Structure of 5779-93-1
                                
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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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                        | CAS No. : | 5779-93-1 | 
| Formula : | C9H10O | 
| M.W : | 134.18 | 
| SMILES Code : | CC1=C(C=O)C=CC=C1C | 
| MDL No. : | MFCD00798004 | 
| InChI Key : | UIFVCPMLQXKEEU-UHFFFAOYSA-N | 
| Pubchem ID : | 34224 | 
| GHS Pictogram: | 
                                
                                
                                     
                                
                                
                             | 
| Signal Word: | Warning | 
| Hazard Statements: | H227-H315-H319-H335 | 
| Precautionary Statements: | P305+P351+P338 | 
| Num. heavy atoms | 10 | 
| Num. arom. heavy atoms | 6 | 
| Fraction Csp3 | 0.22 | 
| Num. rotatable bonds | 1 | 
| Num. H-bond acceptors | 1.0 | 
| Num. H-bond donors | 0.0 | 
| Molar Refractivity | 41.76 | 
| TPSA ? Topological Polar Surface Area: Calculated from   | 
                                            17.07 Ų | 
| Log Po/w (iLOGP)? iLOGP: in-house physics-based method implemented from   | 
                                            1.82 | 
| Log Po/w (XLOGP3)? XLOGP3: Atomistic and knowledge-based method calculated by   | 
                                            2.3 | 
| Log Po/w (WLOGP)? WLOGP: Atomistic method implemented from   | 
                                            2.12 | 
| Log Po/w (MLOGP)? MLOGP: Topological method implemented from   | 
                                            2.1 | 
| Log Po/w (SILICOS-IT)? SILICOS-IT: Hybrid fragmental/topological method calculated by   | 
                                            2.92 | 
| Consensus Log Po/w? Consensus Log Po/w: Average of all five predictions  | 
                                            2.25 | 
| Log S (ESOL):? ESOL: Topological method implemented from   | 
                                            -2.5 | 
| Solubility | 0.425 mg/ml ; 0.00317 mol/l | 
| Class? Solubility class: Log S scale   | 
                                            Soluble | 
| Log S (Ali)? Ali: Topological method implemented from   | 
                                            -2.3 | 
| Solubility | 0.678 mg/ml ; 0.00505 mol/l | 
| Class? Solubility class: Log S scale   | 
                                            Soluble | 
| Log S (SILICOS-IT)? SILICOS-IT: Fragmental method calculated by   | 
                                            -3.09 | 
| Solubility | 0.11 mg/ml ; 0.000818 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)  | 
                                            No | 
| Log Kp (skin permeation)? Skin permeation: QSPR model implemented from   | 
                                            -5.49 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   | 
                                            2.0 | 
| 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)  | 
                                            1.0 | 
* 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 | 
|---|---|---|
| 95% | Methanol (70OmL), sodium bicarbonate (43.4 g, 516 mmol), <strong>[5779-93-1]2,3-dimethylbenzaldehyde</strong> (46.2g, 344 mmol), and cyclopropylamine (29 mL, 413 mmol) were combined. The mixture was heated to 67 0C for 30 min. The mixture was cooled to 5 0C and sodium borohydride (15.6 g. 413 mmol) was added in portions to keep temperature below 20 0C. Once addition was completed, the reaction mixture was concentrated to remove MeOH. The white residue was taken up in 50OmL CH2Cb and 50OmL water. Water layer was cut and organic layer was washed twice with 50OmL Na2CO3 10percent aq., then dried over MgSO4. Organics were concentrated to give a colorless oil. The oil was dissolved in 500 mL MTBE and stirred at 5 0C as HCl in Et2O (189 mL of 2 N) was added slowly. After addition was complete, solids were filtered off and washed with MTBE. Solids were dried under vacuum to give 57.36g (79percent yield) of a white solid.; Preparation of 2,3-Dimethylbenzylamine 1 1-4:<strong>[5779-93-1]2,3-Dimethylbenzaldehyde</strong> (16.14 g, 120 mmol) was added to a mixture OfNaHCO3 (15.2 g, 180 mmol) and cyclopropylamine (8.24 g, 144 mmol) in MeOH (32 mL) and the resulting suspension was refluxed for 4 h, then cooled to 0 0C. NaBH4 (5.46 g, 144 mmol) was added portion-wise and the mixture was aged 18 h. The mixture was concentrated and partitioned between CH2Cl2 (100 mL) and water (200 mL). The organic layer was washed with brine (100 mL), filtered through cotton and <n="54"/>concentrated. The residue assayed at 20 g (95percent). The material was dissolved in Et2O (200 mL) and 2N HCl (1.1 equiv) was added. The resulting suspension was filtered to afford 20.5 g of white solid HCl salt of the desired amine UA- 1H NMR (400 MHz, DMSO): delta 9.23 (s, 2H), 7.31 (d, IH), 7.20 (d, IH), 7.13 (t, IH), 4.22 (s, 2H), 2.71 (s, IH), 2.26 (d, 5H), 0.90 (s, 2H), 0.79-0.73 (m, 2H). | |
| 87% | Cyclopr opyl-(2,3-dimethylbenzyl)amine (11); EPO <DP n="18"/>A mixture of 2,3-dichlorobenzaldehyde (68.9 g, 514 mmol) and cyclopropylamine (72 mL, 1.02 mol) in dry MeOH (1300 mL) was stirred at rt overnight. The reaction mixture was cooled to 0 °C, and NaBH4 (25.3 g, 668 mmol) was added. The reaction mixture was stirred again at rt overnight. Ice was added to the reaction mixture, and the solvents were evaporated under reduced pressure. The residue was dissolved in EtOAc, and was washed with aq. IM NaOH. The aq. layer was extracted with EtOAc (3x). The combined org. extracts were dried over MgSO4, filtered, and the solvents were removed under reduced pressure. Purification of the residue by FC (EtOAc / heptane 9:1 - > 1:1) yielded the title compound (78.4 g, 87percent). LC-MS: tR = 0.84 min; ES+: 176.13. | |
| Amine 1N-(2,3-Dimethylbenzyl)cyclopropanamineA mixture of <strong>[5779-93-1]2,3-dimethylbenzaldehyde</strong> (1 eq.), cyclopropylamine (1.2 eq.) and sodium bicarbonate (1.5 eq.) were heated at reflux in MeOH (0.5 M) for 1 h. The reaction mixture was then cooled in ice and sodium borohydride (1.2 eq.) was introduced portionwise. Following the completion of addition, the reaction mixture was warmed to RT and stirred at RT for 1 h. The volatiles were then removed in vacuo and the resulting residue was partitioned between H2O and CH2Cl2. The organic layer was separated, washed with brine, dried over MgSO4 and filtered. Concentration of the filtrate in vacuo afforded the title compound as a light yellow oil | 
                                                    
