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Su X, Ma W, Feng D, Cheng B, Wang Q, Guo Z, Zhou D, Tang X. Efficient Inhibition of SARS‐CoV‐2 Using Chimeric Antisense Oligonucleotides through RNase L Activation**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Xiaoxuan Su
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Road Beijing 100191 China
| | - Wenxiao Ma
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Road Beijing 100191 China
| | - Di Feng
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Road Beijing 100191 China
| | - Boyang Cheng
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Road Beijing 100191 China
| | - Qian Wang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Road Beijing 100191 China
| | - Zefeng Guo
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Road Beijing 100191 China
| | - Demin Zhou
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Road Beijing 100191 China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38, Xueyuan Road Beijing 100191 China
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102
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Panigrahi D. Molecular Docking Analysis of the Phytochemicals from Tinospora Cordifolia as Potential Inhibitor Against Multi Targeted SARS-CoV-2 & Cytokine Storm. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416521500277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV)-2, a novel coronavirus, is a member of the Coronoviridae family that has spread worldwide. Developing efficacious therapeutics for the treatment of SARS-CoV-2 is of high priority. Therefore, in this study, the chemical constituents obtained from Tinospora cordifolia are investigated for their in-silico interaction with protein targets crucial for SARSCoV-2 infection and cytokine storm. The five important targets chosen for SARSCoV-2 were the main protease (Mpro), Spike receptor binding domain (Spike-RBD), RNA-dependent RNA polymerase (RdRp or Nsp12), nonstructural protein 15 (Nsp15) of SARS-CoV-2 and the host angiotensin converting enzyme-2 (ACE-2) spike-RBD binding domain and cytokine receptors TNF-[Formula: see text] (Tumor Necrosis Factor-[Formula: see text]) and IL-6 (Interleukine-6). This was accomplished using Maestro 12.4 (Schrodinger Suite) to obtain docking scores. Also, the absorption, distribution, metabolism, elimination, and toxicity parameters (ADMET) were determined using Maestro QikProp modules. The results of computational study revealed that four constituents Cordifolioside-A, Palmatoside-E, Tinocordioside and Tinosporaside significantly antagonize the five targets of SARS-CoV-2 by binding in the binding pocket with docking score ranging from −9.664 to −6.488 kcal/mol and shows drug-like property and also effectively inhibit cytokine storm by antagonizing the TNF-[Formula: see text] and IL-6 receptors. Promising drug-like properties, excellent docking scores, and binding pose against each target makes the screened compounds as possible lead candidate which can be further evaluated in future studies to assess their in vitro and in vivo efficacy against SARS-CoV-2. The structure of these compounds can be used further for optimization and design of drugs against COVID-19.
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Affiliation(s)
- Debadash Panigrahi
- Drug Research Laboratory, Nodal Research Centre, College of Pharmaceutical Sciences, Puri, Baliguali, Puri-Konark Marine Drive Road, Puri, Odisha 752002, India
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103
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Nguyen HT, Falzarano D, Gerdts V, Liu Q. Construction of a Noninfectious SARS-CoV-2 Replicon for Antiviral-Drug Testing and Gene Function Studies. J Virol 2021; 95:e0068721. [PMID: 34191580 PMCID: PMC8387049 DOI: 10.1128/jvi.00687-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/25/2021] [Indexed: 01/01/2023] Open
Abstract
The emerging coronavirus disease 2019 (COVID-19) outbreak caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread worldwide, resulting in global public health emergencies and economic crises. In the present study, a noninfectious and biosafety level 2 (BSL2)-compatible SARS-CoV-2 replicon expressing a nano luciferase (nLuc) reporter was constructed in a bacterial artificial chromosomal (BAC) vector by reverse genetics. The nLuc reporter is highly sensitive, easily quantifiable, and high throughput adaptable. Upon transfecting the SARS-CoV-2 replicon BAC plasmid DNA into Vero E6 cells, we could detect high levels of nLuc reporter activity and viral RNA transcript, suggesting the replication of the replicon. The replicon replication was further demonstrated by the findings that deleting nonstructural protein 15 or mutating its catalytic sites significantly reduced replicon replication, whereas providing the nucleocapsid protein in trans enhanced replicon replication in a dose-dependent manner. Finally, we showed that remdesivir, a U.S. Food and Drug Administration-approved antiviral drug, significantly inhibited the replication of the replicon, providing proof of principle for the application of our replicon as a useful tool for developing antivirals. Taken together, this study established a sensitive and BSL2-compatible reporter system in a single BAC plasmid for investigating the functions of SARS-CoV-2 proteins in viral replication and evaluating antiviral compounds. This should contribute to the global effort to combat this deadly viral pathogen. IMPORTANCE The COVID-19 pandemic caused by SARS-CoV-2 is having a catastrophic impact on human lives. Combatting the pandemic requires effective vaccines and antiviral drugs. In the present study, we developed a SARS-CoV-2 replicon system with a sensitive and easily quantifiable reporter. Unlike studies involving infectious SARS-CoV-2 virus that must be performed in a biosafety level 3 (BSL3) facility, the replicon is noninfectious and thus can be safely used in BSL2 laboratories. The replicon will provide a valuable tool for testing antiviral drugs and studying SARS-CoV-2 biology.
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Affiliation(s)
- Hai Trong Nguyen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Darryl Falzarano
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Volker Gerdts
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Qiang Liu
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Vaccinology and Immunotherapeutics, School of Public Health, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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104
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Frazier MN, Dillard LB, Krahn JM, Perera L, Williams JG, Wilson IM, Stewart ZD, Pillon MC, Deterding LJ, Borgnia MJ, Stanley RE. Characterization of SARS2 Nsp15 nuclease activity reveals it's mad about U. Nucleic Acids Res 2021; 49:10136-10149. [PMID: 34403466 PMCID: PMC8385992 DOI: 10.1093/nar/gkab719] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/04/2021] [Accepted: 08/09/2021] [Indexed: 12/18/2022] Open
Abstract
Nsp15 is a uridine specific endoribonuclease that coronaviruses employ to cleave viral RNA and evade host immune defense systems. Previous structures of Nsp15 from across Coronaviridae revealed that Nsp15 assembles into a homo-hexamer and has a conserved active site similar to RNase A. Beyond a preference for cleaving RNA 3′ of uridines, it is unknown if Nsp15 has any additional substrate preferences. Here, we used cryo-EM to capture structures of Nsp15 bound to RNA in pre- and post-cleavage states. The structures along with molecular dynamics and biochemical assays revealed critical residues involved in substrate specificity, nuclease activity, and oligomerization. Moreover, we determined how the sequence of the RNA substrate dictates cleavage and found that outside of polyU tracts, Nsp15 has a strong preference for purines 3′ of the cleaved uridine. This work advances our understanding of how Nsp15 recognizes and processes viral RNA, and will aid in the development of new anti-viral therapeutics.
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Affiliation(s)
- Meredith N Frazier
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Lucas B Dillard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Juno M Krahn
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Lalith Perera
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Jason G Williams
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Isha M Wilson
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Zachary D Stewart
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Monica C Pillon
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Leesa J Deterding
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Robin E Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
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105
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Detection of SARS-CoV-2 Derived Small RNAs and Changes in Circulating Small RNAs Associated with COVID-19. Viruses 2021; 13:v13081593. [PMID: 34452458 PMCID: PMC8402885 DOI: 10.3390/v13081593] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 12/17/2022] Open
Abstract
Cleavage of double-stranded RNA is described as an evolutionary conserved host defense mechanism against viral infection. Small RNAs are the product and triggers of post transcriptional gene silencing events. Up until now, the relevance of this mechanism for SARS-CoV-2-directed immune responses remains elusive. Herein, we used high throughput sequencing to profile the plasma of active and convalescent COVID-19 patients for the presence of small circulating RNAs. The existence of SARS-CoV-2 derived small RNAs in plasma samples of mild and severe COVID-19 cases is described. Clusters of high siRNA abundance were discovered, homologous to the nsp2 3′-end and nsp4 virus sequence. Four virus-derived small RNA sequences have the size of human miRNAs, and a target search revealed candidate genes associated with ageusia and long COVID symptoms. These virus-derived small RNAs were detectable also after recovery from the disease. The additional analysis of circulating human miRNAs revealed differentially abundant miRNAs, discriminating mild from severe cases. A total of 29 miRNAs were reduced or absent in severe cases. Several of these are associated with JAK-STAT response and cytokine storm.
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106
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Bhavaniramya S, Ramar V, Vishnupriya S, Palaniappan R, Sibiya A, Baskaralingam V. Comprehensive analysis of SARS-COV-2 drug targets and pharmacological aspects in treating the COVID-19. Curr Mol Pharmacol 2021; 15:393-417. [PMID: 34382513 DOI: 10.2174/1874467214666210811120635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/27/2021] [Accepted: 02/22/2021] [Indexed: 11/22/2022]
Abstract
Corona viruses are enveloped, single-stranded RNA (Ribonucleic acid) viruses and they cause pandemic diseases having a devastating effect on both human healthcare and the global economy. To date, six corona viruses have been identified as pathogenic organisms which are significantly responsible for the infection and also cause severe respiratory diseases. Among them, the novel SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) caused a major outbreak of corona virus diseases 2019 (COVID-19). Coronaviridae family members can affects both humans and animals. In human, corona viruses cause severe acute respiratory syndrome with mild to severe outcomes. Several structural and genomics have been investigated, and the genome encodes about 28 proteins most of them with unknown function though it shares remarkable sequence identity with other proteins. There is no potent and licensed vaccine against SARS-CoV-2 and several trials are underway to investigate the possible therapeutic agents against viral infection. However, some of the antiviral drugs that have been investigated against SARS-CoV-2 are under clinical trials. In the current review we comparatively emphasize the emergence and pathogenicity of the SARS-CoV-2 and their infection and discuss the various putative drug targets of both viral and host receptors for developing effective vaccines and therapeutic combinations to overcome the viral outbreak.
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Affiliation(s)
- Sundaresan Bhavaniramya
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Karaikudi 630004, Tamil Nadu. India
| | - Vanajothi Ramar
- Department of Biomedical Science, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024. India
| | - Selvaraju Vishnupriya
- College of Food and Dairy Technology, Tamil Nadu Veterinary and Animal Sciences University, Chennai 600052. India
| | - Ramasamy Palaniappan
- Research and Development Wing, Sree Balaji Medical College and Hospital, Bharath Institute of Higher Education (BIHER), Chennai-600044, Tamilnadu. India
| | - Ashokkumar Sibiya
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Karaikudi 630004, Tamil Nadu. India
| | - Vaseeharan Baskaralingam
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Karaikudi 630004, Tamil Nadu. India
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107
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Bai C, Zhong Q, Gao GF. Overview of SARS-CoV-2 genome-encoded proteins. SCIENCE CHINA-LIFE SCIENCES 2021; 65:280-294. [PMID: 34387838 PMCID: PMC8362648 DOI: 10.1007/s11427-021-1964-4] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/17/2021] [Indexed: 02/06/2023]
Abstract
Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) has spread rapidly throughout the world. SARS-CoV-2 is an enveloped, plus-stranded RNA virus with a single-stranded RNA genome of approximately 30,000 nucleotides. The SARS-CoV-2 genome encodes 29 proteins, including 16 nonstructural, 4 structural and 9 accessory proteins. To date, over 1,228 experimental structures of SARS-CoV-2 proteins have been deposited in the Protein Data Bank (PDB), including 16 protein structures, two functional domain structures of nucleocapsid (N) protein, and scores of complexes. Overall, they exhibit high similarity to SARS-CoV proteins. Here, we summarize the progress of structural and functional research on SARS-CoV-2 proteins. These studies provide structural and functional insights into proteins of SARS-CoV-2, and further elucidate the daedal relationship between different components at the atomic level in the viral life cycle, including attachment to the host cell, viral genome replication and transcription, genome packaging and assembly, and virus release. It is important to understand the structural and functional properties of SARS-CoV-2 proteins as it will facilitate the development of anti-CoV drugs and vaccines to prevent and control the current SARS-CoV-2 pandemic.
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Affiliation(s)
- Chongzhi Bai
- CAS Key Laboratory of Pathogenic Microbiology & Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,Central Laboratory, Shanxi Province Hospital of Traditional Chinese Medicine, Taiyuan, 030012, China.,Shanxi Academy of Advanced Research and Innovation, Taiyuan, 030032, China
| | - Qiming Zhong
- Central Laboratory, Shanxi Province Hospital of Traditional Chinese Medicine, Taiyuan, 030012, China
| | - George Fu Gao
- CAS Key Laboratory of Pathogenic Microbiology & Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China. .,Shanxi Academy of Advanced Research and Innovation, Taiyuan, 030032, China.
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108
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Inde Z, Croker BA, Yapp C, Joshi GN, Spetz J, Fraser C, Qin X, Xu L, Deskin B, Ghelfi E, Webb G, Carlin AF, Zhu YP, Leibel SL, Garretson AF, Clark AE, Duran JM, Pretorius V, Crotty-Alexander LE, Li C, Lee JC, Sodhi C, Hackam DJ, Sun X, Hata AN, Kobzik L, Miller J, Park JA, Brownfield D, Jia H, Sarosiek KA. Age-dependent regulation of SARS-CoV-2 cell entry genes and cell death programs correlates with COVID-19 severity. SCIENCE ADVANCES 2021; 7:eabf8609. [PMID: 34407940 PMCID: PMC8373124 DOI: 10.1126/sciadv.abf8609] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 06/25/2021] [Indexed: 05/02/2023]
Abstract
Novel coronavirus disease 2019 (COVID-19) severity is highly variable, with pediatric patients typically experiencing less severe infection than adults and especially the elderly. The basis for this difference is unclear. We find that mRNA and protein expression of angiotensin-converting enzyme 2 (ACE2), the cell entry receptor for the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes COVID-19, increases with advancing age in distal lung epithelial cells. However, in humans, ACE2 expression exhibits high levels of intra- and interindividual heterogeneity. Further, cells infected with SARS-CoV-2 experience endoplasmic reticulum stress, triggering an unfolded protein response and caspase-mediated apoptosis, a natural host defense system that halts virion production. Apoptosis of infected cells can be selectively induced by treatment with apoptosis-modulating BH3 mimetic drugs. Notably, epithelial cells within young lungs and airways are more primed to undergo apoptosis than those in adults, which may naturally hinder virion production and support milder COVID-19 severity.
