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Structure of 55876-84-1
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The BI-3802 was designed by Boehringer Ingelheim and could be obtained free of charge through the Boehringer Ingelheim open innovation portal opnMe.com, associated with its negative control.
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CAS No. : | 55876-84-1 |
Formula : | C8H8BrNO2 |
M.W : | 230.06 |
SMILES Code : | O=C(OC)C1=NC=C(CBr)C=C1 |
MDL No. : | MFCD07367952 |
InChI Key : | SIMKVUKTEMRUSF-UHFFFAOYSA-N |
Pubchem ID : | 19699469 |
GHS Pictogram: |
![]() ![]() |
Signal Word: | Danger |
Hazard Statements: | H302-H314 |
Precautionary Statements: | P501-P260-P270-P264-P280-P303+P361+P353-P301+P330+P331-P363-P301+P312+P330-P304+P340+P310-P305+P351+P338+P310-P405 |
Class: | 8 |
UN#: | 1759 |
Packing Group: | Ⅱ |
Num. heavy atoms | 12 |
Num. arom. heavy atoms | 6 |
Fraction Csp3 | 0.25 |
Num. rotatable bonds | 3 |
Num. H-bond acceptors | 3.0 |
Num. H-bond donors | 0.0 |
Molar Refractivity | 48.35 |
TPSA ? Topological Polar Surface Area: Calculated from |
39.19 Ų |
Log Po/w (iLOGP)? iLOGP: in-house physics-based method implemented from |
1.96 |
Log Po/w (XLOGP3)? XLOGP3: Atomistic and knowledge-based method calculated by |
2.05 |
Log Po/w (WLOGP)? WLOGP: Atomistic method implemented from |
1.61 |
Log Po/w (MLOGP)? MLOGP: Topological method implemented from |
1.13 |
Log Po/w (SILICOS-IT)? SILICOS-IT: Hybrid fragmental/topological method calculated by |
2.2 |
Consensus Log Po/w? Consensus Log Po/w: Average of all five predictions |
1.79 |
Log S (ESOL):? ESOL: Topological method implemented from |
-2.73 |
Solubility | 0.429 mg/ml ; 0.00186 mol/l |
Class? Solubility class: Log S scale |
Soluble |
Log S (Ali)? Ali: Topological method implemented from |
-2.5 |
Solubility | 0.725 mg/ml ; 0.00315 mol/l |
Class? Solubility class: Log S scale |
Soluble |
Log S (SILICOS-IT)? SILICOS-IT: Fragmental method calculated by |
-3.37 |
Solubility | 0.099 mg/ml ; 0.000431 mol/l |
Class? Solubility class: Log S scale |
Soluble |
GI absorption? Gatrointestinal absorption: according to the white of the BOILED-Egg |
High |
BBB permeant? BBB permeation: according to the yolk of the BOILED-Egg |
Yes |
P-gp substrate? P-glycoprotein substrate: SVM model built on 1033 molecules (training set) |
No |
CYP1A2 inhibitor? Cytochrome P450 1A2 inhibitor: SVM model built on 9145 molecules (training set) |
Yes |
CYP2C19 inhibitor? Cytochrome P450 2C19 inhibitor: SVM model built on 9272 molecules (training set) |
No |
CYP2C9 inhibitor? Cytochrome P450 2C9 inhibitor: SVM model built on 5940 molecules (training set) |
No |
CYP2D6 inhibitor? Cytochrome P450 2D6 inhibitor: SVM model built on 3664 molecules (training set) |
No |
CYP3A4 inhibitor? Cytochrome P450 3A4 inhibitor: SVM model built on 7518 molecules (training set) |
No |
Log Kp (skin permeation)? Skin permeation: QSPR model implemented from |
-6.25 cm/s |
Lipinski? Lipinski (Pfizer) filter: implemented from |
0.0 |
Ghose? Ghose filter: implemented from |
None |
Veber? Veber (GSK) filter: implemented from |
0.0 |
Egan? Egan (Pharmacia) filter: implemented from |
0.0 |
Muegge? Muegge (Bayer) filter: implemented from |
0.0 |
Bioavailability Score? Abbott Bioavailability Score: Probability of F > 10% in rat |
0.55 |
PAINS? Pan Assay Interference Structures: implemented from |
0.0 alert |
Brenk? Structural Alert: implemented from |
1.0 alert: heavy_metal |
Leadlikeness? Leadlikeness: implemented from |
No; 1 violation:MW<1.0 |
Synthetic accessibility? Synthetic accessibility score: from 1 (very easy) to 10 (very difficult) |
2.02 |
* All experimental methods are cited from the reference, please refer to the original source for details. We do not guarantee the accuracy of the content in the reference.
