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Structure of 1885-29-6
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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.
4.5
*For Research Use Only !
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Selective and Cell-Active PBRM1 Bromodomain Inhibitors Discovered through NMR Fragment Screening
Shifali Shishodia ; Raymundo Nuñez ; Brayden P. Strohmier ; Karina L. Bursch ; Christopher J. Goetz ; Michael D. Olp , et al.
Abstract: PBRM1 is a subunit of the PBAF chromatin remodeling complex that uniquely contains six bromodomains. PBRM1 can operate as a tumor suppressor or tumor promoter. PBRM1 is a tumor promoter in prostate cancer, contributing to migratory and immunosuppressive phenotypes. Selective chemical probes targeting PBRM1 bromodomains are desired to elucidate the association between aberrant PBRM1 chromatin binding and cancer pathogenesis and the contributions of PBRM1 to immunotherapy. Previous PBRM1 inhibitors unselectively bind SMARCA2 and SMARCA4 bromodomains with nanomolar potency. We used our protein-detected NMR screening pipeline to screen 1968 fragments against the second PBRM1 bromodomain, identifying 17 hits with Kd values from 45 μM to >2 mM. Structure–activity relationship studies on the tightest-binding hit resulted in nanomolar inhibitors with selectivity for PBRM1 over SMARCA2 and SMARCA4. These chemical probes inhibit the association of full-length PBRM1 to acetylated histone peptides and selectively inhibit growth of a PBRM1-dependent prostate cancer cell line.
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Purchased from AmBeed: 77326-36-4 ; 104-87-0 ; 2148-56-3 ; 63329-53-3 ; 1591-37-3 ; 387-45-1 ; 936-08-3 ; 1123-56-4 ; 2819989-75-6 ; 703-80-0 ; 1885-29-6 ; 115643-59-9 ; 15764-16-6 ; 487-68-3 ; 145737-61-7 ; 5779-95-3 ; 88-68-6 ; 6575-11-7 ; 77326-62-6 ; 88-65-3 ; 4635-59-0 ; 5779-94-2 ; 56043-01-7 ; 5779-93-1 ; 1591-38-4 ; 446-52-6 ; 62803-47-8 ; 1885-31-0 ; 620-23-5 ; 54166-95-9 ; 22179-72-2 ; 529-20-4 ; 100-52-7 ; 123-11-5 ; 1711-06-4 ; 454-89-7 ; 170875-01-1 ; 883032-29-9 ; 2819989-61-0 ; 1915012-21-3 ; 2819989-58-5 ; 2819989-60-9 ; 2819989-57-4 ; 2819989-68-7 ; 2819989-67-6 ; 111478-13-8 ; 73096-42-1 ; 2835-78-1 ; 118-92-3 ; 22458-07-7 ; 80258-99-7 ; 24782-64-7 ; 1108790-90-4 ; 175204-03-2 ; 97-96-1 ; 780802-33-7 ; 89-98-5
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CAS No. : | 1885-29-6 |
Formula : | C7H6N2 |
M.W : | 118.14 |
SMILES Code : | C1=CC(=C(C=C1)C#N)N |
MDL No. : | MFCD00007631 |
InChI Key : | HLCPWBZNUKCSBN-UHFFFAOYSA-N |
Pubchem ID : | 72913 |
GHS Pictogram: |
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Signal Word: | Danger |
Hazard Statements: | H301+H311+H331-H315-H319-H317 |
Precautionary Statements: | P501-P261-P272-P270-P271-P264-P280-P337+P313-P305+P351+P338-P361+P364-P333+P313-P301+P310+P330-P302+P352+P312-P304+P340+P311-P403+P233-P405 |
Class: | 6.1 |
UN#: | 3439 |
Packing Group: | Ⅲ |
Num. heavy atoms | 9 |
Num. arom. heavy atoms | 6 |
Fraction Csp3 | 0.0 |
Num. rotatable bonds | 0 |
Num. H-bond acceptors | 1.0 |
Num. H-bond donors | 1.0 |
Molar Refractivity | 35.56 |
TPSA ? Topological Polar Surface Area: Calculated from |
49.81 Ų |
Log Po/w (iLOGP)? iLOGP: in-house physics-based method implemented from |
1.22 |
Log Po/w (XLOGP3)? XLOGP3: Atomistic and knowledge-based method calculated by |
1.4 |
Log Po/w (WLOGP)? WLOGP: Atomistic method implemented from |
1.15 |
Log Po/w (MLOGP)? MLOGP: Topological method implemented from |
0.79 |
Log Po/w (SILICOS-IT)? SILICOS-IT: Hybrid fragmental/topological method calculated by |
1.1 |
Consensus Log Po/w? Consensus Log Po/w: Average of all five predictions |
1.13 |
Log S (ESOL):? ESOL: Topological method implemented from |
-1.95 |
Solubility | 1.33 mg/ml ; 0.0113 mol/l |
Class? Solubility class: Log S scale |
Very soluble |
Log S (Ali)? Ali: Topological method implemented from |
-2.05 |
Solubility | 1.05 mg/ml ; 0.00891 mol/l |
Class? Solubility class: Log S scale |
Soluble |
Log S (SILICOS-IT)? SILICOS-IT: Fragmental method calculated by |