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Affiliation(s)
- Zintis Inde
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
| | - Ben A Croker
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Clarence Yapp
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
- Image and Data Analysis Core, Harvard Medical School, Boston, MA, USA
| | - Gaurav N Joshi
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
- Integrated Cellular Imaging Core, Emory University, Atlanta, GA, USA
| | - Johan Spetz
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
| | - Cameron Fraser
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
| | - Xingping Qin
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
| | - Le Xu
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Brian Deskin
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Elisa Ghelfi
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Gabrielle Webb
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Aaron F Carlin
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Yanfang Peipei Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Sandra L Leibel
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - Aaron F Garretson
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Alex E Clark
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jason M Duran
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Victor Pretorius
- Department of Surgery, University of California San Diego, La Jolla, CA, USA
| | | | - Chendi Li
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jamie Casey Lee
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Chhinder Sodhi
- Department of Surgery, Johns Hopkins University, Baltimore, MD, USA
| | - David J Hackam
- Department of Surgery, Johns Hopkins University, Baltimore, MD, USA
| | - Xin Sun
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Aaron N Hata
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Lester Kobzik
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jeffrey Miller
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jin-Ah Park
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Douglas Brownfield
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Hongpeng Jia
- Department of Surgery, Johns Hopkins University, Baltimore, MD, USA
| | - Kristopher A Sarosiek
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA
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109
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Min YQ, Huang M, Sun X, Deng F, Wang H, Ning YJ. Immune evasion of SARS-CoV-2 from interferon antiviral system. Comput Struct Biotechnol J 2021; 19:4217-4225. [PMID: 34336145 PMCID: PMC8310780 DOI: 10.1016/j.csbj.2021.07.023] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 12/18/2022] Open
Abstract
The on-going pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to unprecedented medical and socioeconomic crises. Although the viral pathogenesis remains elusive, deficiency of effective antiviral interferon (IFN) responses upon SARS-CoV-2 infection has been recognized as a hallmark of COVID-19 contributing to the disease pathology and progress. Recently, multiple proteins encoded by SARS-CoV-2 have been shown to act as potential IFN antagonists with diverse possible mechanisms. Here, we summarize and discuss the strategies of SARS-CoV-2 for evasion of innate immunity (particularly the antiviral IFN responses), understanding of which will facilitate not only the elucidation of SARS-CoV-2 infection and pathogenesis but also the development of antiviral intervention therapies.
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Affiliation(s)
- Yuan-Qin Min
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071/430207, China
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071/430207, China
| | - Mengzhuo Huang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071/430207, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Xiulian Sun
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071/430207, China
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071/430207, China
| | - Fei Deng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071/430207, China
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071/430207, China
| | - Hualin Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071/430207, China
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071/430207, China
| | - Yun-Jia Ning
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071/430207, China
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071/430207, China
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110
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Huang C. Pathogenesis of Coronaviruses Through Human Monocytes and Tissue Macrophages. Viral Immunol 2021; 34:597-606. [PMID: 34297627 DOI: 10.1089/vim.2021.0038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Coronaviruses (CoVs) contribute significantly to the burden of respiratory diseases, frequently as upper respiratory tract infections. Recent emergence of novel coronaviruses in the last few decades has highlighted the potential transmission, disease, and mortality related to these viruses. In this literature review, we shall explore the disease-causing mechanism of the virus through human monocytes and macrophages. Common strains will be discussed; however, this review will center around coronaviruses responsible for epidemics, namely severe acute respiratory syndrome coronavirus (SARS-CoV)-1 and -2 and the Middle East Respiratory Syndrome Coronavirus (MERS-CoV). Macrophages are key players in the immune system and have been found to play a role in the pathogenesis of lethal coronaviruses. In physiology, they are white blood cells that engulf and digest cellular debris, foreign substances, and microbes. They play a critical role in innate immunity and help initiate adaptive immunity. Human coronaviruses utilize various mechanisms to undermine the innate immune response through its interaction with macrophages and monocytes. It is capable of entering immune cells through DPP4 (dipeptidyl-peptidase 4) receptors and antibody-dependent enhancement, delaying initial interferon response which supports robust viral replication. Pathogenesis includes triggering the production of overwhelming pro-inflammatory cytokines that attract other immune cells to the site of infection, which propagate prolonged pro-inflammatory response. The virus has also been found to suppress the release of anti-inflammatory mediators such as IL-10, leading to an aberrant inflammatory response. Elevated serum cytokines are also believed to contribute to pathological features seen in severe disease such as coagulopathy, acute lung injury, and multiorgan failure.
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Affiliation(s)
- Chenghao Huang
- Medical School, The University of Sheffield, Sheffield, United Kingdom
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111
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Batool M, Kim MS, Choi S. Structural insights into the distinctive RNA recognition and therapeutic potentials of RIG-I-like receptors. Med Res Rev 2021; 42:399-425. [PMID: 34287999 DOI: 10.1002/med.21845] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 06/11/2021] [Accepted: 07/04/2021] [Indexed: 12/12/2022]
Abstract
RNA viruses, including the coronavirus, develop a unique strategy to evade the host immune response by interrupting the normal function of cytosolic retinoic acid-inducible gene-I (RIG-I)-like receptors (RLRs). RLRs rapidly detect atypical nucleic acids, thereby triggering the antiviral innate immune signaling cascade and subsequently activates the interferons transcription and induction of other proinflammatory cytokines and chemokines. Nonetheless, these receptors are manipulated by viral proteins to subvert the host immune system and sustain the infectivity and replication potential of the virus. RIG-I senses the single-stranded, double-stranded, and short double-stranded RNAs and recognizes the key signature, a 5'-triphosphate moiety, at the blunt end of the viral RNA. Meanwhile, the melanoma differentiation-associated gene 5 (MDA5) is triggered by longer double stranded RNAs, messenger RNAs lacking 2'-O-methylation in their 5'-cap, and RNA aggregates. Therefore, structural insights into the nucleic-acid-sensing and downstream signaling mechanisms of these receptors hold great promise for developing effective antiviral therapeutic interventions. This review highlights the critical roles played by RLRs in viral infections as well as their ligand recognition mechanisms. In addition, we highlight the crosstalk between the toll-like receptors and RLRs and provide a comprehensive overview of RLR-associated diseases as well as the therapeutic potential of RLRs for the development of antiviral-drugs. Moreover, we believe that these RLR-based antivirals will serve as a step toward countering the recent coronavirus disease 2019 pandemic.
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Affiliation(s)
- Maria Batool
- Department of Molecular Science and Technology, Ajou University, Suwon, Korea
- S&K Therapeutics, Campus Plaza 418, Ajou University, Suwon, Korea
| | - Moon Suk Kim
- Department of Molecular Science and Technology, Ajou University, Suwon, Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, Korea
- S&K Therapeutics, Campus Plaza 418, Ajou University, Suwon, Korea
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Su X, Ma W, Feng D, Cheng B, Wang Q, Guo Z, Zhou D, Tang X. Efficient Inhibition of SARS-CoV-2 Using Chimeric Antisense Oligonucleotides through RNase L Activation*. Angew Chem Int Ed Engl 2021; 60:21662-21667. [PMID: 34278671 PMCID: PMC8426974 DOI: 10.1002/anie.202105942] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Indexed: 12/14/2022]
Abstract
There is an urgent need to develop antiviral drugs and alleviate the current COVID-19 pandemic. Herein we report the design and construction of chimeric oligonucleotides comprising a 2'-OMe-modified antisense oligonucleotide and a 5'-phosphorylated 2'-5' poly(A)4 (4A2-5 ) to degrade envelope and spike RNAs of SARS-CoV-2. The oligonucleotide was used for searching and recognizing target viral RNA sequence, and the conjugated 4A2-5 was used for guided RNase L activation to sequence-specifically degrade viral RNAs. Since RNase L can potently cleave single-stranded RNA during innate antiviral response, degradation efficiencies with these chimeras were twice as much as those with only antisense oligonucleotides for both SARS-CoV-2 RNA targets. In pseudovirus infection models, chimera-S4 achieved potent and broad-spectrum inhibition of SARS-CoV-2 and its N501Y and/or ΔH69/ΔV70 mutants, indicating a promising antiviral agent based on the nucleic acid-hydrolysis targeting chimera (NATAC) strategy.
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Affiliation(s)
- Xiaoxuan Su
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Road, Beijing, 100191, China
| | - Wenxiao Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Road, Beijing, 100191, China
| | - Di Feng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Road, Beijing, 100191, China
| | - Boyang Cheng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Road, Beijing, 100191, China
| | - Qian Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Road, Beijing, 100191, China
| | - Zefeng Guo
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Road, Beijing, 100191, China
| | - Demin Zhou
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Road, Beijing, 100191, China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Road, Beijing, 100191, China
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113
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de Leon VNO, Manzano JAH, Pilapil DYH, Fernandez RAT, Ching JKAR, Quimque MTJ, Agbay JCM, Notarte KIR, Macabeo APG. Anti-HIV reverse transcriptase plant polyphenolic natural products with in silico inhibitory properties on seven non-structural proteins vital in SARS-CoV-2 pathogenesis. J Genet Eng Biotechnol 2021; 19:104. [PMID: 34272647 PMCID: PMC8284420 DOI: 10.1186/s43141-021-00206-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/06/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Accessing COVID-19 vaccines is a challenge despite successful clinical trials. This burdens the COVID-19 treatment gap, thereby requiring accelerated discovery of anti-SARS-CoV-2 agents. This study explored the potential of anti-HIV reverse transcriptase (RT) phytochemicals as inhibitors of SARS-CoV-2 non-structural proteins (nsps) by targeting in silico key sites in the structures of SARS-CoV-2 nsps. One hundred four anti-HIV phytochemicals were subjected to molecular docking with nsp3, 5, 10, 12, 13, 15, and 16. Top compounds in complex with the nsps were investigated further through molecular dynamics. The drug-likeness and ADME (absorption, distribution, metabolism, and excretion) properties of the top compounds were also predicted using SwissADME. Their toxicity was likewise determined using OSIRIS Property Explorer. RESULTS Among the top-scoring compounds, the polyphenolic functionalized natural products comprised of biflavones 1, 4, 11, 13, 14, 15; ellagitannin 9; and bisisoquinoline alkaloid 19 were multi-targeting and exhibited strongest binding affinities to at least two nsps (binding energy = - 7.7 to - 10.8 kcal/mol). The top ligands were stable in complex with their target nsps as determined by molecular dynamics. Several top-binding compounds were computationally druggable, showed good gastrointestinal absorptive property, and were also predicted to be non-toxic. CONCLUSIONS Twenty anti-HIV RT phytochemicals showed multi-targeting inhibitory potential against SARS-CoV-2 non-structural proteins 3, 5, 10, 12, 13, 15, and 16. Our results highlight the importance of polyhydroxylated aromatic substructures for effective attachment in the binding/catalytic sites of nsps involved in post-translational mechanism pathways. As such with the nsps playing vital roles in viral pathogenesis, our findings provide inspiration for the design and discovery of novel anti-COVID-19 drug prototypes.
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Affiliation(s)
- Von Novi O de Leon
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for the Natural and Applied Sciences, University of Santo Tomas, España Blvd., 1015, Manila, Philippines
- Department of Biological Sciences, College of Science, University of Santo Tomas, España Blvd., 1015, Manila, Philippines
| | - Joe Anthony H Manzano
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for the Natural and Applied Sciences, University of Santo Tomas, España Blvd., 1015, Manila, Philippines
- Department of Biological Sciences, College of Science, University of Santo Tomas, España Blvd., 1015, Manila, Philippines
| | - Delfin Yñigo H Pilapil
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for the Natural and Applied Sciences, University of Santo Tomas, España Blvd., 1015, Manila, Philippines
- Department of Biological Sciences, College of Science, University of Santo Tomas, España Blvd., 1015, Manila, Philippines
| | - Rey Arturo T Fernandez
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for the Natural and Applied Sciences, University of Santo Tomas, España Blvd., 1015, Manila, Philippines
| | - James Kyle Anthony R Ching
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for the Natural and Applied Sciences, University of Santo Tomas, España Blvd., 1015, Manila, Philippines
- Department of Chemistry, College of Science, University of Santo Tomas, España Blvd., 1015, Manila, Philippines
| | - Mark Tristan J Quimque
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for the Natural and Applied Sciences, University of Santo Tomas, España Blvd., 1015, Manila, Philippines
- The Graduate School, University of Santo Tomas, España Blvd., 1015, Manila, Philippines
- Chemistry Department, College of Science and Mathematics, Mindanao State University - Iligan Institute of Technology, Tibanga, 9200, Iligan City, Philippines
| | - Jay Carl M Agbay
- Chemistry Department, College of Science and Mathematics, Mindanao State University - Iligan Institute of Technology, Tibanga, 9200, Iligan City, Philippines
- Philippine Science High School - Central Mindanao Campus, 9217 Balo-I, Lanao del Norte, Philippines
| | - Kin Israel R Notarte
- Faculty of Medicine and Surgery, University of Santo Tomas, España Blvd., 1015, Manila, Philippines
| | - Allan Patrick G Macabeo
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for the Natural and Applied Sciences, University of Santo Tomas, España Blvd., 1015, Manila, Philippines.
