Azzindani/Open_Reaction_Data huggingface dataset:
Reaction SMILES: [NH2:1][C:2]1[NH:3][C:4](=[O:12])[C:5]2[S:10][C:9](=[O:11])[NH:8][C:6]=2[N:7]=1.[C:13]([O:21][CH:22]([CH:36]1[CH2:40][CH2:39][CH2:38][CH2:37]1)[C@@H:23]1[CH2:27][C@@H:26]([O:28][C:29](=[O:31])[CH3:30])[CH:25](OC(=O)C)[O:24]1)(=[O:20])[C:14]1[CH:19]=[CH:18][CH:17]=[CH:16][CH:15]=1.[Si](OS(C(F)(F)F)(=O)=O)(C)(C)C>C(#N)C>[C:13]([O:21][CH:22]([C@@H:23]1[CH2:27][C@@H:26]([O:28][C:29](=[O:31])[CH3:30])[C@H:25]([N:8]2[C:6]3[N:7]=[C:2]([NH2:1])[NH:3][C:4](=[O:12])[C:5]=3[S:10][C:9]2=[O:11])[O:24]1)[CH:36]1[CH2:37][CH2:38][CH2:39][CH2:40]1)(=[O:20])[C:14]1[CH:19]=[CH:18][CH:17]=[CH:16][CH:15]=1
Reactant: Nc1nc2[nH]c(=O)sc2c(=O)[nH]1
Reactant: CC(=O)OC1O[C@H](C(OC(=O)c2ccccc2)C2CCCC2)C[C@H]1OC(C)=O
Agent: C[Si](C)(C)OS(=O)(=O)C(F)(F)F
Solvent: CC#N
Product: CC(=O)O[C@@H]1C[C@@H](C(OC(=O)c2ccccc2)C2CCCC2)O[C@H]1n1c(=O)sc2c(=O)[nH]c(N)nc21
Temperature: 70 °C
Reaction time: 0.5 h
Yield: 31.1 %

Procedure:
To a suspension of 5-amino-3,6-dihydrothiazolo[4,5-d]pyrimidine-2,7-dione (370 mg, 2.0 mmol) in ACN (20 mL) was added BSA (2.1 g, 10 mmol). The resulting reaction mixture was then stirred at 70° C. for 0.5 hour under argon to form a clear solution. After the solution was cooled to room temperature, [cyclopentyl-[(2S,4R)-4,5-diacetoxytetrahydrofuran-2-yl]methyl] benzoate (compound 11c, 400 mg, 1.0 mmol) and TMSOTf (2.25 g, 10 mmol) were added in sequence. After being heated with stirring at 70° C. for 14 hours, the solvent was evaporated in vacuo. The residue was partitioned between EtOAc and saturated NaHCO3 solution (30 mL). The organic layer was collected and the aqueous phase was extracted with EtOAc (30 mL) twice. The combined organic layers were washed with brine, dried over Na2SO4 and concentrated in vacuo. The residue was purified by column chromatography on silica gel (eluting with 1:1 EtOAc in petroleum ether) to afford 160 mg of [[(2S,4R,5R)-4-acetoxy-5-(5-amino-2,7-dioxo-6H-thiazolo[4,5-d]pyrimidin-3-yl)tetrahydrofuran-2-yl]-cyclopentyl-methyl] benzoate (compound 11d).
Reaction SMILES: [Cl:1][C:2]1[CH:25]=[CH:24][C:5]2[N:6]=[C:7]([NH:9][C:10]3[N:14]([CH2:15][CH3:16])[C:13]4[CH:17]=[CH:18][C:19]([C:21](O)=[O:22])=[CH:20][C:12]=4[N:11]=3)[S:8][C:4]=2[CH:3]=1.[CH2:26]([O:28][CH2:29][CH2:30][NH2:31])[CH3:27].CN(C(ON1N=NC2C=CC=CC1=2)=[N+](C)C)C.F[P-](F)(F)(F)(F)F.CCN(C(C)C)C(C)C>CN(C=O)C>[CH2:26]([O:28][CH2:29][CH2:30][NH:31][C:21]([C:19]1[CH:18]=[CH:17][C:13]2[N:14]([CH2:15][CH3:16])[C:10]([NH:9][C:7]3[S:8][C:4]4[CH:3]=[C:2]([Cl:1])[CH:25]=[CH:24][C:5]=4[N:6]=3)=[N:11][C:12]=2[CH:20]=1)=[O:22])[CH3:27]
Reactant: CCn1c(Nc2nc3ccc(Cl)cc3s2)nc2cc(C(=O)O)ccc21
Reactant: CCOCCN
Agent: CN(C)C(On1nnc2ccccc21)=[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: CCOCCNC(=O)c1ccc2c(c1)nc(Nc1nc3ccc(Cl)cc3s1)n2CC
Yield: 44.2 %

