1
|
Petkidis A, Andriasyan V, Murer L, Volle R, Greber UF. A versatile automated pipeline for quantifying virus infectivity by label-free light microscopy and artificial intelligence. Nat Commun 2024; 15:5112. [PMID: 38879641 PMCID: PMC11180103 DOI: 10.1038/s41467-024-49444-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 06/03/2024] [Indexed: 06/19/2024] Open
Abstract
Virus infectivity is traditionally determined by endpoint titration in cell cultures, and requires complex processing steps and human annotation. Here we developed an artificial intelligence (AI)-powered automated framework for ready detection of virus-induced cytopathic effect (DVICE). DVICE uses the convolutional neural network EfficientNet-B0 and transmitted light microscopy images of infected cell cultures, including coronavirus, influenza virus, rhinovirus, herpes simplex virus, vaccinia virus, and adenovirus. DVICE robustly measures virus-induced cytopathic effects (CPE), as shown by class activation mapping. Leave-one-out cross-validation in different cell types demonstrates high accuracy for different viruses, including SARS-CoV-2 in human saliva. Strikingly, DVICE exhibits virus class specificity, as shown with adenovirus, herpesvirus, rhinovirus, vaccinia virus, and SARS-CoV-2. In sum, DVICE provides unbiased infectivity scores of infectious agents causing CPE, and can be adapted to laboratory diagnostics, drug screening, serum neutralization or clinical samples.
Collapse
Affiliation(s)
- Anthony Petkidis
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
- Life Science Zurich Graduate School, ETH and University of Zürich, 8057, Zurich, Switzerland
| | - Vardan Andriasyan
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Luca Murer
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
- Roche Diagnostics, Forrenstrasse 2, 6343, Rotkreuz, Switzerland
| | - Romain Volle
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland.
| |
Collapse
|
2
|
Catching A, Te Yeh M, Bianco S, Capponi S, Andino R. A tradeoff between enterovirus A71 particle stability and cell entry. Nat Commun 2023; 14:7450. [PMID: 37978288 PMCID: PMC10656440 DOI: 10.1038/s41467-023-43029-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/26/2023] [Indexed: 11/19/2023] Open
Abstract
A central role of viral capsids is to protect the viral genome from the harsh extracellular environment while facilitating initiation of infection when the virus encounters a target cell. Viruses are thought to have evolved an optimal equilibrium between particle stability and efficiency of cell entry. In this study, we genetically perturb this equilibrium in a non-enveloped virus, enterovirus A71 to determine its structural basis. We isolate a single-point mutation variant with increased particle thermotolerance and decreased efficiency of cell entry. Using cryo-electron microscopy and molecular dynamics simulations, we determine that the thermostable native particles have acquired an expanded conformation that results in a significant increase in protein dynamics. Examining the intermediate states of the thermostable variant reveals a potential pathway for uncoating. We propose a sequential release of the lipid pocket factor, followed by internal VP4 and ultimately the viral RNA.
Collapse
Affiliation(s)
- Adam Catching
- Department of Microbiology and Immunology, University of California in San Francisco, San Francisco, CA, 94158, USA
- Graduate Program in Biophysics, University of California in San Francisco, San Francisco, CA, 94158, USA
| | - Ming Te Yeh
- Department of Microbiology and Immunology, University of California in San Francisco, San Francisco, CA, 94158, USA
| | - Simone Bianco
- Industrial and Applied Genomics, AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA, 95120, USA
- Center for Cellular Construction, San Francisco, CA, 94158, USA
- Altos Labs, Redwood City, CA, 94022, USA
| | - Sara Capponi
- Industrial and Applied Genomics, AI and Cognitive Software, IBM Almaden Research Center, San Jose, CA, 95120, USA.