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Canal B, Fujisawa R, McClure AW, Deegan TD, Wu M, Ulferts R, Weissmann F, Drury LS, Bertolin AP, Zeng J, Beale R, Howell M, Labib K, Diffley JF. Identifying SARS-CoV-2 antiviral compounds by screening for small molecule inhibitors of nsp15 endoribonuclease. Biochem J 2021; 478:2465-2479. [PMID: 34198324 PMCID: PMC8286823 DOI: 10.1042/bcj20210199] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/05/2021] [Accepted: 05/07/2021] [Indexed: 02/07/2023]
Abstract
SARS-CoV-2 is responsible for COVID-19, a human disease that has caused over 2 million deaths, stretched health systems to near-breaking point and endangered economies of countries and families around the world. Antiviral treatments to combat COVID-19 are currently lacking. Remdesivir, the only antiviral drug approved for the treatment of COVID-19, can affect disease severity, but better treatments are needed. SARS-CoV-2 encodes 16 non-structural proteins (nsp) that possess different enzymatic activities with important roles in viral genome replication, transcription and host immune evasion. One key aspect of host immune evasion is performed by the uridine-directed endoribonuclease activity of nsp15. Here we describe the expression and purification of nsp15 recombinant protein. We have developed biochemical assays to follow its activity, and we have found evidence for allosteric behaviour. We screened a custom chemical library of over 5000 compounds to identify nsp15 endoribonuclease inhibitors, and we identified and validated NSC95397 as an inhibitor of nsp15 endoribonuclease in vitro. Although NSC95397 did not inhibit SARS-CoV-2 growth in VERO E6 cells, further studies will be required to determine the effect of nsp15 inhibition on host immune evasion.
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Affiliation(s)
- Berta Canal
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Ryo Fujisawa
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Allison W. McClure
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Tom D. Deegan
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Mary Wu
- High Throughput Screening, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Rachel Ulferts
- Cell Biology of Infection Laboratory, the Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Florian Weissmann
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Lucy S. Drury
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Agustina P. Bertolin
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Jingkun Zeng
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Rupert Beale
- Cell Biology of Infection Laboratory, the Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Michael Howell
- High Throughput Screening, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Karim Labib
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - John F.X. Diffley
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
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Abstract
Thus far, in 2021, 219 countries with over 175 million people have been infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 is a positive sense, single-stranded RNA virus, and is the causal agent for coronavirus disease (COVID-19). Due to the urgency of the situation, virtual screening as a computational modeling method offers a fast and effective modality of identifying drugs that may be effective against SARS-CoV-2. There has been an overwhelming abundance of molecular docking against SARS-CoV-2 in the last year. Due to the massive volume of computational studies, this systematic review has been created to evaluate and summarize the findings of existing studies. Herein, we report on computational articles of drugs which target, (1) viral protease, (2) Spike protein-ACE 2 interaction, (3) RNA-dependent RNA polymerase, and (4) other proteins and nonstructural proteins of SARS-CoV-2. Based on the studies presented, there are 55 identified natural or drug compounds with potential anti-viral activity. The next step is to show anti-viral activity in vitro and translation to determine effectiveness into human clinical trials.
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116
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Inhibition of Antiviral Innate Immunity by Foot-and-Mouth Disease Virus L pro through Interaction with the N-Terminal Domain of Swine RNase L. J Virol 2021; 95:e0036121. [PMID: 33980594 DOI: 10.1128/jvi.00361-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Foot-and-mouth disease virus (FMDV) is the pathogen of foot-and-mouth disease (FMD), which is a highly contagious disease in cloven-hoofed animals. To survive in the host, FMDV has evolved multiple strategies to antagonize host innate immune responses. In this study, we showed that the leader protease (Lpro) of FMDV, a papain-like proteinase, promoted viral replication by evading the antiviral interferon response through counteracting the 2',5'-oligoadenylate synthetase (OAS)/RNase L system. Specifically, we observed that the titers of Lpro deletion virus were significantly lower than those of wild-type FMDV (FMDV-WT) in cultured cells. Our mechanistic studies demonstrated that Lpro interfered with the OAS/RNase L pathway by interacting with the N-terminal domain of swine RNase L (sRNase L). Remarkably, Lpro of FMDV exhibited species-specific binding to RNase L in that the interaction was observed only in swine cells, not human, monkey, or canine cells. Lastly, we presented evidence that by interacting with sRNase L, FMDV Lpro inhibited cellular apoptosis. Taken together, these results demonstrate a novel mechanism that Lpro utilizes to escape the OAS/RNase L-mediated antiviral defense pathway. IMPORTANCE FMDV is a picornavirus that causes a significant disease in agricultural animals. FMDV has developed diverse strategies to escape the host interferon response. Here, we show that Lpro of FMDV antagonizes the OAS/RNase L pathway, an important interferon effector pathway, by interacting with the N-terminal domain of sRNase L. Interestingly, such a virus-host interaction is species-specific because the interaction is detected only in swine cells, not in human, monkey, or canine cells. Furthermore, Lpro inhibits apoptosis through interacting with sRNase L. This study demonstrates a novel mechanism by which FMDV has evolved to inhibit host innate immune responses.
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117
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Mishra GP, Bhadane RN, Panigrahi D, Amawi HA, Asbhy CR, Tiwari AK. The interaction of the bioflavonoids with five SARS-CoV-2 proteins targets: An in silico study. Comput Biol Med 2021; 134:104464. [PMID: 34020130 PMCID: PMC8108478 DOI: 10.1016/j.compbiomed.2021.104464] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 12/16/2022]
Abstract
Flavonoids have been shown to have antioxidant, anti-inflammatory, anti-proliferative, antibacterial and antiviral efficacy. Therefore, in this study, we choose 85 flavonoid compounds and screened them to determine their in-silico interaction with protein targets crucial for SARS-CoV-2 infection. The five important targets chosen were the main protease (Mpro), Spike receptor binding domain (Spike-RBD), RNA - dependent RNA polymerase (RdRp or Nsp12), non-structural protein 15 (Nsp15) of SARS-CoV-2 and the host angiotensin converting enzyme-2 (ACE-2) spike-RBD binding domain. The compounds were initially docked at the selected sites and further evaluated for binding free energy, using the molecular mechanics/generalized Born surface area (MMGBSA) method. The three compounds with the best binding scores were subjected to molecular dynamics (MD) simulations. The compound, tribuloside, had a high average binding free energy of -86.99 and -88.98 kcal/mol for Mpro and Nsp12, respectively. The compound, legalon, had an average binding free energy of -59.02 kcal/mol at the ACE2 spike-RBD binding site. The compound, isosilybin, had an average free binding energy of -63.06 kcal/mol for the Spike-RBD protein. Overall, our results suggest that tribuloside, legalon and isosilybin should be evaluated in future studies to determine their efficacy to inhibit SARS-CoV-2 infectivity.
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Affiliation(s)
- Ganesh Prasad Mishra
- Kharvel Subharti College of Pharmacy, Swami VivekanandSubharti University, Subhartipuram, NH-58, Delhi-Haridwar Bypass Road, Meerut, U.P, 250005, India,Corresponding author
| | - Rajendra N. Bhadane
- Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, FI, 20520, Turku, Finland,Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, FI, 20520, Turku, Finland
| | - Debadash Panigrahi
- Drug Research Laboratory, Nodal Research Centre, College of Pharmaceutical Sciences, Puri, Baliguali, Puri- Konark Marine Drive Road, Puri, Odisha, 752002, India
| | - Haneen A. Amawi
- Department of Clinical Pharmacy and Pharmacy Practice, College of Pharmacy, Yarmouk University, Shafiq Irshidat St, Irbid, Jordan
| | - Charles R. Asbhy
- Department of Pharmaceutical Sciences, College of Pharmacy & Pharmaceutical Sciences, St. John's University, Queens, NY, USA, 10049
| | - Amit K. Tiwari
- Department of Pharmacology & Experimental Therapeutics, College of Pharmacy & Pharmaceutical Sciences, The University of Toledo, Toledo, OH, 43614, USA,Department of Cancer Biology, College of Medicine & Life Sciences, The University of Toledo, Toledo, OH, 43614, USA,Corresponding author. Department of Pharmacology & Experimental Therapeutics, College of Pharmacy & Pharmaceutical Sciences, The University of Toledo, Toledo, OH, 43614, USA
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Jonsson CB, Golden JE, Meibohm B. Time to 'Mind the Gap' in novel small molecule drug discovery for direct-acting antivirals for SARS-CoV-2. Curr Opin Virol 2021; 50:1-7. [PMID: 34256351 PMCID: PMC8238655 DOI: 10.1016/j.coviro.2021.06.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/11/2021] [Accepted: 06/21/2021] [Indexed: 12/17/2022]
Abstract
A pipeline of effective direct-acting antivirals (DAAs) remains a critical gap in addressing the current pandemic given vaccination hesitancy, the emergence of viral variants of concern, susceptible populations for which vaccination is ineffective or unavailable, and the possibility that coronavirus disease 2019 (COVID-19) is here to stay. Since the start of the pandemic, global efforts in small molecule drug discovery have focused largely on testing of FDA-approved drugs to accelerate evaluation in clinical trials in hospitalized patients. With 80% of the population who test positive for SARS-CoV-2 having asymptomatic to mild COVID-19, early stage, DAAs would be of enormous benefit to reduce spread, duration of symptoms and quarantine length. We highlight a few of the most promising DAAs in clinical trials and discuss considerations in how to navigate the challenges and pitfalls of novel small molecule discovery and thereby accelerate the advancement of new, safe, and oral DAAs.
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Affiliation(s)
- Colleen B Jonsson
- Department of Microbiology, Immunology, Biochemistry, University of Tennessee Health Science Center, 858 Madison Avenue, Memphis, TN 38163 USA; Regional Biocontainment Laboratory, University of Tennessee Health Science Center, 901 Monroe Avenue, Memphis, TN 38163 USA; Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, 38163 USA.
| | - Jennifer E Golden
- School of Pharmacy, Pharmaceutical Sciences Division, University of Wisconsin, Madison, Madison, WI 53705 USA
| | - Bernd Meibohm
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, 38163 USA
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119
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Miljanovic D, Milicevic O, Loncar A, Abazovic D, Despot D, Banko A. The First Molecular Characterization of Serbian SARS-CoV-2 Isolates From a Unique Early Second Wave in Europe. Front Microbiol 2021; 12:691154. [PMID: 34220784 PMCID: PMC8250835 DOI: 10.3389/fmicb.2021.691154] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 05/19/2021] [Indexed: 12/23/2022] Open
Abstract
March 6, 2020 is considered as the official date of the beginning of the COVID-19 epidemic in Serbia. In late spring and early summer 2020, Europe recorded a decline in the rate of SARS-CoV-2 infection and subsiding of the first wave. This trend lasted until the fall, when the second wave of the epidemic began to appear. Unlike the rest of Europe, Serbia was hit by the second wave of the epidemic a few months earlier. Already in June 2020, newly confirmed cases had risen exponentially. As the COVID-19 pandemic is the first pandemic in which there has been instant sharing of genomic information on isolates around the world, the aim of this study was to analyze whole SARS-CoV-2 viral genomes from Serbia, to identify circulating variants/clade/lineages, and to explore site-specific mutational patterns in the unique early second wave of the European epidemic. This analysis of Serbian isolates represents the first publication from Balkan countries, which demonstrates the importance of specificities of local transmission especially when preventive measures differ among countries. One hundred forty-eight different genome variants among 41 Serbian isolates were detected in this study. One unique and seven extremely rare mutations were identified, with locally specific continuous dominance of the 20D clade. At the same time, amino acid substitutions of newly identified variants of concern were found in our isolates from October 2020. Future research should be focused on functional characterization of novel mutations in order to understand the exact role of these variations.
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Affiliation(s)
- Danijela Miljanovic
- Virology Laboratory, Faculty of Medicine, Institute of Microbiology and Immunology, University of Belgrade, Belgrade, Serbia
| | - Ognjen Milicevic
- Faculty of Medicine, Institute for Medical Statistics and Informatics, University of Belgrade, Belgrade, Serbia
| | - Ana Loncar
- Laboratory of Molecular Microbiology, Institute for Biocides and Medical Ecology, Belgrade, Serbia
| | - Dzihan Abazovic
- Biocell Hospital, Belgrade, Serbia
- Emergency Medical Centre of Montenegro, Podgorica, Montenegro
| | - Dragana Despot
- Laboratory of Molecular Microbiology, Institute for Biocides and Medical Ecology, Belgrade, Serbia
| | - Ana Banko
- Virology Laboratory, Faculty of Medicine, Institute of Microbiology and Immunology, University of Belgrade, Belgrade, Serbia
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120
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The Role of Coronavirus RNA-Processing Enzymes in Innate Immune Evasion. Life (Basel) 2021; 11:life11060571. [PMID: 34204549 PMCID: PMC8235370 DOI: 10.3390/life11060571] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 01/21/2023] Open
Abstract
Viral RNA sensing triggers innate antiviral responses in humans by stimulating signaling pathways that include crucial antiviral genes such as interferon. RNA viruses have evolved strategies to inhibit or escape these mechanisms. Coronaviruses use multiple enzymes to synthesize, modify, and process their genomic RNA and sub-genomic RNAs. These include Nsp15 and Nsp16, whose respective roles in RNA capping and dsRNA degradation play a crucial role in coronavirus escape from immune surveillance. Evolutionary studies on coronaviruses demonstrate that genome expansion in Nidoviruses was promoted by the emergence of Nsp14-ExoN activity and led to the acquisition of Nsp15- and Nsp16-RNA-processing activities. In this review, we discuss the main RNA-sensing mechanisms in humans as well as recent structural, functional, and evolutionary insights into coronavirus Nsp15 and Nsp16 with a view to potential antiviral strategies.
