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Allen JD, Ivory D, Ge Song S, He WT, Capozzola T, Yong P, Burton DR, Andrabi R, Crispin M. The diversity of the glycan shield of sarbecoviruses closely related to SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.08.24.505118. [PMID: 36052375 PMCID: PMC9435400 DOI: 10.1101/2022.08.24.505118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The animal reservoirs of sarbecoviruses represent a significant risk of emergent pandemics, as evidenced by the impact of SARS-CoV-2. Vaccines remain successful at limiting severe disease and death, however the continued emergence of SARS-CoV-2 variants, together with the potential for further coronavirus zoonosis, motivates the search for pan-coronavirus vaccines that induce broadly neutralizing antibodies. This necessitates a better understanding of the glycan shields of coronaviruses, which can occlude potential antibody epitopes on spike glycoproteins. Here, we compare the structure of several sarbecovirus glycan shields. Many N-linked glycan attachment sites are shared by all sarbecoviruses, and the processing state of certain sites is highly conserved. However, there are significant differences in the processing state at several glycan sites that surround the receptor binding domain. Our studies reveal similarities and differences in the glycosylation of sarbecoviruses and show how subtle changes in the protein sequence can have pronounced impacts on the glycan shield.
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Affiliation(s)
- Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Dylan Ivory
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Sophie Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Wan-Ting He
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tazio Capozzola
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Peter Yong
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 13 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
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Ouologuem DT, Maiga FO, Dara A, Djimdé A, Traore DAK, Nji E. Hands-on training in structural biology, a tool for sustainable development in Africa series 4. Biol Open 2022; 11:276295. [PMID: 35972051 PMCID: PMC9411641 DOI: 10.1242/bio.059487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Structural biology is an essential tool for understanding the molecular basis of diseases, which can guide the rational design of new drugs, vaccines, and the optimisation of existing medicines. However, most African countries do not conduct structural biology research due to limited resources, lack of trained persons, and an exodus of skilled scientists. The most urgent requirement is to build on the emerging centres in Africa – some well-established, others growing. This can be achieved through workshops that improve networking, grow skills, and develop mechanisms for access to light source beamlines for defining X-ray structures across the continent. These would encourage the growth of structural biology, which is central to understanding biological functions and developing new antimicrobials and other drugs. In this light, a hands-on training workshop in structural biology series 4 was organised by BioStruct-Africa and the Malaria Research and Training Center (MRTC) in Bamako, Mali, to help bridge this gap. The workshop was hosted by MRTC from the 25th to 28th of April 2022. Through a series of lectures and practicals, the workshop enlightened the participants on how structural biology can be utilised to find solutions to the prevalent diseases in Africa. The short training gave them an overview of target selection, protein production and purification, structural determination techniques, and analysis in combination with high-throughput, structure-guided, fragment-based drug design. Summary: BioStruct-Africa has been building capacity in structural biology for Africa-based biologists and researchers.
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Affiliation(s)
- Dinkorma T Ouologuem
- Malaria Research and Training Center, Department of Epidemiology of Parasitic Diseases, Faculty of Pharmacy, University of Science, Techniques, and Technologies of Bamako, Bamako BP 1805, Mali
| | - Fatoumata O Maiga
- Malaria Research and Training Center, Department of Epidemiology of Parasitic Diseases, Faculty of Pharmacy, University of Science, Techniques, and Technologies of Bamako, Bamako BP 1805, Mali
| | - Antoine Dara
- Malaria Research and Training Center, Department of Epidemiology of Parasitic Diseases, Faculty of Pharmacy, University of Science, Techniques, and Technologies of Bamako, Bamako BP 1805, Mali
| | - Abdoulaye Djimdé
- Malaria Research and Training Center, Department of Epidemiology of Parasitic Diseases, Faculty of Pharmacy, University of Science, Techniques, and Technologies of Bamako, Bamako BP 1805, Mali
