Structure of 1174321-06-2
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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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Evaluation of Pyrazinamide and Pyrazinoic Acid Analogues for Control of Key Weeds in Multiple Crops
Gregory R. Armel ; James T. Brosnan ; Nilda R. Burgos ; Peter J. Porpiglia ; Jose J. Vargas ;
Abstract: Numerous similarities exist between the structure–activity relationships of pharmaceutical drugs and pesticides, creating the potential for finding new crop management tools with novel mechanisms of action. Analogues of pyrazinamide and its active metabolite pyrazinoic acid were evaluated on a variety of monocot and dicot species to assess their potential as commercial herbicides. Six analogues, applied postemergence at 3 kg ai/ha, controlled yellow nutsedge (Cyperus esculentus) ≥ the commercial standards bentazon or imazethapyr. The compound 5-fluoropyrazine-2-carboxylic acid provided between 71 and 95% control of barnyardgrass (Echinochloa crus-galli) and yellow nutsedge with only modest injury (8–25%) to soybean (Glycine max). A similar compound containing a bromine atom in the 5-position controlled yellow nutsedge greater than bentazon and affected soybean, sweet corn (Zea mays convar. saccharata var. rugosa), and rice (Oryza sativa) in a similar fashion to bentazon as well. The herbicidal sites of action targeted by these analogues of pyrazinamide and pyrazinoic acid are unknown, but it is hypothesized that they may be disrupting targets in the biosynthesis pathways of nicotinamide adenine dinucleotide (NAD) and/or ethylene.
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Keywords: herbicide ; rice ; pyrazinamide ; pharmaceutical ; prodrug ; soybean ; sweet corn
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Purchased from AmBeed: 23688-89-3 ; 86873-60-1 ; 54013-04-6 ; 374068-01-6 ; 40155-43-9 ; 36070-80-1 ; 40155-42-8 ; 312736-49-5 ; 356783-15-8 ; 34604-60-9 ; 27398-39-6 ; 21279-64-1 ; 38275-61-5 ; 1211533-09-3 ; 876161-05-6 ; 5326-23-8 ; 1174321-06-2 ; 5096-73-1 ; 1060814-50-7 ; 1211584-50-7
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CAS No. : | 1174321-06-2 |
Formula : | C6H4F2N2O2 |
M.W : | 174.11 |
SMILES Code : | O=C(C1=NC=C(C(F)F)N=C1)O |
MDL No. : | MFCD20640530 |
InChI Key : | UYWJPTNAOQSWOS-UHFFFAOYSA-N |
Pubchem ID : | 57468575 |
GHS Pictogram: |
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Signal Word: | Warning |
Hazard Statements: | H302-H315-H319-H335 |
Precautionary Statements: | P261-P305+P351+P338 |
Num. heavy atoms | 12 |
Num. arom. heavy atoms | 6 |
Fraction Csp3 | 0.17 |
Num. rotatable bonds | 2 |
Num. H-bond acceptors | 6.0 |
Num. H-bond donors | 1.0 |
Molar Refractivity | 34.06 |
TPSA ? Topological Polar Surface Area: Calculated from |
63.08 Ų |
Log Po/w (iLOGP)? iLOGP: in-house physics-based method implemented from |
0.71 |
Log Po/w (XLOGP3)? XLOGP3: Atomistic and knowledge-based method calculated by |
0.3 |
Log Po/w (WLOGP)? WLOGP: Atomistic method implemented from |
1.63 |
Log Po/w (MLOGP)? MLOGP: Topological method implemented from |
-0.26 |
Log Po/w (SILICOS-IT)? SILICOS-IT: Hybrid fragmental/topological method calculated by |
1.16 |
Consensus Log Po/w? Consensus Log Po/w: Average of all five predictions |
0.71 |
Log S (ESOL):? ESOL: Topological method implemented from |
-1.35 |
Solubility | 7.84 mg/ml ; 0.045 mol/l |
Class? Solubility class: Log S scale |
Very soluble |
Log S (Ali)? Ali: Topological method implemented from |
-1.19 |
Solubility | 11.3 mg/ml ; 0.065 mol/l |
Class? Solubility class: Log S scale |
Very soluble |
Log S (SILICOS-IT)? SILICOS-IT: Fragmental method calculated by |
-1.63 |
Solubility | 4.09 mg/ml ; 0.0235 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) |
No |
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 |
-7.15 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 |
1.0 |
Bioavailability Score? Abbott Bioavailability Score: Probability of F > 10% in rat |
0.56 |
PAINS? Pan Assay Interference Structures: implemented from |
0.0 alert |
Brenk? Structural Alert: implemented from |
0.0 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) |
1.85 |
* 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 |
---|---|---|
