Role of changes in SARS-CoV-2 spike protein in the interaction with the human ACE2 receptor: An in silico analysis
Identifieur interne : 001756 ( Ncbi/Merge ); précédent : 001755; suivant : 001757Role of changes in SARS-CoV-2 spike protein in the interaction with the human ACE2 receptor: An in silico analysis
Auteurs : Joseph Thomas Ortega [États-Unis] ; Maria Luisa Serrano [Venezuela] ; Flor Helene Pujol [Venezuela] ; Hector Rafael Rangel [Venezuela]Source :
- EXCLI Journal [ 1611-2156 ] ; 2020.
Abstract
Many human viral diseases are a consequence of a zoonotic event. Some of the diseases caused by these zoonotic events have affected millions of people around the world, some of which have resulted in high rates of morbidity/mortality in humans. Changes in the viral proteins that function as ligands of the host receptor may promote the spillover between species. The most recent of these zoonotic events that have caused an ongoing epidemic of high magnitude is the Covid-19 epidemics caused by SARS-CoV-2. The aim of this study was to determine the mutation(s) in the sequence of the spike protein of the SARS-CoV-2 that might be favoring human to human transmission. An
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DOI: 10.17179/excli2020-1167
PubMed: NONE
PubMed Central: 7081066
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first="Maria Luisa" last="Serrano">Maria Luisa Serrano</name><affiliation wicri:level="1"><nlm:aff id="A2">Unidad de Química Medicinal, Facultad de Farmacia, Universidad Central de Venezuela, Caracas, Venezuela</nlm:aff><country xml:lang="fr">Venezuela</country><wicri:regionArea>Unidad de Química Medicinal, Facultad de Farmacia, Universidad Central de Venezuela, Caracas</wicri:regionArea><wicri:noRegion>Caracas</wicri:noRegion></affiliation></author><author><name sortKey="Pujol, Flor Helene" sort="Pujol, Flor Helene" uniqKey="Pujol F" first="Flor Helene" last="Pujol">Flor Helene Pujol</name><affiliation wicri:level="1"><nlm:aff id="A3">Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela</nlm:aff><country xml:lang="fr">Venezuela</country><wicri:regionArea>Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas</wicri:regionArea><wicri:noRegion>Caracas</wicri:noRegion></affiliation></author><author><name sortKey="Rangel, Hector Rafael" sort="Rangel, Hector Rafael" uniqKey="Rangel H" first="Hector Rafael" last="Rangel">Hector Rafael Rangel</name><affiliation wicri:level="1"><nlm:aff id="A3">Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela</nlm:aff><country xml:lang="fr">Venezuela</country><wicri:regionArea>Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas</wicri:regionArea><wicri:noRegion>Caracas</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmc">7081066</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7081066</idno><idno type="RBID">PMC:7081066</idno><idno type="doi">10.17179/excli2020-1167</idno><idno type="pmid">NONE</idno><date when="2020">2020</date><idno type="wicri:Area/Pmc/Corpus">000838</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000838</idno><idno type="wicri:Area/Pmc/Curation">000838</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000838</idno><idno type="wicri:Area/Pmc/Checkpoint">000047</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000047</idno><idno type="wicri:Area/Ncbi/Merge">001756</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Role of changes in SARS-CoV-2 spike protein in the interaction with the human ACE2 receptor: An <italic>in silico</italic> analysis</title><author><name sortKey="Ortega, Joseph Thomas" sort="Ortega, Joseph Thomas" uniqKey="Ortega J" first="Joseph Thomas" last="Ortega">Joseph Thomas Ortega</name><affiliation wicri:level="2"><nlm:aff id="A1">Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106</wicri:regionArea><placeName><region type="state">Ohio</region></placeName></affiliation></author><author><name sortKey="Serrano, Maria Luisa" sort="Serrano, Maria