Discovery of a highly potent NPAS3 heterodimer inhibitor by covalently modifying ARNT

Peizhuo Li; Yucheng Tian; Qinghong Shang; Cailing Tang; Zeng Hou; Yuanqing Li; Liyuan Cao; Shengyu Xue; Jinlei Bian; Cheng Luo; Dalei Wu; Zhiyu Li; Hong Ding

doi:10.1016/j.bioorg.2023.106676

Discovery of a highly potent NPAS3 heterodimer inhibitor by covalently modifying ARNT

Bioorg Chem. 2023 Oct:139:106676. doi: 10.1016/j.bioorg.2023.106676. Epub 2023 Jun 10.

Authors

Peizhuo Li¹, Yucheng Tian², Qinghong Shang³, Cailing Tang¹, Zeng Hou⁴, Yuanqing Li¹, Liyuan Cao⁵, Shengyu Xue¹, Jinlei Bian², Cheng Luo¹, Dalei Wu⁶, Zhiyu Li⁷, Hong Ding⁸

Affiliations

¹ School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
² Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
³ Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
⁴ School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310053, China.
⁵ School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
⁶ Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China. Electronic address: dlwu@sdu.edu.cn.
⁷ Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China. Electronic address: zhiyuLi@cpu.edu.cn.
⁸ State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China. Electronic address: hding@simm.ac.cn.

PMID: 37352720
DOI: 10.1016/j.bioorg.2023.106676

Abstract

Neuronal PAS domain protein 3 (NPAS3), a basic helix-loop-helix PER-ARNT-SIM (bHLH-PAS) family member, is a pivotal transcription factor in neuronal regeneration, development, and related diseases, regulating the expression of downstream genes. Despite several modulators of certain bHLH-PAS family proteins being identified, the NPAS3-targeted compound has yet to be reported. Herein, we discovered a hit compound BI-78D3 that directly blocks the NPAS3-ARNT heterodimer formation by covalently binding to the aryl hydrocarbon receptor nuclear translocator (ARNT) subunit. Further optimization based on the hit scaffold yielded a highly potent Compound 6 with a biochemical EC₅₀ value of 282 ± 61 nM and uncovered the 5-nitrothiazole-2-sulfydryl as a cysteine-targeting covalent warhead. Compound 6 effectively down-regulated NPAS3's transcriptional function by disrupting the interface of NPAS3-ARNT complexes at cellular level. In conclusion, our study identifies the 5-nitrothiazole-2-sulfydryl as a cysteine-modified warhead and provides a strategy that blocks the NPAS3-ARNT heterodimerization by covalently conjugating ARNT Cys336 residue. Compound 6 may serve as a promising chemical probe for exploring NPAS3-related physiological functions.

Keywords: 5-nitrothiazole warhead; Covalent inhibitor; NPAS3; Protein–protein interaction.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Aryl Hydrocarbon Receptor Nuclear Translocator* / chemistry
Aryl Hydrocarbon Receptor Nuclear Translocator* / metabolism
Basic Helix-Loop-Helix Transcription Factors / metabolism
Cysteine / metabolism
Protein Binding
Receptors, Aryl Hydrocarbon* / metabolism

Substances

Aryl Hydrocarbon Receptor Nuclear Translocator
5-nitrothiazole
Receptors, Aryl Hydrocarbon
Cysteine
Basic Helix-Loop-Helix Transcription Factors