Selective inhibition of ALDH1A3 impedes breast cancer growth and metastasis by blocking ALDH1A3-driven transcriptional programs.

Aldehyde dehydrogenase 1A3 (ALDH1A3) promotes tumor growth, metastasis, and chemoresistance in multiple cancers, including triple-negative breast cancer (TNBC), yet no clinically approved, isoform-selective inhibitors exist. Here, we present CLM296, a novel, rationally designed, highly potent ALDH1A3 inhibitor. CLM296 exhibits nanomolar inhibition of ALDH1A3 in TNBC cells (half-maximal inhibitory concentration = 2 nM) with no off-target effects on ALDH1A1. Transcriptomic analysis shows that CLM296 selectively suppresses ALDH1A3-driven gene expression, confirming on-target activity. Functionally, CLM296 impedes ALDH1A3-mediated cell invasion in vitro and, with daily dosing in vivo, significantly reduces only ALDH1A3-dependent tumor growth and lung metastasis in TNBC xenografts. These effects are accompanied by selective inhibition of ALDH1A3 target genes in tumors, while pharmacokinetic studies demonstrate broad tissue distribution to metastatic sites, sustained target engagement, and favorable oral bioavailability. CLM296 shows no observable toxicity in preclinical models, supporting its potential as a first-in-class ALDH1A3 inhibitor for ALDH1A3-positive cancers.