Luisa" uniqKey="Serrano M" first="Maria Luisa" last="Serrano">Maria Luisa Serrano</name><affiliation wicri:level="1"><nlm:aff id="A2">Unidad de Química Medicinal, Facultad de Farmacia, Universidad Central de Venezuela, Caracas, Venezuela</nlm:aff><country xml:lang="fr">Venezuela</country><wicri:regionArea>Unidad de Química Medicinal, Facultad de Farmacia, Universidad Central de Venezuela, Caracas</wicri:regionArea><wicri:noRegion>Caracas</wicri:noRegion></affiliation></author><author><name sortKey="Pujol, Flor Helene" sort="Pujol, Flor Helene" uniqKey="Pujol F" first="Flor Helene" last="Pujol">Flor Helene Pujol</name><affiliation wicri:level="1"><nlm:aff id="A3">Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela</nlm:aff><country xml:lang="fr">Venezuela</country><wicri:regionArea>Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas</wicri:regionArea><wicri:noRegion>Caracas</wicri:noRegion></affiliation></author><author><name sortKey="Rangel, Hector Rafael" sort="Rangel, Hector Rafael" uniqKey="Rangel H" first="Hector Rafael" last="Rangel">Hector Rafael Rangel</name><affiliation wicri:level="1"><nlm:aff id="A3">Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela</nlm:aff><country xml:lang="fr">Venezuela</country><wicri:regionArea>Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas</wicri:regionArea><wicri:noRegion>Caracas</wicri:noRegion></affiliation></author></analytic><series><title level="j">EXCLI Journal</title><idno type="eISSN">1611-2156</idno><imprint><date when="2020">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Many human viral diseases are a consequence of a zoonotic event. Some of the diseases caused by these zoonotic events have affected millions of people around the world, some of which have resulted in high rates of morbidity/mortality in humans. Changes in the viral proteins that function as ligands of the host receptor may promote the spillover between species. The most recent of these zoonotic events that have caused an ongoing epidemic of high magnitude is the Covid-19 epidemics caused by SARS-CoV-2. The aim of this study was to determine the mutation(s) in the sequence of the spike protein of the SARS-CoV-2 that might be favoring human to human transmission. An <italic>in silico</italic> approach was performed, and changes were detected in the S1 subunit of the receptor-binding domain of spike. The observed changes have significant effect on SARS-CoV-2 spike/ACE2 interaction and produce a reduction in the binding energy, compared to the one of the Bat-CoV to this receptor. The data presented in this study suggest a higher affinity of the SARS-Cov-2 spike protein to the human ACE2 receptor, compared to the one of Bat-CoV spike and ACE2. This could be the cause of the rapid viral spread of SARS-CoV-2 in humans. </p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Arnold, K" uniqKey="Arnold K">K Arnold</name></author><author><name sortKey="Bordoli, L" uniqKey="Bordoli L">L Bordoli</name></author><author><name sortKey="Kopp, J" uniqKey="Kopp J">J Kopp</name></author><author><name sortKey="Schwede, T" uniqKey="Schwede T">T Schwede</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chen, Y" uniqKey="Chen Y">Y Chen</name></author><author><name sortKey="Guo, Y" uniqKey="Guo Y">Y Guo</name></author><author><name sortKey="Pan, Y" uniqKey="Pan Y">Y Pan</name></author><author><name sortKey="Zhao, Zj" uniqKey="Zhao Z">ZJ Zhao</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Coutard, B" uniqKey="Coutard B">B Coutard</name></author><author><name sortKey="Valle, C" uniqKey="Valle C">C 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<front><journal-meta><journal-id journal-id-type="nlm-ta">EXCLI J</journal-id><journal-id journal-id-type="iso-abbrev">EXCLI J</journal-id><journal-id journal-id-type="publisher-id">EXCLI J</journal-id><journal-title-group><journal-title>EXCLI Journal</journal-title></journal-title-group><issn