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Liu C, Huang W, He X, Feng Z, Chen Q. Research Advances on Swine Acute Diarrhea Syndrome Coronavirus. Animals (Basel) 2024; 14:448. [PMID: 38338091 PMCID: PMC10854734 DOI: 10.3390/ani14030448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Swine acute diarrhea syndrome coronavirus (SADS-CoV) is a virulent pathogen that causes acute diarrhea in piglets. The virus was first discovered in Guangdong Province, China, in 2017 and has since emerged in Jiangxi, Fujian, and Guangxi Provinces. The outbreak exhibited a localized and sporadic pattern, with no discernable temporal continuity. The virus can infect human progenitor cells and demonstrates considerable potential for cross-species transmission, representing a potential risk for zoonotic transmission. Therefore, continuous surveillance of and comprehensive research on SADS-CoV are imperative. This review provides an overview of the temporal and evolutionary features of SADS-CoV outbreaks, focusing on the structural characteristics of the virus, which serve as the basis for discussing its potential for interspecies transmission. Additionally, the review summarizes virus-host interactions, including the effects on host cells, as well as apoptotic and autophagic behaviors, and discusses prevention and treatment modalities for this viral infection.
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Affiliation(s)
- Chuancheng Liu
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
| | - Weili Huang
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
| | - Xinyan He
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
| | - Zhihua Feng
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
| | - Qi Chen
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
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2
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Neitthoffer B, Alvarez F, Larrous F, Caillet-Saguy C, Etienne-Manneville S, Boëda B. A short sequence in the tail of SARS-CoV-2 envelope protein controls accessibility of its PDZ-binding motif to the cytoplasm. J Biol Chem 2024; 300:105575. [PMID: 38110034 PMCID: PMC10821599 DOI: 10.1016/j.jbc.2023.105575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/28/2023] [Accepted: 12/08/2023] [Indexed: 12/20/2023] Open
Abstract
The carboxy-terminal tail of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) envelope protein (E) contains a PDZ-binding motif (PBM) which is crucial for coronavirus pathogenicity. During SARS-CoV-2 infection, the viral E protein is expressed within the Golgi apparatus membrane of host cells with its PBM facing the cytoplasm. In this work, we study the molecular mechanisms controlling the presentation of the PBM to host PDZ (PSD-95/Dlg/ZO-1) domain-containing proteins. We show that at the level of the Golgi apparatus, the PDZ-binding motif of the E protein is not detected by E C-terminal specific antibodies nor by the PDZ domain-containing protein-binding partner. Four alanine substitutions upstream of the PBM in the central region of the E protein tail is sufficient to generate immunodetection by anti-E antibodies and trigger robust recruitment of the PDZ domain-containing protein into the Golgi organelle. Overall, this work suggests that the presentation of the PBM to the cytoplasm is under conformational regulation mediated by the central region of the E protein tail and that PBM presentation probably does not occur at the surface of Golgi cisternae but likely at post-Golgi stages of the viral cycle.
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Affiliation(s)
- Benoit Neitthoffer
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR3691 CNRS, Université Paris Cité, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Flavio Alvarez
- Laboratory Channel Receptors, UMR CNRS 3571, Institut Pasteur, Université Paris Cité, Paris, France
| | - Florence Larrous
- Lyssavirus Epidemiology and Neuropathology Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Célia Caillet-Saguy
- Laboratory Channel Receptors, UMR CNRS 3571, Institut Pasteur, Université Paris Cité, Paris, France
| | - Sandrine Etienne-Manneville
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR3691 CNRS, Université Paris Cité, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Batiste Boëda
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR3691 CNRS, Université Paris Cité, Equipe Labellisée Ligue Contre le Cancer, Paris, France.
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3
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Fan S, Wang H, Wu D, Liu L. Pharmaceutical approaches for COVID-19: An update on current therapeutic opportunities. ACTA PHARMACEUTICA (ZAGREB, CROATIA) 2023; 73:157-173. [PMID: 37307372 DOI: 10.2478/acph-2023-0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/18/2022] [Indexed: 06/14/2023]
Abstract
SARS-CoV-2, a newly discovered coronavirus, has been linked to the COVID-19 pandemic and is currently an important public health issue. Despite all the work done to date around the world, there is still no viable treatment for COVID-19. This study examined the most recent evidence on the efficacy and safety of several therapeutic options available including natural substances, synthetic drugs and vaccines in the treatment of COVID-19. Various natural compounds such as sarsapogenin, lycorine, biscoclaurine, vitamin B12, glycyrrhizic acid, riboflavin, resveratrol and kaempferol, various vaccines and drugs such as AZD1222, mRNA-1273, BNT162b2, Sputnik V, and remdesivir, lopinavir, favipiravir, darunavir, oseltamivir, and umifenovir, resp., have been discussed comprehensively. We attempted to provide exhaustive information regarding the various prospective therapeutic approaches available in order to assist researchers and physicians in treating COVID-19 patients.
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Affiliation(s)
- Sijia Fan
- 1Department of Intensive Care Unit, South China Hospital, Health Science Center Shenzhen University Guangdong, Shenzhen 518116, P. R. China
| | - Hongling Wang
- 2Department of Cardiothoracic Surgery 940th Hospital of Joint Logistic Support Force of PLA, Lanzhou, Gansu, 730050, P. R. China
| | - Dean Wu
- 3Department of Respiratory Medicine, The Third People's Hospital of Gansu Province Lanzhou University, Lanzhou, Gansu 730050, P. R. China
| | - Lu Liu
- 4The First Pulmonary and Critical Care Medicine, The Fourth Affiliated Hospital of China Medical University, Shenyang Liaoning, 110032, P. R. China
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4
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Manan A, Pirzada RH, Haseeb M, Choi S. Toll-like Receptor Mediation in SARS-CoV-2: A Therapeutic Approach. Int J Mol Sci 2022; 23:ijms231810716. [PMID: 36142620 PMCID: PMC9502216 DOI: 10.3390/ijms231810716] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/10/2022] [Accepted: 09/10/2022] [Indexed: 01/18/2023] Open
Abstract
The innate immune system facilitates defense mechanisms against pathogen invasion and cell damage. Toll-like receptors (TLRs) assist in the activation of the innate immune system by binding to pathogenic ligands. This leads to the generation of intracellular signaling cascades including the biosynthesis of molecular mediators. TLRs on cell membranes are adept at recognizing viral components. Viruses can modulate the innate immune response with the help of proteins and RNAs that downregulate or upregulate the expression of various TLRs. In the case of COVID-19, molecular modulators such as type 1 interferons interfere with signaling pathways in the host cells, leading to an inflammatory response. Coronaviruses are responsible for an enhanced immune signature of inflammatory chemokines and cytokines. TLRs have been employed as therapeutic agents in viral infections as numerous antiviral Food and Drug Administration-approved drugs are TLR agonists. This review highlights the therapeutic approaches associated with SARS-CoV-2 and the TLRs involved in COVID-19 infection.
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Affiliation(s)
- Abdul Manan
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
| | | | - Muhammad Haseeb
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
- S&K Therapeutics, Ajou University Campus Plaza 418, 199 Worldcup-ro, Yeongtong-gu, Suwon 16502, Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
- S&K Therapeutics, Ajou University Campus Plaza 418, 199 Worldcup-ro, Yeongtong-gu, Suwon 16502, Korea
- Correspondence:
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5
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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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Markarian NM, Galli G, Patel D, Hemmings M, Nagpal P, Berghuis AM, Abrahamyan L, Vidal SM. Identifying Markers of Emerging SARS-CoV-2 Variants in Patients With Secondary Immunodeficiency. Front Microbiol 2022; 13:933983. [PMID: 35847101 PMCID: PMC9283111 DOI: 10.3389/fmicb.2022.933983] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 05/31/2022] [Indexed: 12/03/2022] Open
Abstract
Since the end of 2019, the world has been challenged by the coronavirus disease 2019 (COVID-19) pandemic. With COVID-19 cases rising globally, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve, resulting in the emergence of variants of interest (VOI) and of concern (VOC). Of the hundreds of millions infected, immunodeficient patients are one of the vulnerable cohorts that are most susceptible to this virus. These individuals include those with preexisting health conditions and/or those undergoing immunosuppressive treatment (secondary immunodeficiency). In these cases, several researchers have reported chronic infections in the presence of anti-COVID-19 treatments that may potentially lead to the evolution of the virus within the host. Such variations occurred in a variety of viral proteins, including key structural ones involved in pathogenesis such as spike proteins. Tracking and comparing such mutations with those arisen in the general population may provide information about functional sites within the SARS-CoV-2 genome. In this study, we reviewed the current literature regarding the specific features of SARS-CoV-2 evolution in immunocompromised patients and identified recurrent de novo amino acid changes in virus isolates of these patients that can potentially play an important role in SARS-CoV-2 pathogenesis and evolution.
