Synthesis and Use of QCy7-derived Modular Probes for Detection and. Imaging of Biologically Relevant Analytes. Supplementary Methods

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1 Synthesis and Use of QCy7-derived Modular Probes for Detection and Imaging of Biologically Relevant Analytes Supplementary Methods Orit Redy a, Einat Kisin-Finfer a, Shiran Ferber b Ronit Satchi-Fainaro b *, and Doron Shabat a * a School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences and b Department of Physiology and Pharmacology, Sackler School of Medicine, Tel Aviv University, Tel Aviv Israel. chdoron@post.tau.ac.il S1

2 General methods. All reactions requiring anhydrous conditions were performed under an Argon atmosphere. All reactions were carried out at room temperature unless stated otherwise. Chemicals and solvents were either A.R. grade or purified by standard techniques. Thin layer chromatography (TLC): silica gel plates Merck 60 F254: compounds were visualized by irradiation with UV light. Flash chromatography (FC): silica gel Merck 60 (particle size mm), eluent given in parentheses. 1 H-NMR spectra were measured using Bruker Avance operated at 400MHz as mentioned. 13 C-NMR spectra were measured using Bruker Avance operated at 100MHz as mentioned. The chemical shifts are expressed in δ relative to TMS (δ = 0 ppm) and coupling constants J in Hz. The spectra were recorded in CDCl3 as solvent at room temperature unless stated otherwise. Abbreviations. DCM- Dichloromethane, EtOAc- Ethylacetate, Hex- n-hexanes, MeOH- Methanol, THF- Tetrahydrofurane, PTSA- p-toluenesulfonic acid. Synthesis of intermediates: 2-(4-(Iodomethyl) phenyl)-4,4,5,5-tetramethyl-1,3,2-dioxaborolane (Compound 1a) can be prepared as described in Ref. 18 of the Protocol, starting from 2-(4-(formyl) phenyl)-4,4,5,5- tetramethyl-1,3,2-dioxaborolane. Reduction of an aldehyde group with sodium borohydride to obtain the corresponded benzyl alcohol and iodination with TMSCl/I 2 should afford compound 1a. 3-(2,3,3-Trimethyl-3H-indolium-1-yl) propane-1-sulfonate (Compound 4) can be prepared as described in Ref. 19 of the Protocol by alkylation of the corresponded indole with sultan. Compound 2d Compound 2c 1 (500 mg, 1 equivalent), was dissolved in MeOH (100 ml). NaOMe (580 mg, 5 equivalents) and formaldehyde (35% in H 2 O, 840 µl, 5 equivalents) were added, and the solution was heated to reflux. After 2 hours in reflux, the solution was cooled to 0 o C, and NaBH 4 (400 mg, 5 equivalents) was added slowly. The solution was heated to reflux for 1 hour, and was then poured into ice water, and extracted with EtOAc. The organic layer was dried over sodium sulfate and the solvent was removed under reduced pressure. The crude product was purified by column chromatography on silica gel (EtOAc/Hex 20:80) to afford compound 2d (400 mg, 76%). 1 H NMR (400 MHz, CDCl 3 ): δ = 7.19 (2H, d, J = 8.4 Hz), 6.62 (2H, d, J = 8.4), 4.67 (2H, s), 2.84 (3H, s), 0.97 (9H, s), 0.12 (6H, s). 13 C NMR (100MHz, CDCl 3 ): δ = , , , 113.0, 65.88, 31.63, 26.8, 19.22, MS (ES + ): m/z calc. for C 14 H 25 NOSi: ; found: [M+H] +. Compound 2e Compound 2d (400 mg, 1 equivalent) was dissolved in pyridine, and the solution was cooled to 0 o C. 2,4-Dinitrobenzenesulfonyl chloride (467 mg, 1.1 equivalents) was S2

3 added, and the reaction mixture was stirred at 0 o C for 30 minutes, before warming it to room temperature. The reaction was monitored by TLC (EtOAc/Hex 20: 80). Upon completion, the reaction mixture was diluted with EtOAc and washed twice with a solution of 1 M HCl. The organic layer was dried over sodium sulfate and the solvent was removed under reduced pressure. The crude product was purified by column chromatography on silica gel (EtOAc/Hex 20:80) to afford compound 2e (584 mg, 76%). 1 H NMR (400 MHz, CDCl 3 ): δ = 8.42 (1H, d, J = 2 Hz), 8.3 (1H, dd, J = 2, 8.8 Hz), 7.68 (1H, d, J = 8.8 Hz), 7.33 (2H, d, J = 8.4 Hz), 7.18 (2H, d, J = 8.4 Hz), 4.74 (2H, s), 3.39 (3H, s), 0.93 (9H, s), 0.1 (6H, s). 13 C NMR (100MHz, CDCl 3 ): δ = , , , , , , , , , , 64.92, 40.56, 26.63, 19.09, MS (ES + ): m/z calc. for C 20 H 27 N 3 O 7 SSi: ; found: [M+Na] +. Compound 2f Compound 2e (370 mg) was dissolved in 3 ml MeOH. A catalytic amount of PTSA was added to the suspension, and the reaction mixture was stirred at room temperature and monitored by TLC (EtOAc/Hex 40: 60). After completion of the reaction, the solvent was removed under reduced pressure. The crude product was purified by column chromatography on silica gel (EtOAc/Hex 70:30) to give compound 2f (243 mg, 86%) as yellow oil. 1 H NMR (400 MHz, CDCl 3 ): δ = 8.57 (1H, d, J = 2.2 Hz), 8.4 (1H, dd, J = 2.2, 8.7 Hz), 7.83 (1H, d, J= 8.7 Hz), 7.34 (2H, d, J= 8.5 Hz), 7.2 (2H, d, J = 8.5 Hz), 4.57 (2H, s), 3.35 (3H, s). 13 C NMR (100MHz, CDCl 3 ): δ = , , , 139.3, , , , , , , 63.72, MS (ES + ): m/z calc. for C 14 H 13 N 3 O 7 S: ; found: [M+Na] +. Compound 2a Compound 2f (400 mg, 1 equivalent) was dissolved in THF, and the solution was cooled to 0 o C. PPh 3 (655 mg, 2.3 equivalents) was added and after 3 minutes CBr 4 (830 mg, 2.3 equivalents) was added. The reaction mixture was stirred at room temperature and the progress was monitored by TLC (EtOAc/Hex 30: 70). After completion, the reaction mixture was evaporated under reduced pressure. The crude product was purified by column chromatography on silica gel (EtOAc/Hex 40:60) to afford compound 2a (330 mg, 77%) as yellow solid. 1 H NMR (400 MHz, CDCl 3 ): δ = 8.43 (1H, d, J = 2.2 Hz), 8.32 (1H, dd, J = 2.2, 8.6 Hz), 7.74 (1H, d, J= 8.6 Hz), 7.39 (2H, d, J= 8.5 Hz), 7.25 (2H, d, J = 8.5 Hz), 4.46 (2H, s), 3.41 (3H, s). 13 C NMR (100MHz, CDCl 3 ): δ = , , , , , , , , , , 40.46, MS (ES + ): m/z calc. for C 14 H 12 BrN 3 O 6 S: ; found: 454.0[M+Na] +. Compound 3e 4-hydroxybenzaldehyde (772 mg, 1 equivalent) dissolved in 1M NaOH solution (6 ml), was added dropwise to a solution of 3d 2 (2.6 gr, 1 equivalent) in acetone (11 ml). The reaction mixture was stirred for 12 hr at room temperature was monitored S3

