Novel Small Molecule RNA m6A Demethylase AlkBH5 Inhibitors for Treating Cancer

Important Compound Classes

Title

Method of Suppressing Cancer by RNA m6A Demethylase AlkBH5 Inhibitors

Patent Publication Number

WO 2020/207550 A1

Publication Date

October 15, 2020

Priority Application

EP PCT/EP2019/058737

Priority Date

April 7, 2019

Inventors

Selberg, S.; Karelson, M.

Assignee Company

Chemestmed Ltd.; Estonia

Disease Area

Cancer

Biological Target

RNA m6A Demethylase AlkBH5

Summary

Chemical modifications of RNA have recently been identified to have an impact on several critical cellular functions, such as proliferation, survival, and differentiation, mostly through regulation of RNA stability. The most common modification in mRNA is N6-methyladenosine (m6A). It has been shown that m6A modifications of RNA affect its splicing, intracellular distribution, translation, and cytoplasmic degradation, thus playing a crucial role in regulating cell differentiation, neuronal signaling, carcinogenesis, and immune tolerance. The m6A presence in RNA is regulated by specific enzymes, i.e., the RNA methyltransferases, RNA methylases, and RNA reader proteins.

The N-methylation of the adenosine is a reversible process catalyzed by specific proteins. Those include the RNA methyltransferase enzyme complex METTL3/METTL14/WTAP consisting of the following three components: METTL3 (methyltransferase-like 3), METTL14 (methyltransferase-like 14), and WTAP (Wilm’s tumor-1-associated protein). RNA m6A methyltransferase Mettl16, the RNA demethylase FTO (fat mass and obesity-associated protein) and ALKBH5 (ALKB family member 5) are called “erasers”. The fate of the RNA in post-transcriptomic processes is also directed by the “reader” enzymes that recognize specific m6A methylation in RNA. Several RNA reader enzymes have been identified, including YTHDF1 (YTH N6-Methyladenosine RNA Binding Protein 1), YTHDF2 (YTH N6-Methyladenosine RNA Binding Protein 2), YTHDF3 (YTH N6-Methyladenosine RNA Binding Protein 3), YTHDC1 (YTH domain-containing protein 1), and YTHDC2 (YTH domain-containing protein 2). These three types of enzymes collectively coordinate the m6A RNA methylome in eukaryotic cells.

The methyl group from m6A can be removed by two RNA demethylases, FTO and α-ketoglutarate dependent dioxygenase homologue 5 (ALKBH5). Both the FTO and ALKBH5 RNA demethylases belong to the AlkB subfamily of the nonheme Fe(II)/2-oxoglutarate (2OG) dependent dioxygenase subfamily. Specific and efficient ALKBH5 inhibitors or activators would enable a closer examination of the physiological and pathological processes related to the m6A demethylation of RNA. ALKBH5 has been reported to promote tumorigenesis and proliferation in glioblastoma stem-like cells (GSCs) and breast cancer stem cells (BCSCs). Therefore, the compounds inhibiting AlkBH5 activity can act as suppressors of cancer.

The present application describes a series of novel small molecule RNA m6A demethylase AlkBH5 inhibitors for the treatment of cancer. Further, the application discloses compounds, their preparation, use, pharmaceutical composition, and treatment.

Definitions

R₁ and R₂ are independently selected from the group consisting of H, alkyl, aryl, aralkyl, acyl, alkoxycarbonyl, aryloxycarbonyl, araloxycarbonyl, carbamoyl, alkylcarbamoyl, dialkylcarbamoyl, aminoalkyl, and amonoalaryl.

Key Structures

Biological Assay

The RNA m6A demethylase AlkBH5 ligand enzyme inhibition assay was performed. The compounds described in this application were tested for their ability to inhibit RNA m6A demethylase AlkBH5. The RNA m6A demethylase AlkBH5 IC₅₀ values (μM) are shown in the following Table.

Biological Data

The Table below shows representative compounds tested for RNA m6A demethylase AlkBH5 inhibition. The biological data obtained from testing representative examples are listed in the following Table.

Claims

Total claims: 16. Compound claims: 8. Pharmaceutical composition claims: 4. Method for inhibition claims: 4.

Recent Review Articles

• 1.Huang H.; Weng H.; Chen J.. Cancer Cell 2020, 37, 270.
• 2.Muthusamy S.Gene 2020, 736, 144415.
• 3.Gu J.; Xu J.; You Q.; Guo X.. Eur. J. Med. Chem. 2020, 196, 112325.
• 4.Xu Z.; Peng B.; Cai Y.; Wu G.; Huang J.; Gao M.; Guo G.; Zeng S.; Gong Z.; Yan Y.. Biochem. Pharmacol. 2020, 182, 114258.
• 5.Hu Y.; Wang S.; Liu J.; Huang Y.; Gong C.; Liu J.; Xiao Y.; Yang S.. Biomed. Pharmacother. 2020, 122, 109694.
• 6.Zhao W.; Qi X.; Liu L.; Ma S.; Liu J.; Wu J.. Mol. Ther. Nucleic Acids 2020, 19, 405.

The author declares no competing financial interest.