1
|
Bardiot D, Vangeel L, Koukni M, Arzel P, Zwaagstra M, Lyoo H, Wanningen P, Ahmad S, Zhang L, Sun X, Delpal A, Eydoux C, Guillemot JC, Lescrinier E, Klaassen H, Leyssen P, Jochmans D, Castermans K, Hilgenfeld R, Robinson C, Decroly E, Canard B, Snijder EJ, van Hemert MJ, van Kuppeveld F, Chaltin P, Neyts J, De Jonghe S, Marchand A. Synthesis, Structure–Activity Relationships, and Antiviral Profiling of 1-Heteroaryl-2-Alkoxyphenyl Analogs As Inhibitors of SARS-CoV-2 Replication. Molecules 2022; 27:molecules27031052. [PMID: 35164317 PMCID: PMC8840742 DOI: 10.3390/molecules27031052] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/13/2022] [Accepted: 01/24/2022] [Indexed: 02/05/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, has led to a pandemic, that continues to be a huge public health burden. Despite the availability of vaccines, there is still a need for small-molecule antiviral drugs. In an effort to identify novel and drug-like hit matter that can be used for subsequent hit-to-lead optimization campaigns, we conducted a high-throughput screening of a 160 K compound library against SARS-CoV-2, yielding a 1-heteroaryl-2-alkoxyphenyl analog as a promising hit. Antiviral profiling revealed this compound was active against various beta-coronaviruses and preliminary mode-of-action experiments demonstrated that it interfered with viral entry. A systematic structure–activity relationship (SAR) study demonstrated that a 3- or 4-pyridyl moiety on the oxadiazole moiety is optimal, whereas the oxadiazole can be replaced by various other heteroaromatic cycles. In addition, the alkoxy group tolerates some structural diversity.
Collapse
Affiliation(s)
- Dorothée Bardiot
- Centre for Innovation and Stimulation of Drug Discovery (CISTIM), Gaston Geenslaan 2, 3001 Leuven, Belgium; (D.B.); (M.K.); (P.A.); (H.K.); (K.C.); (P.C.)
| | - Laura Vangeel
- Laboratory of Virology and Chemotherapy, KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Herestraat 49, 3000 Leuven, Belgium; (L.V.); (P.L.); (D.J.); (J.N.)
| | - Mohamed Koukni
- Centre for Innovation and Stimulation of Drug Discovery (CISTIM), Gaston Geenslaan 2, 3001 Leuven, Belgium; (D.B.); (M.K.); (P.A.); (H.K.); (K.C.); (P.C.)
| | - Philippe Arzel
- Centre for Innovation and Stimulation of Drug Discovery (CISTIM), Gaston Geenslaan 2, 3001 Leuven, Belgium; (D.B.); (M.K.); (P.A.); (H.K.); (K.C.); (P.C.)
| | - Marleen Zwaagstra
- Virology Section, Infectious Disease and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; (M.Z.); (H.L.); (F.v.K.)
| | - Heyrhyoung Lyoo
- Virology Section, Infectious Disease and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; (M.Z.); (H.L.); (F.v.K.)
| | - Patrick Wanningen
- Department of Medical Microbiology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (P.W.); (E.J.S.); (M.J.v.H.)
| | - Shamshad Ahmad
- Drug Discovery Unit, School of Life Sciences, University of Dundee, Dundee DDI 5EH, UK; (S.A.); (C.R.)
| | - Linlin Zhang
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany; (L.Z.); (X.S.); (R.H.)
| | - Xinyuanyuan Sun
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany; (L.Z.); (X.S.); (R.H.)
| | - Adrien Delpal
- Laboratory Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, CEDEX 9, 13288 Marseille, France; (A.D.); (C.E.); (J.-C.G.); (E.D.); (B.C.)
| | - Cecilia Eydoux
- Laboratory Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, CEDEX 9, 13288 Marseille, France; (A.D.); (C.E.); (J.-C.G.); (E.D.); (B.C.)
| | - Jean-Claude Guillemot
- Laboratory Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, CEDEX 9, 13288 Marseille, France; (A.D.); (C.E.); (J.-C.G.); (E.D.); (B.C.)
| | - Eveline Lescrinier
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium;
| | - Hugo Klaassen
- Centre for Innovation and Stimulation of Drug Discovery (CISTIM), Gaston Geenslaan 2, 3001 Leuven, Belgium; (D.B.); (M.K.); (P.A.); (H.K.); (K.C.); (P.C.)
| | - Pieter Leyssen
- Laboratory of Virology and Chemotherapy, KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Herestraat 49, 3000 Leuven, Belgium; (L.V.); (P.L.); (D.J.); (J.N.)
| | - Dirk Jochmans
- Laboratory of Virology and Chemotherapy, KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Herestraat 49, 3000 Leuven, Belgium; (L.V.); (P.L.); (D.J.); (J.N.)
| | - Karolien Castermans
- Centre for Innovation and Stimulation of Drug Discovery (CISTIM), Gaston Geenslaan 2, 3001 Leuven, Belgium; (D.B.); (M.K.); (P.A.); (H.K.); (K.C.); (P.C.)
| | - Rolf Hilgenfeld
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany; (L.Z.); (X.S.); (R.H.)