| | - Daouda A K Traore
- BioStruct-Africa, 14343 Vårby, Stockholm, Sweden.,Faculty of Natural Sciences, School of Life Sciences, Keele University, Staffordshire ST5 5BG, UK.,Life Sciences Group, Institute Laue Langevin, Grenoble 38000, France.,Faculté des Sciences et Techniques, University of Science, Techniques, and Technologies of Bamako, Bamako BP E423, Mali.,Infection Program, Biomedicine Discovery Institute, Departments of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Victoria, Australia
| | - Emmanuel Nji
- BioStruct-Africa, 14343 Vårby, Stockholm, Sweden.,Centre for Research in Therapeutic Sciences (CREATES), Strathmore University, Madaraka Estate, Ole Sangale Road, 59857-00200, Nairobi, Kenya
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3
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Farhadian S, Heidari-Soureshjani E, Hashemi-Shahraki F, Hasanpour-Dehkordi A, Uversky VN, Shirani M, Shareghi B, Sadeghi M, Pirali E, Hadi-Alijanvand S. Identification of SARS-CoV-2 surface therapeutic targets and drugs using molecular modeling methods for inhibition of the virus entry. J Mol Struct 2022; 1256:132488. [PMID: 35125515 PMCID: PMC8797986 DOI: 10.1016/j.molstruc.2022.132488] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 12/24/2021] [Accepted: 01/24/2022] [Indexed: 01/02/2023]
Abstract
Although COVID-19 emerged as a major concern to public health around the world, no licensed medication has been found as of yet to efficiently stop the virus spread and treat the infection. The SARS-CoV-2 entry into the host cell is driven by the direct interaction of the S1 domain with the ACE-2 receptor followed by conformational changes in the S2 domain, as a result of which fusion peptide is inserted into the target cell membrane, and the fusion process is mediated by the specific interactions between the heptad repeats 1 and 2 (HR1 and HR2) that form the six-helical bundle. Since blocking this interaction between HRs stops virus fusion and prevents its subsequent replication, the HRs inhibitors can be used as anti-COVID drugs. The initial drug selection is based on existing molecular databases to screen for molecules that may have a therapeutic effect on coronavirus. Based on these premises, we chose two approved drugs to investigate their interactions with the HRs (based on docking methods). To this end, molecular dynamics simulations and molecular docking were carried out to investigate the changes in the structure of the SARS-CoV-2 spike protein. Our results revealed, cefpiramide has the highest affinity to S protein, thereby revealing its potential to become an anti-COVID-19 clinical medicine. Therefore, this study offers new ways to re-use existing drugs to combat SARS-CoV-2 infection.
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Affiliation(s)
- Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, P. O. Box.115, Shahrekord, Iran
- Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Ehsan Heidari-Soureshjani
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Fatemeh Hashemi-Shahraki
- Department of Biology, Faculty of Science, Shahrekord University, P. O. Box.115, Shahrekord, Iran
- Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Ali Hasanpour-Dehkordi
- Social Determinants of Health Research Center, School of allied medical sciences, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Majid Shirani
- Department of Urology, Shahrekord University of Medical Science, Shahrekord, Iran
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, P. O. Box.115, Shahrekord, Iran
- Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Mehraban Sadeghi
- Department of Environmental Health Engineering Shahrekord University of Medical Science, Shahrekord, Iran
| | - Esmaeil Pirali
- Aquatic Animal Diseases, Department of Fisheries, Faculty of natural Science, Shahrekord University, Iran
| | - Saeid Hadi-Alijanvand
- Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
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4
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Adashi EY, Cohen IG. CRISPR immunity: a case study for justified somatic genetic modification? JOURNAL OF MEDICAL ETHICS 2022; 48:83-85. [PMID: 33658335 DOI: 10.1136/medethics-2020-106838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 01/25/2021] [Accepted: 02/05/2021] [Indexed: 06/12/2023]
Abstract
The current SARS-CoV-2 pandemic has killed thousands across the world. SARS-CoV-2 is the latest but surely not the last such global pandemic we will face. The biomedical response to such pandemics includes treatment, vaccination, and so on. In this paper, though, we argue that it is time to consider an additional strategy: the somatic (non-heritable) enhancement of human immunity. We argue for this approach and consider bioethics objections we believe can be overcome.
