1
|
Liao Y, Wang H, Liao H, Sun Y, Tan L, Song C, Qiu X, Ding C. Classification, replication, and transcription of Nidovirales. Front Microbiol 2024; 14:1291761. [PMID: 38328580 PMCID: PMC10847374 DOI: 10.3389/fmicb.2023.1291761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 11/06/2023] [Indexed: 02/09/2024] Open
Abstract
Nidovirales is one order of RNA virus, with the largest single-stranded positive sense RNA genome enwrapped with membrane envelope. It comprises four families (Arterividae, Mesoniviridae, Roniviridae, and Coronaviridae) and has been circulating in humans and animals for almost one century, posing great threat to livestock and poultry,as well as to public health. Nidovirales shares similar life cycle: attachment to cell surface, entry, primary translation of replicases, viral RNA replication in cytoplasm, translation of viral proteins, virion assembly, budding, and release. The viral RNA synthesis is the critical step during infection, including genomic RNA (gRNA) replication and subgenomic mRNAs (sg mRNAs) transcription. gRNA replication requires the synthesis of a negative sense full-length RNA intermediate, while the sg mRNAs transcription involves the synthesis of a nested set of negative sense subgenomic intermediates by a discontinuous strategy. This RNA synthesis process is mediated by the viral replication/transcription complex (RTC), which consists of several enzymatic replicases derived from the polyprotein 1a and polyprotein 1ab and several cellular proteins. These replicases and host factors represent the optimal potential therapeutic targets. Hereby, we summarize the Nidovirales classification, associated diseases, "replication organelle," replication and transcription mechanisms, as well as related regulatory factors.
Collapse
Affiliation(s)
- Ying Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huan Wang
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huiyu Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yingjie Sun
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Lei Tan
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Cuiping Song
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xusheng Qiu
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chan Ding
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| |
Collapse
|
2
|
Desmarets L, Danneels A, Burlaud-Gaillard J, Blanchard E, Dubuisson J, Belouzard S. The KxGxYR and DxE motifs in the C-tail of the Middle East respiratory syndrome coronavirus membrane protein are crucial for infectious virus assembly. Cell Mol Life Sci 2023; 80:353. [PMID: 37940699 PMCID: PMC10632273 DOI: 10.1007/s00018-023-05008-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/21/2023] [Accepted: 10/17/2023] [Indexed: 11/10/2023]
Abstract
The coronavirus' (CoV) membrane (M) protein is the driving force during assembly, but this process remains poorly characterized. Previously, we described two motifs in the C-tail of the Middle East respiratory syndrome CoV (MERS-CoV) M protein involved in its endoplasmic reticulum (ER) exit (211DxE213) and trans-Golgi network (TGN) retention (199KxGxYR204). Here, their function in virus assembly was investigated by two different virus-like particle (VLP) assays and by mutating both motifs in an infectious MERS-CoV cDNA clone. It was shown that the 199KxGxYR204 motif was essential for VLP and infectious virus assembly. Moreover, the mislocalization of the M protein induced by mutation of this motif prevented M-E interaction. Hampering the ER export of M by mutating its 211DxE213 motif still allowed the formation of nucleocapsid-empty VLPs, but prevented the formation of fully assembled VLPs and infectious particles. Taken together, these data show that the MERS-CoV assembly process highly depends on the correct intracellular trafficking of its M protein, and hence that not only specific protein-protein interacting motifs but also correct subcellular localization of the M protein in infected cells is essential for virus formation and should be taken into consideration when studying the assembly process.
Collapse
Affiliation(s)
- Lowiese Desmarets
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, 59000, Lille, France
| | - Adeline Danneels
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, 59000, Lille, France
| | - Julien Burlaud-Gaillard
- INSERM U1259 MAVIVH, Université de Tours and CHRU de Tours, Tours, France
- Plate-Forme IBiSA de Microscopie Electronique, Université de Tours and CHRU de Tours, Tours, France
| | - Emmanuelle Blanchard
- INSERM U1259 MAVIVH, Université de Tours and CHRU de Tours, Tours, France
- Plate-Forme IBiSA de Microscopie Electronique, Université de Tours and CHRU de Tours, Tours, France
| | - Jean Dubuisson
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, 59000, Lille, France
| | - Sandrine Belouzard
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, 59000, Lille, France.
| |
Collapse
|
3
|
Shan T, Li LY, Yang JM, Cheng Y. Role and clinical implication of autophagy in COVID-19. Virol J 2023; 20:125. [PMID: 37328875 PMCID: PMC10276507 DOI: 10.1186/s12985-023-02069-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/10/2023] [Indexed: 06/18/2023] Open
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic constitutes a serious public health concern worldwide. Currently, more than 6 million deaths have occurred despite drastic containment measures, and this number is still increasing. Currently, no standard therapies for COVID-19 are available, which necessitates identifying effective preventive and therapeutic agents against COVID-19. However, developing new drugs and vaccines is a time-consuming process, and therefore, repurposing the existing drugs or redeveloping related targets seems to be the best strategy to develop effective therapeutics against COVID-19. Autophagy, a multistep lysosomal degradation pathway contributing to nutrient recycling and metabolic adaptation, is involved in the initiation and progression of numerous diseases as a part of an immune response. The key role of autophagy in antiviral immunity has been extensively studied. Moreover, autophagy can directly eliminate intracellular microorganisms by selective autophagy, that is, "xenophagy." However, viruses have acquired diverse strategies to exploit autophagy for their infection and replication. This review aims to trigger the interest in the field of autophagy as an antiviral target for viral pathogens (with an emphasis on COVID-19). We base this hypothesis on summarizing the classification and structure of coronaviruses as well as the process of SARS-CoV-2 infection and replication; providing the common understanding of autophagy; reviewing interactions between the mechanisms of viral entry/replication and the autophagy pathways; and discussing the current state of clinical trials of autophagy-modifying drugs in the treatment of SARS-CoV-2 infection. We anticipate that this review will contribute to the rapid development of therapeutics and vaccines against COVID-19.
Collapse
Affiliation(s)
- Tianjiao Shan
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
- Hunan Provincial Engineering Research Centre of Translational Medicine and Innovative Drug, Changsha, 410011, China
| | - Lan-Ya Li
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
- Hunan Provincial Engineering Research Centre of Translational Medicine and Innovative Drug, Changsha, 410011, China
| | - Jin-Ming Yang
- Department of Toxicology and Cancer Biology, Department of Pharmacology, and Markey Cancer Center, University of Kentucky, Lexington, KY, 40536, USA.
| | - Yan Cheng
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, 410011, China.
- Hunan Provincial Engineering Research Centre of Translational Medicine and Innovative Drug, Changsha, 410011, China.
| |
Collapse
|
4
|
Gullberg RC, Frydman J. Novel Mode of nanoLuciferase Packaging in SARS-CoV-2 Virions and VLPs Provides Versatile Reporters for Virus Production. Viruses 2023; 15:1335. [PMID: 37376634 DOI: 10.3390/v15061335] [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: 05/16/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
SARS-CoV-2 is a positive-strand RNA virus in the Coronaviridae family that is responsible for morbidity and mortality worldwide. To better understand the molecular pathways leading to SARS-CoV-2 virus assembly, we examined a virus-like particle (VLP) system co-expressing all structural proteins together with an mRNA reporter encoding nanoLuciferase (herein nLuc). Surprisingly, the 19 kDa nLuc protein itself was encapsidated into VLPs, providing a better reporter than nLuc mRNA itself. Strikingly, infecting nLuc-expressing cells with the SARS-CoV-2, NL63 or OC43 coronaviruses yielded virions containing packaged nLuc that served to report viral production. In contrast, infection with the flaviviruses, dengue or Zika, did not lead to nLuc packaging and secretion. A panel of reporter protein variants revealed that the packaging is size-limited and requires cytoplasmic expression, indicating that the large virion of coronaviruses can encaspidate a small cytoplasmic reporter protein. Our findings open the way for powerful new approaches to measure coronavirus particle production, egress and viral entry mechanisms.
Collapse
Affiliation(s)
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Poggio E, Vallese F, Hartel AJW, Morgenstern TJ, Kanner SA, Rauh O, Giamogante F, Barazzuol L, Shepard KL, Colecraft HM, Clarke OB, Brini M, Calì T. Perturbation of the host cell Ca 2+ homeostasis and ER-mitochondria contact sites by the SARS-CoV-2 structural proteins E and M. Cell Death Dis 2023; 14:297. [PMID: 37120609 PMCID: PMC10148623 DOI: 10.1038/s41419-023-05817-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 04/11/2023] [Accepted: 04/18/2023] [Indexed: 05/01/2023]
Abstract
Coronavirus disease (COVID-19) is a contagious respiratory disease caused by the SARS-CoV-2 virus. The clinical phenotypes are variable, ranging from spontaneous recovery to serious illness and death. On March 2020, a global COVID-19 pandemic was declared by the World Health Organization (WHO). As of February 2023, almost 670 million cases and 6,8 million deaths have been confirmed worldwide. Coronaviruses, including SARS-CoV-2, contain a single-stranded RNA genome enclosed in a viral capsid consisting of four structural proteins: the nucleocapsid (N) protein, in the ribonucleoprotein core, the spike (S) protein, the envelope (E) protein, and the membrane (M) protein, embedded in the surface envelope. In particular, the E protein is a poorly characterized viroporin with high identity amongst all the β-coronaviruses (SARS-CoV-2, SARS-CoV, MERS-CoV, HCoV-OC43) and a low mutation rate. Here, we focused our attention on the study of SARS-CoV-2 E and M proteins, and we found a general perturbation of the host cell calcium (Ca2+) homeostasis and a selective rearrangement of the interorganelle contact sites. In vitro and in vivo biochemical analyses revealed that the binding of specific nanobodies to soluble regions of SARS-CoV-2 E protein reversed the observed phenotypes, suggesting that the E protein might be an important therapeutic candidate not only for vaccine development, but also for the clinical management of COVID designing drug regimens that, so far, are very limited.
Collapse
Affiliation(s)
- Elena Poggio
- Department of Biology, University of Padova, Padova, Italy
| | - Francesca Vallese
- Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Andreas J W Hartel
- Department of Electrical Engineering, Columbia University, New York, NY, USA
| | - Travis J Morgenstern
- Department of Molecular Pharmacology and Therapeutics, Columbia University Irving Medical Center, New York, NY, USA
| | - Scott A Kanner
- Doctoral Program in Neurobiology and Behavior, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Oliver Rauh
- Membrane Biophysics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Flavia Giamogante
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Lucia Barazzuol
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Kenneth L Shepard
- Department of Electrical Engineering, Columbia University, New York, NY, USA
| | - Henry M Colecraft
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
- Department of Molecular Pharmacology and Therapeutics, Columbia University Irving Medical Center, New York, NY, USA
- Doctoral Program in Neurobiology and Behavior, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Oliver Biggs Clarke
- Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Marisa Brini
- Department of Biology, University of Padova, Padova, Italy
- Study Center for Neurodegeneration (CESNE), University of Padova, Padova, Italy
| | - Tito Calì
- Department of Biomedical Sciences, University of Padova, Padova, Italy.
- Study Center for Neurodegeneration (CESNE), University of Padova, Padova, Italy.
