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Parthasarathy S, Saenjamsai P, Hao H, Ferkul A, Pfannenstiel JJ, Suder EL, Bejan DS, Chen Y, Schwarting N, Aikawa M, Muhlberger E, Orozco RC, Sullivan CS, Cohen MS, Davido DJ, Hume AJ, Fehr AR. PARP14 is pro- and anti-viral host factor that promotes IFN production and affects the replication of multiple viruses. bioRxiv 2024:2024.04.26.591186. [PMID: 38712082 PMCID: PMC11071520 DOI: 10.1101/2024.04.26.591186] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
PARP14 is a 203 kDa multi-domain protein that is primarily known as an ADP-ribosyltransferase, and is involved in a variety of cellular functions including DNA damage, microglial activation, inflammation, and cancer progression. In addition, PARP14 is upregulated by interferon (IFN), indicating a role in the antiviral response. Furthermore, PARP14 has evolved under positive selection, again indicating that it is involved in host-pathogen conflict. We found that PARP14 is required for increased IFN-I production in response to coronavirus infection lacking ADP-ribosylhydrolase (ARH) activity and poly(I:C), however, whether it has direct antiviral function remains unclear. Here we demonstrate that the catalytic activity of PARP14 enhances IFN-I and IFN-III responses and restricts ARH-deficient murine hepatitis virus (MHV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication. To determine if PARP14's antiviral functions extended beyond CoVs, we tested the ability of herpes simplex virus 1 (HSV-1) and several negative-sense RNA viruses, including vesicular stomatitis virus (VSV), Ebola virus (EBOV), and Nipah virus (NiV), to infect A549 PARP14 knockout (KO) cells. HSV-1 had increased replication in PARP14 KO cells, indicating that PARP14 restricts HSV-1 replication. In contrast, PARP14 was critical for the efficient infection of VSV, EBOV, and NiV, with EBOV infectivity at less than 1% of WT cells. A PARP14 active site inhibitor had no impact on HSV-1 or EBOV infection, indicating that its effect on these viruses was independent of its catalytic activity. These data demonstrate that PARP14 promotes IFN production and has both pro- and anti-viral functions targeting multiple viruses.
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Affiliation(s)
| | - Pradtahna Saenjamsai
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Hongping Hao
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Anna Ferkul
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | | | - Ellen L. Suder
- Department of Microbiology, Boston University School of Medicine, Boston, MA, 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA
- Center for Emerging Infectious Diseases Policy & Research, Boston University, Boston, MA, 02118, USA
| | - Daniel S. Bejan
- Department of Chemical Physiology and Biochemistry, Oregon Health Sciences University, Portland, OR, 97239, USA
| | - Yating Chen
- Department of Molecular Biosciences, University of Texas, Austin, TX, 78712, USA
| | - Nancy Schwarting
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Masanori Aikawa
- Center for Excellence in Vascular Biology (P.K.J., M.A., E.A.), Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Center for Interdisciplinary Cardiovascular Sciences (M.A., E.A.), Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Channing Division of Network Medicine (M.A.), Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Elke Muhlberger
- Department of Microbiology, Boston University School of Medicine, Boston, MA, 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA
- Center for Emerging Infectious Diseases Policy & Research, Boston University, Boston, MA, 02118, USA
| | - Robin C. Orozco
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | | | - Michael S. Cohen
- Department of Chemical Physiology and Biochemistry, Oregon Health Sciences University, Portland, OR, 97239, USA
| | - David J. Davido
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Adam J. Hume
- Department of Microbiology, Boston University School of Medicine, Boston, MA, 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA
- Center for Emerging Infectious Diseases Policy & Research, Boston University, Boston, MA, 02118, USA
| | - Anthony R. Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
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Wazir S, Parviainen TAO, Pfannenstiel JJ, Duong MTH, Cluff D, Sowa ST, Galera-Prat A, Ferraris D, Maksimainen MM, Fehr AR, Heiskanen JP, Lehtiö L. Discovery of 2-Amide-3-methylester Thiophenes that Target SARS-CoV-2 Mac1 and Repress Coronavirus Replication, Validating Mac1 as an Antiviral Target. J Med Chem 2024; 67:6519-6536. [PMID: 38592023 DOI: 10.1021/acs.jmedchem.3c02451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has made it clear that further development of antiviral therapies will be needed. Here, we describe small-molecule inhibitors for SARS-CoV-2 Mac1, which counters ADP-ribosylation-mediated innate immune responses. Three high-throughput screening hits had the same 2-amide-3-methylester thiophene scaffold. We studied the compound binding mode using X-ray crystallography, allowing us to design analogues. Compound 27 (MDOLL-0229) had an IC50 of 2.1 μM and was selective for CoV Mac1 proteins after profiling for activity against a panel of viral and human proteins. The improved potency allowed testing of its effect on virus replication, and indeed, 27 inhibited replication of both murine hepatitis virus (MHV) prototypes CoV and SARS-CoV-2. Sequencing of a drug-resistant MHV identified mutations in Mac1, further demonstrating the specificity of 27. Compound 27 is the first Mac1-targeted small molecule demonstrated to inhibit coronavirus replication in a cell model.
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Affiliation(s)
- Sarah Wazir
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Tomi A O Parviainen
- Research Unit of Sustainable Chemistry, University of Oulu, P.O. Box 4300, 90014 Oulu, Finland
| | - Jessica J Pfannenstiel
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| | - Men Thi Hoai Duong
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Daniel Cluff
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| | - Sven T Sowa
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Albert Galera-Prat
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Dana Ferraris
- McDaniel College Department of Chemistry, 2 College Hill, Westminster, Maryland 21157, United States
| | - Mirko M Maksimainen
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Anthony R Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| | - Juha P Heiskanen
- Research Unit of Sustainable Chemistry, University of Oulu, P.O. Box 4300, 90014 Oulu, Finland
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
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Otter CJ, Bracci N, Parenti NA, Ye C, Asthana A, Blomqvist EK, Tan LH, Pfannenstiel JJ, Jackson N, Fehr AR, Silverman RH, Burke JM, Cohen NA, Martinez-Sobrido L, Weiss SR. SARS-CoV-2 nsp15 endoribonuclease antagonizes dsRNA-induced antiviral signaling. Proc Natl Acad Sci U S A 2024; 121:e2320194121. [PMID: 38568967 PMCID: PMC11009620 DOI: 10.1073/pnas.2320194121] [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: 11/20/2023] [Accepted: 02/26/2024] [Indexed: 04/05/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 has caused millions of deaths since its emergence in 2019. Innate immune antagonism by lethal CoVs such as SARS-CoV-2 is crucial for optimal replication and pathogenesis. The conserved nonstructural protein 15 (nsp15) endoribonuclease (EndoU) limits activation of double-stranded (ds)RNA-induced pathways, including interferon (IFN) signaling, protein kinase R (PKR), and oligoadenylate synthetase/ribonuclease L (OAS/RNase L) during diverse CoV infections including murine coronavirus and Middle East respiratory syndrome (MERS)-CoV. To determine how nsp15 functions during SARS-CoV-2 infection, we constructed a recombinant SARS-CoV-2 (nsp15mut) expressing catalytically inactivated nsp15, which we show promoted increased dsRNA accumulation. Infection with SARS-CoV-2 nsp15mut led to increased activation of the IFN signaling and PKR pathways in lung-derived epithelial cell lines and primary nasal epithelial air-liquid interface (ALI) cultures as well as significant attenuation of replication in ALI cultures compared to wild-type virus. This replication defect was rescued when IFN signaling was inhibited with the Janus activated kinase (JAK) inhibitor ruxolitinib. Finally, to assess nsp15 function in the context of minimal (MERS-CoV) or moderate (SARS-CoV-2) innate immune induction, we compared infections with SARS-CoV-2 nsp15mut and previously described MERS-CoV nsp15 mutants. Inactivation of nsp15 had a more dramatic impact on MERS-CoV replication than SARS-CoV-2 in both Calu3 cells and nasal ALI cultures suggesting that SARS-CoV-2 can better tolerate innate immune responses. Taken together, SARS-CoV-2 nsp15 is a potent inhibitor of dsRNA-induced innate immune response and its antagonism of IFN signaling is necessary for optimal viral replication in primary nasal ALI cultures.
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Affiliation(s)
- Clayton J. Otter
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Nicole Bracci
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Nicholas A. Parenti
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Chengjin Ye
- Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX78227
| | - Abhishek Asthana
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH44195
| | - Ebba K. Blomqvist
- Department of Molecular Medicine, The Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL33458
- Department of Immunology and Microbiology, The Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL33458
| | - Li Hui Tan
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Pennsylvania, Philadelphia, PA19104
- Department of Surgery, Corporal Michael J. Crescenz Veterans Administration Medical Center, Philadelphia, PA19104
| | | | - Nathaniel Jackson
- Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX78227
| | - Anthony R. Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS66045
| | - Robert H. Silverman
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH44195
| | - James M. Burke
- Department of Molecular Medicine, The Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL33458
- Department of Immunology and Microbiology, The Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL33458
| | - Noam A. Cohen
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Pennsylvania, Philadelphia, PA19104
- Department of Surgery, Corporal Michael J. Crescenz Veterans Administration Medical Center, Philadelphia, PA19104
| | - Luis Martinez-Sobrido
- Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX78227
| | - Susan R. Weiss
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
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Kerr CM, Pfannenstiel JJ, Alhammad YM, Roy A, O’Connor JJ, Ghimire R, Khattabi R, Shrestha R, McDonald PR, Gao P, Johnson DK, More S, Channappanavar R, Fehr AR. Mutation of highly conserved residues in loop 2 of the coronavirus macrodomain demonstrates that enhanced ADP-ribose binding is detrimental to infection. bioRxiv 2024:2024.01.03.574082. [PMID: 38260573 PMCID: PMC10802294 DOI: 10.1101/2024.01.03.574082] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
All coronaviruses (CoVs) encode for a conserved macrodomain (Mac1) located in nonstructural protein 3 (nsp3). Mac1 is an ADP-ribosylhydrolase that binds and hydrolyzes mono-ADP-ribose from target proteins. Previous work has shown that Mac1 is important for virus replication and pathogenesis. Within Mac1, there are several regions that are highly conserved across CoVs, including the GIF (glycine-isoleucine-phenylalanine) motif. To determine how the biochemical activities of these residues impact CoV replication, the isoleucine and the phenylalanine residues were mutated to alanine (I-A/F-A) in both recombinant Mac1 proteins and recombinant CoVs, including murine hepatitis virus (MHV), Middle East respiratory syndrome coronavirus (MERS-CoV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The F-A mutant proteins had ADP-ribose binding and/or hydrolysis defects that led to attenuated replication and pathogenesis in cell culture and mice. In contrast, the I-A mutations had normal enzyme activity and enhanced ADP-ribose binding. Despite increased ADP-ribose binding, I-A mutant MERS-CoV and SARS-CoV-2 were highly attenuated in both cell culture and mice, indicating that this isoleucine residue acts as a gate that controls ADP-ribose binding for efficient virus replication. These results highlight the function of this highly conserved residue and provide unique insight into how macrodomains control ADP-ribose binding and hydrolysis to promote viral replication and pathogenesis.
