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Individual research projects

List of Individual Research Projects

LevelPartnerTitle project
ESR-1Utrecht University (NL)Developing host-targeted, broad-spectrum inhibitors of enterovirus replication - The genus Enterovirus of the picornavirus family contains many important human and animal pathogens, such as poliovirus, coxsackievirus, enterovirus 71, and rhinovirus. All enteroviruses exploit the same host factors and pathways for replication. Inhibiting host factors is an emerging approach to develop broad-range antiviral therapy. Recently, we identified several (druggable) host factors essential for coxsackievirus B3 using a genome-wide siRNA screen. The ESR will test available inhibitors of these host factors for their antiviral activity against a broad panel of enteroviruses. The stage of the viral life cycle in which the host factor is involved will be determined and the mode of action of the inhibitor will be investigated in detail using an integrated approach involving molecular biological (e.g. subgenomic replicon analysis, resistance culturing, reverse genetics), biochemical (e.g. interaction analysis), and cell biological (e.g. advanced microscopy) techniques.
ESR-2Utrecht University (NL)Identifying FDA-approved drugs as novel inhibitors of virus replication - Previously, we performed comparative small molecule screens using libraries of FDA-approved drugs to identify inhibitors of coxsackievirus B3 (CVB3, an enterovirus), mouse hepatitis virus (MHV, a coronavirus), respiratory syncytial virus and influenza virus. Following this approach, several novel inhibitors of these viruses were identified. ESR2 determines the spectrum of activity of a selection of inhibitors and characterize their mode of action in detail using a combination of molecular virological, biochemical, cell biological and microscopy techniques. These studies include the analysis of the stage of the viral life cycle that is inhibited by the inhibitor and the identification of its molecular target (e.g. by selecting and genotyping drug-resistant mutants). Together with other ANTIVIRALS partner, strategies to improve the efficacy of the inhibitors will be explored and the antiviral efficacy of a selected group of inhibitors will be evaluated in infection models in mice.
ESR-3Leiden University Medical Center (NL) Development and mode of action of chikungunya virus inhibitors - Chikungunya virus (CHIKV) is a mosquito-borne positive-strand RNA virus that causes a severe arthritis that can persist for months. Registered vaccines or antiviral drugs to prevent or treat CHIKV infections are not available. Massive outbreaks have occurred since 2006 (millions of cases) and the geographic distribution of CHIKV has expanded dramatically. Last year, the virus also became endemic in South and Central America, causing ~1 million infections. This PhD project is aimed at identifying and developing CHIKV inhibitors, including compounds affecting host factors or functions that are important for CHIKV replication. Chikungunya virus is a BSL-3 agent and the ESR will be trained in performing experiments under the appropriate bio-containment conditions. Following identification of antiviral hits, the mode of action of selected inhibitors will be studied in detail and strategies to improve their efficacy will be explored. To this end, a combination of techniques from virus genetics, molecular biology, biochemistry, and cell biology will be integrated into a research program that will also benefit from established collaborations with other ANTIVIRALS partners.
ESR-4Leiden University Medical Center (NL) The quest for broad-spectrum coronavirus inhibitors - Coronaviruses infect a wide variety of human and animal hosts and are commonly associated with respiratory and enteric disease. The 2003 outbreak of Severe Acute Respiratory Syndrome (SARS) and the ongoing Middle East Respiratory Syndrome (MERS) epidemic (approaching 1,000 cases, mortality rate ~40%) demonstrate the potentially lethal consequences of zoonotic coronavirus infection in humans. There are no registered treatments to prevent or combat coronavirus infections. This PhD project is aimed at identifying and developing broad-spectrum coronavirus inhibitors, including compounds affecting host factors or functions that are important for coronavirus replication. The SARS- and MERS-coronaviruses are BSL-3 agents and the ESR will be trained in performing experiments under the appropriate bio-containment conditions. Following identification of antiviral hits, the mode of action of selected inhibitors will be studied in detail and strategies to improve their efficacy will be explored. To this end, a combination of techniques from virus genetics, molecular biology, biochemistry, and cell biology will be integrated into a research program that will also benefit from established collaborations with other ANTIVIRALS partners.
