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Consistency checking: file format, valence, and structural integrity.
Removal of inorganics and separation of mixtures into individual components.
Removal of salts and counterions (the salts list is available in Additional file
Conversion of tautomers and mesomers to consistent representations. Examples include: nitro and azide mesomers, keto–enol tautomers, enamine–imine tautomers, enol-ketenes, etc. [37 (link)–39 ].
Neutralization of charged structures and removal of stereochemistry information.
Addition of explicit hydrogen atoms and aromatization of structures.
Removal of duplicates using InChIKey [40 ].
Original substances (left) and processed, linked chemical structures (right) indicating similarities and differences between the QSAR-Ready and MS-Ready workflows.
Example 20
Following step 1 in the preparation of I-49, tert-butyl 3-(7-bromo-4-chloro-8-methoxyquinolin-2-yl) benzoate was prepared from Intermediate 17.
Step 1: tert-Butyl 3-(7-bromo-4-(1H-imidazol-1-yl)-8-methoxyquinolin-2-yl)benzoate. To a mixture of tert-butyl 3-(7-bromo-4-chloro-8-methoxyquinolin-2-yl) benzoate (125 mg) and Cs2CO3 (136.8 mg) in DMF (2 mL) was added imidazole (96 mg). The suspended solution was stirred and heated at 130° C. over 2 h. Aqueous work-up with EtOAc and a column chromatography eluting with EtOAc/Hexane afforded the desired product tert-butyl 3-(7-bromo-4-(1H-imidazol-1-yl)-8-methoxyquinolin-2-yl) benzoate (120 mg) (MS: [M+1]+ 480).
Step 2: 3-(7-Bromo-4-(1H-imidazol-1-yl)-8-methoxyquinolin-2-yl)benzoic acid. To a solution of tert-butyl 3-(7-bromo-4-(1H-imidazol-1-yl)-8-methoxyquinolin-2-yl)benzoate (65 mg) in DCM (0.2 mL) and MeOH (0.2 mL) was added TFA (0.4 mL). The resultant solution was stirred over 5 h and concentrated to dryness. The resultant oily residue was suspended in water (0.5 mL) and lyophilized to afford the title compound 3-(7-bromo-4-(1H-imidazol-1-yl)-8-methoxyquinolin-2-yl) benzoic acid (60 mg) as light brown powder (MS: [M+1]+ 424).
Example 93
Methyl 2-acrylamido-6-(2-((4-(4-methylpiperazin-1-yl)phenyl)amino)quinazolin-8-yl)benzoate (21.2 mg) was prepared as described for (S)—N-(3-(2-((4-((1-acetylpyrrolidin-3-yl)oxy)phenyl)amino)quinazolin-8-yl)phenyl)acrylamide. LRMS (M+H+) m/z calculated 523.2, found 523.2. 1H NMR (CD3OD, 400 MHz) δ 9.13 (s, 1H), 8.34 (d, 1H), 7.65-7.83 (m, 3H), 7.54-7.57 (m, 2H), 7.41-7.44 (m, 1H), 7.28 (d, 1H), 6.77 (d, 2H), 6.39-6.42 (m, 2H), 5.83-5.87 (m, 1H), 3.13-3.18 (m, 7H), 2.90-2.94 (m, 4H), 2.60 (s, 3H).
Example 21
7-Bromo-4-chloro-8-methoxy-2-phenylquinoline was prepared following step 1 in the preparation procedure of methyl 3-(4-chloro-7-(trifluoromethyl)quinolin-2-yl)benzoate.
To a solution of 7-bromo-4-chloro-8-methoxy-2-phenylquinoline (63 mg) in DMF (2.0 mL) were added imidazole (129 mg) and Cs2CO3 (62 mg). The resultant mixture was heated at 80° C. overnight. The reaction mixture was diluted with water (4 mL) to precipitate the desired product. Isolation of the product and rinsing with water (2 mL) afforded the title compound (55 mg) 7-bromo-4-(1H-imidazol-1-yl)-8-methoxy-2-phenylquinoline (MS: [M+1]+ 380).
Example 3
Combined tert-butyl 2-[1-[2-[3-(1-cyano-1-methyl-ethyl)phenyl]-6-methyl-4-oxo-chromen-8-yl]ethylamino]benzoate (110.0 mg, 210.5 μmol) and TFA (3.0 g, 2.0 mL, 26 mmol) in DCM (2 mL) and heated at 40° C. for 3 hours. Concentrated the reaction and purified using a C-18 column, eluted with 10-90% acetonitrile in water (0.1% TFA additive), to give the product (45.0 mg, 46%). MS ES+ m/z 467 [M+H]+.
Example 94
Methyl 2-((8-(3-acrylamidophenyl)quinazolin-2-yl)amino)-5-(4-methylpiperazin-1-yl)benzoate (10.9 mg) was prepared as described for (S)—N-(3-(2-((4-((1-acetylpyrrolidin-3-yl)oxy)phenyl)amino)quinazolin-8-yl)phenyl)acrylamide. LRMS (M+H+) m/z calculated 523.2, found 523.2. 1H NMR (CD3OD, 400 MHz) δ7.69 (s, 1H), 7.44 (d, 1H), 7.40-7.43 (m, 2H), 7.25-7.28 (m, 3H), 7.09-7.13 (m, 2H), 6.98-7.03 (m, 2H), 6.24-6.28 (m, 2H), 5.64-5.68 (m, 1H), 3.19-3.24 (m, 3H), 3.08-3.17 (m, 4H), 2.67-2.69 (m, 4H), 2.37 (s, 3H).