New enzymatic pathways for the reduction of reactive oxygen species in Entamoeba histolytica

Identification of Small Molecule Inhibitors Targeting Phosphoserine Phosphatase: A Novel Target for the Development of Antiamoebic Drugs

Amoebiasis, a widespread disease caused by the protozoan parasite Entamoeba histolytica, poses challenges due to the adverse effects of existing antiamoebic drugs and rising drug resistance. Novel targeted drugs are in need of the hour to combat the prevalence of this disease. Given the significance of cysteine for Entamoeba survival, the rate-determining step in the serine (the sole substrate of cysteine synthesis) biosynthetic pathway, i.e., the conversion of 3-phosphoserine to l-serine catalyzed by phosphoserine phosphatase (PSP), emerges as a promising drug target. Our previous study unveils the essential role of EhPSP in amoebas' survival, particularly under oxidative stress, by increasing cysteine production. The study also revealed that EhPSP differs significantly from its human counterpart, both structurally and biochemically, highlighting its potential as a viable target for developing new antiamoebic drugs. In the present study, employing in silico screening of vast natural and synthetic small chemical compound libraries, we identified 21 potential EhPSP inhibitor molecules. Out of the 21 compounds examined, only five could inhibit the catalytic activity of EhPSP. The inhibition capability of these five compounds was subsequently validated by in silico binding free energy calculations, SPR-based real-time binding studies, and molecular simulations to assess the stability of the EhPSP-inhibitor complexes. By identifying the five potential inhibitors that can target cysteine synthesis via EhPSP, our findings establish EhPSP as a drug candidate that can serve as a foundation for antiamoebic drug research.

In Vitro Evaluation of the Antiamoebic Activity of Kaempferol against Trophozoites of Entamoeba histolytica and in the Interactions of Amoebae with Hamster Neutrophils

Entamoeba histolytica (E. histolytica) is a parasite in humans that provokes amoebiasis. The most employed drug is metronidazole (MTZ); however, some studies have reported that this drug induces genotoxic effects. Therefore, it is necessary to explore new compounds without toxicity that can eliminate E. histolytica. Flavonoids are polyphenolic compounds that have demonstrated inhibition of growth and dysregulation of amoebic proteins. Despite the knowledge acquired to date, action mechanisms are not completely understood. The present work evaluates the effect of kaempferol against E. histolytica trophozoites and in the interactions with neutrophils from hamster, which is a susceptibility model. Our study demonstrated a significant reduction in the amoebic viability of trophozoites incubated with kaempferol at 150 μM for 90 min. The gene expression analysis showed a significant downregulation of Pr (peroxiredoxin), Rr (rubrerythrin), and TrxR (thioredoxin reductase). In interactions with amoebae and neutrophils for short times, we observed a reduction in ROS (reactive oxygen species), NO (nitric oxide), and MPO (myeloperoxidase) neutrophil activities. In conclusion, we confirmed that kaempferol is an effective drug against E. histolytica through the decrease in E. histolytica antioxidant enzyme expression and a regulator of several neutrophil mechanisms, such as MPO activity and the regulation of ROS and NO.

Apoptosis-inducing factor-like protein-mediated stress and metronidazole-responsive programmed cell death pathway in Entamoeba histolytica

Apoptosis-inducing factor (AIF) is the major component of the caspase-independent cell death pathway that is considered to be evolutionarily ancient. Apoptosis is generally evolved with multicellularity as a prerequisite for the elimination of aged, stressed, or infected cells promoting the survival of the organism. Our study reports the presence of a putative AIF-like protein in Entamoeba histolytica, a caspase-deficient primitive protozoan, strengthening the concept of occurrence of apoptosis in unicellular organisms as well. The putative cytoplasmic EhAIF migrates to the nucleus on receiving stresses that precede its binding with DNA, following chromatin degradation and chromatin condensation as evident from both in vitro and in vivo experiments. Down-regulating the EhAIF expression attenuates the apoptotic features of insulted cells and increases the survival potency in terms of cell viability and vitality of the trophozoites, whereas over-expression of the EhAIF effectively enhances the phenomena. Interestingly, metronidazole, the most widely used drug for amoebiasis treatment, is also potent to elicit similar AIF-mediated cell death responses like other stresses indicating the AIF-mediated cell death could be the probable mechanism of trophozoite-death by metronidazole treatment. The occurrence of apoptosis in a unicellular organism is an interesting phenomenon that might signify the altruistic death that overall improves the population health.