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562 Lübeck, Germany
| | - Colin Robinson
- Drug Discovery Unit, School of Life Sciences, University of Dundee, Dundee DDI 5EH, UK; (S.A.); (C.R.)
| | - Etienne Decroly
- Laboratory Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, CEDEX 9, 13288 Marseille, France; (A.D.); (C.E.); (J.-C.G.); (E.D.); (B.C.)
| | - Bruno Canard
- Laboratory Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, CEDEX 9, 13288 Marseille, France; (A.D.); (C.E.); (J.-C.G.); (E.D.); (B.C.)
| | - Eric J. Snijder
- Department of Medical Microbiology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (P.W.); (E.J.S.); (M.J.v.H.)
| | - Martijn J. van Hemert
- Department of Medical Microbiology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (P.W.); (E.J.S.); (M.J.v.H.)
| | - Frank van Kuppeveld
- Virology Section, Infectious Disease and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; (M.Z.); (H.L.); (F.v.K.)
| | - Patrick Chaltin
- Centre for Innovation and Stimulation of Drug Discovery (CISTIM), Gaston Geenslaan 2, 3001 Leuven, Belgium; (D.B.); (M.K.); (P.A.); (H.K.); (K.C.); (P.C.)
- Center for Drug Design and Development (CD3), KU Leuven R&D, Waaistraat 6, 3000 Leuven, Belgium
| | - Johan Neyts
- Laboratory of Virology and Chemotherapy, KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Herestraat 49, 3000 Leuven, Belgium; (L.V.); (P.L.); (D.J.); (J.N.)
| | - Steven De Jonghe
- Laboratory of Virology and Chemotherapy, KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Herestraat 49, 3000 Leuven, Belgium; (L.V.); (P.L.); (D.J.); (J.N.)
- Correspondence: (S.D.J.); (A.M.)
| | - Arnaud Marchand
- Centre for Innovation and Stimulation of Drug Discovery (CISTIM), Gaston Geenslaan 2, 3001 Leuven, Belgium; (D.B.); (M.K.); (P.A.); (H.K.); (K.C.); (P.C.)
- Correspondence: (S.D.J.); (A.M.)
| |
Collapse
|
2
|
Haagmans BL, Noack D, Okba NMA, Li W, Wang C, Bestebroer T, de Vries R, Herfst S, de Meulder D, Verveer E, van Run P, Lamers MM, Rijnders B, Rokx C, van Kuppeveld F, Grosveld F, Drabek D, Geurts van Kessel C, Koopmans M, Bosch BJ, Kuiken T, Rockx B. SARS-CoV-2 Neutralizing Human Antibodies Protect Against Lower Respiratory Tract Disease in a Hamster Model. J Infect Dis 2021; 223:2020-2028. [PMID: 34043806 PMCID: PMC8243397 DOI: 10.1093/infdis/jiab289] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/25/2021] [Indexed: 01/08/2023] Open
Abstract
Effective clinical intervention strategies for COVID-19 are urgently needed.
Although several clinical trials have evaluated the use of convalescent plasma
containing virus-neutralizing antibodies, the levels of neutralizing antibodies
are usually not assessed and the effectiveness has not been proven. We show that
hamsters treated prophylactically with a 1:2560 titer of human convalescent
plasma or a 1:5260 titer of monoclonal antibody were protected against weight
loss, had a significant reduction of virus replication in the lungs and showed
reduced pneumonia . Interestingly, this protective effect was lost with a titer
of 1:320 of convalescent plasma. These data highlight the importance of
screening plasma donors for high levels of neutralizing antibodies. Our data show that prophylactic administration of high levels of neutralizing
antibody, either monoclonal or from convalescent plasma, prevent severe
SARS-CoV-2 pneumonia in a hamster model, and could be used as an alternative or
complementary to other antiviral treatments for COVID-19.
