Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [NH2:1][C:2]1[N:10]=[CH:9][N:8]=[C:7]2[C:3]=1[N:4]=[C:5](I)[N:6]2[C:11]1[CH:16]=[CH:15][C:14]([NH:17][C:18]([NH:20][C:21]2[CH:26]=[CH:25][C:24]([Cl:27])=[C:23]([C:28]([F:31])([F:30])[F:29])[CH:22]=2)=[O:19])=[CH:13][CH:12]=1.[CH3:33][O-:34].[Na+]>CO>[NH2:1][C:2]1[N:10]=[CH:9][N:8]=[C:7]2[C:3]=1[N:4]=[C:5]([O:34][CH3:33])[N:6]2[C:11]1[CH:16]=[CH:15][C:14]([NH:17][C:18]([NH:20][C:21]2[CH:26]=[CH:25][C:24]([Cl:27])=[C:23]([C:28]([F:31])([F:30])[F:29])[CH:22]=2)=[O:19])=[CH:13][CH:12]=1
Reactant: Nc1ncnc2c1nc(I)n2-c1ccc(NC(=O)Nc2ccc(Cl)c(C(F)(F)F)c2)cc1
Reactant: C[O-]
Agent: [Na+]
Solvent: CO
Product: COc1nc2c(N)ncnc2n1-c1ccc(NC(=O)Nc2ccc(Cl)c(C(F)(F)F)c2)cc1
Reaction time: 14 h
Yield: 36.6 %

Procedure:
In 2 mL of methanol, 25 mg (0.04 mmol) of 1-[4-(6-amino-8-iodopurin-9-yl)phenyl]-3-(4-chloro-3-(trifluoromethyl)phenyl)urea was dissolved, and 5.6 mg (0.10 mmol) of sodium methylate was added thereto, and the mixture solution was refluxed with stirring for 14 hours. The reaction solution was concentrated and purified by a silica gel column (dichloromethane:methanol=9:1) to obtain 7 mg (34%) of a target product as a white solid.
Reaction SMILES: [OH:1][C:2]1[CH:9]=[CH:8][C:5]([CH:6]=[O:7])=[CH:4][CH:3]=1.C(=O)([O-])[O-].[K+].[K+].[I-].[K+].I[CH:19]([CH3:21])[CH3:20]>CC(=O)CC>[CH:19]([O:1][C:2]1[CH:9]=[CH:8][C:5]([CH:6]=[O:7])=[CH:4][CH:3]=1)([CH3:21])[CH3:20]
Reactant: O=Cc1ccc(O)cc1
Reactant: CC(C)I
Agent: O=C([O-])[O-]
Agent: [I-]
Agent: [K+]
Solvent: CCC(C)=O
Product: CC(C)Oc1ccc(C=O)cc1

Procedure:
A mixture of 4-hydroxybenzaldehyde (20 g), anhydrous potassium carbonate (25 g), potassium iodide (0.5 g) and 2-iodopropane (27 g) in 2-butanone (300 ml) was heated overnight, under reflux, with stirring, cooled, filtered and evaporated to dryness. The residue was dissolved in diethyl ether, washed with aqueous sodium hydroxide and brine, dried (magnesium sulphate), filtered and evaporated to dryness. Distillation of the residue gave the title compound, bp 108°-112°/3 mm as an oil.
Reaction SMILES: [OH2:1].[ClH:2].Cl.[Cl:4][C:5]1[CH:32]=[CH:31][C:8]([CH2:9][N:10]2[CH2:15][CH2:14][N:13]([CH2:16][CH2:17][CH2:18][NH:19][C:20]([NH:22][C:23]3[CH:28]=[CH:27][C:26]([C:29]#[N:30])=[CH:25][CH:24]=3)=[O:21])[CH2:12][CH2:11]2)=[CH:7][CH:6]=1.Cl.[OH-].[K+]>C(O)(=O)C>[ClH:4].[ClH:2].[Cl:4][C:5]1[CH:6]=[CH:7][C:8]([CH2:9][N:10]2[CH2:11][CH2:12][N:13]([CH2:16][CH2:17][CH2:18][NH:19][C:20]([NH:22][C:23]3[CH:24]=[CH:25][C:26]([C:29](=[O:1])[NH2:30])=[CH:27][CH:28]=3)=[O:21])[CH2:14][CH2:15]2)=[CH:31][CH:32]=1
Reactant: O
Reactant: N#Cc1ccc(NC(=O)NCCCN2CCN(Cc3ccc(Cl)cc3)CC2)cc1
Agent: Cl
Agent: [K+]
Agent: [OH-]
Solvent: CC(=O)O
Product: NC(=O)c1ccc(NC(=O)NCCCN2CCN(Cc3ccc(Cl)cc3)CC2)cc1
Yield: 70.8 %