Procedure:
2-(6-Chloro-benzothiazol-2-ylamino)-1-ethyl-1H-benzoimidazole-5-carboxylic acid (2-ethoxy-ethyl)-amide (79.0 mg) was prepared by following General Procedure F starting from 2-(6-chloro-benzothiazol-2-ylamino)-1-ethyl-1H-benzoimidazole-5-carboxylic acid (150.0 mg), 2-ethoxy-ethylamine (53.0 mg), HBTU (190.0 mg) and DIEA (0.2 mL) in DMF (1.0 mL). LCMS: m/z 445; and 1H NMR (DMSO-d6, 400 MHz): δ 8.47 (1H, br. s), 8.08 (1H, br. s), 7.92 (1H, br. s), 7.76-7.63 (2H, m), 7.52 (1H, m), 7.40-7.38 (1H, m), 4.22 (2H, m), 3.53-3.41 (6H, m), 1.34-1.30 (3H, t), 1.14-1.11 (3H, t), —NH proton signal was not observed.
Reaction SMILES: F[C:2]1[CH:9]=[CH:8][C:7]([F:10])=[CH:6][C:3]=1[CH:4]=O.[H-].[Na+].[SH:13][CH2:14][C:15]([O:17][CH3:18])=[O:16]>>[CH3:18][O:17][C:15]([C:14]1[S:13][C:2]2[CH:9]=[CH:8][C:7]([F:10])=[CH:6][C:3]=2[CH:4]=1)=[O:16]
Reactant: O=Cc1cc(F)ccc1F
Reactant: COC(=O)CS
Agent: [H-]
Agent: [Na+]
Product: COC(=O)c1cc2cc(F)ccc2s1

Procedure:
Using 5.0 g (35.2 mmol) of 2,5-difluorobenzaldehyde, 2.11 g (52.78 mmol) of sodium hydride (60% pure) and 4.11 g (38.7 mmol) of methyl mercaptoacetate, 1.1 g (14.3% of theory) of the title compound are obtained.
Reaction SMILES: [CH3:1][CH2:2][N:3]1[C:9]2[N:10]=[C:11]([N:14]3[CH2:19][CH2:18][NH:17][CH2:16][CH2:15]3)[N:12]=[CH:13][C:8]=2[C:6](=[O:7])[C:5]([C:20]([OH:22])=[O:21])=[CH:4]1.[CH3:23][C:24]1[CH:25]=[C:26]([N:31]=[C:32]=[S:33])[CH:27]=[C:28]([CH3:30])[CH:29]=1.C(N(CC)CC)C>>[CH3:23][C:24]1[CH:25]=[C:26]([NH:31][C:32]([N:17]2[CH2:18][CH2:19][N:14]([C:11]3[N:12]=[CH:13][C:8]4[C:6](=[O:7])[C:5]([C:20]([OH:22])=[O:21])=[CH:4][N:3]([CH2:2][CH3:1])[C:9]=4[N:10]=3)[CH2:15][CH2:16]2)=[S:33])[CH:27]=[C:28]([CH3:30])[CH:29]=1
Reactant: Cc1cc(C)cc(N=C=S)c1
Reactant: CCn1cc(C(=O)O)c(=O)c2cnc(N3CCNCC3)nc21
Solvent: CCN(CC)CC
Product: CCn1cc(C(=O)O)c(=O)c2cnc(N3CCN(C(=S)Nc4cc(C)cc(C)c4)CC3)nc21

Procedure:
Pipemidic acid (45 mg, 0.148 mmol), 3,5-dimethylphenyl isothiocyanate (24 mg, 0.148 mmol) and triethylamine (41 μL, 296 mmol) were used. Purification on silica yielded compound 22 in Table 1, below (41.6 mg, 67%). 1H NMR (300 MHz, CDCl3) δ 9.30 (s, 1H), 8.66 (s, 1H), 7.48 (s, 1H), 6.86-6.75 (m, 3H), 4.33 (q, J=7.10 Hz, 2H), 4.22-3.91 (m, 8H), 2.30 (s, 6H), 1.48 (t, J=7.11 Hz, 3H) ppm.
Reaction SMILES: [CH:1]12[N:8]([C:9]3[CH:18]=[N:17][C:16]4[C:11](=[CH:12]C=CC=4)[N:10]=3)[CH2:7][CH:6]1[CH2:5][CH2:4][NH:3][CH2:2]2.[C:19](OC(N1CCC2C(NC2)C1)=O)(C)(C)C.ClC1C(C)=NC=C(C)N=1.ClC1C=NC2C(=CC=CC=2)N=1>>[CH3:19][C:18]1[C:9]([N:8]2[C@@H:1]3[C@@H:6]([CH2:5][CH2:4][NH:3][CH2:2]3)[CH2:7]2)=[N:10][C:11]([CH3:12])=[CH:16][N:17]=1
Reactant: c1ccc2nc(N3CC4CCNCC43)cnc2c1
Reactant: CC(C)(C)OC(=O)N1CCC2CNC2C1
Agent: Cc1cnc(C)c(Cl)n1
Agent: Clc1cnc2ccccc2n1
Product: Cc1cnc(C)c(N2C[C@@H]3CCNC[C@@H]32)n1