Collapse
Affiliation(s)
- Bart L Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Danny Noack
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Nisreen M A Okba
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Wentao Li
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Chunyan Wang
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Theo Bestebroer
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Rory de Vries
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Sander Herfst
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Dennis de Meulder
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Elwin Verveer
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Peter van Run
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Mart M Lamers
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Bart Rijnders
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Casper Rokx
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Frank van Kuppeveld
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, the Netherlands.,Harbour BioMed, Rotterdam, the Netherlands
| | - Dubravka Drabek
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, the Netherlands.,Harbour BioMed, Rotterdam, the Netherlands
| | | | - Marion Koopmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Berend Jan Bosch
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Thijs Kuiken
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Barry Rockx
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| |
Collapse
|
3
|
Vogelzang EH, Loeff FC, Derksen NIL, Kruithof S, Ooijevaar-de Heer P, van Mierlo G, Linty F, Mok JY, van Esch W, de Bruin S, Vlaar APJ, Seppen B, Leeuw M, van Oudheusden AJG, Buiting AGM, Jim KK, Vrielink H, Swaneveld F, Vidarsson G, van der Schoot CE, Wever PC, Li W, van Kuppeveld F, Murk JL, Bosch BJ, Wolbink GJ, Rispens T. Development of a SARS-CoV-2 Total Antibody Assay and the Dynamics of Antibody Response over Time in Hospitalized and Nonhospitalized Patients with COVID-19. J Immunol 2020; 205:3491-3499. [PMID: 33127820 DOI: 10.4049/jimmunol.2000767] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/08/2020] [Indexed: 12/16/2022]
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 infections often cause only mild disease that may evoke relatively low Ab titers compared with patients admitted to hospitals. Generally, total Ab bridging assays combine good sensitivity with high specificity. Therefore, we developed sensitive total Ab bridging assays for detection of SARS-CoV-2 Abs to the receptor-binding domain (RBD) and nucleocapsid protein in addition to conventional isotype-specific assays. Ab kinetics was assessed in PCR-confirmed, hospitalized coronavirus disease 2019 (COVID-19) patients (n = 41) and three populations of patients with COVID-19 symptoms not requiring hospital admission: PCR-confirmed convalescent plasmapheresis donors (n = 182), PCR-confirmed hospital care workers (n = 47), and a group of longitudinally sampled symptomatic individuals highly suspect of COVID-19 (n = 14). In nonhospitalized patients, the Ab response to RBD is weaker but follows similar kinetics, as has been observed in hospitalized patients. Across populations, the RBD bridging assay identified most patients correctly as seropositive. In 11/14 of the COVID-19-suspect cases, seroconversion in the RBD bridging assay could be demonstrated before day 12; nucleocapsid protein Abs emerged less consistently. Furthermore, we demonstrated the feasibility of finger-prick sampling for Ab detection against SARS-CoV-2 using these assays. In conclusion, the developed bridging assays reliably detect SARS-CoV-2 Abs in hospitalized and nonhospitalized patients and are therefore well suited to conduct seroprevalence studies.
Collapse
Affiliation(s)
- Erik H Vogelzang
- Department of Rheumatology, Amsterdam Rheumatology and Immunology Center, 1056 AB Reade, Amsterdam, the Netherlands.,Department of Medical Microbiology and Infection Control, Amsterdam University Medical Center, Location Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - Floris C Loeff
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory Academic Medical Centre, 1066 CX Amsterdam, the Netherlands.,Biologics Laboratory, Sanquin Diagnostic Services, 1066 CX Amsterdam, the Netherlands
| | - Ninotska I L Derksen
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory Academic Medical Centre, 1066 CX Amsterdam, the Netherlands
| | - Simone Kruithof
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory Academic Medical Centre, 1066 CX Amsterdam, the Netherlands
| | - Pleuni Ooijevaar-de Heer
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory Academic Medical Centre, 1066 CX Amsterdam, the Netherlands
| | - Gerard van Mierlo
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory Academic Medical Centre, 1066 CX Amsterdam, the Netherlands
| | - Federica Linty
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory Academic Medical Centre, 1066 CX Amsterdam, the Netherlands
| | - Juk Yee Mok
- Sanquin Reagents, 1066 CX Amsterdam, the Netherlands
| | - Wim van Esch
- Sanquin Reagents, 1066 CX Amsterdam, the Netherlands
