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Developing Allosteric Inhibitors of SARS-CoV-2 RNA-dependent RNA polymerase
Chayka, Artem ; Danda, Matěj ; Dostálková, Alžběta , et al. ChemMedChem,2024,e202400367. DOI: 10.1002/cmdc.202400367 PubMed ID: 39140451
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Abstract: The use of Fpocket and virtual screening techniques enabled us to identify potential allosteric druggable pockets within the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp). Of the compounds screened, compound 1 was identified as a promising inhibitor, lowering a SARS-CoV-2 RdRp activity to 57% in an enzymatic assay at 10 µM concentration. The structure of compound 1 was subsequently optimized in order to preserve or enhance inhibitory activity. This involved the substitution of problematic ester and aromatic nitro groups with more inert functionalities. The N,N’-diphenylurea scaffold with two NH groups was identified as essential for the compound's activity but also exhibited high toxicity in Calu-3 cells. To address this issue, a scaffold hopping approach was employed to replace the urea core with potentially less toxic urea isosteres. This approach yielded several structural analogues with notable activity, specifically 2,2’-bisimidazol (in compound 55 with residual activity RA = 42%) and (1H-imidazol-2-yl)urea (in compounds 59 and 60, with RA = 50 and 28%, respectively). Despite these advances, toxicity remained a major concern. These compounds represent a promising starting point for further structure-activity relationship studies of allosteric inhibitors of SARS-CoV-2 RdRp, with the goal of reducing their cytotoxicity and improving aqueous solubility.
Purchased from AmBeed: 99-31-0 ; 328-74-5 ; 99-05-8 ; 873-74-5
CAS No. : | 873-74-5 | MDL No. : | MFCD00007821 |
Formula : | C7H6N2 | Boiling Point : | - |
Linear Structure Formula : | - | InChI Key : | YBAZINRZQSAIAY-UHFFFAOYSA-N |
M.W : | 118.14 | Pubchem ID : | 13396 |
Synonyms : |
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Signal Word: | Warning | Class: | N/A |
Precautionary Statements: | P261-P280-P301+P312-P302+P352-P305+P351+P338 | UN#: | N/A |
Hazard Statements: | H302-H315-H319-H335 | Packing Group: | N/A |
GHS Pictogram: |
* All experimental methods are cited from the reference, please refer to the original source for details. We do not guarantee the accuracy of the content in the reference.
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
86% | With sodium azide In water at 100℃; for 5 h; Green chemistry | General procedure: Benzonitrile (1 mmol, 0.103 g), sodium azide (1.1 mmol, 0.0759 g), and 2 mL water were taken in a reaction tube and stirred at room temperature to make homogeneous suspension, and then 20 wtpercent catalyst (ZnO–RGO) was added to the reaction mixture. The reaction mixture was heated to 100 °C for 2 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was cooled to room temperature and centrifuged. The filtrate was treated with 5N HCl (10 mL) and then with ethyl acetate. The organic layer was separated, washed with deionized water, and then dried over anhydrous sodium sulfate and concentrated to give the crude solid crystalline 5-phenyl-1H-tetrazole. It was recrystallized from n-hexane, ethyl acetate, and the yield was about 0.143 g. |
81% | With sodium azide; silver nitrate In N,N-dimethyl-formamide at 20 - 120℃; for 5.5 h; | General procedure: Sodiumazide (0.378 g, 0.046 mmol) was added to a solution of AgNO3 (5 mg, 10 mmol)in DMF (5 ml) and reaction mixture was stirred for 5 min, to this stirredsolution benzonitrile 1a (0.4 ml, 0.033 mmol) was added dropwise over theperiod of 1 min at room temperature and stirring continued for 10 min at thesame temperature and then heated at 120 C for 5 h. After consumption of 1a,the reaction mixture was cooled to room temperature and chilled by addingcrushed ice into the reaction mixture followed by addition of 2 N HCl tillreaction mixture reached the pH 2. The reaction mixture was then extractedwith ethyl acetate. The organic layer was dried with anhydrous Na2SO4, andconcentrated to obtain tetrazole 2a in 83percent yield as an off white solid (268 mg). |
