1
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Carlson RJ, Patten JJ, Stefanakis G, Soong BY, Radhakrishnan A, Singh A, Thakur N, Amarasinghe GK, Hacohen N, Basler CF, Leung D, Uhler C, Davey RA, Blainey PC. Single-cell image-based genetic screens systematically identify regulators of Ebola virus subcellular infection dynamics. bioRxiv 2024:2024.04.06.588168. [PMID: 38617272 PMCID: PMC11014611 DOI: 10.1101/2024.04.06.588168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Ebola virus (EBOV) is a high-consequence filovirus that gives rise to frequent epidemics with high case fatality rates and few therapeutic options. Here, we applied image-based screening of a genome-wide CRISPR library to systematically identify host cell regulators of Ebola virus infection in 39,085,093 million single cells. Measuring viral RNA and protein levels together with their localization in cells identified over 998 related host factors and provided detailed information about the role of each gene across the virus replication cycle. We trained a deep learning model on single-cell images to associate each host factor with predicted replication steps, and confirmed the predicted relationship for select host factors. Among the findings, we showed that the mitochondrial complex III subunit UQCRB is a post-entry regulator of Ebola virus RNA replication, and demonstrated that UQCRB inhibition with a small molecule reduced overall Ebola virus infection with an IC50 of 5 μM. Using a random forest model, we also identified perturbations that reduced infection by disrupting the equilibrium between viral RNA and protein. One such protein, STRAP, is a spliceosome-associated factor that was found to be closely associated with VP35, a viral protein required for RNA processing. Loss of STRAP expression resulted in a reduction in full-length viral genome production and subsequent production of non-infectious virus particles. Overall, the data produced in this genome-wide high-content single-cell screen and secondary screens in additional cell lines and related filoviruses (MARV and SUDV) revealed new insights about the role of host factors in virus replication and potential new targets for therapeutic intervention.
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Affiliation(s)
- Rebecca J Carlson
- Massachusetts Institute of Technology, Department of Health Sciences and Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - J J Patten
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - George Stefanakis
- Laboratory for Information & Decision Systems, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brian Y Soong
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Adityanarayanan Radhakrishnan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard School of Engineering and Applied Sciences, Cambridge, MA, USA
| | - Avtar Singh
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Naveen Thakur
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gaya K Amarasinghe
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
| | - Christopher F Basler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daisy Leung
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Caroline Uhler
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Laboratory for Information & Decision Systems, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Robert A Davey
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts Institute of Technology, Department of Biological Engineering, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
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2
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Vogel OA, Nafziger E, Sharma A, Pasolli HA, Davey RA, Basler CF. The Role of Ebola Virus VP24 Nuclear Trafficking Signals in Infectious Particle Production. bioRxiv 2024:2024.03.13.584761. [PMID: 38559040 PMCID: PMC10980025 DOI: 10.1101/2024.03.13.584761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Ebola virus (EBOV) protein VP24 carries out at least two critical functions. It promotes condensation of viral nucleocapsids, which is crucial for infectious virus production, and it suppresses interferon (IFN) signaling, which requires interaction with the NPI-1 subfamily of importin-α (IMPA) nuclear transport proteins. Interestingly, over-expressed IMPA leads to VP24 nuclear accumulation and a carboxy-terminus nuclear export signal (NES) has been reported, suggesting that VP24 may undergo nuclear trafficking. For the first time, we demonstrate that NPI-1 IMPA overexpression leads to the nuclear accumulation of VP24 during EBOV infection. To assess the functional impact of nuclear trafficking, we generated tetracistronic minigenomes encoding VP24 nuclear import and/or export signal mutants. The minigenomes, which also encode Renilla luciferase and viral proteins VP40 and GP, were used to generate transcription and replication competent virus-like particles (trVLPs) that can be used to assess EBOV RNA synthesis, gene expression, entry and viral particle production. With this system, we confirmed that NES or IMPA binding site mutations altered VP24 nuclear localization, demonstrating functional trafficking signals. While these mutations minimally affected transcription and replication, the trVLPs exhibited impaired infectivity and formation of shortened nucleocapsids for the IMPA binding mutant. For the NES mutants, infectivity was reduced approximately 1000-fold. The NES mutant could still suppress IFN signaling but failed to promote nucleocapsid formation. To determine whether VP24 nuclear export is required for infectivity, the residues surrounding the wildtype NES were mutated to alanine or the VP24 NES was replaced with the Protein Kinase A Inhibitor NES. While nuclear export remained intact for these mutants, infectivity was severely impaired. These data demonstrate that VP24 undergoes nuclear trafficking and illuminates a separate and critical role for the NES and surrounding sequences in infectivity and nucleocapsid assembly.
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Affiliation(s)
- Olivia A. Vogel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Elias Nafziger
- National Emerging Infectious Diseases Laboratories and Department of Virology, Immunology, and Microbiology, Boston University, Boston, MA 02118
| | - Anurag Sharma
- Electron Microscopy Resource Center, The Rockefeller University, New York ,NY 10065, USA
| | - H. Amalia Pasolli
- Electron Microscopy Resource Center, The Rockefeller University, New York ,NY 10065, USA
| | - Robert A. Davey
- National Emerging Infectious Diseases Laboratories and Department of Virology, Immunology, and Microbiology, Boston University, Boston, MA 02118
| | - Christopher F. Basler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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3
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Xu D, Powell AE, Utz A, Sanyal M, Do J, Patten JJ, Moliva JI, Sullivan NJ, Davey RA, Kim PS. Design of universal Ebola virus vaccine candidates via immunofocusing. Proc Natl Acad Sci U S A 2024; 121:e2316960121. [PMID: 38319964 PMCID: PMC10873634 DOI: 10.1073/pnas.2316960121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/19/2023] [Indexed: 02/08/2024] Open
Abstract
The Ebola virus causes hemorrhagic fever in humans and poses a significant threat to global public health. Although two viral vector vaccines have been approved to prevent Ebola virus disease, they are distributed in the limited ring vaccination setting and only indicated for prevention of infection from orthoebolavirus zairense (EBOV)-one of three orthoebolavirus species that have caused previous outbreaks. Ebola virus glycoprotein GP mediates viral infection and serves as the primary target of neutralizing antibodies. Here, we describe a universal Ebola virus vaccine approach using a structure-guided design of candidates with hyperglycosylation that aims to direct antibody responses away from variable regions and toward conserved epitopes of GP. We first determined the hyperglycosylation landscape on Ebola virus GP and used that to generate hyperglycosylated GP variants with two to four additional glycosylation sites to mask the highly variable glycan cap region. We then created vaccine candidates by displaying wild-type or hyperglycosylated GP variants on ferritin nanoparticles (Fer). Immunization with these antigens elicited potent neutralizing antisera against EBOV in mice. Importantly, we observed consistent cross-neutralizing activity against Bundibugyo virus and Sudan virus from hyperglycosylated GP-Fer with two or three additional glycans. In comparison, elicitation of cross-neutralizing antisera was rare in mice immunized with wild-type GP-Fer. These results demonstrate a potential strategy to develop universal Ebola virus vaccines that confer cross-protective immunity against existing and emerging filovirus species.
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Affiliation(s)
- Duo Xu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Abigail E. Powell
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Ashley Utz
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA94305
- Stanford Biophysics Program, Stanford University School of Medicine, Stanford, CA94305
| | - Mrinmoy Sanyal
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Jonathan Do
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - J. J. Patten
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA02118
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA02118
| | - Juan I. Moliva
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA02118
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA02118
| | - Nancy J. Sullivan
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA02118
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA02118
- Department of Biology, Boston University, Boston, MA02118
| | - Robert A. Davey
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA02118
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA02118
| | - Peter S. Kim
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- Chan Zuckerberg Biohub, San Francisco, CA94158
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Bird GH, Patten JJ, Zavadoski W, Barucci N, Godes M, Moyer BM, Owen CD, DaSilva-Jardine P, Neuberg DS, Bowen RA, Davey RA, Walensky LD. A stapled lipopeptide platform for preventing and treating highly pathogenic viruses of pandemic potential. Nat Commun 2024; 15:274. [PMID: 38177138 PMCID: PMC10766962 DOI: 10.1038/s41467-023-44361-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 12/11/2023] [Indexed: 01/06/2024] Open
Abstract
The continued emergence of highly pathogenic viruses, which either thwart immune- and small molecule-based therapies or lack interventions entirely, mandates alternative approaches, particularly for prompt and facile pre- and post-exposure prophylaxis. Many highly pathogenic viruses, including coronaviruses, employ the six-helix bundle heptad repeat membrane fusion mechanism to achieve infection. Although heptad-repeat-2 decoys can inhibit viral entry by blocking six-helix bundle assembly, the biophysical and pharmacologic liabilities of peptides have hindered their clinical development. Here, we develop a chemically stapled lipopeptide inhibitor of SARS-CoV-2 as proof-of-concept for the platform. We show that our lead compound blocks infection by a spectrum of SARS-CoV-2 variants, exhibits mucosal persistence upon nasal administration, demonstrates enhanced stability compared to prior analogs, and mitigates infection in hamsters. We further demonstrate that our stapled lipopeptide platform yields nanomolar inhibitors of respiratory syncytial, Ebola, and Nipah viruses by targeting heptad-repeat-1 domains, which exhibit strikingly low mutation rates, enabling on-demand therapeutic intervention to combat viral outbreaks.
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Affiliation(s)
- Gregory H Bird
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - J J Patten
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA
| | | | | | - Marina Godes
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Benjamin M Moyer
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Callum D Owen
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA
| | | | - Donna S Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Richard A Bowen
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Robert A Davey
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA
| | - Loren D Walensky
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
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5
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Xu D, Powell AE, Utz A, Sanyal M, Do J, Patten J, Moliva JI, Sullivan NJ, Davey RA, Kim PS. Design of universal Ebola virus vaccine candidates via immunofocusing. bioRxiv 2023:2023.10.14.562364. [PMID: 37904982 PMCID: PMC10614775 DOI: 10.1101/2023.10.14.562364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Ebola virus causes hemorrhagic fever in humans and poses a significant threat to global public health. Although two viral vector vaccines have been approved to prevent Ebola virus disease, they are distributed in the limited ring vaccination setting and only indicated for prevention of infection from orthoebolavirus zairense (EBOV) - one of three orthoebolavirus species that have caused previous outbreaks. Ebola virus glycoprotein GP mediates viral infection and serves as the primary target of neutralizing antibodies. Here we describe a universal Ebola virus vaccine approach using structure-guided design of candidates with hyperglycosylation that aims to direct antibody responses away from variable regions and toward conserved epitopes of GP. We first determined the hyperglycosylation landscape on Ebola virus GP and used that to generate hyperglycosylated GP variants with two to four additional glycosylation sites to mask the highly variable glycan cap region. We then created vaccine candidates by displaying wild-type or hyperglycosylated GP variants on ferritin nanoparticles (Fer). Immunization with these antigens elicited potent neutralizing antisera against EBOV in mice. Importantly, we observed consistent cross-neutralizing activity against Bundibugyo virus and Sudan virus from hyperglycosylated GP-Fer with two or three additional glycans. In comparison, elicitation of cross-neutralizing antisera was rare in mice immunized with wild-type GP-Fer. These results demonstrate a potential strategy to develop universal Ebola virus vaccines that confer cross-protective immunity against existing and emerging filovirus species.
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Affiliation(s)
- Duo Xu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Abigail E. Powell
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Ashley Utz
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA 94305, USA
- Stanford Biophysics Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mrinmoy Sanyal
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Jonathan Do
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - J.J. Patten
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Juan I. Moliva
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Nancy J. Sullivan
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Biology, Boston University, Boston, MA 02118, USA
| | - Robert A. Davey
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Peter S. Kim
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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Wu C, Wagner ND, Moyle AB, Feng A, Sharma N, Stubbs SH, Donahue C, Davey RA, Gross ML, Leung DW, Amarasinghe GK. Disruption of Ebola NP 0VP35 Inclusion Body-like Structures reduce Viral Infection. J Mol Biol 2023; 435:168241. [PMID: 37598728 DOI: 10.1016/j.jmb.2023.168241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 08/04/2023] [Accepted: 08/11/2023] [Indexed: 08/22/2023]
Abstract
Viral inclusion bodies (IBs) are potential sites of viral replication and assembly. How viral IBs form remains poorly defined. Here we describe a combined biophysical and cellular approach to identify the components necessary for IB formation during Ebola virus (EBOV) infection. We find that the eNP0VP35 complex containing Ebola nucleoprotein (eNP) and viral protein 35 (eVP35), the functional equivalents of nucleoprotein (N) and phosphoprotein (P) in non-segmented negative strand viruses (NNSVs), phase separates to form inclusion bodies. Phase separation of eNP0VP35 is reversible and modulated by ionic strength. The multivalency of eVP35, and not eNP, is also critical for phase separation. Furthermore, overexpression of an eVP35 peptide disrupts eNP0VP35 complex formation, leading to reduced frequency of IB formation and limited viral infection. Together, our results show that upon EBOV infection, the eNP0VP35 complex forms the minimum unit to drive IB formation and viral replication.
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Affiliation(s)
- Chao Wu
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
| | - Nicole D Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA; Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Austin B Moyle
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Annie Feng
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Nitin Sharma
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Sarah H Stubbs
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Callie Donahue
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Robert A Davey
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Daisy W Leung
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
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7
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Aguilar-Briseño JA, Elliff JM, Patten JJ, Wilson LR, Davey RA, Bailey AL, Maury WJ. Effect of Interferon Gamma on Ebola Virus Infection of Primary Kupffer Cells and a Kupffer Cell Line. Viruses 2023; 15:2077. [PMID: 37896854 PMCID: PMC10611415 DOI: 10.3390/v15102077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Ebola virus disease (EVD) represents a global health threat. The etiological agents of EVD are six species of Orthoebolaviruses, with Orthoebolavirus zairense (EBOV) having the greatest public health and medical significance. EVD pathogenesis occurs as a result of broad cellular tropism of the virus, robust viral replication and a potent and dysregulated production of cytokines. In vivo, tissue macrophages are some of the earliest cells infected and contribute significantly to virus load and cytokine production. While EBOV is known to infect macrophages and to generate high titer virus in the liver, EBOV infection of liver macrophages, Kupffer cells, has not previously been examined in tissue culture or experimentally manipulated in vivo. Here, we employed primary murine Kupffer cells (KC) and an immortalized murine Kupffer cell line (ImKC) to assess EBOV-eGFP replication in liver macrophages. KCs and ImKCs were highly permissive for EBOV infection and IFN-γ polarization of these cells suppressed their permissiveness to infection. The kinetics of IFN-γ-elicited antiviral responses were examined using a biologically contained model of EBOV infection termed EBOV ΔVP30. The antiviral activity of IFN-γ was transient, but a modest ~3-fold reduction of infection persisted for as long as 6 days post-treatment. To assess the interferon-stimulated gene products (ISGs) responsible for protection, the efficacy of secreted ISGs induced by IFN-γ was evaluated and secreted ISGs failed to block EBOV ΔVP30. Our studies define new cellular tools for the study of EBOV infection that can potentially aid the development of new antiviral therapies. Furthermore, our data underscore the importance of macrophages in EVD pathogenesis and those IFN-γ-elicited ISGs that help to control EBOV infection.
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Affiliation(s)
| | - Jonah M. Elliff
- Graduate Program in Immunology, University of Iowa, Iowa City, IA 52242, USA;
| | - Justin J. Patten
- Department of Virology, Immunology, and Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA; (J.J.P.); (R.A.D.)
| | - Lindsay R. Wilson
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53726, USA; (L.R.W.); (A.L.B.)
| | - Robert A. Davey
- Department of Virology, Immunology, and Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA; (J.J.P.); (R.A.D.)
| | - Adam L. Bailey
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53726, USA; (L.R.W.); (A.L.B.)
| | - Wendy J. Maury
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA;
- Graduate Program in Immunology, University of Iowa, Iowa City, IA 52242, USA;
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8
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Zou C, Yoon H, Park PMC, Patten JJ, Pellman J, Carreiro J, Tsai JM, Li YD, Roy Burman SS, Donovan KA, Gasser J, Sperling AS, Nowak RP, Fischer ES, Davey RA, Ebert BL, Słabicki M. The human E3 ligase RNF185 is a regulator of the SARS-CoV-2 envelope protein. iScience 2023; 26:106601. [PMID: 37095859 PMCID: PMC10082641 DOI: 10.1016/j.isci.2023.106601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 01/31/2023] [Accepted: 03/29/2023] [Indexed: 04/26/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hijacks multiple human proteins during infection and viral replication. To examine whether any viral proteins employ human E3 ubiquitin ligases, we evaluated the stability of SARS-CoV-2 proteins with inhibition of the ubiquitin proteasome pathway. Using genetic screens to dissect the molecular machinery involved in the degradation of candidate viral proteins, we identified human E3 ligase RNF185 as a regulator of protein stability for the SARS-CoV-2 envelope protein. We found that RNF185 and the SARS-CoV-2 envelope co-localize to the endoplasmic reticulum (ER). Finally, we demonstrate that the depletion of RNF185 significantly increases SARS-CoV-2 viral titer in a cellular model. Modulation of this interaction could provide opportunities for novel antiviral therapies.