| | - Sanne de Bruin
- Department of Intensive Care Medicine, Amsterdam University Medical Center, Location Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - Alexander P J Vlaar
- Department of Intensive Care Medicine, Amsterdam University Medical Center, Location Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | | | - Bart Seppen
- Department of Rheumatology, Amsterdam Rheumatology and Immunology Center, 1056 AB Reade, Amsterdam, the Netherlands
| | - Maureen Leeuw
- Department of Rheumatology, Amsterdam Rheumatology and Immunology Center, 1056 AB Reade, Amsterdam, the Netherlands
| | - Anne J G van Oudheusden
- Department of Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, 5042 AD Tilburg, the Netherlands
| | - Anton G M Buiting
- Department of Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, 5042 AD Tilburg, the Netherlands
| | - Kin Ki Jim
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Center, Location Academic Medical Center, 1105 AZ Amsterdam, the Netherlands.,Departments of Medical Microbiology, Jeroen Bosch Hospital, 5223 GZ 's Hertogenbosch, the Netherlands
| | - Hans Vrielink
- Department of Transfusion Medicine, Sanquin Blood Bank, 1066 CX Amsterdam, the Netherlands
| | - Francis Swaneveld
- Department of Transfusion Medicine, Sanquin Blood Bank, 1066 CX Amsterdam, the Netherlands
| | - Gestur Vidarsson
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory Academic Medical Centre, 1066 CX Amsterdam, the Netherlands
| | - C Ellen van der Schoot
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory Academic Medical Centre, 1066 CX Amsterdam, the Netherlands
| | - Peter C Wever
- Departments of Medical Microbiology, Jeroen Bosch Hospital, 5223 GZ 's Hertogenbosch, the Netherlands
| | - Wentao Li
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, the Netherlands; and
| | - Frank van Kuppeveld
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, the Netherlands; and
| | - Jean-Luc Murk
- Department of Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, 5042 AD Tilburg, the Netherlands
| | - Berend Jan Bosch
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, the Netherlands; and
| | - Gerrit-Jan Wolbink
- Department of Rheumatology, Amsterdam Rheumatology and Immunology Center, 1056 AB Reade, Amsterdam, the Netherlands.,Department of Immunopathology, Sanquin Research and Landsteiner Laboratory Academic Medical Centre, 1066 CX Amsterdam, the Netherlands.,Department of Rheumatology, OLVG Hospital, 1091 AC Amsterdam, the Netherlands
| | - Theo Rispens
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory Academic Medical Centre, 1066 CX Amsterdam, the Netherlands;
| |
Collapse
|
4
|
Dirmeier S, Dächert C, van Hemert M, Tas A, Ogando NS, van Kuppeveld F, Bartenschlager R, Kaderali L, Binder M, Beerenwinkel N. Host factor prioritization for pan-viral genetic perturbation screens using random intercept models and network propagation. PLoS Comput Biol 2020; 16:e1007587. [PMID: 32040506 PMCID: PMC7034926 DOI: 10.1371/journal.pcbi.1007587] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 02/21/2020] [Accepted: 12/05/2019] [Indexed: 12/16/2022] Open
Abstract
Genetic perturbation screens using RNA interference (RNAi) have been conducted successfully to identify host factors that are essential for the life cycle of bacteria or viruses. So far, most published studies identified host factors primarily for single pathogens. Furthermore, often only a small subset of genes, e.g., genes encoding kinases, have been targeted. Identification of host factors on a pan-pathogen level, i.e., genes that are crucial for the replication of a diverse group of pathogens has received relatively little attention, despite the fact that such common host factors would be highly relevant, for instance, for devising broad-spectrum anti-pathogenic drugs. Here, we present a novel two-stage procedure for the identification of host factors involved in the replication of different viruses using a combination of random effects models and Markov random walks on a functional interaction network. We first infer candidate genes by jointly analyzing multiple perturbations screens while at the same time adjusting for high variance inherent in these screens. Subsequently the inferred estimates are spread across a network of functional interactions thereby allowing for the analysis of missing genes in the biological studies, smoothing the effect sizes of previously found host factors, and considering a priori pathway information defined over edges of the network. We applied the procedure to RNAi screening data of four different positive-sense single-stranded RNA viruses, Hepatitis C virus, Chikungunya virus, Dengue virus and Severe acute respiratory syndrome coronavirus, and detected novel host factors, including UBC, PLCG1, and DYRK1B, which are predicted to significantly impact the replication cycles of these viruses. We validated the detected host factors experimentally using pharmacological inhibition and an additional siRNA screen and found that some of the predicted host factors indeed influence the replication of these pathogens.
