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Corresponding authors: Mai, Antonello ([email protected]); Epigenetics and chromatin structure play an important
Rotili, Dante ([email protected]) role in mammalian and in parasitic development.
a
Rossella Fioravanti and Nicola Mautone contributed equally to this Therefore, the impact of histone and histone modifying
review. proteins in parasites with complex life cycles and mul-
tiple developmental stages is expected to be strong.
Current Opinion in Chemical Biology 2020, 57:65–74
Moreover, recent studies have shown the role played by
these conserved proteins in conferring to parasites the
This review comes from a themed issue on Chemical Genetics and
Epigenetics
capability to quickly adapt to a different environment of
the host, to evade the host immune responses or to alter
Edited by Akane Kawamura and Arasu Ganesan
their phenotypes at several key points of the life cycles
For a complete overview see the Issue and the Editorial [2].
Available online 29 June 2020
https://doi.org/10.1016/j.cbpa.2020.05.008 Interestingly, it has been suggested that the ability to
1367-5931/© 2020 Elsevier Ltd. All rights reserved. survive within the host by hiding and escaping from its
immune system and by increasing the metabolic rate
activity, owing to higher dependence on lactase
Keywords
Histone acetylation/deacetylation, Bromodomain inhibitors, Sirtuins,
fermentation as a preferential energy source, are
Neglected tropical disease, Drug discovery. common features between cancer cells and parasites,
Abbreviations particularly those that proliferate within human host.
BiP, binding immunoglobulin protein; BNIP, bisnaphthalimidopropyl; Thus, targeting the epigenome with epidrugs developed
BRD, bromodomain; CHD, chromodomain–helicase–DNA–binding for cancer pathologies has been proposed as a new
protein; CBP, CREB-binding protein; EEF, exo-erythrocytic forms; ESG,
early stage gametocytes; GCN5, general control of amino-acid
strategy for the treatment of parasitic diseases [3,4].
In early 2017, we summarized the researches about the at 0.2 mM with no effect of cell proliferation in
identification and characterization of lysine deacetylase mammalian fibroblast cells up to 20 mM [12].
inhibitors (histone deacetylase [HDAC] and sirtuin in-
hibitors) in some of the most relevant parasitic condi- In the genome of P. falciparum there are at least eight
tions [5]. In this opinion article, we give an updated putative P. falciparum BRD-containing proteins [13,14].
overview of the main studies reported from 2017 to early In silico docking studies performed on the crystal struc-
2020, focusing on modulators of histone lysine acetyla- tures of BRDs of PfGCN5 (PDB 4QNS) and PfBDP1
tion at different levels, including histone acetyl- (PDB 3FKM) with a series of BRD inhibitors showed for
transferase (HAT) inhibitors, bromodomain (BRD) all compounds the formation of an hydrogen bond
inhibitors, and HDAC/sirtuin inhibitors, proposed for interaction with the conserved N1436 residue of
the treatment of malaria, schistosomiasis, leishmaniasis, PfGCN5, and only for the selective CREBBP (CBP)/
and Chagas disease. EP300 BRDs inhibitor SGC-CBP30 3 (Figure 1) the
formation of a salt bridge between its morpholine ni-
Malaria trogen and the E1389 residue. In in vitro assays, 3 after
A recent genome-wide study identified 10 putative 72 h treatment inhibited synchronous asexual stage
HAT and seven HDAC enzymes in the Plasmodium fal- P. falciparum Dd2 parasites with low micromolar IC50
ciparum genome (Table 1) [6e8]. values and 7-fold better selectivity for the parasites
versus the human cell line HEK293. Another BRD in-
Among the PfHATs only PfGCN5 and PfMYST, hibitor, L-45 4 (Figure 1), has been crystalized in com-
featuring the highest identity percentage with human plex with the PfGCN5 BRD (PDB 5TPX) owing to its
GCN5 (hGCN5) and hMYST, have a demonstrated strong binding capability (KD 280 nM) [15]. Unfortu-
acetyltransferase activity. Among the PfHDACs, five nately, no data are available about the effects of 4 on
have been already reported, the sixth is a pseudogene P. falciparum strains growth.
considered as a putative HDAC, and the seventh is an
unclassified new putative HDAC belonging to the The ability of HDAC inhibitors (HDACi) to inhibit
CHD subfamily [6]. Thus, both PfHATs and Plasmodium growth is known since a long time [5,16,17].