88% | With trifluoroacetic acid; In dichloromethane; at 0 - 20℃; for 4.0h; | To a solution of A3-5 (1.5 g, 6.5 mmol) in DCM (20 mL) at 0 C was added TFA (2 mL) dropwise. The solution was stirred at RT for 4 h, and then concentrated to afford A3-6 (1 g, 88%). 1H NMR (400 MHz, MeOD): 9.30 (s, 1H), 8.98 (s, 1H), 6.92 (t, J= 14.4 Hz, 1H). |
(5) Synthesis of 5-difluoromethylpyrazine-2-carboxylic acid Trifluoroacetic acid (1 mL) was added to a solution of t-butyl 5-difluoromethylpyrazine-2-carboxylate (175 mg) in dichloromethane (1 mL), and the mixture was stirred at room temperature for five hours. Ether and 5 N sodium hydroxide were added to the reaction solution. The aqueous layer was separated and made acidic with 5 N hydrochloric acid. Ethyl acetate was added to the aqueous layer, and the organic layer was separated. The organic layer was dried over anhydrous magnesium sulfate, and the insoluble matter was separated by filtration. The filtrate was concentrated to obtain the title compound (100 mg). 1H-NMR (CDCl3) delta (ppm): 6.80 (t, J=54.4 Hz, 1H), 9.02 (s, 1H), 9.47 (s, 1H). | ||
Trifluoroacetic acid (1 mL) was added to a solution of t-butyl 5-difluoromethylpyrazine-2-carboxylate (175 mg) in dichloromethane (1 mL), and the mixture was stirred at room temperature for five hours. Ether and 5 N sodium hydroxide were added to the reaction solution. The aqueous layer was separated and made acidic with 5 N hydrochloric acid. Ethyl acetate was added to the aqueous layer, and the organic layer was separated. The organic layer was dried over anhydrous magnesium sulfate, and the insoluble matter was separated by filtration. The filtrate was concentrated to obtain the title compound (100 mg).1H-NMR (CDCl3) delta (ppm): 6.80 (t, J=54.4 Hz, 1H), 9.02 (s, 1H), 9.47 (s, 1H). |
(5) Synthesis of 5-difluoromethylpyrazine-2-carboxylic acidTrifluoroacetic acid (1 mL) was added to a solution of t-butyl 5- difluoromethylpyrazine-2-carboxylate (175 mg) in dichloromethane (1 mL), and the mixture was stirred at RT for 5 h. Ether and 5 N NaOH were added to the reaction solution. The aqueous layer was separated and made acidic with 5 N hydrochloric acid.EtOAc was added to the aqueous layer, and the organic layer was separated. The organic layer was dried over anhydrous MgSO4, and the insoluble matter was separated by filtration. The filtrate was concentrated to obtain the title compound (100 mg).1 H-NMR (CDCl3 ) delta (ppm): 6.80 (t, J = 54.4 Hz, IH), 9.02 (s, IH), 9.47 (s, IH). | ||
(5) Synthesis of 5-difluoromethylpyrazine-2-carboxylic acidTrifluoroacetic acid (1 mL) was added to a solution of t-butyl 5- difluoromethylpyrazine-2-carboxylate (175 mg) in dichloromethane (1 mL), and the mixture was stirred at RT for 5 h. Ether and 5 N NaOH were added to the reaction solution. The aqueous layer was separated and made acidic with 5 N hydrochloric acid. EtOAc was added to the aqueous layer, and the organic layer was separated. The organic layer was dried over anhydrous MgSO4, and the insoluble matter was separated by filtration. The filtrate was concentrated to obtain the title compound (100 mg).1 H-NMR (CDCl3 ) delta (ppm): 6.80 (t, J = 54.4 Hz, IH), 9.02 (s, IH), 9.47 (s, IH). | ||
With trifluoroacetic acid; In dichloromethane; at 20℃; for 5.0h; | Trifluoroacetic acid (1 mL) was added to a solution of t-butyl 5-difluoromethylpyrazine-2-carboxylate (175 mg) in dichloromethane (1 mL), and the mixture was stirred at RT for 5 h. Ether and 5 N NaOH were added to the reaction solution. The aqueous layer was separated and made acidic with 5 N hydrochloric acid. EtOAc was added to the aqueous layer, and the organic layer was separated. The organic layer was dried over anhydrous MgSO4, and the insoluble matter was separated by filtration. The filtrate was concentrated to obtain the title compound (100 mg). 1H-NMR (CDCl3) delta (ppm): 6.80 (t, J=54.4 Hz, 1H), 9.02 (s, 1H), 9.47 (s, 1H). | |
