Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [CH3:1][C:2]1([CH3:28])[C:6]([CH3:8])([CH3:7])[O:5][B:4]([C:9]2[CH:18]=[CH:17][C:16]3[C:11](=[CH:12][CH:13]=[C:14](B4OC(C)(C)C(C)(C)O4)[CH:15]=3)[CH:10]=2)[O:3]1.Br[C:30]1[N:31]=[C:32]2[N:38]=[C:37]([C@@H:39]3[CH2:43][CH2:42][CH2:41][N:40]3[C:44]([O:46][C:47]([CH3:50])([CH3:49])[CH3:48])=[O:45])[N:36]([CH2:51][O:52][CH2:53][CH2:54][Si:55]([CH3:58])([CH3:57])[CH3:56])[C:33]2=[N:34][CH:35]=1.C(=O)([O-])[O-].[Cs+].[Cs+].C1(P(C2CCCCC2)C2C=CC=CC=2C2C(OC)=CC=CC=2OC)CCCCC1>C([O-])(=O)C.[Pd+2].C([O-])(=O)C.C1COCC1.O>[CH3:7][C:6]1([CH3:8])[C:2]([CH3:1])([CH3:28])[O:3][B:4]([C:9]2[CH:10]=[C:11]3[C:16](=[CH:17][CH:18]=2)[CH:15]=[C:14]([C:30]2[N:31]=[C:32]4[N:38]=[C:37]([C@@H:39]5[CH2:43][CH2:42][CH2:41][N:40]5[C:44]([O:46][C:47]([CH3:50])([CH3:49])[CH3:48])=[O:45])[N:36]([CH2:51][O:52][CH2:53][CH2:54][Si:55]([CH3:58])([CH3:57])[CH3:56])[C:33]4=[N:34][CH:35]=2)[CH:13]=[CH:12]3)[O:5]1
Reactant: CC1(C)OB(c2ccc3cc(B4OC(C)(C)C(C)(C)O4)ccc3c2)OC1(C)C
Reactant: CC(C)(C)OC(=O)N1CCC[C@H]1c1nc2nc(Br)cnc2n1COCC[Si](C)(C)C
Agent: [Pd+2]
Agent: CC(=O)[O-]
Agent: COc1cccc(OC)c1-c1ccccc1P(C1CCCCC1)C1CCCCC1
Solvent: C1CCOC1
Solvent: O
Product: CC(C)(C)OC(=O)N1CCC[C@H]1c1nc2nc(-c3ccc4cc(B5OC(C)(C)C(C)(C)O5)ccc4c3)cnc2n1COCC[Si](C)(C)C
Temperature: 120 °C

Procedure:
In a microwave vial, 2,6-bis(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)naphthalene (149 mg, 0.393 mmol), (S)-tert-butyl 2-(5-bromo-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-imidazo[4,5-b]pyrazin-2-yl)pyrrolidine-1-carboxylate (294 mg, 0.590 mmol) (or a SEM regioisomer), cesium carbonate (384 mg, 1.18 mmol) and dicyclohexyl(2′,6′-dimethoxybiphenyl-2-yl)phosphine (32.3 mg, 0.079 mmol) were dissolved into THF (4 mL) and water (0.4 mL). An additional 1.5 mL of THF was added and the reaction was sparged with bubbling nitrogen until the 1.5 mL had evaporated away. To the clear solution was added palladium(II) acetate (8.83 mg, 0.039 mmol). The vial was flushed with nitrogen, sealed and then heated with microwave irradiation at 120° C. for 30 min. The reaction was diluted with EtOAc (˜3 mL) and washed with water (2 mL) and brine (2 mL). The reaction was dried (MgSO4), filtered and concentrated to a yellow oil which was purified by flash chromatography (12 g SiO2, 25-75% EtOAc/hexanes) to yield (2S,2′S)-tert-butyl 2,2′-(5,5′-(naphthalene-2,6-diyl)bis(1-((2-(trimethylsilyl)ethoxy)methyl)-1H-imidazo[4,5-b]pyrazine-5,2-diyl))dipyrrolidine-1-carboxylate (or a SEM regioisomer) (210 mg) as a yellow solidified foam and (S)-tert-butyl 2-(5-(6-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)naphthalen-2-yl)-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-imidazo[4,5-b]pyrazin-2-yl)pyrrolidine-1-carboxylate (or a SEM regioisomer) (53.5 mg) as a colorless oil.
Reaction SMILES: [OH:1][CH2:2][CH2:3][C:4]1[CH:9]=[CH:8][C:7]([NH:10][CH:11]([CH3:20])[C:12]([C:14]2[CH:19]=[CH:18][CH:17]=[CH:16][CH:15]=2)=O)=[CH:6][CH:5]=1.[N:21]#[C:22][NH2:23]>C(O)C>[NH2:23][C:22]1[N:10]([C:7]2[CH:8]=[CH:9][C:4]([CH2:3][CH2:2][OH:1])=[CH:5][CH:6]=2)[C:11]([CH3:20])=[C:12]([C:14]2[CH:19]=[CH:18][CH:17]=[CH:16][CH:15]=2)[N:21]=1
Reactant: N#CN
Reactant: CC(Nc1ccc(CCO)cc1)C(=O)c1ccccc1
Solvent: CCO
Product: Cc1c(-c2ccccc2)nc(N)n1-c1ccc(CCO)cc1
Yield: 33.4 %