75% | With sodium azide; acetic acid; urea In water; N,N-dimethyl-formamide at 60 - 110℃; for 9 h; | General procedure: The procedure for the synthesis of the tetrazole 2a is representative. A mixture of sodium azide (0.39 g 0.0060 mol), urea (0.36 g, 0.0060 mol) and water (2.5 mL) was taken in a round–bottom flask and stirred at 60 °C for 1 h. Charged benzonitrile 1a (0.5 g 0.0048 mol), acetic acid(0.5 mL) and DMF (2.5mL) at 60 °C and heat to 110°C stirred for 8 h. After completion of the reaction (as indicated by TLC), the reaction mixture was cooled to room temperature and diluted the reaction mass with water (2.5 mL)and ethyl acetate (5.0 mL) at 25-35 °C. Add 5N aqueous hydrochloric acid (2.5 mL) at 25-35 °C. Stirred for 20- 30 min, the resultant organic layer was separated and the aqueous layer was extracted with ethyl acetate (2.5 mL). The combined organic layer was washed with 40 percent aq.NaCl solution (2.5 mL) and dried over anhydrous Na2SO4 and concentrated to give a crude product, which was isolated using chilled water after 3-4 h maintenance, and eventually filtered off to give 0.67 g (95percent) of an off-white solid. |
74% | With sodium azide; ammonium chloride In N,N-dimethyl-formamide at 125℃; for 24 h; | Synthesis of 4-(1H-tetrazol-5-yl) aniline (p).A mixture of 4-aminobenzonitrile (100 mg, 0.85 mmol), sodium azide (110.2 mg, 1.69 mmol), DMF (8.5 mL) and ammonium chloride (45.3 mg, 0.85 mmol) was heated in an oil bath for 24 h at 125 °C. When the reaction was deemed complete by TLC the mixture wasacidified with iN HCL and extracted with ethyl acetate (3x). The combined ethyl acetate was washed with brine and dried over Na2SO4, filtered and concentrated to give the crude product. The tetrazole compound was purified by column chromatography on silica gel (90percent CH2C12/MeOH) to yield the desired product (102mg, 74percent).Example 50 - Compound 24 N=N 4-(1 H-tetrazol-5-yl)aniline Chemical Formula: C7H7N5 Molecular Weight: 161.1640 Compound 24 was synthesized according to procedure p, yielding the final product 24 as white powder (74percent). δ (400 MHz, d-MeOD3) 4.34 (brs, 2H, NH2), 6.51 (d, J = 8.9 Hz, 2H, CH), 7.71 (s, J = 8.9 Hz, 2H, CH); d (100 MHz, i -C2D6CO) 1 13.4, 121.6, 126.8, 143.1 , 154.2; LRMS (ES+) Calcd for [C7H7N5 + H] 161.07 found 162.16. |
60% | With sodium azide; triethylamine hydrochloride In toluene at 95℃; for 24 h; | [0343] To a solution of 4-aminobenzonitrile (11.8 g, 100 mmol) and triethylamine hydrochloride (17.9 g, 130 mmol) in toluene (550 ml) was added sodium azide (8.45 g, 130 mmol). After stirring for 24 h at 95° C., the reaction mixture was cooled to room temperature and was extraced with water (3.x.60 ml). The combined aqueous phases were acidified with concentrated aqueous HCl to pH 2-3. The product was collected by filtration, washed with water and dried in vacuum. Yield 9.59 g (60percent) pale brown solid. M.p.: 280-281° C., TLC (CH2Cl2/MeOH/AcOH 9:1:0.1): Rf 0.30 |
54% | With sodium azide; ammonium chloride In N,N-dimethyl-formamideReflux | Example 33. Synthesis of 4-(lH-Tetrazol-5-yl)-phenylamine. The title compound was synthesized following the scheme below and used for synthesis of Compound 285 via Scheme 1.To a solution of 4-amino-benzonitrile (2.36 g, 20 mmol) in dry DMF (20 ml) was added NaN3 (1.6 g, 30 mmol) and NH4C1 (1.6 g, 30 mmol) and the reaction mixture was refluxed overnight. After cooling to room temperature, the resulting mixture was diluted with 40 ml of water and extracted with EtOAc (3x30 ml). The organic layer was washed with brine, dried over Na2S04, filtered and evaporated to give the 4-(lH-Tetrazol-5-yl)-phenylamine (1.5 g, 54percent yield). 1H NMR (400 MHz, DMSO-d6): δ 16.26 (s, 1H), 7.70-7.68 (d, 2H, J = 8.4), 6.70-6.67 (d, 2H, J = 8.4), 5.79-5.76 (s, 2H). |
44.4% | With sodium azide; ammonium chloride In N,N-dimethyl-formamide at 120℃; for 12 h; | 57.1 4-(1H-Tetrazol-5-yl)-phenylamine To a stirred solution of 4-amino-benzonitrile (300 mg, 2.53 mmol; CAS Reg. No. 873-74-5) in dry DMF (6 ml) was added NH4Cl (547 mg, 10.2 mmol) and NaN3 (660 mg, 10.2 mmol) at room temperature. The reaction mixture was then heated at 120° C. for 12 h. After cooling, TLC shows formation of new spot, filtered the solid material by sintered funnel and washed the solid residue by EtOAc (4*5 ml). Combined organic layers were reduced under pressure at 60° C. and diluted the residue with EtOAc (25 mL). Organic layer was washed with H2O (15 ml), brine (12 ml) and dried over Na2SO4; which was then concentrated under reduced pressure to give the crude material (300 mg). Crude product was then purified by column chromatography [SiO2 (230-400 mesh), MeOH:DCM 5:95] to give the title compound (180 mg, 44.4percent) as light yellow solid. |
44% | With sodium azide; triethylamine hydrochloride In toluene for 24 h; Heating / reflux | A mixture of p-amino benzonitrile (2g, 16.9mmol), triethylamine hydrochloride (3.49g, 25.38mmol) and sodium azide (1.65g, 25.38mmol) were taken in anhydrous toluene (20ml) and heated to reflux for 24 hr. The reaction mixture was cooled to room temperature and neutralized with dilute hydrochloric acid. The resultant precipitate was filtered, washed with water then dried to give 4-(lH-tetrazol-5-yl)-ρhenylamine (1.2g, 44percent). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