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Affiliation(s)
- Catherine M. Kerr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | | | - Yousef M. Alhammad
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Anuradha Roy
- High Throughput Screening Laboratory, University of Kansas, Lawrence, Kansas 66047, USA
| | - Joseph J. O’Connor
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Roshan Ghimire
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, Oklahoma 74078, USA
| | - Reem Khattabi
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Rakshya Shrestha
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, Oklahoma 74078, USA
| | - Peter R. McDonald
- High Throughput Screening Laboratory, University of Kansas, Lawrence, Kansas 66047, USA
| | - Philip Gao
- Protein Production Group, University of Kansas, Lawrence, Kansas 66047, USA
| | - David K. Johnson
- Molecular Graphics and Modeling Laboratory and the Computational Chemical Biology Core, University of Kansas, Lawrence, Kansas 66047, USA
| | - Sunil More
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, Oklahoma 74078, USA
- Oklahoma Center for Respiratory and Infectious Diseases, College of Veterinary Medicine, Stillwater, Oklahoma 74078, USA
| | - Rudragouda Channappanavar
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, Oklahoma 74078, USA
- Oklahoma Center for Respiratory and Infectious Diseases, College of Veterinary Medicine, Stillwater, Oklahoma 74078, USA
| | - Anthony R. Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
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Wazir S, Parviainen TAO, Pfannenstiel JJ, Duong MTH, Cluff D, Sowa ST, Galera-Prat A, Ferraris D, Maksimainen MM, Fehr AR, Heiskanen JP, Lehtiö L. Discovery of 2-amide-3-methylester thiophenes that target SARS-CoV-2 Mac1 and repress coronavirus replication, validating Mac1 as an anti-viral target. bioRxiv 2023:2023.08.28.555062. [PMID: 38234730 PMCID: PMC10793406 DOI: 10.1101/2023.08.28.555062] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has made it clear that further development of antiviral therapies will be needed to combat additional SARS-CoV-2 variants or novel CoVs. Here, we describe small molecule inhibitors for SARS-CoV-2 Mac1, which counters ADP-ribosylation mediated innate immune responses. The compounds inhibiting Mac1 were discovered through high-throughput screening (HTS) using a protein FRET-based competition assay and the best hit compound had an IC50 of 14 μM. Three validated HTS hits have the same 2-amide-3-methylester thiophene scaffold and the scaffold was selected for structure-activity relationship (SAR) studies through commercial and synthesized analogs. We studied the compound binding mode in detail using X-ray crystallography and this allowed us to focus on specific features of the compound and design analogs. Compound 27 (MDOLL-0229) had an IC50 of 2.1 μM and was generally selective for CoV Mac1 proteins after profiling for activity against a panel of viral and human ADP-ribose binding proteins. The improved potency allowed testing of its effect on virus replication and indeed, 27 inhibited replication of both MHVa prototype CoV, and SARS-CoV-2. Furthermore, sequencing of a drug-resistant MHV identified mutations in Mac1, further demonstrating the specificity of 27. Compound 27 is the first Mac1 targeted small molecule demonstrated to inhibit coronavirus replication in a cell model. This, together with its well-defined binding mode, makes 27 a good candidate for further hit/lead-optimization efforts.
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Affiliation(s)
- Sarah Wazir
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Tomi A. O. Parviainen
- Research Unit of Sustainable Chemistry, University of Oulu, P.O. Box 4300, FI-90014 Oulu, Finland
| | - Jessica J. Pfannenstiel
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Men Thi Hoai Duong
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Daniel Cluff
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Sven T. Sowa
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Albert Galera-Prat
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Dana Ferraris
- McDaniel College Department of Chemistry, 2 College Hill, Westminster, MD, USA
| | - Mirko M. Maksimainen
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Anthony R. Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Juha P. Heiskanen
- Research Unit of Sustainable Chemistry, University of Oulu, P.O. Box 4300, FI-90014 Oulu, Finland
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
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Otter CJ, Bracci N, Parenti NA, Ye C, Tan LH, Asthana A, Pfannenstiel JJ, Jackson N, Fehr AR, Silverman RH, Cohen NA, Martinez-Sobrido L, Weiss SR. SARS-CoV-2 nsp15 endoribonuclease antagonizes dsRNA-induced antiviral signaling. bioRxiv 2023:2023.11.15.566945. [PMID: 38014074 PMCID: PMC10680701 DOI: 10.1101/2023.11.15.566945] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 has caused millions of deaths since emerging in 2019. Innate immune antagonism by lethal CoVs such as SARS-CoV-2 is crucial for optimal replication and pathogenesis. The conserved nonstructural protein 15 (nsp15) endoribonuclease (EndoU) limits activation of double-stranded (ds)RNA-induced pathways, including interferon (IFN) signaling, protein kinase R (PKR), and oligoadenylate synthetase/ribonuclease L (OAS/RNase L) during diverse CoV infections including murine coronavirus and Middle East respiratory syndrome (MERS)-CoV. To determine how nsp15 functions during SARS-CoV-2 infection, we constructed a mutant recombinant SARS-CoV-2 (nsp15mut) expressing a catalytically inactive nsp15. Infection with SARS-CoV-2 nsp15 mut led to increased activation of the IFN signaling and PKR pathways in lung-derived epithelial cell lines and primary nasal epithelial air-liquid interface (ALI) cultures as well as significant attenuation of replication in ALI cultures compared to wild-type (WT) virus. This replication defect was rescued when IFN signaling was inhibited with the Janus activated kinase (JAK) inhibitor ruxolitinib. Finally, to assess nsp15 function in the context of minimal (MERS-CoV) or moderate (SARS-CoV-2) innate immune induction, we compared infections with SARS-CoV-2 nsp15mut and previously described MERS-CoV nsp15 mutants. Inactivation of nsp15 had a more dramatic impact on MERS-CoV replication than SARS-CoV-2 in both Calu3 cells and nasal ALI cultures suggesting that SARS-CoV-2 can better tolerate innate immune responses. Taken together, SARS-CoV-2 nsp15 is a potent inhibitor of dsRNA-induced innate immune response and its antagonism of IFN signaling is necessary for optimal viral replication in primary nasal ALI culture.
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Affiliation(s)
- Clayton J Otter
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicole Bracci
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicholas A Parenti
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Chengjin Ye
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Li Hui Tan
- Department of Otorhinolaryngology-Head and Neck Surgery, Division of Rhinology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Abhishek Asthana
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | | | - Anthony R Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Robert H Silverman
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Noam A Cohen
- Department of Otorhinolaryngology-Head and Neck Surgery, Division of Rhinology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
| | | | - Susan R Weiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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O’Connor JJ, Ferraris D, Fehr AR. An Update on the Current State of SARS-CoV-2 Mac1 Inhibitors. Pathogens 2023; 12:1221. [PMID: 37887737 PMCID: PMC10610136 DOI: 10.3390/pathogens12101221] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 10/28/2023] Open
Abstract
Non-structural protein 3 (nsp3) from all coronaviruses (CoVs) contains a conserved macrodomain, known as Mac1, that has been proposed as a potential therapeutic target for CoVs due to its critical role in viral pathogenesis. Mac1 is an ADP-ribose binding protein and ADP-ribosylhydrolase that promotes replication and blocks IFN responses, though the precise mechanisms it uses to carry out these functions remain unknown. Over the past 3 years following the onset of COVID-19, several groups have used high-throughput screening with multiple assays and chemical modifications to create unique chemical inhibitors of the SARS-CoV-2 Mac1 protein. Here, we summarize the current efforts to identify selective and potent inhibitors of SARS-CoV-2 Mac1.
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Affiliation(s)
- Joseph J. O’Connor
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA;
| | - Dana Ferraris
- Department of Chemistry, McDaniel College, 2 College Hill, Westminster, MD 21157, USA;
| | - Anthony R. Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA;
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8
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Kerr CM, Parthasarathy S, Schwarting N, O'Connor JJ, Pfannenstiel JJ, Giri E, More S, Orozco RC, Fehr AR. PARP12 is required to repress the replication of a Mac1 mutant coronavirus in a cell- and tissue-specific manner. J Virol 2023; 97:e0088523. [PMID: 37695054 PMCID: PMC10537751 DOI: 10.1128/jvi.00885-23] [Citation(s) in RCA: 1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 07/13/2023] [Indexed: 09/12/2023] Open
Abstract
ADP-ribosyltransferases (ARTs) mediate the transfer of ADP-ribose from NAD+ to protein or nucleic acid substrates. This modification can be removed by several different types of proteins, including macrodomains. Several ARTs, also known as PARPs, are stimulated by interferon indicating ADP-ribosylation is an important aspect of the innate immune response. All coronaviruses (CoVs) encode for a highly conserved macrodomain (Mac1) that is critical for CoVs to replicate and cause disease, indicating that ADP-ribosylation can effectively control coronavirus infection. Our siRNA screen indicated that PARP12 might inhibit the replication of a murine hepatitis virus (MHV) Mac1 mutant virus in bone-marrow-derived macrophages (BMDMs). To conclusively demonstrate that PARP12 is a key mediator of the antiviral response to CoVs both in cell culture and in vivo, we produced PARP12-/-mice and tested the ability of MHV A59 (hepatotropic/neurotropic) and JHM (neurotropic) Mac1 mutant viruses to replicate and cause disease in these mice. Notably, in the absence of PARP12, Mac1 mutant replication was increased in BMDMs and mice. In addition, liver pathology was also increased in A59-infected mice. However, the PARP12 knockout did not restore Mac1 mutant virus replication to WT virus levels in all cell or tissue types and did not significantly increase the lethality of Mac1 mutant viruses. These results demonstrate that while PARP12 inhibits MHV Mac1 mutant virus infection, additional PARPs or innate immune factors must contribute to the extreme attenuation of this virus in mice. IMPORTANCE Over the last decade, the importance of ADP-ribosyltransferases (ARTs), also known as PARPs, in the antiviral response has gained increased significance as several were shown to either restrict virus replication or impact innate immune responses. However, there are few studies showing ART-mediated inhibition of virus replication or pathogenesis in animal models. We found that the CoV macrodomain (Mac1) was required to prevent ART-mediated inhibition of virus replication in cell culture. Using knockout mice, we found that PARP12, an interferon-stimulated ART, was required to repress the replication of a Mac1 mutant CoV both in cell culture and in mice, demonstrating that PARP12 represses coronavirus replication. However, the deletion of PARP12 did not fully rescue Mac1 mutant virus replication or pathogenesis, indicating that multiple PARPs function to counter coronavirus infection.
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Affiliation(s)
- Catherine M. Kerr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | | | - Nancy Schwarting
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Joseph J. O'Connor
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | | | - Emily Giri
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Sunil More
- Department of Veterinary Pathology, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Robin C. Orozco
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Anthony R. Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
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9
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Alhammad YM, Parthasarathy S, Ghimire R, Kerr CM, O’Connor JJ, Pfannenstiel JJ, Chanda D, Miller CA, Baumlin N, Salathe M, Unckless RL, Zuñiga S, Enjuanes L, More S, Channappanavar R, Fehr AR. SARS-CoV-2 Mac1 is required for IFN antagonism and efficient virus replication in cell culture and in mice. Proc Natl Acad Sci U S A 2023; 120:e2302083120. [PMID: 37607224 PMCID: PMC10468617 DOI: 10.1073/pnas.2302083120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [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: 02/06/2023] [Accepted: 06/30/2023] [Indexed: 08/24/2023] Open
Abstract
Several coronavirus (CoV) encoded proteins are being evaluated as targets for antiviral therapies for COVID-19. Included in these drug targets is the conserved macrodomain, or Mac1, an ADP-ribosylhydrolase and ADP-ribose binding protein encoded as a small domain at the N terminus of nonstructural protein 3. Utilizing point mutant recombinant viruses, Mac1 was shown to be critical for both murine hepatitis virus (MHV) and severe acute respiratory syndrome (SARS)-CoV virulence. However, as a potential drug target, it is imperative to understand how a complete Mac1 deletion impacts the replication and pathogenesis of different CoVs. To this end, we created recombinant bacterial artificial chromosomes (BACs) containing complete Mac1 deletions (ΔMac1) in MHV, MERS-CoV, and SARS-CoV-2. While we were unable to recover infectious virus from MHV or MERS-CoV ΔMac1 BACs, SARS-CoV-2 ΔMac1 was readily recovered from BAC transfection, indicating a stark difference in the requirement for Mac1 between different CoVs. Furthermore, SARS-CoV-2 ΔMac1 replicated at or near wild-type levels in multiple cell lines susceptible to infection. However, in a mouse model of severe infection, ΔMac1 was quickly cleared causing minimal pathology without any morbidity. ΔMac1 SARS-CoV-2 induced increased levels of interferon (IFN) and IFN-stimulated gene expression in cell culture and mice, indicating that Mac1 blocks IFN responses which may contribute to its attenuation. ΔMac1 infection also led to a stark reduction in inflammatory monocytes and neutrophils. These results demonstrate that Mac1 only minimally impacts SARS-CoV-2 replication, unlike MHV and MERS-CoV, but is required for SARS-CoV-2 pathogenesis and is a unique antiviral drug target.
