Supplemental Information Supplemental information contains 6 figures and Supplemental Experimental Procedures.

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1 Supplemental Information Supplemental information contains 6 figures and Supplemental Experimental Procedures. Supplemental Figure Legends Fig. S1. HTS of Vpr inhibitors in the RIKE PDepo, related to Fig. 1. verall primary screening results for plates A. AA009 AA165 and B. AA The hit inhibitor 3 is indicated by the arrow, and the hit zone is denoted by the area above the dotted lines (100% growth in the presence of control 1). We screened 6664 natural products at four concentrations (33, 11, 3.7 and 1.2 µg/ml) depicted by the darker to lighter shades of blue. Symbols represent average of readings from two plates at 48 hours. Fig. S2. Paper Disc Assay for Hit Compound 3 and its Derivatives (4-10), related to Fig. 2. Compounds tested included 3*, a resynthesis of hit 3; D, DMS and L, leucine to silent Vpr expression (control). All paper discs contained 50 µg compound except for 1, which contained 20 µg, as the latter was toxic at high concentrations. Relative potency was gauged by comparing the diameter of the yeast growth around the paper discs (ø = 6 mm), and is shown in Fig. 2. Fig. S3. Inhibitory Assay of Vpr Mutants with 1 and 3, related to Fig. 4. Growth of wild-type and mutant Vpr-expressing yeasts at 36 hours in the presence or absence of compounds. Single point alanine mutants of Vpr A and B were assayed for their response towards 1 and 3 on a 96-well plate format. A profile of attenuated Vpr cell cycle arrest activity can be seen. otably, the inhibitory activity of 3 was cancelled or reduced in selected mutants (asterisks). In this analysis, compounds 1 and 3 were used at their optimum concentrations (final concentrations are 1, 5.5 µm; 3, 100 µm). Error bars denote s.d. Fig. S4. Vpr Binds to Hit Compound 3, related to Fig. 5. Flag-tagged Vpr proteins bound to beads were detected by Western blot after SDS-PAGE. Vpr in yeast total cell lysates (2 µg in 500 µl binding buffer) was incubated with 10 µl of beads. The amounts of Vpr in total cell lysate relative to the inputs used in the binding reactions are shown as fractions of input (1/20, 1/10 and 1/5). 3, 3-immobilized beads and C, control beads. Fig. S5. Vipirinin did not have any cytotoxic effect on macrophages and T cells. A. Macrophages prepared in essentially same condition as the virus infection assays were cultured in the presence (1 µg/ml) or absence of compounds and examined under microscopes. Size bar= 100 µm B. T cells (PHA and IL-2 stimulated peripheral blood mononuclear cells) were cultured in the presence or absence of compounds at the concentrations indicated. The growth of compounds treated cells were determined by MTT assays and shown in relative values to that of non-treated cells. Fig. S6. Vipirinin