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Affiliation(s)
- Charles Zou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Hojong Yoon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paul M C Park
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - J J Patten
- Department of Microbiology, Boston University School of Medicine and NEIDL, Boston University, Boston, MA 02118, USA
| | - Jesse Pellman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jeannie Carreiro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan M Tsai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yen-Der Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shourya S Roy Burman
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jessica Gasser
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Adam S Sperling
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Radosław P Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert A Davey
- Department of Microbiology, Boston University School of Medicine and NEIDL, Boston University, Boston, MA 02118, USA
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Mikołaj Słabicki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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9
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Boytz R, Słabicki M, Ramaswamy S, Patten J, Zou C, Meng C, Hurst BL, Wang J, Nowak RP, Yang PL, Sattler M, Stone RM, Griffin JD, Gray NS, Gummuluru S, Davey RA, Weisberg E. Anti-SARS-CoV-2 activity of targeted kinase inhibitors: Repurposing clinically available drugs for COVID-19 therapy. J Med Virol 2023; 95:e28157. [PMID: 36117402 PMCID: PMC9538324 DOI: 10.1002/jmv.28157] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/10/2022] [Accepted: 09/13/2022] [Indexed: 01/17/2023]
Abstract
Coronavirus disease 2019 (COVID-19) remains a major public health concern, and vaccine unavailability, hesitancy, or failure underscore the need for discovery of efficacious antiviral drug therapies. Numerous approved drugs target protein kinases associated with viral life cycle and symptoms of infection. Repurposing of kinase inhibitors is appealing as they have been vetted for safety and are more accessible for COVID-19 treatment. However, an understanding of drug mechanism is needed to improve our understanding of the factors involved in pathogenesis. We tested the in vitro activity of three kinase inhibitors against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), including inhibitors of AXL kinase, a host cell factor that contributes to successful SARS-CoV-2 infection. Using multiple cell-based assays and approaches, gilteritinib, nintedanib, and imatinib were thoroughly evaluated for activity against SARS-CoV-2 variants. Each drug exhibited antiviral activity, but with stark differences in potency, suggesting differences in host dependency for kinase targets. Importantly, for gilteritinib, the amount of compound needed to achieve 90% infection inhibition, at least in part involving blockade of spike protein-mediated viral entry and at concentrations not inducing phospholipidosis (PLD), approached a clinically achievable concentration. Knockout of AXL, a target of gilteritinib and nintedanib, impaired SARS-CoV-2 variant infectivity, supporting a role for AXL in SARS-CoV-2 infection and supporting further investigation of drug-mediated AXL inhibition as a COVID-19 treatment. This study supports further evaluation of AXL-targeting kinase inhibitors as potential antiviral agents and treatments for COVID-19. Additional mechanistic studies are needed to determine underlying differences in virus response.
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Affiliation(s)
- RuthMabel Boytz
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA
| | - Mikołaj Słabicki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sita Ramaswamy
- Department of Microbiology, Boston University, Boston, MA
| | - J.J. Patten
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA
| | - Charles Zou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Chengcheng Meng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brett L. Hurst
- Institute for Antiviral Research, Utah State University, Logan, UT
| | - Jinhua Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Radosław P. Nowak
- Department of Medicine, Harvard Medical School, Boston, MA, USA,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Priscilla L. Yang
- Cancer Biology, Dana-Farber Cancer Institute, MA, USA,Department of Microbiology, Harvard Medical School, Boston, MA, USA; current address Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Martin Sattler
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Richard M. Stone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - James D. Griffin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nathanael S. Gray
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | | | - Robert A. Davey
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA
| | - Ellen Weisberg
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Department of Medicine, Harvard Medical School, Boston, MA, USA
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10
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Boytz R, Seitz S, Gaudiano E, Patten JJ, Keiser PT, Connor JH, Sharpe AH, Davey RA. Inactivation of Ebola Virus and SARS-CoV-2 in Cell Culture Supernatants and Cell Pellets by Gamma Irradiation. Viruses 2022; 15:43. [PMID: 36680083 PMCID: PMC9866162 DOI: 10.3390/v15010043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
Viral pathogens with the potential to cause widespread disruption to human health and society continue to emerge or re-emerge around the world. Research on such viruses often involves high biocontainment laboratories (BSL3 or BSL4), but the development of diagnostics, vaccines and therapeutics often uses assays that are best performed at lower biocontainment. Reliable inactivation is necessary to allow removal of materials to these spaces and to ensure personnel safety. Here, we validate the use of gamma irradiation to inactivate culture supernatants and pellets of cells infected with a representative member of the Filovirus and Coronavirus families. We show that supernatants and cell pellets containing SARS-CoV-2 are readily inactivated with 1.9 MRad, while Ebola virus requires higher doses of 2.6 MRad for supernatants and 3.8 MRad for pellets. While these doses of radiation inactivate viruses, proinflammatory cytokines that are common markers of virus infection are still detected with low losses. The doses required for virus inactivation of supernatants are in line with previously reported values, but the inactivation of cell pellets has not been previously reported and enables new approaches for analysis of protein-based host responses to infection.
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Affiliation(s)
- RuthMabel Boytz
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115, USA
| | - Scott Seitz
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115, USA
| | - Emily Gaudiano
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - J. J. Patten
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115, USA
| | - Patrick T. Keiser
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115, USA
| | - John H. Connor
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115, USA
| | - Arlene H. Sharpe
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert A. Davey
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115, USA
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11
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Edwards MR, Vogel OA, Mori H, Davey RA, Basler CF. Marburg Virus VP30 Is Required for Transcription Initiation at the Glycoprotein Gene. mBio 2022; 13:e0224322. [PMID: 35997284 PMCID: PMC9601197 DOI: 10.1128/mbio.02243-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 08/08/2022] [Indexed: 12/04/2022] Open
Abstract
Marburg virus (MARV) is an enveloped, negative-sense RNA virus from the filovirus family that causes outbreaks of severe, frequently fatal illness in humans. Of the seven MARV proteins, the VP30 protein stands out because it is essential for viral growth but lacks a definitive function. Here, we used model MARV genome RNAs for one or two reporter genes and the MARV VP40, glycoprotein (GP), and VP24 genes to demonstrate that VP30 is dispensable for the transcription of some genes but critical for transcription reinitiation at the GP gene. This results in the loss of the expression of GP and downstream genes and the impaired production of infectious particles when VP30 is absent. Bicistronic minigenome assays demonstrate that the VP40 gene end/GP gene start junction specifically confers VP30 dependence. A region at the GP gene start site predicted to form a stem-loop contributes to VP30 dependence because the replacement of the GP stem-loop with corresponding sequences from the MARV VP35 gene relieves VP30 dependence. Finally, a Cys3-His zinc binding motif characteristic of filovirus VP30 proteins was demonstrated to be critical for reinitiation at GP. These findings address a long-standing gap in our understanding of MARV biology by defining a critical role for VP30 in MARV transcription. IMPORTANCE Marburg virus and Ebola virus encode VP30 proteins. While the role of VP30 in Ebola virus transcription has been well studied, the role of VP30 in the Marburg virus life cycle is not well understood. The work here demonstrates that different gene start sites within the Marburg viral genome have variable levels of dependence on Marburg virus VP30, with its expression being critical for transcription reinitiation at the GP gene start site. These findings address a long-standing question regarding Marburg virus VP30 function and further our understanding of how Marburg virus gene expression is regulated.
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Affiliation(s)
- Megan R. Edwards
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, USA
| | - Olivia A. Vogel
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Hiroyuki Mori
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Robert A. Davey
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Christopher F. Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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12
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Patten J, Keiser PT, Morselli-Gysi D, Menichetti G, Mori H, Donahue CJ, Gan X, Valle ID, Geoghegan-Barek K, Anantpadma M, Boytz R, Berrigan JL, Stubbs SH, Ayazika T, O’Leary C, Jalloh S, Wagner F, Ayehunie S, Elledge SJ, Anderson D, Loscalzo J, Zitnik M, Gummuluru S, Namchuk MN, Barabási AL, Davey RA. Identification of potent inhibitors of SARS-CoV-2 infection by combined pharmacological evaluation and cellular network prioritization. iScience 2022; 25:104925. [PMID: 35992305 PMCID: PMC9374494 DOI: 10.1016/j.isci.2022.104925] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 07/08/2022] [Accepted: 08/08/2022] [Indexed: 11/30/2022] Open
Abstract
Pharmacologically active compounds with known biological targets were evaluated for inhibition of SARS-CoV-2 infection in cell and tissue models to help identify potent classes of active small molecules and to better understand host-virus interactions. We evaluated 6,710 clinical and preclinical compounds targeting 2,183 host proteins by immunocytofluorescence-based screening to identify SARS-CoV-2 infection inhibitors. Computationally integrating relationships between small molecule structure, dose-response antiviral activity, host target, and cell interactome produced cellular networks important for infection. This analysis revealed 389 small molecules with micromolar to low nanomolar activities, representing >12 scaffold classes and 813 host targets. Representatives were evaluated for mechanism of action in stable and primary human cell models with SARS-CoV-2 variants and MERS-CoV. One promising candidate, obatoclax, significantly reduced SARS-CoV-2 viral lung load in mice. Ultimately, this work establishes a rigorous approach for future pharmacological and computational identification of host factor dependencies and treatments for viral diseases.
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Affiliation(s)
- J.J. Patten
- Department of Microbiology, Boston University School of Medicine and NEIDL, Boston University, Boston, MA 02118, USA
| | - Patrick T. Keiser
- Department of Microbiology, Boston University School of Medicine and NEIDL, Boston University, Boston, MA 02118, USA
| | - Deisy Morselli-Gysi
- Network Science Institute, Northeastern University, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Giulia Menichetti
- Network Science Institute, Northeastern University, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hiroyuki Mori
- Department of Microbiology, Boston University School of Medicine and NEIDL, Boston University, Boston, MA 02118, USA
| | - Callie J. Donahue
- Department of Microbiology, Boston University School of Medicine and NEIDL, Boston University, Boston, MA 02118, USA
| | - Xiao Gan
- Network Science Institute, Northeastern University, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Italo do Valle
- Network Science Institute, Northeastern University, Boston, MA 02115, USA
| | - Kathleen Geoghegan-Barek
- Department of Microbiology, Boston University School of Medicine and NEIDL, Boston University, Boston, MA 02118, USA
| | - Manu Anantpadma
- Department of Microbiology, Boston University School of Medicine and NEIDL, Boston University, Boston, MA 02118, USA
| | - RuthMabel Boytz
- Department of Microbiology, Boston University School of Medicine and NEIDL, Boston University, Boston, MA 02118, USA
| | - Jacob L. Berrigan
- Department of Microbiology, Boston University School of Medicine and NEIDL, Boston University, Boston, MA 02118, USA
| | - Sarah H. Stubbs
- Department of Microbiology, Boston University School of Medicine and NEIDL, Boston University, Boston, MA 02118, USA
| | - Tess Ayazika
- Department of Microbiology, Boston University School of Medicine and NEIDL, Boston University, Boston, MA 02118, USA
| | - Colin O’Leary
- Department of Genetics, Program in Virology, Harvard Medical School, Division of Genetics, Brigham and Women’s Hospital, Howard Hughes Medical Institute, Boston, MA, USA
| | - Sallieu Jalloh
- Department of Microbiology, Boston University School of Medicine and NEIDL, Boston University, Boston, MA 02118, USA
| | - Florence Wagner
- Center for the Development of Therapeutics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Stephen J. Elledge
- Department of Genetics, Program in Virology, Harvard Medical School, Division of Genetics, Brigham and Women’s Hospital, Howard Hughes Medical Institute, Boston, MA, USA
| | - Deborah Anderson
- Department of Microbiology, Boston University School of Medicine and NEIDL, Boston University, Boston, MA 02118, USA
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Marinka Zitnik
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Suryaram Gummuluru
- Department of Microbiology, Boston University School of Medicine and NEIDL, Boston University, Boston, MA 02118, USA
| | - Mark N. Namchuk
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Albert-László Barabási
- Network Science Institute, Northeastern University, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Network and Data Science, Central European University, Budapest 1051, Hungary
| | - Robert A. Davey
- Department of Microbiology, Boston University School of Medicine and NEIDL, Boston University, Boston, MA 02118, USA
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13
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Wang LL, Estrada L, Wiggins J, Anantpadma M, Patten JJ, Davey RA, Xiang SH. Ligand-based design of peptide entry inhibitors targeting the endosomal receptor binding site of filoviruses. Antiviral Res 2022; 206:105399. [PMID: 36007601 DOI: 10.1016/j.antiviral.2022.105399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 11/25/2022]
Abstract
Filoviruses enter cells through micropinocytosis and trafficking into the endosomes in which they bind to the receptor Niemann-Pick C1 protein (NPC1) for membrane fusion and entry into the cytoplasm. The endosomal receptor-binding is critical step for filovirus entry. Designing inhibitors to block receptor binding will prevent viral entry. Using available binding structural information from the co-crystal structures of the viral GP with the receptor NPC1 or with monoclonal antibodies, we have conducted structure-based design of peptide inhibitors to target the receptor binding site (RBS). The designed peptides were tested for their inhibition activity against pseudo-typed or replication-competent viruses in a cell-based assay. The results indicate that these peptides exhibited strong activities against both Ebola and Marburg virus infection. It is expected that these peptides can be further developed for therapeutic use to treat filovirus infection and combat the outbreaks.
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Affiliation(s)
- Leah Liu Wang
- School of Veterinary Medicine and Biomedical Sciences, USA; Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Leslie Estrada
- School of Veterinary Medicine and Biomedical Sciences, USA; Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Joshua Wiggins
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA; School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Manu Anantpadma
- Department of Microbiology & National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, 02115, USA
| | - J J Patten
- Department of Microbiology & National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, 02115, USA
| | - Robert A Davey
- Department of Microbiology & National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, 02115, USA
| | - Shi-Hua Xiang
- School of Veterinary Medicine and Biomedical Sciences, USA; Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA.
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14
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Mishra N, Teyra J, Boytz R, Miersch S, Merritt TN, Cardarelli L, Gorelik M, Mihalic F, Jemth P, Davey RA, Sidhu SS, Leung DW, Amarasinghe GK. Development of Monoclonal Antibodies to Detect for SARS-CoV-2 Proteins. J Mol Biol 2022; 434:167583. [PMID: 35405107 PMCID: PMC8993412 DOI: 10.1016/j.jmb.2022.167583] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/29/2022] [Accepted: 04/02/2022] [Indexed: 12/16/2022]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 infection has impacted the world economy and healthcare infrastructure. Key reagents with high specificity to SARS-CoV-2 proteins are currently lacking, which limits our ability to understand the pathophysiology of SARS-CoV-2 infections. To address this need, we initiated a series of studies to generate and develop highly specific antibodies against proteins from SARS-CoV-2 using an antibody engineering platform. These efforts resulted in 18 monoclonal antibodies against nine SARS-CoV-2 proteins. Here we report the characterization of several antibodies, including those that recognize Nsp1, Nsp8, Nsp12, and Orf3b viral proteins. Our validation studies included evaluation for use of antibodies in ELISA, western blots, and immunofluorescence assays (IFA). We expect that availability of these antibodies will enhance our ability to further characterize host-viral interactions, including specific roles played by viral proteins during infection, to acquire a better understanding of the pathophysiology of SARS-CoV-2 infections.
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Affiliation(s)
- Nawneet Mishra
- Department of Pathology and Immunology, Washington University School of Medicine in St Louis, St Louis, MO 63110, USA
| | - Joan Teyra
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | - RuthMabel Boytz
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Shane Miersch
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | - Trudy N Merritt
- Department of Medicine, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Lia Cardarelli
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | - Maryna Gorelik
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | - Filip Mihalic
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, Husargatan 3, 751 23 Uppsala, Sweden
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, Husargatan 3, 751 23 Uppsala, Sweden
| | - Robert A Davey
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | | | - Daisy W Leung
- Department of Medicine, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine in St Louis, St Louis, MO 63110, USA.