- Center for Cellular Construction, San Francisco, CA, 94158, USA.
| | - Raul Andino
- Department of Microbiology and Immunology, University of California in San Francisco, San Francisco, CA, 94158, USA.
| |
Collapse
|
3
|
Martín-González N, Gómez-González A, Hernando-Pérez M, Bauer M, Greber UF, San Martín C, de Pablo PJ. Adenovirus core protein V reinforces the capsid and enhances genome release from disrupted particles. SCIENCE ADVANCES 2023; 9:eade9910. [PMID: 37027464 PMCID: PMC10081844 DOI: 10.1126/sciadv.ade9910] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 03/02/2023] [Indexed: 06/19/2023]
Abstract
Out of the three core proteins in human adenovirus, protein V is believed to connect the inner capsid surface to the outer genome layer. Here, we explored mechanical properties and in vitro disassembly of particles lacking protein V (Ad5-ΔV). Ad5-ΔV particles were softer and less brittle than the wild-type ones (Ad5-wt), but they were more prone to release pentons under mechanical fatigue. In Ad5-ΔV, core components did not readily diffuse out of partially disrupted capsids, and the core appeared more condensed than in Ad5-wt. These observations suggest that instead of condensing the genome, protein V antagonizes the condensing action of the other core proteins. Protein V provides mechanical reinforcement and facilitates genome release by keeping DNA connected to capsid fragments that detach during disruption. This scenario is in line with the location of protein V in the virion and its role in Ad5 cell entry.
Collapse
Affiliation(s)
- Natalia Martín-González
- Departament of Condensed Matter Physics, Universidad Autónoma de Madrid and Institute of Condensed Matter Physics (IFIMAC), 28049 Madrid, Spain
| | - Alfonso Gómez-González
- Department of Molecular Life Sciences, University of Zurich, CH-8057 Zurich, Switzerland
| | - Mercedes Hernando-Pérez
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
| | - Michael Bauer
- Department of Molecular Life Sciences, University of Zurich, CH-8057 Zurich, Switzerland
| | - Urs F. Greber
- Department of Molecular Life Sciences, University of Zurich, CH-8057 Zurich, Switzerland
| | - Carmen San Martín
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
| | - Pedro J. de Pablo
- Departament of Condensed Matter Physics, Universidad Autónoma de Madrid and Institute of Condensed Matter Physics (IFIMAC), 28049 Madrid, Spain
| |
Collapse
|
4
|
Molecular Determinants of Human Rhinovirus Infection, Assembly, and Conformational Stability at Capsid Protein Interfaces. J Virol 2022; 96:e0084022. [PMID: 36374110 PMCID: PMC9749468 DOI: 10.1128/jvi.00840-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Human rhinovirus (HRV), one of the most frequent human pathogens, is the major causative agent of common colds. HRVs also cause or exacerbate severe respiratory diseases, such as asthma or chronic obstructive pulmonary disease. Despite the biomedical and socioeconomic importance of this virus, no anti-HRV vaccines or drugs are available yet. Protein-protein interfaces in virus capsids have increasingly been recognized as promising virus-specific targets for the development of antiviral drugs. However, the specific structural elements and residues responsible for the biological functions of these extended capsid regions are largely unknown. In this study, we performed a thorough mutational analysis to determine which particular residues along the capsid interpentamer interfaces are relevant to HRV infection as well as the stage(s) in the viral cycle in which they are involved. The effect on the virion infectivity of the individual mutation to alanine of 32 interfacial residues that, together, removed most of the interpentamer interactions was analyzed. Then, a representative sample that included many of those 32 single mutants were tested for capsid and virion assembly as well as virion conformational stability. The results indicate that most of the interfacial residues, and the interactions they establish, are biologically relevant, largely because of their important roles in virion assembly and/or stability. The HRV interpentamer interface is revealed as an atypical protein-protein interface, in which infectivity-determining residues are distributed at a high density along the entire interface. Implications for a better understanding of the relationship between the molecular structure and function of HRV and the development of novel capsid interface-binding anti-HRV agents are discussed. IMPORTANCE The rising concern about the serious medical and socioeconomic consequences of respiratory infections by HRV has elicited a renewed interest in the development of anti-HRV drugs. The conversion into effective drugs of compounds identified via screening, as well as antiviral drug design, rely on the acquisition of fundamental knowledge about the targeted viral elements and their roles during specific steps of the infectious cycle. The results of this study provide a detailed view on structure-function relationships in a viral capsid protein-protein interface, a promising specific target for antiviral intervention. The high density and scattering of the interfacial residues found to be involved in HRV assembly and/or stability support the possibility that any compound designed to bind any particular site at the interface will inhibit infection by interfering with virion morphogenesis or stabilization of the functional virion conformation.
