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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.
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CAS No. : | 936-08-3 | MDL No. : | MFCD00672930 |
Formula : | C7H4BrClO2 | Boiling Point : | No data available |
Linear Structure Formula : | - | InChI Key : | USMQLFCVCDEXAK-UHFFFAOYSA-N |
M.W : | 235.46 | Pubchem ID : | 33126 |
Synonyms : |
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Signal Word: | Warning | Class: | |
Precautionary Statements: | P261-P301+P312-P302+P352-P304+P340-P305+P351+P338 | UN#: | |
Hazard Statements: | H302-H315-H319-H335 | Packing Group: | |
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 |
---|---|---|
99% | Step 1: Synthesis of 1-(2-bromo-4-chloro-phenyl)-2,2,2-trifluoro-ethanone. To a 500 ml 2 necked RB flask containing anhydrous methanol (300 ml) was added thionyl chloride (29.2 ml, 400 mmol) dropwise at 0-5 C. (ice water bath) over 10 min. The ice water bath was removed, and 2-bromo-4-chloro-benzoic acid (25 g, 106 mmol) was added. The mixture was heated to mild reflux for 12 h. Progress of the reaction was monitored by TLC and LCMS. After completion of the reaction, the reaction mixture was concentrated. Crude product was dissolved in dichloromethane (DCM, 250 ml), washed with water (50 ml), sat. aq. NaHCO3 (50 ml), brine (50 ml), dried over sodium sulfate, and concentrated to give the 2-bromo-4-chloro-benzoic acid methyl ester (26 g, 99%), which was directly used in the following step. | |
99% | With thionyl chloride; at 0℃;Reflux; | Thionyl chloride (29.2 ml, 400 mmol) was added dropwise over 10 minutes at 0-5 C (ice-water bath) in a 500 ml 2-necked RB flask containing anhydrous methanol (300 ml).Remove the ice-water bath and add 2-bromo-4-chloro-benzoic acid (25 g, 106 mmol).The mixture was heated to moderate reflux for 12 hours.Reaction progress was monitored by TLC and LCMS. After completion of the reaction, the reaction mixture was concentrated.The crude product was dissolved in dichloromethane (DCM, 250 ml)Washed with water (50 ml), saturated aqueous NaHCO3 (50 ml), brine (50 ml)Dried over sodium sulfate,Concentration gave 2-bromo-4-chloro-benzoic acid methyl ester (26 g, 99%) which was used directly in the next step. |
98% | With sulfuric acid;Cooling with ice; Heating; Reflux; | Concentrated sulfuric acid (5 ml_) was added drop-wise to an ice-cold mixture of 2- bromo-4-chloro-benzoic acid (10.14 g, 0.0431 mol) and methanol (40 ml_). The resulting mixture was heated at reflux for 17 hours. After this time, the reaction mixture was cooled to room temperature, and then poured into ice-cold water (150 ml_), creating a white suspension. The suspension was extracted with ethyl acetate (150 ml_). The organic phase was washed with saturated aqueous NaHCO3 (I OO ml_), followed by saturated aqueous NaCI (100 ml_). The organic layer was dried over Na2SO4, filtered, and concentrated to afford 2-bromo-4-chloro-benzoic acid methyl ester (10.57 g, 98% yield) as a clear oil. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
99% | With thionyl chloride; In methanol; dichloromethane; | Step 1: Synthesis of 1-(2-bromo-4-chloro-phenyl)-2,2,2-trifluoro-ethanone. To a 500 ml 2 necked RB flask containing anhydrous methanol (300 ml) was added thionyl chloride (29.2 ml, 400 mmol) dropwise at 0-5° C. (ice water bath) over 10 min. The ice water bath was removed, and 2-bromo-4-chloro-benzoic acid (25 g, 106 mmol) was added. The mixture was heated to mild reflux for 12 h. Progress of the reaction was monitored by TLC and LCMS. After completion of the reaction, the reaction mixture was concentrated. Crude product was dissolved in dichloromethane (DCM, 250 ml), washed with water (50 ml), sat. aq. NaHCO3 (50 ml), brine (50 ml), dried over sodium sulfate, and concentrated to give the 2-bromo-4-chloro-benzoic acid methyl ester (26 g, 99percent), which was directly used in the following step. |
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