RNA viruses, including those from the Coronaviridae family, are the etiological agents responsible numerous epidemics and pandemics. SARS-CoV-2, first detected at the end of 2019, infected over 770... Show moreRNA viruses, including those from the Coronaviridae family, are the etiological agents responsible numerous epidemics and pandemics. SARS-CoV-2, first detected at the end of 2019, infected over 770 million people over the following 4 years, according to official numbers, and continues to evolve and give rise to numerous variants.This thesis outlines the efforts to contribute to the SARS-CoV-2 antiviral field, initiated at the onset of the COVID-19 pandemic. In here we detail the establishment and characterization of the H1299/ACE2 cell line, engineered to express high levels of the Angiotensin-Converting Enzyme 2 (ACE2) receptor, which is used by SARS-CoV-2 for entry into the host cell. These newly generated cells are highly susceptible to SARS-CoV-2 infection and offer significant advantages over other existing cell lines. Concurrently, our early efforts in repurposed compound screening identified several hit molecules with antiviral activity against SARS-CoV-2, including suramin and honokiol. The antiparasitic drug Suramin inhibits SARS-CoV-2 replication in monkey Vero E6 cells, human Calu-3 cells and in a primary human airway epithelial cell culture model by inhibiting early steps of the replication cycle, most likely virus binding and/or entry. Honokiol, a small molecule extracted from magnolia trees, inhibits SARS-CoV-2 replication in Vero E6 cells and in human A549 cells by acting on a post-entry step of the replication cycle, most likely by modulation of host signaling pathways. Both compounds efficiently inhibited SARS-CoV-2 replication with 50% effective concentration values well below the achievable maximum plasma levels in animal models or humans. Altogether, the advances described in this thesis promise to significantly contribute to the antiviral field, by providing a new practical and robust cell model system for antiviral and virus-host interaction studies, and by characterizing new potential antiviral drugs, which are essential to enhance our understanding of this virus and to better prepare against future (corona)virus outbreaks. Show less
The use of data derived from genomics and transcriptomic to further develop our understanding of Polycystic Kidney Diseases and identify novel drugs for its treatment.
Background: Autosomal Dominant Polycystic Kidney Disease (ADPKD) is one of the most common causes of end-stage renal failure, caused by mutations in PKD1 or PKD2 genes. Tolvaptan, the only drug... Show moreBackground: Autosomal Dominant Polycystic Kidney Disease (ADPKD) is one of the most common causes of end-stage renal failure, caused by mutations in PKD1 or PKD2 genes. Tolvaptan, the only drug approved for ADPKD treatment, results in serious side-effects, warranting the need for novel drugs.Methods: In this study, we applied RNA-sequencing of Pkd1cko mice at different disease stages, and with/without drug treatment to identify genes involved in ADPKD progression that were further used to identify novel drug candidates for ADPKD. We followed an integrative computational approach using a combination of gene expression profiling, bioinformatics and cheminformatics data.Findings: We identified 1162 genes that had a normalized expression after treating the mice with drugs proven effective in preclinical models. Intersecting these genes with target affinity profiles for clinically-approved drugs in ChEMBL, resulted in the identification of 116 drugs targeting 29 proteins, of which several are previously linked to Polycystic Kidney Disease such as Rosiglitazone. Further testing the efficacy of six candidate drugs for inhibition of cyst swelling using a human 3D-cyst assay, revealed that three of the six had cyst-growth reducing effects with limited toxicity.Interpretation: Our data further establishes drug repurposing as a robust drug discovery method, with three promising drug candidates identified for ADPKD treatment (Meclofenamic Acid, Gamolenic Acid and Birinapant). Our strategy that combines multiple-omics data, can be extended for ADPKD and other diseases in the future. (C) 2019 The Authors. Published by Elsevier B.V. Show less
Autosomal Dominant Polycystic Kidney Disease (ADPKD) is one of the most common causes of end-stage renal failure, caused by mutations in PKD1 or PKD2 genes. Tolvaptan, the only drug approved for... Show moreAutosomal Dominant Polycystic Kidney Disease (ADPKD) is one of the most common causes of end-stage renal failure, caused by mutations in PKD1 or PKD2 genes. Tolvaptan, the only drug approved for ADPKD treatment, results in serious side-effects, warranting the need for novel drugs.\nIn this study, we applied RNA-sequencing of Pkd1cko mice at different disease stages, and with/without drug treatment to identify genes involved in ADPKD progression that were further used to identify novel drug candidates for ADPKD. We followed an integrative computational approach using a combination of gene expression profiling, bioinformatics and cheminformatics data.\nWe identified 1162 genes that had a normalized expression after treating the mice with drugs proven effective in preclinical models. Intersecting these genes with target affinity profiles for clinically-approved drugs in ChEMBL, resulted in the identification of 116 drugs targeting 29 proteins, of which several are previously linked to Polycystic Kidney Disease such as Rosiglitazone. Further testing the efficacy of six candidate drugs for inhibition of cyst swelling using a human 3D-cyst assay, revealed that three of the six had cyst-growth reducing effects with limited toxicity.\nOur data further establishes drug repurposing as a robust drug discovery method, with three promising drug candidates identified for ADPKD treatment (Meclofenamic Acid, Gamolenic Acid and Birinapant). Our strategy that combines multiple-omics data, can be extended for ADPKD and other diseases in the future.\nEuropean Union's Seventh Framework Program, Dutch Technology Foundation Stichting Technische Wetenschappen and the Dutch Kidney Foundation. Show less
