Discovery of a potent, selective and cell active inhibitor of m6A demethylase ALKBH5

Zhen Fang; Bo Mu; Yang Liu; Nihong Guo; Liang Xiong; Yinping Guo; Anjie Xia; Rong Zhang; Hailin Zhang; Rui Yao; Yan Fan; Linli Li; Shengyong Yang; Rong Xiang

doi:10.1016/j.ejmech.2022.114446

Discovery of a potent, selective and cell active inhibitor of m⁶A demethylase ALKBH5

Eur J Med Chem. 2022 Aug 5:238:114446. doi: 10.1016/j.ejmech.2022.114446. Epub 2022 May 11.

Authors

Zhen Fang¹, Bo Mu², Yang Liu³, Nihong Guo⁴, Liang Xiong³, Yinping Guo³, Anjie Xia³, Rong Zhang³, Hailin Zhang³, Rui Yao³, Yan Fan⁵, Linli Li⁴, Shengyong Yang⁶, Rong Xiang⁷

Affiliations

¹ Department of Medicinal Chemistry, School of Medicine, Nankai University, Tianjin, 300071, China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, 610041, China.
² State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, 610041, China; School of Basic Medical Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan, 637000, China.
³ State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, 610041, China.
⁴ Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, 610041, China.
⁵ Department of Medicinal Chemistry, School of Medicine, Nankai University, Tianjin, 300071, China.
⁶ State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, 610041, China. Electronic address: yangsy@scu.edu.cn.
⁷ Department of Medicinal Chemistry, School of Medicine, Nankai University, Tianjin, 300071, China. Electronic address: rxiang@nankai.edu.cn.

PMID: 35597008
DOI: 10.1016/j.ejmech.2022.114446

Abstract

AlkB homolog 5 (ALKBH5) is an RNA m⁶A demethylase involved in the regulation of genes transcription, translation and metabolism and has been considered as a promising therapeutic target for various human diseases, especially cancers. However, there is still a lack of potent and selective ALKBH5 inhibitors. Herein, we report a new class of ALKBH5 inhibitors containing the 1-aryl-1H-pyrazole scaffold, which were obtained through fluorescence polarization-based screening, structural optimization and structure-activity relationship analysis. Among these compounds, 20m was the most potent one, which showed an IC₅₀ value of 0.021 μM in fluorescence polarization assay. Compound 20m exhibited high selectivity towards ALKBH5 versus FTO as well as other AlkB subfamily members, indicating good selectivity for ALKBH5. Cellular thermal shift assay (CETSA) analysis showed that 20m could efficiently stabilize ALKBH5 in HepG2 cells. Dot blot assay demonstrated that 20m could increase m⁶A level in intact cells. Collectively, 20m is a potent, selective and cell active ALKBH5 inhibitor and could be used as a versatile chemical probe to explore the biological function of ALKBH5.

Keywords: ALKBH5; Epigenetics; N(6)-methyladenosine; RNA modification; Structure-activity relationship analysis.

MeSH terms

AlkB Homolog 5, RNA Demethylase* / chemistry
AlkB Homolog 5, RNA Demethylase* / metabolism
Alpha-Ketoglutarate-Dependent Dioxygenase FTO / metabolism
Humans
RNA* / chemistry
Structure-Activity Relationship

Substances

RNA
ALKBH5 protein, human
AlkB Homolog 5, RNA Demethylase
Alpha-Ketoglutarate-Dependent Dioxygenase FTO
FTO protein, human