did not affect PIC transport. Primary macrophages were infected with L-Luc-E-R in the presence or absence of compounds and total cellular DA was extracted 48 h after infection. Early and late viral reverse transcription products of proviral DA and two-ltr circles in the nucleus were analysed by PCR as described in EXPERIMETAL PRCEDURES. DAs from noninfected cells (lane 1), infected cells in the absence of compounds (lane 2), in the presence of 0.1µg/ml and 1.0 µg/ml of fumagillin 1 (lanes 3, 4, respectively), 0.1µg/ml and 1.0 µg/ml of vipirinin 9 (lanes 5, 6, respectively) and 0.1µg/ml and 1.0 µg/ml of PD (lanes 7, 8, respectively) were used as template for PCR reaction, respectively. GAPDH gene was also amplified and analyzed as a control of PCR reaction. Sizes of each PCR products are shown. 1

2 Supplemental Experimental Procedures HTS Parameters Category Parameters Description Assay ature of the assay Vpr cell cycle arrest activity in yeast Assay strategy Reagents and sources Assay Protocol Additional comments Library Size 6664 screened. Source Details Additional comments Identification of Vpr inhibitors by the growth recovery of yeast expressing Vpr in the presence of small molecules. Yeast strain MLC30 carrying a copper inducible Vpr expression plasmid pyex-bx (AMRAD BITECH, Vic., Australia) 99 µl Vpr expressing yeast (D 620 ~0.085) were dispensed into 96-well plates (IWAKI) and 1 µl of small molecules at the concentrations of 3.33, 1.11, 0.37 and 0.12 mg/ml were added respectively, with mixing. D 620 readings were measured at 0, 24 and 48h. RIKE atural Products Depository (PDepo) RIKE PDepo is a public repository consisting mainly of natural products Web: HTS Process Format Concentrations tested Plate Controls Liquid handling workstation Detection Instrument and Software ormalization Additional comments 96-well plates, flat bottom (IWAKI) 33.33, 11.11, 3.70 and 1.23 µg/ml; 1% DMS one. Fumagillin (2.2 µg/ml), leucine and DMS controls were measured on separate plates. Beckman Coulter Biomek 2000 D 620 was measured using Wallac ARV SX 1420 Multilabel Counter and Wallac1420 Manager (Perkin Elmer) ormalization and standardization were performed to reduce the effects of optically interfering compounds. Post-HTS Analysis Hit criteria Growth of Vpr expressing yeast was converted into a percentage relative to the positive control fumagillin Inhibitors allowing 100% growth were considered hits. Hit rate 3.16% Additional assays Confirmation of hit purity and structure Additional comments Secondary confirmatory screen included visual inspection to identify false positives, see text. Tertiary screen involved reproducibility in shaking culture and Vpr expression check by Western blot. Chemical synthesis. Structure available from PEdia. Dot graph represents the average of readings from two plates. 2