Procedure:
A solution of 1-{3-[4-(4-chlorobenzyl)piperazin-1-yl]-propyl}-3-(4-cyanophenyl)urea dihydrochloride monohydrate (10.0 g; 19.9 mmole), glacial acetic acid (120 ml), and concentrated hydrochloric acid (80 ml) was heated at 80° C. for 30 minutes. The mixture was then poured over ice, and basified with aqueous potassium hydroxide. The product was extracted with methylene chloride, dried (sodium sulfate), and the salt precipitated out ethereal hydrochloric acid. Several recrystallizations from ethanol provided the title compound (3.54 g; 38% yield) as colorless crystals, m.p. 224°-226° C.
Reaction SMILES: [Cl:1][C:2]1[CH:3]=[C:4]([C:8]2[CH:9]=[C:10]([CH2:16][N:17]3[CH:21]=[N:20][C:19]([C:22]([O:24]C)=O)=[N:18]3)[CH:11]=[N:12][C:13]=2[O:14][CH3:15])[CH:5]=[CH:6][CH:7]=1.[NH3:26]>CO>[Cl:1][C:2]1[CH:3]=[C:4]([C:8]2[CH:9]=[C:10]([CH2:16][N:17]3[CH:21]=[N:20][C:19]([C:22]([NH2:26])=[O:24])=[N:18]3)[CH:11]=[N:12][C:13]=2[O:14][CH3:15])[CH:5]=[CH:6][CH:7]=1
Reactant: COC(=O)c1ncn(Cc2cnc(OC)c(-c3cccc(Cl)c3)c2)n1
Reactant: N
Solvent: CO
Product: COc1ncc(Cn2cnc(C(N)=O)n2)cc1-c1cccc(Cl)c1
Yield: 77 %

Procedure:
To a solution of methyl 1-((5-(3-chlorophenyl)-6-methoxypyridin-3-yl)methyl)-1H-1,2,4-triazole-3-carboxylate (Example 141, 103 mg, 0.28 mmol) in methanol (2 mL) was added ammonia in methanol (2 mL of 7N solution, 14 mmol). The mixture was heated using microwave irradiation at 130° C. for 20 min. The LCMS showed incomplete conversion. To the reaction mixture was added more ammonia in methanol (2 mL, 14 mmol) and irradiated in a microwave at 120° C. for an additional 20 min. The solvent was removed under reduced pressure. Purification (FCC, SiO2, 0-5% MeOH/DCM) afforded the title compound (77 mg, 77%). 1H NMR (400 MHz, DMSO-d6) δ 8.74 (s, 1H), 8.25 (d, J=2.3 Hz, 1H), 7.85 (d, J=2.3 Hz, 1H), 7.78-7.70 (m, 1H), 7.62-7.40 (m, 5H), 5.45 (s, 2H), 3.87 (s, 3H). [M+H]=354.18.
Reaction SMILES: [C:1]([C:3](=[C:7]([S:10][CH3:11])SC)[C:4]([NH2:6])=O)#[N:2].[NH2:12][C:13]1[CH:14]=[N:15][CH:16]=[CH:17][CH:18]=1>CCO>[CH3:11][S:10][C:7]([NH:12][C:13]1[CH:14]=[N:15][CH:16]=[CH:17][CH:18]=1)=[C:3]([C:1]#[N:2])[C:4]#[N:6]
Reactant: Nc1cccnc1
Reactant: CSC(SC)=C(C#N)C(N)=O
Solvent: CCO
Product: CSC(Nc1cccnc1)=C(C#N)C#N
Temperature: 25 °C
Reaction time: 48 h

Procedure:
Dissolved 2-cyano-3,3-bis(methylthio)acrylamide I-2 (1.0 g) in EtOH (15 mL), and heated to 75° C. until solids dissolved. 3-Aminopyridine (1.0 eq., 0.608 g) was then added and solution continued stirring for 2 days. Precipitate formed which was found to be product. Reaction was cooled to room temperature and filtered to obtain 2-((methylthio)(pyridin-3-ylamino)methylene)malononitrile as a yellow powder.
Reaction SMILES: [CH3:1][C:2]1[NH:3][C:4]2[C:9]([C:10]=1[CH:11]=O)=[CH:8][CH:7]=[CH:6][CH:5]=2.[C:13]([C:16]1[CH:21]=[CH:20][N:19]=[CH:18][CH:17]=1)(=[O:15])[CH3:14].N1CCCCC1>CO>[CH3:1][C:2]1[NH:3][C:4]2[C:9]([C:10]=1/[CH:11]=[CH:14]/[C:13]([C:16]1[CH:21]=[CH:20][N:19]=[CH:18][CH:17]=1)=[O:15])=[CH:8][CH:7]=[CH:6][CH:5]=2
Reactant: CC(=O)c1ccncc1
Reactant: Cc1[nH]c2ccccc2c1C=O
Solvent: CO
Solvent: C1CCNCC1
Product: Cc1[nH]c2ccccc2c1/C=C/C(=O)c1ccncc1
Yield: 69.6 %

