Journal of Natural Products
Article
(rel int) 144 [M + H]+ (100), 116 (15), 89 (4); HRESMS m/z
285.9732 [M + H]+ (calcd for C10H9INO 285.9729).
through Celite, which was washed with CH2Cl2 (15 mL). The
combined fractions were washed with H2O (2 × 10 mL) and saturated
brine (2 × 10 mL) and dried over anhydrous MgSO4, and the organic
fraction was concentrated in vacuo to yield an orange oil (118 mg). A
portion of the crude reaction mixture (46 mg) was dissolved in EtOH
(2 mL) followed by the addition of NH4OAc (60 mg, 5 equiv) and
allowed to stir (5 h). The bright orange solution was concentrated in
vacuo and redissolved in CH2Cl2 (10 mL). The organic solution was
once again washed with H2O (2 × 10 mL) and saturated brine (2 × 10
mL) and dried over anhydrous MgSO4 to yield a yellow, amorphous
solid (40 mg). Purification via Si flash chromatography (hexane/
EtOAc, 5:1), yielded 33 (20 mg, 0.035 mmol, 51% over two steps).
The same procedure was applied to varying quantities of N-Boc-
protected 3-acetylindoles 27−30 depending on availability using the
same equivalents and solvent ratios above. For spectroscopic data of
compounds 33−37 see the Supporting Information.
General Procedure for the Thermal Cleavage of N-tert-
Butoxycarbonyl-Substituted Deoxytopsentins (5−10). Com-
pounds 32−37 were heated to 180 °C as dry solids under an inert
atmosphere of argon. Once the desired temperature was achieved, gas
bubbles were generated and subsided after 5 min, at which time the
heat source was removed and the compounds were allowed to reach
room temperature, yielding compounds 5−10 in quantitative yield. All
compounds were routinely subjected to RP-HPLC (MeOH/H2O,
3:1), to deliver compounds suitably pure for bioassay. For
spectroscopic data of compounds 5−7, 9, and 10 see the Supporting
Information. Compounds 527 and 628 have been reported previously as
marine natural products.
General Procedure for the Synthesis of N-tert-Butoxycar-
bonyl-Substituted 3-Acetylindoles (25−31). Boc2O (2020 mg,
1.5 equiv) and DMAP (77 mg, 0.1 equiv) were added to a stirring
solution of 12 (1000 mg, 6.3 mmol, 1 equiv) in HPLC grade MeCN
(15 mL) at 0 °C under an atmosphere of argon. After 3 h the MeCN
was removed in vacuo and the solid recrystallized from MeOH to yield
25 (1565 mg, 6.04 mmol, 96%) The same procedure was applied to
varying quantities of 3-acetylindoles 13−18 depending on availability
using the same equivalents and solvent ratios as above. For
spectroscopic data of compounds 25, 26, and 28−31 see the
Supporting Information. Compounds 2540 and 2941 have been
reported previously.
6-Chloro-3-acetyl-1-(tert-butoxycarbonyl)indole (27): white nee-
dles from MeOH; yield 94%; mp 180−182 °C; IR (cm−1) 2970 2162
1732 1665 1548 1361 1272 1150; 1H NMR (600 MHz, CDCl3) δ 8.28
(1H, d, J = 8.4 Hz, H-4), 8.18 (1H, s, H-2), 8.15 (1H, s, H-7), 7.32
(1H, dd, J = 8.5, 1.7 Hz, H-5), 2.55 (3H, s, H-2′), 1.71 (9H, s, H-3″);
13C NMR (150 MHz, CDCl3) δ 193.6 (C, C-1′), 148.7 (C, C-1″),
135.9 (C, C-7a), 132.5 (CH, C-2), 131.5, (C, C-6), 125.8 (C, C-3a),
124.9 (CH, C-5), 123.5 (CH, C-4), 120.3 (C, C-3), 115.3 (CH, C-7),
85.9 (C, C-2″), 28.0 (3 × CH3, C-3″), 27.6 (CH3, C-2′) ppm; ESMS
m/z (rel int) 238 [M + H]+ (5), 194 (7), 152 (17), 117 (100), 89
(10), 57 (15); HRESMS m/z 294.0889 [M + H]+ (calcd for
C15H1735ClNO3 294.0897).