56% | Stage #1: at 13.5℃; for 1 h; Stage #2: With sodium carbonate In water |
Step A: 2-Chlorobenzothiazole-6-carbonitrile; To a mixture of 4-aminobenzonitrile (23.6 g, 0.2 mol) and ammonium rhodanate (30.4 g, 0.4 mol) was added glacial acetic acid (600 ml.) and the resulting solution was cooled to 13.5 0C on an ice-bath. A mixture of bromine and glacial acetic acid was added drop-wise and slowly. The resulting mixture was stirred for 1 hour at 13.5 0C and filtered. The filter cake was washed with glacial acetic (6 x 100 ml.) and placed in hot water (1000 ml.) with stirring. The mixture was filtered and pH of the filtrate was adjusted to 7 with a saturated sodium carbonate solution. The precipitate was isolated and dried to give 19.5 g (56 percent) of 2-aminobenzo- thiazole-6-carbonitrile. A mixture of concentrated hydrochloric acid (1 13 ml.) and water (52 ml.) was heated at 90 0C while 2-aminobenzothiazole-6-carbonitrile (19 g, 0.108 mol) was added. The mixture was cooled to -5 0C on an ice-bath and a solution of sodium nitrite (7.72 g, 0.1 12 mol) in water (20 ml.) was added drop-wise, keeping the temperature below than 0 0C. When addition was complete the mixture was stirred for 0.5 hour and a solution of CuCI2 (16 g) in water (108 ml.) was added drop-wise. When addition was complete the mixture was stirred for 10 min, and the ice-bath was removed. Stirring was continued for 2 h and the mix- ture was cooled to room temperature. The mixture was filtered and the solid was washed to neutrality with water and dried. This afforded 12.8 g (61 percent) of 2-chlorobenzothiazole-6-carbo- nitrile. 1H-NMR δ 8.14 (s, 1 H), 8.03 (d, 1 H), 7.75 (d, 1 H). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
0.70 g | Stage #1: at 10 - 20℃; for 0.5 h; Stage #2: at 20℃; for 16 h; |
To a solution of 4-aminobenzonitrile (1.00 g, 8.47 mmol) in acetic acid (12 ml) was added potassium thiocyanate (1.00 g, 16.9 mmol) at 10°C. The reaction mixture was stirred at rt for 30 mm. A solution of bromine (0.5 ml, 10.16 mmol) in acetic acid (3 ml) was added dropwise to the reaction at rt. The reaction mixture was stirred at rt for 16 h. The resulting solid precipitates were collected byfiltration under reduced pressure, washed with acetic acid (10 ml) and dried under vacuum. The obtained precipitates were suspended in ice cold aqueous solution of NH4OH (10 ml) and stirred at rt for 30 mm. The resulting solid precipitates were collected by filtration under reduced pressure, dried under vacuum yielding 2-aminobenzo[djthiazole-6-carbonitrile (0.70 g, 4.00 mmol). This material was directly used in the next step without further purification. LCMS: Method C, 1.62 mi MS: ES+176.13. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
95% | With N-chloro-succinimide In acetonitrile at 90℃; for 2 h; | Step 1: To a stirred solution of 4-aminobenzonitrile (10.0 g, 84.7 mmol) in MeCN (100 mL) at 90 °C was slowlyadded N-chlorosuccinimide (12.4 g, 93 mmol). After the addition of N-chlorosuccinimide, the reaction mixture was stirredat 90 °C for 2 h. The reaction mixture was then cooled to rt and concentrated under reduced pressure. The residue wasdissolved in 500 mL of CH2Cl2 and washed with 5percent aq NaOH. The organic layer was dried over MgSO4 and concentratedunder reduced pressure to give 4-amino-3-chlorobenzonitrile as a tan solid (12.2 g, 95percent). 1H NMR (300 MHz, CDCl3)δ 7.54 (d, J= 1.7 Hz, 1H), 7.35 (dd, J= 1.8, 8.4 Hz, 1H), 6.77 (d, J = 8.5 Hz, 1H), 4.63 (br s, 2H). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
95% | With N-chloro-succinimide In dichloromethane; acetonitrile | 3-chloro-4-cyanoaniline. PREPARATION 2 (2-chloro-4-cyanoaniline) To a stirred, 60° C. solution of 4-cyanoaniline (20 g, 0.169 mol) in acetonitrile (200 mL) was added slowly N-chlorosuccinimide (24.8 g, 0.186 mol) to keep the reaction at reflux. After the addition of the N-chlorosuccinimide was complete, the reaction mixture was stirred at 60° C. for two hours. The solvent was then removed under reduced pressure. The residue was then dissolved in dichloromethane, washed with a 5percent sodium hydroxide solution, dried (Na2 SO4) and evaporated under reduced pressure to afford 24.5 g (95percent) of the title compound, 2-chloro-4-cyanoaniline, as a tan solid; m.p. 93°-95° C. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
5.2 g | Stage #1: With hydrogenchloride; sodium nitrite In water at -15 - 10℃; for 0.25 h; Stage #2: With hydrogenchloride; tin(ll) chloride In water at -15℃; for 0.5 h; |
