Structure of 6971-44-4
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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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Ingraham, Charles H. IV ; Stalinska, Joanna ; Carson, Sean C. ; Colley, Susan B. ; Rak, Monika ; Lassak, Adam , et al.
Abstract: Glioblastomas are highly aggressive brain tumors for which therapeutic options are very limited. In a quest for new anti-glioblastoma drugs, we focused on specific structural modifications to the benzoyl-phenoxy-acetamide (BPA) structure present in a common lipid-lowering drug, fenofibrate, and in our first prototype glioblastoma drug, PP1. Here, we propose extensive computational analyses to improve the selection of the most effective glioblastoma drug candidates. Initially, over 100 structural BPA variations were analyzed and their physicochemical properties, such as water solubility (- logS), calculated partition coefficient (ClogP), probability for BBB crossing (BBB_SCORE), probability for CNS penetration (CNS-MPO) and calculated cardiotoxicity (hERG), were evaluated. This integrated approach allowed us to select pyridine variants of BPA that show improved BBB penetration, water solubility, and low cardiotoxicity. Herein the top 24 compounds were synthesized and analyzed in cell culture. Six of them demonstrated glioblastoma toxicity with IC50 ranging from 0.59 to 3.24 µM. Importantly, one of the compounds, HR68, accumulated in the brain tumor tissue at 3.7 ± 0.5 µM, which exceeds its glioblastoma IC50 (1.17 µM) by over threefold.
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CAS No. : | 6971-44-4 |
Formula : | C7H10N2 |
M.W : | 122.17 |
SMILES Code : | CNCC1=CC=NC=C1 |
MDL No. : | MFCD00066937 |
InChI Key : | DNBWGFKLIBQQSL-UHFFFAOYSA-N |
Pubchem ID : | 81436 |
GHS Pictogram: |
![]() |
Signal Word: | Warning |
Hazard Statements: | H315-H319-H335 |
Precautionary Statements: | P261-P305+P351+P338 |
Num. heavy atoms | 9 |
Num. arom. heavy atoms | 6 |
Fraction Csp3 | 0.29 |
Num. rotatable bonds | 2 |
Num. H-bond acceptors | 2.0 |
Num. H-bond donors | 1.0 |
Molar Refractivity | 36.81 |
TPSA ? Topological Polar Surface Area: Calculated from |
24.92 Ų |
Log Po/w (iLOGP)? iLOGP: in-house physics-based method implemented from |
1.55 |
Log Po/w (XLOGP3)? XLOGP3: Atomistic and knowledge-based method calculated by |
0.31 |
Log Po/w (WLOGP)? WLOGP: Atomistic method implemented from |
0.65 |
Log Po/w (MLOGP)? MLOGP: Topological method implemented from |
0.22 |
Log Po/w (SILICOS-IT)? SILICOS-IT: Hybrid fragmental/topological method calculated by |
1.35 |
Consensus Log Po/w? Consensus Log Po/w: Average of all five predictions |
0.82 |
Log S (ESOL):? ESOL: Topological method implemented from |
-1.15 |
Solubility | 8.57 mg/ml ; 0.0701 mol/l |
Class? Solubility class: Log S scale |
Very soluble |
Log S (Ali)? Ali: Topological method implemented from |
-0.4 |
Solubility | 49.1 mg/ml ; 0.402 mol/l |
Class? Solubility class: Log S scale |
Very soluble |
Log S (SILICOS-IT)? SILICOS-IT: Fragmental method calculated by |
-2.82 |
Solubility | 0.184 mg/ml ; 0.00151 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 |
-6.83 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 |
0.55 |
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) |
1.0 |
* 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 |
---|---|---|