-2.07 |
Solubility | 1.0 mg/ml ; 0.00847 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) |
Yes |
Log Kp (skin permeation)? Skin permeation: QSPR model implemented from |
-6.03 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 |
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) |
1.02 |
* 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 |
---|---|---|
With boron trifluoride; In toluene; for 24.0h;Reflux; | General procedure: To a solution of 2-aminobenzonitrile (1.0 mmol) and cyclic ketones (2a-c, n=1, 2 and 3; 1.0 mmol) in dry toluene(8 mL), boron triflurodietherate (1.28 mL) was added slowly with a syringe. The mixture was refluxed for 24 hours with stirring. After cooling the mixture to room temperature, the mixture was dried and the residue thus obtained was treated with 2M NaOH (24 mL) and refluxedfurther for 24 hours. After cooling, the mixture was extracted with CHCl3. The combined organic extracts were evaporated to give colorless to yellow solids (3a-c). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
92.6% | With ammonium iodide; dihydrogen peroxide; acetic acid; at 20℃; for 12h; | General procedure: Followed previous procedures: 1 a mixture of 2-aminobenzonitrile (0.02 mol) and ammonium iodide (0.02 mol) were dissolved in acetic acid (50 mL), and then 30% aqueous hydrogen peroxide solution (0.13 mol) was slowly added at room temperature and stirred for 12 h. After reaction completion, the reaction solution was treated with aqueous sodium thiosulfate solution 40 mL (0.03 mol) and basified to about pH~8 by the addition of 20% sodium hydroxide. The reaction mixture was stirred at room temperature for 0.5 h. The desired product, which was partially precipitated during this step, was isolated by vacuum filtration to afford A as silvery white flake solid (yield 92.6%). |
84.9% | With Iodine monochloride; acetic acid; at 20℃; for 3h; | The 2.0g (16.9mmol) 2- aminobenzonitrile (Compound of Formula II) was dissolved in 20mL glacial acetic acid; was slowly added dropwise 2.8g (17.2 mmol) 10mL glacial acetic acid solution of iodine monochloride dropwise was completed, the reaction mixture was stirred 3H at room temperature; the reaction mixture was poured into 150mL ice water, Suction filtered, the filter cake was washed with water, dried with cyclohexane - toluene: Recrystallization (9 1, v / v), to give 2-amino-5-iodobenzonitrile (formula III Compound) (3.5g, molar yield of 84.9%, HPLC purity 98.7%), |
48% | With ammonium iodide; dihydrogen peroxide; acetic acid; In water; at 20℃; for 12h; | [612] Preparation 52: Synthesis of 2-amino-5-iodo-benzonitrile [613] [614] 2-Amino-benzonitrile (10g, 0.085mol) and ammonium iodide (13.5g, 0.094mol) were dissolved in acetic acid (200mL). 30% aqueous hydrogen peroxide solution (5.3mL, 0.094mL) was slowly added at room temperature and stirred for 12 h. After completion of the reaction, the reaction solution was filtered through celite. The filtrate was treated with aqueous sodium thiosulfate solution and extracted with ethyl acetate. The organic layer was dried over sodium sulfate and filtered. The solid obtained using dichloromethane (10mL) and hexane (200mL) was filtered and dried under nitrogen gas to give the title compound (10g, Yield 48%). [615] NMR: 1H-NMR(CDCl3) delta 7.64 (1H, d), 7.56 (1H, dd), 6.35 (1H, d), 4.44 (2H, br s) [616] Mass(EI) 245 (M++1) [617] |
With Iodine monochloride; acetic acid; at 25 - 35℃; | Example-2; Preparation of N{3-chloro-4-[(3-fluorobenzyloxy]phenyl}-6-[5-([2-methanesulphonyl) ethyl]amino}methyl)-2-furyl]-4-quinazoIinamine. (or) Lapatinib base (1)(i) Preparation of 2-amino-5-iodobenzonitrile (7)Into a one liter four necked round bottomed flask, acetic acid (200 mL), 2-aminobenzonitrile(30.0 g) were charged. To this reaction mass, iodinemonochloride (44 g) in acetic acid (200 mL) solution was added drop-wise at 25-35C. The reaction mass was maintained at 25-350C for about 3 hrs. The completion of the reaction was monitored by TLC. The reaction mass was poured into ice cold water, stirred