Fragment-Based Discovery of Bromodomain Inhibitors Part 2: Optimization of Phenylisoxazole Sulfonamides

Abstract

Bromodomains are epigenetic reader modules that regulate gene transcription through their recognition of acetyl-lysine modified histone tails. Inhibitors of this protein-protein interaction have the potential to modulate multiple diseases as demonstrated by the profound anti-inflammatory and antiproliferative effects of a recently disclosed class of BET compounds. While these compounds were discovered using phenotypic assays, here we present a highly efficient alternative approach to find new chemical templates, exploiting the abundant structural knowledge that exists for this target class. A phenyl dimethyl isoxazole chemotype resulting from a focused fragment screen has been rapidly optimized through structure-based design, leading to a sulfonamide series showing anti-inflammatory activity in cellular assays. This proof-of-principle experiment demonstrates the tractability of the BET family and bromodomain target class to fragment-based hit discovery and structure-based lead optimization.

Modulation of Epigenetic Targets for Anticancer Therapy: Clinicopathological Relevance, Structural Data and Drug Discovery Perspectives

“…The research focused on inhibition of BDs has been stimulated by the discovery of two potent compounds (I-BET762 and JQ1) with in vivo efficacy in murine models of NUT (nuclear protein in testis) midline carcinoma, as well as AML and severe immune inflammation [347][348][349][350]. Other recent works show the application of fragment-based drug discovery techniques for the identification of new BD inhibitors [316,347,348,351,352] in addition to evidence that the pharmacological inhibition of BET (bromodomains and extra terminal domain) family proteins leads to rapid and potent abrogation of MYC gene transcription [353].…”

Fragment-based drug discovery and protein–protein interactions

“…Primary screening techniques include protein-and ligandobserved nuclear magnetic resonance (NMR), X-ray crystallography, surface plasmon resonance, thermal shift assay (TSA), and biochemical assays. Notably, two-dimensional heteronuclear single quantum coherence (HSQC) NMR and X-ray crystallography, employed as frontline approaches at Abbott Laboratories (Abbott Park, IL, USA) and Astex Pharmaceuticals ( Cambridge, UK), respectively, deliver detailed information about fragment-binding modes at the earliest XiAP/ciAP1 primary screening and complex structure determination [62][63][64] HCv NS3 primary screening and complex structure determination 20 Bromodomain primary screening 73 and complex structure determination [71][72][73][74] Arf1-Arno complex structure determination 77 …”

“…Primary HCv NS3 iC 50 determination using FReT-based assay 20 Bromodomain primary screening using FP and FReTbased assays 71,72,74 Arf1-Arno FP assay to triage virtual screening hits 77 Notes: A typical screening cascade comprises two or more orthogonal techniques to identify binders and triage hits. "Primary screening" refers to high-throughput techniques that can be used to screen a fragment library and detect preliminary hits.…”

“…68 The AcK pocket can bind selective small-molecule inhibitors with low nanomolar affinity, 69,70 and several efforts have been pursued to identify candidate inhibitors through FBDD. [71][72][73][74][75] In these studies, the fragment hits interact with conserved water molecules and residues by mimicking the AcK head group, whilst lipophilic parts of the fragments engage with hydrophobic side chains.…”

Bromodomains: Are Readers Right for Epigenetic Therapy?

“…12 The availability of Xray structures of ligands bound to the BET bromodomains has enabled a structure-based design approach to the optimization of the 3,5-dimethylisoxazole-based ligands, and a good understanding of SAR is beginning to emerge.…”