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Andrabi SM, Sharma NS, Karan A, Shahriar SMS, Cordon B, Ma B, Xie J. Nitric Oxide: Physiological Functions, Delivery, and Biomedical Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303259. [PMID: 37632708 PMCID: PMC10602574 DOI: 10.1002/advs.202303259] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Indexed: 08/28/2023]
Abstract
Nitric oxide (NO) is a gaseous molecule that has a central role in signaling pathways involved in numerous physiological processes (e.g., vasodilation, neurotransmission, inflammation, apoptosis, and tumor growth). Due to its gaseous form, NO has a short half-life, and its physiology role is concentration dependent, often restricting its function to a target site. Providing NO from an external source is beneficial in promoting cellular functions and treatment of different pathological conditions. Hence, the multifaceted role of NO in physiology and pathology has garnered massive interest in developing strategies to deliver exogenous NO for the treatment of various regenerative and biomedical complexities. NO-releasing platforms or donors capable of delivering NO in a controlled and sustained manner to target tissues or organs have advanced in the past few decades. This review article discusses in detail the generation of NO via the enzymatic functions of NO synthase as well as from NO donors and the multiple biological and pathological processes that NO modulates. The methods for incorporating of NO donors into diverse biomaterials including physical, chemical, or supramolecular techniques are summarized. Then, these NO-releasing platforms are highlighted in terms of advancing treatment strategies for various medical problems.
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Affiliation(s)
- Syed Muntazir Andrabi
- Department of Surgery‐Transplant and Mary & Dick Holland Regenerative Medicine ProgramCollege of MedicineUniversity of Nebraska Medical CenterOmahaNE68198USA
| | - Navatha Shree Sharma
- Department of Surgery‐Transplant and Mary & Dick Holland Regenerative Medicine ProgramCollege of MedicineUniversity of Nebraska Medical CenterOmahaNE68198USA
| | - Anik Karan
- Department of Surgery‐Transplant and Mary & Dick Holland Regenerative Medicine ProgramCollege of MedicineUniversity of Nebraska Medical CenterOmahaNE68198USA
| | - S. M. Shatil Shahriar
- Department of Surgery‐Transplant and Mary & Dick Holland Regenerative Medicine ProgramCollege of MedicineUniversity of Nebraska Medical CenterOmahaNE68198USA
| | - Brent Cordon
- Department of Surgery‐Transplant and Mary & Dick Holland Regenerative Medicine ProgramCollege of MedicineUniversity of Nebraska Medical CenterOmahaNE68198USA
| | - Bing Ma
- Cell Therapy Manufacturing FacilityMedStar Georgetown University HospitalWashington, DC2007USA
| | - Jingwei Xie
- Department of Surgery‐Transplant and Mary & Dick Holland Regenerative Medicine ProgramCollege of MedicineUniversity of Nebraska Medical CenterOmahaNE68198USA
- Department of Mechanical and Materials EngineeringCollege of EngineeringUniversity of Nebraska LincolnLincolnNE68588USA
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2
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Duan Z, Zhang Q, Liu M, Hu Z. Multifunctionality of matrix protein in the replication and pathogenesis of Newcastle disease virus: A review. Int J Biol Macromol 2023; 249:126089. [PMID: 37532184 DOI: 10.1016/j.ijbiomac.2023.126089] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 07/28/2023] [Accepted: 07/30/2023] [Indexed: 08/04/2023]
Abstract
As an important structural protein in virion morphogenesis, the matrix (M) protein of Newcastle disease virus (NDV) is demonstrated to be a nuclear-cytoplasmic trafficking protein and plays essential roles in viral assembly and budding. In recent years, increasing lines of evidence have indicated that the M protein has obvious influence on the pathotypes of NDV, and the interaction of M protein with cellular proteins is also closely associated with the replication and pathogenicity of NDV. Although substantial progress has been made in the past 40 years towards understanding the structure and function of NDV M protein, the available information is scattered. Therefore, this review article summarizes and updates the research progress on the structural feature, virulence and pathotype correlation, and nucleocytoplasmic transport mechanism of NDV M protein, as well as the functions of M protein and cellular protein interactions in M's intracellular localization, viral RNA synthesis and transcription, viral protein synthesis, viral immune evasion, and viral budding and release, which will provide an in-depth understanding of the biological functions of M protein in the replication and pathogenesis of NDV, and also contribute to the development of effective antiviral strategies aiming at blocking the early or late steps of NDV lifecycles.
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Affiliation(s)
- Zhiqiang Duan
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China; College of Animal Science, Guizhou University, Guiyang, China.
| | - Qianyong Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China; College of Animal Science, Guizhou University, Guiyang, China
| | - Menglan Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China; College of Animal Science, Guizhou University, Guiyang, China
| | - Zenglei Hu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China
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3
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Lee YB, Jung M, Kim J, Charles A, Christ W, Kang J, Kang MG, Kwak C, Klingström J, Smed-Sörensen A, Kim JS, Mun JY, Rhee HW. Super-resolution proximity labeling reveals anti-viral protein network and its structural changes against SARS-CoV-2 viral proteins. Cell Rep 2023; 42:112835. [PMID: 37478010 DOI: 10.1016/j.celrep.2023.112835] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 05/31/2023] [Accepted: 07/05/2023] [Indexed: 07/23/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replicates in human cells by interacting with host factors following infection. To understand the virus and host interactome proximity, we introduce a super-resolution proximity labeling (SR-PL) method with a "plug-and-playable" PL enzyme, TurboID-GBP (GFP-binding nanobody protein), and we apply it for interactome mapping of SARS-CoV-2 ORF3a and membrane protein (M), which generates highly perturbed endoplasmic reticulum (ER) structures. Through SR-PL analysis of the biotinylated interactome, 224 and 272 peptides are robustly identified as ORF3a and M interactomes, respectively. Within the ORF3a interactome, RNF5 co-localizes with ORF3a and generates ubiquitin modifications of ORF3a that can be involved in protein degradation. We also observe that the SARS-CoV-2 infection rate is efficiently reduced by the overexpression of RNF5 in host cells. The interactome data obtained using the SR-PL method are presented at https://sarscov2.spatiomics.org. We hope that our method will contribute to revealing virus-host interactions of other viruses in an efficient manner.
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Affiliation(s)
- Yun-Bin Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Minkyo Jung
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Jeesoo Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea; Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea
| | - Afandi Charles
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, 17164 Stockholm, Sweden
| | - Wanda Christ
- Centre for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, 14183 Stockholm, Sweden
| | - Jiwoong Kang
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Myeong-Gyun Kang
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Chulhwan Kwak
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Jonas Klingström
- Centre for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, 14183 Stockholm, Sweden; Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
| | - Anna Smed-Sörensen
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, 17164 Stockholm, Sweden
| | - Jong-Seo Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea; Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea.
| | - Ji Young Mun
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea.
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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4
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Gonzalez Lopez Ledesma MM, Costa Navarro G, Pallares HM, Paletta A, De Maio F, Iglesias NG, Gebhard L, Oviedo Rouco S, Ojeda DS, de Borba L, Giraldo M, Rajsbaum R, Ceballos A, Krogan NJ, Shah PS, Gamarnik AV. Dengue virus NS5 degrades ERC1 during infection to antagonize NF-kB activation. Proc Natl Acad Sci U S A 2023; 120:e2220005120. [PMID: 37252973 PMCID: PMC10266027 DOI: 10.1073/pnas.2220005120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/28/2023] [Indexed: 06/01/2023] Open
Abstract
Dengue virus (DENV) is the most important human virus transmitted by mosquitos. Dengue pathogenesis is characterized by a large induction of proinflammatory cytokines. This cytokine induction varies among the four DENV serotypes (DENV1 to 4) and poses a challenge for live DENV vaccine design. Here, we identify a viral mechanism to limit NF-κB activation and cytokine secretion by the DENV protein NS5. Using proteomics, we found that NS5 binds and degrades the host protein ERC1 to antagonize NF-κB activation, limit proinflammatory cytokine secretion, and reduce cell migration. We found that ERC1 degradation involves unique properties of the methyltransferase domain of NS5 that are not conserved among the four DENV serotypes. By obtaining chimeric DENV2 and DENV4 viruses, we map the residues in NS5 for ERC1 degradation, and generate recombinant DENVs exchanging serotype properties by single amino acid substitutions. This work uncovers a function of the viral protein NS5 to limit cytokine production, critical to dengue pathogenesis. Importantly, the information provided about the serotype-specific mechanism for counteracting the antiviral response can be applied to improve live attenuated vaccines.
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Affiliation(s)
| | | | | | - Ana Paletta
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA, Universidad de Buenos Aires-National Scientific and Technical Research Council, Buenos AiresC1121, Argentina
| | - Federico De Maio
- Fundación Instituto Leloir-CONICET, Buenos AiresC1405, Argentina
| | | | - Leopoldo Gebhard
- Fundación Instituto Leloir-CONICET, Buenos AiresC1405, Argentina
| | | | - Diego S. Ojeda
- Fundación Instituto Leloir-CONICET, Buenos AiresC1405, Argentina
| | - Luana de Borba
- Fundación Instituto Leloir-CONICET, Buenos AiresC1405, Argentina
| | - María Giraldo
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX77555
| | - Ricardo Rajsbaum
- Department of Medicine, Center for Virus-Host-Innate-Immunity, Rutgers Biomedical and Health Sciences, Newark, NJ07101
| | - Ana Ceballos
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA, Universidad de Buenos Aires-National Scientific and Technical Research Council, Buenos AiresC1121, Argentina
| | | | - Priya S. Shah
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA95616
- Department of Chemical Engineering, University of California, Davis, CA95616
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5
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Kakavandi S, Zare I, VaezJalali M, Dadashi M, Azarian M, Akbari A, Ramezani Farani M, Zalpoor H, Hajikhani B. Structural and non-structural proteins in SARS-CoV-2: potential aspects to COVID-19 treatment or prevention of progression of related diseases. Cell Commun Signal 2023; 21:110. [PMID: 37189112 DOI: 10.1186/s12964-023-01104-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 03/15/2023] [Indexed: 05/17/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by a new member of the Coronaviridae family known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). There are structural and non-structural proteins (NSPs) in the genome of this virus. S, M, H, and E proteins are structural proteins, and NSPs include accessory and replicase proteins. The structural and NSP components of SARS-CoV-2 play an important role in its infectivity, and some of them may be important in the pathogenesis of chronic diseases, including cancer, coagulation disorders, neurodegenerative disorders, and cardiovascular diseases. The SARS-CoV-2 proteins interact with targets such as angiotensin-converting enzyme 2 (ACE2) receptor. In addition, SARS-CoV-2 can stimulate pathological intracellular signaling pathways by triggering transcription factor hypoxia-inducible factor-1 (HIF-1), neuropilin-1 (NRP-1), CD147, and Eph receptors, which play important roles in the progression of neurodegenerative diseases like Alzheimer's disease, epilepsy, and multiple sclerosis, and multiple cancers such as glioblastoma, lung malignancies, and leukemias. Several compounds such as polyphenols, doxazosin, baricitinib, and ruxolitinib could inhibit these interactions. It has been demonstrated that the SARS-CoV-2 spike protein has a stronger affinity for human ACE2 than the spike protein of SARS-CoV, leading the current study to hypothesize that the newly produced variant Omicron receptor-binding domain (RBD) binds to human ACE2 more strongly than the primary strain. SARS and Middle East respiratory syndrome (MERS) viruses against structural and NSPs have become resistant to previous vaccines. Therefore, the review of recent studies and the performance of current vaccines and their effects on COVID-19 and related diseases has become a vital need to deal with the current conditions. This review examines the potential role of these SARS-CoV-2 proteins in the initiation of chronic diseases, and it is anticipated that these proteins could serve as components of an effective vaccine or treatment for COVID-19 and related diseases. Video Abstract.
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Affiliation(s)
- Sareh Kakavandi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Iman Zare
- Research and Development Department, Sina Medical Biochemistry Technologies Co. Ltd., Shiraz, 7178795844, Iran
| | - Maryam VaezJalali
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoud Dadashi
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
- Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Maryam Azarian
- Department of Radiology, Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Abdullatif Akbari
- Shiraz Neuroscience Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Marzieh Ramezani Farani
- Department of Biological Sciences and Bioengineering, Nano Bio High-Tech Materials Research Center, Inha University, Incheon, 22212, Republic of Korea
| | - Hamidreza Zalpoor
- Shiraz Neuroscience Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran.
| | - Bahareh Hajikhani
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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6
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Beeraka NM, Sukocheva OA, Lukina E, Liu J, Fan R. Development of antibody resistance in emerging mutant strains of SARS CoV-2: Impediment for COVID-19 vaccines. Rev Med Virol 2022; 32:e2346. [PMID: 35416390 PMCID: PMC9111059 DOI: 10.1002/rmv.2346] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/28/2022] [Accepted: 03/06/2022] [Indexed: 02/05/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a highly infectious agent associated with unprecedented morbidity and mortality. A failure to stop growth of COVID-19-linked morbidity rates is caused by SARS-CoV-2 mutations and the emergence of new highly virulent SARS-CoV-2 strains. Several acquired SARS-CoV-2 mutations reflect viral adaptations to host immune defence. Mutations in the virus Spike-protein were associated with the lowered effectiveness of current preventive therapies, including vaccines. Recent in vitro studies detected diminished neutralisation capacity of vaccine-induced antibodies, which are targeted to bind Spike receptor-binding and N-terminal domains in the emerging strains. Lower than expected inhibitory activity of antibodies was reported against viruses with E484K Spike mutation, including B.1.1.7 (UK), P.1 (Brazil), B.1.351 (South African), and new Omicron variant (B.1.1.529) with E484A mutation. The vaccine effectiveness is yet to be examined against new mutant strains of SARS-CoV-2 originating in Europe, Nigeria, Brazil, South Africa, and India. To prevent the loss of anti-viral protection in vivo, often defined as antibody resistance, it is required to target highly conserved viral sequences (including Spike protein) and enhance the potency of antibody cocktails. In this review, we assess the reported mutation-acquiring potential of coronaviruses and compare efficacies of current COVID-19 vaccines against 'parent' and 'mutant' strains of SARS-CoV-2 (Kappa (B.1.617.1), Delta (B.1.617.2), and Omicron (B.1.1.529)).