3 Synthesis of 3-phenyl coumarin derivatives All commercially available chemicals for chemical synthesis were used without further purification. All reactions were carried out under an argon atmosphere and monitored by thin-layer chromatography with 0.25 mm pre-coated silica gel plates 60F254 Art 5715 (Merck). Silica gel 60 (Kanto Chemical Co.) was used for silica gel column chromatography. 1 H-MR spectra (300 MHz) and 13 C-MR spectra (75 MHz) were recorded on a JEL JM-AL300 spectrometer, and fast atom bombardment (FAB) mass spectra were obtained using a JMS-HX110 mass spectrometer. Representative Experimental Procedure for the Synthesis of 3-phenylcoumarin derivatives Ac DIPEA, Ac 2 + H LiH MeH 14 Cl K 2 C 3, DMF 3 A mixture of 2,4-dihydroxyacetophenone 11 (500 mg, 3.29 mmol) and 2,5-dimethoxyphenylacetic acid 12 (645 mg, 3.29 mmol) in the presence of diisopropylethylamine was refluxed in acetic anhydride for 60 h (1). The reaction mixture was quenched with ice water and extracted with AcEt. The organic phase was washed with water, saturated aqueous ahc 3 and brine, and then dried (a 2 S 4 ). Filtration, concentration, and silica gel column chromatography (Hex/AcEt, 10:1~1:1) yielded 202 mg (0.57 mmol, 17%) of 13 as a white powder. To a solution of III (195 mg, 0.55 mmol) in MeH was added LiH-H 2 (46 mg, 1.10 mmol) at 0 C. After stirring for 12 h at room temperature, the reaction mixture was c6ncentrated and extracted with CHCl 3. The organic phase was washed with water and brine, and then dried (a 2 S 4 ). Filtration, concentration, and silica gel column chromatography (CHCl 3 /MeH, 30:1~10:1) yielded 130 mg (0.41 mmol, 76%) 14 as a white powder (2). To a solution of 14 (20 mg, mmol) and K 2 C 3 (10.5 mg, mmol) in DMF was added dimethylcarbamyl chloride (7.5 mg, mmol). After stirring for 12 h at room temperature, the reaction mixture was quenched with water and extracted with CHCl 3. The organic phase was washed with water and brine, and dried (a 2 S 4 ). Filtration, concentration, and silica gel column chromatography (CHCl 3 /MeH, 50:1~20:1) yielded 19 mg (0.051 mmol, 85%) of 3 (PD4456) as a white powder. 3-(2,5-dimethoxyphenyl)-4-methyl-2-oxo-2H-chromen-7-yl dimethylcarbamate (3) (PD4456) 1 H-MR (300 MHz, CDCl 3 ) δ: 7.57 (1H, d, J = 8.7 Hz), 7.07 (1H, br s), 7.05 (1H, dd, J = 2.4, 8.7 Hz), 6.85 (2H, br s), 6.68 (1H, br s), 3.72 (3H, s), 3.66 (3H, s), 3.07 (3H, s), 2.97 (3H, s), 2.16 (3H, s); 13 C- MR (75 MHz, CDCl 3 ) δ: 160.4, 154.0, 153.6, , , 151.5, 148.4, 125.6, 124.2, 123.1, 118.2, 117.8, 116.9, 114.6, 112.5, 110.3, 56.3, 55.7, 36.8, 36.6, 16.4; FABMS (m/z) 385 (24), 384 (M+H, 100), 383 (51), 72 (69). 3