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
66% | With N-Bromosuccinimide; 2,2'-azobis(isobutyronitrile); In tetrachloromethane; for 5h;Reflux; | A mixture of methyl 2-methylisonicotinate (leq) and a,a'-Azoisobutyronitrile (AIBN) (10%) was dissolved in carbontetrachloride (CC14). The solution was heated at 48C and N-bromosuccinimide (NBS) (1.1 eq) solution in CC14 was added drop wise and stirred for 5 hours. The reaction was cooled to room temperature and the solvent evaporated. The mixture was then extracted using dichloromethane and water followed by washing the organic layer with brine. The organic layer was dried over sodium sulfate, filtered, evaporated and the crude product was purified using SiO2 column chromatography and eluted with the solvent system EtOAc: hexanes = 2:3 to obtain pure product as white powder and the yield was 66%. 1H-NMR (400 MHz, DMSO-d6): d 8.78 (t, J= 1.48 Hz, 1H), 8.06 (d, J= 1.36 Hz, 2H), 4.82 (s, 2H), 3.89 (s, 3H). HRMS (ESI) m/z found 229.98 [M+H]+, Calculated 230.0586 [M]+. |
57% | With N-Bromosuccinimide; 2,2'-azobis(isobutyronitrile); In tetrachloromethane; at 80℃; for 16h; | 5-(Bromomethyl)pyridine-2-carboxylate In a 500-mL round bottom flask, NBS (14.13 g, 79.38 mmol, 1.20 equiv) and AIBN (217 mg, 1.32 mmol, 0.02 equiv) were added to a solution of methyl 5-methylpyridine-2-carboxylate (10 g, 66.15 mmol, 1.00 equiv) in CCl4 (200 mL) at room temperature. The resulting solution was stirred for 16 h at 80 C. After the reaction was done, the reaction mixture was concentrated under reduced pressure. The residue was purified in a silica gel column eluting with ethyl acetate in petroleum ether (5% to 25% gradient) to afford methyl 5-(bromomethyl)pyridine-2-carboxylate (9.6 g, 57%) as yellow solid. MS: m/z=229.9 [M+H]+ |
50% | With N-Bromosuccinimide;VAZO; In tetrachloromethane; for 18h;Heating / reflux; | To a solution of 5-methylpyridirie-2-carboxylic acid methyl ester (140 mg, 0.93 mmol) in CCl4 (8 mL) was added NBS (181 mg, 1.02 mmol) and VAZO (23 mg, 0.09 mmol). The reaction was stirred at reflux for 18 h. Standard work-up and purification by flash chromatography on silica gel (10% ether in CH2Cl2) afforded 5-bromomethylpyridine-2- carboxylic acid methyl ester (107 mg, 50%). |
24% | With N-Bromosuccinimide; dibenzoyl peroxide; In tetrachloromethane; for 18h;Reflux; | INTERMEDIATE 37 - PREPARATION of Methyl 5-(bromomethyl)picolinate. To a mixture of methyl 5-methylpicolinate (1.25 g; 8.27 mmol) in carbon tetrachloride (45 mL) was added N-bromosuccinimide (1.78 g, 9.92 mmol) and benzoyl peroxide (0.205 g; 0.827 mmol). The mixture was refluxed for 18 hours and the resulting suspension was concentrated under reduced pressure. The residue was purified by flash chromatography on silica gel (eluent 0 to 8% ethyl acetate in dichloromethane) to 0.450g (24%) of methyl 5- (bromomethyl)picolinate as a beige solid.ESI/APCI(+): 230 (M+H). |
24% | With N-Bromosuccinimide; dibenzoyl peroxide; In tetrachloromethane; for 18h;Reflux; | To a mixture of methyl 5-methylpicolinate (1.25 g; 8.27 mmol) in carbon tetrachloride (45 mL) was added N-bromosuccinimide (1.78 g, 9.92 mmol) and benzoyl peroxide (0.205 g; 0.827 mmol). The mixture was refluxed for 18 hours and the resulting suspension was concentrated under reduced pressure. The residue was purified by flash chromatography on silica gel (eluent 0 to 8% ethyl acetate in dichloromethane) to 0.450 g (24%) of methyl 5-(bromomethyl)picolinate as a beige solid. [0623] ESI/APCI(+): 230 (M+H). |
