Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [N:1]1(C(OC(C)(C)C)=O)C[CH2:63][CH2:62][C@H:2]1[C:3]([NH:5][C@@H:6]([C:17]([NH:19][C@H:20]([C:28]([NH:30][C@@H:31]([C:42]([NH:44][C@H:45]([C:50]([N:52]([CH3:61])[C@H:53]([C:58]([NH2:60])=[O:59])[CH2:54][CH2:55][CH2:56][CH3:57])=[O:51])[CH2:46][CH:47]([CH3:49])[CH3:48])=[O:43])[CH2:32][C:33]1[C:41]2[C:36](=[CH:37][CH:38]=[CH:39][CH:40]=2)[NH:35][CH:34]=1)=[O:29])[CH2:21][C:22]1[CH:27]=[CH:26][CH:25]=[CH:24][CH:23]=1)=[O:18])[CH2:7][C:8]1[C:16]2[C:11](=[CH:12][CH:13]=[CH:14][CH:15]=2)[NH:10][CH:9]=1)=[O:4].FC(F)(F)C(O)=O.[CH:79](S)(S)[CH3:80]>CSC>[NH:1]1[CH2:80][CH2:79][CH2:63][CH2:62][C@H:2]1[C:3]([NH:5][C@@H:6]([C:17]([NH:19][C@H:20]([C:28]([NH:30][C@@H:31]([C:42]([NH:44][C@H:45]([C:50]([N:52]([CH3:61])[C@H:53]([C:58]([NH2:60])=[O:59])[CH2:54][CH2:55][CH2:56][CH3:57])=[O:51])[CH2:46][CH:47]([CH3:49])[CH3:48])=[O:43])[CH2:32][C:33]1[C:41]2[C:36](=[CH:37][CH:38]=[CH:39][CH:40]=2)[NH:35][CH:34]=1)=[O:29])[CH2:21][C:22]1[CH:23]=[CH:24][CH:25]=[CH:26][CH:27]=1)=[O:18])[CH2:7][C:8]1[C:16]2[C:11](=[CH:12][CH:13]=[CH:14][CH:15]=2)[NH:10][CH:9]=1)=[O:4]
Reactant: CC(S)S
Reactant: CCCC[C@@H](C(N)=O)N(C)C(=O)[C@H](CC(C)C)NC(=O)[C@@H](Cc1c[nH]c2ccccc12)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@H](Cc1c[nH]c2ccccc12)NC(=O)[C@@H]1CCCN1C(=O)OC(C)(C)C
Solvent: O=C(O)C(F)(F)F
Solvent: CSC
Product: CCCC[C@@H](C(N)=O)N(C)C(=O)[C@H](CC(C)C)NC(=O)[C@@H](Cc1c[nH]c2ccccc12)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@H](Cc1c[nH]c2ccccc12)NC(=O)[C@@H]1CCCCN1

Procedure:
Condensation of BocPro-DTrp-PheOH (part B of Example 17, 0.700 g.) and HDTrp-Leu-MeNleNH2 (0.520 g.) using dicyclohexylcarbodiimide and 1-hydroxybenzotriazole gave BocPro-DTrp-Phe-DTrp-Leu-MeNleNH2 in 64% yield. De-t-butoxycarbonylation of BocPro-DTrp-Phe-DTrp-Leu-MeNleNH2 (0.750 g.) using trifluoroacetic acid in dimethyl sulfide and ethanedithiol gave HPro-DTrp-Phe-DTrp-Leu-MeNleNH2, which was isolated as the amorphous white solid phosphate (1:1) salt tetrahydrate in 30% yield.
Reaction SMILES: [CH2:1]([C:3]1[CH:8]=[CH:7][C:6]([C:9]2[N:14]=[C:13]([N:15]([CH3:35])[CH2:16][CH2:17][CH2:18][O:19][C:20]3[CH:21]=[C:22]4[C:26](=[CH:27][CH:28]=3)[C@H:25]([CH2:29][C:30]([O:32]CC)=[O:31])[CH2:24][CH2:23]4)[C:12]([C:36]([F:39])([F:38])[F:37])=[CH:11][CH:10]=2)=[CH:5][CH:4]=1)[CH3:2].[Li+].[OH-].O.[CH2:43]1COC[CH2:44]1>CO>[CH2:43]([CH:29]([C@H:25]1[C:26]2[C:22](=[CH:21][C:20]([O:19][CH2:18][CH2:17][CH2:16][N:15]([C:13]3[C:12]([C:36]([F:37])([F:38])[F:39])=[CH:11][CH:10]=[C:9]([C:6]4[CH:7]=[CH:8][C:3]([CH2:1][CH3:2])=[CH:4][CH:5]=4)[N:14]=3)[CH3:35])=[CH:28][CH:27]=2)[CH2:23][CH2:24]1)[C:30]([OH:32])=[O:31])[CH3:44]
Reactant: C1CCOC1
Reactant: CCOC(=O)C[C@@H]1CCc2cc(OCCCN(C)c3nc(-c4ccc(CC)cc4)ccc3C(F)(F)F)ccc21
Agent: [Li+]
Agent: [OH-]
Solvent: O
Solvent: CO
Product: CCc1ccc(-c2ccc(C(F)(F)F)c(N(C)CCCOc3ccc4c(c3)CC[C@H]4C(CC)C(=O)O)n2)cc1