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Affiliation(s)
- Narasimha M. Beeraka
- Department of Radiation OncologyCancer CenterThe First Affiliated Hospital of ZhengzhouZhengzhouChina
- Department of Human AnatomyI.M. Sechenov First Moscow State Medical University (Sechenov University)MoscowRussian Federation
| | - Olga A. Sukocheva
- Discipline of Health SciencesCollege of Nursing and Health SciencesFlinders University of South AustraliaBedford ParkAustralia
| | - Elena Lukina
- Discipline of BiologyCollege of SciencesFlinders University of South AustraliaBedford ParkAustralia
| | - Junqi Liu
- Department of Radiation OncologyCancer CenterThe First Affiliated Hospital of ZhengzhouZhengzhouChina
| | - Ruitai Fan
- Department of Radiation OncologyCancer CenterThe First Affiliated Hospital of ZhengzhouZhengzhouChina
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7
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Cortés-Sarabia K, Cruz-Rangel A, Flores-Alanis A, Salazar-García M, Jiménez-García S, Rodríguez-Martínez G, Reyes-Grajeda JP, Rodríguez-Téllez RI, Patiño-López G, Parra-Ortega I, Del Moral-Hernández O, Illades-Aguiar B, Klünder-Klünder M, Márquez-González H, Chávez-López A, Luna-Pineda VM. Clinical features and severe acute respiratory syndrome-coronavirus-2 structural protein-based serology of Mexican children and adolescents with coronavirus disease 2019. PLoS One 2022; 17:e0273097. [PMID: 35969583 PMCID: PMC9377623 DOI: 10.1371/journal.pone.0273097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 08/02/2022] [Indexed: 12/24/2022] Open
Abstract
Severe acute respiratory syndrome (SARS)-coronavirus (CoV)-2 infection in children and adolescents primarily causes mild or asymptomatic coronavirus disease 2019 (COVID-19), and severe illness is mainly associated with comorbidities. However, the worldwide prevalence of COVID-19 in this population is only 1%–2%. In Mexico, the prevalence of COVID-19 in children has increased to 10%. As serology-based studies are scarce, we analyzed the clinical features and serological response (SARS-CoV-2 structural proteins) of children and adolescents who visited the Hospital Infantil de México Federico Gómez (October 2020–March 2021). The majority were 9-year-old children without comorbidities who were treated as outpatients and had mild-to-moderate illness. Children aged 6–10 years and adolescents aged 11–15 years had the maximum number of symptoms, including those with obesity. Nevertheless, children with comorbidities such as immunosuppression, leukemia, and obesity exhibited the lowest antibody response, whereas those aged 1–5 years with heart disease had the highest levels of antibodies. The SARS-CoV-2 spike receptor-binding domain-localized peptides and M and E proteins had the best antibody response. In conclusion, Mexican children and adolescents with COVID-19 represent a heterogeneous population, and comorbidities play an important role in the antibody response against SARS-CoV-2 infection.
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Affiliation(s)
- Karen Cortés-Sarabia
- Laboratorio de Inmunobiología y Diagnóstico Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Guerrero, México
| | - Armando Cruz-Rangel
- Laboratorio de Bioquímica de Enfermedades Crónicas, Instituto Nacional de Medicina Genómica, Mexico City (Ciudad de México), México
| | - Alejandro Flores-Alanis
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City (Ciudad de México), México
| | - Marcela Salazar-García
- Laboratorio de Biología del Desarrollo y Teratogénesis Experimental, Hospital Infantil de México Federico Gómez, Mexico City (Ciudad de México), México
- Laboratorio de Investigación en COVID-19, Hospital Infantil de México Federico Gómez, Mexico City (Ciudad de México), México
| | - Samuel Jiménez-García
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Guerrero, México
| | - Griselda Rodríguez-Martínez
- Laboratorio de Investigación en COVID-19, Hospital Infantil de México Federico Gómez, Mexico City (Ciudad de México), México
| | - Juan Pablo Reyes-Grajeda
- Laboratorio de Bioquímica de Enfermedades Crónicas, Instituto Nacional de Medicina Genómica, Mexico City (Ciudad de México), México
| | - Rosa Isela Rodríguez-Téllez
- Unidad de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Mexico City (Ciudad de México), México
| | - Genaro Patiño-López
- Unidad de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Mexico City (Ciudad de México), México
| | - Israel Parra-Ortega
- Laboratorio Central, Hospital Infantil de México Federico Gómez, Mexico City (Ciudad de México), México
| | - Oscar Del Moral-Hernández
- Laboratorio de Virología, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Guerrero, México
| | - Berenice Illades-Aguiar
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Guerrero, México
| | - Miguel Klünder-Klünder
- Subdirección de Gestión de la Investigación, Hospital Infantil de México Federico Gómez, Mexico City (Ciudad de México), México
| | - Horacio Márquez-González
- Investigación Clínica, Hospital Infantil de México Federico Gómez, Mexico City (Ciudad de México), México
| | - Adrián Chávez-López
- Departamento de la Unidad de Terapia Intensiva Pediátrica, Hospital Infantil de México Federico Gómez, Mexico City (Ciudad de México), México
| | - Victor M. Luna-Pineda
- Laboratorio de Investigación en COVID-19, Hospital Infantil de México Federico Gómez, Mexico City (Ciudad de México), México
- Unidad de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Mexico City (Ciudad de México), México
- * E-mail:
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8
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Duan Z, Xing J, Shi H, Wang Y, Zhao C. The matrix protein of Newcastle disease virus inhibits inflammatory response through IRAK4/TRAF6/TAK1/NF-κB signaling pathway. Int J Biol Macromol 2022; 218:295-309. [PMID: 35872314 DOI: 10.1016/j.ijbiomac.2022.07.132] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/23/2022] [Accepted: 07/17/2022] [Indexed: 11/25/2022]
Abstract
The matrix (M) protein of several cytoplasmic RNA viruses has been reported to be an NF-κB pathway antagonist. However, the function and mechanism of NDV M protein antagonizing NF-κB activation remain largely unknown. In this study, we found that the expression levels of IRAK4, TRAF6, TAK1, and RELA/p65 were obviously reduced late in NDV infection. In addition, the cytoplasmic M protein rather than other viral proteins decreased the expression of these proteins in a dose-dependent manner. Further indepth analysis showed that the N-terminal 180 amino acids of M protein were not only responsible for the reduced expression of these proteins, but also responsible for the inhibition of NF-κB activation and nuclear translocation of RELA/p65, as well as the production of inflammatory cytokines. Moreover, small interference RNA-mediated knockdown of IRAK4 or overexpression of IRAK4 markedly enhanced or reduced NDV replication by decreasing or increasing inflammatory cytokines production through the IRAK4/TRAF6/TAK1/NF-κB signaling pathway. Strangely, there were no interactions detected between NDV M protein and IRAK4, TRAF6, TAK1 or RELA/p65. Our findings described here contribute to a better understanding of the innate immune antagonism function of M protein and the molecular mechanism underlying the replication and pathogenesis of NDV.
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Affiliation(s)
- Zhiqiang Duan
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China; College of Animal Science, Guizhou University, Guiyang, China.
| | - Jingru Xing
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China; College of Animal Science, Guizhou University, Guiyang, China
| | - Haiying Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China; College of Animal Science, Guizhou University, Guiyang, China
| | - Yanbi Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China; College of Animal Science, Guizhou University, Guiyang, China
| | - Caiqin Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China; College of Animal Science, Guizhou University, Guiyang, China
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9
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Li J, Jia H, Tian M, Wu N, Yang X, Qi J, Ren W, Li F, Bian H. SARS-CoV-2 and Emerging Variants: Unmasking Structure, Function, Infection, and Immune Escape Mechanisms. Front Cell Infect Microbiol 2022; 12:869832. [PMID: 35646741 PMCID: PMC9134119 DOI: 10.3389/fcimb.2022.869832] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 04/06/2022] [Indexed: 12/24/2022] Open
Abstract
As of April 1, 2022, over 468 million COVID-19 cases and over 6 million deaths have been confirmed globally. Unlike the common coronavirus, SARS-CoV-2 has highly contagious and attracted a high level of concern worldwide. Through the analysis of SARS-CoV-2 structural, non-structural, and accessory proteins, we can gain a deeper understanding of structure-function relationships, viral infection mechanisms, and viable strategies for antiviral therapy. Angiotensin-converting enzyme 2 (ACE2) is the first widely acknowledged SARS-CoV-2 receptor, but researches have shown that there are additional co-receptors that can facilitate the entry of SARS-CoV-2 to infect humans. We have performed an in-depth review of published papers, searching for co-receptors or other auxiliary membrane proteins that enhance viral infection, and analyzing pertinent pathogenic mechanisms. The genome, and especially the spike gene, undergoes mutations at an abnormally high frequency during virus replication and/or when it is transmitted from one individual to another. We summarized the main mutant strains currently circulating global, and elaborated the structural feature for increased infectivity and immune evasion of variants. Meanwhile, the principal purpose of the review is to update information on the COVID-19 outbreak. Many countries have novel findings on the early stage of the epidemic, and accruing evidence has rewritten the timeline of the outbreak, triggering new thinking about the origin and spread of COVID-19. It is anticipated that this can provide further insights for future research and global epidemic prevention and control.
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Affiliation(s)
| | | | | | | | | | | | | | - Feifei Li
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Hongjun Bian
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
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10
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Evaluation of the Potential Risk of Mortality from SARS-CoV-2 Infection in Hospitalized Patients According to the Charlson Comorbidity Index. Healthcare (Basel) 2022; 10:healthcare10020362. [PMID: 35206976 PMCID: PMC8872141 DOI: 10.3390/healthcare10020362] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/25/2022] [Accepted: 02/10/2022] [Indexed: 12/15/2022] Open
Abstract
Background: The pandemic of COVID-19 has represented a major threat to global public health in the last century and therefore to identify predictors of mortality among COVID-19 hospitalized patients is widely justified. The aim of this study was to evaluate the possible usefulness of Charlson Comorbidity Index (CCI) as mortality predictor in patients hospitalized because COVID-19. Methods: This study was carried out in Zacatecas, Mexico, and it included 705 hospitalized patients with suspected of SARS-CoV-2 infection. Clinical data were collected, and the CCI score was calculated online using the calculator from the Sociedad Andaluza de Medicina Intensiva y Unidades Coronarias; the result was evaluated as mortality predictor among the patients with COVID-19. Results: 377 patients were positive for SARS-COV-2. Obesity increased the risk of intubation among the study population (odds ratio (OR) = 2.59; 95 CI: 1.36–4.92; p = 0.003). The CCI values were higher in patients who died because of COVID-19 complications than those observed in patients who survived (p < 0.001). Considering a CCI cutoff > 31.69, the area under the ROC curve was 0.75, with a sensitivity and a specificity of 63.6% and 87.7%, respectively. Having a CCI value > 31.69 increased the odds of death by 12.5 times among the study population (95% CI: 7.3–21.4; p < 0.001). Conclusions: The CCI is a suitable tool for the prediction of mortality in patients hospitalized for COVID-19. The presence of comorbidities in hospitalized patients with COVID-19 reflected as CCI > 31.69 increased the risk of death among the study population, so it is important to take precautionary measures in patients due to their condition and their increased vulnerability to SARS-CoV-2 infection.
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11
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Ahmadi K, Zahedifard F, Mafakher L, Einakian MA, Ghaedi T, Kavousipour S, Faezi S, Karmostaji A, Sharifi-Sarasiabi K, Gouklani H, Hassaniazad M. Active site-based analysis of structural proteins for drug targets in different human Coronaviruses. Chem Biol Drug Des 2021; 99:585-602. [PMID: 34914204 DOI: 10.1111/cbdd.14004] [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: 08/05/2021] [Revised: 11/03/2021] [Accepted: 12/09/2021] [Indexed: 11/30/2022]
Abstract
Seven types of Coronaviruses (CoVs) have been identified that can cause infection in humans, including HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1, SARS-CoV, HCoV-MERS, and SARS-CoV-2. In this study, we investigated the genetic structure, the homology of the structural protein sequences, as well as the investigation of the active site of structural proteins. The active site of structural proteins was determined based on the previous studies, and the homology of their amino acid sequences and structure was compared. Multiple sequence alignment of Spike protein of HCoVs showed that the receptor-binding domain of SARS-CoV-2, SARS-CoV, and MERS-CoV was located at a similar site to the S1 subunit. The binding motif of PDZ (postsynaptic density- 95/discs large/zona occludens-1) of the envelope protein, was conserved in SARS-CoV and SARS-CoV-2 according to multiple sequence alignment but showed different changes in the other HCoVs. Overall, Spike protein showed the most variation in its active sites, but the other structural proteins were highly conserved. In this study, for the first time, the active site of all structural proteins of HCoVs as a drug target was investigated. The binding site of these proteins can be suitable targets for drugs or vaccines among HCoVs.