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Affiliation(s)
- Eli Y Adashi
- Medical Science, Brown University, Providence, Rhode Island, USA
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5
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Park JJ, Chen S. Metaviromic identification of discriminative genomic features in SARS-CoV-2 using machine learning. PATTERNS 2022; 3:100407. [PMID: 34812427 PMCID: PMC8598947 DOI: 10.1016/j.patter.2021.100407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/12/2021] [Accepted: 11/11/2021] [Indexed: 01/18/2023]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has become a major threat across the globe. Here, we developed machine learning approaches to identify key pathogenic regions in coronavirus genomes. We trained and evaluated 7,562,625 models on 3,665 genomes including SARS-CoV-2, MERS-CoV, SARS-CoV, and other coronaviruses of human and animal origins to return quantitative and biologically interpretable signatures at nucleotide and amino acid resolutions. We identified hotspots across the SARS-CoV-2 genome, including previously unappreciated features in spike, RdRp, and other proteins. Finally, we integrated pathogenicity genomic profiles with B cell and T cell epitope predictions for enrichment of sequence targets to help guide vaccine development. These results provide a systematic map of predicted pathogenicity in SARS-CoV-2 that incorporates sequence, structural, and immunologic features, providing an unbiased collection of genetic elements for functional studies. This metavirome-based framework can also be applied for rapid characterization of new coronavirus strains or emerging pathogenic viruses. Machine learning identifies discriminative signatures in coronavirus genomes Hotspots in key viral proteins have evolutionary and structural significance Integration of hotspots with B cell and T cell epitopes identify joint features Hotspots correlate with emerging variants of concern for mutation prioritization
Identifying which genomic regions of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus are pathogenic remains a major challenge in COVID-19 research. However, there is currently a lack of systematic and unbiased methods for such functional characterization. In this study, we set up a machine learning-based approach to identify which genomic regions distinguish SARS-CoV-2 and other high case fatality rate coronaviruses from other coronaviruses. Discriminative scores were obtained for every nucleotide in the SARS-CoV-2 genome. We then performed a series of evolutionary and structural analyses of candidate hotspots, as well as integrative analyses with predicted B cell and T cell epitopes and emerging variants of concern. Our approach can be extended to other viral genomes or microbial pathogens to gain insights on which sequence features are pathogenic or immunogenic.
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6
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Makky S, Dawoud A, Safwat A, Abdelsattar AS, Rezk N, El-Shibiny A. The bacteriophage decides own tracks: When they are with or against the bacteria. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100050. [PMID: 34841341 PMCID: PMC8610337 DOI: 10.1016/j.crmicr.2021.100050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/09/2021] [Accepted: 07/20/2021] [Indexed: 11/18/2022] Open
Abstract
Bacteriophages, bacteria-infecting viruses, are considered by many researchers a promising solution for antimicrobial resistance. On the other hand, some phages have shown contribution to bacterial resistance phenomenon by transducing antimicrobial resistance genes to their bacterial hosts. Contradictory consequences of infections are correlated to different phage lifecycles. Out of four known lifecycles, lysogenic and lytic pathways have been riddles since the uncontrolled conversion between them could negatively affect the intended use of phages. However, phages still can be engineered for applications against bacterial and viral infections to ensure high efficiency. This review highlights two main aspects: (1) the different lifecycles as well as the different factors that affect lytic-lysogenic switch are discussed, including the intracellular and molecular factors control this decision. In addition, different models which describe the effect of phages on the ecosystem are compared, besides the approaches to study the switch. (2) An overview on the contribution of the phage in the evolution of the bacteria, instead of eating them, as a consequence of different mode of actions. As well, how phage display has helped in restricting phage cheating and how it could open new gates for immunization and pandemics control will be tacked.
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Affiliation(s)
- Salsabil Makky
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578, Egypt
| | - Alyaa Dawoud
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578, Egypt
- Faculty of Pharmacy and Biotechnology, German University in Cairo, New Cairo, 16482, Egypt
| | - Anan Safwat
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578, Egypt
| | - Abdallah S. Abdelsattar
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578, Egypt
- Center for X-Ray and Determination of Structure of Matter, Zewail City of Science and Technology, October Gardens, 6th of October, Giza, 12578, Egypt
| | - Nouran Rezk
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578, Egypt
| | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578, Egypt
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7
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Sarkar A, Mandal K. Repurposing an Antiviral Drug against SARS‐CoV‐2 Main Protease. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Arighna Sarkar
- TIFR Centre for Interdisciplinary Sciences Tata Institute of Fundamental Research Hyderabad 36/p Gopanpally Hyderabad Telangana 500046 India
| | - Kalyaneswar Mandal
- TIFR Centre for Interdisciplinary Sciences Tata Institute of Fundamental Research Hyderabad 36/p Gopanpally Hyderabad Telangana 500046 India
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8
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Sarkar A, Mandal K. Repurposing an Antiviral Drug against SARS-CoV-2 Main Protease. Angew Chem Int Ed Engl 2021; 60:23492-23494. [PMID: 34545983 PMCID: PMC8652770 DOI: 10.1002/anie.202107481] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Indexed: 01/05/2023]
Abstract
This article highlights recent pioneering work by Günther et al. towards the discovery of potential repurposed antiviral compounds (peptidomimetic and non-peptidic) against the SARS-CoV-2 main protease (Mpro ). The antiviral activity of the most potent drugs is discussed along with their binding mode to Mpro as observed through X-ray crystallographic screening.
