COVID-19 spike-host cell receptor GRP78 binding site prediction
Identifieur interne : 000B56 ( Ncbi/Merge ); précédent : 000B55; suivant : 000B57COVID-19 spike-host cell receptor GRP78 binding site prediction
Auteurs : Ibrahim M. Ibrahim [Égypte] ; Doaa H. Abdelmalek [Égypte] ; Mohammed E. Elshahat [Égypte] ; Abdo A. Elfiky [Égypte, Arabie saoudite]Source :
- The Journal of Infection [ 0163-4453 ] ; 2020.
Abstract
Understanding the novel coronavirus (COVID-19) mode of host cell recognition may help to fight the disease and save lives. The spike protein of coronaviruses is the main driving force for host cell recognition.
In this study, the COVID-19 spike binding site to the cell-surface receptor (Glucose Regulated Protein 78 (GRP78)) is predicted using combined molecular modeling docking and structural bioinformatics. The COVID-19 spike protein is modeled using its counterpart, the SARS spike.
Sequence and structural alignments show that four regions, in addition to its cyclic nature have sequence and physicochemical similarities to the cyclic Pep42. Protein-protein docking was performed to test the four regions of the spike that fit tightly in the GRP78 Substrate Binding Domain β (SBDβ). The docking pose revealed the involvement of the SBDβ of GRP78 and the receptor-binding domain of the coronavirus spike protein in recognition of the host cell receptor.
We reveal that the binding is more favorable between regions III (C391-C525) and IV (C480-C488) of the spike protein model and GRP78. Region IV is the main driving force for GRP78 binding with the predicted binding affinity of -9.8 kcal/mol. These nine residues can be used to develop therapeutics specific against COVID-19.
Url:
DOI: 10.1016/j.jinf.2020.02.026
PubMed: 32169481
PubMed Central: 7102553
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000735
- to stream Pmc, to step Curation: 000735
- to stream Pmc, to step Checkpoint: 000580
Links to Exploration step
PMC:7102553Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">COVID-19 spike-host cell receptor GRP78 binding site prediction</title><author><name sortKey="Ibrahim, Ibrahim M" sort="Ibrahim, Ibrahim M" uniqKey="Ibrahim I" first="Ibrahim M." last="Ibrahim">Ibrahim M. Ibrahim</name><affiliation wicri:level="1"><nlm:aff id="aff0001">Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt</nlm:aff><country xml:lang="fr">Égypte</country><wicri:regionArea>Biophysics Department, Faculty of Sciences, Cairo University, Giza</wicri:regionArea><wicri:noRegion>Giza</wicri:noRegion></affiliation></author><author><name sortKey="Abdelmalek, Doaa H" sort="Abdelmalek, Doaa H" uniqKey="Abdelmalek D" first="Doaa H." last="Abdelmalek">Doaa H. Abdelmalek</name><affiliation wicri:level="1"><nlm:aff id="aff0001">Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt</nlm:aff><country xml:lang="fr">Égypte</country><wicri:regionArea>Biophysics Department, Faculty of Sciences, Cairo University, Giza</wicri:regionArea><wicri:noRegion>Giza</wicri:noRegion></affiliation></author><author><name sortKey="Elshahat, Mohammed E" sort="Elshahat, Mohammed E" uniqKey="Elshahat M" first="Mohammed E." last="Elshahat">Mohammed E. Elshahat</name><affiliation wicri:level="1"><nlm:aff id="aff0001">Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt</nlm:aff><country xml:lang="fr">Égypte</country><wicri:regionArea>Biophysics Department, Faculty of Sciences, Cairo University, Giza</wicri:regionArea><wicri:noRegion>Giza</wicri:noRegion></affiliation></author><author><name sortKey="Elfiky, Abdo A" sort="Elfiky, Abdo A" uniqKey="Elfiky A" first="Abdo A." last="Elfiky">Abdo A. Elfiky</name><affiliation wicri:level="1"><nlm:aff id="aff0001">Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt</nlm:aff><country xml:lang="fr">Égypte</country><wicri:regionArea>Biophysics Department, Faculty of Sciences, Cairo University, Giza</wicri:regionArea><wicri:noRegion>Giza</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff0002">College of Applied Medical Sciences, University of Al-Jouf, Saudi Arabia</nlm:aff><country xml:lang="fr">Arabie saoudite</country><wicri:regionArea>College of Applied Medical Sciences, University of