Procedure:
A mixture of 2-{[4-(2-hydroxyethyl)phenyl]amino}-1-phenyl-1-propanone (1.3 g, 5.0 mmol) and cyanamide (420 mg, 10 mmol) in ethanol (60 mL) was refluxed for 16 h. After removal of solvent, the residue was diluted with dichloromethane. The organic layer was washed with water, dried (Na2SO4) and concentrated under reduced pressure. The residue was purified by flash column chromatography on silica gel eluting with ethyl acetate/ethanol (10:1) to give 490 mg (33%) of the title compound as yellow solids: 1H-NMR (CDCl3) δ 2.16 (3H, s), 2.96 (2H, t, J=5.6 Hz), 3.96 (2H, t, J=5.6 Hz), 4.24 (1H, br), 7.29-7.21 (2H, m), 7.46-7.38 (4H, m), 7.66-7.63 (2H, m).
Reaction SMILES: [Si:1]([O:8][C:9]1[CH:42]=[CH:41][C:12]([C:13]([NH:15][NH:16][C:17](=O)[C@H:18]([NH:29][C:30]2[CH:35]=[CH:34][C:33]([C:36]#[N:37])=[C:32]([Cl:38])[C:31]=2[CH3:39])[C@H:19]([O:21][Si:22]([C:25]([CH3:28])([CH3:27])[CH3:26])([CH3:24])[CH3:23])[CH3:20])=[O:14])=[CH:11][CH:10]=1)([C:4]([CH3:7])([CH3:6])[CH3:5])([CH3:3])[CH3:2].C1C=CC(P(C2C=CC=CC=2)C2C=CC=CC=2)=CC=1.[Si](O[C@@H](C)[C@@H](NC1C=CC(C#N)=C(Cl)C=1C)C1OC(C2C=CC=C(O[Si](C(C)(C)C)(C)C)C=2)=NN=1)(C(C)(C)C)(C)C>>[Si:22]([O:21][C@H:19]([CH3:20])[C@@H:18]([NH:29][C:30]1[CH:35]=[CH:34][C:33]([C:36]#[N:37])=[C:32]([Cl:38])[C:31]=1[CH3:39])[C:17]1[O:14][C:13]([C:12]2[CH:41]=[CH:42][C:9]([O:8][Si:1]([C:4]([CH3:6])([CH3:5])[CH3:7])([CH3:3])[CH3:2])=[CH:10][CH:11]=2)=[N:15][N:16]=1)([C:25]([CH3:26])([CH3:27])[CH3:28])([CH3:23])[CH3:24]
Reactant: Cc1c(N[C@@H](C(=O)NNC(=O)c2ccc(O[Si](C)(C)C(C)(C)C)cc2)[C@@H](C)O[Si](C)(C)C(C)(C)C)ccc(C#N)c1Cl
Agent: Cc1c(N[C@@H](c2nnc(-c3cccc(O[Si](C)(C)C(C)(C)C)c3)o2)[C@H](C)O[Si](C)(C)C(C)(C)C)ccc(C#N)c1Cl
Agent: c1ccc(P(c2ccccc2)c2ccccc2)cc1
Product: Cc1c(N[C@@H](c2nnc(-c3ccc(O[Si](C)(C)C(C)(C)C)cc3)o2)[C@@H](C)O[Si](C)(C)C(C)(C)C)ccc(C#N)c1Cl