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Affiliation(s)
- Khadijeh Ahmadi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Farnaz Zahedifard
- Drug discovery and Evaluation unit, Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ladan Mafakher
- Thalassemia & Hemoglobinopathy Research center, Health research institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Ali Einakian
- Food Health Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Tayebeh Ghaedi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Soudabeh Kavousipour
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Sobhan Faezi
- Department of Microbiology, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Afsaneh Karmostaji
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Khojasteh Sharifi-Sarasiabi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Hamed Gouklani
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mehdi Hassaniazad
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
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12
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SARS-CoV-2, Zika viruses and mycoplasma: Structure, pathogenesis and some treatment options in these emerging viral and bacterial infectious diseases. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166264. [PMID: 34481867 PMCID: PMC8413106 DOI: 10.1016/j.bbadis.2021.166264] [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: 02/23/2021] [Revised: 07/22/2021] [Accepted: 08/30/2021] [Indexed: 01/28/2023]
Abstract
The molecular evolution of life on earth along with changing environmental, conditions has rendered mankind susceptible to endemic and pandemic emerging infectious diseases. The effects of certain systemic viral and bacterial infections on morbidity and mortality are considered as examples of recent emerging infections. Here we will focus on three examples of infections that are important in pregnancy and early childhood: SARS-CoV-2 virus, Zika virus, and Mycoplasma species. The basic structural characteristics of these infectious agents will be examined, along with their general pathogenic mechanisms. Coronavirus infections, such as caused by the SARS-CoV-2 virus, likely evolved from zoonotic bat viruses to infect humans and cause a pandemic that has been the biggest challenge for humanity since the Spanish Flu pandemic of the early 20th century. In contrast, Zika Virus infections represent an expanding infectious threat in the context of global climate change. The relationship of these infections to pregnancy, the vertical transmission and neurological sequels make these viruses highly relevant to the topics of this special issue. Finally, mycoplasmal infections have been present before mankind evolved, but they were rarely identified as human pathogens until recently, and they are now recognized as important coinfections that are able to modify the course and prognosis of various infectious diseases and other chronic illnesses. The infectious processes caused by these intracellular microorganisms are examined as well as some general aspects of their pathogeneses, clinical presentations, and diagnoses. We will finally consider examples of treatments that have been used to reduce morbidity and mortality of these infections and discuss briefly the current status of vaccines, in particular, against the SARS-CoV-2 virus. It is important to understand some of the basic features of these emerging infectious diseases and the pathogens involved in order to better appreciate the contributions of this special issue on how infectious diseases can affect human pregnancy, fetuses and neonates.
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13
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Arslan Gulen T, Bayraktar M, Yaksi N, Kayabas U. Is the course of COVID-19 associated with tuberculin skin test diameter? A retrospective study. J Med Virol 2021; 94:1020-1026. [PMID: 34676582 PMCID: PMC8662280 DOI: 10.1002/jmv.27414] [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: 09/21/2021] [Accepted: 10/20/2021] [Indexed: 01/08/2023]
Abstract
The pathogenesis of coronavirus disease 2019 (COVID‐19) is still not fully understood. As severe acute respiratory syndrome coronavirus 2 (SARS‐COV‐2) has a similar pathogenetic pathway to Mycobacterium tuberculosis, it has been reported that there may be a relationship between Bacille Calmette–Guérin (BCG) vaccination rate and COVID‐19 severity. This study investigated the relationship between tuberculin skin test (TST) induration diameter and the clinical course of COVID‐19. Of 1963 adult patients who underwent TST, 76 patients with SARS‐COV‐2 infection confirmed by RT‐PCR analysis of respiratory tract samples were included in the study. Relationships between COVID‐19 clinical severity and TST positivity, induration size, and other clinical parameters were analyzed. Of the 76 patients, TST results were negative for 53 patients (69.7%) and positive for 23 patients (30.3%). COVID‐19 severity was mild in 47 patients (61.8%), moderate in 22 patients (28.9%), and severe in seven patients (9.3%). All TST‐positive patients had mild disease. Patients with mild disease had a significantly higher TST positivity rate (p < 0.001) and larger induration diameter (p < 0.001). The area under the receiver operating characteristic (ROC) curve of TST induration size for the differentiation of mild with moderate and severe disease was 0.768 (p < 0.001). The maximum Youden J index value was 0.522 at an induration diameter of 6.5 mm, which had a sensitivity of 66.0% and specificity of 86.2%. COVID‐19 patients with positive TST showed a significantly higher rate of mild disease than those with negative TST. TST positivity is favorably associated with the course of COVID‐19. TST induration diameters larger than 6.5 mm were highly specific in predicting a milder clinical presentation of COVID‐19. Patients with positive tuberculin skin test (TST) had milder COVID‐19 symptoms. TST induration diameter is favorably associated with the course of COVID‐19.
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Affiliation(s)
- Tugba Arslan Gulen
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Muhammet Bayraktar
- Department of Public Health, Faculty of Medicine, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Nese Yaksi
- Division of Community Health Center, City Health Directorate, Nigde, Turkey
| | - Uner Kayabas
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Nigde Omer Halisdemir University, Nigde, Turkey
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14
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Myocardial Damage by SARS-CoV-2: Emerging Mechanisms and Therapies. Viruses 2021; 13:v13091880. [PMID: 34578462 PMCID: PMC8473126 DOI: 10.3390/v13091880] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/06/2021] [Accepted: 09/18/2021] [Indexed: 01/01/2023] Open
Abstract
Evidence is emerging that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can infect various organs of the body, including cardiomyocytes and cardiac endothelial cells in the heart. This review focuses on the effects of SARS-CoV-2 in the heart after direct infection that can lead to myocarditis and an outline of potential treatment options. The main points are: (1) Viral entry: SARS-CoV-2 uses specific receptors and proteases for docking and priming in cardiac cells. Thus, different receptors or protease inhibitors might be effective in SARS-CoV-2-infected cardiac cells. (2) Viral replication: SARS-CoV-2 uses RNA-dependent RNA polymerase for replication. Drugs acting against ssRNA(+) viral replication for cardiac cells can be effective. (3) Autophagy and double-membrane vesicles: SARS-CoV-2 manipulates autophagy to inhibit viral clearance and promote SARS-CoV-2 replication by creating double-membrane vesicles as replication sites. (4) Immune response: Host immune response is manipulated to evade host cell attacks against SARS-CoV-2 and increased inflammation by dysregulating immune cells. Efficiency of immunosuppressive therapy must be elucidated. (5) Programmed cell death: SARS-CoV-2 inhibits programmed cell death in early stages and induces apoptosis, necroptosis, and pyroptosis in later stages. (6) Energy metabolism: SARS-CoV-2 infection leads to disturbed energy metabolism that in turn leads to a decrease in ATP production and ROS production. (7) Viroporins: SARS-CoV-2 creates viroporins that lead to an imbalance of ion homeostasis. This causes apoptosis, altered action potential, and arrhythmia.
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15
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Su CM, Wang L, Yoo D. Activation of NF-κB and induction of proinflammatory cytokine expressions mediated by ORF7a protein of SARS-CoV-2. Sci Rep 2021; 11:13464. [PMID: 34188167 PMCID: PMC8242070 DOI: 10.1038/s41598-021-92941-2] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/17/2021] [Indexed: 02/07/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent for coronavirus disease 2019 (COVID-19) that emerged in human populations recently. Severely ill COVID-19 patients exhibit the elevation of proinflammatory cytokines, and such an unbalanced production of proinflammatory cytokines is linked to acute respiratory distress syndrome with high mortality in COVID-19 patients. Our study provides evidence that the ORF3a, M, ORF7a, and N proteins of SARS-CoV-2 were NF-κB activators. The viral sequence from infected zoo lions belonged to clade V, and a single mutation of G251V is found for ORF3a gene compared to all other clades. No significant functional difference was found for clade V ORF3a, indicating the NF-κB activation is conserved among COVID-19 variants. Of the four viral proteins, the ORF7a protein induced the NF-κB dictated proinflammatory cytokines including IL-1α, IL-1β, IL-6, IL-8, IL-10, TNF-α, and IFNβ. The ORF7a protein also induced IL-3, IL-4, IL-7, IL-23. Of 15 different chemokines examined in the study, CCL11, CCL17, CCL19, CCL20, CCL21, CCL22, CCL25, CCL26, CCL27, and CXCL9 were significantly upregulated by ORF7. These cytokines and chemokines were frequently elevated in severely ill COVID-19 patients. Our data provide an insight into how SARS-CoV-2 modulates NF-κB signaling and inflammatory cytokine expressions. The ORF7a protein may be a desirable target for strategic developments to minimize uncontrolled inflammation in COVID-19 patients.
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Affiliation(s)
- Chia-Ming Su
- Department of Pathobiology, University of Illinois at Urbana-Champaign, 2001 Lincoln Ave, Urbana, IL, 61802, USA
| | - Leyi Wang
- Department of Veterinary Diagnostic Laboratory and Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Dongwan Yoo
- Department of Pathobiology, University of Illinois at Urbana-Champaign, 2001 Lincoln Ave, Urbana, IL, 61802, USA.
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16
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Clementi N, Ghosh S, De Santis M, Castelli M, Criscuolo E, Zanoni I, Clementi M, Mancini N. Viral Respiratory Pathogens and Lung Injury. Clin Microbiol Rev 2021; 34:e00103-20. [PMID: 33789928 PMCID: PMC8142519 DOI: 10.1128/cmr.00103-20] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Several viruses target the human respiratory tract, causing different clinical manifestations spanning from mild upper airway involvement to life-threatening acute respiratory distress syndrome (ARDS). As dramatically evident in the ongoing SARS-CoV-2 pandemic, the clinical picture is not always easily predictable due to the combined effect of direct viral and indirect patient-specific immune-mediated damage. In this review, we discuss the main RNA (orthomyxoviruses, paramyxoviruses, and coronaviruses) and DNA (adenoviruses, herpesviruses, and bocaviruses) viruses with respiratory tropism and their mechanisms of direct and indirect cell damage. We analyze the thin line existing between a protective immune response, capable of limiting viral replication, and an unbalanced, dysregulated immune activation often leading to the most severe complication. Our comprehension of the molecular mechanisms involved is increasing and this should pave the way for the development and clinical use of new tailored immune-based antiviral strategies.
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Affiliation(s)
- Nicola Clementi
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, Milan, Italy
- Laboratory of Microbiology and Virology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sreya Ghosh
- Harvard Medical School, Boston Children's Hospital, Division of Immunology, Boston, Massachusetts, USA
| | - Maria De Santis
- Department of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center-IRCCS, Rozzano, Italy
| | - Matteo Castelli
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, Milan, Italy
| | - Elena Criscuolo
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, Milan, Italy
| | - Ivan Zanoni
- Harvard Medical School, Boston Children's Hospital, Division of Immunology, Boston, Massachusetts, USA
- Harvard Medical School, Boston Children's Hospital, Division of Gastroenterology, Boston, Massachusetts, USA
| | - Massimo Clementi
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, Milan, Italy
- Laboratory of Microbiology and Virology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Nicasio Mancini
- Laboratory of Microbiology and Virology, Vita-Salute San Raffaele University, Milan, Italy
- Laboratory of Microbiology and Virology, IRCCS San Raffaele Scientific Institute, Milan, Italy
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17
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Peele KA, Kumar V, Parate S, Srirama K, Lee KW, Venkateswarulu TC. Insilico drug repurposing using FDA approved drugs against Membrane protein of SARS-CoV-2. J Pharm Sci 2021; 110:2346-2354. [PMID: 33684397 PMCID: PMC7934671 DOI: 10.1016/j.xphs.2021.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The novel coronavirus (SARS-CoV-2) outbreak has started taking away the millions of lives worldwide. Identification of known and approved drugs against novel coronavirus disease (COVID-19) seems to be an urgent need for the repurposing of the existing drugs. So, here we examined a safe strategy of using approved drugs of SuperDRUG2 database against modeled membrane protein (M-protein) of SARS-CoV-2 which is essential for virus assembly by using molecular docking-based virtual screening. A total of 3639 drugs from SuperDRUG2 database and additionally 14 potential drugs reported against COVID-19 proteins were selected. Molecular docking analyses revealed that nine drugs can bind the active site of M-protein with desirable molecular interactions. We therefore applied molecular dynamics simulations and binding free energy calculation using MM-PBSA to analyze the stability of the compounds. The complexes of M-protein with the selected drugs were simulated for 50 ns and ranked according to their binding free energies. The binding mode of the drugs with M-protein was analyzed and it was observed that Colchicine, Remdesivir, Bafilomycin A1 from COVID-19 suggested drugs and Temozolomide from SuperDRUG2 database displayed desirable molecular interactions and higher binding affinity towards M-protein. Interestingly, Colchicine was found as the top most binder among tested drugs against M-protein. We therefore additionally identified four Colchicine derivatives which can bind efficiently with M-protein and have better pharmacokinetic properties. We recommend that these drugs can be tested further through in vitro studies against SARS-CoV-2 M-protein.
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Affiliation(s)
- K Abraham Peele
- Department of Bio-Technology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, 522213, Andhra Pradesh, India
| | - Vikas Kumar
- Division of Life Science, Department of Bio & Medical Big Data (BK4 Program), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea
| | - Shraddha Parate
- Division of Applied Life Sciences, Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Krupanidhi Srirama
- Department of Bio-Technology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, 522213, Andhra Pradesh, India
| | - Keun Woo Lee
- Division of Life Science, Department of Bio & Medical Big Data (BK4 Program), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea.
| | - T C Venkateswarulu
- Department of Bio-Technology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, 522213, Andhra Pradesh, India.