Procedure:
To a dried 500 mL round bottom flask under argon, 2-methylindole-3-carboxaldehyde (400 mg, 2.51 mmol) was dissolved in anhydrous MeOH (10 mL). 4-Acetyl-pyridine (305 μL, 2.76 mmol, 1.1 equiv.) and piperidine (82 μL, 0.83 mmol) were added and the reaction was stirred under reflux. A red-orange precipitate gradually formed, and after twelve hours this solid was isolated by filtration, rinsed with chilled methanol and dried under vacuum, producing 458 mg (69%) of yellow solid. NMR: 1H NMR (600 MHz, d6-DMSO): δ 12.017 (s, 1H, N—H), 8.816-8.806 (dd, J1=4.5, J2=2.1, 2H, pyr-2,6H), 8.121-8.095 (d, J=15.6, 1H, C═CH), 8.077-8.063 (m, 1H, indole-4H), 7.975-7.965 (dd, J1=4.5, J2=1.5, 2H, pyr-3,5H), 7.489-7.464 (d, J=15.6, 1H, C═CH), 7.415-7.400 (m, 1H, indole-7H), 7.220-7.200 (m, 2H, indole-5,6H), 2.596 (s, 3H, methyl). 13C NMR (150 MHz, d6-DMSO): δ 188.0, 150.7, 145.6, 144.9, 139.5, 136.3, 125.8, 122.4, 121.50, 121.46, 120.4, 113.1, 111.7, 109.4, 11.9. Melting Point: 268-272° C. TLC: (ethyl acetate:hexanes 4:1) Rf=0.18. Elemental analysis calculated for C17H14N2O: C, 77.84; H, 5.38; N, 10.68. found: C, 77.96; H, 5.28; N, 10.59.
Reaction SMILES: [NH2:1][C:2]1[CH:7]=[CH:6][C:5]([S:8][C:9]2[CH:24]=[CH:23][C:12]([C:13]([NH:15][C:16]3[CH:21]=[CH:20][C:19]([Br:22])=[CH:18][CH:17]=3)=[O:14])=[CH:11][C:10]=2[N+:25]([O-:27])=[O:26])=[CH:4][CH:3]=1.N1C=CC=CC=1.Cl[C:35]([O:37][CH2:38][C:39]([Cl:42])([Cl:41])[Cl:40])=[O:36]>ClCCl>[Cl:40][C:39]([Cl:42])([Cl:41])[CH2:38][O:37][C:35](=[O:36])[NH:1][C:2]1[CH:7]=[CH:6][C:5]([S:8][C:9]2[CH:24]=[CH:23][C:12]([C:13](=[O:14])[NH:15][C:16]3[CH:21]=[CH:20][C:19]([Br:22])=[CH:18][CH:17]=3)=[CH:11][C:10]=2[N+:25]([O-:27])=[O:26])=[CH:4][CH:3]=1
Reactant: O=C(Cl)OCC(Cl)(Cl)Cl
Reactant: Nc1ccc(Sc2ccc(C(=O)Nc3ccc(Br)cc3)cc2[N+](=O)[O-])cc1
Solvent: c1ccncc1
Solvent: ClCCl
Product: O=C(Nc1ccc(Sc2ccc(C(=O)Nc3ccc(Br)cc3)cc2[N+](=O)[O-])cc1)OCC(Cl)(Cl)Cl
Reaction time: 16 h
Yield: 82.7 %

Procedure:
To a slurry of the product of Example 60A (3.6 g, 8.1 mmol) in dichloromethane (100 mL) and pyridine (1.3 g, 16.2 mmol) was added 2,2,2-Trichloroethyl chloroformate (2.16 g, 10.2 mmol). The solution was stirred for 16 hours, washed with water, brine, dried over sodium sulfate and concentrated under vacuum. The resulting residue was triturated in 9:1 hexane/ethyl acetate to give the title compound as an orange powder (4.15 g, 83%).
Reaction SMILES: [Cl:1][C:2]1[CH:7]=[CH:6][C:5]([CH:8]2[CH2:14][CH:13]3[N:15](C(OCC(Cl)(Cl)Cl)=O)[CH:10]([CH2:11][CH2:12]3)[CH:9]2[O:24][CH2:25][C:26]2[CH:35]=[CH:34][C:33]3[C:28](=[CH:29][CH:30]=[CH:31][CH:32]=3)[CH:27]=2)=[CH:4][CH:3]=1>C(O)(=O)C.O.[Zn]>[Cl:1][C:2]1[CH:7]=[CH:6][C:5]([CH:8]2[CH2:14][CH:13]3[NH:15][CH:10]([CH2:11][CH2:12]3)[CH:9]2[O:24][CH2:25][C:26]2[CH:35]=[CH:34][C:33]3[C:28](=[CH:29][CH:30]=[CH:31][CH:32]=3)[CH:27]=2)=[CH:4][CH:3]=1
Reactant: O=C(OCC(Cl)(Cl)Cl)N1C2CCC1C(OCc1ccc3ccccc3c1)C(c1ccc(Cl)cc1)C2
Agent: [Zn]
Solvent: O
Solvent: CC(=O)O
Product: Clc1ccc(C2CC3CCC(N3)C2OCc2ccc3ccccc3c2)cc1
Temperature: 25 °C
Reaction time: 12 h
Yield: 61.7 %

