Development of small molecule inhibitors of the bromodomain-histone interaction

Thesis

Bromodomains bind to acetylated lysine residues 1 to mediate a wide range of biological processes, including the assembly of transcriptional machinery at modified histones. This thesis describes the design of small molecule inhibitors of bromodomains, with particular focus on the bromodomain of CREBBP.

A fragment based approach was employed to investigate bicyclic amides as acetyl lysine mimics. Initially the benzoxazinone scaffold (BNZ) 2 was shown to be a novel, ligand efficient bromodomain inhibitor. Structure based elaboration of the BNZ scaffold was employed to direct substitutions towards the region of CREBBP with greatest variability compared to other bromodomains. Ultimately, the compounds in this series were limited to micromolar affinity for CREBBP, but provided useful structure activity relationships.

Subsequently the dihydroquinoxalinone scaffold (DHQN) 3 was also shown to be a novel acetyl lysine mimic. Attachment of the optimum side group identified in the BNZ series led to the discovery of the first sub micromolar inhibitor of CREBBP. A co crystal structure with CREBBP revealed that the side group of this compound bound in a newly identified induced fit pocket, mediated by a cation π interaction. A combination of structural, functional and computational studies confirmed that the cation π interaction contributed significantly towards the binding affinity of these ligands. Further work to elaborate the DHQN core, or develop an alternative acetyl lysine mimic into a CREBBP inhibitor, did not lead to an improvement. However, the optimum compound 4 was shown to displace CREBBP from chromatin in a cell based assay.

Overall, cyclic amide based fragments were developed as CREBBP inhibitors, providing some of the first bromodomain ligands with nanomolar affinity outside of the BET family. In the process, key structural information about binding of ligands to CREBBP was revealed. Compound 4 provides a tool with which to study the biological implications of aberrant CREBBP activity and to investigate the therapeutic potential of bromodomain inhibition.

Authors: Rooney, TPC

• Publication date: 2014
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: University of Oxford
• Language: English
• Keywords: organic chemistry; bromodomain; ligand discovery; epigenetics
• Subjects: Organic chemistry; Chemical biology; Synthetic organic chemistry; Chemistry & allied sciences; Physical Sciences