Procedure:
4-(tert-butyldimethylsilyloxy)-N′-((2R,3R)-3-(tert-butyldimethylsilyloxy)-2-(3-chloro-4-cyano-2-methylphenylamino)butanoyl)benzohydrazide (intermediate 10b) (202 mg, 0.3 mmol) was cyclized with PS-PPh3 (3.0 mmol/g, 209 mg, 0.63 mmol), 12 (152 mg, 0.6 mmol), and TEA (0.33 mL, 2.4 mmol) as described for the preparation of intermediate 7c. After column chromatography (20% EtOAc/hexanes) the title compound was isolated as a white solid (147 mg, 75%). 1H NMR (500 MHz, CDCl3, δ in ppm) 7.86 (AA′XX′, J=8.7 Hz, 2H), 7.34 (d, J=8.6 Hz, 1H), 6.91 (AA′XX′, J=8.7 Hz, 2H), 6.62 (d, J=8.7 Hz, 1H), 5.11 (d, J=8.8 Hz, 1H), 4.81 (dd, J=3.9, 8.8 Hz, 1H), 4.43 (m, 1H), 2.32 (s, 3H), 1.28 (d, J=6.3 Hz, 3H), 0.98 (s, 9H), 0.93 (s, 9H), 0.22 (s, 6H), 0.13 (s, 3H), 0.10 (s, 3H).
Reaction SMILES: [CH3:1][C:2]1[CH:7]=[CH:6][CH:5]=[C:4]([CH3:8])[C:3]=1[C:9]#[C:10][C:11]1[CH:20]=[CH:19][C:14]([C:15]([O:17][CH3:18])=[O:16])=[CH:13][C:12]=1[NH:21]C(=O)C(F)(F)F.C1(P(C2C=CC=CC=2)C2C=CC=CC=2)C=CC=CC=1.[O-]P([O-])([O-])=O.[K+].[K+].[K+]>O1CCOCC1.[Cu]I>[CH3:1][C:2]1[CH:7]=[CH:6][CH:5]=[C:4]([CH3:8])[C:3]=1[C:9]1[NH:21][C:12]2[C:11]([CH:10]=1)=[CH:20][CH:19]=[C:14]([C:15]([O:17][CH3:18])=[O:16])[CH:13]=2
Reactant: COC(=O)c1ccc(C#Cc2c(C)cccc2C)c(NC(=O)C(F)(F)F)c1
Agent: [Cu]I
Agent: O=P([O-])([O-])[O-]
Agent: [K+]
Solvent: C1COCCO1
Product: COC(=O)c1ccc2cc(-c3c(C)cccc3C)[nH]c2c1
Temperature: 115 °C

Procedure:
A mixture of methyl 4-(2,6-dimethylphenylethynyl)-3-(2,2,2-trifluoroacetylamino)-benzoate (103 mg, 270 μmol), copper (I) iodide (2 mg, 10 μmol), triphenylphosphine (6 mg, 23 μmol), and K3PO4 (117 mg, 550 μmol) in dioxane (2 mL) was heated at 115° C. in a microwave apparatus for 15 min. The solution was concentrated, then chromatographed using a gradient of 0-40% heptane/ethyl acetate to afford methyl 2-(2,6-dimethylphenyl)-1H-indole-6-carboxylate.
Reaction SMILES: [S:1]1[CH:5]=[CH:4][CH:3]=[C:2]1[C:6](=[O:10])[C:7](O)=O.S1C=CC=C1C(Cl)=O.[C-]#[N:20].[Na+]>C(Cl)Cl>[S:1]1[CH:5]=[CH:4][CH:3]=[C:2]1[C:6]([C:7]#[N:20])=[O:10]
Reactant: O=C(O)C(=O)c1cccs1
Reactant: [C-]#N
Agent: O=C(Cl)c1cccs1
Agent: [Na+]
Solvent: ClCCl
Product: N#CC(=O)c1cccs1

Procedure:
A process for preparing thienylglyoxylic acid which comprises reacting thiophene carboxylic acid chloride with aqueous sodium cyanide in methylene chloride solvent and in the presence of a phase transfer catalyst to form thiophene carboxylic acid cyanide and then reacting said thiophene carboxylic acid cyanide with concentrated hydrochloric acid at a temperature and for a time sufficient to form thienylglyoxylic acid.
Reaction SMILES: [Cl:1][C:2]1[CH:3]=[N:4][N:5]([CH3:16])[C:6]=1[C:7]1[CH:8]=[C:9]([C:13]([OH:15])=O)[S:10][C:11]=1[CH3:12].[NH2:17][C@@H:18]([CH2:31][C:32]1[CH:37]=[CH:36][CH:35]=[C:34]([F:38])[CH:33]=1)[CH2:19][N:20]1[C:28](=[O:29])[C:27]2[C:22](=[CH:23][CH:24]=[CH:25][CH:26]=2)[C:21]1=[O:30].CC(OC(N[C@H](C(O)=O)CC1C=CC=CC=1C(F)(F)F)=O)(C)C.C1CN([P+](Br)(N2CCCC2)N2CCCC2)CC1.F[P-](F)(F)(F)(F)F.CCN(C(C)C)C(C)C>C(Cl)(Cl)Cl>[Cl:1][C:2]1[CH:3]=[N:4][N:5]([CH3:16])[C:6]=1[C:7]1[CH:8]=[C:9]([C:13]([NH:17][C@@H:18]([CH2:31][C:32]2[CH:37]=[CH:36][CH:35]=[C:34]([F:38])[CH:33]=2)[CH2:19][N:20]2[C:28](=[O:29])[C:27]3[C:22](=[CH:23][CH:24]=[CH:25][CH:26]=3)[C:21]2=[O:30])=[O:15])[S:10][C:11]=1[CH3:12]
Reactant: Cc1sc(C(=O)O)cc1-c1c(Cl)cnn1C
Reactant: N[C@@H](Cc1cccc(F)c1)CN1C(=O)c2ccccc2C1=O
Agent: Br[P+](N1CCCC1)(N1CCCC1)N1CCCC1
Agent: CC(C)(C)OC(=O)N[C@@H](Cc1ccccc1C(F)(F)F)C(=O)O
Agent: F[P-](F)(F)(F)(F)F
Solvent: ClC(Cl)Cl
Solvent: CCN(C(C)C)C(C)C
Product: Cc1sc(C(=O)N[C@@H](Cc2cccc(F)c2)CN2C(=O)c3ccccc3C2=O)cc1-c1c(Cl)cnn1C
Temperature: 25 °C
Reaction time: 8 h
Yield: 42.9 %