Procedure:
The title compound was prepared in a manner analogous to Intermediate 2, substituting (1R,6S)-(3,8-diaza-bicyclo[4.2.0]octane-3-carboxylic acid tert-butyl ester for 3,8-diaza-bicyclo[4.2.0]octane-3-carboxylic acid tert-butyl ester and 3-chloro-2,5-dimethyl-pyrazine for 2-chloro-quinoxaline in Step A. MS (ESI) mass calcd. for C12H18N4, 218.30. The compound was used as such in the subsequent reactions.
Reaction SMILES: [C:1]([O:5][C:6]([N:8]1[C:16]2[C:11](=[CH:12][CH:13]=[CH:14][CH:15]=2)[C:10](/[CH:17]=[CH:18]/[C:19](O)=[O:20])=[CH:9]1)=[O:7])([CH3:4])([CH3:3])[CH3:2].[CH:22]([NH:25][NH:26][C:27](=[O:34])[C:28]1[CH:33]=[CH:32][CH:31]=[CH:30][CH:29]=1)([CH3:24])[CH3:23].CN(C(ON1N=NC2C=CC=NC1=2)=[N+](C)C)C.F[P-](F)(F)(F)(F)F.C(N(CC)C(C)C)(C)C>CN(C=O)C.CCOC(C)=O>[C:27]([NH:26][N:25]([C:19](=[O:20])/[CH:18]=[CH:17]/[C:10]1[C:11]2[C:16](=[CH:15][CH:14]=[CH:13][CH:12]=2)[N:8]([C:6]([O:5][C:1]([CH3:3])([CH3:4])[CH3:2])=[O:7])[CH:9]=1)[CH:22]([CH3:24])[CH3:23])(=[O:34])[C:28]1[CH:33]=[CH:32][CH:31]=[CH:30][CH:29]=1
Reactant: CC(C)NNC(=O)c1ccccc1
Reactant: CC(C)(C)OC(=O)n1cc(/C=C/C(=O)O)c2ccccc21
Agent: CN(C)C(On1nnc2cccnc21)=[N+](C)C
Agent: F[P-](F)(F)(F)(F)F
Solvent: CCN(C(C)C)C(C)C
Solvent: CCOC(C)=O
Solvent: CN(C)C=O
Product: CC(C)N(NC(=O)c1ccccc1)C(=O)/C=C/c1cn(C(=O)OC(C)(C)C)c2ccccc12
Temperature: 25 °C
Reaction time: 12 h
Yield: 62.3 %

Procedure:
To solution containing (E)-3-(1-(tert-butoxycarbonyl)-1H-indol-3-yl)acrylic acid (1000 mg, 3.48 mmol), N′-isopropylbenzohydrazide (930.51 mg, 5.22 mmol) and HATU (1985.12 mg, 5.22 mmol) dissolved in DMF (15.0 ml), N,N-diisopropylethylamine (DIPEA)(0.90943 ml, 5.22 mmol) was slowly drop-wise added and stirred at room temperature for 12 hr. The reaction mixture was diluted with EtOAc, washed with water and brine, dried with anhydrous MgSO4 filtered, and concentrated under reduced pressure. The residue was separated through silica gel chromatography (n-hexane:EtOAc=3:1) and dried so that ivory (E)-tert-butyl 3-(3-(2-benzoyl-1-isopropylhydrazinyl)-3-oxoprop-1-enyl)-1H-indole-1-carboxylate was obtained as white solid (970 mg, 62.3%).
Reaction SMILES: [Br:1][C:2]1[S:6][C:5]([CH2:7][OH:8])=[N:4][CH:3]=1.N1C=CN=C1.CN(C)C=O.Cl[Si:20]([CH:27]([CH3:29])[CH3:28])([CH:24]([CH3:26])[CH3:25])[CH:21]([CH3:23])[CH3:22]>C(OC(=O)C)C>[Br:1][C:2]1[S:6][C:5]([CH2:7][O:8][Si:20]([CH:27]([CH3:29])[CH3:28])([CH:24]([CH3:26])[CH3:25])[CH:21]([CH3:23])[CH3:22])=[N:4][CH:3]=1
Reactant: CC(C)[Si](Cl)(C(C)C)C(C)C
Reactant: OCc1ncc(Br)s1
Agent: c1c[nH]cn1
Solvent: CCOC(C)=O
Solvent: CN(C)C=O
Product: CC(C)[Si](OCc1ncc(Br)s1)(C(C)C)C(C)C
Temperature: 25 °C
Reaction time: 72 h
Yield: 104 %