Procedure:
Following the procedure described in Example 308 and starting with ethyl ((1S)-5-[(3-{[6-(4-ethylphenyl)-3-(trifluoromethyl)-2-pyridinyl](methyl)amino]propoxy}-2,3-dihydro-1H-inden-1-yl)acetate (Example 319, 10 mg, 0.018 mmol), LiOH (0.1 mg, 0.004 mmol) in THF (1 mL), MeOH (1 mL), and water (0.5 mL), the title compound was obtained (0.0024 g, 51%). 1H NMR (400 MHz, CD2Cl2) δ 7.98 (d, 2H), 7.85 (d, 1H), 7.35-7.25 (m, 3H), 7.01 (d, 1H), 6.72 (d, 1H), 6.65 (dd, 1H), 4.02 (t, 2H), 3.83 (t, 2H), 3.47 (qt, 1H), 3.08 (s, 3H), 2.90-2.68 (m, 5H), 2.42-2.30 (m, 2H), 2.15 (qt, 2H), 1.78-1.68 (m, 1H), 1.33 (m, 3H); LC-MS: RT=4.50 min, (M+H)+ 513.2.
Reaction SMILES: [C:1]([O:7][CH3:8])(=[O:6])[CH2:2][C:3]([CH3:5])=[O:4].[H-].[Na+].C([Li])CCC.[CH3:16][O:17][C:18]1[CH:25]=[CH:24][C:21](C=O)=[CH:20][CH:19]=1>CCCCCC.O1CCCC1>[OH:4][C:3]1[CH2:5][CH:8]([C:21]2[CH:24]=[CH:25][C:18]([O:17][CH3:16])=[CH:19][CH:20]=2)[O:7][C:1](=[O:6])[CH:2]=1
Reactant: COC(=O)CC(C)=O
Reactant: COc1ccc(C=O)cc1
Agent: [H-]
Agent: [Li]CCCC
Agent: [Na+]
Solvent: CCCCCC
Solvent: C1CCOC1
Product: COc1ccc(C2CC(O)=CC(=O)O2)cc1
Temperature: 0 °C
Reaction time: 0.25 h

Procedure:
The title compound was prepared as described in General Method 1 using 5 mL of methyl acetoacetate, 2.0 g of NaH 60% dispersion in oil, 25 mL of 2.0M n-butyl lithium in hexane, 7.0 mL of 4-methoxybenzaldehyde and 150 mL of tetrahydrofuran. After addition of the aldehyde, the reaction was stirred for 15 minutes at 0° C. then allowed to warm to room temperature overnight. The crude product was triturated from diethyl ether to afford a solid (m.p.159°-162° C. (dec.)). 1H NMR (CDCl3) δ 2.91 (dd, 2 H), 3.57 (dd, 2 H), 3.83 (s, 3 H), 5.66 (dd, 1 H), 6.93-6.97 (m, 2 H), 7.30-7.34 (m, 2 H).
Reaction SMILES: Cl.O.[NH:3]1[CH2:8][CH2:7][C:6](=[O:9])[CH2:5][CH2:4]1.C(=O)([O-])[O-].[Na+].[Na+].Cl[C:17]1[CH:22]=[CH:21][N:20]=[C:19]([C:23]([F:26])([F:25])[F:24])[N:18]=1>C(Cl)Cl>[F:24][C:23]([F:26])([F:25])[C:19]1[N:20]=[C:21]([N:3]2[CH2:8][CH2:7][C:6](=[O:9])[CH2:5][CH2:4]2)[CH:22]=[CH:17][N:18]=1
Reactant: O=C1CCNCC1
Reactant: FC(F)(F)c1nccc(Cl)n1
Agent: Cl
Agent: O=C([O-])[O-]
Agent: [Na+]
Solvent: O
Solvent: ClCCl
Product: O=C1CCN(c2ccnc(C(F)(F)F)n2)CC1
Reaction time: 48 h
Yield: 91.2 %

