Discovery of an MLLT1/3 YEATS Domain Chemical Probe

Abstract

YEATS domain (YD) containing proteins are an emerging class of epigenetic targets in drug discovery.D ysregulation of these modified lysine-binding proteins has been linked to the onset and progression of cancers.Weherein report the discovery and characterisation of the first small-molecule chemical probe, SGC-iMLLT,f or the YD of MLLT1 (ENL/ YEATS1) and MLLT3 (AF9/YEATS3). SGC-iMLLT is ap otent and selective inhibitor of MLLT1/3-histone interactions.E xcellent 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.

Structural insights into interaction mechanisms of alternative piperazine-urea YEATS domain binders in MLLT1

“…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 21,30 , 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 featured on the N-linked portion of the amide.…”

“…Piperazine-urea compound 1-3 were purchased from Enamine 25 , while benzimidazole-amide derivative 4-6 were obtained from our previous study 26 .…”

“…Our recent screening efforts alternatively revealed a number of small molecule binders for MLLT1/3 21,25 . One chemotype identified was benzimidazole-amide, and extensive modification focused on this scaffold led to the development of the potent and selective MLLT1/3 inhibitor (SGC-iMLLT) with IC50 of ~0.26 μM and KD of 113 nM 26 . Unfortunately, moderate metabolic stability of this SGC-iMLLT chemical probe has limited its further use in chemotherapeutics.…”

“…Based on our previous work 25,30 , 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.…”

A structure-based approach towards identification of inhibitory fragments for eleven-nineteen-leukemia protein (ENL) YEATS domain

“…The information provided by this structurebased fragment study will facilitate this design and the development of more potent inhibitors. In our laboratory, we used benzimidazole amides for the development of a potent chemical probe for ELN and AF9 31 , which will facilitate further study of the role of this interesting reader domain in normal physiology and disease.…”