4 by TLC (EtOAc/Hex 50:50). Upon completion, the reaction mixture was diluted with DCM and washed with water. The organic layer was dried over sodium sulfate and the solvent was removed under reduced pressure. The crude product was purified by column chromatography on silica gel (EtOAc/Hex 50:50) to afford compound 3e (1.72 gr, 60%). 1 H NMR (400 MHz, CDCl 3 ): δ = 9.86 (1H, s), 7.81 (2H, d, J = 8.6 Hz), 7.08 (2H, d, J = 8.6Hz), (2H, m), 5.17 (1H, d, J = 7.9 Hz), 5.12 (1H, dd, J = 10.4, 3.3 Hz), (3H, m), 2.14 (3H, s), 2.01 (6H, s), 1.97 (3H, s). 13 C NMR (100MHz, CDCl 3 ): δ = , , , 170.8, , , , , 99.22, 72.0, 71.37, 69.13, 67.51, 62.08, MS (ES + ): m/z calc. for C 21 H 24 O 11 : ; found: [M+Na] +. Compound 3f Compound 3e (1.65 gr, 1 equivalent), was dissolved in MeOH, and the solution was cooled to 0 o C. NaBH 4 (267 mg, 2 equivalents) was added slowly. The reaction was monitored by TLC (EtOAc/Hex 60:40). Upon completion, the reaction mixture was diluted with EtOAc and washed with a saturated NH 4 Cl solution, followed by Brine. The organic layer was dried over sodium sulfate and the solvent was removed under reduced pressure. The crude product was purified by column chromatography on silica gel (EtOAc/Hex 75:25) to afford compound 3f (800 mg, 50%). 1 H NMR (400 MHz, CDCl 3 ): δ = 7.25 (2H, d, J = 8.6 Hz), 6.95 (2H, d, J = 8.6 Hz), (2H, m), 5.08 (1H, dd, J = 10.4, 3.3 Hz), 5.01 (1H, d, J = 7.9 Hz), 4.57 (2H, s), (3H, m), 2.13 (3H, s), 2.01 (3H, s), 2.0 (3H, s), 1.96 (3H, s). 13 C NMR (100MHz, CDCl 3 ): δ = , , , , , , , , , 71.68, 71.53, 69.4, 67.64, 65.2, MS (ES + ): m/z calc. for C 21 H 26 O 11 : ; found: [M+Na] +. Compound 3a Compound 3f (688 mg, 1 equivalent) was dissolved in THF, and the solution was cooled to 0 o C. PPh 3 (913 mg, 2.3 equivalents) was added and after 3 minutes CBr 4 (1.155 gr, 2.3 equivalents) was added. The reaction mixture was stirred for 10 minutes at room temperature and the progress was monitored by TLC (EtOAc/Hex 40: 60). After completion, the reaction mixture was evaporated under reduced pressure. The crude product was purified by column chromatography on silica gel (EtOAc/Hex 50:50) to afford compound 3a (701 mg, 90%). 1 H NMR (400 MHz, CDCl 3 ): δ = 7.33 (2H, d, J = 8.6 Hz), 6.96 (2H, d, J = 8.6 Hz), (2H, m), 5.11 (1H, dd, J = 10.4, 3.3 Hz), 5.04 (1H, d, J = 7.9 Hz), 4.47 (2H, s), (3H, m), 2.17 (3H, s), 2.05 (6H, s), 2.0 (3H, s). 13 C NMR (100MHz, CDCl 3 ): δ = , , , , , , , , , 71.81, 71.5, 69.29, 67.57, 62.08, 33.84, MS (ES + ): m/z calc. for C 21 H 26 O 11 : ; found: [M+Na] +. S4

5 References (1) Bernardo, P. H. et al. J. Med. Chem., 2008, 51, (2) Orth, R.; Pitscheider, M.; Sieber, S. A.; SYNTHESIS, 2010, 13, S5

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