Small-molecule inhibition of METTL3 as a strategy against myeloid leukaemia

Abstract

The N6-methyladenosine (m 6 A) is an abundant internal RNA modification 1,2 catalysed predominantly by the METTL3-METTL14 methyltransferase complex 3,4 . The m 6 A writer METTL3 has been linked to the initiation and maintenance of acute myeloid leukaemia (AML), but its true therapeutic importance is still unknown [5][6][7] . Here we present the identification and characterisation of a highly potent and selective first-in-class catalytic inhibitor of METTL3 (STM2457) and its co-crystal structure bound to METTL3/METTL14. Treatment with (Extended Data Fig. 2f). These data demonstrate that STM2457 is a highly potent, specific and bioavailable inhibitor of METTL3, suitable for in vivo investigations. Cellular and molecular effects of STM2457To study the anti-leukaemic potential of STM2457 we examined the proliferation of a panel of human AML cell lines post-treatment and detected significant growth reduction in a concentration-dependent manner (Fig. 2a) while we found that STM2457 did not affect the colony-forming ability of normal human cord blood CD34 + cells (Extended Data Fig. 3a). We also observed no impact on the proliferation of MOLM-13 cells treated with the control small molecule STM2120, unlike our observations with STM2457 (Extended Data Fig. 3b). Additionally, treatment with STM2457 significantly reduced the clonogenic potential of primary murine AML cells (Fig. 2b and Extended Data Fig. 3c), while having no effect on normal haematopoietic stem and progenitor cells (HSPCs) (Fig. 2c). Pharmacological inhibition of METTL3 also caused significant myeloid differentiation 6,11 and cell cycle arrest in MOLM-13 and primary murine AML cells (Fig. 2d, e). In contrast, the same effects were not identified using the non-leukaemic haemopoietic cell line HPC7 (Fig. 3e and Extended Data Fig. 3d). Moreover, treatment with STM2457 induced apoptosis in human and mouse AML models but not in normal non-leukaemic haemopoietic cells (Fig. 2f and Extended Data Fig. 3e). To assess the impact of pharmacological inhibition of METTL3 on two known METTL3 biomarkers associated with AML, SP1 6,12 and BRD4 13,14 , we treated MOLM-13 cells with STM2457 and observed a dose-dependent reduction of SP1 and BRD4 protein levels (Fig. 2g). Notably, ectopic expression of SP1 significantly reduced the sensitivity of MOLM-13 cells to STM2457 (Extended Data Fig. 3f, g). These data establish that the catalytic function of METTL3 is important for leukaemia growth, in line with previous findings 6,7,15 . We next sought to investigate the molecular mechanism by which STM2457 affects AML. RNAseq analysis of MOLM-13 cells treated with STM2457 revealed 1,338 up-regulated and 489 down-regulated genes (Extended Data Fig. 4a and Supplementary Table 1). Gene ontology (GO) analysis of the differentially expressed genes showed enrichment in pathways related to myeloid differentiation, cell cycle and leukaemia progression (Extended Data Fig. 4b, c) in close agreement with our phenotypic observations (Supplementary Table 2). To examine the impact of the pharmac...

Targeting the m6A RNA modification pathway blocks SARS-CoV-2 and HCoV-OC43 replication

“…Indeed, there was good agreement between sites detected using this DRS approach and peak regions identified by meRIP-seq for polyadenylated RNAs isolated from human adenovirus type 5 (Ad5)-infected cells. To test whether DRS could effectively detect m 6 A installation on β-coronavirus RNAs, cells were infected with SARS-CoV-2 (A549 +ACE2 ) or HCoV-OC43 (MRC-5) under the same conditions used for meRIP-seq in the presence of STM2457, a new and highly selective small molecule inhibitor of METTL3 activity (Yankova et al 2021), or a structurally related control compound STM2120 that is >3000-fold less potent as an METTL3 inhibitor as measured by in vitro methylation assay (Supplemental Fig. S6).…”

Epitranscriptomics of Ischemic Heart Disease—The IHD-EPITRAN Study Design and Objectives

“…Indeed, small molecule ligands for METTL3 writer complex [ 116 ], FTO [ 170 ], and ALKBH5 [ 171 ] erasers have already been described by the members of the IHD-EPITRAN Consortium. Remarkably, just recently, a potent METTL3 inhibitor has also been reported with leukemia-repressing effects in vivo in mice, providing simultaneously an enchanting proof-of-principle and a seminal endeavor to thrust the door ajar into the yet uncharted realm of epitranscriptomics-based pharmacology in vivo—ultimately shifting eyes also increasingly towards the clinic [ 172 ]. Hence, both the existing and future breakthroughs regarding epitranscriptomic pharmacology is closely monitored and implemented accordingly to the mid/late phases of the IHD-EPITRAN study as a further applicatory dimension.…”

Immunotherapeutic Potential of m6A-Modifiers and MicroRNAs in Controlling Acute Myeloid Leukaemia

“…Recently, Eliza et al, 2021 [ 48 ] have discovered the selective inhibitor of Mettl3 and Mettl14 (STM2457, IC50 = 16.9 nM) in controlling AML via high-throughput screening of 250,000 drug-like compounds. Functionally, authors showed a significant effect of STM2457 in reducing clonogenic potential and inducing apoptosis in human and mouse AML model without affecting normal human cord blood (CD34 + /HSPCs) and non-leukaemia (HPC7) hematopoietic cells [ 48 ]. Moreover, in vivo studies on AML patient-derived xenograft (PDX) model and primary murine MLL-AF9/Flt3 ltd/+ model showed convincing anti-leukaemia effect of STM2120 inhibitors [ 48 ].…”

“…Functionally, authors showed a significant effect of STM2457 in reducing clonogenic potential and inducing apoptosis in human and mouse AML model without affecting normal human cord blood (CD34 + /HSPCs) and non-leukaemia (HPC7) hematopoietic cells [ 48 ]. Moreover, in vivo studies on AML patient-derived xenograft (PDX) model and primary murine MLL-AF9/Flt3 ltd/+ model showed convincing anti-leukaemia effect of STM2120 inhibitors [ 48 ]. Similar findings have been reported from other research groups summarised in Table 3 [ 6 , 45 , 47 ].…”