Procedure:
A suspension of 1.14 g (2.06 mmol) of 2,2,2-trichloroethyl (1RS,2RS,3RS,5SR)-3-(4-chloro-phenyl)-2-(naphthalen-2-ylmethoxy)-8-aza-bicyclo[3.2.1]octane-8-carboxylate and 400 mg of zinc in 10 ml of acetic acid was stirred at room temperature for 12 hours. The reaction solution was diluted with 50 ml of water and extracted four times with 40 ml of methylene chloride. The organic phase was washed twice with 50 ml of 1 N sodium hydroxide solution, dried over sodium sulphate, filtered and evaporated. The residue was chromatographed on silica gel using a 9:1 mixture of methylene chloride and methanol as the eluent. There was obtained 0.480 g (61% of theory) of (1RS,2RS,3RS,5SR)-3-(4-chloro-phenyl)-2-(naphthalen-2-ylmethoxy)-8-aza-bicyclo[3.2.1]octane of m.p. 184-185°; MS: 379 (M+H)+.
Reaction SMILES: CC1C=CC(S(O[CH2:12][CH:13]2[CH2:22][CH2:21][C:20]3[C:15](=[CH:16][C:17]([S:23]([CH3:26])(=[O:25])=[O:24])=[CH:18][CH:19]=3)[O:14]2)(=O)=O)=CC=1.[NH:27]1[CH2:30][CH2:29][CH2:28]1>C(#N)C>[CH3:26][S:23]([C:17]1[CH:16]=[C:15]2[C:20]([CH2:21][CH2:22][CH:13]([CH2:12][N:27]3[CH2:30][CH2:29][CH2:28]3)[O:14]2)=[CH:19][CH:18]=1)(=[O:24])=[O:25]
Reactant: Cc1ccc(S(=O)(=O)OCC2CCc3ccc(S(C)(=O)=O)cc3O2)cc1
Reactant: C1CNC1
Solvent: CC#N
Product: CS(=O)(=O)c1ccc2c(c1)OC(CN1CCC1)CC2

Procedure:
Preparation according to Example 25: [7-(methylsulfonyl)-3,4-dihydro-2H-chromen-2-yl]methyl 4-methylbenzenesulfonate (0.020 g, 0.0504 mmol), azetidine (0.2 ml), ACN (3 ml). MS m/z (rel. intensity, 70 eV) 281 (M+, 3), 131 (6), 77 (5), 71 (5), 70 (bp).
Reaction SMILES: [CH3:1][O:2][C:3]([C@H:5]1[CH2:10][CH2:9][C@H:8]([C:11]2[N:15]3[CH:16]=[CH:17][N:18]=[C:19]([NH2:20])[C:14]3=[C:13](Br)[N:12]=2)[CH2:7][CH2:6]1)=[O:4].[O:22]([C:29]1[CH:34]=[CH:33][C:32](B(O)O)=[CH:31][CH:30]=1)[C:23]1[CH:28]=[CH:27][CH:26]=[CH:25][CH:24]=1.O.O.[F-].[K+]>COCCOC.O.C1C=CC([P]([Pd]([P](C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)([P](C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)[P](C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)(C2C=CC=CC=2)C2C=CC=CC=2)=CC=1>[CH3:1][O:2][C:3]([C@H:5]1[CH2:10][CH2:9][C@H:8]([C:11]2[N:15]3[CH:16]=[CH:17][N:18]=[C:19]([NH2:20])[C:14]3=[C:13]([C:32]3[CH:33]=[CH:34][C:29]([O:22][C:23]4[CH:28]=[CH:27][CH:26]=[CH:25][CH:24]=4)=[CH:30][CH:31]=3)[N:12]=2)[CH2:7][CH2:6]1)=[O:4]
Reactant: COC(=O)[C@H]1CC[C@H](c2nc(Br)c3c(N)nccn32)CC1
Reactant: OB(O)c1ccc(Oc2ccccc2)cc1
Agent: c1ccc([P](c2ccccc2)(c2ccccc2)[Pd]([P](c2ccccc2)(c2ccccc2)c2ccccc2)([P](c2ccccc2)(c2ccccc2)c2ccccc2)[P](c2ccccc2)(c2ccccc2)c2ccccc2)cc1
Agent: [F-]
Agent: [K+]
Solvent: COCCOC
Solvent: O
Product: COC(=O)[C@H]1CC[C@H](c2nc(-c3ccc(Oc4ccccc4)cc3)c3c(N)nccn32)CC1
Temperature: 100 °C