Al-Jouf</wicri:regionArea><wicri:noRegion>University of Al-Jouf</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">32169481</idno><idno type="pmc">7102553</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7102553</idno><idno type="RBID">PMC:7102553</idno><idno type="doi">10.1016/j.jinf.2020.02.026</idno><date when="2020">2020</date><idno type="wicri:Area/Pmc/Corpus">000735</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000735</idno><idno type="wicri:Area/Pmc/Curation">000735</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000735</idno><idno type="wicri:Area/Pmc/Checkpoint">000580</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000580</idno><idno type="wicri:Area/Ncbi/Merge">000B56</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">COVID-19 spike-host cell receptor GRP78 binding site prediction</title><author><name sortKey="Ibrahim, Ibrahim M" sort="Ibrahim, Ibrahim M" uniqKey="Ibrahim I" first="Ibrahim M." last="Ibrahim">Ibrahim M. Ibrahim</name><affiliation wicri:level="1"><nlm:aff id="aff0001">Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt</nlm:aff><country xml:lang="fr">Égypte</country><wicri:regionArea>Biophysics Department, Faculty of Sciences, Cairo University, Giza</wicri:regionArea><wicri:noRegion>Giza</wicri:noRegion></affiliation></author><author><name sortKey="Abdelmalek, Doaa H" sort="Abdelmalek, Doaa H" uniqKey="Abdelmalek D" first="Doaa H." last="Abdelmalek">Doaa H. Abdelmalek</name><affiliation wicri:level="1"><nlm:aff id="aff0001">Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt</nlm:aff><country xml:lang="fr">Égypte</country><wicri:regionArea>Biophysics Department, Faculty of Sciences, Cairo University, Giza</wicri:regionArea><wicri:noRegion>Giza</wicri:noRegion></affiliation></author><author><name sortKey="Elshahat, Mohammed E" sort="Elshahat, Mohammed E" uniqKey="Elshahat M" first="Mohammed E." last="Elshahat">Mohammed E. Elshahat</name><affiliation wicri:level="1"><nlm:aff id="aff0001">Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt</nlm:aff><country xml:lang="fr">Égypte</country><wicri:regionArea>Biophysics Department, Faculty of Sciences, Cairo University, Giza</wicri:regionArea><wicri:noRegion>Giza</wicri:noRegion></affiliation></author><author><name sortKey="Elfiky, Abdo A" sort="Elfiky, Abdo A" uniqKey="Elfiky A" first="Abdo A." last="Elfiky">Abdo A. Elfiky</name><affiliation wicri:level="1"><nlm:aff id="aff0001">Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt</nlm:aff><country xml:lang="fr">Égypte</country><wicri:regionArea>Biophysics Department, Faculty of Sciences, Cairo University, Giza</wicri:regionArea><wicri:noRegion>Giza</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff0002">College of Applied Medical Sciences, University of Al-Jouf, Saudi Arabia</nlm:aff><country xml:lang="fr">Arabie saoudite</country><wicri:regionArea>College of Applied Medical Sciences, University of Al-Jouf</wicri:regionArea><wicri:noRegion>University of Al-Jouf</wicri:noRegion></affiliation></author></analytic><series><title level="j">The Journal of Infection</title><idno type="ISSN">0163-4453</idno><idno type="eISSN">1532-2742</idno><imprint><date when="2020">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Summary</title><sec><title>Objectives</title><p>Understanding the novel coronavirus (COVID-19) mode of host cell recognition may help to fight the disease and save lives. The spike protein of coronaviruses is the main driving force for host cell recognition.</p></sec><sec><title>Methods</title><p>In this study, the COVID-19 spike binding site to the cell-surface receptor (Glucose Regulated Protein 78 (GRP78)) is predicted using combined molecular modeling docking and structural bioinformatics. The COVID-19 spike protein is modeled using its counterpart, the SARS spike.</p></sec><sec><title>Results</title><p>Sequence and structural alignments show that four regions, in addition to its cyclic nature have sequence and physicochemical similarities to the cyclic Pep42. Protein-protein docking was performed to test the four regions of the spike that fit tightly in the GRP78 Substrate Binding Domain β (SBDβ). The docking pose revealed the involvement of the SBDβ of GRP78 and the receptor-binding domain of the coronavirus spike protein in recognition of the host cell receptor.