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1 Supporting Information Synthesis and biological evaluation of Aryl-hospho-Indole (AI) as novel IV-1 non-nucleoside reverse transcriptase inhibitors. François-René Alexandre a *, Agnès Amador a, Stéphanie Bot a, Catherine Caillet a, Thierry Convard a, Jocelyn Jakubik c, Chiara Musiu b, Barbara oddesu b, Luana Vargiu b, Michel Liuzzi b, Arlène Roland a, David Standring c, Richard Storer a and Cyril B. Dousson a. a Laboratoires Idenix, Département de Chimie Médicinale, 1682 rue de la Valsière, B50001, Montpellier Cedex 4, France; b Idenix harmaceuticals, Cooperative Lab Idenix-Universita Di Cagliari, Sesta Strada vest, Zona Industriale di Macchiareddu (UTA), 09010, Cagliary, Italy ; c Idenix harmaceuticals, 60 ampshire Street, Cambridge, MA 02139, USA. Contents of Supporting Information I. General Experimental Methods II. Synthesis of ethyl 3-bromo-5-chloro-1-(phenylsulfonyl)-1-indole-2-carboxylate 3 III. Synthesis of phosphinates 4,5 and 8 and phosphinamidate 6 IV. Synthesis of phosphine oxides 7 and 9 V. Synthesis AI VI. Synthesis of phoshinic acid 16 VII. Synthesis of phosphotioate 17 I. General Experimental Methods. All reactions were performed with reagent-grade materials under an atmosphere of nitrogen. Solvents were reagent-grade or better. Evaporation of the solvents was carried out in a rotary evaporator under reduced pressure. Thin layer chromatography (TLC) was performed on precoated aluminium sheets of silica gel 60 F254 (Merck, Art. 5554), visualization of products being accomplished by UV absorbance at 254 nm; column chromatography on silica 60 (40-63µm, Merck 11567). 1 (400 Mz), 13 C (100 Mz) and 31 (162 Mz) MR spectra were recorded on a Brucker DRX 400 Advance II spectrometer using DMS-d 6 or CD 3 as solvents. MR chemical shift (δ) are quoted in parts per million (ppm) referenced to the residual solvent peak [DMS-d 6 ] set at 2.49 ppm or [CD 3 ] set at 7.26 ppm. The accepted abbreviations are as followed: s, singulet; d, doublet; t, triplet; q, quartet; m, multiplet. Lowresolution LC mass spectra (LR LCMS) were recorded on a WATERS unit [Alliance 2695, hotodiode Array detector 2996, ZQ 2000 (ESCI source), Mass Lynx 4.1] using a reverse phase analytical column Synergy 4 µm Fusion 80A 50x2.0 mm (henomenex 100B B). The compound to be analyzed was eluted using a linear gradient of 5% -95% acetonitrile in water with 0.05 % formic acid programmed over a 8 or 20 minutes period with a flow rate of 0.4 ml/min. urity of all compounds was determined to be >95% by analytical LC using a WATERS unit [Alliance 2695, hotodiode Array detector 2996] using a reverse phase analytical column Waters ovapack C18 4µm 150x3.9 mm. The compound to be analyzed was eluted using a linear gradient of 5 95% acetonitrile over a 20 min period with a flow rate of 1 ml/min and the chromatogram was recorded using an UV detection from 210 to 400 nm (DA Max lot). II. Synthesis of ethyl 3-bromo-5-chloro-1-(phenylsulfonyl)-1-indole-2-carboxylate 3 S1