To a cold solution of 4-cyanoaniline (6.0 g, 0.050 mol) in cone. HCl was added aq. solution of sodium nitrite (3.85 g, 0.055 mmol) at -15°C. The reaction mass was stirred at 0-10°C for 15 minutes and filtered off to remove insolubles. The filtrate was added to stannous chloride in cone. HCl (24.0 g, 0.166 mmol). The reaction mass was stirred at -15°C for 30 minutes. The reaction mass was filtered to afford 5.2 g of desired product.1H NMR (300 MHz, DMSO d6): δ 7.04 (d, 2H), 7.70 (d, 2H), 9.17 (br s, 1H), 10.66 (br s, 2H). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
78% | With sodium nitrite In hydrogenchloride; water | 1. 4-Cyanophenylhydrazine. Hydrochloride To a cooled (-15° C.) and stirred suspension of 4-aminobenzonitrile (50 g, 423 mmol) in concentrated hydrochloric acid (550 ml) was added dropwise a solution of sodium nitrite (31.5 g, 457 mmol) in water (200 ml) at such a rate as to maintain the temperature below -10° C. After the addition was finished, the reaction mixture was quickly filtered to remove solids and the filtrate was added portionwise to a cooled (-20° C.) and stirred solution of tin (II) chloride dihydrate (477 g, 2.1 mol) in concentrated hydrochloric acid (370 ml) at such a rate as to maintain the temperature below -10° C. After further 15 minutes at -10° to 0° C., the white precipitate was collected by filtration, washed with diethyl ether (4*250ml) and dried to give 56 g (78percent) of the title compound; mp 235°-237° C. (ethanol-water 1:1); 1 H NMR (250MHz, D6 -DMSO) δ10.50 (3H, br s, -N+H3) 9.10 (1H, br s, --NH--), 7.71 (2H, d, J=8.8Hz, Ar--H), 7.03 (2H, d, J=8.8Hz, Ar--H); m/z (CI) 132 (M+ -1). |
78% | With sodium nitrite In hydrogenchloride; water | 1.4-Cyanophenylhydrazine. Hydrochloride To a cooled (-15° C.) and stirred suspension of 4-aminobenzonitrile (50 g, 423 mmol) in concentrated hydrochloric acid (550 ml) was added dropwise a solution of sodium nitrite (31.5 g, 457 mmol) in water (200 ml) at such a rate as to maintain the temperature below -10° C. After the addition was finished, the reaction mixture was quickly filtered to remove solids and the filtrate was added portionwise to a cooled (-20° C.) and stirred solution of tin (II) chloride dihydrate (477 g, 2.1 mol) in concentrated hydrochloric acid (370 ml) at such a rate as to maintain the temperature below -10° C. After further 15 minutes at -10° to 0° C., the white precipitate was collected by filtration, washed with diethyl ether (4*250 ml) and dried to give 56 g (78percent) of the title compound; mp 235°-237° C. (ethanolwater 1:1); 1 H NMR (250 MHz, DMSO-d6) δ 10.50 (3H, br s, --N+ H3), 9.10 (1H, br s, --NH--), 7.71 (2H, d, J=8.8 Hz, Ar-H), 7.03 (2H, d, J=8.8 Hz, Ar-H); m/z (CI) 132 (M+ - 1). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
74% | With bromine In 1,4-dioxane; sodium hydroxide | EXAMPLE 25 PREPARATION OF 4-AMINO-3,5-DIBROMOBENZONITRILE STR37 To a stirred solution of 100 mg (0.847 mmoles) of p-aminobenzonitrile in 3.6 mL dioxane chilled in an ice-bath was added sequentially 356 μL (1.78 moles) of 5N sodium hydroxide solution and mg (1.78 mmoles) of bromine. The ice-water bath was removed and the reaction mixture was stirred further for 1.5 hours. After this time, 21.8 μL (0.423 mmoles) of bromine was added to drive the reaction to completion and stirring was continued for 10 minutes. The mixture was partitioned between ethyl acetate and ice-water and the organic phase was separated. It was washed with brine, dried over anhydrous sodium sulfate, filtered, and evaporated. Purification by plate layer chromatography using hexane-ethyl acetate (7:3) as the eluant provided 175 mg (74percent) of the entitled product. NMR(CDCl3) δ5.1 (bs, 2H), 7.66 (s, 2H). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
74% | With bromine In 1,4-dioxane; sodium hydroxide | EXAMPLE 1 Preparation of 4-Amino-3,5-dibromobenzonitrile STR15 To a stirred solution of 100 mg (0.847 mmoles) of p-aminobenzonitrile in 3.6 mL dioxane chilled in an ice-bath was added sequentially 356 μL (1.78 mmoles) of 5 N sodium hydroxide solution and 284 mg (1.78 mmoles) of bromine. The ice-water bath was removed and the reaction mixture was stirred further for 1.5 hours. After this time, 21.8 μL (0.423 mmoles) of bromine was added to drive the reaction to completion and stirring was continued for 10 minutes. The mixture was partitioned between ethyl acetate and ice-water and the organic phase was separated. It was washed with brine, dried over anhydrous sodium sulfate, filtered, and evaporated. Purification by plate layer chromatography using hexane-ethyl acetate (7:3) as eluant provided 175 mg (74percent) of the entitled product. NMR(CDCl3) δ: 5.1 (bs, 2H), 7.66 (s, 2H). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
33 g | Stage #1: With nitric acid In ethanol; water for 16 h; Reflux Stage #2: With sodium hydroxide In water |