Procedure:
To a 50 mL round-bottomed flask was added 4-(4-chloro-1-methyl-1H-pyrazol-5-yl)-5-methyl-2-thiophenecarboxylic acid (187 mg, 0.73 mmol) [prepared according to the procedure of Example 158], 2-[(2S)-2-amino-3-(3-fluorophenyl)propyl]-1H-isoindole-1,3(2H)-dione (233 mg, 0.70 mmol) [prepared according to the procedure of Preparation 6 except substituting N-{[(1,1-dimethylethyl)oxy]carbonyl}-3-fluoro-L-phenylalanine (5.03 g, 17.8 mmol) for N-{[(1,1-dimethylethyl)oxy]carbonyl}-2-(trifluoromethyl)-L-phenylalanine] and PyBrop (412 mg, 0.88 mmol) in Chloroform (9 mL). DIEA (640 μL, 3.66 mmol) was added and the reaction stirred overnight at room temperature. The mixture was adsorbed onto silica and purified via column chromatography (25-70% EtOAc/Hex) affording the title compound (180 mg, 0.30 mmol, 42%): LC-MS (ES) m/z=537 (M+H)+.
Reaction SMILES: CC(C)=CCC1C(O)=CC2OC3C=C(O)C(O)=C(CC=C(C)C)C=3C(=O)C=2C=1O.[CH3:30][C:31]([CH3:60])=[CH:32][CH2:33][C:34]1[C:39]([OH:40])=[C:38]2[C:41]([C:43]3[C:48]([CH2:49][CH:50]=[C:51]([CH3:53])[CH3:52])=[C:47]([O:54][CH3:55])[C:46]([OH:56])=[CH:45][C:44]=3[O:57][C:37]2=[CH:36][C:35]=1[O:58]C)=[O:42].[C-]#N.[Na+].Cl>CS(C)=O>[CH3:30][C:31]([CH3:60])=[CH:32][CH2:33][C:34]1[C:39]([OH:40])=[C:38]2[C:41]([C:43]3[C:44]([O:57][C:37]2=[CH:36][C:35]=1[OH:58])=[CH:45][C:46]([OH:56])=[C:47]([O:54][CH3:55])[C:48]=3[CH2:49][CH:50]=[C:51]([CH3:53])[CH3:52])=[O:42]
Reactant: COc1cc2oc3cc(O)c(OC)c(CC=C(C)C)c3c(=O)c2c(O)c1CC=C(C)C
Agent: CC(C)=CCc1c(O)cc2oc3cc(O)c(O)c(CC=C(C)C)c3c(=O)c2c1O
Agent: Cl
Agent: [C-]#N
Solvent: CS(C)=O
Product: COc1c(O)cc2oc3cc(O)c(CC=C(C)C)c(O)c3c(=O)c2c1CC=C(C)C
Temperature: 195 °C
Reaction time: 6 h
Yield: 37 %

Procedure:
γ-Mangostin from β-mangostin: To a solution of β-mangostin (0.25 g, 0.58 mmol) in DMSO (LR, 15 mL) was added sodium cyanide (0.52 g, 10.61 mmol) at RT and the mixture was stirred at 190-200° C. for 6 h. The reaction mixture was allowed to cool to ambient temperature and then poured into ice water and the mixture was acidified with dil. HCl. The solution was extracted with ethyl acetate (5×50 mL). The combined ethyl acetate layer was washed with aqueous potassium permanganate (10%), water, brine and dried over sodium sulfate. The solution was filtered and treated with few drops of triethyl amine and the solvent evaporated. The residue was chromatographed over silica gel column using hexane/ethyl acetate mixture (80:20) as an eluent to give α-mangostin (90 mg, 37%). The α-mangostin was then converted to γ-mangostin using the inventive demethylation procedure as described in example 12.
Reaction SMILES: BrCC1CCC(CBr)CC1.BrCC1C=CC(CBr)=CC=1.[Cl:21][C:22]1[CH:37]=[C:36]([O:38][CH3:39])[CH:35]=[CH:34][C:23]=1[O:24][CH2:25][C:26]1[CH:33]=[CH:32][C:29]([CH2:30][Br:31])=[CH:28][CH:27]=1>>[Br:31][CH2:30][CH:29]1[CH2:28][CH2:27][CH:26]([CH2:25][O:24][C:23]2[CH:34]=[CH:35][C:36]([O:38][CH3:39])=[CH:37][C:22]=2[Cl:21])[CH2:33][CH2:32]1
Reactant: COc1ccc(OCc2ccc(CBr)cc2)c(Cl)c1
Agent: BrCC1CCC(CBr)CC1
Agent: BrCc1ccc(CBr)cc1
Product: COc1ccc(OCC2CCC(CBr)CC2)c(Cl)c1