- Padova Neuroscience Center (PNC), University of Padova, Padova, Italy.
| |
Collapse
|
7
|
Hassan SS, Kodakandla V, Redwan EM, Lundstrom K, Choudhury PP, Serrano-Aroca Á, Azad GK, Aljabali AAA, Palu G, Abd El-Aziz TM, Barh D, Uhal BD, Adadi P, Takayama K, Bazan NG, Tambuwala M, Sherchan SP, Lal A, Chauhan G, Baetas-da-Cruz W, Uversky VN. Non-uniform aspects of the SARS-CoV-2 intraspecies evolution reopen question of its origin. Int J Biol Macromol 2022; 222:972-993. [PMID: 36174872 PMCID: PMC9511875 DOI: 10.1016/j.ijbiomac.2022.09.184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 05/04/2022] [Accepted: 09/20/2022] [Indexed: 12/01/2022]
Abstract
Several hypotheses have been presented on the origin of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) from its identification as the agent causing the current coronavirus disease 19 (COVID-19) pandemic. So far, no solid evidence has been found to support any hypothesis on the origin of this virus, and the issue continue to resurface over and over again. Here we have unfolded a pattern of distribution of several mutations in the SARS-CoV-2 proteins in 24 geo-locations across different continents. The results showed an evenly uneven distribution of the unique protein variants, distinct mutations, unique frequency of common conserved residues, and mutational residues across these 24 geo-locations. Furthermore, ample mutations were identified in the evolutionarily conserved invariant regions in the SARS-CoV-2 proteins across almost all geo-locations studied. This pattern of mutations potentially breaches the law of evolutionary conserved functional units of the beta-coronavirus genus. These mutations may lead to several novel SARS-CoV-2 variants with a high degree of transmissibility and virulence. A thorough investigation on the origin and characteristics of SARS-CoV-2 needs to be conducted in the interest of science and for the preparation of meeting the challenges of potential future pandemics.
Collapse
Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur, 721140, West Bengal, India.
| | - Vaishnavi Kodakandla
- Department of Life sciences, Sophia College For Women, University of Mumbai, Bhulabhai Desai Road, Mumbai 400026, India
| | - Elrashdy M Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications, New Borg EL-Arab 21934, Alexandria, Egypt.
| | | | - Pabitra Pal Choudhury
- Indian Statistical Institute, Applied Statistics Unit, 203 B T Road, Kolkata 700108, India
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigacion Traslacional San Alberto Magno, Universidad Cat'olica de Valencia San Vicente Martir, c/Guillem de Castro, 94, 46001 Valencia, Valencia, Spain.
| | | | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University, Faculty of Pharmacy, Irbid 566, Jordan.
| | - Giorgio Palu
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy.
| | - 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, San Antonio, TX 78229-3900, USA.
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB, India; Departamento de Geńetica, Ecologia e Evolucao, Instituto de Cíencias Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Bruce D Uhal
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin 9054, New Zealand
| | - Kazuo Takayama
- Center for iPS Cell Research and Application, Kyoto University, Kyoto 6068507, Japan.
| | - Nicolas G Bazan
- Neuroscience Center of Excellence, School of Medicine, LSU Health New Orleans, New Orleans, LA 70112, USA.
| | - Murtaza Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK.
| | - Samendra P Sherchan
- Lincoln Medical School, University of Lincoln, Brayford Pool Campus, Lincoln LN6 7TS, UK.
| | - Amos Lal
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, USA
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501 Sur, 64849 Monterrey, Nuevo León, Mexico.
| | - 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
| | - Vladimir N Uversky
- Department of Molecular Medicineand USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny 141700, Russia.
| |
Collapse
|
8
|
Rath SL, Tripathy M, Mandal N. How Does Temperature Affect the Dynamics of SARS-CoV-2 M Proteins? Insights from Molecular Dynamics Simulations. J Membr Biol 2022; 255:341-356. [PMID: 35552785 PMCID: PMC9101995 DOI: 10.1007/s00232-022-00244-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 05/07/2022] [Indexed: 11/30/2022]
Abstract
Enveloped viruses, in general, have several transmembrane proteins and glycoproteins, which assist the virus in entry and attachment onto the host cells. These proteins also play a significant role in determining the shape and size of the newly formed virus particles. The lipid membrane and the embedded proteins affect each other in non-trivial ways during the course of the viral life cycle. Unraveling the nature of the protein-protein and protein-lipid interactions, under various environmental and physiological conditions, could therefore prove to be crucial in development of therapeutics. Here, we study the M protein of SARS-CoV-2 to understand the effect of temperature on the properties of the protein-membrane system. The membrane-embedded dimeric M proteins were studied using atomistic and coarse-grained molecular dynamics simulations at temperatures ranging between 10 and 50 °C. While temperature-induced fluctuations are expected to be monotonic, we observe a steady rise in the protein dynamics up to 40 °C, beyond which it surprisingly reverts back to the low-temperature behavior. Detailed investigation reveals disordering of the membrane lipids in the presence of the protein, which induces additional curvature around the transmembrane region. Coarse-grained simulations indicate temperature-dependent aggregation of M protein dimers. Our study clearly indicates that the dynamics of membrane lipids and integral M protein of SARS-CoV-2 enables it to better associate and aggregate only at a certain temperature range (i.e., ~ 30-40 °C). This can have important implications in the protein aggregation and subsequent viral budding/fission processes.
Collapse
Affiliation(s)
- Soumya Lipsa Rath
- Department of Biotechnology, National Institute of Technology Warangal (NITW), Telangana, 506004, India.
| | - Madhusmita Tripathy
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, 64287, Darmstadt, Germany.
| | - Nabanita Mandal
- Department of Biotechnology, National Institute of Technology Warangal (NITW), Telangana, 506004, India
| |
Collapse
|
9
|
Goyal R, Bala R, Sindhu RK, Zehravi M, Madaan R, Ramproshad S, Mondal B, Dey A, Rahman MH, Cavalu S. Bioactive Based Nanocarriers for the Treatment of Viral Infections and SARS-CoV-2. NANOMATERIALS 2022; 12:nano12091530. [PMID: 35564239 PMCID: PMC9104170 DOI: 10.3390/nano12091530] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/21/2022] [Accepted: 04/27/2022] [Indexed: 02/01/2023]
Abstract
Since ancient times, plants have been used for their medicinal properties. They provide us with many phytomolecules, which serve a synergistic function for human well-being. Along with anti-microbial, plants also possess anti-viral activities. In Western nations, about 50% of medicines were extracted from plants or their constituents. The spread and pandemic of viral diseases are becoming a major threat to public health and a burden on the financial prosperity of communities worldwide. In recent years, SARS-CoV-2 has made a dramatic lifestyle change. This has promoted scientists not to use synthetic anti-virals, such as protease inhibitors, nucleic acid analogs, and other anti-virals, but to study less toxic anti-viral phytomolecules. An emerging approach includes searching for eco-friendly therapeutic molecules to develop phytopharmaceuticals. This article briefly discusses numerous bioactive molecules that possess anti-viral properties, their mode of action, and possible applications in treating viral diseases, with a special focus on coronavirus and various nano-formulations used as a carrier for the delivery of phytoconstituents for improved bioavailability.
Collapse
Affiliation(s)
- Ravi Goyal
- Department of Pharmacognosy, Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India; (R.G.); (R.B.); (R.M.)
| | - Rajni Bala
- Department of Pharmacognosy, Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India; (R.G.); (R.B.); (R.M.)
| | - Rakesh K. Sindhu
- Department of Pharmacognosy, Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India; (R.G.); (R.B.); (R.M.)
- Correspondence: (R.K.S.); (M.H.R.); (S.C.)
| | - Mehrukh Zehravi
- Department of Clinical Pharmacy Girls Section, Prince Sattam Bin Abdul Aziz University, Al-Kharj 11942, Saudi Arabia;
| | - Reecha Madaan
- Department of Pharmacognosy, Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India; (R.G.); (R.B.); (R.M.)
| | - Sarker Ramproshad
- Department of Pharmacy, Ranada Prasad Shaha University, Narayanganj 1400, Bangladesh; (S.R.); (B.M.)
| | - Banani Mondal
- Department of Pharmacy, Ranada Prasad Shaha University, Narayanganj 1400, Bangladesh; (S.R.); (B.M.)
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata 700073, West Bengal, India;
| | - Md. Habibur Rahman
- Department of Global Medical Science, Wonju College of Medicine, Yonsei University, Wonju 26426, Gangwon-do, Korea
- Correspondence: (R.K.S.); (M.H.R.); (S.C.)
| | - Simona Cavalu
- Faculty of Medicine and Pharmacy, University of Oradea, P-ta 1 Decembrie 10, 410087 Oradea, Romania
- Correspondence: (R.K.S.); (M.H.R.); (S.C.)
| |
Collapse
|
10
|
Kim J, Kim M, Kim D, Park S, Kang M, Baek K, Choi JK, Maharjan S, Akauliya M, Lee Y, Kwon HJ. Targeting the Interaction Between Spike Protein and Nucleocapsid Protein for Suppression and Detection of Human Coronavirus OC43. Front Immunol 2022; 13:835333. [PMID: 35359936 PMCID: PMC8960273 DOI: 10.3389/fimmu.2022.835333] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/18/2022] [Indexed: 01/09/2023] Open
Abstract
Human coronavirus OC43 (HCoV-OC43) is the coronavirus most associated with "common colds", infections of the upper respiratory tract. Previously, we reported that direct interactions of nucleocapsid (N) protein and C-terminal domain of Spike protein (Spike CD) are essential for replication of SARS-CoV-2 and MERS-CoV. Thus, we developed a novel ELISA-based strategy targeting these specific interactions to detect SARS-CoV-2 and MERS-CoV. Here, we investigated whether the same principles apply to HCoV-OC43. We discovered that the S protein of HCoV-OC43 interacts with N protein and that cell penetrating Spike CD peptide inhibits virus protein expression and replication of HCoV-OC43. The interaction between HCoV-OC43 S and N proteins were recapitulated with a recombinant HCoV-OC43 Spike CD fusion protein and a recombinant HCoV-OC43 N fusion protein in vitro. By producing an anti-HCoV-OC43 N protein-specific monoclonal antibody, we established a virus detection system based on the interaction between recombinant Spike CD and N protein of HCoV-OC43. We suggest that the interaction between Spike CD and N protein is conserved in coronaviruses and therefore could be a target for therapeutics against both novel coronavirus and its variants.
Collapse
Affiliation(s)
- Jinsoo Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, South Korea
| | - Minyoung Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, South Korea
| | - Dongbum Kim
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, South Korea
| | - Sangkyu Park
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, South Korea
| | - Mijeong Kang
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, South Korea
| | - Kyeongbin Baek
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, South Korea
| | - Jun-Kyu Choi
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, South Korea
| | - Sony Maharjan
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, South Korea
| | - Madhav Akauliya
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, South Korea
| | - Younghee Lee
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, South Korea,*Correspondence: Younghee Lee, ; Hyung-Joo Kwon,
| | - Hyung-Joo Kwon
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, South Korea,Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, South Korea,*Correspondence: Younghee Lee, ; Hyung-Joo Kwon,
| |
Collapse
|
11
|
Lu W, Zhao Z, Huang YW, Wang B. Review: A systematic review of virus-like particles of coronavirus: Assembly, generation, chimerism and their application in basic research and in the clinic. Int J Biol Macromol 2022; 200:487-497. [PMID: 35065135 PMCID: PMC8769907 DOI: 10.1016/j.ijbiomac.2022.01.108] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 12/27/2022]
Abstract
Virus-like particles (VLPs) are nano-scale particles that are morphologically similar to a live virus but which lack a genetic component. Since the pandemic spread of COVID-19, much focus has been placed on coronavirus (CoV)-related VLPs. CoVs contain four structural proteins, though the minimum requirement for VLP formation differs among virus species. CoV VLPs are commonly produced in mammalian and insect cell systems, sometimes in the form of chimeric VLPs that enable surface display of CoV epitopes. VLPs are an ideal model for virological research and have been applied as vaccines and diagnostic reagents to aid in clinical disease control. This review summarizes and updates the research progress on the characteristics of VLPs from different known CoVs, mainly focusing on assembly, in vitro expression systems for VLP generation, VLP chimerism, protein-based nanoparticles and their applications in basic research and clinical settings, which may aid in development of novel VLP vaccines against emerging coronavirus diseases such as SARS-CoV-2.