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Affiliation(s)
- Nathan M. Markarian
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- McGill University Research Centre on Complex Traits, Montréal, QC, Canada
- Swine and Poultry Infectious Diseases Research Center and Research Group on Infectious Diseases in Production Animals, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | - Gaël Galli
- McGill University Research Centre on Complex Traits, Montréal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- CNRS, ImmunoConcEpT, UMR 5164, Université de Bordeaux, Bordeaux, France
- CHU de Bordeaux, FHU ACRONIM, Centre National de Référence des Maladies Auto-Immunes et Systémiques Rares Est/Sud-Ouest, Bordeaux, France
| | - Dhanesh Patel
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- McGill University Research Centre on Complex Traits, Montréal, QC, Canada
| | - Mark Hemmings
- Department of Biochemistry, McGill University, Montréal, QC, Canada
| | - Priya Nagpal
- Department of Pharmacology, McGill University, Montréal, QC, Canada
| | | | - Levon Abrahamyan
- Swine and Poultry Infectious Diseases Research Center and Research Group on Infectious Diseases in Production Animals, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | - Silvia M. Vidal
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- McGill University Research Centre on Complex Traits, Montréal, QC, Canada
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Erukainure OL, Matsabisa MG, Muhammad A, Abarshi MM, Amaku JF, Katsayal SB, Nde AL. Targeting of Protein's Messenger RNA for Viral Replication, Assembly and Release in SARS-CoV-2 Using Whole Genomic Data From South Africa: Therapeutic Potentials of Cannabis Sativa L. Front Pharmacol 2021; 12:736511. [PMID: 34539415 PMCID: PMC8448283 DOI: 10.3389/fphar.2021.736511] [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: 07/06/2021] [Accepted: 08/17/2021] [Indexed: 12/16/2022] Open
Abstract
The possible evolutionary trend of COVID-19 in South Africa was investigated by comparing the genome of SARS-CoV-2 isolated from a patient in KwaZulu-Natal, South Africa with those isolated from China, Spain, Italy, and United States, as well as the genomes of Bat SARS CoV, Middle East Respiratory Syndrome Coronavirus (MERS-CoV), Mouse Hepatitis Virus (MHV), and Infectious Bronchitis Virus (IBV). Phylogenetic analysis revealed a strong homology (96%) between the genomes of SARS-CoV-2 isolated from KwaZulu-Natal, South Africa and those isolated from the study countries as well as those isolated from bat SARS CoV, MERS-CoV, MHV and IBV. The ability of phytocannabinoids from Cannabis sativa infusion to interact with gene segments (mRNAs) coding for proteins implicated in viral replication, assembly and release were also investiagted using computational tools. Hot water infusion of C. sativa leaves was freeze-dried and subjected to Gas Chromatography-Mass Spectroscopy analysis which revealed the presence of tetrahydrocannabivarin, cannabispiran, cannabidiol tetrahydrocannabinol, cannabigerol, and cannabinol. Molecular docking analysis revealed strong binding affinities and interactions between the phytocannabinoids and codon mRNAs for ORF1ab, Surface glycoprotein, Envelope protein and Nucleocapsid phosphoprotein from SARS-CoV-2 whole genome which may be due to chemico-biological interactions as a result of nucleophilic/electrophilic attacks between viral nucleotides and cannabinoids. These results depict the spread of SARS-CoV-2 is intercontinental and might have evolved from other coronaviruses. The results also portray the phytocannabinoids of C. sativa infusion as potential therapies against COVID-19 as depicted by their ability to molecularly interact with codon mRNAs of proteins implicated in the replication, translation, assembly, and release of SARS-CoV-2. However, further studies are needed to verify these activities in pre-clinical and clinical studies.
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Affiliation(s)
- Ochuko L. Erukainure
- Department of Pharmacology, School of Clinical Medicine, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Motlalepula G. Matsabisa
- Department of Pharmacology, School of Clinical Medicine, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Aliyu Muhammad
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Musa M. Abarshi
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - James F. Amaku
- Department of Chemistry, Michael Okpara University of Agriculture, Umudike, Nigeria
| | - Sanusi B. Katsayal
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Adeline Lum Nde
- Department of Pharmacology, School of Clinical Medicine, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
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8
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Chen W, Wang Z, Wang Y, Li Y. Natural Bioactive Molecules as Potential Agents Against SARS-CoV-2. Front Pharmacol 2021; 12:702472. [PMID: 34483904 PMCID: PMC8416071 DOI: 10.3389/fphar.2021.702472] [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: 04/29/2021] [Accepted: 07/12/2021] [Indexed: 12/24/2022] Open
Abstract
In the past two decades, pandemics of several fatal coronaviruses have posed enormous challenges for public health, including SARS-CoV (2003), MERS-CoV (2012), and SARS-CoV-2 (2019). Among these, SARS-CoV-2 continues to ravage the world today and has lead to millions of deaths and incalculable economic damage. Till now, there is no clinically proven antiviral drug available for SARS-CoV-2. However, the bioactive molecules of natural origin, especially medicinal plants, have been proven to be potential resources in the treatment of SARS-CoV-2, acting at different stages of the viral life cycle and targeting different viral or host proteins, such as PLpro, 3CLpro, RdRp, helicase, spike, ACE2, and TMPRSS2. They provide a viable strategy to develop therapeutic agents. This review presents fundamental biological information on SARS-CoV-2, including the viral biological characteristics and invasion mechanisms. It also summarizes the reported natural bioactive molecules with anti-coronavirus properties, arranged by their different targets in the life cycle of viral infection of human cells, and discusses the prospects of these bioactive molecules for the treatment of COVID-19.
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Affiliation(s)
- Wei Chen
- Department of Medicinal Chemistry, School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Zhihao Wang
- Biobank, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Yawen Wang
- Biobank, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Laboratory Medicine, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Yiping Li
- Department of Medicinal Chemistry, School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
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9
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Mou K, Abdalla M, Wei DQ, Khan MT, Lodhi MS, Darwish DB, Sharaf M, Tu X. Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. INFORMATICS IN MEDICINE UNLOCKED 2021; 25:100675. [PMID: 34337139 PMCID: PMC8314890 DOI: 10.1016/j.imu.2021.100675] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/11/2021] [Accepted: 07/19/2021] [Indexed: 12/23/2022] Open
Abstract
Structural proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are potential drug targets due to their role in the virus life cycle. The envelope (E) protein is one of the structural proteins; plays a critical role in virulency. However, the emergence of mutations oftenly leads to drug resistance and may also play a vital role in virus stabilization and evolution. In this study, we aimed to identify mutations in E proteins that affect the protein stability. About 0.3 million complete whole genome sequences were analyzed to screen mutations in E protein. All these mutations were subjected to stability prediction using the DynaMut server. The most common mutations that were detected at the C-terminal domain, Ser68Phe, Pro71Ser, and Leu73Phe, were examined through molecular dynamics (MD) simulations for a 100ns period. The sequence analysis shows the existence of 259 mutations in E protein. Interestingly, 16 of them were detected in the DFLV amino acid (aa) motif (aa72-aa75) that binds the host PALS1 protein. The results of root mean square deviation, fluctuations, radius of gyration, and free energy landscape show that Ser68Phe, Pro71Ser, and Leu73Phe are exhibiting a more stabilizing effect. However, a more comprehensive experimental study may be required to see the effect on virus pathogenicity. Potential antiviral drugs, and vaccines may be developed used after screening the genomic variations for better management of SARS-CoV-2 infections.
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Affiliation(s)
- Kejie Mou
- Department of Neurosurgery, Bishan Hospital of Chongqing, Chongqing, China
| | - Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 Cultural West Road, Shandong Province, 250012, PR China
| | - Dong Qing Wei
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Research Laboratory of Metabolic & Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, PR China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong, 518055, PR China
| | - Muhammad Tahir Khan
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, KM Defence Road, Lahore, Pakistan, 58810
| | - Madeeha Shahzad Lodhi
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, KM Defence Road, Lahore, Pakistan, 58810
| | - Doaa B Darwish
- Department of Biology, Faculty of Science, University of Tabuk, 71491, Saudi Arabia
| | - Mohamed Sharaf
- Department of Biochemistry and Molecular Biology, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, PR China
- Department of Biochemistry, Faculty of Agriculture, AL-Azhar University, Nasr City, Cairo, 11751, Egypt
| | - Xudong Tu
- Chongqing Medical and Pharmaceutical College, Chongqing, China
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10
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Richter J, Fanis P, Tryfonos C, Koptides D, Krashias G, Bashiardes S, Hadjisavvas A, Loizidou M, Oulas A, Alexandrou D, Kalakouta O, Panayiotidis MI, Spyrou GM, Christodoulou C. Molecular epidemiology of SARS-CoV-2 in Cyprus. PLoS One 2021; 16:e0248792. [PMID: 34288921 PMCID: PMC8294526 DOI: 10.1371/journal.pone.0248792] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/22/2021] [Indexed: 12/14/2022] Open
Abstract
Whole genome sequencing of viral specimens following molecular diagnosis is a powerful analytical tool of molecular epidemiology that can critically assist in resolving chains of transmission, identifying of new variants or assessing pathogen evolution and allows a real-time view into the dynamics of a pandemic. In Cyprus, the first two cases of COVID-19 were identified on March 9, 2020 and since then 33,567 confirmed cases and 230 deaths were documented. In this study, viral whole genome sequencing was performed on 133 SARS-CoV-2 positive samples collected between March 2020 and January 2021. Phylogenetic analysis was conducted to evaluate the genomic diversity of circulating SARS-CoV-2 lineages in Cyprus. 15 different lineages were identified that clustered into three groups associated with the spring, summer and autumn/winter wave of SARS-CoV-2 incidence in Cyprus, respectively. The majority of the Cypriot samples belonged to the B.1.258 lineage first detected in September that spread rapidly and largely dominated the autumn/winter wave with a peak prevalence of 86% during the months of November and December. The B.1.1.7 UK variant (VOC-202012/01) was identified for the first time at the end of December and spread rapidly reaching 37% prevalence within one month. Overall, we describe the changing pattern of circulating SARS-CoV-2 lineages in Cyprus since the beginning of the pandemic until the end of January 2021. These findings highlight the role of importation of new variants through travel towards the emergence of successive waves of incidence in Cyprus and demonstrate the importance of genomic surveillance in determining viral genetic diversity and the timely identification of new variants for guiding public health intervention measures.
