Zinc Affinity of Benzamide-Based Histone Deacetylase Inhibitors: A DFT Study

Histone deacetylase inhibitors (HDACi) are an emerging class of epigenetic anticancer drugs that exert their activity through coordination to the catalytic Zn²⁺ ion within the active site of histone deacetylases (HDACs). Due to the limited isoform-selectivity of hydroxamic acid-based inhibitors, benzamide-based HDACi (BBHDACi) have been developed as subtype-selective alternatives. Clinically relevant representatives include Chidamide, Entinostat, Mocetinostat, Zabadinostat, and Tacedinaline. Although these compounds share a conserved o-aminoanilide zinc-binding group (ZBG), they differ in linker and cap region structure, raising questions regarding their intrinsic Zn²⁺ affinity and coordination behavior. Herein, density functional theory (DFT) calculations were performed at the B3LYP/6-311++g(d,p) level of theory combined with the PCM solvation in methanol (ε = 33) and water (ε = 78). Geometry optimization confirmed that the trans (E) isomer of Chidamide is thermodynamically preferred. Coordination studies showed that the remaining BBHDACi adopt stable geometries, with the o-aminoanilide group preferentially forming tetracoordinated complexes that are more stable than hexacoordinated ones in polar media. Interestingly, calculated substitution free energies differed by less than ± 2 kcal.mol^-1, indicating nearly identical intrinsic Zn²⁺ affinities across the series. These results suggest that the ZBG contributes similarly to metal coordination across all BBHDACi, whereas the overall binding strength is mainly governed by interactions of the linker and cap regions rather than by the conserved zinc-binding group itself.