PfHDACs can be valuable targets to gain anti-Plas- Recently, novel series of HDACi acquired great impor-
modium activity. In particular, PfGCN5 upregulates tance because of their behavior as dual stage anti-Plas-
virulence gene expression upon stress induction and modium agents. One pot, multicomponent syntheses
plays a crucial role in the emergence of artemisinin afforded peptoid-based HDACi highly potent at single-
resistance in P. falciparum [9]. Garcinol 1 (Figure 1), a digit nanomolar level against drug-sensitive (3D7) and
natural p300/CBP and GCN5/PCAF inhibitor, exhibi- drug-resistant (Dd2) P. falciparum asexual blood stage
ted single-digit micromolar activity against erythro- forms, at submicromolar level against exo-erythrocytic
cytic asexual chloroquine-sensitive (HB3) and forms (EEFs) of P. berghei, and at low micromolar level
chloroquine-resistant (Dd2) P. falciparum strains [10]. against P. falciparum gametocytes, with high parasite
When tested against PfGCN5, 1 showed an IC50 of selectivity, measured determining the toxicity of such
15 mM and in P. falciparum artemisinin-resistant strains compounds for human HepG2 cells (selectivity index
reverted the resistance with decrease of the expres- up to 9990) [18,19]. The most potent examples of such
sion levels of BiP and TRiC, two chaperone genes compounds (5, 6) are depicted in Figure 1. The same
upregulated by PfGCN5 in stress conditions [9]. groups previously reported two further series of
However, because natural products such as 1 have hydroxamate HDACi bearing an alkoxyamide function
pleiotropic effects, the presence of multiple mecha- (see 7 and 8 in Figure 1 as examples), which were less
nisms of action cannot be excluded. A comparison potent than the peptoid-based compounds and showed
between the modeled PfGCN5 structure and the submicromolar inhibition of both 3D7 and Dd2
crystal structure of hGCN5 [11] revealed the presence P. falciparum strains, as well as of P. berghei EEFs, and
of three non-identical residues (A1205, L1207, and micromolar inhibition of P. falciparum gametocytes, while
F1245) in the PfGCN5 active site that could allow the the parasite selectivity for the best compound was
design of novel specific PfGCN5 inhibitors. The vir- around 500 [20,21]. Western blot analyses performed on
tual screening performed on this PfGCN5 structure all these compounds in P. falciparum trophozoite stage
using 1e10 ChEMBL compounds known as antima- parasites using the anti-(tetra)acetyl-histone H4 anti-
larial agents confirmed this potential, and a following bodies furnished increased signals for acetyl-H4 (band
virtual screening made with 11e20 ZINC compounds of w11 kDa), acetyl-H2B/H2Bv (bands of w13e
structurally close to the first 1e10 highlighted com- 14 kDa) and acetyl-H2A.Z (band of w16 kDa).
pound C14 2 (Figure 1) as the most potent and se-
lective PfGCN5 inhibitor [12]. In vitro and in vivo Today hybrid compounds represent a modern approach
acetylation assays confirmed the inhibiting activity of for chemotherapy to overcome the main limits of single
2, which arrested the growth of P. falciparum 3D7 strain target therapy, such as the potential mechanism(s) of
Table 1
Parasitic protein targets involved in lysine acetylation/deacetylation. Homo sapiens homologs are reported at the bottom for compar-
ison. When known, the belonging family (for HATs) or class (for HDACs), based on the sequence similarity percentage, has been re-
ported in italics in brackets.
resistance caused by robustness and redundancy of vorinostat) a series of hybrid compounds named
biological pathways [22]. Merging the structure of SAHAquines has been obtained, with low micromolar
primaquine, a known antimalarial agent, with that of the potency against 3D7 and Dd2 P. falciparum erythrocytic
pan-HDACi SAHA (suberoylanilide hydroxamic acid, strains and P. berghei exo-erythrocytic stages, as well as
Figure 1
HAT, BRD, and HDAC inhibitors active against Plasmodium. Color code: black, cellular activity; blue, enzyme activity. EEF, exo-erythrocytic forms; SVG,
stage V gametocytes; NFF, neonatal foreskin fibroblasts; ESG, early stage gametocytes; LSG, late stage gametocytes; HFF, human foreskin fibroblasts;
HDAC, histone deacetylase.
against a panel of cancer cells and HEK293 cells. administration or a combination of oral/iv injections
However, the most potent SAHAquines 9 and 10 [25].
