Strategy to Target the Substrate Binding site of SET Domain Protein Methyltransferases

Protein methyltransferases (PMTs) are a novel gene family of therapeutic relevance involved in chromatin-mediated signaling and other biological mechanisms. Most PMTs are organized around the structurally conserved SET domain that catalyzes the methylation of a substrate lysine. A few potent chemical inhibitors compete with the protein substrate, and all are anchored in the channel recruiting the methyl-accepting lysine. We propose a novel strategy to design focused chemical libraries targeting the substrate binding site, where a limited number of warheads each occupying the lysine-channel of multiple enzymes would be decorated by different substituents. A variety of sequence and structure-based approaches used to analyze the diversity of the lysine channel of SET domain PMTs support the relevance of this strategy. We show that chemical fragments derived from published inhibitors are valid warheads that can be used in the design of novel focused libraries targeting other PMTs

Discovery of Bisubstrate Inhibitors of Nicotinamide <i>N</i>‑Methyltransferase (NNMT)

Nicotinamide <i>N</i>-methyltransferase (NNMT) catalyzes the N-methylation of pyridine-containing compounds using the cofactor <i>S</i>-5′-adenosyl-l-methionine (SAM) as the methyl group donor. Through the regulation of the levels of its substrates, cofactor, and products, NNMT plays an important role in physiology and pathophysiology. Overexpression of NNMT has been implicated in various human diseases. Potent and selective small-molecule NNMT inhibitors are valuable chemical tools for testing biological and therapeutic hypotheses. However, very few NNMT inhibitors have been reported. Here, we describe the discovery of a bisubstrate NNMT inhibitor MS2734 (<b>6</b>) and characterization of this inhibitor in biochemical, biophysical, kinetic, and structural studies. Importantly, we obtained the first crystal structure of human NNMT in complex with a small-molecule inhibitor. The structure of the NNMT–<b>6</b> complex has unambiguously demonstrated that <b>6</b> occupied both substrate and cofactor binding sites. The findings paved the way for developing more potent and selective NNMT inhibitors in the future

Structure of the Catalytic Domain of EZH2 Reveals Conformational Plasticity in Cofactor and Substrate Binding Sites and Explains Oncogenic Mutations

<div><p>Polycomb repressive complex 2 (PRC2) is an important regulator of cellular differentiation and cell type identity. Overexpression or activating mutations of EZH2, the catalytic component of the PRC2 complex, are linked to hyper-trimethylation of lysine 27 of histone H3 (H3K27me3) in many cancers. Potent EZH2 inhibitors that reduce levels of H3K27me3 kill mutant lymphoma cells and are efficacious in a mouse xenograft model of malignant rhabdoid tumors. Unlike most SET domain methyltransferases, EZH2 requires PRC2 components, SUZ12 and EED, for activity, but the mechanism by which catalysis is promoted in the PRC2 complex is unknown. We solved the 2.0 Å crystal structure of the EZH2 methyltransferase domain revealing that most of the canonical structural features of SET domain methyltransferase structures are conserved. The site of methyl transfer is in a catalytically competent state, and the structure clarifies the structural mechanism underlying oncogenic hyper-trimethylation of H3K27 in tumors harboring mutations at Y641 or A677. On the other hand, the I-SET and post-SET domains occupy atypical positions relative to the core SET domain resulting in incomplete formation of the cofactor binding site and occlusion of the substrate binding groove. A novel CXC domain N-terminal to the SET domain may contribute to the apparent inactive conformation. We propose that protein interactions within the PRC2 complex modulate the trajectory of the post-SET and I-SET domains of EZH2 in favor of a catalytically competent conformation.</p> </div

Discovery of Potent and Selective Inhibitors for G9a-Like Protein (GLP) Lysine Methyltransferase

G9a-like protein (GLP) and G9a are highly homologous protein lysine methyltransferases (PKMTs) sharing approximately 80% sequence identity in their catalytic domains. GLP and G9a form a heterodimer complex and catalyze mono- and dimethylation of histone H3 lysine 9 and nonhistone substrates. Although they are closely related, GLP and G9a possess distinct physiological and pathophysiological functions. Thus, GLP or G9a selective small-molecule inhibitors are useful tools to dissect their distinct biological functions. We previously reported potent and selective G9a/GLP dual inhibitors including UNC0638 and UNC0642. Here we report the discovery of potent and selective GLP inhibitors including <b>4</b> (MS0124) and <b>18</b> (MS012), which are >30-fold and 140-fold selective for GLP over G9a and other methyltransferases, respectively. The cocrystal structures of GLP and G9a in the complex with either <b>4</b> or <b>18</b> displayed virtually identical binding modes and interactions, highlighting the challenges in structure-based design of selective inhibitors for either enzyme

