Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [O:1]=[C:2]1[CH:11]=[CH:10][C:9]2[C:4](=[N:5][CH:6]=[CH:7][CH:8]=2)[N:3]1[CH2:12][CH:13]=O.[O:15]1[C:20]2[CH:21]=[CH:22][C:23]([CH2:25][N:26]([CH:34]3[CH2:39][CH2:38][NH:37][CH2:36][CH2:35]3)[C:27](=[O:33])[O:28][C:29]([CH3:32])([CH3:31])[CH3:30])=[CH:24][C:19]=2[O:18][CH2:17][CH2:16]1.C(O)(=O)C.C(O[BH-](OC(=O)C)OC(=O)C)(=O)C.[Na+]>ClCCl.O>[O:15]1[C:20]2[CH:21]=[CH:22][C:23]([CH2:25][N:26]([CH:34]3[CH2:39][CH2:38][N:37]([CH2:13][CH2:12][N:3]4[C:4]5[C:9](=[CH:8][CH:7]=[CH:6][N:5]=5)[CH:10]=[CH:11][C:2]4=[O:1])[CH2:36][CH2:35]3)[C:27](=[O:33])[O:28][C:29]([CH3:32])([CH3:30])[CH3:31])=[CH:24][C:19]=2[O:18][CH2:17][CH2:16]1
Reactant: CC(C)(C)OC(=O)N(Cc1ccc2c(c1)OCCO2)C1CCNCC1
Reactant: O=CCn1c(=O)ccc2cccnc21
Agent: CC(=O)O[BH-](OC(C)=O)OC(C)=O
Agent: [Na+]
Solvent: ClCCl
Solvent: O
Solvent: CC(=O)O
Product: CC(C)(C)OC(=O)N(Cc1ccc2c(c1)OCCO2)C1CCN(CCn2c(=O)ccc3cccnc32)CC1
Temperature: 25 °C
Reaction time: 2 h
Yield: 67.5 %

Procedure:
To a solution of 0.75 g of (2-oxo-1,8-naphthyridin-1(2H)-yl)acetaldehyde in 40 mL of dichloromethane, 1.4 g of tert-butyl (2,3-dihydro-1,4-benzodioxin-6-ylmethyl)(piperidin-4-yl)carbamate, 0.23 mL of acetic acid and 1.3 g of sodium triacetoxyborohydride were added, and the mixture was stirred at room temperature for 2 hours. Thereto were added water, a saturated aqueous sodium hydrogen carbonate solution and chloroform, the organic layer was separated, and the aqueous layer was extracted with chloroform. The organic layer and the extract were combined, the resultant solution was washed with a saturated aqueous sodium chloride solution and dried over anhydrous magnesium sulfate, and the solvent was distilled off under reduced pressure. The resultant residue was purified by silica gel column chromatography using an eluent of chloroform:methanol=200:3 to obtain 1.4 g of tert-butyl (2,3-dihydro-1,4-benzodioxin-6-ylmethyl)(1-(2-(2-oxo-1,8-naphthyridin-1(2H)-yl)ethyl)piperidin-4-yl)carbamate as a white foam.
Reaction SMILES: [C:1]([O:5][P:6]([O:13][CH2:14][C@@H:15]([NH:24]C(=O)OCC1C2C=CC=CC=2C2C1=CC=CC=2)[C:16]1[CH:21]=[C:20]([I:22])[CH:19]=[C:18]([F:23])[CH:17]=1)([O:8][C:9]([CH3:12])([CH3:11])[CH3:10])=[O:7])([CH3:4])([CH3:3])[CH3:2].CN(C=O)C.N1CCCCC1.C(N1CCCCC1)(OCC1C2C(=CC=CC=2)C2C1=CC=CC=2)=O>C(OCC)(=O)C>[P:6]([O:8][C:9]([CH3:12])([CH3:11])[CH3:10])([O:5][C:1]([CH3:2])([CH3:4])[CH3:3])([O:13][CH2:14][C@@H:15]([NH2:24])[C:16]1[CH:21]=[C:20]([I:22])[CH:19]=[C:18]([F:23])[CH:17]=1)=[O:7]
Reactant: CC(C)(C)OP(=O)(OC[C@@H](NC(=O)OCC1c2ccccc2-c2ccccc21)c1cc(F)cc(I)c1)OC(C)(C)C
Agent: O=C(OCC1c2ccccc2-c2ccccc21)N1CCCCC1
Solvent: CN(C)C=O
Solvent: CCOC(C)=O
Solvent: C1CCNCC1
Product: CC(C)(C)OP(=O)(OC[C@@H](N)c1cc(F)cc(I)c1)OC(C)(C)C
Temperature: 25 °C
Reaction time: 0.5 h

Procedure:
To (S)-(9H-fluoren-9-yl)methyl (2-((di-tert-butoxyphosphoryl)oxy)-1-(3-fluoro-5-iodophenyl)ethyl)carbamate (6450 mg, 9.27 mmol) was added DMF (Volume: 90 mL) followed by piperidine (25 mL, 253 mmol) and stirred at room temperature for 30 minutes, followed by LCMS. To the crude reaction mixture was added 750 ml of ethyl acetate, washed with saturated sodium bicarbonate (2×), water (5×), saturated salt solution, dried sodium sulfate, and filtered. The solvent was concentrated off to constant mass under high vacuum to give the desire crude product which includes FMOC piperidine impurity, used as is. LCMS (m/z): 474.2 (MH+), 0.80 min.
