Identification of GPI anchor attachment signals by a Kohonen self-organizing map

Motivation: Anchoring of proteins to the extracytosolic leaflet of membranes via C-terminal attachment of glycosylphosphatidylinositol (GPI) is ubiquitous and essential in eukaryotes. The signal for GPI-anchoring is confined to the C-terminus of the target protein. In order to identify anchoring signals in silico, we have trained neural networks on known GPI-anchored proteins, systematically optimizing input parameters. Results: A Kohonen self-organizing map, GPI-SOM, was developed that predicts GPI-anchored proteins with high accuracy. In combination with SignalP, GPI-SOM was used in genome-wide surveys for GPI-anchored proteins in diverse eukaryotes. Apart from specialized parasites, a general trend towards higher percentages of GPI-anchored proteins in larger proteomes was observed. Availability: GPI-SOM is accessible on-line at http://gpi.unibe.ch. The source code (written in C) is available on the same website. Contact: [email protected] Supplementary information: Positive training set, performance test sets and lists of predicted GPI-anchored proteins from different eukaryotes in fasta forma

Beyond immune escape:a variant surface glycoprotein causes suramin resistance in Trypanosoma brucei

Suramin is one of the first drugs developed in a medicinal chemistry program (Bayer, 1916), and it is still the treatment of choice for the hemolymphatic stage of African sleeping sickness caused by Trypanosoma brucei rhodesiense. Cellular uptake of suramin occurs by endocytosis, and reverse genetic studies with T. b. brucei have linked downregulation of the endocytic pathway to suramin resistance. Here we show that forward selection for suramin resistance in T. brucei spp. cultures is fast, highly reproducible and linked to antigenic variation. Bloodstream-form trypanosomes are covered by a dense coat of variant surface glycoprotein (VSG), which protects them from their mammalian hosts' immune defenses. Each T. brucei genome contains over 2000 different VSG genes, but only one is expressed at a time. An expression switch to one particular VSG, termed VSGSur , correlated with suramin resistance. Reintroduction of the originally expressed VSG gene in resistant T. brucei restored suramin susceptibility. This is the first report of a link between antigenic variation and drug resistance in African trypanosomes

Editorial: Swiss TPH: 30 Years of R&D Towards New Drugs for Tropical Diseases

The year 2023 marks the 80th anniversary of the Swiss Tropical and Public Health Institute (Swiss TPH). Associated with the University of Basel, Swiss TPH combines research, education and services, working across a value chain from innovation and validation to application to improve people’s health and well-being. Around 700 staff and students work in Swiss TPH’s new headquarters in an emerging life-science cluster in Allschwil, Switzerland, focusing on infectious and non-communicable diseases, environment, society and health as well as health systems and interventions. In this special issue of Chimia, we highlight 30 years of research and development (R&D) at Swiss TPH, deeply grounded in partnership, towards new drugs for tropical diseases

Global impact of parasitic infections and the importance of parasite control

Parasites have a severe impact on animal and human health. Parasites like worms, ticks, mites, fleas, biting flies, mosquitoes, and pathogenic protozoa affect humans and their pets as well as their livestock globally, both in terms of severity and numbers. Parasitic infections are a global phenomenon, and they can be associated with severe or mild symptoms but represent a continuous risk of severe diseases for animals and humans. Therefore, effective treatment options and the prevention of infection are key for the wellbeing of pets, livestock, and humans, including the reduction of zoonotic risk of infection. The effective control of parasites in animals can greatly improve their quality of life and is also beneficial for humans; this is threatened by drug-resistant parasite populations. Today’s key areas for improvement of parasite control are as follows: a) convenience of prevention and treatment, b) effectiveness against drug-resistant parasites, c) availability and reduced costs of treatment, and d) control measurements that are environmentally friendly

In vitro activity of anti-malarial ozonides against an artemisinin-resistant isolate