                                                    [ 82074-39-3 ]
                                                    
                                                    [ 5779-93-1 ]
                                                    
                                                    [ 14205-39-1 ]
| Yield | Reaction Conditions | Operation in experiment | 
|---|---|---|
| In methanol; ethanol; | EXAMPLE 17 4-(2,3-Dimethylphenyl)-1,4,5,6,7,8-hexahydro-2,7-dimethyl-5-oxo-1,7-naphthyridine-3-carboxylic acid methyl ester 1-Methyl-3-oxo-5-hydroxy-1,2,3,6-tetrahydropyridine (6.36 g.), 5.93 g. of methyl-3-aminocrotonate (97percent), 11 g. of <strong>[5779-93-1]2,3-dimethylbenzaldehyde</strong> and 100 ml. of ethanol were refluxed for 3 hours. The mixture was filtered while hot and then left standing overnight. The precipitated solid was separated by filtration. The solid was suspended in methanol and saturated with hydrogen chloride. The solvent removed in vacuo. The residue was recrystallized from ethanol to obtain the title compound as the hydrochloride, m.p. 244°-247° C. dec. Analysis for: C20 H24 N2 O3.HCl: Calculated: C, 63.73; H, 6.68; N, 7.43; Cl, 9.41. Found: C, 63.85; H, 6.77; N, 7.38; Cl, 9.33. | 
                                                    
                                                    [ 5779-93-1 ]
                                                    
                                                    [ 15057-43-9 ]
                                                    