for 1 hour and filtered and dried under vacuum to get55.0 g of brick-red coloured powder.Purity: 97.1% by HPLC To enhance the purity of the product the following recrystallization process was adopted.Purification:Into a two liter four necked round bottomed flask, 275 mL of toluene and 55 g of crude 2- aminobenzonitrile as obtained above were charged. The mass was stirred for 30 min and clarified with activated carbon (5g) and filtered. To the filtrate 825 mL of hexane was added and stirred for 1 hr. at 25-30 C to crystallize out the product. The product was filtered and dried under vacuum at 30-40 C to get 46.5 g of 2-amino-5-iodobenzonitrile as a pinkish coloured crystalline powder.Melting -range: 85 to 87 CPurity : 99.89% by HPLC | |
With Iodine monochloride; acetic acid; at 25 - 35℃; for 3h; | Example-1 Preparation of N {3-chloro-4-[(3-fluorobenzyloxy] phenyl}-6-[5-([2- methanesulphonyl)ethyl]amino}methyl)-2-furyl]-4-quinazoIinamine. (or) Lapatinib base (1)(i) Preparation of 2-amino-S-iodobenzonitrile (7)Into a one liter four necked round bottomed flask, acetic acid (200 mL), 2- aminobenzonitrile (30.0 g) were charged. To this reaction mass, iodinemonochloride (44 g) in acetic acid (200 mL) solution was added drop-wise at 25-35C. The reaction mass was maintained at 25-35C for about 3 hrs. The completion of the reaction was monitored by TLC. The reaction mass was poured into ice cold water, stirred for 1 hour and filtered and dried under vacuum to get 55.0 g of brick -red coloured powder. Purity: 97.1% by HPLCTo enhance the purity of the product the following recrystall ization process was adopted. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
73% | In DMF (N,N-dimethyl-formamide); at 20℃; for 18h; | N-iodosuccinimide (11.35 g, 50.4 mmol) was added in several portions at room temperature to a solution of anthranilonitrile (Aldrich, 5.87 g, 49.7 mmol) in DMF (80 mL) and stirred under N2 for 18 h. The reaction mixture was concentrated to [1/4] volume and diluted with [H20] (200 mL) and [CH2C12.] The phases were separated. The organic phase was washed with H2O, dried [(NA2SO4),] and concentrated in vacuo to give 14 g of dark liquid that was dissolved in hot ethanol and diluted with ca. 100 mL of hot H2O. The solution was cooled to room temperature overnight. The crystallized mixture was filtered and the pink mica-like sheets were washed with [H20] and dried in a vacuum oven at [40 C] to give 8. 85 g (73%) of product; mp [76-78 C] : MS (EI) [INTO] (rel. intensity) 244 (M+, 99), 245 (12), 127 (9), 118 (9), 117 (72), 90 (75), 84 (11), 64 (14), 63 (42), 62 (13). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
In acetic acid; at 25 - 35℃; for 3h; | (i) Preparation of 2-amino-5-iodobenzonitrile (7)Into a one liter four necked round bottomed flask, acetic acid (200 mL), 2-aminobenzonitrile (30.0 g) were charged. To this reaction mass, iodinemonochloride (44 g) in acetic acid (200 mL) solution was added drop-wise at 25-35 C. The reaction mass was maintained at 25-35 C. for about 3 hrs. The completion of the reaction was monitored by TLC. The reaction mass was poured into ice cold water, stirred for 1 hour and filtered and dried under vacuum to get 55.0 g of brick-red coloured powder.Purity: 97.1% by HPLCTo enhance the purity of the product the following recrystallization process was adopted.Purification:Into a two liter four necked round bottomed flask, 275 mL of toluene and 55 g of crude 2-aminobenzonitrile as obtained above were charged. The mass was stirred for 30 min and clarified with activated carbon (5 g) and filtered. To the filtrate 825 mL of hexane was added and stirred for 1 hr. at 25-30 C. to crystallize out the product. The product was filtered and dried under vacuum at 30-40 C. to get 46.5 g of 2-amino-5-iodobenzonitrile as a pinkish coloured crystalline powder.Melting-range: 85 to 87 C.Purity: 99.89% by HPLC |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