A solution of P-aminobenzonitrile (100 gm), ethanol (500 ml), concentrated nitric acid (36 ml) and aqueous cyanamide (50percent, 54 ml) was heated at reflux. The solution was maintained for 16 hours at reflux. The reaction mass was further cooled to 0° C. and then added methyl tert-butyl ether (500 ml) at 0 to 5° C. The reaction mass was maintained for 5 hours at 0 to 5° C. and separated solid obtained was collected by filtration to obtain 59 gm of guanidine nitrate. Guanidine nitrate (59 gm) was dissolved in water (590 ml) and then added sodium hydroxide solution (1M, 325 ml). The separated solid obtained was filtered and dried to obtain 33 gm of 1-(4-cyanophenyl)guanidine. |
30 g | With nitric acid In methanol; water at 10 - 65℃; for 8 h; | 100 g of 4-aminobenzonitrile was dissolved in 500 mL of methanol and cooled the reaction mixture to 10-15° C. 161 mL of con. Nitric acid was added to the reaction mixture followed by 65.6 ml of 50percent aqueous solution cynamide to the reaction mixture and maintained the reaction at 65° C. for 8 hrs. Cooled the reaction mass to 0° C. and charged 500 ml of methyl-t-butyl ether at 0° C. The solids were filtered, washed with water and acetone and dried to give 30 g of the product as a solid. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
95% | With N-chloro-succinimide In dichloromethane; acetonitrile | 3-chloro-4-cyanoaniline. PREPARATION 2 (2-chloro-4-cyanoaniline) To a stirred, 60° C. solution of 4-cyanoaniline (20 g, 0.169 mol) in acetonitrile (200 mL) was added slowly N-chlorosuccinimide (24.8 g, 0.186 mol) to keep the reaction at reflux. After the addition of the N-chlorosuccinimide was complete, the reaction mixture was stirred at 60° C. for two hours. The solvent was then removed under reduced pressure. The residue was then dissolved in dichloromethane, washed with a 5percent sodium hydroxide solution, dried (Na2 SO4) and evaporated under reduced pressure to afford 24.5 g (95percent) of the title compound, 2-chloro-4-cyanoaniline, as a tan solid; m.p. 93°-95° C. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
67% | With potassium carbonate; nickel(II) hydroxide In dimethyl sulfoxide at 35℃; for 2 h; | The preparation method of the trifluoromethyl aromatic amine of the present embodiment, the aromatic amine is p-cyanoaniline, the reaction time is 12 h, and the other reaction and post-treatment processes are the same as in the embodiment 28. The preparation method of the trifluoromethyl aromatic amine of the present embodiment, the aromatic amine is aniline, and the nickel compound is nickel hydroxide.The base is potassium carbonate, and the reaction process parameters are: 1-trifluoromethyl-1,2-phenyliodo-3(H)-one (0.5 mmol, 1.0 eq).Aromatic amine (1.5 mmol, 3.0 eq), nickel hydroxide 10 molpercent, potassium carbonate (1.5 mmol, 3.0 eq),DMSO (2 mL) was reacted at 35 ° C for 2 h, and the other reactions and workup procedures were the same as in Example 1. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
61% | With fac-tris(2-phenylpyridinato-N,C2')iridium(III); potassium carbonate In 1,2-dichloro-ethane at 20℃; for 24 h; Inert atmosphere; Schlenk technique; Irradiation | General procedure: A 25 mL of Schlenk tube equipped with a magnetic stir bar were charged with aniline (1.2 mmol, 3.0 equiv) or heterocycles (0.8 mmol, 2.0 equiv), K2CO3 (0.8 mmol, 2.0 equiv) and fac-Ir(ppy)3 (2.6 mg, 0.004 mmol, 1 mol percent), under air. The vessel was evacuated and backfilled with Ar (3 times), CF3I stock solution (0.56 mL, 0.71 mmol/mL in 1,2-chloroethane or 0.36 mL, 1.11 mmol/mL in DMSO, 1.0 equiv), anhydrous 1,2-dichloroethane (3 mL) were then added. The tube was screw capped and stirred at room temperature under irradiation of blue LEDs (12 W) for 24 hours. The reaction S15 mixture was filtered through a pad of Celite and washed with ethyl acetate (3×5 mL). The filtrate was concentrated. The residue was subjected to column chromatography on silica gel to afford the pure product. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
88% | at 100 - 110℃; for 3 h; | 3.2.3 Preparation of [(4-cyanophenyl)amino]acetic acid (V) C7H6N2 C2H3DPψ2 C9H8N2O2 MoI. Wt.: 1 18,14 MoI. Wt.: 138,95 MoI. Wt.: 176,17VIngredientsF: 90 g - 0.75 molG: 211.7 g - 1.5 molSodium bicarbonate: 35 g, 0.42 molThe starting substances F and G were mixed in 1250 ml of water and this suspension was inserted into a bath heated up to 100-110 0C. After three hours of heating the reaction container was removed from the bath, cooled in the fridge and the separated substance was sucked off. The substance was dried in a vacuum drier at the temperature of 100 °C. Yield: Crude product: 122 g (92.8percent), HPLC: 97percentThe crude product was purified by conversion to the sodium salt and re-acidification using an aqueous solution of sodium bicarbonate. The acid was released by means of diluted hydrochloric acid (1 :1). After sucking off and washing with water the product was dried in a vacuum drier (105 °C). Yield: Purified product: 115 g (88percent), HPLC: 99.1percent, water content: 0.13percent; sulphate ash: 1.8percent |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