Reaction SMILES: [Cl-].O[NH3+:3].[C:4](=[O:7])([O-])[OH:5].[Na+].CS(C)=O.[CH2:13]([C:17]1[N:18]=[C:19]([CH3:50])[N:20]([C:39]2[CH:40]=[CH:41][C:42]3[O:46][C:45]([CH3:48])([CH3:47])[CH2:44][C:43]=3[CH:49]=2)[C:21](=[O:38])[C:22]=1[CH2:23][C:24]1[CH:29]=[CH:28][C:27]([C:30]2[C:31]([C:36]#[N:37])=[CH:32][CH:33]=[CH:34][CH:35]=2)=[CH:26][CH:25]=1)[CH2:14][CH2:15][CH3:16]>O.C(OCC)(=O)C>[CH2:13]([C:17]1[N:18]=[C:19]([CH3:50])[N:20]([C:39]2[CH:40]=[CH:41][C:42]3[O:46][C:45]([CH3:48])([CH3:47])[CH2:44][C:43]=3[CH:49]=2)[C:21](=[O:38])[C:22]=1[CH2:23][C:24]1[CH:25]=[CH:26][C:27]([C:30]2[CH:35]=[CH:34][CH:33]=[CH:32][C:31]=2[C:36]2[NH:3][C:4](=[O:7])[O:5][N:37]=2)=[CH:28][CH:29]=1)[CH2:14][CH2:15][CH3:16]
Reactant: O=C([O-])O
Reactant: [NH3+]O
Reactant: CCCCc1nc(C)n(-c2ccc3c(c2)CC(C)(C)O3)c(=O)c1Cc1ccc(-c2ccccc2C#N)cc1
Agent: [Cl-]
Agent: [Na+]
Solvent: CCOC(C)=O
Solvent: CS(C)=O
Solvent: O
Product: CCCCc1nc(C)n(-c2ccc3c(c2)CC(C)(C)O3)c(=O)c1Cc1ccc(-c2ccccc2-c2noc(=O)[nH]2)cc1
Temperature: 40 °C
Reaction time: 0.5 h
Yield: 60.6 %

Procedure:
A mixture of hydroxylammonium chloride (1.1 g), sodium hydrogen carbonate (1.69 g) and dimethyl sulfoxide (7 mL) was stirred at 40° C. for 30 min, 4′-{[4-butyl-1-(2,2-dimethyl-2,3-dihydro-1-benzofuran-5-yl)-2-methyl-6-oxo-1,6-dihydropyrimidin-5-yl]methyl}biphenyl-2-carbonitrile (0.68 g) was added, and the mixture was stirred at 90° C. for 18 hr. The reaction mixture was allowed to cool to room temperature, ethyl acetate and water were added, and the mixture was extracted with ethyl acetate. The organic layer was washed with saturated brine and dried over anhydrous magnesium sulfate, and the solvent was evaporated. The residue was dissolved in tetrahydrofuran (7 mL), N,N′-carbonyldiimidazole (0.33 g) and then 1,8-diazabicyclo[5.4.0]undec-7-ene (0.30 mL) were added, and the mixture was stirred at room temperature for 3 hr. The reaction mixture was diluted with ethyl acetate, washed with 1 M hydrochloric acid and then with saturated brine, and dried over anhydrous magnesium sulfate. The solvent was evaporated under reduced pressure and the residue was purified by silica gel column chromatography to give the title compound as a colorless solid (0.46 g, 61%).
