Sertraline, chlorprothixene, and chlorpromazine characteristically interact with the REST-binding site of the corepressor mSin3, showing medulloblastoma cell growth inhibitory activities

Jun-Ichi Kurita,Yuuka Hirao,Hirofumi Nakano,Yoshifumi Nishimura,Yoshifumi Fukunishi

doi:10.1038/s41598-018-31852-1

Abstract

Dysregulation of repressor-element 1 silencing transcription factor REST/NRSF is related to several neuropathies, including medulloblastoma, glioblastoma, Huntington’s disease, and neuropathic pain. Inhibitors of the interaction between the N-terminal repressor domain of REST/NRSF and the PAH1 domain of its corepressor mSin3 may ameliorate such neuropathies. In-silico screening based on the complex structure of REST/NRSF and mSin3 PAH1 yielded 52 active compounds, including approved neuropathic drugs. We investigated their binding affinity to PAH1 by NMR, and their inhibitory activity toward medulloblastoma cell growth. Interestingly, three antidepressant and antipsychotic medicines, sertraline, chlorprothixene, and chlorpromazine, were found to strongly bind to PAH1. Multivariate analysis based on NMR chemical shift changes in PAH1 residues induced by ligand binding was used to identify compound characteristics associated with cell growth inhibition. Active compounds showed a new chemo-type for inhibitors of the REST/NRSF-mSin3 interaction, raising the possibility of new therapies for neuropathies caused by dysregulation of REST/NRSF.

Highlights

Repressor-element 1 silencing transcription factor (REST) or neural restrictive silencer factor (NRSF)[1,2] was originally identified as a fundamental repressor, which binds to repressor-element 1 or neural restrictive silencer element of many neuronal genes[3,4] in both non-neuronal cells and neuronal progenitor cells
The binding ability of the 52 compounds was examined by NMR screening methods[30], including two ligand-based screening methods, saturation transfer difference (STD)[31,32] and WaterLOGSY33,34, and one protein-based screening method, heteronuclear single quantum coherence (HSQC), while their inhibitor activity was examined by using a medulloblastoma cell line, DAOY35–37
To identify potential inhibitors of the interaction between mSin[3] and Repressor-element silencing transcription factor (REST)/NRSF, we performed two types of in-silico screening: ligandbased drug screening (LBDS) to identify compounds similar to known active compounds; and structure-based drug screening (SBDS) based on the target protein structure to identify new active chemo-types that differ from the chemo-types of known active compounds

Summary

Introduction

Repressor-element 1 silencing transcription factor (REST) or neural restrictive silencer factor (NRSF)[1,2] was originally identified as a fundamental repressor, which binds to repressor-element 1 (re1) or neural restrictive silencer element (nrse) of many neuronal genes[3,4] in both non-neuronal cells and neuronal progenitor cells. MSin[3] contains four paired amphipathic helix domains (PAH1–PAH4), of which PAH1 is responsible for interacting with the N-terminal repressor domain of REST/NRSF25. In the NMR structure of the complex, the short helix of NRSF/REST is deeply buried in the hydrophobic groove of PAH1. Compounds that bind to the mSin3B PAH1 groove are presumably inhibitors of REST/NRSF function[21,25], and potentially drug candidates to ameliorate disorders originating from up-regulation of REST/NRSF21,26–29. We obtained the NMR-docking structures of two of the identified active compounds (sertraline and chlorpromazine), on the mSin3B PAH1 domain based on their chemical shift perturbations (CSPs) and compared them with the binding mode of sertraline to a serotonin transporter

Methods

Results

Conclusion