11% | With N-Bromosuccinimide; dibenzoyl peroxide; In tetrachloromethane;Reflux; | Example 8. Synthesis of 1-548-101. Into a 2000-mL 4-necked round-bottom flask, was placed a solution of methyl 5-methylpicolinate (85 g, 539.68 mmol, 1.00 equiv, 96%) in CC14 (1000 mL), N-bromosuccinimide (1 10 g, 617.98 mmol, 1.10 equiv), and benzoyl peroxide (3.5 g, 14.45 mmol, 0.03 equiv). The resulting solution was heated to reflux overnight. The solids were removed by filtration. The filtrate was concentrated under vacuum. The residue was applied onto a silica gel column with ethyl acetate/petroleum ether (1 :30-l :5). This resulted in 15 g (1 1%) of methyl 5-(bromomethyl)picolinate as a light-yellow solid.LC-MS: (ES, m/z): 232 [M+H]+ |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
40% | With N-ethyl-N,N-diisopropylamine;tetrakis(triphenylphosphine) palladium(0); In 1,2-dimethoxyethane; water; at 130℃; for 0.333333h;Microwave irradiation; | INTERMEDIATE 38 - PREPARATION of methyl 5-(3-fluorobenzyl)picolinate. A mixture of 3-fluorophenylboronic acid (0.319 g; 2.28 mmol), methyl 5- (bromomethyl)picolinate (0.350 g; 0.230 mmol), tetrakis-(triphenylphosphine)-palladium(0) (0.175; 0.152 mmol) and N,N diisopropylethylamine (0.524 g; 3.04 mmol) in dimethoxyethane (9 mL) and water (3 mL) was irradiated in a microwave oven at 130°C for 20 minutes. The resulting solution was partitioned between water and ethyl acetate. The organic layer was separated and concentrated under reduced pressure. The crude residue was purified by flash chromatography on silica gel (eluent 1 to 10 percent ethyl acetate in dichlomethane) to afford 0.149 g (40percent) of the title compound as a yellow oil.ESI/APCI(+): 246 (M+H), 268(M+Na). |
40% | With tetrakis(triphenylphosphine) palladium(0); N-ethyl-N,N-diisopropylamine; In 1,2-dimethoxyethane; water; at 130℃; for 0.333333h;Microwave irradiation; | A mixture of 3-fluorophenylboronic acid (0.319 g; 2.28 mmol), <strong>[55876-84-1]methyl 5-(bromomethyl)picolinate</strong> (0.350 g; 0.230 mmol), tetrakis-(triphenylphosphine)-palladium(0) (0.175; 0.152 mmol) and N,N diisopropylethylamine (0.524 g; 3.04 mmol) in dimethoxyethane (9 mL) and water (3 mL) was irradiated in a microwave oven at 130° C. for 20 minutes. The resulting solution was partitioned between water and ethyl acetate. The organic layer was separated and concentrated under reduced pressure. The crude residue was purified by flash chromatography on silica gel (eluent 1 to 10percent ethyl acetate in dichlomethane) to afford 0.149 g (40percent) of the title compound as a yellow oil. [0625] ESI/APCI(+): 246 (M+H), 268 (M+Na). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
92% | With potassium carbonate; In acetonitrile; at 85℃; for 2h; | Example 9. Synthesis of 1-548-102. Into a 50-mL round-bottom flask, was placed a solution of <strong>[55876-84-1]methyl 5-(bromomethyl)picolinate</strong> (500 mg, 2.09 mmol, 1.00 equiv, 96percent) in acetonitrile (20 mL), 3-ethylphenol (280 mg, 2.29 mmol, 1.05 equiv), and potassium carbonate (900 mg, 6.51 mmol, 3.00 equiv). The resulting solution was stirred for 2 h at 85°C. The mixture was concentrated under vacuum. The residue was diluted with 30 mL of water and extracted with 2x20 mL of ethyl acetate and the organic layers combined and dried over anhydrous sodium sulfate and concentrated under vacuum. This resulted in 0.6 g (92percent) of methyl 5-((3- ethylphenoxy)methyl)picolinate as a brown solid.LC-MS: (ES, m/z): 272 [M+H]+ |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
89% | With potassium carbonate; In acetonitrile; for 2h;Reflux; | Example 12. Synthesis of 1-554-1. Into a 50-mL round-bottom flask, was placed a solution of <strong>[55876-84-1]methyl 5-(bromomethyl)picolinate</strong> (500 mg, 2.17 mmol, 1.00 equiv) in CH3CN (25 mL), m-cresol (250 mg, 2.31 mmol, 1.05 equiv), and potassium carbonate (900 mg, 6.52 mmol, 3.00 equiv). The solution was heated to reflux for 2 h in an oil bath. The resulting mixture was concentrated under vacuum and diluted with 50 mL of H20. The resulting solution was extracted with 3x20 mL of ethyl acetate and the organic layers combined and dried over anhydrous sodium sulfate and concentrated under vacuum. This resulted in 0.6 g (89percent) of methyl 5-(m- tolyloxymethyl)picolinate as a brown solid.LC-MS: (ES, m/z): [M+H]+ 258 |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