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Affiliation(s)
- Yousef M. Alhammad
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS66047
| | | | - Roshan Ghimire
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK74078
| | - Catherine M. Kerr
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS66047
| | - Joseph J. O’Connor
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS66047
| | | | - Debarati Chanda
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK74078
| | - Caden A. Miller
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK74078
| | - Nathalie Baumlin
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS66160
| | - Matthias Salathe
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS66160
| | - Robert L. Unckless
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS66047
| | - Sonia Zuñiga
- Department of Molecular and Cell Biology, National Center of Biotechnology, Madrid28049, Spain
| | - Luis Enjuanes
- Department of Molecular and Cell Biology, National Center of Biotechnology, Madrid28049, Spain
| | - Sunil More
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK74078
| | | | - Anthony R. Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS66047
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10
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O’Connor JJ, Voth L, Athmer J, George NM, Connelly CM, Fehr AR. Two Commercially Available Blood-Stabilization Reagents Serve as Potent Inactivators of Coronaviruses. Pathogens 2023; 12:1082. [PMID: 37764890 PMCID: PMC10534660 DOI: 10.3390/pathogens12091082] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/22/2023] [Accepted: 08/22/2023] [Indexed: 09/29/2023] Open
Abstract
The continued circulation of SARS-CoV-2 and the increasing frequency of coronavirus (CoV) outbreaks over the decades demonstrates the enduring threat that the CoV family poses. There remains a significant need to develop tools to monitor and prevent the spread of these viruses. We tested blood-stabilization reagents from two commercially available blood collection tubes (BCTs) for their ability to inactivate three different coronaviruses (MHV, OC-43, and SARS-CoV-2) and stabilize their RNA. Both Cell-Free DNA BCT® (cfDNA) and Cyto-Chex® BCT (CytoChex) reagents reduced infectious virus in the buffer to below the limit of detection within 18 h of treatment, with some conditions showing this effect in as little as 3 h. CytoChex had more potent activity than cfDNA as in all cases it more rapidly reduced the actively replicating virus to the limit of detection. Despite the rapid inactivation of the virus, both reagents effectively preserved viral RNA for 7 days. Finally, both reagents accelerated viral inactivation in blood compared to the control samples. These results indicate that cfDNA and CytoChex could be used to inactivate and preserve CoV RNA for detection and further testing.
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Affiliation(s)
- Joseph J. O’Connor
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
| | - Lynden Voth
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
| | - Jeremiah Athmer
- Streck LLC, 7002 S. 109th Street, La Vista, Omaha, NE 68128, USA (C.M.C.)
| | - Nicholas M. George
- Streck LLC, 7002 S. 109th Street, La Vista, Omaha, NE 68128, USA (C.M.C.)
| | | | - Anthony R. Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
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11
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Kerr CM, Parthasarathy S, Schwarting N, O’Connor JJ, Giri E, More S, Orozco RC, Fehr AR. PARP12 is required to repress the replication of a Mac1 mutant coronavirus in a cell and tissue specific manner. bioRxiv 2023:2023.06.16.545351. [PMID: 37398292 PMCID: PMC10312760 DOI: 10.1101/2023.06.16.545351] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
ADP-ribosyltransferases (ARTs) mediate the transfer of ADP-ribose from NAD + to protein or nucleic acid substrates. This modification can be removed by several different types of proteins, including macrodomains. Several ARTs, also known as PARPs, are stimulated by interferon, indicating ADP-ribosylation is an important aspect of the innate immune response. All coronaviruses (CoVs) encode for a highly conserved macrodomain (Mac1) that is critical for CoVs to replicate and cause disease, indicating that ADP-ribosylation can effectively control coronavirus infection. Our siRNA screen indicated that PARP12 might inhibit the replication of a MHV Mac1 mutant virus in bone-marrow derived macrophages (BMDMs). To conclusively demonstrate that PARP12 is a key mediator of the antiviral response to CoVs both in cell culture and in vivo , we produced PARP12 -/- mice and tested the ability of MHV A59 (hepatotropic/neurotropic) and JHM (neurotropic) Mac1 mutant viruses to replicate and cause disease in these mice. Notably, in the absence of PARP12, Mac1 mutant replication was increased in BMDMs and in mice. In addition, liver pathology was also increased in A59 infected mice. However, the PARP12 knockout did not restore Mac1 mutant virus replication to WT virus levels in all cell or tissue types and did not significantly increase the lethality of Mac1 mutant viruses. These results demonstrate that while PARP12 inhibits MHV Mac1 mutant virus infection, additional PARPs or innate immune factors must contribute to the extreme attenuation of this virus in mice. IMPORTANCE Over the last decade, the importance of ADP-ribosyltransferases (ARTs), also known as PARPs, in the antiviral response has gained increased significance as several were shown to either restrict virus replication or impact innate immune responses. However, there are few studies showing ART-mediated inhibition of virus replication or pathogenesis in animal models. We found that the CoV macrodomain (Mac1) was required to prevent ART-mediated inhibition of virus replication in cell culture. Here, using knockout mice, we found that PARP12, an interferon-stimulated ART, was required to repress the replication of a Mac1 mutant CoV both in cell culture and in mice, demonstrating that PARP12 represses coronavirus replication. However, the deletion of PARP12 did not fully rescue Mac1 mutant virus replication or pathogenesis, indicating that multiple PARPs function to counter coronavirus infection.
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Affiliation(s)
- Catherine M. Kerr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | | | - Nancy Schwarting
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Joseph J. O’Connor
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Emily Giri
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Sunil More
- Department of Veterinary Pathology, Oklahoma State University, Stillwater Oklahoma 74048, USA
| | - Robin C. Orozco
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Anthony R. Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
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12
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Alhammad YM, Parthasarathy S, Ghimire R, O’Connor JJ, Kerr CM, Pfannenstiel JJ, Chanda D, Miller CA, Unckless RL, Zuniga S, Enjuanes L, More S, Channappanavar R, Fehr AR. SARS-CoV-2 Mac1 is required for IFN antagonism and efficient virus replication in mice. bioRxiv 2023:2023.04.06.535927. [PMID: 37066301 PMCID: PMC10104158 DOI: 10.1101/2023.04.06.535927] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Several coronavirus (CoV) encoded proteins are being evaluated as targets for antiviral therapies for COVID-19. Included in this set of proteins is the conserved macrodomain, or Mac1, an ADP-ribosylhydrolase and ADP-ribose binding protein. Utilizing point mutant recombinant viruses, Mac1 was shown to be critical for both murine hepatitis virus (MHV) and severe acute respiratory syndrome (SARS)-CoV virulence. However, as a potential drug target, it is imperative to understand how a complete Mac1 deletion impacts the replication and pathogenesis of different CoVs. To this end, we created recombinant bacterial artificial chromosomes (BACs) containing complete Mac1 deletions (ΔMac1) in MHV, MERS-CoV, and SARS-CoV-2. While we were unable to recover infectious virus from MHV or MERS-CoV ΔMac1 BACs, SARS-CoV-2 ΔMac1 was readily recovered from BAC transfection, indicating a stark difference in the requirement for Mac1 between different CoVs. Furthermore, SARS-CoV-2 ΔMac1 replicated at or near wild-type levels in multiple cell lines susceptible to infection. However, in a mouse model of severe infection, ΔMac1 was quickly cleared causing minimal pathology without any morbidity. ΔMac1 SARS-CoV-2 induced increased levels of interferon (IFN) and interferon-stimulated gene (ISG) expression in cell culture and mice, indicating that Mac1 blocks IFN responses which may contribute to its attenuation. ΔMac1 infection also led to a stark reduction in inflammatory monocytes and neutrophils. These results demonstrate that Mac1 only minimally impacts SARS-CoV-2 replication, unlike MHV and MERS-CoV, but is required for SARS-CoV-2 pathogenesis and is a unique antiviral drug target. SIGNIFICANCE All CoVs, including SARS-CoV-2, encode for a conserved macrodomain (Mac1) that counters host ADP-ribosylation. Prior studies with SARS-CoV-1 and MHV found that Mac1 blocks IFN production and promotes CoV pathogenesis, which has prompted the development of SARS-CoV-2 Mac1 inhibitors. However, development of these compounds into antivirals requires that we understand how SARS-CoV-2 lacking Mac1 replicates and causes disease in vitro and in vivo . Here we found that SARS-CoV-2 containing a complete Mac1 deletion replicates normally in cell culture but induces an elevated IFN response, has reduced viral loads in vivo , and does not cause significant disease in mice. These results will provide a roadmap for testing Mac1 inhibitors, help identify Mac1 functions, and open additional avenues for coronavirus therapies.
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Affiliation(s)
- Yousef M. Alhammad
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, USA
| | | | - Roshan Ghimire
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, Oklahoma, United States
| | - Joseph J. O’Connor
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, USA
| | - Catherine M. Kerr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, USA
| | | | - Debarati Chanda
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, Oklahoma, United States
| | - Caden A. Miller
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, Oklahoma, United States
| | - Robert L. Unckless
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, USA
| | - Sonia Zuniga
- National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Luis Enjuanes
- National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Sunil More
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, Oklahoma, United States
| | - Rudragouda Channappanavar
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, Oklahoma, United States
| | - Anthony R. Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, USA
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13
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Ly CY, Pfannenstiel J, Pant A, Yang Z, Fehr AR, Rodzkin MS, Davido DJ. Inhibitors of One or More Cellular Aurora Kinases Impair the Replication of Herpes Simplex Virus 1 and Other DNA and RNA Viruses with Diverse Genomes and Life Cycles. Microbiol Spectr 2023; 11:e0194322. [PMID: 36537798 PMCID: PMC9927324 DOI: 10.1128/spectrum.01943-22] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 11/11/2022] [Indexed: 02/16/2023] Open
Abstract
We utilized a high-throughput cell-based assay to screen several chemical libraries for inhibitors of herpes simplex virus 1 (HSV-1) gene expression. From this screen, four aurora kinase inhibitors were identified that potently reduced gene expression during HSV-1 lytic infection. HSV-1 is known to interact with cellular kinases to regulate gene expression by modulating the phosphorylation and/or activities of viral and cellular proteins. To date, the role of aurora kinases in HSV-1 lytic infection has not been reported. We demonstrated that three aurora kinase inhibitors strongly reduced the transcript levels of immediate-early (IE) genes ICP0, ICP4, and ICP27 and impaired HSV-1 protein expression from all classes of HSV-1, including ICP0, ICP4, ICP8, and gC. These restrictions caused by the aurora kinase inhibitors led to potent reductions in HSV-1 viral replication. The compounds TAK 901, JNJ 7706621, and PF 03814735 decreased HSV-1 titers by 4,500-, 13,200-, and 8,400-fold, respectively, when present in a low micromolar range. The antiviral activity of these compounds correlated with an apparent decrease in histone H3 phosphorylation at serine 10 (H3S10ph) during viral infection, suggesting that the phosphorylation status of H3 influences HSV-1 gene expression. Furthermore, we demonstrated that the aurora kinase inhibitors also impaired the replication of other RNA and DNA viruses. These inhibitors significantly reduced yields of vaccinia virus (a poxvirus, double-stranded DNA, cytoplasmic replication) and mouse hepatitis virus (a coronavirus, positive-sense single-strand RNA [ssRNA]), whereas vesicular stomatitis virus (rhabdovirus, negative-sense ssRNA) yields were unaffected. These results indicated that the activities of aurora kinases play pivotal roles in the life cycles of diverse viruses. IMPORTANCE We have demonstrated that aurora kinases play a role during HSV-1 lytic infection. Three aurora kinase inhibitors significantly impaired HSV-1 immediate-early gene expression. This led to a potent reduction in HSV-1 protein expression and viral replication. Together, our results illustrate a novel role for aurora kinases in the HSV-1 lytic cycle and demonstrate that aurora kinase inhibitors can restrict HSV-1 replication. Furthermore, these aurora kinase inhibitors also reduced the replication of murine coronavirus and vaccinia virus, suggesting that multiple viral families utilize the aurora kinases for their own replication.