Procedure:
To a stirred mixture of trans-4-(8-amino-1-bromo-imidazo[1,5-a]pyrazin-3-yl)-cyclohexanecarboxylic acid methyl ester (2.00 g, 5.66 mmol) and 4-phenoxyphenylboronic acid (1.454 g, 6.7 mmol) in DME (25.00 mL) and H2O (8.3 mL) was added potassium fluoride dihydrate (1.865 g, 19.82 mmol). The mixture was bubbled with nitrogen for 5 min before Pd(PPh3)4 (330 mg, 0.28 mmol) was added to. The resulting mixture was refluxed overnight at 100° C. Solvent was removed under reduced pressure and the product was purified by flash chromatography (2% MeOH in DCM). 1H NMR (400 MHz, CD3OD) δ 1.59-1.87 (m, 4H), 2.02-2.18 (m, 4H), 2.41-2.53 (m, 1H), 3.09-3.19 (m, 1H), 3.68 (s, 3H), 6.94-7.20 (m, 6H), 7.32-7.44 (m, 2H), 7.52-7.63 (m, 3H). MS (ES+): m/z: 442.97 [MH+]. HPLC: tR=2.48 min (OpenLynx: polar—5 min).
Reaction SMILES: [OH:1][CH:2]([CH:6]([CH3:8])[CH3:7])[C:3](O)=[O:4].CCN(C(C)C)C(C)C.CN(C(ON1N=NC2C=CC=NC1=2)=[N+](C)C)C.F[P-](F)(F)(F)(F)F.[CH3:42][N:43]1[C:52]2[C:47](=[CH:48][N:49]=[C:50]([CH3:53])[CH:51]=2)[CH:46]=[C:45]([C:54]2[CH:55]=[C:56]([NH:61]/[C:62](/[NH2:65])=[N:63]/O)[CH:57]=[CH:58][C:59]=2[CH3:60])[C:44]1=[O:66]>CN(C=O)C>[OH:1][CH:2]([C:3]1[O:4][N:63]=[C:62]([NH:61][C:56]2[CH:57]=[CH:58][C:59]([CH3:60])=[C:54]([C:45]3[C:44](=[O:66])[N:43]([CH3:42])[C:52]4[C:47]([CH:46]=3)=[CH:48][N:49]=[C:50]([CH3:53])[CH:51]=4)[CH:55]=2)[N:65]=1)[CH:6]([CH3:8])[CH3:7]
Reactant: CC(C)C(O)C(=O)O
Reactant: Cc1cc2c(cn1)cc(-c1cc(N/C(N)=N/O)ccc1C)c(=O)n2C
Agent: CN(C)C(On1nnc2cccnc21)=[N+](C)C
Agent: F[P-](F)(F)(F)(F)F
Solvent: CN(C)C=O
Solvent: CCN(C(C)C)C(C)C
Product: Cc1cc2c(cn1)cc(-c1cc(Nc3noc(C(O)C(C)C)n3)ccc1C)c(=O)n2C
Temperature: 100 °C

Procedure:
To a solution of 2-hydroxy-3-methylbutanoic acid (70 mg, 0.6 mmol) in DMF (6 mL) were added DIPEA (0.125 mL, 0.7 mmol) and HATU (0.23 g, 0.6 mmol). After stirring at rt for 15 min 17 (0.2 g, 0.6 mmol) was added as a solution in DMF (2 mL). The reaction was stirred at rt until complete consumption of 17 was determined by LC/MS and then was heated at 100° C. for 1 h. The reaction was cooled to rt, purified by preparative LCMS to afford crude material, which was further purified by flash column chromatography on silica with DCM/2% MeOH as eluant to give 3-(5-(5-(1-hydroxy-2-methylpropyl)-1,2,4-oxadiazol-3-ylamino)-2-methylphenyl)-1,7-dimethyl-1,6-naphthyridin-2(1H)-one (A64) as an off white solid. 1H NMR (400 MHz, CD4OD) δ 8.76 (s, 1H), 7.93 (s, 1H), 7.47 (s, 1H), 7.39 (dd, J=8, 2 Hz, 1H), 7.36 (d, J=2 Hz, 1H), 7.22 (d, J=8 Hz, 1H), 4.51 (d, J=6 Hz, 1H), 3.76 (s, 3H), 2.69 (s, 3H), 2.16 (m, 1H), 2.14 (s, 3H), 1.02 (d, J=6 Hz, 3H), 0.94 (d, J=6 Hz, 3H). MS m/z 420.4 (M+1).
Reaction SMILES: [O:1]=[C:2]1[C:7]2[CH:8]=[C:9]([C:11]3[CH:12]=[CH:13][CH:14]=[C:15]4[C:20]=3[N:19]=[C:18]([NH:21][C@@H:22]3[CH2:27][CH2:26][CH2:25][N:24](C(OC(C)(C)C)=O)[CH2:23]3)[CH:17]=[CH:16]4)[NH:10][C:6]=2[CH2:5][CH2:4][NH:3]1.[C:35]([OH:41])([C:37]([F:40])([F:39])[F:38])=[O:36]>C(Cl)Cl>[F:38][C:37]([F:40])([F:39])[C:35]([OH:41])=[O:36].[NH:24]1[CH2:25][CH2:26][CH2:27][C@@H:22]([NH:21][C:18]2[CH:17]=[CH:16][C:15]3[C:20](=[C:11]([C:9]4[NH:10][C:6]5[CH2:5][CH2:4][NH:3][C:2](=[O:1])[C:7]=5[CH:8]=4)[CH:12]=[CH:13][CH:14]=3)[N:19]=2)[CH2:23]1
Reactant: CC(C)(C)OC(=O)N1CCC[C@@H](Nc2ccc3cccc(-c4cc5c([nH]4)CCNC5=O)c3n2)C1
Solvent: ClCCl
Solvent: O=C(O)C(F)(F)F
Product: O=C1NCCc2[nH]c(-c3cccc4ccc(N[C@@H]5CCCNC5)nc34)cc21
Temperature: 0 °C
Reaction time: 0.17 h
Yield: 38.5 %

