GNE-371, a Potent and Selective Chemical Probe for the Second Bromodomains of Human Transcription-Initiation-Factor TFIID Subunit 1 and Transcription-Initiation-Factor TFIID Subunit 1-like

Abstract

The biological functions of the dual bromodomains of human transcription-initiation-factor TFIID subunit 1 (TAF1(1,2)) remain unknown, although TAF1 has been identified as a potential target for oncology research. Here, we describe the discovery of a potent and selective in vitro tool compound for TAF1(2), starting from a previously reported lead. A cocrystal structure of lead compound 2 bound to TAF1(2) enabled structure-based design and structure−activity-relationship studies that ultimately led to our in vitro tool compound, 27 (GNE-371). Compound 27 binds TAF1(2) with an IC 50 of 10 nM while maintaining excellent selectivity over other bromodomain-family members. Compound 27 is also active in a cellular-TAF1(2) target-engagement assay (IC 50 = 38 nM) and exhibits antiproliferative synergy with the BET inhibitor JQ1, suggesting engagement of endogenous TAF1 by 27 and further supporting the use of 27 in mechanistic and target-validation studies.

Advancements in the Development of non‐BET Bromodomain Chemical Probes

“…Substitution of the N ‐methyl group of hit molecule 62 for a 1‐butene group ( 92 ) dramatically reduced the potency for BRD4, BRD9, BRPF1, CREBBP and CECR2, whilst maintaining sub‐micromolar potency for TAF1(2) (pIC 50 =7.3) (Figure c). Compound 92 was subjected to iterative structure‐based design leading to TAF1(2)/TAF1L(2) chemical probe GNE‐371 ( 93 ) . Introduction of a morpholine group to the benzamide provided an optimal occupancy of the lipophilic‐shelf region and an accompanying boost in TAF1(2) potency.…”

Optimization of Naphthyridones into Selective TATA-Binding Protein Associated Factor 1 (TAF1) Bromodomain Inhibitors

“…Additionally, a bivalent molecule designed to inhibit the BET bromodomains was also reported to inhibit TAF1(2), although it is unclear whether the TAF1 inhibition is bivalent . The selective and potent TAF1(2)/TAF1L(2) chemical probe GNE-371 ( 6 ) was recently developed by Genentech and Constellation Pharmaceuticals . The 1-butenyl group in GNE-371 functions as the KAc methyl mimetic and takes advantage of the differential stability of conserved bromodomain water networks to induce selectivity at TAF1(2) through rearrangement and stabilization of the waters in the KAc binding site .…”

“…It has been previously demonstrated that TAF1(2) is able to recognize not just methyl acetyl lysine, but also atypical crotonyl and butyryl substituted acetyl lysines . Genentech and Constellation Pharmaceuticals have elegantly utilized this facet of the TAF1(2) bromodomain with the 1-butenyl group as an atypical acetyl lysine methyl mimetic on a pyrrolopyridinone scaffold to induce TAF1(2) selectivity through the rearrangement and stabilization of the KAc binding site water molecules. , This approach was also successfully applied to a dihydropyridopyrazine scaffold in the development of a dual BET, TAF1(2) inhibitor 4 . Overlaying the published structure of GNE-371 bound to TAF1(2) with 18 bound to TAF1(2) indicated that the methyl groups occupied approximately the same space, even if the angle of the C–C bond was slightly different (Supporting Information Figure S1).…”

“…21 The selective and potent TAF1(2)/TAF1L(2) chemical probe GNE-371 (6) was recently developed by Genentech and Constellation Pharmaceuticals. 22 The 1-butenyl group in GNE-371 functions as the KAc methyl mimetic and takes advantage of the differential stability of conserved bromodomain water networks to induce selectivity at TAF1(2) through rearrangement and stabilization of the waters in the KAc binding site. 23 To aid TAF1 target validation efforts, we sought to develop a structurally diverse, potent and selective small molecule inhibitor of the second bromodomain of these targets.…”

Dual Inhibition of TAF1 and BET Bromodomains from the BI-2536 Kinase Inhibitor Scaffold

“…Several recent studies have reported small molecule ligands for the dual bromodomain containing TAF1. − As the largest of approximately 13 Tata-binding protein (TBP) associated factors “TAFs” that assemble to comprise the general transcription factor IID (TFIID), , TAF1 scaffolds the pioneer factor for general eukaryotic transcription. − In-vitro transcription and temperature sensitive mutant experiments have implied that TAF1 may be dispensable for basal transcription but directly mediates transcription downstream of RB, B-Myb, and C-Jun and is also critical to transcription downstream of key cell cycle drivers. , Despite these roles, no direct phenotypes of TAF1 bromodomain inhibition have been reported, suggesting that as recently observed for other non-BET bromodomain targets, existing probes may not dramatically impact protein function. − However, recent studies have suggested that TAF1 may collaborate with BRD4 to control cancer cell proliferation in a bromodomain dependent manner, potentially through cooperating transicriptional effects . Indeed, two structurally dissimilar TAF1 inhibitors have now been independently demonstrated to potentiate the activity of BET inhibition in cultured cancer models. , These findings have engendered interest in compounds that may offer dual BRD4/TAF1 inhibition. Toward this objective, we herein report structure activity relationships (SAR) toward dual TAF1/BRD4 inhibitors, as well as TAF1-biased derivatives, from a single kinase inhibitor derived scaffold.…”