With trifluoroacetic acid; In dichloromethane; at 20℃; for 5.0h; | Trifluoroacetic acid (1 mL) was added to a solution of t-butyl 5-difluoromethylpyrazine-2-carboxylate (175 mg) in dichloromethane (1 mL), and the mixture was stirred at RT for 5 h. Ether and 5 N NaOH were added to the reaction solution. The aqueous layer was separated and made acidic with 5 N hydrochloric acid. EtOAc was added to the aqueous layer, and the organic layer was separated. The organic layer was dried over anhydrous MgSO4, and the insoluble matter was separated by filtration. The filtrate was concentrated to obtain the title compound (100 mg). 1H-NMR (CDCl3) delta (ppm): 6.80 (t, J=54.4 Hz, 1H), 9.02 (s, 1H), 9.47 (s, 1H). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With (benzotriazol-1-yloxy)tripyrrolidinophosphonium hexafluorophosphate; N-ethyl-N,N-diisopropylamine; In dichloromethane; at 20℃; for 16.0h;Inert atmosphere; | Step 6: tert-Butyl ((4aS,5SJaS)-7a-(5-(5-(difluoromethyl)pyrazine-2-carboxamido)-2- fluorophenyl)-3-ethyl-4-oxo-5-(trifluoromethyl)-3,4,4a,5JJa-hexahvdrofuror3,4- dlpyrimidin-2-yl)carbamate N-Ethyl-N-(propan-2-yl)propan-2-amine (190 muL, 1.1 mmol) was added to a stirred mixture of tert-butyl ((4aS,5S,7aS)-7a-(5-amino-2-fluorophenyl)-3-ethyl-4-oxo-5- (trifluoromethyl)-3,4,4a,5,7,7a-hexahydrofuro[3,4-d]pyrimidin-2-yl)carbamate (100 mg, 0.21 mmol), <strong>[1174321-06-2]5-(difluoromethyl)pyrazine-2-carboxylic acid</strong> (57 mg, 0.33 mmol) and (lH-benzotriazol-l-yloxy)(tripyrrolidin-l-yl)phosphonium hexafluorophosphate (170 mg, 0.33 mmol) in dry DCM (1 mL) at RT under nitrogen. The reaction was stirred at this temperature for 16 h, and then partitioned between DCM and NaHCO3 (aq.). The aqueous layer was extracted with DCM (x2). The combined extracts were dried by passing through a hydrophobic frit and then evaporated. The residue was purified by column chromatography (normal phase, 1Og, Biotage SNAP cartridge KP-SiI, 12mL per min, gradient 5% to 30% EtOAc in n-hexane) to give the title compound (118 mg, cream foam). 1H NMR (400 MHz, CDCl3-d) delta ppm 1.14 (t, J=7.07 Hz, 3H) 1.56 (s, 9H) 3.96 - 4.15 (m, 3H) 4.39 (d, J=9.60 Hz, IH) 4.50 (dd, J=9.73, 2.91 Hz, IH) 4.53 - 4.62 (m, IH) 6.81 (t, J=54.60 Hz, IH) 7.22 (dd, J=10.74, 8.97 Hz, IH) 7.76 (dd, J=6.69, 2.65 Hz, IH) 7.79 - 7.84 (m, IH) 8.93 (s, IH) 9.52 (s, IH) 9.65 (s, IH) 10.64 (s, IH). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With N-(3-dimethylaminopropyl)-N-ethylcarbodiimide; N-ethyl-N,N-diisopropylamine; In dichloromethane; for 0.25h; | Step 12: (+/-)-N-(3-((4aS*,7aS*)-2-amino-3-methyl-4-oxo-3,4,4a,5,7,7a-hexahydrofuro r3,4-dlpyrimidin-7a-yl)-4-fluorophenyl)-5-(difluoromethyl)picolinamide.(+/-)-tert-Butyl ((4aS*,7aS*)-7a-(5-amino-2-fluorophenyl)-3-methyl-4-oxo-3,4,4a,5,7,7a- hexahydrofuro[3,4-d]pyrimidin-2-yl)carbamate (11 mg , 0.03 mmol) was dissolved in DCM (2 mL). <strong>[1174321-06-2]5-(difluoromethyl)pyrazine-2-carboxylic acid</strong> (8 mg , 0.04 mmol) was transferred into the reaction vessel. N-ethyl-N-(propan-2-yl)propan-2-amine (7.5 mg, 0.06 mmol) was transferred in to the reaction vessel. N-[3-(dimethylamino)propyl]- N'-ethylcarbodiimide (7 mg, 0.04 mmol) was transferred into the reaction vessel.After 15 mins the reaction mixture was washed with HCl (IM, 2 x 2 mL) then with saturated aqueous NaHCO3 (2 x 2 mL). The organic phase was then concentrated and the crude mixture was taken directly to the next reaction. LCMS (Method A) Rt 5.44 min; ESI-MS: m/z 535 [M+H]+. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With (benzotriazol-1-yloxy)tripyrrolidinophosphonium hexafluorophosphate; N-ethyl-N,N-diisopropylamine; In N,N-dimethyl-formamide; at 20℃; for 72.0h; | Step 7: tert-Butyl ((4aS,5R,7aS)-7a-(5-(5-(difluoromethyl)pyrazine-2-carboxamido)-2- fluorophenyl)-3,5-dimethyl-4-oxo-3,4,4a,5JJa-hexahvdrofuror3,4-dlpyrimidin-2- yl)(N-tert-butoxycarbonyl)carbamateA mixture of tert-butyl ((4aS,5R,7aS)-7a-(5-amino-2-fluorophenyl)-3,5-dimethyl-4- oxo-3,4,4a,5,7,7a-hexahydrofuro[3,4-d]pyrimidin-2-yl)(N-tert- butoxycarbonyl)carbamate (77 mg, 0.156 mmol), 5-(difluoromethyl)pyrazine-2- carboxylic acid (41 mg, 0.23 mmol), N-ethyl-N-(propan-2-yl)propan-2-amine (136 mul, 0.78 mmol) and (lH-benzotriazol-l-yloxy)(tripyrrolidin-l-yl)phosphoniumhexafluorophosphate (122 mg, 0.23 mmol) in dry DMF (2 mL) was stirred at RT for 3 days. The mixture was partitioned between EtOAc / NaHCO3 (aq.). The aqueous layer was extracted with EtOAc (x2). The combined extracts were washed with brine (xl), dried (Na2SO4), filtered and evaporated. The residue was purified by column chromatography (normal phase, 1Og, Biotage SNAP cartridge KP-SiI, 12mL per min, gradient 5% to 50% EtOAc in n-hexane) to give the title compound (30 mg, solid). 1H NMR (400 MHz, CDCl3) delta ppm 1.38 (s, 9H) 1.49 (d, J=6.06 Hz, 3H) 1.54 (s, 9H) 3.16 (s, 3H) 3.50 (d, J=4.80 Hz, IH) 4.25 - 4.33 (m, IH) 4.46 - 4.54 (m, 2H) 6.80 (t, J=54.80 Hz, IH) 7.15 (dd, J=10.86, 8.84 Hz, IH) 7.56 (dd, J=6.57, 2.78 Hz, IH) 8.05 - 8.11 (m, IH) 8.84 - 8.89 (m, IH) 9.53 (s, IH) 9.65 (s, IH). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With (benzotriazol-1-yloxy)tripyrrolidinophosphonium hexafluorophosphate; N-ethyl-N,N-diisopropylamine; In dichloromethane; at 20℃; for 16.0h;Inert atmosphere; | Step 9: tert- Butyl ((4aS,5SJaS)-7a-(5-(5-(difluoromethyl)pyrazine-2-carboxamido)-2- fluorophenyl)-3-methyl-4-oxo-5-(trifluoromethyl)-3,4,4a,5J,7a-hexahydrofuror3,4- dlpyrimidin-2-yl)carbamate N- Ethyl-N-(propan-2-yl)propan-2- amine (300 muL, 1.7 mmol) was added to a stirred mixture of tert-butyl ((4aS,5S,7aS)-7a-(5-amino-2-fluorophenyl)-3-methyl-4-oxo-5- (trifluoromethyl)-3,4,4a,5,7,7a-hexahydrofuro[3,4-d]pyrimidin-2-yl)carbamate amine (150 mg, 0.34 mmol), <strong>[1174321-06-2]5-(difluoromethyl)pyrazine-2-carboxylic acid</strong> (90 mg, 0.50 mmol) and (lH-benzotriazol-l-yloxy)(tripyrrolidin-l-yl)phosphoniumhexafluorophosphate (265 mg, 0.50 mmol) in dry DCM (2 mL) at RT under nitrogen. The reaction was stirred at this temperature for 16 h, then partitioned between DCM and NaHCO3 (aq). The aqueous layer was extracted with DCM (x2). The combined extracts were dried by passing through a hydrophobic frit and then evaporated. The residue was purified by column chromatography (normal phase, 25 g, Biotage SNAP cartridge KP-SiI, 25mL per min, gradient 5% to 30% EtOAc in n-hexane) to give the title compound (92 mg, light yellow solid). 1H NMR (400 MHz, CDCl3) delta ppm 1.58 (s, 9H) 3.36 (s, 3H) 4.06 (d, J=7.83 Hz, IH) 4.40 (d, J=9.85 Hz, IH) 4.50 (dd, J=9.73, 2.91 Hz, IH) 4.57 - 4.65 (m, IH) 6.81 (t, J=54.60 Hz, IH) 7.22 (dd, J=10.86, 9.09 Hz, IH) 7.74 (dd, J=6.69, 2.65 Hz, IH) 7.84 (ddd, J=8.84, 4.17, 2.65 Hz, IH) 8.93 (s, IH) 9.52 (s, IH) 9.65 (s, IH) 10.64 (s, IH) |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With N-ethyl-N,N-diisopropylamine; HATU; In dichloromethane; at 20℃; for 0.25h; | 3Q-(Il) synthesis of ((lS,4aS,5R,7aS)-7a-{5-r(5-Difluoromethyl-pyrazine-2-carbonyl)- aminol-2-fluoro-phenyl|-5-methyl-4-trifluoromethyl-4a,5JJa-tetrahydro-4H-furor3,4- diri,31oxazin-2-yl)-carbamic acid tert-butyl estertert-butyl ((4S,4aS,5R,7aS)-7a-(5-amino-2-fluorophenyl)-5-methyl-4-(trifluoromethyl)- 4a,5,7,7a-tetrahydro-4H-furo[3,4-d][l,3]oxazin-2-yl)carbamate (Preparation Example 30-(1O)) (110.25 mg, 0.25 mmol) dissolved in DCM. 5-(difluoromethyl)pyrazine-2- carboxylic acid (66.43 mg, 0.38 mmol) added. Followed by N-ethyl-N-(propan-2- yl)propan-2-amine (65.75 mg, 0.51 mmol) and N-[(dimethylamino)(3H- [l,2,3]triazolo[4,5-b]pyridin-3-yloxy)methylidene]-N-methylmethanaminiumhexafluorophosphate (0.14 g, 0.38 mmol). The reaction was stirred at RT. LCMS (Agilent Method A) Retention time 5.44min, ES+: 535 [MH]+. After 15 min, the reaction mixture was washed with HCl IM (2 x 5mL) then washed with sat. NaHCO3 (2 x 5mL). The organic phase was then concentrated and the crude mixture was purified by flash chromatography. 140 mg (100%) of the title compound (85%) and its isomer (15%) were isolated as a mixture. 1H NMR (400 MHz, CDCl3) ppm 1.45 (d, /=6.19 Hz, 3H) 1.55 (s, 9H) 2.95 (dd, /=8.84, 2.65 Hz, IH) 3.89 (dd, /=8.84, 2.53 Hz, IH) 4.30 (qd, /=6.91, 2.27 Hz, IH) 4.48 (quin, /=6.44 Hz, IH) 4.56 (dd, /=(dd, /=11.68, 9.03 Hz, IH) 6.82 (t, /=54.20 Hz, IH) 7.22 (dd, /=11.6, 7.87 Hz, IH) 7.55 (dd, /=6.88, 2.84 Hz, IH) 8.26 (ddd, /=8.87, 4.14, 2.78 Hz, IH) 8.97 (s, IH) 9.55 (s, IH) 9.70 (s, IH) |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With (benzotriazol-1-yloxy)tripyrrolidinophosphonium hexafluorophosphate; N-ethyl-N,N-diisopropylamine; In dichloromethane; at 20℃; | General Procedure A: the coupling of anilines prepared in Preparation Examples 25- (14) and 26-Q2) with aryl carboxylic acidsThe aniline (100 mg) was dissolved in DCM (2 mL) and the aryl carboxylic acid (1.2 - 1.6 equiv.), N,N-diisopropylethylamine (3 equiv.) and (lH-benzotriazol-1- yloxy)tripyrrolidin-l-yl)phosphonium hexafluorophophate (1.2 - 1.6 equiv.) were added. The reaction mixture was stirred at RT for 16 h - 3 days, and sodium bicarbonate (sat., aq., 25 mL) was added. The mixture was extracted with EtOAc (2 x40 mL), the combined organic portions were dried over MgSO4, evaporated and purified by silica gel chromatography (EtOAc/hexanes gradient) to afford the amide as a white solid. The amide was dissolved in