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15
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Gourronc FA, Rebagliati M, Kramer-Riesberg B, Fleck AM, Patten JJ, Geohegan-Barek K, Messingham KN, Davey RA, Maury W, Klingelhutz AJ. Adipocytes are susceptible to Ebola Virus infection. Virology 2022; 573:12-22. [DOI: 10.1016/j.virol.2022.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 12/23/2022]
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16
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El-Sayed NS, Jureka AS, Edwards MR, Lohan S, Williams CG, Keiser PT, Davey RA, Totonchy J, Tiwari RK, Basler CF, Parang K. Synthesis and antiviral activity of fatty acyl conjugates of remdesivir against severe acute respiratory syndrome coronavirus 2 and Ebola virus. Eur J Med Chem 2021; 226:113862. [PMID: 34583312 PMCID: PMC8454092 DOI: 10.1016/j.ejmech.2021.113862] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/30/2021] [Accepted: 09/18/2021] [Indexed: 01/18/2023]
Abstract
We report here the synthesis, purification, and characterization of mono- and di-fatty acyl conjugates of remdesivir (RDV) and their in vitro antiviral activity against SAR-CoV-2, an Ebola virus transcription- and replication-competent virus-like particle (trVLP) system, and infectious Ebola virus. The most potent monofatty acyl conjugate was 4b, containing a 4-oxatetradecanolyl at the 3' position. Monofatty acyl conjugates, 3'-O-tetradecanoyl (4a) (IC50(VeroE6) = 2.3 μM; IC50(Calu3) = 0.24 μM), 3'-O-4-oxatetradodecanoyl (4b) (IC50(VeroE6) = 2.0 μM; IC50(Calu3) = 0.18 μM), and 3'-O-(12-ethylthiododecanoyl) (4e) (IC50(VeroE6) = 2.4 μM; IC50(Calu3) = 0.25 μM) derivatives exhibited less activity than RDV (IC50(VeroE6) = 0.85 μM; IC50(Calu3) = 0.06 μM) in both VeroE6 and Calu3 cells. Difatty acylation led to a significant reduction in the antiviral activity of RDV (as shown in conjugates 5a and 5b) against SARS-CoV-2 when compared with monofatty acylation (3a-e and 4a-e). About 77.9% of 4c remained intact after 4 h incubation with human plasma while only 47% of parent RDV was observed at the 2 h time point. The results clearly indicate the effectiveness of fatty acylation to improve the half-life of RDV. The antiviral activities of a number of monofatty acyl conjugates of RDV, such as 3b, 3e, and 4b, were comparable with RDV against the Ebola trVLP system. Meanwhile, the corresponding physical mixtures of RDV and fatty acids 6a and 6b showed 1.6 to 2.2 times less antiviral activity than the corresponding conjugates, 4a and 4c, respectively, against SARS-CoV-2 in VeroE6 cells. A significant reduction in viral RNA synthesis was observed for selected compounds 3a and 4b consistent with the IC50 results. These studies indicate the potential of these compounds as long-acting antiviral agents or prodrugs of RDV.
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Affiliation(s)
- Naglaa Salem El-Sayed
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA, 92618, USA; AJK Biopharmaceutical, 5270 California Ave, Irvine, CA, 92617, USA; Cellulose & Paper Department, National Research Centre, 33 El-Bohouth St. former (El-Tahrir St.), Dokki, Giza P.O. Box, 12622, Egypt
| | - Alexander S Jureka
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, 686 Petit Science Center, Atlanta, GA, 30302, USA
| | - Megan R Edwards
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, 686 Petit Science Center, Atlanta, GA, 30302, USA
| | - Sandeep Lohan
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA, 92618, USA; AJK Biopharmaceutical, 5270 California Ave, Irvine, CA, 92617, USA
| | - Caroline G Williams
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, 686 Petit Science Center, Atlanta, GA, 30302, USA
| | | | - Robert A Davey
- NEIDL, 620 Albany St, Boston University, Boston, MA, 02118, USA
| | - Jennifer Totonchy
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA, 92618, USA
| | - Rakesh K Tiwari
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA, 92618, USA; AJK Biopharmaceutical, 5270 California Ave, Irvine, CA, 92617, USA.
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, 686 Petit Science Center, Atlanta, GA, 30302, USA.
| | - Keykavous Parang
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA, 92618, USA; AJK Biopharmaceutical, 5270 California Ave, Irvine, CA, 92617, USA.
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17
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Batra J, Mori H, Small GI, Anantpadma M, Shtanko O, Mishra N, Zhang M, Liu D, Williams CG, Biedenkopf N, Becker S, Gross ML, Leung DW, Davey RA, Amarasinghe GK, Krogan NJ, Basler CF. Non-canonical proline-tyrosine interactions with multiple host proteins regulate Ebola virus infection. EMBO J 2021; 40:e105658. [PMID: 34260076 DOI: 10.15252/embj.2020105658] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/23/2021] [Accepted: 07/09/2021] [Indexed: 01/08/2023] Open
Abstract
The Ebola virus VP30 protein interacts with the viral nucleoprotein and with host protein RBBP6 via PPxPxY motifs that adopt non-canonical orientations, as compared to other proline-rich motifs. An affinity tag-purification mass spectrometry approach identified additional PPxPxY-containing host proteins hnRNP L, hnRNPUL1, and PEG10, as VP30 interactors. hnRNP L and PEG10, like RBBP6, inhibit viral RNA synthesis and EBOV infection, whereas hnRNPUL1 enhances. RBBP6 and hnRNP L modulate VP30 phosphorylation, increase viral transcription, and exert additive effects on viral RNA synthesis. PEG10 has more modest inhibitory effects on EBOV replication. hnRNPUL1 positively affects viral RNA synthesis but in a VP30-independent manner. Binding studies demonstrate variable capacity of the PPxPxY motifs from these proteins to bind VP30, define PxPPPPxY as an optimal binding motif, and identify the fifth proline and the tyrosine as most critical for interaction. Competition binding and hydrogen-deuterium exchange mass spectrometry studies demonstrate that each protein binds a similar interface on VP30. VP30 therefore presents a novel proline recognition domain that is targeted by multiple host proteins to modulate viral transcription.
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Affiliation(s)
- Jyoti Batra
- J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA
| | - Hiroyuki Mori
- Department of Microbiology, NEIDL, Boston University School of Medicine, Boston, MA, USA
| | - Gabriel I Small
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.,John T. Milliken Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Manu Anantpadma
- Department of Microbiology, NEIDL, Boston University School of Medicine, Boston, MA, USA
| | - Olena Shtanko
- Host-Pathogen Interactions, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Nawneet Mishra
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Mengru Zhang
- Department of Chemistry, Washington University School of Medicine, St. Louis, MO, USA
| | - Dandan Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Caroline G Williams
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Nadine Biedenkopf
- Institute of Virology, Philipps University of Marburg, Marburg, Germany
| | - Stephan Becker
- Institute of Virology, Philipps University of Marburg, Marburg, Germany
| | - Michael L Gross
- Department of Chemistry, Washington University School of Medicine, St. Louis, MO, USA
| | - Daisy W Leung
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.,John T. Milliken Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Robert A Davey
- Department of Microbiology, NEIDL, Boston University School of Medicine, Boston, MA, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Nevan J Krogan
- J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA, USA
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
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18
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Morselli Gysi D, do Valle Í, Zitnik M, Ameli A, Gan X, Varol O, Ghiassian SD, Patten JJ, Davey RA, Loscalzo J, Barabási AL. Network medicine framework for identifying drug-repurposing opportunities for COVID-19. Proc Natl Acad Sci U S A 2021; 118:e2025581118. [PMID: 33906951 PMCID: PMC8126852 DOI: 10.1073/pnas.2025581118] [Citation(s) in RCA: 164] [Impact Index Per Article: 54.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The COVID-19 pandemic has highlighted the need to quickly and reliably prioritize clinically approved compounds for their potential effectiveness for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. Here, we deployed algorithms relying on artificial intelligence, network diffusion, and network proximity, tasking each of them to rank 6,340 drugs for their expected efficacy against SARS-CoV-2. To test the predictions, we used as ground truth 918 drugs experimentally screened in VeroE6 cells, as well as the list of drugs in clinical trials that capture the medical community's assessment of drugs with potential COVID-19 efficacy. We find that no single predictive algorithm offers consistently reliable outcomes across all datasets and metrics. This outcome prompted us to develop a multimodal technology that fuses the predictions of all algorithms, finding that a consensus among the different predictive methods consistently exceeds the performance of the best individual pipelines. We screened in human cells the top-ranked drugs, obtaining a 62% success rate, in contrast to the 0.8% hit rate of nonguided screenings. Of the six drugs that reduced viral infection, four could be directly repurposed to treat COVID-19, proposing novel treatments for COVID-19. We also found that 76 of the 77 drugs that successfully reduced viral infection do not bind the proteins targeted by SARS-CoV-2, indicating that these network drugs rely on network-based mechanisms that cannot be identified using docking-based strategies. These advances offer a methodological pathway to identify repurposable drugs for future pathogens and neglected diseases underserved by the costs and extended timeline of de novo drug development.
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Affiliation(s)
- Deisy Morselli Gysi
- Network Science Institute, Northeastern University, Boston, MA 02115
- Department of Physics, Northeastern University, Boston, MA 02115
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115
| | - Ítalo do Valle
- Network Science Institute, Northeastern University, Boston, MA 02115
- Department of Physics, Northeastern University, Boston, MA 02115
| | - Marinka Zitnik
- Department of Biomedical Informatics, Harvard University, Boston, MA 02115
- Harvard Data Science Initiative, Harvard University, Cambridge, MA 02138
| | - Asher Ameli
- Department of Physics, Northeastern University, Boston, MA 02115
- Data Science Department, Scipher Medicine, Waltham, MA 02453
| | - Xiao Gan
- Network Science Institute, Northeastern University, Boston, MA 02115
- Department of Physics, Northeastern University, Boston, MA 02115
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115
| | - Onur Varol
- Network Science Institute, Northeastern University, Boston, MA 02115
- Department of Physics, Northeastern University, Boston, MA 02115
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
| | | | - J J Patten
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118
| | - Robert A Davey
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115
| | - Albert-László Barabási
- Network Science Institute, Northeastern University, Boston, MA 02115;
- Department of Physics, Northeastern University, Boston, MA 02115
- Department of Network and Data Science, Central European University, Budapest 1051, Hungary
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19
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Mena EL, Donahue CJ, Vaites LP, Li J, Rona G, O'Leary C, Lignitto L, Miwatani-Minter B, Paulo JA, Dhabaria A, Ueberheide B, Gygi SP, Pagano M, Harper JW, Davey RA, Elledge SJ. ORF10-Cullin-2-ZYG11B complex is not required for SARS-CoV-2 infection. Proc Natl Acad Sci U S A 2021; 118:e2023157118. [PMID: 33827988 PMCID: PMC8092598 DOI: 10.1073/pnas.2023157118] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In order to understand the transmission and virulence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), it is necessary to understand the functions of each of the gene products encoded in the viral genome. One feature of the SARS-CoV-2 genome that is not present in related, common coronaviruses is ORF10, a putative 38-amino acid protein-coding gene. Proteomic studies found that ORF10 binds to an E3 ubiquitin ligase containing Cullin-2, Rbx1, Elongin B, Elongin C, and ZYG11B (CRL2ZYG11B). Since CRL2ZYG11B mediates protein degradation, one possible role for ORF10 is to "hijack" CRL2ZYG11B in order to target cellular, antiviral proteins for ubiquitylation and subsequent proteasomal degradation. Here, we investigated whether ORF10 hijacks CRL2ZYG11B or functions in other ways, for example, as an inhibitor or substrate of CRL2ZYG11B While we confirm the ORF10-ZYG11B interaction and show that the N terminus of ORF10 is critical for it, we find no evidence that ORF10 is functioning to inhibit or hijack CRL2ZYG11B Furthermore, ZYG11B and its paralog ZER1 are dispensable for SARS-CoV-2 infection in cultured cells. We conclude that the interaction between ORF10 and CRL2ZYG11B is not relevant for SARS-CoV-2 infection in vitro.
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Affiliation(s)
- Elijah L Mena
- Division of Genetics, Department of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115
- Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115
| | - Callie J Donahue
- Department of Microbiology, National Emerging Infectious Disease Laboratories, Boston University Medical Campus, Boston, MA 02118
| | - Laura Pontano Vaites
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Jie Li
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016
| | - Gergely Rona
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016
| | - Colin O'Leary
- Division of Genetics, Department of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115
| | - Luca Lignitto
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016
| | - Bearach Miwatani-Minter
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016
| | - Joao A Paulo
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Avantika Dhabaria
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY 10016
| | - Beatrix Ueberheide
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY 10016
- Department of Neurology, New York University Grossman School of Medicine, New York, NY 10016
| | - Steven P Gygi
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016;
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016
| | - J Wade Harper
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115;
| | - Robert A Davey
- Department of Microbiology, National Emerging Infectious Disease Laboratories, Boston University Medical Campus, Boston, MA 02118;
| | - Stephen J Elledge
- Division of Genetics, Department of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115;
- Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115
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20
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Patten JJ, Keiser PT, Gysi D, Menichetti G, Mori H, Donahue CJ, Gan X, Do Valle I, Geoghegan-Barek K, Anantpadma M, Berrigan JL, Jalloh S, Ayazika T, Wagner F, Zitnik M, Ayehunie S, Anderson D, Loscalzo J, Gummuluru S, Namchuk MN, Barabasi AL, Davey RA. Multidose evaluation of 6,710 drug repurposing library identifies potent SARS-CoV-2 infection inhibitors In Vitro and In Vivo. bioRxiv 2021. [PMID: 33907750 DOI: 10.1101/2021.04.20.440626] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The SARS-CoV-2 pandemic has caused widespread illness, loss of life, and socioeconomic disruption that is unlikely to resolve until vaccines are widely adopted, and effective therapeutic treatments become established. Here, a well curated and annotated library of 6710 clinical and preclinical molecules, covering diverse chemical scaffolds and known host targets was evaluated for inhibition of SARS-CoV-2 infection in multiple infection models. Multi-concentration, high-content immunocytofluorescence-based screening identified 172 strongly active small molecules, including 52 with submicromolar potencies. The active molecules were extensively triaged by in vitro mechanistic assays, including human primary cell models of infection and the most promising, obatoclax, was tested for in vivo efficacy. Structural and mechanistic classification of compounds revealed known and novel chemotypes and potential host targets involved in each step of the virus replication cycle including BET proteins, microtubule function, mTOR, ER kinases, protein synthesis and ion channel function. In the mouse disease model obatoclax effectively reduced lung virus load by 10-fold. Overall, this work provides an important, publicly accessible, foundation for development of novel treatments for COVID-19, establishes human primary cell-based pharmacological models for evaluation of therapeutics and identifies new insights into SARS-CoV-2 infection mechanisms. Significance A bioinformatically rich library of pharmacologically active small molecules with diverse chemical scaffolds and including known host targets were used to identify hundreds of SARS-CoV-2 replication inhibitors using in vitro, ex vivo, and in vivo models. Extending our previous work, unbiased screening demonstrated a propensity for compounds targeting host proteins that interact with virus proteins. Representatives from multiple chemical classes revealed differences in cell susceptibility, suggesting distinct dependencies on host factors and one, Obatoclax, showed 90% reduction of lung virus loads in the mouse disease model. Our findings and integrated analytical approaches will have important implications for future drug screening and how therapies are developed against SARS-CoV-2 and other viruses.