Collapse
Affiliation(s)
- Simon Dirmeier
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Christopher Dächert
- Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response” (division F170), German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Martijn van Hemert
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ali Tas
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Natacha S. Ogando
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Frank van Kuppeveld
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Ralf Bartenschlager
- Department for Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
- Division Virus-Associated Carcinogenesis, German Cancer Research Center, Heidelberg, Germany
| | - Lars Kaderali
- University Medicine Greifswald, Institute of Bioinformatics, Greifswald, Germany
| | - Marco Binder
- Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response” (division F170), German Cancer Research Center, Heidelberg, Germany
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
- * E-mail:
| |
Collapse
|
5
|
Domsgen E, Lind K, Kong L, Hühn MH, Rasool O, van Kuppeveld F, Korsgren O, Lahesmaa R, Flodström-Tullberg M. An IFIH1 gene polymorphism associated with risk for autoimmunity regulates canonical antiviral defence pathways in Coxsackievirus infected human pancreatic islets. Sci Rep 2016; 6:39378. [PMID: 28000722 PMCID: PMC5175199 DOI: 10.1038/srep39378] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 11/23/2016] [Indexed: 02/08/2023] Open
Abstract
The IFIH1 gene encodes the pattern recognition receptor MDA5. A common polymorphism in IFIH1 (rs1990760, A946T) confers increased risk for autoimmune disease, including type 1-diabetes (T1D). Coxsackievirus infections are linked to T1D and cause beta-cell damage in vitro. Here we demonstrate that the rs1990760 polymorphism regulates the interferon (IFN) signature expressed by human pancreatic islets following Coxsackievirus infection. A strong IFN signature was associated with high expression of IFNλ1 and IFNλ2, linking rs1990760 to the expression of type III IFNs. In the high-responding genotype, IRF-1 expression correlated with that of type III IFN, suggesting a positive-feedback on type III IFN transcription. In summary, our study uncovers an influence of rs1990760 on the canonical effector function of MDA5 in response to an acute infection of primary human parenchymal cells with a clinically relevant virus linked to human T1D. It also highlights a previously unrecognized connection between the rs1990760 polymorphism and the expression level of type III IFNs.
Collapse
Affiliation(s)
- Erna Domsgen
- The Center for Infectious Medicine, Department of Medicine HS, Karolinska Institutet, Karolinska University Hospital, Stockholm, 141 86, Sweden
| | - Katharina Lind
- The Center for Infectious Medicine, Department of Medicine HS, Karolinska Institutet, Karolinska University Hospital, Stockholm, 141 86, Sweden
| | - Lingjia Kong
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, 205 20, Finland
| | - Michael H Hühn
- The Center for Infectious Medicine, Department of Medicine HS, Karolinska Institutet, Karolinska University Hospital, Stockholm, 141 86, Sweden
| | - Omid Rasool
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, 205 20, Finland
| | - Frank van Kuppeveld
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584, The Netherlands
| | - Olle Korsgren
- Department of Immunology, Genetics, and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, 751 05, Sweden
| | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, 205 20, Finland
| | - Malin Flodström-Tullberg
- The Center for Infectious Medicine, Department of Medicine HS, Karolinska Institutet, Karolinska University Hospital, Stockholm, 141 86, Sweden.,Institute of Biosciences and Medical Technologies, University of Tampere, Tampere, 33520, Finland
| |
Collapse
|
6
|
Mauthe M, Langereis M, Jung J, Zhou X, Jones A, Omta W, Tooze SA, Stork B, Paludan SR, Ahola T, Egan D, Behrends C, Mokry M, de Haan C, van Kuppeveld F, Reggiori F. An siRNA screen for ATG protein depletion reveals the extent of the unconventional functions of the autophagy proteome in virus replication. J Cell Biol 2016; 214:619-35. [PMID: 27573464 PMCID: PMC5004442 DOI: 10.1083/jcb.201602046] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 07/25/2016] [Indexed: 02/06/2023] Open
Abstract
Autophagy is a catabolic process regulated by the orchestrated action of the autophagy-related (ATG) proteins. Recent work indicates that some of the ATG proteins also have autophagy-independent roles. Using an unbiased siRNA screen approach, we explored the extent of these unconventional functions of ATG proteins. We determined the effects of the depletion of each ATG proteome component on the replication of six different viruses. Our screen reveals that up to 36% of the ATG proteins significantly alter the replication of at least one virus in an unconventional fashion. Detailed analysis of two candidates revealed an undocumented role for ATG13 and FIP200 in picornavirus replication that is independent of their function in autophagy as part of the ULK complex. The high numbers of unveiled ATG gene-specific and pathogen-specific functions of the ATG proteins calls for caution in the interpretation of data, which rely solely on the depletion of a single ATG protein to specifically ablate autophagy.