Procedure:
4-Piperidone monohydrate hydrochloride (XXVII, 3.37 g, 21.9 mmol) was added to a stirred mixture of methylene chloride (50 mL) and saturated aqueous sodium carbonate (8 mL). 4-Chloro-2-(trifluoromethyl)pyrimidine (IV, 4.0 g, 21.9 mmol) was then added to the mixture which was then stirred for 2 days. The organic layer was separated, dried over magnesium sulfate, and concentrated in vacuo to give the product as a white solid (4.9 g, 92%) which was used in the next step without further purification.
Reaction SMILES: Br[C:2]1[CH:3]=[C:4]([N:8]2[CH2:16][CH:15]3[CH2:17][N:11]4[CH2:12][CH:13]([CH2:18][CH:9]2[CH2:10]4)[CH2:14]3)[CH:5]=[N:6][CH:7]=1.[CH3:19][O:20][C:21]1[CH:26]=[CH:25][CH:24]=[C:23]([O:27][CH3:28])[C:22]=1B(O)O>>[CH3:19][O:20][C:21]1[CH:26]=[CH:25][CH:24]=[C:23]([O:27][CH3:28])[C:22]=1[C:2]1[CH:3]=[C:4]([N:8]2[CH2:16][CH:15]3[CH2:17][N:11]4[CH2:12][CH:13]([CH2:18][CH:9]2[CH2:10]4)[CH2:14]3)[CH:5]=[N:6][CH:7]=1
Reactant: COc1cccc(OC)c1B(O)O
Reactant: Brc1cncc(N2CC3CC4CC2CN(C4)C3)c1
Product: COc1cccc(OC)c1-c1cncc(N2CC3CC4CC2CN(C4)C3)c1

Procedure:
The title compound was prepared from the product of Example 65A and 2,6-dimethoxyphenylboronic acid according to General Method B: LC-MS Method D (ESI+) m/z 366.0 (M+H)+, retention time 1.34 minutes.
Reaction SMILES: [CH3:1][N:2]1[CH2:7][CH2:6][N:5]([CH2:8][C:9]2[CH:10]=[CH:11][C:12]3[N:16]=[CH:15][N:14]([C:17]4[S:18][C:19]([C:28](O)=[O:29])=[C:20]([C:22]5[CH:27]=[CH:26][CH:25]=[CH:24][CH:23]=5)[N:21]=4)[C:13]=3[CH:31]=2)[CH2:4][CH2:3]1.C[N:33](C(N(C)C)=[N+]1C2C(=NC=CC=2)N=N1)C.F[P-](F)(F)(F)(F)F.[Cl-].[NH4+].C(N(C(C)C)C(C)C)C>CN(C)C=O>[CH3:1][N:2]1[CH2:3][CH2:4][N:5]([CH2:8][C:9]2[CH:10]=[CH:11][C:12]3[N:16]=[CH:15][N:14]([C:17]4[S:18][C:19]([C:28]([NH2:33])=[O:29])=[C:20]([C:22]5[CH:23]=[CH:24][CH:25]=[CH:26][CH:27]=5)[N:21]=4)[C:13]=3[CH:31]=2)[CH2:6][CH2:7]1
Reactant: CN(C)C(N(C)C)=[N+]1N=Nc2ncccc21
Reactant: CN1CCN(Cc2ccc3ncn(-c4nc(-c5ccccc5)c(C(=O)O)s4)c3c2)CC1
Agent: F[P-](F)(F)(F)(F)F
Agent: [Cl-]
Agent: [NH4+]
Solvent: CCN(C(C)C)C(C)C
Solvent: CN(C)C=O
Product: CN1CCN(Cc2ccc3ncn(-c4nc(-c5ccccc5)c(C(N)=O)s4)c3c2)CC1
Temperature: 25 °C
Reaction time: 1 h
Yield: 64.7 %

Procedure:
To a mixture of 0.022 g (0.05 mmole) of 2-[6-(4-methyl-piperazin-1-ylmethyl)-benzoimidazol-1-yl]-4-phenyl-thiazole-5-carboxylic acid (I.1b), 0.023 g (0.06 mmole) of 1-[bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium, 3-oxide, hexafluorophosphate(1-) (1:1), 0.004 g of ammonium chloride and 1 mL of dimethylformamide was added 0.026 mL (0.15 mmole) of ethyldiisopropylamine. The mixture was stirred at ambient temperature for 1 hour. Solids were removed by filtration and the filtrate purified by reverse phase silica gel chromatography, eluting with acetonitrile-water (gradient 10:90-90:10) to give 0.014 g of 2-[6-(4-methyl-piperazin-1-ylmethyl)-benzoimidazol-1-yl]-4-phenyl-thiazole-5-carboxylic acid amide (I.1) as a white powder. MH+/Z=433.
Reaction SMILES: [Br:1][C:2]1[C:6]([CH2:7]Br)=[CH:5][S:4][CH:3]=1.[C:9]([O-:12])(=[O:11])[CH3:10].[K+].O>CC(C)=O>[C:9]([O:12][CH2:7][C:6]1[C:2]([Br:1])=[CH:3][S:4][CH:5]=1)(=[O:11])[CH3:10]
Reactant: CC(=O)[O-]
Reactant: BrCc1cscc1Br
Agent: [K+]
Solvent: O
Solvent: CC(C)=O
Product: CC(=O)OCc1cscc1Br
Temperature: 25 °C
Reaction time: 5 h