Oxygen levels are key to understanding "Anaerobic" protozoan pathogens with micro-aerophilic lifestyles

Publications abound on the physiology, biochemistry and molecular biology of "anaerobic" protozoal parasites as usually grown under "anaerobic" culture conditions. The media routinely used are poised at low redox potentials using techniques that remove O₂ to "undetectable" levels in sealed containers. However there is growing understanding that these culture conditions do not faithfully resemble the O₂ environments these organisms inhabit. Here we review for protists lacking oxidative energy metabolism, the oxygen cascade from atmospheric to intracellular concentrations and relevant methods of measurements of O₂, some well-studied parasitic or symbiotic protozoan lifestyles, their homeodynamic metabolic and redox balances, organism-drug-oxygen interactions, and the present and future prospects for improved drugs and treatment regimes.

Diversity of structures and functions of oxo-bridged non-heme diiron proteins

Oxo-bridged diiron proteins are a distinct class of non-heme iron proteins. Their active sites are composed of two irons that are coordinated by amino acid side chains, and a bridging oxygen that interacts with each iron. These proteins are members of the ferritin superfamily and share the structural feature of a four α-helix bundle that provides the residues that coordinate the irons. The different proteins also display a wide range of structures and functions. A prototype of this family is hemerythrin, which functions as an oxygen transporter. Several other hemerythrin-like proteins have been described with a diversity of functions including oxygen and iron sensing, and catalytic activities. Rubrerythrins react with hydrogen peroxide and rubrerythrin-like proteins possess a rubredoxin domain, in addition to the oxo-bridged diiron center. Other redox enzymes with oxo-bridged irons include flavodiiron proteins that act as O2 or NO reductases, ribonucleotide reductase and methane monooxygenase. Ferritins have an oxo-bridged diiron in the ferroxidase center of the protein, which plays a role in the iron storage function of these proteins. There are also bacterial ferritins that exhibit catalytic activities. The structures and functions of this broad class of oxo-bridged diiron proteins are described and compared in this review.

Rubredoxin from the green sulfur bacterium Chlorobaculum tepidum donates a redox equivalent to the flavodiiron protein in an NAD(P)H dependent manner via ferredoxin-NAD(P)+ oxidoreductase

The green sulfur bacterium, Chlorobaculum tepidum, is an anaerobic photoautotroph that performs anoxygenic photosynthesis. Although genes encoding rubredoxin (Rd) and a putative flavodiiron protein (FDP) were reported in the genome, a gene encoding putative NADH-Rd oxidoreductase is not identified. In this work, we expressed and purified the recombinant Rd and FDP and confirmed dioxygen reductase activity in the presence of ferredoxin-NAD(P)⁺ oxidoreductase (FNR). FNR from C. tepidum and Bacillus subtilis catalyzed the reduction of Rd at rates comparable to those reported for NADH-Rd oxidoreductases. Also, we observed substrate inhibition at high concentrations of NADPH similar to that observed with ferredoxins. In the presence of NADPH, B. subtilis FNR and Rd, FDP promoted dioxygen reduction at rates comparable to those reported for other bacterial FDPs. Taken together, our results suggest that Rd and FDP participate in the reduction of dioxygen in C. tepidum and that FNR can promote the reduction of Rd in this bacterium.

