Inhibition of histone binding by supramolecular hosts

Abstract

The tandem PHD (plant homeodomain) fingers of the CHD4 (chromodomain helicase DNA-binding protein 4) ATPase are epigenetic readers that bind either unmodified histone H3 tails or H3K9me3 (histone H3 trimethylated at Lys9). This dual function is necessary for the transcriptional and chromatin remodelling activities of the NuRD (nucleosome remodelling and deacetylase) complex. In the present paper, we show that calixarene-based supramolecular hosts disrupt binding of the CHD4 PHD2 finger to H3K9me3, but do not affect the interaction of this protein with the H3K9me0 (unmodified histone H3) tail. A similar inhibitory effect, observed for the association of chromodomain of HP1γ (heterochromatin protein 1γ) with H3K9me3, points to a general mechanism of methyl-lysine caging by calixarenes and suggests a high potential for these compounds in biochemical applications. Immunofluorescence analysis reveals that the supramolecular agents induce changes in chromatin organization that are consistent with their binding to and disruption of H3K9me3 sites in living cells. The results of the present study suggest that the aromatic macrocyclic hosts can be used as a powerful new tool for characterizing methylation-driven epigenetic mechanisms.

Molecular Insights into Inhibition of the Methylated Histone-Plant Homeodomain Complexes by Calixarenes

“…The set of calixarenes included analogs of p-sulfonatocalixarene (1) carrying amide-or sulfonamide-linked substituents at one or two positions of its upper rim (2-8) (Fig. 1c) (26,32). The bulkiness and electrostatic properties of the substituents varied to determine how change in polarity, size, and charge affects the ability of calixarenes to disrupt the PHD-H3K4me3 complexes.…”

“…Supramolecular caging compounds, including synthetic receptors, chelating macrocycles, and calixarenes, have been shown to coordinate unmodified and posttranslationally modified amino acids and, therefore, can be applied for studying epigenetic mechanisms (25-31, 45, 46). We have demonstrated previously that calixarenes inhibit binding of the second PHD finger of CHD4 to histone H3 trimethylated at Lys-9, although this binding does not involve the formation of a methyllysine-recognizing aromatic cage (32,33). Here we characterize the mechanisms by which calixarenes interact with the canonical PHDH3K4me3 complexes and examine the effect of the aromatic cage architecture on these interactions.…”

Host–guest chemistry that directly targets lysine methylation: synthetic host molecules as alternatives to bio-reagents

“…56 This is a different result than could be achieved with the traditional medicinal chemistry approach, which would target the concave binding pocket of CHD4 and would disrupt both complexes of CHD4 equally well. 56 This is a different result than could be achieved with the traditional medicinal chemistry approach, which would target the concave binding pocket of CHD4 and would disrupt both complexes of CHD4 equally well.…”

“…67 Sulfonated calixarenes look like terrible candidates for cellbased studies. 29,56,[70][71][72][73][74] Our collaborators in the Strahl lab used a proximity ligation assay that probes the co-localization of H3K4me3 and MLL5 in C2C12 cells (Fig. 68 They are highly charged at neutral pH.…”

Towards understanding methyllysine readout

“…Supramolecular host compounds that can cage histone methyllysines are now available. For example, the calixarene-based supramolecular host can associate with methylated lysine in chromatin to selectively disrupt binding of the CHD4 PHD finger and HP1γ CD to H3K9me3 [84]. …”