Discovery of Selective Small-Molecule Inhibitors for the ENL YEATS Domain

Abstract

Eleven-nineteen leukemia (ENL) protein is a histone acetylation reader essential for disease maintenance in acute leukemias, in particular, the mixed-lineage leukemia (MLL)rearranged leukemia. In this study, we carried out high-throughput screening of a small-molecule library to identify inhibitors for the ENL YEATS domain. Structure−activity relationship studies of the hits and structure-based inhibitor design led to two compounds, 11 and 24, with IC 50 values below 100 nM in inhibiting the ENL− acetyl-H3 interaction. Both compounds, and their precursor compound 7, displayed strong selectivity toward the ENL YEATS domain over all other human YEATS domains. Moreover, 7 exhibited on-target inhibition of ENL in cultured cells and a synergistic effect with the bromodomain and extraterminal domain inhibitor JQ1 in killing leukemia cells. Together, we have developed selective chemical probes for the ENL YEATS domain, providing the basis for further medicinal chemistry-based optimization to advance both basic and translational research of ENL.

A novel bis-triazole scaffold accessed via two tandem [3 + 2] cycloaddition events including an uncatalyzed, room temperature azide–alkyne click reaction

“…However, 5,6,7,8-tetrahydro [1,4]diazepine (B) scaffolds are of high medicinal importance, as evident from the literature. The range of biologically active compounds based on these two closely related scaffolds (both incorporated as fragments in the structure of compound 5a) include compound 6 for the treatment of cognitive impairment [7], BET bromodomain inhibitors 7 [8] and 8 [9] for cancer treatment, σ 1 receptor modulator 9 for diverse disorders [10] and bacterial regulatory RNA binder 10 [11] (scaffold A) as well as antidiuretic 11 [12], glycogen phosphorylase inhibitor 12 [13], MK2 kinase inhibitor 13 [14], ENL YEATS domain inhibitor 14 for leukemia treatment [15] and hepatitis C NS5B polymerase inhibitor 15 [16] (scaffold B, Figure 2).…”

Fragment-Based Discovery of AF9 YEATS Domain Inhibitors

“…Small-molecule inhibitors and peptide-mimics have recently been discovered to block the recognition of acyl-lysines by the ENL YEATS domain. However, the ENL inhibitor SGC-iMLLT and its analogs failed to suppress the proliferation of cancer cells, while compound 7 with a new chemotype did [ 27 ]. The large-scale prioritization of cancer targets nominated 9 out of 324 cell lines as AF9-sensitive cell lines, thus reigniting the campaign toward the discovery of AF9 YEATS inhibitors.…”

“…Although these peptides and small-molecule inhibitors interact with AF9/ENL in living cells, it is frustrating that these inhibitors in all cases have failed to suppress the proliferation of tumor cells and thus cannot recapitulate the phenotype induced by the depletion of the ENL gene [ 19 , 20 ]. Most recently, a new inhibitor 7 of ENL displayed selectivity over all other human YEATS domains and on-target inhibition of MLL-rearranged leukemia cell lines [ 27 ]. Additionally, 7 suppressed two ENL target genes’ expression, including MYC and HOXA9 in MOLM13 cells.…”

The Prioritization of Eleven-Nineteen-Leukemia Inhibitors as Potential Drug Candidates to Treat Acute Myeloid Leukemia

“…In a previous study, we synthesized a series of potent small-molecule inhibitors that show preferential binding to the ENL YEATS domain rather than the AF9 YEATS domain in vitro . 31 However, these inhibitors showed variable cellular potency in two MLL-rearranged leukemia cells, MOLM-13 and MV4-11, which is likely due to their differences in cellular permeability, stability, etc . 31 To prioritize some of these inhibitors as potential drug leads for the treatment of AML and further optimization, in this study, we developed a fluorescence tracer based on a reported selective ENL/AF9 YEATS domain inhibitor SR-0813 32 and constructed a NanoBRET system for the evaluation of cellular permeability, potency, selectivity, and stability of our developed ENL inhibitors.…”

“…31 However, these inhibitors showed variable cellular potency in two MLL-rearranged leukemia cells, MOLM-13 and MV4-11, which is likely due to their differences in cellular permeability, stability, etc . 31 To prioritize some of these inhibitors as potential drug leads for the treatment of AML and further optimization, in this study, we developed a fluorescence tracer based on a reported selective ENL/AF9 YEATS domain inhibitor SR-0813 32 and constructed a NanoBRET system for the evaluation of cellular permeability, potency, selectivity, and stability of our developed ENL inhibitors. Potent inhibitors were then selected according to the IC 50 values determined by the NanoBRET assay and subjected to in vitro metabolic stability, cell viability and anti-proliferation evaluation to screen inhibitors with optimal characteristics.…”