(Figure 1) displayed one magnitude order higher activity
against Plasmodium than toward cancer and Schistosomiasis
HEK293 cells [23]. Combination of the structures of In Schistosoma mansoni class I (SmHDAC1/2, 3,
BIX-01294, a known G9a histone methyltransferase in- and 8), class II (SmHDAC6, SmHDAC10,
hibitor, with SAHA afforded the dual HDAC3/6 inhibi- Smp_069380 and Smp_191310) and class III (SmSIRT1,
tor 11 (Figure 1) devoid of activity against G9a, and able -2, -5, -6, and -7) HDACs have been identified and/or
to inhibit the P. falciparum D37 and the chloroquine- cloned and characterized (Table 1) [3,27e29]. The four
resistant K1 strains growth at submicromolar level, and Food and Drug Administration (FDA)-approved HDACi
to exhibit antiproliferative activity in a panel of cancer vorinostat (SAHA) 13, romidepsin 14, belinostat 15 and
cells with no or low toxicity in mammalian normal cells panobinostat 16 (Figure 2) have been tested in
[24]. Recently we reported the effect of 51 epidrugs on S. mansoni at 10 mM to determine their effects in
the growth of P. falciparum 3D7 and the drug-resistant schistosomula, adult worm pairs, and egg production
W2 and Dd2 parasites [25]. One of the most potent [30]. Vorinostat displayed 20e30% of inhibition in the
compounds in vitro was MC1742 12 (Figure 1), a class I/ three assays, whereas panobinostat was inactive against
IIb HDACi [26] displaying single-digit nanomolar ac- schistosomula and pretty active against adult worms and
tivity against the P. falciparum strains, low toxicity against egg laying (60 and 70% of inhibition, respectively), and
murine and human cell lines and promising PK data belinostat reduced of 30 and 35% the schistosomula
[25]. Unfortunately, when tested in a P. berghei-infected viability and the egg production, respectively, being
rodent model of malaria, 12 failed to reduce peripheral inactive against adult worms. Differently, romidepsin
blood parasitemia at day 4 pi or beyond, either after oral did not exert any effect against parasite larvae but
Figure 2
hHDAC, SmHDAC8, and SmSIRT2 inhibitors active against Schistosoma. Color code: black, cellular activity; blue, enzyme activity. HDAC, histone
deacetylase.
displayed almost 100% of inhibition of adult worm pairs the use of molecular modeling and virtual screening
and egg laying. A high-throughput screening performed techniques based on the crystal structure of SmHDAC8
on 1500 nonhydroxamate HDACi identified SmI-124, (PDB 4BZ8) [34] diverse series of SmHDAC8 inhibitors
SmI-148 and SmI-558 (17, Figure 2) as inhibitors of with various degrees of selectivity toward hHDAC8,
schistosomula viability, as well as adult worm pairs, hHDAC1 and hHDAC6 have been reported: N-phenyl-
leading to an adult phenotype with defects in the succinimides (J1036 18, Figure 2), not selective for
reproductive system [31]. For these three compounds SmHDAC8 in enzyme assays and able to induce
only activities against hHDAC1 and HeLa cell nuclear apoptosis in schistosomula [35]; triazole-based in-
extracts, indicative of a mixture of class I HDACs, have hibitors (19 and 20, Figure 2), displaying a favorable
been reported. All three S. mansoni class I HDACs are selectivity profile but having no or very low effects in
expressed at all life-cycle stages, with SmHDAC8 tran- worms [36], and spiroindolines and thieno[3,2-b]indoles
scripts being the most abundant [32], differently to (21 and 22 in Figure 2), exhibiting low micromolar in-
what happens in human cells where levels of HDAC8 hibition of SmHDAC8 but scarce selectivity toward
transcripts are generally lower than those of HDAC1 and hHDAC1, and reducing schistosomula, as well as juve-
HDAC3, apart from some cancers where HDAC8 nile and adult worms’ viability and egg laying with
expression is often highly upregulated [33]. Through
Figure 3
HDAC and SIRT (including parasite SIR2rp) inhibitors active against Leishmania and T. cruzi. Color code: black, cellular activity; blue, enzyme activity.
NA, no activity; HDAC, histone deacetylase.
toxicity for THP-1 and HFF cells [44]. Interestingly, the Chagas disease
related phenylhydroxamate and sulfonylamino counter- In a comparative study describing the effects on T. cruzi of
parts were totally inactive, while the 4-(2-(3- the HDACi trichostatin A, the SIRTi sirtinol, and the
methoxyphenyl)acetamido)phenylhydroxamate analog SIRT activator resveratrol, the latter emerged as the only
(but not its 2-methoxyphenyl isomer [45]) displayed no one effective in reducing the parasite infection and pro-
effect in Leishmania but strong, submicromolar potency liferation, but at high micromolar doses [57]. In a suc-
against Toxoplasma gondi (IC50 = 0.35 mM) [44]. Anti- cessive report, trichostatin A has been shown to influence
monial drugs have been used for treatment of leish- T. cruzi proliferation and viability through promotion of
maniasis for more than a century. By reaction of cell cycle arrest in the G2/M phase and hyperacetylation
hydroxamates with SbCl3 or Sb(OEt)3 a series of anti- of parasite histones, as well as a-tubulin, thus promoting
mony(III) hydroxamic acid complexes was obtained and changes in microtubule cytoskeleton [58].
