Structure-Based Optimization of a Small Molecule Antagonist of the Interaction Between WD Repeat-Containing Protein 5 (WDR5) and Mixed-Lineage Leukemia 1 (MLL1)

Abstract

WD repeat-containing protein 5 (WDR5) is an important component of the multiprotein complex essential for activating mixed-lineage leukemia 1 (MLL1). Rearrangement of the MLL1 gene is associated with onset and progression of acute myeloid and lymphoblastic leukemias, and targeting the WDR5-MLL1 interaction may result in new cancer therapeutics. Our previous work showed that binding of small molecule ligands to WDR5 can modulate its interaction with MLL1, suppressing MLL1 methyltransferase activity. Initial structure-activity relationship studies identified N-(2-(4-methylpiperazin-1-yl)-5-substituted-phenyl) benzamides as potent and selective antagonists of this protein-protein interaction. Guided by crystal structure data and supported by in silico library design, we optimized the scaffold by varying the C-1 benzamide and C-5 substituents. This allowed us to develop the first highly potent (Kdisp < 100 nM) small molecule antagonists of the WDR5-MLL1 interaction and demonstrate that N-(4-(4-methylpiperazin-1-yl)-3'-(morpholinomethyl)-[1,1'-biphenyl]-3-yl)-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide 16d (OICR-9429) is a potent and selective chemical probe suitable to help dissect the biological role of WDR5.

Targeted Disruption of the Interaction between WD-40 Repeat Protein 5 (WDR5) and Mixed Lineage Leukemia (MLL)/SET1 Family Proteins Specifically Inhibits MLL1 and SETd1A Methyltransferase Complexes

“…Inhibition data were plotted as relative methyltransferase activity versus log[Win6mer] (nM). The Win6mer IC 50 values for MLL1 and SETd1A core complexes were determined by fitting the data to a dose response with variable slope equation in SigmaPlot 11 as follows. …”

“…Last, our data suggest that the MLL1 and SETd1A complexes have lower overall stabilities compared with other complexes. Consistent with this hypothesis, we observed that the IC 50 (Fig. 5D).…”

Recent Advances in Chemical Tools for the Regulation and Study of Protein Lysine Methyltransferases

“…In addition to the activity of DOT1 L (described in the next section), retention of wild‐type MLL1 is also a common feature of leukemia, so several inhibitors of MLL1 have been developed as candidate drugs . Although no practically useful inhibitors of the catalytic activity of MLL1 have yet been reported, several inhibitors of the PPI of MLL1 with WDR5 (WD repeat‐containing protein 5), which is necessary for optimal methyltransferase activity, have been developed (Figure ), including peptidomimetic compounds, MM‐102 and MM‐401, and small‐molecule‐based compounds, WDR5‐0103 and OICR‐9429 . MI‐503 inhibits the PPI between MLL and menin …”

Recent progress in developing selective inhibitors of protein methyltransferases

“…[15] Furthermore, inhibitors that are disrupting the protein-protein interactions such as OICR-9429 (WDR5-MLL), MI-503 (MENIN-MLL) and A-395, EED226 (EED-PRC2) were also recently reported introducing yet another approach for the inhibition of the PMTs (Table 1). [16–19] The design, synthesis and biological studies of many of these aforementioned inhibitors have already been discussed in detail in literature. [9,10] The following sections will focus only on the potent, selective small-molecule PMT inhibitors that are discovered very recently (indicated in bold type in Table 1).…”

“…[31] Small molecules that perturb protein-protein interactions (PPI) of MLL with its partners, such as WDR5 (OICR-9429) and menin (MI-503) have been discovered. [9,16,17]…”