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Affiliation(s)
- Arighna Sarkar
- TIFR Centre for Interdisciplinary SciencesTata Institute of Fundamental Research Hyderabad36/p GopanpallyHyderabadTelangana500046India
| | - Kalyaneswar Mandal
- TIFR Centre for Interdisciplinary SciencesTata Institute of Fundamental Research Hyderabad36/p GopanpallyHyderabadTelangana500046India
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9
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Kuo CW, Yang TJ, Chien YC, Yu PY, Hsu STD, Khoo KH. Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. Glycobiology 2021; 32:60-72. [PMID: 34735575 PMCID: PMC8689840 DOI: 10.1093/glycob/cwab102] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/07/2021] [Accepted: 09/12/2021] [Indexed: 12/23/2022] Open
Abstract
Extensive glycosylation of the spike protein of severe acute respiratory syndrome coronavirus 2 virus not only shields the major part of it from host immune responses, but glycans at specific sites also act on its conformation dynamics and contribute to efficient host receptor binding, and hence infectivity. As variants of concern arise during the course of the coronavirus disease of 2019 pandemic, it is unclear if mutations accumulated within the spike protein would affect its site-specific glycosylation pattern. The Alpha variant derived from the D614G lineage is distinguished from others by having deletion mutations located right within an immunogenic supersite of the spike N-terminal domain (NTD) that make it refractory to most neutralizing antibodies directed against this domain. Despite maintaining an overall similar structural conformation, our mass spectrometry-based site-specific glycosylation analyses of similarly produced spike proteins with and without the D614G and Alpha variant mutations reveal a significant shift in the processing state of N-glycans on one specific NTD site. Its conversion to a higher proportion of complex type structures is indicative of altered spatial accessibility attributable to mutations specific to the Alpha variant that may impact its transmissibility. This and other more subtle changes in glycosylation features detected at other sites provide crucial missing information otherwise not apparent in the available cryogenic electron microscopy-derived structures of the spike protein variants.
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Affiliation(s)
- Chu-Wei Kuo
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec 2, Nankang, Taipei 11529, Taiwan
| | - Tzu-Jing Yang
- Institute of Biochemical Sciences, National Taiwan University, 1 Roosevelt Road Sec 4, Daan, Taipei 10617, Taiwan
| | - Yu-Chun Chien
- Institute of Biochemical Sciences, National Taiwan University, 1 Roosevelt Road Sec 4, Daan, Taipei 10617, Taiwan
| | - Pei-Yu Yu
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec 2, Nankang, Taipei 11529, Taiwan
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec 2, Nankang, Taipei 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, 1 Roosevelt Road Sec 4, Daan, Taipei 10617, Taiwan
| | - Kay-Hooi Khoo
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec 2, Nankang, Taipei 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, 1 Roosevelt Road Sec 4, Daan, Taipei 10617, Taiwan
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10
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Takahashi JA, Barbosa BVR, Lima MTNS, Cardoso PG, Contigli C, Pimenta LPS. Antiviral fungal metabolites and some insights into their contribution to the current COVID-19 pandemic. Bioorg Med Chem 2021; 46:116366. [PMID: 34438338 PMCID: PMC8363177 DOI: 10.1016/j.bmc.2021.116366] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/23/2021] [Accepted: 08/03/2021] [Indexed: 12/11/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak, which started in late 2019, drove the scientific community to conduct innovative research to contain the spread of the pandemic and to care for those already affected. Since then, the search for new drugs that are effective against the virus has been strengthened. Featuring a relatively low cost of production under well-defined methods of cultivation, fungi have been providing a diversity of antiviral metabolites with unprecedented chemical structures. In this review, we present viral RNA infections highlighting SARS-CoV-2 morphogenesis and the infectious cycle, the targets of known antiviral drugs, and current developments in this area such as drug repurposing. We also explored the metabolic adaptability of fungi during fermentation to produce metabolites active against RNA viruses, along with their chemical structures, and mechanisms of action. Finally, the state of the art of research on SARS-CoV-2 inhibitors of fungal origin is reported, highlighting the metabolites selected by docking studies.