Lateral Acquisitions Repeatedly Remodel the Oxygen Detoxification Pathway in Diplomonads and Relatives

Oxygen and reactive oxygen species (ROS) are important stress factors for cells because they can oxidize many large molecules. Fornicata, a group of flagellated protists that includes diplomonads, have anaerobic metabolism but are still able to tolerate fluctuating levels of oxygen. We identified 25 protein families putatively involved in detoxification of oxygen and ROS in this group using a bioinformatics approach and propose how these interact in an oxygen detoxification pathway. These protein families were divided into a central oxygen detoxification pathway and accessory pathways for the synthesis of nonprotein thiols. We then used a phylogenetic approach to investigate the evolutionary origin of the components of this putative pathway in Diplomonadida and other Fornicata species. Our analyses suggested that the diplomonad ancestor was adapted to low-oxygen levels, was able to reduce O₂ to H₂O in a manner similar to extant diplomonads, and was able to synthesize glutathione and l-cysteine. Several genes involved in the pathway have complex evolutionary histories and have apparently been repeatedly acquired through lateral gene transfer and subsequently lost. At least seven genes were acquired independently in different Fornicata lineages, leading to evolutionary convergences. It is likely that acquiring these oxygen detoxification proteins helped anaerobic organisms (like the parasitic Giardia intestinalis) adapt to low-oxygen environments (such as the digestive tract of aerobic hosts).

How superoxide reductases and flavodiiron proteins combat oxidative stress in anaerobes

Microbial anaerobes are exposed in the natural environment and in their hosts, even if transiently, to fluctuating concentrations of oxygen and its derived reactive species, which pose a considerable threat to their anoxygenic lifestyle. To counteract these stressful conditions, they contain a multifaceted array of detoxifying systems that, in conjugation with cellular repairing mechanisms and in close crosstalk with metal homeostasis, allow them to survive in the presence of O₂ and reactive oxygen species. Some of these systems are shared with aerobes, but two families of enzymes emerged more recently that, although not restricted to anaerobes, are predominant in anaerobic microbes. These are the iron-containing superoxide reductases, and the flavodiiron proteins, endowed with O₂ and/or NO reductase activities, which are the subject of this Review. A detailed account of their physicochemical, physiological and molecular mechanisms will be presented, highlighting their unique properties in allowing survival of anaerobes in oxidative stress conditions, and comparing their properties with the most well-known detoxifying systems.

Control and regulation of the pyrophosphate-dependent glucose metabolism in Entamoeba histolytica

Entamoeba histolytica has neither Krebs cycle nor oxidative phosphorylation activities; therefore, glycolysis is the main pathway for ATP supply and provision of carbon skeleton precursors for the synthesis of macromolecules. Glucose is metabolized through fermentative glycolysis, producing ethanol as its main end-product as well as some acetate. Amoebal glycolysis markedly differs from the typical Embden-Meyerhof-Parnas pathway present in human cells: (i) by the use of inorganic pyrophosphate, instead of ATP, as the high-energy phospho group donor; (ii) with one exception, the pathway enzymes can catalyze reversible reactions under physiological conditions; (iii) there is no allosteric regulation and sigmoidal kinetic behavior of key enzymes; and (iv) the presence of some glycolytic and fermentation enzymes similar to those of anaerobic bacteria. These peculiarities bring about alternative mechanisms of control and regulation of the PPi-dependent fermentative glycolysis in the parasite in comparison to the ATP-dependent and allosterically regulated glycolysis in many other eukaryotic cells. In this review, the current knowledge of the carbohydrate metabolism enzymes in E. histolytica is analyzed. Thermodynamics and stoichiometric analyses indicate 2 to 3.5 ATP yield per glucose metabolized, instead of the often presumed 5 ATP/glucose ratio. PPi derived from anabolism seems insufficient for PPi-glycolysis; hence, alternative ways of PPi supply are also discussed. Furthermore, the underlying mechanisms of control and regulation of the E. histolytica carbohydrate metabolism, analyzed by applying integral and systemic approaches such as Metabolic Control Analysis and kinetic modeling, contribute to unveiling alternative and promising drug targets.