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Affiliation(s)
- Cindy Y. Ly
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Jessica Pfannenstiel
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Anil Pant
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Zhilong Yang
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M, College Station, Texas, USA
| | - Anthony R. Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Maxim S. Rodzkin
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - David J. Davido
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
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14
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Lüscher B, Ahel I, Altmeyer M, Ashworth A, Bai P, Chang P, Cohen M, Corda D, Dantzer F, Daugherty MD, Dawson TM, Dawson VL, Deindl S, Fehr AR, Feijs KLH, Filippov DV, Gagné JP, Grimaldi G, Guettler S, Hoch NC, Hottiger MO, Korn P, Kraus WL, Ladurner A, Lehtiö L, Leung AKL, Lord CJ, Mangerich A, Matic I, Matthews J, Moldovan GL, Moss J, Natoli G, Nielsen ML, Niepel M, Nolte F, Pascal J, Paschal BM, Pawłowski K, Poirier GG, Smith S, Timinszky G, Wang ZQ, Yélamos J, Yu X, Zaja R, Ziegler M. ADP-ribosyltransferases, an update on function and nomenclature. FEBS J 2022; 289:7399-7410. [PMID: 34323016 PMCID: PMC9027952 DOI: 10.1111/febs.16142] [Citation(s) in RCA: 123] [Impact Index Per Article: 61.5] [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: 06/03/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 01/13/2023]
Abstract
ADP-ribosylation, a modification of proteins, nucleic acids, and metabolites, confers broad functions, including roles in stress responses elicited, for example, by DNA damage and viral infection and is involved in intra- and extracellular signaling, chromatin and transcriptional regulation, protein biosynthesis, and cell death. ADP-ribosylation is catalyzed by ADP-ribosyltransferases (ARTs), which transfer ADP-ribose from NAD+ onto substrates. The modification, which occurs as mono- or poly-ADP-ribosylation, is reversible due to the action of different ADP-ribosylhydrolases. Importantly, inhibitors of ARTs are approved or are being developed for clinical use. Moreover, ADP-ribosylhydrolases are being assessed as therapeutic targets, foremost as antiviral drugs and for oncological indications. Due to the development of novel reagents and major technological advances that allow the study of ADP-ribosylation in unprecedented detail, an increasing number of cellular processes and pathways are being identified that are regulated by ADP-ribosylation. In addition, characterization of biochemical and structural aspects of the ARTs and their catalytic activities have expanded our understanding of this protein family. This increased knowledge requires that a common nomenclature be used to describe the relevant enzymes. Therefore, in this viewpoint, we propose an updated and broadly supported nomenclature for mammalian ARTs that will facilitate future discussions when addressing the biochemistry and biology of ADP-ribosylation. This is combined with a brief description of the main functions of mammalian ARTs to illustrate the increasing diversity of mono- and poly-ADP-ribose mediated cellular processes.
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Affiliation(s)
- Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Germany
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, UK
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Switzerland
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Peter Bai
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Hungary
| | | | - Michael Cohen
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, USA
| | - Daniela Corda
- Department of Biomedical Sciences, National Research Council, Rome, Italy
| | | | - Matthew D Daugherty
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sebastian Deindl
- Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Anthony R Fehr
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, USA
| | - Karla L H Feijs
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Germany
| | | | - Jean-Philippe Gagné
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec City, QC, Canada
| | | | - Sebastian Guettler
- Divisions of Structural Biology and Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Nicolas C Hoch
- Department of Biochemistry, University of São Paulo, Brazil
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, Switzerland
| | - Patricia Korn
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Germany
| | - W Lee Kraus
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andreas Ladurner
- Department of Physiological Chemistry, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Christopher J Lord
- CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | - Ivan Matic
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster for Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Germany
| | - Jason Matthews
- Institute of Basic Medical Sciences, University of Oslo, Norway
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Joel Moss
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan, Italy
| | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | | | - Friedrich Nolte
- Institut für Immunologie, Universitätsklinikum Hamburg-Eppendorf, Germany
| | - John Pascal
- Biochemistry and Molecular Medicine, Université de Montréal, Canada
| | - Bryce M Paschal
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guy G Poirier
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec City, QC, Canada
| | - Susan Smith
- Department of Pathology, Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, NY, USA
| | - Gyula Timinszky
- Lendület Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Zhao-Qi Wang
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
- Faculty of Biological Sciences, Friedrich-Schiller University of Jena, Germany
| | - José Yélamos
- Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Xiaochun Yu
- School of Life Sciences, Westlake University, Hangzhou, China
| | - Roko Zaja
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Germany
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15
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Sherrill LM, Joya EE, Walker A, Roy A, Alhammad YM, Atobatele M, Wazir S, Abbas G, Keane P, Zhuo J, Leung AKL, Johnson DK, Lehtiö L, Fehr AR, Ferraris D. Design, synthesis and evaluation of inhibitors of the SARS-CoV-2 nsp3 macrodomain. Bioorg Med Chem 2022; 67:116788. [PMID: 35597097 PMCID: PMC9093066 DOI: 10.1016/j.bmc.2022.116788] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 03/15/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 01/25/2023]
Abstract
A series of amino acid based 7H-pyrrolo[2,3-d]pyrimidines were designed and synthesized to discern the structure activity relationships against the SARS-CoV-2 nsp3 macrodomain (Mac1), an ADP-ribosylhydrolase that is critical for coronavirus replication and pathogenesis. Structure activity studies identified compound 15c as a low-micromolar inhibitor of Mac1 in two ADP-ribose binding assays. This compound also demonstrated inhibition in an enzymatic assay of Mac1 and displayed a thermal shift comparable to ADPr in the melting temperature of Mac1 supporting binding to the target protein. A structural model reproducibly predicted a binding mode where the pyrrolo pyrimidine forms a hydrogen bonding network with Asp22 and the amide backbone NH of Ile23 in the adenosine binding pocket and the carboxylate forms hydrogen bonds to the amide backbone of Phe157 and Asp156, part of the oxyanion subsite of Mac1. Compound 15c also demonstrated notable selectivity for coronavirus macrodomains when tested against a panel of ADP-ribose binding proteins. Together, this study identified several low MW, low µM Mac1 inhibitors to use as small molecule chemical probes for this potential anti-viral target and offers starting points for further optimization.
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Affiliation(s)
- Lavinia M Sherrill
- McDaniel College, Department of Chemistry, 2 College Hill, Westminster, MD 21157, USA
| | - Elva E Joya
- McDaniel College, Department of Chemistry, 2 College Hill, Westminster, MD 21157, USA
| | - AnnMarie Walker
- McDaniel College, Department of Chemistry, 2 College Hill, Westminster, MD 21157, USA
| | - Anuradha Roy
- Infectious Disease Assay Development Laboratory/HTS, University of Kansas, Lawrence, KS 66047, USA
| | - Yousef M Alhammad
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
| | - Moriama Atobatele
- Infectious Disease Assay Development Laboratory/HTS, University of Kansas, Lawrence, KS 66047, USA
| | - Sarah Wazir
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - George Abbas
- McDaniel College, Department of Chemistry, 2 College Hill, Westminster, MD 21157, USA
| | - Patrick Keane
- McDaniel College, Department of Chemistry, 2 College Hill, Westminster, MD 21157, USA
| | - Junlin Zhuo
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Oncology, McKusick-Nathans Department of Genetic Medicine and Department of Molecular Biology and Genetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - David K Johnson
- Molecular Graphics and Modeling Laboratory and the Computational Chemical Biology Core, University of Kansas, Lawrence, KS 66047, USA
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Anthony R Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA.
| | - Dana Ferraris
- McDaniel College, Department of Chemistry, 2 College Hill, Westminster, MD 21157, USA.
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16
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Affiliation(s)
- Srivatsan Parthasarathy
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Anthony R. Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
- * E-mail:
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17
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Comar CE, Otter CJ, Pfannenstiel J, Doerger E, Renner DM, Tan LH, Perlman S, Cohen NA, Fehr AR, Weiss SR. MERS-CoV endoribonuclease and accessory proteins jointly evade host innate immunity during infection of lung and nasal epithelial cells. Proc Natl Acad Sci U S A 2022; 119:e2123208119. [PMID: 35594398 PMCID: PMC9173776 DOI: 10.1073/pnas.2123208119] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [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: 12/24/2021] [Accepted: 04/13/2022] [Indexed: 12/25/2022] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) emerged into humans in 2012, causing highly lethal respiratory disease. The severity of disease may be, in part, because MERS-CoV is adept at antagonizing early innate immune pathways—interferon (IFN) production and signaling, protein kinase R (PKR), and oligoadenylate synthetase/ribonuclease L (OAS/RNase L)—activated in response to viral double-stranded RNA (dsRNA) generated during genome replication. This is in contrast to severe acute respiratory syndrome CoV-2 (SARS-CoV-2), which we recently reported to activate PKR and RNase L and, to some extent, IFN signaling. We previously found that MERS-CoV accessory proteins NS4a (dsRNA binding protein) and NS4b (phosphodiesterase) could weakly suppress these pathways, but ablation of each had minimal effect on virus replication. Here we investigated the antagonist effects of the conserved coronavirus endoribonuclease (EndoU), in combination with NS4a or NS4b. Inactivation of EndoU catalytic activity alone in a recombinant MERS-CoV caused little if any effect on activation of the innate immune pathways during infection. However, infection with recombinant viruses containing combined mutations with inactivation of EndoU and deletion of NS4a or inactivation of the NS4b phosphodiesterase promoted robust activation of dsRNA-induced innate immune pathways. This resulted in at least tenfold attenuation of replication in human lung–derived A549 and primary nasal cells. Furthermore, replication of these recombinant viruses could be rescued to the level of wild-type MERS-CoV by knockout of host immune mediators MAVS, PKR, or RNase L. Thus, EndoU and accessory proteins NS4a and NS4b together suppress dsRNA-induced innate immunity during MERS-CoV infection in order to optimize viral replication.
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Affiliation(s)
- Courtney E. Comar
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Clayton J. Otter
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | | | - Ethan Doerger
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045
| | - David M. Renner
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Li Hui Tan
- Otorhinolaryngology-Head and Neck Surgery, University of Pennsylvania, Philadelphia, PA 19104
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242
| | - Noam A. Cohen
- Otorhinolaryngology-Head and Neck Surgery, University of Pennsylvania, Philadelphia, PA 19104
- Department of Surgery, Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA 19104
| | - Anthony R. Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242
| | - Susan R. Weiss
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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18
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Roy A, Alhammad YM, McDonald P, Johnson DK, Zhuo J, Wazir S, Ferraris D, Lehtiö L, Leung AKL, Fehr AR. Discovery of compounds that inhibit SARS-CoV-2 Mac1-ADP-ribose binding by high-throughput screening. bioRxiv 2022:2022.03.01.482536. [PMID: 35262075 PMCID: PMC8902866 DOI: 10.1101/2022.03.01.482536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The emergence of several zoonotic viruses in the last twenty years, especially the pandemic outbreak of SARS-CoV-2, has exposed a dearth of antiviral drug therapies for viruses with pandemic potential. Developing a diverse drug portfolio will be critical for our ability to rapidly respond to novel coronaviruses (CoVs) and other viruses with pandemic potential. Here we focus on the SARS-CoV-2 conserved macrodomain (Mac1), a small domain of non-structural protein 3 (nsp3). Mac1 is an ADP-ribosylhydrolase that cleaves mono-ADP-ribose (MAR) from target proteins, protects the virus from the anti-viral effects of host ADP-ribosyltransferases, and is critical for the replication and pathogenesis of CoVs. In this study, a luminescent-based high-throughput assay was used to screen ∼38,000 small molecules for those that could inhibit Mac1-ADP-ribose binding. We identified 5 compounds amongst 3 chemotypes that inhibit SARS-CoV-2 Mac1-ADP-ribose binding in multiple assays with IC 50 values less than 100 µ M, inhibit ADP-ribosylhydrolase activity, and have evidence of direct Mac1 binding. These chemotypes are strong candidates for further derivatization into highly effective Mac1 inhibitors.