Recently published data suggest that artemisinin derivatives and synthetic peroxides, such as the ozonides OZ277 and OZ439, have a similar mode of action. Here the cross-resistance of OZ277 and OZ439 and four additional next-generation ozonides was probed against the artemisinin-resistant clinical isolate Plasmodium falciparum Cam3.I, which carries the K13-propeller mutation R539T (Cam3.I(R539T)).; The previously described in vitro ring-stage survival assay (RSA0-3h) was employed and a simplified variation of the original protocol was developed.; At the pharmacologically relevant concentration of 700 nM, all six ozonides were highly effective against the dihydroartemisinin-resistant P. falciparum Cam3.I(R539T) parasites, showing a per cent survival ranging from <0.01 to 1.83%. A simplified version of the original RSA0-3h method was developed and gave similar results, thus providing a practical drug discovery tool for further optimization of next-generation anti-malarial peroxides.; The absence of in vitro cross-resistance against the artemisinin-resistant clinical isolate Cam3.I(R539T) suggests that ozonides could be effective against artemisinin-resistant P. falciparum. How this will translate to the human situation in clinical settings remains to be investigated

Phylogenetic Analysis of Pyruvate-Ferredoxin Oxidoreductase, a Redox Enzyme Involved in the Pharmacological Activation of Nitro-Based Prodrugs in Bacteria and Protozoa

The present frontrunners in the chemotherapy of infections caused by protozoa are nitro-based prodrugs that are selectively activated by PFOR-mediated redox reactions. This study seeks to analyze the distribution of PFOR in selected protozoa and bacteria by applying comparative genomics to test the hypothesis that PFOR in eukaryotes was acquired through horizontal gene transfer (HGT) from bacteria. Furthermore, to identify other putatively acquired genes, proteome-wide and gene enrichment analyses were used. A plausible explanation for the patchy occurrence of PFOR in protozoa is based on the hypothesis that bacteria are potential sources of genes that enhance the adaptation of protozoa in hostile environments. Comparative genomics of Entamoeba histolytica and the putative gene donor, Desulfovibrio vulgaris, identified eleven candidate genes for HGT involved in intermediary metabolism. If these results can be reproduced in other PFOR-possessing protozoa, it would provide more validated evidence to support the horizontal transfer of pfor from bacteria

HMM-based profiling identifies the binding to divalent cations and nucleotides as common denominators of suramin targets

Introduction: Suramin is one of the pharmacopeia’s most promiscuous drugs. Originally developed for African trypanosomiasis, suramin was also used for onchocerciasis and it has been proposed as an anticancer agent, antiviral drug, therapy for arthritis, autism, and antidote for snake bites. Target proteins of suramin have been described from different species. Here we identify the common motifs among these various targets, aiming to explain the promiscuous nature of suramin.Methods: We have searched for suramin target proteins in the literature and in chemical databases. Applying rigorous inclusion criteria, a list of 44 diverse proteins was assembled with experimental evidence for direct interaction with, and inhibition by, suramin. Hidden Markov model-based target profiling was performed by running the full set of Pfam protein family domains against these proteins.Results: Common denominators were identified by mapping the identified Pfam domains to molecular function gene ontology terms. This in silico pipeline identified nucleotide binding, nucleic acid binding, and binding to divalent cations as the most common denominators of the suramin targets.Discussion: Our results suggest that the extraordinary polypharmacology of suramin may be caused by its ability to inhibit the interaction of proteins with nucleotides or nucleic acids and with divalent cations (Mg2+, Ca2+, Zn2+). Suramin is well known to inhibit nucleotide receptors and nucleic acid-binding enzymes. The association with divalent cations is new and might be key towards the design of better, more selective inhibitors

Comparative genomics of metabolic networks of free-living and parasitic eukaryotes

BACKGROUND: Obligate endoparasites often lack particular metabolic pathways as compared to free-living organisms. This phenomenon comprises anabolic as well as catabolic reactions. Presumably, the corresponding enzymes were lost in adaptation to parasitism. Here we compare the predicted core metabolic graphs of obligate endoparasites and non-parasites (free living organisms and facultative parasites) in order to analyze how the parasites' metabolic networks shrunk in the course of evolution. RESULTS: Core metabolic graphs comprising biochemical reactions present in the presumed ancestor of parasites and non-parasites were reconstructed from the Kyoto Encyclopedia of Genes and Genomes. While the parasites' networks had fewer nodes (metabolites) and edges (reactions), other parameters such as average connectivity, network diameter and number of isolated edges were similar in parasites and non-parasites. The parasites' networks contained a higher percentage of ATP-consuming reactions and a lower percentage of NAD-requiring reactions. Control networks, shrunk to the size of the parasites' by random deletion of edges, were scale-free but exhibited smaller diameters and more isolated edges. CONCLUSIONS: The parasites' networks were smaller than those of the non-parasites regarding number of nodes or edges, but not regarding network diameters. Network integrity but not scale-freeness has acted as a selective principle during the evolutionary reduction of parasite metabolism. ATP-requiring reactions in particular have been retained in the parasites' core metabolism whil

