Selective and Cell-Active PBRM1 Bromodomain Inhibitors Discovered through NMR Fragment Screening

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 K d 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.

Rational design and development of selective BRD7 bromodomain inhibitors and their activity in prostate cancer

“…48,[51][52][53][54][55][56] Therefore, we also performed RNA-Seq with a BRG1/BRM degrader that eliminates all BAF complexes (ACBI1), a cBAF-specific inhibitor (BD98), a BRD9 degrader that eliminates GBAF complexes (dBRD9), and a PBRM1-specific BD inhibitor to target PBAF (PB16) (Figure 8F). 23,24,31,38 In agreement with their modes of action, we found the largest changes in gene expression with ACBI1, which eliminates all BAF functions, and the next largest with BD98, which targets the most abundant cBAF subcomplex. In contrast, we found smaller changes in gene expression with dBRD9 or PB16, which target the less abundant GBAF and PBAF subcomplexes, respectively.…”

“…We observed that reduced expression of BRD7 decreased cell proliferation in AR-positive cells while having little to no effect on normal epithelial prostate cells or AR-negative PCa cells, an effect similar to, but more pronounced than what we previously observed for PBRM1 (Figure 7D). 31 Both 1-78 and 2-77 inhibited cell growth of LNCaP cells at all three tested concentrations (5, 1 and 0.1 µM) while being active in PC-3 only at the highest concentration (5 µM), in agreement with a greater BRD7 dependency in AR-positive PCa (Figure 7E and 7F). To evaluate if the activity of the compounds could be related to off-target BRD9 or BRPF1 inhibition, we treated LNCaP and PC-3 cells with BI7273 and GSK-5959 at 5, 1 and 0.1 µM and observed little to no effect with either compound (Figure 7E and 7F).…”

“…57 The second, fourth, and fifth BDs of PBRM1 (BD2, BD4, and BD5, respectively) are most critical for PBAF function by binding H3K14Ac (BD2 and BD5) and acetylated p53 (BD4), and as such, BD inhibitors have been developed for BD5 and BD2. 31,36,46,58,59 The functional role of the BD of BRD7 in PBAF is less defined. PBAF has recently been implicated in prostate and breast cancer progression through response to oxidative stress; however, the contribution of the BRD7 BD is yet to be addressed.…”

“…[19][20][21][22] Multiple compounds have been developed to target BAF complex subunits, including small molecules and proteolysis targeting chimeras (PROTACs); however, most of the subunits have yet to be explored as targets in disease. [23][24][25][26][27][28][29][30][31][32][33][34][35][36][37][38][39][40] In the human proteome, there are forty-six bromodomain-containing proteins that are predicted to recognize acetylated Lys in proteins, most commonly histones. 1 Bromodomains (BDs) are therapeutic targets in multiple diseases, and several BD inhibitors are currently under phase I, II, or III clinical studies (www.clinicaltrials.gov).…”

Rational Design and Development of Selective BRD7 Bromodomain Inhibitors and Their Activity in Prostate Cancer

“…The BRG1-associated factor (BAF) complexes function as ATP-dependent chromatin remodelers and consist of three biochemically distinct complexes: canonical BAF (cBAF), polybromo-associated BAF (PBAF), and GLTSCR1/like-containing BAF (GBAF or ncBAF) (Figure A). − All three types of BAF complexes share the ATPase and several core subunits but also contain unique subunits. BAF complexes are the most frequently mutated chromatin remodeling complex in cancer, and different subunits, in cooperation with the catalytic subunits BRM and BRG1, play crucial roles in regulating chromatin accessibility. − Multiple compounds have been developed to target BAF complex subunits, including small molecules and proteolysis targeting chimeras (PROTACs); however, most of the subunits have yet to be explored as targets in disease. − …”