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Affiliation(s)
- Jan Richter
- Molecular Virology Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Pavlos Fanis
- The Cyprus School of Molecular Medicine, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Molecular Genetics, Function & Therapy Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Christina Tryfonos
- Molecular Virology Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Dana Koptides
- Molecular Virology Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - George Krashias
- Molecular Virology Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Stavros Bashiardes
- Molecular Virology Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Andreas Hadjisavvas
- The Cyprus School of Molecular Medicine, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cancer Genetics, Therapeutics & Ultrastructural Pathology Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Maria Loizidou
- The Cyprus School of Molecular Medicine, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cancer Genetics, Therapeutics & Ultrastructural Pathology Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Anastasis Oulas
- The Cyprus School of Molecular Medicine, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Bioinformatics Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Denise Alexandrou
- Medical and Public Health Services, Ministry of Health, Nicosia, Cyprus
| | - Olga Kalakouta
- Medical and Public Health Services, Ministry of Health, Nicosia, Cyprus
| | - Mihalis I. Panayiotidis
- The Cyprus School of Molecular Medicine, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cancer Genetics, Therapeutics & Ultrastructural Pathology Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - George M. Spyrou
- The Cyprus School of Molecular Medicine, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Bioinformatics Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Christina Christodoulou
- Molecular Virology Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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11
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In silico analysis of the aggregation propensity of the SARS-CoV-2 proteome: Insight into possible cellular pathologies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140693. [PMID: 34237472 PMCID: PMC8256665 DOI: 10.1016/j.bbapap.2021.140693] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 12/12/2022]
Abstract
The SARS-CoV-2 virus causes the coronavirus disease 19 emerged in 2020. The pandemic triggered a turmoil in public health and is having a tremendous social and economic impact around the globe. Upon entry into host cells, the SARS-CoV-2 virus hijacks cellular machineries to produce and maintain its own proteins, spreading the infection. Although the disease is known for prominent respiratory symptoms, accumulating evidence is also demonstrating the involvement of the central nervous system, with possible mid- and long-term neurological consequences. In this study, we conducted a detailed bioinformatic analysis of the SARS-CoV-2 proteome aggregation propensity by using several complementary computational tools. Our study identified 10 aggregation prone proteins in the reference SARS-CoV-2 strain: the non-structural proteins Nsp4, Nsp6 and Nsp7 as well as ORF3a, ORF6, ORF7a, ORF7b, ORF10, CovE and CovM. By searching for the available mutants of each protein, we have found that most proteins are conserved, while ORF3a and ORF7b are variable and characterized by the occurrence of a large number of mutants with increased aggregation propensity. The geographical distribution of the mutants revealed interesting differences in the localization of aggregation-prone mutants of each protein. Aggregation-prone mutants of ORF7b were found in 7 European countries, whereas those of ORF3a in only 2. Aggregation-prone sequences of ORF7b, but not of ORF3a, were identified in Australia, India, Nepal, China, and Thailand. Our results are important for future analysis of a possible correlation between higher transmissibility and infection, as well as the presence of neurological symptoms with aggregation propensity of SARS-CoV-2 proteins.
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12
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Aldaais EA, Yegnaswamy S, Albahrani F, Alsowaiket F, Alramadan S. Sequence and structural analysis of COVID-19 E and M proteins with MERS virus E and M proteins-A comparative study. Biochem Biophys Rep 2021; 26:101023. [PMID: 34013072 PMCID: PMC8120451 DOI: 10.1016/j.bbrep.2021.101023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 05/05/2021] [Accepted: 05/11/2021] [Indexed: 12/23/2022] Open
Abstract
The outbreak of SARS in 2003, MERS in 2012, and now COVID-19 in 2019 has demonstrated that Coronaviruses are capable of causing primary lethal infections in humans, and the pandemic is now a global concern. The COVID-19 belongs to the beta coronavirus family encoding 29 proteins, of which four are structural, the Spike, Membrane, Envelope, and Nucleocapsid proteins. Here we have analyzed and compared the Membrane (M) and Envelope (E) proteins of COVID-19 and MERS with SARS and Bat viruses. The sequence analysis of conserved regions of both E and M proteins revealed that many regions of COVID-19 are similar to Bat and SARS viruses while the MERS virus showed variations. The essential binding motifs found in SARS appeared in COVID-19. Besides, the M protein of COVID-19 showed a distinct serine phosphorylation site in the C-terminal domain, which looked like a catalytic triad seen in serine proteases. A Dileucine motif occurred many times in the sequence of the M protein of all the four viruses compared. Concerning the structural part, the COVID-19 E protein showed more similarity to Bat while MERS shared similarity with the SARS virus. The M protein of both COVID-19 and MERS displayed variations in the structure. The interaction between M and E proteins was also studied to know the additional binding regions. Our study highlights the critical motifs and structural regions to be considered for further research to design better inhibitors for the infection caused by these viruses.
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Affiliation(s)
- Ebtisam A. Aldaais
- Department of Radiological Sciences, Imam Abdulrahman Bin Faisal University, Dammam, P.O. Box 2435, 31441, Saudi Arabia
| | - Subha Yegnaswamy
- Aldaais Research Group, Imam Abdulrahman bin Faisal University, Dammam, P.O. Box 2435, 31451, Saudi Arabia
| | - Fatimah Albahrani
- Department of Biomedical Engineering, Imam Abdulrahman Bin Faisal University, Dammam, P.O. Box 2435, 31451, Saudi Arabia
| | - Fatima Alsowaiket
- Department of Biomedical Engineering, Imam Abdulrahman Bin Faisal University, Dammam, P.O. Box 2435, 31451, Saudi Arabia
| | - Sarah Alramadan
- Department of Biomedical Engineering, Imam Abdulrahman Bin Faisal University, Dammam, P.O. Box 2435, 31451, Saudi Arabia
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13
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Cao Y, Yang R, Lee I, Zhang W, Sun J, Wang W, Meng X. Characterization of the SARS-CoV-2 E Protein: Sequence, Structure, Viroporin, and Inhibitors. Protein Sci 2021; 30:1114-1130. [PMID: 33813796 PMCID: PMC8138525 DOI: 10.1002/pro.4075] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 12/19/2022]
Abstract
The COVID-19 epidemic is one of the most influential epidemics in history. Understanding the impact of coronaviruses (CoVs) on host cells is very important for disease treatment. The SARS-CoV-2 envelope (E) protein is a small structural protein involved in many aspects of the viral life cycle. The E protein promotes the packaging and reproduction of the virus, and deletion of this protein weakens or even abolishes the virulence. This review aims to establish new knowledge by combining recent advances in the study of the SARS-CoV-2 E protein and by comparing it with the SARS-CoV E protein. The E protein amino acid sequence, structure, self-assembly characteristics, viroporin mechanisms and inhibitors are summarized and analyzed herein. Although the mechanisms of the SARS-CoV-2 and SARS-CoV E proteins are similar in many respects, specific studies on the SARS-CoV-2 E protein, for both monomers and oligomers, are still lacking. A comprehensive understanding of this protein should prompt further studies on the design and characterization of effective targeted therapeutic measures.
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Affiliation(s)
- Yipeng Cao
- Tianjin Medical University Cancer Institute and HospitalKey Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for CancerTianjinPeople's Republic of China
- National Supercomputer Center in TianjinTEDA‐Tianjin Economic‐Technological Development AreaTianjinPeople's Republic of China
| | - Rui Yang
- Department of Infection and ImmunityTianjin Union Medical Center, Nankai University Affiliated HospitalTianjinPeople's Republic of China
| | - Imshik Lee
- College of PhysicsNankai UniversityTianjinPeople's Republic of China
| | - Wenwen Zhang
- Tianjin Medical University Cancer Institute and HospitalKey Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for CancerTianjinPeople's Republic of China
| | - Jiana Sun
- Tianjin Medical University Cancer Institute and HospitalKey Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for CancerTianjinPeople's Republic of China
| | - Wei Wang
- Tianjin Medical University Cancer Institute and HospitalKey Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for CancerTianjinPeople's Republic of China
| | - Xiangfei Meng
- National Supercomputer Center in TianjinTEDA‐Tianjin Economic‐Technological Development AreaTianjinPeople's Republic of China
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14
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Yerukala Sathipati S, Ho SY. Identification and Characterization of Species-Specific Severe Acute Respiratory Syndrome Coronavirus 2 Physicochemical Properties. J Proteome Res 2021; 20:2942-2952. [PMID: 33856796 PMCID: PMC8056951 DOI: 10.1021/acs.jproteome.1c00156] [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: 02/23/2021] [Indexed: 12/28/2022]
Abstract
There is an urgent need to elucidate the underlying mechanisms of coronavirus disease (COVID-19) so that vaccines and treatments can be devised. Severe acute respiratory syndrome coronavirus 2 has genetic similarity with bats and pangolin viruses, but a comprehensive understanding of the functions of its proteins at the amino acid sequence level is lacking. A total of 4320 sequences of human and nonhuman coronaviruses was retrieved from the Global Initiative on Sharing All Influenza Data and the National Center for Biotechnology Information. This work proposes an optimization method COVID-Pred with an efficient feature selection algorithm to classify the species-specific coronaviruses based on physicochemical properties (PCPs) of their sequences. COVID-Pred identified a set of 11 PCPs using a support vector machine and achieved 10-fold cross-validation and test accuracies of 99.53% and 97.80%, respectively. These findings could provide key insights into understanding the driving forces during the course of infection and assist in developing effective therapies.
