Inhibitors of Protein Methyltransferases and Demethylases

Abstract

Post-translational modifications of histones by protein methyltransferases (PMTs) and histone demethylases (KDMs) play an important role in the regulation of gene expression and transcription and are implicated in cancer and many other diseases. Many of these enzymes also target various nonhistone proteins impacting numerous crucial biological pathways. Given their key biological functions and implications in human diseases, there has been a growing interest in assessing these enzymes as potential therapeutic targets. Consequently, discovering and developing inhibitors of these enzymes has become a very active and fast-growing research area over the past decade. In this review, we cover the discovery, characterization, and biological application of inhibitors of PMTs and KDMs with emphasis on key advancements in the field. We also discuss challenges, opportunities, and future directions in this emerging, exciting research field.

Figure 1

Known methylation and demethylation sites for histone H3 and H4 tails and corresponding protein methyltransferases and histone demethylases.

Figure 2

(A) Methylation of lysine (K) and arginine (R) residues of histone tails and nonhistone proteins by protein methyltransferases. (B) Methylation states of K and R residues.

Figure 3

Phylogenetic tree of PMTs. The PMTs with known inhibitors are indicated in boxes.

Figure 4

Structures of G9a/GLP inhibitors.

Figure 5

Co-crystal structures of UNC0224 (cyan) and UNC0638 (blue) in complex with G9a are superimposed (PDB ID: 3K5K and 3RJW, respectively). H3K9me2 peptide (magenta) overlaid for reference. Hydrogen bonds with G9a residues are represented as yellow dashed lines.

Figure 6

Structures of EZH2/EZH1 inhibitors.

Figure 7

(A) X-ray structure of Ct-PRC2 complex (PDB ID: 5CH1). (B) Co-crystal structure of PRC2 with a derivative of CPI-1205 (PDB ID: 5LS6). The key residues and interactions are indicated. SAH (blue) is overlaid for reference (PDB ID: 5HYN). Hydrogen bonds are represented as yellow dashed lines.

Figure 8

Structures of SETD7 inhibitors.

Figure 9

(A) SETD7 (light blue) in complex with (R)-PFI-2 (magenta) and SAM (yellow) (PDB ID: 4JLG) is superimposed with SETD7 structure in complex with SAH (1O9S) depicting the conformational variability of the post-SET loop. Hydrogen bonds are represented as orange dashed lines with key residues. (B) Surface representation of (R)-PFI-2-bound SETD7 highlighting an induced conformational modification of the post-SET loop.

Figure 10

Structures of SMYD3 inhibitors.

Figure 11

(A) Co-crystal structure of EPZ030456 (orange) in complex with SMYD3 (green) and SAM (yellow) (PDB ID: 5CCM). (B) Co-crystal structure of GSK2807 (orange) (PDB ID: 5HI7) in complex with SMYD3. MEKK2 (MAP3K2) peptide (magenta) and SAH (gray) is overlaid for reference (PDB ID: 5HQ8). Selected SET (green), SET-I (yellow), and post-SET (aqua) residues are indicated. Hydrogen bonds are represented as yellow dashed lines and water molecules as red spheres.

Figure 12

Structures of SMYD2 inhibitors.

Figure 13

X-ray cocrystal structure of the SMYD2-AZ-505 complex (PDB ID: 3S7B).

Figure 14

Structures of Sinefungin and Pr-Sinefungin (Pr-SNF).

Figure 15

(A) Co-crystal structure of SETD2 in complex with SAH (PDB ID: 4H12). SET domain (light orange), N-SET domain (light blue), pre-SET domain (cyan), and post-SET motif (red) are highlighted. (B) The SAH binding pocket between SET and Post-SET domains of SETD2. (C) Co-crystal structure of SETD2 in complex with Pr-SNF (PDB ID: 4FMU). (D) The key residues stabilizing the alternative configuration of the post-SET loop and interacting with Pr-SNF’s N-propyl chain.

Figure 16

Structures of SETD8 inhibitors.

Figure 17

(A) Co-crystal structure of MS2177 (orange) in complex with SETD8 (PDB ID: 5T5G). Hydrogen bonds are represented as magenta dashed lines and water molecule as red sphere. (B) Co-crystal structure of MS453 (green and cyan) in complex with SETD8 homodimer (subunits depicted in cyan and green, PDB ID: 5TH7).

Figure 18

Structures of additional SETD8 inhibitors.

Figure 19

Structure of A-196, an inhibitor of SUV420H1 and SUV420H2.

Figure 20

Structures of DOT1L inhibitors.