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21
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Novelli G, Liu J, Biancolella M, Alonzi T, Novelli A, Patten JJ, Cocciadiferro D, Agolini E, Colona VL, Rizzacasa B, Giannini R, Bigio B, Goletti D, Capobianchi MR, Grelli S, Mann J, McKee TD, Cheng K, Amanat F, Krammer F, Guarracino A, Pepe G, Tomino C, Tandjaoui-Lambiotte Y, Uzunhan Y, Tubiana S, Ghosn J, Notarangelo LD, Su HC, Abel L, Cobat A, Elhanan G, Grzymski JJ, Latini A, Sidhu SS, Jain S, Davey RA, Casanova JL, Wei W, Pandolfi PP. Inhibition of HECT E3 ligases as potential therapy for COVID-19. Cell Death Dis 2021; 12:310. [PMID: 33762578 PMCID: PMC7987752 DOI: 10.1038/s41419-021-03513-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 02/01/2023]
Abstract
SARS-CoV-2 is responsible for the ongoing world-wide pandemic which has already taken more than two million lives. Effective treatments are urgently needed. The enzymatic activity of the HECT-E3 ligase family members has been implicated in the cell egression phase of deadly RNA viruses such as Ebola through direct interaction of its VP40 Protein. Here we report that HECT-E3 ligase family members such as NEDD4 and WWP1 interact with and ubiquitylate the SARS-CoV-2 Spike protein. Furthermore, we find that HECT family members are overexpressed in primary samples derived from COVID-19 infected patients and COVID-19 mouse models. Importantly, rare germline activating variants in the NEDD4 and WWP1 genes are associated with severe COVID-19 cases. Critically, I3C, a natural NEDD4 and WWP1 inhibitor from Brassicaceae, displays potent antiviral effects and inhibits viral egression. In conclusion, we identify the HECT family members of E3 ligases as likely novel biomarkers for COVID-19, as well as new potential targets of therapeutic strategy easily testable in clinical trials in view of the established well-tolerated nature of the Brassicaceae natural compounds.
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Affiliation(s)
- Giuseppe Novelli
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133, Rome, Italy.
- IRCCS Neuromed, Pozzilli, (IS), Italy.
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, NV, 89557, USA.
| | - Jing Liu
- Department of Pathology, Beth Israel Deaconess Cancer Center, Harvard Medical School, Boston, MA, 02215, USA
| | | | - Tonino Alonzi
- Translational Research Unit, Department of Epidemiology and Preclinical Research, National Institute for Infectious Diseases Lazzaro Spallanzani - IRCCS, 00149, Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, IRCCS Bambino Gesù Children's Hospital, 00165, Rome, Italy
| | - J J Patten
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Dario Cocciadiferro
- Laboratory of Medical Genetics, IRCCS Bambino Gesù Children's Hospital, 00165, Rome, Italy
| | - Emanuele Agolini
- Laboratory of Medical Genetics, IRCCS Bambino Gesù Children's Hospital, 00165, Rome, Italy
| | - Vito Luigi Colona
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133, Rome, Italy
| | - Barbara Rizzacasa
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133, Rome, Italy
| | - Rosalinda Giannini
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133, Rome, Italy
| | - Benedetta Bigio
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, 10065, USA
| | - Delia Goletti
- Translational Research Unit, Department of Epidemiology and Preclinical Research, National Institute for Infectious Diseases Lazzaro Spallanzani - IRCCS, 00149, Rome, Italy
| | - Maria Rosaria Capobianchi
- Laboratory of Virology, Department of Epidemiology and Preclinical Research, National Institute for Infectious Diseases Lazzaro Spallanzani - IRCCS, 00149, Rome, Italy
| | - Sandro Grelli
- Department of Experimental Medicine, Tor Vergata University of Rome, 00133, Rome, Italy
| | | | | | - Ke Cheng
- HistoWiz Inc, Brooklyn, NY, 11226, USA
| | - Fatima Amanat
- Department of Microbiology, Icahn school of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Florian Krammer
- Department of Microbiology, Icahn school of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Gerardo Pepe
- Department of Biology, Tor Vergata University, 00133, Rome, Italy
| | - Carlo Tomino
- San Raffaele University of Rome, 00166, Rome, Italy
| | - Yacine Tandjaoui-Lambiotte
- Intensive Care Unit, Avicenne Hospital, APHP, Bobigny, France
- INSERM U1272 Hypoxia & Lung, Bobigny, France
| | - Yurdagul Uzunhan
- Pneumology Department, Reference Center for Rare Pulmonary Diseases, Hôpital Avicenne, APHP, Bobigny; INSERM UMR1272, Université Paris 13, Bobigny, France
| | - Sarah Tubiana
- Hôpital Bichat Claude Bernard, APHP, Paris, France
- Centre d'investigation Clinique, Inserm CIC, 1425, Paris, France
| | - Jade Ghosn
- Infection, Antimicrobials, Modelling, Evolution (IAME), INSERM, UMRS1137, University of Paris, Paris, France
- AP-HP, Bichat Claude Bernard Hospital, Infectious and Tropical Disease Department, Paris, France
| | | | - Helen C Su
- Laboratory of Clinical Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, 10065, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Aurélie Cobat
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, 10065, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Gai Elhanan
- Center for Genomic Medicine, Desert Research Institute, Reno, NV, 89502, USA
- Renown Institute for Cancer, Nevada System of Higher Education, Reno, NV, 89502, USA
| | - Joseph J Grzymski
- Center for Genomic Medicine, Desert Research Institute, Reno, NV, 89502, USA
- Renown Institute for Cancer, Nevada System of Higher Education, Reno, NV, 89502, USA
| | - Andrea Latini
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133, Rome, Italy
| | - Sachdev S Sidhu
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada, M5S 3E1 416-946-0863
| | | | - Robert A Davey
- Department of Microbiology Boston University, National Emerging Infectious Diseases Laboratories, Boston, MA, 02118, USA
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, 10065, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- Howard Hughes Medical Institute, New York, NY, USA
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Cancer Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Pier Paolo Pandolfi
- Department of Pathology, Beth Israel Deaconess Cancer Center, Harvard Medical School, Boston, MA, 02215, USA.
- Renown Institute for Cancer, Nevada System of Higher Education, Reno, NV, 89502, USA.
- MBC, Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, TO, 10126, Italy.
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22
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Wang LL, Palermo N, Estrada L, Thompson C, Patten JJ, Anantpadma M, Davey RA, Xiang SH. Identification of filovirus entry inhibitors targeting the endosomal receptor NPC1 binding site. Antiviral Res 2021; 189:105059. [PMID: 33705865 DOI: 10.1016/j.antiviral.2021.105059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/27/2021] [Accepted: 03/04/2021] [Indexed: 12/20/2022]
Abstract
Filoviruses, mainly consisting of Ebola viruses (EBOV) and Marburg viruses (MARV), are enveloped negative-strand RNA viruses which can infect humans to cause severe hemorrhagic fevers and outbreaks with high mortality rates. The filovirus infection is mediated by the interaction of viral envelope glycoprotein (GP) and the human endosomal receptor Niemann-Pick C1 (NPC1). Blocking this interaction will prevent the infection. Therefore, we utilized an In silico screening approach to conduct virtual compound screening against the NPC1 receptor-binding site (RBS). Twenty-six top-hit compounds were purchased and evaluated by in vitro cell based inhibition assays against pseudotyped or replication-competent filoviruses. Two classes (A and U) of compounds were identified to have potent inhibitory activity against both Ebola and Marburg viruses. The IC50 values are in the lower level of micromolar concentrations. One compound (compd-A) was found to have a sub-micromolar IC50 value (0.86 μM) against pseudotyped Marburg virus. The cytotoxicity assay (MTT) indicates that compd-A has a moderate cytotoxicity level but the compd-U has much less toxicity and the CC50 value was about 100 μM. Structure-activity relationship (SAR) study has found some analogs of compd-A and -U have reduced the toxicity and enhanced the inhibitory activity. In conclusion, this work has identified several qualified lead-compounds for further drug development against filovirus infection.
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Affiliation(s)
- Leah Liu Wang
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA; Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Nicholas Palermo
- Computational Chemistry Core Facility, VCR Cores, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Leslie Estrada
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Colton Thompson
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - J J Patten
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 0211, USA
| | - Manu Anantpadma
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 0211, USA
| | - Robert A Davey
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 0211, USA
| | - Shi-Hua Xiang
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA; Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA.
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23
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Gorgulla C, Padmanabha Das KM, Leigh KE, Cespugli M, Fischer PD, Wang ZF, Tesseyre G, Pandita S, Shnapir A, Calderaio A, Gechev M, Rose A, Lewis N, Hutcheson C, Yaffe E, Luxenburg R, Herce HD, Durmaz V, Halazonetis TD, Fackeldey K, Patten J, Chuprina A, Dziuba I, Plekhova A, Moroz Y, Radchenko D, Tarkhanova O, Yavnyuk I, Gruber C, Yust R, Payne D, Näär AM, Namchuk MN, Davey RA, Wagner G, Kinney J, Arthanari H. A multi-pronged approach targeting SARS-CoV-2 proteins using ultra-large virtual screening. iScience 2021; 24:102021. [PMID: 33426509 PMCID: PMC7783459 DOI: 10.1016/j.isci.2020.102021] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/28/2020] [Accepted: 12/29/2020] [Indexed: 02/07/2023] Open
Abstract
The unparalleled global effort to combat the continuing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic over the last year has resulted in promising prophylactic measures. However, a need still exists for cheap, effective therapeutics, and targeting multiple points in the viral life cycle could help tackle the current, as well as future, coronaviruses. Here, we leverage our recently developed, ultra-large-scale in silico screening platform, VirtualFlow, to search for inhibitors that target SARS-CoV-2. In this unprecedented structure-based virtual campaign, we screened roughly 1 billion molecules against each of 40 different target sites on 17 different potential viral and host targets. In addition to targeting the active sites of viral enzymes, we also targeted critical auxiliary sites such as functionally important protein-protein interactions.
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Affiliation(s)
- Christoph Gorgulla
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA 02138, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Krishna M. Padmanabha Das
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kendra E. Leigh
- Max Planck Institute of Biophysics, Frankfurt am Main, Hessen 60438, Germany
| | | | - Patrick D. Fischer
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Saarland 66123, Germany
| | - Zi-Fu Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | | | | | | | - Anthony Calderaio
- VirtualFlow Organization, https://virtual-flow.org/, Boston, MA 02115, USA
| | | | - Alexander Rose
- Mol∗ Consortium, https://molstar.org, San Diego, CA 92109, USA
| | | | | | | | | | - Henry D. Herce
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | | | - Konstantin Fackeldey
- Zuse Institute Berlin (ZIB), Berlin 14195, Germany
- Institute of Mathematics, Technical University Berlin, Berlin 10587, Germany
| | - J.J. Patten
- Department of Microbiology, Boston University Medical School, Boston University, Boston, MA 02118, USA
| | | | | | | | - Yurii Moroz
- Chemspace, Kyiv 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Kyiv 01601, Ukraine
| | - Dmytro Radchenko
- Enamine, Kyiv 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Kyiv 01601, Ukraine
| | | | | | - Christian Gruber
- Innophore GmbH, Graz 8010, Austria
- Institute of Molecular Biosciences, University of Graz, Graz 8010, Austria
| | - Ryan Yust
- Google, Mountain View, CA 94043, USA
| | | | - Anders M. Näär
- Department of Nutritional Sciences & Toxicology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Mark N. Namchuk
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Robert A. Davey
- Department of Microbiology, Boston University Medical School, Boston University, Boston, MA 02118, USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | | | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
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24
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Keiser PT, Anantpadma M, Staples H, Carrion R, Davey RA. Automation of Infectious Focus Assay for Determination of Filovirus Titers and Direct Comparison to Plaque and TCID 50 Assays. Microorganisms 2021; 9:microorganisms9010156. [PMID: 33445537 PMCID: PMC7826780 DOI: 10.3390/microorganisms9010156] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/09/2021] [Accepted: 01/10/2021] [Indexed: 11/16/2022] Open
Abstract
Ongoing efforts to develop effective therapies against filoviruses rely, to different extents, on quantifying the amount of viable virus in samples by plaque, TCID50, and focus assays. Unfortunately, these techniques have inherent variance, and laboratory-specific preferences make direct comparison of data difficult. Additionally, human errors such as operator errors and subjective bias can further compound the differences in outcomes. To overcome these biases, we developed a computer-based automated image-processing method for a focus assay based on the open-source CellProfiler software platform, which enables high-throughput screening of many treatment samples at one time. We compared virus titers calculated using this platform to plaque and TCID50 assays using common stocks of virus for 3 major Filovirus species, Zaire ebolavirus, Sudan ebolavirus, and Marburg marburgvirus with each assay performed by multiple operators on multiple days. We show that plaque assays give comparable findings that differ by less than 3-fold. Focus-forming unit (FFU) and TCID50 assays differ by 10-fold or less from the plaque assays due a higher (FFU) and lower (TCID50) sensitivity. However, reproducibility and accuracy of each assay differs significantly with Neutral Red Agarose Overlay plaque assays and TCID50 with the lowest reproducibility due to subjective analysis and operator error. Both crystal violet methylcellulose overlay plaque assay and focus assays perform best for accuracy and the focus assay performs best for speed and throughput.
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Affiliation(s)
- Patrick T. Keiser
- Department of Microbiology, National Emerging Infectious Disease Laboratories, Boston University, Boston, MA 02215, USA; (P.T.K.); (M.A.)
- Disease Intervention & Prevention, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (H.S.); (R.C.)
| | - Manu Anantpadma
- Department of Microbiology, National Emerging Infectious Disease Laboratories, Boston University, Boston, MA 02215, USA; (P.T.K.); (M.A.)
- Disease Intervention & Prevention, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (H.S.); (R.C.)
| | - Hilary Staples
- Disease Intervention & Prevention, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (H.S.); (R.C.)
| | - Ricardo Carrion
- Disease Intervention & Prevention, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (H.S.); (R.C.)
| | - Robert A. Davey
- Department of Microbiology, National Emerging Infectious Disease Laboratories, Boston University, Boston, MA 02215, USA; (P.T.K.); (M.A.)
- Disease Intervention & Prevention, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (H.S.); (R.C.)
- Correspondence: ; Tel.: +1-617-358-9166
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25
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Luthra P, Anantpadma M, De S, Sourimant J, Davey RA, Plemper RK, Basler CF. High-Throughput Screening Assay to Identify Small Molecule Inhibitors of Marburg Virus VP40 Protein. ACS Infect Dis 2020; 6:2783-2799. [PMID: 32870648 DOI: 10.1021/acsinfecdis.0c00512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Marburg virus (MARV) causes sporadic outbreaks of severe disease with high case fatality rates in humans. To date, neither therapeutics nor prophylactic approaches have been approved for MARV disease. The MARV matrix protein VP40 (mVP40) plays central roles in virus assembly and budding. mVP40 also inhibits interferon signaling by inhibiting the function of Janus kinase 1. This suppression of host antiviral defenses likely contributes to MARV virulence and therefore is a potential therapeutic target. We developed and optimized a cell-based high-throughput screening (HTS) assay in 384-well format to measure mVP40 interferon (IFN) antagonist function such that inhibitors could be identified. We performed a pilot screen of 1280 bioactive compounds and identified 3 hits, azaguanine-8, tosufloxacin hydrochloride, and linezolid, with Z scores > 3 and no significant cytotoxicity. Of these, azaguanine-8 inhibited MARV growth at noncytotoxic concentrations. These data demonstrate the suitability of the HTS mVP40 assay for drug discovery and suggest potential directions for anti-MARV therapeutic development.
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Affiliation(s)
- Priya Luthra
- Trudeau Institute, Saranac Lake, New York 12983-2100, United States
| | - Manu Anantpadma
- WuXi App Tec, Philadelphia, Pennsylvania 19112, United States
| | - Sampriti De
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Julien Sourimant
- Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Robert A. Davey
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts 02118, United States
| | - Richard K. Plemper
- Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Christopher F. Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia 30302-3965, United States
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26
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Cooper L, Schafer A, Li Y, Cheng H, Medegan Fagla B, Shen Z, Nowar R, Dye K, Anantpadma M, Davey RA, Thatcher GRJ, Rong L, Xiong R. Screening and Reverse-Engineering of Estrogen Receptor Ligands as Potent Pan-Filovirus Inhibitors. J Med Chem 2020; 63:11085-11099. [PMID: 32886512 DOI: 10.1021/acs.jmedchem.0c01001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Filoviridae, including Ebola (EBOV) and Marburg (MARV) viruses, are emerging pathogens that pose a serious threat to public health. No agents have been approved to treat filovirus infections, representing a major unmet medical need. The selective estrogen receptor modulator (SERM) toremifene was previously identified from a screen of FDA-approved drugs as a potent EBOV viral entry inhibitor, via binding to EBOV glycoprotein (GP). A focused screen of ER ligands identified ridaifen-B as a potent dual inhibitor of EBOV and MARV. Optimization and reverse-engineering to remove ER activity led to a novel compound 30 (XL-147) showing potent inhibition against infectious EBOV Zaire (0.09 μM) and MARV (0.64 μM). Mutagenesis studies confirmed that inhibition of EBOV viral entry is mediated by the direct interaction with GP. Importantly, compound 30 displayed a broad-spectrum antifilovirus activity against Bundibugyo, Tai Forest, Reston, and Měnglà viruses and is the first submicromolar antiviral agent reported for some of these strains, therefore warranting further development as a pan-filovirus inhibitor.