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Affiliation(s)
- Srinivasulu Yerukala Sathipati
- Center for Precision Medicine Research,
Marshfield Clinic Research Institute, Marshfield, Wisconsin
54449, United States
- Institute of Bioinformatics and Systems Biology,
National Chiao Tung University, Hsinchu 300,
Taiwan
- Institute of Population Health Sciences,
National Health Research Institutes, Miaoli 350,
Taiwan
| | - Shinn-Ying Ho
- Institute of Bioinformatics and Systems Biology,
National Chiao Tung University, Hsinchu 300,
Taiwan
- Institute of Bioinformatics and Systems Biology,
National Yang Ming Chiao Tung University, Hsinchu 300,
Taiwan
- Department of Biological Science and Technology,
National Yang Ming Chiao Tung University, Hsinchu 300,
Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices
(IDSB), National Yang Ming Chiao Tung University,
Hsinchu 300, Taiwan
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15
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Hassan SS, Aljabali AAA, Panda PK, Ghosh S, Attrish D, Choudhury PP, Seyran M, Pizzol D, Adadi P, Abd El-Aziz TM, Soares A, Kandimalla R, Lundstrom K, Lal A, Azad GK, Uversky VN, Sherchan SP, Baetas-da-Cruz W, Uhal BD, Rezaei N, Chauhan G, Barh D, Redwan EM, Dayhoff GW, Bazan NG, Serrano-Aroca Á, El-Demerdash A, Mishra YK, Palu G, Takayama K, Brufsky AM, Tambuwala MM. A unique view of SARS-CoV-2 through the lens of ORF8 protein. Comput Biol Med 2021; 133:104380. [PMID: 33872970 PMCID: PMC8049180 DOI: 10.1016/j.compbiomed.2021.104380] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 01/07/2023]
Abstract
Immune evasion is one of the unique characteristics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) attributed to its ORF8 protein. This protein modulates the adaptive host immunity through down-regulation of MHC-1 (Major Histocompatibility Complex) molecules and innate immune responses by surpassing the host's interferon-mediated antiviral response. To understand the host's immune perspective in reference to the ORF8 protein, a comprehensive study of the ORF8 protein and mutations possessed by it have been performed. Chemical and structural properties of ORF8 proteins from different hosts, such as human, bat, and pangolin, suggest that the ORF8 of SARS-CoV-2 is much closer to ORF8 of Bat RaTG13-CoV than to that of Pangolin-CoV. Eighty-seven mutations across unique variants of ORF8 in SARS-CoV-2 can be grouped into four classes based on their predicted effects (Hussain et al., 2021) [1]. Based on the geo-locations and timescale of sample collection, a possible flow of mutations was built. Furthermore, conclusive flows of amalgamation of mutations were found upon sequence similarity analyses and consideration of the amino acid conservation phylogenies. Therefore, this study seeks to highlight the uniqueness of the rapidly evolving SARS-CoV-2 through the ORF8.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, 721140, India
| | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University-Faculty of Pharmacy, Irbid, 566, Jordan
| | - Pritam Kumar Panda
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20, Uppsala, Sweden
| | - Shinjini Ghosh
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, 700009, West Bengal, India
| | - Diksha Attrish
- Dr. B. R. Ambedkar Centre for Biomedical Research (ACBR), University of Delhi (North Campus), Delhi, 110007, India
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, Kolkata, 700108, West Bengal, India
| | - Murat Seyran
- Doctoral Studies in Natural and Technical Sciences (SPL 44), University of Vienna, Austria
| | - Damiano Pizzol
- Italian Agency for Development Cooperation - Khartoum, Sudan Street 33, Al Amarat, Sudan
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin, 9054, New Zealand
| | - Tarek Mohamed Abd El-Aziz
- Zoology Department, Faculty of Science, Minia University, El-Minia, 61519, Egypt; Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229-3900, USA
| | - Antonio Soares
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229-3900, USA
| | - Ramesh Kandimalla
- CSIR-Indian Institute of Chemical Technology Uppal Road, Tarnaka, Hyderabad, 500007, Telangana State, India
| | | | - Amos Lal
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA, 70112, USA
| | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Bruce D Uhal
- Department of Physiology, Michigan State University, East Lansing, MI, 48824, USA
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran and Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Stockholm, Sweden
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501, Sur, 64849, Monterrey, NL, Mexico Tecnológico De Monterrey, Campus Monterrey, Monterrey, Nuevo León, Mexico
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), PatnaPatna, India
| | - Elrashdy M Redwan
- King Abdulazizi University, Faculty of Science, Department of Biological Science, Saudi Arabia
| | - Guy W Dayhoff
- Department of Chemistry, College of Art and Sciences, University of South Florida, Tampa, FL, 33620, USA
| | - Nicolas G Bazan
- Neuroscience Center of Excellence, School of Medicine, Louisiana State University Health New Orleans, New Orleans, LA, 70112, USA
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Translational Research Centre San Alberto Magno, Catholic University of Valencia San Vicente Mártir, C/Guillem de Castro 94, 46001, Valencia, Spain
| | - Amr El-Demerdash
- Natural Products and Medicinal Chemistry Department, Institute de Chimie des Substances Naturelles, Gif-sur-Yvette, France
| | - Yogendra K Mishra
- University of Southern Denmark, Mads Clausen Institute, NanoSYD, Alsion 2, 6400 Sønderborg, Denmark
| | - Giorgio Palu
- Department of Molecular Medicine, University of Padova, Italy
| | - Kazuo Takayama
- Center for IPS Cell Research and Application, Kyoto University, Kyoto, 606-8397, Japan
| | - Adam M Brufsky
- University of Pittsburgh School of Medicine, Department of Medicine, Division of Hematology/Oncology, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Murtaza M Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK.
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16
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Sadat SM, Aghadadeghi MR, Yousefi M, Khodaei A, Sadat Larijani M, Bahramali G. Bioinformatics Analysis of SARS-CoV-2 to Approach an Effective Vaccine Candidate Against COVID-19. Mol Biotechnol 2021; 63:389-409. [PMID: 33625681 PMCID: PMC7902242 DOI: 10.1007/s12033-021-00303-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/21/2021] [Indexed: 02/07/2023]
Abstract
The emerging Coronavirus Disease 2019 (COVID-19) pandemic has posed a serious threat to the public health worldwide, demanding urgent vaccine provide. According to the virus feature as an RNA virus, a high rate of mutations imposes some vaccine design difficulties. Bioinformatics tools have been widely used to make advantage of conserved regions as well as immunogenicity. In this study, we aimed at immunoinformatic evaluation of SARS-CoV-2 proteins conservancy and immunogenicity to design a preventive vaccine candidate. Spike, Membrane and Nucleocapsid amino acid sequences were obtained, and four possible fusion proteins were assessed and compared in terms of structural features and immunogenicity, and population coverage. MHC-I and MHC-II T-cell epitopes, the linear and conformational B-cell epitopes were evaluated. Among the predicted models, the truncated form of Spike in fusion with M and N protein applying AAY linker has high rate of MHC-I and MCH-II epitopes with high antigenicity and acceptable population coverage of 82.95% in Iran and 92.51% in Europe. The in silico study provided truncated Spike-M-N SARS-CoV-2 as a potential preventive vaccine candidate for further in vivo evaluation.
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Affiliation(s)
- Seyed Mehdi Sadat
- Department of Hepatitis and AIDS and Blood Borne Diseases, Pasteur Institute of Iran, No: 69, Pasteur Ave, 13165, Tehran, Iran
| | - Mohammad Reza Aghadadeghi
- Department of Hepatitis and AIDS and Blood Borne Diseases, Pasteur Institute of Iran, No: 69, Pasteur Ave, 13165, Tehran, Iran.
| | - Masoume Yousefi
- Department of Hepatitis and AIDS and Blood Borne Diseases, Pasteur Institute of Iran, No: 69, Pasteur Ave, 13165, Tehran, Iran
| | - Arezoo Khodaei
- Department of Hepatitis and AIDS and Blood Borne Diseases, Pasteur Institute of Iran, No: 69, Pasteur Ave, 13165, Tehran, Iran
| | - Mona Sadat Larijani
- Department of Hepatitis and AIDS and Blood Borne Diseases, Pasteur Institute of Iran, No: 69, Pasteur Ave, 13165, Tehran, Iran
| | - Golnaz Bahramali
- Department of Hepatitis and AIDS and Blood Borne Diseases, Pasteur Institute of Iran, No: 69, Pasteur Ave, 13165, Tehran, Iran.
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17
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Kalhori MR, Saadatpour F, Arefian E, Soleimani M, Farzaei MH, Aneva IY, Echeverría J. The Potential Therapeutic Effect of RNA Interference and Natural Products on COVID-19: A Review of the Coronaviruses Infection. Front Pharmacol 2021; 12:616993. [PMID: 33716745 PMCID: PMC7953353 DOI: 10.3389/fphar.2021.616993] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/14/2021] [Indexed: 01/08/2023] Open
Abstract
The SARS-CoV-2 virus was reported for the first time in Wuhan, Hubei Province, China, and causes respiratory infection. This pandemic pneumonia killed about 1,437,835 people out of 61,308,161cases up to November 27, 2020. The disease's main clinical complications include fever, recurrent coughing, shortness of breath, acute respiratory syndrome, and failure of vital organs that could lead to death. It has been shown that natural compounds with antioxidant, anticancer, and antiviral activities and RNA interference agents could play an essential role in preventing or treating coronavirus infection by inhibiting the expression of crucial virus genes. This study aims to introduce a summary of coronavirus's genetic and morphological structure and determine the role of miRNAs, siRNAs, chemical drugs, and natural compounds in stimulating the immune system or inhibiting the virus's structural and non-structural genes that are essential for replication and infection of SARS-CoV-2.