Collapse
Affiliation(s)
- Mario Mauthe
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, Netherlands Department of Cell Biology, University Medical Center Utrecht, 3584 CX Utrecht, Netherlands
| | - Martijn Langereis
- Virology Division, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, 3584 CL Utrecht, Netherlands
| | - Jennifer Jung
- Institute of Biochemistry II, Goethe University School of Medicine, 60590 Frankfurt am Main, Germany
| | - Xingdong Zhou
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, Netherlands Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Alex Jones
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, Netherlands Department of Cell Biology, University Medical Center Utrecht, 3584 CX Utrecht, Netherlands
| | - Wienand Omta
- Department of Cell Biology, University Medical Center Utrecht, 3584 CX Utrecht, Netherlands
| | - Sharon A Tooze
- Lincoln's Inn Fields Laboratories, The Francis Crick Institute, London WC2A 3LY, England, UK
| | - Björn Stork
- Institute of Molecular Medicine I, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | | | - Tero Ahola
- Department of Food and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Dave Egan
- Department of Cell Biology, University Medical Center Utrecht, 3584 CX Utrecht, Netherlands
| | - Christian Behrends
- Institute of Biochemistry II, Goethe University School of Medicine, 60590 Frankfurt am Main, Germany
| | - Michal Mokry
- Regenerative Medicine Center Utrecht, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CX Utrecht, Netherlands Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3584 EA Utrecht, Netherlands
| | - Cornelis de Haan
- Virology Division, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, 3584 CL Utrecht, Netherlands
| | - Frank van Kuppeveld
- Virology Division, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, 3584 CL Utrecht, Netherlands
| | - Fulvio Reggiori
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, 9713 AV Groningen, Netherlands Department of Cell Biology, University Medical Center Utrecht, 3584 CX Utrecht, Netherlands
| |
Collapse
|
7
|
Humoud MN, Doyle N, Royall E, Willcocks MM, Sorgeloos F, van Kuppeveld F, Roberts LO, Goodfellow IG, Langereis MA, Locker N. Feline Calicivirus Infection Disrupts Assembly of Cytoplasmic Stress Granules and Induces G3BP1 Cleavage. J Virol 2016; 90:6489-6501. [PMID: 27147742 PMCID: PMC4936126 DOI: 10.1128/jvi.00647-16] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 04/27/2016] [Indexed: 12/24/2022] Open
Abstract
UNLABELLED In response to stress such as virus infection, cells can stall translation by storing mRNAs away in cellular compartments called stress granules (SGs). This defense mechanism favors cell survival by limiting the use of energy and nutrients until the stress is resolved. In some cases it may also block viral propagation as viruses are dependent on the host cell resources to produce viral proteins. Human norovirus is a member of the Caliciviridae family responsible for gastroenteritis outbreaks worldwide. Previous studies on caliciviruses have identified mechanisms by which they can usurp the host translational machinery, using the viral protein genome-linked VPg, or regulate host protein synthesis through the mitogen-activated protein kinase (MAPK) pathway. Here, we examined the effect of feline calicivirus (FCV) infection on SG accumulation. We show that FCV infection impairs the assembly of SGs despite an increased phosphorylation of eukaryotic initiation factor eIF2α, a hallmark of stress pathway activation. Furthermore, SGs did not accumulate in FCV-infected cells that were stressed with arsenite or hydrogen peroxide. FCV infection resulted in the cleavage of the SG-nucleating protein Ras-GTPase activating SH3 domain-binding protein (G3BP1), which is mediated by the viral 3C-like proteinase NS6(Pro) Using mutational analysis, we identified the FCV-induced cleavage site within G3BP1, which differs from the poliovirus 3C proteinase cleavage site previously identified. Finally, we showed that NS6(Pro)-mediated G3BP1 cleavage impairs SG assembly. In contrast, murine norovirus (MNV) infection did not impact arsenite-induced SG assembly or G3BP1 integrity, suggesting that related caliciviruses have distinct effects on the stress response pathway. IMPORTANCE Human noroviruses are a major cause of viral gastroenteritis, and it is important to understand how they interact with the infected host cell. Feline calicivirus (FCV) and murine norovirus (MNV) are used as models to understand norovirus biology. Recent studies have suggested that the assembly of stress granules is central in orchestrating stress and antiviral responses to restrict viral replication. Overall, our study provides the first insight on how caliciviruses impair stress granule assembly by targeting the nucleating factor G3BP1 via the viral proteinase NS6(Pro) This work provides new insights into host-pathogen interactions that regulate stress pathways during FCV infection.
