Appendix S1 : Synthesis procedure for compound BAR0329
O
O
N
H
O
Cl
4
O
O
a
O
N
H
O
c
O
Cl
N
d
HO
N
Cl
X
2 X = Cl
1
O
Cl
5
b
3 X = OMe
O O
S
O
e
N
6
O
Cl
NH
Boct
HN
N
f
N
Boct
HN
N
N
O
Cl
N
N
H2N
N
N
O
Cl
NH
tBoc
7
8
BAR0329
N
tBoc
Scheme 1: Synthetic route to compound BAR0329: (a)POCl3, DMF, 80°C, 16h; (b) NaOMe/MeOH, 48h,
reflux, 48%; (c) LiAlH4, THF, 0°-10°C, 31%; (d) MsCl, Et3N, CH2Cl2, 0°-10°C, 3h, 100%; (e) KI, Et3N,
CH3CN, reflux, 16h (27%); (f) 1 :1 TFA/CH2Cl2, 95%.
1
H NMR spectra were recorded on a Bruker Avance DRX-400 spectrometer with standard pulse
sequences, operating at 400 MHz and using DMSO-d6 as solvent. Chemical shifts (δ) are reported
in parts per million (ppm). Elemental analyses were carried out using a on a Carlo-Erba EA1110
analyser. DMF: dimethylformamide; THF: tetrahydrofurane.
Ethyl 2-chloro-3-(4-chlorobenzyl)quinoline-6-carboxylate (2).
Phosphoroxychloride (34.4
mL; 0.369 mol) was added dropwise to stirred dry DMF (12.6 mL; 0.158 mol) under nitrogen
atmosphere at 0°C. The mixture was stirred for one hour at 0°C to 5°C and treated portionwise
with Ethyl-4-[[3-(4-Chlorophenyl)propionyl]amino]benzoate (1) (17.5 g; 0.053 mol) [1]. The
mixture was brought to room temperature, heated to 80°C and stirred for 16 hours, cooled, and
poured into a mixture of ice and ethyl acetate (300 mL). The mixture was extracted with Ethyl
acetate (3 × 100 mL), and the combined organic layers were subsequently washed with saturated
Appendix S1 : Synthesis procedure for compound BAR0329
NaHCO3 water (2 × 50 mL), water, brine, and dried (MgSO4), filtered, and the solvent was
evaporated yielding compound 2 (19 g), which was used without further purification in the next
reaction.
Methyl 3-(4-chlorobenzyl)-2-oxo-1,2-dihydroquinoline-6-carboxylate (3). A 30 % sodium
methoxide in methanol (100 mL; 0.527 mol) was added to a solution of compound 2 (19 g;
0.0527 mol) in methanol (100 mL) and the solution was stirred for 48 hours reflux temperature.
The reaction was cooled to room temperature and the solvent was evaporated under reduced
pressure. The residue was treated with a 1:1 mixture of water and CH2Cl2 (200 mL) and filtered.
The precipitate contained mainly compound 4, which was treated with 3N HCl (2 × 5 mL),
washed with water, diethyl ether and dried in vacuo to yield compound 4 as a solid (Mp (Kofler)
= 228°C) (3 g; 17%). The organic layer of the water/CH2Cl2 fraction was separated, dried
(MgSO4) and the solvent was evaporated yielding compound 3 as a white solid (8.7 g; 48%). Mp
(Kofler) = 149 °C. 1H NMR (400 MHz, DMSO-d6) δ ppm 3.9 (s, 3 H), 4.0 - 4.05 (m, 5 H), 7.29
(d, J=7.7 Hz, 2 H), 7.35 (d, J=7.7 Hz, 2 H), 7.82 (d, J=9.5 Hz, 1 H), 8.1 (dd, J=9.5, 2.8 Hz, 1 H),
8.2 (s, 1 H), 8.51 (d, 2.8 Hz, 1 H). Anal. calcd for (C19H16ClNO3): C, 66.77; H, 4.72; N, 4.10.
Found: C, 67.02; H, 4.73; N, 4.06.
[3-(4-chlorobenzyl)-2-methoxyquinolin-6-yl]methanol (5). Compound 3 (8.7 g; 0.0255 mol)
was added portionwise at 0°C to a suspension of LiAlH4 (1.35 g; 0.355 mol) in dry THF (130
mL) under nitrogen atmosphere. The mixture was stirred at between 5°C and 10°C for 1 hour.