DCM (2 mL) and TFA (1 mL) was added. After stirring at RT for 1-3 h, the reaction mixture was evaporated and sodium bicarbonate (sat., aq., 25 mL) was added. The mixture was extracted with EtOAc (2 x 40 mL), and the combined organic portions dried over MgSO4 and evaporated to afford the desired compound as a white solid. On occasions where the product was not pure, purification was effected by silica gel chromatography (MeOH/EtOAc/DCM gradients). Example 1 : N-(3-(('4aR,5S,7aS)-2-amino-5-('fluoromethyl)-4a,5,7,7a-tetrahvdro-4H- furor3,4-diri,31oxazin-7a-yl)-4-fluorophenyl)-5-(difluoromethyl)pyrazine-2- carboxamideSynthesized from tert-butyl [(4aR,5S,7aS)-7a-(5-amino-2-fluorophenyl)-5- fluoromethyl-4a,5,7,7a-tetrahydro-4H-furo[3,4-d][l,3]oxazin-2-yl]carbamate 25-(14) and <strong>[1174321-06-2]5-difluoromethyl-pyrazine-2-carboxylic acid</strong> according to General Procedure A. 1H NMR (400 MHz, CDCl3) delta (ppm): 2.94 (d, /=7.8 Hz, IH), 3.79 (dd, /=8.6, 2.5 Hz, IH), 3.89 - 4.05 (m, 2H), 4.28 - 4.66 (m, 4H), 6.72 (t, J 54.3 Hz, IH), 7.05 (dd, /=11.6, 8.8 Hz, IH), 7.67 (dd, /=7.1, 2.8 Hz, IH), 7.91 - 8.03 (m, IH), 8.85 (s, IH), 9.45 (s, IH), 9.61 (br s, IH) |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
79% | To a mixture of wet solids (235 g including 2-propanol) of benzyl amine salt of 5-[carboxy(difluoro)methyl]pyrazine-2-carboxylic acid (IV, 214 g, 0.495 mol,) and toluene (1070 mL) were added water (303 mL) and an aqueous sodium hydroxide solution (48%, 68,3 mL) , and the aqueous layer was separated. After the organic layer was re-extracted with water (107 mL), the aqueous layers were combined. To the aqueous layer were added cyclopentyl methyl ether (2141 mL) and concentrated hydrochloric acid (165 mL), and the organic layer was separated.The aqueous layer was re-extracted with cyclopentyl methyl ether (963 mL), and the vessel rinsed with cyclopentyl methyl ether (107 mL) followed by combining the obtained three organic layers. After the mixture was stirred at 90 C for 30 h and cooled to room temperature, water (828 mL) and sodium hydroxide solution (48%, 54.6 mL) were added to the mixture. After phase separation, the organic layer was re-extracted with water (107 mL), and the obtained two aqueous layers were combined. Phase separation was conducted after addition of isopropyl acetate (2141 mL) and concentrated hydrochloric acid (86.6 mL), and the aqueous layer was re-extracted with isopropyl acetate (1070 mL). After combining the obtained two organic layers, the organic layers were washed with water (321 mL). Insoluble materials in the organic layer was removed by polish filtration through aand the filter was rinsed with isopropyl acetate (107 mL). The obtained organic layer was concentrated at 50 C under reduced pressure, and the residue (about 188 mL) was diluted with isopropyl acetate (46 mL) followed by cooling to 30 C. After addition of ^-heptane (640 mL) over 1 h, the mixture was cooled to -10 C. The precipitated solids were collected by filtration, washed with rc-heptane (117 mL), and dried at 50 C under reduced pressure to afford the title compound (V, 68.2 g, 79% yield) as flesh colored solids. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
64% | With sulfuric acid; In Isopropyl acetate; water; at 75 - 80℃; for 22.5h; | (l-4)-C Preparation of 5-(difluoromethyl pyrazine-2-carboxylic acid (V)To a mixture of potassium salt of 5-[carboxy(difluoro)methyl]pyrazine-2- carboxylic acid (IV, 1.00 g, 3.32 mmol) which was obtained from example (l-3)-B, isopropyl acetate (4 mL), and water (2 mL) were added concentrated sulfuric acid (0.60 mL, 10.8 mmol), and the organic layer was separated. The aqueous layer was re-extracted with isopropyl acetate (4 mL) followed by combining the obtained two organic layers. After stirring the mixture at 75 C for 16.5 h, the mixture was stirred at 80 C for 6 h and cooled to room temperature. After polish filtration of the mixture through a filter and rising the filter with isopropyl acetate (1 mL), water (4 mL) and aqueous sodium hydroxide solution (48%, 973 mg, 8.33 mmol) were added to the filtrate, and then the aqueous layer was separated. To the aqueous layer was added concentrated hydrochloric acid (0.83 mL, 10.0 mmol), and the resulting mixture was stirred while in ice-cooling for 17 h. The precipitated solids were collected by filtration, washed with water (0.5 mL), and dried at 50 C under reduced pressure to afford the title compound (V, 371 mg, 64% yield) as pale brown solids. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
