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.
Abstract: In this study, we developed a metal-free and highly chemoselective method for the reduction of aromatic nitro compounds. This reduction was performed using tetrahydroxydiboron [B2(OH)4] as the reductant and 4,4'-bipyridine as the organocatalyst and could be completed within 5 min at room temperature. Under optimal conditions, nitroarenes with sensitive functional groups, such as vinyl, ethynyl, carbonyl, and halogen, were converted into the corresponding anilines with excellent selectivity while avoiding the undesirable reduction of the sensitive functional groups.
* 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.
With 1,2-diphenyl-1,1,2,2-tetrahydroperoxyethane; hydrogen bromide In water; acetonitrile at 20℃; for 2.5 h;
General procedure: To a solution of aniline/phenol (1 mmol) in CH3CN (4 mL), HBr and THPDPE (depending on the substrate as shown in Table 7) were added and the solution was stirred at room temperature. After the reaction was completed, Na2SO3 (3M, 1mL) was added to the stirring mixture followed by the addition of H2O (10 mL). The solution was stirred until the desired precipitates appeared. The products were filtered and more purification was carried out using silica- packed column chromatography (Hexane–EtOAc). All of the products were characterized on the basis of their melting points, IR, 1H NMR, and 13C NMR spectral analysis and compared with those reported
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).
Reference：
[1] RSC Advances, 2016, vol. 6, # 93, p. 90184 - 90187
[2] Journal fuer Praktische Chemie (Leipzig), 1986, vol. 328, # 4, p. 497 - 514
[3] Tetrahedron, 2018, vol. 74, # 45, p. 6584 - 6592
[4] Journal of Organic Chemistry, 1998, vol. 63, # 5, p. 1555 - 1565
[5] Journal of the American Chemical Society, 1960, vol. 82, p. 3454 - 3456
[6] Synthesis (Germany), 2013, vol. 45, # 11, p. 1497 - 1504
[7] Patent: US5455239, 1995, A,
3
[ 873-74-5 ]
[ 58633-04-8 ]
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).
(c) 4-(4-Cyanophenyl)amino-2,6-dimethyl-3-nitropyridine A solution of <strong>[15513-48-1]4-chloro-2,6-dimethyl-3-nitropyridine</strong> (9.80 g, 52.5 mmol) and 4-aminobenzonitrile (6.20 g, 52.5 mmol) in ethanol (160 ml) was stirred at room temperature for 16 hours. The solvent was removed under reduced pressure and the residue was dissolved in dichloromethane (200 ml), and washed with saturated aqueous sodium bicarbonate (100 ml). The organic phase was dried (MgSO4) and concentrated under reduced pressure to give a gum which was crystallized by adding ether (100 ml) and sonicating for 5 minutes.
In ethanol; dichloromethane;
(c) 4-[N-(4-Cyanophenyl)amino]-2,6-dimethyl-3-nitropyridine A solution of <strong>[15513-48-1]4-chloro-2,6-dimethyl-3-nitropyridine</strong> (see part (b)) (9.80 g, 52.5 mmol) and 4-aminobenzonitrile (6.20 g, 52.5 mmol) in ethanol (160 ml) was stirred at room temperature for 16 hours. The solvent was removed under reduced pressure and the residue was dissolved in dichloromethane (200 ml) and washed with saturated aqueous sodium bicarbonate (100 ml). The organic phase was dried (MgSO4) and concentrated under reduced pressure to give a gum which was crystallized by adding ether (100 ml) and sonicating for 5 minutes. The title compound was obtained as a yellow solid which was filtered off and dried in vacuo, (9.80 g, 70percent) m.p. 171°-172° C. 1 H-NMR (300 MHz, CDCl3): delta=2.49 (3H, s), 2.76 (3H, s), 6.96 (1H, s), 7.35 (2H, d, J 8 Hz), 7.74 (2H, d, J 8 Hz), 8.69 (1H, br s) p.p.m.
In ethanol; dichloromethane;
(c) 4-(4-Cyanophenyl)amino-2,6-dimethyl-3-nitropyridine A solution of <strong>[15513-48-1]4-chloro-2,6-dimethyl-3-nitropyridine</strong> (9.80 g, 52.5 mmol) and 4-aminobenzonitrile (6.20 g, 52.5 mmol) in ethanol (160 ml) was stirred at room temperature for 16 hours. The solvent was removed under reduced pressure and the residue was dissolved in dichloromethane (200 ml), and washed with saturated aqueous sodium bicarbonate (100 ml). The organic phase was dried (MgSO4) and concentrated under reduced pressure to give a gum which was crystallized by adding either (100 ml) and sonicating for 5 minutes. The yellow solid (9.80 g, 70percent) was filtered off and dried in vacuo , mp 171-172°C. 1H NMR (300 MHz, CDCl3) 2.49 (3H, s), 2.76 (3H, s), 6.96 (1H, s), 7.35 (2H, d, J 8Hz), 7.74 (2H, d, J 8Hz), (1H, br s).
With sodium hydroxide; sulfuryl dichloride; In chloroform;
EXAMPLE 15 (+-)-(2E,4E) N-(1,2-Dimethylpropyl)-5-[trans-2-(3,5-dichloro-4-bromophenyl)cyclopropyl]penta-2,4-dienamide (compound 61) P-Aminobenzonitrile (11.8 g) (ex Aldrich) in dry chloroform (250 ml) under nitrogen was treated with sulphuryl chloride (4.05 g) (ex BDH) maintaining reaction temperature below 35. After 2 hours at reflux the mixture was poured onto ice and made alkaline with 2M sodium hydroxide solution. Work up in the usual manner gave 3,5-dichloro-4-aminobenzonitrile (18.2 g) NMR 1 H 7.35(2H,s), 4.70(2H,bs).