With potassium carbonate; In N,N-dimethyl-formamide; at 80℃; for 16h; | Step II: Preparation of 2-[2-(methylpyridin-4-ylmethylamino) ethylisoindole-l,3-dione; Potassium carbonate (55.2 mmol) and 2-bromoethylfthalimide (66.2 mmol) was added to a solution of N* l*-pyridin-4-yl-methylethane-l, 2-diamine (55.2 mmol) in EPO <DP n="82"/>dimethylformamide (50 mL). The reaction mixture was heated to 800C and stirred for about 16 hours. The reaction mixture was cooled to ambient temperature, poured into water and extracted with dichloromethane. The organic layer was washed with water, dried over anhydrous sodium sulfate and concentrated under reduced pressure to yield the title product. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
(c) wherein W = -(CH2)2-N (CH3)-CH2-; Step I: Preparation of methylpyridin-4-ylmethylamine40% methyl amine (68.7 mmol) was added to a solution of pyridine 4- carbaldehyde (57.3 mmol) in methanol (90 mL) at 0-5 0C and stirred for about 15minutes, followed by adding sodium borohydride (57.3 mmol). The reaction mixture was refluxed for about 1 hour, cooled to ambient temperature and solvent was removed under reduced pressure. Water was added to the resulting residue the mixture was extracted with dichloromethane. The dichloromethane layers were combined, mixed and washed successively with water and then brine, and dried over anhydrous sodium sulfate. Solvent was evaporated under reduced pressure to yield a crude product. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
21% | With triethylamine; In methanol; dichloromethane; | (b) 4-Methoxy-N-methyl-N-(4-picolyl)benzamide To a solution of N-methyl-N-(4-picolyl)amine (0.40 g, 3.3 mmol) and triethylamine (1.5 mL, 10.8 mmol) in CH2 Cl2 (15 mL) was added 4-methoxybenzoyl chloride (1.2 g, 7.3 mmol). The resulting mixture was stirred at rt for 15 min, and then partitioned between 2.5N NaOH and Et2 O. The organic extract was washed with saturated aqueous NaCl and dried (MgSO4). The solvent was removed in vacuo, and the residue was purified by flash chromatography, eluding with a solvent gradient of 2-4% MeOH/CHCl3. The material that was isolated was triturated with Et2 O to provide the title compound as a light yellow solid (0.18 g, 21%): 1 H NMR (CDCl3): δ8.60 (d, 2H); 7.43 (br d, 2H); 7.20 (br s, 2H); 6.90 (br d, 2H); 4.66 (br s, 2H); 3.80 (s, 3H); 3.00 (s, 3H). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With hydrogenchloride; sodium hydroxide; triethylamine; In chloroform; toluene; | PREPARATION 14 Preparation of 1,3-Dimethyl-1-(4-pyridylmethyl)-3-phenylurea Phosgene in toluene (50 ml, 121/2% solution was stirred at 0-10 whilst a mixture of N-methylaniline (5.4 g) and triethylamine (15 ml) in dry chloroform (100 ml) was added slowly dropwise. On completion of the addition the mixture was stirred for 19 hours at room temperature, then cooled to 0-10 whilst a solution of 4-(N-methylaminomethyl)pyridine (3.1 g) in dry chloroform (70 ml) was slowly added. The mixture was stirred at room temperature overnight followed by the cautious addition of 2 N hydrochloric acid (20 ml). After 1 hour, 5 N sodium hydroxide (12 ml) was added and the organic phase was separated, washed (H2 O, 50 ml), dried (Na2 CO3) and evaporated in vacuo to give a dark oil. The oil was dissolved in the minimum quantity of chloroform and chromatographed on a "Florisil" (Trademark) column eluted with chloroform. Appropriate fractions were identified by thin layer chromatography, combined and evaporated in vacuo to give 1,3-dimethyl-1-(4-pyridylmethyl)-3-phenylurea as a dark oil (3 g). The n.m.r. spectrum was compatible with the required structure. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