Collapse
|
5
|
Olszewski D, Georgi F, Murer L, Andriasyan V, Kuttler F, Petkidis A, Witte R, Yakimovich A, Fischer L, Rozanova A, Yamauchi Y, Turcatti G, Greber UF. High-content, arrayed compound screens with rhinovirus, influenza A virus and herpes simplex virus infections. Sci Data 2022; 9:610. [PMID: 36209289 PMCID: PMC9547564 DOI: 10.1038/s41597-022-01733-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022] Open
Abstract
Viruses are genetically and structurally diverse, and outnumber cells by orders of magnitude. They can cause acute and chronic infections, suppress, or exacerbate immunity, or dysregulate survival and growth of cells. To identify chemical agents with pro- or antiviral effects we conducted arrayed high-content image-based multi-cycle infection screens of 1,280 mainly FDA-approved compounds with three human viruses, rhinovirus (RV), influenza A virus (IAV), and herpes simplex virus (HSV) differing in genome organization, composition, presence of an envelope, and tropism. Based on Z’-factors assessing screening quality and Z-scores ranking individual compounds, we identified potent inhibitors and enhancers of infection: the RNA mutagen 5-Azacytidine against RV-A16; the broad-spectrum antimycotic drug Clotrimazole inhibiting IAV-WSN; the chemotherapeutic agent Raltitrexed blocking HSV-1; and Clobetasol enhancing HSV-1. Remarkably, the topical antiseptic compound Aminacrine, which is clinically used against bacterial and fungal agents, inhibited all three viruses. Our data underscore the versatility and potency of image-based, full cycle virus propagation assays in cell-based screenings for antiviral agents. Measurement(s) | transmission of virus • drug toxicity | Technology Type(s) | fluorescence microscopy | Factor Type(s) | virus genotype • cell line • incubation temperature • number of cells seeded/ seeding density • inoculation time • virus input FFU • drug concentration | Sample Characteristic - Organism | Homo sapiens • Rhinovirus A • Influenza A virus • Human alphaherpesvirus 1 | Sample Characteristic - Environment | epithelium | Sample Characteristic - Location | Switzerland |
Collapse
Affiliation(s)
- Dominik Olszewski
- Department of Molecular Life Sciences, University of Zurich (UZH), Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Fanny Georgi
- Department of Molecular Life Sciences, University of Zurich (UZH), Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Luca Murer
- Department of Molecular Life Sciences, University of Zurich (UZH), Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Vardan Andriasyan
- Department of Molecular Life Sciences, University of Zurich (UZH), Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Fabien Kuttler
- Biomolecular Screening Facility, School of Life Sciences, Ecole Polytechnique Fédérale (EPFL) de Lausanne, Station 15, Lausanne, 1015, Switzerland
| | - Anthony Petkidis
- Department of Molecular Life Sciences, University of Zurich (UZH), Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Robert Witte
- Department of Molecular Life Sciences, University of Zurich (UZH), Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Artur Yakimovich
- Center for Advanced Systems Understanding (CASUS), Helmholtz Center Dresden-Rossendorf, Untermarkt 20, 82026, Görlitz, Germany.,Bladder Infection and Immunity Group (BIIG), Department of Renal Medicine, Division of Medicine, University College London, Royal Free Hospital Campus, London, NW3 2PF, United Kingdom
| | - Lucy Fischer
- Department of Molecular Life Sciences, University of Zurich (UZH), Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Alina Rozanova
- Department of Molecular Life Sciences, University of Zurich (UZH), Winterthurerstrasse 190, 8057, Zurich, Switzerland.,University of Bristol, Bristol, BS8 1TH, United Kingdom
| | - Yohei Yamauchi
- University of Bristol, Bristol, BS8 1TH, United Kingdom.,Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Gerardo Turcatti
- Biomolecular Screening Facility, School of Life Sciences, Ecole Polytechnique Fédérale (EPFL) de Lausanne, Station 15, Lausanne, 1015, Switzerland
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich (UZH), Winterthurerstrasse 190, 8057, Zurich, Switzerland.