Collapse
Affiliation(s)
- Wan Lu
- Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China
| | - Zhuangzhuang Zhao
- Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yao-Wei Huang
- Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
| | - Bin Wang
- Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China.
| |
Collapse
|
12
|
Behl T, Kaur I, Aleya L, Sehgal A, Singh S, Sharma N, Bhatia S, Al-Harrasi A, Bungau S. CD147-spike protein interaction in COVID-19: Get the ball rolling with a novel receptor and therapeutic target. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 808:152072. [PMID: 34863742 PMCID: PMC8634688 DOI: 10.1016/j.scitotenv.2021.152072] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/26/2021] [Accepted: 11/26/2021] [Indexed: 05/03/2023]
Abstract
The combat against the Corona virus disease of 2019 (COVID-19), has created a chaos among the healthcare institutions and researchers, in turn accelerating the dire need to curtail the infection spread. The already established entry mechanism, via ACE2 has not yet successfully aided in the development of a suitable and reliable therapy. Taking in account the constant progression and deterioration of the cases worldwide, a different perspective and mechanistic approach is required, which has thrown light onto the cluster of differentiation 147 (CD147) transmembrane protein, as a novel route for SARS-CoV-2 entry. Despite lesser affinity towards COVID-19 virus, as compared to ACE2, this receptor provides a suitable justification behind elevated blood glucose levels in infected patients, retarded COVID-19 risk in women, enhanced susceptibility in geriatrics, greater infection susceptibility of T cells, infection prevalence in non-susceptible human cardiac pericytes and so on. The manuscript invokes the title role and distribution of CD147 in COVID-19 as an entry receptor and mediator of endocytosis-promoted entry of the virus, along with the "catch and clump" hypothesis, thereby presenting its Fundamental significance as a therapeutic target for potential candidates, such as Azithromycin, melatonin, statins, beta adrenergic blockers, ivermectin, Meplazumab etc. Thus, the authors provide a comprehensive review of a different perspective in COVID-19 infection, aiming to aid the researchers and virologists in considering all aspects of viral entry, in order to develop a sustainable and potential cure for the 2019 COVID-19 disease.
Collapse
Affiliation(s)
- Tapan Behl
- Chitkara College of Pharmacy, Chitkara University, Punjab, India.
| | - Ishnoor Kaur
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Lotfi Aleya
- Chrono-Environment Laboratory, UMR CNRS 6249, Bourgogne Franche-Comté University, France
| | - Aayush Sehgal
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Sukhbir Singh
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Neelam Sharma
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Saurabh Bhatia
- Natural & Medical Sciences Research Centre, University of Nizwa, Nizwa, Oman
| | - Ahmed Al-Harrasi
- Natural & Medical Sciences Research Centre, University of Nizwa, Nizwa, Oman
| | - Simona Bungau
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, Romania.
| |
Collapse
|
13
|
Sholukh AM, Fiore-Gartland A, Ford ES, Miner MD, Hou YJ, Tse LV, Kaiser H, Zhu H, Lu J, Madarampalli B, Park A, Lempp FA, St. Germain R, Bossard EL, Kee JJ, Diem K, Stuart AB, Rupert PB, Brock C, Buerger M, Doll MK, Randhawa AK, Stamatatos L, Strong RK, McLaughlin C, Huang ML, Jerome KR, Baric RS, Montefiori D, Corey L. Evaluation of Cell-Based and Surrogate SARS-CoV-2 Neutralization Assays. J Clin Microbiol 2021; 59:e0052721. [PMID: 34288726 PMCID: PMC8451402 DOI: 10.1128/jcm.00527-21] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/25/2021] [Indexed: 11/22/2022] Open
Abstract
Determinants of protective immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection require the development of well-standardized, reproducible antibody assays. This need has led to the emergence of a variety of neutralization assays. Head-to-head evaluation of different SARS-CoV-2 neutralization platforms could facilitate comparisons across studies and laboratories. Five neutralization assays were compared using 40 plasma samples from convalescent individuals with mild to moderate coronavirus disease 2019 (COVID-19): four cell-based systems using either live recombinant SARS-CoV-2 or pseudotyped viral particles created with lentivirus (LV) or vesicular stomatitis virus (VSV) packaging and one surrogate enzyme-linked immunosorbent assay (ELISA)-based test that measures inhibition of the spike protein receptor binding domain (RBD) binding its receptor human angiotensin converting enzyme 2 (hACE2). Vero cells, Vero E6 cells, HEK293T cells expressing hACE2, and TZM-bl cells expressing hACE2 and transmembrane serine protease 2 were tested. All cell-based assays showed 50% neutralizing dilution (ND50) geometric mean titers (GMTs) that were highly correlated (Pearson r = 0.81 to 0.89) and ranged within 3.4-fold. The live virus assay and LV pseudovirus assays with HEK293T/hACE2 cells showed very similar mean titers, 141 and 178, respectively. ND50 titers positively correlated with plasma IgG targeting SARS-CoV-2 spike protein and RBD (r = 0.63 to 0.89), but moderately correlated with nucleoprotein IgG (r = 0.46 to 0.73). ND80 GMTs mirrored ND50 data and showed similar correlation between assays and with IgG concentrations. The VSV pseudovirus assay and LV pseudovirus assay with HEK293T/hACE2 cells in low- and high-throughput versions were calibrated against the WHO SARS-CoV-2 IgG standard. High concordance between the outcomes of cell-based assays with live and pseudotyped virions enables valid cross-study comparison using these platforms.
Collapse
Affiliation(s)
- Anton M. Sholukh
- Vaccine and Infectious Diseases Division, Fred Hutch Cancer Research Center, Seattle, Washington, USA
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Diseases Division, Fred Hutch Cancer Research Center, Seattle, Washington, USA
| | - Emily S. Ford
- Vaccine and Infectious Diseases Division, Fred Hutch Cancer Research Center, Seattle, Washington, USA
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Maurine D. Miner
- Vaccine and Infectious Diseases Division, Fred Hutch Cancer Research Center, Seattle, Washington, USA
| | - Yixuan J. Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Longping V. Tse
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Haiying Zhu
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Joyce Lu
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Bhanupriya Madarampalli
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Arnold Park
- Vir Biotechnology, San Francisco, California, USA
| | | | - Russell St. Germain
- Vaccine and Infectious Diseases Division, Fred Hutch Cancer Research Center, Seattle, Washington, USA
| | - Emily L. Bossard
- Vaccine and Infectious Diseases Division, Fred Hutch Cancer Research Center, Seattle, Washington, USA
| | - Jia Jin Kee
- Vaccine and Infectious Diseases Division, Fred Hutch Cancer Research Center, Seattle, Washington, USA
| | - Kurt Diem
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Andrew B. Stuart
- Vaccine and Infectious Diseases Division, Fred Hutch Cancer Research Center, Seattle, Washington, USA
| | - Peter B. Rupert
- Basic Sciences Division, Fred Hutch Cancer Research Center, Seattle, Washington, USA
| | - Chance Brock
- Basic Sciences Division, Fred Hutch Cancer Research Center, Seattle, Washington, USA
| | - Matthew Buerger
- Basic Sciences Division, Fred Hutch Cancer Research Center, Seattle, Washington, USA
| | - Margaret K. Doll
- Department of Population Health Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - April Kaur Randhawa
- Vaccine and Infectious Diseases Division, Fred Hutch Cancer Research Center, Seattle, Washington, USA
| | - Leonidas Stamatatos
- Vaccine and Infectious Diseases Division, Fred Hutch Cancer Research Center, Seattle, Washington, USA
| | - Roland K. Strong
- Vaccine and Infectious Diseases Division, Fred Hutch Cancer Research Center, Seattle, Washington, USA
- Basic Sciences Division, Fred Hutch Cancer Research Center, Seattle, Washington, USA
| | - Colleen McLaughlin
- Department of Population Health Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Keith R. Jerome
- Vaccine and Infectious Diseases Division, Fred Hutch Cancer Research Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Lawrence Corey
- Vaccine and Infectious Diseases Division, Fred Hutch Cancer Research Center, Seattle, Washington, USA
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| |
Collapse
|
14
|
Alsobaie S. Understanding the Molecular Biology of SARS-CoV-2 and the COVID-19 Pandemic: A Review. Infect Drug Resist 2021; 14:2259-2268. [PMID: 34163190 PMCID: PMC8215902 DOI: 10.2147/idr.s306441] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 05/04/2021] [Indexed: 12/12/2022] Open
Abstract
Coronaviruses are named after the crown-like spike proteins on their surface. In the 21st century, three coronaviruses, namely severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), SARS-CoV, and Middle East respiratory syndrome related coronavirus (MERS-CoV), have emerged in the human population, presumably evolving from pathogens infecting other animals. Coronaviruses are enveloped viruses responsible for 15-30% of the atypical pneumonia cases in humans worldwide. The current coronavirus disease 2019 (COVID-19) pandemic is caused by the newest SARS virus, SARS-CoV-2, an enveloped, positive-sense, single-stranded RNA betacoronavirus of the family Coronaviridae. As of April 2021, the World Health Organization has reported more than 3 million deaths from COVID-19 and more than 140 million people have been infected with the virus, thereby making it the worst SARS pandemic of all time. Here, I review the current understanding of the molecular biology of coronaviruses and their host interactions, bringing together knowledge of the infection process to aid in the development of therapeutic drugs and/or vaccines against SARS-CoV-2. I also briefly overview the current situation of available treatments, vaccinations, and emerging strains.
Collapse
Affiliation(s)
- Sarah Alsobaie
- Department of Clinical Laboratory Science, King Saud University, Riyadh, 11451, Saudi Arabia
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Alharbi SN, Alrefaei AF. Comparison of the SARS-CoV-2 (2019-nCoV) M protein with its counterparts of SARS-CoV and MERS-CoV species. JOURNAL OF KING SAUD UNIVERSITY. SCIENCE 2021; 33:101335. [PMID: 33432259 PMCID: PMC7787911 DOI: 10.1016/j.jksus.2020.101335] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/13/2020] [Accepted: 12/27/2020] [Indexed: 05/09/2023]
Abstract
Coronaviruses M proteins are well-represented in the major protein component of the viral envelope. During the viral assembly, they play an important role by association with all other viral structural proteins. Despite their crucial functions, very little information regarding the structures and functions of M proteins is available. Here we utilize bioinformatic tools from available sequences and 3D structures of SARS-CoV, SARS-CoV2, and MERS-CoV M proteins in order to predict potential B-cell epitopes and assessing antibody binding affinity. Such study aims to aid finding more effective vaccines and recognize neutralizing antibodies. we found some rather exciting differences between SARS-COV-2, SARS-Cov and MERS-CoV M proteins. Two SARS-CoV-2 peptides with significant antigen presentation scores for human cell surface proteins have been identified. The results reveal that N-terminal domains of M proteins of SARS-CoV and SARS-CoV2 are translocated (outside) whereas it is inside (cytoplasmic side) in MERS-CoV.
Collapse
Affiliation(s)
- Sultan Nafea Alharbi
- National Centre for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
| | - Abdulwahed Fahad Alrefaei
- Department of Zoology, King Saud University, College of Science, P. O. Box 2455, Riyadh 11451, Saudi Arabia
| |
Collapse
|
17
|
Park BK, Kim J, Park S, Kim D, Kim M, Baek K, Bae JY, Park MS, Kim WK, Lee Y, Kwon HJ. MERS-CoV and SARS-CoV-2 replication can be inhibited by targeting the interaction between the viral spike protein and the nucleocapsid protein. Theranostics 2021; 11:3853-3867. [PMID: 33664866 PMCID: PMC7914343 DOI: 10.7150/thno.55647] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/19/2021] [Indexed: 12/20/2022] Open
Abstract
Background: The molecular interactions between viral proteins form the basis of virus production and can be used to develop strategies against virus infection. The interactions of the envelope proteins and the viral RNA-binding nucleocapsid (N) protein are essential for the assembly of coronaviruses including the Middle East respiratory syndrome coronavirus (MERS-CoV). Methods: Using co-immunoprecipitation, immunostaining, and proteomics analysis, we identified a protein interacting with the spike (S) protein in the cells infected with MERS-CoV or SARS-CoV-2. To confirm the interaction, synthetic peptides corresponding to the C-terminal domain of the S protein (Spike CD) were produced and their effect on the interaction was investigated in vitro. In vivo effect of the Spike CD peptides after cell penetration was further investigated using viral plaque formation assay. Phylogeographic analyses were conducted to deduce homology of Spike CDs and N proteins. Results: We identified a direct interaction between the S protein and the N protein of MERS-CoV that takes place during virus assembly in infected cells. Spike CD peptides of MERS-CoV inhibited the interaction between the S and N proteins in vitro. Furthermore, cell penetration by the synthetic Spike CD peptides inhibited viral plaque formation in MERS-CoV-infected cells. Phylogeographic analyses of Spike CDs and N proteins showed high homology among betacoronavirus lineage C strains. To determine if Spike CD peptides can inhibit the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), we used the same strategy and found that the SARS-CoV-2 Spike CD peptide inhibited virus replication in SARS-CoV-2-infected cells. Conclusions: We suggest that the interaction between the S protein and the N protein can be targeted to design new therapeutics against emerging coronaviruses, including SARS-CoV-2.