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18
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Sui L, Zhao Y, Wang W, Wu P, Wang Z, Yu Y, Hou Z, Tan G, Liu Q. SARS-CoV-2 Membrane Protein Inhibits Type I Interferon Production Through Ubiquitin-Mediated Degradation of TBK1. Front Immunol 2021; 12:662989. [PMID: 34084167 PMCID: PMC8168463 DOI: 10.3389/fimmu.2021.662989] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/31/2021] [Indexed: 12/25/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the causative pathogen of current COVID-19 pandemic, and insufficient production of type I interferon (IFN-I) is associated with the severe forms of the disease. Membrane (M) protein of SARS-CoV-2 has been reported to suppress host IFN-I production, but the underlying mechanism is not completely understood. In this study, SARS-CoV-2 M protein was confirmed to suppress the expression of IFNβ and interferon-stimulated genes induced by RIG-I, MDA5, IKKϵ, and TBK1, and to inhibit IRF3 phosphorylation and dimerization caused by TBK1. SARS-CoV-2 M could interact with MDA5, TRAF3, IKKϵ, and TBK1, and induce TBK1 degradation via K48-linked ubiquitination. The reduced TBK1 further impaired the formation of TRAF3-TANK-TBK1-IKKε complex that leads to inhibition of IFN-I production. Our study revealed a novel mechanism of SARS-CoV-2 M for negative regulation of IFN-I production, which would provide deeper insight into the innate immunosuppression and pathogenicity of SARS-CoV-2.
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Affiliation(s)
- Liyan Sui
- Laboratory of Emerging Infectious Disease, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, China
| | - Yinghua Zhao
- Laboratory of Emerging Infectious Disease, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, China
| | - Wenfang Wang
- College of Basic Medical Science, Jilin University, Changchun, China
| | - Ping Wu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Zedong Wang
- Laboratory of Emerging Infectious Disease, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, China
| | - Yang Yu
- Hospital of Stomatology, Jilin University, Changchun, China
| | - Zhijun Hou
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Guangyun Tan
- Department of Immunology, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, China
| | - Quan Liu
- Laboratory of Emerging Infectious Disease, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, China
- School of Life Sciences and Engineering, Foshan University, Foshan, China
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19
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Hachem M. SARS-CoV-2 journey to the brain with a focus on potential role of docosahexaenoic acid bioactive lipid mediators. Biochimie 2021. [DOI: 10.1016/j.biochi.2021.02.012
expr 870642717 + 972675317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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Hachem M. SARS-CoV-2 journey to the brain with a focus on potential role of docosahexaenoic acid bioactive lipid mediators. Biochimie 2021; 184:95-103. [PMID: 33639198 PMCID: PMC7904461 DOI: 10.1016/j.biochi.2021.02.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 02/12/2021] [Accepted: 02/19/2021] [Indexed: 12/27/2022]
Abstract
Coronavirus Disease 2019 or COVID-19 have infected till day 82,579,768 confirmed cases including 1,818,849 deaths, reported by World Health Organization WHO. COVID-19, originated by Severe Acute respiratory syndrome Coronavirus 2 (SARS-CoV-2), contributes to respiratory distress in addition to neurological symptoms in some patients. In the current review, we focused on the neurological complications associated with COVID-19. We discussed different pathways followed by RNA-virus, especially Flaviviridae family in the brain and passage through the Blood-Brain-Barrier BBB. Then, we explored SARS-CoV-2 mechanisms responsible of neuroinvasion and BBB disruption as well as the immunopathogenesis of SARS-CoV-2 in the central nervous system CNS. Since SARS-CoV-2 is an enveloped virus, enclosed in a lipid bilayer and that lipids are essential cell components playing numerous biological roles in viral infection and replication, we investigated the lipid metabolism remodeling upon coronavirus replication. We also highlighted the anti-inflammatory and neuroprotective potential of an omega-3 polyunsaturated fatty acid, docosahexaenoic acid DHA, as well as several bioactive lipid mediators. Altogether, our data allow better understanding of SARS-CoV-2 neuroinvasion and could assist in drug targeting to decline the burden of short-term and long-term neurological manifestations of SARS-CoV-2.
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Affiliation(s)
- Mayssa Hachem
- Khalifa University, Department of Chemistry, Abu Dhabi, United Arab Emirates.
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21
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Teodorescu M. An Overview of a Year with COVID-19: What We Know? ELECTRONIC JOURNAL OF GENERAL MEDICINE 2021. [DOI: 10.29333/ejgm/9765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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22
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Kadam SB, Sukhramani GS, Bishnoi P, Pable AA, Barvkar VT. SARS-CoV-2, the pandemic coronavirus: Molecular and structural insights. J Basic Microbiol 2021; 61:180-202. [PMID: 33460172 PMCID: PMC8013332 DOI: 10.1002/jobm.202000537] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 12/12/2022]
Abstract
The outbreak of a novel coronavirus associated with acute respiratory disease, called COVID-19, marked the introduction of the third spillover of an animal coronavirus (CoV) to humans in the last two decades. The genome analysis with various bioinformatics tools revealed that the causative pathogen (SARS-CoV-2) belongs to the subgenus Sarbecovirus of the genus Betacoronavirus, with highly similar genome as bat coronavirus and receptor-binding domain (RBD) of spike glycoprotein as Malayan pangolin coronavirus. Based on its genetic proximity, SARS-CoV-2 is likely to have originated from bat-derived CoV and transmitted to humans via an unknown intermediate mammalian host, probably Malayan pangolin. Further, spike protein S1/S2 cleavage site of SARS-CoV-2 has acquired polybasic furin cleavage site which is absent in bat and pangolin suggesting natural selection either in an animal host before zoonotic transfer or in humans following zoonotic transfer. In the current review, we recapitulate a preliminary opinion about the disease, origin and life cycle of SARS-CoV-2, roles of virus proteins in pathogenesis, commonalities, and differences between different corona viruses. Moreover, the crystal structures of SARS-CoV-2 proteins with unique characteristics differentiating it from other CoVs are discussed. Our review also provides comprehensive information on the molecular aspects of SARS-CoV-2 including secondary structures in the genome and protein-protein interactions which can be useful to understand the aggressive spread of the SARS-CoV-2. The mutations and the haplotypes reported in the SARS-CoV-2 genome are summarized to understand the virus evolution.
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Affiliation(s)
| | | | | | - Anupama A. Pable
- Department of MicrobiologySavitribai Phule Pune UniversityPuneIndia
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23
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Garren MR, Ashcraft M, Qian Y, Douglass M, Brisbois EJ, Handa H. Nitric oxide and viral infection: Recent developments in antiviral therapies and platforms. APPLIED MATERIALS TODAY 2021; 22:100887. [PMID: 38620577 PMCID: PMC7718584 DOI: 10.1016/j.apmt.2020.100887] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 11/11/2020] [Accepted: 11/14/2020] [Indexed: 05/09/2023]
Abstract
Nitric oxide (NO) is a gasotransmitter of great significance to developing the innate immune response to many bacterial and viral infections, while also modulating vascular physiology. The generation of NO from the upregulation of endogenous nitric oxide synthases serves as an efficacious method for inhibiting viral replication in host defense and warrants investigation for the development of antiviral therapeutics. With increased incidence of global pandemics concerning several respiratory-based viral infections, it is necessary to develop broad therapeutic platforms for inhibiting viral replication and enabling more efficient host clearance, as well as to fabricate new materials for deterring viral transmission from medical devices. Recent developments in creating stabilized NO donor compounds and their incorporation into macromolecular scaffolds and polymeric substrates has created a new paradigm for developing NO-based therapeutics for long-term NO release in applications for bactericidal and blood-contacting surfaces. Despite this abundance of research, there has been little consideration of NO-releasing scaffolds and substrates for reducing passive transmission of viral infections or for treating several respiratory viral infections. The aim of this review is to highlight the recent advances in developing gaseous NO, NO prodrugs, and NO donor compounds for antiviral therapies; discuss the limitations of NO as an antiviral agent; and outline future prospects for guiding materials design of a next generation of NO-releasing antiviral platforms.
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Key Words
- ACE, angiotensin converting enzyme
- AP1, activator protein 1
- COVID-19
- COVID-19, coronavirus disease 2019
- ECMO, extracorporeal membrane oxygenation, FDA, United States Food and Drug Administration
- GNSO, S-nitrosoglutathione
- H1N1, influenza A virus subtype H1N1
- HI, Host Immunology
- HIV, human immunodeficiency virus
- HPV, human papillomavirus
- HSV, herpes simplex virus
- I/R, pulmonary ischemia-reperfusion
- IC50, inhibitory concentration 50
- IFN, interferon
- IFNγ, interferon gamma
- IKK, inhibitor of nuclear factor kappa B kinase
- IRF-1, interferon regulatory factor 1
- Inhalation therapy
- Medical Terminology: ARDS, acute respiratory distress syndrome
- NF-κB, nuclear factor kappa-light-chain enhancer of activated B cells
- NO, nitric oxide
- NOS, nitric oxide synthase
- Nitric Oxide and Related Compounds: eNOS/NOS 3, endothelial nitric oxide synthase
- Nitric oxide
- Other: DNA, deoxyribonucleic acid
- P38-MAPK, P38 mitogen-activated protein kinases
- PAMP, pathogen-associated molecular pattern
- PCV2, porcine circovirus type 2
- PHT, pulmonary hypertension
- PKR, protein kinase R
- RNA, ribonucleic acid
- RNI, reactive nitrogen intermediate
- RSNO, S-nitrosothiol
- SARS, severe acute respiratory syndrome
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- SNAP, S-nitroso-N-acetyl-penicillamine
- STAT-1, signal transducer and activator of transcription 1
- Severe acute respiratory distress
- TAK1, transforming growth factor β-activated kinases-1
- TLR, toll-like receptor
- VAP, ventilator associated pneumonia
- Viral infection
- Viruses: CVB3, coxsackievirus
- dsRNA, double stranded (viral) ribonucleic acid
- gNO, gaseous nitric oxide
- iNOS/NOS 2, inducible nitric oxide synthase
- mtALDH, mitochondrial aldehyde dehydrogenase
- nNOS/NOS 1, neuronal nitric oxide synthase
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Affiliation(s)
- Mark R Garren
- School of Chemical, Materials, and Biochemical Engineering, College of Engineering, University of Georgia, Athens, GA, USA
| | - Morgan Ashcraft
- School of Chemical, Materials, and Biochemical Engineering, College of Engineering, University of Georgia, Athens, GA, USA
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, USA
| | - Yun Qian
- School of Chemical, Materials, and Biochemical Engineering, College of Engineering, University of Georgia, Athens, GA, USA
| | - Megan Douglass
- School of Chemical, Materials, and Biochemical Engineering, College of Engineering, University of Georgia, Athens, GA, USA
| | - Elizabeth J Brisbois
- School of Chemical, Materials, and Biochemical Engineering, College of Engineering, University of Georgia, Athens, GA, USA
| | - Hitesh Handa
- School of Chemical, Materials, and Biochemical Engineering, College of Engineering, University of Georgia, Athens, GA, USA
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24
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Kozlov EM, Ivanova E, Grechko AV, Wu WK, Starodubova AV, Orekhov AN. Involvement of Oxidative Stress and the Innate Immune System in SARS-CoV-2 Infection. Diseases 2021; 9:diseases9010017. [PMID: 33668325 PMCID: PMC8005963 DOI: 10.3390/diseases9010017] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/15/2021] [Accepted: 02/20/2021] [Indexed: 12/13/2022] Open
Abstract
The emergence of the novel coronavirus in December 2019 in China marked the beginning of a pandemic that impacted healthcare systems and economic life all over the world. The virus primarily targets the respiratory system causing severe acute respiratory syndrome (SARS) in some patients, and therefore received the name of SARS-CoV-2. The pathogen stands out among other coronaviruses by its rapid transmission from human to human, with the majority of infected individuals being asymptomatic or presenting with only minor illness, therefore facilitating the pathogen spread. At the same time, people from the risk groups, such as the elderly, patients suffering from chronic diseases, or obese individuals, have increased chances of developing a severe or even fatal disease. The search for risk factors explaining this phenomenon continues. In this review, we focus on the known mechanisms of SARS-CoV-2 infection affecting the functioning of the immune system and discuss potential risk factors responsible for the severe disease course. Oxidative stress is one of such factors, which plays a prominent role in innate immunity activity, and recent research has revealed its tight involvement in SARS-CoV-2 infection. We discuss these recent findings and the development of excessive inflammation and cytokine storm observed during SARS-CoV-2 infection. Finally, we consider potential use of antioxidant drugs for alleviating the severe symptoms in affected patients.
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Affiliation(s)
- Evgenii M. Kozlov
- Laboratory of Immunopathology, Department of Clinical Immunology and Allergy, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
| | - Ekaterina Ivanova
- Department of Basic Research, Institute of Atherosclerosis Research, 121609 Moscow, Russia
- Correspondence: ; Tel./Fax: +7-(495)4159594
| | - Andrey V. Grechko
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 14-3 Solyanka Street, 109240 Moscow, Russia;
| | - Wei-Kai Wu
- Department of Medical Research, National Taiwan University Hospital, Taipei 10617, Taiwan;
| | - Antonina V. Starodubova
- Federal Research Centre for Nutrition, Biotechnology and Food Safety, 2/14 Ustinsky Passage, 109240 Moscow, Russia;
- Pirogov Russian National Research Medical University, 1 Ostrovitianov Street, 117997 Moscow, Russia
| | - Alexander N. Orekhov
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia;
- Laboratory of Infectious Pathology and Molecular Microecology, Institute of Human Morphology, 117418 Moscow, Russia
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25
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Prates ET, Garvin MR, Pavicic M, Jones P, Shah M, Demerdash O, Amos BK, Geiger A, Jacobson D. Potential Pathogenicity Determinants Identified from Structural Proteomics of SARS-CoV and SARS-CoV-2. Mol Biol Evol 2021; 38:702-715. [PMID: 32941612 PMCID: PMC7543629 DOI: 10.1093/molbev/msaa231] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Despite SARS-CoV and SARS-CoV-2 being equipped with highly similar protein arsenals, the corresponding zoonoses have spread among humans at extremely different rates. The specific characteristics of these viruses that led to such distinct outcomes remain unclear. Here, we apply proteome-wide comparative structural analysis aiming to identify the unique molecular elements in the SARS-CoV-2 proteome that may explain the differing consequences. By combining protein modeling and molecular dynamics simulations, we suggest nonconservative substitutions in functional regions of the spike glycoprotein (S), nsp1, and nsp3 that are contributing to differences in virulence. Particularly, we explain why the substitutions at the receptor-binding domain of S affect the structure–dynamics behavior in complexes with putative host receptors. Conservation of functional protein regions within the two taxa is also noteworthy. We suggest that the highly conserved main protease, nsp5, of SARS-CoV and SARS-CoV-2 is part of their mechanism of circumventing the host interferon antiviral response. Overall, most substitutions occur on the protein surfaces and may be modulating their antigenic properties and interactions with other macromolecules. Our results imply that the striking difference in the pervasiveness of SARS-CoV-2 and SARS-CoV among humans seems to significantly derive from molecular features that modulate the efficiency of viral particles in entering the host cells and blocking the host immune response.