                                                    [ 14205-39-1 ]
| Yield | Reaction Conditions | Operation in experiment | 
|---|---|---|
| In methanol; ethanol; | EXAMPLE 20 4-(2,3-dimethylphenyl)-1,4,5,6,7,8-hexahydro-2-methyl-5-oxo-7-(phenylmethyl)-1,7-naphthyridine-3-carboxylic acid methyl ester A mixture of 16.2 g. of 1-benzyl-3-oxo-5-hydroxy-1,2,3,6-tetrahydropyridine, 9.2 g. of methyl-3-aminocrotonate, 11.6 g. of <strong>[5779-93-1]2,3-dimethylbenzaldehyde</strong> and 180 ml. of ethanol was heated at reflux for 3 hours. The solvent was removed in vacuo and the residue was recrystallized from ethanol to obtain 14 g. of solid, m.p. 208°-211° C. The solid was suspended in methanol and saturated with hydrogen chloride. The solvent was removed in vacuo. The residue was recrystallized from methanol to obtain the title compound as the hydrochloride, m.p. 238°-239° C. d. Analysis for: C26 H28 N2 O3.HCl: Calculated: C, 68.94; H, 6.45; N, 6.18; Cl, 7.83. Found: C, 68.78; H, 6.51; N, 6.41; Cl, 7.77. | 

                                                    
                                                    [ 5779-93-1 ]
| Yield | Reaction Conditions | Operation in experiment | 
|---|---|---|
| With pyridine; zinc diiodide; In dichloromethane; aluminium; | A mixture of <strong>[5779-93-1]2,3-dimethylbenzaldehyde</strong> (2 g) and (1-ethoxycyclopropyl)oxy]trimethylsilane (3.6 mL) in dry dichloromethane (20 mL) is added dropwise to a stirred suspension of zinc iodide (<100 mg) in dry dichloromethane (25 mL) under nitrogen. The reaction flask is wrapped in aluminium foil and stirring is continued for 3 hours. The reaction mixture is treated with dry pyridine (10 mL) and stirring continued for 15 minutes. The reaction mixture is washed three times with water (50 mL), twice with brine (50 mL), dried over magnesium sulphate and evaporated to give ethyl (RS)-4-(2,3-dimethylphenyl)-4-hydroxybutanoate (3.6 g) as a yellow oil. | 
| Yield | Reaction Conditions | Operation in experiment | 
|---|---|---|
| 26% | With hydrogenchloride; sodium hydroxide; tetrabutylammomium bromide; In dichloromethane; water; at 20℃; for 6h; | To a mixture of tetrabutylammonium bromide (1.08 g, 3.3 mmol) in dichloromethane (80 mL) and aqueous NaOH (50percent w/w solution, 10 mL) was added 4 (13.7 mL, 67 mmol) and 5 (4.50 g, 33.5 mmol). The mixture was stirred at room temperature for 6 h followed by the addition of 1 M HCl (200 mL). The product was extracted with dichloromethane (250 mL) and the organic phase washed with 1 M HCl (200 mL), dried over Na2SO4 and concentrated under vacuum. The resulting thick yellow oil was purified over silica gel with ether and hexanes as eluent to give 6 (3.06 g, 26percent) as a yellow solid, along with an additional 1.67 g of less pure material. LRMS (M+H+) m/z = 357.1 | 
                                                    
                                                    [ 610321-50-1 ]
                                                    