Procedure:
A mixture of (R)-tert-butyl 3-((8-(4-oxo-4,5,6,7-tetrahydro-1H-pyrrolo[3,2-c]pyridin-2-yl)quinolin-2-yl)amino)piperidine-1-carboxylate (78.0 mg, 0.169 mmol) and TFA (0.45 mL, 5.84 mmol) in DCM (1.5 mL) was stirred at 0° C. for 10 min, then at 25° C. for 1 h. The mixture was concentrated in vacuo, and the residue was taken up in DMSO (2.0 mL) and purified by reversed-phase HPLC (Phenomenex Gemini C18 column (150×30 mm, 10 μm), 35 mL/min, 5-100% ACN/H2O+0.1% TFA) to provide (R)-2-(2-(piperidin-3-ylamino)quinolin-8-yl)-6,7-dihydro-1H-pyrrolo[3,2-c]pyridin-4(5H)-one 2,2,2-trifluoroacetate (30.7 mg, 0.065 mmol, 38% yield) as a yellowish-brown solid: 1H NMR (400 MHz, MeOH-d4) δ ppm 8.08 (1H, dd, J=9.6, 4.1 Hz), 7.85 (1H, dd, J=7.5, 1.3 Hz), 7.65 (1H, d, J=7.4 Hz), 7.43 (1H, br. s.), 7.37 (1H, t, J=7.5 Hz), 6.96 (1H, d, J=7.2 Hz), 4.40-4.50 (1H, m), 3.79 (1H, dd, J=11.7, 2.3 Hz), 3.66 (2H, t, J=7.0 Hz), 3.43 (1H, dt, J=12.8, 4.3 Hz), 3.06-3.18 (2H, m), 3.03 (2H, t, J=7.1 Hz), 2.27-2.38 (1H, m), 2.10-2.22 (1H, m), 1.93-2.07 (1H, m), 1.72-1.85 (1H, m). 19F NMR (377 MHz, MeOH-d4) δ ppm −77.29 (3F, s). m/z (ESI, +ve) 362.1 (M+H)+.
Reaction SMILES: Cl[C:2]1[C:7]2[C:8](=[O:22])[N:9]([CH2:11][C:12]3[CH:17]=[CH:16][C:15]([O:18][CH3:19])=[CH:14][C:13]=3[O:20][CH3:21])[CH2:10][C:6]=2[C:5]([F:23])=[C:4]([NH:24][C@H:25]([CH2:29][CH:30]([CH3:32])[CH3:31])[C:26]([OH:28])=[O:27])[N:3]=1.[CH3:33][N:34]1[CH:38]=[C:37](B2OC(C)(C)C(C)(C)O2)[CH:36]=[N:35]1>O1CCOCC1.C([O-])([O-])=O.[Na+].[Na+].Cl[Pd](Cl)([P](C1C=CC=CC=1)(C1C=CC=CC=1)C1C=CC=CC=1)[P](C1C=CC=CC=1)(C1C=CC=CC=1)C1C=CC=CC=1>[CH3:21][O:20][C:13]1[CH:14]=[C:15]([O:18][CH3:19])[CH:16]=[CH:17][C:12]=1[CH2:11][N:9]1[CH2:10][C:6]2[C:5]([F:23])=[C:4]([NH:24][C@H:25]([CH2:29][CH:30]([CH3:32])[CH3:31])[C:26]([OH:28])=[O:27])[N:3]=[C:2]([C:37]3[CH:36]=[N:35][N:34]([CH3:33])[CH:38]=3)[C:7]=2[C:8]1=[O:22]
Reactant: Cn1cc(B2OC(C)(C)C(C)(C)O2)cn1
Reactant: COc1ccc(CN2Cc3c(F)c(N[C@H](CC(C)C)C(=O)O)nc(Cl)c3C2=O)c(OC)c1
Agent: Cl[Pd](Cl)([P](c1ccccc1)(c1ccccc1)c1ccccc1)[P](c1ccccc1)(c1ccccc1)c1ccccc1
Agent: O=C([O-])[O-]
Agent: [Na+]
Solvent: C1COCCO1
Product: COc1ccc(CN2Cc3c(F)c(N[C@H](CC(C)C)C(=O)O)nc(-c4cnn(C)c4)c3C2=O)c(OC)c1