4 3-(2-methoxyphenyl)-4-methyl-2-oxo-2H-chromen-7-yl dimethylcarbamate (4) was derived from 3-(2-methoxyphenyl)-7-hydroxy-4-methyl- chromen-2-one(15) (3). 83%; 1 H-MR (300 MHz, CDCl 3 ) δ: 7.57 (1H, d, J = 8.4 Hz), 7.32 (1H, dt, J = 1.8, 8.1 Hz), (2H, m), 7.05 (1H, dd, J = 2.4, 8.4 Hz), 6.98 (1H, d, J = 8.1 Hz), 6.92 (1H, d, J = 8.1 Hz), 3.71 (3H, s), 3.07 (3H, s), 2.97 (3H, s), 2.15 (3H, s); 13 C-MR (75 MHz, CDCl 3 ) δ: 160.5, 157.2, 154.0, 153.6, 153.4, 148.3, 131.2, 129.9, 125.5, 123.3, 120.6, 118.2, 117.9, 111.2, 110.1, 55.6, 36.8, 36.6, 16.4; FABMS (m/z) 355 (25), 354 (M+H, 100), 353 (21); FAB-HRMS calculated for C 20 H 20 5 [M+H] +, ; found: (3-methoxyphenyl)-4-methyl-2-oxo-2H-chromen-7-yl derivatives + H Cl K 2 C 3, DMF DIPEA, Ac 2 Ac 18 LiH MeH Cl K 2 C 3, DMF (3-methoxyphenyl)-4-methyl-2-oxo-2H-chromen-7-yl acetate (18) 33%; 1 H-MR (300 MHz, CDCl 3 ) δ: 7.71 (1H, d, J = 8.4 Hz), 7.41 (1H, t, J = 7.8 Hz), 7.19 (1H, d, J = 2.1 Hz), 7.14 (1H, dd, J = 2.1, 8.4 Hz), 6.98 (1H, dd, J= 2.1, 7.8 Hz), 6.90 (1H, d, J = 7.8 Hz), 6.87 (1H, d, J = 2.4 Hz), 3.90 (3H, s), 2.47 (3H, s), 2.34 (3H, s); FABMS (m/z) 326 (22), 325 (M+H, 100), 324 (18), 283 (52). 3-(3-methoxyphenyl)-7-hydroxy-4-methyl-chromen-2-one (19) 3 72%; 1 H-MR (300 MHz, 10% CD 3 D in CDCl 3 ) δ: 7.44 (1H, d, J = 8.4 Hz), 7.28 (1H, t, J = 7.8 Hz), 6.85 (1H, dd, J = 2.4, 8.4 Hz), (4H, m); 13 C-MR (75 MHz, CDCl 3 ) δ: 162.1, 160.6, 159.3, 154.0, 149.1, 135.8, 129.3, 126.3, 122.8, 122.4, 115.6, 113.3, 113.2, 113.0, 102.4, 55.1, 16.3; FABMS (m/z) 284 (20), 283 (M+H, 100), 282 (28), 216 (37). 3-(3-methoxyphenyl)-4-methyl-2-oxo-2H-chromen-7-yl dimethylcarbamate (5) 77%; 1 H-MR (300 MHz, CDCl 3 ) δ: 7.63 (1H, d, J = 8.4 Hz), 7.35 (1H, t, J = 7.8 Hz), 7.14 (1H, br s), (1H, m), 6.92 (1H, dd, J = 2.4, 8.4 Hz), 6.85 (1H, d, J = 7.8 Hz), 6.82 (1H, d, J = 2.4 Hz), 3.81 (3H, s), 3.12 (3H, s), 3.02 (3H, s), 2.28 (3H, s); 13 C-MR (75 MHz, CDCl 3 ) δ: 160.8, 159.5, 153.9, 153.8, 153.2, 147.5, 135.7, 129.5, 126.3, 125.7, 122.3, 118.4, 117.8, 115.6, 113.8, 110.1, 55.2, 36.8, 36.6, 16.7; FABMS (m/z) 355 (24), 354 (M+H, 100), 353 (24); FAB-HRMS calculated for C 20 H 20 5 [M+H] +, ; found:

5 3-(3-trifluoromethoxyphenyl)-4-methyl-2-oxo-2H-chromen-7-yl dimethylcarbamate (6) Ac DIPEA, Ac 2 + CF 3 H CF3 LiH MeH Cl K 2 C 3, DMF 23 CF3 6 CF3 3-(3-trifluoromethoxyphenyl)-4-methyl-2-oxo-2H-chromen-7-yl acetate (22) 17%; 1 H-MR (300 MHz, CDCl 3 )δ: 7.68 (1H, d, J = 8.1 Hz), 7.48 (1H, t, J = 8.1 Hz), (2H, m), 7.15 (1H, d, J = 1.8 Hz), 7.11 (1H, dd, J = 2.1, 8.7 Hz), 2.34 (3H, s), 2.30 (3H, s); 13 C-MR (75 MHz, CDCl 3 ) δ: 168.7, 160.3, 153.3, 153.0, 149.1, 148.0, 136.1, 129.9, 128,6, 126.1, 125.3, 122.8, 120.7, 118.3, 118.1, 110.3, 21.1, 16.7; FABMS (m/z) 380 (22), 379 (M+H, 100), 378 (13), 337 (43), 336 (37); FAB- HRMS calculated for C 19 H 14 5 F 3 [M+H] +, ; found: (3-trifluoromethoxyphenyl)-7-hydroxy-4-methyl- chromen-2-one (23) 27%; 1 H-MR (300 MHz, 10% CD 3 D in CDCl 3 )δ: 7.54 (1H, d, J = 87 Hz), 7.45 (1H, t, J = 7.8 Hz), (2H, m), 7.15 (1H, br s), 6.84 (1H, dd, J = 2.1, 8.7 Hz), 6.79 (1H, d, J = 2.1 Hz), 2.26 (3H, s); 13 C-MR (75 MHz, CDCl 