-β-D-glucopyranoside (13)
A mixture of crude methyl 2-[amino-5ꢀ-methylene-1ꢀ,3ꢀ-
dimethypyrimidine-2,4,6-(1H,3H,5H)trione]-4,6-O-benzylidene-
2-deoxy-1-thio-β-d-glucopyranoside (12) from the previous step
(184 g) and benzoic anhydride (135 g, 0.597 mol) in anhy-
drous pyridine (720 mL) was stirred overnight at room tem-
perature. The solvent was evaporated under reduced pressure,
co-evaporated from toluene (2 × 400 mL), and the residue taken
up in DCM (2 L). The organic phase was washed with 10% citric
acid solution (2 × 1.4 L) and brine (1.6 L), dried over anhydrous
magnesium sulfate and evaporated under reduced pressure to
give a golden foam 13, which was used directly in the follow-
ing step. HPLC Rt 5.59 min. m/z (ESMS) 568 [M + H]+, 1135
[2M + H]+.
Methyl 2-[Amino-5ꢀ-methylene-1ꢀ,3ꢀ-dimethypyrimidine-
2,4,6-(1H,3H,5H)trione]-4-azido-3-O-benzoyl-6-O-tert-
butyldiphenylsilyl-2,4-dideoxy-1-thio-β-D-
galactopyranoside (3)
Methyl 2-[Amino-5ꢀ-methylene-1ꢀ,3ꢀ-dimethypyrimidine-
2,4,6-(1H,3H,5H)trione]-3-O-benzoyl-2-deoxy-1-thio-
β-D-glucopyranoside (14)
A suspension of methyl 2-[amino-5ꢀ-methylene-1ꢀ,3ꢀ-dimethy-
pyrimidine-2,4,6-(1H,3H,5H)trione]-3-O-benzoyl-6-O-tert-butyl-
diphenylsilyl-2-deoxy-1-thio-4-O-trifluoromethanesulfonyl-β-
d-glucopyranoside (16) (crude residue from previous reaction)
andsodiumazide(80.8 g, 1.24 mol)inanhydrousDMF(400 mL)
was heated under nitrogen at 60◦C for 16 h. The mixture was
allowed to cool to room temperature, diluted with ethyl acetate
(1.5 L) and washed with water (2 × 1 L) and brine (1 L). The
organicphasewasdriedoveranhydroussodiumsulfateandevap-
orated under reduced pressure to give a golden glass, which was
dried under high vacuum to give the title compound (3) (94 g).
The crude product was dissolved in toluene and chro-
matographed on silica gel (300 g) eluting first with toluene (2 L)
followed by toluene/ethyl acetate (20:1, 7.5 L) to yield pure 3
(62 g; 60.5% over 2 steps) as a white solid after solvent evapo-
ration. HPLC Rt 7.31 min. δH (500 MHz, CDCl3): 8.19 (1H, d,
JCH,NH 13.6, CH=), 8.09 (2H, d, J 7.7, Ar-H), 7.16–7.75 (13H,
m, Ar-H), 5.19 (1H, t, JH3,H4 9.4, JH2,H3 9.4, H-3), 4.37 (1H,
d, JH1,H2 10.1, H-1), 5.49 (1H, dd, JH2,H3 10.3, H-3), 4.49 (1H,
d, JH1,H2 10.0, H-1), 4.41 (1H, dd, JH3,H4 3.4, H-4), 3.80–3.95
(4H, m, H-2, H-5, H-6a, H-6b), 3.29 (3H, s, NCH3), 3.28 (3H,
s, NCH3), 2.17 (3H, s, SMe), 1.10 (9H, s, tBu). δC (100.6 MHz,
CDCl3): 165.45 (all C=O), 164.92, 162.45, 159.55 (CH=C),
151.88 (C=O), 135.49, 134.04, 132.78, 132.60, 130.06, 130.02,
129.00, 128.73, 128.20, 128.11, 127.89 (all Ar-C), 92.28
(C=CH), 84.08 (C-1), 77.11 (C-5), 73.87 (C-3), 61.88 (C-6),
60.38 (C-2), 59.92(C-4), 27.78 (NMe), 27.16 (NMe), 26.84
(tBuC), 19.15 (tBuC), 11.90 (SMe). m/z (ESMS) 743 [M + H]+,
1485 [2M + H]+. m/z (HRMS, ESI +ve) [M + Na]+ Anal. Calc.