Procedure:
A solution of (R)-2-(4-chloro-2-(2,4-dimethoxybenzyl)-7-fluoro-3-oxo-2,3-dihydro-1H-pyrrolo[3,4-c]pyridin-6-ylamino)-4-methylpentanoic acid (1.1 g, 2.361 mmol), 1-methyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazole (2.456 g, 11.81 mmol) and bis(triphenylphosphine)palladium chloride (1.657 g, 2.361 mmol) in dioxane (10 mL) and saturated aq Na2CO3 (10.00 mL) was heated to 120° C. for 30 min. After filtering out the solids, the solvent was removed from the filtrate. The resulting residue was dissolved in MeOH and DCM and was purified via preparative HPLC eluting with water (0.05% TFA) and ACN (40-70% gradient, 0.035% TFA). The collected fractions were combined and the solvent stripped to dryness via rotary evaporation to yield the title compound. [M+H] calc'd for C26H30FN5O5, 512; found, 512.
Reaction SMILES: [O:1]1[CH2:6][CH2:5][N:4]([CH2:7][C:8]([O:10]C)=O)[CH2:3][CH2:2]1.O.[NH2:13][NH2:14]>C(O)C>[O:1]1[CH2:6][CH2:5][N:4]([CH2:7][C:8]([NH:13][NH2:14])=[O:10])[CH2:3][CH2:2]1
Reactant: NN
Reactant: COC(=O)CN1CCOCC1
Solvent: CCO
Solvent: O
Product: NNC(=O)CN1CCOCC1
Temperature: 95 °C
Yield: 92 %

Procedure:
In a 25 mL, 3-neck round-bottom flask, methyl 2-morpholinoacetate (0.25 g, 1.0 eq.) was dissolved in ethanol (5 mL) at RT. Hydrazine hydrate (0.087 g, 1.1 eq.) was introduced dropwise at RT and the reaction mixture was refluxed at 95° C. for 20 h. The reaction mixture was concentrated under reduced pressure (40° C., 20 mm Hg) to afford the crude 2-morpholinoacetohydrazide (0.23 g) which was used without further purification in the following step.
Reaction SMILES: [C:1]([C:4]1[CH:5]=[C:6]2[C:11](=[CH:12][CH:13]=1)[N:10]([CH:14]1[CH2:19][CH2:18][O:17][CH2:16][CH2:15]1)[C:9](=[O:20])[N:8]([CH2:21][C:22]1[CH:27]=[CH:26][C:25]([O:28][CH3:29])=[C:24]([O:30][CH3:31])[CH:23]=1)[C:7]2=[O:32])(=[O:3])[CH3:2].[CH3:33][Mg]I>CCOCC>[CH3:31][O:30][C:24]1[CH:23]=[C:22]([CH:27]=[CH:26][C:25]=1[O:28][CH3:29])[CH2:21][N:8]1[C:7](=[O:32])[C:6]2[C:11](=[CH:12][CH:13]=[C:4]([C:1]([OH:3])([CH3:33])[CH3:2])[CH:5]=2)[N:10]([CH:14]2[CH2:15][CH2:16][O:17][CH2:18][CH2:19]2)[C:9]1=[O:20]
Reactant: COc1ccc(Cn2c(=O)c3cc(C(C)=O)ccc3n(C3CCOCC3)c2=O)cc1OC
Reactant: C[Mg]I
Solvent: CCOCC
Product: COc1ccc(Cn2c(=O)c3cc(C(C)(C)O)ccc3n(C3CCOCC3)c2=O)cc1OC
Temperature: 0 °C
Reaction time: 0.5 h
Yield: 9.6 %