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Affiliation(s)
- Jacqueline Aparecida Takahashi
- Department of Chemistry, Exact Sciences Institute, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, CEP 31270-901 Belo Horizonte, MG, Brazil.
| | - Bianca Vianna Rodrigues Barbosa
- Department of Chemistry, Exact Sciences Institute, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, CEP 31270-901 Belo Horizonte, MG, Brazil
| | - Matheus Thomaz Nogueira Silva Lima
- Department of Food Science, Faculty of Pharmacy, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, CEP 31270-901 Belo Horizonte, MG, Brazil.
| | - Patrícia Gomes Cardoso
- Department of Biology, Universidade Federal de Lavras, Av. Dr. Sylvio Menicucci, 1001, CEP 37200-900 Lavras, MG, Brazil.
| | - Christiane Contigli
- Cell Biology Service, Research and Development Department, Fundação Ezequiel Dias, R. Conde Pereira Carneiro, 80, CEP 30510-010 Belo Horizonte, MG, Brazil
| | - Lúcia Pinheiro Santos Pimenta
- Department of Chemistry, Exact Sciences Institute, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, CEP 31270-901 Belo Horizonte, MG, Brazil
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11
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Slavin M, Zamel J, Zohar K, Eliyahu T, Braitbard M, Brielle E, Baraz L, Stolovich-Rain M, Friedman A, Wolf DG, Rouvinski A, Linial M, Schneidman-Duhovny D, Kalisman N. Targeted in situ cross-linking mass spectrometry and integrative modeling reveal the architectures of three proteins from SARS-CoV-2. Proc Natl Acad Sci U S A 2021; 118:e2103554118. [PMID: 34373319 PMCID: PMC8403911 DOI: 10.1073/pnas.2103554118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Atomic structures of several proteins from the coronavirus family are still partial or unavailable. A possible reason for this gap is the instability of these proteins outside of the cellular context, thereby prompting the use of in-cell approaches. In situ cross-linking and mass spectrometry (in situ CLMS) can provide information on the structures of such proteins as they occur in the intact cell. Here, we applied targeted in situ CLMS to structurally probe Nsp1, Nsp2, and nucleocapsid (N) proteins from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and obtained cross-link sets with an average density of one cross-link per 20 residues. We then employed integrative modeling that computationally combined the cross-linking data with domain structures to determine full-length atomic models. For the Nsp2, the cross-links report on a complex topology with long-range interactions. Integrative modeling with structural prediction of individual domains by the AlphaFold2 system allowed us to generate a single consistent all-atom model of the full-length Nsp2. The model reveals three putative metal binding sites and suggests a role for Nsp2 in zinc regulation within the replication-transcription complex. For the N protein, we identified multiple intra- and interdomain cross-links. Our integrative model of the N dimer demonstrates that it can accommodate three single RNA strands simultaneously, both stereochemically and electrostatically. For the Nsp1, cross-links with the 40S ribosome were highly consistent with recent cryogenic electron microscopy structures. These results highlight the importance of cellular context for the structural probing of recalcitrant proteins and demonstrate the effectiveness of targeted in situ CLMS and integrative modeling.
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Affiliation(s)
- Moriya Slavin
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Joanna Zamel
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Keren Zohar
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Tsiona Eliyahu
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Merav Braitbard
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Esther Brielle
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Leah Baraz
- Hadassah Academic College Jerusalem, Jerusalem 9101001, Israel
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Miri Stolovich-Rain
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Ahuva Friedman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Dana G Wolf
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, 9190401 Jerusalem, Israel
| | - Alexander Rouvinski
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Michal Linial
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
| | - Dina Schneidman-Duhovny
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Nir Kalisman
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
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12
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Lau EY, Negrete OA, Bennett WFD, Bennion BJ, Borucki M, Bourguet F, Epstein A, Franco M, Harmon B, He S, Jones D, Kim H, Kirshner D, Lao V, Lo J, McLoughlin K, Mosesso R, Murugesh DK, Saada EA, Segelke B, Stefan MA, Stevenson GA, Torres MW, Weilhammer DR, Wong S, Yang Y, Zemla A, Zhang X, Zhu F, Allen JE, Lightstone FC. Discovery of Small-Molecule Inhibitors of SARS-CoV-2 Proteins Using a Computational and Experimental Pipeline. Front Mol Biosci 2021; 8:678701. [PMID: 34327214 PMCID: PMC8315004 DOI: 10.3389/fmolb.2021.678701] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/22/2021] [Indexed: 12/21/2022] Open
Abstract
A rapid response is necessary to contain emergent biological outbreaks before they can become pandemics. The novel coronavirus (SARS-CoV-2) that causes COVID-19 was first reported in December of 2019 in Wuhan, China and reached most corners of the globe in less than two months. In just over a year since the initial infections, COVID-19 infected almost 100 million people worldwide. Although similar to SARS-CoV and MERS-CoV, SARS-CoV-2 has resisted treatments that are effective against other coronaviruses. Crystal structures of two SARS-CoV-2 proteins, spike protein and main protease, have been reported and can serve as targets for studies in neutralizing this threat. We have employed molecular docking, molecular dynamics simulations, and machine learning to identify from a library of 26 million molecules possible candidate compounds that may attenuate or neutralize the effects of this virus. The viability of selected candidate compounds against SARS-CoV-2 was determined experimentally by biolayer interferometry and FRET-based activity protein assays along with virus-based assays. In the pseudovirus assay, imatinib and lapatinib had IC50 values below 10 μM, while candesartan cilexetil had an IC50 value of approximately 67 µM against Mpro in a FRET-based activity assay. Comparatively, candesartan cilexetil had the highest selectivity index of all compounds tested as its half-maximal cytotoxicity concentration 50 (CC50) value was the only one greater than the limit of the assay (>100 μM).