Procedure:
A mixture of 3-bromo-4-methylthiophene (8.85 g), N-bromosuccinimide (8.85 g), 2,2'-azobis(isobutyronitrile) (0.16 g) and carbon tetrachloride (100 ml) was stirred under reflux for 6 hours. The mixture was concentrated under reduced pressure to give a crude product of 3-bromo-4-bromomethylthiophene. A suspension of this crude product of 3-bromo-4-bromomethylthiophene and potassium acetate (30 g) in acetone (100 ml) was stirred at room temperature for 5 hours. The mixture was poured into water and extracted with ethyl acetate. The extract was dried over anhydrous magnesium sulfate and concentrated under reduced pressure to give a crude product of 4-acetoxymethyl-3-bromothiophene. This crude product was dissolved in tetrahydrofuran (50 ml), and 1N aqueous sodium hydroxide (50 ml) and ethanol (20 ml) were added. The mixture was stirred at room temperature for 2 hours and washed with diethyl ether. The aqueous layer was acidified with 1N hydrochloric acid and extracted with ethyl acetate. The extract was dried over anhdrous magnesium sulfate and concentrated under reduced pressure. The residue was purified by silica gel column chromatography to give 3-bromo-4-hydroxymethylthiophene (5.33 g) as oil. 3-Bromo-4-hydroxymethylthiophene was dissolved in methylene chloride (100 ml), and manganese dioxide (15 g) was added. The mixture was stirred at room temperature for 6 hours, and insoluble substances were removed by filtration. The filtrate was concentrated under reduced pressure to give a crude product of 4-bromo-3-thiophenecarbaldehyde. The crude product of 4-bromo-3-thiophenecarbaldehyde was dissolved in acetonitrile (50 ml), and sodium dihydrogen phosphate (1.2 g) in water (15 ml) and 30% aqueous hydrogen peroxide (3.5 ml) were added. Further, sodium chlorite (3.7 g) in water (40 ml) was added dropwise under ice-cooling. The mixture was stirred at room temperature for 2 hours, alkalified with 1N aqueous sodium hydroxide and washed with diethyl ether. The aqueous layer was acidified with 1N hydrochloric acid and extracted with ethyl acetate. The extract was dried over anhydrous magnesium sulfate and concentrated under reduced pressure to give 4-bromo-3-thiophenecarboxylic acid (3.40 g) as crystals.
Reaction SMILES: [Cl:1][C:2]1[CH:3]=[C:4]([N:9]2[C:13]3=[CH:14][CH2:15][CH2:16][CH2:17][C:12]3([CH2:18][C:19]3[CH:26]=[CH:25][C:22]([C:23]#[N:24])=[CH:21][CH:20]=3)[NH:11][C:10]2=[O:27])[CH:5]=[C:6]([Cl:8])[CH:7]=1.[H-].[Na+].[CH3:30]I>CN(C=O)C>[Cl:1][C:2]1[CH:3]=[C:4]([N:9]2[C:13]3=[CH:14][CH2:15][CH2:16][CH2:17][C:12]3([CH2:18][C:19]3[CH:20]=[CH:21][C:22]([C:23]#[N:24])=[CH:25][CH:26]=3)[N:11]([CH3:30])[C:10]2=[O:27])[CH:5]=[C:6]([Cl:8])[CH:7]=1
Reactant: N#Cc1ccc(CC23CCCC=C2N(c2cc(Cl)cc(Cl)c2)C(=O)N3)cc1
Reactant: CI
Agent: [H-]
Agent: [Na+]
Solvent: CN(C)C=O
Product: CN1C(=O)N(c2cc(Cl)cc(Cl)c2)C2=CCCCC21Cc1ccc(C#N)cc1
Temperature: 25 °C
Reaction time: 1 h

Procedure:
4-[1-(3,5-Dichlorophenyl)-2-oxo-1,2,3,4,5,6-hexahydro-benzimidazol-3a-ylmethyl]benzonitrile (200 mg) (0.5 mmol) in DMF (6 ml) was carefully dropped on a suspension of NaH 60% (24.1 mg) (1.2 eq) in DMF (5 ml) at RT. The reaction mixture was stirred 1 h at RT then methyl iodide (0.095 ml) (3 eq) was added. After one night, the reaction mixture was poured on water and extracted with tBuOMe. The organic layer was washed with water, dried over Na2SO4, and concentrated to yield a solid which was washed with diisopropyl ether to give 4-[1-(3,5-Dichlorophenyl)-3-methyl-2-oxo-1,2,3,4,5,6-hexahydro-benzimidazol-3a-ylmethyl]benzonitrile (115 mg) as a white solid. 1H NMR (CDCl3): 7.55 (2H, d), 7.25 (2H, d), 7.10 (1H, m), 6.75 (2H, m), 4.95 (1H, m), 3.10-3.0 (5H, m), 2.45-1.65 (6H, m).
Reaction SMILES: [CH3:1][N:2]([CH2:4][C:5]([OH:7])=O)[CH3:3].C(N1C=CN=C1)(N1C=CN=C1)=O.[NH2:20][CH2:21][CH2:22][N:23]1[C:27]([CH3:28])=[CH:26][CH:25]=[C:24]1[CH3:29]>COCCOC>[CH3:29][C:24]1[N:23]([CH2:22][CH2:21][NH:20][C:5](=[O:7])[CH2:4][N:2]([CH3:3])[CH3:1])[C:27]([CH3:28])=[CH:26][CH:25]=1
Reactant: CN(C)CC(=O)O
Reactant: Cc1ccc(C)n1CCN
Agent: O=C(n1ccnc1)n1ccnc1
Solvent: COCCOC
Product: Cc1ccc(C)n1CCNC(=O)CN(C)C
Temperature: 25 °C
Reaction time: 5 h

