Identification and Development of 2,3-Dihydropyrrolo[1,2-a]quinazolin-5(1H)-one Inhibitors Targeting Bromodomains within the Switch/Sucrose Nonfermenting Complex

Abstract

Bromodomain containing proteins PB1, SMARCA4, and SMARCA2 are important components of SWI/SNF chromatin remodeling complexes. We identified bromodomain inhibitors that target these proteins and display unusual binding modes involving water displacement from the KAc binding site. The best compound binds the fifth bromodomain of PB1 with a KD of 124 nM, SMARCA2B and SMARCA4 with KD values of 262 and 417 nM, respectively, and displays excellent selectivity over bromodomains other than PB1, SMARCA2, and SMARCA4.

DNA binding drives the association of BRG1/hBRM bromodomains with nucleosomes

“…These studies demonstrate that under normal cellular levels of histone acetylation, inhibition of hBRM/BRG1 BRD acetyl-lysine binding does not lead to a measureable decrease in recovery time in FRAP assays171825. However, treatment of ESCs with the BRD inhibitor PFI-3 did lead to defects in stem cell maintenance and differentiation, suggesting that acetyl-lysine binding is in fact critical for proper BAF function17.…”

“…In addition, deletion of the BRM BRD led to a modest effect on the ability of BRM to bind nucleosome templates in vitro and to reverse the transformed phenotype in Ras-transformed fibroblasts. However, BRG1 BRD has only millimolar affinity for acetylated histone tails2324, and small molecule inhibition of BRG1/BRM BRD does not decrease BRG1/BRM chromatin association in cells unless pre-treated with HDAC inhibitors171825. Therefore, the potential role of the BRD in targeting the BAF complex to acetylated chromatin and its therapeutic potential has not yet been resolved.…”

Large-scale analysis of water stability in bromodomain binding pockets with grand canonical Monte Carlo

“…Gerstenberger et al 11 started from the same fragment and developed another potent chemical probe with a similar selectivity profile. At the same time, Sutherell et al 12 reported the discovery of another series of ligands, also targeting Family VIII and displacing all four waters from their pocket, based on a 2,3-dihydropyrrolo[1,2-a]quinazolin-5(1H)-one scaffold. Myrianthopoulos et al 13 reported the discovery of a pyrazoloisocoumarin ligand, selective for PB1 (5), which too displaces the conserved water network of the protein.…”

Advancements in the Development of non‐BET Bromodomain Chemical Probes

“…Sutherell and co‐workers have developed a collection of potent and selective SMARCA2/4/PB1 bromodomain inhibitors (Figure b). Starting from a weakly potent, and poorly soluble, dihydropyrroloquinazolinone hit compound 98 , structure guided optimization led to lead compound 99 . X‐ray crystallography was used to identify the two key hydrogen bond interactions between the carbonyl group and nitrogen atom of the 4‐quinazolinone scaffold, and the conserved Tyr696 and Asn739 respectively.…”

“…Starting from aw eakly potent, and poorly soluble, dihydropyrroloquinazolinone hit compound 98,s tructure guidedo ptimization led to lead compound 99. [124] X-ray crystallography was used to identify the two key hydrogen bond interactions between the carbonyl group andn itrogen atom of the 4-quinazolinone scaffold, and the conserved Tyr696 and Asn739r espectively.S imilarly to SMARCA2/4/PB1(5)i nhibitors 96 and 97,c ompound 99 demonstratedc omplete displacement of the conserved water molecules found within the bind- ing pocket of SMARCA4 ( Figure 16 f). Ah alogen bond between the chlorine atom and the carbonyl of am ethionine residue (Met731) was also observed via X-ray crystallography.S ubstitution of the chlorine for ab romine, in an attemptt oc reate a stronger halogenb ond, was countered by the steric constraint of the cavity.C ompound 99 demonstrated potency forP B1 (pK D = 6.9), SMARCA2B (pK D = 6.6) and SMARCA4 (pK D = 6.4), and selectivity against as election of other representative bromodomains (BRD4, PCAF,C REBBP,T RIM33B).…”