Collapse
Affiliation(s)
- Majid N Humoud
- University of Surrey, Faculty of Health and Medical Sciences, School of Biosciences and Medicine, Guildford, United Kingdom
| | - Nicole Doyle
- University of Surrey, Faculty of Health and Medical Sciences, School of Biosciences and Medicine, Guildford, United Kingdom
| | - Elizabeth Royall
- University of Surrey, Faculty of Health and Medical Sciences, School of Biosciences and Medicine, Guildford, United Kingdom
| | - Margaret M Willcocks
- University of Surrey, Faculty of Health and Medical Sciences, School of Biosciences and Medicine, Guildford, United Kingdom
| | - Frederic Sorgeloos
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, United Kingdom
| | - Frank van Kuppeveld
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Lisa O Roberts
- University of Surrey, Faculty of Health and Medical Sciences, School of Biosciences and Medicine, Guildford, United Kingdom
| | - Ian G Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, United Kingdom
| | - Martijn A Langereis
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Nicolas Locker
- University of Surrey, Faculty of Health and Medical Sciences, School of Biosciences and Medicine, Guildford, United Kingdom
| |
Collapse
|
8
|
Kuppeveld FV. Understanding virus replication is key to develop antiviral drugs. Future Virol 2014. [DOI: 10.2217/fvl.14.67] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Frank van Kuppeveld* speaks to James Potticary, Commissioning Editor: Frank van Kuppeveld is a Professor of Molecular Virology at the Faculty of Veterinary Medicine, Utrecht University (The Netherlands). Having published over 100 original research papers, he is also the scientific coordinator of the European Training Network on (+)RNA Virus Replication and Antiviral Drug Development (EUVIRNA) consortium, a European training network for young researchers in the field of RNA viruses and antiviral drug development. van Kuppeveld spoke to Future Virology about his own contributions to the molecular virology field, as well as discussing the progress of the EUVIRNA training network.
Collapse
|
9
|
|
10
|
van Kuppeveld F, Snijder E, Gorbalenya A, Canard B, Bartenschlager R, Neyts J, Brancale A, McGuigan C. European Training Network on (+)RNA Virus Replication and Antiviral Drug Development. Antiviral Res 2011. [DOI: 10.1016/j.antiviral.2011.03.129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
11
|
De Palma AM, Heggermont W, Lanke K, Coutard B, Bergmann M, Monforte AM, Canard B, De Clercq E, Chimirri A, Pürstinger G, Rohayem J, van Kuppeveld F, Neyts J. The thiazolobenzimidazole TBZE-029 inhibits enterovirus replication by targeting a short region immediately downstream from motif C in the nonstructural protein 2C. J Virol 2008; 82:4720-30. [PMID: 18337578 PMCID: PMC2346740 DOI: 10.1128/jvi.01338-07] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Accepted: 03/03/2008] [Indexed: 11/20/2022] Open
Abstract
TBZE-029 {1-(2,6-difluorophenyl)-6-trifluoromethyl-1H,3H-thiazolo[3,4-a]benzimidazole} is a novel selective inhibitor of the replication of several enteroviruses. We show that TBZE-029 exerts its antiviral activity through inhibition of viral RNA replication, without affecting polyprotein processing. To identify the viral target of TBZE-029, drug-resistant coxsackievirus B3 (CVB3) was selected. Genotyping of resistant clones led to the identification of three amino acid mutations in nonstructural protein 2C, clustered at amino acid positions 224, 227, and 229, immediately downstream of NTPase/helicase motif C. The mutations were reintroduced, either alone or combined, into an infectious full-length CVB3 clone. In particular the mutations at positions 227 and 229 proved essential for the altered sensitivity of CVB3 to TBZE-029. Resistant virus exhibited cross-resistance to the earlier-reported antienterovirus agents targeting 2C, namely, guanidine hydrochloride, HBB [2-(alpha-hydroxybenzyl)-benzimidazole], and MRL-1237 {1-(4-fluorophenyl)-2-[(4-imino-1,4-dihydropyridin-1-yl)methyl]benzimidazole hydrochloride}. The ATPase activity of 2C, however, remained unaltered in the presence of TBZE-029.
