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

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

Genotypic status of the TbAT1/P2 adenosine transporter of Trypanosoma brucei gambiense isolates from northwestern Uganda following melarsoprol withdrawal

Human African trypanosomiasis (HAT) manifests as a chronic infection caused by <i>Trypanosoma brucei gambiense</i>, or as a more acute form due to <i>T. b. rhodesiense</i>. Both manifestations occur in Uganda and melarsoprol use against the former was jeopardised in the 1990s as reports of reduced efficacy increased to the point where it was dismissed as first-line treatment at some treatment centers. Previous work to elucidate possible mechanisms leading to melarsoprol resistance pointed to a P2 type adenosine transporter known to mediate melarsoprol uptake and previously shown to be mutated in significant numbers of patients not responding to the drug. Our present findings indicate that there is a low prevalence of mutants in foci where melarsoprol relapses are infrequent. In addition we observe that at the Omugo focus where the drug was withdrawn as first line over 6 years ago, the mutant alleles have disappeared, suggesting that drug pressure is responsible for fuelling their spread. Thus constant monitoring for mutants could play a key role in cost-effective HAT management by identifying which foci can still use the less logistically demanding melarsoprol as opposed to the alternative drug eflornithine. What is required now is a simple method for identifying such mutants at the point of care, enabling practitioners to make informed prescriptions at first diagnosis

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

Neue Parameter für die Wirkstofftestung gegen Trypanosoma cruzi

Chagas disease is a zoonosis caused by Trypanosoma cruzi and transmitted by triatomine bugs. Autochthonous to Latin America, Chagas disease has spread globally through travel and migration. New drugs are needed urgently, in particular drugs that cure the chronic stage. This is where high-content imaging makes a key contribution: assays with fluorescent parasites in cell culture allow to determine pharmacodynamic parameters and to better assess the antichagasic potential of new molecules

Fexinidazole for human African trypanosomiasis, the fruit of a successful public-private partnership

After 100 years of chemotherapy with impractical and toxic drugs, an oral cure for human African trypanosomiasis (HAT) is available: Fexinidazole. In this case, we review the history of drug discovery for HAT with special emphasis on the discovery, pre-clinical development, and operational challenges of the clinical trials of fexinidazole. The screening of the Drugs for Neglected Diseases initiative (DNDi) HAT-library by the Swiss TPH had singled out fexinidazole, originally developed by Hoechst (now Sanofi), as the most promising of a series of over 800 nitroimidazoles and related molecules. In cell culture, fexinidazole has an IC50 of around 1 microM against Trypanosoma brucei and is more than 100-fold less toxic to mammalian cells. In the mouse model, fexinidazole cures both the first, haemolymphatic, and the second, meningoencephalitic stage of the infection, the latter at 100 mg/kg twice daily for 5 days. In patients, the clinical trials managed by DNDi and supported by Swiss TPH mainly conducted in the Democratic Republic of the Congo demonstrated that oral fexinidazole is safe and effective for use against first- and early second-stage sleeping sickness. Based on the positive opinion issued by the European Medicines Agency in 2018, the WHO has released new interim guidelines for the treatment of HAT including fexinidazole as the new therapy for first-stage and non-severe second-stage sleeping sickness caused by Trypanosoma brucei gambiense (gHAT). This greatly facilitates the diagnosis and treatment algorithm for gHAT, increasing the attainable coverage and paving the way towards the envisaged goal of zero transmission by 2030

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

Spielboden

Die Alternativkultur, welche sich parallel zu den Festspielen und einem Theater für Vorarlberg – den konventionellen Arten der Kultur in Vorarlberg – Anfang der 1970er Jahre zu entwickeln begonnen hat, ist ein oftmals unbeachtetes Gebiet der Theatergeschichte. Der Spielboden – das eigentliche Thema meiner Arbeit hat sich in einer sehr spannenden Zeit zu Beginn der 1980er Jahre entwickelt, und sehr viel zum heutigen Kulturverständnis der Vorarlberger und der heutigen Kulturpolitik in Vorarlberg beigetragen. Die vorliegende Arbeit erforscht wie diese Entwicklung der Alternativkultur in Vorarlberg von Statten ging, und wie der Spielboden vom kleinen Verein auf freiwilliger Basis zu einer Kulturveranstaltungs-GmbH gewachsen ist. Besonderes Augenmerk wird hierbei auf die Wahrnehmung der Öffentlichkeit, den Schwierigkeiten der Spielbodenverantwortlichen mit den konservativen Stadtverantwortlichen und der Entwicklung der Kulturpolitik in Vorarlberg und den Beitrag des Spielbodens gelegt. Um einen besseren Einblick in die Mentalität der Vorarlberger, und somit auch die Probleme die durch diese verursacht werden, geben zu können, beschäftigt sich das erste Kapitel mit dem „Volkscharakter des Vorarlbergers“. Weiters wird im darauf folgenden Kapitel die Theatergeschichte Vorarlbergs näher betrachtet. Das dritte Kapitel behandelt die Gesellschaft im westlichsten Bundesland nach dem zweiten Weltkrieg sowie die Entwicklung einer Alternativ- und Jugendkultur. In dieser Zeit wirken auch bereits sehr viele Personen, die dann später für den Spielboden von Bedeutung sind. Erst das vierte Kapitel der Arbeit behandelt den Spielboden, seine Entstehung, seine Grundsätze und die Geschichte desselben. Hier werden besonders die Impulse zur Kulturpolitik in Vorarlberg, den Standpunkt zur Kultur und die Querelen mit der konservativen Stadtführung behandelt. Im letzten Kapitel werden lediglich die Zahlen und Fakten, die größtenteils schon in den vorigen Kapiteln erwähnt wurden zusammengefasst und zur Vollständigkeit gebracht

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

Anti-malarial ozonides OZ439 and OZ609 tested at clinically relevant compound exposure parameters in a novel ring-stage survival assay

BACKGROUND: Drug efficacy against kelch 13 mutant malaria parasites can be determined in vitro with the ring-stage survival assay (RSA). The conventional assay protocol reflects the exposure profile of dihydroartemisinin. METHODS: Taking into account that other anti-malarial peroxides, such as the synthetic ozonides OZ439 (artefenomel) and OZ609, have different pharmacokinetics, the RSA was adjusted to the concentration-time profile of these ozonides in humans and a novel, semi-automated readout was introduced. RESULTS: When tested at clinically relevant parameters, it was shown that OZ439 and OZ609 are active against the Plasmodium falciparum clinical isolate Cam3.I(R539T). CONCLUSION: If the in vitro RSA does indeed predict the potency of compounds against parasites with increased tolerance to artemisinin and its derivatives, then the herein presented data suggest that following drug-pulses of at least 48 h, OZ439 and OZ609 will be highly potent against kelch 13 mutant isolates, such as P. falciparum Cam3.I(R539T)