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Affiliation(s)
- Erica T Prates
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN.,National Virtual Biotechnology Laboratory, US Department of Energy, TN
| | - Michael R Garvin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN.,National Virtual Biotechnology Laboratory, US Department of Energy, TN
| | - Mirko Pavicic
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN.,National Virtual Biotechnology Laboratory, US Department of Energy, TN
| | - Piet Jones
- National Virtual Biotechnology Laboratory, US Department of Energy, TN.,The Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee Knoxville, Knoxville, TN
| | - Manesh Shah
- Genome Science and Technology, The University of Tennessee Knoxville, Knoxville, TN
| | - Omar Demerdash
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN
| | - B Kirtley Amos
- Department of Horticulture, N-318 Ag Sciences Center, University of Kentucky, Lexington, KY
| | - Armin Geiger
- National Virtual Biotechnology Laboratory, US Department of Energy, TN.,The Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee Knoxville, Knoxville, TN
| | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN.,National Virtual Biotechnology Laboratory, US Department of Energy, TN.,The Bredesen Center for Interdisciplinary Research and Graduate Education, The University of Tennessee Knoxville, Knoxville, TN.,Genome Science and Technology, The University of Tennessee Knoxville, Knoxville, TN.,Department of Psychology, The University of Tennessee Knoxville, Knoxville, TN
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26
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Garvin MR, T Prates E, Pavicic M, Jones P, Amos BK, Geiger A, Shah MB, Streich J, Felipe Machado Gazolla JG, Kainer D, Cliff A, Romero J, Keith N, Brown JB, Jacobson D. Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. Genome Biol 2020; 21:304. [PMID: 33357233 PMCID: PMC7756312 DOI: 10.1186/s13059-020-02191-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/29/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND A mechanistic understanding of the spread of SARS-CoV-2 and diligent tracking of ongoing mutagenesis are of key importance to plan robust strategies for confining its transmission. Large numbers of available sequences and their dates of transmission provide an unprecedented opportunity to analyze evolutionary adaptation in novel ways. Addition of high-resolution structural information can reveal the functional basis of these processes at the molecular level. Integrated systems biology-directed analyses of these data layers afford valuable insights to build a global understanding of the COVID-19 pandemic. RESULTS Here we identify globally distributed haplotypes from 15,789 SARS-CoV-2 genomes and model their success based on their duration, dispersal, and frequency in the host population. Our models identify mutations that are likely compensatory adaptive changes that allowed for rapid expansion of the virus. Functional predictions from structural analyses indicate that, contrary to previous reports, the Asp614Gly mutation in the spike glycoprotein (S) likely reduced transmission and the subsequent Pro323Leu mutation in the RNA-dependent RNA polymerase led to the precipitous spread of the virus. Our model also suggests that two mutations in the nsp13 helicase allowed for the adaptation of the virus to the Pacific Northwest of the USA. Finally, our explainable artificial intelligence algorithm identified a mutational hotspot in the sequence of S that also displays a signature of positive selection and may have implications for tissue or cell-specific expression of the virus. CONCLUSIONS These results provide valuable insights for the development of drugs and surveillance strategies to combat the current and future pandemics.
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Affiliation(s)
- Michael R Garvin
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - Erica T Prates
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - Mirko Pavicic
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - Piet Jones
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA
| | - B Kirtley Amos
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
- Department of Horticulture, N-318 Ag Sciences Center, University of Kentucky, Lexington, KY, USA
| | - Armin Geiger
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Manesh B Shah
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - Jared Streich
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | | | - David Kainer
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - Ashley Cliff
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Jonathon Romero
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Nathan Keith
- Lawrence Berkeley National Laboratory, Environmental Genomics & Systems Biology, Berkeley, CA, USA
| | - James B Brown
- Lawrence Berkeley National Laboratory, Environmental Genomics & Systems Biology, Berkeley, CA, USA
| | - Daniel Jacobson
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA.
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA.
- Department of Psychology, University of Tennessee Knoxville, Knoxville, TN, USA.
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27
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Vlachakis D, Papakonstantinou E, Mitsis T, Pierouli K, Diakou I, Chrousos G, Bacopoulou F. Molecular mechanisms of the novel coronavirus SARS-CoV-2 and potential anti-COVID19 pharmacological targets since the outbreak of the pandemic. Food Chem Toxicol 2020; 146:111805. [PMID: 33038452 PMCID: PMC7543766 DOI: 10.1016/j.fct.2020.111805] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 12/26/2022]
Abstract
The novel coronavirus SARS-CoV-2 has emerged as a severe threat against public health and global economies. COVID-19, the disease caused by this virus, is highly contagious and has led to an ongoing pandemic. SARS-CoV-2 affects, mainly, the respiratory system, with most severe cases primarily showcasing acute respiratory distress syndrome. Currently, no targeted therapy exists, and since the number of infections and death toll keeps rising, it has become a necessity to study possible therapeutic targets. Antiviral drugs can target various stages of the viral infection, and in the case of SARS-CoV-2, both structural and non-structural proteins have been proposed as potential drug targets. This review focuses on the most researched SARS-CoV-2 proteins, their structure, function, and possible therapeutic approaches.
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Affiliation(s)
- Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos, Athens, 11855, Greece; University Research Institute of Maternal and Child Health & Precision Medicine, and UNESCO Chair on Adolescent Health Care, National and Kapodistrian University of Athens, Aghia Sophia Children's Hospital, 8 Levadias Street, Athens, 11527, Greece; Lab of Molecular Endocrinology, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou Street, Athens, 11527, Greece; Department of Informatics, Faculty of Natural and Mathematical Sciences, King's College London, Strand, London WC2R 2LS, UK
| | - Eleni Papakonstantinou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos, Athens, 11855, Greece
| | - Thanasis Mitsis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos, Athens, 11855, Greece
| | - Katerina Pierouli
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos, Athens, 11855, Greece
| | - Io Diakou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos, Athens, 11855, Greece
| | - George Chrousos
- University Research Institute of Maternal and Child Health & Precision Medicine, and UNESCO Chair on Adolescent Health Care, National and Kapodistrian University of Athens, Aghia Sophia Children's Hospital, 8 Levadias Street, Athens, 11527, Greece; Lab of Molecular Endocrinology, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou Street, Athens, 11527, Greece
| | - Flora Bacopoulou
- University Research Institute of Maternal and Child Health & Precision Medicine, and UNESCO Chair on Adolescent Health Care, National and Kapodistrian University of Athens, Aghia Sophia Children's Hospital, 8 Levadias Street, Athens, 11527, Greece.
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28
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Pasrija R, Naime M. The deregulated immune reaction and cytokines release storm (CRS) in COVID-19 disease. Int Immunopharmacol 2020; 90:107225. [PMID: 33302033 PMCID: PMC7691139 DOI: 10.1016/j.intimp.2020.107225] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/11/2020] [Accepted: 11/18/2020] [Indexed: 12/12/2022]
Abstract
COVID-19 caused by the SARS-CoV-2 virus, accompanies an unprecedented spike in cytokines levels termed cytokines release syndrome (CRS), in critically ill patients. Clinicians claim that the surge demonstrates a deregulated immune defence in host, as infected cell expression analysis depicts a delay in type-I (interferon-I) and type-III IFNs expression, along with a limited Interferon-Stimulated Gene (ISG) response, which later resume and culminates in elicitation of several cytokines including- IL-6, IL-8, IL-12, TNFα, IL-17, MCP-1, IP-10 and IL-10 etc. Although cytokines are messenger molecules of the immune system, but their increased concentration results in inflammation, infiltration of macrophages, neutrophils and lung injury in patients. This inflammatory response results in the precarious pathogenesis of COVID-19; thus, a complete estimation of the immune response against SARS-CoV-2 is vital in designing a harmless and effective vaccine. In pathogenesis analysis, it emerges that a timely forceful type-I IFN production (18-24hrs post infection) promotes innate and acquired immune responses, while a delay in IFNs production (3-4 days post infection) actually renders both innate and acquired responses ineffective in fighting infection. Further, underlying conditions including hypertension, obesity, cardio-vascular disease etc may increase the chances of putting people in risk groups, which end up having critical form of infection. This review summarizes the events starting from viral entry, its struggle with the immune system and failure of host immunological parameters to obliterate the infections, which finally culminate into massive release of CRS and inflammation in gravely ill patients.
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Affiliation(s)
- Ritu Pasrija
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Mohammad Naime
- Central Research Institute of Unani Medicine, Central Council for Research in Unani Medicine, Ministry of AYUSH, Government of India, Lucknow, Uttar Pradesh, India
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29
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Amor S, Fernández Blanco L, Baker D. Innate immunity during SARS-CoV-2: evasion strategies and activation trigger hypoxia and vascular damage. Clin Exp Immunol 2020; 202:193-209. [PMID: 32978971 PMCID: PMC7537271 DOI: 10.1111/cei.13523] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/11/2020] [Accepted: 09/11/2020] [Indexed: 12/18/2022] Open
Abstract
Innate immune sensing of viral molecular patterns is essential for development of antiviral responses. Like many viruses, SARS-CoV-2 has evolved strategies to circumvent innate immune detection, including low cytosine-phosphate-guanosine (CpG) levels in the genome, glycosylation to shield essential elements including the receptor-binding domain, RNA shielding and generation of viral proteins that actively impede anti-viral interferon responses. Together these strategies allow widespread infection and increased viral load. Despite the efforts of immune subversion, SARS-CoV-2 infection activates innate immune pathways inducing a robust type I/III interferon response, production of proinflammatory cytokines and recruitment of neutrophils and myeloid cells. This may induce hyperinflammation or, alternatively, effectively recruit adaptive immune responses that help clear the infection and prevent reinfection. The dysregulation of the renin-angiotensin system due to down-regulation of angiotensin-converting enzyme 2, the receptor for SARS-CoV-2, together with the activation of type I/III interferon response, and inflammasome response converge to promote free radical production and oxidative stress. This exacerbates tissue damage in the respiratory system, but also leads to widespread activation of coagulation pathways leading to thrombosis. Here, we review the current knowledge of the role of the innate immune response following SARS-CoV-2 infection, much of which is based on the knowledge from SARS-CoV and other coronaviruses. Understanding how the virus subverts the initial immune response and how an aberrant innate immune response contributes to the respiratory and vascular damage in COVID-19 may help to explain factors that contribute to the variety of clinical manifestations and outcome of SARS-CoV-2 infection.
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Affiliation(s)
- S. Amor
- Pathology DepartmentVUMC, Amsterdam UMCAmsterdamthe Netherlands
- Blizard InstituteBarts and The London School of Medicine and DentistryQueen Mary University of LondonUK
| | | | - D. Baker
- Blizard InstituteBarts and The London School of Medicine and DentistryQueen Mary University of LondonUK
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30
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Ivanisenko NV, Seyrek K, Kolchanov NA, Ivanisenko VA, Lavrik IN. The role of death domain proteins in host response upon SARS-CoV-2 infection: modulation of programmed cell death and translational applications. Cell Death Discov 2020; 6:101. [PMID: 33072409 PMCID: PMC7547561 DOI: 10.1038/s41420-020-00331-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/17/2020] [Indexed: 02/08/2023] Open
Abstract
The current pandemic of novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) poses a significant global public health threat. While urgent regulatory measures in control of the rapid spread of this virus are essential, scientists around the world have quickly engaged in this battle by studying the molecular mechanisms and searching for effective therapeutic strategies against this deadly disease. At present, the exact mechanisms of programmed cell death upon SARS-CoV-2 infection remain to be elucidated, though there is increasing evidence suggesting that cell death pathways play a key role in SARS-CoV-2 infection. There are several types of programmed cell death, including apoptosis, pyroptosis, and necroptosis. These distinct programs are largely controlled by the proteins of the death domain (DD) superfamily, which play an important role in viral pathogenesis and host antiviral response. Many viruses have acquired the capability to subvert the program of cell death and evade the host immune response, mainly by virally encoded gene products that control cell signaling networks. In this mini-review, we will focus on SARS-CoV-2, and discuss the implication of restraining the DD-mediated signaling network to potentially suppress viral replication and reduce tissue damage.
