Indolizine-Based Hydroxamates as New HDAC6 Inhibitors: From Docking-Guided SAR Analysis to Model Validation

Histone deacetylase 6 (HDAC6) is a zinc-dependent epigenetic target involved in inflammatory signaling and antiviral immune responses, contributing to pro-inflammatory pathways triggered by viral infections. Known inhibitors include hydroxamate-based compounds, which however lack isoform selectivity. Consequently, selective HDAC6 inhibition represents a promising strategy to attenuate neuroinflammation while minimizing off-target effects associated with pan-HDAC inhibitors. This work investigates the structure–activity relationships (SAR) of a series of novel hydroxamic acid derivatives featuring an indolizine-based recognition scaffold as selective HDAC6 inhibitors, to elucidate the binding mode and prospectively support the design of optimized analogues. Docking studies were performed on the catalytic domain 2 of human HDAC6 (PDB ID: 5EDU) using Glide with a Zn2+ coordination constraint on the hydroxamic acid moiety. Docking poses were analyzed to rationalize SAR and guide optimization of the indolizine cap group. Docking studies showed a prototypical derivative adopted the canonical HDAC6 binding mode: bidentate hydroxamate-mediated Zn2+ chelation, hydrogen bonding with the selectivity-determining Ser568, and occupation of the Loop 2-adjacent lipophilic cavity, which is poorly conserved among HDAC isoforms. Binding-site analysis suggested that larger amide substituents could be accommodated within the wide surface recognition region of HDAC6, improving ligand–protein interactions and selectivity. This supported the synthesis of an amide-based series to explore steric and stereoelectronic effects within the cap group. A qualitative correlation between experimental pIC50 and computed Gscores after pose refinement was observed across the entire compound series. Experimental data confirmed the computational predictions, and the morpholine derivative (5g) emerged as the optimal analogue, displaying low-nanomolar HDAC6 inhibition, fair selectivity and a good in vitro ADME profile. Docking guided the rational optimization of selective indolizine-based HDAC6 inhibitors. The identification of a morpholine-based derivative validates the proposed structure-based design strategy and supports the development of HDAC6-targeted modulators for virus-associated neuroinflammation.