                                                    [ 5779-93-1 ]
| Yield | Reaction Conditions | Operation in experiment | 
|---|---|---|
| 65% | Example 1; J-6-1 [ (2, 3-dimeLhyl-benzyl)- (1 (2) H-tetrazol-5-ylme I- amino]-methyl}-1, 2, 3, 4, 4a, 5, 6, 7, 8, 8a-decahYdroisoquinoline-3-carboxylic acid dihydrochloride; A. Ethyl (3S, 4aR, 6S, 8aR)-6-[(2, 3-dimethyl-benzyl)-(1 (2) H-tetrazol-5- ylmethyl)-amino]-methyl}-2- (methoxycarbonyl)-1, 2,3, 4,4a, 5,6, 7,8, 8a- decahydroisoquinoline-3-carboxylate; To a solution of 1.30 g (3.42 mmol) of ethyl (3S, 4aR, 6S, 8aR)-6- [(1 (2) H- tetrazol-5-ylmethyl)-amino]-methyl}-2-methoxycarbonyl-1, 2,3, 4,4a, 5,6, 7,8, 8a- decahydroisoquinoline-3-carboxylate (Preparation 2) in 50 mL of 1,2-dichloroethane at room temperature is added <strong>[5779-93-1]2,3-dimethylbenzaldehyde</strong> (800 mg, 5.96 mmol) and acetic acid (1.18 mL, 20.62 mmol). After stirring 3 hours, 2.01 g (9.57 mmol) of sodium triacetoxyborohydride is added. The reaction mixture is stirred overnight at room temperature, quenched with a saturated solution of sodium bicarbonate and extracted with three portions of ethyl acetate. The combined organic extracts are dried over sodium sulfate, filtered and concentrated to dryness. The crude reaction product is purified by flash chromatography (Silica gel, ethyl acetate, ethyl acetate-acetic acid, 10: 1) to afford 1.53g (65percent yield) of the title compound. Ion Electrospray Mass Spectrum M+1 : 499 | 
| Yield | Reaction Conditions | Operation in experiment | 
|---|---|---|
| 84% | Example 1 (step a); Preparation of (2,3-Dimethylphenyl)-(3-trityl-3H-imidazol-4-yl)methanol A solution of isopropylmagnesium bromide in tetrahydrofuran (48 mL, 0.046 mol) was added to a stirred solution of 4-iodo-1-trityl-1 H-imidazole (19.0 g, 0.046 mol) in dichloromethane (180 mL) at 10 to 15°C. The reaction mixture was allowed to warm to the ambient temperature and was stirred at ambient temperature for 1 hour. The reaction mixture was then cooled to 10-15°C, at which point a solution of <strong>[5779-93-1]2,3-dimethylbenzaldehyde</strong> (6.2 mL, 0.046 mol) in dichloromethane (10 mL) was added, while not exceeding 20 to 25°C. After additional stirring for 1 hour at ambient temperature a 10percent aqueous ammonium chloride solution (200 mL) was added to the reaction mixture. The organic layer was separated and washed with an aqueous sodium chloride solution (150 mL), thereafter the organic layer was concentrated to a volume of 40 mL. A precipitate of (2,3-dimethylphenyl)-(3-trityl-3H-imidazol-4-yl)methanol was obtained upon cooling the distillation residue to 4°C and it was separated by filtration, then washed with dichloromethane (50 mL). The intermediate (2,3-dimethylphenyl)-(3-trityl-3H-imidazol-4-yl)methanol was dried at ambient temperature. The yield was 17.4 g (84 percent) of a white or off-white powder, having a melting temperature of 203.0 to 207.0°C. | 
| Yield | Reaction Conditions | Operation in experiment | 
|---|---|---|
| 83% | Step 2: A solution of <strong>[5779-93-1]2,3-dimethylbenzaldehyde</strong> (50.0 g) in 200 ml of THF was treated at room temperature with a solution of lithium hexamethyl disilazane (LiHMDS) in toluene (410 ml, 1.0 M-solution, 1.1 equivalent) dropwise and the stirring was continued for 1.5 hours.To this solution was added the solution of 3,5-dimethylbenzyl magnesium chloride prepared as described above dropwise. Stirring was continued afterwards for 2 hours at 35°C. . The reaction was quenched by the cautious addition of 300 ml of potassium carbonate solution (5 wtpercent in water), extracted three times with diethyl ether and the combined organic phases were washed with water, dried over sodium sulphate and the solvent evaporated. The residue was purified on silica gel with a gradient of petrol ether/ethyl acetate and methanol/ethyl ace- tate. This yielded 78 g (83percent) of the title compound 2-(3,5-dimethylphenyl)-1-(2,3-dimethylphenyl)-ethylamine as a yellowish oil. | 
| Yield | Reaction Conditions | Operation in experiment | 
|---|---|---|
| In tetrahydrofuran; at 20℃; | Step 2; Methylmagnesium chloride solution 3M in THF at about 20 0C. Workup with methylene chloride |