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Affiliation(s)
- Laura Cooper
- Department of Pharmaceutical Sciences, College of Pharmacy, and UICentre, University of Illinois at Chicago, Chicago, Illinois 60612, United States.,Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Adam Schafer
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Yangfeng Li
- Department of Pharmaceutical Sciences, College of Pharmacy, and UICentre, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Han Cheng
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Bani Medegan Fagla
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Zhengnan Shen
- Department of Pharmaceutical Sciences, College of Pharmacy, and UICentre, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Raghad Nowar
- Department of Pharmaceutical Sciences, College of Pharmacy, and UICentre, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Katherine Dye
- Department of Pharmaceutical Sciences, College of Pharmacy, and UICentre, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Manu Anantpadma
- Department of Microbiology, Boston University School of Medicine, National Emerging Infectious Diseases Laboratories, Boston, Massachusetts 02118, United States.,Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas 78227, United States
| | - Robert A Davey
- Department of Microbiology, Boston University School of Medicine, National Emerging Infectious Diseases Laboratories, Boston, Massachusetts 02118, United States.,Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas 78227, United States
| | - Gregory R J Thatcher
- Department of Pharmaceutical Sciences, College of Pharmacy, and UICentre, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Lijun Rong
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Rui Xiong
- Department of Pharmaceutical Sciences, College of Pharmacy, and UICentre, University of Illinois at Chicago, Chicago, Illinois 60612, United States
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27
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Lane TR, Massey C, Comer JE, Freiberg AN, Zhou H, Dyall J, Holbrook MR, Anantpadma M, Davey RA, Madrid PB, Ekins S. Pyronaridine tetraphosphate efficacy against Ebola virus infection in guinea pig. Antiviral Res 2020; 181:104863. [PMID: 32682926 PMCID: PMC8194506 DOI: 10.1016/j.antiviral.2020.104863] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 12/22/2022]
Abstract
The recent outbreaks of the Ebola virus (EBOV) in Africa have brought global visibility to the shortage of available therapeutic options to treat patients infected with this or closely related viruses. We have recently computationally identified three molecules which have all demonstrated statistically significant efficacy in the mouse model of infection with mouse adapted Ebola virus (ma-EBOV). One of these molecules is the antimalarial pyronaridine tetraphosphate (IC50 range of 0.82-1.30 μM against three strains of EBOV and IC50 range of 1.01-2.72 μM against two strains of Marburg virus (MARV)) which is an approved drug in the European Union and used in combination with artesunate. To date, no small molecule drugs have shown statistically significant efficacy in the guinea pig model of EBOV infection. Pharmacokinetics and range-finding studies in guinea pigs directed us to a single 300 mg/kg or 600 mg/kg oral dose of pyronaridine 1hr after infection. Pyronaridine resulted in statistically significant survival of 40% at 300 mg/kg and protected from a lethal challenge with EBOV. In comparison, oral favipiravir (300 mg/kg dosed once a day) had 43.5% survival. All animals in the vehicle treatment group succumbed to disease by study day 12 (100% mortality). The in vitro metabolism and metabolite identification of pyronaridine and another of our EBOV active molecules, tilorone, suggested significant species differences which may account for the efficacy or lack thereof, respectively in guinea pig. In summary, our studies with pyronaridine demonstrates its utility for repurposing as an antiviral against EBOV and MARV.
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Affiliation(s)
- Thomas R. Lane
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC 27606, USA
| | - Christopher Massey
- Institutional Office of Regulated Nonclinical Studies, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555, USA
| | - Jason E. Comer
- Institutional Office of Regulated Nonclinical Studies, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555, USA
| | - Alexander N. Freiberg
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555, USA
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555, USA
| | - Huanying Zhou
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Julie Dyall
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Michael R. Holbrook
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Manu Anantpadma
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Robert A. Davey
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Peter B. Madrid
- SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC 27606, USA
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28
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Akinci E, Cha M, Lin L, Yeo G, Hamilton MC, Donahue CJ, Bermudez-Cabrera HC, Zanetti LC, Chen M, Barkal SA, Khowpinitchai B, Chu N, Velimirovic M, Jodhani R, Fife JD, Sovrovic M, Cole PA, Davey RA, Cassa CA, Sherwood RI. Elucidation of remdesivir cytotoxicity pathways through genome-wide CRISPR-Cas9 screening and transcriptomics. bioRxiv 2020:2020.08.27.270819. [PMID: 32869031 PMCID: PMC7457617 DOI: 10.1101/2020.08.27.270819] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The adenosine analogue remdesivir has emerged as a front-line antiviral treatment for SARS-CoV-2, with preliminary evidence that it reduces the duration and severity of illness1.Prior clinical studies have identified adverse events1,2, and remdesivir has been shown to inhibit mitochondrial RNA polymerase in biochemical experiments7, yet little is known about the specific genetic pathways involved in cellular remdesivir metabolism and cytotoxicity. Through genome-wide CRISPR-Cas9 screening and RNA sequencing, we show that remdesivir treatment leads to a repression of mitochondrial respiratory activity, and we identify five genes whose loss significantly reduces remdesivir cytotoxicity. In particular, we show that loss of the mitochondrial nucleoside transporter SLC29A3 mitigates remdesivir toxicity without a commensurate decrease in SARS-CoV-2 antiviral potency and that the mitochondrial adenylate kinase AK2 is a remdesivir kinase required for remdesivir efficacy and toxicity. This work elucidates the cellular mechanisms of remdesivir metabolism and provides a candidate gene target to reduce remdesivir cytotoxicity.
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Affiliation(s)
- Ersin Akinci
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
- Department of Agricultural Biotechnology, Faculty of Agriculture, Akdeniz University, Antalya, 07070, Turkey
| | - Minsun Cha
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Lin Lin
- Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Grace Yeo
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Marisa C Hamilton
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Callie J Donahue
- Department of Microbiology, National Emerging Infectious Disease Laboratories, Boston University Medical Campus, Boston, MA 02118, USA
| | - Heysol C Bermudez-Cabrera
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Larissa C Zanetti
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
- Hospital Israelita Albert Einstein, São Paulo, SP 05652-900, Brazil
| | - Maggie Chen
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Sammy A Barkal
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Benyapa Khowpinitchai
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Nam Chu
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Minja Velimirovic
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
- Centre Hospitalier Universitaire de Québec Research Center-Université Laval, Québec, Québec G1V 4G2, Canada
| | - Rikita Jodhani
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - James D Fife
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Miha Sovrovic
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Robert A Davey
- Department of Microbiology, National Emerging Infectious Disease Laboratories, Boston University Medical Campus, Boston, MA 02118, USA
| | - Christopher A Cassa
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Richard I Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
- Hubrecht Institute, 3584 CT Utrecht, the Netherlands
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29
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Gorgulla C, Padmanabha Das KM, Leigh KE, Cespugli M, Fischer PD, Wang ZF, Tesseyre G, Pandita S, Shnapir A, Calderaio A, Gechev M, Rose A, Lewis N, Hutcheson C, Yaffe E, Luxenburg R, Herce HD, Durmaz V, Halazonetis TD, Fackeldey K, Patten JJ, Chuprina A, Dziuba I, Plekhova A, Moroz Y, Radchenko D, Tarkhanova O, Yavnyuk I, Gruber C, Yust R, Payne D, Näär AM, Namchuk MN, Davey RA, Wagner G, Kinney J, Arthanari H. A Multi-Pronged Approach Targeting SARS-CoV-2 Proteins Using Ultra-Large Virtual Screening. ChemRxiv 2020:12682316. [PMID: 33200116 PMCID: PMC7668741 DOI: 10.26434/chemrxiv.12682316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 07/24/2020] [Indexed: 11/23/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), previously known as 2019 novel coronavirus (2019-nCoV), has spread rapidly across the globe, creating an unparalleled global health burden and spurring a deepening economic crisis. As of July 7th, 2020, almost seven months into the outbreak, there are no approved vaccines and few treatments available. Developing drugs that target multiple points in the viral life cycle could serve as a strategy to tackle the current as well as future coronavirus pandemics. Here we leverage the power of our recently developed in silico screening platform, VirtualFlow, to identify inhibitors that target SARS-CoV-2. VirtualFlow is able to efficiently harness the power of computing clusters and cloud-based computing platforms to carry out ultra-large scale virtual screens. In this unprecedented structure-based multi-target virtual screening campaign, we have used VirtualFlow to screen an average of approximately 1 billion molecules against each of 40 different target sites on 17 different potential viral and host targets in the cloud. In addition to targeting the active sites of viral enzymes, we also target critical auxiliary sites such as functionally important protein-protein interaction interfaces. This multi-target approach not only increases the likelihood of finding a potent inhibitor, but could also help identify a collection of anti-coronavirus drugs that would retain efficacy in the face of viral mutation. Drugs belonging to different regimen classes could be combined to develop possible combination therapies, and top hits that bind at highly conserved sites would be potential candidates for further development as coronavirus drugs. Here, we present the top 200 in silico hits for each target site. While in-house experimental validation of some of these compounds is currently underway, we want to make this array of potential inhibitor candidates available to researchers worldwide in consideration of the pressing need for fast-tracked drug development.
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Affiliation(s)
- Christoph Gorgulla
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
- Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| | - Krishna M. Padmanabha Das
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| | | | | | - Patrick D. Fischer
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Zi-Fu Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
| | | | | | | | | | | | | | | | | | | | | | - Henry D. Herce
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| | | | | | - Konstantin Fackeldey
- Zuse Institute Berlin (ZIB), Berlin, Germany
- Institute of Mathematics, Technical University Berlin, Berlin, Germany
| | - Justin J. Patten
- Department of Microbiology, Boston University Medical School, Boston University, Boston, USA
| | | | | | | | - Yurii Moroz
- Chemspace, Kyiv, Ukraine
- Taras Shevchenko National University of Kyiv, Ukraine
| | - Dmytro Radchenko
- Enamine, Kyiv, Ukraine
- Taras Shevchenko National University of Kyiv, Ukraine
| | | | | | - Christian Gruber
- Innophore GmbH, Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Austria
| | | | | | - Anders M. Näär
- Department of Nutritional Sciences & Toxicology, University of California Berkeley, USA
| | - Mark N. Namchuk
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
| | - Robert A. Davey
- Department of Microbiology, Boston University Medical School, Boston University, Boston, USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
| | | | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
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30
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Gaisina IN, Peet NP, Wong L, Schafer AM, Cheng H, Anantpadma M, Davey RA, Thatcher GRJ, Rong L. Discovery and Structural Optimization of 4-(Aminomethyl)benzamides as Potent Entry Inhibitors of Ebola and Marburg Virus Infections. J Med Chem 2020; 63:7211-7225. [PMID: 32490678 DOI: 10.1021/acs.jmedchem.0c00463] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The recent Ebola epidemics in West Africa underscore the great need for effective and practical therapies for future Ebola virus outbreaks. We have discovered a new series of remarkably potent small molecule inhibitors of Ebola virus entry. These 4-(aminomethyl)benzamide-based inhibitors are also effective against Marburg virus. Synthetic routes to these compounds allowed for the preparation of a wide variety of structures, including a conformationally restrained subset of indolines (compounds 41-50). Compounds 20, 23, 32, 33, and 35 are superior inhibitors of Ebola (Mayinga) and Marburg (Angola) infectious viruses. Representative compounds (20, 32, and 35) have shown good metabolic stability in plasma and liver microsomes (rat and human), and 32 did not inhibit CYP3A4 nor CYP2C9. These 4-(aminomethyl)benzamides are suitable for further optimization as inhibitors of filovirus entry, with the potential to be developed as therapeutic agents for the treatment and control of Ebola virus infections.
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Affiliation(s)
- Irina N Gaisina
- UICentre (Drug Discovery @ UIC) and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States.,Chicago BioSolutions Inc., 2242 W Harrison Street, Chicago, Illinois 60612, United States
| | - Norton P Peet
- Chicago BioSolutions Inc., 2242 W Harrison Street, Chicago, Illinois 60612, United States
| | - Letitia Wong
- Chicago BioSolutions Inc., 2242 W Harrison Street, Chicago, Illinois 60612, United States
| | - Adam M Schafer
- College of Medicine, Department of Microbiology and Immunology, University of Illinois at Chicago, 909 S Wolcott Ave, Chicago, Illinois 60612, United States
| | - Han Cheng
- College of Medicine, Department of Microbiology and Immunology, University of Illinois at Chicago, 909 S Wolcott Ave, Chicago, Illinois 60612, United States
| | - Manu Anantpadma
- Texas Biomedical Research Institute, 8715 W Military Drive, San Antonio, Texas 78227, United States.,Department of Microbiology, Boston University, 620 Albany Street, Boston, Massachusetts 02118, United States
| | - Robert A Davey
- Texas Biomedical Research Institute, 8715 W Military Drive, San Antonio, Texas 78227, United States.,Department of Microbiology, Boston University, 620 Albany Street, Boston, Massachusetts 02118, United States
| | - Gregory R J Thatcher
- UICentre (Drug Discovery @ UIC) and Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, United States
| | - Lijun Rong
- College of Medicine, Department of Microbiology and Immunology, University of Illinois at Chicago, 909 S Wolcott Ave, Chicago, Illinois 60612, United States
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31
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Pavlovich SS, Darling T, Hume AJ, Davey RA, Feng F, Mühlberger E, Kepler TB. Egyptian Rousette IFN-ω Subtypes Elicit Distinct Antiviral Effects and Transcriptional Responses in Conspecific Cells. Front Immunol 2020; 11:435. [PMID: 32231668 PMCID: PMC7083018 DOI: 10.3389/fimmu.2020.00435] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/25/2020] [Indexed: 12/15/2022] Open
Abstract
Bats host a number of viruses that cause severe disease in humans without experiencing overt symptoms of disease themselves. While the mechanisms underlying this ability to avoid sickness are not known, deep sequencing studies of bat genomes have uncovered genetic adaptations that may have functional importance in the antiviral response of these animals. Egyptian rousette bats (Rousettus aegyptiacus) are the natural reservoir hosts of Marburg virus (MARV). In contrast to humans, these bats do not become sick when infected with MARV. A striking difference to the human genome is that Egyptian rousettes have an expanded repertoire of IFNW genes. To probe the biological implications of this expansion, we synthesized IFN-ω4 and IFN-ω9 proteins and tested their antiviral activity in Egyptian rousette cells. Both IFN-ω4 and IFN-ω9 showed antiviral activity against RNA viruses, including MARV, with IFN-ω9 being more efficient than IFN-ω4. Using RNA-Seq, we examined the transcriptional response induced by each protein. Although the sets of genes induced by the two IFNs were largely overlapping, IFN-ω9 induced a more rapid and intense response than did IFN-ω4. About 13% of genes induced by IFN-ω treatment are not found in the Interferome or other ISG databases, indicating that they may be uniquely IFN-responsive in this bat.
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Affiliation(s)
- Stephanie S Pavlovich
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States.,National Emerging Infectious Diseases Laboratory, Boston University, Boston, MA, United States
| | - Tamarand Darling
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Adam J Hume
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States.,Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Robert A Davey
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States.,National Emerging Infectious Diseases Laboratory, Boston University, Boston, MA, United States.,Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Feng Feng
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States
| | - Elke Mühlberger
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States.,National Emerging Infectious Diseases Laboratory, Boston University, Boston, MA, United States
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States.,National Emerging Infectious Diseases Laboratory, Boston University, Boston, MA, United States.,Department of Mathematics and Statistics, Boston University, Boston, MA, United States
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32
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Yurdakul C, Avci O, Matlock A, Devaux AJ, Quintero MV, Ozbay E, Davey RA, Connor JH, Karl WC, Tian L, Ünlü MS. High-Throughput, High-Resolution Interferometric Light Microscopy of Biological Nanoparticles. ACS Nano 2020; 14:2002-2013. [PMID: 32003974 DOI: 10.1021/acsnano.9b08512] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Label-free, visible light microscopy is an indispensable tool for studying biological nanoparticles (BNPs). However, conventional imaging techniques have two major challenges: (i) weak contrast due to low-refractive-index difference with the surrounding medium and exceptionally small size and (ii) limited spatial resolution. Advances in interferometric microscopy have overcome the weak contrast limitation and enabled direct detection of BNPs, yet lateral resolution remains as a challenge in studying BNP morphology. Here, we introduce a wide-field interferometric microscopy technique augmented by computational imaging to demonstrate a 2-fold lateral resolution improvement over a large field-of-view (>100 × 100 μm2), enabling simultaneous imaging of more than 104 BNPs at a resolution of ∼150 nm without any labels or sample preparation. We present a rigorous vectorial-optics-based forward model establishing the relationship between the intensity images captured under partially coherent asymmetric illumination and the complex permittivity distribution of nanoparticles. We demonstrate high-throughput morphological visualization of a diverse population of Ebola virus-like particles and a structurally distinct Ebola vaccine candidate. Our approach offers a low-cost and robust label-free imaging platform for high-throughput and high-resolution characterization of a broad size range of BNPs.