</p></sec><sec><title>Conclusions</title><p>We reveal that the binding is more favorable between regions III (C391-C525) and IV (C480-C488) of the spike protein model and GRP78. Region IV is the main driving force for GRP78 binding with the predicted binding affinity of -9.8 kcal/mol. These nine residues can be used to develop therapeutics specific against COVID-19.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Hui, D S" uniqKey="Hui D">D.S. Hui</name></author><author><name sortKey="I Azhar, E" uniqKey="I Azhar E">E. I Azhar</name></author><author><name sortKey="Madani, T A" uniqKey="Madani T">T.A. Madani</name></author><author><name sortKey="Ntoumi, F" uniqKey="Ntoumi F">F. Ntoumi</name></author><author><name sortKey="Kock, R" uniqKey="Kock R">R. Kock</name></author><author><name sortKey="Dar, O" uniqKey="Dar O">O. Dar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bogoch, I I" uniqKey="Bogoch I">I.I. Bogoch</name></author><author><name sortKey="Watts, A" uniqKey="Watts A">A. Watts</name></author><author><name sortKey="Thomas Bachli, A" uniqKey="Thomas Bachli A">A. Thomas-Bachli</name></author><author><name sortKey="Huber, C" uniqKey="Huber C">C. Huber</name></author><author><name sortKey="Kraemer, M U G" uniqKey="Kraemer M">M.U.G. Kraemer</name></author><author><name sortKey="Khan, K" uniqKey="Khan K">K. Khan</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Parr, J" uniqKey="Parr J">J. Parr</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yang, L" uniqKey="Yang L">L. Yang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Elfiky, A A" uniqKey="Elfiky A">A.A. Elfiky</name></author><author><name sortKey="Mahdy, S M" uniqKey="Mahdy S">S.M. Mahdy</name></author><author><name sortKey="Elshemey, W M" uniqKey="Elshemey W">W.M. Elshemey</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chan, J F" uniqKey="Chan J">J.F. Chan</name></author><author><name sortKey="Lau, S K" uniqKey="Lau S">S.K. Lau</name></author><author><name sortKey="To, K K" uniqKey="To K">K.K. To</name></author><author><name sortKey="Cheng, V C" uniqKey="Cheng V">V.C. Cheng</name></author><author><name sortKey="Woo, P C" uniqKey="Woo P">P.C. Woo</name></author><author><name sortKey="Yuen, K Y" uniqKey="Yuen K">K.-.Y. Yuen</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Hemida, M G" uniqKey="Hemida M">M.G. Hemida</name></author><author><name sortKey="Alnaeem, A" uniqKey="Alnaeem A">A. Alnaeem</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Baez Santos, Y M" uniqKey="Baez Santos Y">Y.M. Báez-Santos</name></author><author><name sortKey="Mielech, A M" uniqKey="Mielech A">A.M. Mielech</name></author><author><name sortKey="Deng, X" uniqKey="Deng X">X. Deng</name></author><author><name sortKey="Baker, S" uniqKey="Baker S">S. Baker</name></author><author><name sortKey="Mesecar, A D" uniqKey="Mesecar A">A.D. Mesecar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Organization, W H" uniqKey="Organization W">W.H. Organization</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ibrahim, I M" uniqKey="Ibrahim I">I.M. Ibrahim</name></author><author><name sortKey="Abdelmalek, D H" uniqKey="Abdelmalek D">D.H. Abdelmalek</name></author><author><name sortKey="Elfiky, A A" uniqKey="Elfiky A">A.A. Elfiky</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Belouzard, S" uniqKey="Belouzard S">S. Belouzard</name></author><author><name sortKey="Millet, J K" uniqKey="Millet J">J.K. Millet</name></author><author><name sortKey="Licitra, B N" uniqKey="Licitra B">B.N. Licitra</name></author><author><name sortKey="Whittaker, G R" uniqKey="Whittaker G">G.R. Whittaker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lee, A S" uniqKey="Lee A">A.S. Lee</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, J" uniqKey="Li J">J. Li</name></author><author><name sortKey="Lee, A S" uniqKey="Lee A">A.S. Lee</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rao, R V" uniqKey="Rao R">R.V. Rao</name></author><author><name sortKey="Peel, A" uniqKey="Peel A">A. Peel</name></author><author><name