Procedure:
By replacing the 1,4-bis(bromomethyl)cyclohexane in the foregoing preparation by a molar equivalent amount of 1,4-bis(bromomethyl)benzene, it is contemplated that 4-(2-chloro-4-methoxyphenoxymethyl)benzyl bromide can be prepared.
Reaction SMILES: [Cl:1][C:2]1[C:7]([CH2:8]Cl)=[CH:6][CH:5]=[C:4]([Cl:10])[N:3]=1.[C-:11]#[N:12].[Na+]>C(O)C>[Cl:1][C:2]1[C:7]([CH2:8][C:11]#[N:12])=[CH:6][CH:5]=[C:4]([Cl:10])[N:3]=1
Reactant: ClCc1ccc(Cl)nc1Cl
Reactant: [C-]#N
Agent: [Na+]
Solvent: CCO
Product: N#CCc1ccc(Cl)nc1Cl

Procedure:
2 g of 2,6-dichloro-3-chloromethyl-pyridine in 8 ml of ethanol at ambient temperature was treated with 0.57 g of NaCN. The resulting brown suspension was refluxed for 2 h. Ethanol was removed by evaporation under reduced pressure and the residue was taken-up in water and ethyl acetate. The aqueous layer was washed twice with ethyl acetate. The organic phases were combined, dried over anhydrous sodium sulphate, filtered and concentrated. 2.05 g of crude 2,6-dichloro-pyridin-3-yl)-acetonitrile was obtained as brown solid which was used in the next step without further purification. 1H-NMR (CDCl3): 7.86 ppm (d, 1H), 7.38 ppm (d, 1H), 3.84 ppm (s, 2H).
Reaction SMILES: N[C:2]1[S:3][C:4]2[CH:10]=[C:9]([C:11]3[CH:12]=[C:13]([N:23]4[CH:28]=[CH:27][C:26](=[O:29])[NH:25][C:24]4=[O:30])[CH:14]=[C:15]([C:19]([CH3:22])([CH3:21])[CH3:20])[C:16]=3[O:17][CH3:18])[CH:8]=[CH:7][C:5]=2[N:6]=1.N(OCCC(C)C)=O>O1CCOCC1>[S:3]1[C:4]2[CH:10]=[C:9]([C:11]3[CH:12]=[C:13]([N:23]4[CH:28]=[CH:27][C:26](=[O:29])[NH:25][C:24]4=[O:30])[CH:14]=[C:15]([C:19]([CH3:22])([CH3:21])[CH3:20])[C:16]=3[O:17][CH3:18])[CH:8]=[CH:7][C:5]=2[N:6]=[CH:2]1
Reactant: COc1c(-c2ccc3nc(N)sc3c2)cc(-n2ccc(=O)[nH]c2=O)cc1C(C)(C)C
Agent: CC(C)CCON=O
Solvent: C1COCCO1
Product: COc1c(-c2ccc3ncsc3c2)cc(-n2ccc(=O)[nH]c2=O)cc1C(C)(C)C
Yield: 48.4 %

Procedure:
To a solution of the product from Example 53 (30 mg, 0.071 mmol) in anhydrous 1,4-dioxane (3 mL) under N2 was added isoamyl nitrite (19 μL, 0.142 mmol). The resulting mixture was stirred at reflux for 1 h, and concentrated in vacuo. The crude product was purified by C-18 reverse-phase HPLC using an acetonitrile:H2O (0.1% TFA) gradient to give the title compound (14 mg, 48%). 1H NMR (300 MHz, DMSO-d6) δ 11.42 (d, J=1.84 Hz, 1H) 9.44 (s, 1H) 8.34 (d, J=1.47 Hz, 1H) 8.19 (d, J=8.46 Hz, 1H) 7.79 (d, J=7.72 Hz, 1H) 7.73 (dd, J=8.46, 1.84 Hz, 1H) 7.32-7.37 (m, 2H) 5.65 (dd, J=7.91, 2.39 Hz, 1H) 3.24 (s, 3H) 1.42 (s, 9H).
Reaction SMILES: C[C@]1(O)[C@@H]2C(=[C:12]([OH:30])[C@:13]3([OH:29])[C:20](=[O:21])[C:19](C(N)=O)=[C:18]([OH:25])[C@@H:17](N(C)C)[C@@H]3C2)C(=O)C2C(O)=CC=CC1=2.CC1(C)S[C@@H]2[C@H](NC([C@H](N)C3C=CC=CC=3)=O)C(=[O:41])N2[C@H]1C(O)=O>>[O:30]=[CH:12][C@@H:13]([C@@H:20]([C@H:19]([C@H:18]([CH3:17])[OH:25])[OH:41])[OH:21])[OH:29]
Reactant: CC1(C)S[C@@H]2[C@H](NC(=O)[C@H](N)c3ccccc3)C(=O)N2[C@H]1C(=O)O
Reactant: CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@@]2(O)C(O)=C3C(=O)c4c(O)cccc4[C@@](C)(O)[C@H]3C[C@@H]12
Product: C[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)C=O