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19
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Sherrill LM, Joya EE, Walker A, Roy A, Alhammad YM, Atobatele M, Wazir S, Abbas G, Keane P, Zhuo J, Leung AKL, Johnson DK, Lehtiö L, Fehr AR, Ferraris D. Design, Synthesis and Evaluation of Inhibitors of the SARS-CoV2 nsp3 Macrodomain. bioRxiv 2022:2022.02.27.482176. [PMID: 35262078 PMCID: PMC8902877 DOI: 10.1101/2022.02.27.482176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A series of amino acid based 7H -pyrrolo[2,3- d ]pyrimidines were designed and synthesized to discern the structure activity relationships against the SARS-CoV-2 nsp3 macrodomain (Mac1), an ADP-ribosylhydrolase that is critical for coronavirus replication and pathogenesis. Structure activity studies identified compound 15c as a low-micromolar inhibitor of Mac1 in two ADP-ribose binding assays. This compound also demonstrated inhibition in an enzymatic assay of Mac1 and displayed a thermal shift comparable to ADPr in the melting temperature of Mac1 supporting binding to the target protein. A structural model reproducibly predicted a binding mode where the pyrrolo pyrimidine forms a hydrogen bonding network with Asp 22 and the amide backbone NH of Ile 23 in the adenosine binding pocket and the carboxylate forms hydrogen bonds to the amide backbone of Phe 157 and Asp 156 , part of the oxyanion subsite of Mac1. Compound 15c also demonstrated notable selectivity for coronavirus macrodomains when tested against a panel of ADP-ribose binding proteins. Together, this study identified several low MW, low μM Mac1 inhibitors to use as small molecule chemical probes for this potential anti-viral target and offers starting points for further optimization.
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20
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Dasovich M, Zhuo J, Goodman JA, Thomas A, McPherson RL, Jayabalan AK, Busa VF, Cheng SJ, Murphy BA, Redinger KR, Alhammad YMO, Fehr AR, Tsukamoto T, Slusher BS, Bosch J, Wei H, Leung AKL. High-Throughput Activity Assay for Screening Inhibitors of the SARS-CoV-2 Mac1 Macrodomain. ACS Chem Biol 2022; 17:17-23. [PMID: 34904435 PMCID: PMC8691451 DOI: 10.1021/acschembio.1c00721] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/16/2021] [Indexed: 12/11/2022]
Abstract
Macrodomains are a class of conserved ADP-ribosylhydrolases expressed by viruses of pandemic concern, including coronaviruses and alphaviruses. Viral macrodomains are critical for replication and virus-induced pathogenesis; therefore, these enzymes are a promising target for antiviral therapy. However, no potent or selective viral macrodomain inhibitors currently exist, in part due to the lack of a high-throughput assay for this class of enzymes. Here we developed a high-throughput ADP-ribosylhydrolase assay using the SARS-CoV-2 macrodomain Mac1. We performed a pilot screen that identified dasatinib and dihydralazine as ADP-ribosylhydrolase inhibitors. Importantly, dasatinib inhibits SARS-CoV-2 and MERS-CoV Mac1 but not the closest human homologue, MacroD2. Our study demonstrates the feasibility of identifying selective inhibitors based on ADP-ribosylhydrolase activity, paving the way for the screening of large compound libraries to identify improved macrodomain inhibitors and to explore their potential as antiviral therapies for SARS-CoV-2 and future viral threats.
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Affiliation(s)
- Morgan Dasovich
- Department of Biochemistry and Molecular Biology,
Bloomberg School of Public Health, Johns Hopkins University,
Baltimore, Maryland 21205, United States
- Department of Chemistry, Krieger School of Arts and
Sciences, Johns Hopkins University, Baltimore, Maryland 21218,
United States
| | - Junlin Zhuo
- Department of Biochemistry and Molecular Biology,
Bloomberg School of Public Health, Johns Hopkins University,
Baltimore, Maryland 21205, United States
| | - Jack A. Goodman
- Department of Biochemistry and Molecular Biology,
Bloomberg School of Public Health, Johns Hopkins University,
Baltimore, Maryland 21205, United States
| | - Ajit Thomas
- Johns Hopkins Drug Discovery,
Baltimore, Maryland 21205, United States
- Department of Neurology, School of Medicine,
Johns Hopkins University, Baltimore, Maryland 21205,
United States
| | - Robert Lyle McPherson
- Department of Biochemistry and Molecular Biology,
Bloomberg School of Public Health, Johns Hopkins University,
Baltimore, Maryland 21205, United States
| | - Aravinth Kumar Jayabalan
- Department of Biochemistry and Molecular Biology,
Bloomberg School of Public Health, Johns Hopkins University,
Baltimore, Maryland 21205, United States
| | - Veronica F. Busa
- Department of Biochemistry and Molecular Biology,
Bloomberg School of Public Health, Johns Hopkins University,
Baltimore, Maryland 21205, United States
- McKusick-Nathans Department of Genetics Medicine,
School of Medicine, Johns Hopkins
University, Baltimore, Maryland 21205, United
States
| | - Shang-Jung Cheng
- Department of Biochemistry and Molecular Biology,
Bloomberg School of Public Health, Johns Hopkins University,
Baltimore, Maryland 21205, United States
| | - Brennan A. Murphy
- Johns Hopkins Drug Discovery,
Baltimore, Maryland 21205, United States
| | - Karli R. Redinger
- Center for Global Health and Diseases, Case
Western Reserve University, Cleveland, Ohio 44106, United
States
| | - Yousef M. O. Alhammad
- Department of Molecular Biosciences,
University of Kansas, Lawrence, Kansas 66045, United
States
| | - Anthony R. Fehr
- Department of Molecular Biosciences,
University of Kansas, Lawrence, Kansas 66045, United
States
| | - Takashi Tsukamoto
- Johns Hopkins Drug Discovery,
Baltimore, Maryland 21205, United States
- Department of Neurology, School of Medicine,
Johns Hopkins University, Baltimore, Maryland 21205,
United States
| | - Barbara S. Slusher
- Johns Hopkins Drug Discovery,
Baltimore, Maryland 21205, United States
- Department of Neurology, School of Medicine,
Johns Hopkins University, Baltimore, Maryland 21205,
United States
| | - Jürgen Bosch
- Center for Global Health and Diseases, Case
Western Reserve University, Cleveland, Ohio 44106, United
States
- InterRayBio, LLC,
Cleveland, Ohio 44106, United States
| | - Huijun Wei
- Johns Hopkins Drug Discovery,
Baltimore, Maryland 21205, United States
- Department of Neurology, School of Medicine,
Johns Hopkins University, Baltimore, Maryland 21205,
United States
| | - Anthony K. L. Leung
- Department of Biochemistry and Molecular Biology,
Bloomberg School of Public Health, Johns Hopkins University,
Baltimore, Maryland 21205, United States
- McKusick-Nathans Department of Genetics Medicine,
School of Medicine, Johns Hopkins
University, Baltimore, Maryland 21205, United
States
- Department of Oncology and Department of
Molecular Biology and Genetics, School of Medicine, Johns Hopkins
University, Baltimore, Maryland 21205, United
States
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21
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Leung AKL, Griffin DE, Bosch J, Fehr AR. The Conserved Macrodomain Is a Potential Therapeutic Target for Coronaviruses and Alphaviruses. Pathogens 2022; 11:pathogens11010094. [PMID: 35056042 PMCID: PMC8780475 DOI: 10.3390/pathogens11010094] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 12/04/2022] Open
Abstract
Emerging and re-emerging viral diseases pose continuous public health threats, and effective control requires a combination of non-pharmacologic interventions, treatment with antivirals, and prevention with vaccines. The COVID-19 pandemic has demonstrated that the world was least prepared to provide effective treatments. This lack of preparedness has been due, in large part, to a lack of investment in developing a diverse portfolio of antiviral agents, particularly those ready to combat viruses of pandemic potential. Here, we focus on a drug target called macrodomain that is critical for the replication and pathogenesis of alphaviruses and coronaviruses. Some mutations in alphavirus and coronaviral macrodomains are not tolerated for virus replication. In addition, the coronavirus macrodomain suppresses host interferon responses. Therefore, macrodomain inhibitors have the potential to block virus replication and restore the host’s protective interferon response. Viral macrodomains offer an attractive antiviral target for developing direct acting antivirals because they are highly conserved and have a structurally well-defined (druggable) binding pocket. Given that this target is distinct from the existing RNA polymerase and protease targets, a macrodomain inhibitor may complement current approaches, pre-empt the threat of resistance and offer opportunities to develop combination therapies for combating COVID-19 and future viral threats.
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Affiliation(s)
- Anthony K. L. Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- McKusick-Nathans Department of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Molecular Biology and Genetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Correspondence: (A.K.L.L.); (D.E.G.); (A.R.F.); Tel.: +1-(410)-5028939 (A.K.L.L.); +1-(410)-955-3459 (D.E.G.); +1-(785)-864-6626 (A.R.F.)
| | - Diane E. Griffin
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
- Correspondence: (A.K.L.L.); (D.E.G.); (A.R.F.); Tel.: +1-(410)-5028939 (A.K.L.L.); +1-(410)-955-3459 (D.E.G.); +1-(785)-864-6626 (A.R.F.)
| | - Jürgen Bosch
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH 44106, USA;
- InterRayBio, LLC, Cleveland, OH 44106, USA
| | - Anthony R. Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
- Correspondence: (A.K.L.L.); (D.E.G.); (A.R.F.); Tel.: +1-(410)-5028939 (A.K.L.L.); +1-(410)-955-3459 (D.E.G.); +1-(785)-864-6626 (A.R.F.)
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22
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Comar CE, Otter CJ, Pfannenstiel J, Doerger E, Renner DM, Tan LH, Perlman S, Cohen NA, Fehr AR, Weiss SR. MERS-CoV endoribonuclease and accessory proteins jointly evade host innate immunity during infection of lung and nasal epithelial cells. bioRxiv 2021. [PMID: 34981054 DOI: 10.1101/2021.12.20.473564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) emerged into humans in 2012, causing highly lethal respiratory disease. The severity of disease may be in part because MERS-CoV is adept at antagonizing early innate immune pathways - interferon (IFN) production and signaling, protein kinase R (PKR), and oligoadenylate synthetase ribonuclease L (OAS/RNase L) - generated in response to viral double-stranded (ds)RNA generated during genome replication. This is in contrast to SARS-CoV-2, which we recently reported activates PKR and RNase L and to some extent, IFN signaling. We previously found that MERS-CoV accessory proteins NS4a (dsRNA binding protein) and NS4b (phosphodiesterase) could weakly suppress these pathways, but ablation of each had minimal effect on virus replication. Here we investigated the antagonist effects of the conserved coronavirus endoribonuclease (EndoU), in combination with NS4a or NS4b. Inactivation of EndoU catalytic activity alone in a recombinant MERS-CoV caused little if any effect on activation of the innate immune pathways during infection. However, infection with recombinant viruses containing combined mutations with inactivation of EndoU and deletion of NS4a or inactivation of the NS4b phosphodiesterase promoted robust activation of the dsRNA-induced innate immune pathways. This resulted in ten-fold attenuation of replication in human lung derived A549 and primary nasal cells. Furthermore, replication of these recombinant viruses could be rescued to the level of WT MERS-CoV by knockout of host immune mediators MAVS, PKR, or RNase L. Thus, EndoU and accessory proteins NS4a and NS4b together suppress dsRNA-induced innate immunity during MERS-CoV infection in order to optimize viral replication. IMPORTANCE Middle East Respiratory Syndrome Coronavirus (MERS-CoV) causes highly lethal respiratory disease. MERS-CoV encodes several innate immune antagonists, accessory proteins NS4a and NS4b unique to the merbeco lineage and the nsp15 protein endoribonuclease (EndoU), conserved among all coronaviruses. While mutation of each antagonist protein alone has little effect on innate immunity, infections with recombinant MERS-CoVs with mutations of EndoU in combination with either NS4a or NS4b, activate innate signaling pathways and are attenuated for replication. Our data indicate that EndoU and accessory proteins NS4a and NS4b together suppress innate immunity during MERS-CoV infection, to optimize viral replication. This is in contrast to SARS-CoV-2 which activates these pathways and consistent with greater mortality observed during MERS-CoV infection compared to SARS-CoV-2.
