Discovery of a selective YTHDC1 inhibitor that targets acute myeloid leukemia

Abstract

N6-methyladenosine (m6A) is the most prevalent modification of eukaryotic RNA, which is recognized by m6A-binding proteins (“readers”) and thereby mediates multiple biological processes. Dysregulation of the m6A readers has been linked to various pathologies, but the therapeutic potential of small molecule inhibitors targeting the m6A readers is unknown. Here we report the identification and characterization of a highly potent and selective first-in-class inhibitor (YL-5092) of YT521-B homology (YTH) domain-containing protein 1 (YTHDC1), which is a nuclear RNA m6A reader and plays essential roles in the pathological process of acute myeloid leukemia (AML). The crystal structure of YTHDC1 in complex with YL-5092 well explained its potency and selectivity. YL-5092 treatment substantially suppressed the proliferation and induced the differentiation and apoptosis of AML cells. It also efficiently inhibited the colony-forming ability of CD34+ AML stem cells, but had no effect on normal hematopoietic stem cells and early progenitors (Lin− Sca1+ Kit+). Moreover, YL-5092 treatment impaired leukemogenesis and improved the animal survival rate in mouse AML xenograft models. Collectively, this research reveals a therapeutic potential of YTHDC1 inhibitors against AML, and provides proof of concept that targeting m6A readers represents a promising strategy for cancer treatment.

Structure-Based Design of a Potent and Selective YTHDC1 Ligand

“…On the other hand, a bigger and more lipophilic bromide substituent present in compound 24 resulted in a 2-fold decrease in potency (IC 50 = 2 μM) in comparison to compound 25. Because of the positive effect observed with carboxylic acid functionality, we also prepared derivatives of carboxylic acid (28,29) and benzyl alcohol derivative 30 in the para position. However, these compounds did not exhibit improved binding compared to the ones with functional groups in meta position, presumably due to an unfavorable orientation of the substituents that lead toward solvent exposed area out of the pocket.…”

“…The crude product was purified using flash column chromatography (SiO 2 ; EtOAc/Hept = 2:1) and the desired compound was obtained as a white solid (0.034 g, 69%). 1 (28). The N 9 alkylation was performed following General procedure 1 using 2,6-dichloropurine 44 (0.2 g, 1.06 mmol) and methyl-4-(bromomethyl)benzoate (0.242 g, 1.06 mmol).…”

“…23,24 Other studies in the literature have reported inhibition using rather promiscuous binders providing limited selectivity toward proteins of the YTH family, 25−27 except for a recent report which describes a selective YTHDC1 inhibitor identified by in vitro highthroughput screening followed by a structure-based optimization. 28 In this study, we present a structure-based design campaign aimed at developing a potent and selective ligand of YTHDC1. Additionally, we provide biochemical evaluation based on the homogeneous time-resolved fluorescence assay (HTRF), isothermal titration calorimetry (ITC), thermal shift assay (TSA), and protein X-ray crystallography.…”

“…Our group recently reported fragments binding to YTHDC1 or YTHDF2, respectively. , Other studies in the literature have reported inhibition using rather promiscuous binders providing limited selectivity toward proteins of the YTH family, − except for a recent report which describes a selective YTHDC1 inhibitor identified by in vitro high-throughput screening followed by a structure-based optimization …”

Structure-based design of a potent and selective YTHDC1 ligand

“…21,22 Other studies in the literature have reported inhibition using rather promiscuous binders providing limited selectivity towards proteins of the YTH family, [23][24][25] except for a recent report which describes a selective YTHDC1 inhibitor identified by in vitro high-throughput screening followed by a structure-based optimization. 26 In this study, we present a structure-based design campaign aimed at developing a potent and selective ligand of YTHDC1. Additionally, we provide a biochemical evaluation (HTRF assay, ITC, TSA, X-Ray) and report a direct connection between YTHDC1 inhibition and the effect on the cell proliferation of acute monocytic leukemia (THP-1, MOLM-13, NOMO1).…”