Discovery of an MLLT1/3 YEATS Domain Chemical Probe

Abstract

<p>YEATS domain (YD) containing proteins are an emerging</p> <p>class of epigenetic targets in drug discovery. Dysregulation of these modified lysine binding proteins has been linked to the onset and progression of cancers. We herein report the discovery and characterisation of the first small molecule chemical probe, SGC-iMLLT, for the YD of MLLT1 (ENL/YEATS1) and MLLT3 (AF9/YEATS3). SGC-iMLLT is a potent and selective inhibitor of MLLT1/3 -histone interactions. Excellent selectivity over other human YD proteins (YEATS2/4) and bromodomains was observed. Furthermore, our probe displays cellular target engagement of MLLT1 and MLLT3. The first small molecule X-ray co-crystal structures with the MLLT1 YD are also reported. This first in class probe molecule can be used to understand MLLT1/3 associated biology and the therapeutic potential of small molecule YD inhibitors.</p>

Targeting the SAGA and ATAC Transcriptional Coactivator Complexes in MYC-Driven Cancers

“…The discovery that YEATS domains, which are structurally distinct from bromodomains, also read acetyl-lysine moieties raises the possibility that chemical probes against these domains, including the YEATS2 protein in ATAC, may have therapeutic potential [85,86].…”

Structural Insights into Interaction Mechanisms of Alternative Piperazine-urea YEATS Domain Binders in MLLT1

“…Comparable binding modes between the secondary amide central core of the piperazine-1-carboxamide compounds and acetyl-lysine confirmed our previous hypothesis on the use of the amide group as an acetyl-lysine mimetic moiety for YEATS domains. 21 Earlier crystal structures suggested an important role of aromatic moieties on both ends of the amide central core for achieving aromatic stacking with Phe28, Phe59, and His56, 21,26 as exemplified also here in the interactions of 4, 5, and 6 (Figure 1E−G). However, in contrast to benzimidazoles, all piperazine-urea 1, 2, and 3 did not follow this scheme and contained instead an sp 3 piperazine on the C-linked region of the amide, whereas a benzyl substituent was featured on the Nlinked portion of the amide.…”

“…Piperazine-urea compound 1−3 were purchased from Enamine, 25 while benzimidazole-amide derivatives 4−6 were obtained from our previous study. 26 Protein purification and crystallization: MLLT1 YEATS domain (aa 1−148) was purified using the procedure described previously. 21 Apo crystals were produced using sitting drop vapor diffusion method at 20 °C and the condition containing 25% PEG 3350, 0.2 M NaCl, and either 0.1 M bis-tris, pH 6.5, or 0.1 M HEPES, pH 7.5.…”

“…21, 25 One chemotype identified was benzimidazoleamide, and extensive modification focused on this scaffold led to the development of the potent and selective MLLT1/3 inhibitor (SGC-iMLLT) with IC 50 of ∼0.26 μM and K D of 113 nM. 26 Unfortunately, moderate metabolic stability of this SGC-iMLLT chemical probe has limited its further use in chemotherapeutics. Nevertheless, the discovery of this chemical probe has demonstrated, therefore, a potential of targeting YEATS domains using small molecule inhibitor.…”

“…29 For the potential application as an alternative scaffold for YEATS domain inhibitors, we investigated interaction mechanisms of the piperazine-urea chemotype in MLLT1. Based on our previous work, 25,26 we selected three piperazine-1-carboxamide hits (1, 2, and 3) and for comparison three benzimidazole-amide derivatives of similar sizes (4, 5, and 6), and first determined the crystal structures of their complexes with MLLT1 (Figure 1). We observed surprisingly different binding modes and interactions between these two chemotypes to the protein.…”