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23
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Heer CD, Sanderson DJ, Voth LS, Alhammad YMO, Schmidt MS, Trammell SAJ, Perlman S, Cohen MS, Fehr AR, Brenner C. Coronavirus infection and PARP expression dysregulate the NAD metabolome: An actionable component of innate immunity. J Biol Chem 2020; 295:17986-17996. [PMID: 33051211 PMCID: PMC7834058 DOI: 10.1074/jbc.ra120.015138] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [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: 07/07/2020] [Revised: 09/30/2020] [Indexed: 11/17/2022] Open
Abstract
Poly(ADP-ribose) polymerase (PARP) superfamily members covalently link either a single ADP-ribose (ADPR) or a chain of ADPR units to proteins using NAD as the source of ADPR. Although the well-known poly(ADP-ribosylating) (PARylating) PARPs primarily function in the DNA damage response, many noncanonical mono(ADP-ribosylating) (MARylating) PARPs are associated with cellular antiviral responses. We recently demonstrated robust up-regulation of several PARPs following infection with murine hepatitis virus (MHV), a model coronavirus. Here we show that SARS-CoV-2 infection strikingly up-regulates MARylating PARPs and induces the expression of genes encoding enzymes for salvage NAD synthesis from nicotinamide (NAM) and nicotinamide riboside (NR), while down-regulating other NAD biosynthetic pathways. We show that overexpression of PARP10 is sufficient to depress cellular NAD and that the activities of the transcriptionally induced enzymes PARP7, PARP10, PARP12 and PARP14 are limited by cellular NAD and can be enhanced by pharmacological activation of NAD synthesis. We further demonstrate that infection with MHV induces a severe attack on host cell NAD+ and NADP+ Finally, we show that NAMPT activation, NAM, and NR dramatically decrease the replication of an MHV that is sensitive to PARP activity. These data suggest that the antiviral activities of noncanonical PARP isozyme activities are limited by the availability of NAD and that nutritional and pharmacological interventions to enhance NAD levels may boost innate immunity to coronaviruses.
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Affiliation(s)
- Collin D Heer
- Free Radical and Radiation Biology Program, Department of Radiation Oncology, University of Iowa, Iowa City, Iowa, USA; Department of Biochemistry, University of Iowa, Iowa City, Iowa, USA
| | - Daniel J Sanderson
- Department of Chemical Physiology & Biochemistry, Oregon Health Sciences University, Portland, Oregon, USA
| | - Lynden S Voth
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Yousef M O Alhammad
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Mark S Schmidt
- Department of Biochemistry, University of Iowa, Iowa City, Iowa, USA
| | | | - Stanley Perlman
- Department of Microbiology & Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Michael S Cohen
- Department of Chemical Physiology & Biochemistry, Oregon Health Sciences University, Portland, Oregon, USA
| | - Anthony R Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA.
| | - Charles Brenner
- Department of Biochemistry, University of Iowa, Iowa City, Iowa, USA.
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24
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Alhammad YMO, Kashipathy MM, Roy A, Gagné JP, McDonald P, Gao P, Nonfoux L, Battaile KP, Johnson DK, Holmstrom ED, Poirier GG, Lovell S, Fehr AR. The SARS-CoV-2 conserved macrodomain is a mono-ADP-ribosylhydrolase. bioRxiv 2020:2020.05.11.089375. [PMID: 32511412 PMCID: PMC7263559 DOI: 10.1101/2020.05.11.089375] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
UNLABELLED Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other SARS-like-CoVs encode 3 tandem macrodomains within non-structural protein 3 (nsp3). The first macrodomain, Mac1, is conserved throughout CoVs, and binds to and hydrolyzes mono-ADP-ribose (MAR) from target proteins. Mac1 likely counters host-mediated anti-viral ADP-ribosylation, a posttranslational modification that is part of the host response to viral infections. Mac1 is essential for pathogenesis in multiple animal models of CoV infection, implicating it as a virulence factor and potential therapeutic target. Here we report the crystal structure of SARS-CoV-2 Mac1 in complex with ADP-ribose. SARS-CoV-2, SARS-CoV and MERS-CoV Mac1 exhibit similar structural folds and all 3 proteins bound to ADP-ribose with low μM affinities. Importantly, using ADP-ribose detecting binding reagents in both a gel-based assay and novel ELISA assays, we demonstrated de-MARylating activity for all 3 CoV Mac1 proteins, with the SARS-CoV-2 Mac1 protein leading to a more rapid loss of substrate compared to the others. In addition, none of these enzymes could hydrolyze poly-ADP-ribose. We conclude that the SARS-CoV-2 and other CoV Mac1 proteins are MAR-hydrolases with similar functions, indicating that compounds targeting CoV Mac1 proteins may have broad anti-CoV activity. IMPORTANCE SARS-CoV-2 has recently emerged into the human population and has led to a worldwide pandemic of COVID-19 that has caused greater than 900 thousand deaths worldwide. With, no currently approved treatments, novel therapeutic strategies are desperately needed. All coronaviruses encode for a highly conserved macrodomain (Mac1) that binds to and removes ADP-ribose adducts from proteins in a dynamic post-translational process increasingly recognized as an important factor that regulates viral infection. The macrodomain is essential for CoV pathogenesis and may be a novel therapeutic target. Thus, understanding its biochemistry and enzyme activity are critical first steps for these efforts. Here we report the crystal structure of SARS-CoV-2 Mac1 in complex with ADP-ribose, and describe its ADP-ribose binding and hydrolysis activities in direct comparison to SARS-CoV and MERS-CoV Mac1 proteins. These results are an important first step for the design and testing of potential therapies targeting this unique protein domain.
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25
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Heer CD, Sanderson DJ, Voth LS, Alhammad YMO, Schmidt MS, Trammell SAJ, Perlman S, Cohen MS, Fehr AR, Brenner C. Coronavirus infection and PARP expression dysregulate the NAD Metabolome: an actionable component of innate immunity. bioRxiv 2020. [PMID: 32511303 PMCID: PMC7217258 DOI: 10.1101/2020.04.17.047480] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Poly-ADP-ribose polymerase (PARP) superfamily members covalently link either a single ADP-ribose (ADPR) or a chain of ADPR units to proteins using nicotinamide adenine dinucleotide (NAD) as the source of ADPR. While the well-known poly-ADP-ribosylating (PARylating) PARPs primarily function in the DNA damage response, many non-canonical mono-ADP-ribosylating (MARylating) PARPs are associated with cellular antiviral responses. We recently demonstrated robust upregulation of several PARPs following infection with Murine Hepatitis Virus (MHV), a model coronavirus. Here we show that SARS-CoV-2 infection strikingly upregulates MARylating PARPs and induces the expression of genes encoding enzymes for salvage NAD synthesis from nicotinamide (NAM) and nicotinamide riboside (NR), while downregulating other NAD biosynthetic pathways. We show that overexpression of PARP10 is sufficient to depress cellular NAD and that the activities of the transcriptionally induced enzymes PARP7, PARP10, PARP12 and PARP14 are limited by cellular NAD and can be enhanced by pharmacological activation of NAD synthesis. We further demonstrate that infection with MHV induces a severe attack on host cell NAD+ and NADP+. Finally, we show that NAMPT activation, NAM and NR dramatically decrease the replication of an MHV virus that is sensitive to PARP activity. These data suggest that the antiviral activities of noncanonical PARP isozyme activities are limited by the availability of NAD, and that nutritional and pharmacological interventions to enhance NAD levels may boost innate immunity to coronaviruses.
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Affiliation(s)
- Collin D Heer
- Free Radical and Radiation Biology Program, Department of Radiation Oncology, University of Iowa, Iowa City, IA, USA.,Department of Biochemistry, University of Iowa, Iowa City, IA, USA
| | - Daniel J Sanderson
- Department of Chemical Physiology & Biochemistry, Oregon Health Sciences University, Portland, OR, USA
| | - Lynden S Voth
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Yousef M O Alhammad
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Mark S Schmidt
- Department of Biochemistry, University of Iowa, Iowa City, IA, USA
| | | | - Stanley Perlman
- Department of Microbiology & Immunology, University of Iowa, Iowa City, IA, USA
| | - Michael S Cohen
- Department of Chemical Physiology & Biochemistry, Oregon Health Sciences University, Portland, OR, USA
| | - Anthony R Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Charles Brenner
- Department of Biochemistry, University of Iowa, Iowa City, IA, USA
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26
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Abstract
Over the past two decades, several coronavirus (CoV) infectious clones have been engineered, allowing for the manipulation of their large viral genomes (~30 kb) using unique reverse genetic systems. These reverse genetic systems include targeted recombination, in vitro ligation, vaccinia virus vectors, and bacterial artificial chromosomes (BACs). Quickly after the identification of Middle East respiratory syndrome-CoV (MERS-CoV), both in vitro ligation and BAC-based reverse genetic technologies were engineered for MERS-CoV to study its basic biological properties, develop live-attenuated vaccines, and test antiviral drugs. Here, I will describe how lambda red recombination can be used with the MERS-CoV BAC to quickly and efficiently introduce virtually any type of genetic modification (point mutations, insertions, deletions) into the MERS-CoV genome and recover recombinant virus.
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Affiliation(s)
- Anthony R Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA.
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27
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Abstract
Macrodomains, enzymes that remove ADP-ribose from proteins, are encoded by several families of RNA viruses and have recently been shown to counter innate immune responses to virus infection. ADP-ribose is covalently attached to target proteins by poly-ADP-ribose polymerases (PARPs), using nicotinamide adenine dinucleotide (NAD+) as a substrate. This modification can have a wide variety of effects on proteins including alteration of enzyme activity, protein-protein interactions, and protein stability. Several PARPs are induced by interferon (IFN) and are known to have antiviral properties, implicating ADP-ribosylation in the host defense response and suggesting that viral macrodomains may counter this response. Recent studies have demonstrated that viral macrodomains do counter the innate immune response by interfering with PARP-mediated antiviral defenses, stress granule formation, and pro-inflammatory cytokine production. Here, we will describe the known functions of the viral macrodomains and review recent literature demonstrating their roles in countering PARP-mediated antiviral responses.
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Affiliation(s)
| | - Anthony R. Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA;
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28
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Abstract
Poly-adenosine diphosphate-ribose polymerases (PARPs) promote ADP-ribosylation, a highly conserved, fundamental posttranslational modification (PTM). PARP catalytic domains transfer the ADP-ribose moiety from NAD+ to amino acid residues of target proteins, leading to mono- or poly-ADP-ribosylation (MARylation or PARylation). This PTM regulates various key biological and pathological processes. In this review, we focus on the roles of the PARP family members in inflammation and host-pathogen interactions. Here we give an overview the current understanding of the mechanisms by which PARPs promote or suppress proinflammatory activation of macrophages, and various roles PARPs play in virus infections. We also demonstrate how innovative technologies, such as proteomics and systems biology, help to advance this research field and describe unanswered questions.