73% | Reflux | In the 4-cyanato aniline (6.0g, 0 . 05mol) and 1-chloro acetic acid (10g, 0.11mol) adding water in 150 ml, heating to reflux until a large amount of yellow solid is separated out so far, the filter at room temperature, with water, anhydrous ethanol, anhydrous ethyl ether eluviation, that is, to get the yellow solid 4-cyanato anilino-acetic acid (6.4g, yield 73percent). Mass spectrometric (ESI-MS): 177.3(M+H) +, 199.2(M+Na) +; C 9 H 8 N 2 O 2 (176). |
58% | Heating / reflux | a) (4-Cyano-phenylamino)-acetic acid A solution of 4-aminobenzonitrile (12 g, 101.6 mmol) and chloroacetic acid (20 g, 211.6 mmol) in water (250 mL) was refluxed until the product began to separate out. After cooled down to the room temperature, the solids were collected by filtration, washed with ether, and dried in vacuo to afford 10.35 g (58percent) of the title compound which was pure enough for the next reaction. 1H NMR (400 MHz, DMSO-d6) δ 12.73 (s, 1H), 7.46 (dd, 2H), 6.93 (t, 1H), 6.65 (dd, 2H), 3.91 (d, 2H). |
Yield | Reaction Conditions | Operation in experiment |
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73.2% | for 6.5 h; Reflux | e) 2-(4-Cyanophenylamino)acetic acid (compound III) 77.4 g (0.66 mol) of 4-aminobenzonitrile and 150 g (1.31 mol) of sodium chloroacetate were suspended in 1.1 L of water, and the resulting mixture was stirred at reflux temperature for 6.5 hours. After cooling to 0°C, the resulting suspension was stirred at this temperature overnight. The solid was filtered and washed with 200 mL of water. The resulting solid was suspended in 200 mL of ethyl acetate and stirred at room temperature for 1 hour. The solid was filtered, washed with 400 mL of ethyl acetate and dried at 60°C under vacuum for 5 hours to yield 84.5 g of 2-(4-cyanophenylamino)acetic acid as an off-white solid. Yield: 73.2 percent. Purity (HPLC, method 3): 98.4 percent. |
73.2% | at 0℃; Reflux | e) 2-(4-Cyanophenylamino)acetic acid (compound III) 77.4 g (0.66 mol) of 4-aminobenzonitrile and 150 g (1.31 mol) of sodium chloroacetate were suspended in 1.1 L of water, and the resulting mixture was stirred at reflux temperature for 6.5 hours. After cooling to 0°C, the resulting suspension was stirred at this temperature overnight. The solid was filtered and washed with 200 mL of water. The resulting solid was suspended in 200 mL of ethyl acetate and stirred at room temperature for 1 hour. The solid was filtered, washed with 400 mL of ethyl acetate and dri e d at 60 ° C under v acuum for 5 hours to yield 84.5 g of 2-(4- cyanophenylamino)acetic acid as an off-white solid. Yield: 73.2 percent. Purity (HPLC, method 3): 98.4 percent. |
131 g | With tetrabutylammomium bromide; sodium hydrogencarbonate; potassium iodide In water at 90 - 95℃; for 24 h; | Sodium bicarbonate (21.35 g) was added to a mixture of 4-aminobenzonitrile compound of formula-12 (100 g) and water (1000 ml) followed by sodium 2-chloroacetate (197.42 g). Potassium iodide (5 g) followed by tertiary butyl ammonium bromide (2.5 g) were added to the reaction mixture. The reaction mixture was heated to the 90-95° C. and stirred for 24 hours at the same temperature. After completion of the reaction, the reaction mixture was cooled to 20-25° C. and pH was adjusted to 7.5 with ammonia. The reaction mixture was stirred for 20 minutes at 20-30° C. Filtered the reaction mixture and ethylacetate was added to the filtrate. The reaction mixture was stirred for 15 minutes. Both the ethylacetate and aqueous layers were separated and the pH of aqueous layer was adjusted to 2.5 using hydrochloric acid. The reaction mixture was stirred for 3 hours at 20-30° C. to precipitate the solid. Filtered the precipitated solid, water followed by hydrochloric acid were added to the obtained solid and stirred for 4 hours at 25-30° C. Filtered the solid, the obtained solid was slurried twice in water for 30-45 minutes and then dried to get the title compound. The same process can be repeated one more time to eliminates the impurities if present. Yield: 131 g |
120 g | With tetrabutylammomium bromide; sodium hydrogencarbonate; potassium iodide In water at 85 - 90℃; for 24 h; | Sodium mono chloroacetate (197.42 g), followed by potassium iodide (5 g) and tetrabutyl ammonium bromide (2.5 g) were added to a mixture of 4-aminobenzonitrile (100 g), water (1000 ml) and sodium bicarbonate (42.71 g). The reaction mixture was heated to 85-90° C. and stirred for 24 hours. The reaction mixture was cooled to 25-30° C. and treated with ammonia followed by hydrochloric acid. Filtered the solid, washed with water and then dried to get title compound. Yield: 120 g. |
