Graphical AbstractHighlights d Structure-guided design and optimization yield potent FTO inhibitors d mRNA m 6 A acts as the major effector of the inhibitor/FTO axis in AML cells d FTO inhibitor FB23-2 displays therapeutic effects in PDX AML models d Targeting epitranscriptomic RNA methylation holds potential to treat AML SUMMARY FTO, an mRNA N 6 -methyladenosine (m 6 A) demethylase, was reported to promote leukemogenesis. Using structure-based rational design, we have developed two promising FTO inhibitors, namely FB23 and FB23-2, which directly bind to FTO and selectively inhibit FTO's m 6 A demethylase activity. Mimicking FTO depletion, FB23-2 dramatically suppresses proliferation and promotes the differentiation/apoptosis of human acute myeloid leukemia (AML) cell line cells and primary blast AML cells in vitro. Moreover, FB23-2 significantly inhibits the progression of human AML cell lines and primary cells in xeno-transplanted mice. Collectively, our data suggest that FTO is a druggable target and that targeting FTO by small-molecule inhibitors holds potential to treat AML. SignificanceAs the most abundant internal mRNA modification, m 6 A impacts various biological processes. As a major m 6 A demethylase, FTO is overexpressed in certain subtypes of AMLs and promotes leukemogenesis. Thus, the development of effective inhibitors to target FTO's aberrant m 6 A demethylase activity is urgently needed for leukemia therapy. Here we report two selective FTO inhibitors that efficiently reverse/suppress FTO-mediated aberrant epitranscriptome in AML cells and significantly inhibit AML progression in vivo. Our studies provide the proof-of-concept evidence demonstrating that small-molecule inhibitors targeting oncogenic FTO represent a promising targeted therapeutic strategy for the effective treatment of AML. Moreover, given the overexpression of FTO in various cancers, our work may have a broad impact on cancer therapy by targeting the FTO-mediated epitranscriptome.
Two human demethylases, the fat mass and obesity-associated (FTO) enzyme and ALKBH5, oxidatively demethylate abundant N6-methyladenosine (m6A) residues in mRNA. Achieving a method for selective inhibition of FTO over ALKBH5 remains a challenge, however. Here, we have identified meclofenamic acid (MA) as a highly selective inhibitor of FTO. MA is a non-steroidal, anti-inflammatory drug that mechanistic studies indicate competes with FTO binding for the m6A-containing nucleic acid. The structure of FTO/MA has revealed much about the inhibitory function of FTO. Our newfound understanding, revealed herein, of the part of the nucleotide recognition lid (NRL) in FTO, for example, has helped elucidate the principles behind the selectivity of FTO over ALKBH5. Treatment of HeLa cells with the ethyl ester form of MA (MA2) has led to elevated levels of m6A modification in mRNA. Our collective results highlight the development of functional probes of the FTO enzyme that will (i) enable future biological studies and (ii) pave the way for the rational design of potent and specific inhibitors of FTO for use in medicine.
Members of the ribonuclease III (RNase III) family are double-stranded RNA (dsRNA) specific endoribonucleases characterized by a signature motif in their active centers and a two-base 3' overhang in their products. While Dicer, which produces small interfering RNAs, is currently the focus of intense interest, the structurally simpler bacterial RNase III serves as a paradigm for the entire family. Here, we present the crystal structure of an RNase III-product complex, the first catalytic complex observed for the family. A 7 residue linker within the protein facilitates induced fit in protein-RNA recognition. A pattern of protein-RNA interactions, defined by four RNA binding motifs in RNase III and three protein-interacting boxes in dsRNA, is responsible for substrate specificity, while conserved amino acid residues and divalent cations are responsible for scissile-bond cleavage. The structure reveals a wealth of information about the mechanism of RNA hydrolysis that can be extrapolated to other RNase III family members.
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