Abstract by Daniela Danková

Histone deacetylases (HDACs) are Zn²⁺-dependent enzymes that remove post-translational acyl modifications from ε-amino lysine residues. This affects various cellular functions, like gene transcription, protein cellular localization, and stability. HDAC11 is the most recently discovered isozyme that acts as demyristoylase. This thesis describes strategies to generate selectivity between different HDAC isozymes.

In the past decades, the drug discovery toolbox expanded significantly with the emergence of beyond-the-rule-of-five drugs, like chemical degraders or peptide macrocycles. The novel modalities yielded tool compounds with enhanced potency and selectivity to study human biology in health and disease.

The first part of the thesis describes the development and the use of chemical degraders of HDACs. HDAC3-selective degrader was employed to investigate the role of this isozyme in histone lactylation. The thesis also outlines the design, synthesis, and screening of a series of covalent, RNF126-recruiting molecular glue degraders targeting HDACs that yielded an HDAC1/3 degrader that was derived from vorinostat, a broad-spectrum HDAC inhibitor.

Secondly, a focused HDAC11-targeting macrocycle library of 4608 members was screened in a high‑throughput that identified a potent and selective HDAC11 macrocycle. SAR study identified N‑alkylation of the hydroxamic acid moiety as a key feature of compound selectivity (>1000-fold) and potency (K_i = 40 nM). HDAC11-selective macrocycle exhibited excellent cell permeability, as assessed by a modified chloroalkane penetration assay (CP₅₀ = 96 nM).

Finally, a methodology was developed to employ sulfur (VI) fluoride exchange chemistry for generating a diverse library of hydroxamic acid containing biaryl sulfates. Subsequent biochemical screening identified an HDAC11-selective scaffold and a potent HDAC6 inhibitor.