A specific inhibitor of ALDH1A3 regulates retinoic acid biosynthesis in glioma stem cells

Jianfeng Li,Andrzej Wierzbicki,Andrea Moretti,Carlos J Camacho,Steven J Mullett,Alla Klyuyeva ,Md Ibrahim ,Steven Mcclellan ,Olga V Belyaeva,E Alan Salter,Anna Wilk,Marie E Migaud,Menico Rizzi,Zhaofeng Ye,Kelli R Goggans,Silvia Garavaglia,Nathan A Yates,Alison Beiser,Natalia Y Kedishvili,Robert W Sobol

doi:10.1038/s42003-021-02949-7

Abstract

Elevated aldehyde dehydrogenase (ALDH) activity correlates with poor outcome for many solid tumors as ALDHs may regulate cell proliferation and chemoresistance of cancer stem cells (CSCs). Accordingly, potent, and selective inhibitors of key ALDH enzymes may represent a novel CSC-directed treatment paradigm for ALDH+ cancer types. Of the many ALDH isoforms, we and others have implicated the elevated expression of ALDH1A3 in mesenchymal glioma stem cells (MES GSCs) as a target for the development of novel therapeutics. To this end, our structure of human ALDH1A3 combined with in silico modeling identifies a selective, active-site inhibitor of ALDH1A3. The lead compound, MCI-INI-3, is a selective competitive inhibitor of human ALDH1A3 and shows poor inhibitory effect on the structurally related isoform ALDH1A1. Mass spectrometry-based cellular thermal shift analysis reveals that ALDH1A3 is the primary binding protein for MCI-INI-3 in MES GSC lysates. The inhibitory effect of MCI-INI-3 on retinoic acid biosynthesis is comparable with that of ALDH1A3 knockout, suggesting that effective inhibition of ALDH1A3 is achieved with MCI-INI-3. Further development is warranted to characterize the role of ALDH1A3 and retinoic acid biosynthesis in glioma stem cell growth and differentiation.

Highlights

Elevated aldehyde dehydrogenase (ALDH) activity correlates with poor outcome for many solid tumors as ALDHs may regulate cell proliferation and chemoresistance of cancer stem cells (CSCs)
Mass spectrometry-based cellular thermal shift analysis revealed that MCI-INI-3 binds selectively to the 1A3 isoform of ALDHs in cell lysates, and we show by analysis of a co-crystal of MCI-INI-3 and ALDH1A3 that the inhibitor binds in the active site
We reported that there are two major subtypes of glioma stem cells (GSCs), proneural (PN) and mesenchymal (MES), and each present with distinct phenotypes and molecular signatures, in which ALDH1A3 mRNA expression is elevated in the MES subtype[3]

Summary

Introduction

Elevated aldehyde dehydrogenase (ALDH) activity correlates with poor outcome for many solid tumors as ALDHs may regulate cell proliferation and chemoresistance of cancer stem cells (CSCs). Of the many ALDH isoforms, we and others have implicated the elevated expression of ALDH1A3 in mesenchymal glioma stem cells (MES GSCs) as a target for the development of novel therapeutics To this end, our structure of human ALDH1A3 combined with in silico modeling identifies a selective, active-site inhibitor of ALDH1A3. The Aldefluor assay, developed for rapid analysis of the enzymatic activity of ALDHs in cells, is a well-established method to identify CSCs within a mixed population of heterogeneous tumor cells[21,22] This is of value since it has been suggested that subpopulations of ALDHHigh cancer cells show increased clonogenic potential, migration capacity, and tumor initiation as compared to ALDHLow cancer cells[23]. It is critical to determine the dominant ALDH isoform in different cancer and tumor types

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