The WD40-repeat protein WDR5 plays a critical role in maintaining the integrity of MLL complexes and fully activating their methyltransferase function. MLL complexes, the trithorax-like family of SET1 methyltransferases, catalyze trimethylation of lysine 4 on histone 3, and they have been widely implicated in various cancers. Antagonism of WDR5 and MLL subunit interaction by small molecules has recently been presented as a practical way to inhibit activity of the MLL1 complex, and N-(2-(4-methylpiperazin-1-yl)-5-substituted-phenyl) benzamides were reported as potent and selective antagonists of such an interaction. Here, we describe the protein crystal structure guided optimization of prototypic compound 2 (K dis = 7 μM), leading to identification of more potent antagonist 47 (K dis = 0.3 μM). KEYWORDS: WDR5, MLL, SET1 methyltransferase complex, peptide binding site, small molecule antagonists T he SET1-family of human histone methyltransferases (SET1A, SET1B, MLL1, MLL2, MLL3, and MLL4) contribute to active chromatin via mono-, di-, and trimethylation of lysine 4 on histone H3. 1−3 MLLs are S-adenosyl methionine (SAM) dependent lysine methyltransferases that work optimally when in complex with other components; WDR5 (WD40 repeat protein 5), RbBP5 (retinoblastomabinding protein-5), ASH2L (absent small homeotic disks-2-like), and DPY-30 (WRAD). 4 WDR5 has been shown to be essential for complex integrity and for fully activating MLL methyltransferase function. 5−7 In the peptide-bound structure, WDR5 adopts a donutshaped WD40-repeat fold with a deep central cavity that normally accommodates an arginine side chain of interacting peptides. 8 WDR5 binds to the "WDR5 INteracting" (WIN) motif of MLL1 through the peptidyl arginine-binding cleft. 8−12 A crystal structure of WDR5 in complex with MLL1 WIN peptide revealed the critical role of arginine 3765 of MLL1 in complex formation. 9 A similar interaction has been reported for WDR5 and the WIN region of all SET1 family lysine methyltransferases, with reported K D values of 1.13, 0.16, 2.03, 0.03, 0.26, and 0.10 μM for MLL1-4, SET1A, and SET1B WIN peptides, respectively. 13 Although there is significant divergence in the amino acid sequences of WIN motifs close to the critical arginine residue, the plasticity of the WDR5 arginine binding pocket allows such an interaction with the WIN motifs of all MLLs. 13 MLLs have been reported to be essential for embryonic development and biological processes 14−17 and have been widely implicated in a variety of cancers. 18−22 As almost all MLLs show minimal or no activity in the absence of the complex components (WDR5 in particular), 13 identifying WDR5−MLL interaction antagonists has been proposed as a potentially selective alternative to active site directed inhibitors of MLL methyltransferase activity. Such antagonists could serve as a starting point for the development of potential therapeutics to treat MLL-rearranged leukemias or other related cancers. 23 Recent reports detailing the use of short arginine contain...