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Affiliation(s)
- Edmond Y Lau
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biotechnology and Biosciences Division, Livermore, CA, United States
| | - Oscar A Negrete
- Sandia National Laboratory, Department of Biotechnologies and Bioengineering, Livermore, CA, United States
| | - W F Drew Bennett
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biotechnology and Biosciences Division, Livermore, CA, United States
| | - Brian J Bennion
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biotechnology and Biosciences Division, Livermore, CA, United States
| | - Monica Borucki
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biotechnology and Biosciences Division, Livermore, CA, United States
| | - Feliza Bourguet
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biotechnology and Biosciences Division, Livermore, CA, United States
| | - Aidan Epstein
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Division, Livermore, CA, United States
| | - Magdalena Franco
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biotechnology and Biosciences Division, Livermore, CA, United States
| | - Brooke Harmon
- Sandia National Laboratory, Department Systems Biology, Livermore, CA, United States
| | - Stewart He
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Division, Livermore, CA, United States
| | - Derek Jones
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Division, Livermore, CA, United States
| | - Hyojin Kim
- Lawrence Livermore National Laboratory, Computing Directorate, Center for Applied Scientific Computing, Livermore, CA, United States
| | - Daniel Kirshner
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biotechnology and Biosciences Division, Livermore, CA, United States
| | - Victoria Lao
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biotechnology and Biosciences Division, Livermore, CA, United States
| | - Jacky Lo
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biotechnology and Biosciences Division, Livermore, CA, United States
| | - Kevin McLoughlin
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Division, Livermore, CA, United States
| | - Richard Mosesso
- Sandia National Laboratory, Department Systems Biology, Livermore, CA, United States
| | - Deepa K Murugesh
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biotechnology and Biosciences Division, Livermore, CA, United States
| | - Edwin A Saada
- Sandia National Laboratory, Department Systems Biology, Livermore, CA, United States
| | - Brent Segelke
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biotechnology and Biosciences Division, Livermore, CA, United States
| | - Maxwell A Stefan
- Sandia National Laboratory, Department Systems Biology, Livermore, CA, United States
| | - Garrett A Stevenson
- Lawrence Livermore National Laboratory, Engineering Directorate, Computational Engineering Division, Livermore, CA, United States
| | - Marisa W Torres
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Division, Livermore, CA, United States
| | - Dina R Weilhammer
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biotechnology and Biosciences Division, Livermore, CA, United States
| | - Sergio Wong
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biotechnology and Biosciences Division, Livermore, CA, United States
| | - Yue Yang
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biotechnology and Biosciences Division, Livermore, CA, United States
| | - Adam Zemla
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Division, Livermore, CA, United States
| | - Xiaohua Zhang
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biotechnology and Biosciences Division, Livermore, CA, United States
| | - Fangqiang Zhu
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biotechnology and Biosciences Division, Livermore, CA, United States
| | - Jonathan E Allen
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Division, Livermore, CA, United States
| | - Felice C Lightstone
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biotechnology and Biosciences Division, Livermore, CA, United States
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13
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Lucas-Dominguez R, Alonso-Arroyo A, Vidal-Infer A, Aleixandre-Benavent R. The sharing of research data facing the COVID-19 pandemic. Scientometrics 2021; 126:4975-4990. [PMID: 33935332 PMCID: PMC8072296 DOI: 10.1007/s11192-021-03971-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/24/2021] [Indexed: 11/25/2022]
Abstract
During the previous Ebola and Zika outbreaks, researchers shared their data, allowing many published epidemiological studies to be produced only from open research data, to speed up investigations and control of these infections. This study aims to evaluate the dissemination of the COVID-19 research data underlying scientific publications. Analysis of COVID-19 publications from December 1, 2019, to April 30, 2020, was conducted through the PubMed Central repository to evaluate the research data available through its publication as supplementary material or deposited in repositories. The PubMed Central search generated 5,905 records, of which 804 papers included complementary research data, especially as supplementary material (77.4%). The most productive journals were The New England Journal of Medicine, The Lancet and The Lancet Infectious Diseases, the most frequent keyword was pneumonia, and the most used repositories were GitHub and GenBank. An expected growth in the number of published articles following the course of the pandemics is confirmed in this work, while the underlying research data are only 13.6%. It can be deduced that data sharing is not a common practice, even in health emergencies, such as the present one. High-impact generalist journals have accounted for a large share of global publishing. The topics most often covered are related to epidemiological and public health concepts, genetics, virology and respiratory diseases, such as pneumonia. However, it is essential to interpret these data with caution following the evolution of publications and their funding in the coming months.