Reaction SMILES: [C:1]([C:5]1[NH:6][C:7](=[O:20])[C:8]([C:17]([OH:19])=O)=[C:9]([NH:11][CH2:12][CH2:13][CH2:14][O:15][CH3:16])[N:10]=1)([CH3:4])([CH3:3])[CH3:2].[CH3:21][CH:22]([CH3:46])[CH2:23][NH:24][C@H:25]1[CH2:30][C@@H:29]([C:31]([N:33]2[CH2:38][CH2:37][O:36][CH2:35][CH2:34]2)=[O:32])[CH2:28][N:27](C(OC(C)(C)C)=O)[CH2:26]1.C(N(CC)C(C)C)(C)C.F[P-](F)(F)(F)(F)F.ClC(N(C)C)=[N+](C)C>ClCCCl>[C:1]([C:5]1[NH:6][C:7](=[O:20])[C:8]([C:17]([N:24]([CH2:23][CH:22]([CH3:46])[CH3:21])[C@H:25]2[CH2:30][C@@H:29]([C:31]([N:33]3[CH2:34][CH2:35][O:36][CH2:37][CH2:38]3)=[O:32])[CH2:28][NH:27][CH2:26]2)=[O:19])=[C:9]([NH:11][CH2:12][CH2:13][CH2:14][O:15][CH3:16])[N:10]=1)([CH3:2])([CH3:3])[CH3:4]
Reactant: COCCCNc1nc(C(C)(C)C)[nH]c(=O)c1C(=O)O
Reactant: CC(C)CN[C@H]1C[C@@H](C(=O)N2CCOCC2)CN(C(=O)OC(C)(C)C)C1
Agent: CN(C)C(Cl)=[N+](C)C
Agent: F[P-](F)(F)(F)(F)F
Solvent: ClCCCl
Solvent: CCN(C(C)C)C(C)C
Product: COCCCNc1nc(C(C)(C)C)[nH]c(=O)c1C(=O)N(CC(C)C)[C@@H]1CNC[C@H](C(=O)N2CCOCC2)C1
Temperature: 25 °C
Reaction time: 3 h
Yield: 4.4 %

Procedure:
2-tert-Butyl-4-[(3-methoxypropyl)amino]-6-oxo-1,6-dihydropyrimidine-5-carboxylic acid (280 mg), tert-butyl (3S,5R)-3-[(2-methylpropyl)amino]-5-(morpholin-4-ylcarbonyl)piperidine-1-carboxylate (250 mg) and N,N-diisopropylethylamine (640 mg) were dissolved in 1,2-dichloroethane (10 ml), chloro-N,N,N′,N′-tetramethylformamidinium hexafluorophosphate (420 mg) was added and the mixture was stirred at room temperature for 3 hr. The reaction mixture was concentrated, and diluted with aqueous calcium carbonate solution, and the mixture was extracted with ethyl acetate. The extract was washed with saturated brine, and dried over anhydrous magnesium sulfate. The solvent was evaporated under reduced pressure. The residue was dissolved in TFA (1 ml), and the mixture was stirred at room temperature for 0.5 hr. The reaction mixture was concentrated and purified by HPLC to give the object compound (15.8 mg).
Reaction SMILES: [NH:1]1[CH2:6][CH2:5][C:4](=[O:7])[CH2:3][CH2:2]1.Cl[CH2:9][CH2:10][CH2:11][O:12][CH2:13][C:14]1[CH:19]=[CH:18][CH:17]=[CH:16][CH:15]=1>>[CH2:13]([O:12][CH2:11][CH2:10][CH2:9][N:1]1[CH2:6][CH2:5][C:4](=[O:7])[CH2:3][CH2:2]1)[C:14]1[CH:19]=[CH:18][CH:17]=[CH:16][CH:15]=1
Reactant: ClCCCOCc1ccccc1
Reactant: O=C1CCNCC1
Product: O=C1CCN(CCCOCc2ccccc2)CC1

Procedure:
1-(3-Benzyloxypropyl)-4-piperidone is prepared from 4-piperidone and 1-chloro-3-benzyloxypropane essentially as described above in Example 38, Scheme C, step a.