Procedure:
The plasmid pBRsacH3 (Example 1) was used for cloning the rMET1 antibody (Example 9). In this case, the kappa and heavy chains were engineered with human ceruloplasmin and human neutrophil defensin signal sequences, respectively (Example 9). This plasmid was electroporated into E. coli strain DH10B rha+ to generate clone rMET1.LS.1, which was cultured under 10 μg/mL tetracycline selection. The plasmid was also electroporated into E. coli strain ECL339 rha− to generate clone rMET1.ECL.1 which was cultured under 100 μg/mL ampicillin selection.
Reaction SMILES: [CH3:1][N:2]1[C:6]([C:7]2[CH:12]=[CH:11][CH:10]=[CH:9][C:8]=2[C:13]([F:16])([F:15])[F:14])=[N:5][N:4]=[C:3]1[C:17]12[CH2:24][CH2:23][C:20]([C:25]([NH:27][NH2:28])=[O:26])([CH2:21][CH2:22]1)[CH2:19][CH2:18]2.[F:29][C:30]([F:35])([CH3:34])[C:31](O)=O>C(Cl)Cl>[F:29][C:30]([C:34]1[O:26][C:25]([C:20]23[CH2:23][CH2:24][C:17]([C:3]4[N:2]([CH3:1])[C:6]([C:7]5[CH:12]=[CH:11][CH:10]=[CH:9][C:8]=5[C:13]([F:15])([F:14])[F:16])=[N:5][N:4]=4)([CH2:18][CH2:19]2)[CH2:22][CH2:21]3)=[N:27][N:28]=1)([F:35])[CH3:31]
Reactant: CC(F)(F)C(=O)O
Reactant: Cn1c(-c2ccccc2C(F)(F)F)nnc1C12CCC(C(=O)NN)(CC1)CC2
Solvent: ClCCl
Product: Cn1c(-c2ccccc2C(F)(F)F)nnc1C12CCC(c3nnc(C(C)(F)F)o3)(CC1)CC2
Temperature: 25 °C
Reaction time: 48 h

Procedure:
A mixture of 4-{4-methyl-5-[2-(trifluoromethyl)phenyl]-4H-1,2,4-triazol-3-yl}bicyclo[2.2.2]octane-1-carbohydrazide (4-A) (334 mg, 0.850 mmol) and 2,2-difluoropropionic acid (78 mg, 0.708 mmol) was suspended in methylene chloride, and DMC (1.2 g, 7.08 mmol) was added as solid. The mixture was stirred at room temperature under nitrogen for 48 hours before it was diluted with methylene chloride, washed with water, saturated sodium bicarbonate and brine. The crude product was purified by column chromatography to give 4-B as a white solid. MS (ESI+)=468.3 (M+1); 1H NMR (500 MHz, CDCl3): δ 2.15-2.33 (15H, m), 3.52 (3H, s), 7.61 (1H, m), 7.72 (2H, m), 7.85 (1H, m) ppm.
Reaction SMILES: [Cl:1][C:2]1[C:3]([C:9]2[N:10]=[C:11]([NH:18][CH2:19][CH:20]3[CH2:25][CH2:24][O:23][CH2:22][CH2:21]3)[C:12]([C:15]([NH2:17])=[O:16])=[N:13][CH:14]=2)=[CH:4][C:5](F)=[N:6][CH:7]=1.[NH2:26][CH:27]1[CH2:32][CH2:31][CH:30]([NH2:33])[CH2:29][CH2:28]1>CS(C)=O>[NH2:26][C@H:27]1[CH2:32][CH2:31][C@H:30]([NH:33][C:5]2[CH:4]=[C:3]([C:9]3[N:10]=[C:11]([NH:18][CH2:19][CH:20]4[CH2:25][CH2:24][O:23][CH2:22][CH2:21]4)[C:12]([C:15]([NH2:17])=[O:16])=[N:13][CH:14]=3)[C:2]([Cl:1])=[CH:7][N:6]=2)[CH2:29][CH2:28]1
Reactant: NC1CCC(N)CC1
Reactant: NC(=O)c1ncc(-c2cc(F)ncc2Cl)nc1NCC1CCOCC1
Solvent: CS(C)=O
Product: NC(=O)c1ncc(-c2cc(N[C@H]3CC[C@H](N)CC3)ncc2Cl)nc1NCC1CCOCC1
Temperature: 100 °C