2 a) Synthesis of ethyl 5-chloro-1-(phenylsulfonyl)-1-indole-2-carboxylate 2: S To a stirred and cooled (0 C) solution of ethyl-5-chloroindole-2-carboxylate (1.052g, 4.70 mmol) in DMF (25 ml) under 2, was added a (60% in oil, 230 mg, 5.64 mmol) portionwise. After the end of gas evolution, phenylsulfonyl chloride (0.72 ml, 5.64 mmol) was added. The reaction mixture was stirred for 1 h (TLC monitoring, eluant dichloromethane). A little amount of water was added carefully and DMF was evaporated. Crude residue was dissolved in EtAc and washed with water and brine. After drying and evaporation of solvents the compound was purified by chromatography on silica gel (eluant: cyclohexane/etac 9/1 to 7/3) to afford protected indole (1.547 g, 90% yield. ff-white solid; 1 MR (d 6 -DMS) δ 1,30 (t, J = 7.2 z, 3), 4.35 (q, J = 7.2 z, 2), 7.37 (s, 1), 7.53 (dd, J = 2.2 and 9.1 z), (m, 3), 7.80 (d, J = 2.2 z, 1), 7.99 (m, 2), 8.06 (d, J = 9.1 z); MS (ESI, El + ) m/z = 364 (M + ). b) Synthesis of ethyl 3-bromo-5-chloro-1-(phenylsulfonyl)-1-indole-2-carboxylate 3: Br S To a stirred solution of ethyl 5-chloro-1-(phenylsulfonyl)-1-indole-2-carboxylate (4.83 g, mmol) in DMF (40 ml) under 2, was added a solution of bromine (1.3 ml, mmol) in DMF (10 ml). Reaction media was stirred at room temperature for 4 h, water was added (150 ml) and was extracted with dichloromethane (3 100 ml). rganic layer was washed with a saturated solution of a 2 S 5, dried and evaporated to give a crude yellow oil. urification by chromatography on silica gel (eluant: cyclohexane/etac 9/1) afforded 3- brominated indole (5.548 g, 93% yield). ff white solid; 1 MR (d 6 -DMS) δ 1,37 (t, J = 7.2 z, 3), 4.48 (q, J = 7.2 z, 2), (m, 4), 7.77 (m, 1), (m, 3) ; MS (ESI, El + ) m/z = (M + ). III. Synthesis of phosphinates 4,5 and 8 and phosphinamidate 6 Typical procedure : To a stirred and cooled (-90 C) solution of ethyl 3-bromo-5-chloro-1- (phenylsulfonyl)-1-indole-2-carboxylate 3 ( 0.50 mmol) in anhydrous TF (2.5 ml) under 2, was added n-buli (2.5M in hexanes, 0.24 ml, 0.60 mmol) dropwise. After 5 min at - 90 C, appropriate chorophosphosphus reagent (0.60 mmol) was added dropwise at the same temperature. The reaction was allowed to warm up to room temperature over 3 h (TLC monitoring, eluant dichloromethane/ EtAc 9/1). Water was then added (5 ml). Extraction with EtAc (3 20 ml) drying and evaporation led to a crude oil that was purified by chromatography on silica gel. S2

3 a) Synthesis of Ethyl 5-chloro-3-[ethoxy(phenyl)phosphoryl]-1-(phenylsulfonyl)-1-indole- 2-carboxylate 4: S urification by chromatography on silica gel (eluant: dichloromethane/etac 9/1); 41% yield; colorless oil; 1 MR (d 6 -DMS, 300 Mz) δ 1,27 (t, J = 7.1 z, 3), 1,36 (t, J = 7.1 z, 3), 4.03 (m, 2), 4.38 (q, J = 7.1 z, 2), (m, 11), (m, 3); 31 MR (d 6 -DMS, 101 Mz) δ 23.3; MS (ESI, El + ) m/z = 532 (M + ). b) Synthesis of Ethyl 5-chloro-3-[benzyloxy(phenyl)phosphoryl]-1-(phenylsulfonyl)-1indole-2-carboxylate 5: S urification by chromatography on silica gel (eluant: dichloromethane/etac 8/2); 29% yield; thick yellow oil, 1 MR (CD 3, 300 Mz) δ 1.30 (t, J = 7.2 z,3), (m, 2), (m, 2), (m, 6), (m, 5), (m, 1), (m, 1), (m, 3), (m, 2), 31 MR (CD 3, Mz) δ 25.24, MS (ESI, El + ) m/z = 594 (M + ). d) Synthesis of ethyl 5-chloro-3-[(dimethylamino)phenylphosphinyl]-1-(phenylsulfonyl)- 1indole-2-carboxylate 6 S3

