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Targeting Lysine Deacetylases (KDACs) in Parasites.

Wang Q, Rosa BA, Nare B, Powell K, Valente S, Rotili D, Mai A, Marshall GR, Mitreva M - PLoS Negl Trop Dis (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America.

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.

No MeSH data available.


Related in: MedlinePlus

Compound MC2776 docked to the KDAC1 protein.(A) in the B. malayi protein and (B) in the H. sapiens protein. MC2776 is shown as yellow stick model along with important residues for ligand binding. (C) shows a close-up view of the zinc-centered square based pyramid, Distances for these are shown in Table 2. (D) and (E) show the rendered surface models of the cartoon representations from (A) and (B).
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pntd.0004026.g004: Compound MC2776 docked to the KDAC1 protein.(A) in the B. malayi protein and (B) in the H. sapiens protein. MC2776 is shown as yellow stick model along with important residues for ligand binding. (C) shows a close-up view of the zinc-centered square based pyramid, Distances for these are shown in Table 2. (D) and (E) show the rendered surface models of the cartoon representations from (A) and (B).

Mentions: To validate our docking procedure, a benchmark docking study was also performed for the crystal structure, using the bound ligand (acetate ion). The experimental pose was successfully obtained for acetate (RMSD between lowest energy ligand conformation and crystal structure: 0.74 Å). This validates the potential utility of the docking procedure. The subsequent docking of the two ligands from the screening suggests that both ligands could bind relatively well with the orthologs, but shows some differences at the different ortholog binding sites, especially for the roundworm-selective ligand MC2776 (Fig 4). The models showed that when viewed from above, the ligand the pyrrole ring was almost perfectly in the plane of the hydroxymate in human KDAC1 with the hydroxymate group chelated with catalytic zinc. However, in the B. malayi ortholog, the pyrrole ring rotated counter-clockwise in order to accommodate the tyrosine residue (Y296) at the opening at the binding channel (Fig 4a). The tyrosine residue is conserved across all the KDAC isotypes among almost all organisms, and has been implicated to play a critical role in the selective ligand binding to KDAC8 of S. mansoni [16]. The different orientation of the Y296 in B. malayi could be attributed to a nearby point mutation (C254N). The small hydrophobic residue in other species is tightly packed beneath the binding pocket; while in B. malayi, the bulkier, more hydrophilic asparagine led to a propagation of rearrangements of the two strands nearby, resulting in a misaligned tyrosine residue at the protein surface. In contrast, because of the lack of the pyrrole ring, MC2780 showed very similar binding modes in the KDAC1 proteins of human and B. malayi (Fig 5). The tert-butylcarbamate group at position 3 of the terminal phenyl ring extended toward the outer portion of the binding gorge, contacting one of the loops lining the rim of the catalytic tunnel (residues G677–G686), while in the protist proteins, the same group tilted away to the other side of the channel (S1 Fig). The different binding modes of MC2776 and MC2780 at KDAC1 may partially explain the different affinities among different organisms. Although quantitative binding energies cannot be obtained from simple docking simulations, the distances of the catalytic zinc atom to its coordinating atoms from the protein and ligand were measured in all the models for comparison (Table 2). In general, the ortholog protein with higher binding affinity with the ligand shows shorter distance (both mean and standard deviation) to the zinc atom for most of the coordinating atoms, to maintain the optimal square-based pyramidal geometry. Docking results showed that both MC2776 and MC2780 could bind the KDAC1 of the protists (L. donovani and P. falciparum); However, MC2776 did not show any efficacy in any of the protists, while MC2780 demonstrated pan-parasite potential. This may be due to its inability to reach its target under assay conditions due to metabolism, transport, or other issues [54].


Targeting Lysine Deacetylases (KDACs) in Parasites.

Wang Q, Rosa BA, Nare B, Powell K, Valente S, Rotili D, Mai A, Marshall GR, Mitreva M - PLoS Negl Trop Dis (2015)

Compound MC2776 docked to the KDAC1 protein.(A) in the B. malayi protein and (B) in the H. sapiens protein. MC2776 is shown as yellow stick model along with important residues for ligand binding. (C) shows a close-up view of the zinc-centered square based pyramid, Distances for these are shown in Table 2. (D) and (E) show the rendered surface models of the cartoon representations from (A) and (B).
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pntd.0004026.g004: Compound MC2776 docked to the KDAC1 protein.(A) in the B. malayi protein and (B) in the H. sapiens protein. MC2776 is shown as yellow stick model along with important residues for ligand binding. (C) shows a close-up view of the zinc-centered square based pyramid, Distances for these are shown in Table 2. (D) and (E) show the rendered surface models of the cartoon representations from (A) and (B).
Mentions: To validate our docking procedure, a benchmark docking study was also performed for the crystal structure, using the bound ligand (acetate ion). The experimental pose was successfully obtained for acetate (RMSD between lowest energy ligand conformation and crystal structure: 0.74 Å). This validates the potential utility of the docking procedure. The subsequent docking of the two ligands from the screening suggests that both ligands could bind relatively well with the orthologs, but shows some differences at the different ortholog binding sites, especially for the roundworm-selective ligand MC2776 (Fig 4). The models showed that when viewed from above, the ligand the pyrrole ring was almost perfectly in the plane of the hydroxymate in human KDAC1 with the hydroxymate group chelated with catalytic zinc. However, in the B. malayi ortholog, the pyrrole ring rotated counter-clockwise in order to accommodate the tyrosine residue (Y296) at the opening at the binding channel (Fig 4a). The tyrosine residue is conserved across all the KDAC isotypes among almost all organisms, and has been implicated to play a critical role in the selective ligand binding to KDAC8 of S. mansoni [16]. The different orientation of the Y296 in B. malayi could be attributed to a nearby point mutation (C254N). The small hydrophobic residue in other species is tightly packed beneath the binding pocket; while in B. malayi, the bulkier, more hydrophilic asparagine led to a propagation of rearrangements of the two strands nearby, resulting in a misaligned tyrosine residue at the protein surface. In contrast, because of the lack of the pyrrole ring, MC2780 showed very similar binding modes in the KDAC1 proteins of human and B. malayi (Fig 5). The tert-butylcarbamate group at position 3 of the terminal phenyl ring extended toward the outer portion of the binding gorge, contacting one of the loops lining the rim of the catalytic tunnel (residues G677–G686), while in the protist proteins, the same group tilted away to the other side of the channel (S1 Fig). The different binding modes of MC2776 and MC2780 at KDAC1 may partially explain the different affinities among different organisms. Although quantitative binding energies cannot be obtained from simple docking simulations, the distances of the catalytic zinc atom to its coordinating atoms from the protein and ligand were measured in all the models for comparison (Table 2). In general, the ortholog protein with higher binding affinity with the ligand shows shorter distance (both mean and standard deviation) to the zinc atom for most of the coordinating atoms, to maintain the optimal square-based pyramidal geometry. Docking results showed that both MC2776 and MC2780 could bind the KDAC1 of the protists (L. donovani and P. falciparum); However, MC2776 did not show any efficacy in any of the protists, while MC2780 demonstrated pan-parasite potential. This may be due to its inability to reach its target under assay conditions due to metabolism, transport, or other issues [54].

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America.

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.

No MeSH data available.


Related in: MedlinePlus