METTL3 from Target Validation to the First Small-Molecule Inhibitors: A Medicinal Chemistry Journey

Abstract

RNA methylation is a critical mechanism for regulating the transcription and translation of specific sequences or for eliminating unnecessary sequences during RNA maturation. METTL3, an RNA methyltransferase that catalyzes the transfer of a methyl group to the N⁶-adenosine of RNA, is one of the key mediators of this process. METTL3 dysregulation may result in the emergence of a variety of diseases ranging from cancer to cardiovascular and neurological disorders beyond contributing to viral infections. Hence, the discovery of METTL3 inhibitors may assist in furthering the understanding of the biological roles of this enzyme, in addition to contributing to the development of novel therapeutics. Through this work, we will examine the existing correlations between METTL3 and diseases. We will also analyze the development, mode of action, pharmacology, and structure-activity relationships of the currently known METTL3 inhibitors. They include both nucleoside and non-nucleoside compounds, with the latter comprising both competitive and allosteric inhibitors.

Figure 1

(A) Structure of METTL3–METTL14 in complex with SAM (green) (PDB ID 5IL1). (B) Focus on the catalytic pocket indicating the key interactions of SAM with METTL3 residues. Dashed gray lines indicate polar interactions, and red spheres indicate water molecules. (C) Roles and topologies of the different components of the MTC. The topology of the METTL3–METTL14–WTAP–VIRMA–ZC3H13–HAKAI complex is based on cryo-EM structures and cross-linking mass spectrometry. The connection between ZC3H13 and RBM15 is based on the literature.

Figure 2

Summary of the implications of METTL3 in cancer. The figure depicts the main protein interactors and pathways regulated by METTL3 as both (A) a tumor promoter and (B) a tumor suppressor.

Figure 3

(A) Nucleoside-based METTL3 inhibitors 1a–h related to cosubstrate SAM. (B) Crystal structure of METTL3–METTL14 in complex with compound 1b (green) (PDB ID 6TTT). (C) Crystal structure of METTL3–METTL14 in complex with compound 1g (light blue) (PDB ID 6TU1). Key residues are labeled. Dashed gray lines indicate polar interactions, and red spheres indicate water molecules.

Figure 4

(A) METTL3 inhibitor UZH1a (R-2a) and its derivatives 2b–f. (B) Crystal structure of METTL3–METTL14 in complex with compound R-2a (green) (PDB ID 7ACD). (C) Development of compound 2h starting from 2f. (D) Crystal structure of METTL3–METTL14 in complex with compound 2h (yellow) (PDB ID 7O0L). Key residues are labeled. Dashed gray lines indicate polar interactions, and red spheres indicate water molecules.

Figure 5

(A) Optimization strategy of the Caflisch group starting from compound 2f derivatives bearing a phenyl ring instead of the pyridine (2i–m) and finally leading to fluorinated derivatives (2n–p), which include the single-digit nanomolar METTL3 inhibitor UZH2 (2p). (B) Crystal structure of METTL3–METTL14 in complex with compound 2p (yellow) (PDB ID 7O2F). Key residues are labeled. Dashed gray lines indicate polar interactions, dashed yellow lines indicate fluorine−π interactions, and red spheres indicate water molecules.

Figure 6

(A) Structures of the inhitial hit STM1760 (3a) and the optimized METTL3 inhibitor STM2457 (3b). (B) Crystal structure of METTL3–METTL14 in complex with compound 3b (green) (PDB ID 7O2I). Key residues are labeled. Dashed gray lines indicate polar interactions, and red spheres indicate water molecules.

Figure 7

Structures of METTL3–METTL14 inhibitors (A) 4a–h and (B) 5a–d developed by Accent Therapeutics. All inhibitors possess IC₅₀ < 10 nM.

Figure 8

Structures of METTL3–METTL14 inhibitors (A) 6a–e, (B) 7a–f, (C) 8a–c, and (D) 9a–d developed by Storm Therapeutics. All inhibitors possess IC₅₀ < 8 nM.

Figure 9

(A) Structures of METTL3 allosteric inhibitors 10a–h. (B) Structures of eltrombopag (11a) and its inactive analogues 11b–d.

Figure 10

(A) Structures of natural products 12a–c reported as METTL3 inhibitors. (B) Structure of the METTL3 degrader elvitegravir (13).