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121
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Ramasamy S, Subbian S. Critical Determinants of Cytokine Storm and Type I Interferon Response in COVID-19 Pathogenesis. Clin Microbiol Rev 2021; 34:e00299-20. [PMID: 33980688 PMCID: PMC8142516 DOI: 10.1128/cmr.00299-20] [Citation(s) in RCA: 127] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), a rapidly evolving pandemic worldwide with at least 68 million COVID-19-positive cases and a mortality rate of about 2.2%, as of 10 December 2020. About 20% of COVID-19 patients exhibit moderate to severe symptoms. Severe COVID-19 manifests as acute respiratory distress syndrome (ARDS) with elevated plasma proinflammatory cytokines, including interleukin 1β (IL-1β), IL-6, tumor necrosis factor α (TNF-α), C-X-C motif chemokine ligand 10 (CXCL10/IP10), macrophage inflammatory protein 1 alpha (MIP-1α), and chemokine (C-C motif) ligand 2 (CCL2), with low levels of interferon type I (IFN-I) in the early stage and elevated levels of IFN-I during the advanced stage of COVID-19. Most of the severe and critically ill COVID-19 patients have had preexisting comorbidities, including hypertension, diabetes, cardiovascular diseases, and respiratory diseases. These conditions are known to perturb the levels of cytokines, chemokines, and angiotensin-converting enzyme 2 (ACE2), an essential receptor involved in SARS-CoV-2 entry into the host cells. ACE2 downregulation during SARS-CoV-2 infection activates the angiotensin II/angiotensin receptor (AT1R)-mediated hypercytokinemia and hyperinflammatory syndrome. However, several SARS-CoV-2 proteins, including open reading frame 3b (ORF3b), ORF6, ORF7, ORF8, and the nucleocapsid (N) protein, can inhibit IFN type I and II (IFN-I and -II) production. Thus, hyperinflammation, in combination with the lack of IFN responses against SARS-CoV-2 early on during infection, makes the patients succumb rapidly to COVID-19. Therefore, therapeutic approaches involving anti-cytokine/anti-cytokine-signaling and IFN therapy would favor the disease prognosis in COVID-19. This review describes critical host and viral factors underpinning the inflammatory "cytokine storm" induction and IFN antagonism during COVID-19 pathogenesis. Therapeutic approaches to reduce hyperinflammation and their limitations are also discussed.
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Affiliation(s)
- Santhamani Ramasamy
- Public Health Research Institute (PHRI) at New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Selvakumar Subbian
- Public Health Research Institute (PHRI) at New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
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Hong S, Seo SH, Woo SJ, Kwon Y, Song M, Ha NC. Epigallocatechin Gallate Inhibits the Uridylate-Specific Endoribonuclease Nsp15 and Efficiently Neutralizes the SARS-CoV-2 Strain. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:5948-5954. [PMID: 34015930 PMCID: PMC8146138 DOI: 10.1021/acs.jafc.1c02050] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 05/05/2023]
Abstract
SARS-CoV-2, the coronavirus strain that initiated the COVID-19 pandemic, and its subsequent variants present challenges to vaccine development and treatment. As the coronavirus evades the host innate immune response at the initial stage of infection, the disease can have a long nonsymptomatic period. The uridylate-specific endoribonuclease Nsp15 processes the viral genome for replication and cleaves the polyU sequence in the viral RNA to interfere with the host immune system. This study screened natural compounds in vitro to identify inhibitors against Nsp15 from SARS-CoV-2. Three natural compounds, epigallocatechin gallate (EGCG), baicalin, and quercetin, were identified as potential inhibitors. Potent antiviral activity of EGCG was confirmed in plaque reduction neutralization tests with a SARS-CoV-2 strain (PRNT50 = 0.20 μM). Because the compound has been used as a functional food ingredient due to its beneficial health effects, we theorize that this natural compound may help inhibit viral replication while minimizing safety issues.
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Affiliation(s)
- Seokho Hong
- Department
of Agricultural Biotechnology, Center for Food and Bioconvergence,
and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic
of Korea
| | - Sang Hwan Seo
- Science
Unit, International Vaccine Institute, Seoul 08826, Republic of Korea
| | - Sun-Je Woo
- Science
Unit, International Vaccine Institute, Seoul 08826, Republic of Korea
| | - Yonghoon Kwon
- Department
of Applied Biology and Chemistry, Seoul
National University, Seoul 08826, Republic of Korea
| | - Manki Song
- Science
Unit, International Vaccine Institute, Seoul 08826, Republic of Korea
| | - Nam-Chul Ha
- Department
of Agricultural Biotechnology, Center for Food and Bioconvergence,
and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic
of Korea
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123
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Kehrer T, García-Sastre A, Miorin L. Control of Innate Immune Activation by Severe Acute Respiratory Syndrome Coronavirus 2 and Other Coronaviruses. J Interferon Cytokine Res 2021; 41:205-219. [PMID: 34161170 PMCID: PMC8336211 DOI: 10.1089/jir.2021.0060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 05/07/2021] [Indexed: 12/25/2022] Open
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), represents a public health crisis of unprecedented proportions. After the emergence of SARS-CoV-1 in 2002, and Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012, this is the third outbreak of a highly pathogenic zoonotic coronavirus (CoV) that the world has witnessed in the last 2 decades. Infection with highly pathogenic human CoVs often results in a severe respiratory disease characterized by a delayed and blunted interferon (IFN) response, accompanied by an excessive production of proinflammatory cytokines. This indicates that CoVs developed effective mechanisms to overcome the host innate immune response and promote viral replication and pathogenesis. In this review, we describe the key innate immune signaling pathways that are activated during infection with SARS-CoV-2 and other well studied pathogenic CoVs. In addition, we summarize the main strategies that these viruses employ to modulate the host immune responses through the antagonism of IFN induction and effector pathways.
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Affiliation(s)
- Thomas Kehrer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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124
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Bibert S, Guex N, Lourenco J, Brahier T, Papadimitriou-Olivgeris M, Damonti L, Manuel O, Liechti R, Götz L, Tschopp J, Quinodoz M, Vollenweider P, Pagani JL, Oddo M, Hügli O, Lamoth F, Erard V, Voide C, Delorenzi M, Rufer N, Candotti F, Rivolta C, Boillat-Blanco N, Bochud PY. Transcriptomic Signature Differences Between SARS-CoV-2 and Influenza Virus Infected Patients. Front Immunol 2021; 12:666163. [PMID: 34135895 PMCID: PMC8202013 DOI: 10.3389/fimmu.2021.666163] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/10/2021] [Indexed: 12/19/2022] Open
Abstract
The reason why most individuals with COVID-19 have relatively limited symptoms while other develop respiratory distress with life-threatening complications remains unknown. Increasing evidence suggests that COVID-19 associated adverse outcomes mainly rely on dysregulated immunity. Here, we compared transcriptomic profiles of blood cells from 103 patients with different severity levels of COVID-19 with that of 27 healthy and 22 influenza-infected individuals. Data provided a complete overview of SARS-CoV-2-induced immune signature, including a dramatic defect in IFN responses, a reduction of toxicity-related molecules in NK cells, an increased degranulation of neutrophils, a dysregulation of T cells, a dramatic increase in B cell function and immunoglobulin production, as well as an important over-expression of genes involved in metabolism and cell cycle in patients infected with SARS-CoV-2 compared to those infected with influenza viruses. These features also differed according to COVID-19 severity. Overall and specific gene expression patterns across groups can be visualized on an interactive website (https://bix.unil.ch/covid/). Collectively, these transcriptomic host responses to SARS-CoV-2 infection are discussed in the context of current studies, thereby improving our understanding of COVID-19 pathogenesis and shaping the severity level of COVID-19.
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Affiliation(s)
- Stéphanie Bibert
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
| | - Joao Lourenco
- SIB Swiss Institute of Bioinformatics and Department of Fundamenal Oncology, University of Lausanne, Lausanne, Switzerland
| | - Thomas Brahier
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | | | - Lauro Damonti
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
- Department of Infectious Diseases, Bern University Hospital, Bern, Switzerland
| | - Oriol Manuel
- Infectious Diseases Service and Transplantation Center, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Robin Liechti
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics and Department of Fundamenal Oncology, University of Lausanne, Lausanne, Switzerland
| | - Lou Götz
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics and Department of Fundamenal Oncology, University of Lausanne, Lausanne, Switzerland
| | - Jonathan Tschopp
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Peter Vollenweider
- Internal Medicine Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Jean-Luc Pagani
- Department of Adult Intensive Care Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Mauro Oddo
- Department of Adult Intensive Care Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Olivier Hügli
- Emergency Department, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Frédéric Lamoth
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
- Department of Laboratory Medicine, Institute of Microbiology, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Véronique Erard
- Clinique de Médecine et spécialités, Infectiologie, Hôpital Fribourgeois-Fribourg, Fribourg, Switzerland
| | - Cathy Voide
- Department of Infectious Diseases, Central Institute, Valais Hospital, Sion, Switzerland
| | - Mauro Delorenzi
- SIB Swiss Institute of Bioinformatics and Department of Fundamenal Oncology, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, University Hospital and University of Lausanne, Epalinges, Switzerland
| | - Nathalie Rufer
- Department of Oncology, University Hospital and University of Lausanne, Epalinges, Switzerland
| | - Fabio Candotti
- Division of Immunology and Allergy, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Noémie Boillat-Blanco
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Pierre-Yves Bochud
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
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125
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Stevaert A, Krasniqi B, Van Loy B, Nguyen T, Thomas J, Vandeput J, Jochmans D, Thiel V, Dijkman R, Dehaen W, Voet A, Naesens L. Betulonic Acid Derivatives Interfering with Human Coronavirus 229E Replication via the nsp15 Endoribonuclease. J Med Chem 2021; 64:5632-5644. [PMID: 33877845 PMCID: PMC8084268 DOI: 10.1021/acs.jmedchem.0c02124] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Indexed: 02/08/2023]
Abstract
To develop antiviral therapeutics against human coronavirus (HCoV) infections, suitable coronavirus drug targets and corresponding lead molecules must be urgently identified. Here, we describe the discovery of a class of HCoV inhibitors acting on nsp15, a hexameric protein component of the viral replication-transcription complexes, endowed with immune evasion-associated endoribonuclease activity. Structure-activity relationship exploration of these 1,2,3-triazolo-fused betulonic acid derivatives yielded lead molecule 5h as a strong inhibitor (antiviral EC50: 0.6 μM) of HCoV-229E replication. An nsp15 endoribonuclease active site mutant virus was markedly less sensitive to 5h, and selected resistance to the compound mapped to mutations in the N-terminal part of HCoV-229E nsp15, at an interface between two nsp15 monomers. The biological findings were substantiated by the nsp15 binding mode for 5h, predicted by docking. Hence, besides delivering a distinct class of inhibitors, our study revealed a druggable pocket in the nsp15 hexamer with relevance for anti-coronavirus drug development.
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Affiliation(s)
- Annelies Stevaert
- Laboratory of Virology and Chemotherapy,
Rega Institute, KU Leuven, 3000 Leuven,
Belgium
| | - Besir Krasniqi
- Molecular Design and Synthesis, Department of
Chemistry, KU Leuven, 3001 Leuven,
Belgium
| | - Benjamin Van Loy
- Laboratory of Virology and Chemotherapy,
Rega Institute, KU Leuven, 3000 Leuven,
Belgium
| | - Tien Nguyen
- Biochemistry, Molecular and Structural Biology,
Department of Chemistry, KU Leuven, 3001 Leuven,
Belgium
| | - Joice Thomas
- Molecular Design and Synthesis, Department of
Chemistry, KU Leuven, 3001 Leuven,
Belgium
| | - Julie Vandeput
- Laboratory of Virology and Chemotherapy,
Rega Institute, KU Leuven, 3000 Leuven,
Belgium
| | - Dirk Jochmans
- Laboratory of Virology and Chemotherapy,
Rega Institute, KU Leuven, 3000 Leuven,
Belgium
| | - Volker Thiel
- Institute of Virology and Immunology
(IVI), 3012 Bern and 3012 Bern, Switzerland
- Department of Infectious Diseases and Pathobiology,
Vetsuisse Faculty, University of Bern, 3012 Bern,
Switzerland
| | - Ronald Dijkman
- Institute of Virology and Immunology
(IVI), 3012 Bern and 3012 Bern, Switzerland
- Department of Infectious Diseases and Pathobiology,
Vetsuisse Faculty, University of Bern, 3012 Bern,
Switzerland
- Institute for Infectious Diseases (IFIK),
University of Bern, 3012 Bern,
Switzerland
| | - Wim Dehaen
- Molecular Design and Synthesis, Department of
Chemistry, KU Leuven, 3001 Leuven,
Belgium
| | - Arnout Voet
- Biochemistry, Molecular and Structural Biology,
Department of Chemistry, KU Leuven, 3001 Leuven,
Belgium
| | - Lieve Naesens
- Laboratory of Virology and Chemotherapy,
Rega Institute, KU Leuven, 3000 Leuven,
Belgium
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126
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Altincekic N, Korn SM, Qureshi NS, Dujardin M, Ninot-Pedrosa M, Abele R, Abi Saad MJ, Alfano C, Almeida FCL, Alshamleh I, de Amorim GC, Anderson TK, Anobom CD, Anorma C, Bains JK, Bax A, Blackledge M, Blechar J, Böckmann A, Brigandat L, Bula A, Bütikofer M, Camacho-Zarco AR, Carlomagno T, Caruso IP, Ceylan B, Chaikuad A, Chu F, Cole L, Crosby MG, de Jesus V, Dhamotharan K, Felli IC, Ferner J, Fleischmann Y, Fogeron ML, Fourkiotis NK, Fuks C, Fürtig B, Gallo A, Gande SL, Gerez JA, Ghosh D, Gomes-Neto F, Gorbatyuk O, Guseva S, Hacker C, Häfner S, Hao B, Hargittay B, Henzler-Wildman K, Hoch JC, Hohmann KF, Hutchison MT, Jaudzems K, Jović K, Kaderli J, Kalniņš G, Kaņepe I, Kirchdoerfer RN, Kirkpatrick J, Knapp S, Krishnathas R, Kutz F, zur Lage S, Lambertz R, Lang A, Laurents D, Lecoq L, Linhard V, Löhr F, Malki A, Bessa LM, Martin RW, Matzel T, Maurin D, McNutt SW, Mebus-Antunes NC, Meier BH, Meiser N, Mompeán M, Monaca E, Montserret R, Mariño Perez L, Moser C, Muhle-Goll C, Neves-Martins TC, Ni X, Norton-Baker B, Pierattelli R, Pontoriero L, Pustovalova Y, Ohlenschläger O, Orts J, Da Poian AT, Pyper DJ, Richter C, Riek R, Rienstra CM, Robertson A, Pinheiro AS, Sabbatella R, Salvi N, Saxena K, Schulte L, Schiavina M, Schwalbe H, Silber M, Almeida MDS, Sprague-Piercy MA, Spyroulias GA, Sreeramulu S, Tants JN, Tārs K, Torres F, Töws S, Treviño MÁ, Trucks S, Tsika AC, Varga K, Wang Y, Weber ME, Weigand JE, Wiedemann C, Wirmer-Bartoschek J, Wirtz Martin MA, Zehnder J, Hengesbach M, Schlundt A. Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications. Front Mol Biosci 2021; 8:653148. [PMID: 34041264 PMCID: PMC8141814 DOI: 10.3389/fmolb.2021.653148] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/04/2021] [Indexed: 01/18/2023] Open
Abstract
The highly infectious disease COVID-19 caused by the Betacoronavirus SARS-CoV-2 poses a severe threat to humanity and demands the redirection of scientific efforts and criteria to organized research projects. The international COVID19-NMR consortium seeks to provide such new approaches by gathering scientific expertise worldwide. In particular, making available viral proteins and RNAs will pave the way to understanding the SARS-CoV-2 molecular components in detail. The research in COVID19-NMR and the resources provided through the consortium are fully disclosed to accelerate access and exploitation. NMR investigations of the viral molecular components are designated to provide the essential basis for further work, including macromolecular interaction studies and high-throughput drug screening. Here, we present the extensive catalog of a holistic SARS-CoV-2 protein preparation approach based on the consortium's collective efforts. We provide protocols for the large-scale production of more than 80% of all SARS-CoV-2 proteins or essential parts of them. Several of the proteins were produced in more than one laboratory, demonstrating the high interoperability between NMR groups worldwide. For the majority of proteins, we can produce isotope-labeled samples of HSQC-grade. Together with several NMR chemical shift assignments made publicly available on covid19-nmr.com, we here provide highly valuable resources for the production of SARS-CoV-2 proteins in isotope-labeled form.