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Affiliation(s)
- Anthony R Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Sasha A Singh
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Catherine M Kerr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
| | - Shin Mukai
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Hideyuki Higashi
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.,Center for Excellence in Vascular Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Human Pathology, I.M. Sechenov First Moscow State Medical University of the Ministry of Health, Moscow 119146, Russian Federation
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29
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Grunewald ME, Shaban MG, Mackin SR, Fehr AR, Perlman S. Murine Coronavirus Infection Activates the Aryl Hydrocarbon Receptor in an Indoleamine 2,3-Dioxygenase-Independent Manner, Contributing to Cytokine Modulation and Proviral TCDD-Inducible-PARP Expression. J Virol 2020; 94:e01743-19. [PMID: 31694960 PMCID: PMC7000979 DOI: 10.1128/jvi.01743-19] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [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: 10/10/2019] [Accepted: 11/04/2019] [Indexed: 11/20/2022] Open
Abstract
The aryl hydrocarbon receptor (AhR) is a cytoplasmic receptor/transcription factor that modulates several cellular and immunological processes following activation by pathogen-associated stimuli, though its role during virus infection is largely unknown. Here, we show that AhR is activated in cells infected with mouse hepatitis virus (MHV), a coronavirus (CoV), and contributes to the upregulation of downstream effector TCDD-inducible poly(ADP-ribose) polymerase (TiPARP) during infection. Knockdown of TiPARP reduced viral replication and increased interferon expression, suggesting that TiPARP functions in a proviral manner during MHV infection. We also show that MHV replication induced the expression of other genes known to be downstream of AhR in macrophages and dendritic cells and in livers of infected mice. Further, we found that chemically inhibiting or activating AhR reciprocally modulated the expression levels of cytokines induced by infection, specifically, interleukin 1β (IL-1β), IL-10, and tumor necrosis factor alpha (TNF-α), consistent with a role for AhR activation in the host response to MHV infection. Furthermore, while indoleamine 2,3-dioxygenase (IDO1) drives AhR activation in other settings, MHV infection induced equal expression of downstream genes in wild-type (WT) and IDO1-/- macrophages, suggesting an alternative pathway of AhR activation. In summary, we show that coronaviruses elicit AhR activation by an IDO1-independent pathway, contributing to upregulation of downstream effectors, including the proviral factor TiPARP, and to modulation of cytokine gene expression, and we identify a previously unappreciated role for AhR signaling in CoV pathogenesis.IMPORTANCE Coronaviruses are a family of positive-sense RNA viruses with human and agricultural significance. Characterizing the mechanisms by which coronavirus infection dictates pathogenesis or counters the host immune response would provide targets for the development of therapeutics. Here, we show that the aryl hydrocarbon receptor (AhR) is activated in cells infected with a prototypic coronavirus, mouse hepatitis virus (MHV), resulting in the expression of several effector genes. AhR is important for modulation of the host immune response to MHV and plays a role in the expression of TiPARP, which we show is required for maximal viral replication. Taken together, our findings highlight a previously unidentified role for AhR in regulating coronavirus replication and the immune response to the virus.
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Affiliation(s)
- Matthew E Grunewald
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Mohamed G Shaban
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Samantha R Mackin
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Anthony R Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
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30
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Channappanavar R, Fehr AR, Zheng J, Wohlford-Lenane C, Abrahante JE, Mack M, Sompallae R, McCray PB, Meyerholz DK, Perlman S. IFN-I response timing relative to virus replication determines MERS coronavirus infection outcomes. J Clin Invest 2019; 129:3625-3639. [PMID: 31355779 DOI: 10.1172/jci126363] [Citation(s) in RCA: 399] [Impact Index Per Article: 79.8] [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: 11/21/2018] [Accepted: 06/04/2019] [Indexed: 12/12/2022] Open
Abstract
Type 1 IFNs (IFN-I) generally protect mammalian hosts from virus infections, but in some cases, IFN-I is pathogenic. Because IFN-I is protective, it is commonly used to treat virus infections for which no specific approved drug or vaccine is available. The Middle East respiratory syndrome-coronavirus (MERS-CoV) is such an infection, yet little is known about the role of IFN-I in this setting. Here, we show that IFN-I signaling is protective during MERS-CoV infection. Blocking IFN-I signaling resulted in delayed virus clearance, enhanced neutrophil infiltration, and impaired MERS-CoV-specific T cell responses. Notably, IFN-I administration within 1 day after infection (before virus titers peak) protected mice from lethal infection, despite a decrease in IFN-stimulated gene (ISG) and inflammatory cytokine gene expression. In contrast, delayed IFN-β treatment failed to effectively inhibit virus replication, increased infiltration and activation of monocytes, macrophages, and neutrophils in the lungs, and enhanced proinflammatory cytokine expression, resulting in fatal pneumonia in an otherwise sublethal infection. Together, these results suggest that the relative timing of the IFN-I response and maximal virus replication is key in determining outcomes, at least in infected mice. By extension, IFN-αβ or combination therapy may need to be used cautiously to treat viral infections in clinical settings.
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Affiliation(s)
- Rudragouda Channappanavar
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA.,Department of Acute and Tertiary Care, and.,Department of Microbiology and Immunology, University of Tennessee Health Sciences Center, Memphis, Tennessee, USA
| | - Anthony R Fehr
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Jian Zheng
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
| | | | - Juan E Abrahante
- University of Minnesota Informatics Institute, University of Minnesota, Minneapolis, Minnesota, USA
| | - Matthias Mack
- Department of Internal Medicine, University Hospital Regensburg, Regensburg, Germany
| | | | - Paul B McCray
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA.,Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA
| | | | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA.,Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA.,State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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31
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Grunewald ME, Chen Y, Kuny C, Maejima T, Lease R, Ferraris D, Aikawa M, Sullivan CS, Perlman S, Fehr AR. The coronavirus macrodomain is required to prevent PARP-mediated inhibition of virus replication and enhancement of IFN expression. PLoS Pathog 2019; 15:e1007756. [PMID: 31095648 PMCID: PMC6521996 DOI: 10.1371/journal.ppat.1007756] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [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: 01/25/2019] [Accepted: 04/09/2019] [Indexed: 12/20/2022] Open
Abstract
ADP-ribosylation is a ubiquitous post-translational addition of either monomers or polymers of ADP-ribose to target proteins by ADP-ribosyltransferases, usually by interferon-inducible diphtheria toxin-like enzymes known as PARPs. While several PARPs have known antiviral activities, these activities are mostly independent of ADP-ribosylation. Consequently, less is known about the antiviral effects of ADP-ribosylation. Several viral families, including Coronaviridae, Togaviridae, and Hepeviridae, encode for macrodomain proteins that bind to and hydrolyze ADP-ribose from proteins and are critical for optimal replication and virulence. These results suggest that macrodomains counter cellular ADP-ribosylation, but whether PARPs or, alternatively, other ADP-ribosyltransferases cause this modification is not clear. Here we show that pan-PARP inhibition enhanced replication and inhibited interferon production in primary macrophages infected with macrodomain-mutant but not wild-type coronavirus. Specifically, knockdown of two abundantly expressed PARPs, PARP12 and PARP14, led to increased replication of mutant but did not significantly affect wild-type virus. PARP14 was also important for the induction of interferon in mouse and human cells, indicating a critical role for this PARP in the regulation of innate immunity. In summary, these data demonstrate that the macrodomain is required to prevent PARP-mediated inhibition of coronavirus replication and enhancement of interferon production. ADP-ribosylation, an understudied post-translational modification, facilitates the host response to virus infection. Several viruses, including all members of the coronavirus family, encode a macrodomain to reverse ADP-ribosylation and combat this immune response. As such, viruses with mutations in the macrodomain are highly attenuated and cause minimal disease in vivo. Here, using primary macrophages and mice infected with a pathogenic murine coronavirus, we identify PARPs, specifically PARP12 and PARP14, as host cell ADP-ribosylating enzymes important for the attenuation of these mutant viruses and confirm their importance using inhibitors and siRNAs. These data demonstrate a broad strategy of virus-host interactions and indicate that the macrodomain may be a useful target for antiviral therapy.
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Affiliation(s)
- Matthew E. Grunewald
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, United States of America
| | - Yating Chen
- Department of Molecular Biosciences, University of Texas, Austin, TX, United States of America
| | - Chad Kuny
- Department of Molecular Biosciences, University of Texas, Austin, TX, United States of America
| | - Takashi Maejima
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Robert Lease
- McDaniel College, Westminster, MD, United States of America
| | - Dana Ferraris
- McDaniel College, Westminster, MD, United States of America
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Christopher S. Sullivan
- Department of Molecular Biosciences, University of Texas, Austin, TX, United States of America
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, United States of America
- * E-mail: (SP); (ARF)
| | - Anthony R. Fehr
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, United States of America
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States of America
- * E-mail: (SP); (ARF)
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32
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Fehr AR, Jankevicius G, Ahel I, Perlman S. Viral Macrodomains: Unique Mediators of Viral Replication and Pathogenesis. Trends Microbiol 2018; 26:598-610. [PMID: 29268982 PMCID: PMC6003825 DOI: 10.1016/j.tim.2017.11.011] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [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: 09/27/2017] [Revised: 11/16/2017] [Accepted: 11/30/2017] [Indexed: 12/20/2022]
Abstract
Viruses from the Coronaviridae, Togaviridae, and Hepeviridae families all contain genes that encode a conserved protein domain, called a macrodomain; however, the role of this domain during infection has remained enigmatic. The recent discovery that mammalian macrodomain proteins enzymatically remove ADP-ribose, a common post-translation modification, from proteins has led to an outburst of studies describing both the enzymatic activity and function of viral macrodomains. These new studies have defined these domains as de-ADP-ribosylating enzymes, which indicates that these viruses have evolved to counteract antiviral ADP-ribosylation, likely mediated by poly-ADP-ribose polymerases (PARPs). Here, we comprehensively review this rapidly expanding field, describing the structures and enzymatic activities of viral macrodomains, and discussing their roles in viral replication and pathogenesis.
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Affiliation(s)
- Anthony R Fehr
- University of Iowa, Department of Microbiology and Immunology, Iowa City, IA 52242, USA; These authors contributed equally to this manuscript.
| | - Gytis Jankevicius
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK; These authors contributed equally to this manuscript
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Stanley Perlman
- University of Iowa, Department of Microbiology and Immunology, Iowa City, IA 52242, USA.
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33
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Galasiti Kankanamalage AC, Kim Y, Damalanka VC, Rathnayake AD, Fehr AR, Mehzabeen N, Battaile KP, Lovell S, Lushington GH, Perlman S, Chang KO, Groutas WC. Structure-guided design of potent and permeable inhibitors of MERS coronavirus 3CL protease that utilize a piperidine moiety as a novel design element. Eur J Med Chem 2018; 150:334-346. [PMID: 29544147 PMCID: PMC5891363 DOI: 10.1016/j.ejmech.2018.03.004] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [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: 10/07/2017] [Revised: 02/28/2018] [Accepted: 03/01/2018] [Indexed: 01/17/2023]
Abstract
There are currently no approved vaccines or small molecule therapeutics available for the prophylaxis or treatment of Middle East Respiratory Syndrome coronavirus (MERS-CoV) infections. MERS-CoV 3CL protease is essential for viral replication; consequently, it is an attractive target that provides a potentially effective means of developing small molecule therapeutics for combatting MERS-CoV. We describe herein the structure-guided design and evaluation of a novel class of inhibitors of MERS-CoV 3CL protease that embody a piperidine moiety as a design element that is well-suited to exploiting favorable subsite binding interactions to attain optimal pharmacological activity and PK properties. The mechanism of action of the compounds and the structural determinants associated with binding were illuminated using X-ray crystallography.
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Affiliation(s)
| | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Vishnu C Damalanka
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | - Athri D Rathnayake
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
| | - Anthony R Fehr
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Nurjahan Mehzabeen
- Protein Structure Laboratory, The University of Kansas, Lawrence, KS 66047, USA
| | - Kevin P Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, APS Argonne National Laboratory, Argonne, IL 60439, USA
| | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Lawrence, KS 66047, USA
| | | | - Stanley Perlman
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
| | - William C Groutas
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA.
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34
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Abstract
ADP-ribosylation is a common post-translational modification, although how it modulates RNA virus infection is not well understood. While screening for ADP-ribosylated proteins during coronavirus (CoV) infection, we detected a ~55kDa ADP-ribosylated protein in mouse hepatitis virus (MHV)-infected cells and in virions, which we identified as the viral nucleocapsid (N) protein. The N proteins of porcine epidemic diarrhea virus (PEDV), severe acute respiratory syndrome (SARS)-CoV and Middle East respiratory syndrome (MERS)-CoV were also ADP-ribosylated. ADP-ribosylation of N protein was also observed in cells exogenously expressing N protein by transduction using Venezuelan equine encephalitis virus replicon particles (VRPs). However, plasmid-derived N protein was not ADP-ribosylated following transient transfection but was ADP-ribosylated after MHV infection, indicating that this modification requires virus infection. In conclusion, we have identified a novel post-translation modification of the CoV N protein that may play a regulatory role for this important structural protein.
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Affiliation(s)
- Matthew E Grunewald
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, 51 Newton Road, Iowa City, IA 52242, United States
| | - Anthony R Fehr
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, 51 Newton Road, Iowa City, IA 52242, United States
| | - Jeremiah Athmer
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, 51 Newton Road, Iowa City, IA 52242, United States
| | - Stanley Perlman
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, 51 Newton Road, Iowa City, IA 52242, United States.