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Affiliation(s)
- Mohammad Reza Kalhori
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Fatemeh Saadatpour
- Molecular Virology Lab, Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Ehsan Arefian
- Molecular Virology Lab, Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Masoud Soleimani
- Department of Hematology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Hosien Farzaei
- Medical Technology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ina Yosifova Aneva
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Javier Echeverría
- Departamento de Ciencias del Ambiente, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
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18
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Aggregation hot spots in the SARS-CoV-2 proteome may constitute potential therapeutic targets for the suppression of the viral replication and multiplication. ACTA ACUST UNITED AC 2021; 12:1-13. [PMID: 33613009 PMCID: PMC7882052 DOI: 10.1007/s42485-021-00057-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 01/23/2021] [Accepted: 01/27/2021] [Indexed: 12/15/2022]
Abstract
The emergence of novel coronavirus SARS-CoV-2 is responsible for causing coronavirus disease-19 (COVID-19) imposing serious threat to global public health. Infection of SARS-CoV-2 to the host cell is characterized by direct translation of positive single stranded (+ ss) RNA to form large polyprotein polymerase 1ab (pp1ab), which acts as precursor for a number of nonstructural and structural proteins that play vital roles in replication of viral genome and biosynthesis of new virus particles. The maintenance of viral protein homeostasis is essential for continuation of viral life cycle in the host cell. To test whether the protein homeostasis of SARS-CoV-2 can be disrupted by inducing specific protein aggregation, we made an effort to examine whether the viral proteome contains any aggregation prone regions (APRs) that can be explored for inducing toxic protein aggregation specifically in viral proteins and without affecting the host cell. This curiosity leads to the identification of several (> 70) potential APRs in SARS-CoV-2 proteome. The length of the APRs ranges from 5 to 25 amino acid residues. Nearly 70% of total APRs investigated are relatively smaller and found to be in the range of 5–10 amino acids. The maximum number of ARPs (> 50) was observed in pp1ab. On the other hand, the structural proteins such as, spike (S), nucleoprotein (N), membrane (M) and envelope (E) proteins also possess APRs in their primary structures which altogether constitute 30% of the total APRs identified. Our findings may provide new windows of opportunities to design specific peptide-based, anti-SARS-CoV-2 therapeutic molecules against COVID-19.
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19
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Qin P, Luo WT, Su Q, Zhao P, Zhang Y, Wang B, Yang YL, Huang YW. The porcine deltacoronavirus accessory protein NS6 is expressed in vivo and incorporated into virions. Virology 2021; 556:1-8. [PMID: 33515858 PMCID: PMC7825830 DOI: 10.1016/j.virol.2021.01.011] [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: 10/11/2020] [Revised: 01/17/2021] [Accepted: 01/18/2021] [Indexed: 01/12/2023]
Abstract
Porcine deltacoronavirus (PDCoV) is one of the emerged coronaviruses posing a significant threat to the swine industry. Previous work showed the presence of a viral accessory protein NS6 in PDCoV-infected cells. In this study, we detected the expression of the NS6 protein in small intestinal tissues of PDCoV-infected piglets. In addition, SDS-PAGE and Western blot analysis of sucrose gradient-purified virions showed the presence of a 13-kDa NS6 protein. Further evidences of the presence of NS6 in the PDCoV virions were obtained by immunogold staining of purified virions with anti-NS6 antiserum, and by immunoprecipitation of NS6 from purified virions. Finally, the anti-NS6 antibody was not able to neutralize PDCoV in cultured cells. These data establish for the first time that the accessory protein NS6 is expressed during infection in vivo and incorporated into PDCoV virions.
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Affiliation(s)
- Pan Qin
- Institute of Preventive Veterinary Science and Key Laboratory of Animal Virology of Ministry of Agriculture, Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Wen-Ting Luo
- Institute of Preventive Veterinary Science and Key Laboratory of Animal Virology of Ministry of Agriculture, Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Quan Su
- Institute of Preventive Veterinary Science and Key Laboratory of Animal Virology of Ministry of Agriculture, Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Pengwei Zhao
- Institute of Preventive Veterinary Science and Key Laboratory of Animal Virology of Ministry of Agriculture, Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Yuqi Zhang
- Institute of Preventive Veterinary Science and Key Laboratory of Animal Virology of Ministry of Agriculture, Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Bin Wang
- Institute of Preventive Veterinary Science and Key Laboratory of Animal Virology of Ministry of Agriculture, Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Yong-Le Yang
- Institute of Preventive Veterinary Science and Key Laboratory of Animal Virology of Ministry of Agriculture, Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Yao-Wei Huang
- Institute of Preventive Veterinary Science and Key Laboratory of Animal Virology of Ministry of Agriculture, Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China.
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20
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Xu C, Ke Z, Liu C, Wang Z, Liu D, Zhang L, Wang J, He W, Xu Z, Li Y, Yang Y, Huang Z, Lv P, Wang X, Han D, Li Y, Qiao N, Liu B. Systemic In Silico Screening in Drug Discovery for Coronavirus Disease (COVID-19) with an Online Interactive Web Server. J Chem Inf Model 2020; 60:5735-5745. [PMID: 32786695 PMCID: PMC7460831 DOI: 10.1021/acs.jcim.0c00821] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Indexed: 01/18/2023]
Abstract
The emergence of the new coronavirus (nCoV-19) has impacted human health on a global scale, while the interaction between the virus and the host is the foundation of the disease. The viral genome codes a cluster of proteins, each with a unique function in the event of host invasion or viral development. Under the current adverse situation, we employ virtual screening tools in searching for drugs and natural products which have been already deposited in DrugBank in an attempt to accelerate the drug discovery process. This study provides an initial evaluation of current drug candidates from various reports using our systemic in silico drug screening based on structures of viral proteins and human ACE2 receptor. Additionally, we have built an interactive online platform (https://shennongproject.ai/) for browsing these results with the visual display of a small molecule docked on its potential target protein, without installing any specialized structural software. With continuous maintenance and incorporation of data from laboratory work, it may serve not only as the assessment tool for the new drug discovery but also an educational web site for the public.
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Affiliation(s)
- Chi Xu
- Laboratory of Health Intelligence,
Huawei Technologies Co., Ltd,
Shenzhen 518100, China
| | - Zunhui Ke
- Wuhan Children’s Hospital,
Tongji Medical College, Huazhong University of Science
& Technology, Wuhan 430000,
China
| | - Chuandong Liu
- Key Laboratory of Genomic and Precision
Medicine, Beijing Institute of Genomics, Chinese Academy
of Sciences, Beijing 100101,
China
- College of Future Technology,
Sino-Danish College, University of Chinese Academy of
Sciences, Beijing, 100049
China
| | - Zhihao Wang
- BioBank, The First
Affiliated Hospital of Xi’an Jiaotong
University, Shaanxi 710061,
China
- MRC Centre for Molecular Bacteriology and
Infection, Imperial College London, London
SW7 2AZ, U.K.
| | - Denghui Liu
- Laboratory of Health Intelligence,
Huawei Technologies Co., Ltd,
Shenzhen 518100, China
| | - Lei Zhang
- Laboratory of Health Intelligence,
Huawei Technologies Co., Ltd,
Shenzhen 518100, China
| | - Jingning Wang
- Department of Pathogen Biology, School
of Basic Medicine, Tongji Medical College, Huazhong
University of Science and Technology, Wuhan
430030, China
| | - Wenjun He
- Laboratory of Health Intelligence,
Huawei Technologies Co., Ltd,
Shenzhen 518100, China
| | - Zhimeng Xu
- Laboratory of Health Intelligence,
Huawei Technologies Co., Ltd,
Shenzhen 518100, China
| | - Yanqing Li
- BioBank, The First
Affiliated Hospital of Xi’an Jiaotong
University, Shaanxi 710061,
China
| | - Yanan Yang
- BioBank, The First
Affiliated Hospital of Xi’an Jiaotong
University, Shaanxi 710061,
China
| | - Zhaowei Huang
- Laboratory of Health Intelligence,
Huawei Technologies Co., Ltd,
Shenzhen 518100, China
| | - Panjing Lv
- Department of Pathogen Biology, School
of Basic Medicine, Tongji Medical College, Huazhong
University of Science and Technology, Wuhan
430030, China
| | - Xin Wang
- BioBank, The First
Affiliated Hospital of Xi’an Jiaotong
University, Shaanxi 710061,
China
| | - Dali Han
- Key Laboratory of Genomic and Precision
Medicine, Beijing Institute of Genomics, Chinese Academy
of Sciences, Beijing 100101,
China
- College of Future Technology,
Sino-Danish College, University of Chinese Academy of
Sciences, Beijing, 100049
China
- Institute for
Stem Cell and Regeneration, Chinese Academy of
Sciences, Beijing 100101,
China
- China National Center for
Bioinformation, Beijing 100101,
China
| | - Yan Li
- Department of Pathogen Biology, School
of Basic Medicine, Tongji Medical College, Huazhong
University of Science and Technology, Wuhan
430030, China
- Department of Pediatrics, Tongji
Hospital, Tongji Medical College, Huazhong University of
Science and Technology, Wuhan 430030,
China
| | - Nan Qiao
- Laboratory of Health Intelligence,
Huawei Technologies Co., Ltd,
Shenzhen 518100, China
| | - Bing Liu
- BioBank, The First
Affiliated Hospital of Xi’an Jiaotong
University, Shaanxi 710061,
China
- MRC Centre for Molecular Bacteriology and
Infection, Imperial College London, London
SW7 2AZ, U.K.
- Instrument Analysis
Centre, of Xi’an Jiaotong University,
Shaanxi 710049, China
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21
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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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22
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Lin P, Wang M, Wei Y, Kim T, Wei X. Coronavirus in human diseases: Mechanisms and advances in clinical treatment. MedComm (Beijing) 2020; 1:270-301. [PMID: 33173860 PMCID: PMC7646666 DOI: 10.1002/mco2.26] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 02/05/2023] Open
Abstract
Coronaviruses (CoVs), a subfamily of coronavirinae, are a panel of single-stranded RNA virus. Human coronavirus (HCoV) strains (HCoV-229E, HCoV-OC43, HCoV-HKU1, HCoV-NL63) usually cause mild upper respiratory diseases and are believed to be harmless. However, other HCoVs, associated with severe acute respiratory syndrome, Middle East respiratory syndrome, and COVID-19, have been identified as important pathogens due to their potent infectivity and lethality worldwide. Moreover, currently, no effective antiviral drugs treatments are available so far. In this review, we summarize the biological characters of HCoVs, their association with human diseases, and current therapeutic options for the three severe HCoVs. We also highlight the discussion about novel treatment strategies for HCoVs infections.