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Affiliation(s)
- Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Sophie Marianne Korn
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Nusrat Shahin Qureshi
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marie Dujardin
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Martí Ninot-Pedrosa
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Rupert Abele
- Institute for Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marie Jose Abi Saad
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Caterina Alfano
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, Palermo, Italy
| | - Fabio C. L. Almeida
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Islam Alshamleh
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Gisele Cardoso de Amorim
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Multidisciplinary Center for Research in Biology (NUMPEX), Campus Duque de Caxias Federal University of Rio de Janeiro, Duque de Caxias, Brazil
| | - Thomas K. Anderson
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, United States
| | - Cristiane D. Anobom
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Chelsea Anorma
- Department of Chemistry, University of California, Irvine, CA, United States
| | - Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Adriaan Bax
- LCP, NIDDK, NIH, Bethesda, MD, United States
| | | | - Julius Blechar
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Louis Brigandat
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Anna Bula
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Matthias Bütikofer
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | | | - Teresa Carlomagno
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Hannover, Germany
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Icaro Putinhon Caruso
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São José do Rio Preto, Brazil
| | - Betül Ceylan
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Feixia Chu
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Laura Cole
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Marquise G. Crosby
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Vanessa de Jesus
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Karthikeyan Dhamotharan
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Isabella C. Felli
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Jan Ferner
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Yanick Fleischmann
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | | | - Christin Fuks
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Angelo Gallo
- Department of Pharmacy, University of Patras, Patras, Greece
| | - Santosh L. Gande
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Juan Atilio Gerez
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Dhiman Ghosh
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Francisco Gomes-Neto
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratory of Toxinology, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Oksana Gorbatyuk
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | | | | | - Sabine Häfner
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Jena, Germany
| | - Bing Hao
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Bruno Hargittay
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - K. Henzler-Wildman
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, United States
| | - Jeffrey C. Hoch
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Katharina F. Hohmann
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marie T. Hutchison
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Katarina Jović
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Janina Kaderli
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Gints Kalniņš
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Iveta Kaņepe
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Robert N. Kirchdoerfer
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, United States
| | - John Kirkpatrick
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Hannover, Germany
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Robin Krishnathas
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Felicitas Kutz
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Susanne zur Lage
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Roderick Lambertz
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Andras Lang
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Jena, Germany
| | - Douglas Laurents
- “Rocasolano” Institute for Physical Chemistry (IQFR), Spanish National Research Council (CSIC), Madrid, Spain
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Verena Linhard
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Frank Löhr
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anas Malki
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | | | - Rachel W. Martin
- Department of Chemistry, University of California, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Tobias Matzel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Damien Maurin
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Seth W. McNutt
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Nathane Cunha Mebus-Antunes
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Beat H. Meier
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Nathalie Meiser
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Miguel Mompeán
- “Rocasolano” Institute for Physical Chemistry (IQFR), Spanish National Research Council (CSIC), Madrid, Spain
| | - Elisa Monaca
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, Palermo, Italy
| | - Roland Montserret
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | | | - Celine Moser
- IBG-4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | | | - Thais Cristtina Neves-Martins
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Xiamonin Ni
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Brenna Norton-Baker
- Department of Chemistry, University of California, Irvine, CA, United States
| | - Roberta Pierattelli
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Letizia Pontoriero
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Yulia Pustovalova
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | | | - Julien Orts
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Andrea T. Da Poian
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Dennis J. Pyper
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Roland Riek
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Chad M. Rienstra
- Department of Biochemistry and National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, United States
| | | | - Anderson S. Pinheiro
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Nicola Salvi
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Krishna Saxena
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Linda Schulte
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marco Schiavina
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Mara Silber
- IBG-4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Marcius da Silva Almeida
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marc A. Sprague-Piercy
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | | | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jan-Niklas Tants
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Kaspars Tārs
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Felix Torres
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Sabrina Töws
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Miguel Á. Treviño
- “Rocasolano” Institute for Physical Chemistry (IQFR), Spanish National Research Council (CSIC), Madrid, Spain
| | - Sven Trucks
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Krisztina Varga
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Ying Wang
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Hannover, Germany
| | - Marco E. Weber
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Julia E. Weigand
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Christoph Wiedemann
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Maria Alexandra Wirtz Martin
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Johannes Zehnder
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Andreas Schlundt
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
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Analysis of natural compounds against the activity of SARS-CoV-2 NSP15 protein towards an effective treatment against COVID-19: a theoretical and computational biology approach. J Mol Model 2021; 27:160. [PMID: 33963942 PMCID: PMC8105700 DOI: 10.1007/s00894-021-04750-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 04/15/2021] [Indexed: 12/26/2022]
Abstract
Coronavirus infectious disease 2019 (COVID-19), a viral infection caused by a novel coronavirus (nCoV), continues to emerge as a serious threat to public health. This pandemic caused by SARS-CoV-2 (severe acute respiratory syndrome-coronavirus-2) has infected globally with 1,550,000 plus deaths to date, representing a high risk to public health. No effective drug or vaccine is available to curb down this deadly virus. The expedition for searching for a potential drug or vaccine against COVID-19 is of massive potential and favour to the community. This study is focused on finding an effective natural compound that can be processed further into a potential inhibitor to check the activity of SARS-CoV-2 with minimal side effects targeting NSP15 protein, which belongs to the EndoU enzyme family. The natural screening suggested two efficient compounds (PubChem ID: 95372568 and 1776037) with dihydroxyphenyl region of the compound, found to be important in the interaction with the viral protein showing promising activity which may act as a potent lead inhibitory molecule against the virus. In combination with virtual screening, modelling, drug likeliness, molecular docking, and 500 ns cumulative molecular dynamics simulations (100 ns for each complex) along with the decomposition analysis to calculate and confirm the stability and fold, we propose 95372568 and 1776037 as novel compounds of natural origin capable of getting developed into potent lead molecules against SARS-CoV-2 target protein NSP15.
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128
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Kasuga Y, Zhu B, Jang KJ, Yoo JS. Innate immune sensing of coronavirus and viral evasion strategies. Exp Mol Med 2021; 53:723-736. [PMID: 33953325 PMCID: PMC8099713 DOI: 10.1038/s12276-021-00602-1] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/01/2021] [Accepted: 03/03/2021] [Indexed: 12/13/2022] Open
Abstract
The innate immune system is the first line of the host defense program against pathogens and harmful substances. Antiviral innate immune responses can be triggered by multiple cellular receptors sensing viral components. The activated innate immune system produces interferons (IFNs) and cytokines that perform antiviral functions to eliminate invading viruses. Coronaviruses are single-stranded, positive-sense RNA viruses that have a broad range of animal hosts. Coronaviruses have evolved multiple means to evade host antiviral immune responses. Successful immune evasion by coronaviruses may enable the viruses to adapt to multiple species of host organisms. Coronavirus transmission from zoonotic hosts to humans has caused serious illnesses, such as severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and coronavirus disease-2019 (COVID-19), resulting in global health and economic crises. In this review, we summarize the current knowledge of the mechanisms underlying host sensing of and innate immune responses against coronavirus invasion, as well as host immune evasion strategies of coronaviruses. Understanding how the innate immune system senses coronaviruses and how coronaviruses can escape detection could provide novel approaches to tackle infections. Coronaviruses, including SARS-CoV-2, constantly evolve to manipulate, obstruct and evade host immune responses. A team led by Ji-Seung Yoo, Hokkaido University, Sapporo, Japan, reviewed understanding of innate immune responses to coronaviruses and viral evasion strategies. Two major receptor families recognise RNA viruses upon infection, but how they respond to SARS-CoV-2 is unclear. One receptor, TLR7, plays a critical role in sensing coronavirus infections, and mutations in the TLR7 gene are associated with severe illness and mortality in young Covid-19 patients. Activating host TLR pathways may prove a useful therapeutic approach. Further in-depth investigations are needed into specific coronavirus proteins and viral mechanisms that suppress host immunity.
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Affiliation(s)
- Yusuke Kasuga
- Department of Immunology, Hokkaido University Graduate School of Medicine, Sapporo, 060-8638, Japan
| | - Baohui Zhu
- Department of Immunology, Hokkaido University Graduate School of Medicine, Sapporo, 060-8638, Japan
| | - Kyoung-Jin Jang
- Department of Pathology, School of Medicine, Institute of Biomedical Science and Technology, Konkuk University, Chungju, 27478, Republic of Korea.
| | - Ji-Seung Yoo
- Department of Immunology, Hokkaido University Graduate School of Medicine, Sapporo, 060-8638, Japan.
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Vafaeinezhad A, Atashzar MR, Baharlou R. The Immune Responses against Coronavirus Infections: Friend or Foe? Int Arch Allergy Immunol 2021; 182:863-876. [PMID: 33951640 PMCID: PMC8247827 DOI: 10.1159/000516038] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/19/2021] [Indexed: 01/19/2023] Open
Abstract
Coronaviruses (CoVs) were first discovered in the 1960s. Severe acute respiratory syndrome CoV-2 (SARS-CoV-2) has been identified as the cause of COVID-19, which spread throughout China and subsequently, across the world. As COVID-19 causes serious public health concerns across the world, investigating the characteristics of SARS-CoV-2 and its interaction with the host immune responses may provide a clearer picture of how the pathogen causes disease in some individuals. Interestingly, SARS-CoV-2 has 80% sequence homology with SARS-CoV-1 and 96-98% homology with CoVs isolated from bats. Therefore, the experience acquired in SARS and Middle East Respiratory Syndrome (MERS) epidemics may improve our understanding of the immune response and immunopathological changes in COVID-19 patients. In the present paper, we have reviewed the immune responses (including the innate and adaptive immunities) to SARS-CoV, MERS-CoV, and SARS-CoV-2, so as to improve our understanding of the concept of the COVID-19 disease, which will be helpful in developing vaccines and medications for treating the COVID-19 patients.
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Affiliation(s)
- Arefe Vafaeinezhad
- Cancer Research Center, Semnan University of Medical Sciences, Semnan, Iran
- Department of Immunology, School of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Mohammad Reza Atashzar
- Department of Immunology, School of Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Rasoul Baharlou
- Cancer Research Center, Semnan University of Medical Sciences, Semnan, Iran
- Department of Immunology, School of Medicine, Semnan University of Medical Sciences, Semnan, Iran
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130
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Mechanism involved in the pathogenesis and immune response against SARS-CoV-2 infection. Virusdisease 2021; 32:211-219. [PMID: 33969150 PMCID: PMC8096142 DOI: 10.1007/s13337-021-00687-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/08/2021] [Indexed: 12/18/2022] Open
Abstract
SARS CoV-2, a causative agent of human respiratory tract infection, was first identified in late 2019. It is a newly emerging viral disease with unsatisfactory treatments. The virus is highly contagious and has caused pandemic globally. The number of deaths is increasing exponentially, which is an alarming situation for mankind. The detailed mechanism of the pathogenesis and host immune responses to this virus are not fully known. Here we discuss an overview of SARS CoV-2 pathogenicity, its entry and replication mechanism, and host immune response against this deadly pathogen. Understanding these processes will help to lead the development and identification of drug targets and effective therapies.
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131
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Markiewicz L, Drazkowska K, Sikorski PJ. Tricks and threats of RNA viruses - towards understanding the fate of viral RNA. RNA Biol 2021; 18:669-687. [PMID: 33618611 PMCID: PMC8078519 DOI: 10.1080/15476286.2021.1875680] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/22/2020] [Accepted: 01/09/2021] [Indexed: 12/24/2022] Open
Abstract
Human innate cellular defence pathways have evolved to sense and eliminate pathogens, of which, viruses are considered one of the most dangerous. Their relatively simple structure makes the identification of viral invasion a difficult task for cells. In the course of evolution, viral nucleic acids have become one of the strongest and most reliable early identifiers of infection. When considering RNA virus recognition, RNA sensing is the central mechanism in human innate immunity, and effectiveness of this sensing is crucial for triggering an appropriate antiviral response. Although human cells are armed with a variety of highly specialized receptors designed to respond only to pathogenic viral RNA, RNA viruses have developed an array of mechanisms to avoid being recognized by human interferon-mediated cellular defence systems. The repertoire of viral evasion strategies is extremely wide, ranging from masking pathogenic RNA through end modification, to utilizing sophisticated techniques to deceive host cellular RNA degrading enzymes, and hijacking the most basic metabolic pathways in host cells. In this review, we aim to dissect human RNA sensing mechanisms crucial for antiviral immune defences, as well as the strategies adopted by RNA viruses to avoid detection and degradation by host cells. We believe that understanding the fate of viral RNA upon infection, and detailing the molecular mechanisms behind virus-host interactions, may be helpful for developing more effective antiviral strategies; which are urgently needed to prevent the far-reaching consequences of widespread, highly pathogenic viral infections.