1. Preparation of 4-cyano-2,6-dichlorobenzamine. Reaction of 4-cyanobenzamine (10 g., 0.085 m, Aldrich Chem. Co.) with 292 ml of 6N HCl and 30% H2 O2 (17.2 mL, 0.17 m) led to the formation of a white crystalline compound with a melting point of 113-115 C. The yield of this compound was 12.3 g.
N-[5-(5,6-dimethoxy-3-methyl-1,4-benzoquinon-2-yl)methyl-2-acetoxybenzoyl]-4-cyanoaniline[ No CAS ]
Yield
Reaction Conditions
Operation in experiment
With triethylamine; In dichloromethane;
Example 111 N-[5-(5,6-Dimethoxy-3-methyl-1,4-benzoquinon-2-yl)methyl-2-acetoxybenzoyl]-4-cyanoaniline 4-Cyanoaniline (0.189 g, 1.60 mmol), triethylamine (0.162 g, 1.60 mmol) and <strong>[37091-73-9]2-chloro-1,3-dimethylimidazolinium chloride</strong> (0.271 g, 1.60 mmol) were added to a methylene chloride solution (20 ml) of 5-(5,6-dimethoxy-3-methyl-1,4-benzoquinon-2-yl)methyl-2-acetoxybenzoic acid (0.200 g, 0.535 mmol) and the resulting solution was stirred at room temperature for 12 hours. The reaction solution was poured into ice water and then extracted with methylene chloride. The extract was washed with water and then dried, and the solvent was removed by distillation. The obtained residue was purified by preparative thin-layer chromatography (hexane: ethyl acetate = 1:2) to obtain the titled compound (0.141 g, 0.297 mmol, 56percent).
A solution of P-aminobenzonitrile (100 gm), ethanol (500 ml), concentrated nitric acid (36 ml) and aqueous cyanamide (50%, 54 ml) was heated at reflux. The solution was maintained for 16 hours at reflux. The reaction mass was further cooled to 0C and then added methyl tert-butyl ether (500 ml) at 0 to 5C. The reaction mass was maintained for 5 hours at 0 to 5C 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 l-(4-cyanophenyl)guanidine.
33 g
A solution of P-aminobenzonitrile (100 gm), ethanol (500 ml), concentrated nitric acid (36 ml) and aqueous cyanamide (50%, 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 8h;
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 50% 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.
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 %) of 4-(4-amino-6-chloropyrimidin-2-ylamino)benzonitrile hydrochloride.Purity (HPLC/ MS): 99.0 Area %
With toluene-4-sulfonic acid; In isopropyl alcohol; at 20 - 85℃; for 4h;
Example 5:Preparation of rilpivirineTo a mixture of (E)-3-( 4-(2-chloropyrimidin-4-ylamino )-3,5-dimethylphenyl)acrylonitrile ( 40 gm), 4-aminobenzonitrile (17 gm), isopropanol ( 400 ml)5 and p-toluenesulfonic acid (20 ml) were added at room temperature. The reaction mixturewas then heated to 80 to 85C and stirred for 4 hours. The reaction mass was then cooledto 0C and pH was adjusted to 10 to 11 with aqueous ammonia solution. The separatedsolid was filtered and then dried to provide 40 gm of rilpivirine.Chromatographic purity: 96.0%;10 Content of Z-isomer: 3.5%.
N-(4-cyanophenyl)-2-methoxybenzimidamide[ No CAS ]
Yield
Reaction Conditions
Operation in experiment
68%
To a stirred solution of 2-mcthoxyi enzonitrile (10 g, 0075 mol) in tolucne (200ml) at 0 C was added trimcthylaiuminum (90 mL. 0.09 mol) drop-wise over a period of 10 mi The reaction mixture was then stirred at room temperature for 3 h followed byaddition of 4-aminobcnzonitrilc (8.6g. 0,074mo1) in tohienc 100 mL. The reaction mixturewas heated to 70 C for 1 6 h. After confirming the completion by LCMS the reactionmixture was quenched with ice-cold water; the aqueous layer was filtered through a pad of diatomaccous earth, and the resultant filtrate was washed with ethyl acetate. The aqueous layer was extracted with ethyl acetate (2 x 100 mL). The combined organic extracts were washed with brine, dried over anhydrous Na2504, filtered, and concentrated under reducedpressure to provide a residue. Purification by column chromatography on silica gel (100-200 mesh) using ethyl acetate in hcxane afforded the title compound as a white solid. (12.8 g, 68%).
68%
Example 1 Preparation of intermediate A1; N-(4-cyanophenyl)-2-methoxybenzimidamide To a stirred solution of 2-methoxybenzonitrile (10 g, 0.075 mol) in toluene (200 ml) at 0 C. was added trimethylaluminum (90 mL, 0.09 mol) drop-wise over a period of 10 min. The reaction mixture was then stirred at room temperature for 3 h followed by addition of 4-aminobenzonitrile (8.6 g, 0.074 mol) in toluene 100 mL. The reaction mixture was heated to 70 C. for 16 h. After confirming the completion by LCMS the reaction mixture was quenched with ice-cold water; the aqueous layer was filtered through a pad of diatomaceous earth, and the resultant filtrate was washed with ethyl acetate. The aqueous layer was extracted with ethyl acetate (2*100 mL). The combined organic extracts were washed with brine, dried over anhydrous Na2SO4, filtered, and concentrated under reduced pressure to provide a residue. Purification by column chromatography on silica gel (100-200 mesh) using ethyl acetate in hexane afforded the title compound as a white solid. (12.8 g, 68%). By using analogous protocols as described in the foregoing example the intermediates described in Table 1 have been prepared using appropriate starting materials
Chemistry
Pharmaceutical Intermediates
Inhibitors/Agonists
Material Science