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Affiliation(s)
- Panpan Lin
- Laboratory of Aging Research and Cancer Drug Target State Key Laboratory of Biotherapy and Cancer Center National Clinical Research Center for Geriatrics West China Hospital Sichuan University Chengdu China
| | - Manni Wang
- Laboratory of Aging Research and Cancer Drug Target State Key Laboratory of Biotherapy and Cancer Center National Clinical Research Center for Geriatrics West China Hospital Sichuan University Chengdu China
| | - Yuquan Wei
- Laboratory of Aging Research and Cancer Drug Target State Key Laboratory of Biotherapy and Cancer Center National Clinical Research Center for Geriatrics West China Hospital Sichuan University Chengdu China
| | - Taewan Kim
- Wexner Medical Center The Ohio State University Columbus Ohio 43210 USA
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target State Key Laboratory of Biotherapy and Cancer Center National Clinical Research Center for Geriatrics West China Hospital Sichuan University Chengdu China
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23
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Hadi J, Dunowska M, Wu S, Brightwell G. Control Measures for SARS-CoV-2: A Review on Light-Based Inactivation of Single-Stranded RNA Viruses. Pathogens 2020; 9:E737. [PMID: 32911671 PMCID: PMC7558314 DOI: 10.3390/pathogens9090737] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/04/2020] [Accepted: 09/05/2020] [Indexed: 12/20/2022] Open
Abstract
SARS-CoV-2 is a single-stranded RNA virus classified in the family Coronaviridae. In this review, we summarize the literature on light-based (UV, blue, and red lights) sanitization methods for the inactivation of ssRNA viruses in different matrixes (air, liquid, and solid). The rate of inactivation of ssRNA viruses in liquid was higher than in air, whereas inactivation on solid surfaces varied with the type of surface. The efficacy of light-based inactivation was reduced by the presence of absorptive materials. Several technologies can be used to deliver light, including mercury lamp (conventional UV), excimer lamp (UV), pulsed-light, and light-emitting diode (LED). Pulsed-light technologies could inactivate viruses more quickly than conventional UV-C lamps. Large-scale use of germicidal LED is dependent on future improvements in their energy efficiency. Blue light possesses virucidal potential in the presence of exogenous photosensitizers, although femtosecond laser (ultrashort pulses) can be used to circumvent the need for photosensitizers. Red light can be combined with methylene blue for application in medical settings, especially for sanitization of blood products. Future modelling studies are required to establish clearer parameters for assessing susceptibility of viruses to light-based inactivation. There is considerable scope for improvement in the current germicidal light-based technologies and practices.
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Affiliation(s)
- Joshua Hadi
- AgResearch Ltd., Hopkirk Research Institute, Cnr University Ave and Library Road, Massey University, Palmerston North 4442, New Zealand; (J.H.); (S.W.)
| | - Magdalena Dunowska
- School of Veterinary Science, Massey University Manawatu (Turitea) Tennent Drive, Palmerston North 4474, New Zealand;
| | - Shuyan Wu
- AgResearch Ltd., Hopkirk Research Institute, Cnr University Ave and Library Road, Massey University, Palmerston North 4442, New Zealand; (J.H.); (S.W.)
| | - Gale Brightwell
- AgResearch Ltd., Hopkirk Research Institute, Cnr University Ave and Library Road, Massey University, Palmerston North 4442, New Zealand; (J.H.); (S.W.)
- New Zealand Food Safety Science and Research Centre, Massey University Manawatu (Turitea) Tennent Drive, Palmerston North 4474, New Zealand
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24
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Gentile D, Fuochi V, Rescifina A, Furneri PM. New Anti SARS-Cov-2 Targets for Quinoline Derivatives Chloroquine and Hydroxychloroquine. Int J Mol Sci 2020; 21:E5856. [PMID: 32824072 PMCID: PMC7461590 DOI: 10.3390/ijms21165856] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/01/2020] [Accepted: 08/12/2020] [Indexed: 12/18/2022] Open
Abstract
The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created a severe global health crisis. In this paper, we used docking and simulation methods to identify potential targets and the mechanism of action of chloroquine (CQ) and hydroxychloroquine (HCQ) against SARS-CoV-2. Our results showed that both CQ and HCQ influenced the functionality of the envelope (E) protein, necessary in the maturation processes of the virus, due to interactions that modify the flexibility of the protein structure. Furthermore, CQ and HCQ also influenced the proofreading and capping of viral RNA in SARS-CoV-2, performed by nsp10/nsp14 and nsp10/nsp16. In particular, HCQ demonstrated a better energy binding with the examined targets compared to CQ, probably due to the hydrogen bonding of the hydroxyl group of HCQ with polar amino acid residues.
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Affiliation(s)
- Davide Gentile
- Dipartimento di Scienze del Farmaco, University of Catania, 95125 Catania, Italy;
| | - Virginia Fuochi
- Dipartimento di Scienze Biomediche e Biotecnologiche, University of Catania, 95125 Catania, Italy;
| | - Antonio Rescifina
- Dipartimento di Scienze del Farmaco, University of Catania, 95125 Catania, Italy;
| | - Pio Maria Furneri
- Dipartimento di Scienze Biomediche e Biotecnologiche, University of Catania, 95125 Catania, Italy;
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25
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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: 226] [Impact Index Per Article: 56.5] [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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26
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Li S, Yuan L, Dai G, Chen RA, Liu DX, Fung TS. Regulation of the ER Stress Response by the Ion Channel Activity of the Infectious Bronchitis Coronavirus Envelope Protein Modulates Virion Release, Apoptosis, Viral Fitness, and Pathogenesis. Front Microbiol 2020; 10:3022. [PMID: 32038520 PMCID: PMC6992538 DOI: 10.3389/fmicb.2019.03022] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/17/2019] [Indexed: 01/31/2023] Open
Abstract
Coronavirus (CoV) envelope (E) protein is a small structural protein critical for virion morphogenesis and release. The recently characterized E protein ion channel activity (EIC) has also been implicated in modulating viral pathogenesis. In this study, we used infectious bronchitis coronavirus (IBV) as a model to study EIC. Two recombinant IBVs (rIBVs) harboring EIC-inactivating mutations – rT16A and rA26F – were serially passaged, and several compensatory mutations were identified in the transmembrane domain (TMD). Two rIBVs harboring these putative EIC-reverting mutations – rT16A/A26V and rA26F/F14N – were recovered. Compared with the parental rIBV-p65 control, all four EIC mutants exhibited comparable levels of intracellular RNA synthesis, structural protein production, and virion assembly. Our results showed that the IBV EIC contributed to the induction of ER stress response, as up-regulation of ER stress-related genes was markedly reduced in cells infected with the EIC-defective mutants. EIC-defective mutants also formed smaller plaques, released significantly less infectious virions into the culture supernatant, and had lower levels of viral fitness in cell culture. Significantly, all these defective phenotypes were restored in cells infected with the putative EIC revertants. EIC mutations were also implicated in regulating IBV-induced apoptosis, induction of pro-inflammatory cytokines, and viral pathogenicity in vivo. Taken together, this study highlights the importance of CoV EIC in modulating virion release and various aspects of CoV – host interaction.
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Affiliation(s)
- Shumin Li
- Guangdong Province Key Laboratory of Microbial Signals & Disease Control, and Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Lixia Yuan
- Guangdong Province Key Laboratory of Microbial Signals & Disease Control, and Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Guo Dai
- Guangdong Province Key Laboratory of Microbial Signals & Disease Control, and Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Rui Ai Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Zhaoqing DaHuaNong Biology Medicine Co., Ltd., Zhaoqing, China
| | - Ding Xiang Liu
- Guangdong Province Key Laboratory of Microbial Signals & Disease Control, and Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - To Sing Fung
- Guangdong Province Key Laboratory of Microbial Signals & Disease Control, and Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
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27
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Abstract
Coronavirus particles serve three fundamentally important functions in infection. The virion provides the means to deliver the viral genome across the plasma membrane of a host cell. The virion is also a means of escape for newly synthesized genomes. Lastly, the virion is a durable vessel that protects the genome on its journey between cells. This review summarizes the available X-ray crystallography, NMR, and cryoelectron microscopy structural data for coronavirus structural proteins, and looks at the role of each of the major structural proteins in virus entry and assembly. The potential wider conservation of the nucleoprotein fold identified in the Arteriviridae and Coronaviridae families and a speculative model for the evolution of corona-like virus architecture are discussed.
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Affiliation(s)
- B W Neuman
- School of Biological Sciences, University of Reading, Reading, United Kingdom; College of STEM, Texas A&M University, Texarkana, Texarkana, TX, United States.
| | - M J Buchmeier
- University of California, Irvine, Irvine, CA, United States
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28
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The Emerging Roles of Viroporins in ER Stress Response and Autophagy Induction during Virus Infection. Viruses 2015; 7:2834-57. [PMID: 26053926 PMCID: PMC4488716 DOI: 10.3390/v7062749] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 05/27/2015] [Accepted: 05/29/2015] [Indexed: 01/14/2023] Open
Abstract
Viroporins are small hydrophobic viral proteins that oligomerize to form aqueous pores on cellular membranes. Studies in recent years have demonstrated that viroporins serve important functions during virus replication and contribute to viral pathogenicity. A number of viroporins have also been shown to localize to the endoplasmic reticulum (ER) and/or its associated membranous organelles. In fact, replication of most RNA viruses is closely linked to the ER, and has been found to cause ER stress in the infected cells. On the other hand, autophagy is an evolutionarily conserved "self-eating" mechanism that is also observed in cells infected with RNA viruses. Both ER stress and autophagy are also known to modulate a wide variety of signaling pathways including pro-inflammatory and innate immune response, thereby constituting a major aspect of host-virus interactions. In this review, the potential involvement of viroporins in virus-induced ER stress and autophagy will be discussed.