Procedure:
A 100 mL round bottom flask is charged with (5-bromothiazol-2-yl)methanol (2.5 g, 12.9 mmol), imidazole (1.75 g, 25.8 mmol), dimethylformamide (25 mL), and chlorotriisopropylsilane (3.4 mL, 15.5 mmol). The reaction is stirred at room temperature under nitrogen for 72 hours. Contents are diluted with ethylacetate (150 mL), washed with 0.5M hydrochloric acid (2×100 mL) and brine (100 mL), dried (Na2SO4), and concentrated under vacuum to afford the title compound (4.7 g): m/z (CI) M+H 350+352.
Reaction SMILES: [CH3:1][C:2]1[CH:7]=[C:6]([CH3:8])[N:5]=[C:4](OS(C(F)(F)F)(=O)=O)[CH:3]=1.N1C=CC=CC=1.[N+:23]([C:26]1[CH:31]=[CH:30][C:29]([NH:32][CH2:33][CH2:34][NH2:35])=[CH:28][CH:27]=1)([O-:25])=[O:24]>COCCOCCOC>[CH3:1][C:2]1[CH:7]=[C:6]([CH3:8])[N:5]=[C:4]([NH:35][CH2:34][CH2:33][NH:32][C:29]2[CH:28]=[CH:27][C:26]([N+:23]([O-:25])=[O:24])=[CH:31][CH:30]=2)[CH:3]=1
Reactant: Cc1cc(C)nc(OS(=O)(=O)C(F)(F)F)c1
Reactant: NCCNc1ccc([N+](=O)[O-])cc1
Solvent: c1ccncc1
Solvent: COCCOCCOC
Product: Cc1cc(C)nc(NCCNc2ccc([N+](=O)[O-])cc2)c1
Temperature: 165 °C
Yield: 55 %

Procedure:
To a solution of trifluoro-methanesulfonic acid 4,6-dimethyl-pyridin-2-yl ester (prepared according to J. Org. Chem., 63, 10048-51, 1998), using pyridine as base. 0.6 g, 2.35 mmol) in diglyme (2 mL) was added N*1*-(4-nitro-phenyl)-ethane-1,2-diamine (0.51 g, 2.82 mmol). The reaction mixture was heated to 165° C. for 24 h. The resulting reaction mixture was concentrated under reduced pressure and the residue diluted with chloroform. The organic layer was washed with brine and water and dried over sodium sulfate. The solvent was evaporated and the crude residue was purified by column chromatography (60-120 mesh) using 20% ethyl acetate/petroleum ether as eluent to afford N-(4,6-dimethyl-pyridin-2-yl)-N′-(4-nitro-phenyl)-ethane-1,2-diamine (0.38 g, 55%) as a cream solid.
Reaction SMILES: [Cl:1][C:2]1[CH:3]=[C:4]2[C:8](=[C:9]([Cl:11])[CH:10]=1)[NH:7][C:6]([C:12]1[CH:17]=[C:16]([Cl:18])[CH:15]=[C:14]([Cl:19])[CH:13]=1)=[CH:5]2.[N+:20]([O-])([OH:22])=[O:21]>C(O)(=O)C>[Cl:1][C:2]1[CH:3]=[C:4]2[C:8](=[C:9]([Cl:11])[CH:10]=1)[NH:7][C:6]([C:12]1[CH:13]=[C:14]([Cl:19])[CH:15]=[C:16]([Cl:18])[CH:17]=1)=[C:5]2[N+:20]([O-:22])=[O:21]
Reactant: O=[N+]([O-])O
Reactant: Clc1cc(Cl)cc(-c2cc3cc(Cl)cc(Cl)c3[nH]2)c1
Solvent: CC(=O)O
Product: O=[N+]([O-])c1c(-c2cc(Cl)cc(Cl)c2)[nH]c2c(Cl)cc(Cl)cc12
Temperature: 90 °C
Yield: 42 %

Procedure:
A mixture of 5, 7-dichloro-2-(3,5-dichlorophenyl)indole (1.25 g, 3.8 mmole) in acetic acid is treated dropwise with 3 mL of concentrated HNO3 at 90° C., maintained at 90° C. for 1 hour, cooled and filtered. The filtercake is air-dried and recrystallized from methanol/water to afford the title product as a yellow solid, 0.60 g, (42% yield), mp 272°-273° C., identified by IR, 1HNMR and elemental analyses.
Reaction SMILES: [CH3:1][O:2][C:3]1[N:8]=[C:7]([O:9][CH3:10])[C:6](B(O)O)=[CH:5][N:4]=1.[CH3:14][C:15]1[CH:20]=[CH:19][N:18]=[CH:17][C:16]=1Br.C([O-])([O-])=O.[Na+].[Na+].C1C=CC(P(C2C=CC=CC=2)C2C=CC=CC=2)=CC=1>C(O)CC.CC([O-])=O.CC([O-])=O.[Pd+2]>[CH3:14][C:15]1[CH:20]=[CH:19][N:18]=[CH:17][C:16]=1[C:6]1[C:7]([O:9][CH3:10])=[N:8][C:3]([O:2][CH3:1])=[N:4][CH:5]=1
Reactant: COc1ncc(B(O)O)c(OC)n1
Reactant: Cc1ccncc1Br
Agent: [Pd+2]
Agent: CC(=O)[O-]
Agent: O=C([O-])[O-]
Solvent: CCCO
Product: COc1ncc(-c2cnccc2C)c(OC)n1