Procedure:
0.1 g of 6-acetyl-3-(3,4-dimethoxybenzyl)-1-(tetrahydro-2H-pyran-4-yl)quinazoline-2,4(1H,3H)-dione is added to a solution of 0.143 g of methylmagnesium iodide in 1 ml of Et2O. This mixture is stirred for 30 minutes at 0° C. and then overnight at room temperature. The reaction mixture is evaporated under reduced pressure. The residue is chromatographed on silica gel, eluting with EtOAc to give 0.01 g of the expected product.
Reaction SMILES: C[O:2][C:3](=[O:37])[CH2:4][N:5]([CH2:32][C:33]([O:35]C)=[O:34])[C:6]1[CH:11]=[CH:10][CH:9]=[C:8]([NH:12][C:13](=[O:31])[CH2:14][CH2:15][CH2:16][CH2:17][CH2:18][CH2:19][CH2:20][CH2:21][CH2:22][CH2:23][CH2:24][CH2:25][CH2:26][CH2:27][CH2:28][CH2:29][CH3:30])[CH:7]=1.[OH-].[Na+]>O1CCOCC1.CO>[C:3]([CH2:4][N:5]([C:6]1[CH:11]=[CH:10][CH:9]=[C:8]([NH:12][C:13](=[O:31])[CH2:14][CH2:15][CH2:16][CH2:17][CH2:18][CH2:19][CH2:20][CH2:21][CH2:22][CH2:23][CH2:24][CH2:25][CH2:26][CH2:27][CH2:28][CH2:29][CH3:30])[CH:7]=1)[CH2:32][C:33]([OH:35])=[O:34])([OH:37])=[O:2]
Reactant: CCCCCCCCCCCCCCCCCC(=O)Nc1cccc(N(CC(=O)OC)CC(=O)OC)c1
Agent: [Na+]
Agent: [OH-]
Solvent: CO
Solvent: C1COCCO1
Product: CCCCCCCCCCCCCCCCCC(=O)Nc1cccc(N(CC(=O)O)CC(=O)O)c1
Reaction time: 18 h
Yield: 79.3 %

Procedure:
A mixture of 1.8 g N-(2-methoxy-2-oxoethyl)-N-[3-[(1-oxooctadecyl)amino]phenyl]glycine methyl ester and 2.4 ml of 6N NaOH in 30 ml of dioxane and 30 ml of methanol was heated to dissolve the solid and left at room temperature for 18 hours. The solid which precipitated was filtered, treated with 1N HCl and filtered again. Recrystallization from methanol-THF-water gave 1.35 g (79% yield, mp 135°-140°) of N-(carboxymethyl)-N-[3-[(1-oxooctadecyl)amino]phenyl]glycine.
Reaction SMILES: [NH2:1][CH2:2][CH:3]([C:10]1[CH:15]=[CH:14][CH:13]=[C:12]([Cl:16])[CH:11]=1)[CH2:4][C:5](OCC)=[O:6]>C1(C)C=CC=CC=1>[Cl:16][C:12]1[CH:11]=[C:10]([CH:3]2[CH2:2][NH:1][C:5](=[O:6])[CH2:4]2)[CH:15]=[CH:14][CH:13]=1
Reactant: CCOC(=O)CC(CN)c1cccc(Cl)c1
Solvent: Cc1ccccc1
Product: O=C1CC(c2cccc(Cl)c2)CN1
Yield: 49.2 %

Procedure:
In a 500 ml flask fitted with reflux condenser and magnetic stirrer, 135.7 g (561 mmoles) of ethyl 4-amino-3-(3-chlorophenyl)butanoate 378 are dissolved in 200 ml of toluene, and the mixture is refluxed for 30 min. The solution is concentrated to dryness and the residue purified by PrepLC (1 kg SiO2, CH2Cl2/EtOH, 98:2→95:5) to give 54.4 g of pure 379 (49.2%). GC/MS: 197/197 M+.
Reaction SMILES: [Br:1][C:2]1[CH:3]=[N:4][N:5]2[C:10]([NH:11][C:12]3[CH:17]=[C:16]([CH3:18])[CH:15]=[CH:14][C:13]=3[CH3:19])=[C:9]([C:20](O)=[O:21])[CH:8]=[N:7][C:6]=12.Cl.[F:24][C:25]1([C:31]2[CH:36]=[CH:35][CH:34]=[CH:33][CH:32]=2)[CH2:30][CH2:29][NH:28][CH2:27][CH2:26]1>>[Br:1][C:2]1[CH:3]=[N:4][N:5]2[C:10]([NH:11][C:12]3[CH:17]=[C:16]([CH3:18])[CH:15]=[CH:14][C:13]=3[CH3:19])=[C:9]([C:20]([N:28]3[CH2:29][CH2:30][C:25]([F:24])([C:31]4[CH:32]=[CH:33][CH:34]=[CH:35][CH:36]=4)[CH2:26][CH2:27]3)=[O:21])[CH:8]=[N:7][C:6]=12
Reactant: FC1(c2ccccc2)CCNCC1
Reactant: Cc1ccc(C)c(Nc2c(C(=O)O)cnc3c(Br)cnn23)c1
Agent: Cl
Product: Cc1ccc(C)c(Nc2c(C(=O)N3CCC(F)(c4ccccc4)CC3)cnc3c(Br)cnn23)c1
Yield: 62.2 %

Procedure:
In the same manner as in Example 21, step 5 and using 3-bromo-7-(2,5-dimethylphenylamino)pyrazolo[1,5-a]pyrimidine-6-carboxylic acid (231 mg, 0.64 mmol) obtained in step 2 and 4-fluoro-4-phenylpiperidine hydrochloride (207 mg, 0.96 mmol), the title compound (208 mg, 62%) was obtained.