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Affiliation(s)
- Nikita V. Ivanisenko
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Kamil Seyrek
- Translational Inflammation Research, CDS, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Nikolay A. Kolchanov
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Vladimir A. Ivanisenko
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Inna N. Lavrik
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Translational Inflammation Research, CDS, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
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31
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Xie TA, Han MY, Su XR, Li HH, Chen JC, Guo XG. Identification of Hub genes associated with infection of three lung cell lines by SARS-CoV-2 with integrated bioinformatics analysis. J Cell Mol Med 2020; 24:12225-12230. [PMID: 32924263 PMCID: PMC7579704 DOI: 10.1111/jcmm.15862] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 08/04/2020] [Accepted: 08/10/2020] [Indexed: 02/06/2023] Open
Affiliation(s)
- Tian-Ao Xie
- Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Meng-Yi Han
- Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Xiao-Rui Su
- Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Hou-He Li
- Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Ji-Chun Chen
- Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Xu-Guang Guo
- Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China.,Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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32
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Perrin-Cocon L, Diaz O, Jacquemin C, Barthel V, Ogire E, Ramière C, André P, Lotteau V, Vidalain PO. The current landscape of coronavirus-host protein-protein interactions. J Transl Med 2020; 18:319. [PMID: 32811513 PMCID: PMC7432461 DOI: 10.1186/s12967-020-02480-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 08/07/2020] [Indexed: 12/23/2022] Open
Abstract
In less than 20 years, three deadly coronaviruses, SARS-CoV, MERS-CoV and SARS-CoV-2, have emerged in human population causing hundreds to hundreds of thousands of deaths. Other coronaviruses are causing epizootic representing a significant threat for both domestic and wild animals. Members of this viral family have the longest genome of all RNA viruses, and express up to 29 proteins establishing complex interactions with the host proteome. Deciphering these interactions is essential to identify cellular pathways hijacked by these viruses to replicate and escape innate immunity. Virus-host interactions also provide key information to select targets for antiviral drug development. Here, we have manually curated the literature to assemble a unique dataset of 1311 coronavirus-host protein–protein interactions. Functional enrichment and network-based analyses showed coronavirus connections to RNA processing and translation, DNA damage and pathogen sensing, interferon production, and metabolic pathways. In particular, this global analysis pinpointed overlooked interactions with translation modulators (GIGYF2-EIF4E2), components of the nuclear pore, proteins involved in mitochondria homeostasis (PHB, PHB2, STOML2), and methylation pathways (MAT2A/B). Finally, interactome data provided a rational for the antiviral activity of some drugs inhibiting coronaviruses replication. Altogether, this work describing the current landscape of coronavirus-host interactions provides valuable hints for understanding the pathophysiology of coronavirus infections and developing effective antiviral therapies.
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Affiliation(s)
- Laure Perrin-Cocon
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007, Lyon, France
| | - Olivier Diaz
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007, Lyon, France
| | - Clémence Jacquemin
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007, Lyon, France
| | - Valentine Barthel
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007, Lyon, France
| | - Eva Ogire
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007, Lyon, France.,UMR Processus Infectieux en Milieu Insulaire Tropical, Université de La Réunion, CNRS, 9192 INSERM U1187, IRD 249, Plateforme de Recherche CYROI, Sainte Clotilde La Réunion, France
| | - Christophe Ramière
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007, Lyon, France.,Laboratoire de Virologie, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - Patrice André
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007, Lyon, France
| | - Vincent Lotteau
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007, Lyon, France.
| | - Pierre-Olivier Vidalain
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69007, Lyon, France.
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Satarker S, Nampoothiri M. Structural Proteins in Severe Acute Respiratory Syndrome Coronavirus-2. Arch Med Res 2020; 51:482-491. [PMID: 32493627 PMCID: PMC7247499 DOI: 10.1016/j.arcmed.2020.05.012] [Citation(s) in RCA: 227] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 05/18/2020] [Indexed: 12/22/2022]
Abstract
What began with a sign of pneumonia-related respiratory disorders in China has now become a pandemic named by WHO as Covid-19 known to be caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The SARS-CoV-2 are newly emerged β coronaviruses belonging to the Coronaviridae family. SARS-CoV-2 has a positive viral RNA genome expressing open reading frames that code for structural and non-structural proteins. The structural proteins include spike (S), nucleocapsid (N), membrane (M), and envelope (E) proteins. The S1 subunit of S protein facilitates ACE2 mediated virus attachment while S2 subunit promotes membrane fusion. The presence of glutamine, asparagine, leucine, phenylalanine and serine amino acids in SARS-CoV-2 enhances ACE2 binding. The N protein is composed of a serine-rich linker region sandwiched between N Terminal Domain (NTD) and C Terminal Domain (CTD). These terminals play a role in viral entry and its processing post entry. The NTD forms orthorhombic crystals and binds to the viral genome. The linker region contains phosphorylation sites that regulate its functioning. The CTD promotes nucleocapsid formation. The E protein contains a NTD, hydrophobic domain and CTD which form viroporins needed for viral assembly. The M protein possesses hydrophilic C terminal and amphipathic N terminal. Its long-form promotes spike incorporations and the interaction with E facilitates virion production. As each protein is essential in viral functioning, this review describes the insights of SARS-CoV-2 structural proteins that would help in developing therapeutic strategies by targeting each protein to curb the rapidly growing pandemic.
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Affiliation(s)
- Sairaj Satarker
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Madhavan Nampoothiri
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India.
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Uludağ H, Parent K, Aliabadi HM, Haddadi A. Prospects for RNAi Therapy of COVID-19. Front Bioeng Biotechnol 2020; 8:916. [PMID: 32850752 PMCID: PMC7409875 DOI: 10.3389/fbioe.2020.00916] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/15/2020] [Indexed: 12/12/2022] Open
Abstract
COVID-19 caused by the SARS-CoV-2 virus is a fast emerging disease with deadly consequences. The pulmonary system and lungs in particular are most prone to damage caused by the SARS-CoV-2 infection, which leaves a destructive footprint in the lung tissue, making it incapable of conducting its respiratory functions and resulting in severe acute respiratory disease and loss of life. There were no drug treatments or vaccines approved for SARS-CoV-2 at the onset of pandemic, necessitating an urgent need to develop effective therapeutics. To this end, the innate RNA interference (RNAi) mechanism can be employed to develop front line therapies against the virus. This approach allows specific binding and silencing of therapeutic targets by using short interfering RNA (siRNA) and short hairpin RNA (shRNA) molecules. In this review, we lay out the prospect of the RNAi technology for combatting the COVID-19. We first summarize current understanding of SARS-CoV-2 virology and the host response to viral entry and duplication, with the purpose of revealing effective RNAi targets. We then summarize the past experience with nucleic acid silencers for SARS-CoV, the predecessor for current SARS-CoV-2. Efforts targeting specific protein-coding regions within the viral genome and intragenomic targets are summarized. Emphasizing non-viral delivery approaches, molecular underpinnings of design of RNAi agents are summarized with comparative analysis of various systems used in the past. Promising viral targets as well as host factors are summarized, and the possibility of modulating the immune system are presented for more effective therapies. We place special emphasis on the limitations of past studies to propel the field faster by focusing on most relevant models to translate the promising agents to a clinical setting. Given the urgency to address lung failure in COVID-19, we summarize the feasibility of delivering promising therapies by the inhalational route, with the expectation that this route will provide the most effective intervention to halt viral spread. We conclude with the authors' perspectives on the future of RNAi therapeutics for combatting SARS-CoV-2. Since time is of the essence, a strong perspective for the path to most effective therapeutic approaches are clearly articulated by the authors.
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Affiliation(s)
- Hasan Uludağ
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Kylie Parent
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada
| | | | - Azita Haddadi
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, SK, Canada
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Zhou MY, Xie XL, Peng YG, Wu MJ, Deng XZ, Wu Y, Xiong LJ, Shang LH. From SARS to COVID-19: What we have learned about children infected with COVID-19. Int J Infect Dis 2020; 96:710-714. [PMID: 32389849 PMCID: PMC7204709 DOI: 10.1016/j.ijid.2020.04.090] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/29/2020] [Accepted: 04/30/2020] [Indexed: 12/20/2022] Open
Abstract
INTRODUCTION Coronaviruses, both SARS-CoV and SARS-CoV-2, first appeared in China. They have certain biological, epidemiological and pathological similarities. To date, research has shown that their genes exhibit 79% of identical sequences and the receptor-binding domain structure is also very similar. There has been extensive research performed on SARS; however, the understanding of the pathophysiological impact of coronavirus disease 2019 (COVID-19) is still limited. METHODS This review drew upon the lessons learnt from SARS, in terms of epidemiology, clinical characteristics and pathogenesis, to further understand the features of COVID-19. RESULTS By comparing these two diseases, it found that COVID-19 has quicker and wider transmission, obvious family agglomeration, and higher morbidity and mortality. Newborns, asymptomatic children and normal chest imaging cases emerged in COVID-19 literature. Children starting with gastrointestinal symptoms may progress to severe conditions and newborns whose mothers are infected with COVID-19 could have severe complications. The laboratory test data showed that the percentage of neutrophils and the level of LDH is higher, and the number of CD4+ and CD8+T-cells is decreased in children's COVID-19 cases. CONCLUSION Based on these early observations, as pediatricians, this review put forward some thoughts on children's COVID-19 and gave some recommendations to contain the disease.
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Affiliation(s)
- Meng-Yao Zhou
- Department of Pediatric Infection and Gastroenterology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology, Chengdu, Sichuan, P.R. China
| | - Xiao-Li Xie
- Department of Pediatric Infection and Gastroenterology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology, Chengdu, Sichuan, P.R. China.
| | - Yong-Gang Peng
- Department of Anesthesiology, Department of Anesthesiology, University of Florida College of Medicine, Gainesville, Fl, USA
| | - Meng-Jun Wu
- Department of Anesthesiology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology, Chengdu, Sichuan, P.R. China
| | - Xiao-Zhi Deng
- Department of Pediatric Infection and Gastroenterology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology, Chengdu, Sichuan, P.R. China
| | - Ying Wu
- Department of Pediatric Pneumology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology, Chengdu, Sichuan, P.R. China
| | - Li-Jing Xiong
- Department of Pediatric Infection and Gastroenterology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology, Chengdu, Sichuan, P.R. China
| | - Li-Hong Shang
- Department of Pediatric Infection and Gastroenterology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology, Chengdu, Sichuan, P.R. China
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Michalakis K, Ilias I. SARS-CoV-2 infection and obesity: Common inflammatory and metabolic aspects. Diabetes Metab Syndr 2020; 14:469-471. [PMID: 32387864 PMCID: PMC7189186 DOI: 10.1016/j.dsx.2020.04.033] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 04/22/2020] [Accepted: 04/22/2020] [Indexed: 01/07/2023]
Abstract
BACKROUND AND AIMS According to the World Obesity Federation, "obesity-related conditions seem to worsen the effect of Covid-19 (SARS-CoV-2)"; additionally the Centres for Disease Control and Prevention reported that "people with heart disease and diabetes are at higher risk of SARS-CoV-2 complications and that severe obesity poses a higher risk for severe illness". Recent reports have shown elevated levels of cytokines due to increased inflammation in patients with SARS-CoV-2 disease. On the other hand, obesity represents a state of low-grade inflammation, with various inflammatory products directly excreted by adipose tissue. In this concise report we aimed to assess common elements of obesity and SARS-CoV-2 infection. METHODS Pubmed search on obesity and SARS-CoV-2 infection. RESULTS We present "mechanistic" obesity-related problems that aggravate SARS-CoV-2 infection as well as tentative inflammatory/metabolic links between these diseases. CONCLUSION Obesity and SARS-CoV-2 share common elements of the inflammatory process (and possibly also metabolic disturbances), exacerbating SARS-CoV-2 infection in the obese.
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Affiliation(s)
| | - Ioannis Ilias
- Department of Endocrinology, Diabetes & Metabolism, Elena Venizelou Hospital, 2 Elena Venizelou Sq, Athens, GR11521, Greece.
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37
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Thomas G, Frederick E, Hausburg M, Goldberg L, Hoke M, Roshon M, Mains C, Bar-Or D. The novel immunomodulatory biologic LMWF5A for pharmacological attenuation of the "cytokine storm" in COVID-19 patients: a hypothesis. Patient Saf Surg 2020; 14:21. [PMID: 32431755 PMCID: PMC7220573 DOI: 10.1186/s13037-020-00248-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 05/06/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND A common complication of viral pulmonary infections, such as in the ongoing COVID-19 pandemic, is a phenomenon described as a "cytokine storm". While poorly defined, this hyperinflammatory response results in diffuse alveolar damage. The low molecular weight fraction of commercial human serum albumin (LMWF5A), a novel biologic in development for osteoarthritis, demonstrates beneficial in vitro immunomodulatory effects complimentary to addressing inflammation, thus, we hypothesize that LMWF5A could improve the clinical outcomes of COVID-19 by attenuating hyperinflammation and the potential development of a cytokine storm. PRESENTATION OF THE HYPOTHESIS A variety of human in vitro immune models indicate that LMWF5A reduces the production of pro-inflammatory cytokines implicated in cytokine storm associated with COVID-19. Furthermore, evidence suggests LMWF5A also promotes the production of mediators required for resolving inflammation and enhances the barrier function of endothelial cultures. TESTING THE HYPOTHESIS A randomized controlled trial, to evaluate the safety and efficacy of nebulized LMWF5A in adults with Acute Respiratory Distress Syndrome (ARDS) secondary to COVID-19 infection, was developed and is currently under review by the Food and Drug Administration. IMPLICATIONS OF HYPOTHESIS If successful, this therapy may attenuate the cytokine storm observed in these patients and potentially reduce mortality, increase ventilation free days, improve oxygenation parameters and consequently lessen the burden on patients and the intensive care unit. CONCLUSIONS In conclusion, in vitro findings suggest that the immunomodulatory effects of LMWF5A make it a viable candidate for treating cytokine storm and restoring homeostasis to the immune response in COVID-19.