sortKey="Logvinova, A" uniqKey="Logvinova A">A. Logvinova</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Quinones, Q J" uniqKey="Quinones Q">Q.J. Quinones</name></author><author><name sortKey="Ridder, G G D" uniqKey="Ridder G">G.G.D. Ridder</name></author><author><name sortKey="Pizzo, S V" uniqKey="Pizzo S">S.V. Pizzo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shen, J" uniqKey="Shen J">J. Shen</name></author><author><name sortKey="Chen, X" uniqKey="Chen X">X. Chen</name></author><author><name sortKey="Hendershot, L" uniqKey="Hendershot L">L. Hendershot</name></author><author><name sortKey="Prywes, R" uniqKey="Prywes R">R. Prywes</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kim, Y" uniqKey="Kim Y">Y. Kim</name></author><author><name sortKey="Lillo, A M" uniqKey="Lillo A">A.M. Lillo</name></author><author><name sortKey="Steiniger, S C" uniqKey="Steiniger S">S.C. Steiniger</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Berman, H" uniqKey="Berman H">H. Berman</name></author><author><name sortKey="Henrick, K" uniqKey="Henrick K">K. Henrick</name></author><author><name sortKey="Nakamura, H" uniqKey="Nakamura H">H. Nakamura</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chu, H" uniqKey="Chu H">H. Chu</name></author><author><name sortKey="Chan, C M" uniqKey="Chan C">C.-.M. Chan</name></author><author><name sortKey="Zhang, X" uniqKey="Zhang X">X. Zhang</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Notredame, C" uniqKey="Notredame C">C. Notredame</name></author><author><name sortKey="Higgins, D G" uniqKey="Higgins D">D.G. Higgins</name></author><author><name sortKey="Heringa, J" uniqKey="Heringa J">J. Heringa</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gouet, P" uniqKey="Gouet P">P. Gouet</name></author><author><name sortKey="Courcelle, E" uniqKey="Courcelle E">E. Courcelle</name></author><author><name sortKey="Stuart, D I" uniqKey="Stuart D">D.I. Stuart</name></author><author><name sortKey="M Oz, F" uniqKey="M Oz F">F. M√©toz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Biasini, M" uniqKey="Biasini M">M. Biasini</name></author><author><name sortKey="Bienert, S" uniqKey="Bienert S">S. Bienert</name></author><author><name sortKey="Waterhouse, A" uniqKey="Waterhouse A">A. Waterhouse</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Gasteiger, E" uniqKey="Gasteiger E">E. Gasteiger</name></author><author><name sortKey="Hoogland, C" uniqKey="Hoogland C">C. Hoogland</name></author><author><name sortKey="Gattiker, A" uniqKey="Gattiker A">A. Gattiker</name></author><author><name sortKey="Wilkins, M R" uniqKey="Wilkins M">M.R. Wilkins</name></author><author><name sortKey="Appel, R D" uniqKey="Appel R">R.D. Appel</name></author><author><name sortKey="Bairoch, A" uniqKey="Bairoch A">A. Bairoch</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yang, J" uniqKey="Yang J">J. Yang</name></author><author><name sortKey="Nune, M" uniqKey="Nune M">M. Nune</name></author><author><name sortKey="Zong, Y" uniqKey="Zong Y">Y. Zong</name></author><author><name sortKey="Zhou, L" uniqKey="Zhou L">L. Zhou</name></author><author><name sortKey="Liu, Q" uniqKey="Liu Q">Q. Liu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yang, J" uniqKey="Yang J">J. Yang</name></author><author><name sortKey="Zong, Y" uniqKey="Zong Y">Y. Zong</name></author><author><name sortKey="Su, J" uniqKey="Su J">J. Su</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Dijk, A D" uniqKey="Van Dijk A">A.D. van Dijk</name></author><author><name sortKey="Bonvin, A M" uniqKey="Bonvin A">A.M. Bonvin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="De Vries, S J" uniqKey="De Vries S">S.J. de Vries</name></author><author><name sortKey="Van Dijk, M" uniqKey="Van Dijk M">M. van Dijk</name></author><author><name sortKey="Bonvin, A M" uniqKey="Bonvin A">A.M. Bonvin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="De Vries, S J" uniqKey="De Vries S">S.J. de Vries</name></author><author><name sortKey="Van Dijk, A D J" uniqKey="Van Dijk A">A.D.J. van Dijk</name></author><author><name sortKey="Krzeminski, M" uniqKey="Krzeminski M">M. Krzeminski</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Dijk, A D" uniqKey="Van