Collapse
Affiliation(s)
- Byoung Kwon Park
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
| | - Jinsoo Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
| | - Sangkyu Park
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Dongbum Kim
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
| | - Minyoung Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
| | - Kyeongbin Baek
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
| | - Joon-Yong Bae
- Department of Microbiology, College of Medicine, and the Institute for Viral Diseases, Korea University, Seoul 02841, Republic of Korea
| | - Man-Seong Park
- Department of Microbiology, College of Medicine, and the Institute for Viral Diseases, Korea University, Seoul 02841, Republic of Korea
| | - Won-Keun Kim
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
| | - Younghee Lee
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Hyung-Joo Kwon
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
| |
Collapse
|
18
|
Giri R, Bhardwaj T, Shegane M, Gehi BR, Kumar P, Gadhave K, Oldfield CJ, Uversky VN. Understanding COVID-19 via comparative analysis of dark proteomes of SARS-CoV-2, human SARS and bat SARS-like coronaviruses. Cell Mol Life Sci 2021; 78:1655-1688. [PMID: 32712910 DOI: 10.1101/2020.03.13.990598] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/03/2020] [Accepted: 07/17/2020] [Indexed: 05/18/2023]
Abstract
The recently emerged coronavirus designated as SARS-CoV-2 (also known as 2019 novel coronavirus (2019-nCoV) or Wuhan coronavirus) is a causative agent of coronavirus disease 2019 (COVID-19), which is rapidly spreading throughout the world now. More than 1.21 million cases of SARS-CoV-2 infection and more than 67,000 COVID-19-associated mortalities have been reported worldwide till the writing of this article, and these numbers are increasing every passing hour. The World Health Organization (WHO) has declared the SARS-CoV-2 spread as a global public health emergency and admitted COVID-19 as a pandemic now. Multiple sequence alignment data correlated with the already published reports on SARS-CoV-2 evolution indicated that this virus is closely related to the bat severe acute respiratory syndrome-like coronavirus (bat SARS-like CoV) and the well-studied human SARS coronavirus (SARS-CoV). The disordered regions in viral proteins are associated with the viral infectivity and pathogenicity. Therefore, in this study, we have exploited a set of complementary computational approaches to examine the dark proteomes of SARS-CoV-2, bat SARS-like, and human SARS CoVs by analysing the prevalence of intrinsic disorder in their proteins. According to our findings, SARS-CoV-2 proteome contains very significant levels of structural order. In fact, except for nucleocapsid, Nsp8, and ORF6, the vast majority of SARS-CoV-2 proteins are mostly ordered proteins containing less intrinsically disordered protein regions (IDPRs). However, IDPRs found in SARS-CoV-2 proteins are functionally important. For example, cleavage sites in its replicase 1ab polyprotein are found to be highly disordered, and almost all SARS-CoV-2 proteins contains molecular recognition features (MoRFs), which are intrinsic disorder-based protein-protein interaction sites that are commonly utilized by proteins for interaction with specific partners. The results of our extensive investigation of the dark side of SARS-CoV-2 proteome will have important implications in understanding the structural and non-structural biology of SARS or SARS-like coronaviruses.
Collapse
Affiliation(s)
- Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Mandi, Himachal Pradesh, 175005, India.
| | - Taniya Bhardwaj
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Mandi, Himachal Pradesh, 175005, India
| | - Meenakshi Shegane
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Mandi, Himachal Pradesh, 175005, India
| | - Bhuvaneshwari R Gehi
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Mandi, Himachal Pradesh, 175005, India
| | - Prateek Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Mandi, Himachal Pradesh, 175005, India
| | - Kundlik Gadhave
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Mandi, Himachal Pradesh, 175005, India
| | | | - Vladimir N Uversky
- Department of Molecular Medicine, Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Moscow region, Pushchino, 142290, Russia
| |
Collapse
|
19
|
Chepur SV, Pluzhnikov NN, Chubar OV, Bakulina LS, Litvinenko IV, Makarov VA, Gogolevsky AS, Myasnikov VA, Myasnikova IA, Al-Shehadat RI. Respiratory RNA Viruses: How to Be Prepared for an Encounter with New Pandemic Virus Strains. BIOLOGY BULLETIN REVIEWS 2021; 11. [PMCID: PMC8078390 DOI: 10.1134/s207908642102002x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The characteristics of the biology of influenza viruses and coronavirus that determine the implementation of the infectious process are presented. With provision for pathogenesis of infection possible effects of serine proteinase inhibitors, heparin, and inhibitors of heparan sulfate receptors in the prevention of cell contamination by viruses are examined. It has been determined that chelators of metals of variable valency and antioxidants should be used for the reduction of replicative activity of viruses and anti-inflammatory therapy. The possibility of a pH-dependent impairment of glycosylation of cellular and viral proteins was traced for chloroquine and its derivatives. The use of low-toxicity drugs as part of adjunct therapy increases the effectiveness of synthetic antiviral drugs and interferons and ensures the safety of baseline therapy.
Collapse
Affiliation(s)
- S. V. Chepur
- State Scientific Research Test Institute of Military Medicine of the Ministry of Defense of the Russian Federation, 195043 St. Petersburg, Russia
| | - N. N. Pluzhnikov
- State Scientific Research Test Institute of Military Medicine of the Ministry of Defense of the Russian Federation, 195043 St. Petersburg, Russia
| | - O. V. Chubar
- State Scientific Research Test Institute of Military Medicine of the Ministry of Defense of the Russian Federation, 195043 St. Petersburg, Russia
| | - L. S. Bakulina
- Burdenko Voronezh State Medical University, 394036 Voronezh, Russia
| | | | - V. A. Makarov
- Fundamentals of Biotechnology Federal Research Center, 119071 Moscow, Russia
| | - A. S. Gogolevsky
- State Scientific Research Test Institute of Military Medicine of the Ministry of Defense of the Russian Federation, 195043 St. Petersburg, Russia
| | - V. A. Myasnikov
- State Scientific Research Test Institute of Military Medicine of the Ministry of Defense of the Russian Federation, 195043 St. Petersburg, Russia
| | - I. A. Myasnikova
- State Scientific Research Test Institute of Military Medicine of the Ministry of Defense of the Russian Federation, 195043 St. Petersburg, Russia
| | - R. I. Al-Shehadat
- State Scientific Research Test Institute of Military Medicine of the Ministry of Defense of the Russian Federation, 195043 St. Petersburg, Russia
| |
Collapse
|
20
|
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.
Collapse
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.
| |
Collapse
|
21
|
Lang Y, Chen K, Li Z, Li H. The nucleocapsid protein of zoonotic betacoronaviruses is an attractive target for antiviral drug discovery. Life Sci 2020; 282:118754. [PMID: 33189817 PMCID: PMC7658559 DOI: 10.1016/j.lfs.2020.118754] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/22/2020] [Accepted: 11/10/2020] [Indexed: 12/02/2022]
Abstract
Betacoronaviruses are in one genera of coronaviruses including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome-related coronavirus (MERS-CoV), etc. These viruses threaten public health and cause dramatic economic losses. The nucleocapsid (N) protein is a structural protein of betacoronaviruses with multiple functions such as forming viral capsids with viral RNA, interacting with viral membrane protein to form the virus core with RNA, binding to several cellular kinases for signal transductions, etc. In this review, we highlighted the potential of the N protein as a suitable antiviral target from different perspectives, including structure, functions, and antiviral strategies for combatting betacoronaviruses.
Collapse
Affiliation(s)
- Yuekun Lang
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
| | - Ke Chen
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
| | - Zhong Li
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
| | - Hongmin Li
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA; Department of Biomedical Sciences, School of Public Health, University at Albany, 1 University Place, Rensselaer, NY 12144, USA.
| |
Collapse
|
22
|
Mazzoni A, Maggi L, Capone M, Spinicci M, Salvati L, Colao MG, Vanni A, Kiros ST, Mencarini J, Zammarchi L, Mantengoli E, Menicacci L, Caldini E, Romagnani S, Liotta F, Morettini A, Rossolini GM, Bartoloni A, Cosmi L, Annunziato F. Cell-mediated and humoral adaptive immune responses to SARS-CoV-2 are lower in asymptomatic than symptomatic COVID-19 patients. Eur J Immunol 2020; 50:2013-2024. [PMID: 33080068 DOI: 10.1002/eji.202048915] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/23/2020] [Indexed: 11/11/2022]
Abstract
The characterization of cell-mediated and humoral adaptive immune responses to SARS-CoV-2 is fundamental to understand COVID-19 progression and the development of immunological memory to the virus. In this study, we detected T-cells reactive to SARS-CoV-2 proteins M, S, and N, as well as serum virus-specific IgM, IgA, IgG, in nearly all SARS-CoV-2 infected individuals, but not in healthy donors. Virus-reactive T cells exhibited signs of in vivo activation, as suggested by the surface expression of immune-checkpoint molecules PD1 and TIGIT. Of note, we detected antigen-specific adaptive immune response both in asymptomatic and symptomatic SARS-CoV-2 infected subjects. More importantly, symptomatic patients displayed a significantly higher magnitude of both cell-mediated and humoral adaptive immune response to the virus, as compared to asymptomatic individuals. These findings suggest that an uncontrolled adaptive immune response contribute to the development of the life-threatening inflammatory phase of the disease. Finally, this study might open the way to develop effective vaccination strategies.
Collapse
Affiliation(s)
- Alessio Mazzoni
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Laura Maggi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Manuela Capone
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Michele Spinicci
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Infectious and Tropical Diseases Unit, Careggi University Hospital, Florence, Italy
| | - Lorenzo Salvati
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Maria Grazia Colao
- Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Anna Vanni
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Seble Tekle Kiros
- Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Jessica Mencarini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Infectious and Tropical Diseases Unit, Careggi University Hospital, Florence, Italy
| | - Lorenzo Zammarchi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Infectious and Tropical Diseases Unit, Careggi University Hospital, Florence, Italy
| | | | - Lorenzo Menicacci
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Eleonora Caldini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Sergio Romagnani
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Francesco Liotta
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Immunology and Cell Therapy Unit, Careggi University Hospital, Florence, Italy
| | | | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Alessandro Bartoloni
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Infectious and Tropical Diseases Unit, Careggi University Hospital, Florence, Italy
| | - Lorenzo Cosmi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Immunology and Cell Therapy Unit, Careggi University Hospital, Florence, Italy
| | - Francesco Annunziato
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Flow Cytometry Diagnostic Center and Immunotherapy (CDCI), Careggi University Hospital, Florence, Italy
| |
Collapse
|
23
|
Makarov V, Riabova O, Ekins S, Pluzhnikov N, Chepur S. The past, present and future of RNA respiratory viruses: influenza and coronaviruses. Pathog Dis 2020; 78:ftaa046. [PMID: 32860686 PMCID: PMC7499567 DOI: 10.1093/femspd/ftaa046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022] Open
Abstract
Influenza virus and coronaviruses continue to cause pandemics across the globe. We now have a greater understanding of their functions. Unfortunately, the number of drugs in our armory to defend us against them is inadequate. This may require us to think about what mechanisms to address. Here, we review the biological properties of these viruses, their genetic evolution and antiviral therapies that can be used or have been attempted. We will describe several classes of drugs such as serine protease inhibitors, heparin, heparan sulfate receptor inhibitors, chelating agents, immunomodulators and many others. We also briefly describe some of the drug repurposing efforts that have taken place in an effort to rapidly identify molecules to treat patients with COVID-19. While we put a heavy emphasis on the past and present efforts, we also provide some thoughts about what we need to do to prepare for respiratory viral threats in the future.