Reaction SMILES: [H-].[Na+].[CH3:3][N:4]1[CH2:9][CH2:8][CH2:7][C@@H:6]([CH2:10][OH:11])[CH2:5]1.[CH3:12][C:13]1[CH:18]=[CH:17][C:16]([N:19]2[CH2:24][CH2:23][N:22]([C:25](OC3C=CC([N+]([O-])=O)=CC=3)=[O:26])[CH2:21][CH2:20]2)=[CH:15][CH:14]=1>CCCCCCC.C1COCC1>[CH3:12][C:13]1[CH:14]=[CH:15][C:16]([N:19]2[CH2:20][CH2:21][N:22]([C:25]([O:11][CH2:10][C@@H:6]3[CH2:7][CH2:8][CH2:9][N:4]([CH3:3])[CH2:5]3)=[O:26])[CH2:23][CH2:24]2)=[CH:17][CH:18]=1
Reactant: CN1CCC[C@@H](CO)C1
Reactant: Cc1ccc(N2CCN(C(=O)Oc3ccc([N+](=O)[O-])cc3)CC2)cc1
Agent: [H-]
Agent: [Na+]
Solvent: CCCCCCC
Solvent: C1CCOC1
Product: Cc1ccc(N2CCN(C(=O)OC[C@@H]3CCCN(C)C3)CC2)cc1
Temperature: 0 °C
Reaction time: 18 h
Yield: 32 %

Procedure:
Sodium hydride (0.70 g, 60% dispersion in mineral oil, 17.5 mmol) was suspended in heptane (10 mL) under an argon atmosphere. The heptane was decanted off, and the flask was charged with THF (20 mL) and cooled to 0° C. A solution of (R)-(1-methylpiperidin-3-yl)methanol (0.75 g, 5.83 mmol) in THF (20 mL) was added drop-wise, followed by a solution of 4-nitrophenyl 4-(4-methylphenyl)piperazine-1-carboxylate (Intermediate 1; 2.19 g, 6.42 mmol) in THF (20 mL). The reaction mixture was allowed to warm to room temperature and stirred for 18 hours. The reaction mixture was then cooled to 0° C. and quenched with the drop-wise addition of sat aq NaHCO3 solution and concentrated in vacuo. The residue was dissolved in ethyl acetate (200 mL), washed with sat aq NaHCO3 solution (4×50 mL), dried (MgSO4) and concentrated in vacuo. The residue was purified by reverse phase chromatography (gradient eluting with methanol in water, with 1% formic acid in each solvent, 0-25%). The resulting residue was dissolved in DCM (50 mL) and stirred with solid K2CO3 for 20 min, filtered and concentrated in vacuo. The residue was further purified by normal phase column chromatography (eluting with DCM, followed by a 90:10 mixture of DCM:MeOH) to give [(3R)-1-methylpiperidin-3-yl]methyl 4-(4-methylphenyl)piperazine-1-carboxylate (619 mg, 32%) as a pale brown solid.
Reaction SMILES: [C:1]([O:5][C:6](=[O:25])[NH:7][C@H:8]1[CH2:13][CH2:12][C@H:11]([NH:14][C@@H:15]2[C:24]3[N:23]=[CH:22][CH:21]=[CH:20][C:19]=3[CH2:18][CH2:17][CH2:16]2)[CH2:10][CH2:9]1)([CH3:4])([CH3:3])[CH3:2].[C:26]([O:30][C:31]([N:33]1[C:37]2[CH:38]=[CH:39][CH:40]=[CH:41][C:36]=2[N:35]=[C:34]1[CH2:42]Cl)=[O:32])([CH3:29])([CH3:28])[CH3:27].C(N(C(C)C)CC)(C)C.[I-].[K+]>C(#N)C>[C:26]([O:30][C:31]([N:33]1[C:37]2[CH:38]=[CH:39][CH:40]=[CH:41][C:36]=2[N:35]=[C:34]1[CH2:42][N:14]([C@H:11]1[CH2:12][CH2:13][C@H:8]([NH:7][C:6]([O:5][C:1]([CH3:4])([CH3:2])[CH3:3])=[O:25])[CH2:9][CH2:10]1)[CH:15]1[C:24]2[N:23]=[CH:22][CH:21]=[CH:20][C:19]=2[CH2:18][CH2:17][CH2:16]1)=[O:32])([CH3:29])([CH3:28])[CH3:27]
Reactant: CC(C)(C)OC(=O)n1c(CCl)nc2ccccc21
Reactant: CC(C)(C)OC(=O)N[C@H]1CC[C@H](N[C@H]2CCCc3cccnc32)CC1
Agent: [I-]
Agent: [K+]
Solvent: CCN(C(C)C)C(C)C
Solvent: CC#N
Product: CC(C)(C)OC(=O)N[C@H]1CC[C@H](N(Cc2nc3ccccc3n2C(=O)OC(C)(C)C)C2CCCc3cccnc32)CC1
Temperature: 60 °C
Reaction time: 48 h

Procedure:
To a suspension of [4-((S)-5,6,7,8-tetrahydro-quinolin-8-ylamino)-trans-cyclohexyl]-carbamic acid tert-butyl ester (1.95 g, 5.64 mmol) in dry acetonitrile (60 mL) was added 2-chloromethyl-benzoimidazole-1-carboxylic acid tert-butyl ester (1.65 g, 6.20 mmol), diisopropylethylamine (2.0 mL, 11.4 mmol) and potassium iodide (100 mg, 0.60 mmol). The mixture was warmed to 60° C. and stirred for 2 days under nitrogen. The mixture was concentrated, dissolved in methylene chloride (80 mL) and washed with brine (50 mL). The aqueous layer was extracted with methylene chloride (3×50 mL). The combined organic layers were dried (Na2SO4) and concentrated. The crude mixture was purified by column chromatography on silica gel (80 g) with methanol/methylene chloride (4:96) to afford 2-{[(4-tert-butoxycarbonylamino-trans-cyclohexyl)-(5,6,7,8-tetrahydro-quinolin-8-yl)-amino]-methyl}-benzimidazole-1-carboxylic acid tert-butyl ester as a white solid (1.82 g, 56%). 1H NMR (CDCl3) δ 1.09 (bs, 2H), 1.43 (s, 9H), 1.68 (s, 9H), 1.83-2.14 (m, 6H), 2.47-2.63 (m, 1H), 2.65-2.79 (m, 1H), 2.79-2.95 (m, 1H), 3.32 (bs, 1H), 4.30 (bs, 2H), 4.46 (s, 2H), 6.75-6.89 (m, 1H), 7.00-7.13 (m, 1H), 7.61-7.70 (m, 1H), 7.70-7.79 (m, 1H), 8.32 (bs, 1H).
