G. Lopez et al. / Bioorg. Med. Chem. Lett. 17 (2007) 434–438
437
angles were identified (for 20 independent runs per li-
gand). A grid of 60, 60 and 60 points in x, y and z
directions was built, centred on the acid/base catalyst
(d, 1H, H-1, J1,2 = 2.4 Hz), 4.13 (dd, 1H, H-2,
J2,3 = 4.2 Hz), 4.09–3.92 (m, 2H, H-4 H-3), 3.65–3.55
(m, 2H, H-5a, H-5b); 13C NMR (CD3OD) d(ppm):
160.9 (SCS), 120.7 (2 CHN), 111.5 (CHCHCN), 92.8
(C-1), 89.2 (C-4), 85.7 (C-2), 81.2 (C-3), 65.8 (C-5);
HRMS (ESI+) for C9H12O4N2SNa: m/z [M]+: calcd
267.0415; found 267.0415.
˚
residue Glu-176. A grid spacing of 0.375 A and a dis-
tance-dependent function of the dielectric constant
were used for the calculation of the energetic map.
The default settings were used for all parameters.
At the end of docking, ligands with the most favour-
able free energy of binding and a similar orientation
as the ‘natural’ substrate were selected as the resul-
tant complex structures. All calculations were carried
out on PC based machines. The resultant structure
files were analyzed using Pymol visualization
programs.20
Pyridin-2-yl 1-thio-a-L-arabinofuranoside (4). CH2Cl2/
20
MeOH (9:1), Rf 0.6; mp: 169 °C; ½aꢂ +22 (c 1, MeOH);
D
1H NMR (CD3OD) d (ppm): 8.31 (ddd, 1H, CHN,
J = 0.9 Hz, J = 1.8 Hz, J = 4.9 Hz), 7.52 (ddd, 1H,
CHCHCHN, J = 7.5 Hz, J = 7.6 Hz), 7.21 (ddd, 1H,
CHCHCHCHN, J = 1.1 Hz), 7.00 (ddd, 1H, CHCHN),
6.05 (d, 1H, H-1, J1,2 = 3.1 Hz), 4.10 (dd, 1H, H-2,
J2,3 = 4.3 Hz), 4.00 (dd, 1H, H-3, J3,4 = 4.0 Hz), 3.96-
3.92 (m, 1H, H-4), 3.64 (dd, 1H, H-5a, J5a,5b = 11.9 Hz
J4,5a = 3.3 Hz), 3.56 (dd, 1H, H-5b, J4,5b = 4.0 Hz); 13C
NMR (CD3OD) d (ppm): 159.2 (SCN), 149.7 (CHN),
137.0 (CHCHCHN), 123.0 (CHCHCHCHN), 120.5
(CHCHN), 89.6 (C-1), 85.8 (C-4), 83.3 (C-2), 77.8 (C-
3), 62.3 (C-5); HRMS (ESI+) for C10H13O4NSNa: m/z
[M]+: calcd 243.0565; found 243.0569.
Synthesis. Optical rotations were measured on a Perkin-
Elmer 341 polarimeter. Melting points were determined
on a Reichert microscope and are uncorrected. Thin-
layer chromatography (TLC) analyses were conducted
on E. Merck 60 F254 Silica Gel non-activated plates
and compounds were revealed using a 5% solution of
H2SO4 in EtOH followed by heating. For column chro-
matography, Geduran Si 60 (40–63 lm) Silica Gel was
1
used. H, 13C, HMQC and COSY NMR spectra were
recorded on a Bruker ARX 400 spectrometer at
400 MHz for 1H and 100 MHz for 13C, respectively.
Chemical shifts are given in d-units (ppm) measured
downfield from Me4Si. The HRMS were measured at
the CRMPO with a MS/MS ZabSpec TOF Micromass
using m-nitrobenzylic alcohol as a matrix and accelerat-
ed caesium ions for ionisation.
Benzimidazol-2-yl
1-thio-a-L-arabinofuranoside
(5).
20
D
CH2Cl2/MeOH (9:1), Rf 0.61; mp: 158 °C; ½aꢂ +69
(c 1, MeOH); 1H NMR (CD3OD) d (ppm): 7.51–
7.49 (m, 2H, CHCN, CHCNH), 7.21–7.19 (m, 2H,
CHCHCN, CHCHCNH), 5.76 (d, 1H, H-1,
J1,2 = 3.8 Hz), 4.10 (dd, 1H, H-3, J2,3 = 4.4 Hz,
J3,4 = 3.9 Hz), 4.08 (ddd, 1H, H-4, J4,5a = 2.8 Hz,
J4,5b = 5.5 Hz), 3.88 (dd, 1H, H-2), 3.78 (dd, 1H, H-
5a, J5a,5b = 12.2 Hz), 3.66 (dd, 1H, H-5b); 13C NMR
(CD3OD) d (ppm): 149.6 (SCN), 134.3, 134.1 (CN,
CNH), 130.1, 128.9 (CHCHCN, CHCHCNH), 123.9,
121.3 (CHCN, CHCNH), 92.3 (C-1), 85.7 (C-4),
83.7 (C-2), 77.9 (C-3), 62.5 (C-5); HRMS (ESI+) for
C12H14O4N2SNa: m/z [M]+: calcd 305.0572; found
305.0576.
