Exploiting a water network to achieve enthalpy-driven, bromodomain-selective BET inhibitors

Abstract

Within the last decade, the Bromodomain and Extra-Terminal domain family (BET) of proteins have emerged as promising drug targets in diverse clinical indications including oncology, auto-immune disease, heart failure, and male contraception. The BET family consists of four isoforms (BRD2, BRD3, BRD4, and BRDT/BRDT6) which are distinguished by the presence of two tandem bromodomains (BD1 and BD2) that independently recognize acetylated-lysine (KAc) residues and appear to have distinct biological roles. BET BD1 and BD2 bromodomains differ at five positions near the substrate binding pocket: the variation in the ZA channel induces different water networks nearby. We designed a set of congeneric 2- and 3-heteroaryl substituted tetrahydroquinolines (THQ) to differentially engage bound waters in the ZA channel with the goal of achieving bromodomain selectivity. SJ830599 (9) showed modest, but consistent, selectivity for BRD2-BD2. Using isothermal titration calorimetry, we showed that the binding of all THQ analogs in our study to either of the two bromodomains was enthalpy driven. Remarkably, the binding of 9 to BRD2-BD2 was marked by negative entropy and was entirely driven by enthalpy, consistent with significant restriction of conformational flexibility and/or engagement with bound waters. Co-crystallography studies confirmed that 9 did indeed stabilize a water-mediated hydrogen bond network. Finally, we report that 9 retained cytotoxicity against several pediatric cancer cell lines with EC values comparable to BET inhibitor (BETi) clinical candidates.

The role of ZA channel water-mediated interactions in the design of bromodomain-selective BET inhibitors

“…To explore this hypothesis, we applied our modeling framework to three hetero-aromatic substituted THQs: 2-furan SJ830599 ( 5 ), 2-thiophene SJ830629 ( 6 ), and 2-pyrrole SJ852844 ( 7 ) 27 . These molecules differed by a single atom that was expected to be within close proximity to the W5 and W6 waters in the ZA channel, and therefore, enabled study of the role of water-mediated interactions at that position.…”

Inhibitors of bromodomain and extra‐terminal proteins for treating multiple human diseases

“…Bromodomain and extra‐terminal (BET) proteins are epigenetic “readers” that recognize and bind posttranslational modifications on histones and other transcriptional machinery to facilitate gene expression. BET proteins have received an increasing amount of attention in recent years, 1–49 and BET inhibitor(s) (BETi) that target the BET bromodomains (BD) are unique in drug development in that they are consecutively undergoing clinical investigation in vastly different disease areas. Evidence is mounting to support the use of BETi in treating cancer, metabolic, inflammatory, neurologic, cardiovascular, and musculoskeletal diseases 1–3,14,19,20,29,31,44,50–62 .…”

Flavonoids as Putative Epi-Modulators: Insight into Their Binding Mode with BRD4 Bromodomains Using Molecular Docking and Dynamics

“…One of the main problems in this approach is the increased difficulty of modeling of such phenomena, i.e., identifying “crucial waters” [ 17 , 18 ]. For bromodomains, recent studies showed that the network of structural waters in the ZA channel plays a significant role in binding [ 19 , 20 ] and this topic served as a case study for the development of novel methods in the field [ 21 ].…”