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Affiliation(s)
- Rut Lucas-Dominguez
- Department of the History of Science and Information Science, School of Medicine and Dentistry, University of Valencia, Avda. Blasco Ibañez 15, 46010 Valencia, Spain
- UISYS, Joint Research Unit CSIC–University of Valencia, Pza. Cisneros 4, 46003 Valencia, Spain
- CIBERONC, Valencia, Spain
| | - Adolfo Alonso-Arroyo
- Department of the History of Science and Information Science, School of Medicine and Dentistry, University of Valencia, Avda. Blasco Ibañez 15, 46010 Valencia, Spain
- UISYS, Joint Research Unit CSIC–University of Valencia, Pza. Cisneros 4, 46003 Valencia, Spain
| | - Antonio Vidal-Infer
- Department of the History of Science and Information Science, School of Medicine and Dentistry, University of Valencia, Avda. Blasco Ibañez 15, 46010 Valencia, Spain
- UISYS, Joint Research Unit CSIC–University of Valencia, Pza. Cisneros 4, 46003 Valencia, Spain
| | - Rafael Aleixandre-Benavent
- UISYS, Joint Research Unit CSIC–University of Valencia, Pza. Cisneros 4, 46003 Valencia, Spain
- Ingenio (CSIC-Politechnic University of Valencia), Ciudad Politécnica de La Innovación, Edif 8E 4º, Camino de Vera s/n, 46022 Valencia, Spain
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14
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DeepTracer for fast de novo cryo-EM protein structure modeling and special studies on CoV-related complexes. Proc Natl Acad Sci U S A 2021; 118:2017525118. [PMID: 33361332 PMCID: PMC7812826 DOI: 10.1073/pnas.2017525118] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Electron cryomicroscopy (cryo-EM), a 2017 Nobel prize-awarded technology, provides direct 3D maps of macromolecules and explains the shape and interactions of protein complexes such as SARS-CoV-2 viral proteins and human cell receptors. This understanding can be combined with detailed structural information gathered using other technologies to form the basis for modeling course of diseases and for designing therapeutic drugs. However, ab initio modeling of protein complex structure remains a challenging problem. Here, we present DeepTracer, a fully automated and robust tool that determines the all-atom structure of a protein complex based solely on its cryo-EM map and amino acid sequence, with improved accuracy and efficiency compared to previous methods. We also provide a web service for global access. Information about macromolecular structure of protein complexes and related cellular and molecular mechanisms can assist the search for vaccines and drug development processes. To obtain such structural information, we present DeepTracer, a fully automated deep learning-based method for fast de novo multichain protein complex structure determination from high-resolution cryoelectron microscopy (cryo-EM) maps. We applied DeepTracer on a previously published set of 476 raw experimental cryo-EM maps and compared the results with a current state of the art method. The residue coverage increased by over 30% using DeepTracer, and the rmsd value improved from 1.29 Å to 1.18 Å. Additionally, we applied DeepTracer on a set of 62 coronavirus-related cryo-EM maps, among them 10 with no deposited structure available in EMDataResource. We observed an average residue match of 84% with the deposited structures and an average rmsd of 0.93 Å. Additional tests with related methods further exemplify DeepTracer’s competitive accuracy and efficiency of structure modeling. DeepTracer allows for exceptionally fast computations, making it possible to trace around 60,000 residues in 350 chains within only 2 h. The web service is globally accessible at https://deeptracer.uw.edu.