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132
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Kumar S, Kashyap P, Chowdhury S, Kumar S, Panwar A, Kumar A. Identification of phytochemicals as potential therapeutic agents that binds to Nsp15 protein target of coronavirus (SARS-CoV-2) that are capable of inhibiting virus replication. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2021; 85:153317. [PMID: 32943302 PMCID: PMC7470885 DOI: 10.1016/j.phymed.2020.153317] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/18/2020] [Accepted: 08/30/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) playing havoc across the globe caused 585,727 deaths and 13,616,593 confirmed cases so far as per World Health Organization data released till 17th July 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV- 2) is responsible for causing this pandemic across different continents. It is not only impacting the world economy but also quarantined millions of people in their homes or hospitals. PURPOSE At present, there is no Food and Drug Administration-approved drug or vaccine available to treat this disease. Still, people are trying various pre-existing medicines that are known to have anti-viral or anti-parasitic effects. In view of this, the present study aimed to study the binding potential of various phytochemicals present in multiple natural plant extract as a secondary metabolite to non-structural protein 15 (Nsp15) protein, a drug target known to play a crucial role in virulence of coronavirus. METHOD Nsp15 protein was selected because it shows 89% similarity to the other SARS-CoV, which caused the earlier outbreak. The assumption is that inhibition of Nsp15 slowdowns the viral replication. Phytochemicals are selected as these are present in various plant parts (seed, flower, roots, etc.), which are used in different food cuisines in different geographical regions across the globe. The molecular docking approach was performed using two different software, i.e., Autodock, and Swissdock, to study the interaction of various phytochemicals with Nsp15 protein. Hydroxychloroquine is used as a positive control as it is used by medical professionals showing some positive effects in dealing with coronavirus. RESULTS The present study demonstrated the binding potential of approximately 50 phytochemicals with Nsp15 and capable of inhibiting the viral replication, although in vitro and in vivo tests are required to confirm these findings. CONCLUSIONS In conclusion, the present study successfully demonstrated the binding of phytochemicals such as sarsasapogenin, ursonic acid, curcumin, ajmalicine, novobiocin, silymarin and aranotin, piperine, gingerol, rosmarinic acid, and alpha terpinyl acetate to Nsp15 viral protein and they might play a key role in inhibiting SARS-CoV-2 replication.
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Affiliation(s)
- Suresh Kumar
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, Sector 16C, New Delhi 110075, India.
| | - Priya Kashyap
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, Sector 16C, New Delhi 110075, India
| | - Suman Chowdhury
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, Sector 16C, New Delhi 110075, India
| | - Shivani Kumar
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, Sector 16C, New Delhi 110075, India
| | - Anil Panwar
- Centre for System Biology and Bioinformatics, Panjab University, Chandigarh 160014, India
| | - Ashok Kumar
- Centre for System Biology and Bioinformatics, Panjab University, Chandigarh 160014, India
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Elhady SS, Abdelhameed RFA, Malatani RT, Alahdal AM, Bogari HA, Almalki AJ, Mohammad KA, Ahmed SA, Khedr AIM, Darwish KM. Molecular Docking and Dynamics Simulation Study of Hyrtios erectus Isolated Scalarane Sesterterpenes as Potential SARS-CoV-2 Dual Target Inhibitors. BIOLOGY 2021; 10:389. [PMID: 34062724 PMCID: PMC8147222 DOI: 10.3390/biology10050389] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/16/2021] [Accepted: 04/27/2021] [Indexed: 12/16/2022]
Abstract
Presently, the world is under the toll of pandemic coronavirus disease-2019 (COVID-19) outbreak caused by SARS-CoV-2. Lack of effective and safe therapeutics has stressed the scientific community for developing novel therapeutics capable of alleviating and stopping this pandemic. Within the presented study, molecular docking, ADME properties and all-atom molecular dynamic (MD) simulation, along with two standard antiviral agents (lopinavir and benzopurpurin-4B), were applied to investigate 15 scalaranes sesterterpenes natural compounds, purified from the Red Sea marine sponge Hyrtios erectus, as potential COVID-19 dual-target inhibitors. Following multi-step docking within COVID-19 main protease and Nsp15 endoribonuclease cavities, nine promising drug-like compounds exhibited higher docking scores as well as better interactions with the target's crucial residues than those of reference ligands. Compounds 2, 6, 11, and 15, were predicted to simultaneously subdue the activity of the two COVID-19 targets. Dynamics behavior of the best-docked molecules, compounds 15 and 6, within COVID-19 target pockets showed substantial stability of ligand-protein complexes as presented via several MD simulation parameters. Furthermore, calculated free-binding energies from MD simulation illustrated significant ligand's binding affinity towards respective target pockets. All provided findings supported the utility of scalarane-based sesterterpenes, particularly compounds 15 and 6, as promising lead candidates guiding the development of effective therapeutics against SARS-CoV-2.
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Affiliation(s)
- Sameh S. Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Reda F. A. Abdelhameed
- Department of Pharmacognosy, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt; (R.F.A.A.); (S.A.A.)
| | - Rania T. Malatani
- Department of Pharmacy Practice, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (R.T.M.); (A.M.A.); (H.A.B.)
| | - Abdulrahman M. Alahdal
- Department of Pharmacy Practice, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (R.T.M.); (A.M.A.); (H.A.B.)
| | - Hanin A. Bogari
- Department of Pharmacy Practice, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (R.T.M.); (A.M.A.); (H.A.B.)
| | - Ahmad J. Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (A.J.A.); (K.A.M.)
| | - Khadijah A. Mohammad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (A.J.A.); (K.A.M.)
| | - Safwat A. Ahmed
- Department of Pharmacognosy, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt; (R.F.A.A.); (S.A.A.)
| | - Amgad I. M. Khedr
- Department of Pharmacognosy, Faculty of Pharmacy, Port Said University, Port Said 42526, Egypt;
- Department of Pharmacognosy, Faculty of Pharmacy, Horus University-Egypt, New Damietta 34518, Egypt
| | - Khaled M. Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
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134
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Choi H, Shin EC. Roles of Type I and III Interferons in COVID-19. Yonsei Med J 2021; 62:381-390. [PMID: 33908208 PMCID: PMC8084697 DOI: 10.3349/ymj.2021.62.5.381] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/05/2021] [Accepted: 03/04/2021] [Indexed: 12/23/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is an ongoing global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Type I and III interferon (IFN) responses act as the first line of defense against viral infection and are activated by the recognition of viruses by infected cells and innate immune cells. Dysregulation of host IFN responses has been known to be associated with severe disease progression in COVID-19 patients. However, the reported results are controversial and the roles of IFN responses in COVID-19 need to be investigated further. In the absence of a highly efficacious antiviral drug, clinical studies have evaluated recombinant type I and III IFNs, as they have been successfully used for the treatment of infections caused by two other epidemic coronaviruses, SARS-CoV-1 and Middle East respiratory syndrome (MERS)-CoV. In this review, we describe the strategies by which SARS-CoV-2 evades IFN responses and the dysregulation of host IFN responses in COVID-19 patients. In addition, we discuss the therapeutic potential of type I and III IFNs in COVID-19.
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Affiliation(s)
- Hojun Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
- Laboratory of Immunology and Infectious Diseases, Graduate School of Medical Science and Engineering, KAIST, Daejeon, Korea
| | - Eui Cheol Shin
- Laboratory of Immunology and Infectious Diseases, Graduate School of Medical Science and Engineering, KAIST, Daejeon, Korea
- The Center for Epidemic Preparedness, KAIST Institute, Daejeon, Korea.
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135
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Choi R, Zhou M, Shek R, Wilson JW, Tillery L, Craig JK, Salukhe IA, Hickson SE, Kumar N, James RM, Buchko GW, Wu R, Huff S, Nguyen TT, Hurst BL, Cherry S, Barrett LK, Hyde JL, Van Voorhis WC. High-throughput screening of the ReFRAME, Pandemic Box, and COVID Box drug repurposing libraries against SARS-CoV-2 nsp15 endoribonuclease to identify small-molecule inhibitors of viral activity. PLoS One 2021; 16:e0250019. [PMID: 33886614 PMCID: PMC8062000 DOI: 10.1371/journal.pone.0250019] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/29/2021] [Indexed: 12/20/2022] Open
Abstract
SARS-CoV-2 has caused a global pandemic, and has taken over 1.7 million lives as of mid-December, 2020. Although great progress has been made in the development of effective countermeasures, with several pharmaceutical companies approved or poised to deliver vaccines to market, there is still an unmet need of essential antiviral drugs with therapeutic impact for the treatment of moderate-to-severe COVID-19. Towards this goal, a high-throughput assay was used to screen SARS-CoV-2 nsp15 uracil-dependent endonuclease (endoU) function against 13 thousand compounds from drug and lead repurposing compound libraries. While over 80% of initial hit compounds were pan-assay inhibitory compounds, three hits were confirmed as nsp15 endoU inhibitors in the 1-20 μM range in vitro. Furthermore, Exebryl-1, a ß-amyloid anti-aggregation molecule for Alzheimer's therapy, was shown to have antiviral activity between 10 to 66 μM, in Vero 76, Caco-2, and Calu-3 cells. Although the inhibitory concentrations determined for Exebryl-1 exceed those recommended for therapeutic intervention, our findings show great promise for further optimization of Exebryl-1 as an nsp15 endoU inhibitor and as a SARS-CoV-2 antiviral.
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Affiliation(s)
- Ryan Choi
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
| | - Mowei Zhou
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, United States of America
| | - Roger Shek
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, United States of America
| | - Jesse W. Wilson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, United States of America
| | - Logan Tillery
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, United States of America
| | - Justin K. Craig
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, United States of America
| | - Indraneel A. Salukhe
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Sarah E. Hickson
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Neeraj Kumar
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, United States of America
| | - Rhema M. James
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, United States of America
| | - Garry W. Buchko
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, United States of America
- School of Molecular Bioscience, Washington State University, Pullman, WA, United States of America
| | - Ruilian Wu
- Bioenergy and Biome Sciences, Los Alamos National Laboratory (LANL), Los Alamos, NM, United States of America
| | - Sydney Huff
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
| | - Tu-Trinh Nguyen
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, United States of America
| | - Brett L. Hurst
- Institute for Antiviral Research, Utah State University, Logan, UT, United States of America
| | - Sara Cherry
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Lynn K. Barrett
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, United States of America
| | - Jennifer L. Hyde
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Wesley C. Van Voorhis
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, United States of America
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, United States of America
- Department of Global Health, University of Washington, Seattle, WA, United States of America
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Abstract
C6 deamination of adenosine (A) to inosine (I) in double-stranded RNA (dsRNA) is catalyzed by a family of enzymes known as ADARs (adenosine deaminases acting on RNA) encoded by three genes in mammals. Alternative promoters and splicing produce two ADAR1 proteins, an interferon-inducible cytoplasmic p150 and a constitutively expressed p110 that like ADAR2 is a nuclear enzyme. ADAR3 lacks deaminase activity. A-to-I editing occurs with both viral and cellular RNAs. Deamination activity is dependent on dsRNA substrate structure and regulatory RNA-binding proteins and ranges from highly site selective with hepatitis D RNA and glutamate receptor precursor messenger RNA (pre-mRNA) to hyperediting of measles virus and polyomavirus transcripts and cellular inverted Alu elements. Because I base-pairs as guanosine instead of A, editing can alter mRNA decoding, pre-mRNA splicing, and microRNA silencing. Editing also alters dsRNA structure, thereby suppressing innate immune responses including interferon production and action. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Christian K Pfaller
- Division of Veterinary Medicine, Paul-Ehrlich-Institute, Langen 63225, Germany
| | - Cyril X George
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California 93106, USA;
| | - Charles E Samuel
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California 93106, USA;
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Merino GA, Raad J, Bugnon LA, Yones C, Kamenetzky L, Claus J, Ariel F, Milone DH, Stegmayer G. Novel SARS-CoV-2 encoded small RNAs in the passage to humans. Bioinformatics 2021; 36:5571-5581. [PMID: 33244583 PMCID: PMC7717134 DOI: 10.1093/bioinformatics/btaa1002] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/15/2020] [Accepted: 11/18/2020] [Indexed: 12/14/2022] Open
Abstract
Motivation The Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) has recently emerged as the responsible for the pandemic outbreak of the coronavirus disease (COVID-19). This virus is closely related to coronaviruses infecting bats and Malayan pangolins, species suspected to be an intermediate host in the passage to humans. Several genomic mutations affecting viral proteins have been identified, contributing to the understanding of the recent animal-to-human transmission. However, the capacity of SARS-CoV-2 to encode functional putative microRNAs (miRNAs) remains largely unexplored. Results We have used deep learning to discover 12 candidate stem-loop structures hidden in the viral protein-coding genome. Among the precursors, the expression of eight mature miRNAs-like sequences was confirmed in small RNA-seq data from SARS-CoV-2 infected human cells. Predicted miRNAs are likely to target a subset of human genes of which 109 are transcriptionally deregulated upon infection. Remarkably, 28 of those genes potentially targeted by SARS-CoV-2 miRNAs are down-regulated in infected human cells. Interestingly, most of them have been related to respiratory diseases and viral infection, including several afflictions previously associated with SARS-CoV-1 and SARS-CoV-2. The comparison of SARS-CoV-2 pre-miRNA sequences with those from bat and pangolin coronaviruses suggests that single nucleotide mutations could have helped its progenitors jumping inter-species boundaries, allowing the gain of novel mature miRNAs targeting human mRNAs. Our results suggest that the recent acquisition of novel miRNAs-like sequences in the SARS-CoV-2 genome may have contributed to modulate the transcriptional reprogramming of the new host upon infection.