pub-type="epub">1611-2156</issn><publisher><publisher-name>Leibniz Research Centre for Working Environment and Human Factors</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmc">7081066</article-id><article-id pub-id-type="publisher-id">2020-1167</article-id><article-id pub-id-type="doi">10.17179/excli2020-1167</article-id><article-id pub-id-type="publisher-id">Doc410</article-id><article-categories><subj-group subj-group-type="heading"><subject>Original Article</subject></subj-group></article-categories><title-group><article-title>Role of changes in SARS-CoV-2 spike protein in the interaction with the human ACE2 receptor: An <italic>in silico</italic> analysis</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Ortega</surname><given-names>Joseph Thomas</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib><contrib contrib-type="author"><name><surname>Serrano</surname><given-names>Maria Luisa</given-names></name><xref ref-type="aff" rid="A2">2</xref></contrib><contrib contrib-type="author"><name><surname>Pujol</surname><given-names>Flor Helene</given-names></name><xref ref-type="aff" rid="A3">3</xref></contrib><contrib contrib-type="author"><name><surname>Rangel</surname><given-names>Hector Rafael</given-names></name><xref ref-type="corresp" rid="COR1">*</xref><xref ref-type="aff" rid="A3">3</xref></contrib></contrib-group><aff id="A1"><label>1</label>Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA</aff><aff id="A2"><label>2</label>Unidad de Química Medicinal, Facultad de Farmacia, Universidad Central de Venezuela, Caracas, Venezuela</aff><aff id="A3"><label>3</label>Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela</aff><author-notes><corresp id="COR1">*To whom correspondence should be addressed: Hector Rafael Rangel, Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela, E-mail: <email>hrangel2006@gmail.com</email></corresp></author-notes><pub-date pub-type="epub"><day>18</day><month>3</month><year>2020</year></pub-date><pub-date pub-type="collection"><year>2020</year></pub-date><volume>19</volume><fpage>410</fpage><lpage>417</lpage><history><date date-type="received"><day>25</day><month>2</month><year>2020</year></date><date date-type="accepted"><day>16</day><month>3</month><year>2020</year></date></history><permissions><copyright-statement>Copyright © 2020 Ortega et al.</copyright-statement><copyright-year>2020</copyright-year><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>This is an Open Access article distributed under the terms of the Creative Commons Attribution Licence (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>) You are free to copy, distribute and transmit the work, provided the original author and source are credited.</license-p></license></permissions><self-uri xlink:type="simple" xlink:href="https://www.excli.de/vol19/Rangel_18032020_proof.pdf">This article is available from https://www.excli.de/vol19/Rangel_18032020_proof.pdf</self-uri><abstract><p>Many human viral diseases are a consequence of a zoonotic event. Some of the diseases caused by these zoonotic events have affected millions of people around the world, some of which have resulted in high rates of morbidity/mortality in humans. Changes in the viral proteins that function as ligands of the host receptor may promote the spillover between species. The most recent of these zoonotic events that have caused an ongoing epidemic of high magnitude is the Covid-19 epidemics caused by SARS-CoV-2. The aim of this study was to determine the mutation(s) in the sequence of the spike protein of the SARS-CoV-2 that might be favoring human to human transmission. An <italic>in silico</italic> approach was performed, and changes were detected in the S1 subunit of the receptor-binding domain of spike. The observed changes have significant effect on SARS-CoV-2 spike/ACE2 interaction and produce a reduction in the binding energy, compared to the one of the Bat-CoV to this receptor. The data presented in this