Thiazol-2-yl 1-thio-a-L-arabinofuranoside (1). CH2Cl2/
20
MeOH (9:1), Rf 0.5; mp: 157 °C; ½aꢂ +25 (c 1, MeOH);
D
1H NMR (CD3OD) d (ppm): 7.70 (d, 1H, CHS,
J = 3.3 Hz), 7.50 (d, 1H, CHN), 5.60 (d, 1H, H-1, J1,2
3.3 Hz), 4.07 (dd, 1H, H-2, J2,3 4.2 Hz), 3.99–4.03 (m,
1H, H-4), 3.94 (dd, 1H, H-3, J3,4 = 6.4 Hz), 3.72 (dd,
1H, H-5a, J4,5a = 3.3 Hz, J5a,5b = 12.4 Hz), 3.63 (dd,
1H, H-5b, J4,5b = 4.9 Hz); 13C NMR (CD3OD)
d(ppm): 160.1 (SCN), 144.1 (CHS), 123.5 (CHN), 94.3
(C-1), 88.4 (C-4), 86.5 (C-2), 79.8 (C-3), 62.7 (C-5);
HRMS (ESI+) for C8H11O4NS2Na: m/z [M]+: calcd
272.0027; found 272.0031.
Thiazol-2-yl 1-thio-b-D-galactofuranoside (6). CH2Cl2/
MeOH (9:1), Rf 0.4; H NMR (CD3OD) d (ppm): 7.72
1
(d, 1H, CHN, J = 3.3 Hz), 7.56 (d, 1H, CHS), 5.56 (d,
1H, H-1, J1,2 = 3.8 Hz), 4.12 (dd, 1H, H-3, J2,3 = 4.6 Hz,
J3,4 = 6.6 Hz), 4.07–4.04 (m, 2H, H-2, H-4), 3.72 (ddd,
1H, H-5, J4,5 = 2.8 Hz, J5,6a = 6.1 Hz, J5,6b = 6.1 Hz),
3.60–3.58 (m, 2H, H-6a, H-6b); 13C NMR (CD3OD) d
(ppm): 160.2 (SCN), 144.3 (CHS), 123.5 (CHN), 93.8
(C-1), 85.0 (C-4), 78.7 (C-2), 78.3 (C-3), 72.0 (C-5), 64.4
(C-6); HRMS (ESI+) for C9H13NO5S2Na: m/z [M]+: calcd
302.0133; found 302.00136.
Benzothiazol-2-yl 1-thio-a-L -arabinofuranoside (2).
20
D
CH2Cl2/MeOH (9:1), Rf 0.5; mp: 192 °C; ½aꢂ +74 (c
1
1, MeOH); H NMR (CD3OD) d (ppm): 7.83–7.81 (m,
2H, CHCN, CHCS), 7.49–7.47 (m, 2H, CHCHCN,
CHCHCS), 5.80 (d, 1H, H-1, J1,2 = 4.2 Hz), 3.88 (dd,
1H, H-2, J2,3 4.4 Hz), 3.85–3.75 (m, 2H, H-4, H-3),
3.60 (dd, 1H, H-5a, J4,5a = 3.4 Hz, J5a,5b = 12.1 Hz),
3.48 (dd, 1H, H-5b, J4,5b = 5.0 Hz); 13C NMR (CD3OD)
d (ppm): 150.6 (SCS), 134.9, 134.3 (CHCN, CHCS),
131.1, 129.8 (CHCHCS, CHCHCN), 124.9, 122.3
(CHCS, CHCN), 90.7 (C-1), 85.7 (C-4), 83.9 (C-2),
78.2 (C-3), 62.8 (C-5); HRMS (ESI+) for C12H13O4N-
S2Na: m/z [M]+: calcd 322.0184; found 322.0187.
Enzymatic inhibition. The hydrolytic activity of AbfD3
was quantified after incubation of the enzyme (0.7 IU)
with p-NP-a-L-Araf at 60 °C in water in the absence or
presence of inhibitor. Continuous release of p-nitrophe-
nol was measured at 400 nm. One unit of activity corre-
sponds to the amount of enzyme releasing 1 lmol of p-
nitrophenol per minute. The inhibitor and the substrate
aqueous solutions were mixed and prewarmed before
the addition of enzyme. Initial rates of the hydrolytic
reaction were used in order to determine the relative
activity using various inhibitor concentrations between
Pyrimidin-2-yl
1-thio-a-L
-arabinofuranoside (3).
20
CH2Cl2/MeOH (9:1), Rf 0.5; mp: 201 °C; ½aꢂ : +107 (c
D
1
1, MeOH); H NMR (CD3OD) d (ppm): 8.42 (d, 2H,
CHN, J = 4.9 Hz), 7.40–7.35 (m, 1H, CHCHN), 6.20