Design and synthesis of peptides as stabilizers of histone deacetylase 4

Histone deacetylase 4 (HDAC4) contributes to gene repression by complex formation with HDAC3 and the corepressor silencing mediator for retinoid or thyroid hormone receptors (SMRT). We hypothesized that peptides derived from the class IIa specific binding site of SMRT would stabilize a specific conformation of its target protein and modulate its activity. Based on the SMRT‐motif 1 (SM1) involved in the interaction of SMRT with HDAC4, we systematically developed cyclic peptides that exhibit Ki values that are 9 to 56 times lower than that of the linear SMRT peptide. The peptide macrocycles stabilize the wildtype of the catalytic domain of HDAC4 (cHDAC4) considerably better than its thermally more stable ‘gain‐of‐function’ (GOF) variant, cHDAC4‐H976Y. Molecular docking and mutagenesis studies indicated that the cyclic peptides bind in a similar but not identical manner as the linear SMRT peptide to a discontinuous binding site. Ion mobility mass spectrometry showed no major changes in the protein fold upon peptide binding. Consistent with these results, preliminary hydrogen‐deuterium exchange mass spectrometry measurements indicated only minor conformational changes. Taken together, the cyclic SMRT peptides most likely stabilize the apo form of cHDAC4. Based on the SMRT‐motif 1, cyclic peptides were systematically developed that stabilize the wildtype of the catalytic domain of histone deacetylase 4 (cHDAC4) considerably better than its thermally more stable “gain‐of‐function” variant, cHDAC4‐H976Y. The cyclic peptides bind in a similar but not identical manner as the linear SMRT peptide to a discontinuous binding site.