Procedure:
5.2 g (0.05 mol) of N,N-dimethylaminoacetic acid and 8.1 g (0.05 mol) of carbonyldiimidazole in 20 ml of ethylene glycol dimethyl ether are stirred at 70° C. for 15 min. After addition of 5.5 g (0.04 mol) of 1-(2-aminoethyl)-2,5-dimethylpyrrole, dissolved in 20 ml of ethylene glycol dimethyl ether, to the mixture it is stirred at room temperature for 5 h, then concentrated, water is added, and the mixture is extracted first when acid and then when alkaline. The product contained in the extract from the mixture which has been made alkaline is crystallized using ligroin. Yield: 4.3 g (39% of theory), Melting point: 63°-65° C. Elemental analysis: C12H21N3O (223.32) calculated: C 64.5 H 9.5 N 18.8 O 7.2 found: C 64.0 H 9.4 N 18.5 O 8.0
Reaction SMILES: C[O-].[Na+].[SH:4][C:5]1[CH:10]=[CH:9][CH:8]=[CH:7][N:6]=1.[NH2:11][C:12]1[N:17]=[C:16]([CH2:18]Cl)[CH:15]=[C:14]([O:20][CH3:21])[N:13]=1>CO.O>[NH2:11][C:12]1[N:13]=[C:14]([O:20][CH3:21])[CH:15]=[C:16]([CH2:18][S:4][C:5]2[CH:10]=[CH:9][CH:8]=[CH:7][N:6]=2)[N:17]=1
Reactant: Sc1ccccn1
Reactant: COc1cc(CCl)nc(N)n1
Agent: C[O-]
Agent: [Na+]
Solvent: O
Solvent: CO
Product: COc1cc(CSc2ccccn2)nc(N)n1

Procedure:
18 g of 30% methanolic sodium methylate solution are added to a solution of 11.1 g of 2-mercaptopyridine in 100 ml of methanol, and stirring is then maintained at 20°-25° C. for 1 hours. To this solution are added portionwise 17.4 g of 2-amino-4-chloromethyl-6-methoxy-pyrimidine, and the mixture is stirred at 20°-25° C. for a further 2 hours. In further processing, the mixture is diluted with 1 liter of water, and the precipitating crystalline product is separated and dried. The yield is 22.5 g (91% of theory) of 2-amino-4-methoxy-6-(pyridin-2-yl-thiomethyl)-pyrimidine, m.p. 115°-116° C.
Reaction SMILES: [C:1]([NH:9][C:10]1[N:18]=[CH:17][N:16]=[C:15]2[C:11]=1[N:12]=[CH:13][N:14]2[CH2:19][C:20]([O:22]CC)=[O:21])(=[O:8])[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.[OH-].[Na+].Cl>O>[C:1]([NH:9][C:10]1[N:18]=[CH:17][N:16]=[C:15]2[C:11]=1[N:12]=[CH:13][N:14]2[CH2:19][C:20]([OH:22])=[O:21])(=[O:8])[C:2]1[CH:3]=[CH:4][CH:5]=[CH:6][CH:7]=1
Reactant: CCOC(=O)Cn1cnc2c(NC(=O)c3ccccc3)ncnc21
Agent: Cl
Agent: [Na+]
Agent: [OH-]
Solvent: O
Product: O=C(O)Cn1cnc2c(NC(=O)c3ccccc3)ncnc21
Temperature: 25 °C
Reaction time: 2 h