3 ) δ: 165.8, 165.0, 158.1, 153.7, 152.9, 140.5, 133.6, 132.7, 130.4, 126.8, 125.4, 124.2, 117.4, 116.7, 106.4, 20.2; FABMS (m/z) 338 (49), 338 (M+H, 100), 336 (50); FAB-HRMS calculated for C 17 H 12 4 F 3 [M+H] +, ; found: (3-trifluoromethoxyphenyl)-4-methyl-2-oxo-2H-chromen-7-yl dimethylcarbamate (6) 98%; 1 H-MR (300 MHz, CDCl 3 ) δ: 7.63 (1H, d, J = 8.4 Hz), 7.45 (1H, t, J = 8.1 Hz), (3H, m), 7.14 (1H, br s), (1H, m); 13 C-MR (75 MHz, CDCl 3 ) δ: 160.4, 154.1, 153.8, 153.3, 149.1, 148.1, 136.2, 129.8, 128.7, 125.8, 124.9, 112.8, 122.1, 120.6, 118.5, 117.5, 110.2, 36.8, 36.6, 16.7; FABMS (m/z) 409 (23), 408 (M+H, 100), 407 (18); FABMS (m/z) 385 (24), 384 (M+H, 100), 383 (51); FAB-HRMS calculated for C 20 H 17 5 F 3 [M+H] +, ; found: (3-methoxyphenyl)-4-methyl-2-oxo-2H-chromen-7-yl isobutyrate (7) 5

6 Cl 19 DIPEA, CH 2 Cl 2 7 To a solution of 19 (13 mg, mmol) and DIPEA (24 mg, 0.18 mmol) in CH 2 Cl 2 was added isobutyryl chloride (8.5 mg, mmol). After stirring for 12 h at room temperature, the reaction mixture was quenched with water and extracted with CHCl 3. The organic phase was washed with water and brine, and dried (a 2 S 4 ). Filtration, concentration, and silica gel column chromatography (Hex/AcEt, 10:1~1:1) yielded 13 mg (0.037 mmol, 80%) of 7 as a white powder. 1 H-MR (300 MHz, CDCl 3 ) δ: 7.60 (1H, d, J = 8.7 Hz), 7.31 (1H, t, J = 8.1 Hz), 7.06 (1H, d, J = 2.4 Hz), 7.01 (1H, dd, J = 2.4, 8.7 Hz), 6.87 (1H, dd, J = 1.8, 8.4 Hz), 6.80 (1H, d, J = 8.4 Hz), 6.76 (1H, d, J = 1.8 Hz), 2.78 (1H, septet, J = 6.9 Hz), 2.24 (3H, s), 1.28 (6H, d, J = 6.9 Hz); 13 C-MR (75 MHz, CDCl 3 ) δ: 175.0, 160.6, 159.5, 153.3, 153.0, 147.4, 135.6, 129.5, 126.6, 125.9, 122.3, 118.2, 118.1, 115.6, 113.8, 110.1, 55.3, 34.2, 18.8, 16.7; FABMS (m/z) 354 (23), 353 (M+H, 100), 352 (17), 283 (54); FAB-HRMS calculated for C 21 H 21 5 [M+H] +, ; found: (3-methoxyphenyl)-4-methyl-2-oxo-2H-chromen-7-yl piperidine-1-carboxylate (8) Cl 19 K 2 C 3, DMF 85%; 1 H-MR (300 MHz, CDCl 3 ) δ: 7.58 (1H, d, J = 8.4 Hz), 7.30 (1H, t, J = 8.1 Hz), 7.08 (1H, br s), (1H, m), 6.87 (1H, dd, J = 2.7, 8.4 Hz), 6.80 (1H, d, J = 8.1 Hz), 6.77 (1H, d, J = 2.7 Hz), 3.76 (3H, s), 3.56 (2H, br s), 3.46 (2H, br s), 3.11 (2H, br s), 2.23 (3H, s), (4H, m); 13 C-MR (75 MHz, CDCl 3 ) δ: 160.7, 159.5, 153.8, 153.2, 152.7, 147.5, 135.6, 129.5, 126.2, 125.6, 122.3, 118.4, 117.7, 115.6, 113.7, 110.1, 55.2, 47.9, 45.6, 45.2, 25.8, 25.7, 25.4, 24.7, 24.1, 16.6; FABMS (m/z) 395 (12), 394 (M+H, 42), 393 (9.1), 197 (100), 196 (21); FAB-HRMS calculated for C 23 H 24 5 [M+H] +, ; found: (3-methoxyphenyl)-4-methyl-2-oxo-2H-chromen-7-yl morpholine-4-carboxylate (9) vipirinin 8 Cl 19 K 2 C 3, DMF 9 96%; 1 H-MR (300 MHz, CDCl 3 ) δ: 7.64 (1H, d, J = 8.4 Hz), 7.35 (1H, t, J = 8.1 Hz), 7.14 (1H, d, J = 1 Hz), 7.12 (1H, dd, J = 2.1, 8.4 Hz), 6.93 (1H, dd, J = 1.5, 8.1 Hz), 6.85 (1H, d, J = 8.1 Hz), 6.81 (1H, d, J 6

