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      Graphene BioFET sensors for SARS-CoV-2 detection: a multiscale simulation approach†

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      Nanoscale Advances
      RSC

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          Abstract

          Biological Field-Effect Transistors (BioFETs) have already demonstrated enormous potential for detecting minute amounts of ions and molecules. The use of two-dimensional (2D) materials has been shown to boost their performance and to enable the design of new applications. This combination deserves special interest in the current pandemic caused by the SARS-CoV-2 virus which demands fast, reliable and cheap detection methods. However, in spite of the experimental advances, there is a lack of a comprehensive and in-depth computational approach to capture the mechanisms underlying the sensor behaviour. Here, we present a multiscale platform that combines detailed atomic models of the molecules with mesoscopic device-level simulations. The fine-level description exploited in this approach accounts for the charge distribution of the receptor, its reconfiguration when the target binds to it, and the consequences in terms of sensitivity on the transduction mechanism. The results encourage the further exploration of improved sensor designs and 2D materials combined with diverse receptors selected to achieve the desired specificity.

          Abstract

          Two-dimensional (2D) materials BioFETs have already demonstrated their potential for detecting low amounts of molecules. Here, we present a multiscale simulation platform in the context of Graphene BioFET for the detection of SARS-CoV-2.

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          Most cited references47

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          Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation

          Structure of the nCoV trimeric spike The World Health Organization has declared the outbreak of a novel coronavirus (2019-nCoV) to be a public health emergency of international concern. The virus binds to host cells through its trimeric spike glycoprotein, making this protein a key target for potential therapies and diagnostics. Wrapp et al. determined a 3.5-angstrom-resolution structure of the 2019-nCoV trimeric spike protein by cryo–electron microscopy. Using biophysical assays, the authors show that this protein binds at least 10 times more tightly than the corresponding spike protein of severe acute respiratory syndrome (SARS)–CoV to their common host cell receptor. They also tested three antibodies known to bind to the SARS-CoV spike protein but did not detect binding to the 2019-nCoV spike protein. These studies provide valuable information to guide the development of medical counter-measures for 2019-nCoV. Science, this issue p. 1260
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            Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

            Summary The emergence of SARS-CoV-2 has resulted in >90,000 infections and >3,000 deaths. Coronavirus spike (S) glycoproteins promote entry into cells and are the main target of antibodies. We show that SARS-CoV-2 S uses ACE2 to enter cells and that the receptor-binding domains of SARS-CoV-2 S and SARS-CoV S bind with similar affinities to human ACE2, correlating with the efficient spread of SARS-CoV-2 among humans. We found that the SARS-CoV-2 S glycoprotein harbors a furin cleavage site at the boundary between the S1/S2 subunits, which is processed during biogenesis and sets this virus apart from SARS-CoV and SARS-related CoVs. We determined cryo-EM structures of the SARS-CoV-2 S ectodomain trimer, providing a blueprint for the design of vaccines and inhibitors of viral entry. Finally, we demonstrate that SARS-CoV S murine polyclonal antibodies potently inhibited SARS-CoV-2 S mediated entry into cells, indicating that cross-neutralizing antibodies targeting conserved S epitopes can be elicited upon vaccination.
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              Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor

              A new and highly pathogenic coronavirus (severe acute respiratory syndrome coronavirus-2, SARS-CoV-2) caused an outbreak in Wuhan city, Hubei province, China, starting from December 2019 that quickly spread nationwide and to other countries around the world1-3. Here, to better understand the initial step of infection at an atomic level, we determined the crystal structure of the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 bound to the cell receptor ACE2. The overall ACE2-binding mode of the SARS-CoV-2 RBD is nearly identical to that of the SARS-CoV RBD, which also uses ACE2 as the cell receptor4. Structural analysis identified residues in the SARS-CoV-2 RBD that are essential for ACE2 binding, the majority of which either are highly conserved or share similar side chain properties with those in the SARS-CoV RBD. Such similarity in structure and sequence strongly indicate convergent evolution between the SARS-CoV-2 and SARS-CoV RBDs for improved binding to ACE2, although SARS-CoV-2 does not cluster within SARS and SARS-related coronaviruses1-3,5. The epitopes of two SARS-CoV antibodies that target the RBD are also analysed for binding to the SARS-CoV-2 RBD, providing insights into the future identification of cross-reactive antibodies.
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                Author and article information

                Journal
                Nanoscale Adv
                Nanoscale Adv
                NA
                NAADAI
                Nanoscale Advances
                RSC
                2516-0230
                17 June 2022
                15 July 2022
                17 June 2022
                : 4
                : 14
                : 3065-3072
                Affiliations
                [a] Departamento de Electrónica y Tecnología de Computadores, Facultad de Ciencias, Universidad de Granada Spain atoral@ 123456ugr.es agodoy@ 123456ugr.es
                [b] Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies Schloss-Wolfsbrunnenweg 35 69118 Heidelberg Germany
                [c] Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University Im Neuenheimer Feld 282 69120 Heidelberg Germany
                [d] Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University Im Neuenheimer Feld 205 Heidelberg Germany
                Author information
                https://orcid.org/0000-0001-5612-0536
                https://orcid.org/0000-0002-4687-6572
                https://orcid.org/0000-0002-0302-3764
                https://orcid.org/0000-0001-5951-8670
                https://orcid.org/0000-0002-3014-8765
                Article
                d2na00357k
                10.1039/d2na00357k
                9418999
                36133524
                d5fc8bb6-108c-4c29-8825-c722a59281b3
                This journal is © The Royal Society of Chemistry
                History
                : 6 June 2022
                : 13 June 2022
                Page count
                Pages: 8
                Funding
                Funded by: Consejería de Conocimiento, Investigación y Universidad, Junta de Andalucía, doi 10.13039/501100018943;
                Award ID: B-RNM-375-UGR18
                Funded by: H2020 LEIT Information and Communication Technologies, doi 10.13039/100010669;
                Award ID: Contract 825213
                Funded by: Klaus Tschira Stiftung, doi 10.13039/501100007316;
                Award ID: Unassigned
                Funded by: H2020 Future and Emerging Technologies, doi 10.13039/100010664;
                Award ID: Grant Agreement 945539
                Funded by: Ministerio de Ciencia e Innovación, doi 10.13039/501100004837;
                Award ID: PID2020-116518GB-I00
                Funded by: Ministerio de Educación, Cultura y Deporte, doi 10.13039/501100003176;
                Award ID: FPU16/04043
                Categories
                Chemistry
                Custom metadata
                Paginated Article

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