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15
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Scientists’ pursuit for SARS-COV-2 coronavirus: strategies against pandemic. UKRAINIAN BIOCHEMICAL JOURNAL 2020. [DOI: 10.15407/ubj92.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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16
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Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the identified cause of coronavirus disease 2019 (COVID-19), continues unabated. This fact, coupled with recurrence of COVID-19 in areas where it had been controlled, highlights the critical need for a safe and effective vaccine to prevent and mitigate this novel virus. The spike protein of SARS-CoV-2 is important in its lifecycle as well as in the development of immunity after human infection. This has prompted the selection of this antigen as a focus in developing COVID-19 vaccines. This article provides (1) a summary of the host immune responses to SARS-CoV-2 infection, (2) the vaccine platforms being used with COVID-19 vaccine candidates undergoing, or about to undergo, Phase III clinical trial testing, and (3) an overview of the key criteria necessary for COVID-19 vaccine efficacy and safety. In addition, the unique concept of vaccine-enhanced disease will be discussed. [Pediatr Ann. 2020;49(12):e532-e536.].
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17
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Paliwal P, Sargolzaei S, Bhardwaj SK, Bhardwaj V, Dixit C, Kaushik A. Grand Challenges in Bio-Nanotechnology to Manage the COVID-19 Pandemic. FRONTIERS IN NANOTECHNOLOGY 2020. [DOI: 10.3389/fnano.2020.571284] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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18
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Future antiviral surfaces: Lessons from COVID-19 pandemic. SUSTAINABLE MATERIALS AND TECHNOLOGIES 2020; 25. [PMCID: PMC7376362 DOI: 10.1016/j.susmat.2020.e00203] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
It is an urgent priority for advanced materials researchers to help find solutions to eliminate the COVID-19 pandemic. The transmission of the SARS-CoV-2 coronavirus is majorly through touching the contaminated surfaces and then the vulnerable mouth and eyes besides the direct contact with the infected person. This lesson inspired us to propose a strategy from the view of materials scientists on designing effective antiviral surfaces to prevent the transmission of infectious coronaviruses by disrupting their survival on various surfaces. In this perspective, based on current progress in antiviral and antibacterial coatings, we put forward some general principles for designing effective antiviral surfaces by applying natural viral inhibitors, physical/chemical modifications, and bioinspired patterns, with the mechanisms of direct disinfection, indirect disinfection, and receptor inactivation. This work maps possible solutions to inactivate the receptors of the coronavirus spikes and resist the transmission of the COVID-19 and other infectious diseases, and contribute to the prevention of future outbreaks and control of epidemics.
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19
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Youkharibache P, Cachau R, Madej T, Wang J. Using iCn3D and the World Wide Web for structure-based collaborative research: Analyzing molecular interactions at the root of COVID-19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32637961 PMCID: PMC7337391 DOI: 10.1101/2020.07.01.182964] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The COVID-19 pandemic took us ill-prepared and tackling the many challenges it poses in a timely manner requires world-wide collaboration. Our ability to study the SARS-COV-2 virus and its interactions with its human host in molecular terms efficiently and collaboratively becomes indispensable and mission-critical in the race to develop vaccines, drugs, and neutralizing antibodies. There is already a significant corpus of 3D structures related to SARS and MERS coronaviruses, and the rapid generation of new structures demands the use of efficient tools to expedite the sharing of structural analyses and molecular designs and convey them in their native 3D context in sync with sequence data and annotations. We developed iCn3D (pronounced "I see in 3D")1 to take full advantage of web technologies and allow scientists of different backgrounds to perform and share sequence-structure analyses over the Internet and engage in collaborations through a simple mechanism of exchanging "lifelong" web links (URLs). This approach solves the very old problem of "sharing of molecular scenes" in a reliable and convenient manner. iCn3D links are sharable over the Internet and make data and entire analyses findable, accessible, and reproducible, with various levels of interoperability. Links and underlying data are FAIR2 and can be embedded in preprints and papers, bringing a 3D live and interactive dimension to a world of text and static images used in current publications, eliminating at the same time the need for arcane supplemental materials. This paper exemplifies iCn3D capabilities in visualization, analysis, and sharing of COVID-19 related structures, sequence variability, and molecular interactions.
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Affiliation(s)
- Philippe Youkharibache
- Cancer Data Science Lab, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Raul Cachau
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Tom Madej
- National Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jiyao Wang
- National Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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