Research Article: Targeting Lysine Deacetylases (KDACs) in Parasites

Date Published: September 24, 2015

Publisher: Public Library of Science

Author(s): Qi Wang, Bruce A. Rosa, Bakela Nare, Kerrie Powell, Sergio Valente, Dante Rotili, Antonello Mai, Garland R. Marshall, Makedonka Mitreva, Timothy G. Geary.

Abstract: Due to an increasing problem of drug resistance among almost all parasites species ranging from protists to worms, there is an urgent need to explore new drug targets and their inhibitors to provide new and effective parasitic therapeutics. In this regard, there is growing interest in exploring known drug leads of human epigenetic enzymes as potential starting points to develop novel treatments for parasitic diseases. This approach of repurposing (starting with validated targets and inhibitors) is quite attractive since it has the potential to reduce the expense of drug development and accelerate the process of developing novel drug candidates for parasite control. Lysine deacetylases (KDACs) are among the most studied epigenetic drug targets of humans, and a broad range of small-molecule inhibitors for these enzymes have been reported. In this work, we identify the KDAC protein families in representative species across important classes of parasites, screen a compound library of 23 hydroxamate- or benzamide-based small molecules KDAC inhibitors, and report their activities against a range of parasitic species, including the pathogen of malaria (Plasmodium falciparum), kinetoplastids (Trypanosoma brucei and Leishmania donovani), and nematodes (Brugia malayi, Dirofilaria immitis and Haemonchus contortus). Compound activity against parasites is compared to that observed against the mammalian cell line (L929 mouse fibroblast) in order to determine potential parasite-versus-host selectivity). The compounds showed nanomolar to sub-nanomolar potency against various parasites, and some selectivity was observed within the small panel of compounds tested. The possible binding modes of the active compounds at the different protein target sites within different species were explored by docking to homology models to help guide the discovery of more selective, parasite-specific inhibitors. This current work supports previous studies that explored the use of KDAC inhibitors in targeting Plasmodium to develop new anti-malarial treatments, and also pioneers experiments with these KDAC inhibitors as potential new anthelminthics. The selectivity observed begins to address the challenges of targeting specific parasitic diseases while limiting host toxicity.

Partial Text: Neglected tropical diseases are the most common infections of the poorest populations around the globe, causing massive burdens on the countries’ general population and inhibiting economic development [1]. Treatments for these diseases usually rely on a single drug, or limited options of drugs. Most drugs used for treating neglected diseases are quite old, have unknown mechanisms of action, and often have limited effectiveness with poor safety profiles. Furthermore, drug resistance has been observed following the treatment of almost all parasitic pathogens, including protists, helminthes (roundworms) and Platyhelminthes (flatworms) [2]. Parasitic genome sequencing is now being exploited to help accelerate the development of much-needed compounds with novel mechanisms of action.

We presented the first systematic examinations of all zinc-dependent KDAC proteins in representative parasites from nematode, trematode, kinetoplastid and malaria pathogens, and showed that some human KDAC isotypes lack clear orthologs in the parasites, with the only conserved isotype across all the species studied being KDAC1. KDAC1 enzymes are primarily localized in the nucleus and are expressed in all tissues almost ubiquitously. As a classical KDAC protein, it has been studied extensively both in human and in the parasites such as P. falciparum as a novel drug target [6, 12]. KDAC1 shares high sequence similarities among all the species studied. It has been reported that KDAC1 of P. falciparum shares over 55% sequence identity to yeast, human, chicken, and frog KDAC orthologs [55]. This also consistent for the nematode/trematode KDAC1 in comparison with host orthologs, but the homology was lower in the kinetoplastids, which had ~40% sequence identity with the remaining species (S2 Fig). It was also reflected in active-site residues, with most of the variants coming from the kinetoplastid orthologs. As shown in S2 Fig, out of the 12 active-site variants from all the parasite proteins, 3 are specifically present in the kinetoplastids, indicating a higher level of divergence. It has been found that the KDACs of kinetoplastids branched very early from the eukaryotic lineages, especially for the class I isotopes [56]. This suggests that it would be relatively easier to design selective compounds against the kinetoplastid KDAC1. Achieving species selectivity within the other parasite species would still be difficult, due to the higher level of conservations of protein sequence especially at the active site. In this regard, the molecular ligand binding modeling of B. malayi KDAC1 offered potential insight on improving parasitic selectivity. In fact, a BLAST search of the protein sequence against other nematode proteomes suggests that the C254N mutation was present within KDAC1 of other Brugia species (B. timori and B. pahangi), as well as the Onchocerca species (O. ochengi, O. flexuosa, and O. volvulus).



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