373 mg | With benzotriazol-1-ol; 1-ethyl-(3-(3-dimethylamino)propyl)-carbodiimide hydrochloride; In chloroform; at 20℃; | To an ice-water cooled mixture of tert-butyl[(4'R)-6'-amino-2',2'-dimethyldispiro[cyclopropane-1,3'-chromene-4',4"-[1,3]oxazol]-2"-yl]carbamate (430 mg, 1.15 mmol), <strong>[1174321-06-2]5-(difluoromethyl)pyrazine-2-carboxylic acid</strong> (221 mg, 1.27mmol) and lH-benzotriazol-1-ol (170 mg, 1.26 mmol) in chloroform (8.6 ml) was addedN-[3-(dimethylamino)propyl]-N'-ethylcarbodiimide hydrochloride (244 mg, 1.28 mmol). Themixture was stirred at room temperature overnight and directly purified by silica gel columnchromatography (precolumn: basic silica gel, main column: neutral silica gel, hexane/ethylacetate= 2:1- 1:1- 0:100) to afford tert-butyl[ ( 4'R)-6'-( { [5-( difluoromethyl)pyrazin-2-yl]carbonyl }amino )-2' ,2'-dimethyldispiro[ cyclopropane-1,3'-chromene-4',4"-[1,3]oxazol]-2"-yl]carbamate (373 mg). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
69.3% | Example 140 N-(3-((6S,7R)-9-amino-6-fluoro-7-methyl-5,5-dioxido-5-thia-8-azaspiro[3.5]non-8-en-7-yl)-4-fluorophenyl)-5-(difluoromethyl)pyrazine-2-carboxamide As described in the HATU coupling procedure, tert-butyl ((6S,7R)-7-(5-amino-2-fluorophenyl)-6-fluoro-7-methyl-5,5-dioxido-5-thia-8-azaspiro[3.5]non-8-en-9-yl)carbamate (127 mg, 0.296 mmol) and <strong>[1174321-06-2]5-(difluoromethyl)pyrazine-2-carboxylic acid</strong> (61.8 mg, 0.355 mmol) were combined to provide the title compound (120 mg, 0.205 mmol, 69.3% yield) as an off-white solid. LC/MS (ESI+) m/z=486 (M+H). 1H NMR (400 MHz, DMSO-d6) ppm 10.91 (s, 1H) 9.37-9.39 (m, 1H) 9.08-9.10 (m, 1H) 7.81-7.89 (m, 2H) 7.11-7.42 (m, 2H) 6.59 (br. s., 2H) 5.92 (d, J=1.00 Hz, 1H) 2.58-2.82 (m, 4H) 1.94-2.27 (m, 2H) 1.62 (d, J=3.52 Hz, 3H) |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
Example 211 N-(3-((4S,6S)-2-amino-4-methyl-6-(trifluoromethyl)-5,6-dihydro-4H-1,3-oxazin-4-yl)-5-chloro-4-fluorophenyl)-5-(difluoromethyl)pyrazine-2-carboxamide The title compound was synthesized by procedures and steps analogous to those described in Method A2, Example 206 above, but using <strong>[1174321-06-2]5-(difluoromethyl)pyrazine-2-carboxylic acid</strong> (Aurigene Discovery Technologies Ltd.) in step 10. MS m/z=482.1 [M+H]+. Calculated for C18H14ClF6N5O2: 481.779 1H NMR (400 MHz, CHLOROFORM-d) delta=9.61 (br. s., 1H), 9.51 (s, 1H), 8.91 (s, 1H), 8.18 (dd, J=2.5, 6.1 Hz, 1H), 7.44-7.35 (m, 1H), 7.02-6.60 (m, 1H), 4.35 (br. s., 2H), 4.11-3.96 (m, 1H), 2.80 (dd, J=2.2, 13.9 Hz, 1H), 1.92 (t, J=13.2 Hz, 1H), 1.65 (s, 3H) |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
Example 193 N-(3-((4S,6S)-2-amino-4-methyl-6-(trifluoromethyl)-5,6-dihydro-4H-1,3-oxazin-4-yl)-4,5-difluorophenyl)-5-(difluoromethyl)pyrazine-2-carboxamide The title compound was synthesized by procedures and steps analogous to those described in Method Z, Example 186 above, but using <strong>[1174321-06-2]5-(difluoromethyl)pyrazine-2-carboxylic acid</strong> (Aurigene Discovery Technologies). MS m/z=466.1 [M+H]+. Calculated for C18H14F7N5O2: 465.32 1H NMR (300 MHz, CHLOROFORM-d) delta=9.65 (br. s., 1H), 9.52 (s, 1H), 8.93 (s, 1H), 8.14-8.02 (m, 1H), 7.15 (br. s., 1H), 6.99-6.60 (m, 1H), 4.13-3.98 (m, 1H), 2.81 (d, J=13.6 Hz, 1H), 1.94 (t, J=13.1 Hz, 1H), 1.67 (s, 3H) |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
Example 16 N-(3-((2R,5S)-6-amino-3,3,5-trifluoro-2,5-dimethyl-2,3,4,5-tetrahydropyridin-2-yl)-4-fluorophenyl)-5-(difluoromethyl)pyrazine-2-carboxamide Prepared from (3S,6R)-6-(5-amino-2-fluorophenyl)-3,5,5-trifluoro-3,6-dimethylpiperidine-2-thione and <strong>[1174321-06-2]5-(difluoromethyl)pyrazine-2-carboxylic acid</strong> LC-MS (m/z) 446 (MH+) tR=0.52 minutes (Method A) 1H NMR (600 MHz, CDCl3) delta 9.63 (br s, 1H), 9.53 (s, 1H), 8.92 (s, 1H), 7.90-7.86 (m, 1H), 7.63 (dd, J=6.8, 2.7 Hz, 1H), 7.11 (dd, J=11.6, 8.8 Hz, 1H), 6.80 (t, J=54.5 Hz, 1H), 4.76 (br s, 2H), 2.64-2.34 (m, 2H), 1.80 (t, J=2.7 Hz, 3H), 1.77 (d, J=23.5 Hz, 3H) |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