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Affiliation(s)
- Celalettin Yurdakul
- Department of Electrical and Computer Engineering , Boston University , Boston , Massachusetts 02215 , United States
| | - Oguzhan Avci
- Department of Electrical and Computer Engineering , Boston University , Boston , Massachusetts 02215 , United States
| | - Alex Matlock
- Department of Electrical and Computer Engineering , Boston University , Boston , Massachusetts 02215 , United States
| | - Alexander J Devaux
- Department of Microbiology and National Infectious Diseases Laboratories , Boston University School of Medicine , Boston , Massachusetts 02118 , United States
| | - Maritza V Quintero
- Department of Biochemistry and Structural Biology , University of Texas Health San Antonio , San Antonio , Texas 78229 , United States
| | - Ekmel Ozbay
- Department of Electrical and Electronics Engineering , Bilkent University , 06800 Ankara , Turkey
| | - Robert A Davey
- Department of Microbiology and National Infectious Diseases Laboratories , Boston University School of Medicine , Boston , Massachusetts 02118 , United States
| | - John H Connor
- Department of Microbiology and National Infectious Diseases Laboratories , Boston University School of Medicine , Boston , Massachusetts 02118 , United States
| | - W Clem Karl
- Department of Electrical and Computer Engineering , Boston University , Boston , Massachusetts 02215 , United States
| | - Lei Tian
- Department of Electrical and Computer Engineering , Boston University , Boston , Massachusetts 02215 , United States
| | - M Selim Ünlü
- Department of Electrical and Computer Engineering , Boston University , Boston , Massachusetts 02215 , United States
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33
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Lane TR, Massey C, Comer JE, Anantpadma M, Freundlich JS, Davey RA, Madrid PB, Ekins S. Repurposing the antimalarial pyronaridine tetraphosphate to protect against Ebola virus infection. PLoS Negl Trop Dis 2019; 13:e0007890. [PMID: 31751347 PMCID: PMC6894882 DOI: 10.1371/journal.pntd.0007890] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [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: 07/12/2019] [Revised: 12/05/2019] [Accepted: 10/29/2019] [Indexed: 12/28/2022] Open
Abstract
Recent outbreaks of the Ebola virus (EBOV) have focused attention on the dire need for antivirals to treat these patients. We identified pyronaridine tetraphosphate as a potential candidate as it is an approved drug in the European Union which is currently used in combination with artesunate as a treatment for malaria (EC50 between 420 nM—1.14 μM against EBOV in HeLa cells). Range-finding studies in mice directed us to a single 75 mg/kg i.p. dose 1 hr after infection which resulted in 100% survival and statistically significantly reduced viremia at study day 3 from a lethal challenge with mouse-adapted EBOV (maEBOV). Further, an EBOV window study suggested we could dose pyronaridine 2 or 24 hrs post-exposure to result in similar efficacy. Analysis of cytokine and chemokine panels suggests that pyronaridine may act as an immunomodulator during an EBOV infection. Our studies with pyronaridine clearly demonstrate potential utility for its repurposing as an antiviral against EBOV and merits further study in larger animal models with the added benefit of already being used as a treatment against malaria. To date there is no approved drug for Ebola Virus infection. Our approach has been to assess drugs that are already approved for other uses in various countries. Using computational models, we have previously identified three such drugs and demonstrated their activity against the Ebola virus in vitro. We now report on the in vitro absorption, metabolism, distribution, excretion and pharmacokinetic properties of one of these molecules, namely the antimalarial pyronaridine. We justify efficacy testing in the mouse model of ebola infection. We also demonstrate that a single dose of this drug is 100% effective against the virus. This study provides important preclinical evaluation of this already approved drug and justifies its selection for larger animal efficacy studies.
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Affiliation(s)
- Thomas R. Lane
- Collaborations Pharmaceuticals, Inc., Raleigh, NC, United States of America
| | - Christopher Massey
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Jason E. Comer
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States of America
- Institutional Office of Regulated Nonclinical Studies, University of Texas Medical Branch, Galveston, TX, United States of America
- Sealy Center for Vaccine Development, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Manu Anantpadma
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | - Joel S. Freundlich
- Departments of Pharmacology, Physiology, and Neuroscience & Medicine, Center for Emerging and Reemerging Pathogens, Rutgers University–New Jersey Medical School, NJ, United States of America
| | - Robert A. Davey
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | | | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., Raleigh, NC, United States of America
- * E-mail:
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34
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Pascal KE, Dudgeon D, Trefry JC, Anantpadma M, Sakurai Y, Murin CD, Turner HL, Fairhurst J, Torres M, Rafique A, Yan Y, Badithe A, Yu K, Potocky T, Bixler SL, Chance TB, Pratt WD, Rossi FD, Shamblin JD, Wollen SE, Zelko JM, Carrion R, Worwa G, Staples HM, Burakov D, Babb R, Chen G, Martin J, Huang TT, Erlandson K, Willis MS, Armstrong K, Dreier TM, Ward AB, Davey RA, Pitt MLM, Lipsich L, Mason P, Olson W, Stahl N, Kyratsous CA. Development of Clinical-Stage Human Monoclonal Antibodies That Treat Advanced Ebola Virus Disease in Nonhuman Primates. J Infect Dis 2019; 218:S612-S626. [PMID: 29860496 PMCID: PMC6249601 DOI: 10.1093/infdis/jiy285] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background For most classes of drugs, rapid development of therapeutics to treat emerging infections is challenged by the timelines needed to identify compounds with the desired efficacy, safety, and pharmacokinetic profiles. Fully human monoclonal antibodies (mAbs) provide an attractive method to overcome many of these hurdles to rapidly produce therapeutics for emerging diseases. Methods In this study, we deployed a platform to generate, test, and develop fully human antibodies to Zaire ebolavirus. We obtained specific anti-Ebola virus (EBOV) antibodies by immunizing VelocImmune mice that use human immunoglobulin variable regions in their humoral responses. Results Of the antibody clones isolated, 3 were selected as best at neutralizing EBOV and triggering FcγRIIIa. Binding studies and negative-stain electron microscopy revealed that the 3 selected antibodies bind to non-overlapping epitopes, including a potentially new protective epitope not targeted by other antibody-based treatments. When combined, a single dose of a cocktail of the 3 antibodies protected nonhuman primates (NHPs) from EBOV disease even after disease symptoms were apparent. Conclusions This antibody cocktail provides complementary mechanisms of actions, incorporates novel specificities, and demonstrates high-level postexposure protection from lethal EBOV disease in NHPs. It is now undergoing testing in normal healthy volunteers in preparation for potential use in future Ebola epidemics.
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Affiliation(s)
| | - Drew Dudgeon
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York
| | - John C Trefry
- Virology Division, US Army Medical Research Institute of Infectious Diseases, Ft. Detrick, Maryland
| | - Manu Anantpadma
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio
| | - Yasuteru Sakurai
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio
| | - Charles D Murin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California
| | - Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California
| | | | | | | | - Ying Yan
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York
| | - Ashok Badithe
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York
| | - Kevin Yu
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York
| | - Terra Potocky
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York
| | - Sandra L Bixler
- Virology Division, US Army Medical Research Institute of Infectious Diseases, Ft. Detrick, Maryland
| | - Taylor B Chance
- Pathology Division, US Army Medical Research Institute of Infectious Diseases, Ft. Detrick, Maryland
| | - William D Pratt
- Virology Division, US Army Medical Research Institute of Infectious Diseases, Ft. Detrick, Maryland
| | - Franco D Rossi
- Center for Aerobiological Sciences, US Army Medical Research Institute of Infectious Diseases, Ft. Detrick, Maryland
| | - Joshua D Shamblin
- Virology Division, US Army Medical Research Institute of Infectious Diseases, Ft. Detrick, Maryland
| | - Suzanne E Wollen
- Virology Division, US Army Medical Research Institute of Infectious Diseases, Ft. Detrick, Maryland
| | - Justine M Zelko
- Virology Division, US Army Medical Research Institute of Infectious Diseases, Ft. Detrick, Maryland
| | - Ricardo Carrion
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio
| | - Gabriella Worwa
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio
| | - Hilary M Staples
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio
| | - Darya Burakov
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York
| | - Robert Babb
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York
| | - Gang Chen
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York
| | - Joel Martin
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York
| | - Tammy T Huang
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York
| | - Karl Erlandson
- Biomedical Advanced Research and Development Authority, Office of the Assistant Secretary for Preparedness and Response, US Department of Health and Human Services, Washington, DC
| | - Melissa S Willis
- Biomedical Advanced Research and Development Authority, Office of the Assistant Secretary for Preparedness and Response, US Department of Health and Human Services, Washington, DC
| | - Kimberly Armstrong
- Biomedical Advanced Research and Development Authority, Office of the Assistant Secretary for Preparedness and Response, US Department of Health and Human Services, Washington, DC
| | - Thomas M Dreier
- Biomedical Advanced Research and Development Authority, Office of the Assistant Secretary for Preparedness and Response, US Department of Health and Human Services, Washington, DC
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California
| | - Robert A Davey
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio
| | - Margaret L M Pitt
- Office of the Commander, US Army Medical Research Institute of Infectious Diseases, Ft. Detrick, Maryland
| | - Leah Lipsich
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York
| | - Peter Mason
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York
| | - William Olson
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York
| | - Neil Stahl
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York
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35
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Abstract
Ebola virus (EBOV) enters host cells by macropinocytosis, a poorly understood process. Recent studies have suggested that cell factors involved in autophagy, an evolutionally conserved pathway leading to the lysosomal degradation of protein aggregates and organelles during cellular stress, also have roles in macropinocytosis. Here, we demonstrate that autophagy-associated proteins are required for trafficking of EBOV into the cell body. Depleting cells of beclin 1, autophagy-related protein 7, or microtubule-associated protein 1A/B light chain 3B (LC3B) abolished EBOV uptake, owing to a block in vesicle formation at the cell surface. Both LC3B-I and LC3B-II interacted with macropinocytic structures. Our work indicates that, although various forms of LC3B possess an inherent ability to associate with forming macropinosomes, LC3B-II is critical for internalization of macropinocytic vesicles and, therefore, EBOV from the cell surface.
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Affiliation(s)
- Olena Shtanko
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio
| | - Ann N Reyes
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio
| | - William T Jackson
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore
| | - Robert A Davey
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio
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36
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Wu Y, Pons V, Noël R, Kali S, Shtanko O, Davey RA, Popoff MR, Tordo N, Gillet D, Cintrat JC, Barbier J. DABMA: A Derivative of ABMA with Improved Broad-Spectrum Inhibitory Activity of Toxins and Viruses. ACS Med Chem Lett 2019; 10:1140-1147. [PMID: 31413797 DOI: 10.1021/acsmedchemlett.9b00155] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 07/02/2019] [Indexed: 02/08/2023] Open
Abstract
The small molecule ABMA has been previously shown to protect cells against multiple toxins and pathogens including virus, intracellular bacteria, and parasite. Its mechanism of action is directly associated with host endolysosomal pathway rather than targeting toxin or pathogen itself. However, the relationship of its broad-spectrum anti-infection activity and chemical structure is not yet resolved. Here, we synthesized a series of derivatives and compared their activities against diphtheria toxin (DT). Dimethyl-ABMA (DABMA), one of the most potent analogs with about 20-fold improvement in protection efficacy against DT, was identified with a similar mechanism of action to ABMA. Moreover, DABMA exhibited enhanced efficacy against Clostridium difficile toxin B (TcdB), Clostridium sordellii lethal toxin (TcsL), Pseudomonas Exotoxin A (PE) as well as Rabies and Ebola viruses. The results revealed a structure-activity relationship of ABMA, which is a starting point for its clinical development as broad-spectrum drug against existing and emerging infectious diseases.
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Affiliation(s)
- Yu Wu
- Service d’Ingénierie Moléculaire des Protéines (SIMOPRO), CEA, Université
Paris-Saclay, LabEx LERMIT, 91191 Gif-sur-Yvette, France
| | - Valérie Pons
- Service de Chimie Bio-organique et de Marquage (SCBM), CEA, Université Paris-Saclay, LabEx LERMIT, 91191 Gif-sur-Yvette, France
| | - Romain Noël
- Service de Chimie Bio-organique et de Marquage (SCBM), CEA, Université Paris-Saclay, LabEx LERMIT, 91191 Gif-sur-Yvette, France
| | - Sabrina Kali
- Antiviral Strategies Unit, Virology Department, Institut Pasteur, 75015 Paris, France
| | - Olena Shtanko
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas 78227, United States
| | - Robert A. Davey
- Department of Microbiology, NEIDL, Boston University, Boston, Massachusetts 02118, United States
| | - Michel R. Popoff
- Bactéries anaérobies et Toxines, Institut Pasteur, 75015 Paris, France
| | - Noël Tordo
- Antiviral Strategies Unit, Virology Department, Institut Pasteur, 75015 Paris, France
| | - Daniel Gillet
- Service d’Ingénierie Moléculaire des Protéines (SIMOPRO), CEA, Université
Paris-Saclay, LabEx LERMIT, 91191 Gif-sur-Yvette, France
| | - Jean-Christophe Cintrat
- Service de Chimie Bio-organique et de Marquage (SCBM), CEA, Université Paris-Saclay, LabEx LERMIT, 91191 Gif-sur-Yvette, France
| | - Julien Barbier
- Service d’Ingénierie Moléculaire des Protéines (SIMOPRO), CEA, Université
Paris-Saclay, LabEx LERMIT, 91191 Gif-sur-Yvette, France
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37
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Anantpadma M, Lane T, Zorn KM, Lingerfelt MA, Clark AM, Freundlich JS, Davey RA, Madrid PB, Ekins S. Ebola Virus Bayesian Machine Learning Models Enable New in Vitro Leads. ACS Omega 2019; 4:2353-2361. [PMID: 30729228 PMCID: PMC6356859 DOI: 10.1021/acsomega.8b02948] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/17/2019] [Indexed: 05/08/2023]
Abstract
We have previously described the first Bayesian machine learning models from FDA-approved drug screens, for identifying compounds active against the Ebola virus (EBOV). These models led to the identification of three active molecules in vitro: tilorone, pyronaridine, and quinacrine. A follow-up study demonstrated that one of these compounds, tilorone, has 100% in vivo efficacy in mice infected with mouse-adapted EBOV at 30 mg/kg/day intraperitoneal. This suggested that we can learn from the published data on EBOV inhibition and use it to select new compounds for testing that are active in vivo. We used these previously built Bayesian machine learning EBOV models alongside our chemical insights for the selection of 12 molecules, absent from the training set, to test for in vitro EBOV inhibition. Nine molecules were directly selected using the model, and eight of these molecules possessed a promising in vitro activity (EC50 < 15 μM). Three further compounds were selected for an in vitro evaluation because they were antimalarials, and compounds of this class like pyronaridine and quinacrine have previously been shown to inhibit EBOV. We identified the antimalarial drug arterolane (IC50 = 4.53 μM) and the anticancer clinical candidate lucanthone (IC50 = 3.27 μM) as novel compounds that have EBOV inhibitory activity in HeLa cells and generally lack cytotoxicity. This work provides further validation for using machine learning and medicinal chemistry expertize to prioritize compounds for testing in vitro prior to more costly in vivo tests. These studies provide further corroboration of this strategy and suggest that it can likely be applied to other pathogens in the future.