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Affiliation(s)
- Gregory Thomas
- Ampio Pharmaceuticals, Inc, 373 Inverness Pkwy #200, Englewood, CO 80112 USA
| | - Elizabeth Frederick
- Ampio Pharmaceuticals, Inc, 373 Inverness Pkwy #200, Englewood, CO 80112 USA
| | - Melissa Hausburg
- Trauma Research Department, Swedish Medical Center, 501 E. Hampden, Englewood, CO 80113 USA
- Trauma Research Department, St. Anthony Hospital, 11600 W 2nd Pl, Lakewood, CO 80228 USA
- Trauma Research Department, Medical City Plano, 3901 W 15th St, Plano, TX 75075 USA
- Trauma Research Department, Penrose Hospital, 2222 N Nevada Ave, Colorado Springs, CO 80907 USA
- Trauma Research Department, Research Medical Center, 2316 E Meyer Blvd, Kansas City, MO 64132 USA
- Trauma Research Department, Wesley Medical Center, 550 N Hillside St, Wichita, KS 67214 USA
| | - Laura Goldberg
- Ampio Pharmaceuticals, Inc, 373 Inverness Pkwy #200, Englewood, CO 80112 USA
| | - Marshall Hoke
- Ampio Pharmaceuticals, Inc, 373 Inverness Pkwy #200, Englewood, CO 80112 USA
| | - Michael Roshon
- Emergency Department, Penrose Hospital, Colorado Springs, Colorado USA
| | | | - David Bar-Or
- Trauma Research Department, Swedish Medical Center, 501 E. Hampden, Englewood, CO 80113 USA
- Trauma Research Department, St. Anthony Hospital, 11600 W 2nd Pl, Lakewood, CO 80228 USA
- Trauma Research Department, Medical City Plano, 3901 W 15th St, Plano, TX 75075 USA
- Trauma Research Department, Penrose Hospital, 2222 N Nevada Ave, Colorado Springs, CO 80907 USA
- Trauma Research Department, Research Medical Center, 2316 E Meyer Blvd, Kansas City, MO 64132 USA
- Trauma Research Department, Wesley Medical Center, 550 N Hillside St, Wichita, KS 67214 USA
- Department of Molecular Biology, Rocky Vista University, 8401 S Chambers Rd, Parker, CO 80134 USA
- Swedish Medical Center, 501 E. Hampden Ave. Rm 4-454, Englewood, CO 80013 USA
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Beidas M, Chehadeh W. Effect of Human Coronavirus OC43 Structural and Accessory Proteins on the Transcriptional Activation of Antiviral Response Elements. Intervirology 2018; 61:30-35. [PMID: 30041172 PMCID: PMC7179558 DOI: 10.1159/000490566] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 06/03/2018] [Indexed: 12/25/2022] Open
Abstract
Objectives The molecular mechanisms underlying the pathogenesis of human coronavirus OC43 (HCoV-OC43) infection are poorly understood. In this study, we investigated the ability of HCoV-OC43 to antagonize the transcriptional activation of antiviral response elements. Methods HCoV-OC43 structural (membrane M and nucleocapsid N) and accessory proteins (ns2a and ns5a) were expressed individually in human embryonic kidney 293 (HEK-293) cells. The transcriptional activation of antiviral response elements was assessed by measuring the levels of firefly luciferase expressed under the control of interferon (IFN)-stimulated response element (ISRE), IFN-β promoter, or nuclear factor kappa B response element (NF-κB-RE). The antiviral gene expression profile in HEK-293 cells was determined by PCR array. Results The transcriptional activity of ISRE, IFN-β promoter, and NF-κB-RE was significantly reduced in the presence of HCoV-OC43 ns2a, ns5a, M, or N protein, following the challenge of cells with Sendai virus, IFN-α or tumor necrosis factor-α. The expression of antiviral genes involved in the type I IFN and NF-κB signaling pathways was also downregulated in the presence of HCoV-OC43 structural or accessory proteins. Conclusion Both structural and accessory HCoV-OC43 proteins are able to inhibit antiviral response elements in HEK-293 cells, and to block the activation of different antiviral signaling pathways.
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Affiliation(s)
| | - Wassim Chehadeh
- *Dr. Wassim Chehadeh, Department of Microbiology, Faculty of Medicine, Kuwait University, PO Box 24923, Safat 13310 (Kuwait), E-Mail
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Beidas M, Chehadeh W. PCR array profiling of antiviral genes in human embryonic kidney cells expressing human coronavirus OC43 structural and accessory proteins. Arch Virol 2018; 163:2065-2072. [PMID: 29619598 PMCID: PMC7086905 DOI: 10.1007/s00705-018-3832-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/22/2018] [Indexed: 10/26/2022]
Abstract
Human coronavirus OC43 (HCoV-OC43) is a respiratory virus that usually causes a common cold. However, it has the potential to cause severe infection in young children and immunocompromised adults. Both SARS-CoV and MERS-CoV were shown to express proteins with the potential to evade early innate immune responses. However, the ability of HCoV-OC43 to antagonise the intracellular antiviral defences has not yet been investigated. The potential role of the HCoV-OC43 structural (M and N) and accessory proteins (ns2a and ns5a) in the alteration of antiviral gene expression was investigated in this study. HCoV-OC43M, N, ns2a and ns5a proteins were expressed in human embryonic kidney 293 (HEK-293) cells before challenge with Sendai virus. The Human Antiviral Response PCR array was used to profile the antiviral gene expression in HEK-293 cells. Over 30 genes were downregulated in the presence of one of the HCoV-OC43 proteins, e.g. genes representing mitogen-activated protein kinases, toll-like receptors, interferons, interleukins, and signaling transduction proteins. Our findings suggest that similarly to SARS-CoV and MERS-CoV, HCoV-OC43 has the ability to downregulate the transcription of genes critical for the activation of different antiviral signaling pathways. Further studies are needed to confirm the role of HCoV-OC43 structural and accessory proteins in antagonising antiviral gene expression.
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Affiliation(s)
- Meshal Beidas
- Department of Microbiology, Faculty of Medicine, Kuwait University, PO Box 24923, 13310, Safat, Kuwait
| | - Wassim Chehadeh
- Department of Microbiology, Faculty of Medicine, Kuwait University, PO Box 24923, 13310, Safat, Kuwait.
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40
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Zhou Y, Wu W, Xie L, Wang D, Ke Q, Hou Z, Wu X, Fang Y, Chen H, Xiao S, Fang L. Cellular RNA Helicase DDX1 Is Involved in Transmissible Gastroenteritis Virus nsp14-Induced Interferon-Beta Production. Front Immunol 2017; 8:940. [PMID: 28848548 PMCID: PMC5552718 DOI: 10.3389/fimmu.2017.00940] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 07/24/2017] [Indexed: 12/11/2022] Open
Abstract
Transmissible gastroenteritis virus (TGEV), an enteropathogenic coronavirus (CoV) of porcine, causes lethal watery diarrhea and severe dehydration in piglets and leads to severe economic losses in the swine industry. Unlike most CoVs that antagonize type I interferon (IFN) production, previous studies showed that TGEV infection induces IFN-I production both in vivo and in vitro. However, the underlying mechanism(s) remain largely unknown. In this study, we found that TGEV infection significantly facilitated IFN-β production as well as activation of the transcription factors IFN regulatory factor 3 (IRF3) and nuclear factor-kappaB (NF-κB) in porcine kidney (PK-15) cells. Screening of TGEV-encoded proteins demonstrated that non-structural protein 14 (nsp14) was the most potent IFN-β inducer and induced IFN-β production mainly by activating NF-κB but not IRF3. Further analysis showed that nsp14 interacted with DDX1, a member of the DExD/H helicase family. Knockdown of DDX1 by specific small interfering RNA (siRNA) significantly decreased nsp14-induced IFN-β production and NF-κB activation. Furthermore, TGEV-induced IFN-β production and IFN-stimulated gene (ISG) expression were decreased in cells transfected with DDX1-specific siRNA, indicating the vital role of DDX1 to TGEV-induced IFN-β responses. In summary, our data revealed a potential coactivator role of host RNA helicase DDX1 to the induction of IFN-β response initiated by TGEV and demonstrated that nsp14 is an important IFN inducer among the TGEV-encoded proteins.
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Affiliation(s)
- Yanrong Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Wei Wu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Lilan Xie
- College of Life Science and Technology, Wuhan Institute of Bioengineering, Wuhan, China
| | - Dang Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Qiyun Ke
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Zhenzhen Hou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Xiaoli Wu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Ying Fang
- College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Liurong Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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Inhibition of NF-κB activity by the porcine epidemic diarrhea virus nonstructural protein 1 for innate immune evasion. Virology 2017; 510:111-126. [PMID: 28715653 PMCID: PMC7111422 DOI: 10.1016/j.virol.2017.07.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 06/28/2017] [Accepted: 07/05/2017] [Indexed: 12/29/2022]
Abstract
Porcine epidemic diarrhea virus emerged in the US is known to suppress the type I interferons response during infection. In the present study using porcine epithelial cells, we showed that PEDV inhibited both NF-κB and proinflammatory cytokines. PEDV blocked the p65 activation in infected cells and suppressed the PRD II-mediated NF-κB activity. Of the total of 22 viral proteins, nine proteins were identified as NF-κB antagonists, and nsp1 was the most potent suppressor of proinflammatory cytokines. Nsp1 interfered the phosphorylation and degradation of IκBα, and thus blocked the p65 activation. Mutational studies demonstrated the essential requirements of the conserved residues of nsp1 for NF-κB suppression. Our study showed that PEDV inhibited NF-κB activity and nsp1 was a potent NF-κB antagonist for suppression of both IFN and early production of pro-inflammatory cytokines. PEDV inhibits type I IFNs and NF-κB-mediated pro-inflammatory cytokines. PEDV blocks p65 nuclear translocation in virus-infected cells. Among 22 viral proteins, nsp1, nsp3, nsp5, nsp7, nsp14, nsp15, nsp16, ORF3, and E are NF-κB antagonists. Nsp1 suppresses pro-inflammatory cytokines and p65 activation by blocking IκBα phosphorylation. The conserved residues of nsp1 are crucial for NF-κB suppression.
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42
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Scutigliani EM, Kikkert M. Interaction of the innate immune system with positive-strand RNA virus replication organelles. Cytokine Growth Factor Rev 2017; 37:17-27. [PMID: 28709747 PMCID: PMC7108334 DOI: 10.1016/j.cytogfr.2017.05.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 05/15/2017] [Indexed: 02/08/2023]
Abstract
All +RNA viruses induce replication organelles to shield viral RNA from innate immune surveillance. Recent literature suggests that non-self or aberrant-self membrane structures can be tagged with LC3 or ubiquitin. Interferon-induced GTPases then recognize these tags and destroy the membrane structures, thereby exposing PAMPs. More research will have to indicate whether this is a general antiviral mechanism affecting +RNA virus infections.
The potential health risks associated with (re-)emerging positive-strand RNA (+RNA) viruses emphasizes the need for understanding host-pathogen interactions for these viruses. The innate immune system forms the first line of defense against pathogenic organisms like these and is responsible for detecting pathogen-associated molecular patterns (PAMPs). Viral RNA is a potent inducer of antiviral innate immune signaling, provoking an antiviral state by directing expression of interferons (IFNs) and pro-inflammatory cytokines. However, +RNA viruses developed various methods to avoid detection and downstream signaling, including isolation of viral RNA replication in membranous viral replication organelles (ROs). These structures therefore play a central role in infection, and consequently, loss of RO integrity might simultaneously result in impaired viral replication and enhanced antiviral signaling. This review summarizes the first indications that the innate immune system indeed has tools to disrupt viral ROs and other non- or aberrant-self membrane structures, and may do this by marking these membranes with proteins such as microtubule-associated protein 1A/1B-light chain 3 (LC3) and ubiquitin, resulting in the recruitment of IFN-inducible GTPases. Further studies should evaluate whether this process forms a general effector mechanism in +RNA virus infection, thereby creating the opportunity for development of novel antiviral therapies.
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Affiliation(s)
- Enzo Maxim Scutigliani
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marjolein Kikkert
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.
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The NF-κB-dependent and -independent transcriptome and chromatin landscapes of human coronavirus 229E-infected cells. PLoS Pathog 2017; 13:e1006286. [PMID: 28355270 PMCID: PMC5386326 DOI: 10.1371/journal.ppat.1006286] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 04/10/2017] [Accepted: 03/09/2017] [Indexed: 12/20/2022] Open
Abstract
Coronavirus replication takes place in the host cell cytoplasm and triggers inflammatory gene expression by poorly characterized mechanisms. To obtain more insight into the signals and molecular events that coordinate global host responses in the nucleus of coronavirus-infected cells, first, transcriptome dynamics was studied in human coronavirus 229E (HCoV-229E)-infected A549 and HuH7 cells, respectively, revealing a core signature of upregulated genes in these cells. Compared to treatment with the prototypical inflammatory cytokine interleukin(IL)-1, HCoV-229E replication was found to attenuate the inducible activity of the transcription factor (TF) NF-κB and to restrict the nuclear concentration of NF-κB subunits by (i) an unusual mechanism involving partial degradation of IKKβ, NEMO and IκBα and (ii) upregulation of TNFAIP3 (A20), although constitutive IKK activity and basal TNFAIP3 expression levels were shown to be required for efficient virus replication. Second, we characterized actively transcribed genomic regions and enhancers in HCoV-229E-infected cells and systematically correlated the genome-wide gene expression changes with the recruitment of Ser5-phosphorylated RNA polymerase II and prototypical histone modifications (H3K9ac, H3K36ac, H4K5ac, H3K27ac, H3K4me1). The data revealed that, in HCoV-infected (but not IL-1-treated) cells, an extensive set of genes was activated without inducible p65 NF-κB being recruited. Furthermore, both HCoV-229E replication and IL-1 were shown to upregulate a small set of genes encoding immunomodulatory factors that bind p65 at promoters and require IKKβ activity and p65 for expression. Also, HCoV-229E and IL-1 activated a common set of 440 p65-bound enhancers that differed from another 992 HCoV-229E-specific enhancer regions by distinct TF-binding motif combinations. Taken together, the study shows that cytoplasmic RNA viruses fine-tune NF-κB signaling at multiple levels and profoundly reprogram the host cellular chromatin landscape, thereby orchestrating the timely coordinated expression of genes involved in multiple signaling, immunoregulatory and metabolic processes. Coronaviruses are major human and animal pathogens. They belong to a family of plus-strand RNA viruses that have extremely large genomes and encode a variety of proteins involved in virus-host interactions. The four common coronaviruses (HCoV-229E, NL63, OC43, HKU1) cause mainly upper respiratory tract infections, while zoonotic coronaviruses (SARS-CoV and MERS-CoV) cause severe lung disease, including acute respiratory distress syndrome (ARDS). The molecular basis for this fundamentally different pathology is incompletely understood. Our study provides a genome-wide investigation of epigenetic changes occurring in response to HCoV-229E. We identify at high resolution a large number of regulatory regions in the genome of infected cells that coordinate de novo gene transcription. Many of these genes have immunomodulatory functions and, most likely, contribute to limiting viral replication, while other factors may promote viral replication. The study provides an intriguing example of a virus that completes its entire life cycle in the cytoplasm while sending multiple signals to the nuclear chromatin compartment to adjust the host cell repertoire of transcribed genes. The approach taken in this study is expected to provide a suitable framework for future studies aimed at dissecting and comparing host responses to representative coronaviruses with different pathogenic potential in humans.