ESR-5University Hospital of Heidelberg (DE)Molecular mechanism of highly potent NS5A inhibitors of hepatitis C virus - Hepatitis C virus (HCV) is a major causative agent of acute and chronic liver diseases, including liver cirrhosis and hepatocellular carcinoma. With the advent of robust cell culture systems, highly potent antiviral drugs have been developed and recently approved for treatment of chronic hepatitis C. One class of these inhibitors targeting nonstructural protein 5A is extremely potent and acts via a bimodal activity: blocking the assembly of virus particles and the biogenesis of the membranous replication factory (Berger et al., Gastroenterology 2014; Paul and Bartenschlager Cell Host & Microbe 2014; Bartenschlager et al., Nature Rev. Microbiol. 2013). However, the molecular mechanisms underlying this bimodal activity are not understood and will be addressed in this project. The ESR will use a combination of molecular, biochemical and advanced imaging-based methods, including live-cell imaging and correlative microscopy to decipher how NS5A inhibitors interfere with the formation of infectious virions and at the same block the membrane rearrangements that are essential to build up the viral replication factory. In addition, in a collaborative effort molecular docking will be used, complemented by reverse and forward genetics conducted by the ESR to decipher how NS5A interacts with the membrane, with viral RNA and with itself and how this might be affected by highly potent NS5A inhibitors.
ESR-6University Hospital of Heidelberg (DE)Targeting the biogenesis of dengue virus replication factory for antiviral therapy
ESR-7Cardiff University (UK) Identification of novel anti-RSV inhibitors by a computer-based drug design approach - In this project, we aim to design a novel series of anti-RSV compounds using a series of computational methods, including both ligand-based and structure-based approaches. In particular, we will focus our attention to two viral proteins that are considered suitable targets for antiviral therapy: the viral F protein and the M2-1 protein. X-ray structures of both proteins are available and starting from these structures, we will use several computer-aided drug design methodologies to identify novel potential inhibitors. The most promising compounds will be then purchased or synthesised (depending on their commercial availability) and evaluated in cell-based assays (in collaboration with other network partners). The results obtained will be then used, along with the in silico model, in the design of a second generation of potential inhibitors.
ESR-8Cardiff University (UK) Computer-aided design, synthesis and evaluation of novel anti-CHKV compounds - The aim of this project is to identify a novel series of anti-CHIKV compounds. In particular, we will focus our attention to different viral targets: 1) The nspP2 is a cysteine-protease essential for viral replication and in our previous studies, we have identified an interesting hit with a ~3µM anti-CHKV activity in a cell-based assay. However, this compound also presents some toxicity (selectivity index of 30).The aim of this part of the project is to use a rational approach to design a second generation of inhibitors, more potent and less toxic than our original hit. 2) The nsP3 protein is also essential to viral replication and we aim to use a series of computer-aided drug design approaches to identify novel inhibitors of CHKV replication. All the new compounds will biologically evaluated (at the Catholic University of Leuven) and the data will be used to feedback the in silico model in an iterative optimisation process.
ESR-9Aix Marseille University (FR)Inhibitors of the mRNA capping machinery of Alphaviruses - Alphaviruses are emerging arboviruses which are known to possess a unique capping mechanism carried out by the viral non structural protein nsP1. The enzyme harbours methyltransferase (MTase) and nsP1 guanylylation (GT) activities catalysing the transfer of the methyl group from S-Adenosylmethionine (AdoMet) to a GTP molecule followed by the formation of a m7GMP-nsP1 , the substrate for the RNA capping reaction. Because of its unconventional mechanism, alphavirus mRNA capping is an attractive target for the design of specific inhibitors. In the lab, we have recently characterized the biochemical activities of Venezuelan equine encephalitis virus (VEEV) nsP1. To do so, we have developed enzymatic assays uncoupling the different reaction steps catalysed by nsP1 and used reference capping inhibitors. The ESR will screen series of potential inhibitors by HT enzymatic assays. The most potent ones will be tested on infected cells in order to select viral escape mutants and understand their mechanism of action. This project will foster the development of novel molecules with antiviral activity as well as contribute to a better understanding of nsP1 regulation in the capping process.