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29
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Torres J, Surya W, Li Y, Liu DX. Protein-Protein Interactions of Viroporins in Coronaviruses and Paramyxoviruses: New Targets for Antivirals? Viruses 2015; 7:2858-83. [PMID: 26053927 PMCID: PMC4488717 DOI: 10.3390/v7062750] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 05/21/2015] [Accepted: 05/28/2015] [Indexed: 12/13/2022] Open
Abstract
Viroporins are members of a rapidly growing family of channel-forming small polypeptides found in viruses. The present review will be focused on recent structural and protein-protein interaction information involving two viroporins found in enveloped viruses that target the respiratory tract; (i) the envelope protein in coronaviruses and (ii) the small hydrophobic protein in paramyxoviruses. Deletion of these two viroporins leads to viral attenuation in vivo, whereas data from cell culture shows involvement in the regulation of stress and inflammation. The channel activity and structure of some representative members of these viroporins have been recently characterized in some detail. In addition, searches for protein-protein interactions using yeast-two hybrid techniques have shed light on possible functional roles for their exposed cytoplasmic domains. A deeper analysis of these interactions should not only provide a more complete overview of the multiple functions of these viroporins, but also suggest novel strategies that target protein-protein interactions as much needed antivirals. These should complement current efforts to block viroporin channel activity.
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Affiliation(s)
- Jaume Torres
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
| | - Wahyu Surya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
| | - Yan Li
- 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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30
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Desforges M, Le Coupanec A, Stodola JK, Meessen-Pinard M, Talbot PJ. Human coronaviruses: viral and cellular factors involved in neuroinvasiveness and neuropathogenesis. Virus Res 2014; 194:145-58. [PMID: 25281913 PMCID: PMC7114389 DOI: 10.1016/j.virusres.2014.09.011] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/22/2014] [Accepted: 09/24/2014] [Indexed: 12/15/2022]
Abstract
Human coronavirus (HCoV) are naturally neuroinvasive in both mice and humans. Both transneuronal and hematogenous route may allow virus invasion of the CNS. Infection of neurons leads to excitotoxicity, neurodegeneration and cell-death. HCoV are potentially associated with human neurological disorders.
Among the various respiratory viruses infecting human beings, coronaviruses are important pathogens, which usually infect the upper respiratory tract, where they are mainly associated with common colds. However, in more vulnerable populations, such as newborns, infants, the elderly and immune-compromised individuals, these opportunistic pathogens can also affect the lower respiratory tract, leading to pneumonia, exacerbations of asthma, and various types of respiratory distress syndrome. The respiratory involvement of human coronaviruses has been clearly established since the 1960s. Nevertheless, for almost three decades now, data reported in the scientific literature has also demonstrated that, like it was described for other human viruses, coronaviruses have neuroinvasive capacities since they can spread from the respiratory tract to the central nervous system (CNS). Once there, infection of CNS cells (neurotropism) could lead to human health problems, such as encephalitis and long-term neurological diseases. Neuroinvasive coronaviruses could damage the CNS as a result of misdirected host immune responses that could be associated with autoimmunity in susceptible individuals (virus-induced neuroimmunopathology) and/or viral replication, which directly induces damage to CNS cells (virus-induced neuropathology). Given all these properties, it has been suggested that these opportunistic human respiratory pathogens could be associated with the triggering or the exacerbation of neurologic diseases for which the etiology remains poorly understood. Herein, we present host and viral factors that participate in the regulation of the possible pathogenic processes associated with CNS infection by human coronaviruses and we try to decipher the intricate interplay between virus and host target cells in order to characterize their role in the virus life cycle as well as in the capacity of the cell to respond to viral invasion.
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Affiliation(s)
- Marc Desforges
- Laboratory of Neuroimmunovirology, INRS-Institut Armand-Frappier, Institut national de la recherche scientifique, Université du Québec, 531 boulevard des Prairies, Laval, Québec, Canada H7V 1B7.
| | - Alain Le Coupanec
- Laboratory of Neuroimmunovirology, INRS-Institut Armand-Frappier, Institut national de la recherche scientifique, Université du Québec, 531 boulevard des Prairies, Laval, Québec, Canada H7V 1B7
| | - Jenny K Stodola
- Laboratory of Neuroimmunovirology, INRS-Institut Armand-Frappier, Institut national de la recherche scientifique, Université du Québec, 531 boulevard des Prairies, Laval, Québec, Canada H7V 1B7
| | - Mathieu Meessen-Pinard
- Laboratory of Neuroimmunovirology, INRS-Institut Armand-Frappier, Institut national de la recherche scientifique, Université du Québec, 531 boulevard des Prairies, Laval, Québec, Canada H7V 1B7
| | - Pierre J Talbot
- Laboratory of Neuroimmunovirology, INRS-Institut Armand-Frappier, Institut national de la recherche scientifique, Université du Québec, 531 boulevard des Prairies, Laval, Québec, Canada H7V 1B7.
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31
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Study of Environmental and Antimicrobial Agents Impact on Features of Bacterial Growth. Cell Biochem Biophys 2013; 66:759-64. [DOI: 10.1007/s12013-013-9521-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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32
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Abstract
The article summarises the results of more than 30 years of research on palmitoylation (S‐acylation) of viral proteins, the post‐translational attachment of fatty acids to cysteine residues of integral and peripheral membrane proteins. Analysing viral proteins is not only important to characterise the cellular pathogens but also instrumental to decipher the palmitoylation machinery of cells. This comprehensive review describes methods to identify S‐acylated proteins and covers the fundamental biochemistry of palmitoylation: the location of palmitoylation sites in viral proteins, the fatty acid species found in S‐acylated proteins, the intracellular site of palmitoylation and the enzymology of the reaction. Finally, the functional consequences of palmitoylation are discussed regarding binding of proteins to membranes or membrane rafts, entry of enveloped viruses into target cells by spike‐mediated membrane fusion as well as assembly and release of virus particles from infected cells. The topics are described mainly for palmitoylated proteins of influenza virus, but proteins of other important pathogens, such as the causative agents of AIDS and severe acute respiratory syndrome, and of model viruses are discussed.
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Affiliation(s)
- Michael Veit
- Department of Immunology and Molecular Biology, Free University, Berlin, Germany.
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Abstract
Viroporins are small virally encoded hydrophobic proteins that oligomerize in the membrane of host cells, leading to the formation of hydrophilic pores. This activity modifies several cellular functions, including membrane permeability, Ca2+ homeostasis, membrane remodelling and glycoprotein trafficking. A classification scheme for viroporins is proposed on the basis of their structure and membrane topology. Thus, class I and class II viroporins are defined according to the number of transmembrane domains in the protein (one and two, respectively), and subclasses are defined according to their orientation in the membrane. The main function of viroporins during viral replication is to participate in virion morphogenesis and release from host cells. In addition, some viroporins are involved in viral entry and genome replication. The structure and activity of several viroporins, such as picornavirus protein 2B (P2B), influenza A virus matrix protein 2 (M2), hepatitis C virus p7 and HIV-1 viral protein U (Vpu), have been analysed in detail. New members of this expanding family of viral proteins have been described, from both RNA and DNA viruses. In addition to having a common general structure, all of these new viroporins have the ability to increase membrane permeability. Viroporins represent ideal targets to block viral replication and the spread of infection. Although a number of selective inhibitors of viroporin ion channels have been analysed in detail, optimized screening systems promise to provide new and more potent antiviral compounds in the near future.
Viroporins belong to a growing family of virally encoded proteins that form aqueous channels in the membranes of host cells. Here, Carrasco and colleagues review the structure and diverse biological functions of these proteins during the viral life cycle, as well as their potential as antiviral therapeutic targets. Viroporins are small, hydrophobic proteins that are encoded by a wide range of clinically relevant animal viruses. When these proteins oligomerize in host cell membranes, they form hydrophilic pores that disrupt a number of physiological properties of the cell. Viroporins are crucial for viral pathogenicity owing to their involvement in several diverse steps of the viral life cycle. Thus, these viral proteins, which include influenza A virus matrix protein 2 (M2), HIV-1 viral protein U (Vpu) and hepatitis C virus p7, represent ideal targets for therapeutic intervention, and several compounds that block their pore-forming activity have been identified. Here, we review recent studies in the field that have advanced our knowledge of the structure and function of this expanding family of viral proteins.
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Identification of a Golgi complex-targeting signal in the cytoplasmic tail of the severe acute respiratory syndrome coronavirus envelope protein. J Virol 2011; 85:5794-803. [PMID: 21450821 DOI: 10.1128/jvi.00060-11] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The 2003 global outbreak of progressive respiratory failure was caused by a newly emerged virus, severe acute respiratory syndrome coronavirus (SARS-CoV). In contrast to many well-studied enveloped viruses that assemble and bud at the plasma membrane, coronaviruses assemble by budding into the lumen of the endoplasmic reticulum-Golgi intermediate compartment and are released from the cell by exocytosis. For this to occur, the viral envelope proteins must be efficiently targeted to the Golgi region of the secretory pathway. Although the envelope protein (E) makes up only a small percentage of the viral envelope, it plays an important, as-yet-undefined role in virus production. To dissect the targeting of the SARS-CoV E protein to the Golgi region, we exogenously expressed the protein and various mutants from cDNA and determined their localization using immunofluorescence microscopy and biochemical assays. We show that the cytoplasmic tail of the SARS-CoV E protein is sufficient to redirect a plasma membrane protein to the Golgi region. Through site-directed mutagenesis, we demonstrate that a predicted beta-hairpin structural motif in the tail is sufficient for Golgi complex localization of a reporter protein. This motif is conserved in E proteins of beta and gamma coronaviruses (formerly referred to as group 2 and 3 coronaviruses), where it also functions as a Golgi complex-targeting signal. Dissecting the mechanism of targeting of the SARS-CoV E protein will lead to a better understanding of its role in the assembly and release of virions.