Surface antigens and potential virulence factors from parasites detected by comparative genomics of perfect amino acid repeats

<p>Abstract</p> <p>Background</p> <p>Many parasitic organisms, eukaryotes as well as bacteria, possess surface antigens with amino acid repeats. Making up the interface between host and pathogen such repetitive proteins may be virulence factors involved in immune evasion or cytoadherence. They find immunological applications in serodiagnostics and vaccine development. Here we use proteins which contain perfect repeats as a basis for comparative genomics between parasitic and free-living organisms.</p> <p>Results</p> <p>We have developed Reptile <url>http://reptile.unibe.ch</url>, a program for proteome-wide probabilistic description of perfect repeats in proteins. Parasite proteomes exhibited a large variance regarding the proportion of repeat-containing proteins. Interestingly, there was a good correlation between the percentage of highly repetitive proteins and mean protein length in parasite proteomes, but not at all in the proteomes of free-living eukaryotes. Reptile combined with programs for the prediction of transmembrane domains and GPI-anchoring resulted in an effective tool for in silico identification of potential surface antigens and virulence factors from parasites.</p> <p>Conclusion</p> <p>Systemic surveys for perfect amino acid repeats allowed basic comparisons between free-living and parasitic organisms that were directly applicable to predict proteins of serological and parasitological importance. An on-line tool is available at <url>http://genomics.unibe.ch/dora</url>.</p

Mining sudanese medicinal plants for antiprotozoal agents

Neglected tropical diseases are major health hazards in developing countries. Annually, up to 30 million people are affected by either Chagas disease, African trypansomiasis or leishmaniasis, and more than 200 million by malaria. Most of the currently available drugs have drawbacks in terms of toxicity, limited oral availability, development of resistance, or non-affordability. Tropical plants of the arid zones are a treasure chest for the discovery of bioactive secondary metabolites. This study aims to compile Sudanese medicinal plants, validate their antiprotozoal activities, and identify active molecules. We have performed a survey of medicinal plants of Sudan and selected 62 that are being used in Sudanese traditional medicine. From these, we collected materials such as leaves, stem, bark, or fruit. The plant materials were extracted in 70% ethanol and further fractionated by liquid-liquid partitioning using solvents of increasing polarity. This resulted in a library of 235 fractions. The library was tested; in vitro; against; Plasmodium falciparum; (erythrocytic stages),; Trypanosoma brucei rhodesiense; (bloodstream forms),; Trypanosoma cruzi; (intracellular amastigotes), and; Leishmania donovani; (axenic amastigotes). Active fractions were also tested for cytotoxicity. Of the 235 fractions, 125 showed growth inhibitory activity >80% at 10 μg/ml, and >50% at 2 μg/ml against at least one of the protozoan parasites.; Plasmodium falciparum; was the most sensitive of the parasites, followed by; T. b. rhodesiense; and; L. donovani; . Only few hits were identified for; T. cruzi; , and these were not selective. Contrary to expectation based on phylogeny, but in agreement with previous results, a large number of extracts displayed mutual activity against; T. brucei; and; P. falciparum; . HPLC-based activity profiling for selected active extracts was performed to identify the bioactive principles. Active compounds identified by dereplication were guieranone A from; Guiera senegalensis; J.F.Gmel.; pseudosemiglabrin from; Tephrosia apollinea; (Delile) DC; ellagic acid and quercetin from; Terminalia leiocarpa; (DC.) Baill.; and catechin, ethyl gallate, and epicatechin gallate from; Vachellia nilotica; (L.) P.J.H.Hurter & Mabb. Also the extracts of; Croton gratissimus; var.; gratissimus; and; Cuscuta hyalina; Roth ex Schult. exhibited promising antitrypanosomatid activity. This assessment provides a comprehensive overview of Sudanese medicinal plants and supports the notion that they are a potential source of bioactive molecules against protozoan parasites