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Lim YX, Ng YL, Tam JP, Liu DX. Human Coronaviruses: A Review of Virus-Host Interactions. Diseases 2016; 4:E26. [PMID: 28933406 PMCID: PMC5456285 DOI: 10.3390/diseases4030026] [Citation(s) in RCA: 368] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/18/2016] [Accepted: 07/18/2016] [Indexed: 12/19/2022] Open
Abstract
Human coronaviruses (HCoVs) are known respiratory pathogens associated with a range of respiratory outcomes. In the past 14 years, the onset of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) have thrust HCoVs into spotlight of the research community due to their high pathogenicity in humans. The study of HCoV-host interactions has contributed extensively to our understanding of HCoV pathogenesis. In this review, we discuss some of the recent findings of host cell factors that might be exploited by HCoVs to facilitate their own replication cycle. We also discuss various cellular processes, such as apoptosis, innate immunity, ER stress response, mitogen-activated protein kinase (MAPK) pathway and nuclear factor kappa B (NF-κB) pathway that may be modulated by HCoVs.
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Affiliation(s)
- Yvonne Xinyi Lim
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
| | - Yan Ling Ng
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
| | - Ding Xiang Liu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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45
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Zhang Q, Yoo D. Immune evasion of porcine enteric coronaviruses and viral modulation of antiviral innate signaling. Virus Res 2016; 226:128-141. [PMID: 27212682 PMCID: PMC7111337 DOI: 10.1016/j.virusres.2016.05.015] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 05/16/2016] [Accepted: 05/17/2016] [Indexed: 12/15/2022]
Abstract
Enteric coronaviruses have evolved to modulate the host innate immunity. Viral IFN antagonists have been identified and they are mostly redundant. For protection of intestinal epithelia from enteric viruses, type III IFN plays a major role.
Porcine epidemic diarrhea virus (PEDV) and porcine deltacoronavirus (PDCoV) are emerged and reemerging viruses in pigs, and together with transmissible gastroenteritis virus (TGEV), pose significant economic concerns to the swine industry. These viruses infect epithelial cells of the small intestine and cause watery diarrhea, dehydration, and a high mortality in neonatal piglets. Type I interferons (IFN-α/β) are major antiviral cytokines forming host innate immunity, and in turn, these enteric coronaviruses have evolved to modulate the host innate immune signaling during infection. Accumulating evidence however suggests that IFN induction and signaling in the intestinal epithelial cells differ from other epithelial cells, largely due to distinct features of the gut epithelial mucosal surface and commensal microflora, and it appears that type III interferon (IFN-λ) plays a key role to maintain the antiviral state in the gut. This review describes the recent understanding on the immune evasion strategies of porcine enteric coronaviruses and the role of different types of IFNs for intestinal antiviral innate immunity.
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Affiliation(s)
- Qingzhan Zhang
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana IL, United States
| | - Dongwan Yoo
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana IL, United States.
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Shah M, Anwar MA, Kim JH, Choi S. Advances in Antiviral Therapies Targeting Toll-like Receptors. Expert Opin Investig Drugs 2016; 25:437-53. [DOI: 10.1517/13543784.2016.1154040] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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47
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The Membrane Protein of Severe Acute Respiratory Syndrome Coronavirus Functions as a Novel Cytosolic Pathogen-Associated Molecular Pattern To Promote Beta Interferon Induction via a Toll-Like-Receptor-Related TRAF3-Independent Mechanism. mBio 2016; 7:e01872-15. [PMID: 26861016 PMCID: PMC4752600 DOI: 10.1128/mbio.01872-15] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Most of the intracellular pattern recognition receptors (PRRs) reside in either the endolysosome or the cytoplasm to sense pathogen-derived RNAs, DNAs, or synthetic analogs of double-stranded RNA (dsRNA), such as poly(I:C). However, it remains elusive whether or not a pathogen-derived protein can function as a cytosolic pathogen-associated molecular pattern (PAMP). In this study, we demonstrate that delivering the membrane gene of severe acute respiratory syndrome coronavirus (SARS-CoV) into HEK293T, HEK293ET, and immobilized murine bone marrow-derived macrophage (J2-Mφ) cells significantly upregulates beta interferon (IFN-β) production. Both NF-κB and TBK1-IRF3 signaling cascades are activated by M gene products. M protein rather than M mRNA is responsible for M-mediated IFN-β induction that is preferentially associated with the activation of the Toll-like receptor (TLR) adaptor proteins MyD88, TIRAP, and TICAM2 but not the RIG-I signaling cascade. Blocking the secretion of M protein by brefeldin A (BFA) failed to reverse the M-mediated IFN-β induction. The antagonist of both TLR2 and TLR4 did not impede M-mediated IFN-β induction, indicating that the driving force for the activation of IFN-β production was generated from inside the cells. Inhibition of TRAF3 expression by specific small interfering RNA (siRNA) did not prevent M-mediated IFN-β induction. SARS-CoV pseudovirus could induce IFN-β production in an M rather than M(V68A) dependent manner, since the valine-to-alanine alteration at residue 68 in M protein markedly inhibited IFN-β production. Overall, our study indicates for the first time that a pathogen-derived protein is able to function as a cytosolic PAMP to stimulate type I interferon production by activating a noncanonical TLR signaling cascade in a TRAF3-independent manner. Viral protein can serve as a pathogen-associated molecular pattern (PAMP) that is usually recognized by certain pathogen recognition receptors (PRRs) on the cell surface, such as Toll-like receptor 2 (TLR2) and TLR4. In this study, we demonstrate that the membrane (M) protein of SARS-CoV can directly promote the activation of both beta interferon (IFN-β) and NF-κB through a TLR-related signaling pathway independent of TRAF3. The driving force for M-mediated IFN-β production is most likely generated from inside the cells. M-mediated IFN-β induction was confirmed at the viral infection level since a point mutation at the V68 residue of M markedly inhibited SARS-CoV pseudovirally induced IFN-β production. Thus, the results indicate for the first time that SARS-CoV M protein may function as a cytosolic PAMP to stimulate IFN-β production by activating a TLR-related TRAF3-independent signaling cascade.
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48
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Ma DY, Suthar MS. Mechanisms of innate immune evasion in re-emerging RNA viruses. Curr Opin Virol 2015; 12:26-37. [PMID: 25765605 PMCID: PMC4470747 DOI: 10.1016/j.coviro.2015.02.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 02/18/2015] [Accepted: 02/19/2015] [Indexed: 01/10/2023]
Abstract
RNA viruses passively evade host detection by masking viral PAMPs and replicating within vesicles. Many emerging viruses harbor multiple strategies for innate immune evasion. Viral antagonists have been found to target the pattern recognition receptor and interferon signaling pathways. Knowledge of host–pathogen interactions is essential for vaccine/therapeutic development and understanding innate immunity.
Recent outbreaks of Ebola, West Nile, Chikungunya, Middle Eastern Respiratory and other emerging/re-emerging RNA viruses continue to highlight the need to further understand the virus–host interactions that govern disease severity and infection outcome. As part of the early host antiviral defense, the innate immune system mediates pathogen recognition and initiation of potent antiviral programs that serve to limit virus replication, limit virus spread and activate adaptive immune responses. Concordantly, viral pathogens have evolved several strategies to counteract pathogen recognition and cell-intrinsic antiviral responses. In this review, we highlight the major mechanisms of innate immune evasion by emerging and re-emerging RNA viruses, focusing on pathogens that pose significant risk to public health.
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Affiliation(s)
- Daphne Y Ma
- Department of Pediatrics and Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA 30329, USA; Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Mehul S Suthar
- Department of Pediatrics and Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA 30329, USA; Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA.
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Zhao S, Gao Q, Lin J, Yan M, Yu Q, Yang Q. Differential response of porcine immature monocyte-derived dendritic cells to virulent and inactivated transmissible gastroenteritis virus. Res Vet Sci 2014; 97:623-30. [PMID: 25307113 PMCID: PMC7111762 DOI: 10.1016/j.rvsc.2014.09.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 08/11/2014] [Accepted: 09/15/2014] [Indexed: 12/17/2022]
Abstract
Virulent TGEV down-regulates cell surface markers of immature Mo-DCs. Virulent TGEV limits the immature Mo-DCs to secrete IL-12, IFN-γ and IL-10. Virulent TGEV impairs the ability of immature Mo-DCs to stimulate T cell proliferation. Virulent TGEV inhibits the activation of nuclear factor kappa B (NF-κB) in immature Mo-DCs. UV-inactivated TGEV (UV-SHXB) has the opposite effects in immature Mo-DCs.
Exposure of piglets less than 2 weeks of age to virulent transmissible gastroenteritis virus (TGEV) gives rise to mortality as high as 100%, and adult pigs recovering from its infection often become TGEV carriers. These facts suggest an evasion of the immune system by virulent TGEV. In this study, we showed that a virulent TGEV SHXB strain could infect porcine immature monocyte-derived dendritic cells (Mo-DCs), and down-regulate cell surface markers (SLA-II-DR, CD1a and CD80/86). Moreover, SHXB-infected immature Mo-DCs showed low expression of IL-12 and IFN-γ, and also lost the ability to stimulate T cell proliferation. Finally, SHXB inhibited the activation of nuclear factor kappa B (NF-κB) in these cells. Instead, UV-inactivated SHXB (UV-SHXB) had the opposite effects in immature Mo-DCs. In conclusion, the virulent SHXB could severely impair immature Mo-DCs, which might be involved in the pathogenesis of virulent TGEV in vivo.
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Affiliation(s)
- Shanshan Zhao
- Key Lab of Animal Physiology and Biochemistry, Ministry of Agriculture, Nanjing Agricultural University, Wei gang 1, Jiangsu, China
| | - Qi Gao
- Key Lab of Animal Physiology and Biochemistry, Ministry of Agriculture, Nanjing Agricultural University, Wei gang 1, Jiangsu, China
| | - Jian Lin
- Key Lab of Animal Physiology and Biochemistry, Ministry of Agriculture, Nanjing Agricultural University, Wei gang 1, Jiangsu, China
| | - Mengfei Yan
- Key Lab of Animal Physiology and Biochemistry, Ministry of Agriculture, Nanjing Agricultural University, Wei gang 1, Jiangsu, China
| | - Qinghua Yu
- Key Lab of Animal Physiology and Biochemistry, Ministry of Agriculture, Nanjing Agricultural University, Wei gang 1, Jiangsu, China
| | - Qian Yang
- Key Lab of Animal Physiology and Biochemistry, Ministry of Agriculture, Nanjing Agricultural University, Wei gang 1, Jiangsu, China.
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50
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Amaya M, Keck F, Bailey C, Narayanan A. The role of the IKK complex in viral infections. Pathog Dis 2014; 72:32-44. [PMID: 25082354 PMCID: PMC7108545 DOI: 10.1111/2049-632x.12210] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 06/11/2014] [Accepted: 07/17/2014] [Indexed: 01/21/2023] Open
Abstract
The NF‐κB signal transduction pathway is a critical regulator of multiple cellular functions that ultimately shift the balance between cell survival and death. The cascade is activated by many intrinsic and extrinsic stimuli, which is transduced via adaptor proteins to phosphorylate the IκB kinase (IKK) complex, which in turn phosphorylates the inhibitory IκBα protein to undergo proteasomal degradation and sets in motion nuclear events in response to the initial stimulus. Viruses are important modulators of the NF‐κB cascade and have evolved multiple mechanisms to activate or inhibit this pathway in a manner conducive to viral multiplication and establishment of a productive infectious cycle. This is a subject of extensive research by multiple laboratories whereby unraveling the interactions between specific viral components and members of the NF‐κB signal transduction cascade can shed unique perspectives on infection associated pathogenesis and novel therapeutic targets. In this review, we highlight the interactions between components of the IKK complex and multiple RNA and DNA viruses with the emphasis on mechanisms by which the interaction feeds the infection. Understanding these interactions will shed light on the exploitative capabilities of viruses to maintain an environment favorable for a productive infection.
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Affiliation(s)
- Moushimi Amaya
- National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University, Manassas, VA, USA
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