4 C 2 Et S urification by chromatography on silica gel (eluant: cyclohexane/etac 8/2 to 100% EtAc); 10% yield, yellow oil, 1 MR (CD 3, 300 Mz) δ 1.44 (t, J = 6.5 z, 3), 2.66 (d, J = 11.1 z, 6), 4.48 (q, J = 6.7 z, 2), 7.34 (d, J = 9.9 z, 1), (m, 5), 7.60 (m, 1), (m, 4), (m, 2), 31 MR (CD 3, 101 Mz) δ 25.11, MS (ESI, El + ) m/z = 531 (M + ). IV. Synthesis of phosphine oxides 7 and 9 a) Synthesis of ethyl 5-chloro-3-(diphenylphosphinyl)-1-(phenylsulfonyl)-1-indole-2- carboxylate 7 Et S To a stirred and cooled (-90 C) solution of bromoindole 3 (1eq) was added dropwise n- butyllithium (1.2eq) under 2. After 10 minutes, Diphenylchlorophosphine oxide (1.1eq) in tetrahydrofuran (15ml/mmol) was added dropwise at -70 C. The mixture was allowed to warm up to -30 C (~3 h), quenched with water and extracted with dichloromethane. The organic layer was dried over a 2 S 4, filtered and concentrated under reduce pressure. The crude was purified by chromatography on silica gel (eluent: C 2 2 /Me : 9/1) to give the compound 9 in 46% yield. White solid, 1 MR (CD 3,, 300 Mz) δ 1.18 (t, J = 7.2 z, 3), 3.78 (q, J = 7.2 z, 2), 7.33 (dd, J = 2.1 and 9 z, 1), (m, 14), (m, 1), (m, 2), 31 MR (CD 3, Mz) δ 22.23, MS (ESI, El + ) m/z = 564 (M + ). b) Synthesis of ethyl 5-chloro-3-( methylphenylphosphinyl)-1-(phenylsulfonyl)-1-indole-2- carboxylate 9 S4

5 C 2 Et S To a stirred and cooled (-90 C) solution of bromoindole 3 (1eq) was added dropwise n- butyllithium (1.2eq) under 2. After 10 minutes, benzenephosphonyl dichloride (1.1eq) in tetrahydrofuran (15ml/mmol) was added dropwise at -70 C and, when the addition was finished, after 15 minutes at -90 C, the methylmagnesium bromide (1.1eq) was added. The mixture was allowed to warm up to -40 C (~1 h), quenched with water and extracted with ethyl acetate then dichloromethane. The organic layer was dried over a 2 S 4, filtered and concentrated under reduce pressure. The crude was purified by chromatography on silica gel (eluent: C 2 2 /AcEt : 9/1 to 7/3) to give the compound 9 in 9% yield. Yellow thick oil, 1 MR (CD 3, 300 Mz) δ 1.36 (t, J = 7.2 z, 3), (m, 2), (dd, J = 2.1 z and 9 z, 1), (m, 6), (m, 2), (m, 2), (m, 2), 31 MR (CD 3, Mz) δ 25.04, MS (ESI, El + ) m/z = 502 (M + ). V. Synthesis AI a) Synthesis of Ethyl 2-(aminocarbonyl)-5-chloro-1-indol-3-yl-(phenyl)phosphinate 10 2 Typical procedure : Ethyl-5-chloro-3-[ethoxy(phenyl)phosphoryl]-1-(phenylsulfonyl)-1indole-2-carboxylate (268 mg, 0.50 mmol) was dissolved in a saturated solution of ammonia in methanol (5 ml) in a pressure tube. The tube was heated under microwave irradiation under pressure at 65 C (Maximum power input 100W, CEM discover apparatus) for 2 h. After evaporation of solvents, purification by chromatography on silica gel (eluant: dichloromethane/me 95/5 to 9/1) afforded desired carboxamide indole (107 mg, 81% yield). White solid; 1 MR (d 6 -DMS, 300 Mz) δ 1,34 (t, J = 7.1 z, 3), 4.05 (m, 1), 4.20 (m, 1), 7.32 (dd, J = 2.1 and 8.7z, 1), (m, 5), (m, 2), 8.02 (brs, 1), 10,27 (brs, 1), (brs, 1); 31 MR (d 6 -DMS, 101 Mz) δ 31.1; MS (ESI, El + ) m/z = 363 (M + ). b) Synthesis of Benzyl 2-(aminocarbonyl)-5-chloro-1-indol-3-yl-(phenyl)phosphinate 11 S5