7 = 1.5 Hz), 3.81 (3H, s), (4H, m), (2H, m), (2H, m), 2.29 (3H, s); 13 C-MR (75 MHz, CDCl 3 ) δ: 160.7, 159.5, 153.4, 153.2, 152.7, 147.4, 135.6, 129.5, 126.4, 125.8, 112.3, 118.2, 118.0, 115.6, 113.8, 110.1, 66.5, 66.4, 55.2, 44.9, 44.2, 16.7; FABMS (m/z) 396 (M+H, 22), 281 (17), 207 (21), 147 (45), 73 (100); FAB-HRMS calculated for C 22 H 22 6 [M+H] +, ; found: (3-methoxyphenyl)-4-methyl-2-oxo-2H-chromen-7-yl 4-methylpiperazine-1 carboxylate (10) Cl 19 K 2 C 3, DMF 13%; 1 H-MR (300 MHz, CDCl 3 ) δ: 7.50 (1H, d, J = 8.7 Hz), 7.29 (1H, t, J = 7.8 Hz), (5H, m), 4.11 (2H, t, J = 5.1 Hz), 3.75 (3H, s), 3.56 (2H, t, J = 5.1 Hz), 3.44 (2H, t, J= 8.4 Hz), 3.25 (2H, t, J = 8.4 Hz), 2.73 (3H, s), 2.22 (3H, s); 13 C-MR (75 MHz, CDCl 3 ) δ: 161.4, 161.2, 161.1, 159.5, 154.2, 147.9, 135.9, 129.4, 126.2, 124.3, 122.4, 115.7, 114.3, 113.5, 112.1, 101.5, 67.9, 55.2, 45.2, 44.3, 43.7, 31.3, 16.5; FABMS (m/z) 410 (27), 409 (M+H, 100); FAB-HRMS calculated for C 23 H [M+H] +, ; found: Analysis of the viral reverse transcription and nuclear import processes in primary macrophages. Primary macrophages in 6 well plates were inoculated with 50 ng of VSV-G pseudotyped reporter viruses; L-Luc-E-R+(VSV-G), cultured in the absence or presence of the compounds, and total cellular DA was extracted by QIAamp DA Mini Kit (QIAGE) from the cells 48 h later. DA samples (50 ng) were subjected to PCR with primers (5 -CACACACAAGGCTACTTCCCT-3, and 5 - CTGCTAGAGATTTTCCACACTGAC-3 ) for the early reverse transcription product of proviral DA, primers (5 -CACACACAAGGCTACTTCCCT-3, and 5 -CCGGTCCTGCGTCGAGAGATC-3 ) for its late product (4), or primers (5 -GAGATCCCTCAGACCCTTTTAG-3, and 5 - GTCAGTGGATATCTGATCCCTG-3 ) for two-ltr circle in the nucleus (5), in combination with the glyceraldehydes 3-phosphate dehydrogenase (GAPDH) primers (5 - GTTCCAATATGATTCCACCCATGGC-3, and 5 -CGATACCAAAGTTGTCATGGATGACC-3 ) of the human GAPDH gene, which served as a control. PCR to detect early and late reverse transcription products, and to detect GAPDH was performed with conditions; 30 cycles of 94 o C for 40 sec, 55 o C for 40 sec, and 72 o C for 1 min. PCR to detect two-ltr circle in the nucleus was performed with conditions; 34 cycles of 94 o C for 45 sec, 60 o C for 30 sec, and 72 o C for 2 min. PCR products were resolved by electrophoresis in 1.5% agarose gels and stained with ethidium bromide. References for Supplemental Experimental Procedures 1. Kanojia, R.M., Jain,., Xu, J. and Sui, Z. (2004) Tetr Lett Ebdrup, S., Hansen, H. C., Vedso, P., Cornelis De Jong, J., and Jacobsen, P. (2003) (PCT Int. Appl. W A2) 3. Sreenivasulu, B., Sundara Murthy, V. and Subba Rao,.V. (1969) Curr Sci Koh, K.B., Fujita, M., and Adachi, A. (2000) J Virol Methods Kondo, E., Mammano, F., Cohen, E.A. and Gottlinger, H.G (1995) J Virol

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