Procedure:
Compound 9 (1.63 g, 5 mmol) and NaOH (0.4 g, 10 mmol) were dissolved in water (20 mL) and the solution was stirred for 2 h at room temperature. The pH was adjusted to 3 using 1M HCl, causing precipitation of the product. The precipitate was separated by filtration, washed with water, and dried in vacuo to give 4 as a white solid: yield 1.4 g (95%); MS(+ESI): m/z 298 [M+H]+; 1H NMR (400 MHz, d-DMSO): δ11.682 (s, 1H), 9.11 (s, 1H), 8.81 (s, 1H), 8.52 (s, 1H), 8.09 (d, 2H, J=7.2 Hz), 7.67 (t, 1H, J=7.2 Hz), 7.60 (t, 2H, J=7.2 Hz), 5.16 (s, 2H); 13C NMR (400 MHz, CDCl3): δ169.43, 166.34, 152.89, 152,09, 150.29, 145.63, 133.74, 132.98, 128.45, 122.56, 44.88.
Reaction SMILES: [CH2:1]([O:8][C:9]1[CH:14]=[CH:13][C:12]([CH2:15][CH2:16][CH2:17][CH2:18][NH:19][CH2:20][CH2:21][C:22]2[C:30]3[C:25](=[CH:26][CH:27]=[C:28]([OH:31])[CH:29]=3)[NH:24][C:23]=2[C:32]2[CH:37]=[C:36]([CH3:38])[CH:35]=[C:34]([CH3:39])[CH:33]=2)=[CH:11][CH:10]=1)[C:2]1[CH:7]=[CH:6][CH:5]=[CH:4][CH:3]=1.Cl[C:41]([O:43][CH2:44][C:45]1[CH:50]=[CH:49][CH:48]=[CH:47][CH:46]=1)=[O:42].C(N(C(C)C)CC)(C)C>>[CH2:44]([O:43][C:41](=[O:42])[N:19]([CH2:18][CH2:17][CH2:16][CH2:15][C:12]1[CH:11]=[CH:10][C:9]([O:8][CH2:1][C:2]2[CH:3]=[CH:4][CH:5]=[CH:6][CH:7]=2)=[CH:14][CH:13]=1)[CH2:20][CH2:21][C:22]1[C:30]2[C:25](=[CH:26][CH:27]=[C:28]([OH:31])[CH:29]=2)[NH:24][C:23]=1[C:32]1[CH:37]=[C:36]([CH3:38])[CH:35]=[C:34]([CH3:39])[CH:33]=1)[C:45]1[CH:50]=[CH:49][CH:48]=[CH:47][CH:46]=1
Reactant: O=C(Cl)OCc1ccccc1
Reactant: Cc1cc(C)cc(-c2[nH]c3ccc(O)cc3c2CCNCCCCc2ccc(OCc3ccccc3)cc2)c1
Solvent: CCN(C(C)C)C(C)C
Product: Cc1cc(C)cc(-c2[nH]c3ccc(O)cc3c2CCN(CCCCc2ccc(OCc3ccccc3)cc2)C(=O)OCc2ccccc2)c1
Temperature: 25 °C

Procedure:
To a solution of 3-[2-[4-(4-benzyloxyphenyl)butylamino]ethyl]-2-(3,5-dimethylphenyl)-1H-indol-5-ol (234 mg in 5 mL of dry methylene chloride) at −78° C. was added benzyl chloroformate (0.082 mL) and diisopropylethylamine (0.104 mL) and the mixture stirred at room temperature. After 1 hour the reaction was quenched by the addition of saturated sodium bicarbonate and extracted with ethyl acetate. The organic portion was washed with saturated ammonium chloride, dried over magnesium sulfate and concentrated in vacuo. Purification by flash chromatography on silica gel (hexane:ethyl acetate, 3:1 then 2:1) gave the title compound (155 mg).
Reaction SMILES: Br[C:2]1[S:3][C:4]2[CH:10]=[C:9]([CH2:11][N:12]3[C:16]4[CH:17]=[C:18]([O:23][CH3:24])[C:19]([O:21][CH3:22])=[CH:20][C:15]=4[N:14]=[CH:13]3)[CH:8]=[CH:7][C:5]=2[N:6]=1.[NH2:25][C:26]1[CH:31]=[CH:30][CH:29]=[CH:28][C:27]=1[OH:32].CCN(C(C)C)C(C)C>CC(N(C)C)=O>[CH3:22][O:21][C:19]1[C:18]([O:23][CH3:24])=[CH:17][C:16]2[N:12]([CH2:11][C:9]3[CH:8]=[CH:7][C:5]4[N:6]=[C:2]([NH:25][C:26]5[CH:31]=[CH:30][CH:29]=[CH:28][C:27]=5[OH:32])[S:3][C:4]=4[CH:10]=3)[CH:13]=[N:14][C:15]=2[CH:20]=1
Reactant: COc1cc2ncn(Cc3ccc4nc(Br)sc4c3)c2cc1OC
Reactant: Nc1ccccc1O
Solvent: CCN(C(C)C)C(C)C
Solvent: CC(=O)N(C)C
Product: COc1cc2ncn(Cc3ccc4nc(Nc5ccccc5O)sc4c3)c2cc1OC
Temperature: 110 °C
Yield: 16.3 %