Collapse
Affiliation(s)
- Vadim Makarov
- Federal Research Center Fundamentals of Biotechnology of the Russian Academy of Sciences, 33-2 Leninsky Prospect, Moscow 119071, Russia
| | - Olga Riabova
- Federal Research Center Fundamentals of Biotechnology of the Russian Academy of Sciences, 33-2 Leninsky Prospect, Moscow 119071, Russia
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC 27606, USA
| | - Nikolay Pluzhnikov
- State Research Institute of Military Medicine of the Ministry of Defence of the Russian Federation, St Petersburg 195043, Russia
| | - Sergei Chepur
- State Research Institute of Military Medicine of the Ministry of Defence of the Russian Federation, St Petersburg 195043, Russia
| |
Collapse
|
24
|
Satarker S, Nampoothiri M. Involvement of the nervous system in COVID-19: The bell should toll in the brain. Life Sci 2020; 262:118568. [PMID: 33035589 PMCID: PMC7537730 DOI: 10.1016/j.lfs.2020.118568] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/24/2020] [Accepted: 10/02/2020] [Indexed: 02/06/2023]
Abstract
The world is fuming at SARS-CoV-2 for being the culprit for causing the devastating COVID-19, claiming millions of lives across the globe in the form of respiratory disorders. But lesser known are its effects on the CNS that are slowly surfacing in the worldwide population. Our review illustrates findings that claim SARS-CoV-2's arrival onto the ACE2 receptors of neuronal and glial cells mainly via CSF, olfactory nerve, trigeminal nerve, neuronal dissemination, and hematogenous pathways. The role of SARS-CoV-2 structural proteins in its smooth viral infectivity of the host cannot be ignored, especially the spike proteins that mediate spike attachment and host membrane fusion. Worth mentioning the nucleocapsid, envelope, and membrane proteins make the proliferation of SARS-CoV-2 much simpler than expected in spreading infection. This has led to catastrophic conditions like seizures, Guillain-Barré syndrome, viral encephalitis, meningoencephalitis, acute cerebrovascular disease, and respiratory failures. Placing a magnifying lens on the lesser-explored CNS consequences of COVID-19, we attempt to shift the focus of our readers onto the new supporting threats to which further studies are needed.
Collapse
Affiliation(s)
- Sairaj Satarker
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Madhavan Nampoothiri
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, India.
| |
Collapse
|
25
|
Boozari M, Hosseinzadeh H. Natural products for
COVID
‐19 prevention and treatment regarding to previous coronavirus infections and novel studies. Phytother Res 2020; 35:864-876. [DOI: 10.1002/ptr.6873] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/18/2020] [Accepted: 08/24/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Motahareh Boozari
- Department of Pharmacognosy, School of Pharmacy Mashhad University of Medical Sciences Mashhad Iran
| | - Hossein Hosseinzadeh
- Department of Pharmacodynamics and Toxicology, School of Pharmacy Mashhad University of Medical Sciences Mashhad Iran
- Pharmaceutical Research Center, Pharmaceutical Technology Institute Mashhad University of Medical Sciences Mashhad Iran
| |
Collapse
|
26
|
Cao Y, Yang R, Wang W, Lee I, Zhang R, Zhang W, Sun J, Xu B, Meng X. Computational Study of the Ion and Water Permeation and Transport Mechanisms of the SARS-CoV-2 Pentameric E Protein Channel. Front Mol Biosci 2020; 7:565797. [PMID: 33173781 PMCID: PMC7538787 DOI: 10.3389/fmolb.2020.565797] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/04/2020] [Indexed: 12/28/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by a novel coronavirus (SARS-CoV-2) and represents the causative agent of a potentially fatal disease that is a public health emergency of international concern. Coronaviruses, including SARS-CoV-2, encode an envelope (E) protein, which is a small, hydrophobic membrane protein; the E protein of SARS-CoV-2 shares a high level of homology with severe acute respiratory syndrome coronavirus (SARS-CoV). In this study, we provide insights into the function of the SARS-CoV-2 E protein channel and the ion and water permeation mechanisms using a combination of in silico methods. Based on our results, the pentameric E protein promotes the penetration of cation ions through the channel. An analysis of the potential mean force (PMF), pore radius and diffusion coefficient reveals that Leu10 and Phe19 are the hydrophobic gates of the channel. In addition, the pore exhibits a clear wetting/dewetting transition with cation selectivity under transmembrane voltage, indicating that it is a hydrophobic voltage-dependent channel. Overall, these results provide structure-based insights and molecular dynamic information that are needed to understand the regulatory mechanisms of ion permeability in the pentameric SARS-CoV-2 E protein channel.
Collapse
Affiliation(s)
- Yipeng Cao
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,National Supercomputer Center in Tianjin, TEDA - Tianjin Economic-Technological Development Area, Tianjin, China
| | - Rui Yang
- Department of Infection and Immunity, Tianjin Union Medical Center, Nankai University Affiliated Hospital, Tianjin, China
| | - Wei Wang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Imshik Lee
- College of Physics, Nankai University, Tianjin, China
| | - Ruiping Zhang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Wenwen Zhang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Jiana Sun
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Bo Xu
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Center for Intelligent Oncology, Chongqing University School of Medicine and Chongqing University Cancer Hospital, Chongqing, China
| | - Xiangfei Meng
- National Supercomputer Center in Tianjin, TEDA - Tianjin Economic-Technological Development Area, Tianjin, China
| |
Collapse
|
27
|
Oso BJ, Adeoye AO, Olaoye IF. Pharmacoinformatics and hypothetical studies on allicin, curcumin, and gingerol as potential candidates against COVID-19-associated proteases. J Biomol Struct Dyn 2020; 40:389-400. [DOI: 10.1080/07391102.2020.1813630] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Babatunde Joseph Oso
- Department of Biochemistry, McPherson University, Seriki Sotayo, Ogun State, Nigeria
| | | | - Ige Francis Olaoye
- Department of Biochemistry, McPherson University, Seriki Sotayo, Ogun State, Nigeria
| |
Collapse
|
28
|
Liu C, von Brunn A, Zhu D. Cyclophilin A and CD147: novel therapeutic targets for the treatment of COVID-19. MEDICINE IN DRUG DISCOVERY 2020; 7:100056. [PMID: 32835213 PMCID: PMC7364167 DOI: 10.1016/j.medidd.2020.100056] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 07/05/2020] [Accepted: 07/05/2020] [Indexed: 02/07/2023] Open
Abstract
The outbreak of pneumonia caused by a new coronavirus (SARS-CoV-2) occurred in December 2019, and spread rapidly throughout the world. There have been other severe coronavirus outbreaks worldwide, namely, severe acute respiratory syndrome (SARS-CoV) and Middle East respiratory syndrome (MERS-CoV). Because the genetic diversity of coronaviruses renders the design of vaccines complicated, broad spectrum-anti-coronavirus drugs have become a critical approach to control the coronavirus epidemic. Cyclophilin A is an important protein needed for coronavirus replication, and its inhibitor cyclosporine A has the ability to suppress coronavirus on a broad spectrum. CD147-S protein was found to be one route by which SARS-CoV-2 invades host cells, while CD147 was found to play a functional role in facilitating the infection of host cells by SARS-CoV. The CyPA/CD147 interaction may play a critical role in the ability of the SARS-CoV-2 virus to enter the host cells. However, cyclosporine A has immunosuppressive effects, so the conditions for its use as an antiviral drug are limited. As a result, cyclosporine A analogues without immunosuppressive side effects have attracted lots of interest. This review primarily discusses the drug development prospects of cyclophilin A as a therapeutic target for the treatment of coronavirus infection, especially coronavirus disease 2019 (COVID-19), and non-immunosuppressive cyclosporine analogues.
Collapse
Affiliation(s)
- Chenglong Liu
- School of Pharmacy, Fudan University, Shanghai, China, 201203
| | - Albrecht von Brunn
- Max-von-Pettenkofer Institute, Ludwig-Maximilians-University Munich and German Center for Infection Research, (DZIF), partner site Munich, 80336 Munich, Germany
| | - Di Zhu
- School of Pharmacy, Fudan University, Shanghai, China, 201203,Fudan affiliated Pudong Hospital, Fudan University, Shanghai, China 201100,Corresponding author at: School of Pharmacy, Fudan University, Shanghai, China 201203.
| |
Collapse
|
29
|
Liang XY, Zhu QC, Liang JQ, Liu SY, Liu DX, Fung TS. Development of HiBiT-Tagged Recombinant Infectious Bronchitis Coronavirus for Efficient in vitro and in vivo Viral Quantification. Front Microbiol 2020; 11:2100. [PMID: 32983065 PMCID: PMC7485224 DOI: 10.3389/fmicb.2020.02100] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 08/10/2020] [Indexed: 12/31/2022] Open
Abstract
Coronaviruses (CoVs) are enveloped (+) ssRNA viruses of veterinary and medical importance. Because recombinant CoVs with reporter proteins fused with viral proteins are usually non-viable or unstable, a small and quantifiable epitope tag would be beneficial to CoV research. In this study, we integrated the NanoLuc Binary Technology to the reverse genetics of infectious bronchitis virus (IBV), a prototypic gammacoronavirus. The 11-amino-acid HiBiT tag was inserted to the spike (S) or membrane (M) protein, and the recombinant IBVs (rS-HiBiT and rM-HiBiT) were characterized. Compared with the rIBV-p65 control, rS-HiBiT exhibited comparable growth kinetics, whereas rM-HiBiT replicated slightly slower. The levels of HiBiT-tagged S and M proteins in the infected cells or the culture supernatant could be both rapidly (~15 min) and efficiently (30 μL sample volume) determined using the HiBiT luminescence assay. Notably, replication of the HiBiT-tagged IBV could be monitored continuously in an infected chicken embryo, and rS-HiBiT was genetically stable for at least 20 passages. By integrating the HiBiT tagging system with CoV reverse genetics, this new reporter system may facilitate future study of CoV replication and pathogenesis.
Collapse
Affiliation(s)
- Xiao Ying Liang
- Guangdong Province Key Laboratory of Microbial Signals & Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Qing Chun Zhu
- Guangdong Province Key Laboratory of Microbial Signals & Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Jia Qi Liang
- Guangdong Province Key Laboratory of Microbial Signals & Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Si Ying Liu
- Guangdong Province Key Laboratory of Microbial Signals & Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Ding Xiang Liu
- Guangdong Province Key Laboratory of Microbial Signals & Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - To Sing Fung
- Guangdong Province Key Laboratory of Microbial Signals & Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| |
Collapse
|
30
|
Artika IM, Dewantari AK, Wiyatno A. Molecular biology of coronaviruses: current knowledge. Heliyon 2020; 6:e04743. [PMID: 32835122 PMCID: PMC7430346 DOI: 10.1016/j.heliyon.2020.e04743] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/13/2020] [Accepted: 08/13/2020] [Indexed: 02/07/2023] Open
Abstract
The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) late December 2019 in Wuhan, China, marked the third introduction of a highly pathogenic coronavirus into the human population in the twenty-first century. The constant spillover of coronaviruses from natural hosts to humans has been linked to human activities and other factors. The seriousness of this infection and the lack of effective, licensed countermeasures clearly underscore the need of more detailed and comprehensive understanding of coronavirus molecular biology. Coronaviruses are large, enveloped viruses with a positive sense single-stranded RNA genome. Currently, coronaviruses are recognized as one of the most rapidly evolving viruses due to their high genomic nucleotide substitution rates and recombination. At the molecular level, the coronaviruses employ complex strategies to successfully accomplish genome expression, virus particle assembly and virion progeny release. As the health threats from coronaviruses are constant and long-term, understanding the molecular biology of coronaviruses and controlling their spread has significant implications for global health and economic stability. This review is intended to provide an overview of our current basic knowledge of the molecular biology of coronaviruses, which is important as basic knowledge for the development of coronavirus countermeasures.