In chloroform; | PREPARATION 13 Preparation of 1-Methyl-1-(4-pyridyl-methyl)-3-phenylurea 4-(Methylaminomethyl)pyridine (5 g), dry chloroform (500 ml) and phenyl isocyanate (5 g) were stirred together at room temperature for 2 hours. The chloroform was then evaporated in vacuo and the resultant oil was redissolved in the minimum quantity of chloroform and chromatographed on a "Florisil" (Trade Mark) (100 g) column using chloroform containing gradually increasing quantities of methanol (up to 2.5%) as eluding solvent. Appropriate fractions (identified by t.l.c.) were combined and evaporated in vacuo to give 1-methyl-1-(4-pyridylmethyl)-3-phenylurea as an oil (8.0 g). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With triethylamine; In dichloromethane; chloroform; water; | (A) 4-(N-Methyl-butyramidomethyl)pyridine n-Butyryl chloride (2.8 ml.) in dry methylene chloride (20 ml.) was added slowly to a stirred, cooled mixture of 4-(N-methylaminomethyl)pyridine (3 g.) and triethylamine (5 ml.) in dry methylene chloride (30 ml.). The mixture was then stirred at room temperature for 2.5 hours, after which water (30 ml.) was added. The organic phase was separated, washed with dilute aqueous sodium hydroxide (5%, 30 ml.), dried (Na2 CO3) and evaporated to dryness in vacuo. The resultant dark brown oil (3.8 g.) was chromatographed on a "Florisil" (Trademark) (15 g.) column, using chloroform as eluant. Appropriate fractions were identified by TLC, bulked and evaporated in vacuo to give pure 4-(N-methylbutyramidomethyl)pyridine as an oil (3.2 g.). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With triethylamine; In ethanol; at 20℃; for 14h; | N-[3,5-bis(trifluoromethyl)benzyl]-N-[2-{1-methyl(pyridin-4-ylmethyl)amino]propyl}-5-(trifluoromethyl)benzyl]-2H-tetrazol-5-amine 0.132M solutions of benzotriazole (790 mg/50 ml), triethylamine (0.83 ml/50 ml) and aldehyde from Preparation 8 (3 g/50 ml) in ethanol were prepared.To the solution of amine (60 mmol) in ethanol was added benzotriazole solution (450 uL, 54 mmols), triethylamine solution (450 uL, 54 mmols), and the aldehyde solution (450 uL, 54 mmols) via the TECAN (Model: Genesis RSP 150 TECAN US, Durham, N.C., USA). Reaction mixtures were shaken at room temperature for 14 hours. Organic solvents were evaporated on Genevac HT-24 (Barnstead Genevac, Valley Cottage, N.Y., USA). Toluene (1500 uL) was added followed by 3M ethyl magnesium bromide in ether (80 uL, 240 mmol) via the TECAN. Reaction mixture was heated to 80 C. for 2 hours. Reaction mixture was cooled, diluted with ethyl acetate (2 ml), quenched with saturated aqueous NH4Cl (2 ml) then shaken. The aqueous layer was removed. Organic layer was evaporated. Residue was diluted in 1 ml of DMSO, filtered and purified. MS (ES+) Calc: 645.2, Found: 646.3 (M+1). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
49% | Part A: 5-Fluoro-6-hydrazino-N,2-dimethyl-N-(4-pyridinylmethyl)-4-pyrimidinamine. 4,6-Dichloro-5-fluoro-2-methylpyrimidine (0.18 g, 0.99 mmol) was dissolved in DMSO (1 ml_). To this solution was added triethylamine (0.15 ml_, 1.08 mmol), followed by commercially available N-methyl-1-(4-pyridinyl)methanamine (0.122 g, 1.0 mmol). The reaction was left to stir for 3 hours. Then hydrazine monohydrate was added, and the resulting reaction mixture was stirred overnight at room temperature. The reaction mixture was heated to 6O0C for 90 minutes. After cooling, the reaction mixture was purified by RP-HPLC to provide 5-fluoro-6-hydrazino-N,2-dimethyl-N-(4-pyridinylmethyl)- 4-pyrimidinamine (0.130 g, 49%). LCMS: (M+H)+ = 263.0. |
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