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Affiliation(s)
- Gabriela A Merino
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina.,Bioengineering and Bioinformatics Research and Development Institute (IBB), FI-UNER, CONICET, Entre Ríos 3100, Argentina.,European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridgeshire CB101SD, UK
| | - Jonathan Raad
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
| | - Leandro A Bugnon
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
| | - Cristian Yones
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
| | - Laura Kamenetzky
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Facultad de Medicina, UBA-CONICET, Ciudad Autónoma de Buenos Aires 1121, Argentina.,Laboratorio de Genómica y Bioinformática de Patógenos, iB3, Instituto de Biociencias, Biotecnología y Biología traslacional, Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires 1121, Argentina
| | - Juan Claus
- Laboratorio de Virología, FBCB, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral (IAL), CONICET, FBCB, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Diego H Milone
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
| | - Georgina Stegmayer
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
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Kumar S, Singh B, Kumari P, Kumar PV, Agnihotri G, Khan S, Kant Beuria T, Syed GH, Dixit A. Identification of multipotent drugs for COVID-19 therapeutics with the evaluation of their SARS-CoV2 inhibitory activity. Comput Struct Biotechnol J 2021; 19:1998-2017. [PMID: 33841751 PMCID: PMC8025584 DOI: 10.1016/j.csbj.2021.04.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/04/2021] [Accepted: 04/04/2021] [Indexed: 12/12/2022] Open
Abstract
The SARS-CoV2 is a highly contagious pathogen that causes COVID-19 disease. It has affected millions of people globally with an average lethality of ~3%. There is an urgent need of drugs for the treatment of COVID-19. In the current studies, we have used bioinformatics techniques to screen the FDA approved drugs against nine SARS-CoV2 proteins to identify drugs for repurposing. Additionally, we analyzed if the identified molecules can also affect the human proteins whose expression in lung changed during SARS-CoV2 infection. Targeting such genes may also be a beneficial strategy to curb disease manifestation. We have identified 74 molecules that can bind to various SARS-CoV2 and human host proteins. We experimentally validated our in-silico predictions using vero E6 cells infected with SARS-CoV2 virus. Interestingly, many of our predicted molecules viz. capreomycin, celecoxib, mefloquine, montelukast, and nebivolol showed good activity (IC50) against SARS-CoV2. We hope that these studies may help in the development of new therapeutic options for the treatment of COVID-19.
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Affiliation(s)
- Sugandh Kumar
- Institute of Life Science, Nalco Square, Bhubaneswar, Odisha 751023, India
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT) University, Bhubaneswar, Odisha 751024, India
| | - Bharati Singh
- Institute of Life Science, Nalco Square, Bhubaneswar, Odisha 751023, India
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT) University, Bhubaneswar, Odisha 751024, India
| | - Pratima Kumari
- Institute of Life Science, Nalco Square, Bhubaneswar, Odisha 751023, India
- Regional Centre for Biotechnology (RCB), 3rd Milestone, Faridabad-Gurgaon, Haryana 121001, India
| | - Preethy V. Kumar
- Institute of Life Science, Nalco Square, Bhubaneswar, Odisha 751023, India
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT) University, Bhubaneswar, Odisha 751024, India
| | - Geetanjali Agnihotri
- School of Chemical Technology, Kalinga Institute of Industrial Technology (KIIT) University, Bhubaneswar, Odisha 751024, India
| | - Shaheerah Khan
- Institute of Life Science, Nalco Square, Bhubaneswar, Odisha 751023, India
- Regional Centre for Biotechnology (RCB), 3rd Milestone, Faridabad-Gurgaon, Haryana 121001, India
| | - Tushar Kant Beuria
- Institute of Life Science, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Gulam Hussain Syed
- Institute of Life Science, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Anshuman Dixit
- Institute of Life Science, Nalco Square, Bhubaneswar, Odisha 751023, India
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Pérez-Moraga R, Forés-Martos J, Suay-García B, Duval JL, Falcó A, Climent J. A COVID-19 Drug Repurposing Strategy through Quantitative Homological Similarities Using a Topological Data Analysis-Based Framework. Pharmaceutics 2021; 13:pharmaceutics13040488. [PMID: 33918313 PMCID: PMC8066156 DOI: 10.3390/pharmaceutics13040488] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 02/06/2023] Open
Abstract
Since its emergence in March 2020, the SARS-CoV-2 global pandemic has produced more than 116 million cases and 2.5 million deaths worldwide. Despite the enormous efforts carried out by the scientific community, no effective treatments have been developed to date. We applied a novel computational pipeline aimed to accelerate the process of identifying drug repurposing candidates which allows us to compare three-dimensional protein structures. Its use in conjunction with two in silico validation strategies (molecular docking and transcriptomic analyses) allowed us to identify a set of potential drug repurposing candidates targeting three viral proteins (3CL viral protease, NSP15 endoribonuclease, and NSP12 RNA-dependent RNA polymerase), which included rutin, dexamethasone, and vemurafenib. This is the first time that a topological data analysis (TDA)-based strategy has been used to compare a massive number of protein structures with the final objective of performing drug repurposing to treat SARS-CoV-2 infection.
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Affiliation(s)
- Raul Pérez-Moraga
- ESI International Chair@CEU-UCH, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, Alfara del Patriarca, 46115 Valencia, Spain; (R.P.-M.); (J.F.-M.); (B.S.-G.)
- Departamento de Matemáticas, Física y Ciencias Tecnológicas, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, Alfara del Patriarca, 46115 Valencia, Spain
| | - Jaume Forés-Martos
- ESI International Chair@CEU-UCH, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, Alfara del Patriarca, 46115 Valencia, Spain; (R.P.-M.); (J.F.-M.); (B.S.-G.)
- Departamento de Matemáticas, Física y Ciencias Tecnológicas, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, Alfara del Patriarca, 46115 Valencia, Spain
- Biomedical Research Networking Center of Mental Health (CIBERSAM), 28029 Madrid, Spain
| | - Beatriz Suay-García
- ESI International Chair@CEU-UCH, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, Alfara del Patriarca, 46115 Valencia, Spain; (R.P.-M.); (J.F.-M.); (B.S.-G.)
- Departamento de Matemáticas, Física y Ciencias Tecnológicas, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, Alfara del Patriarca, 46115 Valencia, Spain
| | | | - Antonio Falcó
- ESI International Chair@CEU-UCH, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, Alfara del Patriarca, 46115 Valencia, Spain; (R.P.-M.); (J.F.-M.); (B.S.-G.)
- Departamento de Matemáticas, Física y Ciencias Tecnológicas, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, Alfara del Patriarca, 46115 Valencia, Spain
- Correspondence: (A.F.); (J.C.)
| | - Joan Climent
- ESI International Chair@CEU-UCH, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, Alfara del Patriarca, 46115 Valencia, Spain; (R.P.-M.); (J.F.-M.); (B.S.-G.)
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Universidad Cardenal Herrera-CEU, CEU Universities, C/Tirant lo Blanc 7, Alfara del Patriarca, 46115 Valencia, Spain
- Correspondence: (A.F.); (J.C.)
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140
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Current Understanding of Novel Coronavirus: Molecular Pathogenesis, Diagnosis, and Treatment Approaches. IMMUNO 2021. [DOI: 10.3390/immuno1010004] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
An outbreak of “Pneumonia of Unknown Etiology” occurred in Wuhan, China, in late December 2019. Later, the agent factor was identified and coined as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the disease was named coronavirus disease 2019 (COVID-19). In a shorter period, this newly emergent infection brought the world to a standstill. On 11 March 2020, the WHO declared COVID-19 as a pandemic. Researchers across the globe have joined their hands to investigate SARS-CoV-2 in terms of pathogenicity, transmissibility, and deduce therapeutics to subjugate this infection. The researchers and scholars practicing different arts of medicine are on an extensive quest to come up with safer ways to curb the pathological implications of this viral infection. A huge number of clinical trials are underway from the branch of allopathy and naturopathy. Besides, a paradigm shift on cellular therapy and nano-medicine protocols has to be optimized for better clinical and functional outcomes of COVID-19-affected individuals. This article unveils a comprehensive review of the pathogenesis mode of spread, and various treatment modalities to combat COVID-19 disease.
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141
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Garcia-del-Barco D, Risco-Acevedo D, Berlanga-Acosta J, Martos-Benítez FD, Guillén-Nieto G. Revisiting Pleiotropic Effects of Type I Interferons: Rationale for Its Prophylactic and Therapeutic Use Against SARS-CoV-2. Front Immunol 2021; 12:655528. [PMID: 33841439 PMCID: PMC8033157 DOI: 10.3389/fimmu.2021.655528] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/08/2021] [Indexed: 12/11/2022] Open
Abstract
The pandemic distribution of SARS-CoV-2 together with its particular feature of inactivating the interferon-based endogenous response and accordingly, impairing the innate immunity, has become a challenge for the international scientific and medical community. Fortunately, recombinant interferons as therapeutic products have accumulated a long history of beneficial therapeutic results in the treatment of chronic and acute viral diseases and also in the therapy of some types of cancer. One of the first antiviral treatments during the onset of COVID-19 in China was based on the use of recombinant interferon alfa 2b, so many clinicians began to use it, not only as therapy but also as a prophylactic approach, mainly in medical personnel. At the same time, basic research on interferons provided new insights that have contributed to a much better understanding of how treatment with interferons, initially considered as antivirals, actually has a much broader pharmacological scope. In this review, we briefly describe interferons, how they are induced in the event of a viral infection, and how they elicit signaling after contact with their specific receptor on target cells. Additionally, some of the genes stimulated by type I interferons are described, as well as the way interferon-mediated signaling is torpedoed by coronaviruses and in particular by SARS-CoV-2. Angiotensin converting enzyme 2 (ACE2) gene is one of the interferon response genes. Although for many scientists this fact could result in an adverse effect of interferon treatment in COVID-19 patients, ACE2 expression contributes to the balance of the renin-angiotensin system, which is greatly affected by SARS-CoV-2 in its internalization into the cell. This manuscript also includes the relationship between type I interferons and neutrophils, NETosis, and interleukin 17. Finally, under the subtitle of "take-home messages", we discuss the rationale behind a timely treatment with interferons in the context of COVID-19 is emphasized.
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Affiliation(s)
- Diana Garcia-del-Barco
- Neuroprotection Project, Center for Genetic Engineering and Biotechnology, Pharmaceutical Division, Havana, Cuba
| | - Daniela Risco-Acevedo
- Neuroprotection Project, Center for Genetic Engineering and Biotechnology, Pharmaceutical Division, Havana, Cuba
| | - Jorge Berlanga-Acosta
- Cytoprotection Project, Center for Genetic Engineering and Biotechnology, Pharmaceutical Division, Havana, Cuba
| | | | - Gerardo Guillén-Nieto
- Biomedical Research Direction, Center for Genetic Engineering and Biotechnology, Havana, Cuba
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Lednicky JA, Tagliamonte MS, White SK, Elbadry MA, Alam MM, Stephenson CJ, Bonny TS, Loeb JC, Telisma T, Chavannes S, Ostrov DA, Mavian C, De Rochars VMB, Salemi M, Morris JG. Emergence of porcine delta-coronavirus pathogenic infections among children in Haiti through independent zoonoses and convergent evolution. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021. [PMID: 33791709 PMCID: PMC8010738 DOI: 10.1101/2021.03.19.21253391] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Coronaviruses have caused three major epidemics since 2003, including the ongoing SARS-CoV-2 pandemic. In each case, coronavirus emergence in our species has been associated with zoonotic transmissions from animal reservoirs1,2, underscoring how prone such pathogens are to spill over and adapt to new species. Among the four recognized genera of the family Coronaviridae – Alphacoronavirus, Betacoronavirus, Deltacoronavirus, Gammacoronavirus, – human infections reported to date have been limited to alpha- and betacoronaviruses3. We identify, for the first time, porcine deltacoronavirus (PDCoV) strains in plasma samples of three Haitian children with acute undifferentiated febrile illness. Genomic and evolutionary analyses reveal that human infections were the result of at least two independent zoonoses of distinct viral lineages that acquired the same mutational signature in the nsp15 and the spike glycoprotein genes by convergent evolution. In particular, structural analysis predicts that one of the changes in the Spike S1 subunit, which contains the receptor-binding domain, may affect protein’s flexibility and binding to the host cell receptor. Our findings not only underscore the ability of deltacoronaviruses to adapt and potentially lead to human-to-human transmission, but also raise questions about the role of such transmissions in development of pre-existing immunity to other coronaviruses, such as SARS-CoV-2.
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Structure-based inhibitor screening of natural products against NSP15 of SARS-CoV-2 revealed thymopentin and oleuropein as potent inhibitors. ACTA ACUST UNITED AC 2021; 12:71-80. [PMID: 33776343 PMCID: PMC7985738 DOI: 10.1007/s42485-021-00059-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 02/26/2021] [Accepted: 03/09/2021] [Indexed: 12/26/2022]
Abstract
Coronaviruses are enveloped, non-segmented positive-sense RNA viruses with the largest genome among RNA viruses. Their genome contains a large replicase ORF which encodes nonstructural proteins (NSPs), structural, and accessory genes. NSP15 is a nidoviral RNA uridylate-specific endoribonuclease (NendoU) with C-terminal catalytic domain. The endoribonuclease activity of NSP15 interferes with the innate immune response of the host. Here, we screened Selleckchem Natural product database of the compounds against NSP15, and we found that thymopentin and oleuropein displayed highest binding energies. The binding of these molecules was further validated by molecular dynamic simulations that revealed them as very stable complexes. These drugs might serve as effective counter molecules in the reduction of virulence of this virus; may be more effective if treated in combination with replicase inhibitors. Future validation of both these inhibitors is worth the consideration for patients being treated for COVID-19.