Procedure:
5-(5-chloro-2-fluoropyridin-4-yl)-3-((tetrahydro-2H-pyran-4-yl)methyl)aminopyrazine-2-carboxamide (0.035 g, 0.096 mmol) was dissolved in DMSO (2 ml). This was treated with 1,4-diaminocyclohexane (0.109 g, 0.957 mmol). The reaction mixture was then heated at 100° C. for 4 hr. The material was purified by preparative reverse-phase HPLC to give 0.0053 g of 5-(2-(trans-4-aminocyclohexylamino)-5-chloropyridin-4-yl)-3-((tetrahydro-2H-pyran-4-yl)methyl)aminopyrazine-2-carboxamide as the TFA salt. LCMS (m/z): 460.1 (MH+), retention time=0.54 min.
Reaction SMILES: [NH2:1][C:2]1[CH:3]=[C:4]([OH:12])[C:5]([CH3:11])=[C:6]([CH:10]=1)[C:7]([OH:9])=[O:8].[C:13]1(=O)[O:18][C:16](=[O:17])[C:15]2=[CH:19][CH:20]=[CH:21][CH:22]=[C:14]12>CN(C)C=O>[O:17]=[C:16]1[C:15]2[C:14](=[CH:22][CH:21]=[CH:20][CH:19]=2)[C:13](=[O:18])[N:1]1[C:2]1[CH:3]=[C:4]([OH:12])[C:5]([CH3:11])=[C:6]([CH:10]=1)[C:7]([OH:9])=[O:8]
Reactant: Cc1c(O)cc(N)cc1C(=O)O
Reactant: O=C1OC(=O)c2ccccc21
Solvent: CN(C)C=O
Product: Cc1c(O)cc(N2C(=O)c3ccccc3C2=O)cc1C(=O)O
Temperature: 110 °C
Reaction time: 2 h
Yield: 58.3 %

Procedure:
A mixture of 300 mg 5-amino-3-hydroxy-2-methylbenzoic acid and 265 mg of phtalic anhydride in 12 ml of dimethylformamide was heated to 110° C. for 2 hours, and subsequently to 150° C. for another 2 hours. The solvent was evaporated in vacuo and the residue was crystallized from ethanol/diethylether to give 310 mg of 5-(1,3-dioxo-1,3-dihydro-isoindol-2-yl)-3-hydroxy-2-methylbenzoic acid as white crystals, m.p. >250° C.
Reaction SMILES: [Cl:1][C:2]1[CH:9]=[CH:8][C:7]([C:10]([F:13])([F:12])[F:11])=[CH:6][C:3]=1[CH:4]=O.[NH2:14][C:15]1[CH:16]=[C:17]2[C:21]3=[C:22]([CH2:24][O:25][CH2:26][CH2:27][N:20]3[C@H:19]3[CH2:28][CH2:29][N:30](C(OC(C)(C)C)=O)[CH2:31][C@@H:18]23)[CH:23]=1>>[Cl:1][C:2]1[CH:9]=[CH:8][C:7]([C:10]([F:13])([F:12])[F:11])=[CH:6][C:3]=1[CH2:4][NH:14][C:15]1[CH:16]=[C:17]2[C:21]3=[C:22]([CH2:24][O:25][CH2:26][CH2:27][N:20]3[C@H:19]3[CH2:28][CH2:29][NH:30][CH2:31][C@@H:18]23)[CH:23]=1
Reactant: CC(C)(C)OC(=O)N1CC[C@H]2[C@@H](C1)c1cc(N)cc3c1N2CCOC3
Reactant: O=Cc1cc(C(F)(F)F)ccc1Cl
Product: FC(F)(F)c1ccc(Cl)c(CNc2cc3c4c(c2)[C@@H]2CNCC[C@@H]2N4CCOC3)c1