Global Profiling of Acetyltransferase Feedback Regulation

Lysine acetyltransferases (KATs) are key mediators of cell signaling. Methods capable of providing new insights into their regulation thus constitute an important goal. Here we report an optimized platform for profiling KAT–ligand interactions in complex proteomes using inhibitor-functionalized capture resins. This approach greatly expands the scope of KATs, KAT complexes, and CoA-dependent enzymes accessible to chemoproteomic methods. This enhanced profiling platform is then applied in the most comprehensive analysis to date of KAT inhibition by the feedback metabolite CoA. Our studies reveal that members of the KAT superfamily possess a spectrum of sensitivity to CoA and highlight NAT10 as a novel KAT that may be susceptible to metabolic feedback inhibition. This platform provides a powerful tool to define the potency and selectivity of reversible stimuli, such as small molecules and metabolites, that regulate KAT-dependent signaling

The cofactor binding site of EZH2 is incomplete.

<p>(A) Superimposition of the EZH2 structure (colored mesh; post-SET shown as blue ribbon) with a ternary complex of EHMT1/GLP (white ribbon) shows that the cofactor binding site is only partially formed in EZH2, due to an atypical orientation of the post-SET domain. (B) The cofactor site of EZH2 is occupied by the CXC domain of a second molecule within the crystal lattice. (C) Mapping of the location of lysine-mediated cross-links detected in the purified PRC2 complex [53]. Cross-links between Lys735 and Lys569 as well as Lys713 indicate that the post-SET domain of EZH2 (yellow) can project towards the CXC domain in solution, consistent with the conformation seen in our structure.</p

Catalytic activity and substrate/cofactor binding of EZH2 (520-746) and the trimeric (EZH2-EED-SUZ12) complex.

<p>(A) The full-length trimeric complex (●) was active, and the crystallized EZH2 construct (○) was not. Activity assay conditions were optimized for the full length EZH2 in complex with EED and SUZ12 as a control. Kinetic analysis shows that the trimeric complex binds SAM (B) and a histone peptide (C) (K_m SAM: 900 ± 100 nM; K_m peptide: 205 ± 25 nM; k_cat: 24 ± 2 h^-1). Apparent kinetic parameters are the average of three measurements ± standard deviation. ITC shows that the crystallized construct binds neither SAM (D) nor the peptide substrate (E). </p

Structural basis for altered activity of mutations recurrent in lymphomas.

<p>Hydrogen bonding between Tyr 641 and the substrate lysine’s ε-nitrogen, and steric envelope of the tyrosine hydroxy group impose rotational constraints that penalize proper alignment with the cofactor’s scissile bond, required for displacement of a third methyl group. A677 stabilizes the conformation of Y641 hydrogen-bonded to the substrate lysine. The cofactor and substrate lysine are from a superimposed ternary structure of EHMT1/GLP (2RFI).</p

EZH2 adopts the canonical fold of SET domain methyltransferases.

<p>(A) Linear domain architecture of EZH2 showing the crystallized construct. Residue numbers according to GenBank isoform C (Uniprot isoform 1). (B) The catalytic SET domain (yellow) is folded as previously described for other histone methyltransferases such as EHMT1/GLP and MLL, but the post-SET domain is largely unresolved and its first five residues (blue) are oriented away from its expected position. The unique CXC domain adopts a novel conformation including two clusters of three Zn ions (light blue spheres). (C) A mesh representation of the EZH2 structure in the same orientation. The cofactor is expected to bind at the junction of the SET, post-SET and I-SET (cyan) domains. (D) Residues forming the substrate lysine-binding channel in EHMT1/GLP (beige – PDB code 2RFI) are structurally conserved in EZH2 (color coding as in A-C).</p

The substrate binding site of EZH2 is occluded.

<p>The substrate binding groove is too wide in MLL (right) and too narrow in EZH2 (left), compared with the catalytically competent state observed in the EHMT1/GLP ternary complex (center). Color-coding as in Figure 1.</p