| |
Collapse
|
6
|
Murer L, Volle R, Andriasyan V, Petkidis A, Gomez-Gonzalez A, Yang L, Meili N, Suomalainen M, Bauer M, Policarpo Sequeira D, Olszewski D, Georgi F, Kuttler F, Turcatti G, Greber UF. Identification of broad anti-coronavirus chemical agents for repurposing against SARS-CoV-2 and variants of concern. CURRENT RESEARCH IN VIROLOGICAL SCIENCE 2022; 3:100019. [PMID: 35072124 PMCID: PMC8760634 DOI: 10.1016/j.crviro.2022.100019] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 01/18/2023]
Abstract
Endemic human coronaviruses (hCoVs) 229E and OC43 cause respiratory disease with recurrent infections, while severe acute respiratory syndrome (SARS)-CoV-2 spreads across the world with impact on health and societies. Here, we report an image-based multicycle infection procedure with α-coronavirus hCoV-229E-eGFP in an arrayed chemical library screen of 5440 clinical and preclinical compounds. Toxicity counter selection and challenge with the β-coronaviruses OC43 and SARS-CoV-2 in tissue culture and human airway epithelial explant cultures (HAEEC) identified four FDA-approved compounds with oral availability. Methylene blue (MB, used for the treatment of methemoglobinemia), Mycophenolic acid (MPA, used in organ transplantation) and the anti-fungal agent Posaconazole (POS) had the broadest anti-CoV spectrum. They inhibited the shedding of SARS-CoV-2 and variants-of-concern (alpha, beta, gamma, delta) from HAEEC in either pre- or post exposure regimens at clinically relevant concentrations. Co-treatment of cultured cells with MB and the FDA-approved SARS-CoV-2 RNA-polymerase inhibitor Remdesivir reduced the effective anti-viral concentrations of MB by 2-fold, and Remdesivir by 4 to 10-fold, indicated by BLISS independence synergy modelling. Neither MB, nor MPA, nor POS affected the cell delivery of SARS-CoV-2 or OC43 (+)sense RNA, but blocked subsequent viral RNA accumulation in cells. Unlike Remdesivir, MB, MPA or POS did not reduce the release of viral RNA in post exposure regimen, thus indicating infection inhibition at a post-replicating step as well. In summary, the data emphasize the power of unbiased, full cycle compound screens to identify and repurpose broadly acting drugs against coronaviruses.
Collapse
Affiliation(s)
- Luca Murer
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Romain Volle
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Vardan Andriasyan
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Anthony Petkidis
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Alfonso Gomez-Gonzalez
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Liliane Yang
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Nicole Meili
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Maarit Suomalainen
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Michael Bauer
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Daniela Policarpo Sequeira
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Dominik Olszewski
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Fanny Georgi
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Fabien Kuttler
- Biomolecular Screening Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 15, 1015, Lausanne, Switzerland
| | - Gerardo Turcatti
- Biomolecular Screening Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 15, 1015, Lausanne, Switzerland
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| |
Collapse
|