Procedure:
To a suspension of 2-bromo-6-((5,6-dimethoxy-1H-benzo[d]imidazol-1-yl)methyl)benzo[d]thiazole (70 mg, 0.17 mmol) from Example 2 and 2-aminophenol (95 mg, 0.87 mmol) in anhydrous DMA (300 μL) at rt was added DIEA (90 μL, 0.52 mmol). The mixture was stirred and heated in a sealed tube at 110° C. for 96 h. After cooling to rt, the mixture was purified by reverse-phase preparative HPLC using a mixture of water (5% CH3CN, 0.05% HCOOH) and CH3CN (0.05% HCOOH) as the mobile phase and Varian Pursuit XRs C18 column as the stationary phase to afford 2-((6-((5,6-dimethoxy-1H-benzo[d]imidazol-1-yl)methyl)benzo[d]thiazol-2-yl)amino)phenol (12 mg, 16%) as a white solid. 1H NMR (300 MHz, DMSO-d6) δ 9.77 (br s, 1H), 8.14-8.26 (m, 2H), 7.75 (s, 1H), 7.49 (d, J=8.3 Hz, 1H), 7.24-7.29 (m, 1H), 7.16-7.22 (m, 2H), 6.79-6.92 (m, 3H), 5.46 (s, 2H), 3.76 (s, 6H). LCMS (ESI) m/z 461 (M+H)+.
Reaction SMILES: Cl[C:2]1[C:11]([C:12]2[CH:17]=[CH:16][CH:15]=[CH:14][CH:13]=2)=[CH:10][C:9]2[C:4](=[C:5]([O:20][CH3:21])[CH:6]=[CH:7][C:8]=2[O:18][CH3:19])[N:3]=1.C(O)(=[O:24])C>>[C:12]1([C:11]2[C:2](=[O:24])[NH:3][C:4]3[C:9]([CH:10]=2)=[C:8]([O:18][CH3:19])[CH:7]=[CH:6][C:5]=3[O:20][CH3:21])[CH:17]=[CH:16][CH:15]=[CH:14][CH:13]=1
Reactant: CC(=O)O
Reactant: COc1ccc(OC)c2nc(Cl)c(-c3ccccc3)cc12
Product: COc1ccc(OC)c2[nH]c(=O)c(-c3ccccc3)cc12
Yield: 100 %

Procedure:
A solution of 2-chloro-3-phenyl-5,8-dimethoxyquinoline (200 mg, 0.67 mmol) was refluxed for 3 hours in acetic acid (1.5 ml) and water (0.05 ml.) After the solvent was evaporated, the residue was dissolved in water, basified with aqueous ammonium hydroxide 25% and extracted with chloroform (3×25 ml). The combined chloroform layers were dried over sodium sulfate and evaporated, yielding an essentially pure residue of 187 mg (100%) of 3-phenyl-5,8-dimethoxy-2-(1H)-quinolinone. m.p. 207 (CDCl3).
Reaction SMILES: [C:1]([CH2:3][CH2:4][O:5][C:6]([C:8]1[CH:13]([C:14]2[CH:19]=[CH:18][C:17]([F:20])=[C:16]([F:21])[CH:15]=2)[NH:12][C:11]([O:22][CH3:23])=[N:10][C:9]=1[CH2:24][O:25][CH3:26])=[O:7])#[N:2].Cl[C:28]([O:30][C:31]1[CH:36]=[CH:35][C:34]([N+:37]([O-:39])=[O:38])=[CH:33][CH:32]=1)=[O:29]>CN(C1C=CN=CC=1)C.C(Cl)Cl>[C:1]([CH2:3][CH2:4][O:5][C:6]([C:8]1[CH:13]([C:14]2[CH:19]=[CH:18][C:17]([F:20])=[C:16]([F:21])[CH:15]=2)[N:12]([C:28]([O:30][C:31]2[CH:32]=[CH:33][C:34]([N+:37]([O-:39])=[O:38])=[CH:35][CH:36]=2)=[O:29])[C:11]([O:22][CH3:23])=[N:10][C:9]=1[CH2:24][O:25][CH3:26])=[O:7])#[N:2]
Reactant: O=C(Cl)Oc1ccc([N+](=O)[O-])cc1
Reactant: COCC1=C(C(=O)OCCC#N)C(c2ccc(F)c(F)c2)NC(OC)=N1
Agent: CN(C)c1ccncc1
Solvent: ClCCl
Product: COCC1=C(C(=O)OCCC#N)C(c2ccc(F)c(F)c2)N(C(=O)Oc2ccc([N+](=O)[O-])cc2)C(OC)=N1
Yield: 67.3 %