tested against L. amazonensis and Leishmania infantum
promastigotes [46]. Compared with their corresponding Both Leishmania and Trypanosoma species belong to the
hydroxamates, the antimony(III) complexes were more group of kinetoplastids thus, despite they provoke
toxic for the parasites but also for RAW macrophages, different diseases and are transmitted by distinct insect
used to assess cellular cytotoxicity. The most potent vectors, they could likely be inhibited by the same epi-
complexes were 28 and the SAHA-based 29, whereas 30 drugs targeting parasitic deacetylases. BNIPs, for
(Figure 3) was the complex with the best selectivity instance, have been reported to inhibit TcSIR2rp1, with
indexes. Such compounds also determined changes in BNIPSpd 33 (Figure 3) d already known as an inhibitor
the morphology of parasites with reduction of size and of LiSIR2rp1 [49] d being one of the most potent.
loss of flagellum, reduction of plasma membrane Compound 33 exerted a trypanocidal activity against
permeability, and impairment of mitochondrial meta- TcSIR2rp1-overexpressing epimastigotes with a 2.8-fold
bolism [46]. Generally, SAHA has been reported as increase of the EC50 value compared with wild-type
poorly active against Leishmania parasites (see previ- parasites, thus suggesting that its trypanocidal activity
ously). Intriguingly, its O-benzyl derivative MDG 31 is correlated to TcSIR2rp1 inhibition. When tested in
(Figure 3), inactive toward HDAC1-3, 6, and 8 T. cruzi intracellular amastigotes, 33 displayed single-
(IC50 > 10 mM), was found ineffective against promas- digit micromolar inhibition with low toxicity for
tigotes, but very potent against L. donovani and C2C12 cells (selectivity index = 8.8) [59]. Unfortu-
L. infantum intracellular amastigotes. Adsorbed on gold nately, when tested in vivo in a mouse model of Chagas
nanoparticles, 31 was tested in vivo in infected Balb/c disease 33 had no effect, likely because of pharmacoki-
mice showing reduction of parasite load with no toxicity netic problems [59]. As stated above, KH-TFMDI 32
[47]. Further studies should be performed to determine exerted (sub)micromolar potency against T. cruzi leading
the molecular mechanism of action of this drug. to inhibition of amastigote replication, lysis of trypo-
mastigotes, epimastigote cytokinesis impairment, and
The bisnaphthalimidopropyl (BNIP) compounds are a changes in the parasite Golgi complex and nuclear en-
known series of anti-Leishmania agents acting through velope [55]. TcSIR2rp1 and TcSIR2rp3, the only charac-
inhibition of the parasite sirtuin LiSIR2rp1 at the low terized deacetylases in T. cruzi, seem to be valuable
micromolar level, with some selectivity toward hSIRT1 targets to fight the parasite infections. The anacardic acid
[48e51]. In a recent study a new synthesis of old and derivatives 34 and 35 (Figure 3), well-known inhibitors of
novel analogs, obtained by replacing the polyamine p300 HAT [60], and related compounds were found
linker with a 16-membered spacer containing amide, active at the low micromolar level against both T. cruzi
reverse amide or carbamate function has been sirtuins [61]. In antiparasitic assays, 34 and 35 were
described, but without inhibitory data on Leishmania ineffective against trypomastigotes, but inhibited the
parasites [52]. The Leishmania sirtuins SIR2rp1, growth of T. cruzi amastigotes (EC50 w 40 mM) in
SIR2rp2, recently characterized in L. donovani [53], and infected cells [61]. However, because of the pleiotropic
SIR2rp3 are the putative targets of KH-TFMDI 32 behavior typical of anacardic acid analogs, the involve-
(Figure 3), a hSIRT1/2 inhibitor with moderate potency ment of off-target effects in their parasitic growth inhi-
belonging to the 3-arylideneindolin-2-one series [54] bition cannot be ruled out. From the screening of 33
and found highly potent in inhibiting the growth of chemically different modulators of hSIRTs we have
Tripanosoma cruzi [55], as well as, more recently, recently identified two compounds, 36 and 37 (Figure 3),
L. amazonensis in both its promastigote and amastigote and further five compounds (for example 38 and 39 in
forms [56]. Treatment with 32 in Leishmania also pro- Figure 3), able to inhibit at micromolar concentrations
duced morphological changes with increased levels of TcSIR2rp1 and TcSIR2rp3, respectively. In T. cruzi-infec-
acetyl-tubulin, different size and shape of the promas- ted cells (high content assay), the TcSIR2rp1 inhibitors
tigotes, alteration of mitochondrial function, accumula- displayed high potency being effective at low micromolar
tion of lipid bodies in the cytoplasm and blebs in the doses, whereas the TcSIR2rp3 inhibitors required higher
membrane, and induction of a sort of apoptosis [56]. concentrations to exert their effects [66].
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