Dijk A">A.D. van Dijk</name></author><author><name sortKey="De Vries, S J" uniqKey="De Vries S">S.J. de Vries</name></author><author><name sortKey="Dominguez, C" uniqKey="Dominguez C">C. Dominguez</name></author><author><name sortKey="Chen, H" uniqKey="Chen H">H. Chen</name></author><author><name sortKey="Zhou, H X" uniqKey="Zhou H">H.X. Zhou</name></author><author><name sortKey="Bonvin, A M" uniqKey="Bonvin A">A.M. Bonvin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dominguez, C" uniqKey="Dominguez C">C. Dominguez</name></author><author><name sortKey="Boelens, R" uniqKey="Boelens R">R. Boelens</name></author><author><name sortKey="Bonvin, A M" uniqKey="Bonvin A">A.M. Bonvin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, Y" uniqKey="Zhang Y">Y. Zhang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yoneda, Y" uniqKey="Yoneda Y">Y. Yoneda</name></author><author><name sortKey="Steiniger, S C" uniqKey="Steiniger S">S.C. Steiniger</name></author><author><name sortKey="Capkova, K" uniqKey="Capkova K">K. Capkova</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kim, Y" uniqKey="Kim Y">Y. Kim</name></author><author><name sortKey="Lillo, A M" uniqKey="Lillo A">A.M. Lillo</name></author><author><name sortKey="Steiniger, S C" uniqKey="Steiniger S">S.C. Steiniger</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Salentin, S" uniqKey="Salentin S">S. Salentin</name></author><author><name sortKey="Schreiber, S" uniqKey="Schreiber S">S. Schreiber</name></author><author><name sortKey="Haupt, V J" uniqKey="Haupt V">V.J. Haupt</name></author><author><name sortKey="Adasme, M F" uniqKey="Adasme M">M.F. Adasme</name></author><author><name sortKey="Schroeder, M" uniqKey="Schroeder M">M. Schroeder</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pujhari, S" uniqKey="Pujhari S">S. Pujhari</name></author><author><name sortKey="Macias, V M" uniqKey="Macias V">V.M. Macias</name></author><author><name sortKey="Nissly, R H" uniqKey="Nissly R">R.H. Nissly</name></author><author><name sortKey="Nomura, M" uniqKey="Nomura M">M. Nomura</name></author><author><name sortKey="Kuchipudi, S V" uniqKey="Kuchipudi S">S.V. Kuchipudi</name></author><author><name sortKey="Rasgon, J L" uniqKey="Rasgon J">J.L. Rasgon</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">J Infect</journal-id><journal-id journal-id-type="iso-abbrev">J. Infect</journal-id><journal-title-group><journal-title>The Journal of Infection</journal-title></journal-title-group><issn pub-type="ppub">0163-4453</issn><issn pub-type="epub">1532-2742</issn><publisher><publisher-name>The British Infection Association. Published by Elsevier Ltd.</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">32169481</article-id><article-id pub-id-type="pmc">7102553</article-id><article-id pub-id-type="publisher-id">S0163-4453(20)30107-9</article-id><article-id pub-id-type="doi">10.1016/j.jinf.2020.02.026</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>COVID-19 spike-host cell receptor GRP78 binding site prediction</article-title></title-group><contrib-group><contrib contrib-type="author" id="au0001"><name><surname>Ibrahim</surname><given-names>Ibrahim M.</given-names></name><xref rid="aff0001" ref-type="aff">a</xref></contrib><contrib contrib-type="author" id="au0002"><name><surname>Abdelmalek</surname><given-names>Doaa H.</given-names></name><xref rid="aff0001" ref-type="aff">a</xref></contrib><contrib contrib-type="author" id="au0003"><name><surname>Elshahat</surname><given-names>Mohammed E.</given-names></name><xref rid="aff0001" ref-type="aff">a</xref></contrib><contrib contrib-type="author" id="au0004"><name><surname>Elfiky</surname><given-names>Abdo A.</given-names></name><email>abdo@sci.cu.edu.eg</email><email>aelfiky@ictp.it</email><xref rid="aff0001" ref-type="aff">a</xref><xref rid="aff0002" ref-type="aff">b</xref><xref rid="cor0001" ref-type="corresp">⁎</xref></contrib></contrib-group><aff id="aff0001"><label>a</label>Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt</aff><aff id="aff0002"><label>b</label>College of Applied Medical Sciences, University of Al-Jouf, Saudi Arabia</aff><author-notes><corresp id="cor0001"><label>⁎</label>Corresponding author. <email>abdo@sci.cu.edu.eg</email><email>aelfiky@ictp.it</email></corresp></author-notes><pub-date pub-type="pmc-release"><day>10</day><month>3</month><year>2020</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on .</pmc-comment>