Ethyl acetate (400 mL) was added, and then carefully water (200 mL) was added dropwise. The
mixture was filtered over celite, the organic layer was separated and dried (MgSO4), filtered and
evaporated under reduced pressure. The residue was purified by flash chromatography over
silica gel (CH2Cl2/MeOH 98.5/1.5; 70-200 M) yielding compound 5 as a white solid (2.52 g;
Appendix S1 : Synthesis procedure for compound BAR0329
31%). Mp (Kofler) = 110 °C. 1H NMR (400 MHz, DMSO-d6) δ ppm 3.95 (s, 3 H), 4.01 (s, 2H),
4.61 (d, J=4.0 Hz, 2 H), 5.3 (t, J=4.0 Hz, 1 H), 7.29 (d, J=7.7 Hz, 2 H), 7.35 (d, J=7.7 Hz, 2 H),
7.56 (dd, J=9.5, 2.8 Hz, 1 H), 7.70 - 7.75 (m, 2 H), 7.97 (s, 1 H). Anal. calcd for (C18H16ClNO2):
C, 68.90; H, 5.14; N, 4.46. Found: C, 68.78; H, 5.19; N, 4.42.
[3-(4-chlorobenzyl)-2-methoxyquinolin-6-yl]methyl methanesulfonate (6).
A solution of
methanesulfonyl chloride (1.5 mL; 0.0194 mol) in dry CH2Cl2 (10 mL) was added dropwise at
0°C to a stirred solution of compound 5 (4.05 g; 0.0129 mol) and triethylamine (3.6 mL; 0.0258
mol) in CH2Cl2 (70 mL) under nitrogen atmosphere. After stirring for 3 hours at 10°C the
solvent was evaporated to yield quantitatively compound 6 (5 g), which was used in the next step
as such.
4-{[3-(4-chlorobenzyl)-2-methoxyquinolin-6-yl]methyl}piperazine-1-carboximidamide
(8).
A mixture of compound 6 (5 g ; 0.0129 mol), [tert-Butoxycarbonylimino(piperazin-1yl)methyl]carbamic acid tert-butyl ester [2,3] (4.2 g; 0.0129 mol), triethylamine (2 mL; 0.0142
mol), potassium iodide (few crystals) in acetonitrile (150 mL) was stirred and refluxed for 16
hours. The reaction was cooled to room temperature and the solvent was evaporated under
reduced pressure. The residue was triturated with water (50 mL) and extracted with CH2Cl2 (2 ×
50 mL). The combined organic layers were dried (MgSO4), filtered and evaporated in vacuo.
The residue was purified by column chromatography over silica gel (CH2Cl2/EtOAc 60/40; 15-40
M) yielding compound 7 (2.2 g; 27%). Compound 7 (2.2 g; 0.0035 mol) was dissolved in a 1:1
mixture of trifluoroacetic acid and CH2Cl2 (60 mL) and stirred at room temperature for 2 hours.
The solvent was evaporated in vacuo and the residue was crystallized from iPrOH/diethyl
ether/DIPE to yield a compound 8 as a white solid difluoroacetic acid salt (2.2 g; 95 %). Mp
(Kofler) = 190 °C. 1H NMR (400 MHz, DMSO-d6) δ ppm 3.2 (br. s, 8 H), 4.0 (s, 3 H), 4.05 (s, 2
Appendix S1 : Synthesis procedure for compound BAR0329
H), 4.41 (br.s, 1 H), 7.30 (d, J=7.7 Hz, 2 H), 7.35 (d, J=7.7 Hz, 2 H), 7.58 - 7.79 (m, 5 H), 7.83
(d, J=9.5 Hz, 1 H), 7.90 (br s, 1 H), 7.96 (s, 1 H). Anal. calcd for (C23H26ClN5O).2C2HF3O2: C,
49.74; H, 4.33; N, 10.74. Found: C, 48.26; H, 4.05; N, 9.82.
References
[1] Albright, J.D., DeVries, V.G., Largis, E.E., Miner, T.G., Reich, M.F., Schaffer, S.A.,
Shepherd, R.G. and Upeslacis, J. (1983) Potential antiatherosclerotic agents. 2. (Aralkylamino)and (alkylamino)benzoic acid analogs of cetaben. J. Med. Chem. 26, 1378-1393.
[2] An, H., Wang, T., Mohan, V., Griffey, R.H. and Dan Cook, P. (1998) Solution phase
combinatorial chemistry. Discovery of 13- and 15-membered polyazapyridinocyclophane
libraries with antibacterial activity. Tetrahedron 54, 3999-4012.
[3] Nicolaou, K.C., Trujillo, J.I., Jandeleit, B., Chibale, K., Rosenfeld, M., Diefenbach, B.,
Cheresh, D.A. and Goodman, S.L. (1998) Design, synthesis and biological evaluation of
nonpeptide integrin antagonists. Bioorg. Med. Chem. 6, 1185-1208.