Procedure:
2,4-Dimethoxypyrimidine-5-boronic acid (1.3 g, 7.23 mmol) was dissolved in degassed n-PrOH (20 ml) and then 4-methyl-3-bromo-pyridine (830 g, 4.82 mmol), Na2CO3 (1.02 g, 9.64 mmol), PPh3 (126 mg, 0.48 mmol) and Pd(OAc)2 (40 mg) were added. The suspension was stirred at reflux for 3 hours. The solvent was evaporated under vacuum and the crude was partitioned between water and DCM. The organic phase was dried (Na2SO4) and evaporated to give the title compound that was used without further purification in the next step (quantitative yield).
Reaction SMILES: Cl[C:2]1[N:7]=[C:6]([NH:8][C:9]2[CH:10]=[C:11]3[C:15](=[CH:16][CH:17]=2)[NH:14][C:13]([CH3:18])=[CH:12]3)[CH:5]=[CH:4][N:3]=1.[NH2:19][C:20]1[CH:25]=[CH:24][CH:23]=[CH:22][CH:21]=1>CN(C=O)C.O>[CH3:18][C:13]1[NH:14][C:15]2[C:11]([CH:12]=1)=[CH:10][C:9]([NH:8][C:6]1[CH:5]=[CH:4][N:3]=[C:2]([NH:19][C:20]3[CH:25]=[CH:24][CH:23]=[CH:22][CH:21]=3)[N:7]=1)=[CH:17][CH:16]=2
Reactant: Nc1ccccc1
Reactant: Cc1cc2cc(Nc3ccnc(Cl)n3)ccc2[nH]1
Solvent: O
Solvent: CN(C)C=O
Product: Cc1cc2cc(Nc3ccnc(Nc4ccccc4)n3)ccc2[nH]1
Temperature: 60 °C
Reaction time: 5 h
Yield: 85 %

Procedure:
N-(2-chloropyrimidin-4-yl)-2-methyl-1H-indol-5-amine (0.1 mmol) and aniline (0.1 mmol) were dissolved in 0.5 ml DMF. To this was added p-TsOH monohydrate (0.2 mmol). The reaction mixture was stirred at 60° C. for 5 hours, diluted with water, and extracted with ethyl acetate. The organic layer was washed with water and brine sequentially, dried over anhydrous Na2SO4, and concentrated. The resulting residue was purified by column chromatography to provide the title product in a yield of 85%.
Reaction SMILES: [Cl:1][C:2]1[C:9]([O:10][C:11]2[C:19]3[N:18]=[N:17][NH:16][C:15]=3[CH:14]=[CH:13][C:12]=2[Cl:20])=[CH:8][C:7]([Cl:21])=[CH:6][C:3]=1[C:4]#[N:5].CC(C)([O-])C.[Li+].Cl[CH2:29][C:30]1[C:38]2[C:33](=[N:34][C:35]([NH:39][CH2:40][C:41]3[CH:46]=[CH:45][C:44]([O:47][CH3:48])=[CH:43][CH:42]=3)=[CH:36][CH:37]=2)[N:32]([CH2:49][C:50]2[CH:55]=[CH:54][C:53]([O:56][CH3:57])=[CH:52][CH:51]=2)[N:31]=1.[Cl-].[NH4+]>CN(C=O)C>[Cl:1][C:2]1[C:9]([O:10][C:11]2[C:19]3[N:18]=[N:17][N:16]([CH2:29][C:30]4[C:38]5[C:33](=[N:34][C:35]([NH:39][CH2:40][C:41]6[CH:42]=[CH:43][C:44]([O:47][CH3:48])=[CH:45][CH:46]=6)=[CH:36][CH:37]=5)[N:32]([CH2:49][C:50]5[CH:51]=[CH:52][C:53]([O:56][CH3:57])=[CH:54][CH:55]=5)[N:31]=4)[C:15]=3[CH:14]=[CH:13][C:12]=2[Cl:20])=[CH:8][C:7]([Cl:21])=[CH:6][C:3]=1[C:4]#[N:5]
Reactant: N#Cc1cc(Cl)cc(Oc2c(Cl)ccc3[nH]nnc23)c1Cl
Reactant: COc1ccc(CNc2ccc3c(CCl)nn(Cc4ccc(OC)cc4)c3n2)cc1
Agent: CC(C)(C)[O-]
Agent: [Cl-]
Agent: [Li+]
Solvent: CN(C)C=O
Product: COc1ccc(CNc2ccc3c(Cn4nnc5c(Oc6cc(Cl)cc(C#N)c6Cl)c(Cl)ccc54)nn(Cc4ccc(OC)cc4)c3n2)cc1
Temperature: 25 °C
Reaction time: 0.08 h

