Multicomponent Synthesis and Binding Mode of Imidazo[1,2-a]pyridine-Capped Selective HDAC6 Inhibitors

Abstract

The multicomponent synthesis of a mini library of histone deacetylase inhibitors with imidazo[1,2-a]pyridine-based cap groups is presented. The biological evaluation led to the discovery of the hit compound MAIP-032 as a selective HDAC6 inhibitor with promising anticancer activity. The X-ray structure of catalytic domain 2 from Danio rerio HDAC6 complexed with MAIP-032 revealed a monodentate zinc-binding mode.

Binding of inhibitors to active-site mutants of CD1, the enigmatic catalytic domain of histone deacetylase 6

“…The amide group of SAHA forms water-mediated hydrogen bonds to Ser150 and the zinc ligand His232. Similar hydrogen-bond interactions are observed to the corresponding residues Ser531 and His614 in several HDAC6 CD2inhibitor complexes Hai & Christianson, 2016;Porter et al, 2017;Bhatia et al, 2018;Mackwitz et al, 2018). The benzophenone carbonyl group forms a hydrogen bond to a water molecule, which in turn forms hydrogen bonds to Asp79 and Ser81.…”

“…Thus, X-ray crystallographic studies of HDAC6 CD1 and CD2 have relied on the zebrafish enzyme as a surrogate for the human enzyme. More than 50 structures of zebrafish HDAC6 CD2-inhibitor complexes have since appeared in the literature Bhatia et al, 2018;Mackwitz et al, 2018;Porter et al, 2017;Porter, Osko et al, 2018;Porter, Shen et al, 2018;Porter, Wagner et al, 2018;Shen et al, 2020). In contrast, only seven additional crystal structures of zebrafish HDAC6 CD1inhibitor complexes have since been reported (Osko & Christianson, 2019).…”

Structure–Activity and Structure–Toxicity Relationships of Peptoid‐Based Histone Deacetylase Inhibitors with Dual‐Stage Antiplasmodial Activity

“…Hence, the potent activity against the human class I hHDAC1 isoform seems to be a possible explanation for the increased toxicity of certain compounds against mammalian cells. Notably, compounds 2 e , f , t turned out to be promising selective hHDAC6 inhibitors (IC 50 hHDAC6: 0.032–0.051 μ m , SI HDAC1/HDAC6 : 47–82), similar to other known selective HDAC6i such as ricolinostat (SI HDAC1/HDAC6 : 11), HPOB (SI HDAC1/HDAC6 : 25) and tubastatin A (SI HDAC1/HDAC6 : 178) …”

“…In general, pan‐ and class‐I‐selective human HDACi seem to show increased toxicity. Thus, it has been hypothesized that class‐IIb‐preferential inhibitors may decrease side effects due, in part, to a more precise alteration of biological substrates in the cell . In that regard, we screened selected compounds in a biochemical assay against the class I isoform hHDAC1 and the class IIb isoform hHDAC6 using ZMAL (Z‐Lys(Ac)‐AMC) as substrate to determine if the toxicity against mammalian cells shows any correlation to the human HDAC isoform profile.…”

“…In vitro testing on hHDAC1 and hHDAC6 : The in vitro inhibitory activity of 2 c – i , 2 s , t and SAHA against two human HDAC isoforms (1 and 6) were measured using a previously published protocol . OptiPlate‐96 black microplates (PerkinElmer) were used with an assay volume of 50 μL; 5 μL test compound or control, diluted in assay buffer (50 m m Tris⋅HCl, pH 8.0, 137 m m NaCl, 2.7 m m KCl, 1 m m MgCl 2 , 0.1 mg mL −1 BSA), were incubated with 35 μL of the fluorogenic substrate ZMAL (Z‐(Ac)Lys‐AMC) (21.43 μ m in assay buffer) and 10 μL of human recombinant HDAC1 (BPS Bioscience, Catalog #50051) or HDAC6 (BPS Bioscience, Catalog #50006) at 37 °C.…”