Collapse
Affiliation(s)
- I. Made Artika
- Biosafety Level 3 Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta, 10430, Indonesia
- Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Darmaga Campus, Bogor, 16680, Indonesia
| | - Aghnianditya Kresno Dewantari
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta, 10430, Indonesia
| | - Ageng Wiyatno
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta, 10430, Indonesia
| |
Collapse
|
31
|
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.
Collapse
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.
| |
Collapse
|
32
|
Giri R, Bhardwaj T, Shegane M, Gehi BR, Kumar P, Gadhave K, Oldfield CJ, Uversky VN. Understanding COVID-19 via comparative analysis of dark proteomes of SARS-CoV-2, human SARS and bat SARS-like coronaviruses. Cell Mol Life Sci 2020; 78:1655-1688. [PMID: 32712910 PMCID: PMC7382329 DOI: 10.1007/s00018-020-03603-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/03/2020] [Accepted: 07/17/2020] [Indexed: 01/08/2023]
Abstract
The recently emerged coronavirus designated as SARS-CoV-2 (also known as 2019 novel coronavirus (2019-nCoV) or Wuhan coronavirus) is a causative agent of coronavirus disease 2019 (COVID-19), which is rapidly spreading throughout the world now. More than 1.21 million cases of SARS-CoV-2 infection and more than 67,000 COVID-19-associated mortalities have been reported worldwide till the writing of this article, and these numbers are increasing every passing hour. The World Health Organization (WHO) has declared the SARS-CoV-2 spread as a global public health emergency and admitted COVID-19 as a pandemic now. Multiple sequence alignment data correlated with the already published reports on SARS-CoV-2 evolution indicated that this virus is closely related to the bat severe acute respiratory syndrome-like coronavirus (bat SARS-like CoV) and the well-studied human SARS coronavirus (SARS-CoV). The disordered regions in viral proteins are associated with the viral infectivity and pathogenicity. Therefore, in this study, we have exploited a set of complementary computational approaches to examine the dark proteomes of SARS-CoV-2, bat SARS-like, and human SARS CoVs by analysing the prevalence of intrinsic disorder in their proteins. According to our findings, SARS-CoV-2 proteome contains very significant levels of structural order. In fact, except for nucleocapsid, Nsp8, and ORF6, the vast majority of SARS-CoV-2 proteins are mostly ordered proteins containing less intrinsically disordered protein regions (IDPRs). However, IDPRs found in SARS-CoV-2 proteins are functionally important. For example, cleavage sites in its replicase 1ab polyprotein are found to be highly disordered, and almost all SARS-CoV-2 proteins contains molecular recognition features (MoRFs), which are intrinsic disorder-based protein–protein interaction sites that are commonly utilized by proteins for interaction with specific partners. The results of our extensive investigation of the dark side of SARS-CoV-2 proteome will have important implications in understanding the structural and non-structural biology of SARS or SARS-like coronaviruses.
Collapse
Affiliation(s)
- Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Mandi, Himachal Pradesh, 175005, India.
| | - Taniya Bhardwaj
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Mandi, Himachal Pradesh, 175005, India
| | - Meenakshi Shegane
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Mandi, Himachal Pradesh, 175005, India
| | - Bhuvaneshwari R Gehi
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Mandi, Himachal Pradesh, 175005, India
| | - Prateek Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Mandi, Himachal Pradesh, 175005, India
| | - Kundlik Gadhave
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Mandi, Himachal Pradesh, 175005, India
| | | | - Vladimir N Uversky
- Department of Molecular Medicine, Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Moscow region, Pushchino, 142290, Russia
| |
Collapse
|
33
|
Research Progress of Coronavirus Based on Bibliometric Analysis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17113766. [PMID: 32466477 PMCID: PMC7312058 DOI: 10.3390/ijerph17113766] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/10/2020] [Accepted: 05/23/2020] [Indexed: 01/08/2023]
Abstract
Background: COVID-19 has become one of the most serious global epidemics in the 21st Century. This study aims to explore the distribution of research capabilities of countries, institutions, and researchers, and the hotspots and frontiers of coronavirus research in the past two decades. In it, references for funding support of urgent projects and international cooperation among research institutions are provided. Method: the Web of Science core collection database was used to retrieve the documents related to coronavirus published from 2003 to 2020. Citespace.5.6.R2, VOSviewer1.6.12, and Excel 2016 were used for bibliometric analysis. Results: 11,036 documents were retrieved, of which China and the United States have contributed the most coronavirus studies, Hong Kong University being the top contributor. Regarding journals, the Journal of Virology has contributed the most, while in terms of researchers, Yuen Kwok Yung has made the most contributions. The proportion of documents published by international cooperation has been rising for decades. Vaccines for SARS-CoV-2 are under development, and clinical trials of several drugs are ongoing. Conclusions: international cooperation is an important way to accelerate research progress and achieve success. Developing corresponding vaccines and drugs are the current hotspots and research directions.
Collapse
|
34
|
Saber-Ayad M, Saleh MA, Abu-Gharbieh E. The Rationale for Potential Pharmacotherapy of COVID-19. Pharmaceuticals (Basel) 2020; 13:E96. [PMID: 32423024 PMCID: PMC7281404 DOI: 10.3390/ph13050096] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/09/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022] Open
Abstract
On 11 March 2020, the coronavirus disease (COVID-19) was defined by the World Health Organization as a pandemic. Severe acute respiratory syndrome-2 (SARS-CoV-2) is the newly evolving human coronavirus infection that causes COVID-19, and it first appeared in Wuhan, China in December 2019 and spread rapidly all over the world. COVID-19 is being increasingly investigated through virology, epidemiology, and clinical management strategies. There is currently no established consensus on the standard of care in the pharmacological treatment of COVID-19 patients. However, certain medications suggested for other diseases have been shown to be potentially effective for treating this infection, though there has yet to be clear evidence. Therapies include new agents that are currently tested in several clinical trials, in addition to other medications that have been repurposed as antiviral and immune-modulating therapies. Previous high-morbidity human coronavirus epidemics such as the 2003 SARS-CoV and the 2012 Middle East respiratory syndrome coronavirus (MERS-CoV) prompted the identification of compounds that could theoretically be active against the emerging coronavirus SARS-CoV-2. Moreover, advances in molecular biology techniques and computational analysis have allowed for the better recognition of the virus structure and the quicker screening of chemical libraries to suggest potential therapies. This review aims to summarize rationalized pharmacotherapy considerations in COVID-19 patients in order to serve as a tool for health care professionals at the forefront of clinical care during this pandemic. All the reviewed therapies require either additional drug development or randomized large-scale clinical trials to be justified for clinical use.
Collapse
Affiliation(s)
- Maha Saber-Ayad
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah 27272, UAE; (M.A.S.); (E.A.-G.)
- College of Medicine, Cairo University, Cairo 12613, Egypt
| | - Mohamed A. Saleh
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah 27272, UAE; (M.A.S.); (E.A.-G.)
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Eman Abu-Gharbieh
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah 27272, UAE; (M.A.S.); (E.A.-G.)
| |
Collapse
|
35
|
Perrier A, Bonnin A, Desmarets L, Danneels A, Goffard A, Rouillé Y, Dubuisson J, Belouzard S. The C-terminal domain of the MERS coronavirus M protein contains a trans-Golgi network localization signal. J Biol Chem 2019; 294:14406-14421. [PMID: 31399512 PMCID: PMC6768645 DOI: 10.1074/jbc.ra119.008964] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 08/06/2019] [Indexed: 11/23/2022] Open
Abstract
Coronavirus M proteins represent the major protein component of the viral
envelope. They play an essential role during viral assembly by interacting with
all of the other structural proteins. Coronaviruses bud into the endoplasmic
reticulum (ER)–Golgi intermediate compartment (ERGIC), but the mechanisms
by which M proteins are transported from their site of synthesis, the ER, to the
budding site remain poorly understood. Here, we investigated the intracellular
trafficking of the Middle East respiratory syndrome coronavirus (MERS-CoV) M
protein. Subcellular localization analyses revealed that the MERS-CoV M protein
is retained intracellularly in the trans-Golgi network (TGN),
and we identified two motifs in the distal part of the C-terminal domain as
being important for this specific localization. We identified the first motif as
a functional diacidic DxE ER export signal, because substituting Asp-211 and
Glu-213 with alanine induced retention of the MERS-CoV M in the ER. The second
motif, 199KxGxYR204, was responsible for retaining the M
protein in the TGN. Substitution of this motif resulted in MERS-CoV M leakage
toward the plasma membrane. We further confirmed the role of
199KxGxYR204 as a TGN retention signal by using
chimeras between MERS-CoV M and the M protein of infectious bronchitis virus
(IBV). Our results indicated that the C-terminal domains of both proteins
determine their specific localization, namely TGN and
ERGIC/cis-Golgi for MERS-M and IBV-M, respectively. Our
findings indicate that MERS-CoV M protein localizes to the TGN because of the
combined presence of an ER export signal and a TGN retention motif.
Collapse
Affiliation(s)
- Anabelle Perrier
- Université Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Ariane Bonnin
- Université Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Lowiese Desmarets
- Université Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Adeline Danneels
- Université Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Anne Goffard
- Université Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Yves Rouillé
- Université Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Jean Dubuisson
- Université Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Sandrine Belouzard
- Université Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France
| |
Collapse
|
36
|
Wang SM, Huang KJ, Wang CT. Severe acute respiratory syndrome coronavirus spike protein counteracts BST2-mediated restriction of virus-like particle release. J Med Virol 2019; 91:1743-1750. [PMID: 31199522 PMCID: PMC7166632 DOI: 10.1002/jmv.25518] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/08/2019] [Indexed: 12/12/2022]
Abstract
BST2/tetherin, an interferon‐inducible antiviral factor, can block the cellular release of various enveloped viruses. We previously reported that human coronavirus 229E (HCoV‐229E) infection can alleviate the BST2 tethering of HIV‐1 virions by downregulating cell surface BST2, suggesting that coronaviruses are capable of encoding anti‐BST2 factors. Here we report our new finding that severe acute respiratory syndrome coronavirus (SARS‐CoV) spike (S) glycoprotein, similar to Vpu, is capable of antagonizing the BST2 tethering of SARS‐CoV, HCoV‐229E, and HIV‐1 virus‐like particles via BST2 downregulation. However, unlike Vpu (which downmodulates BST2 by means of proteasomal and lysosomal degradation pathways), BST2 downregulation is apparently mediated by SARS‐CoV S through the lysosomal degradation pathway only. We found that SARS‐CoV S colocalized with both BST2 and reduced cell surface BST2, suggesting an association between SARS‐CoV S and BST2 that targets the lysosomal degradation pathway. According to one recent report, SARS‐CoV ORF7a antagonizes BST2 by interfering with BST2 glycosylation1. Our data provide support for the proposal that SARS‐CoV and other enveloped viruses are capable of evolving supplementary anti‐BST2 factors in a manner that requires virus replication. Further experiments are required to determine whether the BST2‐mediated restriction of authentic SARS‐CoV virions is alleviated by the SARS‐CoV spike protein. BST2/tetherin inhibits the release of various enveloped viruses. SARS‐CoV S antagonizes the BST2 tethering of human coronavirus and HIV‐1 virus‐like particles. SARS‐CoV S colocalizes with BST2 and reduces cell surface BST2. SARS‐CoV S downregulates BST2 through lysosomal degradation pathway.