Synthesis of N-tert-Butoxycarbonyl-Substituted Deoxytop-
sentin (32). Freshly sublimed SeO2 (286 mg, 2.59 mmol, 2.7 equiv)
was added to a mixture of 1,4-dioxane (7 mL) and H2O (200 μL, 11
equiv), after which the reaction mixture was heated to 60 °C to allow
all the SeO2 to dissolve. To this was added 25 (250 mg, 0.96 mmol, 1
equiv), and the temperature increased to 75 °C. After 6 h the crude
reaction mixture was filtered through Celite, which was washed with
CH2Cl2 (20 mL). The combined fractions were washed with H2O (2
× 10 mL) and saturated brine (2 × 10 mL) and dried over anhydrous
MgSO4, and the organic fraction was concentrated in vacuo to yield an
orange oil (287 mg). The crude reaction mixture was dissolved in
EtOH (7 mL) followed by the addition of NH4OAc (374 mg, 5 equiv)
and allowed to stir for 5 h. The bright orange solution was
concentrated in vacuo and redissolved in CH2Cl2 (15 mL). The
organic solution was once again washed with H2O (2 × 10 mL) and
saturated brine (2 × 10 mL) and dried over anhydrous MgSO4 to yield
a yellow, amorphous solid (248 mg). Purification via Si flash
chromatography (hexane/EtOAc, 5:1) yielded 32 (142 mg, 0.27
mmol, 53% over two steps).
6″-Chloro-1H″-indol-3-yl[5-(6′-chloro-1H′-indol-3-yl)-1H-imida-
zole-2-yl]methanone (6′,6″-dichlorodeoxytopsentin) (8): yellow,
amorphous solid; yield 100%; IR (cm−1) 2880 1672 1519 1445
1
1241 1137; H NMR (600 MHz, DMSO-d6, 1 equiv TFA) δ 12.26
(1H, s, NH-1″), 11.54 (1H, s, NH-1′), 9.19 (1H, s, H-2″), 8.35 (1H, d,
J = 8.5 Hz, H-4″), 8.06 (1H, d, J = 8.4 Hz, H-4′), 8.03 (1H, s, H-2′),
7.79 (1H, s, H-4), 7.62 (1H, d, J = 1.6 Hz, H-7″), 7.51 (1H, d, J = 1.6
Hz, H-7′), 7.29 (1H, dd, J = 8.5, 1.8 Hz, H-5″), 7.14 (1H, dd, J = 8.5,
1.7 Hz, H-5′); 13C NMR (150 MHz, DMSO-d6, 1 equiv TFA) δ 175.2
(C, C-8″), 144.3 (C, C-2), 138.0 (CH, C-2″), 136.8 (C, C-7a″), 136.7
(C, C-7a′), 129.8 (C, C-6″), 128.3 (C, C-6′), 127.6 (C, C-3a″), 126.4
(C, C-3a′), 125.3 (C, C-5), 124.8 (CH, C-5″), 123.4 (CH, C-5′),
122.7 (CH, C-4″), 122.4 (CH, C-4′), 122.3 (CH, C-2′), 121.2 (CH,
C-4), 120.0 (C, C-3″), 113.6 (CH, C-3′), 112.2 (CH, C-7″) 111.5
(CH, C-7′) ppm; ESMS m/z (rel int) 244 [M + H]+ (5), 191 (22),
189 (100), 181 (18), 177 (12), 149 (8); HRESMS m/z 395.0455 [M
+ H]+ (calcd for C20H1335Cl2N4O 395.0466).
Synthesis of 7′,7″-Dichlorodeoxytopsentin (11). Compound
11 was synthesized as per the method described above for halogenated
topsentin analogues 6−10 with the exception of the benchtop
purification step, which was omitted in favor of deprotection of the
crude reaction mixture. Routine RP-HPLC (MeOH/H2O, 3:1)
delivered compound 11 as a yellow, amorphous solid (14 mg, 0.035
mmol, 35% over three steps). For spectroscopic data see the
Supporting Information.
