Synthesis of HDAC Substrate Peptidomimetic Inhibitors Using Fmoc Amino Acids Incorporating Zinc-Binding Groups

Abstract

Syntheses of Fmoc amino acids having zinc-binding groups were prepared and incorporated into substrate inhibitor H3K27 peptides using Fmoc/tBu solid-phase peptide synthesis (SPPS). Peptide 11, prepared using Fmoc-Asu(NHOtBu)-OH, is a potent inhibitor (IC50 = 390 nM) of the core NuRD corepressor complex (HDAC1–MTA1–RBBP4). The Fmoc amino acids have the potential to facilitate the rapid preparation of substrate peptidomimetic inhibitor (SPI) libraries in the search for selective HDAC inhibitors.

Hydroxamic Acid-Modified Peptide Microarrays for Profiling Isozyme-Selective Interactions and Inhibition of Histone Deacetylases

“…Hydroxamic acid-modified peptides have been used as substrate mimics and were shown to recapitulate important aspects of HDAC substrate recognition. [32][33][34] Here, we systematically explored the predictive power of this modification. We found that sequence requirements for the recognition of histone tails by HDACs 1, 2, and 8 remain largely conserved for the Asuhamodified peptides, thus allowing for prediction of the turnover of acetylated substrates in response to PTMs and mutations.…”

“…The cap group of such inhibitors interacts with the enzyme surface close to the catalytic pocket and the linker projects a zinc-binding group through a channel to the Zn 2+ ion in the active site (Figure 2A). 31,32 Consequently, the turnover of Kac-containing peptides by Zn 2+ -dependent HDACs can be inhibited by entities where the Kac has been substituted with zinc-binding groups and peptides containing the hydroxamic acid [32][33][34] or the o-aminoanilide 35 functionalities have been shown to bind and/or capture HDAC enzymes. Here, we explored the use of these moieties in histone tail peptide microarrays to interrogate binding of class I HDACs.…”

“…Modification of an acetamidomalonate alkylation/enzymatic resolution strategy [36][37] provided an affordable and scalable synthetic route for Fmoc-Asuha( t Bu)-OH (2 g, 20% overall yield, Scheme S1), which is the largest scale reported to date. [33][34]38 Hydroxamic acid-modified peptide microarrays were then produced using µSPOT, a variant of the widely applied SPOT method. [39][40][41] Successful synthesis of the modified peptides was validated by LC-MS analysis of a subset of the crude peptides in the cleavage cocktail prior to printing the microarrays ( Table S1).…”

“…This is particularly true for class I HDACs (HDACs 1-3 and 8, Figure 1A), which are the HDAC isozymes primarily targeted by clinically used drugs [30][31] and responsible for histone deacetylation. 16 Here, we report the synthesis and application of peptide microarrays that circumvent the aforementioned limitations by introduction of hydroxamic acid-containing residues in place of the Kac residues ( Figure 1B), [32][33][34] which thereby provide a platform to dissect HDAC function in high-throughput ( Figure 1C). Complementary functional assays demonstrate the value of this approach to predict HDAC binding, inhibition, and activity.…”

Asymmetric Synthesis of Tailor-Made Amino Acids Using Chiral Ni(II) Complexes of Schiff Bases. An Update of the Recent Literature

“…In 2019, Jamieson and co-workers successfully used the Ni complex ( S )- 2 for the preparation of three types of amino acids, which were used in the solid-phase peptide synthesis (SPPS) of histone deacetylases (HDACs) substrate peptidomimetic inhibitors ( Scheme 22 ) [ 71 ].…”