Carbamate Prodrug Concept for Hydroxamate HDAC Inhibitors

Abstract

Reversible acetylation of histones and other proteins has emerged over the last 10 years as an important mechanism for cell proliferation and has been identified as a valuable target for anticancer drug design. Acetylation is executed and maintained by the histone acetyltransferases and reversed by their counterparts, histone deacetylases (HDACs). The first HDAC inhibitors have already been approved for therapeutic use, and many additional clinical studies are currently under way. [1][2][3][4] Herein, we describe virtual screening efforts that identified several novel HDAC6 inhibitors with cellular isoform selectivity. In particular, a carbamate-protected hydroxamic acid exhibited improved effects with respect to protein hyperacetylation compared with the parent hydroxamate, possibly because of improved cell permeability. The carbamate structure therefore represents a potential prodrug concept for hydroxamic acidcontaining HDAC inhibitors.HDACs are zinc-dependent amidohydrolases, and 11 human subtypes are known.[5] Among the dozens of nonhistone substrates of HDACs, tubulin has attracted a lot of attention because it is a validated target for established anticancer drugs, such as taxanes, the vinca-alkaloids and their derivatives. Tubulin is deacetylated by a single zinc-dependent HDAC subtype, HDAC6, [6,7] and by the NAD + -dependent histone deacetylase Sirt2.[8] HDAC6-specific inhibitors [9] and nonselective HDAC inhibitors [10] synergize in cytotoxicity with the proteasome inhibitor bortezomib (Velcade), which makes HDAC6 an interesting target for inhibitor development. So far, reports of HDAC6-selective inhibitors are limited [7,11,12,13] compared to nonselective or class I-selective inhibitors.[14] Aiming at novel selective HDAC6 inhibitors, we were particularly interested in whether structure-based virtual screening using a HDAC6 homology model could deliver such compounds.We recently reported a homology model for HDAC6 used for docking studies of hydroxamates.[15] The model was generated by exploiting multiple solved crystal structures of related HDACs as templates. Based on a substructure search for hydroxamates and related zinc binding groups, we identified 252 potential compounds by virtually screening the Maybridge compound collection comprising 55 000 molecules. The docking and subsequent visual inspection of the docking poses showed that, among the compounds with the highest docking scores, several hydroxamate and hydrazide derivatives could be identified. Finally, the five top-ranked compounds (1-5) were selected for in vitro testing.In an initial step, compounds 1-5 were assayed using a rat liver HDAC preparation that contains a mixture of subtypes [14,15] with a fluorescence-based assay. [16] Only the hydroxamate 1 and its carbamate derivative 2 were found to show HDAC inhibition below 100 mm. IC 50 values of 4.8 AE 0.5 mm for 1 and 73.4 AE 5.7 mm for 2 were obtained. The identified hydrazides 3-5 were found to be inactive even though the predicted docking poses suggest an interaction between the ...

HDAC6 as a target for neurodegenerative diseases: what makes it different from the other HDACs?

“…Another structural selective element of the HDAC6 catalytic site was identified by studying new HDAC6 hydroxamate inhibitors isolated from a virtual screening of 55,000 molecules [43]. The selectivity of these compounds was explained by the presence of a small sub-pocket close to the zinc ion, able to stabilize the position of the thiazole and pyridine rings characterizing such compounds.…”

Discovery of a para-Acetoxy-benzyl Ester Prodrug of a Hydroxamate-Based Glutamate Carboxypeptidase II Inhibitor as Oral Therapy for Neuropathic Pain

“…The concept of hydroxamate prodrugs has been only recently reported in the literature, including carbamates, 17,18 O -acyl derivatives, 19 and 1,4,2-dioxazol-5-one. 20 However, little has been investigated on the oral pharmacokinetics of these prodrugs to assess their pharmacological advantages over the parent compounds.…”

Synthesis of hybrid anticancer agents based on kinase and histone deacetylase inhibitors

“…Its promising preliminary data, notably in biochemical and in vitro assays as well as in the NIH cell line, render it an effective potential chemical probe for angiogenisis. 35,36 Current studies are aimed at exploring further SAR in these hybrids with regard to HDAC isoform 37,38 and kinase selectivity 39 as well as improving their physiochemical properties, 40 and will be reported in due course.…”