87% | With aluminum tri-bromide; carbon tetrabromide; In neat (no solvent); at 15 - 20℃; for 0.0833333h;Green chemistry; | General procedure: A mixture of the appropriate adamantane/norbornane (1 mmol), amine (1 mmol), AlBr3 (0.5 mmol) and CBr4 (0.5 mmol) was ground in a mortar and pestle at room temperature till the completion of reaction as indicated by TLC (5-10 min). The product of azole derivatives were purified by recrystallization from ethyl alcohol, and the other amine derivatives were purified by column chromatography using ethyl acetate and petroleum ether mixtures as the mobile phase. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
83% | With p-nitrobenzenesulfonic acid; palladium diacetate; In tetrahydrofuran; water; at 80℃; for 48h;Inert atmosphere; Schlenk technique; | General procedure: Under a N2 atmosphere, a Schlenk tube was charged with 2-aminobenzonitrile 1 (0.3 mmol),sodium arylsulfinate 2 (0.6 mmol), Pd(OAc)2 (10 mol %), bpy (20 mol %), p-NBSA (10 equiv), THF (2 mL), and H2O (1 mL) at room temperature. The reaction mixture was stirred vigorously at 80 C for 48 h. The mixture was poured into ethyl acetate, which was washed with saturated NaHCO3 (2 × 10 mL) and then brine (1 × 10 mL). After the aqueous layer was extracted with ethyl acetate, the combined organic layers were dried over anhydrous MgSO4 and evaporated under reduced pressure. The residue was purified by flash column chromatography (hexane/ethyl acetate) to afford the desired products 3. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
79% | With stannous chloride; In toluene; for 3h;Reflux; | 40 g of 2-aminobenzonitrile was dissolved in 300 ml of toluene.Add 16 grams of the formula V3-cyclopropyl-3-oxo-propionic acid methyl ester (R=methyl)And 73 grams of tin chloride,Then, the temperature was raised to reflux reaction for 3 hours.After the reaction,Down to room temperature,Add water to dilute the layering,The organic layer was washed twice with saturated brine.Dry over anhydrous sodium sulfate,Filtered, and the filtrate was concentrated to dryness under reduced pressure.27 grams of compound IVMethyl 4-amino-2-cyclopropyl-3-quinolinecarboxylate,The yield was 79%.Send feedbackHistorySaved |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
19% | With 1,8-diazabicyclo[5.4.0]undec-7-ene; In 1-methyl-pyrrolidin-2-one; at 250℃; for 0.2h;Flow reactor; | General procedure: Selective N-monomethlyation reactions were performed in a Vapourtec E-series continuous flow system equipped with a high temperature tube reactor (10 mL, stainless steel, 0.03'' i.d., Fig. 2 ) and a membrane back pressure regulator (Zaiput). Stock solutions of aniline (20 mmol, 1.0 equiv, 2 M), DMC (5.05 mL, 60 mmol, 3.0 equiv, 6 M), and DBU (4.47 mL, 30 mmol, 1.5 equiv, 3 M) were prepared in oven-dried 10 mL volumetric flasks using NMP as the solvent. The solutions were transferred to screw-thread vials with septum caps and reagents were pumped directly from the vials. After the high temperature coiled tube reactor was heated to 250 C, peristaltic pumps (Vapourtec V-3) were used to pump the reactant solutions into the system (0.277 mL/min each for a 12 min residence time). The solutions were mixed with a cross-mixer (0.4? i.d.), passed though the high temperature coiled tube reactor. Upon exiting the reactor, the reaction stream was passed through a short segment of stainless steel tubing to enable the reaction to cool and then exited the system by passage through the back pressure regulator (Note: PFA fittings should not be used at the exit of the reactor as they will deform due to the high temperature of the reaction stream and cause leaks in the system. Stainless steel connectors and tubing (12'') were used in our system.). After the flow system was equilibrated for 18 min, the product stream was collected for 5 min (2.77 mmol of aniline). The crude mixture was dissolved in ethyl acetate and washed with brine. The combined organic layers were dried over magnesium sulfate, filtered, and concentrated under reduced pressure. The residue was purified by column chromatography (Biotage 25 g Ultra-sil, 3-15% ethyl acetate in hexanes) to afford the desired product. |