Procedure:
2,5-dichloro-3-[(5-chloro-1H-1,2,3-benzotriazol-4-yl)oxy]benzonitrile (90 mg, 0.265 mmol) and lithium tert-butoxide (22 mg, 0.278 mmol) were dissolved in DMF (1 mL) and the solution stirred for 5 minutes at room temperature. The reaction mixture was cooled to 0° C. and 3-(chloromethyl)-N,1-bis(4-methoxybenzyl)-1H-pyrazolo[3,4-b]pyridin-6-amine (112 mg, 0.265 mmol) in DMF (1.5 mL) was added. After the addition, the solution was allowed to warm to room temperature and stirred for 16 hours, after which saturated aqueous ammonium chloride (1 mL) was added and the mixture was extracted with ethyl acetate (2×15 mL). The combined organic fractions were washed with water (3×15 mL). The combined aqueous layers were back-extracted with EtOAc (25 mL) and the extracts subsequently washed with water (3×15 mL). The combined organic fractions were dried (MgSO4), filtered and the solvent was evaporated under reduced pressure. The resulting residue was purified by column chromatography on silica gel (12 g) eluting with 0-40% EtOAc/hexanes to afford the title compound. LRMS (M+1)=726.3.
Reaction SMILES: [C:1]([OH:5])(=O)[CH2:2][OH:3].[Cl:6][C:7]1[CH:8]=[C:9]([NH:21][C:22]2[C:31]3[C:26](=[CH:27][CH:28]=[CH:29][C:30]=3[O:32][CH2:33][CH2:34][NH:35][CH2:36][CH2:37][CH3:38])[N:25]=[CH:24][N:23]=2)[CH:10]=[CH:11][C:12]=1[O:13][CH2:14][C:15]1[CH:20]=[CH:19][CH:18]=[CH:17][N:16]=1>>[Cl:6][C:7]1[CH:8]=[C:9]([NH:21][C:22]2[C:31]3[C:26](=[CH:27][CH:28]=[CH:29][C:30]=3[O:32][CH2:33][CH2:34][N:35]([CH2:36][CH2:37][CH3:38])[C:1](=[O:5])[CH2:2][OH:3])[N:25]=[CH:24][N:23]=2)[CH:10]=[CH:11][C:12]=1[O:13][CH2:14][C:15]1[CH:20]=[CH:19][CH:18]=[CH:17][N:16]=1
Reactant: CCCNCCOc1cccc2ncnc(Nc3ccc(OCc4ccccn4)c(Cl)c3)c12
Reactant: O=C(O)CO
Product: CCCN(CCOc1cccc2ncnc(Nc3ccc(OCc4ccccn4)c(Cl)c3)c12)C(=O)CO
Yield: 26 %

Procedure:
The procedure described in Example 1 was repeated using glycolic acid and N-[3-chloro-4-(pyridin-2-ylmethoxy)phenyl]-5-[2-(propylamino)ethoxy]quinazolin-4-amine (obtained as described in Example 7, preparation of starting materials) to give the title compound in 26% yield; NMR spectrum (DMSO-d6) 0.84 (t, 3H), 1.53-1.65 (m, 2H), 3.26 (t, 2H), 3.95 (t, 2H), 4.14 (d, 2H), 4.38 (t, 1H), 4.47 (t, 2H), 4.53-4.58 (m, 1H), 5.36 (s, 1H), 7.24 (d, 1H), 7.31 (d, 1H), 7.39-7.44 (m, 2H), 7.63-7.67 (m, 2H), 7.76-7.81 (m, 1H), 7.92-7.96 (m, 1H), 8.05 (s, 1H), 8.51 (s, 1H), 8.66 (d, 1H), 9.87 (s, 1H); Mass spectrum MH+ 522.
Reaction SMILES: [CH3:1][C@@H:2]1[CH2:7][CH2:6][CH2:5][NH:4][C@@H:3]1[CH2:8][N:9]1[C:17](=[O:18])[C:16]2[C:11](=[CH:12][CH:13]=[CH:14][CH:15]=2)[C:10]1=[O:19].[F:20][C:21]1[CH:22]=[C:23]([CH3:31])[C:24]([I:30])=[C:25]([CH:29]=1)[C:26](O)=[O:27].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>CN(C=O)C.C(OCC)(=O)C>[F:20][C:21]1[CH:22]=[C:23]([CH3:31])[C:24]([I:30])=[C:25]([CH:29]=1)[C:26]([N:4]1[CH2:5][CH2:6][CH2:7][C@@H:2]([CH3:1])[C@H:3]1[CH2:8][N:9]1[C:17](=[O:18])[C:16]2[C:11](=[CH:12][CH:13]=[CH:14][CH:15]=2)[C:10]1=[O:19])=[O:27]
Reactant: C[C@@H]1CCCN[C@@H]1CN1C(=O)c2ccccc2C1=O
Reactant: Cc1cc(F)cc(C(=O)O)c1I
Agent: CN(C)C(On1nnc2cccnc21)=[N+](C)C
Agent: F[P-](F)(F)(F)(F)F
Solvent: CN(C)C=O
Solvent: CCOC(C)=O
Solvent: CCN(C(C)C)C(C)C
Product: Cc1cc(F)cc(C(=O)N2CCC[C@@H](C)[C@H]2CN2C(=O)c3ccccc3C2=O)c1I
Temperature: 25 °C
Reaction time: 1 h