<pub-date pub-type="ppub"><month>5</month><year>2020</year></pub-date><pub-date pub-type="epub"><day>10</day><month>3</month><year>2020</year></pub-date><volume>80</volume><issue>5</issue><fpage>554</fpage><lpage>562</lpage><history><date date-type="accepted"><day>27</day><month>2</month><year>2020</year></date></history><permissions><copyright-statement>© 2020 The British Infection Association. Published by Elsevier Ltd. All rights reserved.</copyright-statement><copyright-year>2020</copyright-year><copyright-holder></copyright-holder><license><license-p>Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.</license-p></license></permissions><abstract id="abs0001"><title>Summary</title><sec><title>Objectives</title><p>Understanding the novel coronavirus (COVID-19) mode of host cell recognition may help to fight the disease and save lives. The spike protein of coronaviruses is the main driving force for host cell recognition.</p></sec><sec><title>Methods</title><p>In this study, the COVID-19 spike binding site to the cell-surface receptor (Glucose Regulated Protein 78 (GRP78)) is predicted using combined molecular modeling docking and structural bioinformatics. The COVID-19 spike protein is modeled using its counterpart, the SARS spike.</p></sec><sec><title>Results</title><p>Sequence and structural alignments show that four regions, in addition to its cyclic nature have sequence and physicochemical similarities to the cyclic Pep42. Protein-protein docking was performed to test the four regions of the spike that fit tightly in the GRP78 Substrate Binding Domain β (SBDβ). The docking pose revealed the involvement of the SBDβ of GRP78 and the receptor-binding domain of the coronavirus spike protein in recognition of the host cell receptor.</p></sec><sec><title>Conclusions</title><p>We reveal that the binding is more favorable between regions III (C391-C525) and IV (C480-C488) of the spike protein model and GRP78. Region IV is the main driving force for GRP78 binding with the predicted binding affinity of -9.8 kcal/mol. These nine residues can be used to develop therapeutics specific against COVID-19.</p></sec></abstract><kwd-group id="keys0001"><title>Keywords</title><kwd>GRP78</kwd><kwd>BiP</kwd><kwd>COVID-19 spike</kwd><kwd>Protein-protein docking</kwd><kwd>Structural bioinformatics</kwd><kwd>Pep42</kwd></kwd-group></article-meta></front></pmc><affiliations><list><country><li>Arabie saoudite</li><li>Égypte</li></country></list><tree><country name="Égypte"><noRegion><name sortKey="Ibrahim, Ibrahim M" sort="Ibrahim, Ibrahim M" uniqKey="Ibrahim I" first="Ibrahim M." last="Ibrahim">Ibrahim M. Ibrahim</name></noRegion><name sortKey="Abdelmalek, Doaa H" sort="Abdelmalek, Doaa H" uniqKey="Abdelmalek D" first="Doaa H." last="Abdelmalek">Doaa H. Abdelmalek</name><name sortKey="Elfiky, Abdo A" sort="Elfiky, Abdo A" uniqKey="Elfiky A" first="Abdo A." last="Elfiky">Abdo A. Elfiky</name><name sortKey="Elshahat, Mohammed E" sort="Elshahat, Mohammed E" uniqKey="Elshahat M" first="Mohammed E." last="Elshahat">Mohammed E. Elshahat</name></country><country name="Arabie saoudite"><noRegion><name sortKey="Elfiky, Abdo A" sort="Elfiky, Abdo A" uniqKey="Elfiky A" first="Abdo A." last="Elfiky">Abdo A. Elfiky</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/StressCovidV1/Data/Ncbi/Merge
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000B56 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Ncbi/Merge/biblio.hfd -nk 000B56 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= StressCovidV1
|flux= Ncbi
|étape= Merge
|type= RBID
|clé= PMC:7102553
|texte= COVID-19 spike-host cell receptor GRP78 binding site prediction
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Merge/RBID.i -Sk "pubmed:32169481" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Merge/biblio.hfd \
| NlmPubMed2Wicri -a StressCovidV1
| This area was generated with Dilib version V0.6.33. |  |