Collapse
Affiliation(s)
- Armando M De Palma
- Rega Institute for Medical Research, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Bopegamage S, Kovacova J, Vargova A, Motusova J, Petrovicova A, Benkovicova M, Gomolcak P, Bakkers J, van Kuppeveld F, Melchers WJG, Galama JM. Coxsackie B virus infection of mice: inoculation by the oral route protects the pancreas from damage, but not from infection. J Gen Virol 2005; 86:3271-3280. [PMID: 16298972 DOI: 10.1099/vir.0.81249-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The pathogenesis of coxsackie B virus (CVB) infections is generally studied in mice by intraperitoneal (i.p.) injection, whereas the gastrointestinal tract is the natural porte d'entrée in humans. The present study was undertaken to compare systematically the influence of infection route on morbidity and pathology. Swiss Albino mice were infected with CVB3 (Nancy) at different doses (5 x 10(3), 5 x 10(5), 5 x 10(7), 5 x 10(9) TCID50), given either i.p. or orally. Virus could be isolated from several organs (heart, spleen and pancreas), indicating systemic infection, irrespective of the infection route. Virus titres were 1-2 logs higher after i.p. infection, but kinetics were largely independent of infection route. Organs became negative for virus isolation after 21 days, with the exception of spleen tissue, which remained positive for up to 49 days. Thereafter, virus was detected only by immunohistochemistry and PCR up to 98 days post-infection (oral route). Histopathology showed mild inflammation and necrosis in heart tissue of all mice during the acute phase, with repair at later stages. Strikingly, pancreatic lesions were confined to the exocrine pancreas and observed only after i.p. infection. Under all experimental conditions, the pancreatic islets were spared. In contrast, immunohistochemistry showed the presence of viral VP1, protein 3A and alpha interferon (IFN-alpha) in exocrine as well as endocrine pancreas of all mice, irrespective of route and dose of infection. It is concluded that infection via the oral route protects the pancreas from damage, but not from infection, a process in which IFN-alpha is not the only factor involved.
Collapse
MESH Headings
- Administration, Oral
- Animals
- Cell Line
- Chlorocebus aethiops
- Coxsackievirus Infections/pathology
- Coxsackievirus Infections/virology
- Disease Models, Animal
- Enterovirus B, Human/isolation & purification
- Enterovirus B, Human/pathogenicity
- Heart/virology
- Immunohistochemistry
- Inflammation
- Injections, Intraperitoneal
- Interferon-alpha/analysis
- Intestine, Small/chemistry
- Intestine, Small/pathology
- Intestine, Small/virology
- Mice
- Mice, Inbred ICR
- Myocardium/pathology
- Necrosis
- Pancreas/chemistry
- Pancreas/pathology
- Pancreas/virology
- Polymerase Chain Reaction
- RNA, Viral/analysis
- Spleen/virology
- Viral Proteins/analysis
Collapse
Affiliation(s)
- Shubhada Bopegamage
- Department of Virology, Slovak Medical University, Limbova 12, 83303 Bratislava, Slovak Republic
| | - Jana Kovacova
- Department of Virology, Slovak Medical University, Limbova 12, 83303 Bratislava, Slovak Republic
| | - Agnesa Vargova
- Department of Virology, Slovak Medical University, Limbova 12, 83303 Bratislava, Slovak Republic
| | - Jana Motusova
- Department of Virology, Slovak Medical University, Limbova 12, 83303 Bratislava, Slovak Republic
| | - Anna Petrovicova
- Department of Virology, Slovak Medical University, Limbova 12, 83303 Bratislava, Slovak Republic
| | - Maria Benkovicova
- Institute of Pathology, Derer's Hospital and Clinic, Limbova 5, 83301 Bratislava, Slovak Republic
| | - Pavol Gomolcak
- Institute of Pathology, Derer's Hospital and Clinic, Limbova 5, 83301 Bratislava, Slovak Republic
| | - Judith Bakkers
- Virology Section, Department of Medical Microbiology, Radboud University Medical Center Nijmegen, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Frank van Kuppeveld
- Virology Section, Department of Medical Microbiology, Radboud University Medical Center Nijmegen, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Willem J G Melchers
- Virology Section, Department of Medical Microbiology, Radboud University Medical Center Nijmegen, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Jochem M Galama
- Virology Section, Department of Medical Microbiology, Radboud University Medical Center Nijmegen, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| |
Collapse
|
13
|
Abstract
Cell death is an intrinsic part of metazoan development and mammalian immune regulation. Whereas the molecular events orchestrating apoptosis have been characterized extensively, little is known about the biochemistry of necrotic cell death. Here, we show that, in contrast to apoptosis, the induction of necrosis does not lead to the shut down of protein synthesis. The rapid drop in protein synthesis observed in apoptosis correlates with caspase-dependent breakdown of eukaryotic translation initiation factor (eIF) 4G, activation of the double-stranded RNA-activated protein kinase PKR, and phosphorylation of its substrate eIF2-α. In necrosis induced by tumor necrosis factor, double-stranded RNA, or viral infection, de novo protein synthesis persists and 28S ribosomal RNA fragmentation, eIF2-α phosphorylation, and proteolytic activation of PKR are absent. Collectively, these results show that, in contrast to apoptotic cells, necrotic dying cells retain the opportunity to synthesize proteins.
Collapse
Affiliation(s)
- Xavier Saelens
- Molecular Signalling and Cell Death Unit, Department for Molecular Biomedical Research, Flanders Interuniversity Institute for Biotechnology (VIB) and Ghent University, B9052 Ghent, Belgium
| | | | | | | | | | | | | |
Collapse
|