Ligand−Receptor Docking Studies. All modeled ligands were
constructed using Discovery Studio 3.5 Visualizer,42 and docking
experiments were performed using AutoDock Vina26 against crystal
structures of MRSA pyruvate kinase (PDB accession number 3T0T10
and 3T0715). The crystal structures are in complex with known
inhibitors. Protein crystal structures were prepared for docking by
removing the ligand present in the active site, followed by the addition
of polar hydrogens in AutoDock tools. Atoms were assigned by the
AutoDock 443 typing rules, and electrostatic charges were calculated as
Gasteiger charges. Docking coordinates were defined by X, Y, and Z
coordinates obtained from the originally cocrystallized ligand. The
search space was confined to a cube of 30 Å with docking repeated
eight times in the case of local searches and 80 Å with docking
repeated 64 times in the case of global searches. Our method was
validated by redocking the crystal structure ligands using our defined
criteria. Docking success was evaluated by the lowest relative binding
energy and visual inspection of ligand−receptor interaction.
(N1′,N1″-Di-tert-butoxycarbonyl)indol-3-yl[5-(indol-3-yl)-1H-imi-
dazole-2-yl]-methanone (32): yellow, amorphous solid; yield 53%; IR
(cm−1) 2980, 1741, 1667, 1370, 1150, 749; 1H NMR (600 MHz,
DMSO-d6) δ 13.62 (1H, s, NH-1), 9.69 (1H, s, H-2″), 8.45 (1H, d, J =
7.8 Hz, H-4″), 8.38 (1H, d, J = 7.7 Hz, H-4′), 8.19 (1H, d, J = 8.1 Hz,
H-7″), 8.14 (2H, m, H-2′, H-7′), 8.09 (1H, s, H-4), 7.42 (4H, m, H-5′,
H-5″, H-6′, H-6″), 1.69 (9H, s, H-11″), 1.68 (9H, s, H-10′); 13C NMR
(150 MHz, DMSO-d6) δ 176.2 (C, C-8″), 149.1 (C, C-9″), 148.6 (C,
C-8′), 144.8 (C, C-2), 136.6 (CH, C-2″), 136.4 (C, C-5), 135.1 (C, C-
7a″), 134.7 (C, C-7a′), 127.9 (C, C-3a″), 127.8 (C, C-3a′), 125.5
(CH, C-6″), 124.7 (CH, C-6′), 124.4 (CH, C-5″), 123.1 (CH, C-5′),
122.3 (CH, C-4″), 122.0 (CH, C-2′), 121.1 (CH, C-4′), 118.6 (CH,
C-4), 116.6 (C, C-3″), 116.5 (CH, C-3′), 114.9 (CH, C-7″), 114.8
(CH, C-7′), 85.4 (C, C-10″), 84.1 (C, C-9′), 27.7 (3 × CH3, C-11″),
27.6 (3 × CH3, C-10′) ppm; ESMS m/z (rel int) 415 [M + H]+ (9),
371 (10), 254 (50), 228 (5), 210 (10), 182 (15), 155 (100), 144 (18),
116 (5); HRESMS m/z 527.2308 [M + H]+ (calcd for C30H31N4O5
527.2294).
General Procedure for the Synthesis of N-tert-Butoxycar-
bonyl-Substituted Deoxytopsentins (33−37). Freshly sublimed
SeO2 (248 mg, 2.25 mmol, 6.3 equiv) was added to a mixture of 1,4-
dioxane (4 mL) and H2O (101 μL, 15 equiv), after which the reaction
mixture was heated to 60 °C to allow all the SeO2 to dissolve. To this
was added 26 (100 mg, 0.36 mmol, 1 equiv), and the temperature
increased to 75 °C. After 6 h the crude reaction mixture was filtered
F
dx.doi.org/10.1021/np500755v | J. Nat. Prod. XXXX, XXX, XXX−XXX