Collapse
Affiliation(s)
- Shiu-Mei Wang
- Department of Medical Research, Taipei Veterans General Hospital and Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Kuo-Jung Huang
- Department of Medical Research, Taipei Veterans General Hospital and Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Chin-Tien Wang
- Department of Medical Research, Taipei Veterans General Hospital and Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| |
Collapse
|
37
|
J Alsaadi EA, Jones IM. Membrane binding proteins of coronaviruses. Future Virol 2019; 14:275-286. [PMID: 32201500 PMCID: PMC7079996 DOI: 10.2217/fvl-2018-0144] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 02/19/2019] [Indexed: 12/12/2022]
Abstract
Coronaviruses (CoVs) infect many species causing a variety of diseases with a range of severities. Their members include zoonotic viruses with pandemic potential where therapeutic options are currently limited. Despite this diversity CoVs share some common features including the production, in infected cells, of elaborate membrane structures. Membranes represent both an obstacle and aid to CoV replication - and in consequence - virus-encoded structural and nonstructural proteins have membrane-binding properties. The structural proteins encounter cellular membranes at both entry and exit of the virus while the nonstructural proteins reorganize cellular membranes to benefit virus replication. Here, the role of each protein in membrane binding is described to provide a comprehensive picture of their role in the CoV replication cycle.
Collapse
Affiliation(s)
- Entedar A J Alsaadi
- Biomedical Sciences, School of Biological Sciences, University of Reading, Reading RG6 6AJ, UK.,Department of Microbiology, College of Medicine, Thiqar University, Thiqar, Iraq.,Biomedical Sciences, School of Biological Sciences, University of Reading, Reading RG6 6AJ, UK.,Department of Microbiology, College of Medicine, Thiqar University, Thiqar, Iraq
| | - Ian M Jones
- Biomedical Sciences, School of Biological Sciences, University of Reading, Reading RG6 6AJ, UK.,Biomedical Sciences, School of Biological Sciences, University of Reading, Reading RG6 6AJ, UK
| |
Collapse
|
38
|
Hou L, Liu Y, Gao Q, Xu X, Ning M, Bi J, Liu H, Liu M, Gu W, Wang W, Meng Q. Spiroplasma eriocheiris Adhesin-Like Protein (ALP) Interacts with Epidermal Growth Factor (EGF) Domain Proteins to Facilitate Infection. Front Cell Infect Microbiol 2017; 7:13. [PMID: 28184355 PMCID: PMC5266718 DOI: 10.3389/fcimb.2017.00013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 01/10/2017] [Indexed: 12/20/2022] Open
Abstract
Spiroplasma eriocheiris is a novel pathogen found in recent years, causing the tremor disease (TD) of Chinese mitten crab Eriocheir sinensis. Like Spiroplasma mirum, S. eriocheiris infects the newborn mouse (adult mice are not infected) and can cause cataract. Adhesion-related protein is an important protein involved in the interaction between pathogen and host. In this study, the Adhesin-like Protein (ALP) of S. eriocheiris was detected on its outer membrane by using immune electron microscopy, and was found to be involved in the bacterium's infection of mouse embryo fibroblasts (3T6-Swiss albino). Yeast two-hybrid analysis demonstrated that ALP interacts with a diverse group of mouse proteins. The interactions between recombinant partial fibulin7 (FBLN7; including two epidermal growth factor [EGF] domains) and ALP were confirmed by Far-western blotting and colocalization. We synthetized the domains of FBLN7 [EGF domain: amino acids 136–172 and complement control protein (CCP) domain: 81–134 amino acids], and demonstrated that only EGF domain of FBLN7 can interact with ALP. Because the EGF domain has high degree of similarity to EGF, it can activate the downstream EGFR signaling pathway, in key site amino acids. The EGFR pathway in 3T6 cells was restrained after rALP stimulation resulting from competitive binding of ALP to EGF. The unborn mouse, newborn mouse, and the adult mouse with cataract have a small amount of expressed FBLN7; however, none was detected in the brain and very little expression was seen in the eye of normal adult mice. In short, ALP as a S. eriocheiris surface protein, is critical for infection and further supports the role of ALP in S. eriocheiris infection by competitive effection of the EGF/EGFR axis of the target cells.
Collapse
Affiliation(s)
- Libo Hou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University Nanjing, China
| | - Yuhan Liu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University Nanjing, China
| | - Qi Gao
- Jiangsu Key Laboratory for Biodiversity and Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University Nanjing, China
| | - Xuechuan Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University Nanjing, China
| | - Mingxiao Ning
- Jiangsu Key Laboratory for Biodiversity and Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University Nanjing, China
| | - Jingxiu Bi
- Jiangsu Key Laboratory for Biodiversity and Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University Nanjing, China
| | - Hui Liu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University Nanjing, China
| | - Min Liu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University Nanjing, China
| | - Wei Gu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal UniversityNanjing, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu ProvinceLianYungang, China
| | - Wen Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University Nanjing, China
| | - Qingguo Meng
- Jiangsu Key Laboratory for Biodiversity and Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal UniversityNanjing, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu ProvinceLianYungang, China
| |
Collapse
|
39
|
Characterization of an Immunodominant Epitope in the Endodomain of the Coronavirus Membrane Protein. Viruses 2016; 8:v8120327. [PMID: 27973413 PMCID: PMC5192388 DOI: 10.3390/v8120327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 11/26/2016] [Accepted: 12/06/2016] [Indexed: 11/17/2022] Open
Abstract
The coronavirus membrane (M) protein acts as a dominant immunogen and is a major player in virus assembly. In this study, we prepared two monoclonal antibodies (mAbs; 1C3 and 4C7) directed against the transmissible gastroenteritis virus (TGEV) M protein. The 1C3 and 4C7 mAbs both reacted with the native TGEV M protein in western blotting and immunofluorescence (IFA) assays. Two linear epitopes, 243YSTEART249 (1C3) and 243YSTEARTDNLSEQEKLLHMV262 (4C7), were identified in the endodomain of the TGEV M protein. The 1C3 mAb can be used for the detection of the TGEV M protein in different assays. An IFA method for the detection of TGEV M protein was optimized using mAb 1C3. Furthermore, the ability of the epitope identified in this study to stimulate antibody production was also evaluated. An immunodominant epitope in the TGEV membrane protein endodomain was identified. The results of this study have implications for further research on TGEV replication.
Collapse
|
40
|
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.
Collapse
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
| |
Collapse
|
41
|
The Membrane Protein of Severe Acute Respiratory Syndrome Coronavirus Functions as a Novel Cytosolic Pathogen-Associated Molecular Pattern To Promote Beta Interferon Induction via a Toll-Like-Receptor-Related TRAF3-Independent Mechanism. mBio 2016; 7:e01872-15. [PMID: 26861016 PMCID: PMC4752600 DOI: 10.1128/mbio.01872-15] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Most of the intracellular pattern recognition receptors (PRRs) reside in either the endolysosome or the cytoplasm to sense pathogen-derived RNAs, DNAs, or synthetic analogs of double-stranded RNA (dsRNA), such as poly(I:C). However, it remains elusive whether or not a pathogen-derived protein can function as a cytosolic pathogen-associated molecular pattern (PAMP). In this study, we demonstrate that delivering the membrane gene of severe acute respiratory syndrome coronavirus (SARS-CoV) into HEK293T, HEK293ET, and immobilized murine bone marrow-derived macrophage (J2-Mφ) cells significantly upregulates beta interferon (IFN-β) production. Both NF-κB and TBK1-IRF3 signaling cascades are activated by M gene products. M protein rather than M mRNA is responsible for M-mediated IFN-β induction that is preferentially associated with the activation of the Toll-like receptor (TLR) adaptor proteins MyD88, TIRAP, and TICAM2 but not the RIG-I signaling cascade. Blocking the secretion of M protein by brefeldin A (BFA) failed to reverse the M-mediated IFN-β induction. The antagonist of both TLR2 and TLR4 did not impede M-mediated IFN-β induction, indicating that the driving force for the activation of IFN-β production was generated from inside the cells. Inhibition of TRAF3 expression by specific small interfering RNA (siRNA) did not prevent M-mediated IFN-β induction. SARS-CoV pseudovirus could induce IFN-β production in an M rather than M(V68A) dependent manner, since the valine-to-alanine alteration at residue 68 in M protein markedly inhibited IFN-β production. Overall, our study indicates for the first time that a pathogen-derived protein is able to function as a cytosolic PAMP to stimulate type I interferon production by activating a noncanonical TLR signaling cascade in a TRAF3-independent manner. Viral protein can serve as a pathogen-associated molecular pattern (PAMP) that is usually recognized by certain pathogen recognition receptors (PRRs) on the cell surface, such as Toll-like receptor 2 (TLR2) and TLR4. In this study, we demonstrate that the membrane (M) protein of SARS-CoV can directly promote the activation of both beta interferon (IFN-β) and NF-κB through a TLR-related signaling pathway independent of TRAF3. The driving force for M-mediated IFN-β production is most likely generated from inside the cells. M-mediated IFN-β induction was confirmed at the viral infection level since a point mutation at the V68 residue of M markedly inhibited SARS-CoV pseudovirally induced IFN-β production. Thus, the results indicate for the first time that SARS-CoV M protein may function as a cytosolic PAMP to stimulate IFN-β production by activating a TLR-related TRAF3-independent signaling cascade.
Collapse
|
42
|
Demurtas OC, Massa S, Illiano E, De Martinis D, Chan PKS, Di Bonito P, Franconi R. Antigen Production in Plant to Tackle Infectious Diseases Flare Up: The Case of SARS. FRONTIERS IN PLANT SCIENCE 2016; 7:54. [PMID: 26904039 PMCID: PMC4742786 DOI: 10.3389/fpls.2016.00054] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 01/13/2016] [Indexed: 05/09/2023]
Abstract
Severe acute respiratory syndrome (SARS) is a dangerous infection with pandemic potential. It emerged in 2002 and its aetiological agent, the SARS Coronavirus (SARS-CoV), crossed the species barrier to infect humans, showing high morbidity and mortality rates. No vaccines are currently licensed for SARS-CoV and important efforts have been performed during the first outbreak to develop diagnostic tools. Here we demonstrate the transient expression in Nicotiana benthamiana of two important antigenic determinants of the SARS-CoV, the nucleocapsid protein (N) and the membrane protein (M) using a virus-derived vector or agro-infiltration, respectively. For the M protein, this is the first description of production in plants, while for plant-derived N protein we demonstrate that it is recognized by sera of patients from the SARS outbreak in Hong Kong in 2003. The availability of recombinant N and M proteins from plants opens the way to further evaluation of their potential utility for the development of diagnostic and protection/therapy tools to be quickly manufactured, at low cost and with minimal risk, to face potential new highly infectious SARS-CoV outbreaks.