study suggest a higher affinity of the SARS-Cov-2 spike protein to the human ACE2 receptor, compared to the one of Bat-CoV spike and ACE2. This could be the cause of the rapid viral spread of SARS-CoV-2 in humans. </p></abstract><kwd-group><kwd>Spike</kwd><kwd>SARS-CoV-2</kwd><kwd>ACE2</kwd><kwd>Coronavirus</kwd><kwd>outbreak</kwd></kwd-group></article-meta></front><floats-group><fig id="T1" position="float"><label>Table 1</label><caption><title>Residues involved in the Interaction between viral spike and ACE2 (SARS)</title></caption><graphic xlink:href="EXCLI-19-410-t-001"></graphic></fig><fig id="T2" position="float"><label>Table 2</label><caption><title>Number of protein-protein contacts (PPC) between CoV spikes and ACE2</title></caption><graphic xlink:href="EXCLI-19-410-t-002"></graphic></fig><fig id="T3" position="float"><label>Table 3</label><caption><title>Binding affinity (ΔG) and dissociation constant (Kd) predicted values for the interaction between viral spike and ACE2 receptor</title></caption><graphic xlink:href="EXCLI-19-410-t-003"></graphic></fig><fig id="F1" position="float"><label>Figure 1</label><caption><title>Phylogenetic analysis of SARS-CoV-2 and other coronavirus spike proteins. Phylogenetic tree constructed with Poisson correction and 100 bootstrap replicas. The sequences are named with their accession number. Percent homology with SARS-CoV-2 spike protein is shown for some proteins.</title></caption><graphic xlink:href="EXCLI-19-410-g-001"></graphic></fig><fig id="F2" position="float"><label>Figure 2</label><caption><title>Receptor Binding Domain of the spike protein sequence alignment of SARS-CoV-2 and other related Coronaviruses. Sequence aligment for the interacting domain of SARS-CoV-2 (MN938384), Bat-CoV (MN996532 and MG772933) and SARS-CoV (NC004718). The key amino acids described for the interaction with ACE2 are shown in red, and in blue others amino acid related with the interaction in SARS-CoV2. (Lines (-) = same amino acid, dots (.) =deletion)</title></caption><graphic xlink:href="EXCLI-19-410-g-002"></graphic></fig><fig id="F3" position="float"><label>Figure 3</label><caption><title>Coronavirus spike proteins. The spike proteins in complex with the RBD of ACE2 (dark pink) are shown A) Bat-CoV, B) SARS-CoV, and C) SARS-CoV-2. A comparison between the three spike proteins are shown in D and a 45 degree turn is also shown in E. The location of the main residues mutated in SARS-CoV (position 479 and 487) and SARS-CoV-2 are shown in F (green and blue).</title></caption><graphic xlink:href="EXCLI-19-410-g-003"></graphic></fig></floats-group></pmc><affiliations><list><country><li>Venezuela</li><li>États-Unis</li></country><region><li>Ohio</li></region></list><tree><country name="États-Unis"><region name="Ohio"><name sortKey="Ortega, Joseph Thomas" sort="Ortega, Joseph Thomas" uniqKey="Ortega J" first="Joseph Thomas" last="Ortega">Joseph Thomas Ortega</name></region></country><country name="Venezuela"><noRegion><name sortKey="Serrano, Maria Luisa" sort="Serrano, Maria Luisa" uniqKey="Serrano M" first="Maria Luisa" last="Serrano">Maria Luisa Serrano</name></noRegion><name sortKey="Pujol, Flor Helene" sort="Pujol, Flor Helene" uniqKey="Pujol F" first="Flor Helene" last="Pujol">Flor Helene Pujol</name><name sortKey="Rangel, Hector Rafael" sort="Rangel, Hector Rafael" uniqKey="Rangel H" first="Hector Rafael" last="Rangel">Hector Rafael Rangel</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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|flux= Ncbi
|étape= Merge
|type= RBID
|clé= PMC:7081066
|texte= Role of changes in SARS-CoV-2 spike protein in the interaction with the human ACE2 receptor: An in silico analysis
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Merge/RBID.i -Sk "pubmed:NONE" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Merge/biblio.hfd \
| NlmPubMed2Wicri -a CovidV2
| This area was generated with Dilib version V0.6.33. |  |