Yield | Reaction Conditions | Operation in experiment |
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84% | With hydrogenchloride; tin(II) chloride dihdyrate; sodium nitrite In water at -5 - 0℃; for 0.25 h; | To a cooled (−5 to 0°C) stirred suspension of 4-aminobenzonitrile (50g, 423mmol) in concentrated hydrochloric acid (550mL) was added dropwise aqueous sodium nitrite solution (31.5g, 457mmol in 200mL water). To this diazotised solution cooled (0°C) solution of tin (II) chloride dihydrate (477g, 2.1mol) in concentrated hydrochloric acid (370mL) was added while stirring and maintaining the temperature below 0°C. The resulting solution was further stirred for 15min. White precipitates so formed were collected by filtration, washed with diethylether and crystallized from aqueous ethanol. Mp 234–236°C (Lit. mp 235–237°C), yield 60g (84percent). |
Yield | Reaction Conditions | Operation in experiment |
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88% | With dihydrogen peroxide; iodine In methanol at 20℃; for 48 h; | To a solution of 4-aminobenzonitrile (2.4 g 20 mmol) and -30percent H202 (not titrated before use) in MeOH (30 ml) a solution of l2 (5.05 g, 12 mmol) in MeOH (50 ml) was added at room temperature and the resulting mixture was stirred for 48 h, while a fresh H202 (2 ml) was added every day. The mixture was concentrated under reduced pressure and treated with saturated solution of Na2S203 until most of the colour disappeared. The solid formed was filtered off, diluted to 300 ml with EtOAc, washed with saturated, H20, brine, dried over anhydrous MgS04, filtered and the filtrate evaporated to dryness. The residue was purified by crystallization from EtOH to give the title compound (3 g). The residue was recrystallised from the mixture of CH2CI2/hexane to give more of the title compound (1 .4 g). Total yield 4.4 g (88percent). 1 H NMR (CDCIg) 7.87 (d, 1 H, J = 1 .8 Hz) ; 7.37 (dd, 1 H, J = 1 .8, 8.4), 6.68 (d, 1 H, J = 8.4 Hz), 4.62 (broad s, 2H). |
36% | With iodine; silver sulfate In ethanol at 20℃; for 18 h; | INTERMEDIATE 56 - PREPARATION of 4-Amino-3-iodobenzonitrile. Iodine (0.645 g; 2.54 mmol) was added to a stirred mixture of silver sulphate (0.791 g;2.54 mmol) and 4-aminobenzonitrile (0.300 g; 2.54 mmol) in ethanol (10 ml_). The reaction mixture was then stirred at room temperature for 18 hours and filtered over celite. The volatiles were removed under reduced pressure and the residue was partitioned between ethyl acetate and a saturated aqueous solution of sodium thiosulfate. The organic layer was washed with brine, dried and concentrated under reduced pressure. The crude residue was purified by flash chromatography on silica gel (eluent 2 to 40 percent ethyl acetate in heptane) to afford 0.222 g (36percent) of the title compound as a white solid.1 H NMR (DMSO-de) δ 7.96 (d, 1 H), 7.45 (dd, 1 H), 6.76 (d, 1 H), 6.22 (s, 2H). |
36% | With iodine; silver sulfate In ethanol at 20℃; for 18 h; | Iodine (0.645 g; 2.54 mmol) was added to a stirred mixture of silver sulphate (0.791 g; 2.54 mmol) and 4-aminobenzonitrile (0.300 g; 2.54 mmol) in ethanol (10 mL). The reaction mixture was then stirred at room temperature for 18 hours and filtered over celite. The volatiles were removed under reduced pressure and the residue was partitioned between ethyl acetate and a saturated aqueous solution of sodium thiosulfate. The organic layer was washed with brine, dried and concentrated under reduced pressure. The crude residue was purified by flash chromatography on silica gel (eluent 2 to 40percent ethyl acetate in heptane) to afford 0.222 g (36percent) of the title compound as a white solid. [0654] 1H NMR (DMSO-d6) δ 7.96 (d, 1H), 7.45 (dd, 1H), 6.76 (d, 1H), 6.22 (s, 2H). |
36% | With iodine; silver sulfate In ethanol at 20℃; for 18 h; | INTERMEDIATE 142 - PREPARATION of 4-amino-3-iodobenzonitrile; Iodine (0.645 g; 2.54 mmol) was added to a stirred mixture of silver sulphate (0.791 g; 2.54 mmol) and 4-aminobenzonitrile (0.300 g; 2.54 mmol) in ethanol (10 ml_). The reaction mixture was stirred at room temperature for 18 hours and filtered over celite. The volatiles were removed under reduced pressure and the residue was partitioned between ethyl acetate and a saturated aqueous solution of sodium thiosulphate.. The organic layer was washed with brine, dried and concentrated under reduced pressure. The crude residue was purified by flash chromatography on silica gel (eluent 2 to 40 percent ethyl acetate in heptane) to afford 0.222 g (36percent) of the title compound as a white solid. 1H NMR (DMSO-de) δ 7.96 (d, 1 H), 7.45 (dd, 1 H), 6.76 (d, 1 H), 6.22 (s, 2H). |