Procedure:
To a well stirred solution of (+)-5-(2-cyanoethoxycarbonyl)-1,6-dihydro-2-methoxy-4-methoxymethyl-6-(3,4-difluorophenyl)pyrimidine (0.82 g, 2.24 mmol) and 4-(N,N-dimethylamino)pyridine (0.329 g, 2.69 mmol) in CH2Cl2 (200 mL) was added a powder of 4-nitrophenyl chloroformate (0.543 g, 2.69 mmol) at room temperature. The solvent was evaporated and the residue was purified by column chromatography on silica gel using dichloromethane/hexane (20%-50%) as the eluent to give (+)-5-(2-cyanoethoxycarbonyl)-4-methoxymethyl-1,6-dihydro-2-methoxy-6-(3,4-difluorophenyl)-1-[(4-nitrophenyloxy)carbonyl]pyrimidine (0.80 g, 67%) as a viscous oil.
Reaction SMILES: [CH:1]1[C:10]2[C:5](=[CH:6][CH:7]=[CH:8][CH:9]=2)[CH:4]=[CH:3][C:2]=1[C:11]1[NH:15][C:14]([CH:16]([CH2:20][CH2:21][CH2:22][CH2:23][CH2:24][C:25](=[O:28])[CH2:26][CH3:27])[C:17]([OH:19])=[O:18])=[N:13][CH:12]=1.[H-].[Na+].[CH3:31][Si:32]([CH2:35][CH2:36][O:37][CH2:38]Cl)([CH3:34])[CH3:33]>C1COCC1>[CH2:26]([C:25]1([CH2:24][CH2:23][CH2:22][CH2:21][CH2:20][CH:16]([C:14]2[N:15]([CH2:38][O:37][CH2:36][CH2:35][Si:32]([CH3:34])([CH3:33])[CH3:31])[C:11]([C:2]3[CH:3]=[CH:4][C:5]4[C:10](=[CH:9][CH:8]=[CH:7][CH:6]=4)[CH:1]=3)=[CH:12][N:13]=2)[C:17]([O:19][C:2]([CH3:11])([CH3:3])[CH3:1])=[O:18])[O:18][CH2:17][CH2:16][O:28]1)[CH3:27]
Reactant: CCC(=O)CCCCCC(C(=O)O)c1ncc(-c2ccc3ccccc3c2)[nH]1
Reactant: C[Si](C)(C)CCOCCl
Agent: [H-]
Agent: [Na+]
Solvent: C1CCOC1
Product: CCC1(CCCCCC(C(=O)OC(C)(C)C)c2ncc(-c3ccc4ccccc4c3)n2COCC[Si](C)(C)C)OCCO1
Temperature: 25 °C
Reaction time: 1 h

Procedure:
To a solution of Example 1, A3 in dry THF (0.06 M solution) at 0° C. was added NaH (60%, 1.5 eq.) portionwise, the resulting mixture was stirred for 1 hr and then SEM-Cl (1.5 eq.) was added dropwise. The solution was allowed to warm to RT and stirred for a further 3 hrs. The reaction was quenched by the addition of sat. aq. NH4Cl solution and the mixture extracted with EtOAc. The organic layer was washed with brine, dried (Na2SO4) and concentrated under reduced pressure. The crude was purified by column chromatography on silica gel eluting with 20-50% EtOAc/petroleum ether to obtain D1 as a pale brown foam. 1H NMR (400 MHz, CDCl3) δ: 8.32 (1H, s), 7.91-7.75 (5H, m), 7.49-7.37 (2H, m), 5.43 (1H, d, J=10.9 Hz), 5.26 (1H, d, J=10.9 Hz), 3.90 (4H, s), 3.86 (2H, t, J=7.4 Hz), 3.57 (1H, t, J=8.1 Hz), 2.27-2.14 (2H, m), 1.67-1.57 (4H, m), 1.49 (9H, s), 1.41-1.27 (6H, m), 0.96 (2H, t, J=7.4 Hz), 0.87 (3H, t, J=7.5 Hz), 0.07 (9H, s). MS (ES) C35H52N2O5Si requires: 608, found: 609 (M+H)+.
Reaction SMILES: [C:1]([O:5][C:6](=[O:23])[NH:7][CH:8]([C:15]1[CH:20]=[CH:19][C:18]([Cl:21])=[C:17]([Cl:22])[CH:16]=1)[C:9](=[O:14])N(OC)C)([CH3:4])([CH3:3])[CH3:2].Br[C:25]1[CH:37]=[CH:36][C:28]([O:29][CH2:30][C:31]2([CH3:35])[CH2:34][O:33][CH2:32]2)=[CH:27][C:26]=1[F:38]>>[C:1]([O:5][C:6](=[O:23])[NH:7][CH:8]([C:15]1[CH:20]=[CH:19][C:18]([Cl:21])=[C:17]([Cl:22])[CH:16]=1)[C:9]([C:25]1[CH:37]=[CH:36][C:28]([O:29][CH2:30][C:31]2([CH3:35])[CH2:34][O:33][CH2:32]2)=[CH:27][C:26]=1[F:38])=[O:14])([CH3:2])([CH3:3])[CH3:4]
Reactant: CON(C)C(=O)C(NC(=O)OC(C)(C)C)c1ccc(Cl)c(Cl)c1
Reactant: CC1(COc2ccc(Br)c(F)c2)COC1
Product: CC1(COc2ccc(C(=O)C(NC(=O)OC(C)(C)C)c3ccc(Cl)c(Cl)c3)c(F)c2)COC1

Procedure:
The title compound was prepared from rac-[(3,4-dichloro-phenyl)-(methoxy-methyl-carbamoyl)-methyl]-carbamic acid tert-butyl ester (Intermediate 9) and 3-(4-bromo-3-fluoro-phenoxymethyl)-3-methyl-oxetane (Intermediate 32) in analogy to Example 1a): MS (ISP): 498.3 and 500.2 (M+H)+, 398.2 and 400.0 ((M-Boc)+H)+ (100%); MS (ISN): 496.4 and 498.5 (M−H)−.