ESR-10Aix Marseille University (FR) Viral enzymes in the Coronavirus RNA replication complex: assembly, mechanism and inhibition - The coronavirus (CoV) family contains important respiratory and enteric pathogens. The successive emergence of highly pathogenic CoVs such as the Severe Acute Respiratory Syndrome (SARS-CoV) in 2003 and the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in 2012 highlights their zoonotic potential. To date, there is no treatment against CoVs. In the lab we recently identified and characterized a highly active and processive SARS-CoV polymerase complex in vitro (Subissi et al., PNAS, 2014). We also demonstrated that the viral 3’-5’ exonuclease (ExoN) can excise mismatches generated by the polymerase complex (Bouvet et al., PNAS, 2012). This proofreading system is an unprecedented discovery in RNA viruses and would explain the inefficiency of Ribavirin (a nucleotide analogue) treatment in SARS- and MERS-patients. Goals of the ESR will be to 1) unravel nucleotide polymerisation mechanisms at the molecular and atomic level 2) identify nucleotide analogues that are efficiently incorporated by the SARS-CoV and MERS-CoV polymerase complex, but not excised by the viral 3’-5’ ExoN activity 3) understand in structural terms how these complex work 4) comparatively position these mechanisms in the viral polymerase world.
ESR-11Rega Institute for Medical Research, KU Leuven (BE)Characterisation of novel enterovirus inhibitors - The genus Enterovirus of the picornavirus family contains many important human and animal pathogens, such as poliovirus, coxsackievirus (CV), enterovirus 71 (EV71), and rhinovirus. Recently, a number of novel enterovirus inhibitors were discovered in our laboratory. The ESR will study the particular characteristics and unravel the molecular mechanism of action (MoA) of these inhibitors. The target of the compounds will be identified by selection and characterization of drug-resistant variants (e.g. subgenomic replicon analysis, resistance culturing, reverse genetics). The MoA of compounds targeting viral enzymes will be investigated in more detail by biochemical techniques (e.g. interaction analysis, enzymatic inhibition assays). Structure-based optimization of promising classes of molecules will be performed in close collaboration with structural biologists and medicinal chemists. The efficacy of the most potent molecules will be assessed in CVB3 and EV71 infection models in mice with emphasis on monitoring in vivo resistance development and quasispecies evolution under drug pressure.
ESR-12Aratana Therapeutics (BE)Antiviral mechanisms of foot-and-mouth disease virus inhibitors - Foot-and-mouth disease virus (FMDV) inhibitors have been identified. The ESR will investigate antiviral mechanisms of selected molecules using standardized tests in vitro. Resistance associated mutations will be validated through reverse genetics in replicon and infectious clone systems. To characterize the function of the viral targets, molecular studies will be performed and an academic secondment will allow for the elucidation of the structure of the viral target in order to identify possible binding sites with the selected inhibitors.
ESR-13AiCuris GmbH (DE)Identification and characterisation of hepatitis B virus inhibitors - Available drugs are not capable of reliably eliminating hepatitis B virus (HBV) and achieving a cure of the infection. AiCuris is currently active in the search for inhibitors which differentiate by their molecular targets or mode of action. Based on hits from different screening approaches promising candidates need to be analysed in detail. A special focus will be on the discovery of drugs with the potential to eradicate the virus. As functional cure can currently only be analysed as sustained reduction of surface antigen levels in a surrogate animal model (woodchucks), we will initially focus on developing and establishing suitable biomarkers and in vitro assay systems with a higher throughput which can give a first indication of the inhibitors potential to cure.
ESR-14Complix Luxembourg (LU)Development of Alphabodies that inhibit HIV - The aim of this project is to develop Alphabodies targeting the class I viral entry mechanism of HIV and exploit the stability of Alphabodies to obtain fusion inhibitors with an improved bio-availability and administration flexibility. The ESR will improve the affinity of Alphabodies tackling the fusion protein at 2 different sites by phage-displayed Alphabody library screening and rational design. The best binding Alphabodies will be designed as bi-specific Alphabodies and tested for their antiviral activity including spectrum of activity. The lead candidate will be equipped with serum half-life properties and further characterized for antiviral activity including development of resistance but also serum stability and immunogenicity will be assessed.
ESR-15University of Vienna/Prestwick Chemicals (AS)Development of a non-nucleoside inhibitor of enterovirus polymerases: Computer-aided design, synthesis and biological evaluation - The aim of this project is to develop a new series of non-nucleoside inhibitors of enterovirus polymerases. In particular, analogs of GPC-N114 (a non-nucleoside polymerase inhibitor recently discovered in a collaborative effort between Utrecht University, Aix-Marseille University, and KU Leuven) shall be designed using a variety of computational chemistry approaches. The most promising candidates will then be prepared and submitted to biological evaluation.