76% | With Iodine monochloride In water; acetic acid | EXAMPLE 10 Synthesis of 4-Amino-3-iodobenzonitrile (31) To a solution of 5.9 g (0.05 mole) of 4-aminobenzonitrile (30) (Aldrich 14,775-3) in 25 mL of glacial acetic acid was added dropwise a solution of 8.12 g (0.05 mole) of iodine monochloride (Aldrich 20,822-1) in 5 mL of glacial acetic acid. During the addition, the temperature rose to 40°. The solution was stirred at room temperature for 20 minutes. A solid developed in the reaction mixture and the deep brown color of the solution started fading gradually. The mixture was poured into 250 mL of water and stirred for 10 minutes to give a pale brown solid which was filtered and recrystallized from methanol/water containing one gram of activated charcoal (Darco S51) yielding 9.3 g (76percent) of white crystals of 31, mp 110-112°. Infrared (IR) and NMR analysis gave the following results: IR (potassium bromide): 3454 and 3346 (NH2), 2214 (CN), 1621, 1496 cm1. 1H nmr (90 MHz, CDCI3):δ 7.91 (1H; d, 4JH6-H2=1.8 Hz; H-2), 7.41 (1H; dd, 3JH5-H6=8.4, 4JH2-H6=1.8 Hz; H-6), 6.73 (1 H; d, 3JH6-H5=8.4 Hz, H-5), 4.67 (2H, br s, NH2). |
10 g | With N-iodo-succinimide In N,N-dimethyl acetamide at 45 - 50℃; for 72 h; | Step 1 : Preparation of 4-amino-3-iodobenzonitrile To a solution of 4-aminobenzonitrile (10 g) in DMA (50 mL) was added N- iodosuccinamide (19.80 g).The reaction mixture was stirred at 45-50°C for 72 h. The reaction mass was quenched in water and obtained solid was filtered to afford 10 g of title product. |
10 g | With N-iodo-succinimide In N,N-dimethyl acetamide at 45 - 50℃; for 72 h; | To a solution of 4-aminobenzonitrile (10 g) in DMA (50 mL) was added N-iodosuccinamide (19.80 g).The reaction mixture was stirred at 45-50°C for 72 h. The reaction mass wasquenched in water and obtained solid was filtered to afford 10 g of title product. |
Yield | Reaction Conditions | Operation in experiment |
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42% | With hydrogenchloride In tetrahydrofuran; ethanolReflux | To a solution of S3 (0.13 g, 0.52mmol) in THF:EtOH(1:3, mL) was added S4 (0.07 g, 0.56 mmol) and 1N HCl (1.04 ml, 1.04mmol). The reaction was refluxed overnight and evaporated. The crude product was purified by flash chromatography on silica (50percentEtOAc inhexanes) to afford a white powder (0.07 g, 42percent).1H NMR (CDCl3, 400 MHz) δ 7.99 (d, J= 4.0 Hz, 1H), 7.56-7.76 (m, 5H), 7.00 (s, 2H), 6.53 (brs, 1H), 5.56 (br s, 1H), 2.36 (s, 3H), 2.26 (s, 6H). MS (ESI) m/z 330 [M+H]+. HPLC (214 nm) tr 18.5 min, 100 percent |
Yield | Reaction Conditions | Operation in experiment |
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47% | Stage #1: With sodium tris(acetoxy)borohydride; acetic acid In tetrahydrofuran at 0 - 20℃; for 3.25 h; Stage #2: With sodium hydrogencarbonate In tetrahydrofuran; water; ethyl acetate |
Preparation 31 tert-butyl 4-[(4-cyanophenyl)amino]piperidine-1-carboxylate To a mixture of 4-aminobenzonitrile (0.5g, 4.23mmol) and tert-butyl 4-oxocyclohexanecarboxylate (1.26g, 6.35mmol) in THF (5ml) at 0°C was added acetic acid (0.5ml, 8.5mmol) and sodium triacetoxyborohydride (1.35g, 6.35mmol). The mixture was stirred at this temperature for 15min and at room temperature for 3h. Ethyl acetate and 5percent solution of NaHCO3 were added and the organic layer separated, washed with water, brine and dried over magnesium sulphate. The solvent was concentrated and the residue purified by column chromatography with a mixture of hexane/ethyl acetate (from 5/1 to 1/1) to give the desired compound (yield=47percent). LRMS: m/z 302 (M+1)+ Retention time: 6.33 min (Method B) 1H NMR (300 MHz, CHLOROFORM-d) d ppm 1.37 (m, 2 H) 1.47 (s, 9 H) 2.03 (m, 2 H) 2.93 (t, J=11.95 Hz, 2 H) 3.40 - 3.54 (m, 1 H) 4.04 - 4.13 (m, 3 H) 6.56 (d, J=9.06 Hz, 2 H) 7.43 (d, J=8.79 Hz, 2 H) |
Yield | Reaction Conditions | Operation in experiment |
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73% | at 20 - 102℃; for 21 h; | Example 7: Preparation of 4-(4-amino-6-chloropyrimidin-2-ylamino)benzonitrile ("Compound la")To a solution of 4-aminobenzonitrile (ABN; 7 g; 59.3 mmol) in 2-butanol (190 ml), 2,6- dichloropyrimidin-4-amine ("DCAP"; 10.2 g; 62.2 mmol) was added at room temperature. The resulting suspension was heated to reflux (102 °C) and stirred for 20 hours. The suspension was then cooled to 20-25 °C and stirred for lhour at 20-25 °C. A solid was separated from the suspension by filtration and washed with 2-butanol (20 ml) and dried (2h/ 50 °C/ 10 mbar). Yield: 12.20 g (73.0 percent) of 4-(4-amino-6-chloropyrimidin-2-ylamino)benzonitrile hydrochloride.Purity (HPLC/ MS): 99.0 Area percent |