Reaction SMILES: [CH3:1][S:2]([C:5]1[CH:12]=[CH:11][C:8]([CH:9]=O)=[CH:7][CH:6]=1)(=[O:4])=[O:3].ClC1C=CC(C[CH:19]2[C:24](=[O:25])[O:23][C:22]([CH3:27])([CH3:26])[O:21][C:20]2=[O:28])=CC=1.BrC1C=C2C(=CC=1)N=C(Cl)C(CC1C=CC(Cl)=CC=1)=C2Cl>>[CH3:1][S:2]([C:5]1[CH:12]=[CH:11][C:8]([CH2:9][CH:19]2[C:24](=[O:25])[O:23][C:22]([CH3:27])([CH3:26])[O:21][C:20]2=[O:28])=[CH:7][CH:6]=1)(=[O:4])=[O:3]
Reactant: CC1(C)OC(=O)C(Cc2ccc(Cl)cc2)C(=O)O1
Reactant: CS(=O)(=O)c1ccc(C=O)cc1
Agent: Clc1ccc(Cc2c(Cl)nc3ccc(Br)cc3c2Cl)cc1
Product: CC1(C)OC(=O)C(Cc2ccc(S(C)(=O)=O)cc2)C(=O)O1

Procedure:
The title compound was prepared using 4-(methylsulfonyl)benzaldehyde in place of 4-chlorobenzaldehyde using the procedure described for the preparation of 5-(4-chlorobenzyl)-2,2-dimethyl-1,3-dioxane-4,6-dione (Intermediate 3: step a).
Reaction SMILES: [Cl:1][C:2]1[CH:3]=[CH:4][C:5]([NH:8][C:9]2[CH:34]=[CH:33][C:12]([O:13][C:14]3[C:15]([CH:20]4[CH2:25][CH2:24][N:23]([C:26]([O:28]C(C)(C)C)=O)[CH2:22][CH2:21]4)=[N:16][CH:17]=[CH:18][N:19]=3)=[CH:11][CH:10]=2)=[N:6][CH:7]=1.F[C:36](F)(F)C(O)=O.C(OC(=O)C)(=O)C>ClCCl>[Cl:1][C:2]1[CH:3]=[CH:4][C:5]([NH:8][C:9]2[CH:34]=[CH:33][C:12]([O:13][C:14]3[C:15]([CH:20]4[CH2:25][CH2:24][N:23]([C:26](=[O:28])[CH3:36])[CH2:22][CH2:21]4)=[N:16][CH:17]=[CH:18][N:19]=3)=[CH:11][CH:10]=2)=[N:6][CH:7]=1
Reactant: O=C(O)C(F)(F)F
Reactant: CC(C)(C)OC(=O)N1CCC(c2nccnc2Oc2ccc(Nc3ccc(Cl)cn3)cc2)CC1
Solvent: ClCCl
Solvent: CC(=O)OC(C)=O
Product: CC(=O)N1CCC(c2nccnc2Oc2ccc(Nc3ccc(Cl)cn3)cc2)CC1
Temperature: 25 °C
Reaction time: 2 h

Procedure:
A solution of tert-butyl 4-(3-(4-(5-chloropyridin-2-ylamino)phenoxy)pyrazin-2-yl)piperidine-1-carboxylate (0.14 g, 0.29 mmol) in dichloromethane (1 mL) was added trifluoroacetic acid (0.22 mL, 2.9 mmol) and stirred at room temperature for 2 h. The reaction was concentrated in vacuo, and the residue was partitioned between CH2Cl2 and aqueous saturated NaHCO3 solution. The organic layer was dried (MgSO4), filtered, and concentrated in vacuo to give a golden yellow oil. A solution of the crude golden yellow oil in CH2Cl2 (1 mL) was cooled to 0° C. and added acetic anhydride (0.041 mL, 0.43 mmol). The reaction was gradually allowed to warm to room temperature and stirred for 1 h. The reaction was diluted with CH2Cl2 and washed with aqueous saturated NaHCO3 solution. The organic layer was dried (MgSO4), filtered, and concentrated in vacuo. Flash column chromatography (20% to 70% EtOAc/Hexanes) provided a crude crop of the desired product. Further purification via reverse phase HPLC afforded 1-(4-(3-(4-(5-chloropyridin-2-ylamino)phenoxy)pyrazin-2-yl)piperidin-1-yl)ethanone as an off-white amorphous solid. MS (ESI, pos. ion) m/z: 424.9 (M+1). IC50 (uM) 0.001.
