Discovery of a Selective Series of Inhibitors of Plasmodium falciparum HDACs

Abstract

The identification of a new series of P. falciparum growth inhibitors is described. Starting from a series of known human class I HDAC inhibitors a SAR exploration based on growth inhibitory activity in parasite and human cells-based assays led to the identification of compounds with submicromolar inhibition of P. falciparum growth (EC 50 < 500 nM) and good selectivity over the activity of human HDAC in cells (up to >50-fold). Inhibition of parasital HDACs as the mechanism of action of this new class of selective growth inhibitors is supported by hyperacetylation studies.KEYWORDS: Malaria, Plasmodium falciparum, PfHDAC1, 4-arylimidazoles I nfection with malaria parasites such as Plasmodium falciparum remains a devastating cause of death in tropical geographies with 40% of the world population at risk of acquiring the disease. There are approximately 200 million clinical cases of malaria every year leading to an estimated 600,000 deaths.1 The requirement for improved therapies to treat and to cure malaria is an evident medical and humanitarian need that is exacerbated by an alarming rise in parasite resistance to the current standard of care.2,3 Drugs that operate via novel mechanisms of action for which no innately resistant parasites are expected are therefore especially desirable.DNA is tightly packed around histone proteins in the nucleus of eukaryotic cells with its transcription being regulated by chemical modifications to the nucleosomal histone proteins themselves. Histone deacetylases (HDACs) are zinc-dependent enzymes that play crucial roles in modulating mammalian cell chromatin structure, transcription, and gene expression. 4−6HDACs have also been identified as important regulators of transcription in P. falciparum, 7−10 and inhibition of P. falciparum histone deacetylases (Pf HDACs) has been reported to both effectively kill the parasites (Vorinostat, Figure 1) 11−16 and lead to efficacy in animal models of malaria (compound 2).17 Such findings underscore the potential for Pf HDAC inhibitors to be used for malaria therapy. 18−20 Of the five HDAC encoding genes known in P. falciparum one has homology to mammalian class I isoforms (Pf HDAC1), two are similar class II (Pf HDAC2 and 3) mammalian HDACs, while the remaining two are class III HDACs, or silent information regulator 2 (SIR2) proteins. 19 In light of the close sequence homology between Pf HDAC1 and human class I HDACs 21 an

Design of Potent Panobinostat Histone Deacetylase Inhibitor Derivatives: Molecular Considerations for Enhanced Isozyme Selectivity between HDAC2 and HDAC8

“…Thus, HDAC2 inhibitors may also improve therapeutic options for this patient population. Several researchers are also pursuing histone deacetylase inhibitors (HDACi) as an approach for treatment of parasitic infections ,. HDAC8 is currently one of the targets for treatment of Schistosomiasis …”

Design and Synthesis of Terephthalic Acid‐Based Histone Deacetylase Inhibitors with Dual‐Stage Anti‐Plasmodium Activity

“…However, of the three P. falciparum class I/II HDAC homologues, recombinant protein is only available for Pf HDAC1. Furthermore, in a recent study, the quality of recombinant Pf HDAC1 has been questioned, both in terms of the low purity of this commercially available enzyme and validity of its catalytic activity in the absence of endogenous cofactors. Thus, we decided to study the effect of selected compounds on parasitic deacetylase activity by means of P. falciparum hyperacetylation assays.…”

“…Of the three P. falciparum class I/II HDAC homologues, recombinant protein is only available for Pf HDAC1 . Although this enzyme is inhibited by different anti‐plasmodial HDACi type compounds, its quality has been questioned . While the specificity of anti‐plasmodial HDAC inhibitors for Pf HDAC1 versus the other P. falciparum HDACs is not yet known, we hypothesized that HDACi with potent activity against P. falciparum asexual blood stages and low activity against human class I enzymes and in particular against hHDAC1, are likely to be suitable starting points for the development of anti‐plasmodial HDACi with improved parasite‐selectivity.…”

“…[14] Although this enzyme is inhibited by different anti-plasmodial HDACi type compounds, its quality has been questioned. [15] While the specificity of anti-plasmodial HDAC inhibitors for Pf HDAC1v ersus the other P. falciparum HDACsi s not yet known,w eh ypothesized that HDACi with potent activity against P. falciparum asexualb lood stages and low activity against human class Ie nzymesa nd in particular against hHDAC1, are likely to be suitable starting points for the devel-opment of anti-plasmodial HDACiw ith improved parasite-selectivity. This hypothesis was supported by ar ecent report from De Vreese et al,w ho showed that selectiveh HDAC6 inhibitors( with low activity against human class IH DACs) can possessp otent and selective anti-plasmodial activity.…”

Multistage activity within a diverse set of epi-drugs against Plasmodium falciparum parasites

“…SAHA additionally retained activity in clinical isolates of both P. falciparum and P. vivax (27). These data have led to larger screens for diverse and selective inhibitors of HDACs (14,(28)(29)(30). In P. falciparum, histone lysine methyltransferases (HKMTs) are involved in both transcriptional activation (through H3K4me marking) and repression (e.g.…”