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Selective and Cell-Active PBRM1 Bromodomain Inhibitors Discovered through NMR Fragment Screening
Shifali Shishodia ; Raymundo Nu?ez ; Brayden P. Strohmier , et al. J. Med. Chem.,2022,65(20):13714-13735. DOI: 10.1021/acs.jmedchem.2c00864 PubMed ID: 36227159
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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.
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 ...More
CAS No. : | 1885-29-6 | MDL No. : | MFCD00007631 |
Formula : | C7H6N2 | Boiling Point : | - |
Linear Structure Formula : | C6H4(CN)(NH2) | InChI Key : | HLCPWBZNUKCSBN-UHFFFAOYSA-N |
M.W : | 118.14 | Pubchem ID : | 72913 |
Synonyms : |
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Signal Word: | Danger | Class: | 6.1 |
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 | UN#: | 3439 |
Hazard Statements: | H301+H311+H331-H315-H319-H317 | Packing Group: | Ⅲ |
GHS Pictogram: |
* 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 |
---|---|---|
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. |