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Affiliation(s)
- Manu Anantpadma
- Department
of Virology and Immunology, Texas Biomedical
Research Institute, 8715
West Military Drive, San Antonio, Texas 78227, United
States
| | - Thomas Lane
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Kimberley M. Zorn
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Mary A. Lingerfelt
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Alex M. Clark
- Molecular
Materials Informatics, Inc., 1900 St. Jacques #302, Montreal H3J 2S1, Quebec, Canada
| | - Joel S. Freundlich
- Departments
of Pharmacology, Physiology, and Neuroscience & Medicine, Center
for Emerging and Reemerging Pathogens, Rutgers
University—New Jersey Medical School, 185 South Orange Avenue, Newark, New Jersey 07103, United States
| | - Robert A. Davey
- Department
of Virology and Immunology, Texas Biomedical
Research Institute, 8715
West Military Drive, San Antonio, Texas 78227, United
States
| | - Peter B. Madrid
- SRI
International, 333 Ravenswood Avenue, Menlo Park, California 94025, United States
| | - Sean Ekins
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
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38
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Batra J, Hultquist JF, Liu D, Shtanko O, Von Dollen J, Satkamp L, Jang GM, Luthra P, Schwarz TM, Small GI, Arnett E, Anantpadma M, Reyes A, Leung DW, Kaake R, Haas P, Schmidt CB, Schlesinger LS, LaCount DJ, Davey RA, Amarasinghe GK, Basler CF, Krogan NJ. Protein Interaction Mapping Identifies RBBP6 as a Negative Regulator of Ebola Virus Replication. Cell 2018; 175:1917-1930.e13. [PMID: 30550789 PMCID: PMC6366944 DOI: 10.1016/j.cell.2018.08.044] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 05/17/2018] [Accepted: 08/17/2018] [Indexed: 01/21/2023]
Abstract
Ebola virus (EBOV) infection often results in fatal illness in humans, yet little is known about how EBOV usurps host pathways during infection. To address this, we used affinity tag-purification mass spectrometry (AP-MS) to generate an EBOV-host protein-protein interaction (PPI) map. We uncovered 194 high-confidence EBOV-human PPIs, including one between the viral transcription regulator VP30 and the host ubiquitin ligase RBBP6. Domain mapping identified a 23 amino acid region within RBBP6 that binds to VP30. A crystal structure of the VP30-RBBP6 peptide complex revealed that RBBP6 mimics the viral nucleoprotein (NP) binding to the same interface of VP30. Knockdown of endogenous RBBP6 stimulated viral transcription and increased EBOV replication, whereas overexpression of either RBBP6 or the peptide strongly inhibited both. These results demonstrate the therapeutic potential of biologics that target this interface and identify additional PPIs that may be leveraged for novel therapeutic strategies.
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Affiliation(s)
- Jyoti Batra
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Judd F Hultquist
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Dandan Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63105, USA
| | - Olena Shtanko
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78245, USA
| | - John Von Dollen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Laura Satkamp
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Gwendolyn M Jang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Priya Luthra
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
| | - Toni M Schwarz
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gabriel I Small
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63105, USA
| | - Eusondia Arnett
- Texas Biomedical Research Institute, San Antonio, TX 78245, USA
| | - Manu Anantpadma
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78245, USA
| | - Ann Reyes
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78245, USA
| | - Daisy W Leung
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63105, USA
| | - Robyn Kaake
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Paige Haas
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Carson B Schmidt
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | | | - Douglas J LaCount
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Robert A Davey
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78245, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63105, USA
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA.
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA.
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Cui Q, Cheng H, Xiong R, Zhang G, Du R, Anantpadma M, Davey RA, Rong L. Identification of Diaryl-Quinoline Compounds as Entry Inhibitors of Ebola Virus. Viruses 2018; 10:v10120678. [PMID: 30513600 PMCID: PMC6315506 DOI: 10.3390/v10120678] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 12/14/2022] Open
Abstract
Ebola virus is the causative agent of Ebola virus disease in humans. The lethality of Ebola virus infection is about 50%, supporting the urgent need to develop anti-Ebola drugs. Glycoprotein (GP) is the only surface protein of the Ebola virus, which is functionally critical for the virus to attach and enter the host cells, and is a promising target for anti-Ebola virus drug development. In this study, using the recombinant HIV-1/Ebola pseudovirus platform we previously established, we evaluated a small molecule library containing various quinoline compounds for anti-Ebola virus entry inhibitors. Some of the quinoline compounds specifically inhibited the entry of the Ebola virus. Among them, compound SYL1712 was the most potent Ebola virus entry inhibitor with an IC50 of ~1 μM. The binding of SYL1712 to the vial glycoprotein was computationally modeled and was predicted to interact with specific residues of GP. We used the time of the addition assay to show that compound SYL1712 blocks Ebola GP-mediated entry. Finally, consistent with being an Ebola virus entry inhibitor, compound SYL1712 inhibited infectious Ebola virus replication in tissue culture under biosafety level 4 containment, with an IC50 of 2 μM. In conclusion, we identified several related molecules with a diaryl-quinoline scaffold as potential anti-EBOV entry inhibitors, which can be further optimized for anti-Ebola drug development.
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Affiliation(s)
- Qinghua Cui
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China.
- Department of Microbiology and Immunology, College of Medicine, The University of Illinois at Chicago, Chicago, IL 60612, USA.
| | - Han Cheng
- Department of Microbiology and Immunology, College of Medicine, The University of Illinois at Chicago, Chicago, IL 60612, USA.
| | - Rui Xiong
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, and UICentre, University of Illinois at Chicago, Chicago, IL 60612, USA.
| | - Gang Zhang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China.
| | - Ruikun Du
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China.
| | - Manu Anantpadma
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78227, USA.
- Department of Microbiology, Boston University, National Emerging Infectious Diseases Laboratories, 401P, 620 Albany Street, Boston, MA 02118, USA.
| | - Robert A Davey
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78227, USA.
- Department of Microbiology, Boston University, National Emerging Infectious Diseases Laboratories, 401P, 620 Albany Street, Boston, MA 02118, USA.
| | - Lijun Rong
- Department of Microbiology and Immunology, College of Medicine, The University of Illinois at Chicago, Chicago, IL 60612, USA.
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Luthra P, Naidoo J, Pietzsch CA, De S, Khadka S, Anantpadma M, Williams CG, Edwards MR, Davey RA, Bukreyev A, Ready JM, Basler CF. Inhibiting pyrimidine biosynthesis impairs Ebola virus replication through depletion of nucleoside pools and activation of innate immune responses. Antiviral Res 2018; 158:288-302. [PMID: 30144461 DOI: 10.1016/j.antiviral.2018.08.012] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 08/16/2018] [Accepted: 08/18/2018] [Indexed: 12/27/2022]
Abstract
Specific host pathways that may be targeted therapeutically to inhibit the replication of Ebola virus (EBOV) and other emerging viruses remain incompletely defined. A screen of 200,000 compounds for inhibition of an EBOV minigenome (MG) assay that measures the function of the viral polymerase complex identified as hits several compounds with an amino-tetrahydrocarbazole scaffold. This scaffold was structurally similar to GSK983, a compound previously described as having broad-spectrum antiviral activity due to its impairing de novo pyrimidine biosynthesis through inhibition of dihydroorotate dehydrogenase (DHODH). We generated compound SW835, the racemic version of GSK983 and demonstrated that SW835 and brequinar, another DHODH inhibitor, potently inhibit the MG assay and the replication of EBOV, vesicular stomatitis virus (VSV) and Zika (ZIKV) in vitro. Nucleoside and deoxynucleoside supplementation studies demonstrated that depletion of pyrimidine pools contributes to antiviral activity of these compounds. As reported for other DHODH inhibitors, SW835 and brequinar also induced expression of interferon stimulated genes (ISGs). ISG induction was demonstrated to occur without production of IFNα/β and independently of the IFNα receptor and was not blocked by EBOV-encoded suppressors of IFN signaling pathways. Furthermore, we demonstrated that transcription factor IRF1 is required for this ISG induction, and that IRF1 induction requires the DNA damage response kinase ATM. Therefore, de novo pyrimidine biosynthesis is critical for the replication of EBOV and other RNA viruses and inhibition of this pathway activates an ATM and IRF1-dependent innate immune response that subverts EBOV immune evasion functions.
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Affiliation(s)
- Priya Luthra
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Jacinth Naidoo
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Colette A Pietzsch
- Department of Pathology, Galveston National Laboratory, The University of Texas Medical Branch at Galveston, Galveston, TX, 77555, USA
| | - Sampriti De
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Sudip Khadka
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Manu Anantpadma
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, 78245, USA
| | - Caroline G Williams
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Megan R Edwards
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Robert A Davey
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, 78245, USA
| | - Alexander Bukreyev
- Department of Pathology, Galveston National Laboratory, The University of Texas Medical Branch at Galveston, Galveston, TX, 77555, USA; Department of Microbiology & Immunology, Galveston National Laboratory, The University of Texas Medical Branch at Galveston, Galveston, TX, 77555, USA
| | - Joseph M Ready
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA.
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Tepshi L, Gupta N, Noel R, Goudet A, Hinsinger K, Michau A, Pons V, Abdelkafi H, Secher T, Shima A, Shtanko O, Sakurai Y, Cojean S, Pomel S, Lievin-Le Moal V, Leignel V, Herweg JA, Fischer A, Johannes L, Harrison K, Beard PM, Rudel T, Vacus J, Loiseau PM, Davey RA, Oswald E, Cintrat JC, Barbier J, Gillet D. Retro-2, a small molecule able to protect cells against a broad spectrum of menacing agents: Toxins, viruses, parasites and intracellular bacteria. Toxicon 2018. [DOI: 10.1016/j.toxicon.2017.12.036] [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: 11/30/2022]
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Cui Q, Du R, Anantpadma M, Schafer A, Hou L, Tian J, Davey RA, Cheng H, Rong L. Identification of Ellagic Acid from Plant Rhodiola rosea L. as an Anti-Ebola Virus Entry Inhibitor. Viruses 2018; 10:v10040152. [PMID: 29584652 PMCID: PMC5923446 DOI: 10.3390/v10040152] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 03/23/2018] [Accepted: 03/24/2018] [Indexed: 11/16/2022] Open
Abstract
The recent 2014-2016 West African Ebola virus epidemic underscores the need for the development of novel anti-Ebola therapeutics, due to the high mortality rates of Ebola virus infections and the lack of FDA-approved vaccine or therapy that is available for the prevention and treatment. Traditional Chinese medicines (TCMs) represent a huge reservoir of bioactive chemicals and many TCMs have been shown to have antiviral activities. 373 extracts from 128 TCMs were evaluated using a high throughput assay to screen for inhibitors of Ebola virus cell entry. Extract of Rhodiola rosea displayed specific and potent inhibition against cell entry of both Ebola virus and Marburg virus. In addition, twenty commercial compounds that were isolated from Rhodiola rosea were evaluated using the pseudotyped Ebola virus entry assay, and it was found that ellagic acid and gallic acid, which are two structurally related compounds, are the most effective ones. The activity of the extract and the two pure compounds were validated using infectious Ebola virus. The time-of-addition experiments suggest that, mechanistically, the Rhodiola rosea extract and the effective compounds act at an early step in the infection cycle following initial cell attachment, but prior to viral/cell membrane fusion. Our findings provide evidence that Rhodiola rosea has potent anti-filovirus properties that may be developed as a novel anti-Ebola treatment.
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Affiliation(s)
- Qinghua Cui
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China.
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA.
| | - Ruikun Du
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China.
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA.
| | - Manu Anantpadma
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78227, USA.
| | - Adam Schafer
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA.
| | - Lin Hou
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China.
| | - Jingzhen Tian
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China.
| | - Robert A Davey
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78227, USA.
| | - Han Cheng
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA.
| | - Lijun Rong
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA.
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Abstract
Filovirus entry into cells is complex, perhaps as complex as any viral entry mechanism identified to date. However, over the past 10 years, the important events required for filoviruses to enter into the endosomal compartment and fuse with vesicular membranes have been elucidated (Fig. 1). Here, we highlight the important steps that are required for productive entry of filoviruses into mammalian cells.
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Affiliation(s)
- R A Davey
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - O Shtanko
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - M Anantpadma
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Y Sakurai
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - K Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - W Maury
- Department of Microbiology, The University of Iowa, Iowa City, IA, USA.
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Gupta N, Noël R, Goudet A, Hinsinger K, Michau A, Pons V, Abdelkafi H, Secher T, Shima A, Shtanko O, Sakurai Y, Cojean S, Pomel S, Liévin-Le Moal V, Leignel V, Herweg JA, Fischer A, Johannes L, Harrison K, Beard PM, Clayette P, Le Grand R, Rayner JO, Rudel T, Vacus J, Loiseau PM, Davey RA, Oswald E, Cintrat JC, Barbier J, Gillet D. Inhibitors of retrograde trafficking active against ricin and Shiga toxins also protect cells from several viruses, Leishmania and Chlamydiales. Chem Biol Interact 2016; 267:96-103. [PMID: 27712998 DOI: 10.1016/j.cbi.2016.10.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 08/09/2016] [Accepted: 10/03/2016] [Indexed: 11/25/2022]
Abstract
Medical countermeasures to treat biothreat agent infections require broad-spectrum therapeutics that do not induce agent resistance. A cell-based high-throughput screen (HTS) against ricin toxin combined with hit optimization allowed selection of a family of compounds that meet these requirements. The hit compound Retro-2 and its derivatives have been demonstrated to be safe in vivo in mice even at high doses. Moreover, Retro-2 is an inhibitor of retrograde transport that affects syntaxin-5-dependent toxins and pathogens. As a consequence, it has a broad-spectrum activity that has been demonstrated both in vitro and in vivo against ricin, Shiga toxin-producing O104:H4 entero-hemorrhagic E. coli and Leishmania sp. and in vitro against Ebola, Marburg and poxviruses and Chlamydiales. An effect is anticipated on other toxins or pathogens that use retrograde trafficking and syntaxin-5. Since Retro-2 targets cell components of the host and not directly the pathogen, no selection of resistant pathogens is expected. These lead compounds need now to be developed as drugs for human use.
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Affiliation(s)
- Neetu Gupta
- Institute of Biology and Technology of Saclay (IBITECS), CEA, LabEx LERMIT, Université Paris-Saclay, F-91191, Gif Sur Yvette, France
| | - Romain Noël
- Institute of Biology and Technology of Saclay (IBITECS), CEA, LabEx LERMIT, Université Paris-Saclay, F-91191, Gif Sur Yvette, France
| | - Amélie Goudet
- Institute of Biology and Technology of Saclay (IBITECS), CEA, LabEx LERMIT, Université Paris-Saclay, F-91191, Gif Sur Yvette, France
| | - Karen Hinsinger
- Institute of Biology and Technology of Saclay (IBITECS), CEA, LabEx LERMIT, Université Paris-Saclay, F-91191, Gif Sur Yvette, France
| | - Aurélien Michau
- Institute of Biology and Technology of Saclay (IBITECS), CEA, LabEx LERMIT, Université Paris-Saclay, F-91191, Gif Sur Yvette, France
| | - Valérie Pons
- Institute of Biology and Technology of Saclay (IBITECS), CEA, LabEx LERMIT, Université Paris-Saclay, F-91191, Gif Sur Yvette, France
| | - Hajer Abdelkafi
- Institute of Biology and Technology of Saclay (IBITECS), CEA, LabEx LERMIT, Université Paris-Saclay, F-91191, Gif Sur Yvette, France
| | | | | | - Olena Shtanko
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | | | - Sandrine Cojean
- Antiparasitic Chemotherapy, UMR 8076, CNRS BioCIS, LabEx LERMIT, Université Paris-Sud, Université Paris-Saclay, F-92290, Chatenay-Malabry, France
| | - Sébastien Pomel
- Antiparasitic Chemotherapy, UMR 8076, CNRS BioCIS, LabEx LERMIT, Université Paris-Sud, Université Paris-Saclay, F-92290, Chatenay-Malabry, France
| | - Vanessa Liévin-Le Moal
- Antiparasitic Chemotherapy, UMR 8076, CNRS BioCIS, LabEx LERMIT, Université Paris-Sud, Université Paris-Saclay, F-92290, Chatenay-Malabry, France
| | - Véronique Leignel
- DRUGABILIS (French Research Performer SME), F-92290, Chatenay-Malabry, France
| | - Jo-Ana Herweg
- University of Würzburg, Biocenter, Chair of Microbiology, Am Hubland, D-97074, Würzburg, Germany
| | - Annette Fischer
- University of Würzburg, Biocenter, Chair of Microbiology, Am Hubland, D-97074, Würzburg, Germany
| | - Ludger Johannes
- Institut Curie, PSL Research University, Endocytic Trafficking and Therapeutic Delivery Group, 26 rue d'Ulm, F-75248, Paris Cedex 05, France; CNRS, UMR3666, F-75005, Paris, France; INSERM, U1143, F-75005, Paris, France
| | - Kate Harrison
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, EH25 9RG, United Kingdom
| | - Philippa M Beard
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, EH25 9RG, United Kingdom; The Pirbright Institute, Ash Rd, Pirbright, Surrey GH24 0NF, United Kingdom
| | - Pascal Clayette
- ImmunoPharmacology and Biosafety Laboratory, BERTIN Pharma, CEA, F-92265, Fontenay-aux-Roses, France
| | - Roger Le Grand
- Institute of Emerging Diseases and Innovative Therapies, CEA, U1184, Immunology of Viral Infections and Autoimmune Diseases, Infectious Disease Models and Innovative Therapies Infrastructure, F-92265, Fontenay-aux-Roses, France; INSERM, U1184, F-94276, Le Kremlin-Bicêtre, France; University of Paris South, U1184, F-92265, Fontenay-aux-Roses, France; Vaccine Research Institute, Henri Mondor Hospital, F-94010, Créteil, France
| | - Jonathan O Rayner
- Infectious Disease Research, Southern Research, 2000 Ninth Avenue South, Birmingham, AL 35205, USA
| | - Thomas Rudel
- University of Würzburg, Biocenter, Chair of Microbiology, Am Hubland, D-97074, Würzburg, Germany
| | - Joël Vacus
- DRUGABILIS (French Research Performer SME), F-92290, Chatenay-Malabry, France
| | - Philippe M Loiseau
- Antiparasitic Chemotherapy, UMR 8076, CNRS BioCIS, LabEx LERMIT, Université Paris-Sud, Université Paris-Saclay, F-92290, Chatenay-Malabry, France
| | - Robert A Davey
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | | | - Jean-Christophe Cintrat
- Institute of Biology and Technology of Saclay (IBITECS), CEA, LabEx LERMIT, Université Paris-Saclay, F-91191, Gif Sur Yvette, France
| | - Julien Barbier
- Institute of Biology and Technology of Saclay (IBITECS), CEA, LabEx LERMIT, Université Paris-Saclay, F-91191, Gif Sur Yvette, France
| | - Daniel Gillet
- Institute of Biology and Technology of Saclay (IBITECS), CEA, LabEx LERMIT, Université Paris-Saclay, F-91191, Gif Sur Yvette, France.