Procedure:
Using 2-chloro-5-(trifluoromethyl)benzaldehyde and following the procedures described in EXAMPLE 126, tert-butyl (7bR,11aS)-6-amino-1,2,7b,10,11,11a-hexahydro-4H-[1,4]oxazepino[6,5,4-hi]pyrido[4,3-b]indole-9(8H)-carboxylate from EXAMPLE 56, Part B was converted into the title compound of EXAMPLE 133. 1H NMR(CDCl3) δ: 9.45 (broad s, 1H), 9.20 (broad s, 1H), 7.68 (s, 1H), 7.52-7.45 (m, 2H), 6.41 (d, 1H, J=2.2 Hz), 6.27 (d, 1H, J=2.2 Hz), 4.55 (ABq, 2H, JAB=14.3 Hz), 4.40 (s, 2H), 4.22 (app d, 1H, J=12.8 Hz), 3.69 (app t, 1H), 3.53-3.38 (m, 2H), 3.35-3.10 (m, 4H), 2.70-2.50 (m, 2H), 2.23-2.10 (m, 2H).
Reaction SMILES: [Cl:1][C:2]1[C:3]2[CH:23]=[CH:22][C:21]([OH:24])=[CH:20][C:4]=2[S:5][C:6]=1[CH2:7][CH:8]1[CH2:12][CH2:11][N:10]([CH:13]2[CH2:18][CH2:17][CH2:16][CH2:15][CH2:14]2)[C:9]1=[O:19].[C:25]([O:29][C:30](=[O:35])[CH2:31][CH2:32][CH2:33]Br)([CH3:28])([CH3:27])[CH3:26].[I-].[Na+].C(=O)([O-])[O-].[Cs+].[Cs+]>>[C:25]([O:29][C:30](=[O:35])[CH2:31][CH2:32][CH2:33][O:24][C:21]1[CH:22]=[CH:23][C:3]2[C:2]([Cl:1])=[C:6]([CH2:7][CH:8]3[CH2:12][CH2:11][N:10]([CH:13]4[CH2:14][CH2:15][CH2:16][CH2:17][CH2:18]4)[C:9]3=[O:19])[S:5][C:4]=2[CH:20]=1)([CH3:28])([CH3:27])[CH3:26]
Reactant: O=C1C(Cc2sc3cc(O)ccc3c2Cl)CCN1C1CCCCC1
Reactant: CC(C)(C)OC(=O)CCCBr
Agent: O=C([O-])[O-]
Agent: [Cs+]
Agent: [I-]
Product: CC(C)(C)OC(=O)CCCOc1ccc2c(Cl)c(CC3CCN(C4CCCCC4)C3=O)sc2c1

Procedure:
Using the procedure to synthesize Example 12 and using reagents 3-(3-chloro-6-hydroxy-benzo[b]thiophen-2-ylmethyl)-1-cyclohexyl-pyrrolidin-2-one (175 mg, 0.481 mmol), 4-bromo-butyric acid tert-butyl ester (215 mg, 0.962 mmol), sodium iodide (72 mg, 0.481 mmol), and cesium carbonate (1.25 g, 3.85 mmol) afford crude 4-[3-chloro-2-(1-cyclohexyl-2-oxo-pyrrolidin-3-ylmethyl)-benzo[b]thiophen-6-yloxy]-butyric acid tert-butyl ester. Dissolve ester in trifluoroacetic acid (25 mL) and stir for 1.5 hr. Evaporate and dissolve in 1M NaOH and wash with ether. Bring aqueous layer to a pH of ˜2 with 6M HCl, filter, and dry. Purified on silica gel (30-50% ethyl acetate in hexanes) to give the title compound (105 mg, 49%) as a tan solid: Mass spectrum (apci) m/z=450.1 (M+H).
Reaction SMILES: [Cl:1][C:2]1[C:7]([C:8]#[N:9])=[C:6]([CH3:10])[CH:5]=[C:4](Cl)[N:3]=1.[C:12]([NH2:16])([CH3:15])([CH3:14])[CH3:13]>>[C:12]([NH:16][C:4]1[N:3]=[C:2]([Cl:1])[C:7]([C:8]#[N:9])=[C:6]([CH3:10])[CH:5]=1)([CH3:15])([CH3:14])[CH3:13]
Reactant: CC(C)(C)N
Reactant: Cc1cc(Cl)nc(Cl)c1C#N
Product: Cc1cc(NC(C)(C)C)nc(Cl)c1C#N
Reaction time: 8 h

Procedure:
1 g. (5.35 mmol.) of 2,6-dichloro-3-cyano-4-methylpyridine and approximately 40 ml. of t-butylamine (distilled from sodium hydride) were heated together in a reaction bomb at 200° C. for 5 hrs. Heating for an additional 4 hrs. at the same temperature produced no further change in the reaction mixture. The reaction mixture was allowed to stand overnight and was evaporated at reduced pressure to obtain a gummy solid. The gummy solid was partitioned between water containing a trace of sodium carbonate and chloroform, and the aqueous phase was re-extracted twice with chloroform. The three chloroform phases were combined, dried over anhydrous sodium sulfate and evaporated at reduced pressure. The residue was dissolved in 10 ml. of chloroform and diluted to 70 ml. with hexane. The small amount of crystals that formed were removed by filtration and the filtrate was applied to a column of 50 ml. of silica gel packed in 20% chloroform in hexane and eluted with the same solvent mixture. The first 130 ml. of eluate contained nothing, and the next 100 ml. of eluate were evaporated to obtain 6-t-butylamino-2-chloro-3-cyano-4-methylpyridine (0.49 g.), m.p. 109° C. The next fractions, containing the desired product, were combined and evaporated at reduced pressure and hexane was added. After evaporation of the hexane at reduced pressure, the residue was allowed to crystallize in the freezer to obtain the desired product (0.362 g.), m.p. 134°-138° C.