forC37H42N6NaO7SSi, 765.2503. Found:765.2497.Tworelated
impurities were identified in the final product by LCMS - methyl
The crude methyl 2-[amino-5ꢀ-methylene-1ꢀ,3ꢀ-dimethy-
pyrimidine-2,4,6-(1H,3H,5H)trione]-3-O-benzoyl-4,6-O-benzyl-
idene-2-deoxy-1-thio-β-d-glucopyranoside (13) was dissolved
in a mixture of acetonitrile (800 mL), methanol (400 mL), and
water (40 mL). p-Toluenesulfonic acid (2.27 g, 12 mmol) was
added and the mixture was heated for 3 h at 70◦C. The solu-
tion was neutralized with triethylamine to pH 7 and the solvents
removed under vacuum. The crude product was dissolved in
ethyl acetate (1 L) and precipitated by the addition of petroleum
ether (5 L). The precipitate was collected and crystallized from
methanol:water (80:20, 4 L) to furnish the desired product 14,
which was collected by vacuum filtration and dried under vac-
uum. Yield (167 g, 88%, over three steps). HPLC Rt 3.98 min.
m/z (ESMS) 480 [M + H]+, 959 [2M + H]+.
Methyl 2-[Amino-5ꢀ-methylene-1ꢀ,3ꢀ-dimethypyrimidine-
2,4,6-(1H,3H,5H)trione]-3-O-benzoyl-6-O-tert-
butyldiphenylsilyl-2-deoxy-1-thio-β-D-glucopyranoside (15)
A mixture of methyl 2-[amino-5ꢀ-methylene-1ꢀ,3ꢀ-dimethy-
pyrimidine-2,4,6-(1H,3H,5H)trione]-3-O-benzoyl-2-deoxy-1-
thio-β-d-glucopyranoside (14) (42.179 g, 88.0 mmol) and imi-
dazole (600 mg) in pyridine (100 mL) was stirred and heated at
120◦C for 50 min before tert-butylchlorodiphenylsilane (32 mL,
120 mmol) was added portion-wise. The reaction mixture was
stirredandheatedfor1.5 handthenallowedtocooldowntoroom
temperature.The solvent was evaporated under reduced pressure
and the residue was taken up in DCM (350 mL). The organic
phase was washed with a 10% citric acid solution twice and then

Building Blocks for Diversity Libraries
699
2-[amino-5ꢀ-methylene-1ꢀ,3ꢀ-dimethypyrimidine-2,4,6-(1H,3H,
5H)trione]-3-O-benzoyl-6-O-tert-butyldiphenylsilyl-2-deoxy-
1-thio-β-d-galactopyranoside (0.25%) and methyl 2-[amino-
5ꢀ-methylene-1ꢀ,3ꢀ-dimethypyrimidine-2,4,6-(1H,3H,5H)trione]-
4-azido-3-O-benzoyl-2,4-dideoxy-1-thio-β-d-galactopyranoside
(0.2%).
[5] T. Opatz, C. Kallus, T. Wunberg, W. Schmidt, S. Henke, H. Kunz,
Carbohydr. Res. 2002, 337, 2089. doi:10.1016/S0008-6215(02)
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D. Gange, J. Org. Chem. 1998, 63, 2802. doi:10.1021/JO980164M
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Accessory Publication
gCOSY and HSQC 2D NMR spectra of final products are
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