The Architecture of Thiol Antioxidant Systems among Invertebrate Parasites

The use of oxygen as the final electron acceptor in aerobic organisms results in an improvement in the energy metabolism. However, as a byproduct of the aerobic metabolism, reactive oxygen species are produced, leaving to the potential risk of an oxidative stress. To contend with such harmful compounds, living organisms have evolved antioxidant strategies. In this sense, the thiol-dependent antioxidant defense systems play a central role. In all cases, cysteine constitutes the major building block on which such systems are constructed, being present in redox substrates such as glutathione, thioredoxin, and trypanothione, as well as at the catalytic site of a variety of reductases and peroxidases. In some cases, the related selenocysteine was incorporated at selected proteins. In invertebrate parasites, antioxidant systems have evolved in a diversity of both substrates and enzymes, representing a potential area in the design of anti-parasite strategies. The present review focus on the organization of the thiol-based antioxidant systems in invertebrate parasites. Differences between these taxa and its final mammal host is stressed. An understanding of the antioxidant defense mechanisms in this kind of parasites, as well as their interactions with the specific host is crucial in the design of drugs targeting these organisms.

N-acetyl ornithine deacetylase is a moonlighting protein and is involved in the adaptation of Entamoeba histolytica to nitrosative stress

Adaptation of the Entamoeba histolytica parasite to toxic levels of nitric oxide (NO) that are produced by phagocytes may be essential for the establishment of chronic amebiasis and the parasite's survival in its host. In order to obtain insight into the mechanism of E. histolytica's adaptation to NO, E. histolytica trophozoites were progressively adapted to increasing concentrations of the NO donor drug, S-nitrosoglutathione (GSNO) up to a concentration of 110 μM. The transcriptome of NO adapted trophozoites (NAT) was investigated by RNA sequencing (RNA-seq). N-acetyl ornithine deacetylase (NAOD) was among the 208 genes that were upregulated in NAT. NAOD catalyzes the deacetylation of N-acetyl-L-ornithine to yield ornithine and acetate. Here, we report that NAOD contributes to the better adaptation of the parasite to nitrosative stress (NS) and that this function does not depend on NAOD catalytic activity. We also demonstrated that glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is detrimental to E. histolytica exposed to NS and that this detrimental effect is neutralized by NAOD or by a catalytically inactive NAOD (mNAOD). These results establish NAOD as a moonlighting protein, and highlight the unexpected role of this metabolic enzyme in the adaptation of the parasite to NS.

The dual function of flavodiiron proteins: oxygen and/or nitric oxide reductases

Flavodiiron proteins have emerged in the last two decades as a newly discovered family of oxygen and/or nitric oxide reductases widespread in the three life domains, and present in both aerobic and anaerobic organisms. Herein we present the main features of these fascinating enzymes, with a particular emphasis on the metal sites, as more appropriate for this special issue in memory of the exceptional bioinorganic scientist R. J. P. Williams who pioneered the notion of (metal) element availability-driven evolution. We also compare the flavodiiron proteins with the other oxygen and nitric oxide reductases known until now, highlighting how throughout evolution Nature arrived at different solutions for similar functions, in some cases adding extra features, such as energy conservation. These enzymes are an example of the (bioinorganic) unpredictable diversity of the living world.

Entamoeba thiol-based redox metabolism: A potential target for drug development

Amebiasis is an intestinal infection widespread throughout the world caused by the human pathogen Entamoeba histolytica. Metronidazole has been a drug of choice against amebiasis for decades despite its low efficacy against asymptomatic cyst carriers and emergence of resistance in other protozoa with similar anaerobic metabolism. Therefore, identification and characterization of specific targets is urgently needed to design new therapeutics for improved treatment against amebiasis. Toward this goal, thiol-dependent redox metabolism is of particular interest. The thiol-dependent redox metabolism in E. histolytica consists of proteins including peroxiredoxin, rubrerythrin, Fe-superoxide dismutase, flavodiiron proteins, NADPH: flavin oxidoreductase, and amino acids including l-cysteine, S-methyl-l-cysteine, and thioprolines (thiazolidine-4-carboxylic acids). E. histolytica completely lacks glutathione and its metabolism, and l-cysteine is the major intracellular low molecular mass thiol. Moreover, this parasite possesses a functional thioredoxin system consisting of thioredoxin and thioredoxin reductase, which is a ubiquitous oxidoreductase system with antioxidant and redox regulatory roles. In this review, we summarize and highlight the thiol-based redox metabolism and its control mechanisms in E. histolytica, in particular, the features of the system unique to E. histolytica, and its potential use for drug development against amebiasis.