Example 24 N-(3-((2R,5R)-6-amino-3,3,5-trifluoro-2,5-dimethyl-2,3,4,5-tetrahydropyridin-2-yl)-4-fluorophenyl)-5-(difluoromethyl)pyrazine-2-carboxamide Prepared from (3R,6R)-6-(5-amino-2-fluorophenyl)-3,5,5-trifluoro-3,6-dimethylpiperidine-2-thione and <strong>[1174321-06-2]5-(difluoromethyl)pyrazine-2-carboxylic acid</strong> LC-MS (m/z) 446 (MH+) tR=0.52 minutes (Method A) 1H NMR (600 MHz, DMSO-d6) delta 11.03 (s, 1H), 9.37 (t, J=2.4 Hz, 1H), 9.09 (s, 1H), 7.89-7.80 (m, 2H), 7.26 (t, J=53.9 Hz, 1H), 7.18 (dd, J=11.9, 8.7 Hz, 1H), 6.34 (s, 2H), 2.62-2.51 (m, 1H), 2.29-2.14 (m, 1H), 1.71 (d, J=23.2 Hz, 3H), 1.68 (s, 3H) |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
43 mg | With N-ethyl-N,N-diisopropylamine; N-[(dimethylamino)-3-oxo-1H-1,2,3-triazolo[4,5-b]pyridin-1-yl-methylene]-N-methylmethanaminium hexafluorophosphate; In N,N-dimethyl-formamide; at 20℃; for 0.5h; | A mixture of Example 130E (0.05 g, 0.146 mmol), 5-(difluoromethyl)pyrazine-2- carboxylic acid (0.029 g, 0.168 mmol) and N-ethyl-N-isopropylpropan-2-amine (0.102 mL, 0.583 mmol) in N,N-dimethylformamide (1.5 mL) was treated with 2-(3H-[1,2,3]triazolo[4,5- b]pyridin-3-yl)-1,1,3,3-tetramethylisouronium hexafluorophosphate(V) (0.083 g, 0.219 mmol), and the reaction was stirred at ambient temperature for 30 minutes. Volatiles were removed under high vacuum, and the residue was purified by HPLC (10~95% acetonitrile in 0.1% trifluoroacetic acid/water on Phenomenex C185 mum (250 mm × 21.2 mm) column at a flowrate of 25 mL/minute) to give 43 mg of the title compound as a solid. 1H NMR (400 MHz, DMSO-d6) delta ppm 9.19 (d, J = 1.4 Hz, 1H), 8.94 (d, J = 1.2 Hz, 1H), 8.03 (s, 1H), 7.45 (t, J = 8.9 Hz, 1H), 7.28 (d, J = 6.0 Hz, 1H), 7.16 (m, 1H), 7.076.98 (m, 1H), 6.80 (ddd, J = 9.0, 2.9, 1.2 Hz, 1H), 5.13 (d, J = 4.4 Hz, 1H), 4.44 (s, 2H), 4.08 (ddd, J = 9.9, 5.4, 3.1 Hz, 1H), 2.39 (ddd, J = 12.6, 9.5, 2.5 Hz, 1H), 2.132.01 (m, 2H), 1.95 (q, J = 4.8, 2.6 Hz, 1H), 1.941.76 (m, 6H); MS (ESI+) m/z 499.1 (M+H)+. |
43 mg | With N-ethyl-N,N-diisopropylamine; HATU; In N,N-dimethyl-formamide; at 20℃; for 0.5h; | A mixture of Example 130E (0.05 g, 0.146 mmol), 5-(difluoromethyl)pyrazine-2- carboxylic acid (0.029 g, 0.168 mmol) and N-ethyl-N-isopropylpropan-2-amine (0.102 mL, 0.583 mmol) in N,N-dimethylformamide (1.5 mL) was treated with 2-(3H-[l ,2,3]triazolo[4,5- Z?]pyridin-3-yl)- l ,l ,3,3-tetramethylisouronium hexafluorophosphate(V) (0.083 g, 0.219 mmol), and the reaction was stirred at ambient temperature for 30 minutes. Volatiles were removed under high vacuum, and the residue was purified by HPLC (10-95% acetonitrile in 0.1% trifluoroacetic acid/water on Phenomenex CI 8 5 mupiiota (250 mm x 21.2 mm) column at a flowrate of 25 mL/minute) to give 43 mg of the title compound as a solid. JH NMR (400 MHz, DMSO- ) delta ppm 9.19 (d, J = 1.4 Hz, 1H), 8.94 (d, J = 1.2 Hz, 1H), 8.03 (s, 1H), 7.45 (t, J = 8.9 Hz, 1H), 7.28 (d, J = 6.0 Hz, 1H), 7.16 (m, 1H), 7.07 6.98 (m, 1H), 6.80 (ddd, J = 9.0, 2.9, 1.2 Hz, 1H), 5.13 (d, J = 4.4 Hz, 1H), 4.44 (s, 2H), 4.08 (ddd, J = 9.9, 5.4, 3.1 Hz, 1H), 2.39 (ddd, J = 12.6, 9.5, 2.5 Hz, 1H), 2.13 2.01 (m, 2H), 1.95 (q, J = 4.8, 2.6 Hz, 1H), 1.94 1.76 (m, 6H); MS (ESI+) m/z 499.1 (M+H)+. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
88% | With triethylamine; N-[(dimethylamino)-3-oxo-1H-1,2,3-triazolo[4,5-b]pyridin-1-yl-methylene]-N-methylmethanaminium hexafluorophosphate; In N,N-dimethyl-formamide; at 20℃; for 0.5h; | N,N-Dimethylformamide (2 mL), triethylamine (0.081 mL, 0.58 mmol) and 1- [bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium 3-oxid hexafluorophosphate (48 mg, 0.126 mmol, HATU) were added to a mixture of the product of Example 197B (40 mg, 0.097 mmol) and <strong>[1174321-06-2]5-(difluoromethyl)pyrazine-2-carboxylic acid</strong> (Manchester, 16.9 mg, 0.097 mmol) in sequential order. The reaction mixture was then stirred at ambient temperature for 0.5 hour. The resulting solution was filtered through a glass microfiber frit and purified by preparative HPLC [Waters XBridge C185 mum OBD column, 30 × 100 mm, flow rate 40 mL/minute, 5-100% gradient of acetonitrile in buffer (0.025 M aqueous ammonium bicarbonate, adjusted to pH 10 with ammonium hydroxide)] to give the title compound (39 mg, 0.086 mmol, 88% yield). 1H NMR (500 MHz, DMSO-d6) delta ppm 9.34 (s, 1H), 9.31- 9.22 (m, 1H), 8.99 (s, 1H), 8.53 (s, 1H), 7.50 (t, J = 8.9 Hz, 1H), 7.21 (t, J = 54.0 Hz, 1H), 7.08 (dd, J = 11.4, 2.8 Hz, 1H), 6.86 (ddd, J = 9.0, 3.0, 1.1 Hz, 1H), 4.49 (s, 2H), 2.18 - 2.12 (m, 2H), 1.99- 1.80 (m, 6H); MS (ESI+) m/z 455 (M+H)+. |