Reaction SMILES: [OH-:1].[K+].[Cl:3][C:4]1[C:9]([O:10][CH3:11])=[CH:8][C:7]([O:12][CH3:13])=[C:6]([Cl:14])[C:5]=1[C:15]1[C:24]2[N:23]=[CH:22][C:21]([CH2:25][N:26]3[CH2:31][CH2:30][N:29]([CH2:32][CH3:33])[CH2:28][CH2:27]3)=[N:20][C:19]=2[C:18]([C:34]#N)=[CH:17][CH:16]=1.ClC1C(OC)=CC(OC)=C(Cl)C=1C1C2N=C(CN3CCN(CC)CC3)C=NC=2C(C#N)=CC=1.[OH2:69]>C(O)CO>[Cl:14][C:6]1[C:7]([O:12][CH3:13])=[CH:8][C:9]([O:10][CH3:11])=[C:4]([Cl:3])[C:5]=1[C:15]1[C:24]2[N:23]=[CH:22][C:21]([CH2:25][N:26]3[CH2:31][CH2:30][N:29]([CH2:32][CH3:33])[CH2:28][CH2:27]3)=[N:20][C:19]=2[C:18]([C:34]([OH:69])=[O:1])=[CH:17][CH:16]=1
Reactant: [OH-]
Reactant: CCN1CCN(Cc2cnc3c(-c4c(Cl)c(OC)cc(OC)c4Cl)ccc(C#N)c3n2)CC1
Reactant: O
Agent: CCN1CCN(Cc2cnc3c(C#N)ccc(-c4c(Cl)c(OC)cc(OC)c4Cl)c3n2)CC1
Agent: [K+]
Solvent: OCCO
Product: CCN1CCN(Cc2cnc3c(-c4c(Cl)c(OC)cc(OC)c4Cl)ccc(C(=O)O)c3n2)CC1
Temperature: 150 °C
Reaction time: 3 h

Procedure:
A solution of KOH (0.818 g, 14.6 mmol, 10 equiv) in H2O (20 mL) was added to 710 mg (1.46 equiv) of a mixture of 8-(2,6-dichloro-3,5-dimethoxy-phenyl)-3-(4-ethyl-piperazin-1-ylmethyl)-quinoxaline-5-carbonitrile and 8-(2,6-dichloro-3,5-dimethoxy-phenyl)-2-(4-ethyl-piperazin-1-ylmethyl)-quinoxaline-5-carbonitrile (Step 82.2) (710 mg, 1.46 mmol) in ethylene glycol (20 mL). The reaction mixture was stirred at 150° C. for 3 h, allowed to cool to rt and washed with EtOAc (2×100 mL). The aqueous layer was acidified to pH 3-4 by addition of 1 N HCl. The resulting suspension was filtered. The filtrate contains 8-(2,6-dichloro-3,5-dimethoxy-phenyl)-2-(4-ethyl-piperazin-1-ylmethyl)-quinoxaline-5-carboxylic acid (Step 83.1). The residue in the filter was triturated in 1 N HCl (3 mL) and filtered. The filtrate was basified to pH 5 and extracted with DCM (2×100 mL). The organic layer was dried (Na2SO4), filtered and concentrated to afford 190 mg of the title compound as a white solid: ES-MS: 505.0/506.6 [M+H]+; tR=3.46 min (System 1).