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Teoh KT, Siu YL, Chan WL, Schlüter MA, Liu CJ, Peiris JSM, Bruzzone R, Margolis B, Nal B. The SARS coronavirus E protein interacts with PALS1 and alters tight junction formation and epithelial morphogenesis. Mol Biol Cell 2010; 21:3838-52. [PMID: 20861307 PMCID: PMC2982091 DOI: 10.1091/mbc.e10-04-0338] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Intercellular tight junctions define epithelial apicobasal polarity and form a physical fence which protects underlying tissues from pathogen invasions. PALS1, a tight junction-associated protein, is a member of the CRUMBS3-PALS1-PATJ polarity complex, which is crucial for the establishment and maintenance of epithelial polarity in mammals. Here we report that the carboxy-terminal domain of the SARS-CoV E small envelope protein (E) binds to human PALS1. Using coimmunoprecipitation and pull-down assays, we show that E interacts with PALS1 in mammalian cells and further demonstrate that the last four carboxy-terminal amino acids of E form a novel PDZ-binding motif that binds to PALS1 PDZ domain. PALS1 redistributes to the ERGIC/Golgi region, where E accumulates, in SARS-CoV-infected Vero E6 cells. Ectopic expression of E in MDCKII epithelial cells significantly alters cyst morphogenesis and, furthermore, delays formation of tight junctions, affects polarity, and modifies the subcellular distribution of PALS1, in a PDZ-binding motif-dependent manner. We speculate that hijacking of PALS1 by SARS-CoV E plays a determinant role in the disruption of the lung epithelium in SARS patients.
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Affiliation(s)
- Kim-Tat Teoh
- HKU-Pasteur Research Centre, Pokfulam, Hong Kong SAR China
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36
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McBride CE, Machamer CE. Palmitoylation of SARS-CoV S protein is necessary for partitioning into detergent-resistant membranes and cell-cell fusion but not interaction with M protein. Virology 2010; 405:139-48. [PMID: 20580052 PMCID: PMC2914208 DOI: 10.1016/j.virol.2010.05.031] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 04/27/2010] [Accepted: 05/26/2010] [Indexed: 12/21/2022]
Abstract
Coronaviruses are enveloped RNA viruses that generally cause mild disease in humans. However, the recently emerged coronavirus that caused severe acute respiratory syndrome (SARS-CoV) is the most pathogenic human coronavirus discovered to date. The SARS-CoV spike (S) protein mediates virus entry by binding cellular receptors and inducing fusion between the viral envelope and the host cell membrane. Coronavirus S proteins are palmitoylated, which may affect function. Here, we created a non-palmitoylated SARS-CoV S protein by mutating all nine cytoplasmic cysteine residues. Palmitoylation of SARS-CoV S was required for partitioning into detergent-resistant membranes and for cell–cell fusion. Surprisingly, however, palmitoylation of S was not required for interaction with SARS-CoV M protein. This contrasts with the requirement for palmitoylation of mouse hepatitis virus S protein for interaction with M protein and may point to important differences in assembly and infectivity of these two coronaviruses.
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Affiliation(s)
- Corrin E McBride
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Alvarez E, DeDiego ML, Nieto-Torres JL, Jiménez-Guardeño JM, Marcos-Villar L, Enjuanes L. The envelope protein of severe acute respiratory syndrome coronavirus interacts with the non-structural protein 3 and is ubiquitinated. Virology 2010; 402:281-91. [PMID: 20409569 PMCID: PMC7119183 DOI: 10.1016/j.virol.2010.03.015] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Revised: 01/05/2010] [Accepted: 03/06/2010] [Indexed: 02/02/2023]
Abstract
To analyze the proteins interacting with the severe acute respiratory syndrome coronavirus (SARS-CoV) envelope (E) protein, a SARS-CoV was engineered including two tags associated to the E protein. Using this virus, complexes of SARS-CoV E and other proteins were purified using a tandem affinity purification system. Several viral and cell proteins including spike, membrane, non-structural protein 3 (nsp3), dynein heavy chain, fatty acid synthase and transmembrane protein 43 bound E protein. In the present work, we focused on the binding of E protein to nsp3 in infected cells and cell-free systems. This interaction was mediated by the N-terminal acidic domain of nsp3. Moreover, nsp3 and E protein colocalized during the infection. It was shown that E protein was ubiquitinated in vitro and in cell culture, suggesting that the interaction between nsp3 and E protein may play a role in the E protein ubiquitination status and therefore on its turnover.
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Affiliation(s)
- Enrique Alvarez
- Centro Nacional de Biotecnología (CNB), CSIC, Darwin 3, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
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38
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Thaa B, Hofmann KP, Veit M. Viruses as vesicular carriers of the viral genome: a functional module perspective. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1803:507-19. [PMID: 20100522 PMCID: PMC7114299 DOI: 10.1016/j.bbamcr.2010.01.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Revised: 01/11/2010] [Accepted: 01/13/2010] [Indexed: 12/30/2022]
Abstract
Enveloped viruses and cellular transport vesicles share obvious morphological and functional properties. Both are composed of a closed membrane, which is lined with coat proteins and encases cargo. Transmembrane proteins inserted into the membrane define the target membrane area with which the vesicle or virus is destined to fuse. Here we discuss recent insight into the functioning of enveloped viruses in the framework of the “functional module” concept. Vesicular transport is an exemplary case of a functional module, as defined as a part of the proteome that assembles to perform a specific autonomous function in a living cell. Cellular vesicles serve to transport cargo between membranous organelles inside the cell, while enveloped viruses can be seen as carriers of the viral genome delivering their cargo from an infected to an uninfected cell. The turnover of both vesicles and viruses involves an analogous series of submodular events. This comprises assembly of elements, budding from the donor compartment, uncoating and/or maturation, docking to and finally fusion with the target membrane to release the cargo. This modular perception enables us to define submodular building blocks so that mechanisms and elements can be directly compared. It will be analyzed where viruses have developed their own specific strategy, where they share functional schemes with vesicles, and also where they even have “hijacked” complete submodular schemes from the cell. Such a perspective may also include new and more specific approaches to pharmacological interference with virus function, which could avoid some of the most severe side effects.
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Affiliation(s)
- Bastian Thaa
- Department of Immunology and Molecular Biology, Veterinary Faculty, Free University Berlin, Philippstr. 13, 10115 Berlin, Germany
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39
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Chen Y, Wang M, Zhang Q, Liu J. Construction of an implicit membrane environment for the lattice Monte Carlo simulation of transmembrane protein. Biophys Chem 2009; 147:35-41. [PMID: 20079964 PMCID: PMC7117040 DOI: 10.1016/j.bpc.2009.12.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Revised: 12/17/2009] [Accepted: 12/18/2009] [Indexed: 02/01/2023]
Abstract
Due to the complexity of biological membrane, computer simulation of transmembrane protein's folding is challenging. In this paper, an implicit biological membrane environment has been constructed in lattice space, in which the lipid chains and water molecules were represented by the unoccupied lattice sites. The biological membrane was characterized with three features: stronger hydrogen bonding interaction, membrane lateral pressure, and lipophobicity index for the amino acid residues. In addition to the hydrocarbon core spanning region and the water solution, the lipid interface has also been represented in this implicit membrane environment, which was proved to be effective for the transmembrane protein's folding. The associated Monte Carlo simulations have been performed for SARS-CoV E protein and M2 protein segment (residues 18–60) of influenza A virus. It was found that the coil–helix transition of the transmembrane segment occurred earlier than the coil–globule transition of the two terminal domains. The folding process and final orientation of the amphipathic helical block in water solution are obviously influenced by its corresponding hydrophobicity/lipophobicity. Therefore, this implicit membrane environment, though in lattice space, can make an elaborate balance between different driving forces for the membrane protein's folding, thus offering a potential means for the simulation of transmembrane protein oligomers in feasible time.
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Affiliation(s)
- Yantao Chen
- Shenzhen Key Laboratory of Functional Polymer, College of Chemistry and Chemical Engineering, Shenzhen University, Shenzhen 518060, China.
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40
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Murray CL, Jones CT, Rice CM. Architects of assembly: roles of Flaviviridae non-structural proteins in virion morphogenesis. Nat Rev Microbiol 2009; 6:699-708. [PMID: 18587411 DOI: 10.1038/nrmicro1928] [Citation(s) in RCA: 175] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Viruses of the Flaviviridae family, including hepatitis C, dengue and bovine viral diarrhoea, are responsible for considerable morbidity and mortality worldwide. Recent advances in our understanding of virion assembly have uncovered commonalities among distantly related members of this family. We discuss the emerging hypothesis that physical virion components are not alone in forming the infectious particle, but that non-structural proteins are intimately involved in orchestrating morphogenesis. Pinpointing the roles of Flaviviridae proteins in virion production could reveal new avenues for antiviral therapeutics.
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Expression and membrane integration of SARS-CoV E protein and its interaction with M protein. Virus Genes 2009; 38:365-71. [PMID: 19322648 PMCID: PMC7088807 DOI: 10.1007/s11262-009-0341-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2008] [Accepted: 02/17/2009] [Indexed: 01/22/2023]
Abstract
The severe acute respiratory syndrome (SARS)-CoV E gene fragment was cloned and expressed as a recombinant protein fused with a myc tag at the N-terminus in vitro and in Vero E6 cells. Similar to other N-glycosylated proteins, the glycosylation of SARS-CoV E protein occurred co-translationally in the presence of microsomes. The SARS-CoV E protein is predicted to be a double-spanning membrane protein lacking a conventional signal peptide. Both of the transmembrane regions (a.a. 11–33 and 37–59) are predicted to be α-helices, which penetrate into membranes by themselves. As expected, these two transmembrane regions inserted a cytoplasmic protein into the endoplasmic reticulum membrane. Either of these two transmembrane domains co-localized with M protein. Both the transmembrane domains of E protein are required to interact with M protein, while either of the hydrophilic regions (a.a. 1–10 or 60–76) is dispensable as shown by co-immunoprecipitation assay. These results are important for the study of SARS-CoV assembly.
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