Procedure:
A mixture of 2-(((2S,3R)-3-methylpiperidin-2-yl)methyl)isoindoline-1,3-dione (1.2 eq.), 5-fluoro-2-iodo-3-methylbenzoic acid (1 eq.), DIPEA (3 eq.), and HATU (1 eq.) in DMF (0.2 M) was stirred at rt for 1 h. The reaction mixture was diluted with ethyl acetate and washed with satd. NaHCO3 and brine. The organic layer was separated, dried with MgSO4, and concentrated in vacuo. The crude product was purified by chromatography on silica gel (EtOAc/hexanes) to afford the title compound.
Reaction SMILES: [CH3:1][C:2]1[CH:6]=[CH:5][N:4]([C:7]2[CH:12]=[CH:11][C:10]([OH:13])=[CH:9][CH:8]=2)[N:3]=1.Cl.Cl[CH2:16][CH2:17][N:18]1[CH2:23][CH2:22][CH2:21][CH2:20][CH2:19]1>>[CH3:1][C:2]1[CH:6]=[CH:5][N:4]([C:7]2[CH:12]=[CH:11][C:10]([O:13][CH2:16][CH2:17][N:18]3[CH2:23][CH2:22][CH2:21][CH2:20][CH2:19]3)=[CH:9][CH:8]=2)[N:3]=1
Reactant: ClCCN1CCCCC1
Reactant: Cc1ccn(-c2ccc(O)cc2)n1
Agent: Cl
Product: Cc1ccn(-c2ccc(OCCN3CCCCC3)cc2)n1
Yield: 54 %

Procedure:
The title compound was prepared from 4-(3-methyl-pyrazol-1-yl)-phenol (0.1 g, 0.61 mmol) and 1-(2-chloroethyl)piperidine hydrochloride (0.23 g, 1.25 mmol) using the general procedure C with a yield of 54% (90 mg); 1H NMR (400 MHz, CDCl3) 7.70 (d, J=2 Hz, 1H), 7.52 (d, J=9.2 Hz, 2H), 6.96 (d, J=9.2 Hz, 2H), 6.20 (d, J=2 Hz, 1H), 4.12 (t, J=12, 6 Hz, 2H), 2.78 (t, J=12, 6 Hz, 2H), 2.52 (br, 4H), 2.37 (s, 3H), 1.61-1.47 (m, 6H); LC/MS (ESI): 97%.
Reaction SMILES: [Si:1]([O:8][CH2:9][C:10]1[CH:11]=[C:12]([CH:29]=[CH:30][C:31]=1[CH2:32][O:33][Si:34]([C:37]([CH3:40])([CH3:39])[CH3:38])([CH3:36])[CH3:35])[O:13][CH2:14][C:15]1[S:19][C:18](/[C:20](/[CH2:27][CH3:28])=[CH:21]/[CH2:22][CH2:23][C:24]([OH:26])=[O:25])=[CH:17][CH:16]=1)([C:4]([CH3:7])([CH3:6])[CH3:5])([CH3:3])[CH3:2].[C:41](=O)([O-])[O-].[K+].[K+].IC>CC(=O)CC>[Si:1]([O:8][CH2:9][C:10]1[CH:11]=[C:12]([CH:29]=[CH:30][C:31]=1[CH2:32][O:33][Si:34]([C:37]([CH3:39])([CH3:38])[CH3:40])([CH3:35])[CH3:36])[O:13][CH2:14][C:15]1[S:19][C:18](/[C:20](/[CH2:27][CH3:28])=[CH:21]/[CH2:22][CH2:23][C:24]([O:26][CH3:41])=[O:25])=[CH:17][CH:16]=1)([C:4]([CH3:7])([CH3:6])[CH3:5])([CH3:3])[CH3:2]
Reactant: CC/C(=C\CCC(=O)O)c1ccc(COc2ccc(CO[Si](C)(C)C(C)(C)C)c(CO[Si](C)(C)C(C)(C)C)c2)s1
Reactant: O=C([O-])[O-]
Agent: [K+]
Solvent: CCC(C)=O
Solvent: CI
Product: CC/C(=C\CCC(=O)OC)c1ccc(COc2ccc(CO[Si](C)(C)C(C)(C)C)c(CO[Si](C)(C)C(C)(C)C)c2)s1

Procedure:
4.3 g (7.1 mmol) of (E)-5-{5-[3,4-bis(tert-butyldimethylsilanyloxymethyl)phenoxymethyl]-2-thienyl}-4-heptenoic acid are dissolved in 70 mL of 2-butanone, and 1.1 g of potassium carbonate (7.8 mmol) and 2.2 mL of iodomethane (35 mmol) are added. The medium is refluxed for 12 hours, cooled and filtered. The filtrate is concentrated under reduced pressure and then purified by chromatography on a column of silica. A yellow oil is obtained (m=4.34 g; Y=98%).
Reaction SMILES: [CH:1]1[C:13]2[CH:12]([CH2:14][O:15][C:16]([N:18]3[CH:23]4[CH2:24][N:25](C(OC(C)(C)C)=O)[CH2:26][CH:19]3[CH2:20][O:21][CH2:22]4)=[O:17])[C:11]3[C:6](=[CH:7][CH:8]=[CH:9][CH:10]=3)[C:5]=2[CH:4]=[CH:3][CH:2]=1.[ClH:34].CCOCC>O1CCOCC1>[ClH:34].[CH:10]1[C:11]2[CH:12]([CH2:14][O:15][C:16]([N:18]3[CH:23]4[CH2:24][NH:25][CH2:26][CH:19]3[CH2:20][O:21][CH2:22]4)=[O:17])[C:13]3[C:5](=[CH:4][CH:3]=[CH:2][CH:1]=3)[C:6]=2[CH:7]=[CH:8][CH:9]=1
Reactant: CC(C)(C)OC(=O)N1CC2COCC(C1)N2C(=O)OCC1c2ccccc2-c2ccccc21
Agent: Cl
Solvent: CCOCC
Solvent: C1COCCO1
Product: O=C(OCC1c2ccccc2-c2ccccc21)N1C2CNCC1COC2
Temperature: 25 °C
Reaction time: 1.5 h
Yield: 92 %