Reaction SMILES: [S:1]1(=[O:8])(=[O:7])[CH2:5][CH2:4][C:3](=O)[CH2:2]1.[CH3:9][C:10]1[C:18]2[C:13](=[CH:14][CH:15]=[C:16](/[CH:19]=[C:20](/[C:23](=O)[CH3:24])\[C:21]#[N:22])[CH:17]=2)[NH:12][N:11]=1.C([O-])(=O)C.[NH4+:30]>C(O)(=O)C>[CH3:24][C:23]1[NH:30][C:3]2[CH2:4][CH2:5][S:1](=[O:8])(=[O:7])[C:2]=2[CH:19]([C:16]2[CH:17]=[C:18]3[C:13](=[CH:14][CH:15]=2)[NH:12][N:11]=[C:10]3[CH3:9])[C:20]=1[C:21]#[N:22]
Reactant: O=C1CCS(=O)(=O)C1
Reactant: CC(=O)/C(C#N)=C/c1ccc2[nH]nc(C)c2c1
Reactant: [NH4+]
Agent: CC(=O)[O-]
Solvent: CC(=O)O
Product: CC1=C(C#N)C(c2ccc3[nH]nc(C)c3c2)C2=C(CCS2(=O)=O)N1

Procedure:
850 mg (6.336 mmol) dihydrothiophen-3(2H)-one-1,1-dioxide, 1.78 g (6.336 mmol) (2E)-2-[(3-methyl-1H-indazol-5-yl)methylidene]-3-oxobutanenitrile (Example 2A) and 586 mg (7.603 mmol) ammonium acetate in acetic acid (30 ml) were heated to reflux overnight. After cooling, the mixture was evaporated to dryness, and the residue was taken up in ethyl acetate and washed with water and brine. The organic layer was separated and dried over sodium sulfate. After filtration and evaporation to dryness, the remaining solid was purified by preparative RP-HPLC (acetonitrile/water gradient) to yield 89 mg (4% of th.) of the title compound.
Reaction SMILES: C(OC([N:11]1[CH2:42][CH2:41][C:14]2([O:19][CH2:18][C:17](=[O:20])[N:16]([CH2:21][C:22]3[CH:27]=[CH:26][C:25]([O:28][CH2:29][CH:30]([CH3:32])[CH3:31])=[CH:24][CH:23]=3)[CH:15]2[CH2:33][C:34]2[CH:39]=[CH:38][C:37]([F:40])=[CH:36][CH:35]=2)[CH2:13][CH2:12]1)=O)C1C=CC=CC=1>C(O)C.[Pd]>[F:40][C:37]1[CH:36]=[CH:35][C:34]([CH2:33][CH:15]2[C:14]3([CH2:13][CH2:12][NH:11][CH2:42][CH2:41]3)[O:19][CH2:18][C:17](=[O:20])[N:16]2[CH2:21][C:22]2[CH:27]=[CH:26][C:25]([O:28][CH2:29][CH:30]([CH3:31])[CH3:32])=[CH:24][CH:23]=2)=[CH:39][CH:38]=1
Reactant: CC(C)COc1ccc(CN2C(=O)COC3(CCN(C(=O)OCc4ccccc4)CC3)C2Cc2ccc(F)cc2)cc1
Agent: [Pd]
Solvent: CCO
Product: CC(C)COc1ccc(CN2C(=O)COC3(CCNCC3)C2Cc2ccc(F)cc2)cc1

Procedure:
The spirocycle 103NLS33 (62 mg, 0.107 mmol) in ethanol (5 mL) was N-CBz-deprotected by hydrogenation in presence of Pd/C (10%, 40 mg) under H2-balloon pressure. The catalyst was filtered off and the filtrate evaporated under reduced pressure to give crude 5-(4-fluorobenzyl)-4-(4-isobutoxybenzyl)-1-oxa-4,9-diaza-spiro[5.5]undecan-3-one. The residue was dissolved in methanol (3 mL), formaldehyde (37% in water, 0.017 mL) added, followed by the addition of acetic acid (0.03 mL) and sodium cyanoborohydride (60 mg, 0.95 mmol). The solution was stirred at rt for 5 h, then water was added and the mixture basified with 2 N aq. NaOH solution. The mixture was extracted three times with dichloromethane, the combined organic layers washed with sat ammonium chloride solution and brine, dried over Na2SO4, filtered and evaporated to dryness. The residue was purified by column chromatography on silica gel, eluting with a stepwise gradient of 0-7% methanol in dichloromethane, giving 103NLS35B (43 mg, 88% over both steps) as a colorless oil. The compound was converted to its HCl form by treatment with 2 M HCl in diethylether as described above for 69NLS75, affording the salt as a colorless powder.