Figure 21

(A) Cofactor binding site of DOT1L (PDB ID: 1NW3). (B) Crystal structure of DOT1L in complex with EPZ004777 (PDB ID: 4ER3). Conformational rearrangements of DOT1L create a cavity to accommodate the t-butylphenyl group. (C) Overlay of DOT1L-SAM and DOT1L-EPZ004777 showing conformational rearrangement of substrate-binding and activation loop residues (magenta and yellow, respectively). (D) Overlay of DOT1L-EPZ004777 (PDB ID: 4ER3) and DOT1L-EPZ-5676 (PDB ID: 4HRA) complexes. Key hydrogen bonds are represented as green dashed lines between EPZ004777 (blue) and DOT1L and EPZ-5676 is depicted in orange.

Figure 22

Structures of recently reported DOT1L inhibitors.

Figure 23

Structures of type I PRMT inhibitor MS023 and reported PRMT1 inhibitors.

Figure 24

(A) Structures of PRMT3 inhibitors 11, 12, and 13. (B) Key interactions of 11 with PRMT3 allosteric pocket (3SMQ). (C) Structure of SGC707. (D) Co-crystal structure of PRMT3 in complex with SGC707 (PDB ID: 4RYL).

Figure 25

Structures of CARM1 inhibitors.

Figure 26

(A) Crystal structures of 14 (orange) and 15 (yellow) bound to CARM1 are superimposed (PDB ID: 2Y1W and 2Y1X). Key interactions of 14 in arginine binding channel are indicated. (B) Crystal structures of MS023 (gray) and 16 (blue) bound to PRMT6 are superimposed (PDB ID: 5E8R and 5EGS), and key interactions for 16 are shown. Hydrogen bonds are represented as magenta dashed lines and water molecule as red sphere.

Figure 27

Structures of PRMT5 inhibitors.

Figure 28

Crystal structure of EPZ015666 (orange) bound to PRMT5:MEP50 complex in the presence of SAM (yellow) (PDB ID: 4x61). Hydrogen bonds are represented as magenta dashed lines and water molecule as red spheres.

Figure 29

Structures of PRMT6 inhibitors.

Figure 30

Domain architecture of LSD1 and LSD2.

Figure 31

FAD-dependent enzymatic oxidation mechanism of LSDs.

Figure 32

Structures of mechanism-based MAO inhibitors.

Figure 33

Proposed structures and mechanisms of formation of FAD-(±)-tranylcypromine adduct(s).

Figure 34

(+)-Tranylcypromine-based inhibitors with substitution at the phenyl ring. *Absolute configuration.

Figure 35

(+)-Tranylcypromine-based inhibitors with substitution at both the phenyl ring and amino group. *Absolute configuration.

Figure 36

Structures of LSD1 inhibitors phenelzine and bizine.

Figure 37

Proposed structures and mechanism of formation of FAD-(±)-propargyl-lysine (30) and FAD-(±)-hydrazine-lysine derivatized peptide (32) adduct(s).

Figure 38

Structures of peptide-based LSD1 inhibitors.

Figure 39

Biguanide and bisguanidine polyamine analogues that were reported as LSD1 inhibitors.

Figure 40

Structures of reversible LSD1 inhibitors.

Figure 41

Structures of additional reversible LSD1 inhibitors.

Figure 42

Phylogenetic tree of JmjC KDMs.

Figure 43

Domain architectures of some JmjC KDMs.

Figure 44

Ferrous iron (Fe(II)) and 2-OG-based oxidation mechanism of JmjC KDMs.

Figure 45

Structures of JmjC KDMs inhibitors that contain common motifs.

Figure 46

Structures of KDM2/7 subfamily inhibitors.

Figure 47

Structures of 8HQ-containing KDM4 inhibitors.

Figure 48

Pyridine-4-carboxylic acid containing KDM4 inhibitors.

Figure 49

Structures of peptide-based KDM4 inhibitors.

Figure 50

Structures of other KDM4 inhibitors.

Figure 51

Structures of KDM5 inhibitors.

Figure 52

(A) KDM5-C49 (orange) binding interactions with KDM5B (PDB ID: 5A3T) and (B) GSK467 binding interactions with KDM5B (PDB ID: 5FUN). Side chains are displayed in gray, water molecules as red spheres, and the metal centers as green spheres.

Figure 53

Structures of other KDM5 inhibitors.

Figure 54

Structures of KDM6 inhibitor GSK-J1 and its prodrug GSK-J4.

Figure 55

Co-crystal structure of KDM6B in complex with GSK-J1 (orange). The key residues that formed the catalytic pocked are indicated in blue. Hydrogen bonds are represented as magenta dashed lines and water molecules as red spheres.

Figure 56

Structures of dual LSD1-JmjC KDM inhibitors.