Procedure:
3-Oxa-7,9-diaza-bicyclo[3.3.1]nonane-7,9-dicarboxylic acid 7-tert-butyl ester 9-(9H-fluoren-9-ylmethyl) ester (1.29 g, 2.76 mmol) was dissolved into a 4N solution of HCl in 1,4-dioxane (10 mL). The resulting mixture was stirred at RT for 1.5 hours, and then concentrated under vacuum to give a colorless oil. The oil was taken up with Et2O (20 ml) and a precipitation occurred. The precipitate was filtered off, washed with Et2O (2×) and dried under vacuum to give the title compound as a white powder (1.06 g, 92%). 1H NMR (300 MHz, DMSO-d6) δ 9.81 (s, 1H), 8.22 (s, 1H), 7.90 (d, J=7.3 Hz, 2H), 7.64 (d, J=7.4 Hz, 2H), 7.47-7.31 (m, 4H), 4.61-4.44 (m, 2H), 4.31 (t, J=6.0 Hz, 1H), 4.07 (s, 1H), 4.02-3.84 (m, 3H), 3.62-3.53 (m, 1H), 3.51-3.37 (m, 3H), 3.09-2.90 (m, 2H). HPLC (max plot) 97.4%; Rt 2.94 min. UPLC/MS: (MS+) 351.3 ([M+H]+).
Reaction SMILES: [CH3:1][O:2][C:3]1[CH:40]=[CH:39][C:6]([CH2:7][N:8]([CH2:30][C:31]2[CH:36]=[CH:35][C:34]([O:37][CH3:38])=[CH:33][CH:32]=2)[C:9]2[N:14]=[CH:13][C:12]([C:15]3[C:16]4[CH2:29][CH2:28][NH:27][C:17]=4[N:18]=[C:19]([N:21]4[CH2:26][CH2:25][O:24][CH2:23][CH2:22]4)[N:20]=3)=[CH:11][N:10]=2)=[CH:5][CH:4]=1.Br[C:42]1[CH:43]=[C:44]([C:48]([N:50]2[CH2:55][CH2:54][N:53]([CH2:56][CH3:57])[CH2:52][CH2:51]2)=[O:49])[CH:45]=[N:46][CH:47]=1>>[CH3:38][O:37][C:34]1[CH:33]=[CH:32][C:31]([CH2:30][N:8]([CH2:7][C:6]2[CH:5]=[CH:4][C:3]([O:2][CH3:1])=[CH:40][CH:39]=2)[C:9]2[N:10]=[CH:11][C:12]([C:15]3[C:16]4[CH2:29][CH2:28][N:27]([C:42]5[CH:43]=[C:44]([C:48]([N:50]6[CH2:51][CH2:52][N:53]([CH2:56][CH3:57])[CH2:54][CH2:55]6)=[O:49])[CH:45]=[N:46][CH:47]=5)[C:17]=4[N:18]=[C:19]([N:21]4[CH2:26][CH2:25][O:24][CH2:23][CH2:22]4)[N:20]=3)=[CH:13][N:14]=2)=[CH:36][CH:35]=1
Reactant: COc1ccc(CN(Cc2ccc(OC)cc2)c2ncc(-c3nc(N4CCOCC4)nc4c3CCN4)cn2)cc1
Reactant: CCN1CCN(C(=O)c2cncc(Br)c2)CC1
Product: CCN1CCN(C(=O)c2cncc(N3CCc4c(-c5cnc(N(Cc6ccc(OC)cc6)Cc6ccc(OC)cc6)nc5)nc(N5CCOCC5)nc43)c2)CC1

Procedure:
Using bis-(4-methoxy-benzyl)-[5-(2-morpholin-4-yl-6,7-dihydro-5H-pyrrolo[2,3-d]pyrimidin-4-yl)-pyrimidin-2-yl]-amine (50 mg) and (5-bromo-pyridin-3-yl)-(4-ethyl-piperazin-1-yl)-methanone (42 mg, prepared according to Step A in Example 1-D-25) instead of 4-chloropicolinic acid t-butylamide, in the same manner as Example 1-D-07, a crude product of [5-(4-{2-[bis-(4-methoxy-benzyl)-amino]-pyrimidin-5-yl}-2-morpholin-4-yl-5,6-dihydro-pyrrolo[2,3-d]pyrimidin-7-yl)-pyridin-3-yl]-(4-ethyl-piperazin-1-yl)-methanone was obtained, and then the PMB groups were removed according to the above Deprotection method 3, to obtain the desired compound (D-230) as a pale yellow powder (46 mg, 96%).