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35
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Canton J, Fehr AR, Fernandez-Delgado R, Gutierrez-Alvarez FJ, Sanchez-Aparicio MT, García-Sastre A, Perlman S, Enjuanes L, Sola I. MERS-CoV 4b protein interferes with the NF-κB-dependent innate immune response during infection. PLoS Pathog 2018; 14:e1006838. [PMID: 29370303 PMCID: PMC5800688 DOI: 10.1371/journal.ppat.1006838] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 02/06/2018] [Accepted: 12/21/2017] [Indexed: 12/28/2022] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is a novel human coronavirus that emerged in 2012, causing severe pneumonia and acute respiratory distress syndrome (ARDS), with a case fatality rate of ~36%. When expressed in isolation, CoV accessory proteins have been shown to interfere with innate antiviral signaling pathways. However, there is limited information on the specific contribution of MERS-CoV accessory protein 4b to the repression of the innate antiviral response in the context of infection. We found that MERS-CoV 4b was required to prevent a robust NF-κB dependent response during infection. In wild-type virus infected cells, 4b localized to the nucleus, while NF-κB was retained in the cytoplasm. In contrast, in the absence of 4b or in the presence of cytoplasmic 4b mutants lacking a nuclear localization signal (NLS), NF-κB was translocated to the nucleus leading to the expression of pro-inflammatory cytokines. This indicates that NF-κB repression required the nuclear import of 4b mediated by a specific NLS. Interestingly, we also found that both in isolation and during infection, 4b interacted with α-karyopherin proteins in an NLS-dependent manner. In particular, 4b had a strong preference for binding karyopherin-α4 (KPNA4), which is known to translocate the NF-κB protein complex into the nucleus. Binding of 4b to KPNA4 during infection inhibited its interaction with NF-κB-p65 subunit. Thereby we propose a model where 4b outcompetes NF-κB for KPNA4 binding and translocation into the nucleus as a mechanism of interference with the NF-κB-mediated innate immune response.
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Affiliation(s)
- Javier Canton
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Anthony R. Fehr
- Department of Microbiology and Immunology, University of Iowa Carver College of Medicine, Iowa City, IA, United States of America
| | - Raúl Fernandez-Delgado
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | | | - Maria T. Sanchez-Aparicio
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Global Health and Emerging Pathogens Institute. Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Global Health and Emerging Pathogens Institute. Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa Carver College of Medicine, Iowa City, IA, United States of America
| | - Luis Enjuanes
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Isabel Sola
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
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36
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Channappanavar R, Fehr AR, Vijay R, Mack M, Zhao J, Meyerholz DK, Perlman S. Dysregulated Type I Interferon and Inflammatory Monocyte-Macrophage Responses Cause Lethal Pneumonia in SARS-CoV-Infected Mice. Cell Host Microbe 2016; 19:181-93. [PMID: 26867177 PMCID: PMC4752723 DOI: 10.1016/j.chom.2016.01.007] [Citation(s) in RCA: 1098] [Impact Index Per Article: 137.3] [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] [Received: 07/29/2015] [Revised: 11/30/2015] [Accepted: 01/22/2016] [Indexed: 02/08/2023]
Abstract
Highly pathogenic human respiratory coronaviruses cause acute lethal disease characterized by exuberant inflammatory responses and lung damage. However, the factors leading to lung pathology are not well understood. Using mice infected with SARS (severe acute respiratory syndrome)-CoV, we show that robust virus replication accompanied by delayed type I interferon (IFN-I) signaling orchestrates inflammatory responses and lung immunopathology with diminished survival. IFN-I remains detectable until after virus titers peak, but early IFN-I administration ameliorates immunopathology. This delayed IFN-I signaling promotes the accumulation of pathogenic inflammatory monocyte-macrophages (IMMs), resulting in elevated lung cytokine/chemokine levels, vascular leakage, and impaired virus-specific T cell responses. Genetic ablation of the IFN-αβ receptor (IFNAR) or IMM depletion protects mice from lethal infection, without affecting viral load. These results demonstrate that IFN-I and IMM promote lethal SARS-CoV infection and identify IFN-I and IMMs as potential therapeutic targets in patients infected with pathogenic coronavirus and perhaps other respiratory viruses. SARS-CoV causes a lethal respiratory infection in BALB/c mice Robust SARS-CoV replication and delayed IFN-I signaling promote disease IFN-I induces influx of pathogenic inflammatory monocytes and vascular leakage Disease severity is ameliorated in the absence of IFN signaling
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Affiliation(s)
| | - Anthony R Fehr
- Department of Microbiology, University of Iowa, Iowa City, IA 52242, USA
| | - Rahul Vijay
- Interdisciplinary Program in Immunology, University of Iowa, Iowa City, IA 52242, USA
| | - Matthias Mack
- Department of Internal Medicine, University Hospital Regensburg, Regensburg 93042, Germany
| | - Jincun Zhao
- Department of Microbiology, University of Iowa, Iowa City, IA 52242, USA; State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - David K Meyerholz
- Department of Pathology, University of Iowa, Iowa City, IA 52242, USA
| | - Stanley Perlman
- Department of Microbiology, University of Iowa, Iowa City, IA 52242, USA; Interdisciplinary Program in Immunology, University of Iowa, Iowa City, IA 52242, USA.
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Abstract
In 2012, a zoonotic coronavirus was identified as the causative agent of Middle East respiratory syndrome and was named MERS coronavirus (MERS-CoV). As of August 11, 2016, the virus has infected 1,791 patients, with a mortality rate of 35.6%. Although MERS-CoV generally causes subclinical or mild disease, infection can result in serious outcomes, including acute respiratory distress syndrome and multi-organ failure in patients with comorbidities. The virus is endemic in camels in the Arabian Peninsula and Africa and thus poses a consistent threat of frequent reintroduction into human populations. Disease prevalence will increase substantially if the virus mutates to increase human-to-human transmissibility. No therapeutics or vaccines are approved for MERS; thus, development of novel therapies is needed. Further, since many MERS cases are acquired in healthcare settings, public health measures and scrupulous attention to infection control are required to prevent additional MERS outbreaks.
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Affiliation(s)
| | | | - Stanley Perlman
- Department of Microbiology, University of Iowa, Iowa City, Iowa 52242;
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38
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Abstract
Coronaviruses (CoVs), enveloped positive-sense RNA viruses, are characterized by club-like spikes that project from their surface, an unusually large RNA genome, and a unique replication strategy. Coronaviruses cause a variety of diseases in mammals and birds ranging from enteritis in cows and pigs and upper respiratory disease in chickens to potentially lethal human respiratory infections. Here we provide a brief introduction to coronaviruses discussing their replication and pathogenicity, and current prevention and treatment strategies. We also discuss the outbreaks of the highly pathogenic Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and the recently identified Middle Eastern Respiratory Syndrome Coronavirus (MERS-CoV).
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Affiliation(s)
- Anthony R Fehr
- Department of Microbiology, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
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39
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Caffarelli N, Fehr AR, Yu D. Cyclin A degradation by primate cytomegalovirus protein pUL21a counters its innate restriction of virus replication. PLoS Pathog 2013; 9:e1003825. [PMID: 24385906 PMCID: PMC3873445 DOI: 10.1371/journal.ppat.1003825] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Accepted: 10/28/2013] [Indexed: 12/13/2022] Open
Abstract
Cyclin A is critical for cellular DNA synthesis and S phase progression of the cell cycle. Human cytomegalovirus (HCMV) can reduce cyclin A levels and block cellular DNA synthesis, and cyclin A overexpression can repress HCMV replication. This interaction has only been previously observed in HCMV as murine CMV does not downregulate cyclin A, and the responsible viral factor has not been identified. We previously reported that the HCMV protein pUL21a disrupted the anaphase-promoting complex (APC), but a point mutant abrogating this activity did not phenocopy a UL21a-deficient virus, suggesting that pUL21a has an additional function. Here we identified a conserved arginine-x-leucine (RxL) cyclin-binding domain within pUL21a, which allowed pUL21a to interact with cyclin A and target it for proteasome degradation. Homologous pUL21a proteins from both chimpanzee and rhesus CMVs also contained the RxL domain and similarly degraded cyclin A, indicating that this function is conserved in primate CMVs. The RxL point mutation disabled the virus' ability to block cellular DNA synthesis and resulted in a growth defect similar to pUL21a-deficient virus. Importantly, knockdown of cyclin A rescued growth of UL21a-deficient virus. Together, these data show that during evolution, the pUL21a family proteins of primate CMVs have acquired a cyclin-binding domain that targets cyclin A for degradation, thus neutralizing its restriction on virus replication. Finally, the combined proteasome-dependent degradation of pUL21a and its cellular targets suggests that pUL21a may act as a novel suicide protein, targeting its protein cargos for destruction. Cyclins are evolutionarily conserved proteins that associate with cyclin-dependent kinases (CDKs) to regulate phosphorylation of multiple substrates to promote cell-cycle progression. Many viruses manipulate the cell cycle in order to create an environment suitable for replication; however, only few examples exist where viruses modulate cyclin activity. Here, we identified a cyclin-binding domain within the human cytomegalovirus (HCMV) protein pUL21a that confers its ability to interact with cyclin A and target it for proteasome degradation. Cyclin A promotes cellular DNA replication, which consumes important enzymes and metabolites needed for viral replication, making it important for large viruses like HCMV to block this protein's activity. In accord, the ability of pUL21a to degrade cyclin A was necessary for the virus to block cellular DNA replication and promote viral replication. Importantly, ablating cyclin A expression restored replication to a virus lacking pUL21a, demonstrating that cyclin A has the intrinsic ability to restrict viral replication, but is specifically countered by pUL21a. Together with our previous work showing that pUL21a also regulates the anaphase-promoting complex, another master cell cycle regulator, our studies have now revealed that HCMV has elegantly evolved dual functions within one protein targeting the cell cycle machinery for viral replication.
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Affiliation(s)
- Nicolas Caffarelli
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Anthony R. Fehr
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Dong Yu
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, United States of America
- * E-mail: ,
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Fuchs EL, Brutinel ED, Klem ER, Fehr AR, Yahr TL, Wolfgang MC. In vitro and in vivo characterization of the Pseudomonas aeruginosa cyclic AMP (cAMP) phosphodiesterase CpdA, required for cAMP homeostasis and virulence factor regulation. J Bacteriol 2010; 192:2779-90. [PMID: 20348254 PMCID: PMC2876501 DOI: 10.1128/jb.00168-10] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Accepted: 03/16/2010] [Indexed: 12/19/2022] Open
Abstract
Cyclic AMP (cAMP) is an important second messenger signaling molecule that controls a wide variety of eukaryotic and prokaryotic responses to extracellular cues. For cAMP-dependent signaling pathways to be effective, the intracellular cAMP concentration is tightly controlled at the level of synthesis and degradation. In the opportunistic human pathogen Pseudomonas aeruginosa, cAMP is a key regulator of virulence gene expression. To better understand the role of cAMP homeostasis in this organism, we identified and characterized the enzyme CpdA, a putative cAMP phosphodiesterase. We demonstrate that CpdA possesses 3',5'-cAMP phosphodiesterase activity in vitro and that it utilizes an iron-dependent catalytic mechanism. Deletion of cpdA results in the accumulation of intracellular cAMP and altered regulation of P. aeruginosa virulence traits. Further, we demonstrate that the cAMP-dependent transcription factor Vfr directly regulates cpdA expression in response to intracellular cAMP accumulation, thus providing a feedback mechanism for controlling cAMP levels and fine-tuning virulence factor expression.
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Affiliation(s)
- Erin L. Fuchs
- Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, Department of Microbiology, University of Iowa, Iowa City, Iowa 52242, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Evan D. Brutinel
- Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, Department of Microbiology, University of Iowa, Iowa City, Iowa 52242, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Erich R. Klem
- Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, Department of Microbiology, University of Iowa, Iowa City, Iowa 52242, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Anthony R. Fehr
- Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, Department of Microbiology, University of Iowa, Iowa City, Iowa 52242, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Timothy L. Yahr
- Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, Department of Microbiology, University of Iowa, Iowa City, Iowa 52242, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Matthew C. Wolfgang
- Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, Department of Microbiology, University of Iowa, Iowa City, Iowa 52242, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
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