77% | With potassium carbonate; In acetonitrile; at 85℃; for 1h; | Example 15. Synthesis of 1-546-1. Into a 50-mL round-bottom flask, was placed <strong>[55876-84-1]methyl 5-(bromomethyl)picolinate</strong> (500 mg, 2.17 mmol, 1.00 equiv), 3-bromo-5-fluorophenol (440 mg, 2.30 mmol, 1.06 equiv), CH3CN (6 mL), and potassium carbonate (900 mg, 6.52 mmol, 3.00 equiv). The resulting solution was stirred for 60 min at 85°C. The mixture was concentrated under vacuum and the residue was diluted with 20 mL of H20. The resulting solution was extracted with 3x20 mL of ethyl acetate and the organic layers combined and dried over anhydrous sodium sulfate. The solids were filtered out. The resulting mixture was concentrated under vacuum. This resulted in 0.62 g (77percent) of methyl 5-((3-bromo-5- fluorophenoxy)methyl)picolinate as a yellow solid.LC-MS: ( + |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
74% | With potassium carbonate; In acetonitrile; at 85℃; for 0.5h; | Example 18. Synthesis of 1-549-1. Into a 50-mL round-bottom flask, was placed <strong>[55876-84-1]methyl 5-(bromomethyl)picolinate</strong> (500 mg, 2.17 mmol, 1.00 equiv), 3-(trifluoromethoxy)phenol (410 mg, 2.30 mmol, 1.06 equiv), CH3CN (6 mL), and potassium carbonate (900 mg, 6.52 mmol, 3.00 equiv). The resulting solution was stirred for 30 min at 85°C in an oil bath. The resulting mixture was concentrated under vacuum. The residue was diluted with 20 mL of H20 and extracted with 2x20 mL of ethyl acetate and the organic layers combined and dried over anhydrous sodium sulfate. The solids were filtered out. The filtrate was concentrated under vacuum. This resulted in 0.56 g (74percent) of methyl 5-((3-(trifluoromethoxy)phenoxy)methyl)picolinate as a yellow-tan solid. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
49% | With N-ethyl-N,N-diisopropylamine; In acetonitrile; at 20℃; for 4h; | Methyl 5-[(4-methylpiperazin-1-yl)methyl]pyridine-2-carboxylate In a 50-mL round bottom flask with magnetic stir bar, <strong>[55876-84-1]methyl 5-(bromomethyl)pyridine-2-carboxylate</strong> (940 mg, 4.09 mmol, 1.00 equiv) and 1-methylpiperazine (449.6 mg, 4.49 mmol, 1.10 equiv) were dissolved in ACN (10 mL), to which DIEA (790.8 mg, 6.12 mmol, 1.50 equiv) was added at room temperature. The resulting solution was stirred for 4 h at room temperature. After the reaction was done, the reaction mixture was concentrated under reduced pressure. The residue was purified in a silica gel column eluting with methanol in dichloromethane (1percent to 10percent gradient) to afford methyl 5-[(4-methylpiperazin-1-yl)methyl]pyridine-2-carboxylate (500 mg, 49percent) as brown solid. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
IN NaOH solution was added to a THF (lmL) solution of methyl 5-(bromomethyl) pyridine-2-carboxylate {Ark Pharm, catAK153186, 20 mg, 0.08 mmol) and the mixture was allowed to stir at rt for lh. The mixture was acidified with IN HC1 solution until pH = 4, and then the mixture was extracted with DCM. The organic layers were combined, dried and concentrated. To the residue was added 2.0 M oxalyl chloride in DCM (0.10 mL, 0.20 mmol) and N,N-dimethylformamide (0.6 \L, 0.008 mmol) at 0 °C under N2. The mixture was allowed to stir at rt for 2h, and then the mixture was concentrated and the residue was used for next step without further purification. |
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