88% | With triethylamine; HATU; In N,N-dimethyl-formamide; at 20℃; for 0.5h; | N,N-Dimethylformamide (2 mL), triethylamine (0.081 mL, 0.58 mmol) and 1- [bis(dimethylamino)methylene]-lH-l,2,3-triazolo[4,5-]pyridinium 3-oxid hexafluorophosphate (48 mg, 0.126 mmol, HATU) were added to a mixture of the product of Example 197B (40 mg, 0.097 mmol) and <strong>[1174321-06-2]5-(difluoromethyl)pyrazine-2-carboxylic acid</strong> (Manchester, 16.9 mg, 0.097 mmol) in sequential order. The reaction mixture was then stirred at ambient temperature for 0.5 hour. The resulting solution was filtered through a glass microfiber frit and purified by preparative HPLC [Waters XBridge C18 5 muetaiota OBD column, 30 x 100 mm, flow rate 40 mL/minute, 5-100% gradient of acetonitrile in buffer (0.025 M aqueous ammonium bicarbonate, adjusted to pH 10 with ammonium hydroxide)] to give the title compound (39 mg, 0.086 mmol, 88% yield). JH NMR (500 MHz, DMSO-<) delta ppm 9.34 (s, 1H), 9.31 - 9.22 (m, 1H), 8.99 (s, 1H), 8.53 (s, 1H), 7.50 (t, J = 8.9 Hz, 1H), 7.21 (t, J = 54.0 Hz, 1H), 7.08 (dd, J = 11.4, 2.8 Hz, 1H), 6.86 (ddd, J = 9.0, 3.0, 1.1 Hz, 1H), 4.49 (s, 2H), 2.18 - 2.12 (m, 2H), 1.99 - 1.80 (m, 6H); MS (ESI+) m/z 455 (M+H)+. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
23 mg | With benzotriazol-1-yloxyl-tris-(pyrrolidino)-phosphonium hexafluorophosphate; N-ethyl-N,N-diisopropylamine; In dichloromethane; at 20℃; | 1) Synthesis of Compound F-21: Compound F-19 (18 mg, 0.04 mmol) was dissolved in dichloromethane (3 mL),1H-benzotriazol-1-yloxytripyrrolidinylhexafluorophosphate (PyBOP) (57 mg, 0.1 mmol), diisopropylethylamine (21.6 muL, 0.13 mmol) was added,5-Difluoromethylpyrazine-2-carboxylic acid (16 mg, 0.09 mmol), reacted overnight at room temperature;TLC showed complete reaction of the raw materials, adding dichloromethane (5mL), and then saturated organic saline to wash the organic phase, the organic phase was dried by spin-drying the column product 23mg;Suggest an edit |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
68 mg | With benzotriazol-1-yloxyl-tris-(pyrrolidino)-phosphonium hexafluorophosphate; N-ethyl-N,N-diisopropylamine; In dichloromethane; at 20℃; | 1) Synthesis of Compound A-17: Dissolve A-13 (50 mg, 0.125 mmol) in DCM (5 ml) andAdded diisopropylethylamine (62ul, 0.375mmol), 1H-benzotriazol-1-yloxytripyrrolidinylhexafluorophosphate(PyBOP) (163 mg, 0.313 mmol), <strong>[1174321-06-2]5-difluoromethylpyrazine-2-carboxylic acid</strong> (33 mg, 0.188 mmol), complete by addition, reaction at room temperatureOvernight; TLC monitored the reaction was complete, the solvent was derotated, and the column was purified with petroleum ether and ethyl acetate to give 68 mg of A-17; |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
54.2 g | With 2,4,6-tripropyl-1,3,5,2,4,6-trioxatriphosphinane-2,4,6-trioxide; In ethyl acetate; at 30 - 45℃; | 5-(Difluoromethyl)pyrazine2carboxylic acid (30.0 g, 1.05 equiv) and (4aS,5S,7aS)-7a-(5-amino-2-fluorophenyl)-5-fluoromethyl-4a,5,7,7a-tetrahydro-4H-furo[3,4-d][1,3]thiazin-2-amine (49.2 g, 1.00 equiv.) were charged to a reactor and EtOAc (443 mL) was added to the mixture to give a suspension. A solution of T3P (105 g 1.10 equiv, 50 wt% in EtOAc) (Archimica, Germany) was added at ambient temperature while controlling the internal temperature below 30 C. The reaction mixture was stirred at 4045 C >3 hours and monitored by HPLC. The reaction mixture was cooled to ambient temperature and water (98 mL) was charged. After 1015 minutes charged 28% ammonium hydroxide (137 mL) while controlling the temperature below 30 C. Additional EtOAc (172 mL) was added and the reaction mixture was stirred for 30 minutes at ambient temperature. The aqueous phase was separated and backextracted with EtOAc (246 mL). The organic phases were combined and washed with 15% aq. NaCl (98 mL) and water (98mL). The organic layer was filtered over Celite (0.5 Wt) and concentrated under vacuum to obtain a beige solid (quantitative crude yield) which was recrystallized from 1propanol to afford N-(3-((4aS,5S,7aS)-2-amino-5-(fluoromethyl)-4a,5,7,7a-tetrahydro-4H-furo[3,4-d][1,3]thiazin-7a-yl)-4-fluorophenyl)-5-(difluoromethyl)pyrazine-2-carboxamide as a tan solid (54.2g). |
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