Discovery of HDAC Inhibitors That Lack an Active Site Zn²⁺-Binding Functional Group

Abstract

Natural and synthetic histone deacetylase (HDAC) inhibitors generally derive their strong binding affinity and high potency from a key functional group that binds to the Zn 2+ ion within the enzyme active site. However, this feature is also thought to carry the potential liability of undesirable off-target interactions with other metalloenzymes. As a step toward mitigating this issue, here, we describe the design, synthesis, and structure−activity characterizations of cyclic α 3 β-tetrapeptide HDAC inhibitors that lack the presumed indispensable Zn 2+ -binding group. The lead compounds (e.g., 15 and 26) display good potency against class 1 HDACs and are active in tissue culture against various human cancer cell lines. Importantly, enzymological analysis of 26 indicates that the cyclic α 3 β-tetrapeptide is a fast-on/ off competitive inhibitor of HDACs 1−3 with K i values of 49, 33, and 37 nM, respectively. Our proof of principle study supports the idea that novel classes of HDAC inhibitors, which interact at the activesite opening, but not with the active site Zn 2+ , can have potential in drug design.

An azumamide C analogue without the zinc-binding functionality

“…This is in agreement with previous ndings for SAHA 39 and non-Zn 2+ -binding macrocycles, 24 but to the best of our knowledge, this is the rst investigation of the mechanism of inhibition by azumamide natural products.…”

“…Macrolactamization, under dilute conditions (0.4 mM in DMF), using HATU as the coupling reagent afforded target peptide 9 (Scheme 4). The relatively low yield is similar to those previously achieved for similar compounds [21][22][23][24] and may, at least in part, be attributed to poor solubility in the water-acetonitrile mobile phase used in reversed-phase HPLC purication. However, further optimization of cyclization efficiency, which is known to be notoriously troublesome for small peptides, 33 may also prove worthwhile.…”

“…Trituration with diethyl ether afforded the TFA salt of the linear peptide 16 (53 mg, 81% from 2-chlorotrityl chloride resin, based on theoretical loading of resin) as a white solid. UPLC-MS, t R ¼ 0.84 min, calcd for C 24 Cyclic peptide 9. Linear peptide 16 (50 mg, 0.084 mmol) was dissolved in DMF (200 mL z 0.4 mM) and iPr 2 NEt (73 mL, 0.42 mmol, 5.0 equiv.)…”

“…Not surprisingly, these inhibitors were signi-cantly less potent than their ethylketone-containing counterparts, but still exhibited K i -values of just 30-50 nM against HDACs 1-3. 24 Since a wide variety of enzymes rely on metal ions for catalytic activity, excision of the Zn 2+ -binding group may enable development of more selective HDAC inhibitors with fewer adverse effects.…”

Macrocyclic Peptoid–Peptide Hybrids as Inhibitors of Class I Histone Deacetylases

“…The 1 H NMR spectra of compounds 9 and 10 recorded in DMSO-d 6 at 295 K revealed a single set of signals ( Figures S8 and S9). In contrast, both N-Me-Ala analogs 2 1 and 5, like apicidin, 3,38 exhibited multiple conformations by NMR ( Figures S6 and S7).…”