Proteomic Identification of Oxidized Proteins in Entamoeba histolytica by Resin-Assisted Capture: Insights into the Role of Arginase in Resistance to Oxidative Stress

Entamoeba histolytica is an obligate protozoan parasite of humans, and amebiasis, an infectious disease which targets the intestine and/or liver, is the second most common cause of human death due to a protozoan after malaria. Although amebiasis is usually asymptomatic, E. histolytica has potent pathogenic potential. During host infection, the parasite is exposed to reactive oxygen species that are produced and released by cells of the innate immune system at the site of infection. The ability of the parasite to survive oxidative stress (OS) is essential for a successful invasion of the host. Although the effects of OS on the regulation of gene expression in E. histolytica and the characterization of some proteins whose function in the parasite's defense against OS have been previously studied, our knowledge of oxidized proteins in E. histolytica is lacking. In order to fill this knowledge gap, we performed a large-scale identification and quantification of the oxidized proteins in oxidatively stressed E. histolytica trophozoites using resin-assisted capture coupled to mass spectrometry. We detected 154 oxidized proteins (OXs) and the functions of some of these proteins were associated with antioxidant activity, maintaining the parasite's cytoskeleton, translation, catalysis, and transport. We also found that oxidation of the Gal/GalNAc impairs its function and contributes to the inhibition of E. histolytica adherence to host cells. We also provide evidence that arginase, an enzyme which converts L-arginine into L-ornithine and urea, is involved in the protection of the parasite against OS. Collectively, these results emphasize the importance of OS as a critical regulator of E. histolytica's functions and indicate a new role for arginase in E. histolytica's resistance to OS.

Reactive oxygen species are the most studied of environmental stresses generated by the host immune defense against pathogens. Although most of the studies that have investigated the effect of oxidative stress on an organism have focused on changes which occur at the protein level, only a few studies have investigated the oxidation status of these proteins. Infection with Entamoeba histolytica is known as amebiasis. This condition occurs worldwide, but is most associated with crowded living conditions and poor sanitation. The parasite is exposed inside the host to oxidative stress generated by cells of the host immune system. The nature of oxidized proteins in oxidatively stressed E. histolytica has never been studied. In this report, the authors present their quantitative results of a proteome-wide analysis of oxidized proteins in the oxidatively stressed parasite. They identified crucial redox-regulated proteins that are linked to the virulence of the parasite, such as the Gal/GalNAc lectin. They also discovered that arginase, a protein involved in ornithine synthesis, is also involved in the parasite's resistance to oxidative stress.

The oxygen reduction pathway and heat shock stress response are both required for Entamoeba histolytica pathogenicity

Several species belonging to the genus Entamoeba can colonize the mouth or the human gut; however, only Entamoeba histolytica is pathogenic to the host, causing the disease amoebiasis. This illness is responsible for one hundred thousand human deaths per year worldwide, affecting mainly underdeveloped countries. Throughout its entire life cycle and invasion of human tissues, the parasite is constantly subjected to stress conditions. Under in vitro culture, this microaerophilic parasite can tolerate up to 5 % oxygen concentrations; however, during tissue invasion the parasite has to cope with the higher oxygen content found in well-perfused tissues (4-14 %) and with reactive oxygen and nitrogen species derived from both host and parasite. In this work, the role of the amoebic oxygen reduction pathway (ORP) and heat shock response (HSP) are analyzed in relation to E. histolytica pathogenicity. The data suggest that in contrast with non-pathogenic E. dispar, the higher level of ORP and HSPs displayed by E. histolytica enables its survival in tissues by diminishing and detoxifying intracellular oxidants and repairing damaged proteins to allow metabolic fluxes, replication and immune evasion.