Collapse
Affiliation(s)
- Olivia C. Demurtas
- Department of Sustainability, Biotechnology Laboratory, Italian National Agency for New Technologies, Energy and Sustainable Economic DevelopmentRome, Italy
| | - Silvia Massa
- Department of Sustainability, Biotechnology Laboratory, Italian National Agency for New Technologies, Energy and Sustainable Economic DevelopmentRome, Italy
| | - Elena Illiano
- Department of Sustainability, Biomedical Technology Laboratory, Italian National Agency for New Technologies, Energy and Sustainable Economic DevelopmentRome, Italy
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di MilanoMilan, Italy
| | - Domenico De Martinis
- International Relations Office, Italian National Agency for New Technologies, Energy and Sustainable Economic DevelopmentRome, Italy
| | - Paul K. S. Chan
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales HospitalHong Kong, China
- Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales HospitalHong Kong, China
| | - Paola Di Bonito
- Istituto Superiore di Sanità, Department of Infectious, Parasitic and Immune-Mediated DiseasesRome, Italy
- *Correspondence: Rosella Franconi, ; Paola Di Bonito,
| | - Rosella Franconi
- Department of Sustainability, Biomedical Technology Laboratory, Italian National Agency for New Technologies, Energy and Sustainable Economic DevelopmentRome, Italy
- *Correspondence: Rosella Franconi, ; Paola Di Bonito,
| |
Collapse
|
43
|
Ujike M, Taguchi F. Incorporation of spike and membrane glycoproteins into coronavirus virions. Viruses 2015; 7:1700-25. [PMID: 25855243 PMCID: PMC4411675 DOI: 10.3390/v7041700] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 03/23/2015] [Accepted: 03/24/2015] [Indexed: 12/15/2022] Open
Abstract
The envelopes of coronaviruses (CoVs) contain primarily three proteins; the two major glycoproteins spike (S) and membrane (M), and envelope (E), a non-glycosylated protein. Unlike other enveloped viruses, CoVs bud and assemble at the endoplasmic reticulum (ER)-Golgi intermediate compartment (ERGIC). For efficient virion assembly, these proteins must be targeted to the budding site and to interact with each other or the ribonucleoprotein. Thus, the efficient incorporation of viral envelope proteins into CoV virions depends on protein trafficking and protein–protein interactions near the ERGIC. The goal of this review is to summarize recent findings on the mechanism of incorporation of the M and S glycoproteins into the CoV virion, focusing on protein trafficking and protein–protein interactions.
Collapse
Affiliation(s)
- Makoto Ujike
- Laboratory of Virology and Viral Infections, Faculty of Veterinary Medicine, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino, Tokyo 180-8602, Japan.
| | - Fumihiro Taguchi
- Laboratory of Virology and Viral Infections, Faculty of Veterinary Medicine, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino, Tokyo 180-8602, Japan.
| |
Collapse
|
44
|
Tseng YT, Wang SM, Huang KJ, Wang CT. SARS-CoV envelope protein palmitoylation or nucleocapid association is not required for promoting virus-like particle production. J Biomed Sci 2014; 21:34. [PMID: 24766657 PMCID: PMC4014084 DOI: 10.1186/1423-0127-21-34] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 04/21/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Coronavirus membrane (M) proteins are capable of interacting with nucleocapsid (N) and envelope (E) proteins. Severe acute respiratory syndrome coronavirus (SARS-CoV) M co-expression with either N or E is sufficient for producing virus-like particles (VLPs), although at a lower level compared to M, N and E co-expression. Whether E can release from cells or E/N interaction exists so as to contribute to enhanced VLP production is unknown. It also remains to be determined whether E palmitoylation or disulfide bond formation plays a role in SARS-CoV virus assembly. RESULTS SARS-CoV N is released from cells through an association with E protein-containing vesicles. Further analysis suggests that domains involved in E/N interaction are largely located in both carboxyl-terminal regions. Changing all three E cysteine residues to alanines did not exert negative effects on E release, E association with N, or E enhancement of VLP production, suggesting that E palmitoylation modification or disulfide bond formation is not required for SARS-CoV virus assembly. We found that removal of the last E carboxyl-terminal residue markedly affected E release, N association, and VLP incorporation, but did not significantly compromise the contribution of E to efficient VLP production. CONCLUSIONS The independence of the SARS-CoV E enhancement effect on VLP production from its viral packaging capacity suggests a distinct SARS-CoV E role in virus assembly.
Collapse
Affiliation(s)
| | | | | | - Chin-Tien Wang
- Department of Medical Research, Taipei Veterans General Hospital, 201, Sec, 2, Shih-Pai Road, Taipei 11217, Taiwan.
| |
Collapse
|
45
|
Assembly and immunogenicity of coronavirus-like particles carrying infectious bronchitis virus M and S proteins. Vaccine 2013; 31:5524-30. [PMID: 24099870 PMCID: PMC7115625 DOI: 10.1016/j.vaccine.2013.09.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 08/27/2013] [Accepted: 09/13/2013] [Indexed: 11/23/2022]
Abstract
We generate IBV VLPs carrying M and S proteins using recombinant baculovirus. The VLPs elicit humoral immune responses comparable to inactivated IBV in mice and chickens. The VLPs elicit higher cellular immune responses than inactivated IBV in mice.
Infectious bronchitis virus (IBV) as an avian coronavirus is still posing a persistent and imminent threat to the poultry industry worldwide. Here we report that transfection of Sf9 cells with a single recombinant baculovirus encoding M and S proteins resulted in the assembly of IBV VLPs; this is the first report that S protein plus M protein alone were able to be assembled into VLPs for coronaviruses. We further showed that the generated IBV VLPs could induce humoral immune responses in a level comparable to that of inactivated IBV vaccine, and more importantly the IBV VLPs could elicit significantly higher cellular immune responses than the inactivated IBV vaccine. In summary, the assembly of IBV VLPs with M and S proteins provided a simple strategy for generating VLPs for coronaviruses, and the generated IBV VLPs laid a feasible foundation for the development of an effective vaccine against infection of IBV in the future.
Collapse
|
46
|
Dantas-Lima JJ, Corteel M, Cornelissen M, Bossier P, Sorgeloos P, Nauwynck HJ. Purification of white spot syndrome virus by iodixanol density gradient centrifugation. JOURNAL OF FISH DISEASES 2013; 36:841-851. [PMID: 23384051 DOI: 10.1111/jfd.12082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 12/07/2012] [Accepted: 12/07/2012] [Indexed: 06/01/2023]
Abstract
Up to now, only a few brief procedures for purifying white spot syndrome virus (WSSV) have been described. They were mainly based on sucrose, NaBr and CsCl density gradient centrifugation. This work describes for the first time the purification of WSSV through iodixanol density gradients, using virus isolated from infected tissues and haemolymph of Penaeus vannamei (Boone). The purification from tissues included a concentration step by centrifugation (2.5 h at 60,000 g) onto a 50% iodixanol cushion and a purification step by centrifugation (3 h at 80,000 g) through a discontinuous iodixanol gradient (phosphate-buffered saline, 5%, 10%, 15% and 20%). The purification from infected haemolymph enclosed a dialysis step with a membrane of 1,000 kDa (18 h) and a purification step through the earlier iodixanol gradient. The gradients were collected in fractions and analysed. The number of particles, infectivity titre (in vivo), total protein and viral protein content were evaluated. The purification from infected tissues gave WSSV suspensions with a very high infectivity and an acceptable purity, while virus purified from haemolymph had a high infectivity and a very high purity. Additionally, it was observed that WSSV has an unusually low buoyant density and that it is very sensitive to high external pressures.
Collapse
Affiliation(s)
- J J Dantas-Lima
- Department of Virology, Parasitology and Immunology, Laboratory of Virology, Ghent University, Merelbeke, Belgium
| | | | | | | | | | | |
Collapse
|
47
|
Schley D, Whittaker RJ, Neuman BW. Arenavirus budding resulting from viral-protein-associated cell membrane curvature. J R Soc Interface 2013; 10:20130403. [PMID: 23864502 PMCID: PMC3730687 DOI: 10.1098/rsif.2013.0403] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Viral replication occurs within cells, with release (and onward infection) primarily achieved through two alternative mechanisms: lysis, in which virions emerge as the infected cell dies and bursts open; or budding, in which virions emerge gradually from a still living cell by appropriating a small part of the cell membrane. Virus budding is a poorly understood process that challenges current models of vesicle formation. Here, a plausible mechanism for arenavirus budding is presented, building on recent evidence that viral proteins embed in the inner lipid layer of the cell membrane. Experimental results confirm that viral protein is associated with increased membrane curvature, whereas a mathematical model is used to show that localized increases in curvature alone are sufficient to generate viral buds. The magnitude of the protein-induced curvature is calculated from the size of the amphipathic region hypothetically removed from the inner membrane as a result of translation, with a change in membrane stiffness estimated from observed differences in virion deformation as a result of protein depletion. Numerical results are based on experimental data and estimates for three arenaviruses, but the mechanisms described are more broadly applicable. The hypothesized mechanism is shown to be sufficient to generate spontaneous budding that matches well both qualitatively and quantitatively with experimental observations.
Collapse
Affiliation(s)
- David Schley
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK.
| | | | | |
Collapse
|
48
|
Identifying SARS-CoV membrane protein amino acid residues linked to virus-like particle assembly. PLoS One 2013; 8:e64013. [PMID: 23700447 PMCID: PMC3659117 DOI: 10.1371/journal.pone.0064013] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 04/07/2013] [Indexed: 01/05/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV) membrane (M) proteins are capable of self-assembly and release in the form of membrane-enveloped vesicles, and of forming virus-like particles (VLPs) when coexpressed with SARS-CoV nucleocapsid (N) protein. According to previous deletion analyses, M self-assembly involves multiple M sequence regions. To identify important M amino acid residues for VLP assembly, we coexpressed N with multiple M mutants containing substitution mutations at the amino-terminal ectodomain, carboxyl-terminal endodomain, or transmembrane segments. Our results indicate that a dileucine motif in the endodomain tail (218LL219) is required for efficient N packaging into VLPs. Results from cross-linking VLP analyses suggest that the cysteine residues 63, 85 and 158 are not in close proximity to the M dimer interface. We noted a significant reduction in M secretion due to serine replacement for C158, but not for C63 or C85. Further analysis suggests that C158 is involved in M-N interaction. In addition to mutations of the highly conserved 107-SWWSFNPE-114 motif, substitutions at codons W19, W57, P58, W91, Y94 or F95 all resulted in significantly reduced VLP yields, largely due to defective M secretion. VLP production was not significantly affected by a tryptophan replacement of Y94 or F95 or a phenylalanine replacement of W19, W57 or W91. Combined, these results indicate the involvement of specific M amino acids during SARS-CoV virus assembly, and suggest that aromatic residue retention at specific positions is critical for M function in terms of directing virus assembly.
Collapse
|
49
|
Kushnir N, Streatfield SJ, Yusibov V. Virus-like particles as a highly efficient vaccine platform: diversity of targets and production systems and advances in clinical development. Vaccine 2012; 31:58-83. [PMID: 23142589 PMCID: PMC7115575 DOI: 10.1016/j.vaccine.2012.10.083] [Citation(s) in RCA: 401] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 10/13/2012] [Accepted: 10/25/2012] [Indexed: 12/16/2022]
Abstract
Virus-like particles (VLPs) are a class of subunit vaccines that differentiate themselves from soluble recombinant antigens by stronger protective immunogenicity associated with the VLP structure. Like parental viruses, VLPs can be either non-enveloped or enveloped, and they can form following expression of one or several viral structural proteins in a recombinant heterologous system. Depending on the complexity of the VLP, it can be produced in either a prokaryotic or eukaryotic expression system using target-encoding recombinant vectors, or in some cases can be assembled in cell-free conditions. To date, a wide variety of VLP-based candidate vaccines targeting various viral, bacterial, parasitic and fungal pathogens, as well as non-infectious diseases, have been produced in different expression systems. Some VLPs have entered clinical development and a few have been licensed and commercialized. This article reviews VLP-based vaccines produced in different systems, their immunogenicity in animal models and their status in clinical development.
Collapse
Affiliation(s)
- Natasha Kushnir
- Fraunhofer USA Center for Molecular Biotechnology, Newark, DE 19711, USA
| | | | | |
Collapse
|
50
|
The coronavirus E protein: assembly and beyond. Viruses 2012; 4:363-82. [PMID: 22590676 PMCID: PMC3347032 DOI: 10.3390/v4030363] [Citation(s) in RCA: 187] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2011] [Revised: 02/18/2012] [Accepted: 02/27/2012] [Indexed: 12/14/2022] Open
Abstract
The coronavirus E protein is a small membrane protein that has an important role in the assembly of virions. Recent studies have indicated that the E protein has functions during infection beyond assembly, including in virus egress and in the host stress response. Additionally, the E protein has ion channel activity, interacts with host proteins, and may have multiple membrane topologies. The goal of this review is to highlight the properties and functions of the E protein, and speculate on how they may be related.
Collapse
|