Design, synthesis, and biological evaluation of indazole-based histone deacetylase 6 inhibitors

Abstract

Histone deacetylases (HDACs) have been explored as anticancer targets for over two decades, with six HDAC inhibitors approved for clinical use. However, these pan-HDAC inhibitors exhibit off-target effects, necessitating the development of isoform-selective inhibitors. Among HDACs, HDAC6 has garnered attention due to its dual catalytic domains, cytoplasmic localization, and zinc-finger ubiquitin-binding domain (Zf-UBD). Its role in gene expression, proliferation, protein homeostasis, and cell cycle regulation make it an attractive anticancer target. Here, we report on the design and synthesis of indazole-based HDAC6 inhibitors and evaluate the impact of zinc-binding group (ZBG) modifications on pharmacokinetics. Compound 5j emerged as a selective and potent HDAC6 inhibitor (IC₅₀ = 1.8 ± 0.3 nM), exhibiting strong antiproliferative activity against HCT116 cells (GI₅₀ = 3.1 ± 0.6 μM). It preferentially induced α-tubulin acetylation over histone H3 at concentrations as low as 0.5 μM which is a hallmark of HDAC6 selective inhibition. However, its hydroxamic acid-based ZBG resulted in a very low oral bioavailability (1.2 %). To address this limitation, compound 12 was synthesized with an ethyl hydrazide ZBG, significantly improving oral bioavailability (53 %). These findings highlight compound 12 as a promising lead for further pharmacophore optimization, paving the way for clinically viable HDAC6 selective inhibitors with enhanced drug-like properties.

Keywords: Anticancer; Epigenetics; Histone deacetylase 6; Indazole; Pharmacokinetics; Small molecule.