6 2 32% yield; white solid, 1 MR (d 6 -DMS, 300 Mz) δ 4.98 (dd, J = 7.3 and 11.8 z, 1), 5.22 (dd, J = 7.6 and 11.8 z, 1), 7.29 (dd, J = 1.9 and 8.8 z, 1), (m, 5), (m, 5), (m, 2), 8.05 (brs, 1), (brs, 1), (brs, 1), 31 MR (d 6 -DMS, Mz) δ 31.0, MS (ESI, El + ) m/z = 425 (M + ). c) Synthesis of 5-chloro-3-[(dimethylamino)phenylphosphinyl]-1-Indole-2-carboxamide 12 C 2 54% yield; pale orange powder, 1 MR (d 6 -DMS, 300 Mz) δ 2.64 (d, J = 11.7 z, 6), 7.32 (dd, J = 2.1 and 8.7 z, 1), (m, 4), (m, 3), 7.86 (brs, 1), (brs, 1), (brs, 1), MS (ESI, El + ) m/z = 384 (M+a). d) Synthesis of 5-chloro-3-(diphenylphosphinyl)-1-Indole-2-carboxamide % yield; white solid, 1 MR (d 6 -DMS, 300 Mz) δ 6.13 (d, J = 1.8 z, 1), 7.22 (dd, J = 2.1 and 8.7 z, 1), (m, 11), 7.92 (brs, 1), (brs, 1), (brs, 1), 31 MR (d 6 -DMS, Mz) δ 26.61, MS (ESI, El + ) m/z = 395 (M + ). e) Synthesis of 5-chloro-3-(methylphenylphosphinyl)-1-Indole-2-carboxamide 15 S6

7 2 61% yield, white solid, 1 MR (d 6 -DMS, 300 Mz) δ 2.24 (d, J = 13.5 z, 3), 7.1 (m, 1), 7.25 (dd, J = 1.2 and 8.7 z, 1), (m, 4), (m, 2), (m, 1), (brs, 1), (brs, 1), 31 MR (d 6 -DMS, Mz) δ 30.62, MS (ESI, El + ) m/z = 333 (M + ). VI. Synthesis of [2-(aminocarbonyl)-5-chloro-1-indol-3-yl]phenyl-phosphinic acid 16 2 In a microwave tube, the compound 11 (1eq) was stirred with DMF (5ml/mmol) and TMSBr (5eq) was added. The tube was heated under microwave irradiations under pressure at 60 C (maximum power input 100W, CEM discover apparatus) for 50 min. After cooling down water was added and titled compound 16 collected by filtration. 57% yield, white solid, 1 MR (d 6 -DMS, 300 Mz) δ (m, 1), (m, 7), 8.16 (brs, 1), (brs, 1), 12 (brs, 1), MS (ESI, El + ) m/z 335 (M + ). VII. Synthesis of -methyl ester [2-(aminocarbonyl)-5-chloro-1-indol-3-yl]phenylphosphinothioic acid 17 S 2 The compound Methyl 2-(aminocarbonyl)-5-chloro-1-indol-3-yl-(phenyl)phosphinate, 14 (1eq) and the lawesson s reagent (4eq) were heated in toluene (10ml/mmol) at 90 C under 2 in a pressure tube. The reaction was monitored by TLC and heating was pursued until no starting material was left (~5h30). The crude solution was filtered and the filtrate was evaporated to dryness and purified by chromatography on silica gel to give the compound 17. S7

8 White powder, 1 MR (CD 3, 300 Mz) δ 3.80 (d, J = 14.4 z, 3), 5.92 (brs, 1), 7.32 (dd, J = 1.95 z and 9 z, 1), (m, 4), (m, 3), 9.24 (brs, 1), (brs, 1), 31 MR (CD 3, Mz) δ 80.48, MS (ESI, El + ) m/z = 365 (M + ). S8