Reaction SMILES: [C:1]([C:3]1[CH:51]=[CH:50][C:6]2[N:7]([CH2:36][C:37]3[C:46]4[C:41](=[CH:42][CH:43]=[CH:44][CH:45]=4)[N:40]=[CH:39][C:38]=3[CH:47]3[CH2:49][CH2:48]3)[C:8](=[O:35])[C@@H:9]([NH:21][C:22](=[O:34])[C@@H:23]([N:25](C)[C:26](=O)OC(C)(C)C)[CH3:24])[C@H:10]([CH3:20])[N:11]([C:12]([CH:14]3[CH2:19][CH2:18][O:17][CH2:16][CH2:15]3)=[O:13])[C:5]=2[CH:4]=1)#[N:2].[ClH:52]>O1CCOCC1.CCOCC>[ClH:52].[ClH:52].[C:1]([C:3]1[CH:51]=[CH:50][C:6]2[N:7]([CH2:36][C:37]3[C:46]4[C:41](=[CH:42][CH:43]=[CH:44][CH:45]=4)[N:40]=[CH:39][C:38]=3[CH:47]3[CH2:49][CH2:48]3)[C:8](=[O:35])[C@@H:9]([NH:21][C:22](=[O:34])[C@@H:23]([NH:25][CH3:26])[CH3:24])[C@H:10]([CH3:20])[N:11]([C:12]([CH:14]3[CH2:19][CH2:18][O:17][CH2:16][CH2:15]3)=[O:13])[C:5]=2[CH:4]=1)#[N:2]
Reactant: C[C@@H](C(=O)N[C@@H]1C(=O)N(Cc2c(C3CC3)cnc3ccccc23)c2ccc(C#N)cc2N(C(=O)C2CCOCC2)[C@H]1C)N(C)C(=O)OC(C)(C)C
Agent: Cl
Solvent: CCOCC
Solvent: C1COCCO1
Product: CN[C@@H](C)C(=O)N[C@@H]1C(=O)N(Cc2c(C3CC3)cnc3ccccc23)c2ccc(C#N)cc2N(C(=O)C2CCOCC2)[C@H]1C
Yield: 81 %

Procedure:
A rt solution of tert-butyl(S)-1-((3S,4S)-7-cyano-1-((3-cyclopropylquinolin-4-yl)methyl)-4-methyl-2-oxo-5-(tetrahydro-2H-pyran-4-carbonyl)-2,3,4,5-tetrahydro-1H-benzo[b][1,4]diazepin-3-ylamino)-1-oxopropan-2-yl(methyl)carbamate (53 mg, 76.3 μmol) in 4 M HCl in dioxane (381 μl) was stirred for 2 h. The reaction was diluted with Et2O and the solids were collected by vacuum filtration to provide (S)-N-((3S,4S)-7-cyano-1-((3-cyclopropylquinolin-4-yl)methyl)-4-methyl-2-oxo-5-(tetrahydro-2H-pyran-4-carbonyl)-2,3,4,5-tetrahydro-1H-benzo[b][1,4]diazepin-3-yl)-2-(methylamino)propanamide dihydrochloride (41.4 mg, 81%) as a white solid. MS m/z 595 (MH)+.
Reaction SMILES: C([O-])([O-])=O.[K+].[K+].[CH3:7][NH:8][CH3:9].[CH2:10]([O:12][C:13]([C:15]1[C:16]([S:27][CH2:28][CH3:29])=[N:17][C:18]2[C:23]([C:24]=1[CH3:25])=[CH:22][CH:21]=[C:20](F)[CH:19]=2)=[O:14])[CH3:11].CCCCCC>CCO>[CH2:10]([O:12][C:13]([C:15]1[C:16]([S:27][CH2:28][CH3:29])=[N:17][C:18]2[C:23]([C:24]=1[CH3:25])=[CH:22][CH:21]=[C:20]([N:8]([CH3:9])[CH3:7])[CH:19]=2)=[O:14])[CH3:11]
Reactant: CCOC(=O)c1c(SCC)nc2cc(F)ccc2c1C
Reactant: CNC
Agent: O=C([O-])[O-]
Agent: [K+]
Solvent: CCO
Solvent: CCCCCC
Product: CCOC(=O)c1c(SCC)nc2cc(N(C)C)ccc2c1C
Temperature: 90 °C
Yield: 38 %

Procedure:
2.8 g (20.5 mmol) K2CO3 and a 40% aq. dimethylamine solution (20.5 ml) were added to a solution of 2.0 g (6.8 mmol) 2-ethylsulfanyl-7-fluoro-4-methyl-quinoline-3-carboxylic acid ethyl ester in EtOH (20 ml) and the mixture was heated for 16 h at 90° C. in a closed vessel. Then the reaction solution was concentrated to small volume under vacuum and the residue was taken up with water. It was then extracted with EE. The organic phase was washed with water and brine, dried over Na2SO4, filtered and concentrated to small volume under vacuum. Column chromatography (hexane/EE 25:1) of the residue yielded 810 mg (2.55 mmol, 38%) 7-dimethylamino-2-ethylsulfanyl-4-methyl-quinoline-3-carboxylic acid ethyl ester.