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Coronavirus Endoribonuclease Ensures Efficient Viral Replication and Prevents Protein Kinase R Activation. J Virol 2021; 95:JVI.02103-20. [PMID: 33361429 PMCID: PMC8092692 DOI: 10.1128/jvi.02103-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Coronavirus (CoV) nsp15 is an endoribonuclease conserved throughout the CoV family. The enzymatic activity and crystal structure of infectious bronchitis virus (IBV) nsp15 are undefined, and the protein's role in replication remains unclear. We verified the uridylate-specific endoribonuclease (EndoU) activity of IBV and found that the EndoU active sites were located in the C-terminus of nsp15 and included His223, His238, Lys278 and Tyr334. We further constructed an infectious clone of the IBV-rSD strain (rSD-wild-type [WT]) and EndoU-deficient IBVs by changing the codon for the EndoU catalytic residues to alanine. Both the rSD-WT and EndoU-deficient viruses propagated efficiently in embryonated chicken eggs. Conversely, EndoU-deficient viral propagation was severely impaired in chicken embryonic kidney cells, which was reflected in the lower viral mRNA accumulation and protein synthesis. After infecting chickens with the parental rSD-WT strain and EndoU-deficient viruses, the EndoU-deficient-virus-infected chickens presented reduced mortality, tissue injury and viral shedding.IMPORTANCE Coronaviruses can emerge from animal reservoirs into naive host species to cause pandemic respiratory and gastrointestinal diseases with significant mortality in humans and domestic animals. Infectious bronchitis virus (IBV), a γ-coronavirus, infects respiratory, renal and reproductive systems, causing millions of dollars in lost revenue worldwide annually. Mutating the viral endoribonuclease resulted in an attenuated virus and prevented protein kinase R activation. Therefore, EndoU activity is a virulence factor in IBV infections, thus providing an approach for generating live-attenuated vaccine candidates for emerging coronaviruses.
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145
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Mehrzadi S, Karimi MY, Fatemi A, Reiter RJ, Hosseinzadeh A. SARS-CoV-2 and other coronaviruses negatively influence mitochondrial quality control: beneficial effects of melatonin. Pharmacol Ther 2021; 224:107825. [PMID: 33662449 PMCID: PMC7919585 DOI: 10.1016/j.pharmthera.2021.107825] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 12/25/2020] [Accepted: 02/22/2021] [Indexed: 12/19/2022]
Abstract
Coronaviruses (CoVs) are a group of single stranded RNA viruses, of which some of them such as SARS-CoV, MERS-CoV, and SARS-CoV-2 are associated with deadly worldwide human diseases. Coronavirus disease-2019 (COVID-19), a condition caused by SARS-CoV-2, results in acute lung injury (ALI)/acute respiratory distress syndrome (ARDS) associated with high mortality in the elderly and in people with underlying comorbidities. Results from several studies suggest that CoVs localize in mitochondria and interact with mitochondrial protein translocation machinery to target their encoded products to mitochondria. Coronaviruses encode a number of proteins; this process is essential for viral replication through inhibiting degradation of viral proteins and host misfolded proteins including those in mitochondria. These viruses seem to maintain their replication by altering mitochondrial dynamics and targeting mitochondrial-associated antiviral signaling (MAVS), allowing them to evade host innate immunity. Coronaviruses infections such as COVID-19 are more severe in aging patients. Since endogenous melatonin levels are often dramatically reduced in the aged and because it is a potent anti-inflammatory agent, melatonin has been proposed to be useful in CoVs infections by altering proteasomal and mitochondrial activities. Melatonin inhibits mitochondrial fission due to its antioxidant and inhibitory effects on cytosolic calcium overload. The collective data suggests that melatonin may mediate mitochondrial adaptations through regulating both mitochondrial dynamics and biogenesis. We propose that melatonin may inhibit SARS-CoV-2-induced cell damage by regulating mitochondrial physiology.
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Affiliation(s)
- Saeed Mehrzadi
- Razi Drug Research Center, Iran University of Medical Sciences, Tehran, Iran
| | | | - Alireza Fatemi
- Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Russel J Reiter
- Department of Cellular and Structural Biology, University of Texas Health Science Center, San Antonio, TX, USA
| | - Azam Hosseinzadeh
- Razi Drug Research Center, Iran University of Medical Sciences, Tehran, Iran.
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V'kovski P, Kratzel A, Steiner S, Stalder H, Thiel V. Coronavirus biology and replication: implications for SARS-CoV-2. Nat Rev Microbiol 2021; 19:155-170. [PMID: 33116300 PMCID: PMC7592455 DOI: 10.1038/s41579-020-00468-6] [Citation(s) in RCA: 1665] [Impact Index Per Article: 555.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2020] [Indexed: 02/06/2023]
Abstract
The SARS-CoV-2 pandemic and its unprecedented global societal and economic disruptive impact has marked the third zoonotic introduction of a highly pathogenic coronavirus into the human population. Although the previous coronavirus SARS-CoV and MERS-CoV epidemics raised awareness of the need for clinically available therapeutic or preventive interventions, to date, no treatments with proven efficacy are available. The development of effective intervention strategies relies on the knowledge of molecular and cellular mechanisms of coronavirus infections, which highlights the significance of studying virus-host interactions at the molecular level to identify targets for antiviral intervention and to elucidate critical viral and host determinants that are decisive for the development of severe disease. In this Review, we summarize the first discoveries that shape our current understanding of SARS-CoV-2 infection throughout the intracellular viral life cycle and relate that to our knowledge of coronavirus biology. The elucidation of similarities and differences between SARS-CoV-2 and other coronaviruses will support future preparedness and strategies to combat coronavirus infections.
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Affiliation(s)
- Philip V'kovski
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Annika Kratzel
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Silvio Steiner
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Hanspeter Stalder
- Institute of Virology and Immunology (IVI), Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), Bern, Switzerland.
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
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Wang HT, Hur S. Substrate recognition by TRIM and TRIM-like proteins in innate immunity. Semin Cell Dev Biol 2021; 111:76-85. [PMID: 33092958 PMCID: PMC7572318 DOI: 10.1016/j.semcdb.2020.09.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 09/28/2020] [Indexed: 12/23/2022]
Abstract
TRIM (Tripartite motif) and TRIM-like proteins have emerged as an important class of E3 ligases in innate immunity. Their functions range from activation or regulation of innate immune signaling pathway to direct detection and restriction of pathogens. Despite the importance, molecular mechanisms for many TRIM/TRIM-like proteins remain poorly characterized, in part due to challenges of identifying their substrates. In this review, we discuss several TRIM/TRIM-like proteins in RNA sensing pathways and viral restriction functions. We focus on those containing PRY-SPRY, the domain most frequently used for substrate recognition, and discuss emerging mechanisms that are commonly utilized by several TRIM/TRIM-like proteins to tightly control their interaction with the substrates.
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Affiliation(s)
- Hai-Tao Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Sun Hur
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
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148
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Gao B, Gong X, Fang S, Weng W, Wang H, Chu H, Sun Y, Meng C, Tan L, Song C, Qiu X, Liu W, Forlenza M, Ding C, Liao Y. Inhibition of anti-viral stress granule formation by coronavirus endoribonuclease nsp15 ensures efficient virus replication. PLoS Pathog 2021; 17:e1008690. [PMID: 33635931 PMCID: PMC7946191 DOI: 10.1371/journal.ppat.1008690] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 03/10/2021] [Accepted: 02/01/2021] [Indexed: 12/19/2022] Open
Abstract
Cytoplasmic stress granules (SGs) are generally triggered by stress-induced translation arrest for storing mRNAs. Recently, it has been shown that SGs exert anti-viral functions due to their involvement in protein synthesis shut off and recruitment of innate immune signaling intermediates. The largest RNA viruses, coronaviruses, impose great threat to public safety and animal health; however, the significance of SGs in coronavirus infection is largely unknown. Infectious Bronchitis Virus (IBV) is the first identified coronavirus in 1930s and has been prevalent in poultry farm for many years. In this study, we provided evidence that IBV overcomes the host antiviral response by inhibiting SGs formation via the virus-encoded endoribonuclease nsp15. By immunofluorescence analysis, we observed that IBV infection not only did not trigger SGs formation in approximately 80% of the infected cells, but also impaired the formation of SGs triggered by heat shock, sodium arsenite, or NaCl stimuli. We further demonstrated that the intrinsic endoribonuclease activity of nsp15 was responsible for the interference of SGs formation. In fact, nsp15-defective recombinant IBV (rIBV-nsp15-H238A) greatly induced the formation of SGs, along with accumulation of dsRNA and activation of PKR, whereas wild type IBV failed to do so. Consequently, infection with rIBV-nsp15-H238A strongly triggered transcription of IFN-β which in turn greatly affected rIBV-nsp15-H238A replication. Further analysis showed that SGs function as an antiviral hub, as demonstrated by the attenuated IRF3-IFN response and increased production of IBV in SG-defective cells. Additional evidence includes the aggregation of pattern recognition receptors (PRRs) and signaling intermediates to the IBV-induced SGs. Collectively, our data demonstrate that the endoribonuclease nsp15 of IBV interferes with the formation of antiviral hub SGs by regulating the accumulation of viral dsRNA and by antagonizing the activation of PKR, eventually ensuring productive virus replication. We further demonstrated that nsp15s from PEDV, TGEV, SARS-CoV, and SARS-CoV-2 harbor the conserved function to interfere with the formation of chemically-induced SGs. Thus, we speculate that coronaviruses employ similar nsp15-mediated mechanisms to antagonize the host anti-viral SGs formation to ensure efficient virus replication. Coronavirus encodes the conserved endoribonuclease nsp15, which has been reported to antagonize IFN responses by mediating evasion of recognition by dsRNA sensors. SGs are part of the host cell anti-viral response; not surprisingly, viruses in turn produce an array of antagonists to counteract such host response. Here, we show that IBV prevents the formation of SGs via nsp15, by reducing the accumulation of viral dsRNA, thereby evading the activation of PKR, phosphorylation of eIF2α, and formation of SGs. Depletion of SG scaffold proteins G3BP1/2 decreases IRF3-IFN response and increases the production of IBV. When overexpressed alone, nsp15s from different coronaviruses (IBV, PEDV, TGEV, SARS-CoV, and SARS-CoV-2) interferes with chemically- and physically-induced SGs, probably by targeting essential SGs assembly factors. In this way, coronaviruses antagonize the formation of SGs by nsp15, via reducing the viral dsRNA accumulation and sequestering/depleting critical component of SGs. To our knowledge, this is the first report describing the role of coronavirus nsp15 in the suppression of integral stress response, in crosstalk with anti-innate immune response.
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Affiliation(s)
- Bo Gao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P. R. China
| | - Xiaoqian Gong
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P. R. China
- Cell Biology and Immunology Group, Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands
| | - Shouguo Fang
- College of Agriculture, College of Animal Sciences, Yangtze University, Jingzhou, P. R. China
| | - Wenlian Weng
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P. R. China
| | - Huan Wang
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P. R. China
| | - Hongyan Chu
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P. R. China
| | - Yingjie Sun
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P. R. China
| | - Chunchun Meng
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P. R. China
| | - Lei Tan
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P. R. China
| | - Cuiping Song
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P. R. China
| | - Xusheng Qiu
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P. R. China
| | - Weiwei Liu
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P. R. China
| | - Maria Forlenza
- Cell Biology and Immunology Group, Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands
| | - Chan Ding
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P. R. China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, P. R. China
| | - Ying Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, P. R. China
- * E-mail:
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149
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Mohammed MEA. SARS-CoV-2 proteins: Are they useful as targets for COVID-19 drugs and vaccines? Curr Mol Med 2021; 22:50-66. [PMID: 33622224 DOI: 10.2174/1566524021666210223143243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 01/28/2021] [Accepted: 02/02/2021] [Indexed: 11/22/2022]
Abstract
The proteins of coronavirus are classified to nonstructural, structural, and accessory. There are 16 nonstructural viral proteins beside their precursors (1a and 1ab polyproteins). The nonstructural proteins are named as nsp1 to nsp16 and they act as enzymes, coenzymes, and binding proteins to facilitate the replication, transcription, and translation of the virus. The structural proteins are bound to the RNA in the nucleocapsid (N- protein) or to the lipid bilayer membrane of the viral envelope. The lipid bilayer proteins include the membrane protein (M), envelope protein (E), and spike protein (S). Beside their role as structural proteins, they are essential for the host cells binding and invasion. The SARS-CoV-2 contains six accessory proteins which participates in the viral replication, assembly and virus- host interactions. The SARS-CoV-2 accessory proteins are orf3a, orf6, orf7a, orf7b, orf8, and orf10. The functions of the SARS-CoV-2 are not well known, while the functions of their corresponding proteins in SARS-CoV are either well known or poorly studied. Recently, the Oxford University and Pfizer and BioNTech made SARS-CoV-2 vaccines through targeting the spike protein gene. The US Food and Drug Administration (FDA) and the health authorities of the United Kingdom approved and started vaccination using the Pfizer and BioNTech mRNA vaccine. Also, The FDA of USA approved the treatment of COVID-19 using two monoclonal antibodies produced by Regeneron pharmaceuticals to target the spike protein. The SARS-CoV-2 proteins can be used for the diagnosis, as drug targets and in vaccination trials for COVID-19. For future COVID-19 research, more efforts should be done to elaborate the functions and structure of the SARS-CoV-2 proteins so as to use them as targets for COVID-19 drug and vaccines. Special attention should be drawn to extensive research on the SARS-CoV-2 nsp3, orf8, and orf10.
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150
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Abstract
The ongoing pandemic of the new severe acute respiratory syndrome coronavirus (SARS-CoV-2) has caused more than one million deaths, overwhelmed many public health systems, and led to a worldwide economic recession. This has raised an unprecedented need to develop antiviral drugs and vaccines, which requires profound knowledge of the fundamental pathology of the virus, including its entry, replication, and release from host cells. The genome of coronaviruses comprises around 30 kb of positive single-stranded RNA, representing one of the largest RNA genomes of viruses. The 5′ part of the genome encodes a large polyprotein, PP1ab, which gives rise to 16 non-structural proteins (nsp1– nsp16). Two proteases encoded in nsp3 and nsp5 cleave the polyprotein into individual proteins. Most nsps belong to the viral replicase complex that promotes replication of the viral genome and translation of structural proteins by producing subgenomic mRNAs. The replicase complexes are found on double-membrane vesicles (DMVs) that contain viral double-stranded RNA. Expression of a small subset of viral proteins, including nsp3 and nsp4, is sufficient to induce formation of these DMVs in human cells, suggesting that both proteins deform host membranes into such structures. We will discuss the formation of DMVs and provide an overview of other membrane remodeling processes that are induced by coronaviruses.
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Affiliation(s)
- Jagan Mohan
- Membrane Biochemistry and Transport, Institut Pasteur, UMR3691 CNRS, F-75015, Paris, France
| | - Thomas Wollert
- Membrane Biochemistry and Transport, Institut Pasteur, UMR3691 CNRS, F-75015, Paris, France
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