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Cap AP, Pidcoke HF, Keil SD, Staples HM, Anantpadma M, Carrion R, Davey RA, Frazer-Abel A, Taylor AL, Gonzales R, Patterson JL, Goodrich RP. Treatment of blood with a pathogen reduction technology using ultraviolet light and riboflavin inactivates Ebola virus in vitro. Transfusion 2016; 56 Suppl 1:S6-15. [PMID: 27001363 DOI: 10.1111/trf.13393] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND Transfusion of plasma from recovered patients after Ebolavirus (EBOV) infection, typically called "convalescent plasma," is an effective treatment for active disease available in endemic areas, but carries the risk of introducing other pathogens, including other strains of EBOV. A pathogen reduction technology using ultraviolet light and riboflavin (UV+RB) is effective against multiple enveloped, negative-sense, single-stranded RNA viruses that are similar in structure to EBOV. We hypothesized that UV+RB is effective against EBOV in blood products without activating complement or reducing protective immunoglobulin titers that are important for the treatment of Ebola virus disease (EVD). STUDY DESIGN AND METHODS Four in vitro experiments were conducted to evaluate effects of UV+RB on green fluorescent protein EBOV (EBOV-GFP), wild-type EBOV in serum, and whole blood, respectively, and on immunoglobulins and complement in plasma. Initial titers for Experiments 1 to 3 were 4.21 log GFP units/mL, 4.96 log infectious units/mL, and 4.23 log plaque-forming units/mL. Conditions tested in the first three experiments included the following: 1-EBOV-GFP plus UV+RB; 2-EBOV-GFP plus RB only; 3-EBOV-GFP plus UV only; 4-EBOV-GFP without RB or UV; 5-virus-free control plus UV only; and 6-virus-free control without RB or UV. RESULTS UV+RB reduced EBOV titers to nondetectable levels in both nonhuman primate serum (≥2.8- to 3.2-log reduction) and human whole blood (≥3.0-log reduction) without decreasing protective antibody titers in human plasma. CONCLUSION Our in vitro results demonstrate that the UV+RB treatment efficiently reduces EBOV titers to below limits of detection in both serum and whole blood. In vivo testing to determine whether UV+RB can improve convalescent blood product safety is indicated.
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Affiliation(s)
- Andrew P Cap
- Coagulation and Blood Research, United States Army Institute of Surgical Research, JBSA Fort Sam Houston, Texas
| | - Heather F Pidcoke
- Coagulation and Blood Research, United States Army Institute of Surgical Research, JBSA Fort Sam Houston, Texas
| | | | - Hilary M Staples
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas
| | - Manu Anantpadma
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas
| | - Ricardo Carrion
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas
| | - Robert A Davey
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas
| | | | - Audra L Taylor
- United States Army Blood Program, JBSA Fort Sam Houston, Texas
| | - Richard Gonzales
- Terumo BCT, Lakewood, Colorado.,United States Army Blood Program, JBSA Fort Sam Houston, Texas
| | - Jean L Patterson
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas
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Wang B, Kluwe CA, Lungu OI, DeKosky BJ, Kerr SA, Johnson EL, Tanno H, Lee CH, Jung J, Rezigh AB, Carroll SM, Reyes AN, Bentz JR, Villanueva I, Altman AL, Davey RA, Ellington AD, Georgiou G. Erratum: Corrigendum: Facile Discovery of a Diverse Panel of Anti-Ebola Virus Antibodies by Immune Repertoire Mining. Sci Rep 2016; 6:27229. [PMID: 27282782 PMCID: PMC4901487 DOI: 10.1038/srep27229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Ekins S, Freundlich JS, Clark AM, Anantpadma M, Davey RA, Madrid P. Machine learning models identify molecules active against the Ebola virus in vitro. F1000Res 2016; 4:1091. [PMID: 26834994 DOI: 10.12688/f1000research.7217.2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/23/2015] [Indexed: 12/15/2022] Open
Abstract
The search for small molecule inhibitors of Ebola virus (EBOV) has led to several high throughput screens over the past 3 years. These have identified a range of FDA-approved active pharmaceutical ingredients (APIs) with anti-EBOV activity in vitro and several of which are also active in a mouse infection model. There are millions of additional commercially-available molecules that could be screened for potential activities as anti-EBOV compounds. One way to prioritize compounds for testing is to generate computational models based on the high throughput screening data and then virtually screen compound libraries. In the current study, we have generated Bayesian machine learning models with viral pseudotype entry assay and the EBOV replication assay data. We have validated the models internally and externally. We have also used these models to computationally score the MicroSource library of drugs to select those likely to be potential inhibitors. Three of the highest scoring molecules that were not in the model training sets, quinacrine, pyronaridine and tilorone, were tested in vitro and had EC50 values of 350, 420 and 230 nM, respectively. Pyronaridine is a component of a combination therapy for malaria that was recently approved by the European Medicines Agency, which may make it more readily accessible for clinical testing. Like other known antimalarial drugs active against EBOV, it shares the 4-aminoquinoline scaffold. Tilorone, is an investigational antiviral agent that has shown a broad array of biological activities including cell growth inhibition in cancer cells, antifibrotic properties, α7 nicotinic receptor agonist activity, radioprotective activity and activation of hypoxia inducible factor-1. Quinacrine is an antimalarial but also has use as an anthelmintic. Our results suggest data sets with less than 1,000 molecules can produce validated machine learning models that can in turn be utilized to identify novel EBOV inhibitors in vitro.
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Affiliation(s)
- Sean Ekins
- Collaborations in Chemistry, Fuquay-Varina, NC, 27526, USA
- Collaborations Pharmaceuticals Inc, Fuquay-Varina, NC, 27526, USA
- Collaborative Drug Discovery, Burlingame, CA, 94010, USA
| | - Joel S Freundlich
- Departments of Pharmacology & Physiology and Medicine, Center for Emerging and Reemerging Pathogens, UMDNJ, New Jersey Medical School, Newark, NJ, 07103, USA
| | - Alex M Clark
- Molecular Materials Informatics, Inc., Montreal, 94025, Canada
| | - Manu Anantpadma
- Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Robert A Davey
- Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
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Rhein BA, Powers LS, Rogers K, Anantpadma M, Singh BK, Sakurai Y, Bair T, Miller-Hunt C, Sinn P, Davey RA, Monick MM, Maury W. Interferon-γ Inhibits Ebola Virus Infection. PLoS Pathog 2015; 11:e1005263. [PMID: 26562011 PMCID: PMC4643030 DOI: 10.1371/journal.ppat.1005263] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [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: 04/19/2015] [Accepted: 10/19/2015] [Indexed: 12/31/2022] Open
Abstract
Ebola virus outbreaks, such as the 2014 Makona epidemic in West Africa, are episodic and deadly. Filovirus antivirals are currently not clinically available. Our findings suggest interferon gamma, an FDA-approved drug, may serve as a novel and effective prophylactic or treatment option. Using mouse-adapted Ebola virus, we found that murine interferon gamma administered 24 hours before or after infection robustly protects lethally-challenged mice and reduces morbidity and serum viral titers. Furthermore, we demonstrated that interferon gamma profoundly inhibits Ebola virus infection of macrophages, an early cellular target of infection. As early as six hours following in vitro infection, Ebola virus RNA levels in interferon gamma-treated macrophages were lower than in infected, untreated cells. Addition of the protein synthesis inhibitor, cycloheximide, to interferon gamma-treated macrophages did not further reduce viral RNA levels, suggesting that interferon gamma blocks life cycle events that require protein synthesis such as virus replication. Microarray studies with interferon gamma-treated human macrophages identified more than 160 interferon-stimulated genes. Ectopic expression of a select group of these genes inhibited Ebola virus infection. These studies provide new potential avenues for antiviral targeting as these genes that have not previously appreciated to inhibit negative strand RNA viruses and specifically Ebola virus infection. As treatment of interferon gamma robustly protects mice from lethal Ebola virus infection, we propose that interferon gamma should be further evaluated for its efficacy as a prophylactic and/or therapeutic strategy against filoviruses. Use of this FDA-approved drug could rapidly be deployed during future outbreaks. Filovirus outbreaks occur sporadically, but with increasing frequency. With no current approved filovirus therapeutics, the 2014 Makona Ebola virus epidemic in Guinea, Sierra Leone and Liberia emphasizes the need for effective treatments against this highly pathogenic family of viruses. The use of this FDA-approved drug to inhibit Ebola virus infection would allow rapid implementation of a novel antiviral therapy for future crises. Interferon gamma elicits an antiviral state in antigen-presenting cells and stimulates cellular immune responses. We demonstrate that interferon gamma profoundly inhibits Ebola virus infection of macrophages, which are early cellular targets of Ebola virus. We also identify novel interferon gamma-stimulated genes in human macrophage populations that have not been previously appreciated to inhibit filoviruses or other negative strand RNA viruses. Finally and most importantly, we show that interferon gamma given 24 hours prior to or after virus infection protects mice from lethal Ebola virus challenge, suggesting that this drug may serve as an effective prophylactic and/or therapeutic strategy against this deadly virus.
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Affiliation(s)
- Bethany A. Rhein
- Department of Microbiology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Linda S. Powers
- Department of Internal Medicine, The University of Iowa, Iowa City, Iowa, United States of America
| | - Kai Rogers
- Department of Microbiology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Manu Anantpadma
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Brajesh K. Singh
- Department of Pediatrics, The University of Iowa, Iowa City, Iowa, United States of America
| | - Yasuteru Sakurai
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Thomas Bair
- Iowa Institute for Human Genetics, The University of Iowa, Iowa City, Iowa, United States of America
| | - Catherine Miller-Hunt
- Department of Microbiology, The University of Iowa, Iowa City, Iowa, United States of America
| | - Patrick Sinn
- Department of Pediatrics, The University of Iowa, Iowa City, Iowa, United States of America
| | - Robert A. Davey
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Martha M. Monick
- Department of Internal Medicine, The University of Iowa, Iowa City, Iowa, United States of America
| | - Wendy Maury
- Department of Microbiology, The University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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49
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Ekins S, Freundlich JS, Clark AM, Anantpadma M, Davey RA, Madrid P. Machine learning models identify molecules active against the Ebola virus in vitro. F1000Res 2015; 4:1091. [PMID: 26834994 DOI: 10.12688/f1000research.7217.1] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/15/2015] [Indexed: 12/23/2022] Open
Abstract
The search for small molecule inhibitors of Ebola virus (EBOV) has led to several high throughput screens over the past 3 years. These have identified a range of FDA-approved active pharmaceutical ingredients (APIs) with anti-EBOV activity in vitro and several of which are also active in a mouse infection model. There are millions of additional commercially-available molecules that could be screened for potential activities as anti-EBOV compounds. One way to prioritize compounds for testing is to generate computational models based on the high throughput screening data and then virtually screen compound libraries. In the current study, we have generated Bayesian machine learning models with viral pseudotype entry assay and the EBOV replication assay data. We have validated the models internally and externally. We have also used these models to computationally score the MicroSource library of drugs to select those likely to be potential inhibitors. Three of the highest scoring molecules that were not in the model training sets, quinacrine, pyronaridine and tilorone, were tested in vitro and had EC 50 values of 350, 420 and 230 nM, respectively. Pyronaridine is a component of a combination therapy for malaria that was recently approved by the European Medicines Agency, which may make it more readily accessible for clinical testing. Like other known antimalarial drugs active against EBOV, it shares the 4-aminoquinoline scaffold. Tilorone, is an investigational antiviral agent that has shown a broad array of biological activities including cell growth inhibition in cancer cells, antifibrotic properties, α7 nicotinic receptor agonist activity, radioprotective activity and activation of hypoxia inducible factor-1. Quinacrine is an antimalarial but also has use as an anthelmintic. Our results suggest data sets with less than 1,000 molecules can produce validated machine learning models that can in turn be utilized to identify novel EBOV inhibitors in vitro.
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Affiliation(s)
- Sean Ekins
- Collaborations in Chemistry, Fuquay-Varina, NC, 27526, USA.,Collaborations Pharmaceuticals Inc, Fuquay-Varina, NC, 27526, USA.,Collaborative Drug Discovery, Burlingame, CA, 94010, USA
| | - Joel S Freundlich
- Departments of Pharmacology & Physiology and Medicine, Center for Emerging and Reemerging Pathogens, UMDNJ, New Jersey Medical School, Newark, NJ, 07103, USA
| | - Alex M Clark
- Molecular Materials Informatics, Inc., Montreal, 94025, Canada
| | - Manu Anantpadma
- Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Robert A Davey
- Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
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50
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Abstract
The search for small molecule inhibitors of Ebola virus (EBOV) has led to several high throughput screens over the past 3 years. These have identified a range of FDA-approved active pharmaceutical ingredients (APIs) with anti-EBOV activity
in vitro and several of which are also active in a mouse infection model. There are millions of additional commercially-available molecules that could be screened for potential activities as anti-EBOV compounds. One way to prioritize compounds for testing is to generate computational models based on the high throughput screening data and then virtually screen compound libraries. In the current study, we have generated Bayesian machine learning models with viral pseudotype entry assay and the EBOV replication assay data. We have validated the models internally and externally. We have also used these models to computationally score the MicroSource library of drugs to select those likely to be potential inhibitors. Three of the highest scoring molecules that were not in the model training sets, quinacrine, pyronaridine and tilorone, were tested
in vitro and had EC
50 values of 350, 420 and 230 nM, respectively. Pyronaridine is a component of a combination therapy for malaria that was recently approved by the European Medicines Agency, which may make it more readily accessible for clinical testing. Like other known antimalarial drugs active against EBOV, it shares the 4-aminoquinoline scaffold. Tilorone, is an investigational antiviral agent that has shown a broad array of biological activities including cell growth inhibition in cancer cells, antifibrotic properties, α7 nicotinic receptor agonist activity, radioprotective activity and activation of hypoxia inducible factor-1. Quinacrine is an antimalarial but also has use as an anthelmintic. Our results suggest data sets with less than 1,000 molecules can produce validated machine learning models that can in turn be utilized to identify novel EBOV inhibitors
in vitro.
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Affiliation(s)
- Sean Ekins
- Collaborations in Chemistry, Fuquay-Varina, NC, 27526, USA.,Collaborations Pharmaceuticals Inc, Fuquay-Varina, NC, 27526, USA.,Collaborative Drug Discovery, Burlingame, CA, 94010, USA
| | - Joel S Freundlich
- Departments of Pharmacology & Physiology and Medicine, Center for Emerging and Reemerging Pathogens, UMDNJ, New Jersey Medical School, Newark, NJ, 07103, USA
| | - Alex M Clark
- Molecular Materials Informatics, Inc., Montreal, 94025, Canada
| | - Manu Anantpadma
- Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Robert A Davey
- Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
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